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WO2025155753A2 - Improved gene editing system, guides, and methods - Google Patents

Improved gene editing system, guides, and methods

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Publication number
WO2025155753A2
WO2025155753A2 PCT/US2025/011923 US2025011923W WO2025155753A2 WO 2025155753 A2 WO2025155753 A2 WO 2025155753A2 US 2025011923 W US2025011923 W US 2025011923W WO 2025155753 A2 WO2025155753 A2 WO 2025155753A2
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WIPO (PCT)
Prior art keywords
seq
sequence
polypeptide
amino acid
substitutions
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PCT/US2025/011923
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French (fr)
Other versions
WO2025155753A3 (en
WO2025155753A9 (en
Inventor
Elisabeth NARAYANAN
Kourtney MENDELLO
Giedrius GASIUNAS
Daniel Egan
Sierra HARKEN
Rajat Das
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Renagade Therapeutics Management Inc
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Renagade Therapeutics Management Inc
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Publication of WO2025155753A2 publication Critical patent/WO2025155753A2/en
Publication of WO2025155753A3 publication Critical patent/WO2025155753A3/en
Publication of WO2025155753A9 publication Critical patent/WO2025155753A9/en
Pending legal-status Critical Current
Anticipated expiration legal-status Critical

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases [RNase]; Deoxyribonucleases [DNase]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPR]

Definitions

  • Genome editing tools encompass a diverse set of technologies that can make many types of genomic alterations in various contexts. These technologies have evolved over the last couple of decades to provide a range of user-programmable editing tools that include ZFN (zinc finger) nuclease editing systems, meganuclease editing systems, and TALENS (transcription activator-like effector nucleases).
  • ZFN zinc finger
  • meganuclease editing systems and TALENS (transcription activator-like effector nucleases).
  • CRISPR-Cas9 has been derivatized in numerous ways to expand upon its guide RNA-based programmable double-strand cutting activity to fonn systems ranging from finding alternative CRISPR Cas nuclease enzymes having different PAM requirements and cutting properties (e.g.. Casl2a, Casl2f, Casl3a.
  • twin prime editing (Anzalone et al., “Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing,” Nature Biotechnology, Dec 9, 2021, vol. 40, pp. 731-740) to epigenetic editing (Kungulovski and Jeltsch, “Epigenome Editing: State of the Art, Concepts, and Perspective,” Trends in Genetics, Vol.32, 206, pp. 101-113) to CRISPR-directed integrase editing (Y amell et al., “Drag-and-drop genome insertion of large sequences without double-stranded DNA cleavage using CRISPR-directed integrases,” Nature Biotechnology, Nov 24. 2022, doi.org/10.1038/s41587-022-01527-4 (“PASTE”)).
  • CRISPR-Cas systems CRISPR-associated systems
  • TTT Transfusion-dependent 0-thalassemia
  • SCD sickle cell disease
  • the C-terminus regions of the type V effector nucleases are more highly conserved, however, which comprise a conserved RuvC-like endonuclease (RuvC) domain. It is reported that the RuvC domain of type V effectors is derived from the TnpB protein encoded by autonomous or non-autonomous transposons (Shmakov et al., “Diversity and evolution of class 2 CRISPR-Cas systems,” 2017, Nat. Rev. Microbiol. 15, 169-182. doi: 10.1038/nrmicro.2016.184).
  • RuvC domain of type V effectors is derived from the TnpB protein encoded by autonomous or non-autonomous transposons (Shmakov et al., “Diversity and evolution of class 2 CRISPR-Cas systems,” 2017, Nat. Rev. Microbiol. 15, 169-182. doi: 10.1038/nrmicro.2016.184).
  • the invention provides an isolated or recombinant guide RNA comprising or consisting of a nucleic acid sequence selected from the group consisting of:
  • a Cas Type V gene editing system comprising:
  • the present disclosure provides delivery of a Casl2a-based gene editing system described herein Cast 2a in various viral and non-viral vectors.
  • the LNP comprises: a) one or more ionizable lipids; b) one or more structural lipids; c) one or more PEGylated lipids; and d) one or more phospholipids.
  • compositions comprising a site-specific modification of a target region of a host cell genome comprising a Cas Type V -based gene editing system described herein Cas Type V comprising one or more Cas Type V polypeptides; one or more cognate guide RNA; and LNP suitable for therapeutic administration.
  • the Cas Type V polypeptide or variant thereof is a polypeptide selected from Table S15A (SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419)), or a polypeptide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity’ with a polypeptide from Table S15A (SEQ ID NO: 334 (No.
  • SEQ ID405 SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418).
  • SEQ ID NO: 335 SEQ ID NO: 406
  • SEQ ID NO: 331 SEQ ID NO: 1
  • SEQ ID NO: 20 No. ID41
  • SEQ ID NO: 445 No. ID419)
  • polypeptide from Table S15B (SEQ ID NO: 365 (No. ID405), SEQ ID NO: 75 (No. ID414), or SEQ ID NO:565 (No. ID418), SEQ ID NO: 366 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 30 (No. ID415), or SEQ ID NO: 445 (No. ID419)).
  • Cas Type V guide RNA is selected from any Cas Type V guide sequence disclosed in Table S 15C (SEQ ID NO:28-29. 69-71, 355-360, 542-563), or a nucleic acid molecule having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a Cas Type V guide sequence of Table S15C.
  • accessory domain is a deaminase domain, nuclease domain, reverse transcriptase domain, integrase domain, recombinase domain, transposase domain, endonuclease domain, or exonuclease domain.
  • genome editing system of any one of the above paragraphs wherein the genome editing system further comprises a donor nucleic acid sequence to modify a target region of the host cell genome.
  • Tire genome editing system of claim 19, wherein the one or more edits comprises an edit to the sequence of a gene or to a region of a gene, e.g., an exon or intron.
  • the delivery’ vector is selected from viral vector is selected from a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector.
  • any of the nucleic acid molecules — including any guide RNA or donor DNA — comprises one or more chemical modifications selected from 2'-O-Me, 2'-F, and 2'F-ANA at 2'OH; 2'F-4'-Ca-OMe and 2',4'-di-Ca-OMe at 2' and 4' carbons; phosphodiester modifications comprising sulfide-based Phosphorothioate (PS) or acetate-based phosphonoacetate alterations; combinations of the ribose and phosphodiester modifications; locked nucleic acid (LNA), bridged nucleic acids (BNA), S-constrained ethyl (cEt), and unlocked nucleic acid (UNA); modifications to produce a phosphodiester bond between the 2' and 5' carbons (2',5'-RNA) of adjacent RNAs; and a butane 4-carbon chain link between adjacent RNAs.
  • LNA locked nucleic acid
  • BNA bridged nucleic acids
  • any donor or template DNA comprises one or more chemical modifications selected from 2'-0-Me, 2'-F, and 2'F-ANA at 2'OH; 2'F- 4'-Ca-0Me and 2',4'-di-Ca-OMe at 2' and 4' carbons; phosphodiester modifications comprising sulfide- based Phosphorothioate (PS) or acetate-based phosphonoacetate alterations; combinations of the ribose and phosphodiester modifications; locked nucleic acid (LNA), bridged nucleic acids (BNA), S- constrained ethyl (cEt), and unlocked nucleic acid (UNA); modifications to produce a phosphodiester bond between the 2' and 5' carbons (2',5'-RNA) of adjacent RNAs; and a butane 4-carbon chain link between adjacent nucleotides.
  • LNA locked nucleic acid
  • BNA bridged nucleic acids
  • cEt S- constrained e
  • Tire method of paragraph 37 further comprising introducing into the host cell a second donor nucleic acid sequence paired with a second guide RNA to modify the second target region of the host cell genome.
  • Tire gene editing construct of claim 52 further comprising a donor nucleic acid sequence capable of modifying a target sequence
  • the target region is modified by an insertion, deletion or alteration of one or more base pairs at the target region in the host cell genome.
  • one or more desired modification sequence is selected from one or more sequences associated with one or more monogenic disorders or diseases.
  • FIGs. 5A-5C are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 5 sequences.
  • FIGs. 7A-7C are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 7 sequences.
  • FIGs. 8A-8B are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 8 sequences.
  • FIGs. 9A-9NN are schemes depicting tire predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 9 sequences.
  • FIGs. 10A-10F are schemes depicting tire predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 10 sequences.
  • FIGs. 11A-11C are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 11 sequences.
  • FIGs. 12A-12B are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 12 sequences.
  • FIGs. 13A-13F are schemes depicting tire predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 13 sequences.
  • FIGs. 14A- 14V are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 14 sequences.
  • FIG. 15 is a phylogenetic tree illustrating the location of PAM sequences added at each protein, as described in Example 9.
  • the phylogenetic tree was generated using Geneious Prime 2022.1.1 implementation of FastTree on Muscle multiple sequence alignment of selected protein sequences.
  • PAM sequence weblogos were generated using WebLogo 3 web application from PFMs.
  • FIG. 16 is a blot showing cleavage products of genomic target DNMT] visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ortholog were calculated using Image J software, in accordance with Example 10.
  • FIG. 17 is a blot showing cleavage products of genomic target RUNX 1 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ortholog were calculated using ImageJ software, in accordance with Example 10.
  • FIG. 18 is a blot showing cleavage products of genomic target SCN1A visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ortholog were calculated using ImageJ software, in accordance with Example 10.
  • FIG. 19 is a blot showing cleavage products of genomic target FANCF site 2 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ortholog were calculated using ImageJ software, in accordance with Example 10.
  • FIG. 20 is a blot showing cleavage products of genomic target FANCF site 1 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ortholog were calculated using ImageJ software, in accordance with Example 10.
  • FIG. 22A is a graph showing genome editing efficiency results for ID405, ID414, ID418, LbaCasl2a depicted as indels frequency at RUNX1 and SCN1A target sites as detennined by deep-sequencing in accordance with Example 12.
  • FIG. 280 is a set of blots showing cleavage products of genomic target HBG1 visualized on 2 % agarose gel in the presence of various ID418 mutants. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using ImageJ software.
  • FIG. 31 shows a sequence alignment among each of the Casl2a orthologs provided in Table S15A and tire canonical LbCasl2a sequence of SEQ ID NO: 1382.
  • Bolded-underlined residues are marked with an asterisk (“*”) and denote a fully conserved amino acid residue present in all of the aligned sequences at that alignment position.
  • the amino acid residue positions marked with a colon (“:”) denote aligned amino acid residues which are highly similar although not identically conserved.
  • the highly similar residues are those where the substitutions among the sequences have strongly similar properties.
  • the amino acid residue positions marked with a period (“.”) denote aligned amino acid residues which are moderately similar.
  • FIG. 35 is a set of blots showing cleavage products of genomic target TTR visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a. AsCasl2a Ultra and each 1D405 mutant were calculated using ImageJ software, wt ID405 - wild-type ID405 control, ID405-1 - mutant from the first targeted mutation wave (D169R). [0089]
  • FIG. 37 is a set of blots showing cleavage products of genomic target HBG1 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a. AsCasl2a Ultra and each ID418 mutant were calculated using Image J software, wt ID418 - wild-type ID418 control.
  • FIG. 42 is a set of tables showing the top 5 most common editing outcomes observed in deep sequencing data of ID405 wild type and mutant proteins as well as AsCasl2a Ultra genomic targets as compared to reference sequence in HBG1 gene.
  • FIG. 43 is a set of blots showing cleavage products of genomic target HBG1 visualized on 2 % agarose gel. Editing efficiency values for Alt-R A.s. Casl2a (Cpfl) and each purified Casl2a were calculated using ImageJ software.
  • FIG. 49 compares the interaction betw een Gln492 in ID405-1 with a replaced Arg492 w ith the guide RNA showing a more favorable interaction with the Arg492 residue, as described in Example 16.
  • FIG. 50 compares the interaction between Asn770 in ID405-1 with a replaced Arg770 with the guide RNA showing a more favorable interaction with the Arg770 residue, as described in Example 16.
  • FIG. 51 provides a graph showing the editing efficiency in primary HSPCs of select ID405-1 variants with arginine substitution mutations.
  • WT designated ID405-1.
  • Each variant enzyme, e.g., S972R, designates ID405-1 with a particular arginine substitution (e.g., S972R designates that serine at position 972 relative to ID405-1 has been substituted with an arginine). See Example 16 for details.
  • FIG. 52 is a schematic of ID405-1 variants comprising one or more NLS and optional linkers to improve 1D405-1 editing activity, in accordance with Example 17.
  • FIG. 54A is a schematic representation of the selection scheme for ID405 used in Example 18.
  • Hie ID405 plasmid library was transformed into E. coll cells. Hie most active variants cut ccdB encoding plasmid which led to its subsequent degradation. This allowed for E. colt to grow on selective media promoting ccdB induction. Cells that receive plasmid with WT or non-fiinctional/less active ID405 mutant died due to activity of ccdB.
  • FIG. 55 is a set of photos of test assays evaluating the performance of ID405 constructs against ccdB containing selection plasmids with TCTT and TTGG PAM sequences upstream of the HBG1 target.
  • FIG. 56A is a scatter plot summarizing variant frequency in N-terminus library under the selection against TCTT PAM. Nucleotide positions denote the amplified sequence used for library preparation.
  • FIG. 56C is a scatter plot summarizing variant frequency in N-terminus library under the selection against TTGG PAM under the presence of 0. ImM IPTG. Nucleotide positions denote the amplified sequence used for library preparation.
  • the BCL11A target is the BCL11A binding site in tire HBG1/2 promoters. Targeting this site with a CRISPR-Cas editor and guide RNA can inactivate the binding site of the BCL11A transcriptional repressor, thereby increasing transcription of HBG1/2 genes, which results in increased production of HBG1/2 subunits, and consequently, increased production of HbF.
  • Each of these three guides have same direct repeat sequence (UGAAUUUCUACUGUUGUAGAU; SEQ ID NO: 1744) but have different spacer length for unique DNA targets.
  • FIG. 71B An exemplary guide RNA targeting TTR gene and having the sequence from 5 ' to 3’ of SEQ ID NO: 2585, wherein the bolded sequence as shown in Appendix B, SEQ ID NO:2585, hybridizes to the PNA having the nucleic acid sequence CCACGAAAA fused to the NLS peptide PKKKRKV (SEQ ID NO:584).
  • FIG. 71C An exemplary guide RNA targeting any gene and having the sequence from 5’ to 3' of SEQ ID NO: 2586, wherein the bolded sequence as shown in Appendix B, SEQ ID NO:2586, hybridizes to the PNA having tire nucleic acid sequence AGCCACGAAAA (SEQ ID NO:2305) fused to the NLS peptide PKKKRKV (SEQ ID NO:584). where in “N” designates any nucleotide and will depend upon the target sequence being targeted by the guide RNA.
  • FIG. 75 Modification 6 schema. This figure outlines the positions of 2’-0Me modifications and phosphothiorate modifications in gRNAs with the modification 6 schema.
  • gRNA0260 u*g*AAUuuCUacUguuGuagaUcCUUGUCaagGcUAUUGGU*c*a (SEQ ID NO: 2232) (aka “mod 6” guide);
  • gRNA0390 u*g*AAUuuCUacUguuGuaGAucCUUGUCaaggcuAUUGGu*c*a (SEQ ID NO: 2233);
  • gRNA0391 u*g*AAUUuCUacUguuGuaGAUcCUUGUCaaggCUAUUGGu*c*a (SEQ ID NO:
  • gRNA0392 u*g*AAUUuCUacUguuGUAGAUcCUUGUCaagGCUAUUGGu*c*a (SEQ ID NO:
  • FIG. 76 Shows a graph of % indel formation by 405-1 nuclease with various modified gRNAs in a human HSPC donor at the HBG locus.
  • FIG. 78 Shows a graph of % indel formation by 405-1 with modified gRNAs across three different human HSPC donors at the HBG locus. The results showed that the effect of modified gRNAs on indel formation is consistent across HSPC donors using 405-1 3x NLS nuclease. For each cluster of graphs, the samples appear in the same ordering of (a) Donor 310, (b) Donor 309, and (c) Donor 308.
  • FIG. 80 A schematic representation of luciferase mRNA with miRNA target sites (ts) inserted in the 3’ UTR.
  • Luciferase mRNA consists of 5’ cap. 5' UTR. luciferase coding sequence, 3’ UTR followed by a poly A tail. A single copy (xl) or three copies (x3) of miRNA ts were inserted at the 3’ end of the 3’ UTR.
  • An alternative (alt) insertion site is located at the 5’ end of the 3’ UTR, near the luciferase coding sequence.
  • FIG. 81 depicts (A) A schematic structure of luciferase mRNA with miRNA target sites (ts) inserted in the 3’ UTR.
  • Luciferase mRNA consists of 5' cap, 5 ’UTR, luciferase coding sequence, 3' UTR followed by poly A tail.
  • 3' UTR 3' UTR followed by poly A tail.
  • three copies of miRNA target site are inserted at the 5‘ end of 3‘ UTR, near luciferase coding sequence.
  • the first miRNA target site is inserted near the luciferase coding sequence
  • the second miRNA target site is inserted at the 3’ end of UTR.
  • FIG. 82 depicts four bar graphs showing the result of the miRNAs in Table 22 of Example 23 evaluated for their target-site mediated suppression in various immune cell lines and CD34+CD38- CD90+CD45RA-Ein- long-term hematopoietic stem cells. While the insertion of liver specific miR-122 or epithelial specific miR-200b, 200c. 203a and 205 target sites in the 3 ’ UTR of cargo does not affect its expression in immune cells, hematopoietic miRNAs suppress cargo expression in one or more cell types. miR-142 and let7e effectively suppress cargo expression in all cell lines. miR-223 exhibits mild activity in all cell lines, with the least effect observed in long-term hematopoietic cells.
  • the Cas Type V guide RNA is selected from any Cas Type V guide sequence disclosed in Table S15C (SEQ ID NO:28-29, 69-71, 355-360, 542-563), or a nucleic acid molecule having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a Cas Type V guide sequence of Table S15C (SEQ ID NO:28-29, 69-71, 355-360, 542-563).
  • the Cas Type V guide RNA may comprise (a) a portion that binds or associates with a Cas Type V polypeptide and (b) a region that comprises a targeting sequence, i.e.. a sequence which is complementary to target nucleic acid sequence.
  • a targeting sequence i.e.. a sequence which is complementary to target nucleic acid sequence.
  • the target sequence is typically next to a PAM sequence.
  • the PAM sequence in various embodiments is ty pically TTTV, where V ty pically represents A, C, or G.
  • the “V” of the TTTV is immediately adjacent to the most 5’ base of tire non-targeted strand side of the protospacer element.
  • the PAM sequence is typically not included in the guide RNA design.
  • the Cas Ty pe V-based gene editing systems may comprise one or more additional accessory? proteins having genome modifying functions, including recombinases, invertases, nucleases, polymerases, ligases, deaminases, reverse transcriptases, or epigenetic modifying functions.
  • the accessory proteins may be provided separately.
  • the accessory proteins may be fused to Cas Type V, optionally with a linker.
  • Biologically active as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ⁇ 10%, as such variations are appropriate to perform the disclosed methods.
  • the term “bulge” refers to a small region of unpaired base(s) that interrupts a “stem” of base-paired nucleotides.
  • the bulge may comprise one or two single-stranded or unbase-paired nucleotides joined at both ends by base-paired nucleotides of the stem.
  • the bulge can be symmetrical (viz., the two unbase-paired single-stranded regions have the same number of nucleotides), or asymmetrical (viz., the unbase-paired single stranded region(s) have different or unequal numbers of nucleotides), or there is only one unbase-paired nucleotide on one strand.
  • cDNA refers to a strand of DNA copied from an RNA template, e.g., by a reverse transcriptase.
  • tire “Casl2a polypeptide”, “Casl2a protein” or “Casl2a nuclease” refers to a RNA- binding site-directed CRISPR Cas TypeV polypeptide that recognizes and/or binds RNA and is targeted to a specific DNA sequence.
  • An Cas 12a system as described herein refers to a specific DNA sequence by the RNA molecule to which the Casl2a polypeptide or Casl2a protein is bound.
  • the RNA molecule comprises a sequence that binds, hybridizes to, or is complementary' to a target sequence within the targeted polynucleotide sequence, thus targeting the bound polypeptide to a specific location within the targeted polynucleotide sequence (the target sequence).
  • “Cas 12a” is a type of CRISPR Class II Type V nuclease. The specification may describe the polypeptides contemplated in the scope of this application as Cas 12a polypeptides or alternatively as Cas TypeV polypeptides, or the like.
  • G/U base-pairing is at least partially responsible for the degeneracy (i.e., redundancy) of the genetic code in the context of tRNA anti -codon base-pairing with codons in mRNA.
  • a guanine (G) is considered complementary to both a uracil (U) and to an adenine (A).
  • U uracil
  • A adenine
  • G/U base-pair can be made at a given nucleotide position of a dsRNA duplex of a guide RNA molecule, the position is not considered to be non-complementary, but is instead considered to be complementary.
  • sequence of a polynucleotide need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable or hybridizable. Moreover, a polynucleotide may hybridize over one or more segments such that intervening or adjacent segments are not involved in the hybridization event (e.g., a bulge, a loop structure or hairpin structure, etc.).
  • a polynucleotide can comprise 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 98% or more, 99% or more, 99.5% or more, or 100% sequence complementarity to a target region within the target nucleic acid sequence to which it will hybridize.
  • an antisense nucleic acid in which 18 of 20 nucleotides of the antisense compound are complementary to a target region, and would therefore specifically hybridize, would represent 90 percent complementarity.
  • the remaining noncomplementary nucleotides may be clustered or interspersed with complementary nucleotides and need not be contiguous to each other or to complementary nucleotides.
  • Percent complementarity between particular stretches of nucleic acid sequences within nucleic acids can be determined using any convenient method.
  • Example methods include BEAST programs (basic local alignment search tools) and PowerBLAST programs (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656), the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), e.g., using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482-489), and the like.
  • control sequences is intended to include, at a minimum, all components whose presence is essential for expression, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences.
  • Suitable expression vectors include, without limitation, plasmids and viral vectors derived from, for example, bacteriophage, baculoviruses, tobacco mosaic virus, herpes viruses, cytomegalovirus, retroviruses, vaccinia viruses, adenoviruses, and adeno- associated viruses. Numerous vectors and expression systems are commercially available, such as from Novagen (Madison.
  • Tire tenn “fusion protein” refers to a polypeptide comprising a polypeptide or fragment coupled to heterologous amino acid sequences optionally via an amino acid linker. Fusion proteins are useful because they can be constructed to contain two or more desired functional elements from two or more different proteins.
  • a fusion protein comprises at least 10 contiguous amino acids from a polypeptide of interest, more preferably at least 20 or 30 amino acids, even more preferably at least 40, 50 or 60 amino acids, yet more preferably at least 75, 100 or 125 amino acids.
  • Fusions that include tire entirety of the proteins of the present invention have particular utility.
  • the heterologous polypeptide included within the fusion protein of the present invention is at least 6 amino acids in length, often at least 8 amino acids in length, and usefully at least 15, 20, and 25 amino acids in length.
  • Fusions that include larger polypeptides, such as an IgG Fc region, and even entire proteins, such as the green fluorescent protein (“GFP”) chromophore -containing proteins have particular utility.
  • Fusion proteins can be produced recombinantly by constructing a nucleic acid sequence which encodes the polypeptide or a fragment thereof in frame with a nucleic acid sequence encoding a different protein or peptide and then expressing the fusion protein.
  • a fusion protein can be produced chemically by crosslinking the polypeptide or a fragment thereof to another protein.
  • RNA molecule that binds to the Casl2a polypeptide and targets the polypeptide to a specific location within the targeted polynucleotide sequence is referred to herein as the “guide RNA” or “guide RNA polynucleotide” (also referred to herein as a “guide RNA” or “gRNA” or “crRNA”).
  • a guide RNA comprises two segments, a “DNA-targeting segment” and a “protein-binding segment.”
  • segment it is meant a segment/section/region of a molecule, e.g., a contiguous stretch of nucleotides in an RNA.
  • a protein-binding segment of a guide RNA can comprise base pairs 5-20 of the RNA molecule that is 40 base pairs in length; and the DNA-targeting segment can comprise base pairs 21-40 of the RNA molecule that is 40 base pairs in length.
  • the definition of '‘segment,” unless otherwise specifically defined in a particular context, is not limited to a specific number of total base pairs, is not limited to any particular number of base pairs from a given RNA molecule, is not limited to a particular number of separate molecules within a complex, and may include regions of RNA molecules that are of any total length and may or may not include regions with complementarity to other molecules.
  • site-directed modifying polypeptide is an Casl2a polypeptide
  • site-specific cleavage of the targeted polynucleotide sequence may occur at locations detennined by both (i) base-pairing complementarity between the guide RNA and the targeted polynucleotide sequence; and (ii) a short motif (referred to as the protospacer adjacent motif (PAM)) in the targeted polynucleotide sequence.
  • PAM protospacer adjacent motif
  • isolated means altered or removed from the natural state.
  • a nucleic acid or a peptide naturally present in a living animal is not “isolated,” but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is “isolated.”
  • An isolated nucleic acid or protein can exist in substantially purified fonn. or can exist in a non-native environment such as. for example, a host cell.
  • isolated nucleic acid refers to a nucleic acid segment or fragment, which has been separated from sequences which flank it in a naturally occurring state, i.e., a DNA fragment, which has been removed from the sequences which are normally adjacent to the fragment, i.e., the sequences adjacent to the fragment in a genome in which it naturally occurs.
  • Tire term also applies to nucleic acids which have been substantially purified from other components, which naturally accompany the nucleic acid, i.e., RNA or DNA or proteins, which naturally accompany it in the cell.
  • a “modified derivative” refers to polypeptides or fragments thereof that are substantially homologous in primary structural sequence but which include, e.g., in vivo or in vitro chemical and biochemical modifications or which incorporate amino acids that are not found in the native polypeptide. Such modifications include, for example, acetylation, carboxylation, phosphorylation, glycosylation, ubiquitination, labeling, e.g., with radionuclides, and various enzymatic modifications, as will be readily appreciated by those skilled in the art.
  • a variety of methods for labeling polypeptides and of substituents or labels useful for such purposes are well known in the art, and include radioactive isotopes such as 125 I, 32 P, 35 S.
  • ligands which bind to labeled antiligands e.g.. antibodies
  • fluorophores e.g., fluorophores
  • chemiluminescent agents e.g., chemiluminescent agents
  • enzymes e.g., enzymes, and antiligands which can serve as specific binding pair members for a labeled ligand.
  • the choice of label depends on the sensitivity required, ease of conjugation with the primer, stability requirements, and available instrumentation. Methods for labeling polypeptides are well known in the art. See, e.g, Ausubel et al., Current Protocols in Molecular Biology. Greene Publishing Associates (1992, and Supplements to 2002) (hereby incorporated by reference).
  • moduleating mediating a detectable increase or decrease in the level of a response in a subject compared with the level of a response in the subject in tire absence of a treatment or compound, and/or compared with the level of a response in an otherwise identical but untreated subject.
  • the term encompasses perturbing and/or affecting a native signal or response thereby mediating a beneficial therapeutic response in a subject, preferably, a human.
  • mutated when applied to nucleic acid sequences means that nucleotides in a nucleic acid sequence may be inserted, deleted or changed compared to a reference nucleic acid sequence. A single alteration may be made at a locus (a point mutation) or multiple nucleotides may be inserted, deleted or changed at a single locus. In addition, one or more alterations may be made at any number of loci within a nucleic acid sequence.
  • a nucleic acid sequence may be mutated by any method known in the art including but not limited to mutagenesis techniques such as “error-prone PCR” (a process for performing PCR under conditions where the copying fidelity of the DNA polymerase is low, such that a high rate of point mutations is obtained along the entire length of the PCR product; see, e.g., Leung etal., Technique, 1: 11-15 (1989) and Caldwell and Joyce, PCR Methods Applic.
  • mutagenesis techniques such as “error-prone PCR” (a process for performing PCR under conditions where the copying fidelity of the DNA polymerase is low, such that a high rate of point mutations is obtained along the entire length of the PCR product; see, e.g., Leung etal., Technique, 1: 11-15 (1989) and Caldwell and Joyce, PCR Methods Applic.
  • oligonucleotide -directed mutagenesis a process which enables the generation of site- specific mutations in any cloned DNA segment of interest: see, e.g., Reidhaar-Olson and Sauer, Science 241:53-57 (1988)).
  • non-homologous end joining refers to the repair of double-strand breaks in DNA by direct ligation of the break ends to one another without the need for a homologous template (in contrast to homology -directed repair, which requires a homologous sequence to guide repair). NHEJ often results in the loss (deletion) of nucleotide sequence near the site of the double-strand break.
  • non-peptide analog refers to a compound with properties that are analogous to those of a reference polypeptide.
  • a non-peptide compound may also be termed a "peptide mimetic” or a “peptidomimetic.” See, e.g., Jones, Amino Acid and Peptide Synthesis, Oxford University Press ( 1992); Jung, Combinatorial Peptide and Nonpeptide Libraries: A Handbook, John Wiley (1997); Bodanszky et al., Peptide Chemistry’— A Practical Textbook, Springer Verlag (1993); Synthetic Peptides: A Users Guide, (Grant, ed., W. H. Freeman and Co., 1992); Evans et al., J. Med. Chem.
  • promoter is art-recognized and refers to a nucleic acid molecule with a sequence recognized by the cellular transcription machinery and which is able to initiate transcription of a downstream gene.
  • a promoter can be constitutively active, meaning that the promoter is always active in a given cellular context, or conditionally active, meaning that the promoter is only active in the presence of a specific condition.
  • conditional promoter may only be active in the presence of a specific protein that connects a protein associated with a regulatory element in the promoter to the basic transcriptional machinery, or only in the absence of an inhibitory molecule.
  • programmable nuclease is meant to refer to a polypeptide that has the property of selective localization to a specific desired nucleotide sequence target in a nucleic acid molecule (e.g., to a specific gene target) due to one or more targeting functions.
  • targeting functions can include one or more DNA-binding domains, such as zinc finger domains characteristic of many different types of DNA binding proteins or TALE domains characteristic of TALEN proteins.
  • Such targeting function may also include tire ability to associate and/or form a complex with a guide RNA, which then localizes to a specific site on the DNA which bears a sequence that is complementary to a portion of the guide RNA (i.e., the spacer of the guide RNA).
  • the programmable nuclease may comprise a (a) nuclease -inactive RNA-guided nuclease (which still is capable of binding a guide RNA, localizing to a target DNA, and binding to the target DNA, but not capable of cutting or nicking the strands) fused to a (b) nuclease protein or domain, such as a FokI nuclease.
  • polypeptide encompasses both naturally-occurring and non-naturally- occurring proteins, and fragments, mutants, derivatives and analogs thereof.
  • a polypeptide may be monomeric or polymeric. Further, a polypeptide may comprise a number of different domains each of which has one or more distinct activities.
  • a mutein has at least 85% overall sequence homology to its wild-type counterpart. Even more preferred are muteins having at least 90% overall sequence homology to the wild- type protein. In an even more preferred embodiment, a mutein exhibits at least 95% sequence identity, even more preferably 98%, even more preferably 99% and even more preferably 99.9% overall sequence identity. [00237] Sequence homology may be measured by any common sequence analysis algorithm, such as Gap or Bestfit.
  • an endogenous nucleic acid sequence in the genome of an organism is deemed “recombinant” herein if a heterologous sequence is placed adjacent to the endogenous nucleic acid sequence, such that tire expression of this endogenous nucleic acid sequence is altered.
  • a heterologous sequence is a sequence that is not naturally adjacent to the endogenous nucleic acid sequence, whether or not the heterologous sequence is itself endogenous (originating from the same host cell or progeny thereof) or exogenous (originating from a different host cell or progeny thereof).
  • a promoter sequence can be substituted (e.g., by homologous recombination) for the native promoter of a gene in the genome of a host cell, such that this gene has an altered expression pattern.
  • This gene would now become “recombinant” because it is separated from at least some of the sequences that naturally flank it.
  • recombinant host cell (or simply “host cell”), as used herein, is intended to refer to a cell into which a recombinant vector has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell but to the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein.
  • a recombinant host cell may be an isolated cell or cell line grown in culture or may be a cell which resides in a living tissue or organism.
  • Suitable methods of genetic modification include e.g.. viral or bacteriophage infection, transfection, conjugation, protoplast fusion, lipofection, electroporation, calcium phosphate precipitation, polyethyleneimine (PEI)-mediated transfection, DEAE-dextran mediated transfection, liposome-mediated transfection, particle gun technology, calcium phosphate precipitation, direct micro injection, nanoparticle- mediated nucleic acid delivery (see, e.g., Panyam et al., Adv Drug Deliv Rev. 2012 Sep. 13. pii: S0169-409X(12)00283-9. doi: 10.1016/j.addr.2012.09.023), and the like.
  • transformation include e.g.. viral or bacteriophage infection, transfection, conjugation, protoplast fusion, lipofection, electroporation, calcium phosphate precipitation, polyethyleneimine (PEI)-mediated transfection, DEAE-dextran mediated transfection, liposome-mediated transfection, particle gun
  • a ‘recombinant nucleic acid” or “recombinant nucleotide” refers to a molecule that is constructed by joining nucleic acid molecules, which optionally may self-replicate in a live cell. Recombinant nucleic acids and synthetic nucleic acids also include those molecules that result from the replication of either of the foregoing.
  • Region refers to a physically contiguous portion of the primary structure of a biomolecule. In the case of proteins, a region is defined by a contiguous portion of the amino acid sequence of that protein.
  • RNA-guided nuclease is a type of “programmable nuclease.” and a specific type of “nucleic acid-guided nuclease.”
  • RNA-guided nuclease or “RNA-guided endonuclease” refers to a nuclease that associates covalently or non-covalently with a guide RNA thereby forming a complex between the guide RNA and the RNA-guided nuclease.
  • the guide RNA comprises a spacer sequence which comprises a nucleotide sequence having complementarity with a strand of a target DNA sequence.
  • sequence identity refers to the overall relatedness between polymeric molecules, e.g., between polynucleotide molecules ( ⁇ ?.g, DNA molecules and/or RNA molecules) and/or between polypeptide molecules. Calculation of the percent identity of two polynucleotide sequences, for example, can be performed by aligning the two sequences for optimal comparison purposes (e.g.. gaps can be introduced in one or both of a first and a second nucleic acid sequences for optimal alignment and nonidentical sequences can be disregarded for comparison purposes).
  • Exemplary computer software to determine homology between two sequences include, but are not limited to, GCG program package, Devereux, J., et al., Nucleic Acids Research, 12(1), 387 (1984)), BLASTP, BLASTN, and FASTA (Altschul etal.,J. Mol. Biol. 215:403-410 (1990);
  • FASTA provides alignments and percent sequence identity of tire regions of the best overlap between the query' and search sequences. Pearson, Methods Enzymol. 183:63-98 (1990) (hereby incorporated by reference in its entirety). Percent sequence identity between nucleic acid sequences, for instance, can be determined using FASTA with its default parameters (a word size of 6 and the NOPAM factor for the scoring matrix) or using Gap with its default parameters as provided in GCG Version 6.1.
  • operably linked or “under transcriptional control,” when used in conjunction with the description of a promoter, refers to the correct location and orientation in relation to a polynucleotide (e.g. , a coding sequence) to control the initiation of transcription by RNA polymerase and expression of tire coding sequence.
  • a polynucleotide e.g. , a coding sequence
  • “stringent conditions” are defined for solution phase hybridization as aqueous hybridization (i.e., free of formamide) in 6xSSC (where 20xSSC contains 3.0 M NaCl and 0.3 M sodium citrate), 1% SDS at 65°C for 8-12 hours, followed by two washes in 0.2xSSC, 0.1% SDS at 65°C for 20 minutes. It will be appreciated by the skilled worker that hybridization at 65 °C will occur at different rates depending on a number of factors including the length and percent identity of the sequences which are hybridizing. Hybridization does not require the sequence of the polynucleotide to be 100% com piemen tan to the target polynucleotide. Hybridization also includes one or more segments such that intervening or adjacent segments that are not involved in the hybridization event (e.g., a loop structure or hairpin structure).
  • the nucleic acids (also referred to as polynucleotides) of this present invention may include both sense and antisense strands of RNA, cDNA, genomic DNA, and synthetic forms and mixed polymers of the above. They may be modified chemically or biochemically or may contain non -natural or derivatized nucleotide bases, as will be readily appreciated by those of skill in the art. Such modifications include, for example, labels, methylation, substitution of one or more of the naturally occurring nucleotides with an analog, intemucleotide modifications such as uncharged linkages (e.g., methyl phosphonates.
  • uncharged linkages e.g., methyl phosphonates.
  • phosphotriesters, phosphoramidates, carbamates, etc. charged linkages (e.g., phosphorothioates. phosphorodithioates, etc.), pendent moieties (e.g., polypeptides), intercalators (e.g., acridine, psoralen, etc.), chelators, alkylators, and modified linkages (e.g., alpha anomeric nucleic acids, etc.)
  • synthetic molecules that mimic polynucleotides in their ability to bind to a designated sequence via hydrogen bonding and other chemical interactions. Such molecules are known in tire art and include, for example, those in which peptide linkages substitute for phosphate linkages in the backbone of the molecule.
  • Other modifications can include, for example, analogs in which the ribose ring contains a bridging moiety or other structure such as the modifications found in “locked” nucleic acids.
  • the term “subject” refers to an individual organism, for example, an individual mammal.
  • tire subject is a human.
  • the subject is anon-human mammal.
  • the subject is a non-human primate.
  • the subject is a rodent.
  • the subject is a sheep, a goat, a cattle, a cat, or a dog.
  • the subject is a vertebrate, an amphibian, a reptile, a fish, an insect, a fly, or a nematode.
  • the subject is a research animal.
  • the subject is genetically engineered, e.g., a genetically engineered non-human subject.
  • the subject may be of either sex and at any stage of development.
  • a “synthetic or artificial nucleic acid” refers nucleic acids that are non-naturally occuring sequences. Such sequences do not originate from, or are not known to be present in any living organism (e.g., based on sequence search in existing sequence databases).
  • Targeted polynucleotide sequence refers to a DNA polynucleotide that comprises a “target site” or “target sequence.”
  • target site refers to a DNA polynucleotide that comprises a “target site” or “target sequence.”
  • target site refers to a DNA polynucleotide that comprises a “target site” or “target sequence.”
  • target sequence refers to a nucleic acid sequence present in a targeted polynucleotide sequence to which a DNA-targeting segment of a guide RNA will recognize and/or bind, provided sufficient conditions for binding exist.
  • the target site (or target sequence) 5'- GAGCATATC-3' within a targeted polynucleotide sequence is targeted by (or is bound by, or hybridizes with, or is complementary to) the RNA sequence 5'-GAUAUGCUC-3'.
  • Suitable DNA/RNA binding conditions include physiological conditions normally present in a cell.
  • RNA binding conditions e.g., conditions in a cell -free system
  • tire strand of the targeted polynucleotide sequence that is complementary to and hybridizes with the guide RNA is referred to as the “complementary strand”
  • the strand of the targeted polynucleotide sequence that is complementary to the “complementary strand” (and is therefore not complementary to the guide RNA) is referred to as the “noncomplementary strand” or “non-complementary strand.”
  • a “target site” as used herein is a polynucleotide (e.g., DNA such as genomic DNA) that includes a site or specific locus (“target site” or “target sequence”) targeted by a Cast 2a gene editing system disclosed herein.
  • target site a site or specific locus targeted by a Cast 2a gene editing system disclosed herein.
  • a target sequence is the sequence to which the guide sequence of a guide nucleic acid (e.g., guide RNA) will hybridize.
  • the target site (or target sequence) 5'-GTCAATGGACC-3' (SEQ ID NO:2663) within a target nucleic acid is targeted by (or is bound by, or hybridizes with, or is complementary to) the sequence 5'-GGTCCATTGAC-3' (SEQ ID NO:2664).
  • Suitable hybridization conditions include physiological conditions normally present in a cell.
  • therapeutically effective amount refers to the amount of the subject compound that will elicit the biological or medical response of a tissue, system, or subject that is being sought by the researcher, veterinarian, medical doctor or other clinician.
  • therapeutically effective amount includes that amount of a compound that, when administered, is sufficient to prevent development of, or alleviate to some extent, one or more of the signs or symptoms of the disorder or disease being treated.
  • Tire therapeutically effective amount will vary depending on the compound, the disease and its severity and the age, weight, etc., of the subject to be treated.
  • treatment refers to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease or disorder, or one or more symptoms thereof, as described herein.
  • treatment may be administered after one or more symptoms have developed and/or after a disease has been diagnosed.
  • treatment may be administered in the absence of symptoms, e.g., to prevent or delay onset of a symptom or inhibit onset or progression of a disease.
  • treatment may be administered to a susceptible individual prior to the onset of symptoms (e g ., in light of a history of symptoms and/or in light of genetic or other susceptibility factors). Treatment may also be continued after symptoms have resolved, for example, to prevent or delay their recurrence.
  • tire tenn “halo” or “halogen” alone or as part of another substituent means, unless otherwise stated, a fluorine, chlorine, bromine, or iodine atom, preferably, fluorine, chlorine, or bromine, more preferably, fluorine or chlorine.
  • heteroalkyl by itself or in combination with another term means, unless otherwise stated, a stable straight or branched chain alkyl group consisting of the stated number of carbon atoms and one or tw o or more heteroatoms typically selected from the group consisting of O, N, Si, P, and S, and wherein the nitrogen and sulfur atoms may be optionally oxidized and the nitrogen heteroatom may be a primary, secondary, tertiary or quaternary nitrogen.
  • the heteroatom(s) may be placed at any position of the heteroalkyl group, including between the rest of the heteroalkyl group and the fragment to which it is attached, as well as attached to the most distal carbon atom in the heteroalkyl group.
  • Up to tw o heteroatoms may be consecutive, such as. for example, -CH2-NH-OCH3. or -CH2-CH2-S-S-CH3.
  • heteroaty l or “heteroaromatic” refers to aryl groups which contain at least one heteroatom typically selected from N, O, Si, P, and S; wherein the nitrogen and sulfur atoms may be optionally oxidized, and the nitrogen atom(s) may be optionally teriatry or quatemized. Heteroaryl groups may be substituted or unsubstituted. A heteroaryl group may be attached to the remainder of the molecule through a heteroatom.
  • a polycyclic heteroaryl may include one or more rings that are partially saturated.
  • Examples include tetrahydroquinoline, 2,3-dihydrobenzofuryl, 1 -pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3- pyrazolyl, 2 -imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4- oxazolyl, 5 -oxazolyl, 3- isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-thiazolyl, 4-thiazolyl, 5- thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3- thienyl.
  • heteroaryl groups include pyridyl, pyrazinyl, pyrimidinyl (particularly 2- and 4-pyrimidinyl), pyridazinyl, thienyl, furyl, pyrrolyl (particularly 2-pyrrolyl), imidazolyl, thiazolyl, oxazolyl, pyrazolyl (particularly 3- and 5-pyrazolyl), isothiazolyl, 1,2,3-triazolyl, 1,2,4-triazolyl, 1,3,4- triazolyl, tetrazolyl, 1,2,3-thiadiazolyl, 1,2,3-oxadiazolyl, 1,3,4-thiadiazolyl and 1,3,4- oxadiazolyl.
  • the heterocyclyl radical may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems: and the nitrogen, carbon or sulfur atoms in the heterocyclyl radical may be optionally oxidized; the nitrogen atom may be optionally quatemized; and the heterocyclyl radical may be partially or fully saturated.
  • a heterocyclyl group may be optionally substituted.
  • compounds of the present disclosure may contain '‘optionally substituted” moieties.
  • substituted whether preceded by the term “optionally” or not, means that one or more hydrogens of the designated moiety are replaced with a suitable substituent.
  • an “optionally substituted” group may have a suitable substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position.
  • Combinations of substituents envisioned by this disclosure are preferably those that result in the fonnation of stable or chemically feasible compounds.
  • Tire term “stable”, as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes disclosed herein.
  • Suitable monovalent substituents on a substitutable carbon atom of an “optionally substituted” group are independently halogen; — (CH2)0-4R°; — (CH2)0-4OR°; — O(CH2)0-4R°, — O— (CH2)0-4C(O)OR°;
  • Suitable monovalent substituents on R° are independently halogen, — (CH2)0-2R*, -(haloR*).
  • Suitable divalent substituents that are bound to vicinal substitutable carbons of an “optionally substituted” group include: — O(CR*2)2-3O — , wherein each independent occurrence of R* is selected from hydrogen, Cl-6 aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
  • Suitable substituents on the aliphatic group of R ' are independently halogen, — R*, -(haloR*), — OH, —OR*, — O(haloR*), — CN, — C(O)OH, — C(O)OR*, — NH2, — NHR*, —NR* 2, or — NO2, wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently Cl-4 aliphatic. — CH2Ph, — O(CH2)0-lPh. or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
  • Cas Type V polypeptides of the present disclosure are capable of inducing indel formation when contacted with a population of target sequences and a guide RNA targeting the Cas Type V polypeptide to the target sequence under conditions suitable for inducing indel formation.
  • the target sequence may be a DNA sequence.
  • the target sequence may be associated with a disease or disorder.
  • the substitutions in the Cas Type V polypeptides disclosed herein enhance tire ability of the Cas Type V polypeptide to induce indels in comparison with Cas Type V polypeptides that do not comprise the substitutions.
  • the disclosure provides a gene editing system comprising: (a) one or more Cas Type V polypeptides of tire disclosure or one or more polynucleotides encoding the Cas Type V polypeptide(s); and (b) one or more polynucleotide sequences comprising a guide RNA (gRNA) or one or more polynucleotides encoding the gRNA, wherein the gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
  • the guide RNA may be a guide RNA as disclosed herein.
  • Any Casl2a (or Cas Type V) polypeptide or variant thereof may be used in the present disclosure, including those described in the herein tables and provided in the accompanying sequence listing.
  • the Cas 12a (or Cas Type V) polypeptide is a polypeptide selected from Table S15A (SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419)), or a polypeptide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a polypeptide from Table S15A (SEQ ID NO: 334 (No.
  • the modified mRNA payloads When transfected into mammalian cells, the modified mRNA payloads have a stability of between 12-18 hours, or greater than 18 hours, e.g., 24, 36, 48, 60, 72, or greater than 72 hours.
  • a codon optimized RNA may be one in which the levels of G/C are enhanced.
  • the G/C-content of nucleic acid molecules may influence the stability of the RNA.
  • RNA having an increased amount of guanine (G) and/or cytosine (C) residues may be functionally more stable than RNA containing a large amount of adenine (A) and thymine (T) or uracil (U) nucleotides.
  • WO02/098443 discloses a phannaceutical composition containing an mRNA stabilized by sequence modifications in the translated region. Due to the degeneracy of the genetic code, the modifications work by substituting existing codons forthose that promote greater RNA stability without changing the resulting amino acid. The approach is limited to coding regions of the RNA.
  • the disclosure provides engineered Casl2a variants or mutants which have been modified by introducing one or more amino acid substitutions into a baseline sequence (e.g., a wildtype sequence).
  • a baseline sequence e.g., a wildtype sequence.
  • Any available methods may be utilized to obtain or construct a variant or mutant Cas 12a protein.
  • the term ‘'mutation,” as used herein, refers to a substitution of a residue within a sequence, e.g., a nucleic acid or amino acid sequence, with another residue, or a deletion or insertion of one or more residues w ithin a sequence. Mutations are typically described herein by identifying tire original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue.
  • Mutations are well known in the art (e.g., site-directed mutagenesis or directed evolution engineering), and are provided by, for example, Green and Sambrook, Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)). Mutations can include a variety of categories, such as single base polymorphisms, microduplication regions, indel, and inversions, and is not meant to be limiting in any way. Mutations can include “loss-of-function” mutations w hich is the normal result of a mutation that reduces or abolishes a protein activity.
  • Gain-of-function mutations are recessive, because in a heterozygote the second chromosome copy carries an unmutated version of the gene coding for a fully functional protein w hose presence compensates for the effect of the mutation. Mutations also embrace “gain-of-function” mutations, which confer an abnormal activity on a protein or cell that is otherwise not present in a normal condition. Many gain-of-function mutations are in regulatory sequences rather than in coding regions, and can therefore have a number of consequences. For example, a mutation might lead to one or more genes being expressed in the wrong tissues, these tissues gaining functions that they normally lack. Because of their nature, gain-of-function mutations are usually dominant.
  • telomeres are then transformed into host bacteria and plaques are screened for the desired mutation.
  • site-directed mutagenesis has employed PCR methodologies, w hich have the advantage of not requiring a single-stranded template.
  • methods have been developed that do not require sub-cloning.
  • Several issues must be considered when PCR-based site-directed mutagenesis is performed. First, in these methods it is desirable to reduce the number of PCR cycles to prevent expansion of undesired mutations introduced by the polymerase. Second, a selection must be employed in order to reduce the number of non-mutated parental molecules persisting in the reaction. Third, an extended-length PCR method is preferred in order to allow the use of a single PCR primer set. And fourth, because of the non-template-dependent terminal extension activity of some thermostable polymerases it is often necessary’ to incorporate an end-polishing step into the procedure prior to blunt-end ligation of the PCR-generated mutant product.
  • Mutations may also be introduced by directed evolution processes, such as phage-assisted continuous evolution (PACE) or phage-assisted noncontinuous evolution (PANCE).
  • PACE phage-assisted continuous evolution
  • PANCE phage-assisted noncontinuous evolution
  • PACE technology has been described, for example, in International PCT Application, PCT/US2009/056194, filed Sep. 8, 2009, published as WO 2010/028347 on Mar. 11, 2010; International PCT Application, PCT/US2011/066747, filed Dec. 22, 2011, published as WO 2012/088381 on Jun. 28, 2012; U.S. Pat. No.
  • Variant Casl2as may also be obtain by phage-assisted non-continuous evolution (PANCE),” which as used herein, refers to non-continuous evolution that employs phage as viral vectors.
  • PANCE phage-assisted non-continuous evolution
  • PANCE is a simplified technique for rapid in vivo directed evolution using serial flask transfers of evolving "selection phage’ (SP), which contain a gene of interest to be evolved, across fresh E. coli host cells, thereby allowing genes inside the host E. coli to be held constant while genes contained in the SP continuously evolve.
  • SP selection phage
  • Serial flask transfers have long served as a widely-accessible approach for laboratory evolution of microbes, and, more recently, analogous approaches have been developed for bacteriophage evolution.
  • the PANCE system features lower stringency than the PACE system.
  • the disclosure contemplates any engineered Casl2a variants or mutants which have been modified by introducing one or more amino acid substitutions into a baseline sequence, including conservative substitutions of one amino acid for another.
  • mutation of an amino acid with a hydrophobic side chain e.g.. alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, or tryptophan
  • alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, or tryptophan may be changed to a second amino acid with a different hydrophobic side chain (e.g., alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, or tryptophan).
  • a mutation of an alanine to a threonine may also include a mutation from an alanine to an amino acid that is similar in size and chemical properties to a threonine, for example, serine.
  • mutation of an amino acid with a positively charged side chain e.g., arginine, histidine, or lysine
  • mutation to a second amino acid with a different positively charged side chain e.g., arginine, histidine, or lysine.
  • any amino acid mutations provided herein from one amino acid to a threonine may be an amino acid mutation to a serine.
  • any amino acid mutations provided herein from one amino acid to an arginine may be an amino acid mutation to a lysine.
  • any amino acid mutations provided herein from one amino acid to an isoleucine may be an amino acid mutation to an alanine, valine, methionine, or leucine.
  • any amino acid mutations provided herein from one amino acid to a lysine may be an amino acid mutation to an arginine.
  • any amino acid mutations provided herein from one amino acid to an aspartic acid may be an amino acid mutation to a glutamic acid or asparagine.
  • any amino acid mutations provided herein from one amino acid to a valine may be an amino acid mutation to an alanine, isoleucine, methionine, or leucine.
  • any amino acid mutations provided herein from one amino acid to a glycine may be an amino acid mutation to an alanine. It should be appreciated, however, that additional conserved amino acid residues would be recognized by the skilled artisan and any of the amino acid mutations to other conserved amino acid residues are also within the scope of this disclosure. Tire amino acid substitutions may also be non-conservative amino acid substitutions.
  • an Alanine (A) residue of a Casl2a protein may be substituted with any one of tire following amino acids: Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E) ; Glutamine (N); Glycine (G): Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y): or Valine (V).
  • an Arginine (R) residue of a Casl2a protein may be substituted with any one of the following amino acids: Alanine (A); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E) ; Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S): Threonine (T); Try ptophan (W); Tyrosine (Y); or Valine (V).
  • an Asparagine (N) residue of a Casl2a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Aspartic Acid (D); Cysteine (C); Glutamic acid (E) ; Glutamine (N): Glycine (G); Histidine (H); Isoleucine (I); Leucine (L): Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
  • an Aspartic Acid (D) residue of a Casl2a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Cysteine (C); Glutamic acid (E) ; Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
  • an Isoleucine (I) residue of a Cas 12a protein may be substituted with any one of tire following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T): Tryptophan (W); Tyrosine (Y): or Valine (V).
  • an Leucine (L) residue of a Cast 2a protein may be substituted with any one of tire following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
  • an Methionine (M) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R): Asparagine (N); Aspartic Acid (D): Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I): Leucine (L); Lysine (K); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
  • an Tryptophan (W) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tyrosine (Y); or Valine (V).
  • an Tyrosine (Y) residue of a Cas 12a protein may be substituted with any one of tire following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S): Threonine (T); Tryptophan (W); or Valine (V).
  • an Valine (V) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G): Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); or Tryptophan (W).
  • the Casl2a may be a Casl2a variant based on ID405 (SEQ ID NO: 334), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 334 having any of the following substitutions):
  • the Casl2a may be a Casl2a variant based on ID418 (SEQ ID NO: 564), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 564 having any of the following substitutions):
  • the Casl2a may be a Casl2a variant based on ID418 (SEQ ID NO: 564), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%. 90%. 95%. 99%, or up to 100% sequence identity with SEQ ID NO: 564 having any of tire following substitutions):
  • the Casl2a may be a Casl2a variant based on ID418 (SEQ ID NO: 564), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 564 having any of the following substitutions): a D161 substitution; • a D 161 /R888/R892 substitution;
  • the Casl2a may be a Cast 2a variant based on ID418 (SEQ ID NO: 564), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 564 having any of the following substitutions):
  • WED Wedge
  • REC a-helical recognition lobe
  • PI PAM-interacting
  • RuvC nuclease Bridge Helix
  • BH Bridge Helix
  • NUC domains NUC domains
  • the present disclosure further provides guide RNAs for use in accordance with the disclosed nucleic acid programmable DNA binding proteins (e.g., Casl2a) for use in methods of editing.
  • the disclosure provides guide RNAs that are designed to recognize target sequences.
  • Such gRNAs may be designed to have guide sequences (or “spacers”) having complementarity to a target sequence.
  • Such gRNAs may be designed to have not only a guide sequences having complementarity to a target sequence to be edited, but also to have a backbone sequence that interacts specifically with the nucleic acid programmable DNA binding protein.
  • the gRNA is cleaved and processed into one or more intermediate crRNAs, which are subsequently processed into one or more mature crRNAs.
  • the gRNA comprises a precursor CRISPR RNAs (pre-crRNA) encoding one or more crRNAs or one or more intermediate or mature crRNAs, each guide RNA comprising at a minimum a repeat-spacer in the 5’ to 3‘ direction, wherein the repeat comprises a stem -loop structure and the spacer comprises a DNA-targeting segment complementary to a target sequence in the targeted polynucleotide sequence.
  • the gRNA is cleaved by a RNase activity of the Casl2a polypeptide into one or more mature crRNAs, each comprising at least one repeat and at least one spacer.
  • one or more repeat-spacer directs the Casl2a (or Cas Type V) polypeptides to two or more distinct sites in the targeted polynucleotide sequence.
  • the gRNA is cleaved and processed into one or more intermediate crRNAs, which are subsequently processed into one or more mature crRNAs.
  • the pre- crRNA or intermediate crRNA are processed into mature crRNA by an Cas 12a (or Cas Type V) polypeptide, and the mature crRNA becomes available for directing the Cas 12a (or Cas Type V) endonuclease activity.
  • the gRNA is linked to a single or double strand DNA donor template, and the donor template is cleaved from the gRNA by the Cas 12a (or Cas Type V) polypeptide.
  • the donor polynucleotide template remains linked to gRNA while the Cas 12a (or Cas Type V) polypeptide cleaves gRNA to liberate intermediate or mature crRNAs.
  • the Cas 12a (or Cas Type V) system comprises one or more guide RNA comprising:
  • nucleic acid sequence that is a degenerate variant of (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563;
  • anucleic acid sequence at least 70%, at least 71%, at least 72%. at least 73%. at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81 %, at least 82%, at least 83%, at least 84%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99% or at least 99.9% identical to : (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291- 330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ
  • the Casl2a (or Cas Type V) proteins target and cleave targeted polynucleotides that is complementary to a cognate guide RNA.
  • the guide RNA comprises crRNA, which includes the natural CRISPR array.
  • crRNA which includes the natural CRISPR array.
  • Such variants are derived from the first direct repeat, a “leader” sequence and involved in signaling or the direct repeat retains genetic diversity that doesn’t affect functionality.
  • the direct repeat is degenerate, generally near the 3 ’ end of the repeat array.
  • the crRNA comprises about 15-40 nucleotides or direct repeat sequences comprising about 20-30 nucleotides.
  • the direct repeat is selected from (Group 1) SEQ ID NO:7-12; (Group 2) SEQ ID NO:24-27; (Group 3) SEQ ID NO:36-39; (Group 4) SEQ ID NO:49- 52; (Group 5) SEQ ID NO:63-68; (Group 6) SEQ ID NO:84-91; (Group 7) SEQ ID NO: 106-111; (Group 8) SEQ ID NO: 122-125; (Group 9) SEQ ID Nos:211-290; (Group 10) SEQ ID NO:343-354; (Group 11) SEQ ID NO:374-379; (Group 12) SEQ ID NO:390-393; (Group 13) SEQ ID NO:411-422; and (Group 14) SEQ ID N0:500-541.
  • the crRNA comprises a guide segment of 16-26 nucleotides or 20-24 nucleotides. Accordingly, in various embodiments, tire crRNA of the Casl2a genome editing systems hybridizes to one or more targeted polynucleotide sequence. In certain preferred embodiments, the crRNA is 43- nucleotides. In other embodiments, the crRNA is made up of a 20-nucleotide 5 '-handle and a 23- nucleotide leader sequence. In certain embodiments, the leader sequence comprises a seed region and 3' termini, both of which are complementary to the target region in the genome Li, Bin et al. “Engineering CRISPR-Cpfl crRNAs and rnRNAs to maximize genome editing efficiency.” Nature biomedical engineering vol. 1,5 (2017): 0066. doi: 10.1038/s41551-017-0066.
  • the crRNA-guided endonuclease provides alteration of numerous loci in host cell genomes.
  • the Cast 2a (or Cas Type V) comprises multiplexing performed using two methods.
  • One method involves expressing many single gRNAs under different small RNA promoters either in same vector or in different vectors.
  • Another method multiple single gRNAs are fused with a tRNA recognition sequence, which are expressed as a single transcript under one promoter.
  • the spacer sequence has a length of from 15 to 50 nucleotides (e.g., from 15 nucleotides (nt) to 20 nt, from 20 nt to 25 nt, from 25 nt to 30 nt, from 30 nt to 35 nt, from 35 nt to 40 nt, from 40 nt to 45 nt, or from 45 nt to 50 nt).
  • 15 nucleotides (nt) to 20 nt from 20 nt to 25 nt, from 25 nt to 30 nt, from 30 nt to 35 nt, from 35 nt to 40 nt, from 40 nt to 45 nt, or from 45 nt to 50 nt.
  • a subject guide RNA can interact with a target nucleic acid (e.g., double stranded DNA (dsDNA), single stranded DNA (ssDNA), single stranded RNA (ssRNA), or double stranded RNA (dsRNA)) in a sequence-specific manner via hybridization (i.e., base pairing).
  • a target nucleic acid e.g., double stranded DNA (dsDNA), single stranded DNA (ssDNA), single stranded RNA (ssRNA), or double stranded RNA (dsRNA)
  • dsDNA double stranded DNA
  • ssDNA single stranded DNA
  • ssRNA single stranded RNA
  • dsRNA double stranded RNA
  • the guide RNA can be modified to hybridize to any desired target sequence (e.g., while taking the PAM into account, e.g.. when targeting a dsDNA target) within a target nucleic acid (e.g., a eukaryotic target nucleic acid such as genomic DNA).
  • a target nucleic acid e.g., a eukaryotic target nucleic acid such as genomic DNA.
  • the percent complementarity between tire spacer sequence of the guide and the target site of the target nucleic acid is 60% or more (e.g., 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%).
  • the percent complementarity between the spacer and the target site of the target nucleic acid is 80% or more (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the spacer and the target site of the target nucleic acid is 90% or more (e.g., 95% or more, 97% or more, 98% or more. 99% or more, or 100%). In some cases, the percent complementarity between the spacer and the target site of the target nucleic acid is 100%.
  • the percent complementarity between the spacer sequence and the target site of the target nucleic acid is 100% over an at least 5-nucleotide contiguous region of the spacer. In some cases, the percent complementarity between tire guide sequence and the target site of the target nucleic acid over an at least 6-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%).
  • the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 7-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%).
  • the percent complementarity between tire guide sequence and the target site of the target nucleic acid over an at least 9-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%).
  • the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 10-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more.
  • the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 11 -nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%).
  • the percent complementarity between tire guide sequence and the target site of the target nucleic acid over an at least 12-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more.
  • the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 17-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%).
  • the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 18-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 19-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more.
  • the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 20-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 21 -nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more.
  • the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 22 -nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%).
  • tire percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 16-21 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%).
  • the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 17-22 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more. 75% or more.
  • Examples of various guide RNAs can be found in tire art. and in some cases variations similar to those introduced into Cas9 guide RNAs can also be introduced into guide RNAs of the present disclosure (e.g., mutations to the dsRNA duplex region, extension of the 5’ or 3’ end for added stability for to provide for interaction with another protein, and the like).
  • variations similar to those introduced into Cas9 guide RNAs can also be introduced into guide RNAs of the present disclosure (e.g., mutations to the dsRNA duplex region, extension of the 5’ or 3’ end for added stability for to provide for interaction with another protein, and the like).
  • Jinek et aL Science. 2012 Aug 17;337(6096): 816-21 ; Chylinski ct al., RNA Biol. 2013 May;10(5):726- 37; Ma ct al., Biomcd Res Int.
  • cEt S-constrained ethyl
  • UNA unlocked nucleic acid
  • the position of the modified nucleotide is identified by reference to tire direct repeat sequence of the guide RNA, wherein position 1 is the first nucleotide of the direct repeat sequence. Accordingly, for example, where the direct repeat sequence is 19 nucleotides in length and a modified nucleotide is indicated to be at position 5. the modified nucleotide will be at position 5 of the direct repeat sequence. Where the position of a modification is at aposition beyond the 3' end of the direct repeat sequence, the modified nucleotide will be in another portion of the guide RNA.
  • the direct repeat sequence is contiguous with the spacer sequence.
  • the guide RNAs disclosed herein target a Cas Type V polypeptide to a target sequence, such as a Cas Type V polypeptide disclosed herein or a polypeptide comprising a Cas Type V polypeptide as disclosed herein, and complexes comprising the guide RNA and the Cas Type V polypeptide are capable of inducing indel formation in a target polynucleotide sequence.
  • Tire target sequence may be a DNA sequence.
  • the reference guide RNA consists of the same nucleotide sequence as the guide RNA and wherein the nucleotides are not modified (i.e., the guide RNA does not comprise 2'-0-Me modifications or phosphorothioate linkages).
  • the PNA probes may be modified to enhance solubility.
  • the PNA probe may comprise a solubility enhancing group such as ethylene glycol.
  • Tire PNA probes may comprise a fluorophore such as Cy5.
  • the PNA probe comprises certain sequences and/or structures as described elsewhere herein.
  • any of the guide RNAs; gene editing systems; polynucleotides encoding the guide RNAs or gene editing systems: vectors; cells; or pharmaceutical compositions disclosed herein can be used in medicine, for example for use in treating or preventing a disease or disorder as disclosed elsewhere herein.
  • the tenn modification also includes, for example, the incorporation of non-nucleotide linkages or modified nucleotides into the mRNA sequences of the present invention (e.g., modifications to one or both of the 3' and 5' ends of an mRNA molecule encoding a functional protein or enzyme).
  • modifications include the addition of bases to an mRNA sequence (e.g., the inclusion of a poly A tail or a longer poly A tail), the alteration of the 3' UTR or the 5' UTR, complexing the mRNA with an agent (e.g., a protein or a complementary nucleic acid molecule), and inclusion of elements which change the structure of an RNA molecule (e.g., which form secondary structures).
  • Additional cap analogs include, but are not limited to, a chemical structures selected from the group consisting of m7GpppG, m7GpppA, m7GpppC: unmethylated cap analogs (e.g., GpppG): dimethylated cap analog (e.g., m2,7GpppG), trimethylated cap analog (e.g., m2,2,7GpppG), dimethylated symmetrical cap analogs (e.g., m7Gpppm7G), or anti reverse cap analogs (e.g., ARCA; m7,2'OmcGpppG, m72'dGpppG, m7,3'OmeGpppG, m7,3'dGpppG and their tetraphosphate derivatives) (see. e.g., Jemielity, J. et al., "Novel 'anti-reverse' cap analogs with superior translational properties", RNA, 9:
  • tire presence of a "tail” serves to protect the RNA (e.g., guide RNAs) from exonuclease degradation.
  • a poly A or poly U tail is thought to stabilize natural messengers and synthetic sense RNA. Therefore, in certain embodiments a long poly A or poly U tail can be added to an RNA molecule thus rendering the RNA more stable.
  • Poly A or poly U tails can be added using a variety of art-recognized techniques. For example, long poly A tails can be added to synthetic or in vitro transcribed RNA using poly A polymerase (Yokoe, et al. Nature Biotechnology.1996; 14: 1252-1256).
  • a transcription vector can also encode long poly A tails.
  • RNAs according to tire present disclosure may be synthesized according to any of a variety of known methods.
  • RNAs according to the present invention may be synthesized via in vitro transcription (IVT).
  • IVT in vitro transcription
  • a linear or circular DNA template containing a promoter, a pool of ribonucleotide triphosphates, a buffer system that may include DTT and magnesium ions, and an appropriate RNA polymerase (e.g., T3, T7 or SP6 RNA polymerase), DNAse I, pyrophosphatase, and/or RNAse inhibitor.
  • an appropriate RNA polymerase e.g., T3, T7 or SP6 RNA polymerase
  • the guide RNAs can comprise an MS2 modification, as specific RNA hairpin structure recognized in nature by a certain MS2-binding protein.
  • This domain can help to stabilize the guide RNAs and improve the editing efficiency.
  • the disclosure contemplates other similar modifications. A review of other such MS2-like domains are described in the art, for example, in Johansson et al. ‘RNA recognition by the MS2 phage coat protein/’ Sem Virol., 1997, Vol.8(3): 176-185; Delebecque et al.
  • polypeptide sequences comprising at least 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, or 65% sequence identity to any one of sequences selected from SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419); and
  • the guide RNA may be a guide RNA as disclosed herein.
  • the disclosure further provides one or more polynucleotides encoding the gene editing system, and one or more vectors comprising such polynucleotides.
  • the disclosure further provides a cell comprising the one or more vectors or the one or more polynucleotides.
  • the disclosure provides a method of modifying a targeted polynucleotide sequence, tire method comprising contacting the targeted polynucleotide sequence with a gene editing system as disclosed herein. The method may be carried out in vitro, ex vivo or in vivo.
  • the genome editing system is characterized in enhanced efficiency and precision of site-directed integration.
  • the efficiency and precision of site-directed integration enabled by genome editing system is enhanced by staggered overhangs on the donor nucleic acid sequence.
  • the targeted polynucleotide sequence is double-stranded and contains a 5' overhang wherein the overhang preferably comprises five nucleotides.
  • the nuclease -deficient polypeptide of the genome editing system comprises a nickase activity.
  • the genome editing system comprises fusion of one or more reverse transcriptases to the nuclease deficient Cas (dCas).
  • the fusion of one or more reverse transcriptases is selected from
  • the Cas 12a genome editing system comprises improved genome editing characteristics selected from efficiency, specificity, precision, intended edits: unintended edits, indels relative to Cas9. Accordingly, it is an object of the invention to reduce off-target effects in host cells in comparison to an equivalent endonuclease activity in host cells relative to SpCas9.
  • the compositions and systems herein may further comprise one or more donor templates for use in editing.
  • the donor template may comprise one or more polynucleotides.
  • the donor template may comprise coding sequences for one or more polynucleotides.
  • the donor template may be a DNA template. It may be single stranded or double stranded. It may also be circular single or double stranded. It may also be linear single stranded or double stranded. Without being bound by theoiy, the donor template may become integrated into the genome after a targeted cut by the Cas 12a gene editing system described herein through cellular repair machinery including HDR and NHEJ.
  • the donor template addresses loss of function mutations, deletions, or translocations that may occur, for example, in certain disease contexts by inserting or restoring a functional copy of a gene, or functional fragment thereof, or a functional regulatory sequence or functional fragment of a regulatory sequence.
  • a functional fragment refers to less than the entire copy of a gene by providing sufficient nucleotide sequence to restore the functionality of a wild type gene or non-coding regulatory sequence (e.g. sequences encoding long non-coding RNA).
  • the systems disclosed herein may be used to replace a single allele of a defective gene or defective fragment thereof.
  • the systems disclosed herein may be used to replace both alleles of a defective gene or defective gene fragment.
  • the donor template manipulates a splicing site on the target polynucleotide.
  • the donor template disrupts a splicing site. The disruption may be achieved by inserting the polynucleotide to a splicing site and/or introducing one or more mutations to the splicing site.
  • the donor template may restore a splicing site.
  • the polynucleotide may comprise a splicing site sequence.
  • the donor template to be inserted may has a size from 10 base pair or nucleotides to 50 kb in length, e.g., from 50 to 40k, from 100 and 30 k, from 100 to 10000, from 100 to 300. from 200 to 400, from 300 to 500, from 400 to 600. from 500 to 700, from 600 to 800, from 700 to 900, from 800 to 1000, from 900 to from 1100, from 1000 to 1200, from 1100 to 1300, from 1200 to 1400, from 1300 to 1500, from 1400 to 1600, from 1500 to 1700, from 600 to 1800, from 1700 to 1900, from 1800 to 2000 base pairs (bp) or nucleotides in length.
  • bp base pairs
  • the donor / template may encode or comprises a functional DNA element, such as a promoter, an enhancer, a protein binding sequence, a methylation site, or a homology region for assisting gene editing, etc.
  • a functional DNA element such as a promoter, an enhancer, a protein binding sequence, a methylation site, or a homology region for assisting gene editing, etc.
  • donor DNA or “donor DNA template” it is meant a DNA segment (can be single stranded or double stranded DNA) to be inserted at a site cleaved by a gene-editing nuclease (e.g., a Casl2a nuclease) (e.g., after dsDNA cleavage, after nicking a target DNA, after dual nicking a target DNA. and the like).
  • the donor DNA template can contain sufficient homology to a genomic sequence at the target site, e.g., 70%, 80%, 85%, 90%, 95%, or 100% homology with the nucleotide sequences flanking the target site, e.g.
  • Donor DNA template can be of any length, e.g., 50 nucleotides or more, 100 nucleotides or more, 250 nucleotides or more, 500 nucleotides or more, 1000 nucleotides or more, 5000 nucleotides or more, etc.
  • a suitable donor DNA template can be from 50 nucleotides to 100 nucleotides, from 100 nucleotides to 500 nucleotides, from 500 nucleotides to 1000 nucleotides, from 1000 nucleotides to 5000 nucleotides, or from 5000 nucleotides to 10,000 nucleotides, or more than 10,000 nucleotides, in length.
  • the donor DNA template comprises a first homology arm and a second homology arm.
  • the first homology arm is at or near the 5’ end of the donor DNA; and comprises a nucleotide sequence that is at least partially complementary to a first nucleotide sequence in a target nucleic acid.
  • Tire second homology arm is at or near the 3 ’ end of the donor DNA; and comprises a nucleotide sequence that is at least partially complementary to a second nucleotide sequence in the target nucleic acid.
  • Hie first and second homology anns can each independently have a length of from about 10 nucleotides to 400 nucleotides: e.g., from 10 nucleotides (nt) to 15 nt, from 15 nt to 20 nt, from 20 nt to 25 nt, from 25 nt to 30 nt, from 30 nt to 35 nt, from 35 nt to 40 nt, from 40 nt to 45 nt, from 45 nt to 50 nt, from 50 nt to 75 nt, from 75 nt to 100 nt, from 100 nt to 125 nt, from 125 nt to 150 nt, from 150 nt to 175 nt, from 175 nt to 200 nt, from 200 nt to 225 nt, from 225 nt to 250 nt, from 250 nt to 275 nt, from 275 nt to 300 nt, from 3
  • these defective genes may be associated with one or more disease phenotypes.
  • the defective gene or gene fragment is not replaced but the heterologous nucleic acid is used to insert donor polynucleotides that encode gene or gene fragments that compensate for or override defective gene expression such that cell phenotypes associated with defective gene expression are eliminated or changed to a different or desired cellular phenotype.
  • This can be achieved by including the coding sequence of a therapeutic protein, such as a therapeutic antibody or functional fragment thereof, or a wild-type version of a defective protein associated with one or more disease phenotypes.
  • the donor may include, but not be limited to, genes or gene fragments, encoding proteins or RNA transcripts to be expressed, regulatory elements, repair templates, and the like.
  • tire donor polynucleotides may comprise left end and right end sequence elements that function with transposition components that mediate insertion.
  • the donor DNA template to be inserted has a size from 10 bp to 50 kb in length, e.g., from 50 bp to ⁇ 40kb, from 100 bp to ⁇ 30 kb, from 100 bp to ⁇ 10 kb, from 100 bp to 300 bp, from 200 bp to 400 bp, from 300 bp to 500 bp, from 400 bp to 600 bp, from 500 bp to 700 bp, from 600 bp to 800 bp, from 700 bp to 900 bp, from 800 bp to 1000 bp, from 900 bp to 1100 bp, from 1000 bp to 1200 bp, from 1100 bp to 1300 bp, from 1200 bp to 1400 bp, from 1300 bp to 1500 bp, from 1400 bp to 1600 bp, from 1500 bp to 1700 bp,
  • the first homology arm and the second homology arm of the donor DNA flank a nucleotide sequence (“a nucleotide sequence of interest” or ‘'an intervening nucleotide sequence”) that is to be introduced into a target nucleic acid.
  • the nucleotide sequence of interest can comprise: i) a nucleotide sequence encoding a polypeptide of interest; ii) a nucleotide sequence encoding an exon of a gene; iii) a promoter sequence; iv) an enhancer sequence; v) a nucleotide sequence encoding a non-coding RNA; or vi) any combination of the foregoing.
  • a disease or as an antiviral, antipathogenic, or anticancer therapeutic, the production of genetically modified organisms in agriculture, the large scale production of proteins by cells for therapeutic, diagnostic, or research purposes, the induction of pluripotent stem cells, biological research, the targeting of genes of pathogens for deletion or replacement, etc.
  • the donor DNA comprises a nucleotide sequence encoding a polypeptide of interest.
  • Polypeptides of interest include, e.g., a) functional versions of a polypeptide that comprises one or more amino acid substitutions, insertions, and/or deletions and that exhibits reduced function, e.g., where the reduced function is associated with or causes a pathological condition; b) fluorescent polypeptides; c) hormones; d) receptors for ligands; e) ion channels; f) neurotransmitters; g) and the like.
  • TNF receptor superfamily member 5 LCAT (lecithin-cholesterol acyltransferase), CCR5 (chemokine (C-C motif) receptor 5), MMP1 (matrix metallopeptidase 1 (interstitial collagenase)), TIMP1 (TIMP metallopeptidase inhibitor 1), ADM (adrenomedullin), DYT10 (dystonia 10), STAT3 (signal transducer and activator of transcription 3 (acute-phase response factor)), MMP3 (matrix metallopeptidase 3 (stromelysin 1, progelatinase)), ELN (elastin), USF1 (upstream transcription factor 1), CFH (complement factor H), HSPA4 (heat shock 70 kDa protein 4), MMP12 (matrix metallopeptidase 12 (macrophage elastase)), MME (membrane metallo- endopeptidase), F2R (
  • CHKA choline kinase alpha
  • BEST1 beta (A4) precursor protein
  • CTNNB1 catenin (cadherin-associated protein), beta 1. 88 kDa
  • IL2 interleukin 2
  • CD36 CD36 molecule (thrombospondin receptor)
  • PRKAB1 protein kinase, AMP -activated, beta 1 non-catalytic subunit
  • TPO thyroid peroxidase
  • ALDH7A1 aldehyde dehydrogenase 7 family, member Al
  • CX3CR1 chemokine (C-X3-C motif) receptor 1
  • TH tyrosine hydroxylase
  • F9 coagulation factor IX
  • GH1 growth hormone 1
  • TF transferrin
  • HFE hemochromatosis
  • IE17A interleukin 17A
  • PTEN phosphatase and tensin homolog
  • GSTM1 glutase and tensin homolog
  • CYP1B1 cytochrome P450. family 1, subfamily B, polypeptide 1
  • MIF macrophage migration inhibitory factor (glycosylation-inhibiting factor)
  • MMP13 matrix metallopeptidase 13 (collagenase 3)
  • TIMP2 TIMP metallopeptidase inhibitor 2
  • CYP19A1 cytochrome P450, family 19, subfamily A, polypeptide 1
  • CYP21A2 cytochrome P450, family 21, subfamily A, polypeptide 2
  • PTPN22 protein tyrosine phosphatase, non-receptor type 22 (lymphoid)
  • MYH14 myosin, heavy chain 14, non-muscle
  • MBL2 mannose-binding lectin (protein C) 2, soluble (opsonic defect)
  • SELPLG selectivein P ligand
  • A0C3 amine oxidase, copper containing 3 (vascular adhesion protein 1)
  • CTSL1 cathex
  • CAST (calpastatin), CXCL12 (chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1)), IGHE (immunoglobulin heavy constant epsilon), KCNE1 (potassium voltage-gated channel, Isk-related family, member 1), TFRC (transferrin receptor (p90, CD71)), COL1A1 (collagen, type I, alpha 1), C0L1A2 (collagen, type I, alpha 2), IL2RB (interleukin 2 receptor, beta), PLA2G10 (phospholipase A2, group X), ANGPT2 (angiopoietin 2), PROCR (protein C receptor, endothelial (EPCR)), N0X4 (NADPH oxidase 4), HAMP (hepcidin antimicrobial peptide), PTPN11 (protein tyrosine phosphatase, non-receptor type 11).
  • HSPG2 heparan sulfate proteoglycan 2
  • CCL3 chemokine (C-C motif) ligand 3
  • MYD88 myeloid differentiation primary response gene (88)
  • VIP vaactive intestinal peptide
  • SOAT1 sterol O-acyltransferase 1
  • ADRBK1 adrenergic, beta, receptor kinase 1
  • NR4A2 nuclear receptor subfamily 4, group A, member 2)
  • MMP8 matrix metallopeptidase 8 (neutrophil collagenase)
  • NPR2 natriuretic peptide receptor B/guanylate cyclase B (atrionatriuretic peptide receptor B)
  • GCH1 GTP cyclohydrolase 1
  • EPRS glutamyl-prolyl - tRNA synthetase
  • PPARGC1A peroxisome proliferator-activated receptor gamma
  • CCL4 chemokine (C-C motif) ligand 4
  • SERP1NA3 serotonine (C-C motif) ligand 4
  • SERP1NA3 serotonin peptidase inhibitor, clade A (alpha- 1 antiproteinase, antitrypsin), member 3
  • CASR calcium-sensing receptor
  • GJA5 gap junction protein, alpha 5, 40 kDa
  • FABP2 fatty' acid binding protein 2, intestinal
  • TTF2 transcription termination factor, RNA polymerase II
  • PROS1 protein S (alpha)
  • CTF1 cardiac protein 1
  • SGCB sarcoglycan, beta (43 kDa dystrophin- associated glycoprotein)
  • YME1L1 YMEl-like 1 (S. cerevisiae)
  • MMP7 matrix metallopeptidase 7 (matrilysin, uterine)
  • AHR aryl hydrocarbon receptor
  • CSF1 colony stimulating factor 1 (macrophage)
  • HDAC9 histone deacetylase 9
  • CTGF connective tissue growth factor
  • KCNMA1 potassium large conductance calcium-activated channel, subfamily M, alpha member 1
  • UGT1A UDP glucuronosyltransferase 1 family, polypeptide A complex locus
  • PRKCA protein kinase C, alpha
  • COMT catechol -b- methyltransf erase
  • S100B S100B
  • EGR1 early growth response 1
  • PRL prolactin
  • IL 15 interleukin 1
  • DRD4 dopamine receptor D4
  • CAMK2G calcium/calmodulin- dependent protein kinase II gamma
  • SLC22A2 solute carrier family 22
  • KCND1 potassium voltage-gated channel, Shal- related subfamily, member 1
  • LOC646627 phospholipase inhibitor
  • TBXAS1 thromboxane A synthase 1 (platelet)
  • CYP2J2 cytochrome P450, family 2, subfamily J, polypeptide 2
  • TBXA2R thromboxane A2 receptor
  • ADH1C alcohol dehydrogenase 1C (class I), gamma polypeptide
  • ALOX12 arachidonate 12-lipoxygenase
  • AHSG alpha-2 -HS-glycoprotein
  • BHMT betaine- homocysteine methyltransferase
  • GJA4 gap junction protein, alpha 4, 37 kDa
  • SLC25A4 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4
  • ACLY ATP citrate lyase
  • SFTPD surfactant protein D
  • TAP2 transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)
  • RNF123 ring finger protein 123
  • PTK2B PTK2B protein tyrosine kinase 2 beta
  • NTRK2 neurotrophic tyrosine kinase, receptor, type 2
  • IL6R interleukin 6 receptor
  • ACHE acetylcholinesterase (Yt blood group)
  • GLP1R glucagon-like peptide 1 receptor
  • GHR growth hormone receptor
  • GSR glutthione reductase
  • NQO1 NAD(P)H dehydrogenase, quinone 1
  • NR A1 nuclear receptor subfamily 5, group A, member 1)
  • GJB2 Gap junction protein, beta 2, 26 kDa
  • SLC9A1 solute carrier family 9 (sodium/hydrogen exchanger), member 1)
  • MAOA monoamine oxida
  • EDN3 endothelin 3
  • DHFR dihydrofolate reductase
  • GAS6 growth arrest-specific 6
  • SMPD1 sphingomyelin phosphodiesterase 1, acid lysosomal
  • UCP2 uncoupling protein 2 (mitochondrial, proton carrier)
  • TFAP2A transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)
  • C4BPA complement component 4 binding protein, alpha
  • SERPINF2 serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2).
  • TYMP thymidine phosphorylase
  • ALPP alkaline phosphatase, placental (Regan isozyme)
  • CXCR2 chemokine (C-X-C motif) receptor 2
  • SLC39A3 solute carrier family 39 (zinc transporter), member 3).
  • MECP2 methyl CpG binding protein 2 (Rett syndrome)
  • MYLK myosin light chain kinase
  • BCF1E butyrylcholinesterase
  • EIPE lipase, hormone-sensitive
  • PRDX5 peroxiredoxin 5
  • ADORA1 (adenosine Al receptor), WRN (Werner syndrome, RecQ helicase-like), CXCR3 (chemokine (C-X-C motif) receptor 3), CD81 (CD81 molecule), SMAD7 (SMAD family member 7), LAMC2 (laminin, gamma 2), MAP3K5 (mitogen- activated protein kinase kinase kinase 5), CF1GA (chromogranin A (parathyroid secretory protein 1)), IAPP (islet amyloid polypeptide), RFIO (rhodopsin), ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase 1), PTF1LF1 (parathyroid hormone-like hormone), NRG1 (neuregulin 1), VEGFC (vascular endothelial growth factor C), ENPEP (glutamyl aminopeptidase (aminopeptidase A)), CEBPB (CCAAT/enhancer binding
  • MYOC myocilin, trabecular mesh work inducible glucocorticoid response
  • ATP1A2 ATPase, Na+/K+ transporting, alpha 2 polypeptide
  • NF1 neurofibromin 1
  • GJB1 gap junction protein, beta 1, 32 kDa
  • MEF2A myocyte enhancer factor 2A
  • VCL vinculin
  • BMPR2 bone morphogenetic protein receptor, type II (serine/threonine kinase)
  • TUBB tubulin, beta
  • CDC42 cell division cycle 42 (GTP binding protein, 25 kDa)
  • KRT18 keratin 18
  • F1SF1 heat shock transcription factor 1
  • MYB v-myb myeloblastosis viral oncogene homolog (avian)
  • PRKAA2 protein kinase, AMP-activated, alpha 2 catalytic subunit
  • R0CK2 Ra-associated, coiled
  • VAV2 vav 2 guanine nucleotide exchange factor
  • NPY2R neuropeptide Y receptor Y2
  • IGFBP2 insulin-like growth factor binding protein 2, 36 kDa
  • CD28 CD28 molecule
  • GSTA1 glutthione S-transferase alpha 1
  • PPIA peptidylprolyl isomerase A
  • CF1GB chromogranin B (secretogranin 1)
  • PRKCB protein kinase C, beta
  • SRD A1 steroid-5 -alpha- reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)
  • F1SD11B2 hydroxy steroid (11-beta) dehydrogenase 2)
  • CALCRL calcium receptor-like
  • GALNT2 UDP-N- acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)
  • ANGPTL4 angiopoietin-like 4
  • KCNN4 potassium intennediate/small conductance calcium-activated channel, subfamily N, member 4
  • PIK3C2A phosphoinositide-3-kinase, class 2.
  • HBEGF heparin-binding EGF-like growth factor
  • CYP7A1 cytochrome P450, family 7, subfamily A, polypeptide 1
  • HLA-DRB5 major histocompatibility complex, class II, DR beta 5
  • BNIP3 BCL2/adeno virus E1B 19 kDa interacting protein 3
  • GCKR glucokinase (hexokinase 4) regulator
  • S100A12 S100 calcium binding protein A 12
  • PADI4 peptidyl arginine deaminase, type IV
  • HSPA14 heat shock 70 kDa protein 14
  • CXCR1 chemokine (C-X-C motif) receptor 1)
  • H19 H19, imprinted maternally expressed transcript (non-protein coding)
  • KRTAP19-3 Keratin associated protein 19-3
  • RAC2 ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)
  • RYR1 ryanodine receptor 1 (skeletal)), CLOCK (clock homolog (mouse)), NGFR (nerve growth factor receptor (TNFR superfamily, member 16)), DBH (dopamine beta-hydroxylase (dopamine beta-monooxygenase)), CHRNA4 (cholinergic receptor, nicotinic, alpha 4), CACNA1C (calcium channel, voltage -dependent, L type, alpha 1C subunit), PRKAG2 (protein kinase, AMP-activated, gamma 2 non-catalytic subunit), CHAT (choline acetyltransferase), PTGDS (prostaglandin D2 synthase 21 kDa (brain)).
  • NR1H2 nuclear receptor subfamily 1. group H. member 2).
  • TEK TE
  • PARP2 poly (ADP-ribose) polymerase 2).
  • STAR steroidogenic acute regulatory protein.
  • LBP lipopolysaccharide binding protein
  • ABCC6 ATP- binding cassette, sub-family C(CFTR/MRP), member 6
  • RGS2 regulatory of G-protein signaling 2, 24 kDa
  • EFNB2 ephrin-B2
  • cystic fibrosis transmembrane conductance regulator CFTR
  • GJB6 gap junction protein, beta 6, 30 kDa
  • APOA2 apolipoprotein A-II
  • AMPD1 adenosine monophosphate deaminase 1
  • DYSF dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive)
  • FDFT1 famesyl -diphosphate famesyltransferase 1
  • EDN2 endothelin 2
  • TERC telomerase RNA component
  • GGT2 gamma-glutamyltransf erase 2
  • MT-CO1 mitochondrially encoded cytochrome c oxidase I
  • UOX urate oxidase, pseudogene
  • a CRISPR/Cas effector polypeptide an enzymatically active CRISPR/Cas effector polypeptide (e.g., is capable of cleaving a target nucleic acid) and a CRISPR/Cas effector polypeptide that is not enzymatically active (e.g., does not cleave a target nucleic acid, but retains binding to the target nucleic acid).
  • the donor DNA comprises a nucleotide sequence encoding a fluorescent polypeptide.
  • Suitable fluorescent proteins include, but are not limited to, green fluorescent protein (GFP) or variants thereof, blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP).
  • GFPS65T Emerald, Topaz (TYFP), Venus, Citrine, mCitrine, GFPuv, destabilized EGFP (dEGFP), destabilized ECFP (dECFP), destabilised EYFP (dEYFP), mCFPm, Cerulean, T-Sapphire, CyPet, YPet, mKO, HcRed, t-HcRed, DsRed, DsRed2, DsRed-monomer, J-Red, dimer2, t-dimer2(12), mRFPl, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein and kindling protein.
  • the donor DNA encodes an RNA, e.g., an siRNA, a microRNA, a short hairpin RNA (shRNA), an anti-scnsc RNA, a riboswitch, a ribozyme, an aptamer, a ribosomal RNA, a transfer RNA, and the like.
  • an RNA e.g., an siRNA, a microRNA, a short hairpin RNA (shRNA), an anti-scnsc RNA, a riboswitch, a ribozyme, an aptamer, a ribosomal RNA, a transfer RNA, and the like.
  • a donor DNA can include, in addition to a nucleotide sequence encoding one or more gene products (e.g., an RNA and/or a polypeptide), one or more transcriptional control elements, e.g., a promoter, an enhancer, and the like.
  • the transcriptional control element is inducible.
  • the promoter is reversible.
  • the transcriptional control element is constitutive.
  • the promoter is functional in a eukaryotic cell.
  • the promoter is a cell type- specific promoter.
  • the promoter is a tissue-specific promoter.
  • the donor DNA will include one or more nucleotide sequences to aid in localization of the donor to the nucleus of the recipient cell or to aid in the integration of the donor DNA into tire target nucleic acid.
  • the donor DNA may comprise one or more nucleotide sequences encoding one or more nuclear localization signals (e.g.
  • the donor DNA is delivered as reconstituted chromatin (Cruz-Becerra and Kadonaga (2020) eLife 2020;9:e55780 DOI: 10.7554/eLife.55780).
  • the ends of the donor DNA are protected (e.g., from exonucleolytic degradation) by any convenient method and such methods are known to those of skill in the art.
  • one or more dideoxynucleotide residues can be added to tire 3' terminus of a linear molecule and/or self complementary oligonucleotides can be ligated to one or both ends. See, for example. Chang et al. (1987) Proc. Natl. Acad Sci USA 84:4959-4963; Nehls et al. (1996) Science 272:886-889.
  • Additional methods for protecting exogenous polynucleotides from degradation include, but are not limited to, addition of terminal amino group(s) and the use of modified intemucleotide linkages such as, for example, phosphorothioates, phosphoramidates, and O-methyl ribose or deoxyribose residues.
  • modified intemucleotide linkages such as, for example, phosphorothioates, phosphoramidates, and O-methyl ribose or deoxyribose residues.
  • additional lengths of sequence may be included outside of the regions of homology that can be degraded without impacting recombination.
  • the Casl2a polypeptides are coupled to one or more accessory functions by a linker.
  • Such accessory functions can include deaminases, nucleases, reverse transcriptases, and recombinases.
  • One or more gRNAs directed to such promoters or enhancers may also be provided to direct the binding of the Casl2a polypeptide to such promoters or enhancers.
  • the term linker as used in reference to a fusion protein refers to a molecule which joins the proteins to fonn a fusion protein. Generally, such molecules have no specific biological activity other than to join or to preserve some minimum distance or other spatial relationship between the proteins. However, in one embodiment, the linker may be selected to influence some property of the linker and/or the fusion protein such as the folding, net charge, or hydrophobicity of the linker.
  • Suitable linkers for use in the methods of the present invention are well known to those of skill in the art and include, but are not limited to, straight or branched-chain carbon linkers, heterocyclic carbon linkers, or peptide linkers.
  • tire linker may also be a covalent bond (carbon-carbon bond or carbon-heteroatom bond).
  • the linker is used to separate the Casl2a polypeptide and an accessory protein (e.g., a nucleotide deaminase) by a distance sufficient to ensure that each protein retains its required functional property.
  • Preferred peptide linker sequences adopt a flexible extended conformation and do not exhibit a propensity for developing an ordered secondary structure.
  • the linker can be a chemical moiety which can be monomeric, dimeric, multimeric or polymeric.
  • the linker comprises amino acids. Typical amino acids in flexible linkers include Gly, Asn and Ser.
  • the linker comprises a combination of one or more of Gly, Asn and Ser amino acids.
  • Other near neutral amino acids such as Thr and Ala, also may be used in the linker sequence.
  • Exemplary linkers are disclosed in Maratea et al. (1985). Gene 40: 39-46; Murphy et al. (1986) Proc. Nat'L Acad. Sci. USA 83: 8258-62; U.S. Pat. No. 4,935,233; and U.S. Pat. No. 4,751,180.
  • GlySer linkers may be based on repeating units of GGS (SEQ ID NO:2657), i.e., up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or even 12 or more repeating units, including but not limited to:
  • GlySer linkers may be based on repeating units of GGGGS (SEQ ID NO:2660), i.e., up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or even 12 or more repeating units, including but not limited to:
  • LEPGEKPYKCPECGKSFSQSGALTRHQRTHTR (SEQ ID NO:662) is used as a linker.
  • Casl2a polypeptide is linked C- terminally to the N-terminus of a deaminase protein or its catalytic domain by means of an LEPGEKPYKCPECGKSFSQSGALTRHQRTHTRLEPGEKPYKCPECGKSFSQSGALTRHQRTHTRLEP GEKPYKCPECGKSFSQSGALTRHQRTHTR (SEQ ID NO:665) linker.
  • N-and C-terminal NLSs can also function as linker (e.g., PKKKRKVEASSPKKRKVEAS (SEQ ID NO:666)).
  • the linker may be as simple as a covalent bond, or it may be a polymeric linker many atoms in length.
  • the linker is a polypeptide or based on amino acids. In other embodiments, the linker is not peptide-like.
  • the linker is a covalent bond (e.g., a carbon-carbon bond, disulfide bond, carbon-heteroatom bond, etc.).
  • the linker is a carbon-nitrogen bond of an amide linkage.
  • the linker is a cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic or heteroaliphatic linker.
  • the linker is polymeric (e.g., polyethylene, polyethylene glycol, polyamide, polyester, etc ). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminoalkanoic acid. In certain embodiments, the linker comprises an aminoalkanoic acid (e.g., glycine, ethanoic acid, alanine, beta-alanine, 3 -aminopropanoic acid, 4-aminobutanoic acid, 5-pentanoic acid, etc.). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminoHEXAnoic acid (Ahx).
  • Ahx aminoHEXAnoic acid
  • Tire linker can be, for example, a cleavable linker or protease-sensitive linker.
  • the linker is selected from the group consisting of F2A linker, P2A linker, T2A linker, E2A linker, and combinations thereof.
  • This family of self-cleaving peptide linkers referred to as 2A peptides, has been described in the art (see for example, Kim, J. H. et al. (2011) PLoS ONE 6:el8556).
  • the linker is an F2A linker.
  • the linker is a GGGS linker (SEQ ID NO:632).
  • the fusion protein contains three domains with intervening linkers, having tire structure: domain-linker-domain-linker-domain.
  • an editor component polypeptide comprises at most 6 NLSs.
  • an NLS is considered near the N- or C-terminus when the nearest amino acid of tire NLS is within about 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50, or more amino acids along the polypeptide chain from the N- or C-terminus.
  • Nonlimiting examples of NLSs include an NLS sequence derived from: the NLS of the SV40 virus large T-antigen, having the amino acid sequence PKKKRKV (SEQ ID NO:584); the NLS from nucleoplasmin (e.g.
  • the one or more NLSs are of sufficient strength to drive accumulation of the Cast 2a polypeptide (or an NLS-modified accessory protein, or an NLS-modified chimera comprising a Casl2a protein and an accessory protein) in a detectable amount in the nucleus of a eukaryotic cell.
  • strength of nuclear localization activity may derive from the number of NLSs in tire Cast 2a polypeptide, the particular NLS(s) used, or a combination of these factors. Detection of accumulation in the nucleus may be performed by any suitable technique.
  • a detectable marker may be fused to the Casl2a polypeptide, such that location within a cell may be visualized, such as in combination with a means for detecting the location of the nucleus (e.g., a stain specific for the nucleus such as DAPI).
  • Cell nuclei may also be isolated from cells, the contents of which may then be analyzed by any suitable process for detecting protein, such as immunohistochemistry’, Western blot, or enzyme activity assay.
  • Accumulation in the nucleus may also be determined indirectly, such as by an assay for the effect of complex fonnation (e.g., assay for DNA cleavage or mutation at the target sequence, or assay for altered gene expression activity affected by complex formation and/or Casl2a polypeptide activity ), as compared to a control no exposed to the Casl2a polypeptide or complex, or exposed to a Cas 12a polypeptide lacking the one or more NLSs.
  • an assay for the effect of complex fonnation e.g., assay for DNA cleavage or mutation at the target sequence, or assay for altered gene expression activity affected by complex formation and/or Casl2a polypeptide activity
  • the codon optimized Cas 12a polypeptide proteins comprise an NLS attached to the C-tenninal of the protein.
  • other localization tags may be fused to the Cas 12a polypeptide, such as without limitation for localizing the Casl2a polypeptide to particular sites in a cell, such as organelles, such as mitochondria, plastids, chloroplast, vesicles, golgi, (nuclear or cellular) membranes, ribosomes, nucleolus, ER, cytoskeleton, vacuoles, centrosome, nucleosome, granules, centrioles, etc.
  • organelles such as mitochondria, plastids, chloroplast, vesicles, golgi, (nuclear or cellular) membranes, ribosomes, nucleolus, ER, cytoskeleton, vacuoles, centrosome, nucleosome, granules, centrioles, etc.
  • At least one nuclear localization signal is attached to the nucleic acid sequences encoding the Cas 12a polypeptide.
  • at least one or more C- terminal or N-terminal NLSs are attached (and hence nucleic acid molecule(s) coding for the Cas 12a polypeptide can include coding for NLS(s) so that the expressed product has the NLS(s) attached or connected).
  • a C-terminal NLS is attached for optimal expression and nuclear targeting in eukaryotic cells, preferably human cells.
  • the invention also encompasses methods for delivering multiple nucleic acid components, wherein each nucleic acid component is specific for a different target locus of interest thereby modifying multiple target loci of interest.
  • the nucleic acid component of the complex may comprise one or more protein-binding RNA aptamers.
  • the one or more aptamers may be capable of binding a bacteriophage coat protein.
  • the fusion proteins comprising Cas 12a and another accessory protein contains one or more nuclear localization signals is selected or derived from SV40.
  • c-Myc or NLP-1 contains one or more nuclear localization signals is selected or derived from SV40.
  • Tire NLS examples above are non-limiting.
  • the Cas 12a fusion proteins contemplated herein may comprise any known NLS sequence, including any of those described in Cokol et al. /'Finding nuclear localization signals,” EMBO Rep., 2000, 1(5): 411-415 and Freitas et al. /‘Mechanisms and Signals for the Nuclear Import of Proteins,” Current Genomics, 2009, 10(8): 550-7, each of which are incorporated herein by reference.
  • the Cas 12a editing system peptide may comprise an amino acid tag, such as one or more lysines, histidines, or glutamates, which can be added to the polypeptide sequences (e.g., at the N-terminal or C-tenninal ends). Lysines can be used to increase peptide solubility or to allow for biotinylation.
  • Protein and amino acid tags are peptide sequences genetically grafted onto a recombinant protein. Sequence tags are attached to proteins for various purposes, such as peptide purification, identification, or localization, for use in various applications including, for example, affinity purification, protein array, western blotting, immunofluorescence, and immunoprecipitation. Such tags are subsequently removable by chemical agents or by enzymatic means, such as by specific proteolysis or intein splicing.
  • the nucleic acid components (e.g., guide RNA) of the Casl2a editing systems may further comprise a functional structure designed to improve nucleic acid component molecule structure, architecture, stability, genetic expression, or any combination thereof.
  • a functional structure designed to improve nucleic acid component molecule structure, architecture, stability, genetic expression, or any combination thereof.
  • Such a structure can include an aptamer.
  • Nucleic acid aptamers can for example be selected from pools of random-sequence oligonucleotides, with high binding affinities and specificities for a wide range of biomedically relevant targets, suggesting a wide range of therapeutic utilities for aptamers (Keefe, Anthony
  • RNA aptamers may also be constructed that function as molecular switches, responding to a que by changing properties, such as RNA aptamers that bind fluorophores to mimic the activity of green fluorescent protein (Paige, Jeremy S., Karen Y. Wu, and Sarnie R. Jaffrey. "RNA mimics of green fluorescent protein.” Science 333.6042 (2011): 642-646). It has also been suggested that aptamers may be used as components of targeted siRNA therapeutic delivery systems, for example targeting cell surface proteins (Zhou, Jiehua, and John J. Rossi. "Aptamer-targeted cell-specific RNA interference.” Silence 1.1 (2010): 4).

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Abstract

The present disclosure provides methods and compositions comprising novel Cas Type V programmable nucleases and lipid nanoparticles capable of delivering the Cas Type V programmable nucleases and genome editing systems comprising same. For therapeutic applications, as well as plants and industrial biotechnology.

Description

IMPROVED GENE EDITING SYSTEM, GUIDES, AND METHODS
RELATED APPLICATIONS
[0001] This application refers to and incorporates by reference the contents of tire following U.S. Provisional Application Nos: 63/621,975 [Ref. No. CSG018-P1], filed January 17, 2024. 63/552,429 [Ref. No. CSG018- P2], filed February 12, 2024, 63/648,416 [Ref. No. CSG018-P3]. filed May 16. 2024. and 63/706,484 [Ref. No. CSG018-P4] filed October 11, 2024, in their entireties.
[0002] The foregoing applications, and all documents cited therein and all documents cited or referenced herein, together with any manufacturer’s instructions, descriptions, product specifications, and product sheets for any products mentioned herein or in any document incorporated by reference herein, are hereby incorporated herein by reference, and may be employed in the practice of the disclosed subject matter. More specifically, all referenced documents are incorporated by reference to the same extent as if each individual document was specifically and individually indicated to be incorporated by reference.
SEQUENCE LISTING
[0003] The instant application contains a Sequence Listing which has been submitted via Patent Center and is hereby incorporated by reference in its entirety. Said .xml copy, created on 16 January 2025, is named J0356-99006.xml, and is 4,258.691 bytes in size.
TECHNICAL FIELD
[0004] The present disclosure generally relates to gene editing systems, nucleases, guides, methods and compositions used for precise genome editing, including nucleic acid insertions, replacements, and deletions at targeted and precise genome sites, wherein said systems, methods, and compositions are based on engineered class II/type V Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas systems and engineered guides.
BACKGROUND
[0005] Genome editing tools encompass a diverse set of technologies that can make many types of genomic alterations in various contexts. These technologies have evolved over the last couple of decades to provide a range of user-programmable editing tools that include ZFN (zinc finger) nuclease editing systems, meganuclease editing systems, and TALENS (transcription activator-like effector nucleases). The past decade has seen an explosive growth in a new generation of genome editing systems based on components from bacterial immune pathways, including CRISPR (clustered regularly interspaced short palindromic repeats) and the associated CRISPR-associated proteins (e g., CRISPR-Cas9) (Jinek et al., “A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity,” Science, Vol. 337 (6096), pp. 816- 821), meganuclease editors (Boissel et al., “megaTALs: a rare-cleaving nuclease architecture for therapeutic genome engineering,” Nucleic Acids Research 42: pp. 2591-2601) and bacterial retron systems (Schubert et al., '‘High-throughput functional variant screens via in vivo production of single-stranded DNA,” PNAS, April 27, 2021, Vol. 118(18), pp. 1-10). In particular, CRISPR-Cas9 has been derivatized in numerous ways to expand upon its guide RNA-based programmable double-strand cutting activity to fonn systems ranging from finding alternative CRISPR Cas nuclease enzymes having different PAM requirements and cutting properties (e.g.. Casl2a, Casl2f, Casl3a. and Casl3b) to base editing (Komor et al., “Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage,” Nature, May 19, 2016, 533 (7603); pp. 420-424 [cytosine base editors or CBEs] and Gaudelli et al., “Programmable base editing of A-T to G-C in genomic DNA without DNA cleavage,” Nature, Vol. 551, pp. 464-471 [adenine base editors or ABEs]) to prime editing (Anzalone et al., “Search-and-replace genome editing without double-strand breaks or donor DNA,” Nature, Dec 2019, 576 (7789): pp. 149-157) to twin prime editing (Anzalone et al., “Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing,” Nature Biotechnology, Dec 9, 2021, vol. 40, pp. 731-740) to epigenetic editing (Kungulovski and Jeltsch, “Epigenome Editing: State of the Art, Concepts, and Perspective,” Trends in Genetics, Vol.32, 206, pp. 101-113) to CRISPR-directed integrase editing (Y amell et al., “Drag-and-drop genome insertion of large sequences without double-stranded DNA cleavage using CRISPR-directed integrases,” Nature Biotechnology, Nov 24. 2022, doi.org/10.1038/s41587-022-01527-4 (“PASTE”)).
[0006] In particular, application of CRISPR-associated systems (“CRISPR-Cas systems”) in human therapeutics is anticipated to be curative in ameliorating various monogenic diseases and disorders. Current clinical trials are underway to treat, for instance, Transfusion-dependent 0-thalassemia (TDT) and sickle cell disease (SCD) by tire autologous transfusion of CRISPR/Cas9-edited CD34+ hematopoietic stem cells Frangoul, Haydar et al. “CRISPR-Cas9 Gene Editing for Sickle Cell Disease and |3- Thalassemia.” The New England journal of medicine vol. 384,3 (2021): 252-260. doi:10.1056/NEJMoa2031054 and ATTR amyloidosis Gillmore, Julian D et al. “CRISPR- Cas9 In Vivo Gene Editing for Transthyretin Amyloidosis.” The New England journal of medicine vol. 385,6 (2021): 493-502. doi: 10.1056/NEJMoa2107454, which is incorporated herein by reference.
[0007] The potential of such CRISPR-Cas systems has sparked the discover}' of many novel CRISPR-Cas variants where such systems have been classified into 2 classes (i.e., class I and II) and 6 types and 33 subtypes based on their genes, protein subunits and the structure of their gRNAs. Makarova, K.S.. Wolf, Y.I., Iranzo, J. et al. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat Rev Microbiol 18, 67-83 (2020). doi: 10.1038/s41579-019-0299-x, which is incorporated herein by reference.
[0008] Among the diverse CRISPR-Cas systems, class II has the most extensive applications in gene editing due to its earlier discover}' and by virtue of it having only one effector protein. By contrast, the effector nucleases of the type V family are diverse due to extensive diversity over the N-tenninus of the protein, as evident by comparing the cry stal structures of Casl2a, Casl2b, and Casl2e type V nucleases (Tong et al., “The Versatile Type V CRISPR Effectors and Their Application Prospects,” Front. Cell Dev. Biol., 2021, vol. 8). The C-terminus regions of the type V effector nucleases are more highly conserved, however, which comprise a conserved RuvC-like endonuclease (RuvC) domain. It is reported that the RuvC domain of type V effectors is derived from the TnpB protein encoded by autonomous or non-autonomous transposons (Shmakov et al., “Diversity and evolution of class 2 CRISPR-Cas systems,” 2017, Nat. Rev. Microbiol. 15, 169-182. doi: 10.1038/nrmicro.2016.184). The type V systems are further subdivided into many subty pes, including types V-A to V-I, type V-K, type V-U, and CRISPR Cas® (Hajizadeh et al., “The expanding class 2 CRISPR toolbox: diversity, applicability, and targeting drawbacks,” 2019, BioDrugs 33, 503-513. doi: 10.1007/s40259-019-00369-y). The corresponding effector nucleases in these various subtypes have shown a range of different substrates, including some that act only on double-stranded DNA (dsDNA), but also those that act on both dsDNA as well as single-stranded DNA (ssDNA), and those that act on single-stranded RNA (ssRNA). This multifunctionality has put the type V CRISPR-Cas system into the focus of recent studies. [0009] While a number of CRISPR-Cas type V systems have been used for various applications, including gene editing, reported drawbacks have been published to indicate the need for improved CRISPR-Cas type V systems for suitability of desired applications. Therefore, there remains much room for improvement and design to achieve an effective type V CRISPR-Cas system for gene editing that bears sufficient editing efficiency, improved precision, better deliverability, and which remains affordable, easy to scale, and has improved ability to treat various genetic disorders and complex diseases.
SUMMARY
[0010] Hie present disclosure provides Cas TypeV-based gene editing systems for use in various applications, including precision gene editing in cells, tissues, organs, or organisms. In various embodiments, the Cas TypeV-based gene editing systems comprise (a) a Type V polypeptide and (b) a Type V guide RNA which is capable of associating with a Type V polypeptide to form a complex such that the complex localizes to a target nucleic acid sequence (e.g., a genomic or plasmid target sequence) and binds thereto. In various embodiments, the Type V polypeptide has a nuclease activity which results in the cutting of both strands of DNA
[0011] In various embodiments, the Cas Type V polypeptide is a polypeptide selected from Table S15A, or a polypeptide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%. or 100% sequence identity with a polypeptide from Table S 15A. In various other embodiments, the Cas Type V polypeptide is encoded by a polynucleotide sequence selected from Table S15B, or a polynucleotide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a polynucleotide of Table S15B. In various other embodiments, the Casl2a guide RNA is selected from any Cas Type V guide sequence disclosed in Table S15C, or a nucleic acid molecule having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a Casl2a guide sequence of Table S15C.
[0012] In various embodiments, the Cas Type V guide RNA may comprise (a) a portion that binds or associates with a Cas Type V polypeptide and (b) a region that comprises a targeting sequence, i.e.. a sequence which is complementary to target nucleic acid sequence. For Cas Type V guide RNA designs, just like for Cas9 guide RNA, the target sequence is typically next to a PAM sequence. But for Cas Type V, the PAM sequence in various embodiments is typically TTTV, where V typically represents A, C, or G. In various embodiments, the “V” of the TTTV is immediately adjacent to the most 5’ base of the non-targeted strand side of the protospacer element. As for Cas9 guide RNA designs, the PAM sequence is typically not included in the guide RNA design.
[0013] In various embodiments, the guide RNA for Cas Type V is relatively short at only approximately 40- 44 bases long. The part that base pairs to the protospacer in the target sequence is 20-24 bases in length, and there is also a constant about 20-base section that binds to Cas Type V.
[0014] In various embodiments, nomenclature for a Cas Type V guide RNA is referred to as a “crRNA” and there is no Cas9-like “tracrRNA” component.
[0015] In other aspects, the Cas Type V -based gene editing systems may comprise one or more additional accessory proteins having genome modifying functions, including recombinases, invertases, nucleases, polymerases, ligases, deaminases, reverse transcriptases, or epigenetic modifying functions. In various embodiments, the accessory' proteins may be provided separately. In other embodiments, tire accessory' proteins may be fused to a Cas Type V nuclease, optionally with a linker.
[0016] In still another aspect, the disclosure provides delivery systems for introducing the Cas Type V - based gene editing systems or components thereof into cells, tissues, organs, or organisms. Depending on the chosen format, the Cas Type V -based gene editing systems and/or the individual or combined components thereof may be delivered as DNA molecules (e.g., encoded on one or more plasmids), RNA molecules (e.g., guide RNAs for targeting the Cas Type V protein or linear or circular mRNAs coding for the Cas Type V protein or accessory' protein components of the Cas Type V -based gene editing systems), proteins (e.g., Casl2a polypeptides, accessory proteins having other functions (e.g., recombinases, nucleases, polymerases, ligases, deaminases, or reverse transcriptases), or protein-nucleic acid complexes (e.g., complexes between a guide RNA and a Cas Type V protein or fusion protein comprising a Cas Type V protein).
[0017] In another aspect, the present disclosure provides nucleic acid molecules encoding the Cas Type V - based gene editing systems or components thereof. In yet another aspect, the disclosure provides vectors for transferring and/or expressing said Cas Type V -based gene editing systems, e.g., under in vitro, ex vivo, and in vivo conditions. In still another aspect, the disclosure provides cell-delivery compositions and methods, including compositions for passive and/or active transport to cells (e.g., plasmids), delivery by virus-based recombinant vectors (e.g., AAV and/or lentivirus vectors), delivery by non-virus-based systems (e.g., liposomes and LNPs), and delivery by vims-like particles of the Cas Type V -based gene editing systems described herein. Depending on the delivery system employed, the Cas Type V -based gene editing systems described herein may be delivered in the form of DNA (e.g., plasmids or DNA-based vims vectors), RNA (e.g., guide RNA and mRNA delivered by LNPs), a mixture of DNA and RNA, protein (e.g., vims-like particles), and ribonucleoprotein (RNP) complexes. Any suitable combinations of approaches for delivering the components of the herein disclosed Cas Type V -based gene editing systems may be employed.
[0018] In other embodiments, the Cas Type V -based gene editing systems may comprise a template DNA comprising an edit, e.g., a single strand or double strand donor molecule (linear or circular) which may be used by the cell to repair a single or double cut lesion introduced by a Cas Type V -based gene editing systems by way of cellular repair processes, including homology-dependent repair (HDR) (e.g., in dividing cells) or non-homologous end joining (NHEJ) (in non-dividing cells).
[0019] In one embodiment, each of the components of the Cas Type V -based gene editing systems is delivered by an all-RNA system, e.g., the delivery of one or more RNA molecules (e.g., mRNA and/or guide RNA) by one or more LNPs, wherein the one or more RNA molecules form the guide RNA and/or are translated into the polypeptide components (e.g., the Cas Type V polypeptides and/or any accessory proteins), and a DNA or RNA-encoded template DNA molecule (e.g., donor template), as appropriate or desired.
[0020] In yet another aspect, the disclosure provides methods for genome editing by introducing a Cas Type V -based gene editing system described herein into a cell (e.g., under in vitro, in vivo, or ex vivo conditions) comprising a target edit site, thereby resulting in an edit at the target edit. In other aspects, the disclosure provides formulations comprising any of the aforementioned components for delivery to cells and/or tissues, including in vitro, in vivo, and ex vivo delivery, recombinant cells and/or tissues modified by the recombinant Cas Type V -based gene editing systems and methods described herein, and methods of modifying cells by conducting genome editing using the herein disclosed Cas Type V -based gene editing systems.
[0021] The disclosure also provides methods of making the Cas Type V -based gene editing systems, their protein and nucleic acid molecule components, vectors, compositions and fonnulations described herein, as well as to pharmaceutical compositions and kits for modifying cells under in vitro, in vivo, and ex vivo conditions that comprise the herein disclosed genome editing and/or modification systems.
[0022] In various aspects, the invention provides an isolated or recombinant polynucleotide comprising or consisting of a nucleic acid sequence selected from tire group consisting of: (a) a nucleic acid sequence that encodes a Cas Type V polypeptide having the amino acid sequence of SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), or SEQ ID NO: 445 (No. ID4I9);
(b) a nucleic acid sequence that encodes a polypeptide at least 50%. at least 55%. at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to a Cas Type V polypeptide of SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. 1D414), or SEQ ID NO: 564 (No. 1D418), SEQ ID NO: 335 (No. 1D406), SEQ ID NO: 331 (No. ID41 1), SEQ ID NO: 20 (No. ID415), or SEQ ID NO: 445 (No. ID419);
(c) a nucleic acid sequence that is a degenerate variant of the nucleic acid sequence in (a) or (b); and
(d) a nucleic acid sequence that hybridizes under stringent conditions to the nucleic acid sequence in in (a) or (b).
[0023] In related aspects, the invention provides an isolated or recombinant guide RNA comprising or consisting of a nucleic acid sequence selected from the group consisting of:
(a) one or more crRNA direct repeat sequences or a reverse complement selected from (Group 1) SEQ ID NO:7-12; (Group 2) SEQ ID NO:24-27; (Group 3) SEQ ID NO:36-39; (Group 4) SEQ ID NO:49-52; (Group 5) SEQ ID NO:63-68; (Group 6) SEQ ID NO:84-91; (Group 7) SEQ ID NO: 106-1 1 1 ; (Group 8) SEQ ID NO: 122-125; (Group 9) SEQ ID Nos:21 1- 290; (Group 10) SEQ ID NO:343-354; (Group 11) SEQ ID NO:374-379; (Group 12) SEQ ID NO:390-393; (Group 13) SEQ ID NO:411-422; and (Group 14) SEQ ID N0:500-541;
(b) 20 to 35 nucleotides or up to the length of the crRNA from the 3' end of tire crRNA direct repeat sequences or a reverse complement (a) linked to a targeting guide attached to the 3’ end of the direct repeat sequence that is of 16-30 nucleotides in length;
(c) (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40- 41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291- 330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563;
(d) a nucleic acid sequence that is a degenerate variant of (Group 1 ) SEQ ID NO:13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54;
(Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355- 360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563;
(e) a nucleic acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99% or at least 99.9% identical to : (Group 1) SEQ ID NO: 13- 15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355- 360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563; and
(f) a nucleic acid sequence that hybridizes under stringent conditions to : (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 1 12-1 14; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395;
(Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563.
[0024] In some embodiments, the isolated or recombinant polynucleotide comprising or consisting of a nucleic acid sequence encoding one or more Cas Type V polypeptides of the disclosure is paired with one or more cognate guide RNA of the disclosure.
[0025] In certain exemplary aspects, provided herein is a Cas Type V gene editing system comprising:
(a) one or more polypeptide sequences comprising at least 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, or 65% sequence identity to any one of sequences selected from SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418). SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No.
ID415), and SEQ ID NO: 445 (No. ID419); and
(b) one or more polynucleotide sequences comprising a guide RNA, wherein the guide RNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
[0026] In various embodiments, disclosed is a method of modifying a targeted polynucleotide sequence, said method comprising: (a) one or more polypeptide sequences comprising at least 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, or 65% sequence identity to any one of sequences selected from SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No.
ID415), and SEQ ID NO: 445 (No. ID419); and
(b) one or more polynucleotide sequences comprising a guide RNA, wherein the guide RNA comprises a complementary' sequence to that of a targeted polynucleotide sequence; and
(c) introducing into a host cell the one or more polypeptide sequences of (a) and the one or more polynucleotide sequences of (b) in a delivery’ vector; wherein the polypeptide sequence is configured to form a ribonucleoprotein complex with the guide RNA, and wherein the ribonucleoprotein complex modifies a targeted polynucleotide sequence.
[0027] In certain preferred embodiments, the method comprises contacting the host cell with a guide RNA, wherein the guide RNA optionally forms a ribonucleoprotein complex with the polypeptide and the guide RNA.
[0028] In various aspects, the present disclosure provides delivery of a Casl2a-based gene editing system described herein Cast 2a in various viral and non-viral vectors. In certain preferred embodiments, the LNP comprises: a) one or more ionizable lipids; b) one or more structural lipids; c) one or more PEGylated lipids; and d) one or more phospholipids.
[0029] In certain embodiments, the LNP comprises one or more ionizable lipids selected from the group consisting of those disclosed herein.
[0030] Also provided herein are pharmaceutical compositions comprising a site-specific modification of a target region of a host cell genome comprising a Cas Type V -based gene editing system described herein Cas Type V comprising one or more Cas Type V polypeptides; one or more cognate guide RNA; and LNP suitable for therapeutic administration.
[0031] In various aspects, provided herein is a method of treating a subject in need thereof, comprising administering to the subject a pharmaceutical composition described herein. In some embodiments, the subject is ameliorated from a diseases or disorders including but not limited to various monogenic diseases or disorders.
[0032] In various embodiments, the disclosure relates to the following numbered paragraphs:
1. A genome editing system comprising: a Cas Type V polypeptide or variant thereof, or a nucleic acid sequence encoding a Cas Type V polypeptide or variant thereof; a second nucleic acid sequence encoding a guide RNA; wherein the Cas Type V polypeptide and tire guide RNA form an RNA-protein complex; wherein the genome editing system optionally further comprises a donor nucleic acid sequence capable of modifying a target sequence.
2. The genome editing system of paragraph 1, wherein the Cas Type V polypeptide or variant thereof is a polypeptide selected from Table S15A (SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419)), or a polypeptide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity’ with a polypeptide from Table S15A (SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418). SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419)).
3. The genome editing system of paragraph 1, wherein the Cas 12a polypeptide is encoded by a polynucleotide sequence selected from Table S15B (SEQ ID NO: 365 (No. ID405), SEQ ID NO: 75 (No. ID414). or SEQ ID NO: 565 (No. ID418), SEQ ID NO: 366 (No. ID406), SEQ ID NO: 331 (No. ID411). SEQ ID NO: 30 (No. ID415). or SEQ ID NO: 445 (No. 1D419)), or a polynucleotide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a polypeptide from Table S15B (SEQ ID NO: 365 (No. ID405), SEQ ID NO: 75 (No. ID414), or SEQ ID NO:565 (No. ID418), SEQ ID NO: 366 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 30 (No. ID415), or SEQ ID NO: 445 (No. ID419)).
4. The genome editing system of paragraph 1, wherein the Cas Type V guide RNA is selected from any Cas Type V guide sequence disclosed in Table S 15C (SEQ ID NO:28-29. 69-71, 355-360, 542-563), or a nucleic acid molecule having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a Cas Type V guide sequence of Table S15C.
5. The genome editing system of paragraph 1, wherein the Cas Type V polypeptide or variant thereof is operably fused to an accessory domain.
6. The genome editing system of paragraph 5, wherein the accessory domain is a deaminase domain, nuclease domain, reverse transcriptase domain, integrase domain, recombinase domain, transposase domain, endonuclease domain, or exonuclease domain.
7. The genome editing system of paragraph 1, wherein the Cas Type V polypeptide or variant thereof is operably fused to a deaminase domain. 8. The genome editing system of paragraph 1, wherein the Cas Type V polypeptide or variant thereof is operably fused to a reverse transcriptase domain.
9. The genome editing system of paragraph 1, wherein the Cas Type V polypeptide or variant thereof is operably fused to a recombinase domain.
10. The genome editing system of paragraph 1, wherein the Cas Type V polypeptide or variant thereof is operably fused to an integrase domain.
11. Tire genome editing system of paragraph 1, wherein the Cas Type V polypeptide or variant thereof is operably fused to atransposase domain.
12. The genome editing system of paragraph 1, wherein the Cas Type V polypeptide or variant thereof is engineered to have an enhanced genome editing efficiency relative to a wildtype SpCas9.
13. The genome editing system of paragraph 12, wherein the enhanced genome editing efficiency comprises at least two to fivefold increase in editing efficiency relative to a wildtype SpCas9.
14. Tire genome editing system of any one of the above paragraphs wherein the donor nucleic acid sequence repairs the target region of the genome editing system genome cleaved by the RNA-protein complex.
15. The genome editing system of any one of the above paragraphs wherein the nucleic acid sequence encoding the Cas Type V polypeptide and tire guide RNA are transiently expressed in tire host cell genome.
16. The genome editing system of any one of the above paragraphs wherein the nucleic acid sequence encoding the Cas Type V polypeptide and the guide RNA are integrated into and expressed from the host cell genome.
17. Hie genome editing system of any one of the above paragraphs wherein the nucleic acid sequence encoding the Cas Type V polypeptide and tire guide RNA are integrated into and expressed from a plasmid.
1 . The genome editing system of any one of the above paragraphs wherein the genome editing system further comprises a donor nucleic acid sequence to modify a target region of the host cell genome.
19. The genome editing system of any one of the above paragraphs wherein administering the system to a host cell results in one or more edits.
20. The genome editing system of claim 19, wherein the one or more edits comprises an insertion, deletion, base change/substitution, or inversion, or a combination thereof.
21 . The genome editing system of claim 19, wherein the one or more edits comprises a modification in the nucleobase sequence of a target nucleic acid molecule. 22. The genome editing system of claim 19, wherein the one or more edits comprises a whole-exon insertion, deletion, or substitution.
23. The genome editing system of claim 19, wherein the one or more edits comprises a whole-intron insertion, deletion, or substitution.
24. The genome editing system of claim 19, wherein the one or more edits comprises a whole-gene insertion, deletion, or substitution.
25. Tire genome editing system of claim 19, wherein the one or more edits comprises an edit to the sequence of a gene or to a region of a gene, e.g., an exon or intron.
26. The genome editing system of any one of the above paragraphs wherein the Cas Type V polypeptide recognizes a protospacer-adjacent motif (PAM).
27. Tire genome editing system of any one of the above paragraphs wherein the genome editing system installs one or more desired sequence modifications of one or more monogenic disorders or diseases.
28. Tire genome editing system of any one of the above paragraphs wherein the genome editing system installs one or more desired epigenetic modifications of one or more monogenic disorders or diseases.
29. The genome editing system of any one of the above paragraphs wherein the Cas Type V polypeptide comprises one or more modifications in one or more domains selected from (a) a nuclease domain (e g., RuvC domain) and (b) a PAM-interacting domain.
30. Tire genome editing system of any one of the above paragraphs further comprising a delivery vector.
31. The genome editing system of paragraph 30, wherein the delivery’ vector is selected from viral vector is selected from a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector.
32. Tire genome editing system of paragraph 30, wherein the delivery vector comprises a non-viral vector selected from cationic liposomes, lipid nanoparticles (LNPs). cationic polymers, vesicles, and gold nanoparticles.
33. The genome editing system of any one of the above paragraphs wherein the modification of the target sequence of the host cell genome comprises binding activity, cleavage activity, nickase activity, deaminase activity, reverse transcriptase activity, transcriptional activation activity, transcriptional inhibitory activity, or transcriptional epigenetic activity.
34. Tire genome editing system of any one of the above paragraphs wherein any of the nucleic acid molecules — including any guide RNA or donor DNA — comprises one or more chemical modifications selected from 2'-O-Me, 2'-F, and 2'F-ANA at 2'OH; 2'F-4'-Ca-OMe and 2',4'-di-Ca-OMe at 2' and 4' carbons; phosphodiester modifications comprising sulfide-based Phosphorothioate (PS) or acetate-based phosphonoacetate alterations; combinations of the ribose and phosphodiester modifications; locked nucleic acid (LNA), bridged nucleic acids (BNA), S-constrained ethyl (cEt), and unlocked nucleic acid (UNA); modifications to produce a phosphodiester bond between the 2' and 5' carbons (2',5'-RNA) of adjacent RNAs; and a butane 4-carbon chain link between adjacent RNAs.
35. The genome editing system of any one of the above paragraphs wherein any guide RNA comprises one or more chemical modifications selected from 2'-0-Me, 2'-F. and 2'F-ANA at 2'OH; 2'F-4'-Ca-OMe and 2’,4'-di-Ca-OMe at 2' and 4' carbons; phosphodiester modifications comprising sulfide-based Phosphorothioate (PS) or acetate-based phosphonoacetate alterations; combinations of the ribose and phosphodiester modifications; locked nucleic acid (LNA), bridged nucleic acids (BNA), S-constrained ethyl (cEt), and unlocked nucleic acid (UNA); modifications to produce a phosphodiester bond between the 2' and 5' carbons (2',5'-RNA) of adjacent RNAs; and a butane 4-carbon chain link between adjacent RNAs.
36. Tire genome editing system of any one of the above paragraphs wherein any donor or template DNA comprises one or more chemical modifications selected from 2'-0-Me, 2'-F, and 2'F-ANA at 2'OH; 2'F- 4'-Ca-0Me and 2',4'-di-Ca-OMe at 2' and 4' carbons; phosphodiester modifications comprising sulfide- based Phosphorothioate (PS) or acetate-based phosphonoacetate alterations; combinations of the ribose and phosphodiester modifications; locked nucleic acid (LNA), bridged nucleic acids (BNA), S- constrained ethyl (cEt), and unlocked nucleic acid (UNA); modifications to produce a phosphodiester bond between the 2' and 5' carbons (2',5'-RNA) of adjacent RNAs; and a butane 4-carbon chain link between adjacent nucleotides.
37. A method for editing the DNA of a host cell, producing one or more compositions comprising: a Cas Type V polypeptide or a nucleic acid sequence encoding a Cas Type V polypeptide; a second nucleic acid sequence encoding a guide RNA. wherein the second nucleic acid sequence and the Cas Type V polypeptide form an RNA-protein complex; wherein the genome editing system optionally further comprises a donor nucleic acid sequence capable of modifying a target sequence; and introducing tire composition into a host cell; optionally selecting for the host cell comprising the modification or the donor nucleic acid sequence into the host cell genome; and optionally culturing the edited host cells under conditions sufficient for growth.
38. The method of paragraph 37, wherein the Cas Type V polypeptide is: operably fused to a nuclease; operably fused to a deaminase; operably fused to a reverse transcriptase; operably fused to a recombinase; operably fused to a transposase; operably fused to a epigenetic effector; or operably fused to any combination of a, b, c. d, e and/or f.
39. The method of paragraph 37, further comprising quantifying or characterizing the editing of the target region.
40. The method of paragraph 37, wherein tire method provides editing efficiency of greater than 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99% relative to SpCas9.
41. Tire method of paragraph 37, further comprising introducing into the host cell a second donor nucleic acid sequence paired with a second guide RNA to modify the second target region of the host cell genome.
42. The method of paragraph 37 further comprising introducing into the host cell at least two desired modification sequences for multiplexing.
43. The method of paragraph 37 wherein the method comprises insertion or stable integration of the one or more desired modification sequence into the host cell genome.
44. The method of paragraph 37 wherein the host cell genome comprises a chromosome or chromosome and plasmid.
45. The method of paragraph 37 wherein the target region is modified by an insertion, deletion or alteration of one or more base pairs at the target region in the host cell genome.
46. The method of paragraph 37 wherein the one or more desired modification sequence is selected from one or more sequences associated with one or more monogenic disorders or diseases.
47. The method of paragraph 37 wherein the host cell is a primary human cell.
48. The method of paragraph 37 wherein the step of introducing into the host cell comprises a delivery vector operably linked to the genome editing system.
49. Hie method of paragraph 48 wherein the delivery vector is selected from viral vector is selected from a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector.
50. The method of paragraph 48 wherein the delivery vector comprises a non-viral vectors selected from cationic liposomes, lipid nanoparticles (LNPs), cationic polymers, vesicles, and gold nanoparticles. 51. The method of paragraph 37 wherein the editing method results in enhanced editing efficiency and/or low cytotoxicity.
52. A gene editing construct comprising: an Cas Type V domain; (b) a reverse transcriptase domain; (c) a transcriptional modulating polypeptide; (d) a recombinase domain; (e) a transposose domain; or (f) any combination of a, b. c, d, e, or f.
53. Tire gene editing construct of claim 52, further comprising a donor nucleic acid sequence capable of modifying a target sequence; and
[0033] In various aspects, the target region is modified by an insertion, deletion or alteration of one or more base pairs at the target region in the host cell genome.
[0034] In various embodiments, one or more desired modification sequence is selected from one or more sequences associated with one or more monogenic disorders or diseases.
[0035] In certain preferred embodiments, the methods and compositions provide editing efficiency of greater than 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99% relative to SpCas9.
[0036] Related aspects provide for the use of a Cas Type V-based gene editing system described herein Cas Type Vin the application for plants, yeast, bacteria, and fungi and desired bioindustrial applications for producing value-added components in such systems in a recombinant manner.
[0037] Accordingly, it is an object of the invention not to encompass within the invention any previously known product, process of making the product, or method of using the product such that Applicants reserve the right and hereby disclose a disclaimer of any previously known product, process, or method. It is further noted that tire invention does not intend to encompass within the scope of tire invention any product, process, or making of the product or method of using tire product, which does not meet the written description and enablement requirements of tire USPTO (35 U.S.C. § 112, first paragraph) or the EPO (Article 83 of tire EPC), such that Applicants reserve the right and hereby disclose a disclaimer of any previously described product, process of making the product, or method of using the product. It may be advantageous in the practice of the invention to be in compliance with Art. 53(c) EPC and Rule 28(b) and (c) EPC. All rights to explicitly disclaim any embodiments that are the subject of any granted patent(s) of applicant in the lineage of this application or in any other lineage or in any prior filed application of any third party is explicitly reserved. Nothing herein is to be constmed as a promise.
DESCRIPTION OF THE DRAWINGS
[0038] FIGs. 1 A-l C are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 1 sequences. [0039] FIGs. 2A-2B are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 2 sequences.
[0040] FIGs. 3A-3B are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 3 sequences.
[0041] FIGs. 4A-4B are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 4 sequences.
[0042] FIGs. 5A-5C are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 5 sequences.
[0043] FIGs. 6A-6D are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 6 sequences.
[0044] FIGs. 7A-7C are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 7 sequences.
[0045] FIGs. 8A-8B are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 8 sequences.
[0046] FIGs. 9A-9NN are schemes depicting tire predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 9 sequences.
[0047] FIGs. 10A-10F are schemes depicting tire predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 10 sequences.
[0048] FIGs. 11A-11C are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 11 sequences.
[0049] FIGs. 12A-12B are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 12 sequences.
[0050] FIGs. 13A-13F are schemes depicting tire predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 13 sequences.
[0051] FIGs. 14A- 14V are schemes depicting the predicted stem loop structures of crRNA sequences of the present disclosure corresponding to Group 14 sequences.
[0052] FIG. 15 is a phylogenetic tree illustrating the location of PAM sequences added at each protein, as described in Example 9. The phylogenetic tree was generated using Geneious Prime 2022.1.1 implementation of FastTree on Muscle multiple sequence alignment of selected protein sequences. PAM sequence weblogos were generated using WebLogo 3 web application from PFMs.
[0053] FIG. 16 is a blot showing cleavage products of genomic target DNMT] visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ortholog were calculated using Image J software, in accordance with Example 10. [0054] FIG. 17 is a blot showing cleavage products of genomic target RUNX 1 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ortholog were calculated using ImageJ software, in accordance with Example 10.
[0055] FIG. 18 is a blot showing cleavage products of genomic target SCN1A visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ortholog were calculated using ImageJ software, in accordance with Example 10.
[0056] FIG. 19 is a blot showing cleavage products of genomic target FANCF site 2 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ortholog were calculated using ImageJ software, in accordance with Example 10.
[0057] FIG. 20 is a blot showing cleavage products of genomic target FANCF site 1 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ortholog were calculated using ImageJ software, in accordance with Example 10.
[0058] FIG. 21 is a graph showing a comparison of Casl2a orthologs activity on different targets (n > 3). Results are calculated from T7 endonuclease assay, in accordance with Example 11.
[0059] FIG. 22A is a graph showing genome editing efficiency results for ID405, ID414, ID418, LbaCasl2a depicted as indels frequency at RUNX1 and SCN1A target sites as detennined by deep-sequencing in accordance with Example 12.
[0060] FIG. 22B is a graph showing genome editing efficiency results for 1D405, 1D414, 1D418. LbaCasI2a depicted as indels frequency at RUNX1, SCN1A, DNMT1, FANCF site 1, and FANCF site 2, as determined by deep-sequencing in accordance with Example 12.
[0061] FIGs. 23A-23E are tables showing the top five most common editing outcomes observed in deep sequencing data of ID405, ID414, ID418 and LbaCas 12a genomic targets in RUNX1 (FIG. 23A), SCN1A (FIG. 23B). DNMT1 (FIG. 23C), FANCF Site 1 (FIG. 23D), and FANCF Site 2 (FIG. 23E) genes as compared to reference sequences.
[0062] FIG. 24 is a graph showing genome editing efficiency results depicted as indels frequency as determined by deep-sequencing as described in Example 12.
[0063] FIG. 25 is a set of tables showing the top 5 most common editing outcomes observed in deep sequencing data of ID428 and ID433 genomic targets exhibiting low but observable editing as compared to reference sequences as described in Example 12.
[0064] FIG. 26 is a set of blots showing endonuclease activity comparison between SpyCas9, LbaCas 12a. ID405, and ID414. Blue arrows mark cleavage products of LbaCasl2a, ID405, and ID414 nucleases; black arrows mark cleavage products of SpyCas9 nucleases. Percentages above each gel well show the editing number detennined from the gel using ImageJ software. See Example 13 for further details. [0065] FIG. 27 is a set of blots showing endonuclease activity comparison between SpyCas9. LbaCasl2a, and ID418. Blue arrows mark cleavage products of LbaCasl2a and ID418 nucleases; black arrows mark cleavage products of SpyCas9 nucleases. Percentages above each gel well show the editing number determined from the gel using Image J software. See Example 13 for further details.
[0066] FIG. 28A is a set of blots showing cleavage products of genomic target PCSK9 visualized on 2 % agarose gel in the presence of various ID405 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID405 mutant were calculated using ImageJ software. See Example 13 for further details.
[0067] FIG. 28B is a set of blots showing cleavage products of genomic target CISH visualized on 2 % agarose gel in the presence of various ID405 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID405 mutant were calculated using ImageJ software. See Example 13 for further details.
[0068] FIG. 28C is a set of blots showing cleavage products of genomic target TTR visualized on 2 % agarose gel in the presence of various ID405 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID405 mutant were calculated using ImageJ software. See Example 13 for further details.
[0069] FIG. 28D is a set of blots showing cleavage products of genomic target PCSK9 visualized on 2 % agarose gel in the presence of various ID414 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID414 mutant were calculated using ImageJ software. See Example 13 for further details.
[0070] FIG. 28E is a set of blots showing cleavage products of genomic target CISH visualized on 2 % agarose gel in the presence of various ID414 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID414 mutant were calculated using ImageJ software. See Example 13 for further details.
[0071] FIG. 28F is a set of blots showing cleavage products of genomic target TTR visualized on 2 % agarose gel in the presence of various ID414 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID414 mutant were calculated using ImageJ software. See Example 13 for further details.
[0072] FIG. 28G is a set of blots showing cleavage products of genomic target BCLlla visualized on 2% agarose gel in the presence of various ID405 mutants. Editing efficiency values for LbaCasl2a and each ID405 mutant were calculated using ImageJ software. [0073] FIG. 28H is a set of blots showing cleavage products of genomic target HBG1 visualized on 2 % agarose gel in the presence of various ID405 mutants. Editing efficiency values for LbaCasl2a and each ID405 mutant were calculated using Image J software.
[0074] FIG. 281 is a set of blots showing cleavage products of genomic target BCL1 la visualized on 2 % agarose gel in the presence of various ID414 mutants. Editing efficiency values for LbaCasl2a and each ID414 mutant were calculated using Image J software.
[0075] FIG. 28 J is a set of blots showing cleavage products of genomic target HBG1 visualized on 2 % agarose gel in the presence of various ID414 mutants. Editing efficiency values for LbaCasl2a and each ID414 mutant were calculated using Image J software.
[0076] FIG. 28K is a set of blots showing cleavage products of genomic target PCSK9 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using ImageJ software.
[0077] FIG. 28L is a set of blots showing cleavage products of genomic target CISH visualized on 2 % agarose gel in the presence of various ID418 mutants. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using ImageJ software.
[0078] FIG. 28M is a set of blots showing cleavage products of genomic target CISH visualized on 2 % agarose gel in the presence of various ID418 mutants. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using ImageJ software.
[0079] FIG. 28N is a set of blots showing cleavage products of genomic target BCLlla visualized on 2 % agarose gel in the presence of various ID418 mutants. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using ImageJ software.
[0080] FIG. 280 is a set of blots showing cleavage products of genomic target HBG1 visualized on 2 % agarose gel in the presence of various ID418 mutants. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using ImageJ software.
[0081] FIG. 29A is a graph showing a comparison of ID405 wild-type and ID405-1 mutant editing efficiency on different targets (n > 3). Targets are BCL1 la, CISFI, HBG1, PCSK9, and TTR. Results were calculated from T7 endonuclease assay data. For each gene target in the cluster of bar graphs, beginning on the left-most side of each clusture, the bars correspond to ID405, ID405-1, LbaCasl2a, and AsCasl2a Ultra. Note that no editing activity was observed for the BCL1 la and TTR targets (no left-most bar corresponding to 1D405 activity). See Example 13 for further details.
[0082] FIG. 29B is a graph showing a comparison of ID414 wild-type and ID414- 1 mutant activity on different targets (n > 3). Targets are BCL1 la, CISH, HBG1, PCSK9, and TTR. Results were calculated from T7 endonuclease assay data. For each gene target in the cluster of bar graphs, beginning on the left-most side of each clusture, the bars correspond to ID414, ID414-1, LbaCasl2a, and AsCasl2a Ultra. Note that no editing activity was observed for the BCL1 la and HBG1 targets (no left-most bar corresponding to ID414 activity). See Example 13 for further details.
[0083] FIG. 30 depicts a phylogenetic tree of relationships among each of the Cast 2a ortholog sequences presented in Table S15A versus the canonical LbCasl2a sequence of SEQ ID NO: 1382 (provided in Appendix A, Section Q). The phylogenetic tree was calculated using the Clustal Omega multiple sequence alignment online tools available at EMBL (the European Molecular Biology Laboratory).
[0084] FIG. 31 shows a sequence alignment among each of the Casl2a orthologs provided in Table S15A and tire canonical LbCasl2a sequence of SEQ ID NO: 1382. Bolded-underlined residues are marked with an asterisk (“*”) and denote a fully conserved amino acid residue present in all of the aligned sequences at that alignment position. The amino acid residue positions marked with a colon (“:”) denote aligned amino acid residues which are highly similar although not identically conserved. The highly similar residues are those where the substitutions among the sequences have strongly similar properties. The amino acid residue positions marked with a period (“.”) denote aligned amino acid residues which are moderately similar. The highly similar residues are those where the substitutions among tire sequences have strongly similar properties. The moderately similar residues are those where the substitutions among the sequence have weakly similar properties. The underlined regions are referred to as “highly conserved regions" and include (a) at least one fully conserved residue, and (b) at least one highly similar or moderatly similar residue. See Appendix A, Section Q for further description.
[0085] FIG. 32 is a graph showing genome editing efficiency results depicted as indels frequency as determined by deep-sequencing (n > 4), as described in Example 15.
[0086] FIG. 33 is a set of tables showing the top 5 most common editing outcomes observed in deep sequencing data of ID405, ID414 and ID418 wild type and mutant proteins as well as LbCasl2a and AsCasl2a Ultra genomic targets as compared to reference sequence in HBG1 gene.
[0087] FIG. 34 is a set of blots showing cleavage products of genomic target HBG1 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a, AsCasl2a Ultra and each ID405 mutant were calculated using Image J software, wt ID405 - wild-type ID405 control, ID405-1 - mutant from the first targeted mutation wave (D169R).
[0088] FIG. 35 is a set of blots showing cleavage products of genomic target TTR visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a. AsCasl2a Ultra and each 1D405 mutant were calculated using ImageJ software, wt ID405 - wild-type ID405 control, ID405-1 - mutant from the first targeted mutation wave (D169R). [0089] FIG. 36 is a graph comparing ID405-1 mutants from the first targeted mutation wave, wild type ID405, and ID405 second targeted mutation wave nucleases. NHEJ percentage calculated from T7 Endonuclease I assay results, generated using Image J software (n = 6).
[0090] FIG. 37 is a set of blots showing cleavage products of genomic target HBG1 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a. AsCasl2a Ultra and each ID418 mutant were calculated using Image J software, wt ID418 - wild-type ID418 control.
[0091] FIG. 38 is a set of blots showing cleavage products of genomic target TTR visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a, AsCasl2a Ultra and each ID418 mutant were calculated using Image J software, wt ID418 - wild-type ID418 control.
[0092] FIG. 39 is a set of blots showing cleavage products of genomic target HBG1 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a. AsCasl2a Ultra and each ID414 mutant were calculated using ImageJ software, wt ID448 - wild-type ID414 control: ID414-T154R and ID414-S802L - mutants from the first mutation round (ID414-1 and ID414-6, respectively).
[0093] FIG. 40 is a set of blots showing cleavage products of genomic target TTR visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a, AsCasl2a Ultra and each ID414 mutant were calculated using ImageJ software, wt ID448 - wild-type ID414 control; ID414-T154R and ID414-S802L - mutants from the first mutation round (ID414-1 and ID414-6, respectively).
[0094] FIG. 41 is a graph showing genome editing efficiency results depicted as indels frequency as determined by deep-sequencing (n > 6).
[0095] FIG. 42 is a set of tables showing the top 5 most common editing outcomes observed in deep sequencing data of ID405 wild type and mutant proteins as well as AsCasl2a Ultra genomic targets as compared to reference sequence in HBG1 gene.
[0096] FIG. 43 is a set of blots showing cleavage products of genomic target HBG1 visualized on 2 % agarose gel. Editing efficiency values for Alt-R A.s. Casl2a (Cpfl) and each purified Casl2a were calculated using ImageJ software.
[0097] FIG. 44 is a set of blots showing cleavage products of genomic target TTR visualized on 2 % agarose gel. Editing efficiency values for each purified Casl2a were calculated using ImageJ software.
[0098] FIG. 45 is a graph comparing purified mutant nucleases and Cast 2a variant editing efficiency in HEK293T on HBG1 genomic target. Results are calculated from T7 Endonuclease I assay.
[0099] FIG. 46 is a graph comparing purified mutant nucleases and Casl2a variant editing efficiency in HEK293T on TTR genomic target. Results are calculated from T7 Endonuclease I assay.
[00100] FIG. 47 represents a process for improving a programmable nuclease, such as, but not limited to a type V ortholog (e.g., ID405), by introducing one or more arginine residues in place of a naturally-occurring non-arginine residues at positions predicted to have an impact on the interaction between the ID405 amino acid sequence and a guide RNA (prediction based on computational methodology of Example 16). The substitutable positions are then ranked in accordance w ith the magnitude of stabilizing energetics associated with arginine replacement at any particular position as outlined in Example 16. Variant type V editors are then engineered and tested to determine which variants provide for any improvement in editing efficiency. Results are shown in Example 16.
[00101] FIG. 48 compares the interaction between Lys292 in ID405-1 with a replaced Arg292 with the guide RNA showing a more favorable interaction with the Arg292 residue, as described in Example 16.
[00102] FIG. 49 compares the interaction betw een Gln492 in ID405-1 with a replaced Arg492 w ith the guide RNA showing a more favorable interaction with the Arg492 residue, as described in Example 16.
[00103] FIG. 50 compares the interaction between Asn770 in ID405-1 with a replaced Arg770 with the guide RNA showing a more favorable interaction with the Arg770 residue, as described in Example 16.
[00104] FIG. 51 provides a graph showing the editing efficiency in primary HSPCs of select ID405-1 variants with arginine substitution mutations. WT designated ID405-1. Each variant enzyme, e.g., S972R, designates ID405-1 with a particular arginine substitution (e.g., S972R designates that serine at position 972 relative to ID405-1 has been substituted with an arginine). See Example 16 for details.
[00105] FIG. 52 is a schematic of ID405-1 variants comprising one or more NLS and optional linkers to improve 1D405-1 editing activity, in accordance with Example 17.
[00106] FIG. 53 is a schematic that shows that modified ID405-1 variant containing various linkers and NLSs in various configurations at the N- and/or C-termini improves editing as compared to baseline Construct 1 in primary HSPCs by up to a 5-fold increase. See Example 17 for details.
[00107] FIG. 54A is a schematic representation of the selection scheme for ID405 used in Example 18. Hie ID405 plasmid library was transformed into E. coll cells. Hie most active variants cut ccdB encoding plasmid which led to its subsequent degradation. This allowed for E. colt to grow on selective media promoting ccdB induction. Cells that receive plasmid with WT or non-fiinctional/less active ID405 mutant died due to activity of ccdB.
[00108] FIG. 54B is a schematic of the ID405 containing plasmid pACY CDuet_ID405-HBGl-crRNA-TTR- HDV used for directed evolution.
[00109] FIG. 54C is a schematic of the domain structure of ID405. Domains are labeled in the protein schematic. Marked segments above the protein denote regions selected for mutagenesis.
[00110] FIG. 55 is a set of photos of test assays evaluating the performance of ID405 constructs against ccdB containing selection plasmids with TCTT and TTGG PAM sequences upstream of the HBG1 target. [00111] FIG. 56A is a scatter plot summarizing variant frequency in N-terminus library under the selection against TCTT PAM. Nucleotide positions denote the amplified sequence used for library preparation.
[00112] FIG. 56B is a scatter plot summarizing variant frequency in N-terminus library under the selection against TTGG PAM. Nucleotide positions denote the amplified sequence used for library preparation.
[00113] FIG. 56C is a scatter plot summarizing variant frequency in N-terminus library under the selection against TTGG PAM under the presence of 0. ImM IPTG. Nucleotide positions denote the amplified sequence used for library preparation.
[00114] FIG. 56D is a scatter plot summarizing variant frequency in C-terminus library under the selection against TCTT PAM. Nucleotide positions denote the amplified sequence used for library’ preparation.
[00115] FIG. 56E is a scatter plot summarizing variant frequency in C-terminus library under the selection against TTGG PAM. Nucleotide positions denote the amplified sequence used for library preparation.
[00116] FIG. 56F is a scatter plot summarizing variant frequency in C-terminus library under the selection against TTGG PAM under the presence of 0. 1 mM IPTG. Nucleotide positions denote the amplified sequence used for library? preparation.
[00117] FIG. 56G is a scatter plot summarizing variant frequency in N-2 library’ under the selection against TCTT PAM. Nucleotide positions denote the amplified sequence used for library preparation.
[00118] FIG. 56H is a scatter plot summarizing variant frequency in N-2 library under the selection against TTGG PAM. Nucleotide positions denote the amplified sequence used for library? preparation.
[00119] FIG. 561 is a scatter plot summarizing variant frequency in N-2 library under the selection against TTGG PAM under the presence of 0.1 mM IPTG. Nucleotide positions denote the amplified sequence used for library’ preparation.
[00120] FIG. 56J is a scatter plot summarizing variant frequency in C-2 library under the selection against TCTT PAM. Nucleotide positions denote the amplified sequence used for library preparation.
[00121] FIG. 56K is a scatter plot summarizing variant frequency in C-2 library under the selection against TTGG PAM. Nucleotide positions denote the amplified sequence used for library? preparation.
[00122] FIG. 56L is a scatter plot summarizing variant frequency in C-2 library? under the selection against TTGG PAM under the presence of 0.1 mM IPTG. Nucleotide positions denote the amplified sequence used for library preparation.
[00123] FIG. 56M is a scatter plot summarizing variant frequency in a repeated selection of N-2 library under the selection against TTGG PAM using a greater number of E. colt transformants in round 1. Nucleotide positions denote the amplified sequence used for library preparation. [00124] FIG. 56N is a scatter plot summarizing variant frequency in a repeated selection of N-2 library under the selection against TTGG PAM under the presence of 0. 1 mM IPTG using a greater number of E. coli transformants in round 1. Nucleotide positions denote the amplified sequence used for library preparation.
[00125] FIG. 57A, FIG. 57B, and FIG. 57C show the computationally predicted optimal 2’-0Me guide modification sites in guide RNA for lbCasl2a over the invariant region of nucleotides 1-20 (FIG. 57A), in guide RNA for asCasl9 over the invariant region of nucleotides 1-19 (FIG. 57B). and in guide RNA for fhCasl2 over the scaffold region of nucleotides 1-19 (FIG. 57C). Lower case letters (boxes with white background fill) denote sites selected by the algorithm that have 2’-0Me modifications. Upper case letters (boxes with grey background fill) denote nucleotides sites that are not modified. Scores next to each sequence (one per row) denote the potential loss of hydrogen bonding interactions were that position to be modified with a 2’-OMe modification. Scores over each nucleotide (one per column) denote tire averaged hydrogen bond interaction calculated for that guide nucleotide position. Three exemplary modified guides with varying scores (high; med; low) are also given for each Type V family member (indicated by black stars). The top row guide sequence is modified at every position with 2’-0Me modifications.
[00126] FIG. 58A, FIG. 58B shows optimal 2-OMe guide modification sites in spacer region at nucleotides 20-39 of the asCasl2 guide sequence (FIG. 58A) and at nucleotides 20-39 of the fhCasl2 guide sequence (FIG. 58B). Lower case letters (boxes with white background fill) denote sites selected by the algorithm that may have 2’-OMc modifications. Upper case letters (boxes with grey background fill) denote nucleotides sites that are not modified. Scores next to each sequence (one per row) denote the potential loss of hydrogen bonding interactions due modifications. Scores over each nucleotide (one per column) denote the averaged hydrogen bond interaction calculated for that guide nucleotide. Three-four exemplary modified guides with varying scores are also given for each Type V family member (indicated by black stars).
[00127] FIGs. 59A-59B illustrate results of MOE analysis performed with Cas 12a guide bound protein structure. Based on MOE structural protocol, nucleotide positions are identified where the 2’-OH of gRNA nucleotide is making contact with Cas 12 protein. Dots indicate sum of all interactions at those positions between the 2 ’OH group of a given nucleotide and either the guide itself or with the protein and represent positions that ought not to be modified.
[00128] FIGs. 60A-60C illustrate results of MOE analy sis performed with Cas 12a guide bound protein structure. Based on MOE structural protocol, nucleotide positions are identified where the 2 ’-OH of gRNA nucleotide is making contact with Cas 12 protein. Dots indicate sum of all interactions at those positions between the 2’OH group of a given nucleotide and either the guide itself or with the protein and represent positions that ought not to be modified. [00129] FIG. 61 illustrates, based on the computation methodology of Example 19, nucleotide sites along the length of a type V guide RNA which may permissibly be modified with 2’-OMe modifications.
[00130] FIG. 62, seven different chemical modification patterns are designed for gRNA of three different targets (target 1= PCSK9 gene; target 2 = B2M gene; target 3 = BCL11A gene). The BCL11A target is the BCL11A binding site in tire HBG1/2 promoters. Targeting this site with a CRISPR-Cas editor and guide RNA can inactivate the binding site of the BCL11A transcriptional repressor, thereby increasing transcription of HBG1/2 genes, which results in increased production of HBG1/2 subunits, and consequently, increased production of HbF. Each of these three guides have same direct repeat sequence (UGAAUUUCUACUGUUGUAGAU; SEQ ID NO: 1744) but have different spacer length for unique DNA targets. In every guide, first two and last two phosphates have been converted to phosphorothioate. According to MOE, position 3 may not be suitable for phosphorothioate modification (FIG. 63 and 64) and hence kept unmodified. For this work, it was decided to work with 405-1 gRNA which has UG dinucleotide added before Casl2 guide sequence. For this work, these two nucleotides are assigned with -2 and -1 number. Following nucleotide sequence is identical with Cas 12a gRNA direct repeat (AAUUUCUA . .. .) and they are assigned with 1, 2, 3 ... .as nucleotide identification number.
[00131] FIG. 63. Shows the permissible sites to be modified based on detecting the strength of phosphate interactions for FnCasl2a/guide complexes.
[00132] FIG. 64. Shows the permissible sites to be modified based on detecting the strength of phosphate interactions for Casl2a/guide complexes.
[00133] FIG. 65. Summary of modified guides tested in vitro in Example 20. The modified guides Modi, Mod4, Mod5, Mod6, and Mod7 were tested in accordance with the methodology depicted in FIG. 66.
[00134] FIG. 66. Methodology fortesting modified guide RNAs as detailed in Example 20.
[00135] FIG. 67. Results showing high editing rates in primary HSCs at a clinically relevant locus (up to 77% editing at hB2M locus) as outlined in Example 20.
[00136] FIG. 68 Schematic showing an RNP complex (based on Cas9) wherein the nuclease component comprises an NLS (PKKKRKV)(SEQ ID NO:584). The complex forms in the nuclease and relocates to the nuclease as facilitated by the NLS.
[00137] FIG. 69. Depicts the concept of a PNA-NLS probe to couple an NLS directly to a guide RNA. Here, the exemplary’ PNA is 9 residues in length which is joined through an optional linker to one or more NLS. [00138] FIG. 70. Depicts the concept of a PNA-NLS probe to couple an NLS directly to a guide RNA at an additional sequence element added to the guide RNA referred to as the PNA binder element. This may be configured at either end of the guide RNA. Here, the exemplary PNA is 9 residues in length which is joined through an optional linker to one or more NLS. [00139] FIG. 71 A. An exemplary guide RNA targeting TTR gene and having the sequence from 5’ to 3’ of SEQ ID NO: 2585, wherein the bolded sequence as shown in Appendix B, SEQ ID NO:2585, hybridizes to the PNA having the nucleic acid sequence AGCCACGAAAA (SEQ ID NO:2305) fused to the NLS peptide PKKKRKV (SEQ ID NO:584).
[00140] FIG. 71B. An exemplary guide RNA targeting TTR gene and having the sequence from 5 ' to 3’ of SEQ ID NO: 2585, wherein the bolded sequence as shown in Appendix B, SEQ ID NO:2585, hybridizes to the PNA having the nucleic acid sequence CCACGAAAA fused to the NLS peptide PKKKRKV (SEQ ID NO:584).
[00141] FIG. 71C. An exemplary guide RNA targeting any gene and having the sequence from 5’ to 3' of SEQ ID NO: 2586, wherein the bolded sequence as shown in Appendix B, SEQ ID NO:2586, hybridizes to the PNA having tire nucleic acid sequence AGCCACGAAAA (SEQ ID NO:2305) fused to the NLS peptide PKKKRKV (SEQ ID NO:584). where in “N” designates any nucleotide and will depend upon the target sequence being targeted by the guide RNA.
[00142] FIG. 72. A graph of % indel formation by 405-1 nuclease with various modified gRNAs in a human HSPC donor. These results show that RNA extensions and DNA extensions can improve editing at the HBG locus 3-10 fold in an all RNA format relative to the mod6 benchmark using the 405-1 nuclease.
[00143] FIG. 73. A graph of % indel formation by 405-1 nuclease with various modified gRNAs in a human HSPC donor. These results show that RNA extensions and DNA extensions do not improve editing at the B2M locus in an all RNA format relative to the mod6 benchmark using the 405-1 nuclease.
[00144] FIG. 74. Shows a graph of % indel formation by 405-1 nuclease with various modified gRNAs in a human HSPC donor at the HBG locus. These results show that RNA and DNA extensions are not compatible with the Type V mod6 schema but guides modified with mod7 schema can tolerate RNA extensions.
[00145] FIG. 75. Modification 6 schema. This figure outlines the positions of 2’-0Me modifications and phosphothiorate modifications in gRNAs with the modification 6 schema.
Light grey and uppercase letters = Unmodifed; Dark grey and lowercase letters = modified with phosphothiorate (or in the alternative, indicated below with a post-nt asterisk); White and lowercase letters = modified with 2’-0Me. The sequences of FIG. 75 are: gRNA0260: u*g*AAUuuCUacUguuGuagaUcCUUGUCaagGcUAUUGGU*c*a (SEQ ID NO: 2232) (aka “mod 6” guide); gRNA0390: u*g*AAUuuCUacUguuGuaGAucCUUGUCaaggcuAUUGGu*c*a (SEQ ID NO: 2233); gRNA0391: u*g*AAUUuCUacUguuGuaGAUcCUUGUCaaggCUAUUGGu*c*a (SEQ ID NO:
2234); gRNA0392: u*g*AAUUuCUacUguuGUAGAUcCUUGUCaagGCUAUUGGu*c*a (SEQ ID NO:
2235), wherein A, G, U, C = unmodified RNA nucleotide; a, g, u, c = 2'-O-Methyl-nucleotide; * = Phosphorothioate linkage [00146] FIG. 76. Shows a graph of % indel formation by 405-1 nuclease with various modified gRNAs in a human HSPC donor at the HBG locus. These results show that decreasing the proportion of modification in a gRNA can increase editing 4-5 fold in vitro in CD34+ human HSPCs.
[00147] FIG. 77. Shows a graph of % indel formation at the HBG locus in human CD34+ HSPCs by gRNAs with 3’ extensions that create a hairpin with the spacer region of the gRNA. The results show 3’ extensions creating hairpins with a type V spacer (backfolds) increased editing above the mod6 benchmark gRNA at the HBG locus in human HSPCs. gRNA0260 is “mod6” having the sequence and modification scheme of u*g*AAUuuCUacUguuGuagaUcCUUGUCaagGcUAUUGGU*c*a (SEQ ID NO: 680) (aka “mod 6” guide), wherein A, G, U, C = unmodified RNA nucleotide; a, g, u, c = 2'-O-Methyl-nucleotide; * = Phosphorothioate linkage.
[00148] FIG. 78. Shows a graph of % indel formation by 405-1 with modified gRNAs across three different human HSPC donors at the HBG locus. The results showed that the effect of modified gRNAs on indel formation is consistent across HSPC donors using 405-1 3x NLS nuclease. For each cluster of graphs, the samples appear in the same ordering of (a) Donor 310, (b) Donor 309, and (c) Donor 308.
[00149] FIG. 79. Shows a graph of % indel formation at the HBG locus by modified gRNAs across 405-1 protein variants in human hematopoietic stem cells. The results show that the addition of the point mutant K292R and a 3X NLS increased indel fonnation across all modified gRNAs tested. gRNAs containing a 5‘ DNA extension of a 15bp randomized sequence improved indel formation by up to ~8 fold. Other modified gRNAs tested show more modest increases in indel formation. For each cluster of graphs, the samples appear in the same ordering of (a) 405-1, (b) 405-1 3x NLS, (c) 4051- E1014R + 3xNLS, and (d) 405-1 K292R + 3xNLS.
[00150] FIG. 80 (A) A schematic representation of luciferase mRNA with miRNA target sites (ts) inserted in the 3’ UTR. Luciferase mRNA consists of 5’ cap. 5' UTR. luciferase coding sequence, 3’ UTR followed by a poly A tail. A single copy (xl) or three copies (x3) of miRNA ts were inserted at the 3’ end of the 3’ UTR. An alternative (alt) insertion site is located at the 5’ end of the 3’ UTR, near the luciferase coding sequence. When combining two miRNA target sites in the same UTR, the first miRNA target site is inserted at the ‘alt’ location, and the second miRNA target site is inserted at the 3’ end of the UTR. (B) Incorporation of miR-122 ts into the 3’ UTR of luciferase mRNA results in the suppression of encoded protein in the Huh7 hepatocyte cell line, where miR-122 is expressed. A single copy of the target site at the end of 3’ UTRnear the poly A tail is sufficient to suppress luciferase expression by 5-fold compared to the control. Increasing the number of copies to three does not further enhance suppression. However, when the target site is inserted at the 5’ end of the UTR, near the coding sequence, suppression is enhanced to 10-fold. In contrast, insertion of the target site of miR-142, which is not expressed in hepatocyte cell line, has no impact on luciferase expression by itself and does not influence miR-122 mediated suppression when both target sites are inserted together on the same UTR.
[00151] FIG. 81 depicts (A) A schematic structure of luciferase mRNA with miRNA target sites (ts) inserted in the 3’ UTR. Luciferase mRNA consists of 5' cap, 5 ’UTR, luciferase coding sequence, 3' UTR followed by poly A tail. In this structure, three copies of miRNA target site are inserted at the 5‘ end of 3‘ UTR, near luciferase coding sequence. When combining two miRNA target sites in the same UTR, the first miRNA target site is inserted near the luciferase coding sequence, and the second miRNA target site is inserted at the 3’ end of UTR. (B) Cell type-specific suppression of luciferase expression was achieved by incorporating appropriate miRNA ts in the 3’ UTR. miR-122 ts inserted in the 3’ UTR of luciferase mRNA led to the suppression of protein expression in a hepatocyte cell line, where miR-122 is expressed (left), while no suppression was observed in a monocyte cell line, where miR-122 is not expressed (right). Similarly, miR- 142 ts suppressed luciferase expression exclusively in the monocyte cell line, where miR-142 is expressed. Insertion of miR-122 and miR-142 target sites in the same UTR inhibits luciferase expression in both hepatocyte and monocyte cell line.
[00152] FIG. 82 depicts four bar graphs showing the result of the miRNAs in Table 22 of Example 23 evaluated for their target-site mediated suppression in various immune cell lines and CD34+CD38- CD90+CD45RA-Ein- long-term hematopoietic stem cells. While the insertion of liver specific miR-122 or epithelial specific miR-200b, 200c. 203a and 205 target sites in the 3 ’ UTR of cargo does not affect its expression in immune cells, hematopoietic miRNAs suppress cargo expression in one or more cell types. miR-142 and let7e effectively suppress cargo expression in all cell lines. miR-223 exhibits mild activity in all cell lines, with the least effect observed in long-term hematopoietic cells. miR-155 demonstrates suppression in the monocyte cell line and in long-term hematopoietic cells, albeit weaker in the latter. miR-342 suppresses expression in both monocyte and T-cell lines. Both miR-126 5p and 3p, which are abundantly expressed in endothelial cells, show a substantial suppressive effect in long-term hematopoietic stem cells. [00153] FIG. 83 is a set of bar graphs comparisng genome editing efficiency on the hB2M target, as reported in Example 18. T7E1 = T7 endonuclease I assay; CE = capillary electrophoresis. Results reported as the average of three biological replicates each consisting of three technical replicates in the case of the T7EI assay and two biological replicates, each consisting of three technical replicates in the case of the capillary electrophoresis. Dots represent average values of each biological replicate.
[00154] FIG. 84 is a set of bar graphs comparing the T7Endonuclease 1 assay results reported in Example 18. The graph shows the data from the 13 best performing mutants selected from the study. Results reported as the average of three biological replicates each consisting of three technical replicates. 405-1 = the D169R mutant standard (SEQ ID NO: 585). Each additional mutant indicated in the graph is a cumulative mutant based off of the standard 405-1 sequence.
[00155] FIG. 85 is a set of bar graphs comparing TapeStation DNA assay results reported in Example 18. The graph shows tire data from the 13 best performing mutants selected from the study. Data is representaed as two biological replicates, each consisting of three technical replicates. 405-1 = the D169R mutant standard (SEQ ID NO: 585). Each additional mutant is a cumulative mutant based off of the standard 405-1 sequence. Each additional mutant indicated in the graph is a cumulative mutant based off of the standard 405-1 sequence.
[00156] FIG. 86 is a bar graph demonstrating the effect of various guide RNA extension strategies and the resulting effect in efficacy in editing at the HBG1/2 locus, as reported in Example 22. Extension of gRNA at the 5‘ end improved editing in primary human HSPCs and increased in vitro editing to up to 80% at tire HBG1/2 locus.
[00157] FIG. 87A and FIG. 87B are bar graphs reporting the efficacy of different guide RNA sequences for use with Type V mutant 405-1 K292R, in vitro, at 9.375 ng and 150 ng dosages. As shown in FIG. 86A, gRNAs 1-3 demonstrated the highest editing efficiency at tire B2M locus.
[00158] FIG. 88 is a bar graph showing the efficacy of different guide RNA sequences for use with Type V mutant 405-1 K292R. in vivo, at two dose levels. Utilizing these gRNAs, Type V nuclease 405-1 K292R demonstrated high editing efficiency at the B2M locus, nearly comparable with a literature standard Cas9 system.
DETAILED DESCRIPTION
[00159] Hie present disclosure provides Cas TypeV-based gene editing systems for use in various applications, including precision gene editing in cells, tissues, organs, or organisms. In various embodiments, the Cas TypeV -based gene editing systems comprise (a) a Cas TypeV polypeptide and (b) a Cas TypeV guide RNA which is capable of associating with a Cas TypeV polypeptide to form a complex such that the complex localizes to a target nucleic acid sequence (e.g., a genomic or plasmid target sequence) and binds thereto. In various embodiments, the Cas TypeV polypeptide has a nuclease activity which results in the cutting of at least one strand of DNA.
[00160] In exemplary embodiments, the Cas TypeV systems and/or components thereof described herein are formulated as part of a lipid nanoparticle (LNP). In some embodiments, a lipid nanoparticle comprises an ionizable lipid, a structural lipid, a PEGylated lipid, and a phospholipid.
[00161] In various embodiments, the Cas 12a polypeptide is apolypeptide selected from Table S15A (SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419)), or a polypeptide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a polypeptide from Table S15A (SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415). and SEQ ID NO: 445 (No. ID419)).
[00162] In various embodiments, the Cas Type V polypeptide is encoded by a polynucleotide sequence selected from Table S15B (SEQ ID NO: 365 (No. ID405), SEQ ID NO: 75 (No. ID414), or SEQ ID NO: 565 (No. ID418), SEQ ID NO: 366 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 30 (No. ID415), or SEQ ID NO: 445 (No. ID419)), or a polynucleotide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a polypeptide from Table S 15B (SEQ ID NO: 365 (No. ID405), SEQ ID NO: 75 (No. ID414), or SEQ ID NO:565 (No. ID418). SEQ ID NO: 366 (No. ID406), SEQ ID NO: 331 (No.
ID411). SEQ ID NO: 30 (No. ID415), or SEQ ID NO: 445 (No. ID419)).
[00163] In various embodiments, the Cas Type V guide RNA is selected from any Cas Type V guide sequence disclosed in Table S15C (SEQ ID NO:28-29, 69-71, 355-360, 542-563), or a nucleic acid molecule having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a Cas Type V guide sequence of Table S15C (SEQ ID NO:28-29, 69-71, 355-360, 542-563).
[00164] In various embodiments, the Cas Type V guide RNA may comprise (a) a portion that binds or associates with a Cas Type V polypeptide and (b) a region that comprises a targeting sequence, i.e.. a sequence which is complementary to target nucleic acid sequence. For Cas Type V guide RNA designs, just like for Cas9 guide RNA, the target sequence is typically next to a PAM sequence. But for Cas Type V, the PAM sequence in various embodiments is ty pically TTTV, where V ty pically represents A, C, or G. In various embodiments, the “V” of the TTTV is immediately adjacent to the most 5’ base of tire non-targeted strand side of the protospacer element. As for Cas9 guide RNA designs, the PAM sequence is typically not included in the guide RNA design.
[00165] In various embodiments, the guide RNA for Cas Type V is relatively short at only approximately 40- 44 bases long. The part that base pairs to the protospacer in the target sequence is 20-24 bases in length, and there is also a constant about 20-base section that binds to Cas Type V.
[00166] In various embodiments, nomenclature for a Cas Type V guide RNA is referred to as a “crRNA” and there is no Cas9-like ’tracrRNA" component.
[00167] In other aspects, the Cas Ty pe V-based gene editing systems may comprise one or more additional accessory? proteins having genome modifying functions, including recombinases, invertases, nucleases, polymerases, ligases, deaminases, reverse transcriptases, or epigenetic modifying functions. In various embodiments, the accessory proteins may be provided separately. In other embodiments, the accessory proteins may be fused to Cas Type V, optionally with a linker.
[00168] In still another aspect, the disclosure provides delivery systems for introducing the Cas Type V-based gene editing systems or components thereof into cells, tissues, organs, or organisms. Depending on the chosen format, the Cas Type V-based gene editing systems and/or the individual or combined components thereof may be delivered as DNA molecules (e.g., encoded on one or more plasmids), RNA molecules (e.g., guide RNAs for targeting the Cas Type V protein or linear or circular mRNAs coding for the Cas Type V protein or accessory' protein components of the Cas Type V-based gene editing systems), proteins (e.g., Cas Type V polypeptides, accessory proteins having other functions (e.g., recombinases, nucleases, polymerases, ligases, deaminases, or reverse transcriptases), or protein-nucleic acid complexes (e.g., complexes between a guide RNA and a Cas Type V protein or fusion protein comprising a Cas Type V protein).
[00169] In another aspect, the present disclosure provides nucleic acid molecules encoding the Cas Type V- based gene editing systems or components thereof. In yet another aspect, the disclosure provides vectors for transferring and/or expressing said Cas Type V-based gene editing systems, e.g., under in vitro, ex vivo, and in vivo conditions. In still another aspect, tire disclosure provides cell-delivery compositions and methods, including compositions for passive and/or active transport to cells (e.g., plasmids), delivery by virus-based recombinant vectors (e.g., AAV and/or lentivirus vectors), delivery by non-virus-based systems (e.g.. liposomes and LNPs), and delivery by virus-like particles of the Cas Type V-based gene editing systems described herein. Depending on the delivery system employed, the Cas Type V-based gene editing systems described herein may be delivered in the form of DNA (e.g., plasmids or DNA-based virus vectors), RNA (e.g., guide RNA and rnRNA delivered by LNPs), a mixture of DNA and RNA, protein (e.g., virus-like particles), and ribonucleoprotein (RNP) complexes. Any suitable combinations of approaches for delivering the components of the herein disclosed Cas Type V-based gene editing systems may be employed.
[00170] In other embodiments, the Cas Type V-based gene editing systems may comprise a template DNA comprising an edit, e.g., a single strand or double strand donor molecule (linear or circular) which may be used by the cell to repair a single or double cut lesion introduced by a Cas Type V-based gene editing systems by way of cellular repair processes, including homology-dependent repair (HDR) (e.g., in dividing cells) or non-homologous end joining (NHEJ) (in non-dividing cells).
[00171] In one embodiment, each of the components of the Cas Type V-based gene editing systems is delivered by an all-RNA system, e.g.. the delivery of one or more RNA molecules (e.g., mRNA and/or guide RNA) by one or more LNPs, wherein the one or more RNA molecules form the guide RNA and/or are translated into the polypeptide components (e.g., the Cas Type V polypeptides and/or any accessory proteins), and a DNA or RNA-encoded template DNA molecule (e.g., donor template), as appropriate or desired.
[00172] In yet another aspect, the disclosure provides methods for genome editing by introducing a Cas Type V-based gene editing system described herein into a cell (e.g., under in vitro, in vivo, or ex vivo conditions) comprising a target edit site, thereby resulting in an edit at the target edit. In other aspects, the disclosure provides formulations comprising any of the aforementioned components for delivery to cells and/or tissues, including in vitro, in vivo, and ex vivo delivery, recombinant cells and/or tissues modified by the recombinant Cas Type V-based gene editing systems and methods described herein, and methods of modifying cells by conducting genome editing using the herein disclosed Cas Type V-based gene editing systems.
[00173] The disclosure also provides methods of making the Cas Type V-based gene editing systems, their protein and nucleic acid molecule components, vectors, compositions and fonnulations described herein, as well as to pharmaceutical compositions and kits for modifying cells under in vitro, in vivo, and ex vivo conditions that comprise the herein disclosed genome editing and/or modification systems.
A. General Definitions
[00174] Unless otherwise defined, all terms of art, notations and other scientific terminology used herein are intended to have the meanings commonly understood by those of skill in the art to which this disclosure pertains. In some cases, terms with commonly understood meanings are defined herein for clarity and/or for ready reference, and the inclusion of such definitions herein should not necessarily be construed to represent a difference over what is generally understood in the art. The techniques and procedures described or referenced herein are generally well understood and commonly employed using conventional methodologies by those skilled in the art, such as, for example, tire widely utilized molecular cloning methodologies described in Sambrook et al., Molecular Cloning: A Laboratory Manual 4th ed. (2012) Cold Spring Harbor Laboratory Press. Cold Spring Harbor, NY. As appropriate, procedures involving the use of commercially available kits and reagents are generally carried out in accordance with manufacturer-defined protocols and conditions unless otherwise noted.
An
[00175] The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.
About
[00176] ‘ ‘About” as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±10%, as such variations are appropriate to perform the disclosed methods. Biologically active
[00177] As used herein, the term “biologically active” refers to a characteristic of an agent (e.g., DNA, RNA, or protein) that has activity in a biological system (including in vitro and in vivo biological system), and particularly in a living organism, such as in a mammal, including human and non-human mammals. For instance, an agent when administered to an organism has a biological effect on that organism, is considered to be biologically active.
Bulge
[00178] As used herein, the term “bulge” refers to a small region of unpaired base(s) that interrupts a “stem” of base-paired nucleotides. The bulge may comprise one or two single-stranded or unbase-paired nucleotides joined at both ends by base-paired nucleotides of the stem. The bulge can be symmetrical (viz., the two unbase-paired single-stranded regions have the same number of nucleotides), or asymmetrical (viz., the unbase-paired single stranded region(s) have different or unequal numbers of nucleotides), or there is only one unbase-paired nucleotide on one strand. A bulge can be described as A/B (such as a “2/2 bulge,” or a “1/0 bulge”) wherein A represents the number of impaired nucleotides on the upstream strand of the stem, and B represents the number of unpaired nucleotides on the downstream strand of the stem. An upstream strand of a bulge is more 5’ to a downstream strand of the bulge in the primary nucleotide sequence. cDNA
[00179] As used hereing, the term “cDNA” refers to a strand of DNA copied from an RNA template, e.g., by a reverse transcriptase.
Casl2a or Casl2a polypeptide
[00180] As used herein, tire “Casl2a polypeptide”, “Casl2a protein” or “Casl2a nuclease” refers to a RNA- binding site-directed CRISPR Cas TypeV polypeptide that recognizes and/or binds RNA and is targeted to a specific DNA sequence. An Cas 12a system as described herein refers to a specific DNA sequence by the RNA molecule to which the Casl2a polypeptide or Casl2a protein is bound. The RNA molecule comprises a sequence that binds, hybridizes to, or is complementary' to a target sequence within the targeted polynucleotide sequence, thus targeting the bound polypeptide to a specific location within the targeted polynucleotide sequence (the target sequence). “Cas 12a” is a type of CRISPR Class II Type V nuclease. The specification may describe the polypeptides contemplated in the scope of this application as Cas 12a polypeptides or alternatively as Cas TypeV polypeptides, or the like.
Cleavage
[00181] As used herein, the term “cleavage” refers to the breakage of the covalent backbone of a DNA molecule. Cleavage can be initiated by a variety of methods including, but not limited to, enzymatic or chemical hydrolysis of a phosphodiester bond. Both single -stranded cleavage and double-stranded cleavage are possible, and double-stranded cleavage can occur as a result of two distinct single-stranded cleavage events. DNA cleavage can result in the production of either blunt ends or staggered ends.
Cognate
[00182] The term “cognate” refers to two biomolecules that normally interact or co-exist in nature. Complementary
[00183] As used herein, the terms “complementary” or “substantially complementary" are meant to refer to a nucleic acid (e.g., RNA, DNA) that comprises a sequence of nucleotides that enables it to non-covalently bind, i.e., form Watson-Crick base pairs and/or G/U base pairs, “anneal”, or “hybridize,” to another nucleic acid in a sequence -specific, antiparallel, manner (i.e., a nucleic acid specifically binds to a complementary nucleic acid) under the appropriate in vitro and/or in vivo conditions of temperature and solution ionic strength. Standard Watson-Crick base-pairing includes: adenine (A) pairing with thymidine (T), adenine (A) pairing with uracil (U), and guanine (G) pairing with cytosine (C) [DNA. RNA], In addition, for hybridization between two RNA molecules (e.g., dsRNA), and for hybridization of a DNA molecule with an RNA molecule (e.g., when a DNA target nucleic acid base pairs with a guide RNA, etc.): guanine (G) can also base pair with uracil (U). For example, G/U base-pairing is at least partially responsible for the degeneracy (i.e., redundancy) of the genetic code in the context of tRNA anti -codon base-pairing with codons in mRNA. Thus, in the context of this disclosure, a guanine (G) is considered complementary to both a uracil (U) and to an adenine (A). For example, when a G/U base-pair can be made at a given nucleotide position of a dsRNA duplex of a guide RNA molecule, the position is not considered to be non-complementary, but is instead considered to be complementary.
[00184] It is understood that the sequence of a polynucleotide need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable or hybridizable. Moreover, a polynucleotide may hybridize over one or more segments such that intervening or adjacent segments are not involved in the hybridization event (e.g., a bulge, a loop structure or hairpin structure, etc.). A polynucleotide can comprise 60% or more, 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 98% or more, 99% or more, 99.5% or more, or 100% sequence complementarity to a target region within the target nucleic acid sequence to which it will hybridize. For example, an antisense nucleic acid in which 18 of 20 nucleotides of the antisense compound are complementary to a target region, and would therefore specifically hybridize, would represent 90 percent complementarity. In this example, the remaining noncomplementary nucleotides may be clustered or interspersed with complementary nucleotides and need not be contiguous to each other or to complementary nucleotides. Percent complementarity between particular stretches of nucleic acid sequences within nucleic acids can be determined using any convenient method. Example methods include BEAST programs (basic local alignment search tools) and PowerBLAST programs (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656), the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), e.g., using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482-489), and the like. Consisting essentially of Consisting essentially of
[00185] The phrase “consisting essentially of’ is meant herein to exclude anything that is not the specified active component or components of a system, or that is not the specified active portion or portions of a molecule.
Control sequences
[00186] The term “control sequences” is intended to include, at a minimum, all components whose presence is essential for expression, and can also include additional components whose presence is advantageous, for example, leader sequences and fusion partner sequences. Suitable expression vectors include, without limitation, plasmids and viral vectors derived from, for example, bacteriophage, baculoviruses, tobacco mosaic virus, herpes viruses, cytomegalovirus, retroviruses, vaccinia viruses, adenoviruses, and adeno- associated viruses. Numerous vectors and expression systems are commercially available, such as from Novagen (Madison. WI), Clontech (Palo Alto, CA), Stratagene (La Jolla, CA), and Invitrogen/Life Technologies (Carlsbad, CA). The present invention comprehends recombinant vectors that may include viral vectors, bacterial vectors, protozoan vectors, DNA vectors, or recombinants thereof.
Degenerate variant
[00187] As used herein, the phrase “degenerate variant” of a reference nucleic acid sequence encompasses nucleic acid sequences that can be translated, according to the standard genetic code, to provide an amino acid sequence identical to that translated from the reference nucleic acid sequence. Hie term “degenerate oligonucleotide” or “degenerate primer” is used to signify an oligonucleotide capable of hybridizing with target nucleic acid sequences that are not necessarily identical in sequence butthat are homologous to one another within one or more particular segments.
[00188] Engineered nucleic acid constructs of the present disclosure may be encoded by a single molecule (e.g. , encoded by or present on the same plasmid or other suitable vector) or by multiple different molecules (e.g., multiple independently-replicating vectors).
DNA-guided nuclease
[00189] As used herein, an “DNA-guided nuclease” is a type of “programmable nuclease,” and a specific type of “nucleic acid-guided nuclease.” An example of a DNA-guided nuclease is reported in Varshney et al ., DNA-guided genome editing using structure-guided endonucleases, Genome Biology, 2016, 17(1), 187, which may be used in the context of the present disclosure and is incorporated herein by reference. As used herein, the term “DNA-guided nuclease” or “DNA-guided endonuclease” refers to a nuclease that associates covalently or non-covalently with a guide RNA thereby forming a complex between the guide RNA and the DNA-guided nuclease. The guide RNA comprises a spacer sequence which comprises a nucleotide sequence having complementarity’ with a strand of a target DNA sequence. Thus, the DNA-guided nuclease is indirectly guided or programmed to localize to a specific site in a DNA molecule through its association with the guide RNA. which directly binds or anneals to a strand of the target DNA through its complementarity region via Watson-Crick base-pairing.
DNA regulatory sequences
[00190] As used herein, the terms “DNA regulatory sequences,” “control elements,” and '■regulatory elements,” can be used interchangeably herein to refer to transcriptional and translational control sequences, such as promoters, enhancers, polyadenylation signals, terminators, protein degradation signals, and the like, that provide for and/or regulate transcription of a non-coding sequence (e.g., guide RNA) or a coding sequence and/or regulate translation of a mRNA into an encoded polypeptide.
Domain
[00191] The term “domain” as used herein refers to a structure of a biomolecule that contributes to a known or suspected function of the biomolecule. Domains may be co- extensive with regions or portions thereof; domains may also include distinct, non-contiguous regions of a biomolecule. Examples of protein domains include, but are not limited to, an Ig domain, an extracellular domain, a transmembrane domain, and a cytoplasmic domain. [0062] As used herein, the term “molecule” means any compound, including, but not limited to, a small molecule, peptide, protein, sugar, nucleotide, nucleic acid, lipid, etc., and such a compound can be natural or synthetic.
Donor nucleic acid
[00192] By a “donor nucleic acid” or “donor polynucleotide” or “donor DNA” or “HDR donor DNA” it is meant a single-stranded DNA to be inserted at a site cleaved by a programmable nuclease (e.g.. a CRISPR/Cas effector protein; a TALEN; a ZFN; a meganuclease) (e.g., after dsDNA cleavage, after nicking a target DNA, after dual nicking a target DNA, and the like). Tire donor polynucleotide can contain sufficient homology to a genomic sequence at the target site, e.g. 70%, 80%, 85%, 90%, 95%, or 100% homology with the nucleotide sequences flanking the target site, e.g., within about 200 bases or less of the target site, e.g., within about 190 bases or less of the target site, e.g., within about 180 bases or less of the target site, e.g.. within about 170 bases or less of the target site, e.g., within about 160 bases or less of the target site, e.g.. within about 150 bases or less of the target site, e.g., within about 140 bases or less of the target site, e.g., within about 130 bases or less of the target site, e.g., within about 120 bases or less of the target site, e.g., within about 110 bases or less of the target site, e.g., within about 100 bases or less of the target site, e.g., within about 90 bases or less of the target site, e.g., within about 80 bases or less of the target site, e.g., within about 70 bases or less of the target site, e.g., within about 60 bases or less of the target site, e.g., 50 bases or less of the target site, e.g., within about 30 bases, within about 15 bases, within about 10 bases, within about 5 bases, or immediately flanking the target site, to support homology-directed repair between it and the genomic sequence to which it bears homology.
Effective amount
[00193] An ■‘effective amount” as used herein, means an amount which provides a therapeutic or prophylactic benefit under the conditions of administration.
Encapsulation efficiency
[00194] As used herein, “encapsulation efficiency” refers to the amount of a therapeutic and/or prophylactic that becomes part of a nanoparticle composition, relative to the initial total amount of therapeutic and/or prophylactic used in the preparation of a nanoparticle composition. For example, if 97 mg of a polynucleotide are encapsulated in a nanoparticle composition out of a total 100 mg of therapeutic and/or prophylactic initially provided to the composition, the encapsulation efficiency may be given as 97%. As used herein, “encapsulation” may refer to complete, substantial, or partial enclosure, confinement, surrounding, or encasement.
Encodes
[00195] As used herein, a DNA sequence that “encodes” a particular RNA is a DNA nucleotide sequence that is transcribed into RNA. A DNA polynucleotide may encode an RNA (mRNA) that is translated into protein (and therefore the DNA and the mRNA both encode the protein), or a DNA polynucleotide may encode an RNA that is not translated into protein (e.g. tRNA, rRNA, microRNA (miRNA), a “non-coding” RNA (ncRNA). a guide RNA, etc.).
Exosomes
[00196] As used herein, the term “exosomes” refer to small membrane bound vesicles with an endocytic origin. Without wishing to be bound by theory, exosomes are generally released into an extracellular environment from host/progenitor cells post fusion of multivesicular bodies the cellular plasma membrane. As such, exosomes can include components of the progenitor membrane in addition to designed components. Exosome membranes are generally lamellar, composed of a bilayer of lipids, with an aqueous inter- nanoparticle space.
Expression vector
[00197] As used herein, the term “expression vector” or “expression construct” refers to a vector that includes one or more expression control sequences, and an “expression control sequence” is a DNA sequence that controls and regulates the transcription and/or translation of another DNA sequence. Expression control sequences are sequences which control the transcription, post-transcriptional events and translation of nucleic acid sequences.
[00198] Expression control sequences include appropriate transcription initiation, termination, promoter and enhancer sequences; efficient RNA processing signals such as splicing and polyadenylation signals; sequences that stabilize cytoplasmic mRNA; sequences that enhance translation efficiency (e.g., ribosome binding sites); sequences that enhance protein stability; and when desired, sequences that enhance protein secretion. The nature of such control sequences differs depending upon the host organism; in prokary otes, such control sequences generally include promoter, ribosomal binding site, and transcription termination sequence.
Fusion protein
[00199] Tire tenn “fusion protein" refers to a polypeptide comprising a polypeptide or fragment coupled to heterologous amino acid sequences optionally via an amino acid linker. Fusion proteins are useful because they can be constructed to contain two or more desired functional elements from two or more different proteins. A fusion protein comprises at least 10 contiguous amino acids from a polypeptide of interest, more preferably at least 20 or 30 amino acids, even more preferably at least 40, 50 or 60 amino acids, yet more preferably at least 75, 100 or 125 amino acids.
[00200] Fusions that include tire entirety of the proteins of the present invention have particular utility. The heterologous polypeptide included within the fusion protein of the present invention is at least 6 amino acids in length, often at least 8 amino acids in length, and usefully at least 15, 20, and 25 amino acids in length. Fusions that include larger polypeptides, such as an IgG Fc region, and even entire proteins, such as the green fluorescent protein (“GFP”) chromophore -containing proteins, have particular utility. Fusion proteins can be produced recombinantly by constructing a nucleic acid sequence which encodes the polypeptide or a fragment thereof in frame with a nucleic acid sequence encoding a different protein or peptide and then expressing the fusion protein. Alternatively, a fusion protein can be produced chemically by crosslinking the polypeptide or a fragment thereof to another protein.
Guide RNA
[00201] The RNA molecule that binds to the Casl2a polypeptide and targets the polypeptide to a specific location within the targeted polynucleotide sequence is referred to herein as the “guide RNA" or “guide RNA polynucleotide" (also referred to herein as a “guide RNA" or “gRNA" or “crRNA”). A guide RNA comprises two segments, a “DNA-targeting segment” and a “protein-binding segment.” By “segment” it is meant a segment/section/region of a molecule, e.g., a contiguous stretch of nucleotides in an RNA. As an illustrative, non-limiting example, a protein-binding segment of a guide RNA can comprise base pairs 5-20 of the RNA molecule that is 40 base pairs in length; and the DNA-targeting segment can comprise base pairs 21-40 of the RNA molecule that is 40 base pairs in length. The definition of '‘segment,” unless otherwise specifically defined in a particular context, is not limited to a specific number of total base pairs, is not limited to any particular number of base pairs from a given RNA molecule, is not limited to a particular number of separate molecules within a complex, and may include regions of RNA molecules that are of any total length and may or may not include regions with complementarity to other molecules.
[00202] The DNA-targeting segment (or “DNA-targeting sequence”) comprises a nucleotide sequence that is complementary to a specific sequence within a targeted polynucleotide sequence (the complementary strand of the targeted polynucleotide sequence) designated the “protospacer- like” sequence herein. The proteinbinding segment (or “protein-binding sequence”) interacts with a site-directed modifying polypeptide. When the site-directed modifying polypeptide is an Casl2a polypeptide, site-specific cleavage of the targeted polynucleotide sequence may occur at locations detennined by both (i) base-pairing complementarity between the guide RNA and the targeted polynucleotide sequence; and (ii) a short motif (referred to as the protospacer adjacent motif (PAM)) in the targeted polynucleotide sequence.
Heterologous nucleic acid
[00203] As used herein, the term “heterologous nucleic acid” refers to a genoty pically distinct entity from that of the rest of the entity to which it is compared or into which it is introduced or incorporated. For example, a polynucleotide introduced by genetic engineering techniques into a different cell type is a heterologous polynucleotide (e.g., DNA or RNA) and, if expressed, can encode a heterologous polypeptide. Similarly, a cellular sequence (e.g., a gene or portion thereof) that is incorporated into a viral vector is a heterologous nucleotide sequence with respect to the vector.
Homology
[00204] A protein has “homology” or is “homologous” to a second protein if the nucleic acid sequence that encodes the protein has a similar sequence to the nucleic acid sequence that encodes the second protein. Alternatively, a protein has homology to a second protein if the two proteins have "similar" amino acid sequences. (Thus, the term “homologous proteins” is defined to mean that the two proteins have similar amino acid sequences.) As used herein, homology between two regions of amino acid sequence (especially with respect to predicted structural similarities) is interpreted as implying similarity in function.
[00205] Sequence homology for polypeptides, which is also referred to as percent sequence identity, is typically measured using sequence analysis software. See, e.g.. the Sequence Analysis Software Package of the Genetics Computer Group (GCG), University of Wisconsin Biotechnology Center, 910 University Avenue, Madison, Wis. 53705. Protein analysis software matches similar sequences using a measure of homology assigned to various substitutions, deletions and other modifications, including conservative amino acid substitutions. For instance, GCG contains programs such as “Gap” and “Bestfit” which can be used with default parameters to determine sequence homology or sequence identity between closely related polypeptides, such as homologous polypeptides from different species of organisms or between a wild-type protein and a mutein thereof. See, e.g. , GCG Version 6.1.
[00206] A preferred algorithm when comparing a particular polypeptide sequence to a database containing a large number of sequences from different organisms is the computer program BLAST (Altschul et al., J. Mol. Biol. 215:403-410 (1990); Gish and States, Nature Genet. 3:266-272 (1993); Madden etal.,Meth. Enzymol. 266: 131-141 (1996); Altschul et al.. Nucleic Acids Res. 25:3389-3402 (1997); Zhang and Madden, Genome Res. 7:649-656 (1997)), especially blastp ortblastn (Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)). Preferred parameters for BLASTp are: Expectation value: 10 (default); Filter: seg (default); Cost to open a gap: 11 (default); Cost to extend a gap: 1 (default); Max. alignments: 100 (default); Word size: 11 (default);
No. of descriptions: 100 (default); Penalty Matrix: BLOWSUM62.
[00207] The length of polypeptide sequences compared for homology will generally be at least about 16 amino acid residues, usually at least about 20 residues, more usually at least about 24 residues, typically at least about 28 residues, and preferably more than about 35 residues. When searching a database containing sequences from a large number of different organisms, it is preferable to compare amino acid sequences. Database searching using amino acid sequences can be measured by algorithms other than blastp known in the art. For instance, polypeptide sequences can be compared using FASTA, a program in GCG Version 6.1. [00208] FASTA provides alignments and percent sequence identity of the regions of the best overlap between the query and search sequences. Pearson, Methods Enzymol. 183:63-98 (1990) (incorporated by reference herein). For example, percent sequence identity between amino acid sequences can be determined using FASTA with its default parameters (a word size of 2 and the PAM250 scoring matrix), as provided in GCG Version 6.1, herein incorporated by reference.
Homology-directed repair
[00209] As used herein, “homology-directed repair (HDR)” refers to the specialized form DNA repair that takes place, for example, during repair of double-strand breaks in cells. This process requires nucleotide sequence homology, uses a “donor” molecule to template repair of a “target” molecule (i.e., the one that experienced the double-strand break), and leads to the transfer of genetic infonnation from the donor to the target. Homology-directed repair may result in an alteration of tire sequence of the target molecule (e g ., insertion, deletion, mutation), if the donor polynucleotide differs from tire target molecule and part or all of the sequence of the donor polynucleotide is incorporated into the targeted polynucleotide sequence.
Identical
[00210] As used herein, the term “identical” refers to two or more sequences or subsequences which are the same. In addition, the term “substantially identical,” as used herein, refers to two or more sequences which have a percentage of sequential units which are the same when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using a comparison algorithm or by manual alignment and visual inspection. By way of example only, two or more sequences may be “substantially identical'’ if the sequential units are about 60% identical, about 65% identical, about 70% identical, about 75% identical, about 80% identical, about 85% identical, about 90% identical, or about 95% identical over a specified region. Such percentages to describe the “percent identity” of two or more sequences. The identity of a sequence can exist over a region that is at least about 75-100 sequential units in length, over a region that is about 50 sequential units in length, or, where not specified, across the entire sequence. This definition also refers to the complement of a test sequence.
[00211] Alternatively, substantially identical or similarity exists when a nucleic acid or fragment thereof hybridizes to another nucleic acid, to a strand of another nucleic acid, or to the complementary strand thereof, under stringent hybridization conditions. “Stringent hybridization conditions” and “stringent wash conditions” in the context of nucleic acid hybridization experiments depend upon a number of different physical parameters. Nucleic acid hybridization will be affected by such conditions as salt concentration, temperature, solvents, the base composition of the hybridizing species, length of the complementary regions, and tire number of nucleotide base mismatches betw een the hybridizing nucleic acids, as will be readily appreciated by those skilled in the art. One having ordinary skill in the art knows how to vary these parameters to achieve a particular stringency of hybridization.
Isolated
[00212] ‘ ‘Isolated” means altered or removed from the natural state. For example, a nucleic acid or a peptide naturally present in a living animal is not “isolated,” but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated nucleic acid or protein can exist in substantially purified fonn. or can exist in a non-native environment such as. for example, a host cell. An “isolated nucleic acid” refers to a nucleic acid segment or fragment, which has been separated from sequences which flank it in a naturally occurring state, i.e., a DNA fragment, which has been removed from the sequences which are normally adjacent to the fragment, i.e., the sequences adjacent to the fragment in a genome in which it naturally occurs. Tire term also applies to nucleic acids which have been substantially purified from other components, which naturally accompany the nucleic acid, i.e., RNA or DNA or proteins, which naturally accompany it in the cell. The term therefore includes, for example, a recombinant DNA or RNA, which is incorporated into a vector, into an autonomously replicating plasmid or virus, or into the genomic DNA or RNA of a prokaryote or eukaryote, or which exists as a separate molecule (i.e., as a cDNA or a genomic or cDNA fragment produced by PCR or restriction enzyme digestion) independent of other sequences. It also includes a recombinant DNA or RNA. which is part of a hybrid gene encoding additional polypeptide sequence.
Isolated protein
[00213] The term “isolated protein” or “isolated polypeptide” is a protein or polypeptide that by virtue of its origin or source of derivation (1) is not associated with naturally associated components that accompany it in its native state, (2) exists in a purity not found in nature, where purity can be adjudged with respect to tire presence of other cellular material (e.g. , is free of other proteins from the same species) (3) is expressed by a cell from a different species, or (4) does not occur in nature (e.g., it is a fragment of a polypeptide found in nature or it includes amino acid analogs or derivatives not found in nature or linkages other than standard peptide bonds). Thus, a polypeptide that is chemically synthesized or synthesized in a cellular system different from tire cell from which it naturally originates will be “isolated” from its naturally associated components. A polypeptide or protein may also be rendered substantially free of naturally associated components by isolation, using protein purification techniques well known in the art. As thus defined, “isolated” does not necessarily require that the protein, polypeptide, peptide or oligopeptide so described has been physically removed from its native environment.
Lipid nanoparticle (LNP)
[00214] As used herein, the term “lipid nanoparticle” or LNP refers to a type of lipid particle delivery system formed of small solid or semi-solid particles possessing an exterior lipid layer with a hydrophilic exterior surface that is exposed to the non-LNP environment, an interior space which may aqueous (vesicle like) or non-aqueous (micelle like), and at least one hydrophobic inter-membrane space. LNP membranes may be lamellar or non-lamellar and may be comprised of 1, 2, 3, 4, 5 or more layers. In some embodiments, LNPs may comprise a nucleic acid (e.g. Casl2a editing system) into their interior space, into the inter membrane space, onto their exterior surface, or any combination thereof. In some embodiments, an LNP of the present disclosure comprises an ionizable lipid, a structural lipid, a PEGylated lipid (aka PEG lipid), and a phospholipid. In alternative embodiments, an LNP comprises an ionizable lipid, a structural lipid, a PEGylated lipid (aka PEG lipid), and a zwitterionic amino acid lipid.
[00215] Further discuss of liposomes can be found, for example, in Tenchov et al., “Lipid Nanoparticles - From Liposomes to mRNA Vaccine Delivery, a Landscape of Diversity and Advancement,” ACS Nano, 2021. 15, pp. 16982-17015 (the contents of which are incorporated by reference).
Linker
[00216] As used herein, the term “linker” refers to a molecule linking or joining two other molecules or moieties. Tire linker can be an amino acid sequence in the case of a linker joining Evo fusion proteins. For example, an RNA-guided nuclease (e.g., Casl2a) can be fused to a reverse transcriptase or deaminase by an amino acid linker sequence. The linker can also be a nucleotide sequence in the case of joining two nucleotide sequences together. For example, in the instant case, a guide RNA at its 5' and/or 3' ends may be linked by a nucleotide sequence linker to one or more nucleotide sequences (e.g., a RT template in the case of a prime editor guide RNA). In other embodiments, the linker is an organic molecule, group, polymer, or chemical moiety. In some embodiments, the linker is 5-100 amino acids in length, for example. 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15. 16. 17. 18, 19, 20, 21, 22, 23, 24. 25. 26. 27, 28, 29, 30, 30-35. 35-40, 40- 45, 45-50. 50-60, 60-70, 70-80, 80-90, 90-100, 100-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated.
Liposomes
[00217] As used herein, the tenn “liposomes” refer to small vesicles that contain at least one lipid bilayer membrane surrounding an aqueous inner-nanoparticle space that is generally not derived from a progenitor/host cell.
Micelles
[00218] As used herein, the term “micelles” refer to small particles which do not have an aqueous intraparticle space.
Modified derivative
[00219] A “modified derivative” refers to polypeptides or fragments thereof that are substantially homologous in primary structural sequence but which include, e.g., in vivo or in vitro chemical and biochemical modifications or which incorporate amino acids that are not found in the native polypeptide. Such modifications include, for example, acetylation, carboxylation, phosphorylation, glycosylation, ubiquitination, labeling, e.g., with radionuclides, and various enzymatic modifications, as will be readily appreciated by those skilled in the art. A variety of methods for labeling polypeptides and of substituents or labels useful for such purposes are well known in the art, and include radioactive isotopes such as 125I, 32P, 35S. and 3H. ligands which bind to labeled antiligands (e.g.. antibodies), fluorophores. chemiluminescent agents, enzymes, and antiligands which can serve as specific binding pair members for a labeled ligand. The choice of label depends on the sensitivity required, ease of conjugation with the primer, stability requirements, and available instrumentation. Methods for labeling polypeptides are well known in the art. See, e.g, Ausubel et al., Current Protocols in Molecular Biology. Greene Publishing Associates (1992, and Supplements to 2002) (hereby incorporated by reference).
Modulating
[00220] By the term “modulating,” as used herein, is meant mediating a detectable increase or decrease in the level of a response in a subject compared with the level of a response in the subject in tire absence of a treatment or compound, and/or compared with the level of a response in an otherwise identical but untreated subject. The term encompasses perturbing and/or affecting a native signal or response thereby mediating a beneficial therapeutic response in a subject, preferably, a human.
Mutated
[00221] The term “mutated" when applied to nucleic acid sequences means that nucleotides in a nucleic acid sequence may be inserted, deleted or changed compared to a reference nucleic acid sequence. A single alteration may be made at a locus (a point mutation) or multiple nucleotides may be inserted, deleted or changed at a single locus. In addition, one or more alterations may be made at any number of loci within a nucleic acid sequence. A nucleic acid sequence may be mutated by any method known in the art including but not limited to mutagenesis techniques such as “error-prone PCR” (a process for performing PCR under conditions where the copying fidelity of the DNA polymerase is low, such that a high rate of point mutations is obtained along the entire length of the PCR product; see, e.g., Leung etal., Technique, 1: 11-15 (1989) and Caldwell and Joyce, PCR Methods Applic. 2:28-33 (1992)); and “oligonucleotide -directed mutagenesis” (a process which enables the generation of site- specific mutations in any cloned DNA segment of interest: see, e.g., Reidhaar-Olson and Sauer, Science 241:53-57 (1988)).
Nanoparticle
[00222] As used herein, the term “nanoparticle” refers to any particle ranging in size from 10- 1,000 nm.
Non-homologous end joining
[00223] As used herein, “non-homologous end joining (NHEJ)” refers to the repair of double-strand breaks in DNA by direct ligation of the break ends to one another without the need for a homologous template (in contrast to homology -directed repair, which requires a homologous sequence to guide repair). NHEJ often results in the loss (deletion) of nucleotide sequence near the site of the double-strand break.
Non-peptide analog
[00224] Tire term “non-peptide analog” refers to a compound with properties that are analogous to those of a reference polypeptide. A non-peptide compound may also be termed a "peptide mimetic” or a “peptidomimetic.” See, e.g., Jones, Amino Acid and Peptide Synthesis, Oxford University Press ( 1992); Jung, Combinatorial Peptide and Nonpeptide Libraries: A Handbook, John Wiley (1997); Bodanszky et al., Peptide Chemistry’— A Practical Textbook, Springer Verlag (1993); Synthetic Peptides: A Users Guide, (Grant, ed., W. H. Freeman and Co., 1992); Evans et al., J. Med. Chem. 30: 1229 (1987); Fauchere, J. Adv. Drug Res. 15:29 (1986); Veber and Freidinger, Trends Neurosci.. 8:392-396 (1985); and references sited in each of the above, which are incorporated herein by reference. Such compounds are often developed with the aid of computerized molecular modeling. Peptide mimetics that are structurally similar to useful peptides of the present invention may be used to produce an equivalent effect and are therefore envisioned to be part of the present invention. Nuclear localization sequence (NLS)
[00225] As used herein, the term “nuclear localization sequence” or“NLS” refers to an amino acid sequence that promotes import of a protein (e.g., a RNA-guided nuclease) into the cell nucleus, for example, by nuclear transport. Nuclear localization sequences are known in the art. For example, NLS sequences are described in Plank et al., international PCT application, PCT/EP2000/011690, filed November 23. 2000, published as WO/2001/038547 on May 31, 2001, the contents of which are incorporated herein by reference for its disclosure of exemplary nuclear localization sequences.
Nucleic acid
[00226] As used herein, tire term “nucleic acid” or “nucleic acid molecule” or “nucleic acid sequence” or “polynucleotide” generally refer to deoxyribonucleic or ribonucleic oligonucleotides in either single- or double -stranded fonn. The term may (or may not) encompass oligonucleotides containing known analogues of natural nucleotides. The term also may (or may not) encompass nucleic acid-like structures with synthetic backbones, see, e.g., Eckstein, 1991; Baserga et ah, 1992; Milligan, 1993; WO 97/03211; WO 96/39154; Mata, 1997; Strauss-Soukup, 1997; and Samstag, 1996. The term encompasses both ribonucleic acid (RNA) and DNA, including cDNA, genomic DNA, synthetic, synthesized (e.g., chemically synthesized) DNA, and/or DNA (or RNA) containing nucleic acid analogs. The nucleotides Adenine (A). Thymine (T), Guanine (G) and Cytosine (C) also may (or may not) encompass nucleotide modifications, e.g. , methylated and/or hydroxylated nucleotides, e.g., Cytosine (C) encompasses 5-methylcytosine and 5- hydroxymethylcytosine. The nucleic acid can be in any topological conformation. For instance, the nucleic acid can be singlestranded, double-stranded, triple-stranded, quadruplexed, partially double-stranded, branched, hairpinned, circular, or in a padlocked conformation.
Nucleic acid-guided nuclease
[00227] As used herein, the term “nucleic acid-guided nuclease” or “nucleic acid-guided endonuclease” refers to a nuclease (e.g., Casl2a) that associates covalently or non-covalently with a guide nucleic acid (e.g.. a guide RNA or a guide DNA) thereby forming a complex between the guide nucleic acid and the nucleic acid- guided nuclease. The guide nucleic acid comprises a spacer sequence which comprises a nucleotide sequence having complementarity with a strand of a target DNA sequence. Thus, the nucleic acid-guided nuclease is indirectly guided or programmed to localize to a specific site in a DNA molecule through its association with the guide nucleic acid, which directly binds or anneals to a strand of the target DNA through its complementarity region via Watson-Crick base-pairing. In some embodiments, the nucleic acid-guided nuclease will include a DNA-binding activity (e.g., as in the case for CRISPR Casl2a). Most commonly, the nucleic acid-guided nuclease is programmed by associating with a guide RNA molecule and in such cases the nuclease may be called “RNA-guided nuclease.” When programmed by a guide DNA, the nuclease may be called a “DNA-guided nuclease.” Nucleic acid-guided, RNA-guided, or DNA-guided nucleases may also be referred to as '‘programmable nucleases,” which also include other classes of programmable nucleases which associate with specific DNA sequences through amino acid / nucleotide sequence recognition (e.g., zinc fingers nucleases (ZFN) and transcription activator like effector nucleases (TALEN)) rather than through guide RNAs. In addition, any nuclease contemplated herein may also be engineered to remove, inactivate, or otherwise eliminate one or more nuclease activities (e.g., by introducing a nuclease-inactivating mutation in the active site(s) of a nuclease, e.g., in the RuvC domain of a Casl2a). A nuclease that has been modified to remove, inactivate, or otherwise eliminate all nuclease activity may be referred to as a ‘'dead” nuclease. A dead nuclease is not able to cut either strand of a double-stranded DNA molecule. A nuclease that has been modified to remove, inactivate, or otherwise eliminate at least one nuclease activity but which still retains at least one nuclease activity may be referred to as a “nickase” nuclease. A nickase nuclease cuts one strand of a double -stranded DNA molecule, but not both strands. For example, a CRISPR Cas9 naturally comprises two distinct nuclease activity domains, namely, the HNH domain and the RuvC domain. The HNH domain cuts the strand of DNA bound to the guide RNA and the RuvC domain cuts the protospacer strand. One can obtain a nickase Cas9 by inactivating either the HNH domain or the RuvC domain. One can obtain a dead Cas9 by inactivating both the HNH domain and the RuvC domain. Other RNA-guided nuclease may be similarly converted to nickases and/or dead nucleases by inactivating one or more of the existing nuclease domains.
Off-target effects
[00228] “Off-target effects” refer to non-specific genetic modifications that can occur when the CRISPR nuclease binds at a different genomic site than its intended target due to mismatch tolerance Hsu, P., Scott, D., Weinstein, J. et al. DNA targeting specificity of RNA- guided Cas9 nucleases. Nat Biotechnol 31, 827- 832 (2013). https://doi.org/10.1038/nbt.2647.
Operably linked
[00229] As used herein, the term “operably linked” or “under transcriptional control,” when used in conjunction with the description of a promoter, refers to the correct location and orientation in relation to a polynucleotide e.g., a coding sequence) to control the initiation of transcription by RNA polymerase and expression of the coding sequence, such as one for the msr gene, msd gene, and/or the ret gene. Other transcriptional control regulatory elements (e.g., enhancer sequences, transcription factor binding sites) may also be operably linked to a gene if their location relative to a gene controls or regulates tire expression of the gene.
PEG lipid [00230] As used herein, a '‘PEG lipid” or “PEGylated lipid” refers to a lipid comprising a polyethylene glycol component.
Peptide
[00231] As used herein, the tenns “peptide,” “polypeptide,” and “protein” are used interchangeably, and refer to a compound comprised of amino acid residues covalently linked by peptide bonds. A protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprise a protein’s or peptide’s sequence. Polypeptides include any peptide or protein comprising two or more amino acids joined to each other by peptide bonds. As used herein, the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types. “Polypeptides” include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among others. The polypeptides include natural peptides, recombinant peptides, synthetic peptides, or a combination thereof.
Promoter
[00232] As used herein, the tenn “promoter” is art-recognized and refers to a nucleic acid molecule with a sequence recognized by the cellular transcription machinery and which is able to initiate transcription of a downstream gene. A promoter can be constitutively active, meaning that the promoter is always active in a given cellular context, or conditionally active, meaning that the promoter is only active in the presence of a specific condition. For example, a conditional promoter may only be active in the presence of a specific protein that connects a protein associated with a regulatory element in the promoter to the basic transcriptional machinery, or only in the absence of an inhibitory molecule. Within the promoter sequence will be found a transcription initiation site, as well as protein binding domains responsible for the binding of RNA polymerase. Eukaryotic promoters will often, but not always, contain “TATA” boxes and “CAT” boxes. Various promoters, including inducible promoters, may be used to drive expression by the various vectors of the present disclosure.
Programmable nuclease
[00233] As used herein, the term “programmable nuclease” is meant to refer to a polypeptide that has the property of selective localization to a specific desired nucleotide sequence target in a nucleic acid molecule (e.g., to a specific gene target) due to one or more targeting functions. Such targeting functions can include one or more DNA-binding domains, such as zinc finger domains characteristic of many different types of DNA binding proteins or TALE domains characteristic of TALEN proteins. Such targeting function may also include tire ability to associate and/or form a complex with a guide RNA, which then localizes to a specific site on the DNA which bears a sequence that is complementary to a portion of the guide RNA (i.e., the spacer of the guide RNA). In some embodiments, the programmable nuclease may be a single protein which comprises both a domain that binds directly (e.g., a ZF protein) or indirectly (e.g., an RNA-guided protein) to a target DNA site, as well as a nuclease domain. In other embodiments, the programmable nuclease may be a composite of two or more separate proteins or domains (from different proteins) which together provide the necessary functions of selective DNA binding and nuclease activity. For example, the programmable nuclease may comprise a (a) nuclease -inactive RNA-guided nuclease (which still is capable of binding a guide RNA, localizing to a target DNA, and binding to the target DNA, but not capable of cutting or nicking the strands) fused to a (b) nuclease protein or domain, such as a FokI nuclease.
Polypeptide
[00234] Tire tenn “polypeptide" encompasses both naturally-occurring and non-naturally- occurring proteins, and fragments, mutants, derivatives and analogs thereof. A polypeptide may be monomeric or polymeric. Further, a polypeptide may comprise a number of different domains each of which has one or more distinct activities.
Polypeptide fragment
[00235] The term “polypeptide fragment” as used herein refers to a polypeptide that has a deletion, e.g., an amino-tenninal and/or carboxy-terminal deletion compared to a full-length polypeptide. In a preferred embodiment, the polypeptide fragment is a contiguous sequence in which the amino acid sequence of the fragment is identical to the corresponding positions in the naturally-occurring sequence. Fragments typically are at least 5, 6, 7, 8, 9 or 10 amino acids long, preferably at least 12, 14, 16 or 18 amino acids long, more preferably at least 20 amino acids long, more preferably at least 25, 30, 35, 40 or 45, amino acids, even more preferably at least 50 or 60 amino acids long, and even more preferably at least 70 amino acids long.
Polypeptide mutant
[00236] A “polypeptide mutant" or “mutein" refers to a polypeptide whose sequence contains an insertion, duplication, deletion, rearrangement or substitution of one or more amino acids compared to the amino acid sequence of a native or wild-type protein. A mutein may have one or more amino acid point substitutions, in which a single amino acid at a position has been changed to another amino acid, one or more insertions and/or deletions, in which one or more amino acids are inserted or deleted, respectively, in the sequence of the naturally- occurring protein, and/or truncations of the amino acid sequence at either or both the amino or carboxy termini. A mutein may have the same but preferably has a different biological activity compared to the naturally-occurring protein. A mutein has at least 85% overall sequence homology to its wild-type counterpart. Even more preferred are muteins having at least 90% overall sequence homology to the wild- type protein. In an even more preferred embodiment, a mutein exhibits at least 95% sequence identity, even more preferably 98%, even more preferably 99% and even more preferably 99.9% overall sequence identity. [00237] Sequence homology may be measured by any common sequence analysis algorithm, such as Gap or Bestfit.
[00238] Amino acid substitutions can include those which: (1) reduce susceptibility to proteolysis, (2) reduce susceptibility to oxidation, (3) alter binding affinity for forming protein complexes. (4) alter binding affinity or enzymatic activity, and (5) confer or modify other physicochemical or functional properties of such analogs.
[00239] As used herein, tire twenty conventional amino acids and their abbreviations follow conventional usage. See Immunology-A Synthesis (Golub and Gren eds., Sinauer Associates, Sunderland, Mass., 2nd ed. 1991), which is incorporated herein by reference. Stereoisomers (e.g., D-amino acids) of the twenty conventional amino acids, unnatural amino acids such as a-, a-disubstituted amino acids. N-alkyl amino acids, and other unconventional amino acids may also be suitable components for polypeptides of the present invention. Examples of unconventional amino acids include: 4-hydroxyproline, y-carboxyglutamate, e- N,N,N- trimethyllysine, e-N-acetyllysine, O-phosphoserine, N-acetylserine, N-fonnylmethionine, 3- methylhistidine, 5-hydroxylysine. N-methylarginine, and other similar amino acids and imino acids (e.g., 4- hydroxyproline). In the polypeptide notation used herein, the left-hand end corresponds to tire amino terminal end and the right-hand end corresponds to the carboxy- terminal end, in accordance with standard usage and convention.
Recombinant
[00240] The term “recombinant” refers to a biomolecule, e.g., a gene or protein, that (1) has been removed from its naturally occurring environment, (2) is not associated with all or a portion of a polynucleotide in which the gene is found in nature. (3) is operatively linked to a polynucleotide which it is not linked to in nature, or (4) does not occur in nature. The term “recombinant” can be used in reference to cloned DNA isolates, chemically synthesized polynucleotide analogs, or polynucleotide analogs that are biologically synthesized by heterologous systems, as well as proteins and/or mRNAs encoded by such nucleic acids. [00241] As used herein, an endogenous nucleic acid sequence in the genome of an organism (or the encoded protein product of that sequence) is deemed “recombinant” herein if a heterologous sequence is placed adjacent to the endogenous nucleic acid sequence, such that tire expression of this endogenous nucleic acid sequence is altered. In this context, a heterologous sequence is a sequence that is not naturally adjacent to the endogenous nucleic acid sequence, whether or not the heterologous sequence is itself endogenous (originating from the same host cell or progeny thereof) or exogenous (originating from a different host cell or progeny thereof). By way of example, a promoter sequence can be substituted (e.g., by homologous recombination) for the native promoter of a gene in the genome of a host cell, such that this gene has an altered expression pattern. This gene would now become “recombinant” because it is separated from at least some of the sequences that naturally flank it.
[00242] A nucleic acid is also considered “recombinant” if it contains any modifications that do not naturally occur to the corresponding nucleic acid in a genome. For instance, an endogenous coding sequence is considered “recombinant” if it contains an insertion, deletion or a point mutation introduced artificially, e.g., by human intervention. A “recombinant nucleic acid” also includes a nucleic acid integrated into a host cell chromosome at a heterologous site and a nucleic acid construct present as an episome.
Recombinant host cell
[00243] The term “recombinant host cell” (or simply “host cell”), as used herein, is intended to refer to a cell into which a recombinant vector has been introduced. It should be understood that such terms are intended to refer not only to the particular subject cell but to the progeny of such a cell. Because certain modifications may occur in succeeding generations due to either mutation or environmental influences, such progeny may not, in fact, be identical to the parent cell, but are still included within the scope of the term “host cell” as used herein. A recombinant host cell may be an isolated cell or cell line grown in culture or may be a cell which resides in a living tissue or organism.
[00244] Suitable methods of genetic modification such as “transformation” include e.g.. viral or bacteriophage infection, transfection, conjugation, protoplast fusion, lipofection, electroporation, calcium phosphate precipitation, polyethyleneimine (PEI)-mediated transfection, DEAE-dextran mediated transfection, liposome-mediated transfection, particle gun technology, calcium phosphate precipitation, direct micro injection, nanoparticle- mediated nucleic acid delivery (see, e.g., Panyam et al., Adv Drug Deliv Rev. 2012 Sep. 13. pii: S0169-409X(12)00283-9. doi: 10.1016/j.addr.2012.09.023), and the like. The choice of method of genetic modification is generally dependent on the type of cell being transformed and the circumstances under which the transformation is taking place (e.g., in vitro, ex vivo, or in vivo). A general discussion of these methods can be found in Ausubel, et al.. Short Protocols in Molecular Biology, 3rd ed., Wiley & Sons, 1995.
Recombinant nucleic acid
[00245] A ‘ ‘recombinant nucleic acid” or “recombinant nucleotide” refers to a molecule that is constructed by joining nucleic acid molecules, which optionally may self-replicate in a live cell. Recombinant nucleic acids and synthetic nucleic acids also include those molecules that result from the replication of either of the foregoing.
Region [00246] The term "region" as used herein refers to a physically contiguous portion of the primary structure of a biomolecule. In the case of proteins, a region is defined by a contiguous portion of the amino acid sequence of that protein.
RNA-guided nuclease
[00247] As used herein, an “RNA-guided nuclease" is a type of “programmable nuclease.” and a specific type of “nucleic acid-guided nuclease.” As used herein, the term “RNA-guided nuclease” or “RNA-guided endonuclease” refers to a nuclease that associates covalently or non-covalently with a guide RNA thereby forming a complex between the guide RNA and the RNA-guided nuclease. The guide RNA comprises a spacer sequence which comprises a nucleotide sequence having complementarity with a strand of a target DNA sequence. Thus, the RNA-guided nuclease is indirectly guided or programmed to localize to a specific site in a DNA molecule through its association with the guide RNA, which directly binds or anneals to a strand of the target DNA through its complementarity region via Watson-Crick base-pairing.
Sequence identity
[00248] As used herein, the term “sequence identity" refers to the overall relatedness between polymeric molecules, e.g., between polynucleotide molecules (<?.g, DNA molecules and/or RNA molecules) and/or between polypeptide molecules. Calculation of the percent identity of two polynucleotide sequences, for example, can be performed by aligning the two sequences for optimal comparison purposes (e.g.. gaps can be introduced in one or both of a first and a second nucleic acid sequences for optimal alignment and nonidentical sequences can be disregarded for comparison purposes). For example, the length of a sequence aligned for comparison purposes is at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or 100% of the length of tire reference sequence. The nucleotides at corresponding nucleotide positions are then compared. In other examples, the length of sequence identity comparison may be over a stretch of at least about nine nucleotides, usually at least about 20 nucleotides, more usually at least about 24 nucleotides, typically at least about 28 nucleotides, more typically at least about 32 nucleotides, and preferably at least about 36 or more nucleotides. When a position in the first sequence is occupied by the same nucleotide as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, taking into account the number of gaps, and the length of each gap, which needs to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. For example, the percent identity between two nucleotide sequences can be determined using methods such as those described in Computational Molecular Biology, Lesk, A. M., ed., Oxford University Press, New' York, 1988; Biocomputing: Informatics and Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993; Sequence Analysis in Molecular Biology, von Heinje, G., Academic Press, 1987; Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New Jersey, 1994; and Sequence Analysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press, New York, 1991; each of which is incorporated herein by reference. For example, the percent identity between two nucleotide sequences can be determined using the algorithm of Meyers and Miller (CABIOS, 1989. 4: 11-17). which has been incorporated into the ALIGN program (version 2.0) using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4. The percent identity between two nucleotide sequences can, alternatively, be determined using the GAP program in the GCG software package using an NWSgapdna. CMP matrix. Methods commonly employed to determine percent identity betw een sequences include, but are not limited to those disclosed in Carillo, H. and Lipman, D., SIAM J Applied Math., 48: 1073 (1988); incorporated herein by reference. Techniques for determining identity are codified in publicly available computer programs. Exemplary computer software to determine homology between two sequences include, but are not limited to, GCG program package, Devereux, J., et al., Nucleic Acids Research, 12(1), 387 (1984)), BLASTP, BLASTN, and FASTA (Altschul etal.,J. Mol. Biol. 215:403-410 (1990);
[00249] Gish and States, Nature Genet. 3:266-272 (1993); Madden et al., Meth. Enzymol. 266: 131- 141 (1996); Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997); Zhang and Madden, Genome Res. 7:649-656 (1997)), (Altschul et al., Nucleic Acids Res. 25:3389-3402 (1997)). Polynucleotide sequences, for instance, can be compared using FASTA, Gap or Bestfit. which are programs in Wisconsin Package Version 10.0, Genetics Computer Group (GCG), Madison, Wis. FASTA provides alignments and percent sequence identity of tire regions of the best overlap between the query' and search sequences. Pearson, Methods Enzymol. 183:63-98 (1990) (hereby incorporated by reference in its entirety). Percent sequence identity between nucleic acid sequences, for instance, can be determined using FASTA with its default parameters (a word size of 6 and the NOPAM factor for the scoring matrix) or using Gap with its default parameters as provided in GCG Version 6.1.
Specific binding
[00250] “Specific binding” refers to the ability of two molecules to bind to each other in preference to binding to other molecules in the environment. Typically, “specific binding” discriminates over adventitious binding in a reaction by at least tw o-fold, more typically by at least 10-fold, often at least 100-fold. Typically, the affinity or avidity of a specific binding reaction, as quantified by a dissociation constant, is about 10 7 M or stronger (e.g., about 10'8 M, 10'9 M or even stronger).
Stem and loop
[00251] As used herein, the term “stem” refers to two or more base pairs, such as 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20 or more base pairs, fomied by inverted repeat sequences connected at a “tip,” where the more 5 ’ or ’ upstream” strand of the stem bends to allows the more 3 ' or “downstream” strand to base-pair with the upstream strand. The number of base pairs in a stem is the “length” of the stem. The tip of the stem is typically at least 3 nucleotides, but can be 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more nucleotides.
[00252] Larger tips with more than 5 nucleotides are also referred to as a “loop.” An otherwise continuous stem may be interrupted by one or more bulges as defined herein. The number of unpaired nucleotides in the bulge(s) are not included in the length of the stem. The position of a bulge closest to the tip can be described by the number of base pairs between the bulge and the tip (e.g., the bulge is 4 bps from the tip). The position of tire other bulges (if any) further away from the tip can be described by the number of base pairs in the stem between the bulge in question and the tip, excluding any unpaired bases of other bulges in between. As used herein, the tenn “loop” in the polynucleotide refers to a single stranded stretch of one or more nucleotides, such as 2. 3, 4, 5, 6. 7, 8, 9, or 10 nucleotides, wherein the most 5? nucleotide and the most 3’ nucleotide of the loop are each linked to a base-paired nucleotide in a stem.
[00253] A “stem-loop structure” or a “hairpin” refers to a nucleic acid having a secondary structure that includes a region of nucleotides which are known or predicted to form a double strand (stem portion) that is linked on one side by a region of predominantly single -stranded nucleotides (loop portion). Such structures are well known in the art and these terms are used consistently with their known meanings in the art. As is known in the art, a stem-loop structure does not require exact base-pairing. Tirus, the stem may include one or more base mismatches. Alternatively, the base-pairing may be exact, i.e., not include any mismatches. [0077] As used herein, the term “operably linked” or “under transcriptional control,” when used in conjunction with the description of a promoter, refers to the correct location and orientation in relation to a polynucleotide (e.g. , a coding sequence) to control the initiation of transcription by RNA polymerase and expression of tire coding sequence.
Stringent hybridization
[00254] In general, “stringent hybridization” is performed at about 25°C below the thermal melting point (Tm) for the specific DNA hybrid under a particular set of conditions. “Stringent washing” is performed at temperatures about 5°C lower than the Tm for the specific DNA hybrid under a particular set of conditions. Tire Tm is the temperature at which 50% of the target sequence hybridizes to a perfectly matched probe. See Sambrook et al., Molecular Cloning: A Laboratory Manual, 2d ed.. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989). page 9.51, hereby incorporated by reference. For purposes herein, “stringent conditions” are defined for solution phase hybridization as aqueous hybridization (i.e., free of formamide) in 6xSSC (where 20xSSC contains 3.0 M NaCl and 0.3 M sodium citrate), 1% SDS at 65°C for 8-12 hours, followed by two washes in 0.2xSSC, 0.1% SDS at 65°C for 20 minutes. It will be appreciated by the skilled worker that hybridization at 65 °C will occur at different rates depending on a number of factors including the length and percent identity of the sequences which are hybridizing. Hybridization does not require the sequence of the polynucleotide to be 100% com piemen tan to the target polynucleotide. Hybridization also includes one or more segments such that intervening or adjacent segments that are not involved in the hybridization event (e.g., a loop structure or hairpin structure).
[00255] The nucleic acids (also referred to as polynucleotides) of this present invention may include both sense and antisense strands of RNA, cDNA, genomic DNA, and synthetic forms and mixed polymers of the above. They may be modified chemically or biochemically or may contain non -natural or derivatized nucleotide bases, as will be readily appreciated by those of skill in the art. Such modifications include, for example, labels, methylation, substitution of one or more of the naturally occurring nucleotides with an analog, intemucleotide modifications such as uncharged linkages (e.g., methyl phosphonates. phosphotriesters, phosphoramidates, carbamates, etc.), charged linkages (e.g., phosphorothioates. phosphorodithioates, etc.), pendent moieties (e.g., polypeptides), intercalators (e.g., acridine, psoralen, etc.), chelators, alkylators, and modified linkages (e.g., alpha anomeric nucleic acids, etc.) Also included are synthetic molecules that mimic polynucleotides in their ability to bind to a designated sequence via hydrogen bonding and other chemical interactions. Such molecules are known in tire art and include, for example, those in which peptide linkages substitute for phosphate linkages in the backbone of the molecule. Other modifications can include, for example, analogs in which the ribose ring contains a bridging moiety or other structure such as the modifications found in “locked” nucleic acids.
Subject
[00256] As used herein, the term “subject” refers to an individual organism, for example, an individual mammal. In some embodiments, tire subject is a human. In some embodiments, the subject is anon-human mammal. In some embodiments, the subject is a non-human primate. In some embodiments, the subject is a rodent. In some embodiments, the subject is a sheep, a goat, a cattle, a cat, or a dog. In some embodiments, the subject is a vertebrate, an amphibian, a reptile, a fish, an insect, a fly, or a nematode. In some embodiments, the subject is a research animal. In some embodiments, the subject is genetically engineered, e.g., a genetically engineered non-human subject. The subject may be of either sex and at any stage of development. The terms “individual,” “subject,” “host,” and “patient,” used interchangeably herein.
Synthetic nucleic acid
[00257] A “synthetic or artificial nucleic acid” refers nucleic acids that are non-naturally occuring sequences. Such sequences do not originate from, or are not known to be present in any living organism (e.g., based on sequence search in existing sequence databases).
Targeted polynucleotide sequence [00258] As used herein '‘targeted polynucleotide sequence” refers to a DNA polynucleotide that comprises a “target site” or “target sequence.” The terms “target site,” “target sequence,” “target protospacer DNA,” or “protospacer-like sequence” are used interchangeably herein to refer to a nucleic acid sequence present in a targeted polynucleotide sequence to which a DNA-targeting segment of a guide RNA will recognize and/or bind, provided sufficient conditions for binding exist. For example, the target site (or target sequence) 5'- GAGCATATC-3' within a targeted polynucleotide sequence is targeted by (or is bound by, or hybridizes with, or is complementary to) the RNA sequence 5'-GAUAUGCUC-3'. Suitable DNA/RNA binding conditions include physiological conditions normally present in a cell.
[00259] Other suitable DNA/RNA binding conditions (e.g., conditions in a cell -free system) are known in the art; see, e g., Sambrook, supra. Tire strand of the targeted polynucleotide sequence that is complementary to and hybridizes with the guide RNA is referred to as the “complementary strand” and the strand of the targeted polynucleotide sequence that is complementary to the “complementary strand” (and is therefore not complementary to the guide RNA) is referred to as the “noncomplementary strand” or “non-complementary strand.”
Target site
[00260] As used herein, a “target site” as used herein is a polynucleotide (e.g., DNA such as genomic DNA) that includes a site or specific locus (“target site” or “target sequence”) targeted by a Cast 2a gene editing system disclosed herein. In the context of a Casl2a gene editing system disclosed herein that comprise an RNA-guided nuclease, a target sequence is the sequence to which the guide sequence of a guide nucleic acid (e.g., guide RNA) will hybridize. For example, the target site (or target sequence) 5'-GTCAATGGACC-3' (SEQ ID NO:2663) within a target nucleic acid is targeted by (or is bound by, or hybridizes with, or is complementary to) the sequence 5'-GGTCCATTGAC-3' (SEQ ID NO:2664). Suitable hybridization conditions include physiological conditions normally present in a cell. For a double stranded target nucleic acid, the strand of the target nucleic acid that is complementary to and hybridizes with the guide RNA is referred to as the “complementary strand” or “target strand”; while the strand of the target nucleic acid that is complementary to the “target strand” (and is therefore not complementary to the guide RNA) is referred to as the “non-target strand” or “non-complementary strand.”
Therapeutic
[00261] Tire term “therapeutic” as used herein means a treatment and/or prophylaxis. A therapeutic effect is obtained by suppression, diminution, remission, or eradication of at least one sign or symptom of a disease or disorder state.
Therapeutically effective amount [00262] The term '‘therapeutically effective amount’’ refers to the amount of the subject compound that will elicit the biological or medical response of a tissue, system, or subject that is being sought by the researcher, veterinarian, medical doctor or other clinician. The term “therapeutically effective amount” includes that amount of a compound that, when administered, is sufficient to prevent development of, or alleviate to some extent, one or more of the signs or symptoms of the disorder or disease being treated. Tire therapeutically effective amount will vary depending on the compound, the disease and its severity and the age, weight, etc., of the subject to be treated.
Treat or treatment
[00263] To “treat” a disease as the term is used herein, means to reduce the frequency or severity of at least one sign or symptom of a disease or disorder experienced by a subject. Treatment
[00264] As used herein, the terms “treatment,” “treat,” and “treating,” refer to a clinical intervention aimed to reverse, alleviate, delay the onset of, or inhibit the progress of a disease or disorder, or one or more symptoms thereof, as described herein. In some embodiments, treatment may be administered after one or more symptoms have developed and/or after a disease has been diagnosed. In other embodiments, treatment may be administered in the absence of symptoms, e.g., to prevent or delay onset of a symptom or inhibit onset or progression of a disease. For example, treatment may be administered to a susceptible individual prior to the onset of symptoms (e g ., in light of a history of symptoms and/or in light of genetic or other susceptibility factors). Treatment may also be continued after symptoms have resolved, for example, to prevent or delay their recurrence.
Upstream and downstream
[00265] As used herein, the terms “upstream” and “downstream” are terms of relativity that define the linear position of at least two elements located in a nucleic acid molecule (whether single or double -stranded) that is orientated in a 5'-to-3' direction. A first element is said to be upstream of a second element in a nucleic acid molecule where the first element is positioned somewhere that is 5' to the second element. Conversely, a first element is downstream of a second element in a nucleic acid molecule where the first element is positioned somewhere that is 3' to the second element.
Variant
[00266] As used herein the tenn “variant” should be taken to mean the exhibition of qualities that have a pattern that deviates from what occurs in nature, e.g., a variant retron RT is retron RT comprising one or more changes in amino acid residues as compared to a wild type retron RT amino acid sequence. The term “variant” encompasses homologous proteins having at least 75%, or at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 99% percent identity with a reference sequence and having the same or substantially the same functional activity or activities as the reference sequence. The term also encompasses mutants, truncations, or domains of a reference sequence, and which display the same or substantially the same functional activity or activities as the reference sequence.
Vector
[00267] As used herein, tire term “vector” permits or facilitates the transfer of a polynucleotide from one environment to another. It is a replicon such as a plasmid, phage, or cosmid into which another DNA segment may be inserted so as to bring about the replication of the inserted segment. Generally, a vector is capable of replication when associated with the proper control elements. The term “vector” may include cloning and expression vectors, as well as viral vectors and integrating vectors.
Wild type
[00268] As used herein the term “wild type” is a term of the art understood by skilled persons and means the typical form of an organism, strain, gene, protein, or characteristic as it occurs in nature as distinguished from mutant or variant forms
B. Chemical Definitions
Alkyl
[00269] “Alkyl” refers to a straight or branched hydrocarbon chain radical consisting solely of carbon and hydrogen atoms, which is saturated or unsaturated (i.e., contains one or more double and/or triple bonds), having from one to thirty or more carbon atoms (e.g.. C1-C24 alkyl), one to twelve carbon atoms (C1-C12 alkyl), one to eight carbon atoms (C1-C8 alkyl) or one to six carbon atoms (C1-C6 alkyl) and which is attached to the rest of the molecule by a single bond, e.g., methyl, ethyl, n propyl, 1 -methylethyl (iso propyl), n butyl, n pentyl, 1,1 dimcthylcthyl (t butyl), 3 methylhexyl, 2 methylhexyl, cthcnyl, propyl cnyl, but-l-cnyl, pent- 1-enyl, penta-1, 4-dienyl, ethynyl, propynyl, butynyl, pentynyl, hexynyl, and the like. Alkyl groups that include one or more units of unsaturation (one or more double and/or triple bond) can be C2-C24, C2-C12, C2-C8 or C2-C6 groups, for example. Unless specifically stated otherwise, an alkyl group is optionally substituted. The term “alkyl,” by itself or as part of another substituent means, unless otherwise stated, a straight or branched chain hydrocarbon having the number of carbon atoms designated (i.e., Cl-6 means one to six carbon atoms) and includes straight, branched chain, or cyclic substituent groups.
Alkoxy
[00270] For example, the term “alkoxy” employed alone or in combination with other terms means, unless otherwise stated, an alkyl group having the designated number of carbon atoms, as defined above, connected to the rest of the molecule via an oxygen atom, such as, for example, methoxy, ethoxy, 1 -propoxy, 2 -propoxy (isopropoxy) and the higher homologs and isomers. Preferred are (C1-C3) alkoxy, particularly ethoxy and methoxy.
Alkylamino [00271] As used herein, the terms '‘alkoxy,” “alkylamino” and “alkylthio” are used in their conventional sense, and refer to alkyl groups linked to molecules via an oxygen atom, an amino group, a sulfur atom, respectively.
Alkylene
[00272] “Alkylene” or “alkylene chain” refers to a straight or branched divalent hydrocarbon chain consisting solely of carbon and hydrogen, which is saturated or unsaturated (i.e., contains one or more double (alkenylene) and/or triple bonds (alkynylcnc)). and having, for example, from one to thirty or more carbon atoms (e.g., C1-C24 alkylene), one to fifteen carbon atoms (C1-C15 alkylene), one to twelve carbon atoms (C1-C12 alkylene), one to eight carbon atoms (C1-C8 alkylene), one to six carbon atoms (C1-C6 alkylene), two to four carbon atoms (C2-C4 alkylene), one to two carbon atoms (C1-C2 alkylene), e.g., methylene, ethylene, propylene, n-butylene, ethenylene, propenylene, n-butenylene, propynylene, n-butynylene, and the like. Alkylene groups that include one or more units of unsaturation (one or more double and/or triple bond) can be C2-C24, C2-C12, C2-C8 or C2-C6 groups, for example. Tire alkylene chain is attached to the rest of the molecule through a single or double bond and to the radical group through a single or double bond. The points of attachment of the alkylene chain to the rest of the molecule and to the radical group can be through one carbon or any two carbons within the chain. Unless stated otherwise specifically in the specification, an alkylene chain may be optionally substituted.
Amino aryl
[00273] As used herein, the term “amino aryl" refers to an aryl moiety which contains an amino moiety. Such amino moieties may include, but are not limited to primary amines, secondary amines, tertiary amines, quaternary amines, masked amines, or protected amines. Such tertiary amines, masked amines, or protected amines may be converted to primary amine or secondary amine moieties. Additionally, the amine moiety may include an amine- like moiety which has similar chemical characteristics as amine moieties, including but not limited to chemical reactivity.
Aromatic
[00274] As used herein, the term “aromatic” refers to a carbocycle or heterocycle with one or more polyunsaturated rings and having aromatic character, i.e. having (4n + 2) delocalized p (pi) electrons, where n is an integer.
Aryl
[00275] As used herein, tire term “aryl,” employed alone or in combination with other terms, means, unless otherwise stated, a carbocyclic aromatic system containing one or more rings (typically one, two or three rings) wherein such rings may be attached together in a pendent manner, such as a biphenyl, or may be fused, such as naphthalene. Examples include phenyl, anthracyL and naphthyl. Preferred are phenyl and naphthyl, most preferred is phenyl.
Cvcloakylene
[00276] “Cycloalkylene” is a divalent cycloalkyl group. Unless otherwise stated specifically in the specification, a cycloalkylene group may be optionally substituted.
Cvcloalkyl
[00277] ‘ ‘Cycloalkyl” or “carbocyclic ring” refers to a stable non aromatic monocyclic or polycyclic hydrocarbon radical consisting solely of carbon and hydrogen atoms, which may include fused or bridged ring systems, having from three to fifteen carbon atoms, preferably having from three to ten carbon atoms, and which is saturated or unsaturated and attached to the rest of the molecule by a single bond. Monocyclic radicals include, for example, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl. Polycyclic radicals include, for example, adamantyl, norbomyl. decalinyl, 7,7 dimethyl bicyclo[2.2. l]heptanyl, and the like. Unless specifically stated otherwise, a cycloalkyl group is optionally substituted.
Halo
[00278] As used herein, tire tenn “halo” or “halogen” alone or as part of another substituent means, unless otherwise stated, a fluorine, chlorine, bromine, or iodine atom, preferably, fluorine, chlorine, or bromine, more preferably, fluorine or chlorine.
Heteroalkyl
[00279] As used herein, the term “heteroalkyl” by itself or in combination with another term means, unless otherwise stated, a stable straight or branched chain alkyl group consisting of the stated number of carbon atoms and one or tw o or more heteroatoms typically selected from the group consisting of O, N, Si, P, and S, and wherein the nitrogen and sulfur atoms may be optionally oxidized and the nitrogen heteroatom may be a primary, secondary, tertiary or quaternary nitrogen. The heteroatom(s) may be placed at any position of the heteroalkyl group, including between the rest of the heteroalkyl group and the fragment to which it is attached, as well as attached to the most distal carbon atom in the heteroalkyl group. Examples of heteroalkyl groups include: -O-CH2-CH2-CH3, -CH2-CH2-CH2-OH, - CH2-CH2-NH-CH3, -CH2-S-CH2-CH3, and - CH2CH2-S(=O)-CH3. Up to tw o heteroatoms may be consecutive, such as. for example, -CH2-NH-OCH3. or -CH2-CH2-S-S-CH3.
Heteroaryl
[00280] As used herein, the term "hcteroaty l" or “heteroaromatic” refers to aryl groups which contain at least one heteroatom typically selected from N, O, Si, P, and S; wherein the nitrogen and sulfur atoms may be optionally oxidized, and the nitrogen atom(s) may be optionally teriatry or quatemized. Heteroaryl groups may be substituted or unsubstituted. A heteroaryl group may be attached to the remainder of the molecule through a heteroatom. A polycyclic heteroaryl may include one or more rings that are partially saturated. Examples include tetrahydroquinoline, 2,3-dihydrobenzofuryl, 1 -pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3- pyrazolyl, 2 -imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl, 2-phenyl-4- oxazolyl, 5 -oxazolyl, 3- isoxazolyl, 4-isoxazolyl, 5-isoxazolyl, 2-thiazolyl, 4-thiazolyl, 5- thiazolyl, 2-furyl, 3-furyl, 2-thienyl, 3- thienyl. 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl, 4- pyrimidyl, 5 -benzothiazolyl, purinyl, 2- benzimidazolyl, 5-indolyl, 1 -isoquinolyl, 5- isoquinolyl, 2-quinoxalinyl, 5-quinoxalinyl, 3-quinolyl, and 6- quinolyl. Examples of non-aromatic heterocycles include monocyclic groups such as aziridine, oxirane, thiirane, azetidine, oxetane, thietane, pyrrolidine, pyrroline, imidazoline, pyrazolidine, dioxolane, sulfolane,
2.3 -dihydrofuran, 2,5-dihydrofuran. tetrahydrofuran, thiophane, piperidine, 1,2, 3, 6- tetrahydropyridine, 1,4- dihydropyridine, piperazine, morpholine, thiomorpholine, pyran, 2,3- dihydropyran, tetrahydropyran. 1,4- dioxane, 1,3-dioxane. homopiperazine, homopiperidine, 1,3-dioxepane. 4,7-dihydro-l,3-dioxepin and hexamethyleneoxide. Examples of heteroaryl groups include pyridyl, pyrazinyl, pyrimidinyl (particularly 2- and 4-pyrimidinyl), pyridazinyl, thienyl, furyl, pyrrolyl (particularly 2-pyrrolyl), imidazolyl, thiazolyl, oxazolyl, pyrazolyl (particularly 3- and 5-pyrazolyl), isothiazolyl, 1,2,3-triazolyl, 1,2,4-triazolyl, 1,3,4- triazolyl, tetrazolyl, 1,2,3-thiadiazolyl, 1,2,3-oxadiazolyl, 1,3,4-thiadiazolyl and 1,3,4- oxadiazolyl. Examples of polycyclic heterocycles include indolyl (particularly 3-, 4-, 5-. 6- and 7-indolyl), indolinyl, quinolyl, tetrahydroquinolyl, isoquinolyl (particularly 1- and 5- isoquinolyl), 1.2.3.4-tetrahydroisoquinolyl. cinnolinyl, quinoxalinyl (particularly 2- and 5- quinoxalinyl), quinazolinyl, phthalazinyl, 1,8-naphthyridinyl,
1.4-benzodioxanyl, coumarin, dihydrocoumarin, 1,5-naphthyridinyl, bcnzof'iiryl (particularly 3-, 4-, 5-, 6- and 7-benzofuiy 1), 2,3-dihydrobenzofuryl, 1,2-benzisoxazolyl, benzothienyl (particularly 3-, 4-, 5-, 6-, and 7- benzothienyl), benzoxazolyl, benzothiazolyl (particularly 2-benzothiazolyl and 5- benzothiazolyl), purinyl, benzimidazolyl (particularly 2-benzimidazolyl), benztriazolyl, thioxanthinyl, carbazolyl, carbolinyl, acridinyl, pyrrolizidinyl, and quinolizidinyl. The aforementioned listing of heterocyclyl and heteroaryl moieties is intended to be representative and not limiting.
Heterocyclyl
[00281] As used herein, tire tenn “heterocyclyl” or “heterocyclic ring” refers to a stable 3- to 18-membered non-aromatic ring radical which consists of two to twelve carbon atoms and from one to six heteroatoms typically selected from the group consisting of N. 0, Si, P, and S. Unless stated otherwise specifically in the specification, the heterocyclyl radical may be a monocyclic, bicyclic, tricyclic or tetracyclic ring system, which may include fused or bridged ring systems: and the nitrogen, carbon or sulfur atoms in the heterocyclyl radical may be optionally oxidized; the nitrogen atom may be optionally quatemized; and the heterocyclyl radical may be partially or fully saturated. Examples of such heterocyclyl radicals include, but are not limited to, dioxolanyl, thienyl[l,3]dithianyl, decahydroisoquinolyl, imidazolinyl, imidazolidinyl, isothiazolidinyl, isoxazolidinyl, morpholinyl, octahydroindolyl, octahydroisoindolyl, 2-oxopiperazinyl, 2-oxopiperidinyl, 2- oxopyrrolidinyl, oxazolidinyl, piperidinyl, piperazinyl, 4-piperidonyl, pyrrolidinyl, pyrazolidinyl, quinuclidinyl, thiazolidinyl. tetrahydrofuryl, trithianyl, tetrahydropyranyl, thiomorpholinyl, thiamorpholinyl, 1-oxo-thiomorpholinyl, and 1,1-dioxo-thiomorpholinyl. Unless specifically stated otherwise, a heterocyclyl group may be optionally substituted.
Substituents
[00282] As described herein, compounds of the present disclosure may contain '‘optionally substituted” moieties. In general, the term “substituted”, whether preceded by the term “optionally” or not, means that one or more hydrogens of the designated moiety are replaced with a suitable substituent. Unless otherwise indicated, an “optionally substituted” group may have a suitable substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. Combinations of substituents envisioned by this disclosure are preferably those that result in the fonnation of stable or chemically feasible compounds. Tire term “stable”, as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes disclosed herein. [00283] Suitable monovalent substituents on a substitutable carbon atom of an “optionally substituted” group are independently halogen; — (CH2)0-4R°; — (CH2)0-4OR°; — O(CH2)0-4R°, — O— (CH2)0-4C(O)OR°;
— (CH2)0-4CH(OR°)2; — (CH2)0-4SR°; — (CH2)0-4Ph, which may be substituted with R°; — (CH2)0- 4O(CH2)0-lPh which may be substituted with R°; — CH=CHPh, which may be substituted with R°; — (CH2)0-40(CH2)0-1 -pyridyl which may be substituted with R°; — NO2; — CN; — N3; — (CH2)0-4N(R°)2; — (CH2)0-4N(R°)C(O)R°; — N(R°)C(S)R°; — (CH2)0-4N(R°)C(O)NR° 2; — N(R°)C(S)NR° 2: — (CH2)0- 4N(R°)C(0)0R°; — N(R°)N(R°)C(O)R°; — N(R°)N(R°)C(0)NR° 2; — N(R°)N(R°)C(0)0R°; — (CH2)0- 4C(O)R°; — C(S)R°; — (CH2)0-4C(O)OR°: — (CH2)0-4C(O)SR°; — (CH2)0-4C(O)OSiR° 3; — (CH2)0- 4OC(O)R°; — OC(O)(CH2)0-4SR°, SC(S)SR°; — (CH2)0-4SC(O)R°; — (CH2)0-4C(O)NR° 2; — C(S)NR° 2; — C(S)SR°; — SC(S)SR°, — (CH2)0-4OC(O)NR° 2; — C(0)N(0R°)R°; — C(O)C(O)R°; — C(O)CH2C(O)R°; — C(NOR°)R°; — (CH2)0-4SSR°: — (CH2)0-4S(O)2R°; — (CH2)0-4S(O)2OR°; — (CH2)0-4OS(O)2R°; — S(O)2NR° 2; — (CH2)0-4S(O)R°; — N(R°)S(O)2NR° 2; — N(R°)S(O)2R°; — N(0R°)R°; — C(NH)NR° 2; — P(O)2R°; — P(O)R° 2; — OP(O)R° 2; — OP(O)(OR°)2; SiR° 3; — (Cl-4 straight or branched alkylenejO — N(R°)2; or — (Cl-4 straight or branched alkylene)C(O)O — N(R°)2, wherein each R° may be substituted as defined below and is independently hydrogen, Cl -6 aliphatic, — CH2Ph. — O(CH2)0-lPh. — CH2-(5-6 membered heteroaryl ring), or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R°, taken together with their intervening atom(s), form a 3-12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, which may be substituted as defined below.
[00284] Suitable monovalent substituents on R° (or tire ring formed by taking two independent occurrences of R° together with their intervening atoms), are independently halogen, — (CH2)0-2R*, -(haloR*). — (CH2)0-2OH, — (CH2)0-2OR*, — (CH2)0-2CH(OR*)2: — O(haloR’), — CN, — N3, — (CH2)0-2C(O)R*, — (CH2)0-2C(O)OH, — (CH2)0-2C(O)OR*, — (CH2)0-2SR*, — (CH2)0-2SH, — (CH2)0-2NH2, — (CH2)0- 2NHR*, — (CH2)0-2NR* 2, — NO2, — SiR* 3, — OSiR* 3, — C(O)SR*, — (Cl-4 straight or branched alkylene)C(O)OR*. or — SSR* wherein each R* is unsubstituted or where preceded by "halo" is substituted only with one or more halogens, and is independently selected from Cl-4 aliphatic, — CH2Ph, — O(CH2)0- IPh, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents on a saturated carbon atom of R° include =0 and =S.
[00285] Suitable divalent substituents on a saturated carbon atom of an “optionally substituted” group include the following: =0, =S, =NNR*2, =NNHC(0)R*,
[00286] =NNHC(O)OR*. =NNHS(O)2R*, =NR*, =N0R*, — O(C(R*2))2-3O— , or — S(C(R*2))2-3S— , wherein each independent occurrence of R* is selected from hydrogen, Cl -6 aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents that are bound to vicinal substitutable carbons of an “optionally substituted” group include: — O(CR*2)2-3O — , wherein each independent occurrence of R* is selected from hydrogen, Cl-6 aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. [00287] Suitable substituents on the aliphatic group of R* include halogen, — R*, - (haloR*), — OH, — OR*, — O(haloR*), — CN, — C(O)OH, — C(O)OR*, — NH2, — NHR*, —NR* 2, or — NO2, wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently Cl-4 aliphatic, — CH2Ph, — O(CH2)0- IPh, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. [00288] Suitable substituents on a substitutable nitrogen of an “optionally substituted” group include — R . — NRf 2, — C(O)Rf, — C(O)ORt, — C(O)C(O)Rt, — C(O)CH2C(O)Rt,— S(O)2Rt, — S(O)2NR: 2, — C(S)NRt 2, — C(NH)NRf 2, or — N(R')S(O)2R'; wherein each R' is independently hydrogen, Cl -6 aliphatic which may be substituted as defined below, unsubstituted — OPh, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or. notwithstanding the definition above, two independent occurrences of R:. taken together with their intervening atom(s) form an unsubstituted 3-12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
[00289] Suitable substituents on the aliphatic group of R ' are independently halogen, — R*, -(haloR*), — OH, —OR*, — O(haloR*), — CN, — C(O)OH, — C(O)OR*, — NH2, — NHR*, —NR* 2, or — NO2, wherein each R* is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently Cl-4 aliphatic. — CH2Ph, — O(CH2)0-lPh. or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
[00290] Heteroatoms such as nitrogen may have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valences of the heteroatoms. It is understood that "substitution" or "substituted" includes the implicit proviso that such substitution is in accordance with permitted valence of the substituted atom and the substituent, and that the substitution results in a stable compound, i.e.. a compound that does not spontaneously undergo transformation, for example, by rearrangement, cyclization, or elimination.
[00291] In a broad aspect, the permissible substituents include acyclic and cyclic, branched and unbranched, carbocyclic and heterocyclic, aromatic and nonaromatic substituents of organic compounds. Illustrative substituents include, for example, those described herein. Hie permissible substituents can be one or more and the same or different for appropriate organic compounds. Hie heteroatoms such as nitrogen may have hydrogen substituents and/or any permissible substituents of organic compounds described herein which satisfy the valencies of the heteroatoms.
[00292] In various embodiments, the substituent is selected from alkoxy, aryloxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cyano, cycloalkyl, ester, ether, formyl, halogen, haloalkyl, heteroaryl, heterocyclyl, hydroxyl, ketone, nitro, phosphate, sulfide, sulfinyl, sulfonyl, sulfonic acid, sulfonamide, and thioketone, each of which optionally is substituted with one or more suitable substituents. In some embodiments, the substituent is selected from alkoxy, aryloxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cycloalkyl, ester, ether, formyl, haloalkyl, heteroaryl, heterocyclyl, ketone, phosphate, sulfide, sulfinyl, sulfonyl, sulfonic acid, sulfonamide, and thioketone, wherein each of the alkoxy, aryloxy, alkyl, alkenyl, alkynyl, amide, amino, aryl, arylalkyl, carbamate, carboxy, cycloalkyl, ester, ether, formyl, haloalkyl, heteroaryl, heterocyclyl, ketone, phosphate, sulfide, sulfinyl, sulfonyl, sulfonic acid, sulfonamide, and thioketone can be further substituted with one or more suitable substituents.
[00293] Examples of substituents include, but are not limited to, halogen, azide, alkyl, aralkyl, alkenyl, alkynyl, cycloalkyl, hydroxyl, alkoxyl, amino, nitro, sulfhydryl, imino, amido, phosphonate, phosphinate, carbonyl, carboxyl, silyl, ether, alkylthio, sulfonyl, sulfonamide, ketone, aldehyde, thioketone, ester, heterocyclyl, -CN, aryl, aryloxy, perhaloalkoxy, aralkoxy, heteroaryl, heteroaryloxy. heteroarylalkyl, heteroaralkoxy, azido, alkylthio, oxo, acylalkyl, carboxy esters, carboxamido, acyloxy, aminoalkyl, alkylaminoaryl, alkylaryl, alkylaminoalkyl, alkoxyaryl, arylanuno. aralkylamino, alkylsulfonyl, carboxamidoalkylaryl, carboxamidoaryl, hydroxyalkyl, haloalkyl, alkylaminoalkylcarboxy, aminocarboxamidoalkyl, cyano, alkoxyalkyl, perhaloalkyl, arylalkyloxyalkyl, and the like. In some embodiments, the substituent is selected from cyano, halogen, hydroxyl, and nitro.
[00294] Throughout the disclosure, chemical substituents described in Markush structures are represented by variables. Where a variable is given multiple definitions as applied to different Markush formulas in different sections of the disclosure, it is to be understood that each definition should only apply to the applicable fonnula in the appropriate section of the disclosure.
Abbreviations
[00295] As used herein, the following abbreviations and initialisms have the indicated meanings:
[00296] The details of one or more embodiments of the disclosure are set forth in the accompanying description below. Although any materials and methods similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, the preferred materials and methods are now described. Other features, objects and advantages of the disclosure will be apparent from the description. In the description, the singular forms also include the plural unless the context clearly dictates otherwise. Unless defined otherwise, all technical and scientific tenns used herein have tire same meaning as commonly- understood by one of ordinary skill in the art to which this disclosure belongs. In the case of conflict, the present description will control.
C. Casl2a (or Cas Type V) Sequences
[00297] Hie present disclosure provides a Cas Type V polypeptide comprising an amino acid sequence having at least 80%, 85%, 90%, 91%. 92%. 93%. 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% sequence identity to any one of the amino acid sequence sequences selected from SEQ ID NO: 334 (No.
ID405), SEQ ID NO: 58 (No. TD414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein the poly-peptide comprises one or more substitutions at positions selected from: Q492, T306, L748, A739, F297, N536, D851, N770. D675, K955, S972. N798, K298, H853, E377, V295. K852, F854, N1015, T845. E1019, K745, K292, Q565. K745, 1723, K821, K721, A810, K768. S16, 128. V312, V929, L474. H470, E402, K207, V294, R212, F79. Q299, Q465. F537, K1284, V929, DI 192. Q1203. T838. N735, 11063. K933, N1249, 197. R212, A1251, N1264, R1138, N588, E584, V453, Q475, N76, R304, 1471, E544, V254, D231, H496, V534, D577, 128, A183, D341, K595, V501, S568, H470, V254, D231 and F197, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No.
ID419).
[00298] Particular substitutions and combinations of substitutions are disclosed elsewhere herein. One of skill in the art will be able to identify the corresponding residue in any homologous protein and in the respective encoding nucleic acid by methods well known in the art, e.g., by- sequence alignment and determination of homologous residues. The Cas Type V polypeptide may be isolated, engineered, and/or non-naturally occuring.
[00299] In some embodiments, Cas Type V polypeptides of the present disclosure are capable of inducing indel formation when contacted with a population of target sequences and a guide RNA targeting the Cas Type V polypeptide to the target sequence under conditions suitable for inducing indel formation. The target sequence may be a DNA sequence. In some embodiments, the target sequence may be associated with a disease or disorder. In some embodiments, the substitutions in the Cas Type V polypeptides disclosed herein enhance tire ability of the Cas Type V polypeptide to induce indels in comparison with Cas Type V polypeptides that do not comprise the substitutions. For example, in some embodiments the Cas Type V polypeptide induces indel formation when contacted with a population of target sequences and a guide RNA targeting the Cas Type V polypeptide to the target sequence under conditions suitable for inducing indel formation, wherein the contacting results in an increase in the percentage of target polynucleotide sequences comprising an indel in the population of target sequences of at least 20%. at least 30%, at least 40%, or at least 50% as compared to the percentage of target polynucleotide sequences comprising an indel in the population when the population is contacted with a reference polypeptide comprising the sequence of SEQ ID NO: 1554 (No. ID405-1) and a guide RNA that targets the reference polypeptide to the target polynucleotide sequence.
[00300] The Cas Type V polypeptide may be associated with one or more additional accessory proteins having genome modifying functions, including recombinases, invertases, nucleases, polymerases, ligases, deaminases, reverse transcriptases, or epigenetic modifying functions. In various embodiments, the accessory proteins may be provided separately. In other embodiments, the accessory proteins may be fused to the Cas Type V polypeptide, optionally with a linker. The disclosure provides a fusion protein comprising the Cas Type V polypeptide fused to a heterologous amino acid sequence, such as an accessory protein as described herein.
[00301] The disclosure provides a gene editing system comprising: (a) one or more Cas Type V polypeptides of tire disclosure or one or more polynucleotides encoding the Cas Type V polypeptide(s); and (b) one or more polynucleotide sequences comprising a guide RNA (gRNA) or one or more polynucleotides encoding the gRNA, wherein the gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence. The guide RNA may be a guide RNA as disclosed herein.
[00302] Tire present disclosure also provides polypeptides comprising (i) a Cas Type V polypeptide, (ii) one, two, three or more Nuclear Localization Sequences (NLS); and optionally (iii) one or more linker sequences. The Cas Type V polypeptide may be any of the Cas Type V polypeptides disclosed herein. The polypeptides may comprise any of the NLS sequences, linker sequences, and/or structures as described elsewhere herein.
[00303] In some embodiments, polypeptides of the present disclosure are capable of inducing indel formation when contacted with a population of target sequences and a guide RNA targeting the polypeptide to the target sequence under conditions suitable for inducing indel formation. Tire target sequence may be a DNA sequence. In some embodiments, tire target sequence may be associated with a disease or disorder. In some embodiments, the NLS sequences, linker sequences, and/or structures of the polypeptides disclosed herein enhance tire ability of the polypeptide to induce indels in comparison with polypeptides that do not comprise the structures, NLS sequences, and linker sequences. For example, in some embodiments the polypeptide induces indel formation when contacted with a population of target sequences and a guide RNA targeting the polypeptide to the target sequence under conditions suitable for inducing indel formation, wherein the contacting results in an increase in the percentage of target poly nucleotide sequences comprising an indel in the population of target sequences of at least 40%, at least 50%, at least 60%. or at least 70% as compared to the percentage of target polynucleotide sequences comprising an indel in the population when the population is contacted with a reference polypeptide comprising the structure N-[SEQ ID NO: 1554 (ID405-l)]-[SEQ ID NO: SEQ ID NO: 1556]-C.
[00304] The polypeptide may be associated with one or more additional accessory proteins having genome modifying functions, including recombinases, invertases, nucleases, polymerases, ligases, deaminases, reverse transcriptases, or epigenetic modifying functions. In various embodiments, the accessory proteins may be provided separately. In other embodiments, the accessory proteins may be fused to the polypeptide, optionally with a linker. The disclosure provides a fusion protein comprising the polypeptide fused to a heterologous amino acid sequence, such as an accessory protein as described herein.
[00305] The disclosure provides a gene editing system comprising: (a) one or more polypeptides of the disclosure or one or more polynucleotides encoding the polypeptide(s); and (b) one or more polynucleotide sequences comprising a guide RNA (gRNA) or one or more polynucleotides encoding the gRNA, wherein the gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence. The guide RNA may be a guide RNA as disclosed herein.
[00306] The disclosure provides a method of modifying a targeted polynucleotide sequence, the method comprising contacting the targeted polynucleotide sequence with a gene editing system as disclosed herein. Hie method may be carried out in vitro, ex vivo or in vivo. In some embodiments, the disclosure provides a method of modifying a targeted polynucleotide sequence, the method comprising introducing into a cell the gene editing system of the disclosure. [00307] The disclosure provides one or more polynucleotides encoding: a Cas Type V polypeptide or polypeptide as disclosed herein, a fusion protein as disclosed herein, or a gene editing system as disclosed herein. The disclosure further provides one or more vectors comprising the one or more polynucleotides. The disclosure further provides a cell comprising the one or more vectors or the one or more polynucleotides.
[00308] Any of the Cas Type V polypeptides, polypeptides, fusion proteins, gene editing systems, polynucleotides, vectors, or phannaceutical compositions disclosed herein can be used in medicine, for example for use in treating or preventing a disease or disorder as disclosed elsewhere herein.
[00309] Exemplary amino acid and protein coding sequences of Cas Type V polypeptides of tire present disclosure are provided in Appendix B.
[00310] Hie present disclosure provides Casl2a (or Cas Type V) polypeptides and nucleic acid molecules encoding same for use in the Casl2a-based gene editing systems described herein for use in various applications, including precision gene editing in cells, tissues, organs, or organisms. In various embodiments, the Cas 12a-based gene editing systems comprise (a) a Cas 12a (or Cas Type V) polypeptide (or a nucleic acid molecule encoding a Casl2a (or Cas Type V) polypeptide) and (b) a Casl2a (or Cas Type V) guide RNA which is capable of associating with a Cas 12a (or Cas Type V) polypeptide to form a complex such that the complex localizes to a target nucleic acid sequence (e.g., a genomic or plasmid target sequence) and binds thereto. In various embodiments, the Cas 12a (or Cas Type V) polypeptide has a nuclease activity which results in the cutting of both strands of DNA.
[00311] As outlined in B. Paul. Biomedical Journal, Vol. 43, No. 1, February 2020 pages 8-17. the CRISPR- Cas systems are classified into two classes (Classes 1 and 2) that are subdivided into six types (types I through VI). Class 1 (types I, III and IV) systems use multiple Cas proteins in their CRISPR ribonucleoprotein effector nucleases and Class 2 systems (types II, V and VI) use a single Cas protein. Class 1 CRISPR-Cas systems are most commonly found in bacteria and archaea, and comprise ~90% of all identified CRISPR-Cas loci. The Class 2 CRISPR-Cas systems, comprising the remaining ~10%, exists almost exclusively in bacteria, and assemble a ribonucleoprotein complex, consisting of a CRISPR RNA (crRNA) and a Cas protein. The crRNA contains information to target a specific DNA sequence. These multidomain effector proteins achieve interference by complementarity between the crRNA and the target sequence after recognition of the PAM (Protospacer Adjacent Motif) sequence, which is adjacent to the target DNA. These ribonucleoprotein complexes have been redesigned for precise genome editing by providing a crRNA with a redesigned guide sequence, which is complementary to the sequence of the targeted DNA. Tire most widely characterized CRISPR-Cas system is tire type 11 subtype Il-A that is found in Streptococcus pyogenes (Sp), which uses the protein SpCas9, Cas9 was the first Cas-protein engineered for use in gene editing. Class 2 type V is further classified into 4 subtypes (V-A, V-B, V-C, V-U). At present, V-C and V- U remain widely uncharacterised and no structural information on these systems is available. V-A encodes the protein Casl2a (also known as Cpfl) and recently several high resolution structures of Cast 2a have provided an insight into its working mechanism.
[00312] Type II (e.g., Cas9) and type V (e.g., Casl2a) CRISPR-Cas systems possess a characteristic Ruv-C like nuclease domain, which has been shown to be related to IS605 family transposon encoded TnpB proteins. Crystallographic and cryo-EM data reveal that Cast 2a adopts a bilobed structure formed by the REC and Nuc lobes. The REC lobe is comprised of REC 1 and REC2 domains, and the Nuc lobe is comprised of tire RuvC, the PAM-interacting (PI) and the WED domains, and additionally, the bridge helix (BH). The RuvC endonuclease domain of this effector protein is made up of three discontinuous parts (RuvC I -III) . The RNase site for processing its own crRNA is situated in the WED-III subdomain, and the DNase site is located in the interface between the RuvC and the Nuc domains. These structural studies have also shown that the only the 5 ’ repeat region of the crRNA is involved in the assembly of the binary complex. The 19/20 nt repeat region forms a pseudoknot structure through intramolecular base pairing. Tire crRNA is stabilized through interactions with the WED, RuvC and REC2 domains of the endonuclease, as well as two hydrated Mg2+ ions. This binary interference complex is then responsible for recognizing and degrading foreign DNA.
[00313] PAM recognition is a critical initial step in identifying a prospective DNA molecule for degradation since the PAM allows the CRISPR-Cas systems to distinguish their own genomic DNA from invading nucleic acids. Casl2a employs a multistep quality control mechanism to ensure the accurate and precise recognition of target spacer sequences. The WED II-III. RECI and PAM-interacting domains are responsible for PAM recognition and for initiating the hybridization of the DNA target with the crRNA. After recognition of the dsDNA by WED and REC 1 domains, the conserved loop-lysine helix-loop (LKL) region in the PI domain, containing three conserved lysines (K667, K671, K677 in FnCasl2a), inserts the helix into the PAM duplex with assistance from two conserved prolines in the LKL region. Structural studies show the helix is inserted at an angle of 45° with respect to the dsDNA longitudinal axis, promoting the unwinding of the helical dsDNA. The critical positioning of the three conserved lysines on the dsDNA initiates the uncoupling of the Watson-Crick interaction between the base pairs of the dsDNA after the PAM. The target dsDNA unzipping allows the hybridization of the crRNA w ith the strand containing the PAM, the ‘target strand (TS), w hile the uncoupled DNA strand, non-target strand (NTS), is conducted towards the DNase site by the PAM-interacting domain. Casl2a has been shown to efficiently target spacer sequences following 5'T-rich PAM sequence. The PAM for LbCasl2a and AsCasl2a has a sequence of 5'-TTTN-3' and for FnCasl2a a sequence of 5'-TTN-3' and is situated upstream of the 5’end of the non-target strand. It has also been shown that in addition to the canonical 5'-TTTN-3' PAM, Casl2a also exhibits relaxed PAM recognition for suboptimal C-containing PAM sequences by forming altered interactions with the targeted DNA duplex.
[00314] Thus, Casl2a is another class II CRISPR/Cas system RNA-guided nuclease with similarities to Cas9 and may be used analogously. Unlike Cas9. Casl2a does not require a tracrRNA and only depends on a crRNA in its guide RNA, which provides the advantage that shorter guide RNAs can be used with Cast 2a for targeting than Cas9. Casl2a is capable of cleaving either DNA or RNA. The PAM sites recognized by Casl2a have the sequences 5'-YTN-3' (where “Y’’ is a pyrimidine and C'N” is any nucleobase) or 5'-TTN-3', in contrast to the G-rich PAM site recognized by Cas9. Casl2a cleavage of DNA produces double-stranded breaks with a sticky-ends having a 4 or 5 nucleotide overhang. For further discussion of Casl2a, see, e.g., Ledford et al. (2015) Nature. 526 (7571): 17-17. Zetsche et al. (2015) Cell. 163 (3):759-771, Murovec et al. (2017) Plant Biotechnol. J. 15(8):917-926, Zhang et al. (2017) Front. Plant Sci. 8: 177, Fernandes et al. (2016) Postepy Biochem. 62(3):315-326; herein incorporated by reference.
[00315] Any Casl2a (or Cas Type V) polypeptide or variant thereof may be used in the present disclosure, including those described in the herein tables and provided in the accompanying sequence listing.
[00316] In various embodiments, the Cas 12a (or Cas Type V) polypeptide is a polypeptide selected from Table S15A (SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419)), or a polypeptide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a polypeptide from Table S15A (SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414). or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415). and SEQ ID NO: 445 (No. ID419)).
[00317] In various embodiments, the Cas 12a (or Cas Type V) polypeptide is encoded by a polynucleotide sequence selected from Table S15B (SEQ ID NO: 365 (No. ID405), SEQ ID NO: 75 (No. ID414), or SEQ ID NO: 565 (No. ID418), SEQ ID NO: 366 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 30 (No. ID415), or SEQ ID NO: 445 (No. ID419)), or a polynucleotide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a polypeptide from Table S15B (SEQ ID NO: 365 (No. ID405), SEQ ID NO: 75 (No. ID414), or SEQ ID NO:565 (No. ID418), SEQ ID NO: 366 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 30 (No. ID415). or SEQ ID NO: 445 (No. ID419)).
[00318] Any Cas 12a (or Cas Type V) polypeptide may be utilized with the compositions described herein. Hie Cas 12a editing systems contemplated herein are not meant to be limiting in any way. The Cas 12a editing systems disclosed herein may comprise a canonical or naturally-occurring Casl2a, or any ortholog Casl2a protein, or any variant Cast 2a protein — including any naturally occurring variant, mutant, or otherwise engineered version of Cast 2a — that is known or which can be made or evolved through a directed evolutionary or otherwise mutagenic process. In various embodiments, the Casl2a or Casl2a variants can have a nickase activity, i.e.. only cleave of strand of the target DNA sequence. In other embodiments, the Casl2a or Cast 2a variants have inactive nucleases, i.e.. are “dead” Cast 2a proteins. Other variant Cast 2a proteins that may be used are those having a smaller molecular weight than the canonical Casl2a (e.g., for easier delivery) or having modified amino acid sequences or substitutions.
[00319] In various aspects, the present invention provides one or more modifications of Casl2a (or Cas Type V) polypeptides, including, for example, mutations to increase sufficiency and/or efficiency and modification of the Casl2a. In some embodiments, one or more domains of the Casl2a are modified, e.g., RuvC, REC, WED, BH, PI and NUC domains. In certain preferred embodiments, tire modifications provide editing efficiency of greater than 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%. 90%. 95%, 99% relative to SpCas9. Even more preferably, the methods and compositions provide enhanced transduction efficiency and/or low cytotoxicity.
[00320] The Cas 12a (or Cas Type V) gene editing systems and therapeutics described herein may comprise one or more nucleic acid components (e.g., a guide RNA or a coding RNA that encodes a component of the Casl2a system) which may be codon optimized.
[00321] For example, a nucleotide sequence (e.g., as part of an RNA payload) encoding a nucleobase editing system of the disclosure is codon optimized. Codon optimization methods are known in the art. For example, a protein encoding sequence of any one or more of the sequences provided herein may be codon optimized. Codon optimization, in some embodiments, may be used to match codon frequencies in target and host organisms to ensure proper folding: bias GC content to increase mRNA stability or reduce secondary structures; minimize tandem repeat codons or base runs that may impair gene construction or expression; customize transcriptional and translational control regions; insert or remove protein trafficking sequences; remove/add post translation modification sites in encoded protein (e.g., glycosylation sites); add, remove or shuffle protein domains; insert or delete restriction sites; modify ribosome binding sites and mRNA degradation sites; adjust translational rates to allow the various domains of the protein to fold properly; or reduce or eliminate problem secondary structures within the polynucleotide. Codon optimization tools, algorithms and services are known in the art — non-limiting examples include services from GeneArt (Life Technologies), DNA2.0 (Menlo Park Calif.) and/or proprietary methods. In some embodiments, the protein encoding sequence is optimized using optimization algorithms. In some embodiments, a codon optimized sequence shares less than 95% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding anucleobase editing enzyme). In some embodiments, a codon optimized sequence shares less than 90% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a nucleobase editing enzyme). In some embodiments, a codon optimized sequence shares less than 85% sequence identity to a naturally-occurring or wild-type sequence (e.g.. a naturally-occurring or wild-type mRNA sequence encoding a nucleobase editing enzyme). In some embodiments, a codon optimized sequence shares less than 80% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a nucleobase editing enzyme). In some embodiments, a codon optimized sequence shares less than 75% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally- occurring or wild-type mRNA sequence encoding a nucleobase editing enzyme).
[00322] In some embodiments, a codon optimized sequence shares between 65% and 85% (e.g., between about 67% and about 85% or between about 67% and about 80%) sequence identity to a naturally-occurring or wild-type sequence (e.g.. a naturally-occurring or wild-type mRNA sequence encoding a nucleobase editing enzyme). In some embodiments, a codon optimized sequence shares between 65% and 75% or about 80% sequence identity to a naturally-occurring or wild-type sequence (e.g., a naturally-occurring or wild-type mRNA sequence encoding a nucleobase editing enzyme).
[00323] When transfected into mammalian cells, the modified mRNA payloads have a stability of between 12-18 hours, or greater than 18 hours, e.g., 24, 36, 48, 60, 72, or greater than 72 hours.
[00324] In some embodiments, a codon optimized RNA may be one in which the levels of G/C are enhanced. The G/C-content of nucleic acid molecules (e.g., mRNA) may influence the stability of the RNA. RNA having an increased amount of guanine (G) and/or cytosine (C) residues may be functionally more stable than RNA containing a large amount of adenine (A) and thymine (T) or uracil (U) nucleotides. As an example, WO02/098443 discloses a phannaceutical composition containing an mRNA stabilized by sequence modifications in the translated region. Due to the degeneracy of the genetic code, the modifications work by substituting existing codons forthose that promote greater RNA stability without changing the resulting amino acid. The approach is limited to coding regions of the RNA.
[00325] In some embodiments, the disclosure provides engineered Casl2a variants or mutants which have been modified by introducing one or more amino acid substitutions into a baseline sequence (e.g., a wildtype sequence). [00326] Any available methods may be utilized to obtain or construct a variant or mutant Cas 12a protein. The term ‘'mutation,” as used herein, refers to a substitution of a residue within a sequence, e.g., a nucleic acid or amino acid sequence, with another residue, or a deletion or insertion of one or more residues w ithin a sequence. Mutations are typically described herein by identifying tire original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue. Various methods for making the amino acid substitutions (mutations) provided herein are well known in the art (e.g., site-directed mutagenesis or directed evolution engineering), and are provided by, for example, Green and Sambrook, Molecular Cloning: A Laboratory Manual (4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)). Mutations can include a variety of categories, such as single base polymorphisms, microduplication regions, indel, and inversions, and is not meant to be limiting in any way. Mutations can include “loss-of-function” mutations w hich is the normal result of a mutation that reduces or abolishes a protein activity. Most loss-of-function mutations are recessive, because in a heterozygote the second chromosome copy carries an unmutated version of the gene coding for a fully functional protein w hose presence compensates for the effect of the mutation. Mutations also embrace “gain-of-function” mutations, which confer an abnormal activity on a protein or cell that is otherwise not present in a normal condition. Many gain-of-function mutations are in regulatory sequences rather than in coding regions, and can therefore have a number of consequences. For example, a mutation might lead to one or more genes being expressed in the wrong tissues, these tissues gaining functions that they normally lack. Because of their nature, gain-of-function mutations are usually dominant.
[00327] Mutations can be introduced into a reference Cas 12a protein using site-directed mutagenesis. Older methods of site-directed mutagenesis know n in the art rely on sub-cloning of the sequence to be mutated into a vector, such as an M13 bacteriophage vector, that allows the isolation of single-stranded DNA template. In these methods, one anneals a mutagenic primer (i.e., a primer capable of annealing to the site to be mutated but bearing one or more mismatched nucleotides at the site to be mutated) to the single-stranded template and then polymerizes the complement of the template starting from the 3' end of the mutagenic primer. The resulting duplexes are then transformed into host bacteria and plaques are screened for the desired mutation. More recently, site-directed mutagenesis has employed PCR methodologies, w hich have the advantage of not requiring a single-stranded template. In addition, methods have been developed that do not require sub-cloning. Several issues must be considered when PCR-based site-directed mutagenesis is performed. First, in these methods it is desirable to reduce the number of PCR cycles to prevent expansion of undesired mutations introduced by the polymerase. Second, a selection must be employed in order to reduce the number of non-mutated parental molecules persisting in the reaction. Third, an extended-length PCR method is preferred in order to allow the use of a single PCR primer set. And fourth, because of the non-template-dependent terminal extension activity of some thermostable polymerases it is often necessary’ to incorporate an end-polishing step into the procedure prior to blunt-end ligation of the PCR-generated mutant product.
[00328] Mutations may also be introduced by directed evolution processes, such as phage-assisted continuous evolution (PACE) or phage-assisted noncontinuous evolution (PANCE). Tire term “phage- assisted continuous evolution (PACE)," as used herein, refers to continuous evolution that employs phage as viral vectors. The general concept of PACE technology has been described, for example, in International PCT Application, PCT/US2009/056194, filed Sep. 8, 2009, published as WO 2010/028347 on Mar. 11, 2010; International PCT Application, PCT/US2011/066747, filed Dec. 22, 2011, published as WO 2012/088381 on Jun. 28, 2012; U.S. Pat. No. 9,023,594, issued May 5, 2015, International PCT Application, PCT/US2015/012022, filed Jan. 20, 2015, published as WO 2015/134121 on Sep. 11, 2015, and International PCT Application, PCT/US2016/027795, filed Apr. 15, 2016. published as WO 2016/168631 on Oct. 20, 2016. the entire contents of each of which are incorporated herein by reference. Variant Casl2as may also be obtain by phage-assisted non-continuous evolution (PANCE),” which as used herein, refers to non-continuous evolution that employs phage as viral vectors. PANCE is a simplified technique for rapid in vivo directed evolution using serial flask transfers of evolving "selection phage’ (SP), which contain a gene of interest to be evolved, across fresh E. coli host cells, thereby allowing genes inside the host E. coli to be held constant while genes contained in the SP continuously evolve. Serial flask transfers have long served as a widely-accessible approach for laboratory evolution of microbes, and, more recently, analogous approaches have been developed for bacteriophage evolution. The PANCE system features lower stringency than the PACE system.
[00329] The disclosure contemplates any engineered Casl2a variants or mutants which have been modified by introducing one or more amino acid substitutions into a baseline sequence, including conservative substitutions of one amino acid for another. For example, mutation of an amino acid with a hydrophobic side chain (e.g.. alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, or tryptophan) may be changed to a second amino acid with a different hydrophobic side chain (e.g., alanine, valine, isoleucine, leucine, methionine, phenylalanine, tyrosine, or tryptophan). For example, a mutation of an alanine to a threonine (e.g., a A262T mutation) may also include a mutation from an alanine to an amino acid that is similar in size and chemical properties to a threonine, for example, serine. As another example, mutation of an amino acid with a positively charged side chain (e g., arginine, histidine, or lysine) may include a mutation to a second amino acid with a different positively charged side chain (e.g., arginine, histidine, or lysine). As another example, mutation of an amino acid with a polar side chain (e.g., serine, threonine, asparagine, or glutamine) may also include a mutation to a second amino acid with a different polar side chain (e.g., serine, threonine, asparagine, or glutamine). Additional similar amino acid pairs include, but are not limited to, the following: phenylalanine and tyrosine; asparagine and glutamine: methionine and cysteine; aspartic acid and glutamic acid; and arginine and lysine. The skilled artisan would recognize that such conservative amino acid substitutions may only have minor effects on protein structure and may be well tolerated without compromising function. In some embodiments, any amino acid mutations provided herein from one amino acid to a threonine may be an amino acid mutation to a serine. In some embodiments, any amino acid mutations provided herein from one amino acid to an arginine may be an amino acid mutation to a lysine. In some embodiments, any amino acid mutations provided herein from one amino acid to an isoleucine, may be an amino acid mutation to an alanine, valine, methionine, or leucine. In some embodiments, any amino acid mutations provided herein from one amino acid to a lysine may be an amino acid mutation to an arginine. In some embodiments, any amino acid mutations provided herein from one amino acid to an aspartic acid may be an amino acid mutation to a glutamic acid or asparagine. In some embodiments, any amino acid mutations provided herein from one amino acid to a valine may be an amino acid mutation to an alanine, isoleucine, methionine, or leucine. In some embodiments, any amino acid mutations provided herein from one amino acid to a glycine may be an amino acid mutation to an alanine. It should be appreciated, however, that additional conserved amino acid residues would be recognized by the skilled artisan and any of the amino acid mutations to other conserved amino acid residues are also within the scope of this disclosure. Tire amino acid substitutions may also be non-conservative amino acid substitutions.
[00330] In various embodiments, an Alanine (A) residue of a Casl2a protein may be substituted with any one of tire following amino acids: Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E) ; Glutamine (N); Glycine (G): Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y): or Valine (V).
[00331] In another embodiment, an Arginine (R) residue of a Casl2a protein may be substituted with any one of the following amino acids: Alanine (A); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E) ; Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S): Threonine (T); Try ptophan (W); Tyrosine (Y); or Valine (V).
[00332] In another embodiment, an Asparagine (N) residue of a Casl2a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Aspartic Acid (D); Cysteine (C); Glutamic acid (E) ; Glutamine (N): Glycine (G); Histidine (H); Isoleucine (I); Leucine (L): Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
[00333] In another embodiment, an Aspartic Acid (D) residue of a Casl2a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Cysteine (C); Glutamic acid (E) ; Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
[00334] In another embodiment, an Cysteine (C) residue of a Casl2a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Glutamic acid (E) ; Glutamine (N); Glycine (G): Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T): Tryptophan (W): Tyrosine (Y): or Valine (V).
[00335] In another embodiment, an Glutamic acid (E) residue of a Casl2a protein may be substituted with any one of the following amino acids: Alanine (A): Arginine (R): Asparagine (N); Aspartic Acid (D);
Cysteine (C); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I): Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
[00336] In another embodiment, an Glutamine (N) residue of a Cast 2a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glycine (G); Histidine (H); Isolcucinc (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y): or Valine (V).
[00337] In another embodiment, an Glycine (G) residue of a Casl2a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Histidine (H); Isoleucine (I); Leucine (L): Lysine (K): Methionine (M); Phenylalanine (F); Proline (P); Serine (S): Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
[00338] In another embodiment, an Histidine (H) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
[00339] In another embodiment, an Isoleucine (I) residue of a Cas 12a protein may be substituted with any one of tire following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T): Tryptophan (W); Tyrosine (Y): or Valine (V). [00340] In another embodiment, an Leucine (L) residue of a Cast 2a protein may be substituted with any one of tire following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
[00341] In another embodiment, an Lysine (K) residue of a Cas 12a protein may be substituted with any one of tire following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine CI ): Trvptophan (W): Tyrosine (Y): or Valine (V).
[00342] In another embodiment, an Methionine (M) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R): Asparagine (N); Aspartic Acid (D): Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I): Leucine (L); Lysine (K); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
[00343] In another embodiment, an Phenylalanine (F) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Proline (P); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
[00344] In another embodiment, an Proline (P) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid ( D): Cysteine (C): Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Serine (S); Threonine (T); Tryptophan (W); Tyrosine (Y); or Valine (V).
[00345] In another embodiment, an Serine (S) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Threonine (T); Tryptophan (W); Tyrosine (Y): or Valine (V).
[00346] In another embodiment, an Threonine (T) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D): Cysteine (C): Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H ): Isoleucine (I); Leucine (L): Lysine (K): Methionine (M); Phenylalanine (F); Proline (P): Serine (S); Try ptophan (W); Tyrosine (Y); or Valine (V). [00347] In another embodiment, an Tryptophan (W) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); Tyrosine (Y); or Valine (V).
[00348] In another embodiment, an Tyrosine (Y) residue of a Cas 12a protein may be substituted with any one of tire following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G); Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S): Threonine (T); Tryptophan (W); or Valine (V).
[00349] In another embodiment, an Valine (V) residue of a Cas 12a protein may be substituted with any one of the following amino acids: Alanine (A); Arginine (R); Asparagine (N); Aspartic Acid (D); Cysteine (C); Glutamic acid (E); Glutamine (N); Glycine (G): Histidine (H); Isoleucine (I); Leucine (L); Lysine (K); Methionine (M); Phenylalanine (F); Proline (P); Serine (S); Threonine (T); or Tryptophan (W).
[00350] In addition, the amino acid subsitutions may include that of any non-naturally occurring amino acid analog or amino acid derivative that are known in the art.
[00351] While not intending to be limiting, the following are exemplary' embodiments of mutant variants contemplated by the instant specification and Examples and which are based on Casl2a ID405 (SEQ ID NO: 334), Casl2a ID414 (SEQ ID NO: 58), and Casl2a ID418 (SEQ ID NO: 564). It will be appreciated that any of the following specific substitutions and/or combinations of specific substitutions may be introduced into the corresponding amino acid residues (as determined by a sequence alignment) of any other Type V nuclease enzyme disclosed herein.
Variants based on ID405 (SEO ID NO: 334)
[00352] In various embodiments, the Casl2a may be a Casl2a variant based on ID405 (SEQ ID NO: 334), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 334 having any of the following substitutions):
• a D 169 substitution;
• a C554 substitution;
• a N559 substitution;
• a Q565 substitution;
• a L860 substitution;
• a R950 substitution; and/or
• a R954 substitution. [00353] In various embodiments, the Casl2a may be a Casl2a variant based on ID405 (SEQ ID NO: 334), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 334 having any of the following substitutions):
• a D 169R substitution;
• a C554N substitution;
• a C554R substitution;
• a N559R substitution:
• a Q565R substitution;
• a L860Q substitution;
• a R950K substitution; and/or
• a R954A substitution.
[00354] In various embodiments, the Casl2a may be a Casl2a variant based on ID405 (SEQ ID NO: 334), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 334 having any of the following substitutions):
• a D 169 substitution;
• a D 169/R950/R954 substitution set;
• a D169/N559/Q565 substitution set;
• a C554 substitution;
• a C554 substitution; and/or
• a L860 substitution.
[00355] In various embodiments, the Casl2a may be a Casl2a variant based on ID405 (SEQ ID NO: 334), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 334 having any of the following substitutions):
• a D 169R substitution;
• a D169R/R950K/R954A substitution set;
• a D169R/N559R/Q565R substitution set;
• a C554R substitution;
• a C554N substitution; and/or
• a L860Q substitution.
[00356] The full amino acid and protein coding sequences of these mutant nucleases are provided in Appendix A at Section P (Casl2a Mutant Type V nuclease and associated sequences).
Variants based on ID414 (SEQ ID NO: 58) [00357] In various embodiments, the Casl2a may be a Casl2a variant based on ID414 (SEQ ID NO: 58), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 58 having any of the following substitutions):
• a T154 substitution;
• a N531 substitution;
• a G546 substitution;
• a K542 substitution;
• a S802 substitution;
• a R887 substitution; and/or
• a R891 substitution.
[00358] In various embodiments, the Casl2a may be a Casl2a variant based on ID414 (SEQ ID NO: 58), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%. 90%. 95%. 99%. or up to 100% sequence identity with SEQ ID NO: 58 having any of the following substitutions):
• a T154R substitution;
• a N531R substitution;
• a G546R substitution;
• a K542R substitution;
• a S802L substitution;
• a R887K substitution; and/or
• a R891A substitution.
[00359] In various embodiments, the Casl2a may be a Casl2a variant based on ID414 (SEQ ID NO: 58), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 58 having any of the following substitutions):
• a T154 substitution;
• a T154/R887/R891 substitutions;
• a T154/G536/K542 substitutions;
• a N531/S802 substitutions;
• a N531 substitution; and/or
• a S802 substitution.
[00360] In various embodiments, the Casl2a may be a Casl2a variant based on ID414 (SEQ ID NO: 58), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 58 having any of the following substitutions): • a T 154R substitution;
• a T154R/R887K/R891A substitutions;
• a T154R/G536R/K542R substitutions;
• a N531R/S802L substitutions;
• a N531R substitution; and/or
• a S802L substitution.
[00361] Hie full amino acid and protein coding sequences of these mutant nucleases are provided in Appendix A at Section P (Casl2a Mutant Type V nuclease and associated sequences).
Variants based on ID418 (SEQ ID NO: 564)
[00362] In various embodiments, the Casl2a may be a Casl2a variant based on ID418 (SEQ ID NO: 564), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 564 having any of the following substitutions):
• a D 161 substitution;
• a N527 substitution;
• a T532 substitution;
• a K538 substitution;
• a Q799 substitution;
• a R888 substitution; and/or
• a R892 substitution.
[00363] In various embodiments, the Casl2a may be a Casl2a variant based on ID418 (SEQ ID NO: 564), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%. 90%. 95%. 99%, or up to 100% sequence identity with SEQ ID NO: 564 having any of tire following substitutions):
• a D161R substitution;
• a N527R substitution;
• a T532R substitution;
• a K538R substitution;
• a Q799L substitution;
• a R888K substitution; and/or
• a R892A substitution.
[00364] In various embodiments, the Casl2a may be a Casl2a variant based on ID418 (SEQ ID NO: 564), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 564 having any of the following substitutions): a D161 substitution; • a D 161 /R888/R892 substitution;
• a D161/T532/K538 substitution;
• a N527/Q799 substitution;
• a N527 substitution; and/or
• a Q799 substitution.
[00365] In various embodiments, the Casl2a may be a Cast 2a variant based on ID418 (SEQ ID NO: 564), and may include any of the following substitutions and in any combination (or any amino acid sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with SEQ ID NO: 564 having any of the following substitutions):
• a D 161 R substitution;
• a D161R/R888K/R892A substitution;
• a D161R/T532R/K538R substitution;
• a N527R/Q799L substitution;
• a N527R substitution; and/or
• a Q799L substitution.
[00366] The full amino acid and protein coding sequences of these mutant nucleases are provided in Appendix A at Section P (Casl2a Mutant Type V nuclease and associated sequences).
[00367] In addition, various embodiments of variant Casl2a orthologs are described in Section Q of Appendix A.
[00368] In addition, embodiments of Cast 2a mutant variants based on ID405, ID414, and ID418 are described in the computational approach to directed mutagenesis described in Example 14.
[00369] It is noted that when this disclosure speaks to a polypeptide (including anywhere in this specification, including in tire Appendix A and the Examples) having a percent identity with respect to another amino acid sequence (a reference amino acid sequence), such as a polypeptide at least 50%, at least 55%, at least 60%, at least 65%, at least 70%. at least 75%, at least 80%, at least 85%, at least 90%, at least 91%. at least 92%, at least 93%, at least 94%. at least 95. at least 96%, at least 97%, at least 98%, at least 99%%. at least 99.1%. at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to another amino acid sequence (a reference amino acid sequence), such as one of SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), or SEQ ID NO: 445 (No. ID419), it is advantageous that in the polypeptide having a percent identity to the reference amino acid sequence conserved regions of the reference amino acid sequence (e.g., conserved when compared with other Casl2as, such as those identified herein, such as described in the multi-sequences alignment of FIG. 31) be preserved and/or that the polypeptide has at least one activity selected from endonuclease activity; endoribonuclease activity, or RNA-guided DNase activity and/or that the polypeptide of which comprises: a. one or more a- helical recognition lobe (REC) and a nuclease lobe (NUC); b. a Wedge (WED), a-helical recognition lobe (REC), PAM-interacting (PI), RuvC nuclease, Bridge Helix (BH) and NUC domains; or c. one or more domains selected from RuvC, REC. WED, BH, PI and NUC domains and/or that the polypeptide recognizes or binds crRNA(s) or is bound to crRNA(s), such as a crRNA sequence from Table S15C. Likewise, when this disclosure speaks to a nucleic acid sequence or molecule having a percent identity with respect to a nucleic acid sequence having a percent identity with respect to another nucleic acid sequence or molecule (a reference nucleic acid sequence), such as a nucleic acid sequence at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%. at least 95%, at least 96%, at least 97%, at least 98%, at least 99%%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%. at least 99.8% or at least 99.9% identical to another nucleic acid sequence (a reference nucleic acid sequence, such as a sequence selected from SEQ ID NO: 365 (No. ID405), SEQ ID NO: 74 (No. ID414), or SEQ ID NO: 565 (No. ID418), SEQ ID NO: 366 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 30 (No. ID415), or SEQ ID NO: 445 (No. ID419), it is advantageous that in the nucleic acid sequence that has a percent identity to the reference nucleic acid sequence that conserved regions of the reference nucleic acid sequence (e.g., conserved when compared with other Casl2as, such as those identified herein) be preserved and/or that in the polypeptide that is expressed from the nucleic acid sequence that has a percent identity to the reference nucleic acid sequence that the polypeptide contain conserved region(s) (e.g., conserved when compared with other Casl2as, such as those identified herein) and/or that the polypeptide has at least one activity selected from endonuclease activity; endoribonuclease activity, or RNA-guided DNase activity and/or that the polypeptide of which comprises: a. one or more a-helical recognition lobe (REC) and a nuclease lobe (NUC); b. a Wedge (WED), a-helical recognition lobe (REC), PAM-interacting (PI), RuvC nuclease. Bridge Helix (BH) and NUC domains; or c. one or more domains selected from RuvC. REC. WED, BH. Pl and NUC domains and/or that the polypeptide recognizes or binds crRNA(s) or is bound to crRNA(s), such as a crRNA sequence from Table S15C.
D. Casl2a (or Cas Type V) Guide RNA Sequences
Casl2a (Cas Type V) guide sequences
[00370] The present disclosure further provides guide RNAs for use in accordance with the disclosed nucleic acid programmable DNA binding proteins (e.g., Casl2a) for use in methods of editing. The disclosure provides guide RNAs that are designed to recognize target sequences. Such gRNAs may be designed to have guide sequences (or “spacers”) having complementarity to a target sequence. Such gRNAs may be designed to have not only a guide sequences having complementarity to a target sequence to be edited, but also to have a backbone sequence that interacts specifically with the nucleic acid programmable DNA binding protein.
[00371] In various aspects, provided are one or more guide RNA sequences. In preferred embodiments, the gRNA is cleaved and processed into one or more intermediate crRNAs, which are subsequently processed into one or more mature crRNAs. In some embodiments, the gRNA comprises a precursor CRISPR RNAs (pre-crRNA) encoding one or more crRNAs or one or more intermediate or mature crRNAs, each guide RNA comprising at a minimum a repeat-spacer in the 5’ to 3‘ direction, wherein the repeat comprises a stem -loop structure and the spacer comprises a DNA-targeting segment complementary to a target sequence in the targeted polynucleotide sequence. In certain embodiments, the gRNA is cleaved by a RNase activity of the Casl2a polypeptide into one or more mature crRNAs, each comprising at least one repeat and at least one spacer.
[00372] In other embodiments, one or more repeat-spacer directs the Casl2a (or Cas Type V) polypeptides to two or more distinct sites in the targeted polynucleotide sequence. Preferably, the gRNA is cleaved and processed into one or more intermediate crRNAs, which are subsequently processed into one or more mature crRNAs. More preferably, the pre- crRNA or intermediate crRNA are processed into mature crRNA by an Cas 12a (or Cas Type V) polypeptide, and the mature crRNA becomes available for directing the Cas 12a (or Cas Type V) endonuclease activity. In alternative embodiments, the gRNA is linked to a single or double strand DNA donor template, and the donor template is cleaved from the gRNA by the Cas 12a (or Cas Type V) polypeptide. The donor polynucleotide template remains linked to gRNA while the Cas 12a (or Cas Type V) polypeptide cleaves gRNA to liberate intermediate or mature crRNAs.
[00373] In exemplary embodiments, the Cas 12a (or Cas Type V) system comprises one or more guide RNA comprising:
(a) one or more crRNA direct repeat sequences or a reverse complement selected from (Group 1) SEQ ID NO:7-12; (Group 2) SEQ ID NO:24-27: (Group 3) SEQ ID NO:36-39; (Group 4) SEQ ID NO:49-52; (Group 5) SEQ ID NO:63-68; (Group 6) SEQ ID NO:84-91; (Group 7) SEQ ID NO: 106- 111: (Group 8) SEQ ID NO: 122-125; (Group 9) SEQ ID Nos:211-290; (Group 10) SEQ ID NO:343-354; (Group 11) SEQ ID NO:374-379; (Group 12) SEQ ID NO:390-393; (Group 13) SEQ ID NO:411-422; and (Group 14) SEQ ID N0:500-541;
(b) 20 to 35 nucleotides or up to the length of the crRNA from the 3' end of the crRNA direct repeat sequences or a reverse complement (a) linked to a targeting guide attached to the 3 ’ end of the direct repeat sequence that is of 16-30 nucleotides in length;
(c) (Group 1) SEQ ID NO:13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40- 41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563;
(d) a nucleic acid sequence that is a degenerate variant of (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563;
(e) anucleic acid sequence at least 70%, at least 71%, at least 72%. at least 73%. at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81 %, at least 82%, at least 83%, at least 84%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99% or at least 99.9% identical to : (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291- 330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394- 395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563; and
(f) a nucleic acid sequence that hybridizes under stringent conditions to : (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563.
[00374] In preferred embodiments, the Casl2a (or Cas Type V) proteins target and cleave targeted polynucleotides that is complementary to a cognate guide RNA. In certain embodiments, the guide RNA comprises crRNA, which includes the natural CRISPR array. Such variants are derived from the first direct repeat, a “leader” sequence and involved in signaling or the direct repeat retains genetic diversity that doesn’t affect functionality. The direct repeat is degenerate, generally near the 3 ’ end of the repeat array.
[00375] In various embodiments, the crRNA comprises about 15-40 nucleotides or direct repeat sequences comprising about 20-30 nucleotides. In exemplary embodiments, the direct repeat is selected from (Group 1) SEQ ID NO:7-12; (Group 2) SEQ ID NO:24-27; (Group 3) SEQ ID NO:36-39; (Group 4) SEQ ID NO:49- 52; (Group 5) SEQ ID NO:63-68; (Group 6) SEQ ID NO:84-91; (Group 7) SEQ ID NO: 106-111; (Group 8) SEQ ID NO: 122-125; (Group 9) SEQ ID Nos:211-290; (Group 10) SEQ ID NO:343-354; (Group 11) SEQ ID NO:374-379; (Group 12) SEQ ID NO:390-393; (Group 13) SEQ ID NO:411-422; and (Group 14) SEQ ID N0:500-541. More preferably, the crRNA comprises a guide segment of 16-26 nucleotides or 20-24 nucleotides. Accordingly, in various embodiments, tire crRNA of the Casl2a genome editing systems hybridizes to one or more targeted polynucleotide sequence. In certain preferred embodiments, the crRNA is 43- nucleotides. In other embodiments, the crRNA is made up of a 20-nucleotide 5 '-handle and a 23- nucleotide leader sequence. In certain embodiments, the leader sequence comprises a seed region and 3' termini, both of which are complementary to the target region in the genome Li, Bin et al. “Engineering CRISPR-Cpfl crRNAs and rnRNAs to maximize genome editing efficiency.” Nature biomedical engineering vol. 1,5 (2017): 0066. doi: 10.1038/s41551-017-0066.
[00376] A single crRNA-guided endonuclease and has the ribonuclease activity to process its pre-crRNA into mature crRNA Zetsche, Bernd et al. “A Survey of Genome Editing Activity for 16 Casl2a Orthologs.” The Keio journal of medicine vol. 69,3 (2020): 59-65. doi: 10.2302/kjm.2019-0009-OA; Fonfara, Ines et al. “The CRISPR-associated DNA- cleaving enzyme Cpfl also processes precursor CRISPR RNA.” Nature vol. 532,7600 (2016): 517-21. doi: 10. 1038/nature 17945, which enables multiplex editing in a single crRNA transcript. Campa, Carlo C et al. “Multiplexed genome engineering by Casl2a and CRISPR arrays encoded on single transcripts.” Natu re methods vol. 16,9 (2019): 887-893. doi: 10.1038/s41592-019-0508-6; Zetsche, Bernd et al. “Multiplex gene editing by CRISPR- Cpfl using a single crRNA array.” Nature biotechnology vol. 35,1 (2017): 31-34. doi: 10.1038/nbt.3737
[00377] Preferably, the crRNA-guided endonuclease provides alteration of numerous loci in host cell genomes.
[00378] More preferably, the Cast 2a (or Cas Type V) comprises multiplexing performed using two methods. One method involves expressing many single gRNAs under different small RNA promoters either in same vector or in different vectors. Another method, multiple single gRNAs are fused with a tRNA recognition sequence, which are expressed as a single transcript under one promoter.
[00379] In some embodiments, the guide RNA may be 15-100 nucleotides in length and comprise a sequence of at least 10, at least 15, or at least 20 contiguous nucleotides that is complementary to atarget nucleotide sequence. The guide RNA may comprise a spacer sequence of 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 contiguous nucleotides that is complementary to a target nucleotide sequence. In some cases, the guide sequence has a length in a range of from 17-30 nucleotides (nt) (e.g., from 17-25, 17-22, 17-20, 19-30, 19-25, 19-22. 19-20, 20-30. 20-25, or 20-22 nt). In some cases, the guide sequence has a length in a range of from 17-25 nucleotides (nt) (e.g., from 17-22, 17- 20, 19-25, 19-22, 19-20, 20-25, or 20-22 nt). In some cases, tire guide sequence has a length of 17 or more nt (e.g., 18 or more, 19 or more, 20 or more, 21 or more, or 22 or more nt; 19 nt, 20 nt, 21 nt, 22 nt, 23 nt, 24 nt, 25 nt, etc.). In some cases, the guide sequence has a length of 19 or more nt (e.g., 20 or more, 21 or more, or 22 or more nt; 19 nt, 20 nt, 21 nt, 22 nt, 23 nt, 24 nt, 25 nt, etc.). In some cases, tire guide sequence has a length of 17 nt. In some cases, the guide sequence has a length of 18 nt. In some cases, the guide sequence has a length of 19 nt. In some cases, the guide sequence has a length of 20 nt. In some cases, the guide sequence has a length of 21 nt. In some cases, the guide sequence has a length of 22 nt. In some cases, the guide sequence has a length of 23 nt.
[00380] In some cases, the spacer sequence has a length of from 15 to 50 nucleotides (e.g., from 15 nucleotides (nt) to 20 nt, from 20 nt to 25 nt, from 25 nt to 30 nt, from 30 nt to 35 nt, from 35 nt to 40 nt, from 40 nt to 45 nt, or from 45 nt to 50 nt).
[00381] A subject guide RNA can interact with a target nucleic acid (e.g., double stranded DNA (dsDNA), single stranded DNA (ssDNA), single stranded RNA (ssRNA), or double stranded RNA (dsRNA)) in a sequence-specific manner via hybridization (i.e., base pairing).
[00382] The guide RNA can be modified to hybridize to any desired target sequence (e.g., while taking the PAM into account, e.g.. when targeting a dsDNA target) within a target nucleic acid (e.g., a eukaryotic target nucleic acid such as genomic DNA). In some cases, the percent complementarity between tire spacer sequence of the guide and the target site of the target nucleic acid is 60% or more (e.g., 65% or more, 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the spacer and the target site of the target nucleic acid is 80% or more (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the spacer and the target site of the target nucleic acid is 90% or more (e.g., 95% or more, 97% or more, 98% or more. 99% or more, or 100%). In some cases, the percent complementarity between the spacer and the target site of the target nucleic acid is 100%.
[00383] In some cases, the percent complementarity between the spacer sequence and the target site of the target nucleic acid is 100% over an at least 5-nucleotide contiguous region of the spacer. In some cases, the percent complementarity between tire guide sequence and the target site of the target nucleic acid over an at least 6-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 7-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 8-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between tire guide sequence and the target site of the target nucleic acid over an at least 9-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 10-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more. 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 11 -nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between tire guide sequence and the target site of the target nucleic acid over an at least 12-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more. 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 13-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 14-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more. 75% or more, 80% or more, 85% or more, 90% or more, 95% or more. 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 15-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 16-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more. 90% or more, 95% or more. 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 17-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 18-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 19-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more. 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 20-nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 21 -nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more. 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 22 -nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%).
[00384] In some cases, the percent complementarity between the spacer sequence and the target site of the target nucleic acid is 100% over an at least 5-10 nucleotide contiguous region of tire spacer. In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 6-11 nucleotide contiguous region of the spacer is 60% or more (e.g.. 70% or more. 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 7-12 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 8-13 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 9-14 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more. 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 10-15 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between tire guide sequence and the target site of the target nucleic acid over an at least 11-16 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 12-17 nucleotide contiguous region of the spacer is 60% or more (e.g.. 70% or more. 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of tire target nucleic acid over an at least 13-18 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 14-19 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 15-20 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more. 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, tire percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 16-21 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 17-22 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more. 75% or more. 80% or more, 85% or more, 90% or more, 95% or more, 97% or more. 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 18-23 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 19-24 nucleotide contiguous region of the spacer is 60% or more (e.g.. 70% or more, 75% or more, 80% or more, 85% or more, 90% or more. 95% or more, 97% or more, 98% or more. 99% or more, or 100%). In some cases, tire percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 20-25 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 21-26 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%). In some cases, the percent complementarity between the guide sequence and the target site of the target nucleic acid over an at least 22-27 nucleotide contiguous region of the spacer is 60% or more (e.g., 70% or more. 75% or more. 80% or more, 85% or more, 90% or more, 95% or more, 97% or more. 98% or more, 99% or more, or 100%).
[00385] In various embodiments, the guide RNAs may have a scaffold or core region that complexes with a cognate nucleic acid programmable DNA binding protein (e.g., CRISPR Cas9 or Casl2a). In some cases, a guide scaffold can have two stretches of nucleotides that are complementary to one another and hybridize to form a double stranded RNA duplex (dsRNA duplex). Thus, in some cases, the protein binding segment of a guide RNA includes a dsRNA duplex. In some embodiments, the dsRNA duplex region includes a range of from 5-25 base pairs (bp) (e.g., from 5-22, 5-20, 5-18, 5-15, 5-12, 5-10. 5-8, 8-25, 8-22, 8-18, 8-15, 8-12. 12- 25, 12-22, 12-18. 12- 15, 13-25, 13-22. 13-18, 13-15. 14-25, 14-22. 14-18, 14-15, 15-25, 15-22, 15-18. 17-25, 17-22, or 17-18 bp, e.g., 5 bp, 6 bp, 7 bp, 8 bp, 9 bp, 10 bp, etc.). In some cases, the dsRNA duplex region includes a range of from 6-15 base pairs (bp) (e.g., from 6-12, 6-10, or 6-8 bp, e.g., 6 bp, 7 bp, 8 bp, 9 bp, 10 bp, etc.). In some cases, the duplex region includes 5 or more bp (e.g., 6 or more, 7 or more, or 8 or more bp). In some cases, tire duplex region includes 6 or more bp (e.g., 7 or more, or 8 or more bp). In some cases, not all nucleotides of the duplex region are paired, and therefore the duplex fonning region can include a bulge. Tire term "bulge” herein is used to mean a stretch of nucleotides (which can be one nucleotide) that do not contribute to a double stranded duplex, but which are surround 5’ and 3’ by nucleotides that do contribute, and as such a bulge is considered part of the duplex region. In some cases, the dsRNA includes 1 or more bulges (e.g., 2 or more, 3 or more, 4 or more bulges). In some cases, the dsRNA duplex includes 2 or more bulges (e.g., 3 or more, 4 or more bulges). In some cases, the dsRNA duplex includes 1-5 bulges (e.g., 1-4, 1- 3. 2-5, 2-4, or 2-3 bulges).
[00386] Thus, in some cases, the stretches of nucleotides that hybridize to one another to form the dsRNA duplex in a guide scaffold region have 70%-100% complementarity (e.g.. 75%-100%, 80%-10%. 85%-100%, 90%- 100%, 95%- 100% complementarity) with one another. In some cases, the stretches of nucleotides that hybridize to one another to form the dsRNA duplex have 70%-100% complementarity (e.g., 75%-100%, 80%-10%, 85%- 100%, 90%-100%, 95%-100% complementarity) with one another. In some cases, the stretches of nucleotides that hybridize to one another to form the dsRNA duplex have 85%-100% complementarity (e.g., 90%-100%, 95%-100% complementarity) with one another. In some cases, the stretches of nucleotides that hybridize to one another to form the dsRNA duplex have 70%-95% complementarity (e.g., 75%-95%, 80%-95%, 85%-95%, 90%-95% complementarity) with one another. In other words, in some cases, the dsRNA duplex includes two stretches of nucleotides that have 70%-100% complementarity (e.g., 75%-100%, 80%-10%, 85%-100%, 90%-100%, 95 %- 100% complementarity) with one another. In some cases, the dsRNA duplex includes two stretches of nucleotides that have 85%-100% complementarity (e.g., 90%-100%, 95%-100% complementarity) with one another. In some cases, the dsRNA duplex includes two stretches of nucleotides that have 70%-95% complementarity (e.g., 75%-95%, 80%-95%, 85%-95%, 90%-95% complementarity) with one another.
[00387] In various embodiments, the scaffold region of a guide RNA can also include one or more (1, 2, 3, 4, 5, etc.) mutations relative to a naturally occurring scaffold region. For example, in some cases a base pair can be maintained while the nucleotides contributing to the base pair from each segment can be different. In some cases, the duplex region of a subject guide RNA includes more paired bases, less paired bases, a smaller bulge, a larger bulge, fewer bulges, more bulges, or any convenient combination thereof, as compared to a naturally occurring duplex region (of a naturally occurring guide RNA).
[00388] Examples of various guide RNAs can be found in tire art. and in some cases variations similar to those introduced into Cas9 guide RNAs can also be introduced into guide RNAs of the present disclosure (e.g., mutations to the dsRNA duplex region, extension of the 5’ or 3’ end for added stability for to provide for interaction with another protein, and the like). For example, see Jinek et aL, Science. 2012 Aug 17;337(6096): 816-21 ; Chylinski ct al., RNA Biol. 2013 May;10(5):726- 37; Ma ct al., Biomcd Res Int. 2013;2013:270805; Hou et al., Proc Natl Acad Sci U S A. 2013 Sep 24;110(39): 15644-9; Jinek et al., Elife. 2013;2:e00471; Pattanayak et al., Nat Biotechnol. 2013 Sep;31(9):839-43; Qi et al. Cell. 2013 Feb 28 ;
152(5): 1173-83 ; Wang et al., Cell. 2013 May 9; 153(4):910-8; Auer et al.. Genome Res. 2013 Oct 31; Chen et al., Nucleic Acids Res. 2013 Nov 1 ;41 (20):el9; Cheng et al., Cell Res. 2013 Oct;23(10): 1163-71; Cho et al., Genetics. 2013 Nov;195(3): 1177-80; DiCarlo et al., Nucleic Acids Res. 2013 Apr;41(7):4336-43;
Dickinson ct al., Nat Methods. 2013 Oct; 10(10): 1028-34; Ebina ct al., Sci Rep. 2013;3:2510; Fujii ct. al, Nucleic Acids Res. 2013 Nov I;4 l(20):el87; Hu et al., Cell Res. 2013 Nov;23(ll): 1322-5; Jiang et al., Nucleic Acids Res. 2013 Nov l;41(20):el88; Larson et al.. Nat Protoc. 2013 Nov;8(l 1):2180-96; Mali et. at., Nat Methods. 2013 Oct; 10(10):957-63; Nakayama et al., Genesis. 2013 Dec;51(12):835-43; Ran et al., Nat Protoc. 2013 Nov;8(l 1):2281 -308; Ran et al., Cell. 2013 Sep 12; 154(6): 1380-9; Upadhyay et al., G3 (Bethesda). 2013 Dec 9;3(12):2233-8; Walsh et aL, Proc Natl Acad Sci U S A. 2013 Sep 24; 110(39): 15514- 5; Xie et al., Mol Plant. 2013 Oct 9; Yang et al., Cell. 2013 Sep 12; 154(6): 1370-9; Briner et al., Mol Cell. 2014 Oct 23;56(2):333-9; and U.S. patents and patent applications: 8.906,616; 8,895,308; 8,889,418; 8,889,356: 8,871,445; 8,865,406; 8,795,965; 8,771,945; 8,697,359; 20140068797; 20140170753; 20140179006; 20140179770; 20140186843; 20140186919; 20140186958; 20140189896; 20140227787; 20140234972; 20140242664; 20140242699; 20140242700; 20140242702; 20140248702; 20140256046; 20140273037; 20140273226; 20140273230; 20140273231: 20140273232; 20140273233; 20140273234; 20140273235; 20140287938; 20140295556; 20140295557: 20140298547; 20140304853; 20140309487; 20140310828; 20140310830; 20140315985; 20140335063: 20140335620; 20140342456; 20140342457; 20140342458; 20140349400; 20140349405: 20140356867; 20140356956; 20140356958; 20140356959; 20140357523; 20140357530; 20140364333; and 20140377868; all of which are hereby incorporated by reference in their entirety.
Guide RNA modifications
[00389] In one embodiment, the guide RNAs contemplated herein comprise non-naturally occurring nucleic acids and/or non-naturally occurring nucleotides and/or nucleotide analogs, and/or chemical modifications. Non-naturally occurring nucleic acids can include, for example, mixtures of naturally and non-naturally occurring nucleotides. Non-naturally occurring nucleotides and/or nucleotide analogs may be modified at the ribose, phosphate, and/or base moiety. In an embodiment of the invention, a guide RNA component nucleic acid comprises ribonucleotides and non-ribonucleotides. In one such embodiment, a guide RNA component comprises one or more ribonucleotides and one or more deoxyribonucleotides. In an embodiment of the invention, the guide RNA (including pegRNA) component comprises one or more non-naturally occurring nucleotide or nucleotide analog such as a nucleotide with phosphorothioate linkage, a locked nucleic acid (LNA) nucleotides comprising a methylene bridge between the 2' and 4' carbons of the ribose ring, or bridged nucleic acids (BNA).
[00390] Other examples of modified nucleotides include 2'-O-methyl analogs, 2'-deoxy analogs, or 2'-fluoro analogs. Further examples of modified bases include, but are not limited to, 2-aminopurine, 5-bromo-uridine, pseudouridine, inosine, 7-methylguanosine. Examples of coRNA chemical modifications include, without limitation, incorporation of 2'-O-mcthyl (M), 2'-O-mcthyl 3 'phosphorothioate (MS), S-constraincd ethyl(cEt), or 2'-O-methyl 3 'thioPACE (MSP) at one or more terminal nucleotides. Such chemically modified oRNA components can comprise increased stability and increased activity as compared to unmodified oRNA components, though on-target vs. off-target specificity is not predictable. (See, Hendel, 2015, Nat Biotechnol. 33(9):985-9, doi: 10.1038/nbt.3290, published online 29 June 2015 Ragdarm et al., 0215, PNAS, E7110-E7111; Allerson et al., J. Med. Chem. 2005, 48:901-904; Bramsen et al., Front. Genet., 2012, 3: 154; Deng et al., PNAS, 2015, 112: 11870-11875; Sharma et al., MedChemComm., 2014, 5: 1454- 1471; Hendel et al., Nat. Biotechnol. (2015) 33(9): 985-989; Li et al., Nature Biomedical Engineering, 2017, 1, 0066 DOI: 10.1038/s41551-017-0066). In one embodiment, the 5’ and/or 3’ end of a guide RNA (including pegRNA) component is modified by a variety of functional moieties including fluorescent dyes, polyethylene glycol, cholesterol, proteins, or detection tags. (See Kelly et al., 2016, J. Biotech. 233:74-83). In one embodiment, a guide RNA (including pegRNA) component comprises ribonucleotides in a region that binds to a target sequence and one or more deoxyribonucletides and/or nucleotide analogs in a region that binds to a nucleic acid programmable DNA binding protein (e.g.. Cas9 nickase).
[00391] In an embodiment, deoxyribonucleotides and/or nucleotide analogs are incorporated in engineered guide RNA component structures. In one embodiment, 3-5 nucleotides at either the 3? or the 5’ end of a guide RNA component is chemically modified. In one embodiment, only minor modifications are introduced in the seed region, such as 2’-F modifications. In one embodiment, 2’-F modification is introduced at the 3’ end of a guide RNA component. In one embodiment, three to five nucleotides at the 5’ and/or tire 3’ end of the reRNA component are chemically modified with 2' -O-methyl (M), 2’-O-methyl 3’ phosphorothioate (MS), S- constrained ethyl(cEt), or 2’ -O-methyl 3’ thioPACE (MSP). Such modification can enhance genome editing efficiency (see Hendel et al., Nat. Biotechnol. (2015) 33(9): 985-989). In one embodiment, all of the phosphodiester bonds of a guide RNA (including pegRNA) component are substituted with phosphorothioates (PS) for enhancing levels of gene disruption. In other embodiments, one or more of the phosphodiester bonds of a guide RNA are substituted with phosphorothioate (PS), i.e., a phosphorothioate bond/linkage. For example, at least four of the phosphodiester bonds of a guide RNA may be substituted with phosphorothioates (PS). A phosphorothioate bond may be provided between the first and second nucleotides from the 5 ’ end of the guide RNA, and/or between the second and third nucleotides from the 5 ’ end of the guide RNA, and/or between the first and second nucleotides from the 3’ end of the guide RNA, and/or between the second and third nucleotides from the 3’ end of the guide RNA.
[00392] In one embodiment, more than five nucleotides at the 5’ and/or the 3’ end of the guide RNA (including pegRNA) component are chemically modified with 2’-0-Me, 2’-F or S-constrained ethyl(cEt). Such chemically modified guide RNA (including pegRNA) component can mediate enhanced levels of gene disruption (see Ragdami et al., 0215, PNAS, E7110-E7111). In an embodiment of the invention, a guide RNA (including pegRNA) component is modified to comprise a chemical moiety at its 3’ and/or 5’ end. Such moieties include, but are not limited to amine, azide, alkyne, thio, dibenzocyclooctyne (DBCO), or Rhodamine. In certain embodiment, the chemical moiety is conjugated to the guide RNA (including pegRNA) component by a linker, such as an alkyl chain. In one embodiment, the chemical moiety of the modified nucleic acid component can be used to attach the guide RNA (including pegRNA) component to another molecule, such as DNA, RNA, protein, or nanoparticles. Such chemically modified guide RNA (including pegRNA) component can be used to identify or enrich cells generically edited by a gene editing system described herein.
[00393] Other guide RNA modifications are described in Kim, D.Y., Lee, J.M., Moon, S.B. et al. Efficient CRISPR editing with a hypercompact Casl2fl and engineered guide RNAs delivered by adeno-associated virus. Nat Biotechnol 40, 94-102 (2022).
[00394] Accordingly, in various aspects of the invention, the guide RNA are modified in one or more locations within the molecule. MSI, an internal penta(uridinylate) (UUUUU) sequence in the tracrRNA; MS2, the 3' terminus of the crRNA; MS3, the ‘stem 1’ region of the tracrRNA; MS4, the tracrRNA-crRNA complementary region; and MS5. the ‘stem 2’ region of the tracrRNA.
[00395] Various aspects of the invention provide methods and compositions for improved guide RNA stability via chemical modifications. Braasch, D. A., Jensen, S., Liu, Y ., Kaur, K., Arar, K., White. M. A., et al. (2003). RNA interference in mammalian cells by chemically-modified RNA. Biochemistry 42, 7967- 7975. doi: 10.102 l/bi0343774. Chiu, Y. L , and Rana, T. M. (2003). siRNA function in RNAi: a chemical modification analysis. RNA 9, 1034-1048. doi: 10.1261/ma.5103703. Behlke, M. A. (2008). Chemical modification of siRNAs for in vivo use. Oligonucleotides , 305-319. doi: 10.1089/oli.2008.0164. Bennett, C. F., and Swayze, E. E. (2010). RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform. Annu. Rev. Pharmacol. Toxicol. 50, 259-293. doi:
10.1146/annurev.pharmtox.010909. 105654. Deleavey, G. F., and Damha, M. J. (2012). Designing chemically modified oligonucleotides for targeted gene silencing. Chem. Biol. 19, 937-954. doi: 10.1016/j.chembiol.2012.07.011. Lennox, K. A., and Behlke, M. A. (2020). Chemical modifications in RNA interference and CRISPR/Cas genome editing reagents. Methods Mol. Biol. 2115, 23-55. doi: 10.1007/978-1- 0716-0290-4_2.
[00396] For instance, Hendel et al. improved guide RNA stability by chemically modifying gRNA ends to reduce degradation by exonucleases, RNA nuclease. Hendel. A., Bak, R. O., Clark, J. T.. Kennedy, A. B., Ryan. D. E., Roy. S., et al. (2015a). Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary' cells. Nat. Biotechnol. 33, 985-989. doi: 10.1038/nbt.3290. Chemical modifications of gRNAs may enable more efficient and safer gene-editing in primary cells suitable for clinical applications.
[00397] A review of types of chemical modifications are provided in the table below. Allen, Daniel et al. ‘‘Using Synthetically Engineered Guide RNAs to Enhance CRISPR Genome Editing Systems in Mammalian
Cells.” Frontie rs in genome editing vol. 2 617910. 28 Jan. 2021, doi: 10.3389/fgeed.2020.617910. [00398] Accordingly, in various embodiments of the present invention, the genome editing system comprising a guide RNA and further comprises one or more chemical modifications selected from, but not limited to tire modifications in the above table.
[00399] In exemplary embodiments, chemical modifications to the guide RNA (including pegRNA) include modifications on the ribose rings and phosphate backbone of guide RNA (including pegRNA) and modifications at the 2'OH include 2'-0-Me. 2'-F, and 2'F-ANA. More extensive ribose modifications include 2'F-4'-Ca-OMe and 2',4'-di-Ca-OMe combine modification at both the 2' and 4' carbons. Phosphodiester modifications include sulfide-based Phosphorothioate (PS) or acetate-based phosphonoacetate alterations. Combinations of the ribose and phosphodiester modifications have given way to formulations such as 2'-O- methyl 3 'phosphorothioate (MS), or 2'-O-methyl-3 '-thioPACE (MSP), and 2 '-O-methyl-3 '-phosphonoacetate (MP) RNAs. Locked and unlocked nucleotides such as locked nucleic acid (LNA), bridged nucleic acids (BNA), S-constrained ethyl (cEt), and unlocked nucleic acid (UNA) are examples of sterically hindered nucleotide modifications. Modifications to make a phosphodiester bond between the 2' and 5' carbons (2',5'- RNA) of adjacent RNAs as well as a butane 4-carbon chain link between adjacent RNAs have been described.
[00400] In certain embodiments, the guide RNA comprises one or more hairpins as depicted in the appended Drawings. Preferably, the guide RNA comprises 0 -10 hairpins. In some embodiments, the guide RNA comprises 1-3 hairpins. In some embodiments, the guide RNA comprises 2 hairpins. More preferably, a hairpin comprises 6-20 ribonucleotides.
[00401] Modification of the sgRNA is also an efficient way of enhancing the efficiency of the CRISPR-Cas systems. Kim, Daesik et al. “Evaluating and Enhancing Target Specificity of Gene-Editing Nucleases and Deaminases.’’ A mual review of biochemistry vol. 88 (2019): 191-220. doi: 10. 1146/annurev-biochem- 013118-111730. For instance, adding a “U4AU6” (SEQ ID NO:2662) motif at the end of the crRNA Bin Moon, Su et al. “Highly efficient genome editing by CRISPR-Cpfl using CRISPR RNA with a uridinylate- rich 3’-overhang.” Nature communications vol. 9,1 3651. 7 Sep. 2018, doi: 10.1038/s41467-018-06129-w or using a pol- Il-driven truncated pre-tRNA Zhang, Xuhua et al. “Genetic editing and interrogation with Cpfl and caged truncated pre-tRNA-like crRNA in mammalian cells.” Cell discovery vol. 4 36. 10 Jul. 2018, doi: 10.1038/s41421-018-0035-0 have been demonstrated.
[00402] Accordingly, various embodiments provide for the modification of the sgRNA to enhance the efficiency of the CRISPR-Cas 12a systems and modifications to express the crRNA to improve the activity of the CRISPR- Casl2a system. [00403] Additional embodiments provide guide RNA modifications including but not limited to one or more chemical modifications selected from 2'-0-Me, 2'-F, and 2'F-ANA at 2'OH; 2'F-4'-Ca-OMe and 2',4'-di-Ca- OMe at 2' and 4' carbons; phosphodiester modifications comprising sulfide-based Phosphorothioate (PS) or acetate-based phosphonoacetate alterations; combinations of the ribose and phosphodiester modifications; locked nucleic acid (LNA), bridged nucleic acids (BN A). S-constrained ethyl (cEt), and unlocked nucleic acid (UNA); modifications to produce a phosphodiester bond between the 2' and 5' carbons (2'.5'-RNA) of adjacent RNAs; and a butane 4-carbon chain link between adjacent RNAs.
[00404] The present disclosure provides guide RNAs comprising one or more nucleotides having a 2'-0-Me modification and one or more phosphorothioate linkages. In some embodiments, the guide RNA comprises at least four phosphorothioate linkages, i.e., at least four phosphates of the guide RNA have been converted to phosphorothioate. In some embodiments, four phosphates of the guide RNA have been converted to phosphorothioate. For example, in certain embodiments the first two and last two phosphates of tire guide RNA have been converted to phosphorothioate.
[00405] Hie guide RNA disclosed herein may comprise a direct repeat sequence and a spacer sequence contiguous with the direct repeat sequence. Direct repeat sequences and spacer sequences are described elsewhere herein. In some embodiments, the direct repeat sequence consists of between 10 and 30 nucleotides. For example, the direct repeat sequence may consist of 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In certain embodiments, the direct repeat sequence consists of 19 nucleotides. For example, the direct repeat sequence may consist of AAUUUCUACUGUUGUAGAU (SEQ ID NO: 2584).
[00406] The guide RNA disclosed herein may comprise a modified nucleotide, such as a 2'-0-Me modified nucleotide, at certain positions of the direct repeat sequence, as described elsewhere herein. The guide RNA disclosed herein may comprise a modified nucleotide, such as a 2'-0-Me modified nucleotide, at certain positions of the spacer sequence, as described elsewhere herein. In certain embodiments, one or more nucleotides are added to the 5’ end of the direct repeat sequence. For example, the guide RNA may comprise a UG or UUUU immediately 5’ to the 5’ end of tire direct repeat sequence. In some embodiments, the position of the modified nucleotide is identified by reference to tire direct repeat sequence of the guide RNA, wherein position 1 is the first nucleotide of the direct repeat sequence. Accordingly, for example, where the direct repeat sequence is 19 nucleotides in length and a modified nucleotide is indicated to be at position 5. the modified nucleotide will be at position 5 of the direct repeat sequence. Where the position of a modification is at aposition beyond the 3' end of the direct repeat sequence, the modified nucleotide will be in another portion of the guide RNA. For example, in some embodiments, the direct repeat sequence is contiguous with the spacer sequence. In such embodiments, modified nucleotides indicated to be at positions beyond the 3' end of the direct repeat sequence may be located in the spacer sequence. For example, in some embodiments, if the direct repeat sequence is 19 nucleotides in length and immediately followed by the spacer sequence, a modified nucleotide indicated to be at position 27 is the 8th nucleotide in the spacer sequence. In some embodiments, one or more nucleotides are added to the 5' end of the direct repeat sequence, and the one or more nucleotides are modified. In such embodiments, the modified nucleotides will be at positions preceding the 5’ end of the direct repeat sequence. A first nucleotide immediately preceding the 5’ end of the direct repeat sequence is indicated to be at position -1. A second nucleotide preceding tire first nucleotide is indicated to be at position -2. Accordingly, for example, where the guide RNA comprises a UG immediately 5’ to the 5’ end of the direct repeat sequence, and U and G are modified nucleotides, the modified nucleotides are indicated to be at positions -2 and -1, respectively. In another example, where the guide RNA comprises UUUU immediately 5’ to the 5’ end of the direct repeat sequence, and UUUU are all modified nucleotides, the modified nucleotides are indicated to be at positions -4, -3, -2 and -1.
[00407] In some embodiments, the guide RNAs disclosed herein target a Cas Type V polypeptide to a target sequence, such as a Cas Type V polypeptide disclosed herein or a polypeptide comprising a Cas Type V polypeptide as disclosed herein, and complexes comprising the guide RNA and the Cas Type V polypeptide are capable of inducing indel formation in a target polynucleotide sequence. Tire target sequence may be a DNA sequence. In some embodiments, the target sequence may be associated with a disease or disorder, hi some embodiments, 2'-0-Me modifications and phosphorothioate linkages as disclosed herein enhance the ability of the guide RNA to induce indels in comparison with guide RNAs that do not comprise 2'-0-Me modifications or phosphorothioate linkages. For example, in some embodiments the guide RNA targets a Cas Type V polypeptide to a target sequence, and a complex comprising the guide RNA and the Cas Type V polypeptide induces indel formation when contacted with a population of the target sequences under conditions suitable for inducing indel formation, wherein the contacting results in an increase in the percentage of target polynucleotide sequences comprising an indel in the population of target sequences of at least 20%, at least 30%. at least 40%. at least 50%, at least 60%, at least 70%, at least 80%. at least 90%. at least 100%, at least 110%, or at least 120% as compared to the percentage of target polynucleotide sequences comprising an indel in the population when the population is contacted with a complex comprising a reference guide RNA and the Cas Type V polypeptide, wherein the reference guide RNA consists of the same nucleotide sequence as the guide RNA and wherein the nucleotides are not modified (i.e., the guide RNA does not comprise 2'-0-Me modifications or phosphorothioate linkages). [00408] In still other embodiments, the guide RNAs disclosed herein may be modified by introducing additional RNA motifs into the guide RNAs, e.g., at the 5' and 3' termini of the guide RNAs. Such structures may include, but are not limited to RNA hairpins, RNA step-loops, RNA quadruplexes, cap structures, and poly(A) tails, or ribozyme functions and the like. Also, guide RNAs could also be modified to include one or more nuclear localization sequences.
[00409] The present disclosure provides guide RNAs comprising (i) one or more NLS sequences, optionally wherein the NLS is chemically conjugated to the guide RNA: (ii) one or more RNA-NLS sequences, optionally wherein the gRNA is fused directly or indirectly to the RNA-NLS: and/or (iii) a PNA probe comprising a polynucleotide sequence complementary with one or more portions of the gRNA, wherein the PNA probe is conjugated to one or more NLS sequences; and optionally wherein the gRNA comprises one or more linkers.
[00410] In some embodiments, the PNA binds to the 3’ end of the gRNA. In some embodiments, the guide RNA comprises a PNA binding sequence at the 5’ end or 3’ end, and the PNA probe binds to the PNA binding sequence. In certain embodiments, the PNA may range from 2-30 nucleotides, such as 9 nucleotides.
[00411] The PNA probes may be modified to enhance solubility. For example, the PNA probe may comprise a solubility enhancing group such as ethylene glycol. Tire PNA probes may comprise a fluorophore such as Cy5. In various embodiments, the PNA probe comprises certain sequences and/or structures as described elsewhere herein.
[00412] The present disclosure further provides guide RNAs comprising (i) a 5’ DNA extension sequence and/or a 5’ RNA extension sequence; and/or (ii) a 3’ DNA extension sequence and/or a 3’ RNA extension sequence. The guide RNA may be a guide RNA as described herein. The extension sequence may comprise 4 or more nucleotides. In certain embodiments, the extension sequence consists of 4-25 nucleotides. In certain embodiments, the extension sequence consists of 4 nucleotides. In certain embodiments, the extension sequence consists of 9 nucleotides. In certain embodiments, the extension sequence consists of 15 nucleotides. In certain embodiments, the extension sequence consists of 25 nucleotides. Exemplary extension sequences are described elsewhere herein.
[00413] In some embodiments, the 3’ DNA or 3’ RNA extension sequence anneals to a spacer sequence in the guide RNA to form a hairpin structure. Hairpin structures are described elsewhere herein. In certain embodiments, the 3’DNA or 3’RNA extension sequence anneals to the 3’ end of the spacer sequence, thereby forming a hairpin structure. In certain embodiments, the last nucleotide at the 3’ end of tire extension sequence anneals to the last nucleotide at the 3" end of the spacer sequence. In certain embodiments, the last nucleotide at the 3' end of the extension sequence anneals to a nucleotide within 1, 2. 3, 4, 5, 6. 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 nucleotides of the last nucleotide at the 3’ end of the spacer sequence. As described elsewhere herein, the guide RNA may comprise one or more hairpin structures.
[00414] Guide RNAs disclosed herein may further comprise one or more linkers. In certain embodiments, the guide RNA comprises one or more linkers between the 5 ’ DNA and/or RNA extension sequences, and/or between the 3’ DNA and/or RNA extension sequences. Linkers are described elsewhere herein.
[00415] Any of the features of guide RNAs disclosed herein may be combined.
[00416] In some embodiments, the guide RNAs disclosed herein targets a Cas Type V polypeptide to a target sequence, such as a Cas Type V polypeptide disclosed herein or a polypeptide comprising a Cas Type V polypeptide as disclosed herein, and complexes comprising the guide RNA and the Cas Type V polypeptide are capable of inducing indel fomiation in a target polynucleotide sequence. The target sequence may be a DNA sequence. In some embodiments, the target sequence may be associated with a disease or disorder. In some embodiments, the 5' DNA extension sequences, 5’ RNA extension sequences, 3’ DNA extension sequences, and/or 3’ RNA extension sequences enhance the ability of the guide RNA to induce indels in comparison with guide RNAs that do not comprise 5’ DNA extension sequences, 5’ RNA extension sequences, 3’ DNA extension sequences, or 3’ RNA extension sequences. For example, in some embodiments the guide RNA targets a Cas Type V polypeptide to a target sequence and a complex comprising the guide RNA and the Cas Type V polypeptide induces indel fonnation when contacted with a population of the target sequences under conditions suitable for inducing indel formation, wherein the contacting results in an increase in the percentage of target polynucleotide sequences comprising an indel in the population of target sequences of at least 1.5-fold, at least 2-fold, at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, at least 4.5-fold, at least 5-fold, at least 5.5-fold, at least 6-fold, at least 6.5-fold, at least 7-fold, at least 7.5-fold, at least 8-fold, at least 8.5-fold, at least 9-fold, at least 9.5-fold, or at least 10- fold as compared to the percentage of target polynucleotide sequences comprising an indel in the population when the population is contacted with a reference guide RNA and the Cas Type V polypeptide, wherein the reference guide RNA consists of the same nucleotide sequence as the guide RNA and wherein the guide RNA does not comprise a DNA or RNA extension sequence.
[00417] The disclosure provides a gene editing system comprising: (a) one or more Cas Type V polypeptides or one or more polynucleotides encoding the Cas Type V polypeptide(s); and (b) one or more polynucleotide sequences comprising a guide RNA (gRNA) of the disclosure or one or more polynucleotides encoding the gRNA, wherein the gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence. The Cas Type V polypeptide may be a Cas Type V polypeptide as disclosed herein. [00418] The disclosure provides a method of modifying a targeted polynucleotide sequence, the method comprising contacting the targeted polynucleotide sequence with a gene editing system as disclosed herein. The method may be carried out in vitro, ex vivo or in vivo. In some embodiments, the disclosure provides a method of modifying a targeted polynucleotide sequence, tire method comprising introducing into a cell the gene editing system of the disclosure.
[00419] The disclosure provides one or more polynucleotides encoding a guide RNA as disclosed herein or a gene editing system as disclosed herein. The disclosure further provides one or more vectors comprising the one or more polynucleotides. The disclosure further provides a cell comprising the one or more vectors or the one or more polynucleotides.
[00420] Any of the guide RNAs; gene editing systems; polynucleotides encoding the guide RNAs or gene editing systems: vectors; cells; or pharmaceutical compositions disclosed herein can be used in medicine, for example for use in treating or preventing a disease or disorder as disclosed elsewhere herein.
[00421] Additional RNA motifs could also improve function or stability of the guide RNAs. Addition of dimerization motifs - such as kissing loops or a GNRA tetraloop/tetraloop receptor pair - at the 5' and 3' termini of tire guide RNAs could also result in effective circularization of the guide RNAs, improving stability. Additionally, it is envisioned that addition of these motifs could enable the physical separation of guide RNA components, e.g.. separation of the Casl2a binding region from the spacer sequence. Short 5' extensions or 3 ’ extensions to the guide RNAs that form a small toehold hairpin at either or both ends of the guide RNAs could also compete favorably against the annealing of intracomplcmcntary regions along the length of the guide RNAs. Finally, kissing loops could also be used to recruit other RNAs or proteins to the genomic site targeted by the guide RNA.
[00422] Guide RNAs could be further improved via directed evolution, in an analogous fashion to how7 protein function can be improved. Directed evolution could enhance guide RNA function and/or reduce offsite targeting and/or indels and/or improve precise editing efficiency.
[00423] The present disclosure contemplates any such w ays to further improve tire stability and/or functionality of the guide RNAs disclosed here.
[00424] In some embodiments, the RNAs (including the guide RNAs) used in the compositions of the disclosure have undergone a chemical or biological modification to render them more stable. Exemplary modifications to an RNA include the depletion of a base (e.g., by deletion or by the substitution of one nucleotide for another) or modification of a base, for example, the chemical modification of a base. The phrase "chemical modifications" as used herein, includes modifications which introduce chemistries which differ from those seen in naturally occurring RNA, for example, covalent modifications such as the introduction of modified nucleotides, (e.g., nucleotide analogs, or the inclusion of pendant groups which are not naturally found in such mRNA molecules).
[00425] Other suitable polynucleotide modifications that may be incorporated into the RNAs used in the compositions of the disclosure include, but are not limited to, 4'- thio-modified bases: 4'-thio-adenosine, 4'- thio-guanosine, 4'-thio-cytidine, 4'-thio-uridine, 4'- thio-5-mcthyl-cytidine. 4'-thio-pseudouridine, and 4'-thio- 2-thiouridine. pyridin-4-one ribonucleoside, 5 -aza-uridine, 2-thio-5 -aza-uridine, 2-thiouridine, 4-thio- pseudouridine, 2- thio-pseudouridine. 5-hydroxyuridine, 3 -methyluridine, 5-carboxymethyl-uridine, 1- carboxymethyl-pseudouridine, 5-propynyl-uridine, 1-propynyl-pseudouridine, 5- taurinomethyluridine, 1- taurinomethyl-pseudouridine, 5-taurinomethyl-2 -thio-uridine, 1- taurinomethyl-4-thio-uridine, 5-methy 1- uridine, 1 -methyl -pseudouridine, 4-thio-l -methyl- pseudouridine, 2-thio-l -methyl -pseudouridine, 1-methyl- 1-deaza-pseudouridine, 2-thio-l - methyl- 1-deaza-pseudouridine, dihydrouridine, dihydropseudouridine, 2- thio-dihydrouridine, 2-thio-dihydropseudouridine, 2-methoxyuridine. 2-methoxy-4-thio-uridine, 4-methoxy- pseudouridine, 4-methoxy-2 -thio-pseudouridine, 5 -aza-cytidine, pseudoisocytidine, 3-methyl- cytidine. N4- acetylcytidine, 5 -formylcytidine, N4-methylcytidine, 5 -hydroxymethyl cytidine, 1-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine, 2-thio-cytidine, 2- thio-5 -methyl -cytidine, 4-thio- pseudoisocytidine, 4-thio-l -methyl -pseudoisocytidine, 4-thio- 1 -methy l- 1-deaza-pseudoisocytidine, 1- methyl-l-deaza-pseudoisocytidine, zebularine, 5-aza- zebularine, 5-methyl-zebularine, 5-aza-2-thio- zebularine, 2-thio-zebularine. 2-methoxy- cytidine, 2-methoxy-5-methyl-cytidine, 4-methoxy- pseudoisocytidine, 4-methoxy-l -methyl- pseudoisocytidine, 2-aminopurine, 2,6-diaminopurine, 7-deaza- adenine, 7-deaza-8-aza- adenine, 7-deaza-2-aminopurine, 7-deaza-8-aza-2 -aminopurine, 7-deaza-2,6- diaminopurine, 7-deaza-8-aza-2,6-diaminopurine, 1 -methyladenosine, N6-methyladenosine, N6- isopentenyladenosine, N6-(cis-hydroxyisopentenyl)adenosine, 2-methylthio-N6-(cis- hy droxy isopentenyl)adenosine, N6-glycinylcarbamoyladenosine, N6- threonylcarbamoyladenosine, 2- methy lthio-N6-threonyl carbamoyladenosine. N6,N6- dimethyladenosine, 7-methyladenine, 2-methylthio- adenine, and 2-methoxy-adenine. inosine. 1-methyl-inosine, wyosine, wybutosine, 7-deaza-guanosine. 7- deaza-8-aza-guanosine, 6-thio- guanosine, 6-thio-7-deaza-guanosine, 6-thio-7-deaza-8-aza-guanosine, 7- methyl-guanosine, 6-thio-7-methyl-guanosine, 7-m ethy linosine, 6-methoxy-guanosine, 1 -methylguanosine, N2- mcthylguanosinc, N2,N2-dimcthy Iguanosinc, 8-oxo-guanosinc, 7-mcthyl-8-oxo-guanosinc, l-mcthyl-6- thio-guanosine, N2-methy 1-6-thio-guanosine, and N2,N2-dimethyl-6-thio- guanosine, and combinations thereof. The tenn modification also includes, for example, the incorporation of non-nucleotide linkages or modified nucleotides into the mRNA sequences of the present invention (e.g., modifications to one or both of the 3' and 5' ends of an mRNA molecule encoding a functional protein or enzyme). Such modifications include the addition of bases to an mRNA sequence (e.g., the inclusion of a poly A tail or a longer poly A tail), the alteration of the 3' UTR or the 5' UTR, complexing the mRNA with an agent (e.g., a protein or a complementary nucleic acid molecule), and inclusion of elements which change the structure of an RNA molecule (e.g., which form secondary structures).
[00426] In some embodiments, RNAs (e.g., guide RNAs) include a 5' cap structure. A 5' cap is typically added as follows: first, an RNA terminal phosphatase removes one of tire terminal phosphate groups from the 5' nucleotide, leaving two terminal phosphates; guanosine triphosphate (GTP) is then added to the tenninal phosphates via a guanylyl transferase, producing a 5'5'5 triphosphate linkage: and the 7-nitrogen of guanine is then methylated by a methyltransferase. Examples of cap structures include, but are not limited to, m7G(5')ppp (5'(A,G(5')ppp(5')A and G(5')ppp(5')G. Naturally occurring cap structures comprise a 7- methyl guanosine that is linked via a triphosphate bridge to the 5 '-end of the first transcribed nucleotide, resulting in a dinucleotide cap of m7G(5')ppp(5')N, where N is any nucleoside. In vivo, the cap is added enzymatically. Hie cap is added in the nucleus and is catalyzed by the enzyme guanylyl transferase. The addition of the cap to the 5' terminal end of RNA occurs immediately after initiation of transcription. The terminal nucleoside is typically a guanosine, and is in the reverse orientation to all the other nucleotides, i.e., G(5')ppp(5')GpNpNp.
[00427] Additional cap analogs include, but are not limited to, a chemical structures selected from the group consisting of m7GpppG, m7GpppA, m7GpppC: unmethylated cap analogs (e.g., GpppG): dimethylated cap analog (e.g., m2,7GpppG), trimethylated cap analog (e.g., m2,2,7GpppG), dimethylated symmetrical cap analogs (e.g., m7Gpppm7G), or anti reverse cap analogs (e.g., ARCA; m7,2'OmcGpppG, m72'dGpppG, m7,3'OmeGpppG, m7,3'dGpppG and their tetraphosphate derivatives) (see. e.g., Jemielity, J. et al., "Novel 'anti-reverse' cap analogs with superior translational properties", RNA, 9: 1108-1122 (2003)).
[00428] Typically, tire presence of a "tail" serves to protect the RNA (e.g., guide RNAs) from exonuclease degradation. A poly A or poly U tail is thought to stabilize natural messengers and synthetic sense RNA. Therefore, in certain embodiments a long poly A or poly U tail can be added to an RNA molecule thus rendering the RNA more stable. Poly A or poly U tails can be added using a variety of art-recognized techniques. For example, long poly A tails can be added to synthetic or in vitro transcribed RNA using poly A polymerase (Yokoe, et al. Nature Biotechnology.1996; 14: 1252-1256). A transcription vector can also encode long poly A tails. In addition, poly A tails can be added by transcription directly from PCR products. Poly A may also be ligated to the 3' end of a sense RNA with RNA ligase (see, e.g., Molecular Cloning A Laboratory Manual, 2nd Ed., ed. by Sambrook, Fritsch and Maniatis (Cold Spring Harbor Laboratory Press: 1991 edition)). [00429] Typically, the length of a poly A (SEQ ID NO:2652) or poly U (SEQ ID NO:2653) tail can be at least about 10, 50, 100, 200, 300, 400 at least 500 nucleotides. In some embodiments, a poly-A tail on the 3' terminus of mRNA typically includes about 10 to 300 adenosine nucleotides (e.g., about 10 to 200 adenosine nucleotides, about 10 to 150 adenosine nucleotides, about 10 to 100 adenosine nucleotides, about 20 to 70 adenosine nucleotides, or about 20 to 60 adenosine nucleotides). In some embodiments, mRNAs include a 3' poly(C) tail structure. A suitable poly-C (SEQ ID NO:2654) tail on the 3' terminus of mRNA typically include about 10 to 200 cytosine nucleotides (e.g., about 10 to 150 cytosine nucleotides, about 10 to 100 cytosine nucleotides, about 20 to 70 cytosine nucleotides, about 20 to 60 cytosine nucleotides, or about 10 to 40 cytosine nucleotides). Tire poly-C tail may be added to the poly-A or poly U tail or may substitute the poly-A or poly U tail.
[00430] RNAs according to tire present disclosure (e.g., Casl2a guide RNAs) may be synthesized according to any of a variety of known methods. For example, RNAs according to the present invention may be synthesized via in vitro transcription (IVT). Briefly, IVT is typically perfonned with a linear or circular DNA template containing a promoter, a pool of ribonucleotide triphosphates, a buffer system that may include DTT and magnesium ions, and an appropriate RNA polymerase (e.g., T3, T7 or SP6 RNA polymerase), DNAse I, pyrophosphatase, and/or RNAse inhibitor. The exact conditions will vary according to the specific application.
[00431] In a particular embodiment, the guide RNAs can comprise an MS2 modification, as specific RNA hairpin structure recognized in nature by a certain MS2-binding protein. This domain can help to stabilize the guide RNAs and improve the editing efficiency. The disclosure contemplates other similar modifications. A review of other such MS2-like domains are described in the art, for example, in Johansson et al. ‘RNA recognition by the MS2 phage coat protein/’ Sem Virol., 1997, Vol.8(3): 176-185; Delebecque et al. /‘Organization of intracellular reactions with rationally' designed RNA assemblies,” Science, 2011, Vol.333: 470-474; Mali et al.,“Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering,” Nat. Biotcchnol., 2013, Vol.31: 833- 838; and Zalatan et al. /‘Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds,” Cell. 2015, Vol.160: 339-350, each of which are incorporated herein by reference in their entireties. Other systems include the PP7 hairpin, which specifically recruits the PCP protein, and the ‘ com” hairpin, which specifically recruits the Com protein. See Zalatan et al. The nucleotide sequence of the MS2 hairpin (or equivalently referred to as the “MS2 aptamer”) is: GCCAACATGAGGATCACCCATGTCTGCAGGGCC (SEQ ID NO:2588).
E. Casl2a (or Cas Type V) Editing Systems [00432] The present disclosure relates to novel genome editing systems. In exemplary embodiments, the editing systems comprise:
(a) one or more polypeptide sequences comprising at least 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, or 65% sequence identity to any one of sequences selected from SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419); and
(b) one or more polynucleotide sequences comprising a guide RNA, wherein the guide RNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
[00433] The present disclosure provides a gene editing system comprising: (a) one or more Cas Type V polypeptides, optionally as disclosed herein, or one or more polynucleotides encoding the Cas Type V polypeptide(s), or one or more polypeptides comprising a Cas Type V polypeptide as disclosed herein, or one or more polynucleotides encoding the polypcptidc(s): and (b) one or more polynucleotide sequences comprising a guide RNA (gRNA), or one or more polynucleotides encoding the gRNA, wherein the gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence. The guide RNA may be a guide RNA as disclosed herein. The disclosure further provides one or more polynucleotides encoding the gene editing system, and one or more vectors comprising such polynucleotides. The disclosure further provides a cell comprising the one or more vectors or the one or more polynucleotides. In some embodiments, the disclosure provides a method of modifying a targeted polynucleotide sequence, tire method comprising contacting the targeted polynucleotide sequence with a gene editing system as disclosed herein. The method may be carried out in vitro, ex vivo or in vivo. In some embodiments, the disclosure provides a method of modifying a targeted polynucleotide sequence, tire method comprising introducing into a cell the gene editing system of the disclosure. The gene editing systems disclosed herein can be used in medicine, for example for use in treating or preventing a disease or disorder as disclosed elsewhere herein.
[00434] In other aspects, the Casl2a-bascd gene editing systems may comprise one or more additional accessory proteins having genome modifying functions, including recombinases, invertases, nucleases, polymerases, ligases, deaminases, reverse transcriptases, or epigenetic modifying functions. In various embodiments, the accessory' proteins may be provided separately. In other embodiments, the accessory' proteins may be fused to Cas 12a, optionally with a linker.
[00435] In various embodiments, the genome editing system may comprise a guide RNA, which hybridizes to one or more targeted polynucleotide sequence. In preferred embodiments, the guide RNA of the genome editing system comprises 12-40 nucleotides. [00436] In various embodiments, the genome editing system comprises the targeted polynucleotide sequence comprises one or more protospacer adjacent motif (PAM) recognition domains selected from 5'-TTTN-3', 5'- TTN-3', 5'-TNN-3', 5'-TTV-3', or 5'- TTTV-3', wherein N= A, T, C or G and V = A, C or G. In additional embodiments, the targeted polynucleotide sequence comprises one or more relaxed PAM recognition domains. Jacobsen. Thomas et al. ‘"Characterization of Casl2a nucleases reveals diverse PAM profiles between closely-related orthologs.” Nucleic acids research vol. 48,10 (2020): 5624-5638. doi: 10. 1093/nar/gkaa272. Previous work has demonstrated to address the limitation for the requirement for an extended TTTV protospacer adjacent motif (PAM) by expanding the targeting range for non-canonical PAMs (such as ATTA, CTTA, GTTA, and TCTA) Kleinstiver, Benjamin P et al. “Engineered CRISPR-Casl2a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing.” Nature biotechnology vol. 37,3 (2019): 276-282. doi: 10. 1038/s41587-018-0011-0. Most of the Cpfl nucleases require thymine-rich PAM. Different studies have demonstrated an increased Cpfl targeting range using in vitro and in vivo (E. coli) PAM identification assays. Zhang, Xiaochun, et al. "Multiplex gene regulation by CRISPR-ddCpfl." Cell discovery 3.1 (2017): 1-9. The two Cpfl endonucleases, AsCpfl and LbCpfl, require TTTV as a PAM sequence, where V can be A, C, or G nucleotides. Mutations at position S542R/K607R and S542R/K548V/N552Rproduced AsCpfl variants, and these are able to recognize TYCV and TATV PAMs, respectively, where Y can be C or T. Gao, Linyi, et al. "Engineered Cpfl variants with altered PAM specificities." Nature biotechnology 35.8 (2017): 789-792. The AsCpfl showed increased activity for TTTV PAMs and decreased activity' with TTTT PAM Kim, Hui K., et al. "In vivo high- throughput profiling of CRISPR-Cpfl activity." Nature methods 14.2 (2017): 153-159.
[00437] Accordingly, it is within the scope of the disclosure to devise the Casl2a editing system to recognize altered PAM recognition domains for genome editing. In preferred embodiments, the Cas 12a polypeptide recognizes one or more non-canonical PAM sequence in the targeted polynucleotide sequence, the PAM upstream of the crRNA-complementary DNA sequence on the non-target strand. In related embodiments, the gRNA has a seed sequence of eight nucleotides, located at the 5' end of the spacer, and is proximal to the PAM sequence on the targeted polynucleotide sequence. Preferably, the Cas 12a polypeptide cleaves the targeted polynucleotide sequence about 20 nucleotides upstream of the PAM sequence.
[00438] In further embodiments, the one or more polypeptide sequences and the one or more polynucleotide sequences comprising a cognate guide RNA of the genome editing system form a ribonucleoprotein complex.
[00439] In various embodiments, the one or more polypeptide sequences of the genome editing system comprise: one or more a-helical recognition lobe (REC) and a nuclease lobe (NUC): a Wedge (WED), a-helical recognition lobe (REC), PAM-interacting (PI),
RuvC nuclease. Bridge Helix (BH) and NUC domains; or one or more domains selected from RuvC, REC, WED. BH, PI and NUC domains.
[00440] Preferably, the REC lobe comprises RECI and REC2 domains. More preferably, the NUC lobe comprises tire RuvC, PI, WED, and Bridge Helix (BH) domains. Additionally, the RuvC domain comprises subdomains RuvCl. RuvCll and RuvCIIl. In preferred embodiments, the RuvCIlI domain is located on tire C -terminus.
[00441] In various embodiments, the one or more polypeptide sequences of the genome editing system lack a HNH endonuclease domain.
[00442] Without being bound by theory, the Casl2a genome editing system is characterized as a Class 2, Type V Cas endonuclease.
[00443] In various embodiments, the molecular weight of Cas 12a nuclease is characterized in its molecular weight to be about 50 kDa - lOOkDa, 100 kDa - 200kDa, 200kDa - 500kDa.
[00444] In additional embodiments, the polypeptide sequences comprise at least one activity selected from endonuclease activity; endoribonuclease activity, or RNA-guided DNase activity. In such embodiments, the cognate guide RNA and the Cas 12a protein modifies the targeted polynucleotide sequence of a host cell genome. In certain instances, the targeted polynucleotide sequence is modified by an insertion, deletion or alteration of one or more base pairs at the targeted polynucleotide sequence in tire host cell genome.
[00445] In related embodiments, the genome editing system is characterized in enhanced efficiency and precision of site-directed integration. Preferably, the efficiency and precision of site-directed integration enabled by genome editing system is enhanced by staggered overhangs on the donor nucleic acid sequence. In certain embodiments, the targeted polynucleotide sequence is double-stranded and contains a 5' overhang wherein the overhang preferably comprises five nucleotides.
[00446] In various embodiments, cleavage or cuts in the targeted polynucleotide sequence is preferably repaired by endogenous DNA polymerase repair mechanism present in the cell. In some embodiments, methods provide introducing a donor DNA sequence under conditions that allow editing of the targeted polynucleotide sequence by homology directed repair. Preferably, the Cas 12a genome editing system is characterized as exhibiting reduced specificity, e.g., off-target effects relative to Cas9. More preferably, the Casl2a system comprises enhanced activity of at least 1, 1.5. 2. 2.5, 3, 3.5, 4. 4.5. 5, 5.5, 6. 6.5. 7, 7.5, 8, 8.5. 9, 9.5, 10 or higher-fold improvement. [00447] In various embodiments, the RuvC domain comprising RuvC subdomains I, II and II of the Casl2a polypeptide of the Cast 2a genome editing system cleaves the targeted polynucleotide sequence and/or a nontarget DNA strand. Preferably, the genome editing system expresses multiple copies of guide RNA in a host cell of interest.
[00448] In various other embodiments, the polypeptide of tire genome editing system comprises one or more mutations. Preferably , the mutation is selected from one or more domains selected from RuvC, REC. WED, BH, PI and NUC domains. More preferably, the mutation encodes a nuclease-deficient polypeptide. In various embodiments, the genome editing system comprises a fusion of one or more deaminases to the nuclease deficient polypeptide. Preferably, the one or more deaminases of the genome editing system is selected from adenine deaminase or cytosine deaminase. Use of cytidine deaminase and adenosine deaminase base editing is disclosed in U.S. Pat. No. 9,840,699. One approach is to produce an Casl2a fusion protein, preferably an inactive or nickase variant) and a base- editing enzyme or the active domain of a base editing enzyme. Cytidine deaminase and adenosine deaminase base editing is disclosed in U.S. Pat. No. 9.840,699. In various embodiments, the compositions comprise contacting a targeted polynucleotide sequence with a fusion protein comprising an Casl2a and one or more base-editing polypeptide such as a deaminase; and a gRNA targeting the fusion protein to the targeted polynucleotide sequence of the DNA strand. Accordingly, the fusion of one or more deaminases to the nuclease deficient polypeptide of the Casl2a genome editing system of enables base editing on DNA and/or RNA. In select embodiments, the system modifies one or more nucleobase on DNA and RNA. In related embodiments, the system enables multiplexed gene editing. Preferably, the genome editing system comprises a single crRNA. More preferably, the system enables targeting multiple genes simultaneously.
[00449] Recent studies demonstrate Cast 2a’ s on-target gene editing efficiency approaching 100% through modifications to the NLS framework. Luk et al., GEN Biotechnology.Jun 2022.271- 284.http://doi.org/10. 1089/genbio.2022.0003. Previous work also demonstrated NLS-optimized SpCas9- bascd prime editor that improves genome editing efficiency Liu, Pcngpcng ct al. “Improved prime editors enable pathogenic allele correction and cancer modelling in adult mice.” Nature communications vol. 12.1 2121. 9 Apr. 2021, doi: 10.1038/s41467-021-22295-w.
[00450] In yet other embodiments, the Casl2a polypeptide is operably linked to a nuclear localization signal (NLS). Preferably, the Casl2a polypeptide comprises an NLS on the N-terminus or the C-terminus or both or multiple NLS on the Casl2a polypeptide. In some embodiments, the polypeptide linked to the NLS further comprises crRNA to form a ribonucleoprotein complex. In some embodiments, polypeptide comprises one or more NLS repeats at either N- or C- terminus of the polypeptide. [00451] In select embodiments, the one or more polypeptide sequences of the genome editing system comprises a modification, wherein the modification comprises a nuclease- deficient polypeptide (dCas). In related embodiments, the guide RNA of tire genome editing system of comprises a prime editing guide RNA (pegRNA). Preferably, the pegRNA of tire genome editing sy stem hybridizes to a targeted polynucleotide sequence and acts as a primer to the one or more reverse transcriptases. More preferably, the pegRNA of the genome editing system binds to the nicked strand for initiation of repair through a reverse transcriptase using the repair template.
[00452] In various additional embodiments, the nuclease -deficient polypeptide of the genome editing system comprises a nickase activity. Preferably, the genome editing system comprises fusion of one or more reverse transcriptases to the nuclease deficient Cas (dCas). In certain examples, the fusion of one or more reverse transcriptases is selected from
[00453] Moloney Murine Leukemia Virus (M-MLV). In certain embodiments, the guide RNA or a pegRNA comprises or consists of an extended single guide RNA containing a primer binding site (PBS) and a reverse transcriptase (RT) template sequence.
[00454] The Cas 12a genome editing system comprises improved genome editing characteristics selected from efficiency, specificity, precision, intended edits: unintended edits, indels relative to Cas9. Accordingly, it is an object of the invention to reduce off-target effects in host cells in comparison to an equivalent endonuclease activity in host cells relative to SpCas9.
Optional components/modifications
Donor templates
[00455] In one embodiment, the compositions and systems herein may further comprise one or more donor templates for use in editing. In some cases, the donor template may comprise one or more polynucleotides. In certain cases, the donor template may comprise coding sequences for one or more polynucleotides. The donor template may be a DNA template. It may be single stranded or double stranded. It may also be circular single or double stranded. It may also be linear single stranded or double stranded. Without being bound by theoiy, the donor template may become integrated into the genome after a targeted cut by the Cas 12a gene editing system described herein through cellular repair machinery including HDR and NHEJ.
[00456] Tire donor template may be used for editing the target polynucleotide. In some cases, the donor polynucleotide comprises one or more mutations to be introduced into the target polynucleotide. Examples of such mutations include substitutions, deletions, insertions, or a combination thereof. The mutations may cause a shift in an open reading frame on the target polynucleotide. In some cases, the donor template alters a stop codon in the target polynucleotide. For example, the donor template may correct a premature stop codon. The correction may be achieved by deleting the stop codon or introduces one or more mutations to the stop codon. In other example embodiments, the donor template addresses loss of function mutations, deletions, or translocations that may occur, for example, in certain disease contexts by inserting or restoring a functional copy of a gene, or functional fragment thereof, or a functional regulatory sequence or functional fragment of a regulatory sequence. A functional fragment refers to less than the entire copy of a gene by providing sufficient nucleotide sequence to restore the functionality of a wild type gene or non-coding regulatory sequence (e.g. sequences encoding long non-coding RNA). In certain example embodiments, the systems disclosed herein may be used to replace a single allele of a defective gene or defective fragment thereof. In another example embodiment, the systems disclosed herein may be used to replace both alleles of a defective gene or defective gene fragment. A “defective gene” or “defective gene fragment” is a gene or portion of a gene that when expressed fails to generate a functioning protein or non-coding RNA with functionality of a corresponding wild-type gene. In certain example embodiments, these defective genes may be associated with one or more disease phenotypes. In certain example embodiments, tire defective gene or gene fragment is not replaced but the systems described herein are used to insert donor templates that encode gene or gene fragments that compensate for or override defective gene expression such that cell phenotypes associated with defective gene expression are eliminated or changed to a different or desired cellular phenotype.
[00457] In an embodiment of the invention, the donor template may include, but not be limited to, genes or gene fragments, encoding proteins or RNA transcripts to be expressed, regulatory elements, repair templates, and the like. According to the invention, the donor templates may comprise left end and right end sequence elements that function with transposition components that mediate insertion.
[00458] In certain cases, the donor template manipulates a splicing site on the target polynucleotide. In some examples, the donor template disrupts a splicing site. The disruption may be achieved by inserting the polynucleotide to a splicing site and/or introducing one or more mutations to the splicing site. In certain examples, the donor template may restore a splicing site. For example, the polynucleotide may comprise a splicing site sequence.
[00459] The donor template to be inserted may has a size from 10 base pair or nucleotides to 50 kb in length, e.g., from 50 to 40k, from 100 and 30 k, from 100 to 10000, from 100 to 300. from 200 to 400, from 300 to 500, from 400 to 600. from 500 to 700, from 600 to 800, from 700 to 900, from 800 to 1000, from 900 to from 1100, from 1000 to 1200, from 1100 to 1300, from 1200 to 1400, from 1300 to 1500, from 1400 to 1600, from 1500 to 1700, from 600 to 1800, from 1700 to 1900, from 1800 to 2000 base pairs (bp) or nucleotides in length. [00460] In some embodiments, the heterologous nucleic acid sequence is a donor DNA template that can be integrated into a host genome via HDR. In other embodiments, the heterologous nucleic acid sequence is a donor DNA template that can be integrated into a host genome via NHEJ.
[00461] In certain embodiments, the heterologous nucleic acid comprises or encodes a donor / template sequence, wherein the donor / template corrects / repairs / removes a mutation at the target genome site. For example, the mutation may be a mutated exon in a disease gene.
[00462] In certain embodiments, the donor / template may encode or comprises a functional DNA element, such as a promoter, an enhancer, a protein binding sequence, a methylation site, or a homology region for assisting gene editing, etc.
[00463] By ‘ ‘donor DNA” or “donor DNA template” it is meant a DNA segment (can be single stranded or double stranded DNA) to be inserted at a site cleaved by a gene-editing nuclease (e.g., a Casl2a nuclease) (e.g., after dsDNA cleavage, after nicking a target DNA, after dual nicking a target DNA. and the like). The donor DNA template can contain sufficient homology to a genomic sequence at the target site, e.g., 70%, 80%, 85%, 90%, 95%, or 100% homology with the nucleotide sequences flanking the target site, e.g. within about 50 bases or less of the target site, e.g. within about 30 bases, within about 15 bases, within about 10 bases, within about 5 bases, or immediately flanking tire target site, to support homology-directed repair between it and the genomic sequence to which it bears homology. In the case of repair by NHEJ. no homology is needed on the donor DNA template against the site to which it targets editing.
[00464] Approximately 25, 50, 100. or 200 nucleotides, or more than 200 nucleotides, of sequence homology between a donor DNA template and a genomic sequence (or any integral value between 10 and 200 nucleotides, or more) can support homology-directed repair. Donor DNA template can be of any length, e.g., 50 nucleotides or more, 100 nucleotides or more, 250 nucleotides or more, 500 nucleotides or more, 1000 nucleotides or more, 5000 nucleotides or more, etc. A suitable donor DNA template can be from 50 nucleotides to 100 nucleotides, from 100 nucleotides to 500 nucleotides, from 500 nucleotides to 1000 nucleotides, from 1000 nucleotides to 5000 nucleotides, or from 5000 nucleotides to 10,000 nucleotides, or more than 10,000 nucleotides, in length.
[00465] As noted above, in some embodiments, the donor DNA template comprises a first homology arm and a second homology arm. The first homology arm is at or near the 5’ end of the donor DNA; and comprises a nucleotide sequence that is at least partially complementary to a first nucleotide sequence in a target nucleic acid. Tire second homology arm is at or near the 3 ’ end of the donor DNA; and comprises a nucleotide sequence that is at least partially complementary to a second nucleotide sequence in the target nucleic acid. Hie first and second homology anns can each independently have a length of from about 10 nucleotides to 400 nucleotides: e.g., from 10 nucleotides (nt) to 15 nt, from 15 nt to 20 nt, from 20 nt to 25 nt, from 25 nt to 30 nt, from 30 nt to 35 nt, from 35 nt to 40 nt, from 40 nt to 45 nt, from 45 nt to 50 nt, from 50 nt to 75 nt, from 75 nt to 100 nt, from 100 nt to 125 nt, from 125 nt to 150 nt, from 150 nt to 175 nt, from 175 nt to 200 nt, from 200 nt to 225 nt, from 225 nt to 250 nt, from 250 nt to 275 nt, from 275 nt to 300 nt, from 325 nt to 350 nt, from 350 nt to 375 nt, or from 375 nt to 400 nt.
[00466] In certain embodiments, the donor DNA template is used for editing the target nucleotide sequence. In certain embodiments, the donor DNA template comprises one or more mutations to be introduced into the target polynucleotide. Examples of such mutations include substitutions, deletions, insertions, or a combination thereof. In certain embodiments, the mutation causes a shift in an open reading frame on the target polynucleotide. In certain embodiments, the donor polynucleotide alters a stop codon in the target polynucleotide. In certain embodiments, the donor polynucleotide corrects a premature stop codon. The correction can be achieved by deleting the stop codon, or by introducing one or more sequence changes to alter the stop codon to a codon. In certain embodiments, the donor polynucleotide addresses loss of function mutations, deletions, or translocations that may occur, for example, in certain disease contexts by inserting or restoring a functional copy of a gene, or functional fragment thereof, or a functional regulatory sequence or functional fragment of a regulatory sequence. A functional fragment includes a fragment less than the entire copy of a gene but otherwise provides sufficient nucleotide sequence to restore the functionality of a wild type gene or non-coding regulatory sequence (e.g., sequences encoding long non-coding RNA).
[00467] In certain embodiments, the donor DNA template may be used to replace a single allele of a defective gene or defective fragment thereof. In another embodiment, the donor DNA template is used to replace both alleles of a defective gene or defective gene fragment. A "‘defective gene” or “defective gene fragment” is a gene or portion of a gene that when expressed, fails to generate a functioning protein or non-coding RNA with functionality of the corresponding wild-type gene.
[00468] In certain example embodiments, these defective genes may be associated with one or more disease phenotypes. In certain example embodiments, the defective gene or gene fragment is not replaced but the heterologous nucleic acid is used to insert donor polynucleotides that encode gene or gene fragments that compensate for or override defective gene expression such that cell phenotypes associated with defective gene expression are eliminated or changed to a different or desired cellular phenotype. This can be achieved by including the coding sequence of a therapeutic protein, such as a therapeutic antibody or functional fragment thereof, or a wild-type version of a defective protein associated with one or more disease phenotypes. [00469] In certain embodiments, the donor may include, but not be limited to, genes or gene fragments, encoding proteins or RNA transcripts to be expressed, regulatory elements, repair templates, and the like. According to the invention, tire donor polynucleotides may comprise left end and right end sequence elements that function with transposition components that mediate insertion.
[00470] In certain embodiments, the donor DNA template manipulates a splicing site on the target polynucleotide. In certain embodiments, the donor DNA template disrupts a splicing site. The disruption maybe achieved by inserting tire polynucleotide to a splicing site and/or introducing one or more mutations to the splicing site. In certain embodiments, the donor polynucleotide may restore a splicing site. For example, the polynucleotide may comprise a splicing site sequence.
[00471] In certain embodiments, the donor DNA template to be inserted has a size from 10 bp to 50 kb in length, e.g., from 50 bp to ~40kb, from 100 bp to ~30 kb, from 100 bp to ~10 kb, from 100 bp to 300 bp, from 200 bp to 400 bp, from 300 bp to 500 bp, from 400 bp to 600 bp, from 500 bp to 700 bp, from 600 bp to 800 bp, from 700 bp to 900 bp, from 800 bp to 1000 bp, from 900 bp to 1100 bp, from 1000 bp to 1200 bp, from 1100 bp to 1300 bp, from 1200 bp to 1400 bp, from 1300 bp to 1500 bp, from 1400 bp to 1600 bp, from 1500 bp to 1700 bp, from 1600 bp to 1800 bp, from 1700 bp to 1900 bp, from 1800 bp to 2000 bp nucleotides in length.
[00472] In certain embodiments, the homologous arm on one or both ends of the sequence to be inserted is independently about 20 bp, 40 bp, 60 bp, 80 bp, 100 bp, 120 bp, or 150 bp.
[00473] The first homology arm and the second homology arm of the donor DNA flank a nucleotide sequence (“a nucleotide sequence of interest” or ‘'an intervening nucleotide sequence”) that is to be introduced into a target nucleic acid. The nucleotide sequence of interest can comprise: i) a nucleotide sequence encoding a polypeptide of interest; ii) a nucleotide sequence encoding an exon of a gene; iii) a promoter sequence; iv) an enhancer sequence; v) a nucleotide sequence encoding a non-coding RNA; or vi) any combination of the foregoing.
[00474] The donor DNA can provide for gene correction, gene replacement, gene tagging, transgene insertion, nucleotide deletion, gene disruption, gene mutation, etc. For example, tire donor DNA can be used to add, e.g.. insert or replace, nucleic acid material to a target DNA (e.g. to “knock in” a nucleic acid that encodes a protein, an siRNA, an miRNA, etc.), to add a tag (e.g., 6xHis (SEQ ID NO:2661), a fluorescent protein (e.g., a green fluorescent protein; a yellow fluorescent protein, etc.), hemagglutinin (HA), FLAG, etc.), to add a regulatory' sequence to a gene (e.g. promoter, polyadenylation signal, internal ribosome entrysequence (IRES), 2A peptide, start codon, stop codon, splice signal, localization signal, enhancer, etc.), to modify a nucleic acid sequence (e.g., introduce a mutation), and the like. For example, the donor DNA can be used to modify DNA in a site-specific, i.e. "targeted", way; for example gene knock-out, gene knock-in, gene editing, gene tagging, etc., as used in, for example, gene therapy, e.g. to treat a disease; or as an antiviral, antipathogenic, or anticancer therapeutic, the production of genetically modified organisms in agriculture, the large scale production of proteins by cells for therapeutic, diagnostic, or research purposes, the induction of pluripotent stem cells, biological research, the targeting of genes of pathogens for deletion or replacement, etc.
[00475] In some cases, the donor DNA comprises a nucleotide sequence encoding a polypeptide of interest. Polypeptides of interest include, e.g., a) functional versions of a polypeptide that comprises one or more amino acid substitutions, insertions, and/or deletions and that exhibits reduced function, e.g., where the reduced function is associated with or causes a pathological condition; b) fluorescent polypeptides; c) hormones; d) receptors for ligands; e) ion channels; f) neurotransmitters; g) and the like.
[00476] In some cases, the donor DNA comprises a nucleotide sequence that encodes a wild-type protein that is lacking in the recipient cell. In some cases, the donor DNA encodes a wild type factor (e.g. Factor VII, Factor VIII, Factor IX and tire like) involved in coagulation. In some cases, the donor DNA comprises a nucleotide sequence that encodes a therapeutic antibody. In some cases, tire donor DNA comprises a nucleotide sequence that encodes an engineered protein or receptor, in some cases, the engineered receptor is a T cell receptor (TCR), a natural killer (NK) receptor (NKR), or a B cell receptor (BCR). In some cases, the engineered TCR or NKR targets a cancer marker (e.g., a polypeptide that is expressed (e.g., over-expressed) on the surface of a cancer cell). In some cases, the donor DNA comprises a nucleotide sequence that encodes a chimeric antigen receptor (CAR). In some cases, the CAR targets a cancer marker. Donor DNAs encoding CAR. TCR. and/or NCR proteins may be folded into DNA origami structures (DNA nanostructures) and delivered into T cells or NK cells in vitro or in vivo.
[00477] Non-limiting examples of polypeptides that can be encoded by a donor DNA include, e.g., IL1B (interleukin 1, beta), XDH (xanthine dehydrogenase), TP53 (tumor protein p53), PTGIS (prostaglandin 12 (prostacyclin) synthase), MB (myoglobin), IL4 (interleukin 4), ANGPT1 (angiopoietin 1), ABCG8 (ATP- binding cassette, sub-family G (WHITE), member 8), CTSK (cathepsin K), PTGIR (prostaglandin 12 (prostacyclin) receptor (IP)), KCNJ11 (potassium inwardly-rectifying channel, subfamily J, member 11), INS (insulin), CRP (C -reactive protein, pentraxin-related), PDGFRB (platelet- derived growth factor receptor, beta polypeptide), CCNA2 (cyclin A2). PDGFB (platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)), KCNJ5 (potassium inwardly- rectifying channel, subfamily J, member 5), KCNN3 (potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3), CAPN10 (calpain 10), PTGES (prostaglandin E synthase), ADRA2B (adrenergic, alpha-2B-, receptor), ABCG5 (ATP -binding cassette, sub-family G (WHITE), member 5), PRDX2 (peroxiredoxin 2), CAPN5 (calpain 5), PARP14 (poly (ADP-ribose) polymerase family, member 14), MEX3C (mex-3 homolog C (C. elegans)), ACE angiotensin I converting enzyme (peptidyl-dipeptidase A) 1), TNF (tumor necrosis factor (TNF superfamily, member 2)), IL6 (interleukin 6 (interferon, beta 2)), STN (statin), SERPINE1 (serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1), ALB (albumin), ADIPOQ (adiponectin, C1Q and collagen domain containing), APOB (apolipoprotein B (including Ag(x) antigen)), APOE (apolipoprotein E), LEP (leptin), MTHFR (5,10-methylenetetrahydrofolate reductase (NADPH)), AP0A1 (apolipoprotein A-I), EDN1 (endothelin 1), NPPB (natriuretic peptide precursor B), NOS3 (nitric oxide synthase 3 (endothelial cell)), PPARG (peroxisome proliferator-activated receptor gamma), PLAT (plasminogen activator, tissue), PTGS2 (prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)), CETP (cholesteryl ester transfer protein, plasma), AGTR1 (angiotensin II receptor, type 1), HMGCR (3 -hydroxy-3 -methylglutaryl-Coenzyme A reductase), IGF1 (insulin-like growth factor 1 (somatomedin C)), SELE (selectin E), REN (renin), PPARA (peroxisome proliferator-activated receptor alpha), PON1 (paraoxonase 1), KNG1 (kininogen 1), CCL2 (chemokine (C-C motif) ligand 2), LPL (lipoprotein lipase), vWF (von Willebrand factor), F2 (coagulation factor II (thrombin)), ICAM1 (intercellular adhesion molecule 1), TGFB1 (transforming growth factor, beta 1), NPPA (natriuretic peptide precursor A), IL 10 (interleukin 10), EPO (erythropoietin), SOD1 (superoxide dismutase I. soluble), VCAM1 (vascular cell adhesion molecule 1). IFNG (interferon, gamma). LPA (lipoprotein. Lp(a)), MPO (myeloperoxidase), ESRI (estrogen receptor 1), MAPK1 (mitogen-activated protein kinase 1), HP (haptoglobin), F3 (coagulation factor III (thromboplastin, tissue factor)), CST3 (cystatin C), COG2 (component of oligomeric Golgi complex 2), MMP9 (matrix metallopeptidase 9 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV collagenase)), SERPINC1 (serpin peptidase inhibitor, clade C (antithrombin), member 1), F8 (coagulation factor VIII, procoagulant component), HM0X1 (heme oxygenase (decycling) 1), APOC3 (apolipoprotein C-1I1), IL8 (interleukin 8), PROK1 (prokineticin 1), CBS (cystathionine-beta- synthase), NOS2 (nitric oxide synthase 2, inducible), TLR4 (toll-like receptor 4), SELP (selectin P (granule membrane protein 140 kDa, antigen CD62)), ABCA1 (ATP -binding cassette, sub-family A (ABC1), member 1), AGT (angiotensinogen (serpin peptidase inhibitor, clade A, member 8)), LDLR (low' density lipoprotein receptor), GPT (glutamic -pyruvate transaminase (alanine aminotransferase)), VEGFA (vascular endothelial growth factor A), NR3C2 (nuclear receptor subfamily 3, group C, member 2), IL 18 (interleukin 18 (interferon-gamma-inducing factor)). NOS1 (nitric oxide synthase 1 (neuronal)), NR3CI (nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)), FGB (fibrinogen beta chain), HGF (hepatocyte growth factor (hepapoietin A; scatter factor)), ILIA (interleukin 1, alpha), RETN (resistin), AKT1 (v-akt murine thymoma viral oncogene homolog 1), LIPC (lipase, hepatic), HSPD1 (heat shock 60 kDa protein 1 (chaperonin)), MAPK14 (mitogen-activated protein kinase 14), SPP1 (secreted phosphoprotein 1), ITGB3 (integrin, beta 3 (platelet glycoprotein 11 la, antigen CD61)), CAT (catalase), UTS2 (urotensin 2), THBD (thrombomodulin), F10 (coagulation factor X), CP (ceruloplasmin (ferroxidase)), TNFRSF1 IB (tumor necrosis factor receptor superfamily, member lib), EDNRA (endothelin receptor type A), EGFR (epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)), MMP2 (matrix metallopeptidase 2 (gelatinase A. 72 kDa gelatinase, 72 kDa type IV collagenase)). PLG (plasminogen), NPY (neuropeptide Y), RHOD (ras homolog gene family, member D), MAPK8 (mitogen-activated protein kinase 8), MYC (v-myc myelocytomatosis viral oncogene homolog (avian)), FN1 (fibronectin 1), CMA1 (chymase 1, mast cell), PLAU (plasminogen activator, urokinase), GNB3 (guanine nucleotide binding protein (G protein), beta polypeptide 3), ADRB2 (adrenergic, beta-2-, receptor, surface). AP0A5 (apolipoprotein A-V), SOD2 (superoxide dismutase 2. mitochondrial), F5 (coagulation factor V (proaccelerin, labile factor)), VDR (vitamin D (1,25- dihydroxyvitamin D3) receptor), AL0X5 (arachidonate 5 -lipoxygenase), HLA-DRB1 (major histocompatibility complex, class II, DR beta 1), PARP1 (poly (ADP-ribose) polymerase 1), CD40LG (CD40 ligand), PON2 (paraoxonase 2), AGER (advanced glycosylation end product-specific receptor), IRS 1 (insulin receptor substrate 1), PTGS1 (prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxygenase)), ECE1 (endothelin converting enzyme 1), F7 (coagulation factor VII (serum prothrombin conversion accelerator)), URN (interleukin 1 receptor antagonist), EPHX2 (epoxide hydrolase 2, cytoplasmic). 1GFBP1 (insulin-like growth factor binding protein 1), MAPK10 (mitogen- activated protein kinase 10), FAS (Fas (TNF receptor superfamily, member 6)), ABCB1 (ATP-binding cassette, sub-family B (MDR/TAP), member 1), JUN (jun oncogene), IGFBP3 (insulin-like growth factor binding protein 3), CD 14 (CD 14 molecule), PDE5A (phosphodiesterase 5A, cGMP-specific), AGTR2 (angiotensin II receptor, type 2), CD40 (CD40 molecule. TNF receptor superfamily member 5), LCAT (lecithin-cholesterol acyltransferase), CCR5 (chemokine (C-C motif) receptor 5), MMP1 (matrix metallopeptidase 1 (interstitial collagenase)), TIMP1 (TIMP metallopeptidase inhibitor 1), ADM (adrenomedullin), DYT10 (dystonia 10), STAT3 (signal transducer and activator of transcription 3 (acute-phase response factor)), MMP3 (matrix metallopeptidase 3 (stromelysin 1, progelatinase)), ELN (elastin), USF1 (upstream transcription factor 1), CFH (complement factor H), HSPA4 (heat shock 70 kDa protein 4), MMP12 (matrix metallopeptidase 12 (macrophage elastase)), MME (membrane metallo- endopeptidase), F2R (coagulation factor II (thrombin) receptor), SELL (selectin L), CTSB (cathepsin B). ANXA5 (annexin A5), ADRB1 (adrenergic, beta-1-, receptor). CYBA (cytochrome b-245. alpha polypeptide). FGA (fibrinogen alpha chain), GGT1 (gamma-glutamyltransferase 1), LIPG (lipase, endothelial), HIF1 A (hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)), CXCR4 (chemokine (C-X-C motif) receptor 4), PROC (protein C (inactivator of coagulation factors Va and Villa)), SCARB1 (scavenger receptor class B, member 1), CD79A (CD79a molecule, immunoglobulin-associated alpha), PLTP (phospholipid transfer protein), ADD 1 (adducin 1 (alpha)), FGG (fibrinogen gamma chain), SAA1 (serum amyloid Al), KCNH2 (potassium voltage-gated channel, subfamily H (eag-related), member 2), DPP4 (dipeptidyl-peptidase 4), G6PD (glucose-6-phosphate dehydrogenase), NPR1 (natriuretic peptide receptor A/guanylate cyclase A (atrionatriuretic peptide receptor A)), VTN (vitronectin), KIAA0101 (KIAA0101). FOS (FBJ murine osteosarcoma viral oncogene homolog), TLR2 (toll-like receptor 2). PPIG (peptidylprolyl isomer ase G (cyclophilin G)), IL1R1 (interleukin 1 receptor, type I), AR (androgen receptor), CYP1A1 (cytochrome P450, family 1, subfamily A, polypeptide 1), SERPINA1 (serpin peptidase inhibitor, clade A (alpha- 1 antiproteinase, antitrypsin), member 1), MTR (5- methyltetrahydrofolate-homocysteine methyltransferase), RBP4 (retinol binding protein 4, plasma), AP0A4 (apolipoprotein A-IV), CDKN2A (cyclin-dependent kinase inhibitor 2A (melanoma, pl6, inhibits CDK4)), FGF2 (fibroblast growth factor 2 (basic)), EDNRB (endothelin receptor type B), ITGA2 (integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)), CAB INI (calcineurin binding protein 1), SHBG (sex hormone-binding globulin), HMGB1 (high- mobility group box 1), HSP90B2P (heat shock protein 90 kDa beta (Grp94), member 2 (pseudogene)), CYP3A4 (cytochrome P450, family 3, subfamily A, polypeptide 4), GJA1 (gap junction protein, alpha 1, 43 kDa), CAV1 (caveolin 1, caveolae protein, 22 kDa), ESR2 (estrogen receptor 2 (ER beta)), LTA (lymphotoxin alpha (TNF superfamily, member 1)), GDF15 (growth differentiation factor 15), BDNF (brain-derived neurotrophic factor), CYP2D6 (cytochrome P450, family 2, subfamily D, polypeptide 6), NGF (nerve growth factor (beta polypeptide)), SP1 (Sp 1 transcription factor), TGIF1 (TGFB-induced factor homeobox 1), SRC (v-src sarcoma (Schmidt- Ruppin A-2) viral oncogene homolog (avian)), EGF (epidermal growth factor (beta-urogastrone)), PIK3CG (phosphoinositide-3-kinase, catalytic, gamma poly peptide), HLA-A (major histocompatibility complex, class I, A), KCNQ1 (potassium voltage-gated channel, KQT-like subfamily, member 1), CNR1 (cannabinoid receptor 1 (brain)), FBN1 (fibrillin 1). CHKA (choline kinase alpha), BEST1 (bestrophin 1), APP (amyloid beta (A4) precursor protein), CTNNB1 (catenin (cadherin-associated protein), beta 1. 88 kDa), IL2 (interleukin 2), CD36 (CD36 molecule (thrombospondin receptor)), PRKAB1 (protein kinase, AMP -activated, beta 1 non-catalytic subunit), TPO (thyroid peroxidase), ALDH7A1 (aldehyde dehydrogenase 7 family, member Al), CX3CR1 (chemokine (C-X3-C motif) receptor 1), TH (tyrosine hydroxylase), F9 (coagulation factor IX), GH1 (growth hormone 1), TF (transferrin), HFE (hemochromatosis), IE17A (interleukin 17A), PTEN (phosphatase and tensin homolog), GSTM1 (glutathione S -transferase mu 1), DMD (dystrophin), GATA4 (GATA binding protein 4), F13A1 (coagulation factor XIII. Al polypeptide), TTR (transthyretin). FABP4 (fatty acid binding protein 4, adipocyte), PON3 (paraoxonase 3), APOCI (apolipoprotein C-I), INSR (insulin receptor), TNFRSF1B (tumor necrosis factor receptor superfamily, member IB), HTR2A (5 -hydroxytry ptamine (serotonin) receptor 2A), CSF3 (colony stimulating factor 3 (granulocyte)), CYP2C9 (cytochrome P450, family 2, subfamily C, polypeptide 9), TXN (thioredoxin), CYP11B2 (cytochrome P450, family 11, subfamily B, polypeptide 2), PTH (parathyroid hormone), CSF2 (colony stimulating factor 2 (granulocytemacrophage)), KDR (kinase insert domain receptor (a type III receptor tyrosine kinase)), PLA2G2A (phospholipase A2, group IIA (platelets, synovial fluid)), B2M (beta-2 -microglobulin), THBS1 (thrombospondin 1), GCG (glucagon), RHOA (ras homolog gene family, member A), ALDH2 (aldehyde dehydrogenase 2 family (mitochondrial)), TCF7L2 (transcription factor 7-like 2 (T-cell specific, HMG-box)), BDKRB2 (bradykinin receptor B2), NFE2L2 (nuclear factor (erythroid-derived 2)-like 2), NOTCH 1 (Notch homolog 1, translocation-associated (Drosophila)), UGT1A1 (UDP glucuronosyltransferase 1 family, polypeptide Al), IFNA1 (interferon, alpha 1), PPARD (peroxisome proliferator-activated receptor delta), SIRT1 (sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)), GNRH1 (gonadotropin-releasing hormone 1 (luteinizing- releasing hormone)), PAPPA (pregnancy-associated plasma protein A, pappalysin 1), ARR3 (arrestin 3. retinal (X-arrestin)), NPPC (natriuretic peptide precursor C), AHSP (alpha hemoglobin stabilizing protein), PTK2 (PTK2 protein tyrosine kinase 2), IL 13 (interleukin 13), MTOR (mechanistic target of rapamycin (serine/threonine kinase)), ITGB2 (integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)), GSTT1 (glutathione S-transfcrase theta 1), IL6ST (interleukin 6 signal transducer (gpl30, oncostatin M receptor)), CPB2 (carboxypeptidase B2 (plasma)), CYP1A2 (cytochrome P450, family 1, subfamily A, polypeptide 2), HNF4A (hepatocyte nuclear factor 4, alpha), SLC6A4 (solute carrier family 6 (neurotransmitter transporter, serotonin), member 4), PLA2G6 (phospholipase A2, group VI (cytosolic, calcium -independent)), TNFSF11 (tumor necrosis factor (ligand) superfamily, member 11), SLC8A1 (solute carrier family 8 (sodium/calcium exchanger), member 1), F2RL1 (coagulation factor II (thrombin) receptor-like 1), AKR1A1 (aldo-keto reductase family 1, member Al (aldehyde reductase)), ALDH9A1 (aldehyde dehydrogenase 9 family, member Al), BGLAP (bone gammacarboxyglutamate (gla) protein), MTTP (microsomal triglyceride transfer protein), MTRR (5- methyltetrahydrofolate- homocysteine methyltransferase reductase), SULT1A3 (sulfotransferase family, cytosolic, 1 A, phenol- preferring, member 3), RAGE (renal tumor antigen), C4B (complement component 4B (Chido blood group), P2RY12 (purinergic receptor P2Y, G-protein coupled, 12), RNLS (renalase, FAD- dependent amine oxidase), CREB1 (cAMP responsive element binding protein 1), POMC (proopiomelanocortin), RAC 1 (ras-related C3 botulinum toxin substrate 1 (rho family, small GTP binding protein Rael)), LMNA (lamin NC), CD59 (CD59 molecule, complement regulatory protein), SCN5A (sodium channel, voltage-gated, type V, alpha subunit). CYP1B1 (cytochrome P450. family 1, subfamily B, polypeptide 1), MIF (macrophage migration inhibitory factor (glycosylation-inhibiting factor)), MMP13 (matrix metallopeptidase 13 (collagenase 3)), TIMP2 (TIMP metallopeptidase inhibitor 2), CYP19A1 (cytochrome P450, family 19, subfamily A, polypeptide 1), CYP21A2 (cytochrome P450, family 21, subfamily A, polypeptide 2), PTPN22 (protein tyrosine phosphatase, non-receptor type 22 (lymphoid)), MYH14 (myosin, heavy chain 14, non-muscle), MBL2 (mannose-binding lectin (protein C) 2, soluble (opsonic defect)), SELPLG (selectin P ligand), A0C3 (amine oxidase, copper containing 3 (vascular adhesion protein 1)), CTSL1 (cathepsin LI), PCNA (proliferating cell nuclear antigen), IGF2 (insulin like growth factor 2 (somatomedin A)), ITGB1 (integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)). CAST (calpastatin), CXCL12 (chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1)), IGHE (immunoglobulin heavy constant epsilon), KCNE1 (potassium voltage-gated channel, Isk-related family, member 1), TFRC (transferrin receptor (p90, CD71)), COL1A1 (collagen, type I, alpha 1), C0L1A2 (collagen, type I, alpha 2), IL2RB (interleukin 2 receptor, beta), PLA2G10 (phospholipase A2, group X), ANGPT2 (angiopoietin 2), PROCR (protein C receptor, endothelial (EPCR)), N0X4 (NADPH oxidase 4), HAMP (hepcidin antimicrobial peptide), PTPN11 (protein tyrosine phosphatase, non-receptor type 11). SLC2A1 (solute carrier family 2 (facilitated glucose transporter), member 1), IL2RA (interleukin 2 receptor, alpha), CCL5 (chemokine (C-C motif) ligand 5), IRF1 (interferon regulatory' factor 1), CFLAR (CASP8 and FADD-like apoptosis regulator), CALC A (calcitonin-related polypeptide alpha), EIF4E (eukary otic translation initiation factor 4E), GSTP1 (glutathione S-transferase pi 1), JAK2 (Janus kinase 2), CYP3A5 (cytochrome P450, family 3. subfamily A, polypeptide 5), HSPG2 (heparan sulfate proteoglycan 2), CCL3 (chemokine (C-C motif) ligand 3), MYD88 (myeloid differentiation primary response gene (88)), VIP (vasoactive intestinal peptide), SOAT1 (sterol O-acyltransferase 1), ADRBK1 (adrenergic, beta, receptor kinase 1), NR4A2 (nuclear receptor subfamily 4, group A, member 2), MMP8 (matrix metallopeptidase 8 (neutrophil collagenase)), NPR2 (natriuretic peptide receptor B/guanylate cyclase B (atrionatriuretic peptide receptor B)), GCH1 (GTP cyclohydrolase 1), EPRS (glutamyl-prolyl - tRNA synthetase), PPARGC1A (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha), F12 (coagulation factor XII (Hageman factor)), PEC AMI (platelet/endothelial cell adhesion molecule). CCL4 (chemokine (C-C motif) ligand 4), SERP1NA3 (serpin peptidase inhibitor, clade A (alpha- 1 antiproteinase, antitrypsin), member 3), CASR (calcium-sensing receptor), GJA5 (gap junction protein, alpha 5, 40 kDa), FABP2 (fatty' acid binding protein 2, intestinal), TTF2 (transcription termination factor, RNA polymerase II), PROS1 (protein S (alpha)), CTF1 (cardiotrophin 1), SGCB (sarcoglycan, beta (43 kDa dystrophin- associated glycoprotein)), YME1L1 (YMEl-like 1 (S. cerevisiae)). CAMP (cathelicidin antimicrobial peptide), ZC3H12A (zinc finger CCCH-type containing 12A), AKR1B1 (aldo-keto reductase family 1, member Bl (aldose reductase)). DES (desmin). MMP7 (matrix metallopeptidase 7 (matrilysin, uterine)), AHR (aryl hydrocarbon receptor), CSF1 (colony stimulating factor 1 (macrophage)), HDAC9 (histone deacetylase 9), CTGF (connective tissue growth factor), KCNMA1 (potassium large conductance calcium-activated channel, subfamily M, alpha member 1), UGT1A (UDP glucuronosyltransferase 1 family, polypeptide A complex locus), PRKCA (protein kinase C, alpha), COMT (catechol -b- methyltransf erase), S100B (SI 00 calcium binding protein B), EGR1 (early growth response 1), PRL (prolactin), IL 15 (interleukin 1 ), DRD4 (dopamine receptor D4), CAMK2G (calcium/calmodulin- dependent protein kinase II gamma), SLC22A2 (solute carrier family 22 (organic cation transporter), member 2), CCL11 (chemokine (C-C motif) ligand 11). PGF (placental growth factor), THPO (thrombopoietin), GP6 (glycoprotein VI (platelet)), TACR1 (tachykinin receptor 1). NTS (neurotensin). HNF1A (HNF1 homeobox A), SST (somatostatin). KCND1 (potassium voltage-gated channel, Shal- related subfamily, member 1), LOC646627 (phospholipase inhibitor), TBXAS1 (thromboxane A synthase 1 (platelet)), CYP2J2 (cytochrome P450, family 2, subfamily J, polypeptide 2), TBXA2R (thromboxane A2 receptor), ADH1C (alcohol dehydrogenase 1C (class I), gamma polypeptide), ALOX12 (arachidonate 12-lipoxygenase), AHSG (alpha-2 -HS-glycoprotein), BHMT (betaine- homocysteine methyltransferase), GJA4 (gap junction protein, alpha 4, 37 kDa), SLC25A4 (solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 4), ACLY (ATP citrate lyase), ALOX5AP (arachidonate 5-lipoxygenase-activating protein), NUMA1 (nuclear mitotic apparatus protein 1), CYP27B1 (cytochrome P450, family 27, subfamily B, polypeptide 1), CYSLTR2 (cysteinyl leukotriene receptor 2), SOD3 (superoxide dismutase 3, extracellular), LTC4S (leukotriene C4 synthase), UCN (urocortin), GHRL (ghrelin/obestatin prepropeptide), APOC2 (apolipoprotein C-II), CLEC4A (C-type lectin domain family 4, member A), KBTBD10 (kelch repeat and BTB (POZ) domain containing 10), TNC (tenascin C), TYMS (thymidylate synthetase), SHCI (SHC (Src homology 2 domain containing) transforming protein 1), LRP1 (low density lipoprotein receptor-related protein 1), SOCS3 (suppressor of cytokine signaling 3), ADH1B (alcohol dehydrogenase IB (class I), beta polypeptide), KLK3 (kallikrein- related peptidase 3), HSD11B1 (hydroxysteroid (11 -beta) dehydrogenase 1), VKORC1 (vitamin K epoxide reductase complex, subunit 1), SERPINB2 (serpin peptidase inhibitor, clade B (ovalbumin), member 2), TNS1 (tensin 1), RNF19A (ring finger protein 19A), EPOR (erythropoietin receptor), ITGAM (integrin, alpha M (complement component 3 receptor 3 subunit)), P1TX2 (paired-like homeodomain 2), MAPK7 (mitogen-activated protein kinase 7), FCGR3A (Fc fragment of IgG, low affinity I l la, receptor (CD 16a)), LEPR (leptin receptor), ENG (endoglin), GPX1 (glutathione peroxidase 1), GOT2 (glutamic -oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferase 2)), HRH1 (histamine receptor HI), NR112 (nuclear receptor subfamily 1, group I, member 2), CRH (corticotropin releasing hormone), HTR1A (5- hydroxytryptamine (serotonin) receptor 1A), VDAC1 (voltage-dependent anion channel 1), HPSE (heparanase). SFTPD (surfactant protein D), TAP2 (transporter 2, ATP-binding cassette, sub-family B (MDR/TAP)), RNF123 (ring finger protein 123), PTK2B (PTK2B protein tyrosine kinase 2 beta), NTRK2 (neurotrophic tyrosine kinase, receptor, type 2), IL6R (interleukin 6 receptor), ACHE (acetylcholinesterase (Yt blood group)), GLP1R (glucagon-like peptide 1 receptor), GHR (growth hormone receptor), GSR (glutathione reductase), NQO1 (NAD(P)H dehydrogenase, quinone 1), NR A1 (nuclear receptor subfamily 5, group A, member 1), GJB2 (gap junction protein, beta 2, 26 kDa), SLC9A1 (solute carrier family 9 (sodium/hydrogen exchanger), member 1), MAOA (monoamine oxidase A), PCSK9 (proprotein convertase subtilisin/kexin type 9), FCGR2A (Fc fragment of IgG, low affinity Ila. receptor (CD32)), SERPINF 1 (serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 1). EDN3 (endothelin 3), DHFR (dihydrofolate reductase), GAS6 (growth arrest-specific 6), SMPD1 (sphingomyelin phosphodiesterase 1, acid lysosomal), UCP2 (uncoupling protein 2 (mitochondrial, proton carrier)), TFAP2A (transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)), C4BPA (complement component 4 binding protein, alpha), SERPINF2 (serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2). TYMP (thymidine phosphorylase), ALPP (alkaline phosphatase, placental (Regan isozyme)). CXCR2 (chemokine (C-X-C motif) receptor 2), SLC39A3 (solute carrier family 39 (zinc transporter), member 3). ABCG2 (ATP- binding cassette, sub-family G (WHITE), member 2), ADA (adenosine deaminase), JAK3 (Janus kinase 3), HSPA1A (heat shock 70 kDa protein 1A), FASN (fatty acid synthase), FGF1 (fibroblast growth factor 1 (acidic)), Fll (coagulation factor XI), ATP7A (ATPase, Cu++ transporting, alpha polypeptide), CR1 (complement component (3b/4b) receptor 1 (Knops blood group)), GFAP (glial fibrillary acidic protein), ROCK1 (Rho-associated, coiled-coil containing protein kinase 1). MECP2 (methyl CpG binding protein 2 (Rett syndrome)), MYLK (myosin light chain kinase), BCF1E (butyrylcholinesterase). EIPE (lipase, hormone-sensitive), PRDX5 (peroxiredoxin 5). ADORA1 (adenosine Al receptor), WRN (Werner syndrome, RecQ helicase-like), CXCR3 (chemokine (C-X-C motif) receptor 3), CD81 (CD81 molecule), SMAD7 (SMAD family member 7), LAMC2 (laminin, gamma 2), MAP3K5 (mitogen- activated protein kinase kinase kinase 5), CF1GA (chromogranin A (parathyroid secretory protein 1)), IAPP (islet amyloid polypeptide), RFIO (rhodopsin), ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase 1), PTF1LF1 (parathyroid hormone-like hormone), NRG1 (neuregulin 1), VEGFC (vascular endothelial growth factor C), ENPEP (glutamyl aminopeptidase (aminopeptidase A)), CEBPB (CCAAT/enhancer binding protein (C/EBP), beta), NAGLU (N-acetylglucosaminidase, alpha), F2RL3 (coagulation factor II (thrombin) receptor-like 3), CX3CL1 (chemokine (C-X3-C motif) ligand 1), BDKRB1 (bradykinin receptor Bl), ADAMTS13 (ADAM metallopeptidase w ith thrombospondin type 1 motif, 13), ELANE (elastase, neutrophil expressed), ENPP2 (ectonucleotide pyrophosphatase/phosphodiesterase 2), CISFI (cytokine inducible SF12-containing protein), GAST (gastrin). MYOC (myocilin, trabecular mesh work inducible glucocorticoid response), ATP1A2 (ATPase, Na+/K+ transporting, alpha 2 polypeptide), NF1 (neurofibromin 1), GJB1 (gap junction protein, beta 1, 32 kDa), MEF2A (myocyte enhancer factor 2A), VCL (vinculin), BMPR2 (bone morphogenetic protein receptor, type II (serine/threonine kinase)), TUBB (tubulin, beta), CDC42 (cell division cycle 42 (GTP binding protein, 25 kDa)), KRT18 (keratin 18), F1SF1 (heat shock transcription factor 1), MYB (v-myb myeloblastosis viral oncogene homolog (avian)), PRKAA2 (protein kinase, AMP-activated, alpha 2 catalytic subunit), R0CK2 (Rho-associated, coiled-coil containing protein kinase 2), TFPI (tissue factor pathway inhibitor (lipoprotein- associated coagulation inhibitor)), PRKG1 (protein kinase, cGMP- dependent, type I), BMP2 (bone morphogenetic protein 2), CTNND1 (catenin (cadherin-associated protein), delta 1), CTF1 (cystathionase (cystathionine gamma-lyase)), CTSS (cathepsin S). VAV2 (vav 2 guanine nucleotide exchange factor). NPY2R (neuropeptide Y receptor Y2), IGFBP2 (insulin-like growth factor binding protein 2, 36 kDa), CD28 (CD28 molecule), GSTA1 (glutathione S-transferase alpha 1), PPIA (peptidylprolyl isomerase A (cyclophilin
A)), APOFI (apolipoprotein FI (beta-2- glycoprotein I)), S100A8 (SI 00 calcium binding protein A8), IL11 (interleukin 11), ALOX15 (arachidonate 15 -lipoxygenase), FBLN1 (fibulin 1), NR1F13 (nuclear receptor subfamily 1, group FI, member 3), SCD (stearoyl-CoA desaturase (delta-9-desaturase)), GIP (gastric inhibitory polypeptide). CF1GB (chromogranin B (secretogranin 1)), PRKCB (protein kinase C, beta), SRD A1 (steroid-5 -alpha- reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)), F1SD11B2 (hydroxy steroid (11-beta) dehydrogenase 2), CALCRL (calcitonin receptor-like), GALNT2 (UDP-N- acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)), ANGPTL4 (angiopoietin-like 4), KCNN4 (potassium intennediate/small conductance calcium-activated channel, subfamily N, member 4), PIK3C2A (phosphoinositide-3-kinase, class 2. alpha polypeptide). HBEGF (heparin-binding EGF-like growth factor). CYP7A1 (cytochrome P450, family 7, subfamily A, polypeptide 1), HLA-DRB5 (major histocompatibility complex, class II, DR beta 5), BNIP3 (BCL2/adeno virus E1B 19 kDa interacting protein 3), GCKR (glucokinase (hexokinase 4) regulator), S100A12 (S100 calcium binding protein A 12), PADI4 (peptidyl arginine deaminase, type IV), HSPA14 (heat shock 70 kDa protein 14), CXCR1 (chemokine (C-X-C motif) receptor 1), H19 (H19, imprinted maternally expressed transcript (non-protein coding)), KRTAP19-3 (keratin associated protein 19-3). insulin. RAC2 (ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)). RYR1 (ryanodine receptor 1 (skeletal)), CLOCK (clock homolog (mouse)), NGFR (nerve growth factor receptor (TNFR superfamily, member 16)), DBH (dopamine beta-hydroxylase (dopamine beta-monooxygenase)), CHRNA4 (cholinergic receptor, nicotinic, alpha 4), CACNA1C (calcium channel, voltage -dependent, L type, alpha 1C subunit), PRKAG2 (protein kinase, AMP-activated, gamma 2 non-catalytic subunit), CHAT (choline acetyltransferase), PTGDS (prostaglandin D2 synthase 21 kDa (brain)). NR1H2 (nuclear receptor subfamily 1. group H. member 2). TEK (TEK tyrosine kinase, endothelial), VEGFB (vascular endothelial growth factor
B), MEF2C (myocyte enhancer factor 2C), MAPKAPK2 (mitogen-activated protein kinase-activated protein kinase 2), TNFRSF11 A (tumor necrosis factor receptor superfamily, member 1 la, NFKB activator), HSPA9 (heat shock 70 kDa protein 9 (mortalin)), CYSLTR1 (cysteinyl leukotriene receptor 1), MAT1A (methionine adenosyltransferase I, alpha), OPRL1 (opiate receptor-like 1), IMPA1 (inositol(myo)-l(or 4) - monophosphatase 1), CLCN2 (chloride channel 2), DLD (dihydrolipoamide dehydrogenase), PSMA6 (proteasome (prosome, macropain) subunit, alpha type, 6), PSMB8 (proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional peptidase 7)), CHI3L1 (chitinase 3-like 1 (cartilage glycoprotein- 39)), ALDH1B1 (aldehyde dehydrogenase 1 family, member Bl). PARP2 (poly (ADP-ribose) polymerase 2). STAR (steroidogenic acute regulatory protein). LBP (lipopolysaccharide binding protein), ABCC6 (ATP- binding cassette, sub-family C(CFTR/MRP), member 6), RGS2 (regulator of G-protein signaling 2, 24 kDa), EFNB2 (ephrin-B2), cystic fibrosis transmembrane conductance regulator (CFTR), GJB6 (gap junction protein, beta 6, 30 kDa), APOA2 (apolipoprotein A-II), AMPD1 (adenosine monophosphate deaminase 1), DYSF (dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive)), FDFT1 (famesyl -diphosphate famesyltransferase 1), EDN2 (endothelin 2), CCR6 (chemokine (C-C motif) receptor 6), GJB3 (gap junction protein, beta 3, 31 kDa), IL1RL1 (interleukin 1 receptor-like 1), ENTPD1 (ectonucleoside triphosphate diphosphohydrolase 1), BBS4 (Bardet-Biedl syndrome 4), CELSR2 (cadherin, EGF LAG seven-pass G-type receptor 2 (flamingo homolog, Drosophila)), FUR (Fll receptor), RAPGEF3 (Rap guanine nucleotide exchange factor (GEF) 3), HYAL1 (hyaluronoglucosaminidase 1), ZNF259 (zinc finger protein 259), ATOX1 (ATX1 antioxidant protein 1 homolog (yeast)), ATF6 (activating transcription factor 6), KHK (ketohexokinase (fructokinase)), SAT1 (spermidine/spermine N1 -acetyltransferase 1), GGFI (gammaglutamyl hydrolase (conjugase, folylpolygammaglutamyl hydrolase)), T1MP4 (T1MP metallopeptidase inhibitor 4), SLC4A4 (solute carrier family 4, sodium bicarbonate cotransporter, member 4), PDE2A (phosphodiesterase 2 A, cGMP- stimulated), PDE3B (phosphodiesterase 3B, cGMP-inhibited), FADS1 (fatty acid desaturase 1), FADS2 (fatty acid desaturase 2), TMSB4X (thymosin beta 4, X-linked), TXNIP (thioredoxin interacting protein), LIMSI (LIM and senescent cell antigen-like domains 1), RFIOB (ras homolog gene family, member B), LY96 (lymphocyte antigen 96), FOXO1 (forkhead box 01), PNPLA2 (patatin-like phospholipase domain containing 2). TRH (thyrotropin-releasing hormone). GJC1 (gap junction protein, gamma 1 , 45 kDa), SLC17A5 (solute carrier family 17 (anion/sugar transporter), member 5), FTO (fat mass and obesity associated), GJD2 (gap junction protein, delta 2, 36 kDa), PSRC 1 (proline/serine-rich coiled-coil 1), CASP12 (caspase 12 (gene/pseudogene)), GPBAR1 (G protein-coupled bile acid receptor 1), PXK (PX domain containing serine/threonine kinase), IL33 (interleukin 33), TRIB1 (tribbles homolog 1 (Drosophila)), PBX4 (pre-B-cell leukemia homeobox 4), NUPR1 (nuclear protein, transcriptional regulator, 1), 15-Sep(15 kDa selenoprotein), C1LP2 (cartilage intermediate layer protein 2). TERC (telomerase RNA component), GGT2 (gamma-glutamyltransf erase 2), MT-CO1 (mitochondrially encoded cytochrome c oxidase I), UOX (urate oxidase, pseudogene), a CRISPR/Cas effector polypeptide, an enzymatically active CRISPR/Cas effector polypeptide (e.g., is capable of cleaving a target nucleic acid) and a CRISPR/Cas effector polypeptide that is not enzymatically active (e.g., does not cleave a target nucleic acid, but retains binding to the target nucleic acid). In some cases, the donor DNA encodes a wild-type version of any of the foregoing polypeptides; i.e., the donor DNA can encode a “normal” version that does not include a mutation(s) that results in reduced function, lack of function, or pathogenesis.
[00478] In some cases, the donor DNA comprises a nucleotide sequence encoding a fluorescent polypeptide. Suitable fluorescent proteins include, but are not limited to, green fluorescent protein (GFP) or variants thereof, blue fluorescent variant of GFP (BFP), cyan fluorescent variant of GFP (CFP), yellow fluorescent variant of GFP (YFP), enhanced GFP (EGFP), enhanced CFP (ECFP), enhanced YFP (EYFP). GFPS65T, Emerald, Topaz (TYFP), Venus, Citrine, mCitrine, GFPuv, destabilized EGFP (dEGFP), destabilized ECFP (dECFP), destabilised EYFP (dEYFP), mCFPm, Cerulean, T-Sapphire, CyPet, YPet, mKO, HcRed, t-HcRed, DsRed, DsRed2, DsRed-monomer, J-Red, dimer2, t-dimer2(12), mRFPl, pocilloporin, Renilla GFP, Monster GFP, paGFP, Kaede protein and kindling protein. Phycobiliproteins and Phycobiliprotein conjugates including B-Phycoerythrin, R-Phycoerythrin and Allophycocyanin. Other examples of fluorescent proteins include mHoneydew. mBanana, mOrange, dTomato. tdTomato, mTangerine. mStrawberry. mCherry, mGrapel, mRaspberry, mGrape2, m PI urn (Shaner et al. (2005) Nat. Methods 2:905-909), and the like. Any of a variety of fluorescent and colored proteins from Anthozoan species, as described in, e.g., Matz et al. (1999) Nature Biotechnol. 17:969-973, can be encoded.
[00479] In some cases, the donor DNA encodes an RNA, e.g., an siRNA, a microRNA, a short hairpin RNA (shRNA), an anti-scnsc RNA, a riboswitch, a ribozyme, an aptamer, a ribosomal RNA, a transfer RNA, and the like.
[00480] A donor DNA can include, in addition to a nucleotide sequence encoding one or more gene products (e.g., an RNA and/or a polypeptide), one or more transcriptional control elements, e.g., a promoter, an enhancer, and the like. In some cases, the transcriptional control element is inducible. In some cases, the promoter is reversible. In some cases, the transcriptional control element is constitutive. In some cases, the promoter is functional in a eukaryotic cell. In some cases, the promoter is a cell type- specific promoter. In some cases, the promoter is a tissue-specific promoter.
[00481] The nucleotide sequence of the donor DNA is typically not identical to the target nucleic acid (e.g., genomic sequence) that it replaces. Rather, the donor DNA may contain at least one or more single base changes, insertions, deletions, inversions or rearrangements with respect to the target nucleic acid (e.g., genomic sequence), so long as sufficient homology is present to support homology-directed repair (e g., for gene correction, e.g., to convert a disease-causing base pair or a non-disease-causing base pair). In some cases, the donor DNA comprises a non-homologous sequence flanked by two regions of homology, such that homology-directed repair between the target DNA region and the two flanking sequences results in insertion of tire non-homologous sequence at the target region. Donor DNA may also comprise a vector backbone containing sequences that are not homologous to the DNA region of interest (the target nucleic acid) and that are not intended for insertion into the DNA region of interest (the target nucleic acid). Generally, the homologous region(s) of a donor sequence will have at least 50% sequence identity to a target nucleic acid (e.g., a genomic sequence) with which recombination is desired. In certain cases. 60%, 70%, 80%, 90%, 95%, 98%, 99%, or 99.9% sequence identity is present. Any value between 1% and 100% sequence identity can be present, depending upon the length of the donor polynucleotide.
[00482] The donor DNA may comprise certain nucleotide sequence differences as compared to the target nucleic acid (e.g., genomic sequence), where such difference include, e.g. restriction sites, nucleotide polymorphisms, selectable markers (e.g., drug resistance genes, fluorescent proteins, enzymes etc.), etc., which may be used to assess for successful insertion of the donor DNA at the cleavage site or in some cases may be used for other purposes (e.g., to signify expression at the targeted genomic locus). In some cases, if located in a coding region, such nucleotide sequence differences will not change the amino acid sequence, or will make silent amino acid changes (i .e ., changes which do not affect the structure or function of the protein). Alternatively, these sequences differences may include flanking recombination sequences such as FLPs, loxP sequences, or the like, that can be activated at a later time for removal of the marker sequence. In some cases, the donor DNA will include one or more nucleotide sequences to aid in localization of the donor to the nucleus of the recipient cell or to aid in the integration of the donor DNA into tire target nucleic acid. For example, in some case, the donor DNA may comprise one or more nucleotide sequences encoding one or more nuclear localization signals (e.g. PKKKRKV (SEQ ID NO:584), VSRKRPRP (SEQ ID NO:2665), QRKRKQ (SEQ ID NO:2587), and the like (Frietas et al (2009) Curr Genomics 10:550-7). In some cases, the donor DNA will include nucleotide sequences to recruit DNA repair enzymes to increase insertion efficiency. Fiuman enzymes involved in homology directed repair include MRN-CtIP, BLM-DNA2. ExoL ERCC1, Rad51, Rad52, Ligase 1, RoIQ. PARP1, Ligase 3, BRCA2. RecQ/BLM-ToroIIIa, RTEL. Roid. and Roih (Verma and Greenburg (2016) Genes Dev. 30 (10): 1138-1154). In some cases, the donor DNA is delivered as reconstituted chromatin (Cruz-Becerra and Kadonaga (2020) eLife 2020;9:e55780 DOI: 10.7554/eLife.55780).
[00483] In some cases, the ends of the donor DNA are protected (e.g., from exonucleolytic degradation) by any convenient method and such methods are known to those of skill in the art. For example, one or more dideoxynucleotide residues can be added to tire 3' terminus of a linear molecule and/or self complementary oligonucleotides can be ligated to one or both ends. See, for example. Chang et al. (1987) Proc. Natl. Acad Sci USA 84:4959-4963; Nehls et al. (1996) Science 272:886-889. Additional methods for protecting exogenous polynucleotides from degradation include, but are not limited to, addition of terminal amino group(s) and the use of modified intemucleotide linkages such as, for example, phosphorothioates, phosphoramidates, and O-methyl ribose or deoxyribose residues. As an alternative to protecting the termini of a linear donor DNA, additional lengths of sequence may be included outside of the regions of homology that can be degraded without impacting recombination.
Linkers
[00484] In some embodiments, the Casl2a polypeptides are coupled to one or more accessory functions by a linker. Such accessory functions can include deaminases, nucleases, reverse transcriptases, and recombinases. One or more gRNAs directed to such promoters or enhancers may also be provided to direct the binding of the Casl2a polypeptide to such promoters or enhancers. The term linker as used in reference to a fusion protein refers to a molecule which joins the proteins to fonn a fusion protein. Generally, such molecules have no specific biological activity other than to join or to preserve some minimum distance or other spatial relationship between the proteins. However, in one embodiment, the linker may be selected to influence some property of the linker and/or the fusion protein such as the folding, net charge, or hydrophobicity of the linker.
[00485] Suitable linkers for use in the methods of the present invention are well known to those of skill in the art and include, but are not limited to, straight or branched-chain carbon linkers, heterocyclic carbon linkers, or peptide linkers. However, as used herein tire linker may also be a covalent bond (carbon-carbon bond or carbon-heteroatom bond). In particular embodiments, the linker is used to separate the Casl2a polypeptide and an accessory protein (e.g., a nucleotide deaminase) by a distance sufficient to ensure that each protein retains its required functional property. Preferred peptide linker sequences adopt a flexible extended conformation and do not exhibit a propensity for developing an ordered secondary structure. In one embodiment, the linker can be a chemical moiety which can be monomeric, dimeric, multimeric or polymeric. Preferably, the linker comprises amino acids. Typical amino acids in flexible linkers include Gly, Asn and Ser.
[00486] Accordingly, in particular embodiments, the linker comprises a combination of one or more of Gly, Asn and Ser amino acids. Other near neutral amino acids, such as Thr and Ala, also may be used in the linker sequence. Exemplary linkers are disclosed in Maratea et al. (1985). Gene 40: 39-46; Murphy et al. (1986) Proc. Nat'L Acad. Sci. USA 83: 8258-62; U.S. Pat. No. 4,935,233; and U.S. Pat. No. 4,751,180. For example, GlySer linkers may be based on repeating units of GGS (SEQ ID NO:2657), i.e., up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or even 12 or more repeating units, including but not limited to:
[00487] In another example, GlySer linkers may be based on repeating units of GSG (SEQ ID NO:2658), i.e., up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or even 12 or more repeating units, including but not limited to: [00488] In yet another example, GlySer linkers may be based on repeating units of GGGS (SEQ ID
NO:2659), i.e., up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or even 12 or more repeating units, including but not limited to:
[00489] In still another example, GlySer linkers may be based on repeating units of GGGGS (SEQ ID NO:2660), i.e., up to 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or even 12 or more repeating units, including but not limited to:
[00490] In yet a further embodiment, LEPGEKPYKCPECGKSFSQSGALTRHQRTHTR (SEQ ID NO:662) is used as a linker.
[00491] In yet an additional embodiment, the linker is an XTEN linker, which is TCGGGATCTGAGACGCCTGGGACCTCGGAATCGGCTACGCCCGAAAGT (SEQ ID NO:663). In particular embodiments, the Cast 2a polypeptide is linked to the deaminase protein or its catalytic domain by means of an LEPGEKPYKCPECGKSFSQSGALTRHQRTHTRLEPGEKPYKCPECGKSFSQSGALT RHQRTHTR (SEQ ID NO:664) linker. In further particular embodiments, Casl2a polypeptide is linked C- terminally to the N-terminus of a deaminase protein or its catalytic domain by means of an LEPGEKPYKCPECGKSFSQSGALTRHQRTHTRLEPGEKPYKCPECGKSFSQSGALTRHQRTHTRLEP GEKPYKCPECGKSFSQSGALTRHQRTHTR (SEQ ID NO:665) linker. In addition, N-and C-terminal NLSs can also function as linker (e.g., PKKKRKVEASSPKKRKVEAS (SEQ ID NO:666)).
[00492] The above description of linkers is intended to be non-limiting and includes any combinations of the above linkers or heterologous combinations of repeating GlySer linkers.
[00493] The linker may be as simple as a covalent bond, or it may be a polymeric linker many atoms in length. In certain embodiments, the linker is a polypeptide or based on amino acids. In other embodiments, the linker is not peptide-like. In certain embodiments, the linker is a covalent bond (e.g., a carbon-carbon bond, disulfide bond, carbon-heteroatom bond, etc.). In certain embodiments, the linker is a carbon-nitrogen bond of an amide linkage. In certain embodiments, the linker is a cyclic or acyclic, substituted or unsubstituted, branched or unbranched aliphatic or heteroaliphatic linker. In certain embodiments, the linker is polymeric (e.g., polyethylene, polyethylene glycol, polyamide, polyester, etc ). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminoalkanoic acid. In certain embodiments, the linker comprises an aminoalkanoic acid (e.g., glycine, ethanoic acid, alanine, beta-alanine, 3 -aminopropanoic acid, 4-aminobutanoic acid, 5-pentanoic acid, etc.). In certain embodiments, the linker comprises a monomer, dimer, or polymer of aminoHEXAnoic acid (Ahx). In certain embodiments, the linker is based on a carbocyclic moiety (e.g., cyclopentane, cycloHEXAne). In other embodiments, the linker comprises a polyethylene glycol moiety (PEG). In other embodiments, the linker comprises amino acids. In certain embodiments, the linker comprises a peptide. In certain embodiments, the linker comprises an aryl or heteroaryl moiety. In certain embodiments, the linker is based on a phenyl ring. The linker may included functionalized moieties to facilitate attachment of a nucleophile (e.g., thiol, amino) from the peptide to the linker. Any electrophile may be used as part of the linker. Exemplary electrophiles include, but are not limited to, activated esters, activated amides, Michael acceptors, alkyl halides, aryl halides, acyl halides, and isothiocyanates.
[00494] Tire linker can be, for example, a cleavable linker or protease-sensitive linker. In some embodiments, the linker is selected from the group consisting of F2A linker, P2A linker, T2A linker, E2A linker, and combinations thereof. This family of self-cleaving peptide linkers, referred to as 2A peptides, has been described in the art (see for example, Kim, J. H. et al. (2011) PLoS ONE 6:el8556). In some embodiments, the linker is an F2A linker. In some embodiments, the linker is a GGGS linker (SEQ ID NO:632). In some embodiments, the fusion protein contains three domains with intervening linkers, having tire structure: domain-linker-domain-linker-domain.
[00495] Cleavable linkers known in the art may be used in connection with the disclosure. Exemplary such linkers include: F2A linkers, T2A linkers, P2A linkers, E2A linkers (See. e.g., WO2017127750). Tire skilled artisan will appreciate that other art-recognized linkers may be suitable for use in the constructs of the disclosure (e.g., encoded by the nucleic acids of the disclosure). The skilled artisan will likewise appreciate that other polycistronic constructs (mRNA encoding more than one nucleobase editing system componcnt/polypcptidc separately within the same molecule) may be suitable for use as provided herein.
Nuclear localization domains
[00496] In various embodiments, the gene editing systems or any of the components thereof may fused to one or more nuclear localization sequences (NLSs), such as about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10. or more NLSs. In one embodiment, a gene editor component (e.g., a nucleic acid programmable DNA binding protein or an editing accessory protein) comprises about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the amino-terminus, about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near tire carboxy-terminus, or a combination of these (e.g., zero or at least one or more NLS at the amino-terminus and zero or at one or more NLS at the carboxy terminus). When more than one NLS is present, each may be selected independently of the others, such that a single NLS may be present in more than one copy and/or in combination with one or more other NLSs present in one or more copies. In an embodiment of the invention, an editor component polypeptide comprises at most 6 NLSs. In one embodiment, an NLS is considered near the N- or C-terminus when the nearest amino acid of tire NLS is within about 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50, or more amino acids along the polypeptide chain from the N- or C-terminus. Nonlimiting examples of NLSs include an NLS sequence derived from: the NLS of the SV40 virus large T-antigen, having the amino acid sequence PKKKRKV (SEQ ID NO:584); the NLS from nucleoplasmin (e.g. the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ ID NO:667); the c-myc NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO:668) or RQRRNELKRSP (SEQ ID NO: 669): the hRNPAl M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO:670); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO:671) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO:2501) and PPKKARED (SEQ ID NO:672) of the myoma T protein; the sequence PQPKKKPL (SEQ ID NO:673) of human p53; the sequence SALIKKKKKMAP (SEQ ID NO:674) of mouse c-abl IV; the sequences DRLRR (SEQ ID NO:675) and PKQKKRK (SEQ ID NO:676) of the influenza virus NS 1 ; the sequence RKLKKKIKKL (SEQ ID NO:677) of the Hepatitis virus delta antigen; the sequence REKKKFLKRR (SEQ ID NO:678) of the mouse Mxl protein; the sequence KRKGDEVDGVDEVAKKKSKK (SEQ ID NO:679) of the human poly(ADP-ribose) polymerase; and the sequence RI<CLQAGMNLEARI<TI<I< (SEQ ID NO:2655) of the steroid hormone receptors (human) glucocorticoid.
[00497] In general, the one or more NLSs are of sufficient strength to drive accumulation of the Cast 2a polypeptide (or an NLS-modified accessory protein, or an NLS-modified chimera comprising a Casl2a protein and an accessory protein) in a detectable amount in the nucleus of a eukaryotic cell. In general, strength of nuclear localization activity may derive from the number of NLSs in tire Cast 2a polypeptide, the particular NLS(s) used, or a combination of these factors. Detection of accumulation in the nucleus may be performed by any suitable technique.
[00498] For example, a detectable marker may be fused to the Casl2a polypeptide, such that location within a cell may be visualized, such as in combination with a means for detecting the location of the nucleus (e.g., a stain specific for the nucleus such as DAPI). Cell nuclei may also be isolated from cells, the contents of which may then be analyzed by any suitable process for detecting protein, such as immunohistochemistry’, Western blot, or enzyme activity assay. Accumulation in the nucleus may also be determined indirectly, such as by an assay for the effect of complex fonnation (e.g., assay for DNA cleavage or mutation at the target sequence, or assay for altered gene expression activity affected by complex formation and/or Casl2a polypeptide activity ), as compared to a control no exposed to the Casl2a polypeptide or complex, or exposed to a Cas 12a polypeptide lacking the one or more NLSs. In one embodiment of the herein described Casl2a polypeptide protein complexes and systems the codon optimized Cas 12a polypeptide proteins comprise an NLS attached to the C-tenninal of the protein. In one embodiment, other localization tags may be fused to the Cas 12a polypeptide, such as without limitation for localizing the Casl2a polypeptide to particular sites in a cell, such as organelles, such as mitochondria, plastids, chloroplast, vesicles, golgi, (nuclear or cellular) membranes, ribosomes, nucleolus, ER, cytoskeleton, vacuoles, centrosome, nucleosome, granules, centrioles, etc.
[00499] In one embodiment of the invention, at least one nuclear localization signal (NLS) is attached to the nucleic acid sequences encoding the Cas 12a polypeptide. In preferred embodiments at least one or more C- terminal or N-terminal NLSs are attached (and hence nucleic acid molecule(s) coding for the Cas 12a polypeptide can include coding for NLS(s) so that the expressed product has the NLS(s) attached or connected). In a preferred embodiment a C-terminal NLS is attached for optimal expression and nuclear targeting in eukaryotic cells, preferably human cells. The invention also encompasses methods for delivering multiple nucleic acid components, wherein each nucleic acid component is specific for a different target locus of interest thereby modifying multiple target loci of interest. The nucleic acid component of the complex may comprise one or more protein-binding RNA aptamers. The one or more aptamers may be capable of binding a bacteriophage coat protein.
[00500] In other examples, the fusion proteins comprising Cas 12a and another accessory protein (e.g., RT) contains one or more nuclear localization signals is selected or derived from SV40. c-Myc or NLP-1.
[00501] Tire NLS examples above are non-limiting. The Cas 12a fusion proteins contemplated herein may comprise any known NLS sequence, including any of those described in Cokol et al. /'Finding nuclear localization signals,” EMBO Rep., 2000, 1(5): 411-415 and Freitas et al. /‘Mechanisms and Signals for the Nuclear Import of Proteins,” Current Genomics, 2009, 10(8): 550-7, each of which are incorporated herein by reference.
Tag domains
[00502] In some embodiments, Cas 12a editing system or a component thereof may comprise a polypeptide tag, such as an affinity tag (chitin binding protein (CBP), maltose binding protein (MBP), glutathione-S- transferase (GST), SBP-tag, Strep-tag, AviTag. Calmodulm-tag): solubilization tag; chromatography tag (polyanionic amino acid tag, such as FLAG-tag); epitope tag (short peptide sequences that bind to high- affmity antibodies, such as V5-tag, Myc-tag, VSV-tag, Xpress tag, E-tag, S-tag, and HA-tag); fluorescence tag (e.g., GFP). In some embodiments, the Cas 12a editing system peptide may comprise an amino acid tag, such as one or more lysines, histidines, or glutamates, which can be added to the polypeptide sequences (e.g., at the N-terminal or C-tenninal ends). Lysines can be used to increase peptide solubility or to allow for biotinylation. Protein and amino acid tags are peptide sequences genetically grafted onto a recombinant protein. Sequence tags are attached to proteins for various purposes, such as peptide purification, identification, or localization, for use in various applications including, for example, affinity purification, protein array, western blotting, immunofluorescence, and immunoprecipitation. Such tags are subsequently removable by chemical agents or by enzymatic means, such as by specific proteolysis or intein splicing.
[00503] Alternatively, amino acid residues located at the carboxy and amino terminal regions of the amino acid sequence of a peptide or protein may optionally be deleted providing for truncated sequences. Certain amino acids (e.g., C-terminal or N -terminal residues) may alternatively be deleted depending on the use of the sequence, as for example, expression of the sequence as part of a larger sequence which is soluble, or linked to a solid support.
Aptamers
[00504] In particular embodiments, the nucleic acid components (e.g., guide RNA) of the Casl2a editing systems may further comprise a functional structure designed to improve nucleic acid component molecule structure, architecture, stability, genetic expression, or any combination thereof. Such a structure can include an aptamer.
[00505] Aptamers are biomolecules that can be designed or selected to bind tightly to other ligands, for example using a technique called systematic evolution of ligands by exponential enrichment (SELEX; Tuerk
C, Gold L: ‘‘Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.” Science 1990, 249:505-510). Nucleic acid aptamers can for example be selected from pools of random-sequence oligonucleotides, with high binding affinities and specificities for a wide range of biomedically relevant targets, suggesting a wide range of therapeutic utilities for aptamers (Keefe, Anthony
D., Supriya Pai, and Andrew Ellington. "Aptamers as therapeutics." Nature Reviews Drug Discovery 9.7 (2010): 537-550). These characteristics also suggest a wide range of uses for aptamers as drug deliveryvehicles (Levy-Nissenbaum, Etgar, et al. "Nanotechnology and aptamers: applications in drug delivery." Trends in biotechnology 26.8 (2008): 442-449; and, Hicke BJ, Stephens AW. “Escort aptamers: a delivery service for diagnosis and therapy.” J Clin Invest 2000, 106:923-928.). Aptamers may also be constructed that function as molecular switches, responding to a que by changing properties, such as RNA aptamers that bind fluorophores to mimic the activity of green fluorescent protein (Paige, Jeremy S., Karen Y. Wu, and Sarnie R. Jaffrey. "RNA mimics of green fluorescent protein." Science 333.6042 (2011): 642-646). It has also been suggested that aptamers may be used as components of targeted siRNA therapeutic delivery systems, for example targeting cell surface proteins (Zhou, Jiehua, and John J. Rossi. "Aptamer-targeted cell-specific RNA interference." Silence 1.1 (2010): 4).
[00506] Accordingly, in particular embodiments, a Casl2a gene editing nucleic acid component is modified, e.g., by one or more aptamer(s) designed to improve RNA or DNA component molecule delivery', including delivery across the cellular membrane, to intracellular compartments, or into the nucleus. Such a structure can include, either in addition to the one or more aptamer(s) or without such one or more aptamer(s), moiety(ies) so as to render the nucleic acid component molecule deliverable, inducible or responsive to a selected effector. Tire invention accordingly comprehends a reRNA component molecule that responds to normal or pathological physiological conditions, including without limitation pH, hypoxia, oxygen concentration, temperature, protein concentration, enzymatic concentration, lipid structure, light exposure, mechanical disruption (e.g. ultrasound waves), magnetic fields, electric fields, or electromagnetic radiation.
Agents that modulate DNA-repair
[00507] In certain embodiments, the engineered Casl2a gene editing systems described herein (e.g., an engineered nucleic acid construct or engineered nucleic acid-enzyme construct described herein) further comprises or encodes a DNA-repair modulating biomolecule, which may further enhance the efficiency of integration of a transgene on the heterologous nucleic acid by homology dependent repair (HDR).
[00508] In certain embodiments, the DNA-repair modulating biomolecule comprises a Nonhomologous end joining (NHEJ) inhibitor.
[00509] In certain embodiments, the DNA-repair modulating biomolecule comprises a homologous directed repair (HDR) promoter.
[00510] In certain embodiments, the DNA-repair modulating biomolcculc comprises a NHEJ inhibitor and an HDR promoter.
[00511] In certain embodiments, the DNA-repair modulating biomolecule enhances or improves more precise genome editing and/or the efficiency of homologous recombination, compared to the otherwise identical embodiment without the DNA-repair modulating biomolecule.
[00512] HDR promoters and/or NHEJ inhibitors can, in some embodiments, comprise one or more small molecules. Systems bearing recombination enhancers such as small molecules that activate HDR and suppress NHEJ locally at the genomic site of the DNA damage can be tailored in their placement on the engineered systems to further enhance their efficiency. In general, the small molecule recombination enhancers can be synthesized to bear linkers and a functional group, such as maleimide for reacting with a thiol group on a Cys residue of a protein, for chemical conjugation to the engineered systems. Use of commercially available functionalized PEG linkers (alkyne, azide, cyclooctyne etc.) can also be employed for conjugation, and orthogonal conjugation chemistries can be utilized for the multivalent display.
[00513] Conjugation sites can be readily identified where modifications do not affect the potency of the recombination enhancers selected. [00514] In certain embodiments, multivalent display of one or more DNA-repair modulating biomolecule can be effected, including multiple moieties of NHEJ inhibitors, HDR promoters, or a combination thereof. See, for example, “Genomic targeting of epigenetic probes using a chemically tailored Cas9 system” by Liszczak et al., Proc Natl Acad Set U.S.A. 114: 681-686, 2017 (incorporated herein by reference). In certain embodiments, multivalent display of small molecule compounds can be achieved through sortase loop proteins used as a scaffold for their display.
[00515] In some embodiments, the DNA-repair modulating biomolecule may comprise an HDR promoter. Tire HDR promoter may comprise small molecules, such as RSI or analogs thereof. In certain embodiments, the HDR promoter stimulates RAD51 activity or RAD52 motif protein 1 (RDM1) activity. In certain embodiments, the HDR promoter comprises Nocodazole, which can result in higher HDR selection.
[00516] In certain embodiments, the HDR promoter may be administered prior to the delivery of the engineered Type V systems described herein.
[00517] In certain embodiments, the HDR promoter locally enhances HDR without NHEJ inhibition. For example, RAD51 is a protein involved in strand exchange and tire search for homology regions during HDR repair. In certain embodiments, tire HDR promoter is phenylbenzamide RSI, identified as a small-molecule RAD51 -stimulator (see WO2019/135816 at [0200]-[0204], specifically incorporated herein by reference).
[00518] In certain embodiments, the DNA-repair modulating biomolcculc comprises C-tcrminal binding protein interacting protein (CtIP) or a functional fragment or homolog thereof. CtIP is a key protein in early steps of homologous recombination. According to this embodiment, the CtIP or tire functional fragment or homolog thereof can be linked (e.g., fused) to the RT or the sequence-specific nuclease (e.g., a CRISPR/Cas effector enzyme, a ZFN, a TALEN, a meganuclease, TnpB, IscB, or a restriction endonuclease (RE)), and stimulates transgene integration by HDR.
[00519] In certain embodiments, the CtIP fragment is a minimal N-terminal fragment of the wild-type CtIP, such as the N-terminal fragment comprising residues 1-296 of the full-length CtIP (the HE for HDR enhancer), as described in Charpentier et al. (Nature Comm., DOI: 10.1038/s41467-018-03475-7, incorporated herein by reference), shown to be sufficient to stimulate HDR. The activity of the fragment depends on CDK phosphorylation sites (e.g., S233. T245, and S276) and the multimerization domain essential for CtIP activity in homologous recombination. Thus alternative fragments comprising the CDK phosphorylation sites and the multimerization domain essential for CtIP activity are also within tire scope of the invention. [00520] In certain embodiments, the DNA-repair modulating biomolecule comprises a dominant negative 53BP1.
[00521] In certain embodiments, the DNA-repair modulating biomolecule comprises a cell cycle-specific degradation tag, such as the degradation domain of the (human) Geminin, and the (murine) CyclinB2.
[00522] In certain embodiments, the DNA-repair modulating biomolecule comprises CyclinB2, a member of the B-type cyclins that associate with p34cdc2, and an essential component of the cell cycle regulatory machinery. CRISPR-mediated knock-in efficiency may be increased by promoting the relative increase in Cas9 activity in G2 phase of the cell cycle, when HDR is more active. In certain embodiments, the degradation domains of the (human) Geminin and (murine) CyclinB2 can be used as either N- or C-terminal fusion to serve as the DNA-repair modulating biomolecule. These domains are known to determine a cellcycle specific profile of chimeric proteins, namely an increase in their relative concentration in S and G2 compared to Gl, high-jacking the conventional CyclinB2 and Geminin degradation pathways. This produces active Geminin-Cas9 and CyclinB2-Cas9 chimeric proteins, which are degraded in a cell-cycle-dependent manner. Such chimeras shift the repair of the DSBs to tire HDR repair pathway compared to the commonly used Cas9.
[00523] While not wishing to be bound by particular theory, it is believed that the application of such cell cycle -specific degradation tags permits / promotes more efficient / secure gene editing.
[00524] In certain embodiments, tire DNA-repair modulating biomolecule comprises a Rad family member protein, such as Rad50, Rad51, Rad52, etc., which functions to promote foreign DNA integration into a host chromosome. Specifically, Rad52 is an important homologous recombinant protein, and its complex with Rad51 plays a key role in HDR, mainly involved in the regulation of foreign DNA in eukaryotes. Key steps in the process of HR include repair mediated by Rad51 and strand exchange. Co-expression of Rad52 as a DNA-repair modulating biomolecule significantly enhances the likelihood of HDR by, e.g., three-fold.
[00525] In certain embodiments, the DNA-repair modulating biomolecule comprises a RAD52 protein as, e.g., either an N- or a C-terminal fusion.
[00526] In certain embodiments, the DNA-repair modulating biomolecule comprises a RAD52 motif protein 1 (RDM1) that functions similarly as RAD52. RDM1 has been shown to be able to repair DSBs caused by DNA replication, prevent G2 or M cell cycle arrest, and improve HDR selection.
[00527] In certain embodiments, tire DNA-repair modulating biomolecule comprises a dominant negative version of the tumor suppressor p53-binding protein 1 (53BP1). The wild-type protein 53BP1 is a key regulator of the choice between NHEJ and HDR - it is a pro-NHEJ factor which limits HDR by blocking DNA end resection, and also by inhibiting BRCA 1 recruitment to DSB sites. It has been shown that global inhibition of 53BP1 by a ubiquitin variant significantly improves Cas9-mediated HDR frequency in non- hematopoietic and hematopoietic cells with single-strand oligonucleotide delivery or double-strand donor in AAV.
[00528] In certain embodiments, the dominant negative (DN) version of the 53BP1 comprises the minimal focus forming region, but lacks domains outside this region, e.g., towards the N-terminus and tandem C- terminal BRCT repeats that recruit key effectors involved in NHEJ, such as RIF1-PTIP and EXPAND, respectively. The 53BP1 adapter protein is recruited to specific histone marks at sites of DSBs via this minimal focus forming region, which comprises several conserved domains including an oligomerization domain (OD), a glycine-arginine rich (GAR) motif, a Tudor domain, and an adjacent ubiquitin-dependent recruitment (UDR) motif. The Tudor domain mediates interactions with histone H4 dimethylated at K2023.
[00529] In certain embodiments, a dominant negative version of 53BP 1 (DN 1 S) suppresses the accumulation of endogenous 53BP1 and downstream NHEJ proteins at sites of DNA damage, while upregulating the recruitment of the BRCA1 HDR protein. Such a DN version of the 53BP1 can be used as the DNA-repair modulating biomolecule, either as an N- or a C-terminal fusion (such as a Cas9 fusion, to locally inhibit NHEJ at the Cas9-target site defined by its gRNA, while promoting an increase in HDR, and does not globally affect NHEJ, thereby improving cell viability).
[00530] In certain embodiments, the DNA-repair modulating biomolecule comprises an NHEJ inhibitor, such as an inhibitor of DNA ligase IV, a KU inhibitor (e.g., KU70 or KU80), a DNA-PKc inhibitor, or an artemis inhibitor.
[00531] In certain embodiments, the NHEJ inhibitor inhibits the NHEJ pathway, enhances HDR, or modulates both. In certain embodiments, the NHEJ inhibitor is a small molecule inhibitor.
[00532] In certain embodiments, the small molecule inhibitor of the NHEJ pathway comprises an SCR7 analog, for example, PK66, PK76, PK409.
[00533] In certain embodiments, the NHEJ inhibitor comprises a KU inhibitor, for example, KU5788, and KU0060648.
[00534] In certain embodiments, a small molecule NHEJ inhibitor is linked to a polyglycine tripeptide through PEG for sortase-mediated ligation, as described in WO2019/135816, Guimaraes et al., Nat Protoc 8: 1787-99, 2013; Theile et al., Nat Protoc 8: 1800-7, 2013; and Schmohl et al., Curr Opin Chem Biol 22: 122- 8. 2014 (all incorporated herein by reference). The same means can also be used for attaching small molecule HDR enhancers to protein. [00535] An exemplary method for conjugating a small molecule DNA-repair modulating biomolecule without loss of activity is described in WO2019135816, where SCR-7 conjugation of a poly-glycine peptide with the para-carboxylic moiety at ring 4 retained activity of the inhibitor, with rings 1, 2 and 3 of the molecule having involvement in tire target-engagement, providing a simple and effective strategy to ligate a small molecule NHEJ inhibitor to the system described herein (e.g., to the sequence-specific nuclease including Cas enzymes, or to the RT) to precisely enhance HDR pathway near a nucleic acid target site.
[00536] In certain embodiments, a nucleic acid targeting moiety conjugates based on small molecule inhibitor of DNA-dependent protein kinase (DNA-PK) or heterodimeric Ku (KU70/KU80) can be utilized. KU- 0060648 is one potent KU-inhibitors, which can also be functionalized with poly-glycine and used for recombination enhancement.
[00537] In certain embodiments, the DNA-repair modulating biomolecule comprises the Tumor Suppressor p53. p53 plays a direct role in DNA repair, including HR regulation, where it affects the extension of new DNA, thereby affecting HDR selection. In vivo, p53 binds to the nuclear matrix and is a rate-limiting factor in repairing DNA structure. p53 regulates DNA repair processes in almost all eukaryotes via transactivationdependent and -independent pathways, but only the transactivation-independent function of p53 is involved in HR regulation. Wild-type p53 protein can link double stranded breaks to form intact DNA. as well as also playing a role in inhibiting NHEJ. p53 interacts with HR -related proteins, including Rad51 , where it controls HR through direct interaction with Rad51.
Accessory domains
[00538] In other aspects, the Casl2a-based gene editing systems may comprise one or more additional accessory proteins having genome modifying functions, including recombinases, invertases, nucleases, polymerases, ligases, deaminases, reverse transcriptases, or epigenetic modifying functions. In various embodiments, the accessory proteins may be provided separately. In other embodiments, the accessory proteins may be fused to Cas 12a, optionally with a linker.
[00539] The Casl2a-based gene editing systems may further comprise additional polypeptides polypeptides, proteins and/or peptides known in the art. Non-limiting categories of polypeptides include antigens, antibodies, antibody fragments, cytokines, peptides, hormones, enzymes, oxidants, antioxidants, synthetic polypeptides, and chimeric polypeptides, receptor, enzymes, hormones, transcription factors, ligands, membrane transporters, structural proteins, nucleases, or a component, variant or fragment (e g., a biologically active fragment) thereof.
[00540] As used herein, the tenn “peptide” generally refers to shorter polypeptides of about 50 amino acids or less. Peptides with only two amino acids may be referred to as “dipeptides.” Peptides with only three amino acids may be referred to as ’‘tripeptides.” Polypeptides generally refer to polypeptides with from about 4 to about 50 amino acids. Peptides may be obtained via any method known to those skilled in the art. In some embodiments, peptides may be expressed in culture. In some embodiments, peptides may be obtained via chemical synthesis (e.g., solid phase peptide synthesis).
[00541] In some embodiments, the RNA payloads (e.g., linear and/or circular mRNA payloads encoding one or more encoded products of interest or tire non-coding RNAs such as guide RNAs) may encode a user- programmable DNA binding protein, or a gene editor accessory- proteins, such as, but not limited to a deaminases, nucleases, transposases, polymerases, and reverse transcriptases, etc.
[00542] In some embodiments, the RNA payloads (e.g.. linear and/or circular mRNA payloads encoding one or more encoded products of interest), e.g., the originator constructs and benchmark constructs described herein, may encode a simple protein associated with a non-protein. Non-limiting examples of conjugated proteins include, glycoproteins, hemoglobins, lecithoproteins, nucleoproteins, and phosphoproteins.
[00543] In some embodiments, the RNA payloads (e.g., linear and/or circular mRNA payloads encoding one or more encoded products of interest), e.g., the originator constructs and benchmark constructs described herein, may encode a protein that is derived from a simple or conjugated protein by chemical or physical means. Non-limiting examples of derived proteins include denatured proteins and peptides.
[00544] In some embodiments, the polypeptide, protein or peptide may be unmodified.
[00545] In some embodiments, the polypeptide, protein or peptide may be modified. Types of modifications include, but are not limited to, phosphorylation, glycosylation, acetylation, ubiquity lation/sumoylation, methylation, palmitoylation, quinone, amidation, myristoylation, pyrrolidone carboxylic acid, hydroxylation, phosphopantetheine, prenylation, GPI anchoring, oxidation, ADP-ribosylation, sulfation, S-nitrosylation. citrullination, nitration, gamma-carboxyglutamic acid, formylation, hypusine, topaquinone (TPQ), bromination, lysine topaquinone (LTQ), tryptophan tryptophylquinone (TTQ), iodination, and cysteine tryptophylquinone (CTQ). In some aspects, the polypeptide, protein or peptide may be modified by a post- transcriptional modification which can affect its structure, subcellular localization, and/or function.
[00546] In some embodiments, the polypeptide, protein or peptide may be modified using phosphory lation. Phosphorylation, or tire addition of a phosphate group to serine, threonine, or ty rosine residues, is one of most common forms of protein modification. Protein phosphorylation plays an important role in fine tuning the signal in the intracellular signaling cascades.
[00547] In some embodiments, the polypeptide, protein or peptide may be modified using ubiquitination which is the covalent attachment of ubiquitin to target proteins. Ubiquitination-mediated protein turnover has been shown to play a role in driving the cell cycle as well as in protein-degradation-independent intracellular signaling pathways.
[00548] In some embodiments, the polypeptide, protein or peptide may be modified using acetylation and methylation which can play a role in regulating gene expression. As a non-limiting example, the acetylation and methylation could mediate the formation of chromatin domains (e.g., euchromatin and heterochromatin) which could have an impact on mediating gene silencing.
[00549] In some embodiments, the polypeptide, protein or peptide may be modified using glycosylation.
Glycosylation is tire attachment of one of a large number of glycan groups and is a modification that occurs in about half of all proteins and plays a role in biological processes including, but not limited to. embryonic development, cell division, and regulation of protein structure. The two main types of protein glycosylation are N-glycosylation and O-glycosylation. For N-glycosylation the glycan is attached to an asparagine and for O-glycosylation the glycan is attached to a serine or threonine.
[00550] In some embodiments, the polypeptide, protein or peptide may be modified using sumoylation. Sumoylation is the addition of SUMOs (small ubiquitin-like modifiers) to proteins and is a post-translational modification similar to ubiquitination.
[00551] In other embodiments, the RNA payloads (e.g., linear and/or circular mRNA payloads encoding one or more encoded products of interest), e.g., the originator constructs and benchmark constructs described herein, may encode a therapeutic protein, such as those exemplified below.
[00552] In other embodiments, the RNA payloads (e.g., linear and/or circular mRNA payloads encoding one or more products of interest), e.g., tire originator constructs and benchmark constructs described herein, may encode a gene editing system, such as those exemplified herein. As used herein, a "nucleobase editing system” is a protein, DNA, or RNA composition capable of making edits, modifications or alterations to one or more targeted genes of interest. According to the present invention, one or more nucleobase editing system currently being marketed or in development may be encoded by the RNA payloads (e.g., linear and/or circular mRNA payloads encoding one or more encoded products of interest) described herein of the present invention.
Inducibility modifications
[00553] In one embodiment, a Cast 2a polypeptide may form a component of an inducible gene editing system. The inducible nature of the system would allow for spatiotemporal control of gene editing or gene expression using a form of energy. The form of energy may include but is not limited to electromagnetic radiation, sound energy, chemical energy and thermal energy. Examples of inducible system include tetracycline inducible promoters (Tet-On or Tet-Off), small molecule two-hybrid transcription activations systems (FKBP, ABA, etc.), or light inducible systems (Phytochrome, LOV domains, or cryptochrome). In one embodiment, the Cast 2a polypeptide may be a part of a Light Inducible Transcriptional Effector (LITE) to direct changes in transcriptional activity in a sequence-specific manner. The components of a light may include a Casl2a polypeptide, a light-responsive cytochrome heterodimer (e.g. from Arabidopsis thaliana), and a transcriptional activation/repression domain. Further examples of inducible DNA binding proteins and methods for their use are provided in US Provisional Application Nos. 61/736,465 and US 61/721,283, and International Patent Publication No. WO 2014/018423 A2 which is hereby incorporated by reference in its entirety.
[00554] Once all copies of a gene in the genome of a cell have been edited, continued expression of the system in that cell is no longer necessary. Indeed, sustained expression would be undesirable in case of off- target effects at unintended genomic sites, etc. Thus time-limited expression would be useful. Inducible expression offers one approach, but in addition Applicants have engineered a self-inactivating system that relies on the use of a non-coding nucleic acid component molecule target sequence within the vector itself. Thus, after expression begins, the system will lead to its own destruction, but before destruction is complete it will have time to edit the genomic copies of the target gene (which, with a normal point mutation in a diploid cell, requires at most two edits). Simply, the self-inactivating system includes additional RNA (e.g., nucleic acid component molecule) that targets the coding sequence for the Cas 12a polypeptide itself or that targets one or more non-coding nucleic acid component molecule target sequences complementary to unique sequences present in one or more of the following: (a) within the promoter driving expression of the noncoding RNA elements, (b) within the promoter driving expression of the Cas 12a polypeptide gene, (c) within 100 bp of the ATG translational start codon in the Cas 12a polypeptide coding sequence, (d) within the inverted terminal repeat (iTR) of a viral delivery vector, e.g., in the AAV genome.
[00555] In some aspects, a single nucleic acid component molecule is provided that is capable of hybridization to a sequence downstream of a Cas 12a polypeptide start codon, whereby after a period of time there is a loss of the Cas 12a polypeptide expression. In some aspects, one or more nucleic acid component molecule(s) are provided that are capable of hybridization to one or more coding or non-coding regions of the polynucleotide encoding the system, whereby after a period of time there is a inactivation of one or more, or in some cases all, of the system. In some aspects of the system, and not to be limited by theory, the cell may comprise a plurality of complexes, wherein a first subset of complexes comprise a first nucleic acid component molecule capable of targeting a genomic locus or loci to be edited, and a second subset of complexes comprise at least one second nucleic acid component molecule capable of targeting the polynucleotide encoding the system, wherein the first subset of complexes mediate editing of the targeted genomic locus or loci and the second subset of complexes eventually inactivate the system, thereby inactivating further expression in the cell.
[00556] The various coding sequences (Casl2a polypeptide and nucleic acid component molecule) can be included on a single vector or on multiple vectors. For instance, it is possible to encode the enzyme on one vector and the various RNA sequences on another vector, or to encode the enzyme and one nucleic acid component molecule on one vector, and tire remaining nucleic acid component molecule on another vector, or any other permutation. In general, a system using a total of one or two different vectors is preferred.
Optional editing system formats
[00557] In various embodiments, the Casl2a-based gene editing systems may comprise one or more additional accessory proteins having genome modifying functions, including recombinases, invertases, nucleases, polymerases, ligases, deaminases, reverse transcriptases, or epigenetic modifying functions. In various embodiments, the accessory proteins may be provided separately. In other embodiments, the accessory proteins may be fused to Casl2a, optionally with a linker.
Cast 2a (Cas Type V) base editor fonnat
[00558] In some embodiments, the Casl2a-based gene editing system is combined with one or more deaminases to produce a base editor. In some embodiments, the deaminase is fused, optionally via a linker, to a component of the Casl2a-based gene editing system. For example, the deaminase might be coupled or fused to a Cas 12a domain via a linker.
[00559] Base editing was first described in Komor et al., ‘'Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage,” Nature, May 19, 2016, 533 (7603); pp. 420-424 in the form of cytosine base editors or CBEs followed by the disclosure of Gaudelli et al., “Programmable base editing of A-T to G-C in genomic DNA without DNA cleavage,” Nature, Vol. 551, pp. 464-471 describing adenine base editors or ABEs. Subsequently, base editing has been described in numerous scientific publications, including, but not limited to (i) Kim JS. Precision genome engineering through adenine and cytosine base editing. Nat Plants. 2018 Mar;4(3): 148-151. doi: 10.1038/s41477-018-0115-z. Epub 2018 Feb 26. PMID: 29483683.; (ii) Wei Y, Zhang XH, Li DL. The "new favorite" of gene editing technology-single base editors. Yi Chuan. 2017 Dec 20;39(12): 1115-1121. doi: 10.16288/j.yczz. 17-389. PMID: 29258982; (lii) Tang J, Lee T, Sun T. Single -nucleotide editing: From principle, optimization to application. Hum Mutat. 2019 Dec;40(12):2171-2183. doi: 10.1002/humu.23819. Epub 2019 Sep 15. PMID: 31131955; PMCID: PMC6874907; (iv) Griinewald J, Zhou R. Lareau CA, Garcia SP. Iyer S, Miller BR, Langner LM, Hsu JY, Arycc MJ, Joung JK. A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nat Biotechnol. 2020 Jul;38(7):861-864. doi: 10.1038/s41587-020-0535-y. Epub 2020 Jun 1. PMID: 32483364; PMCID: PMC7723518; (v) Sakata RC, Ishiguro S, Mon H, Tanaka M, Tatsuno K, Ueda H, Yamamoto S, Seki M, Masuyama N, Nishida K, Nishimasu H, Arakawa K, Kondo A, Nureki O, Tomita M, Aburatani H, Yachie N. Base editors for simultaneous introduction of C-to-T and A-to-G mutations. Nat Biotechnol. 2020 Jul;38(7):865-869. doi: 10.1038/s41587-020-0509-0. Epub 2020 Jun 2. Erratum in: Nat Biotechnol. 2020 Jun 5:: PMID: 32483365; (vi) Fan J, Ding Y, Ren C, Song Z. Yuan J. Chen Q, Du C. Li C, Wang X, Shu W. Cytosine and adenine deaminase base-editors induce broad and nonspecific changes in gene expression and splicing. Commun Biol. 2021 Jul 16;4(1):882. doi: 10.1038/s42003-021-02406-5. PMID: 34272468; PMCID: PMC8285404; (vii) Zhang S, Yuan B, Cao J, Song L, Chen J, Qiu J, Qiu Z, Zhao XM, Chen J, Cheng TL. TadA orthologs enable both cytosine and adenine editing of base editors. Nat Commun. 2023 Ian 26; 14( 1):414. doi: 10.1038/s41467-023-36003-3. PMID: 36702837; PMCID: PMC988000; and (viii) Zhang S, Song L, Yuan B, Zhang C, Cao J, Chen J, Qiu J, Tai Y, Chen J, Qiu Z, Zhao XM. Cheng TL. TadA reprogramming to generate potent miniature base editors with high precision. Nat Commun. 2023 Jan 26; 14(1):413. doi: 10.1038/s41467-023-36004-2. PMID: 36702845; PMCID: PMC987999, each of which are incorporated herein by reference in their entireties.
[00560] Amino acid and nucleotide sequences of base editors, including adenosine base editors, cytidine base editors, and others are readily available in the art. For example, exemplary base editors that may be delivered using the LNP compositions described herein can be found in the following published patent applications, each of their contents (including any and all biological sequences) are incorporated herein by reference:
US 2023/0021641 Al CAS9 VARIANTS HAVING NON-CANONICAU
PAM SPECIFICITIES AND USES THEREOF
US 11542496 B2 CYTOSINE TO GUANINE BASE EDITOR
US 11542509 B2 INCORPORATION OF UNNATURAL AMINO
ACIDS INTO PROTEINS USING BASE EDITING
US 2022/0315906 Al BASE EDITORS WITH DIVERSIFIED TARGETING SCOPE
US 2022/0282275 Al G-TO-T BASE EDITORS AND USES THEREOF
US 2022/0249697 Al AAV DELIVERY OF NUCLEOBASE EDITORS [00561] Base editing does not require double -stranded DNA breaks or a DNA donor template. In some embodiments, base editing comprises creating an SSB in a target double-stranded DNA sequence and then converting a nucleobase. In some embodiments, the nucleobase conversion is an adenosine to a guanine. In some embodiments, the nucleobase conversion is a thymine to a cytosine. In some embodiments, the nucleobase conversion is a cytosine to a thymine. In some embodiments, the nucleobase conversion is a guanine to an adenosine. In some embodiments, the nucleobase conversion is an adenosine to inosine. In some embodiments, the nucleobase conversion is a cytosine to uracil.
[00562] A base editing system comprises a base editor which can convert a nucleobase. The base editor (“BE”) comprises a partially inactive Cas 12a protein which is connected to a deaminase that precisely and permanently edits a target nucleobase in a polynucleotide sequence. A base editor comprises a polynucleotide programmable nucleotide binding domain and a nucleobase editing domain (e.g., adenosine deaminase or cytosine deaminase). In some embodiments, the partially inactive Cas 12a protein is a Cas 12a nickase. In some embodiments, the partially inactive Cas protein is a Casl2a nickase (also referred to as “nCasl2a”).
[00563] A polynucleotide programmable nucleotide binding domain, when in conjunction with a bound guide polynucleotide (e.g., gRNA), can specifically bind to a target polynucleotide sequence (i.e.. via complementary base pairing between bases of the bound guide nucleobase and bases of the target polynucleotide sequence) and thereby localize the nucleobase editor to the target polynucleotide sequence desired to be edited. In some embodiments, the target polynucleotide sequence comprises single-stranded DNA or double-stranded DNA. In some embodiments, tire target polynucleotide sequence comprises RNA. In some embodiments, the target polynucleotide sequence comprises a DNA-RNA hybrid.
[00564] In certain embodiments, polynucleotide programmable nucleotide binding domains also include nucleobase programmable proteins that bind RNA. In certain embodiments, the polynucleotide programmable nucleotide binding domain can be associated with a nucleobase that guides the polynucleotide programmable nucleotide binding domain to an RNA.
Casl2a (Cas Type V) CBEs
[00565] In some embodiments, the Cas 12a base editors contemplated herein may comprise a deaminase domain that is a cytidine deaminase domain. A cytidine deaminase domain may also be referred to interchangeably as a cytosine deaminase domain. In some embodiments, the cytidine deaminase catalyzes the hydrolytic deamination of cytidine (C) or deoxycytidine (dC) to uridine (U) or deoxyuridine (dU), respectively. In some embodiments, the cytidine deaminase domain catalyzes the hydrolytic deamination of cytosine (C) to uracil (U). In some embodiments, the cytidine deaminase catalyzes the hydrolytic deamination of cytidine or cytosine in deoxyribonucleic acid (DNA). Without wishing to be bound by any particular theory, fusion proteins comprising a cytidine deaminase are useful inter alia for targeted editing, referred to herein as “base editing,” of nucleic acid sequences in vitro and in vivo.
[00566] One exemplary suitable type of cytidine deaminase is a cytidine deaminase, for example, of the APOBEC family. The apolipoprotein B mRNA-editing complex (APOBEC) family of cytidine deaminase enzymes encompasses eleven proteins that serve to initiate mutagenesis in a controlled and beneficial manner (see, e.g., Conticello S G. The AID/APOBEC family of nucleic acid mutators. Genome Biol. 2008; 9(6):229). One family member, activation-induced cytidine deaminase (AID), is responsible for the maturation of antibodies by converting cytosines in ssDNA to uracils in a transcription-dependent, strand-biased fashion (see, e.g., Reynaud C A, et al. What role for AID: mutator, or assembler of the immunoglobulin mutasome, Nat Immunol. 2003; 4(7):631-638). The apolipoprotein B editing complex 3 (APOBEC3) enzyme provides protection to human cells against a certain HIV-1 strain via the deamination of cytosines in reverse- transcribed viral ssDNA (see, e g., Bhagwat A S. DNA-cytosine deaminases: from antibody maturation to antiviral defense. DNA Repair (Amst). 2004; 3(l):85-89).
[00567] Some aspects of tins disclosure relate to tire recognition that the activity of cytidine deaminase enzymes such as APOBEC enzymes can be directed to a specific site in genomic DNA. Without wishing to be bound by any particular theory, advantages of using a nucleic acid programmable binding protein (e.g., a Cas9 domain) as a recognition agent include (1) the sequence specificity of nucleic acid programmable binding protein (e.g., a Cas9 domain) can be easily altered by simply changing the sgRNA sequence; and (2) the nucleic acid programmable binding protein (e.g., a Cas9 domain) may bind to its target sequence by denaturing the dsDNA, resulting in a stretch of DNA that is single -stranded and therefore a viable substrate for the deaminase. It should be understood that other catalytic domains of napDNAbps. or catalytic domains from other nucleic acid editing proteins, can also be used to generate fusion proteins with Cas9, and that the disclosure is not limited in this regard.
[00568] In some embodiments, the cytidine deaminase is an apolipoprotein B mRNA-editing complex (APOBEC) family deaminase. In some embodiments, the cytidine deaminase is an APOBEC 1 deaminase. In some embodiments, the cytidine deaminase is an APOBEC2 deaminase. In some embodiments, the cy tidine deaminase is an APOBEC3 deaminase. In some embodiments, the cytidine deaminase is an APOBEC3A deaminase. In some embodiments, the cytidine deaminase is an APOBEC3B deaminase. In some embodiments, the cytidine deaminase is an APOBEC3C deaminase. In some embodiments, the cytidine deaminase is an APOBEC3D deaminase. In some embodiments, the cytidine deaminase is an APOBEC3E deaminase. In some embodiments, the cytidine deaminase is an APOBEC3F deaminase. In some embodiments, the cytidine deaminase is an APOBEC3G deaminase. In some embodiments, the cytidine deaminase is an AP0BEC3H deaminase. In some embodiments, the cytidine deaminase is an APOBEC4 deaminase. In some embodiments, the cytidine deaminase is an activation-induced deaminase (AID). In some embodiments, the cytidine deaminase is a vertebrate cytidine deaminase. In some embodiments, the cytidine deaminase is an invertebrate cytidine deaminase. In some embodiments, the cytidine deaminase is a human, chimpanzee, gorilla, monkey, cow, dog, rat, or mouse deaminase. In some embodiments, the cytidine deaminase is a human cytidine deaminase. In some embodiments, the cytidine deaminase is a rat cytidine deaminase, e.g., rAPOBECl.
[00569] In some embodiments, the nucleic acid editing domain is at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any? of the cytidine deaminase domain examples above.
Casl2a (Cas Type V) ABEs
[00570] In other embodiments, the Cas 12a base editors contemplated herein may comprise a deaminase domain that is an adenosine deaminase domain. The disclosure provides fusion proteins that comprise one or more adenosine deaminases. In some aspects, such fusion proteins are capable of deaminating adenosine in a nucleic acid sequence (e.g.. DNA or RNA). As one example, any of the fusion proteins provided herein may be base editors, (e.g.. adenine base editors). Without wishing to be bound by any particular theory, dimerization of adenosine deaminases (e.g., in cis or in trans) may improve the ability (e.g., efficiency) of the fusion protein to modify a nucleic acid base, for example to deaminate adenine. In some embodiments, any of the fusion proteins may comprise 2, 3, 4 or 5 adenosine deaminases. In some embodiments, any of the fusion proteins provided herein comprise two adenosine deaminases. Exemplary, non-limiting, embodiments of adenosine deaminases are provided herein. It should be appreciated that the mutations provided herein (e.g., mutations in ecTadA) may be applied to adenosine deaminases in other adenosine base editors, for example those provided in U.S. Patent Publication No. 2018/0073012, published Mar. 15, 2018, which issued as U.S. Pat. No. 10,113,163, on Oct. 30, 2018; U.S. Patent Publication No. 2017/0121693, published May 4, 2017, which issued as U.S. Pat. No. 10,167,457 on Jan. 1, 2019; International Publication No. WO 2017/070633, published Apr. 27, 2017; U.S. Patent Publication No. 2015/0166980, published Jun. 18, 2015; U.S. Pat. No. 9.840,699, issued Dec. 12, 2017; and U.S. Pat. No. 10,077,453. issued Sep. 18, 2018. all of which are incorporated herein by reference in their entireties.
[00571] In some embodiments, any of the adenosine deaminases provided herein is capable of deaminating adenine. In some embodiments, the adenosine deaminases provided herein are capable of deaminating adenine in a deoxyadenosine residue of DNA. The adenosine deaminase may? be derived from any suitable organism (e.g., E. coli). In some embodiments, the adenosine deaminase is a naturally-occurring adenosine deaminase that includes one or more mutations corresponding to any of the mutations provided herein (e.g., mutations in ecTadA). One of skill in the art will be able to identify the corresponding residue in any homologous protein and in the respective encoding nucleic acid by methods well known in the art, e.g., by sequence alignment and determination of homologous residues. Accordingly, one of skill in the art would be able to generate mutations in any naturally-occurring adenosine deaminase (e.g., having homology to ecTadA) that corresponds to any of the mutations described herein, e.g., any of the mutations identified in ecTadA. In some embodiments, the adenosine deaminase is from a prokaryote. In some embodiments, the adenosine deaminase is from a bacterium. In some embodiments, the adenosine deaminase is from Escherichia coli, Staphylococcus aureus, Salmonella typhi , Shewanella putrefaciens, Haemophilus influenzae, Caulobacter crescentus, or Bacillus subtilis. In some embodiments, the adenosine deaminase is from E. coli.
[00572] Any two or more of the adenosine deaminases described herein may be connected to one another (e.g. by a linker) within an adenosine deaminase domain of the fusion proteins provided herein. For instance, the fusion proteins provided herein may contain only two adenosine deaminases. In some embodiments, the adenosine deaminases are the same. In some embodiments, the adenosine deaminases are any of the adenosine deaminases provided herein. In some embodiments, the adenosine deaminases are different. In some embodiments, the first adenosine deaminase is any of the adenosine deaminases provided herein, and the second adenosine is any of the adenosine deaminases provided herein, but is not identical to the first adenosine deaminase. In some embodiments, the fusion protein comprises two adenosine deaminases (e.g., a first adenosine deaminase and a second adenosine deaminase). In some embodiments, the fusion protein comprises a first adenosine deaminase and a second adenosine deaminase. In some embodiments, the first adenosine deaminase is N-terminal to the second adenosine deaminase in the fusion protein. In some embodiments, the first adenosine deaminase is C-terminal to the second adenosine deaminase in the fusion protein. In some embodiments, the first adenosine deaminase and the second deaminase are fused directly or via a linker.
[00573] In some embodiments, the base editor comprises a deaminase enzyme. In some embodiments, tire base editor comprises a cytidine deaminase. In some embodiments, the base editor comprises a Cas9 protein fused to a cytidine deaminase enzyme. In some embodiments, the base editor comprises an adenosine deaminase. In some embodiments, the base editor comprises a Cas9 protein fused to an adenosine deaminase enzyme.
[00574] In some embodiments, the base editing system comprises an uracil glycosylase inhibitor. In some embodiments, the base editing system comprises a Cas9 protein fused to an uracil glycosylase inhibitor. In some embodiments, the cargo comprises an uracil glycosylase inhibitor or a polynucleotide encoding an uracil glycosylase inhibitor. In some embodiments, the cargo comprises a Cas9 protein fused to an uracil glycosylase inhibitor or a polynucleotide encoding a Cas9 protein fused to an uracil glycosylase inhibitor.
[00575] A variety of nucleobase modifying enzymes are suitable for use in the nucleobase systems disclosed herein. In some embodiments, the nucleobase modifying enzyme is a RNA base editor. In some embodiments, the RNA base editor can be a cytidine deaminase, which converts cytidine into uridine. Nonlimiting examples of cytidine deaminases include cytidine deaminase 1 (CDA1), cytidine deaminase 2 (CDA2), activation-induced cytidine deaminase (AICDA), apolipoprotein B mRNA-editing complex (APOBEC) family cytidine deaminase (e g., APOBEC1, APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D/E, APOBEC3F, APOBEC3G, APOBEC3H, APOBEC4), APOBEC1 complementation factor/APOBECl stimulating factor (ACF1/ASF) cytidine deaminase, cytosine deaminase acting on RNA (CDAR), bacterial long isofonn cytidine deaminase (CDDL), and cytosine deaminase acting on tRNA (CDAT). In other embodiments, the RNA base editor can be an adenosine deaminase, which converts adenosine into inosine, which is read by polymerase enzymes as guanosine. In certain embodiments, adenosine deaminases include tRNA adenine deaminase, adenosine deaminase, adenosine deaminase acting on RNA (ADAR), and adenosine deaminase acting on tRNA (AD AT).
[00576] In some embodiments, in the nucleobase editing systems disclosed herein, the Cas effector may associate with one or more functional domains (e.g., via fusion protein or suitable linkers). In some embodiments, the effector domain comprises one or more cytindinc or nucleotide deaminases that mediate editing of via hy drolytic deamination. In certain embodiments, the effector domain comprises the adenosine deaminase acting on RNA (ADAR) family of enzymes. In certain embodiments, the adenosine deaminase protein or catalytic domain thereof capable of deaminating adenosine or cytidine in RNA or is an RNA specific adenosine deaminase and/or is a bacterial, human, cephalopod, or Drosophila adenosine deaminase protein or catalytic domain thereof, preferably TadA, more preferably ADAR, optionally huADAR, optionally (hu)ADARl or (hu)ADAR2, preferably huADAR2 or catalytic domain thereof.
[00577] In some embodiments, the cytidine deaminase is a human, rat or lamprey cytidine deaminase. In some embodiments, the cytidine deaminase is an apolipoprotein B mRNA-editing complex (APOBEC) family deaminase, an activation-induced deaminase (AID), or a cytidine deaminase 1 (CDA1).
[00578] In certain embodiments, the adenosine deaminase is adenosine deaminase acting on RNA (ADAR). In certain embodiments, the ADAR is ADAR (AD ARI), AD ARBI (ADAR2) or ADARB2 (ADAR3) (see. e.g., Savva et al. Genon. Biol. 2012, 13(12):252). [00579] In some embodiments, the gene editing system comprises AID/APOBEC (apolipoprotein B editing complex) family of enzymes deaminates cytidine to uridine, leading to mutations in RNA and DNA.
[00580] In some embodiments, the nucleobase editing system comprises ADAR and an antisense oligonucleotide. In certain embodiments, the antisense oligonucleotide is chemically optimized antisense oligonucleotide. In certain embodiments, the antisense oligonucleotide is administered for the nucleobase editing, wherein the antisense oligonucleotide activates human endogenous ADAR for nucleobase editing. Such ADAR and antisense oligonucleotide editing system provides a safer site-directed RNA editing with low off-target effect. See, e.g., Merkle et al.. Nature Biotechnology, 2019, 37, 133-138.
[00581] Any of the above base editor embodiments or variants, modifications, or derivatives thereof are contemplated herein to be delivered by the LNP systems disclosed in this specification for gene editing in cells, tissues, and/or organs under in vitro, ex vivo, or in vivo conditions. The various components described herein may be configured and delivered in any suitable manner. Any of the descriptions presented in this section are not intended to be strictly limiting.
Cast 2a (Cas Type V) prime editor format
[00582] In other embodiments, the Casl2a-based gene editing system is combined with one or more reverse transcriptases to produce a prime editor when used in connection with a specialized guide RNA called a prime editing guide RNA ("peg R A"). In some embodiments, the reverse transcriptase is fused, optionally via a linker, to a component of the Casl2a-based gene editing system. For example, the reverse transcriptase might be coupled or fused to a Cas 12a domain via a linker.
[00583] Prime editing technology is a gene editing technology that can make targeted insertions, deletions, and all transversion and transition point mutations in a target genome. Without wishing to be bound by any particular theory, the prime editing process may search and replace endogenous sequences in a target polynucleotide. The spacer sequence of a prime editing guide RNA (“PEgRNA” or “pegRNA”) recognizes and anneals with a search target sequence in a target strand of a double stranded target polynucleotide, e.g.. a double stranded target DNA. A prime editing complex may generate a nick in the target DNA on the edit strand which is the complementary strand of the target strand. The prime editing complex may then use a free 3’ end formed at the nick site of the edit strand to initiate DNA synthesis, where a “primer binding site sequence” (PBS) of the PEgRNA complexes with the free 3’ end, and a single stranded DNA is synthesized (by reverse transcriptase) using an editing template of the PEgRNA as a template. As used herein, a “primer binding site” is a single-stranded portion of the PEgRNA that comprises a region of complementarity to the PAM strand (i.e., the non-target strand or the edit strand). The PBS is complementary or substantially complementary to a sequence on the PAM strand of the double stranded target DNA that is immediately upstream of the nick site.
[00584] The tenn '‘prime editor (PE)” refers to the polypeptide or polypeptide components involved in prime editing, or any polynucleotide (s) encoding the polypeptide or polypeptide components. In various embodiments, a prime editor includes a polypeptide domain having DNA binding activity and a polypeptide domain having DNA polymerase activity. In some embodiments, the prime editor further comprises a polypeptide domain having nuclease activity. In some embodiments, the polypeptide domain having DNA binding activity comprises a nuclease domain or nuclease activity. In some embodiments, the polypeptide domain having nuclease activity comprises a nickase, or a fully active nuclease. As used herein, the term “nickase” refers to a nuclease capable of cleaving only one strand of a double-stranded DNA target. In some embodiments, the prime editor comprises a polypeptide domain that is an inactive nuclease. In some embodiments, the polypeptide domain having programmable DNA binding activity comprises a nucleic acid guided DNA binding domain, for example, a CRISPR-Cas protein, for example, a Cas9 nickase, a Cpfl nickase, or another CRISPR-Cas nuclease. In some embodiments, the polypeptide domain having DNA polymerase activity comprises a template-dependent DNA polymerase, for example, a DNA-dependent DNA polymerase or an RNA-dependent DNA polymerase. In some embodiments, the DNA polymerase is a reverse transcriptase. In some embodiments, the prime editor comprises additional polypeptides involved in prime editing, for example, a polypeptide domain having 5‘ endonuclease activity, e.g.. a 5' endogenous DNA flap endonucleases (e.g., FEN1), for helping to drive the prime editing process towards the edited product formation. In some embodiments, the prime editor further comprises an RNA-protein recruitment polypeptide, for example, a MS2 coat protein.
[00585] A prime editor may be engineered. In some embodiments, the polypeptide components of a prime editor do not naturally occur in the same organism or cellular environment. In some embodiments, the polypeptide components of a prime editor may be of different origins or from different organisms. In some embodiments, a prime editor comprises a DNA binding domain and a DNA polymerase domain that arc derived from different species. In some embodiments, a prime editor comprises a Cas polypeptide (DNA binding domain) and a reverse transcriptase polypeptide (DNA polymerase) that are derived from different species. For example, a prime editor may comprise a S. pyogenes Cas9 polypeptide and a Moloney murine leukemia virus (M-MLV) reverse transcriptase polypeptide.
[00586] In some embodiments, polypeptide domains of a prime editor may be fused or linked by a peptide linker to form a fusion protein. In other embodiments, a prime editor comprises one or more polypeptide domains provided in trans as separate proteins, which are capable of being associated to each other through non-peptide linkages or through aptamers or recruitment sequences. For example, a prime editor may comprise a DNA binding domain and a reverse transcriptase domain associated with each other by an RNA- protein recruitment aptamer, e.g., a MS2 aptamer, which may be linked to a PEgRNA. Prime editor polypeptide components may be encoded by one or more polynucleotides in whole or in part. In some embodiments, a single polynucleotide, construct, or vector encodes the prime editor fusion protein. In some embodiments, multiple polynucleotides, constructs, or vectors each encode a polypeptide domain or portion of a domain of a prime editor, or a portion of a prime editor fusion protein. For example, a prime editor fusion protein may comprise an N-terminal portion fused to an intein-N and a C-terminal portion fused to an intein-C, each of w hich is individually encoded by an AAV vector.
[00587] The editing template may comprise one or more intended nucleotide edits compared to the endogenous double stranded target DNA sequence. Accordingly, the newly synthesized single stranded DNA also comprises tire nucleotide edit(s) encoded by the editing template. Through removal of the editing target sequence on the edit strand of the double stranded target DNA and DNA repair mechanism, the newly synthesized single stranded DNA replaces the editing target sequence, and the desired nucleotide edit(s) are incorporated into the double stranded target DNA.
[00588] Prime editing was first described in Anzalone et al., “Search-and-replace genome editing without double-strand breaks or donor DNA,” Nature, Dec 2019, 576 (7789): pp. 149-157, which is incorporated herein in its entirety. Prime editing has subsequently been described and detailed in numerous follow-on publications, including, for example, (i) Liu ct al., “Prime editing: a search and replace tool w ith versatile base changes,” Yi Chuan. Nov. 20, 2022, 44(11): 993-1008; (ii) Lu C et al., “Prime Editing: An All-Rounder for Genome Editing. Int J Mol Sci. 2022 Aug 30;23(17):9862; (iii) Velimirovic M, Zanetti LC, Shen MW, Fife JD, Lin L, Cha M, Akinci E, Barnum D, Yu T, Sherwood RI. Peptide fusion improves prime editing efficiency. Nat Commun. 2022 Jun 18;13(1):3512. doi: 10.1038/s41467-022-31270-y. PMID: 35717416; PMCID: PMC9206660; (iv) Velimirovic M, Zanetti LC, Shen MW, Fife JD, Lin L, Cha M, Akinci E, Barnum D, Yu T, Sherwood RI. Peptide fusion improves prime editing efficiency. Nat Commun. 2022 Jun 18; 13(1):3512. doi: 10.1038/s41467-022-31270-y. PMID: 35717416; PMCID: PMC9206660; (v) Habib O. Habib G, Hwang GH. Bae S. Comprehensive analysis of prime editing outcomes in human embryonic stem cells. Nucleic Acids Res. 2022 Jan 25;50(2): 1187-1197. doi: 10.1093/nar/gkabl295. PMID: 35018468;
PMCID: PMC8789035; (vi) Marzec M, Brqszewska-Zalew'ska A, Hensel G. Prime Editing: A New' Way for Genome Editing. Trends Cell Biol. 2020 Apr;30(4):257-259. doi: 10.1016/j.tcb.2020.01.004. Epub 2020 Jan 27. PMID: 32001098; (vii) Tao R, Wang Y, Jiao Y, Hu Y, Li L, Jiang L, Zhou L, Qu J, Chen Q, Yao S. Bi- PE: bi-directional priming improves CRISPR/Cas9 prime editing in mammalian cells. Nucleic Acids Res. 2022 Jun 24:50(1 l):6423-6434. doi: 10.1093/nar/gkac506. PMID: 35687127; PMCID: PMC9226529; (vrii) Nelson JW, Randolph PB, Shen SP, Everette KA, Chen PJ, Anzalone AV, An M, Newby GA, Chen JC, Hsu A, Liu DR. Engineered pegRNAs improve prime editing efficiency. Nat BiotechnoL 2022 Mar;40(3):402- 410. doi: 10.1038/s41587-021-01039-7. Epub 2021 Oct 4. Erratum in: Nat BiotechnoL 2021 Dec 8;: PMID: 34608327; PMCID: PMC8930418; (ix) Doman JL, Sousa AA, Randolph PB. Chen PJ, Liu DR. Designing and executing prime editing experiments in mammalian cells. Nat Protoc. 2022 Nov; 17(11):2431-2468. doi: 10.1038/s41596-022-00724-4. Epub 2022 Aug 8. PMID: 35941224; PMCID: PMC9799714; (x) Jiao Y, Zhou L, Tao R, Wang Y, Hu Y, Jiang L, Li L, Yao S. Random-PE: an efficient integration of random sequences into mammalian genome by prime editing. Mol Biomed. 2021 Nov 18;2(1):36. doi: 10.1186/s43556-021- 00057-w. PMID: 35006470; PMCID: PMC8607425; and (xi) Awan MJA, Ali Z, Amin I, Mansoor S. Twin prime editor: seamless repair without damage. Trends BiotechnoL 2022 Apr;40(4):374-376. doi:
10.1016/j tibtech.2022.01.013. Epub 2022 Feb 10. PMID: 35153078. all of which are incorporated herein by reference.
[00589] In addition, prime editing has been described and disclosed in numerous published patent applications, each of which their entire contents, amino acid sequences, nucleotide sequences, and all disclosures therein are incorporated herein by reference in their entireties:
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WO 2023/015309 A2 2/9/2023 IMPROVED PRIME EDITORSAND METHODS OF USE
WO 2023/004439 A2 1/26 2023 GENOME EDITING COMPOSITIONSAND METHODS FOR TREATMENT OF CHRONIC GRANULOMA TO US DISEASE
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WO 2022/234051 Al 11/10/2022 SPLIT PRIME EDITING ENZYME
US 2022/0356469 Al 11/10/2022 METHODSAND COMPOSITIONS FOR EDITING NUCLEOTIDE SEQUENCES METHODS AND COMPOSITIONS FOR EDITING NUCLEOTIDE SEQUENCES
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WO 2022/150790 A3 8'11/2022 PRIME EDITOR VARIANTS, CONSTRUCTS, AND METHODS FOR ENHANCING PRIME EDITING EFFICIENCY AND PRECISION Publication No. Publication Date Title
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US 9458484 B2 10/4/2016 Reverse transcriptase mixtures with improved storage stability
[00590] In some embodiments, the Cast 2 based gene editing system is a prime editing system comprising a Casl2a domain (e.g., a nickase Casl2a domain) fused to a reverse transcriptase or a polynucleotide encoding such a prime editing system.
[00591] Prime editing is a versatile and precise genome editing method that directly writes new genetic information into a specified DNA site using a catalytically impaired Cas fused to an engineered reverse transcriptase, also referred to as a prime editor, which is programmable using a prime editing guide RNA ("pcgRNA") that both specifies the target site and encodes the desired edit (see, e.g., Anzalone et al.. Nature 2019). Prime editing bypasses the need for DNA donor templates by using a prime editor having nickase or catalytically impaired enzymatic activity.
[00592] A prime editing system comprises a prime editor. The prime editor (“PE7’) comprises a catalytically impaired Cas protein (e.g., a Cas 12a) fused to an engineered reverse transcriptase which can precisely and permanently edit one or more target nucleobases in a target polynucleotide. [00593] In some embodiments, the prime editor comprises an engineered Moloney murine leukemia virus (“M-MLV”) reverse transcriptase (‘"RT”) fused to a Cas-H840A nickase (called “PE2”). In some embodiments, the prime editor comprises an engineered M-MLV RT fused to a Cas9-H840A nickase. In some embodiments, the prime editor comprises an engineered M-MLV RT fused to a Streptococcus pyogenes Cas9 (spCas9)-H840A nickase. PE modifications include increased PAM flexibility to increase the utility of PE2 editing, expanding the coverage of targetable pathogenic variants in the ClinVar database that can now be prime edited to 94.4%.
[00594] In some embodiments, the prime editing system further comprises a prime editing guide RNA (“pegRNA”). In some embodiments, the cargo comprises a pegRNA or a polynucleotide encoding a pegRNA.
[00595] In some embodiments, the prime editing system further comprises a second guide RNA targeting the complementary strand, allowing the Cas9 nickase to also nick the non-edited strand (called “PE3”), which biases mismatch DNA repair in favor of the edited sequence. In some embodiments, the second guide RNA is designed to recognize the complementary strand of DNA only after the PE3 edit has occurred (called “PE3b”), which reduces indel fonnation.
[00596] In some embodiments, the prime editing system comprises an uracil glycosylase inhibitor. In some embodiments, the prime editing system comprises a Cas9 protein fused to an uracil glycosylase inhibitor. In some embodiments, the cargo comprises an uracil glycosylase inhibitor or a polynucleotide encoding an uracil glycosylase inhibitor. In some embodiments, the cargo comprises a Cas9 protein fused to an uracil glycosylase inhibitor or a polynucleotide encoding a Cas9 protein fused to an uracil glycosylase inhibitor.
[00597] Any of the above prime editor embodiments or variants, modifications, or derivatives thereof are contemplated herein to be delivered by the LNP systems disclosed in this specification for gene editing in cells, tissues, and/or organs under in vitro, ex vivo, or in vivo conditions. The various components described herein may be configured and delivered in any suitable manner. Any of tire descriptions presented in this section are not intended to be strictly limiting.
Cast 2a (Cas Type V) retron editor format
[00598] In still other embodiments, the herein disclosed Casl2a gene editing system may comprise an engineered retron system. An engineered retron editing system in various embodiments may comprise (a) a retron reverse transcriptase, or a nucleic acid molecule encoding a retron reverse transcriptase, (b) a retron ncRNA (or a nucleic acid molecule encoding same) comprising a modified msd region to include a sequence that is reverse transcribed to form a single strand template DNA sequence (RT-DNA), (c) a Cas 12a domain, and (d) a guide RNA to target the nuclease to a desired target site. [00599] Retrons are defined by their unique ability to produce an unusual satellite DNA known as msDNA (multicopy single-stranded DNA). DNA encoding retrons includes a reverse trancriptase (RT)-coding gene (ret) and a nucleic acid sequence encoding the non-coding RNA (ncRNA), which contains two contiguous and inverted non-coding sequences referred to as the msr and msd. Tire ret gene and the non-coding RNA (including the msr and msd) are transcribed as a single RNA transcript, which becomes folded into a specific secondary structure following post-transcriptional processing. Once translated, the RT binds the RNA template downstream from the msd locus, initiating reverse transcription of the RNA towards its 5' end, assisted by the 2’OH group present in a conserved branching guanosine residue that acts as a primer. Reverse transcription halts before reaching the msr locus, and the resulting DNA, the msDNA, remains covalently attached to the RNA template via a 2"-5' phosphodiester bond and base-pairing between the 3' ends of the msDNA and the RNA template. The external regions, at the 5' and 3' ends of the msd/msr transcript (al and a2, respectively) are complementary and can hybridize, leaving the structures located in the msr and msd regions in internal positions. The msr locus, which is not reverse transcribed, forms one to three short stemloops of variable size, ranging from 3 to 10 base pairs, whereas the msd locus folds into a single/double long hairpin with a highly variable long stem of 10-50 bp in length that is also present in tire final msDNA form.
[00600] It has recently been reported that retrons may be utilized as a means to provide donor DNA template for HDR-dependent genome editing (e.g., see Lopez et al., “Precise genome editing across kingdoms of life using retron-derived DNA/’ Nature Chemical Biology, December 12. 2021, 18. pages 199-206 (2022)). how ever, producing sufficient levels of donor DNA template intracellularly to sufficiently support efficient HDR-dependent editing remains a significant challenge.
[00601] Retrons have previously been described in the scientific literature, including in the context of retron editing. For example, retrons have been described in the following references, each of which are incorporated herein by reference:
[00602] In addition, retrons have previously been described in tire patent literature, including in the context of retron editing. For example, retrons have been described in the following references, each of which are incorporated herein by reference:
[00603] In some embodiments, the Cast 2a retron editing system can be used for genome editing a desired site. A retron is engineered with a heterologous nucleic acid sequence encoding a donor polynucleotide (“template or donor nucleotide sequence” or “template DNA”) suitable for use with nuclease genome editing system. The nuclease is designed to specifically target a location proximal to the desired edit (tire nuclease should be designed such that it will not cut the target once the edit is properly installed). The Cast 2a domain is linked to the retron, either by direct fusion to the RT or by fusion of the msDNA to the gRNA (only applicable for RNA-guided nucleases). A heterologous nucleic acid sequence is inserted into the retron msd.
[00604] In some embodiments, the heterologous nucleic acid sequence has 10-100 or more bp of homologous nucleic acid sequence to the genome on both sides of the desired edit. The desired edit (insertion, deletion, or mutation) is in between the homologous sequence.
[00605] In some embodiments, donor polynucleotides comprise a sequence comprising an intended genome edit flanked by a pair of homology arms responsible for targeting the donor polynucleotide to the target locus to be edited in a cell. Tire donor polynucleotide typically comprises a 5' homology arm that hybridizes to a 5' genomic target sequence and a 3' homology arm that hybridizes to a 3' genomic target sequence. The homology arms are referred to herein as 5' and 3' (z.e., upstream and downstream) homology anns, which relate to the relative position of the homology arms to tire nucleotide sequence comprising the intended edit within the donor polynucleotide. The 5' and 3' homology arms hybridize to regions within the target locus in the genomic DNA to be modified, which are referred to herein as the “5' target sequence” and “3' target sequence,” respectively.
[00606] The homology arm must be sufficiently complementary for hybridization to the target sequence to mediate homologous recombination between the donor polynucleotide and genomic DNA at the target locus. For example, a homology arm may comprise a nucleotide sequence having at least about 80-100% sequence identity to the corresponding genomic target sequence, including any percent identity within this range, such as at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity thereto, wherein the nucleotide sequence comprising the intended edit can be integrated into tire genomic DNA by HDR at the genomic target locus recognized (z.e., having sufficient complementary for hybridization) by the 5' and 3' homology arms.
[00607] In some embodiments, the corresponding homologous nucleotide sequences in the genomic target sequence (i.e., the “5' target sequence” and "‘3' target sequence”) flank a specific site for cleavage and/or a specific site for introducing the intended edit. The distance between the specific cleavage site and the homologous nucleotide sequences (e.g., each homology ann) can be several hundred nucleotides. In some embodiments, the distance between a homology arm and the cleavage site is 200 nucleotides or less (e.g.. 0, 10, 20, 30, 50, 75, 100, 125, 150, 175, and 200 nucleotides). In most cases, a smaller distance may give rise to a higher gene targeting rate. In some embodiments, the donor polynucleotide is substantially identical to the target genomic sequence, across its entire length except for the sequence changes to be introduced to a portion of the genome that encompasses both the specific cleavage site and the portions of the genomic target sequence to be altered.
[00608] A homology arm can be of any length, e.g. 10 nucleotides or more, 15 nucleotides or more, 20 nucleotides or more, 50 nucleotides or more, 100 nucleotides or more, 250 nucleotides or more, 300 nucleotides or more, 350 nucleotides or more, 400 nucleotides or more. 450 nucleotides or more, 500 nucleotides or more, 1000 nucleotides ( 1 kb) or more, 5000 nucleotides (5 kb) or more. 10000 nucleotides (10 kb) or more, etc. In some instances, the 5' and 3' homology arms are substantially equal in length to one another. However, in some instances the 5' and 3' homology arms are not necessarily equal in length to one another. For example, one homology arm may be 30% shorter or less than the other homology arm, 20% shorter or less dian the other homology ann, 10% shorter or less than the other homology arm, 5% shorter or less than the other homology ann, 2% shorter or less than the other homology arm, or only a few nucleotides less than the other homology arm. In other instances, the 5' and 3' homology anns are substantially different in length from one another, e.g. one may be 40% shorter or more, 50% shorter or more, sometimes 60% shorter or more, 70% shorter or more, 80% shorter or more, 90% shorter or more, or 95% shorter or more than the other homology ann.
[00609] The donor polynucleotide may be used in combination with an RNA-guided nuclease, which is targeted to a particular genomic sequence (i.e. , genomic target sequence to be modified) by a guide RNA. A target-specific guide RNA comprises a nucleotide sequence that is complementary to a genomic target sequence, and thereby mediates binding of the nuclease-gRNA complex by hybridization at tire target site. For example, the gRNA can be designed with a sequence complementary to the sequence of a minor allele to target the nuclease-gRNA complex to the site of a mutation. The mutation may comprise an insertion, a deletion, or a substitution. For example, the mutation may include a single nucleotide variation, gene fusion, translocation, inversion, duplication, frameshift, missense, nonsense, or other mutation associated with a phenotype or disease of interest. The targeted minor allele may be a common genetic variant or a rare genetic variant. In some embodiments, the gRNA is designed to selectively bind to a minor allele with single basepair discrimination, for example, to allow binding of the nuclease-gRNA complex to a single nucleotide polymorphism (SNP). In particular, the gRNA may be designed to target disease-relevant mutations of interest for the purpose of genome editing to remove the mutation from a gene. Alternatively, the gRNA can be designed with a sequence complementary to the sequence of a major or wild-type allele to target the nuclease-gRNA complex to the allele for the purpose of genome editing to introduces a mutation into a gene in the genomic DNA of the cell, such as an insertion, deletion, or substitution. Such genetically modified cells can be used, for example, to alter phenotype, confer new properties, or produce disease models for drug screening.
[00610] Hie genomic target site will typically comprise a nucleotide sequence that is complementary to the gRNA and may further comprise a protospacer adjacent motif (PAM). In some embodiments, the target site comprises 20-30 base pairs in addition to a 3 or more base pair PAM. Typically, the first nucleotide of a PAM can be any nucleotide, while the two or more other nucleotides will depend on the specific Cas9 protein that is chosen. Exemplary PAM sequences are known to those of skill in the art and include, without limitation, NNG, NGN, NAG, and NGG, wherein N represents any nucleotide. In some embodiments, the allele targeted by a gRNA comprises a mutation that creates a PAM within the allele, wherein the PAM promotes binding of the Cas9-gRNA complex to the allele.
[00611] In some embodiments, the gRNA is 5-50 nucleotides, 10-30 nucleotides, 15- 25 nucleotides, 18-22 nucleotides, or 19-21 nucleotides in length, or any length between the stated ranges, including, for example, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 nucleotides in length. The guide RNA may be a single guide RNA comprising crRNA and tracrRNA sequences in a single RNA molecule, or the guide RNA may comprise two RNA molecules with crRNA and tracrRNA sequences residing in separate RNA molecules.
[00612] In some embodiments, the Casl2a is provided in the form of a protein, optionally where the nuclease is complexed with a gRNA to form a ribonucleoprotein (RNP) complex. In some embodiments, the RNA- guided nuclease is provided by a nucleic acid encoding the RNA-guided nuclease, such as an RNA (e.g., messenger RNA) or DNA (expression vector). In some embodiments, the RNA-guided nuclease and the gRNA are both provided by vectors, such as the vectors and the vector system described in other parts of the application (all incorporated herein by reference). Both can be expressed by a single vector or separately on different vectors. Tire vectors encoding the RNA-guided nuclease and gRNA may be included in the vector system comprising the engineered retron msr gene, msd gene and ret gene sequences. In some embodiments, the RNA-guided nuclease is fused to the RT and/or the msDNA.
[00613] The RNP complex may be administered to a subject or delivered into a cell by methods known in the art, such as those described in U.S. Pat. No. 11,390,884, which is incorporated by reference herein in its entirety. In some embodiments, the endonuclease/gRNA ribonucleoprotein (RNP) complexes are delivered to cells by electroporation. Direct delivery of the RNP complex to a subject or cell eliminates the need for expression from nucleic acids (e.g., transfection of plasmids encoding Casl2a and gRNA). It also eliminates unwanted integration of DNA segments derived from nucleic acid delivery (e.g., transfection of plasmids encoding Cast 2a and gRNA). An endonuclease/gRNA ribonucleoprotein (RNP) complex usually is formed prior to administration.
[00614] Codon usage may be optimized to further improve production of an RNA-guided nuclease and/or reverse transcriptase (RT) in a particular cell or organism. For example, a nucleic acid encoding an RNA- guided nuclease or reverse transcriptase can be modified to substitute codons having a higher frequency of usage in a yeast cell, a bacterial cell, a human cell, a non-human cell, a mammalian cell, a rodent cell, a mouse cell, a rat cell, or any other host cell of interest, as compared to the naturally occurring polynucleotide sequence. When a nucleic acid encoding the RNA-guided nuclease or reverse transcriptase is introduced into cells, the protein can be transiently, conditionally, or constitutively expressed in the cell.
[00615] In some embodiments, the engineered retron used for genome editing with nuclease genome editing systems can further include accessory7 or enhancer proteins for recombination. Examples of recombination enhancers can include nonhomologous end joining (NHEJ) inhibitors (e.g., inhibitor of DNA ligase IV, a KU inhibitor (e.g., KU70 or KU80), a DNA-PKc inhibitor, or an artemis inhibitor) and homologous directed repair (HDR) promoters, or both, that can enhance or improve more precise genome editing and/or the efficiency of homologous recombination. In some embodiments, the recombination accessory or enhancers can comprise C-terminal binding protein interacting protein (CtIP), cyclinB2, Rad family members (e.g. Rad50, Rad51, Rad52, etc).
[00616] CtIP is a transcription factor containing C2H2 zinc fingers that are involved in early steps of homologous recombination. Mammalian CtIP and its orthologs in other eukaryotes promote the resection of DNA double-strand breaks and are essential for meiotic recombination. HDR may be enhanced by using Cas9 nuclease associated (e.g. fused) to an N-tenninal domain of CtIP, an approach that forces CtIP to the cleavage site and increases transgene integration by HDR. In some embodiments, an N-terminal fragment of CtIP, called HE for HDR enhancer, may be sufficient for HDR stimulation and requires the CtIP multimerization domain and CDK phosphorylation sites to be active. HDR stimulation by the Cas9-HE fusion depends on the guide RNA used, and therefore the guide RNA will be designed accordingly.
[00617] Using the gene editing system described herein, any target gene or sequence in a host cell can be edited or modified for a desired trait, including but not limited to: Myostatin (e.g., GDF8) to increase muscle growth; Pc POLLED to induce hairlessness; KISS 1R to induce bore taint; Dead end protein (dnd) to induce sterility; Nano2 and DDX to induce sterility; CD 163 to induce PRRSV resistance; RELA to induce ASFV resilience; CD 18 to induce Mannheimia (Pasteurella) haemolytica resilience; NRAMP1 to induce tuberculosis resilience; Negative regulators of muscle mass (e.g., Myostatin) to increase muscle mass.
[00618] Any of the above retron editor embodiments or variants, modifications, or derivatives thereof are contemplated herein to be delivered by the LNP systems disclosed in this specification for gene editing in cells, tissues, and/or organs under in vitro, ex vivo, or in vivo conditions. The various components described herein may be configured and delivered in any suitable manner. Any of the descriptions presented in this section are not intended to be strictly limiting.
Casl2a (Cas Type V) integrase editors (e.g., PASTE)
[00619] In some embodiments, the Cas 12a gene editing system comprises one or more integrase domains. In certain embodiments, the Cas 12a gene editing system comprises one or more integrases as described and disclosed in PCT Publications WO2022087235A1, WO2020191245AI, W02022060749A1, WO202I 188840AI, WO2021138469AL US Patent Application Publications US20140349400AL US20210222164A1 or US20150071898A1, each of which is incorporated by reference herein in their entirety.
Casl2a (Cas Type V) epigenetic editors
[00620] In still other embodiments, the Casl2a gene editing systems may comprise one or more epigenetic functionalities for modulating the epigenome of a cell. Epigenetic editors are generally composed of an epigenetic enzyme or their catalytic domain fused with a user-programmable DNA-binding protein, such as a CRISPR-Cas enzyme or Cas 12a disclosed herein. The user-programmable DNA-binding protein (plus a guide RNA for programming the Casl2a) guides the epigenetic enzyme (e.g., a DNA methyltransferase or DNMT) to a specific site (e.g., a CpG island in a promoter region of a gene) in order to induce a change in promoter activity.
[00621] Epigenetic modifications of DNA and histones are known for their multifaceted contributions to transcriptional regulation. As these modifications are faithfully propagated throughout DNA replication, they are considered central players in cellular memory of transcriptional states. Many efforts in the last decade have generated a vast understanding of individual epigenetic modifications and their contribution to transcriptional regulation. Epigenetic editing offers powerful tools to selectively induce epigenetic changes in a genome without altering the sequence of a nucleotide sequence as a means to regulate gene activity. The foundation of epigenetic editing is formed by the ability to generate fusion proteins of epigenetic enzymes or their catalytic domains with programmable DNA-binding platforms such as the clustered regularly interspaced short palindromic repeat (e.g., CRISPR Cas9 or Casl2a) to target these to an endogenous locus of choice. The enzymatic fusion protein then dictates the initial deposited modification while subsequent crosstalk within the local chromatin environment likely influences epigenetic and transcriptional output.
[00622] The following published literature discussing epigenetic editing is incorporated herein by reference each in their entireties.
[00623] Gjaltema RAF. Rots MG. Advances of epigenetic editing. Curr Opin Chem Biol. 2020 Aug;57:75- 81. doi: 10.1016/j.cbpa.2020.04.020. Epub 2020 Jun 30. PMID: 32619853. https://www. sciencedirect.com/science/article/pii/S13675931203006367via%3Dihub
[00624] Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Homg JE, Malagon-Lopez J, Scarf'd I, Maus MV, Pinello L, Aryee MJ, Joung JK. Engineered CRISPR-Casl2a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol.
2019 Mar;37(3):276-282. doi: 10.1038/s41587-018-0011-0. Epub 2019 Feb 11. Erratum in: Nat Biotechnol.
2020 Jul;38(7):901. PMID: 30742127; PMCID: PMC6401248. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6401248/
[00625] Rots MG, Jeltsch A. Editing the Epigenome: Overview, Open Questions, and Directions of Future Development. Methods Mol Biol. 2018;1767:3-18. doi: 10.1007/978- 1-4939-7774- 1 1. PMID: 29524127.
[00626] Liu XS, Jaenisch R. Editing the Epigenome to Tackle Brain Disorders. Trends Neurosci. 2019 Dec:42(12):861-870. doi: 10. 1016/j.tins.2019. 10.003. Epub 2019 Nov 7. PMID: 31706628.
[00627] Waryah CB, Moses C, Arooj M, Blancafort P. Zinc Fingers, TALEs. and CRISPR Systems: A Comparison of Tools for Epigenome Editing. Methods Mol Biol. 2018;1767: 19-63. doi: 10.1007/978-1- 4939-7774-1 2. PMID: 29524128.
[00628] Xu X, Hulshoff MS, Tan X, Zeisberg M, Zeisberg EM. CRISPR/Cas Derivatives as Novel Gene Modulating Tools: Possibilities and In Vivo Applications. Int J Mol Sci. 2020 Apr 25;21(9):3038. doi: 10.3390/ijms21093038. PMID: 32344896; PMCID: PMC7246536. https ://www.ncbi nlm .nih.gov/pmc/articles/PMC7246536/
[00629] In addition, the following published patent literature relating to epigenetic editing is incorporated herein by reference each in their entireties.
Casl2a (Cas Type V) gene writing editor
[00630] In some embodiments, the gene editing system is a gene writing system that comprises a Cas 12a domain. In certain embodiments, the gene editing system is one described and disclosed in US Patent Application Publications US2022039681A1 or US20200109398A1, each of which is incorporated by reference herein in their entirety.
[00631] In certain embodiments, the gene editing system is a system for modifying DNA comprising a polypeptide or a nucleic acid encoding a polypeptide capable of target primed reverse transcription, wherein the polypeptide comprises (a) a reverse transcriptase domain and (b) an endonuclease domain, wherein at least one of (a) or (b) is heterologous; and a template RNA comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence. In certain embodiments, the gene editing system is a system for modifying DNA comprising a polypeptide or a nucleic acid encoding a polypeptide capable of target primed reverse transcription, wherein the polypeptide comprises (a) a target DNA binding domain, (b) a reverse transcriptase domain and (c) an endonuclease domain, wherein at least one of (a), (b) or (c) is heterologous, and a template RNA comprising (i) a sequence that binds the polypeptide and (ii) a heterologous object sequence. In certain embodiments, tire polypeptide comprises a sequence of at least 50 amino acids having at least 80% identity to a reverse transcriptase domain of a sequence of a polypeptide listed in TABLE 1, TABLE 2, or TABLE 3 of US Patent Application Publication US20200109398A1, which is incorporated by reference in its entirety, including the aforementioned sequence tables.
[00632] In certain embodiments, the reverse transcriptase domain is from a retrovirus or a retrotransposon, such as a LTR-retrotransposon, or a non-LTR retrotransposon. In certain embodiments, the reverse transcriptase is from a non-LTR retrotransposon, wherein the non-LTR retrotransposon is a RLE-type non- LTR retrotransposon from the R2, NeSL, HERO, R4, or CRE clade, or an APE-type non-LTR retrotransposon from the Rl, or Txl clade. In certain embodiments, the reverse transcriptase domain is from an avian retrotransposase of column 8 of Table 3 of US20200109398A1, or a sequence having at least 70%, identity thereto. In certain embodiments, the reverse transcriptase domain does not comprise an RNA binding domain and the polypeptide comprises an RNA binding domain heterologous to the reverse transcriptase domain, wherein the RNA binding domain is a B-box protein, a MS2 coat protein, a dCas protein, or a UTR binding protein, or a fragment or variant of any of the foregoing.
[00633] In certain embodiments, the endonuclease domain is heterologous to the reverse transcriptase domain, and wherein the endonuclease is a Fok 1 nuclease (or a functional fragment thereof), a type-II restriction 1 -like endonuclease (RLE-type nuclease), another RLE-type endonuclease, or a Prp8 nuclease. In certain embodiments, the endonuclease domain is heterologous to the reverse transcriptase domain, wherein endonuclease domain contains DNA binding functionality. In certain embodiments, the endonuclease domain is heterologous to the reverse transcriptase domain, and wherein the endonuclease has nickase activity and does not form double stranded breaks.
[00634] In certain embodiments, the polypeptide comprises a DNA binding domain heterologous to the reverse transcriptase domain, and wherein the DNA binding domain is a sequence-guided DNA binding element such as Casl2a. In certain embodiments, the polypeptide comprises a DNA binding domain heterologous to the reverse transcriptase domain, and wherein the DNA binding element is a sequence-guided DNA binding element, further wherein the sequence -guided DNA binding clement is Cas9, Cpfl, or other CRISPR-related protein. In certain embodiments, the polypeptide comprises a DNA binding domain heterologous to the reverse transcriptase domain, and wherein the DNA binding domain is a transcription factor.
[00635] In certain embodiments, the sequence -guided DNA binding element has been altered to have no endonuclease activity. In certain embodiments, the sequence-guided DNA binding element replaces the endonuclease element of the polypeptide. In certain embodiments, the editing system is capable of modifying DNA using reverse transcriptase activity, optionally in the absence of homologous recombination activity.
[00636] In certain embodiments, the gene editing system is a system for modifying DNA comprising: a) a recombinase polypeptide selected from Rec27 (WP 021170377.1, SEQ ID NO: 1241 of US20220396813A1), Rec35 (WP_134161939.1, SEQ ID NO: 1249 of US20220396813A1), or comprising an amino acid sequence of Table 1 or 2 of US20220396813A1, or an amino acid sequence having at least 70%, 75%, 80%, 85%. 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or a nucleic acid encoding the recombinase polypeptide; and b) a double-stranded insert DNA comprising:
(i) a DNA recognition sequence that binds to the recombinase polypeptide of (a), said DNA recognition sequence having a first parapalindromic sequence and a second parapalindromic sequence, wherein each parapalindromic sequence is about 10-30, 12-27, or 10-15 nucleotides, e.g., about 13 nucleotides, and tire first and second parapalindromic sequences together comprise the parapalindromic region of a nucleotide sequence of Table 1, or a nucleotide sequence having at least 70%. 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity thereto, or having no more than 1, 2, 3, 4. 5, 6, 7, 8 sequence alterations (e.g.. substitutions, insertions, or deletions) relative thereto, and said DNA recognition sequence further comprises a core sequence of about 5-10 nucleotides, e.g., about 8 nucleotides, wherein the core sequence is situated between the first and second parapalindromic sequences, and
(ii) a heterologous object sequence.
Cast 2a (Cas Type V) recombinase editors
[00637] In some embodiments, the Cas 12a editing system may also further a recombinase domain, e.g., as a fusion or provided in trans. This domain may be further combined with other domains, such as a reverse transcriptase domain. In certain embodiments, the gene editing system can be based on that described and disclosed in US Patent Application Publications US2022039681A1 or US20200109398A1, each of which is incorporated by reference herein in their entirety, and which may be modified to use a herein disclosed Casl2a domain in place of the programmable nuclease disclosed therein.
[00638] A recombinase refers to a site-specific enzyme that mediates the recombination of DNA between recombinase recognition sequences, which results in the excision, integration, inversion, or exchange (e.g., translocation) of DNA fragments between the recombinase recognition sequences. Recombinases can be classified into two distinct families: serine recombinases (e g., resolvases and invertases) and tyrosine recombinases (e.g., integrases). Examples of serine recombinases include, without limitation. Hin, Gin. Tn3, b-six, CinH, ParA, gd, Bxbl, jC31, TP901, TGI, fBTl, R4, fRVl, fFCl, MR11, Al 18, U153, and gp29. Examples of tyrosine recombinases include, without limitation, Cre, FLP, R, Lambda, HK101, HK022, and pSAM2. The serine and tyrosine recombinase names stem from tire conserved nucleophilic amino acid residue that the recombinase uses to attack the DNA and which becomes covalently linked to tire DNA during strand exchange.
[00639] Recombinases have numerous applications, including the creation of gene knockouts/knock-ins and gene therapy applications. See, e.g., Brown et al., “Serine recombinases as tools for genome engineering." Methods.2011;53(4):372-9; Hirano et al., “Site-specific recombinases as tools for heterologous gene integration.’’ Appl. Microbiol. Biotechnol.2011; 92(2):227-39; Chavez and Calos, “Therapeutic applications of tire FC31 integrase system.” Curr. Gene Ther.2011;11(5):375-81; Turan and Bode, “Site-specific recombinases: from tag-and-target-to tag-and-exchange-based genomic modifications.” FASEB J.2011; 25(12):4088-107;
[00640] Venken and Bellen, “Genome-wide manipulations of Drosophila melanogaster with transposons, Flp recombinase, and FC31 integrase.” Methods Mol. Biol.2012; 859:203-28; Murphy.“Phage recombinases and their applications.” Adv. Virus Res.2012; 83:367-414; Zhang et al..“Conditional gene manipulation: Creating a new biological era.” J. Zhejiang Univ. Sci. B.2012; 13(7):511-24; Karpenshif and Bemstein,“From yeast to mammals: recent advances in genetic control of homologous recombination.” DNA Repair (Amst).2O12; 1;11( 10): 781 -8; the entire contents of each are hereby incorporated by reference in their entirety. The recombinases provided herein are not meant to be exclusive examples of recombinases that can be used in embodiments of the invention. Tire methods and compositions of the invention can be expanded by mining databases for new orthogonal recombinases or designing synthetic recombinases with defined DNA specificities (See, e.g., Groth et al., “Phage integrases: biology and applications.” J. Mol. Biol.2004; 335, 667- 678; Gordley et al., “Synthesis of programmable integrases.” Proc. Natl. Acad. Sci. U S A.2009; 106, 5053- 5058; tire entire contents of each are hereby incorporated by reference in their entirety). Other examples of recombinases that are useful in the methods and compositions described herein are known to those of skill in the art, and any new recombinase that is discovered or generated is expected to be able to be used in the different embodiments of the invention. In some embodiments, the catalytic domains of a recombinase are fused to a nuclease-inactivated RNA-programmable nuclease (e.g., dCas9, or a fragment thereof), such that the recombinase domain does not comprise a nucleic acid binding domain or is unable to bind to a target nucleic acid (e.g., the recombinase domain is engineered such that it does not have specific DNA binding activity). Recombinases lacking DNA binding activity and methods for engineering such are known, and include those described by Klippel et al., “Isolation and characterisation of unusual gin mutants.” EMBO J.1988; 7: 3983-3989: Burke et al..“Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation. Mol Microbiol.2004; 51 : 937-948; Olorunniji et al., “Synapsis and catalysis by activated Tn3 resolvase mutants.” Nucleic Acids Res.2008; 36: 7181-7191; Rowland et al., “Regulatory mutations in Sin recombinase support a structure-based model of the synaptosomc.” Mol Microbiol.2009; 74: 282-298; Akopian et al. /‘Chimeric recombinases with designed DNA sequence recognition.” Proc Natl Acad Sci USA.2003;100: 8688-8691; Gordley et al. ‘Evolution of programmable zinc finger-recombinases with activity in human cells. J Mol Biol.2007; 367: 802-813; Gordley et al., “Synthesis of programmable integrases.” Proc Natl Acad Sci USA.2009;106: 5053-5058; Arnold et al. /'Mutants of Tn3 resolvase which do not require accessory binding sites for recombination activity.” EMBO J.1999; 18: 1407-1414; Gaj et al., “Structure-guided reprogramming of serine recombinase DNA sequence specificity.” Proc Natl Acad Sci USA. 2011;108(2):498-503; and Proudfoot et al., “Zinc finger recombinases with adaptable DNA sequence specificity.” PLoS One.201 l;6(4):el9537; the entire contents of each are hereby incorporated by reference. For example, serine recombinases of the resolvase-invertase group, e.g., Tn3 and gd resolvases and the Hin and Gin invertases, have modular structures with autonomous catalytic and DNA-binding domains (See, e.g., Grindley et al., “Mechanism of site-specific recombination.” Ann Rev Biochem.2006; 75: 567-605, the entire contents of which are incorporated by reference). Tire catalytic domains of these recombinases are thus amenable to being recombined with nuclease-inactivated RNA-programmable nucleases (e.g., dCas9, or a fragment thereof) as described herein, e.g., following the isolation of ‘activated’ recombinase mutants which do not require any accessory factors (e.g., DNA binding activities) (See. e.g., Klippel et al., “Isolation and characterisation of unusual gin mutants.” EMBO J. 1988; 7: 3983-3989: Burke et al. /‘Activating mutations of Tn3 resolvase marking interfaces important in recombination catalysis and its regulation. Mol Microbiol.2004; 51 : 937-948; Olorunniji et al. /‘Synapsis and catalysis by activated Tn3 resolvase mutants.” Nucleic Acids Res.2008; 36: 7181-7191; Rowland et al. /‘Regulatory mutations in Sin recombinase support a structure-based model of the synaptosome.” Mol Microbiol.2009; 74: 282-298; Akopian et al..“Chimeric recombinases with designed DNA sequence recognition.” Proc Natl Acad Sci USA.2003;100: 8688-8691). Additionally, many other natural serine recombinases having an N-terminal catalytic domain and a C-terminal DNA binding domain are known (e.g., phiC31 integrase, TnpX transposase, IS607 transposase), and their catalytic domains can be co-opted to engineer programmable site-specific recombinases as described herein (See, e.g., Smith et al. /‘Diversity in the serine recombinases.” Mol Microbiol.2002;44: 299-307, tire entire contents of which are incorporated by reference). Similarly, the core catalytic domains of tyrosine recombinases (e.g.. Cre, 1 integrase) are known, and can be similarly co-opted to engineer programmable site-specific recombinases as described herein (See. e.g., Guo et al., “Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse.” Nature.1997; 389:40-46; Hartung et al., “Cre mutants with altered DNA binding properties.” J Biol Chem 1998; 273:22884-22891; Shaikh et al. /‘Chimeras of the Flp and Cre recombinases: Tests of the mode of cleavage by Flp and Cre. J Mol Biol.2000; 302:27-48; Rongrong et al. /‘Effect of deletion mutation on the recombination activity of Cre recombinase.” Acta Biochim Pol. 2005; 52:541-544; Kilbride et al., “Determinants of product topology in a hybrid Cre-Tn3 resolvase site-specific recombination system.” J Mol Biol .2006; 355: 185-195; Warren et al., “A chimeric cre recombinase with regulated directionality.” Proc Natl Acad Sci USA.2008 105: 18278-18283; Van Duyne, “Teaching Cre to follow directions.” Proc Natl Acad Sci USA.2009 Jan 6; 106(l):4-5; Numrych et al., “A comparison of the effects of single-base and triple- base changes in the integrase arm-type binding sites on the site-specific recombination of bacteriophage 1.” Nucleic Acids Res.1990; 18:3953-3959; Tirumalai et al. , “The recognition of core-type DNA sites by 1 integrase.” J Mol Biol. 1998; 279:513-527; Aihara et al., “A confonnational switch controls tire DNA cleavage activity of 1 integrase.” Mol Cell.2003; 12: 187-198; Biswas et al., “A structural basis for allosteric control of DNA recombination by 1 integrase.” Nature.2005; 435: 1059-1066; and Warren et al., “Mutations in the amino-terminal domain of 1-integrase have differential effects on integrative and excisive recombination.” Mol Microbiol.2005; 55: 1104-1112; the entire contents of each are incorporated by reference).
Cast 2a (Cas Type V) prime editor / recombinase system
[00641] In another aspect, Cas 12a may be able to be combined with prime editing (“Cas 12a PE” wherein Casl2a is used in place of Cas9) and a recombinase to insert recombinase sites (or “recombinase recognition sequences”) into a desired genomic site. Insertion of recombinase sites provides a programmed location for effecting site-specific genetic changes in a genome. Such genetic changes can include, for example, genomic integration of a plasmid, genomic deletion or insertion, chromosomal translocations, and cassette exchanges, among other genetic changes. The installed recombinase recognition sequences may then be used to conduct site-specific recombination at that site to effecuate a variety of recombination outcomes, such as, excision, integration, inversion, or exchange of DNA fragments.
[00642] The mechanism of installing a recombinase site using a Cas 12a prime editor into the genome is analogous to installing other sequences, such as peptide/protein and RNA tags, into the genome. The process begins with selecting a desired target locus into which the recombinase target sequence will be introduced. Next, a Casl2a prime editor system is provided (“RT-Casl2a:gRNA”). Here, the “gRNA” refers to a PEgRNA, which includes an extended region comprising the RT template that encodes a recombinase integration site for installing in a site in a genome.
[00643] In various aspects, the present disclosure provides for the use of a Cas 12a PE to introduce recombinase recognition sequences at high-value loci in human or other genomes, which, after exposure to site-specific recombinase(s), will direct precise and efficient genomic modifications. In various embodiments, a single SSR target may be installed by Cas 12a PE for use as a site for genomic integration of a DNA donor template. Cas 12a PE-mediated introduction of recombinase recognition sequences could be particularly useful for the treatment of genetic diseases which are caused by large-scale genomic defects, such as gene loss, inversion, or duplication, or chromosomal translocation. For example, Williams-Beuren syndrome is a developmental disorder caused by a deletion of 24 in chromosome 721. No technology exists currently for the efficient and targeted insertion of multiple entire genes in living cells; however, recombinase-mediated integration at a target inserted by Cas 12a PE offers one approach towards a permanent cure for this and other diseases. In addition, targeted introduction of recombinase recognition sequences could be highly enabling for applications including generation of transgenic plants, animal research models, bioproduction cell lines, or other custom eukaryotic cell lines. For example, recombinase-mediated genomic rearrangement in transgenic plants at PE-specific targets could overcome one of the bottlenecks to generating agricultural crops with improved properties8,9.
[00644] In various other aspects, the present disclosure relates to methods of using Casl2a PE to install one or more recombinase recognition sequence and their use in site-specific recombination.
[00645] In some embodiments, tire site-specific recombination may effecuate a variety of recombination outcomes, such as, excision, integration, inversion, or exhange of DNA fragments.
[00646] In some embodiments, the methods are useful for inducing recombination of or between two or more regions of two or more nucleic acid (e.g., DNA) molecules. In other embodiments, the methods are useful for inducing recombination of or between two or more regions in a single nucleic acid molecule (e.g., DNA).
[00647] In some embodiments, the disclosure provides a method for integrating a donor DNA template by site-specific recombination, comprising: (a) installing a recombinase recognition sequence at a genomic locus by prime editing; (b) contacting the genomic locus with a DNA donor template that also comprises the recombinase recognition sequence in the presence of a recombinase.
[00648] In other embodiments, the disclosure provides a method for deleting a genomic region by sitespecific recombination, comprising: (a) installing a pair of recombinase recognition sequences at a genomic locus by prime editing; (b) contacting the genomic locus with a recombinase, thereby catalyzing the deletion of the genomic region between the pair of recombinase recognition sequences.
[00649] In yet other embodiments, the disclosure provides a method for inverting a genomic region by sitespecific recombination, comprising: (a) installing a pair of recombinase recognition sequences at a genomic locus by prime editing; (b) contacting the genomic locus with a recombinase, thereby catalyzing the inversion of the genomic region between the pair of recombinase recognition sequences.
[00650] In still other embodiments, the disclosure provides a method for inducing chromosomal translocation between a first genomic site and a second genomic site, comprising: (a) installing a first recombinase recognition sequence at a first genomic locus by prime editing; (b) installing a second recombinase recognition sequence at a second genomic locus by prime editing; (c) contacting the first and the second genomic loci with a recombinase, thereby catalyzing tire chromosomal translocation of the first and second genomic loci. [00651] In other embodiments, the disclosure provides a method for inducing cassette exchange between a genomic locus and a donor DNA comprising a cassette, comprising: (a) installing a first recombinase recognition sequence at a first genomic locus by prime editing; (b) installing a second recombinase recognition sequence at a second genomic locus by prime editing; (c) contacting the first and tire second genomic loci with a donor DNA comprising a cassette that is flanked by tire first and second recombinase recognition sequences and a recombinase, thereby catalyzing the exchange of the flanked genomic locus and the cassette in the DNA donor.
[00652] In various embodiments involving the insertion of more than one recombinase recognition sequences in the genome, the recombinase recognition sequences can be the same or different. In some embodiments, the recombinase recognition sequences are the same. In other embodiments, that recombinase recognition sequences are different.
[00653] In various embodiments, the recombinase can be a ty rosine recombinase, such as Cre, Dre, Vcre, Sere, Flp, B2, B3, Kw, R, TD1-40, Vika, Nigri, Panto, Kd, Fre, Cre(ALSHG), Tre, Bred, or Cre-R3M3. In such embodiments, the recombinase recognition sequence may be a cognate RRS that corresponds to the recombinase under use.
[00654] In various other embodiments, the recombinase can be a large serine recombinase, such as Bxbl, PhiC31, R4, phiBTl, MJ1, MR11, TP901-1, Al 18. V153, phiRVl. phi370.1. TGI. WB, BL3, SprA, phiJoe, phiK38, Int2, Int3, Int4, Int7, Int8, Int9, IntlO, Inti 1, Intl2, Intl3, LI, peaches, Bxz2, or SV1. In such embodiments, the recombinase recognition sequence may be a cognate RRS that corresponds to the recombinase under use.
[00655] In still other embodiments, the recombinase can be a serine recombinase, such as Bxbl, PhiC31, R4, phiBTl, MJ1, MR11, TP901-1, Al 18, V153, phiRVl, phi370.1, TGI, WB, BL3, SprA, phiJoe, phiK38, Int2, Int3, Int4, Int7, Int8, Int9, IntlO, Intl l, Intl2, Intl3, LI, peaches, Bxz2, or SV1. In such embodiments, the recombinase recognition sequence may be a cognate RRS that corresponds to the recombinase under use.
[00656] In other embodiments, the recombinase can be a serine resolvase, such as Gin, Cin. Hin, Min, or Sin. In such embodiments, the recombinase recognition sequence may be a cognate RRS that corresponds to the recombinase under use.
[00657] In various other embodiments, the recombinase can be a tyrosine integrase, such as HK022, P22, or L5. In such embodiments, tire recombinase recognition sequence may be a cognate RRS that corresponds to the recombinase under use. [00658] In some embodiments, any of the methods for site-specific recombination with Casl2a PE can be performed in vivo or in vitro. In some embodiments, any of tire methods for site-specific recombination are performed in a cell (e.g., recombine genomic DNA in a cell). The cell can be prokary otic or eukary otic. The cell, such as a eukaryotic cell, can be in an individual, such as a subject, as described herein (e.g., a human subject). The methods described herein are useful for the genetic modification of cells in vitro and in vivo, for example, in the context of tire generation of transgenic cells, cell lines, or animals, or in the alteration of genomic sequence, e.g., the correction of a genetic defect, in a cell in a subject.
F. Delivery of Casl2 (or Cas Type V) Gene Editing Systems
Overview
[00659] In yet another aspect, the disclosure provides vectors for transferring and/or expressing said Cas 12a (or Cas Type V)-based gene editing systems, e.g., under in vitro, ex vivo, and in vivo conditions. In still another aspect, the disclosure provides cell-delivery' compositions and methods, including compositions for passive and/or active transport to cells (e.g., plasmids), delivery by virus-based recombinant vectors (e.g., AAV and/or lentivirus vectors), delivery by non-virus-based systems (e.g., liposomes and LNPs), and delivery' by virus-like particles of the Casl2a-based gene editing systems described herein. Depending on the delivery system employed, the Casl2a-based gene editing systems described herein may be delivered in the form of DNA (e.g., plasmids or DNA-based virus vectors), RNA (e.g., guide RNA and mRNA delivered by LNPs), a mixture of DNA and RNA, protein (e.g., virus-like particles), and ribonucleoprotein (RNP) complexes. Any suitable combinations of approaches for delivering the components of the herein disclosed Casl2a-based gene editing systems may be employed.
[00660] The Cas 12a (or Cas Type V) editing systems and/or components thereof can be delivered by any? known delivery' system such as those described above, including (a) without vectors (e.g., electroporation), (b) viral delivery systems and (c) non-viral delivery systems. Viral delivery systems include expression vectors, adeno-associated virus (AAV) vectors, retroviral vectors, lentiviral vectors, and the like. An expression construct can be replicated in a living cell, or it can be made synthetically. Non-viral delivery systems include without limitation lipid particles (e.g. Lipid nanoparticles (LNPs)), non-lipid nanoparticles, exosomes, liposomes, micelles, viral particles, stable nucleic-acid-lipid particles (SNALPs), lipoplexes/polyplexes, DNA nanoclews, Gold nanoparticles, iTOP, Streptolysin O (SLO), multifunctional envelope-type nanodevice (MEND), lipid-coated mesoporous silica particles, inorganic nanoparticles, and polymeric delivery technology (e.g., polymer-based particles).
[00661] Delivery of nucleic acid modalities, including RNA therapeutics, is described further in Paunovska K, Loughrey D. Dahlman JE. Drug delivery systems for RNA therapeutics. Nat Rev Genet. 2022 May;23(5):265-280. doi: 10.1038/s41576-021-00439-4. Epub 2022 Jan 4. PMID: 34983972; PMCID: PMC8724758; Hong CA, Nam YS. Functional nanostructures for effective delivery of small interfering RNA therapeutics. Theranostics. 2014 Sep 19;4(12): 1211-32. doi: 10.7150/thno.849L PMID: 25285170; PMCID: PMC4183999; Liu F, Wang C, Gao Y, Li X, Tian F, Zhang Y, Fu M, Li P, Wang Y, Wang F. Current Transport Systems and Clinical Applications for Small Interfering RNA (siRNA) Drugs. Mol Diagn Ther. 2018 Oct:22(5):551-569. doi: 10.1007/s40291-018-0338-8. PMID: 29926308; Zhang Y, Almazi JG, Ong
HX, Johansen MD, Ledger S, Traini D, Hansbro PM, Kelleher AD, Ahlenstiel CL. Nanoparticle Delivery Platforms for RNAi Therapeutics Targeting COVID-19 Disease in the Respiratory Tract. Int J Mol Sci. 2022 Feb 22;23(5):2408. doi: 10.3390/ijms23052408. PMID: 35269550; PMCID: PMC8909959; Zhang M, Hu S, Liu L, Dang P, Liu Y, Sun Z, Qiao B. Wang C. Engineered exosomes from different sources for cancer- targeted therapy. Signal Transduct Target Ther. 2023 Mar 15 ;8( 1) : 124. doi: 10.1038/s41392-023-01382-y. PMID: 36922504; PMCID: PMC10017761; Hastings ML, Kramer AR. RNA therapeutics. RNA. 2023 Apr;29(4):393-395. doi: 10.1261/ma.079626.123. PMID: 36928165; PMCID: PMC10019368; Miele E, Spinelli GP, Miele E, Di Fabrizio E, Ferretti E, Tomao S, Gulino A. Nanoparticle-based delivery of small interfering RNA: challenges for cancer therapy. Int J Nanomedicine. 2012;7:3637-57. doi:
IO.2147/IJN.S23696. Epub 2012 Jul 20. PMID: 22915840; PMCID: PMC3418108, each of which are incorporated by reference in their entireties.
[00662] Hie engineered Casl2a (or Cas Type V) editing systems (or vectors containing them) may be introduced into any type of cell, including any cell from a prokaryotic, eukary otic, or archaeon organism, including bacteria, archaea, fungi, protists, plants (e.g.. monocotyledonous and dicotyledonous plants); and animals (e.g., vertebrates and invertebrates). Examples of animals that may be transfected with an engineered Cas 12a editing system include, without limitation, vertebrates such as fish, birds, mammals (e.g., human and non-human primates, farm animals, pets, and laboratory animals), reptiles, and amphibians.
[00663] The engineered Cas 12a (or Cas Type V) editing systems can be introduced into a single cell or a population of cells. Cells from tissues, organs, and biopsies, as well as recombinant cells, genetically modified cells, cells from cell lines cultured in vitro, and artificial cells e.g., nanoparticles, liposomes, polymersomes, or microcapsules encapsulating nucleic acids) may all be transfected with the engineered Cas 12a editing systems.
[00664] The engineered Cas 12a (or Cas Type V) editing systems can be introduced into cellular fragments, cell components, or organelles (e.g., mitochondria in animal and plant cells, plastids (e.g., chloroplasts) in plant cells and algae).
[00665] Cells may be cultured or expanded after transfection with the engineered Cas 12a editing systems. [00666] Methods of introducing nucleic acids into a host cell are well known in the art. Commonly used methods include chemically induced transformation, typically using divalent cations (e.g., CaCL). dextran- mediated transfection, polybrene mediated transfection, lipofectamine and LT-1 mediated transfection, electroporation, protoplast fusion, encapsulation of nucleic acids in liposomes, and direct microinjection of the nucleic acids comprising Casl2a editing systems into nuclei. See. e.g., Sambrook et al. (2001) Molecular Cloning, a laboratory manual, 3rd edition, Cold Spring Harbor Laboratories, New York, Davis et al. (1995) Basic Methods in Molecular Biology, 2nd edition, McGraw-Hill, and Chu et al. (1981) Gene 13: 197; herein incorporated by reference in their entireties.
[00667] Plant cells may also be targeted by the Casl2a editing systems disclosed herein. Methods for genetic transformation of plant cells are known in the art and include those set forth in US2022/0145296, and U.S. Pat. Nos. 8,575,425; 7,692,068; 8,802,934; 7,541,517; each of which is herein incorporated by reference in its entirety. See, also, Rakoczy-Trojanowska, M. (2002) Cell Mol Biol Lett. 7:849-858; Jones et al. (2005) Plant Methods 1:5; Rivera et al. (2012) Physics of Life Reviews 9:308-345; Bartlett et al. (2008) Plant Methods 4: 1-12; Bates. G. W. (1999) Methods in Molecular Biology 111:359-366; Binns and Thomashow (1988) Annual Reviews in Microbiology 42:575-606; Christou, P. (1992) The Plant Journal 2:275-281; Christou, P. (1995) Euphytica 85:13-27; Tzfira et al. (2004) TRENDS in Genetics 20:375-383; Yao et al. (2006) Journal of Experimental Botany 57:3737-3746; Zupan and Zambryski (1995) Plant Physiology 107: 1041-1047; and Jones et al. (2005) Plant Methods 1:5.
[00668] The plant cells that have been transformed may be grown into a transgenic organism, such as a plant, in accordance with conventional methods. See, for example, McCormick et al. (1986) Plant Cell Reports 5:81-84.
[00669] Plant material that may be transformed with the Casl2a editing systems described herein includes plant cells, plant protoplasts, plant cell tissue cultures from which plants can be regenerated, plant calli. plant clumps, and plant cells that are intact in plants or parts of plants such as embryos, pollen, ovules, seeds, leaves, flowers, branches, fruit, kernels, ears, cobs, husks, stalks, roots, root tips, anthers, and the like. Progeny, variants, and mutants of tire regenerated plants are also included within the scope of the disclosure, provided that these parts comprise the genetic modification introduced by tire Casl2a editing systems. Further provided is a processed plant product or byproduct that retains the genetic modification introduced by the Cas 12a editing systems.
[00670] Tire Casl2a editing systems described herein may be used to produce transgenic plants with desired phenotypes, including but not limited to, increased disease resistance (e.g., increased viral, bacterial of fungal resistance), increased insect resistance, increased drought resistance, increased yield, and altered fruit ripening characteristics, sugar and oil composition, and color.
[00671] In some embodiments involving Casl2a-based retron editing systems, the retron msr gene, msd gene, and/or ret gene can be expressed in vitro from a vector, such as in an in vitro transcription system. The resulting ncRNA or msDNA can be isolated before being packaged and/or formulated for direct delivery into a host cell. For example, the isolated ncRNA or msDNA can be packaged/formulated in a delivery vehicle such as lipid nanoparticles as described in other sections.
[00672] In some embodiments involving Casl2a-based retron editing systems, the retron msr gene, msd gene, and/or ret gene are expressed in vivo from a vector within a cell. The retron msr gene, msd gene, and/or ret gene can be introduced into a cell with a single vector or in multiple separate vectors to produce msDNA in a host subject.
[00673] In other embodiments, the retron msr gene, msd gene, and/or ret gene, and any other components of the retron-based genome editing systems described herein (e.g., guide RNA in trans, programmable nuclease (e.g., in trans)) may be expressed in vivo from RNA delivered to the cell. The retron msr gene, msd gene, and/or ret gene can be introduced into a cell with a single vector or in multiple separate vectors to produce msDNA in a host subject.
[00674] Vectors and/or nucleic acid molecules encoding the recombinant retron-based genome editing system or components thereof can include control elements operably linked to the retron sequences, which allow for the production of msDNA either in vitro, or in vivo in the subject species. For example, in embodiments relating to Casl2a-based retron editors, the retron msr gene, msd gene, and/or ret gene can be operably linked to a promoter to allow expression of the retron reverse transcriptase and/or the msDNA product. In some embodiments, heterologous sequences encoding desired products of interest e.g., polynucleotide encoding polypeptide or regulatory RNA, donor polynucleotide for gene editing, or protospacer DNA for molecular recording) may be inserted in the msr gene and/or msd gene.
[00675] In some embodiments, the Cast 2a editing systems are produced by a vector system comprising one or more vectors.
[00676] Numerous vectors are available for use in the vector or vector system, including but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses.
Viral vector delivery [00677] In various embodiments, the Cast 2a (or Cas Type V)-based editing systems described herein may be delivered in viral vectors.
[00678] Examples of viral vectors include, but are not limited to, adenoviral vectors, adeno-associated virus (AAV) vectors, retroviral vectors, lentiviral vectors, and the like. An expression construct can be replicated in a living cell, or it can be made synthetically.
[00679] In some embodiments, the nucleic acid comprising an Cas 12a (or Cas Type V) editing system sequence is under transcriptional control of a promoter. In some embodiments, the promoter is competent for initiating transcription of an operably linked coding sequence by a RNA polymerase I, II, or III.
[00680] Exemplary’ promoters for mammalian cell expression include the SV40 early promoter, a CMV promoter such as the CMV immediate early promoter (see, U. S. Patent Nos. 5,168,062 and 5,385,839, incorporated herein by reference in their entireties), the mouse mammary tumor virus LTR promoter, the adenovirus major late promoter (Ad MLP), and the herpes simplex virus promoter, among others. Other nonviral promoters, such as a promoter derived from the murine metallothionein gene, will also find use for mammalian expression.
[00681] Exemplary promoters for plant cell expression include the CaMV 35S promoter (Odell et al., 1985, Nature 313:810-812); the rice actin promoter (McElroy et al., 1990, Plant Cell 2: 163-171); the ubiquitin promoter (Christensen et al., 1989, Plant Mol. Biol. 12:619-632; and Christensen et al., 1992, Plant Mol. Biol. 18:675-689); the pEMU promoter (Last et al., 1991. Theor. Appl. Genet. 81:581-588); and the MAS promoter (Velten et al.. 1984. EMBO J. 3:2723-2730).
[00682] In additional embodiments, tire retron-based vectors may also comprise tissue-specific promoters to start expression only after it is delivered into a specific tissue. Non-limiting exemplary tissue-specific promoters include B29 promoter, CD 14 promoter, CD43 promoter, CD45 promoter, CD68 promoter, desmin promoter, elastase- 1 promoter, endoglin promoter, fibronectin promoter, Flt-1 promoter, GFAP promoter, GPIIb promoter, ICAM- 2 promoter, INF-b promoter, Mb promoter, Nphsl promoter, OG-2 promoter, SP-B promoter, SYN 1 promoter, and WASP promoter.
[00683] These and other promoters can be obtained from or incorporated into commercially available plasmids, using techniques well known in tire art. See, e.g., Sambrook et al., supra.
[00684] In some embodiments, one or more enhancer elements is/are used in association with tire promoter to increase expression levels of the constructs. Examples include the SV40 early gene enhancer, as described in Dijkema et al., EMBOJ (1985) 4:761, the enhancer/promoter derived from the long terminal repeat (LTR) of the Rous Sarcoma Virus, as described in Gorman et al.. Proc. Natl. Acad. Sci. USA ( 1982b) 79:6777, and elements derived from human CMV, as described in Boshart et al., Cell (1985) 41:521, such as elements included in the CMV intron A sequence. All such sequences are incorporated herein by reference.
[00685] In one embodiment, an expression vector for expressing an Casl2a (or Cas Type V) editing system, comprises a promoter operably linked to a polynucleotide encoding the Cas 12a editing system components.
[00686] In some embodiments, the vector or vector system also comprises a transcription terminator/polyadenylation signal. Examples of such sequences include, but are not limited to, those derived from SV40, as described in Sambrook et al., supra, as well as a bovine grow th hormone terminator sequence (see, e.g., U.S. Patent No. 5,122,458).
[00687] Additionally, 5'- UTR sequences can be placed adjacent to the coding sequence to further enhance the expression. Such sequences may include UTRs comprising an internal ribosome entry site (IRES). Inclusion of an IRES permits the translation of one or more open reading frames from a vector. The IRES element attracts a eukaryotic ribosomal translation initiation complex and promotes translation initiation. See, e.g., Kaufman et al., Nuc. Acids Res. (1991) 19:4485-4490; Gurtu et al., Biochem. Biophys. Res. Comm. (1996) 229:295-298: Rees et al., BioTechniques (1996) 20:102-110; Kobayashi et al., BioTechniques (1996) 21:399-402; and Mosser et al., BioTechniques (199722 ISO- 161)c . A multitude of IRES sequences are known and include sequences derived from a wide variety of viruses, such as from leader sequences of picomaviruses such as the encephalomyocarditis virus (EMCV) UTR (Jang et al. . Virol. (1989) 63: 1651- 1660). the polio leader sequence, the hepatitis A virus leader, the hepatitis C virus IRES, human rhinovirus type 2 IRES (Dobrikova et al., Proc. Natl. Acad. Sci. (2003) 100(251: 15125-151301)). an IRES element from the foot and mouth disease virus (Ramesh et al., Nucl. Acid Res. (1996) 24:2697-2700), a giardiavirus IRES (Garlapati et al., J Biol. Chern. (2004) 279(51 ) : 3389-33971 ) and the like. A variety of nonviral IRES sequences will also find use herein, including, but not limited to IRES sequences from yeast, as well as the human angiotensin II type 1 receptor IRES (Martin et al.. Mol. Cell Endocrinol. (2003) 212:51-61), fibroblast growth factor IRESs (FGF-1 IRES and FGF-2 IRES, Martineau et al. (2004) Mol. Cell. Biol. 24( 17): 7622- 7635), vascular endothelial growth factor IRES (Baranick et al. (2008) Proc. Natl. Acad Sci. U.S.A.
105(12):4733-4738, Stein et al. (1998) Mol. Cell. Biol. 18(6):3112-3119, Bert et oZ. (2006) RNA 12(6): 1074-1083), and insulin-like growth factor 2 IRES (Pedersen et al. (2002) Biochem. J. 363(Pt 1) : 37-44).
[00688] These elements are commercially available in plasmids sold, e.g., by Clontech (Mountain View, CA), Invivogen (San Diego, CA), Addgene (Cambridge, MA) and GeneCopoeia (Rockville, MD). See also IRESite: The database of experimentally verified IRES structures (iresite .org). An IRES sequence may be included in a vector, for example, to express multiple bacteriophage recombination proteins for recombineering or an RNA-guided nuclease (e.g., Cas9) for HDR in combination with a retron reverse transcriptase from an expression cassette.
[00689] In some embodiments, a polynucleotide encoding a viral self-cleaving 2A peptide, such as a T2A peptide, can be used to allow production of multiple protein products (e.g., Cas9, bacteriophage recombination proteins, retron reverse transcriptase) from a single vector or a single transcription unit under one promoter. One or more 2A linker peptides can be inserted between the coding sequences in the multicistronic construct. The 2A peptide, which is self-cleaving, allows co-expressed proteins from the multicistronic construct to be produced at equimolar levels. 2A peptides from various viruses may be used, including, but not limited to 2A peptides derived from the foot-and-mouth disease virus, equine rhinitis A virus, Jliosea asigna virus and porcine teschovirus-1. See, e.g., Kim et al. (2011) PLoS One 6(4): el8556, Trichas et al. (2008) BMC Biol. 6:40, Provost et al. (2007) Genesis 45(10): 625-629, Furler c7 r//. (2001) Gene Tlier. 8( 11): 864-873 ; herein incorporated by reference in their entireties.
[00690] In some embodiments, the expression construct comprises a plasmid suitable for transforming a bacterial host. Numerous bacterial expression vectors are known to those of skill in the art, and the selection of an appropriate vector is a matter of choice. Bacterial expression vectors include, but are not limited to. pACYC177, pASK75, pBAD, pBADM, pBAT, pCal, pET. pETM. pGAT. pGEX, pHAT, pKK223, pMal, pProEx, pQE, and pZA31 Bacterial plasmids may contain antibiotic selection markers (e.g., ampicillin, kanamycin, erythromycin, carbenicillin, streptomycin, or tetracycline resistance), a lacZ gene (b- galactosidasc produces blue pigment from x-gal substrate), fluorescent markers (e.g., GFP. mChcrry), or other markers for selection of transfonned bacteria. See, e.g., Sambrook et al., supra.
[00691] In other embodiments, the expression construct comprises a plasmid suitable for transforming a yeast cell. Yeast expression plasmids typically contain a yeast-specific origin of replication (ORI) and nutritional selection markers (e.g., HIS3. URA3. LYS2, LEU2, TRP1. METIS, ura4+, leul+. ade6+), antibiotic selection markers (e.g. , kanamycin resistance), fluorescent markers (e.g. , mCherry), or other markers for selection of transformed yeast cells. The yeast plasmid may further contain components to allow shuttling between a bacterial host (e.g., E coif) and yeast cells. A number of different types of yeast plasmids are available including yeast integrating plasmids (Yip), which lack an ORI and are integrated into host chromosomes by homologous recombination; yeast replicating plasmids (YRp), which contain an autonomously replicating sequence (ARS) and can replicate independently; yeast centromere plasmids (YCp), which are low copy vectors containing a part of an ARS and part of a centromere sequence (CEN); and yeast episomal plasmids (YEp), which are high copy number plasmids comprising a fragment from a 2 micron circle (a natural yeast plasmid) that allows for 50 or more copies to be stably propagated per cell. [00692] In other embodiments, the expression construct does not comprise a plasmid suitable for transforming a yeast cell.
[00693] In other embodiments, the expression construct comprises a virus or engineered construct derived from a viral genome. A number of viral based systems have been developed for gene transfer into mammalian cells. These include adenoviruses, retroviruses (g-retroviruses and lentiviruses), poxviruses, adeno-associated viruses, baculoviruses, and herpes simplex viruses (see e.g.. Warnock et al. (2011) Methods Mol. Biol. 737: 1-25; Walther et al. (2000) Drugs 60(2):249-271; and Lundstrom (2003) Trends Biotechnol. 21(3): 117-122: herein incorporated by reference in their entireties). The ability of certain viruses to enter cells via receptor-mediated endocytosis, to integrate into host cell genomes and express viral genes stably and efficiently have made them attractive candidates for the transfer of foreign genes into mammalian cells.
[00694] For example, retrovimses provide a convenient platform for gene delivery systems. Selected sequences can be inserted into a vector and packaged in retroviral particles using techniques known in the art. The recombinant virus can then be isolated and delivered to cells of the subject either in vivo or ex vivo. A number of retroviral systems have been described (U.S. Pat. No. 5,219,740; Miller and Rosman (1989) BioTechniques 7:980-990; Miller, A. D. (1990) Human Gene Therapy 1:5-14; Scarpa et a/. (1991) Virology 180:849-852: Bums et al. (1993) Proc. Natl. Acad. Sci. USA 90:8033-8037; Bons-Lawne and Temin (1993) Cur. Opin. Genet. Develop. 3: 102-109; and Ferry et al. (201 1) Curr. Pharm. Des. 17(24): 2516-2527).
Lentiviruses are a class of retroviruses that are particularly useful for delivering polynucleotides to mammalian cells because they arc able to infect both dividing and nondividing cells (see e.g., Lois et al. (2002) Science 295:868-872; Durand et al. (2011) Viruses 3(2): 132-159: herein incorporated by reference).
[00695] A number of adenoviral vectors have also been described. Unlike retrovimses which integrate into the host genome, adenoviruses persist extrachromosomally thus minimizing tire risks associated with insertional mutagenesis.
[00696] Additionally, various adeno-associated vims (AAV) vector systems have been developed for gene delivery. AAV vectors can be readily constructed using techniques well known in tire art. See, e.g.. U.S. Pat. Nos. 5,173,414 and 5,139,941; International Publication Nos. WO 92/01070 (published 23 January 1992) and WO 93/03769 (published 4 March 1993); Lebkowski et al., Molec. Cell. Biol. (1988) 8:3988-3996; Vincent et al., Vaccines 90 (1990) (Cold Spring Harbor LaboratoryPress); Carter, B. J. Current Opinion in Biotechnology (1992) 3:533-539; Muzyczka, N. Current Topics in Microbiol and Immunol. (1992) 158:97- 129; Kotin, R. M. Human Gene Urerapy (1994) 5:793-801: Shelling and Smith, Gene Therapy (1994) 1: 165- 169; and Zhou et al., J. Exp. Med. (1994) 179: 1867-1875. [00697] Another vector system useful for delivering nucleic acids encoding the Casl2a editing system components is the enterically administered recombinant poxvirus vaccines described by Small, Jr., P. A., et al. (U.S. Pat. No. 5,676,950, issued Oct. 14, 1997, herein incorporated by reference).
[00698] Other viral vectors include those derived from the pox family of viruses, including vaccinia virus and avian poxvirus. By way of example, vaccinia virus recombinants expressing a nucleic acid molecule of interest (e.g., Casl2a editing system) can be constructed as follows. The DNA encoding the particular nucleic acid sequence is first inserted into an appropriate vector so that it is adjacent to a vaccinia promoter and flanking vaccinia DNA sequences, such as the sequence encoding thymidine kinase (TK). This vector is then used to transfect cells which are simultaneously infected with vaccinia. Homologous recombination serves to insert the vaccinia promoter plus the gene encoding the sequences of interest into the viral genome. The resulting TK-recombinant can be selected by culturing the cells in the presence of 5- bromodeox uridinc and picking viral plaques resistant thereto.
[00699] In some embodiments, avipoxviruses, such as the fowlpox and canarypox viruses, can also be used to deliver tire nucleic acid molecules of interest. Hie use of an avipox vector is particularly desirable in human and other mammalian species since members of the avipox genus can only productively replicate in susceptible avian species and therefore are not infective in mammalian cells. Methods for producing recombinant avipoxviruses are known in the art and employ genetic recombination, as described above with respect to the production of vaccinia viruses. See, e.g., WO 91/12882; WO 89/03429; and WO 92/03545.
[00700] Molecular conjugate vectors, such as the adenovirus chimeric vectors described in Michael et al. , J. Biol. Chem. (1993) 268:6866-6869 and Wagner etal., Proc. Natl. Acad. Sci. USA (1992) 89:6099-6103, can also be used for gene delivery.
[00701] Members of the alphavirus genus, such as, but not limited to, vectors derived from the Sindbis virus (SIN), Semliki Forest virus (SFV), and Venezuelan Equine Encephalitis virus (VEE), will also find use as viral vectors for delivering the polynucleotides of the present invention. For a description of Sindbis-virus derived vectors useful for the practice of the instant methods, see, Dubensky etal. (1996) J. Virol. 70:508- 519; and International Publication Nos. WO 95/07995, WO 96/17072; as well as, Dubensky, Jr., T. W., etal., U.S. Pat. No. 5,843,723, issued Dec. 1, 1998, and Dubensky, Jr., T. W., U.S. Patent No. 5,789,245, issued Aug. 4, 1998, both herein incorporated by reference. Particularly preferred are chimeric alphavirus vectors comprised of sequences derived from Sindbis virus and Venezuelan equine encephalitis virus. See, e.g., Perri et al. (2003) J. Virol. 77: 10394-10403 and International Publication Nos. WO 02/099035, WO 02/080982. WO 01/81609, and WO 00/61772; herein incorporated by reference in their entireties. [00702] A vaccinia-based infection/transfection system can be conveniently used to provide for inducible, transient expression of the nucleic acids of interest (e.g., Casl2a editing system) in a host cell. In this system, cells are first infected in vitro with a vaccinia virus recombinant that encodes the bacteriophage T7 RNA polymerase. This polymerase displays exquisite specificity in that it only transcribes templates bearing T7 promoters. Following infection, cells are transfected with the nucleic acid of interest, driven by a T7 promoter. The polymerase expressed in the cytoplasm from the vaccinia virus recombinant transcribes the transfected DNA into RNA. The method provides for high level, transient, cytoplasmic production of large quantities of RNA. See, e.g., Elroy-Stein and Moss, Proc. Natl. Acad. Sci. USA (1990) 87:6743- 6747; Fuerst et al.. Proc. Natl. Acad. Sci. USA (1986) 83:8122-8126.
[00703] In other approaches to infection with vaccinia or avipox virus recombinants, or to the delivery of nucleic acids using other viral vectors, an amplification system can be used that will lead to high level expression following introduction into host cells. Specifically, a T7 RNA polymerase promoter preceding the coding region for T7 RNA polymerase can be engineered. Translation of RNA derived from this template will generate T7 RNA polymerase which in turn will transcribe more templates. Concomitantly, there will be a cDNA whose expression is under the control of the T7 promoter. Thus, some of the T7 RNA polymerase generated from translation of the amplification template RNA will lead to transcription of the desired gene. Because some T7 RNA polymerase is required to initiate the amplification, T7 RNA polymerase can be introduced into cells along with the template(s) to prime tire transcription reaction. The polymerase can be introduced as a protein or on a plasmid encoding the RNA polymerase. For a further discussion of T7 systems and their use for transfonning cells, see, e.g.. International Publication No. WO 94/26911; Studier and Moffatt, J. Mol. Biol. (1986) 189: 1 13-130; Deng and Wolff, Gene (1994) 143:245-249; Gao etal., Biochem. Biophys. Res. Commun. (1994) 200: 1201-1206; Gao and Huang, Nuc. Acids Res. (1993) 21:2867- 2872; Chen et a/., Nuc. Acids Res. (1994) 22:2114-2120; and U.S. Pat. No. 5,135,855.
[00704] Insect cell expression systems, such as baculovims systems, can also be used and are known to those of skill in the art and described in, e.g, Baculovims and Insect Cell Expression Protocols (Methods in Molecular Biology, D.W. Murhammer ed., Humana Press, 2nd edition, 2007) and E. King The Baculovims Expression System: A laboratory guide (Springer, 1992). Materials and methods for baculovirus/insect cell expression systems are commercially available in kit form from, inter alia, Thermo Fisher Scientific (Waltham, MA) and Clontech (Mountain View, CA).
[00705] Plant expression systems can also be used for transforming plant cells. Generally, such systems use virus-based vectors to transfect plant cells with heterologous genes. For a description of such systems see, e.g, Porta et al., Mol. Biotech. (1996) 5:209-221; and Hackland et al., Arch. Virol. (1994) 139: 1-22. [00706] To obtain expression of the Cast 2a (or Cas Type V) editing system or the ncRNA encoded thereby, the expression construct or the ncRNA must be delivered into a cell. This delivery may be accomplished in vitro, as in laboratory7 procedures for transforming cells lines, or in vivo or ex vivo, as in the treatment of certain disease states. One mechanism for delivery is via viral infection where the expression construct is encapsulated in an infectious viral particle.
Non-viral delivery methods
[00707] Several non-viral methods for the transfer of expression constructs are available for delivering the Cas 12a (or Cas Type V) editing systems or components thereof into cells also are contemplated. These include the use of calcium phosphate precipitation, DEAE-dextran, electroporation, direct microinjection, DNA-loaded liposomes, lipofectamine-DNA complexes, cell sonication, gene bombardment using high velocity microprojectiles, and receptor-mediated transfection (see, e.g., Graham and Van Der Eb (1973) Virology 52:456-467; Chen and Okayama (1987) Mol. Cell Biol. 7:2745-2752; Rippe et al. (1990) Mol. Cell Biol. 10:689-695; Gopal (1985) Mol. Cell Biol. 5: 1188-1190: Tur-Kaspa et al. (1986) Mol. Cell. Biol. 6:716- 718; Potter et al. (1984) Proc. Natl. Acad. Sci. USA 81:7161-7165); Harland and Weintraub (1985) J. Cell Biol. 101 :1094-1099): Nicolau & Sene (1982) Biochim. Biophys. Acta 721: 185-190; Fraley et al. (1979) Proc. Natl. Acad. Sci. USA 76:3348-3352; Fechheimer et al. (1987) Proc Natl. Acad. Sci. USA 84:8463- 8467; Yang et al. (1990) Proc. Natl. Acad. Sci. USA 87:9568-9572; Wu and Wu (1987) J. Biol. Chem.
262:4429-4432; Wu and Wu (1988) Biochemistry 27:887-892; herein incorporated by reference). Some of these techniques may be successfully adapted for in vivo or ex vivo use.
[00708] In some embodiments, nucleic acid molecules encoding the Cas 12a (or Cas Type V) gene editing systems or components thereof may be stably integrated into the genome of the cell. This integration may be in the cognate location and orientation via homologous recombination (gene replacement) or it may be integrated in a random, non-specific location (gene augmentation). In yet further embodiments, the nucleic acid may be stably maintained in the cell as a separate, episomal segment of DNA. Such nucleic acid segments or cpisomcs encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle. How the expression construct is delivered to a cell and where in the cell the nucleic acid remains is dependent on the type of expression construct employed.
[00709] In some embodiments, expression constructs encoding the Cas 12a (or Cas Type V) gene editing systems or components thereof may simply consist of naked recombinant DNA or plasmids comprising nucleotide sequences encoding said Cas 12a gene editing systems or components thereof. Transfer of the construct may be performed by any of the methods mentioned above which physically or chemically permeabilize the cell membrane. This is particularly applicable for transfer in vitro but it may be applied to in vivo use as well. Dubensky et al. (Proc. Natl. Acad. Sci. USA (1984) 81:7529-7533) successfully injected polyomavirus DNA in the form of calcium phosphate precipitates into liver and spleen of adult and newborn mice demonstrating active viral replication and acute infection. Benvenisty & Neshif (Proc. Natl. Acad. Sci. USA (1986) 83:9551-9555) also demonstrated that direct intraperitoneal injection of calcium phosphate- precipitated plasmids results in expression of the transfected genes. It is envisioned that DNA encoding an Casl2a editing system of interest may also be transferred in a similar manner in vivo and express retron products.
[00710] In still another embodiment, DNA expression constructs encoding the Casl2a (or Cas Type V) gene editing systems or components thereof may be transferred into cells by particle bombardment. This method depends on the abi 1 i ty to accelerate DNA-coated microprojectiles to a high velocity allowing them to pierce cell membranes and enter cells without killing them (Klein et al. (1987) Nature 327:70-73). Several devices for accelerating small particles have been developed. One such device relies on a high voltage discharge to generate an electrical current, which in turn provides the motive force (Yang et al. (1990) Proc. Natl. Acad. Sci. USA 87:9568-9572). The microprojectiles may consist of biologically inert substances, such as tungsten or gold beads.
Liposomes
[00711] In a further embodiment, constructs encoding the Cas 12a (or Cas Type V) gene editing systems or components thereof may be delivered using liposomes. Liposomes are vesicular structures characterized by a phospholipid bilaycr membrane and an inner aqueous medium. Multilamcllar liposomes have multiple lipid layers separated by aqueous medium. They fomi spontaneously when phospholipids are suspended in an excess of aqueous solution. Tire lipid components undergo self-rearrangement before the formation of closed structures and entrap water and dissolved solutes between tire lipid bilayers (Ghosh & Bachhawat (1991) Liver Diseases, Targeted Diagnosis and Therapy Using Specific Receptors and Ligands, Wu etal. (Eds.), Marcel Dekker, NY, 87-104). Also contemplated is the use of lipofectamine-DNA complexes.
[00712] In some embodiments, the liposome may be complexed with a hemagglutinating virus (HVJ). This has been shown to facilitate fusion with the cell membrane and promote cell entry of liposome-encapsulated DNA (Kaneda et al. (1989) Science 243:375-378). In other embodiments, the liposome may be complexed or employed in conjunction with nuclear non-histone chromosomal proteins (HMG-I) (Kato et al. (1991) J. Biol. Chem. 266(6):3361-3364).
[00713] In yet further embodiments, the liposome may be complexed or employed in conjunction w ith both HVJ and HMG-I. Where a bacterial promoter is employed in the DNA construct, it also will be desirable to include within the liposome an appropriate bacterial polymerase. [00714] Liposomes can be made from several different types of lipids, e.g., phospholipids. A liposome may comprise natural phospholipids and lipids such as l,2-distearoryl-sn-glycero-3 -phosphatidyl choline (DSPC), sphingomyelin, egg phosphatidylcholines, monosialoganglioside, or any combination thereof.
[00715] Several other additives may be added to liposomes in order to modify their structure and properties. For instance, liposomes may further comprise cholesterol, sphingomyelin, and/or l,2-dioleoyl-sn-glycero-3- phosphoethanolamine (DOPE), e.g., to increase stability and/or to prevent the leakage of the liposomal inner cargo.
[00716] In one embodiment, the liposome comprises a transport polymer, which may optionally be branched, comprising at least 10 amino acids and a ratio of histidine to non-histidine amino acids greater than 1.5 and less than 10. The branched transport polymer can comprise one or more backbones, one or more terminal branches, and optionally, one or more non-terminal branches. See, U.S. Patent No. 7,070,807, incorporated herein by reference in its entirety. In one embodiment, the transposrt polymer is a Histidine-Lysine copolymer (HKP) used to package and deliver mRNA and other cargos. See, U.S. Patent Nos., 7, 163,695, and 7,772,201 , incorporated herein by reference in their entireties,
[00717] In one embodiment, the lipid particles may be stable nucleic acid lipid particles (SNALPs). SNALPs may comprise an ionizable lipid (DLinDMA) (e.g., cationic at low pH), a neutral helper lipid, cholesterol, a diffusible polyethylene glycol (PEG)-lipid, or any combination thereof. In some examples, SNALPs may comprise synthetic cholesterol, dipalmitoylphosphatidylcholine, 3-N-[(w-methoxy polyethylene glycol)2000)carbamoyl]-l,2- dimyrestyloxypropylamine, and cationic l,2-dilinoleyloxy-3- N,Ndimethylaminopropane. In some examples, SNALPs may comprise synthetic cholesterol, 1,2-distearoyl- sn-glycero-3 -phosphocholine, PEG- eDMA, and l,2-dilinoleyloxy-3-(N;N-dimethyl)aminopropane (DLinDMA).
Polymer based vehicles
[00718] In one embodiment, the delivery vehicles may comprise polymer-based particles (e.g., nanoparticles). In one embodiment, the polymer-based particles may mimic a viral mechanism of membrane fusion. Tire polymcr-bascd particles may be a synthetic copy of Influenza virus machinery and form transfection complexes with various types of nucleic acids ((siRNA, miRNA, plasmid DNA or snucleic acid component, mRNA) that cells take up via the endocytosis pathway, a process that involves the formation of an acidic compartment. The low pH in late endosomes acts as a chemical switch that renders the particle surface hydrophobic and facilitates membrane crossing. Once in the cytosol, the particle releases its payload for cellular action. This Active Endosome Escape technology is safe and maximizes transfection efficiency as it is using a natural uptake pathway. In one embodiment, the polymer-based particles may comprise alkylated and carboxyalkylated branched polyethylenimine. In some examples, the polymer-based particles are VIROMER, e.g., VIROMER RNAi, VIROMER RED, VIROMER mRNA. Example methods of delivering the systems and compositions herein include those described in Bawage SS et al.. Synthetic mRNA expressed Cast 3a mitigates RNA virus infections, biorxiv.org/content/10.1101/370460vl. full doi: doi.org/10.1101/370460, Viromer® RED, a powerful tool for transfection of kcratinocytcs. doi: 10.13140/RG.2.2.16993.61281, Viromer® Transfection - Factbook 2018: technology, product overview, users' data., doi: 10.13140/RG.2.2.23912.16642.
Exosomes
[00719] The delivery vehicles may comprise exosomes. Exosomes include membrane bound extracellular vesicles, which can be used to contain and delivery various ty pes of biomolecules, such as proteins, carbohydrates, lipids, and nucleic acids, and complexes thereof (e.g., RNPs). Examples of exosomes include those described in Schroeder A, et al., J Intern Med. 2010 Jan;267(l):9-21; El-Andaloussi S, et al., Nat Protoc. 2012 Dec;7(12):2112-26: Uno Y. et al.. Hum
[00720] Gene Ther. 2011 Jun;22(6):711-9; Zou W, et al., Hum Gene Then 2011 Apr;22(4):465-75. Exemplary exosomes can be generated from 293F cells, with mRNA-loaded exosomes driving higher mRNA expression than mRNA loaded LNPs in some instances. See, e.g. J. Biol. Chem. (2021) 297(5) 101266
[00721] In some examples, the exosome may form a complex (e.g., by binding directly or indirectly) to one or more components of the cargo. In certain examples, a molecule of an exosome may be fused with first adapter protein and a component of the cargo may be fused with a second adapter protein. The first and the second adapter protein may specifically bind each other, thus associating the cargo with the exosome. Examples of such exosomes include those described in Ye Y. et al.. Biomater Sci. 2020 Apr 28. doi: 10.1039/d0bm00427h.
Receptor-mediated delivery
[00722] Other expression constructs encoding the Casl2a (or Cas Type V) gene editing systems or components thereof are receptor-mediated delivery vehicles. These take advantage of the selective uptake of macromolecules by receptor-mediated endocytosis in almost all eukaryotic cells. Because of the cell typespecific distribution of various receptors, the delivery can be highly specific (Wu and Wu (1993) Adv. Drug Delivery Rev. 12: 159- 167). Receptor-mediated gene targeting vehicles generally consist of two components: a cell receptor-specific ligand and a DNA-binding agent. Several ligands have been used for receptor- mediated gene transfer. Tire most extensively characterized ligands are asialoorosomucoid (ASOR) and transferrin (see, e.g., Wu and Wu (1987), supra: Wagner et al. (1990) Proc. Natl. Acad. Sci. USA 87(9):3410- 3414). A synthetic neoglycoprotein, which recognizes the same receptor as ASOR, has been used as a gene delivery' vehicle (Ferkol et al. (1993) FASEB J. 7: 1081-1091; Perales et al. (1994) Proc. Natl. Acad. Sci. USA 91(9):4086-4090), and epidermal grow th factor (EGF) has also been used to deliver genes to squamous carcinoma cells (Myers, EPO 0273085).
[00723] In other embodiments, delivery vehicle comprising one or more expression constructs encoding the Casl2a gene editing systems or components thereof may comprise a ligand and a liposome. For example, Nicolau et al. (Methods Enzymol. (1987) 149: 157-176) employed lactosy 1-ceramide, a galactose-terminal asialoganglioside, incorporated into liposomes and observed an increase in the uptake of the insulin gene by hepatocytes. Thus, it is feasible that a nucleic acid encoding a particular gene also may be specifically delivered into a cell by any number of receptor-ligand systems with or without liposomes. Also, antibodies to surface antigens on cells can similarly be used as targeting moieties.
[00724] In some embodiments, the promoters that may be used in the Casl2a gene editor delivery systems described herein may be constitutive, inducible, or tissue-specific. In some embodiments, the promoters may be a constitutive promoters. Non-limiting exemplary constitutive promoters include cytomegalovirus immediate early promoter (CMV), simian virus (SV40) promoter, adenovirus major late (MLP) promoter, Rous sarcoma virus (RSV) promoter, mouse mammary tumor virus (MMTV) promoter, phosphoglycerate kinase (PGK) promoter, elongation factor-alpha (EFla) promoter, ubiquitin promoters, actin promoters, tubulin promoters, immunoglobulin promoters, a functional fragment thereof, or a combination of any of the foregoing. In some embodiments, tire promoter may be a CMV promoter. In some embodiments, the promoter may be a truncated CMV promoter. In other embodiments, the promoter may be an EFla promoter. In some embodiments, the promoter may be an inducible promoter. Non-limiting exemplary inducible promoters include those inducible by heat shock, light, chemicals, peptides, metals, steroids, antibiotics, or alcohol. In some embodiments, the inducible promoter may be one that has a low basal (non-induced) expression level, such as, e.g., the Tet-On® promoter (Clontech). In some embodiments, the promoter may be a tissue-specific promoter. In some embodiments, the tissue-specific promoter is exclusively or predominantly expressed in liver tissue. Non-limiting exemplary tissue-specific promoters include B29 promoter. CD 14 promoter, CD43 promoter, CD45 promoter, CD68 promoter, desmin promoter, elastase- 1 promoter, endoglin promoter, fibronectin promoter. Fit- 1 promoter, GFAP promoter, GPIIb promoter, ICAM- 2 promoter, INF-b promoter, Mb promoter, Nphsl promoter, OG-2 promoter, SP-B promoter, SYN 1 promoter, and WASP promoter. Lipid nanoparticles (LNPs)
[00725] The payloads (e.g., linear and circular mRNAs; nucleobase editing systems and/or components thereof) described herein may be encapsulated and delivered by lipid nanoparticles (LNPs) and compositions and/or formulations comprising RNA-encapsulated LNPs.
[00726] Below describes LNPs that may be used as the payload delivery vehicles contemplated herein, as well as the various ionizable lipids, structural lipids, PEGylated lipids, and phospholipids that may be used to make the herein LNPs for delivery payloads to cells. In addition, below describes additional LNP components that are contemplated, such as targeting moieties and other lipid components.
[00727] In one aspect, the present disclosure further provides delivery systems for delivery of a therapeutic payload (e.g.. the RNA payloads described herein which may encode a polypeptide of interest, e.g., a nucleobase editing system or a therapeutic protein) disclosed herein. In some embodiments, a delivery system suitable for delivery' of the therapeutic payload disclosed herein comprises a lipid nanoparticle (LNP) formulation.
[00728] In some embodiments, an LNP delivery vehicle of the present disclosure comprises an ionizable lipid, a structural lipid, a PEGylated lipid (aka PEG lipid), and a phospholipid. In alternative embodiments, an LNP delivery vehicle comprises an ionizable lipid, a structural lipid, a PEGylated lipid (aka PEG lipid), and a zwitterionic amino acid lipid. In some embodiments, an LNP delivery vehicle further comprises a 5th lipid, in addition to the aforementioned lipid components. In some embodiments, an LNP delivery vehicle encapsulates one or more nucleic acid cargoes of the present disclosure. For example, in some embodiments, an LNP delivery' vehicle encapsulates one or more mRNA cargoes encoding one or more polypeptides (e.g., a therapeutic protein) with an activity . In some embodiments, an LNP delivery vehicle further comprises one or more targeting moieties covalently or non-covalently bound to the outer surface of the LNP delivery vehicle. In some embodiments, a targeting moiety is a moiety that binds to. or otherwise facilitates uptake by, cells of one or more specific cell populations.
[00729] In some embodiments, an LNP delivery vehicle has a diameter of at least about 20nm, 30 nm, 40nm. 50nm, 60nm, 70nm, 80nm, or 90nm. In some embodiments, an LNP delivery vehicle has a diameter of less than about lOOnm, HOnm, 120nm, 130nm, 140nm, 150nm, or 160nm. In some embodiments, an LNP has a diameter of less than about 120 nm. In some embodiments, an LNP delivery' vehicle has a diameter of less than about lOOnm. In some embodiments, an LNP delivery vehicle has a diameter of less than about 90nm. In some embodiments, an LNP delivery vehicle has a diameter of less than about 80nm. In some embodiments, an LNP delivery vehicle has a diameter of about 60- lOOnm. In some embodiments, an LNP delivery vehicle has a diameter of about 50-120nm. In some embodiments, an LNP delivery vehicle has a diameter of about 75-80nm.
[00730] In some embodiments, the LNP delivery vehicles of the present disclosure are described according to the respective molar ratios of the component lipids in the formulation. As a non-limiting example, the mol-% of tire ionizable lipid may be from about 10 mol-% to about 80 mol-%. As a non-limiting example, the mol-% of tire ionizable lipid may be from about 20 mol-% to about 70 mol-%. As a non-limiting example, the mol-% of the ionizable lipid may be from about 30 mol-% to about 60 mol-%. As a non-limiting example, the mol-% of the ionizable lipid may be from about 35 mol-% to about 55 mol-%. As a non-limiting example, the mol-% of tire ionizable lipid may be from about 40 mol-% to about 50 mol-%. As a non-limiting example, the mol-% of tire ionizable lipid may be from about 30 mol-% to about 40 mol-%. As a non -limiting example, the mol- % of the ionizable lipid may be from about 25 mol-% to about 35 mol-%. In some embodiments, the mol-% of the ionizable lipid is about 10 mol-%. In some embodiments, tire mol-% of the ionizable lipid is about 15 mol-%. In some embodiments, the mol-% of the ionizable lipid is about 20 mol-%. In some embodiments, the mol-% of the ionizable lipid is about 25 mol-%. In some embodiments, the mol-% of the ionizable lipid is about 30 mol-%. In some embodiments, the mol-% of the ionizable lipid is about 33 mol-%. In some embodiments, the mol-% of the ionizable lipid is about 35 mol-%. In some embodiments, the mol-% of the ionizable lipid is about 40 mol-%. In some embodiments, the mol-% of the ionizable lipid is about 45 mol- %. In some embodiments, the mol-% of tire ionizable lipid is about 55 mol-%. In some embodiments, the mol-% of the ionizable lipid is about 60 mol-%.
[00731] In some embodiments, the mol-% of the phospholipid may be from about 1 mol-% to about 50 mol- %. In some embodiments, the mol-% of the phospholipid may be from about 2 mol-% to about 45 mol-%. In some embodiments, the mol-% of the phospholipid may be from about 3 mol-% to about 40 mol-%. In some embodiments, the mol-% of the phospholipid may be from about 4 mol-% to about 35 mol-%. In some embodiments, the mol-% of the phospholipid may be from about 5 mol-% to about 30 mol-%. In some embodiments, the mol-% of the phospholipid may be from about 10 mol-% to about 20 mol-%. In some embodiments, the mol-% of the phospholipid may be from about 5 mol-% to about 20 mol-%. In some embodiments, the mol-% of the phospholipid is from about 30 mol-% to about 60 mol-%. In some embodiments, the mol-% of the phospholipid is from about 35 mol-% to about 55 mol-%. In some embodiments, the mol-% of the phospholipid is from about 35 mol-% to about 45 mol-%. In some embodiments, the mol-% of the phospholipid is about 10 mol-%. In some embodiments, the mol-% of the phospholipid is about 15 mol-%. In some embodiments, the mol-% of the phospholipid is about 20 mol-%. In some embodiments, the mol-% of the phospholipid is about 25 mol-%. In some embodiments, the mol-% of the phospholipid is about 30 mol-%. In some embodiments, the mol-% of the phospholipid is about 35 mol-%. In some embodiments, the mol-% of the phospholipid is about 40 mol-%. In some embodiments, the mol-% of the phospholipid is about 45 mol-%. In some embodiments, the mol-% of the phospholipid is about 55 mol-%. In some embodiments, the mol-% of the phospholipid is about 60 mol-%.
[00732] In some embodiments, the mol-% of the phospholipid as described above comprises two or more phospholipids at an individual mol-% that totals to an aforementioned amount. In certain embodiments, the mol-% of the phospholipid is about 20 mol-% each of two phospholipids. In certain embodiments, the mol- % of the phospholipid is about 15 mol-% each of two phospholipids. In certain embodiments, the mol-% of the phospholipid is about 25 mol-% each of two phospholipids. In certain embodiments, the mol-% of the phospholipid is about 30 mol-% each of two phospholipids. In certain embodiments, the mol-% of the phospholipid is about 15 mol-% of a first phospholipid and about 20 mol-% of a second phospholipid. In certain embodiments, the mol-% of the phospholipid is about 30 mol-% of a first phospholipid and about 10 mol-% of a second phospholipid. In certain embodiments, the mol-% of the phospholipid is about 25 mol-% of a first phospholipid and about 10 mol-% of a second phospholipid. In certain embodiments, the mol-% of the phospholipid is about 25 mol-% of a first phospholipid and about 20 mol-% of a second phospholipid. In certain embodiments, the mol-% of the phospholipid is about 15 mol-% of a first phospholipid and about 20 mol-% of a second phospholipid.
[00733] In some embodiments, the mol-% of the structural lipid may be from about 10 mol-% to about 80 mol-%. In some embodiments, the mol-% of the structural lipid may be from about 20 mol-% to about 70 mol-%. In some embodiments, the mol-% of the structural lipid may be from about 30 mol-% to about 60 mol-%. In some embodiments, the mol-% of the structural lipid may be from about 35 mol-% to about 55 mol-%. In some embodiments, the mol-% of the structural lipid may be from about 40 mol-% to about 50 mol-%.
[00734] In some embodiments, the mol-% of the PEG lipid may be from about 0. 1 mol-% to about 10 mol-%. In some embodiments, the mol-% of the PEG lipid may be from about 0.2 mol-% to about 5 mol-%. In some embodiments, the mol-% of the PEG lipid may be from about 0.5 mol-% to about 3 mol-%. In some embodiments, the mol-% of the PEG lipid may be from about 1 mol-% to about 2 mol-%. In some embodiments, the mol-% of the PEG lipid may be about 1.5 mol-%. In some embodiments, the mol-% of the PEG lipid may be about 2.5 mol-%. i. Ionizable lipids
[00735] In some embodiments, an LNP disclosed herein comprises an ionizable lipid. In some embodiments, an LNP comprises two or more ionizable lipids. [00736] Described below are a number of exemplary ionizable lipids of the present disclosure. In some embodiments, ionizable lipids of the present disclosure are selected from any lipid described below, an enantiomer thereof, or any mixture of enantiomers thereof, or a pharmaceutically acceptable salt of any of the aforementioned.
[00737] In some embodiments, an LNP of the present disclosure comprises an ionizable lipid disclosed in one of US 2023/0053437; US 2019/0240354; US 2010/0130588; US 2021/0087135; WO 2021/204179; US 2021/0128488; US 2020/0121809; US 2017/0119904; US 2013/0108685; US 2013/0195920: US 2015/0005363; US 2014/0308304; US 2013/0053572; WO 2019/232095A1; WO 2021/077067; WO 2019/152557; US 2017/0210697; or WO 2019/089828A1, each of which is incorporated by reference herein in their entirety.
[00738] In some embodiments, an LNP described herein comprises a lipid, e.g., an ionizable lipid, disclosed in US Application publication US2017/0119904, which is incorporated by reference herein, in its entirety.
[00739] In some embodiments, an LNP described herein comprises a lipid, e.g., an ionizable lipid, disclosed in PCT Application Publication WO2021/204179, which is incorporated by reference herein, in its entirety.
[00740] In some embodiments, an LNP described herein comprises a lipid, e.g., an ionizable lipid, disclosed in PCT Application Publication WO2022/251665A1, which is incorporated by reference herein, in its entirety.
[00741] In some embodiments, an LNP described herein comprises a lipid, e.g., an ionizable lipid, disclosed in any one of PCT Application Publications WO2023044343A1, WO2023044333A1, WO2023122752A1, WO2023196931A1, WO2024192277A1, WO2019236673, WO2020237227, WO2021113777, WO2021226597, WO2021189059, WO2021236855, WO2022261490, W02023056033, WO2023081526. WO2023044343, WO2023044333, WO2023122752, WO2024044728, WO2023196931, WO2024102762, WO2024129982, and WO2024102677, and Application PCT/US2024/034752, each of which is incorporated by reference herein, in its entirety.
[00742] In some embodiments, an LNP described herein comprises an ionizable lipid of Formula (AX): or a pharmaceutically acceptable salt thereof, wherein: A is selected from an optionally substituted bridged carbocyclic or heterocyclic core selected from the group n is and integer selected from 1 or 2;
R1 is selected from the group consisting of -OH, -OAc, -NR2, each R is independently -H or Ci-Cs aliphatic;
X1 and XA are each independently a bond or optionally substituted Ci-Ce aliphatic;
Y1 is selected from the group consisting of bond; wherein the bond marked with an is attached to X1; each X2 and X3 is independently a bond or optionally substituted C1-C12 aliphatic; each Y2 and Y3 is independently selected from the group consisting of wherein the bond marked with an is attached to X2 or X3; each X4 and X5 is independently optionally substituted Ci-Ce aliphatic;
R2 is -CH(OR6)(OR7), -CH(SR6)(SR7), -CH(R6)(R7), -R10, optionally substituted C5-C18 aliphatic, or optionally substituted C1-C14 aliphatic-R10, wherein one or more methylene linkages of R2 are each optionally and independently replaced with an optionally substituted Cs-Cg cycloalkylenyl, phenyl, -O-, -NH-, -S-, -SS-, -C(O)-, - OC(O)O-, -OC(O)-, -NHC(O)-, or -C(O)O-; each R3 is independently -CH(OR8)(OR9), -CH(SR8)(SR9), -CH(R8)(R9), -R11, optionally substituted C5-Ci8 aliphatic, or optionally substituted C1-C14 aliphatic-R11, wherein one or more methy lene linkages ofR3 are each optionally and independently replaced with an optionally substituted C3-C8 cycloalkylenyl, phenyl, -O-, -NH-, -S-, -SS-, -C(O)-, -OC(O)O-, -OC(O)-, -NHC(O)-, or -C(O)O-;
R6 and R7 are each independently optionally substituted -C1-C14 aliphatic, -R10, or optionally substituted -C1-C14 aliphatic -R10; wherein one or more methylene linkages of R6 and R7 are each optionally and independently replaced with an optionally substituted Cs-Cs cycloalkylenyl, phenyl, -O-, -NH-, -S-, -SS-, -C(O)-, -OC(O)O-, - OC(O)-, -NHC(O)-, or -C(O)O-;
Rs and R9 are each independently optionally substituted -C1-C14 aliphatic, -R11, or optionally substituted -C1-C14 aliphatic-R11; wherein one or more methylene linkages of R8 and R9 are each optionally and independently replaced with an optionally substituted C--Cs cycloalkylenyl, phenyl, -O-, -NH-, -S-, -SS-, -C(O)-, -OC(O)O-, - OC(O)-, -NHC(O)-, or -C(O)O-; each R10 and R11 is independently an optionally substituted cylic, bicyclic, bridged bicyclic, multicyclic or bridged multicyclic C4-C14 cycloalkyl or optionally substituted cylic, bicyclic, bridged bicyclic, multicyclic or bridged multicyclic 4-14 membered heterocyclyl, or two R1CI or two R11 taken together form an optionally substituted bridged bicyclic or multicyclic C4-C14 cycloalkyl or optionally substituted bridged bicyclic or multicyclic 4-14 membered heterocyclyl.
Additional Formulae
[0001] The present disclosure, in some embodiments, provides compounds of any one of the Formulae below:
(AX-H), 99
(AX-AC), (AX-AC”),
(AX-AF), 11 (AX-AJ), (AX-AK),
(AX-AM), (AX-AN),
(AX-AO), (AX-AO ) or a pharmaceutically acceptable salt thereof, wherein R1, R, X1, XA, X2, X3, X4, X5, Y1, Y2, Y3, R3, R6, R7, R8, R9, R10, and R11 arc as described in Formula (AX).
Table (AX). Non-Limiting Examples of Ionizable ionizable lipids of the present disclosure
ii. Structural lipids
[00743] In some embodiments, an LNP comprises a structural lipid. In some embodiments, an LNP comprises two or more structural lipids. Structural lipids can be selected from the group consisting of, but are not limited to, cholesterol, fccostcrol, fiicostcrol, beta sitosterol, sitosterol, ergosterol, campcstcrol, stigmastcrol, brassicasterol, tomatidine, cholic acid, sitostanol, litocholic acid, tomatine, ursolic acid, alpha-tocopherol, Vitamin D3, Vitamin D2. Calcipotriol, botulin, lupeol, oleanolic acid, beta-sitosterol-acetate and mixtures thereof. In some embodiments, the structural lipid is cholesterol. In some embodiments, the structural lipid is a cholesterol analogue disclosed by Patel, et al., Nat Commun., 11, 983 (2020), which is incorporated herein by reference in its entirety. In some embodiments, the structural lipid comprises cholesterol and a corticosteroid (such as prednisolone, dexamethasone, prednisone, and hydrocortisone), or any combinations thereof. In some embodiments, a structural lipid is described in international patent application WO2019152557A1, which is incorporated herein by reference in its entirety. [00744] In some embodiments, a structural lipid is a cholesterol analog. Using a cholesterol analog may enhance endosomal escape as described in Patel et al.. Naturally-occurring cholesterol analogues in lipid nanoparticles induce polymorphic shape and enhance intracellular deliver of mRNA, Nature Communications (2020), which is incorporated herein by reference.
[00745] In some embodiments, a structural lipid is a phytosterol. Using a phytosterol may enhance endosomal escape as described in Herrera et al ., Illuminating endosomal escape of polymorphic lipid nanoparticles that boost mRNA delivery, Biomaterials Science (2020), which is incorporated herein by reference.
[00746] In some embodiments, a structural lipid contains plant sterol mimetics for enhanced endosomal release.
Hi. PEGylated lipids
[00747] A PEGylated lipid is a lipid modified with polyethylene glycol.
[00748] In some embodiments, an LNP comprises one, two or more PEGylated lipid or PEG-modified lipid. A PEGylated lipid may be selected from the non-limiting group consisting of PEG-modified phosphatidylethanolamines, PEG-modified phosphatidic acids, PEG-modified ceramides, PEG-modified dialkylamines, PEG-modified diacylglycerols, PEG-modified dialkylglycerols, and mixtures thereof. For example, a PEG lipid may be PEG-c-DOMG, PEG-DMG, PEG-DLPE, PEG-DMPE, PEG-DPPC, or a PEG- DSPE lipid.
[00749] In some embodiments, the PEGylated lipid is selected from (R)-2,3-bis(octadecyloxy)propyl-l- (methoxypoly(ethyleneglycol)2000)propylcarbamate, PEG-S-DSG. PEG-S-DMG, PEG-PE, PEG-PAA, PEG-OH DSPE Cl 8, PEG-DSPE, PEG-DSG, PEG-DPG, PEG-DOMG, PEG-DMPE Na, PEG-DMPE. PEG- DMG2000. PEG-DMG Cl 4, PEG-DMG 2000, PEG-DMG, PEG-DMA, PEG-Ceramide Cl 6, PEG-C- DOMG, PEG-c-DMOG, PEG-c-DMA, PEG-cDMA, PEGA, PEG750-C-DMA, PEG400, PEG2k-DMG, PEG2k-Cl l, PEG2000-PE, PEG2000P, PEG2000-DSPE, PEG2000-DOMG, PEG2000-DMG, PEG2000-C- DMA, PEG2000, PEG200, PEG(2k)-DMG, PEG DSPE C18, PEG DMPE C14, PEG DLPE C12, PEG Click DMG C14, PEG Click C12, PEG Click CIO, N(Carbonyl-methoxypolyethylenglycol-2000)-l,2-distearoyl-sn- glycero3 -phosphoethanolamine, Myrj52, mPEG-PLA, MPEG-DSPE. mPEG3000-DMPE, MPEG-2000- DSPE, MPEG2000-DSPE, mPEG2000-DPPE, mPEG2000-DMPE. mPEG2000-DMG. mDPPE-PEG2000. l,2-distearoyl-sn-glycero-3-phosphoethanolamine-PEG2000, HPEG-2K-LIPD, Folate PEG-DSPE, DSPE- PEGMA 500, DSPE-PEGMA, DSPE-PEG6000, DSPE-PEG5000, DSPE-PEG2K-NAG, DSPE-PEG2k, DSPE-PEG2000maleimide, DSPE-PEG2000, DSPE-PEG, DSG-PEGMA, DSG-PEG5000, DPPE-PEG-2K, DPPE-PEG, DPPE-mPEG2000, DPPE-mPEG, DPG-PEGMA, DOPE-PEG2000, DMPE-PEGMA, DMPE- PEG2000, DMPE-Peg, DMPE-mPEG2000, DMG-PEGMA, DMG-PEG2000, DMG-PEG, distearoyl- glycerol-polyethyleneglycol, C18PEG750, CI8PEG5000, CI8PEG3000, CI8PEG2000, CI6PEG2000, CI4PEG2000, C18-PEG5000, C18PEG, C16PEG, C16 mPEG (polyethylene glycol) 2000 Ceramide, C14- PEG-DSPE200, C14-PEG2000, C14PEG2000, C14-PEG 2000, C14-PEG, C14PEG, 14:0-PEG2KPE, 1,2- distearoyl-sn-glycero-3-phosphoethanolamine-PEG2000, (R)-2,3-bis(octadecyloxy)propyl-l- (methoxypoly(ethyleneglycol)2000)propylcarbamate. (PEG)-C-DOMG, PEG-C-DMA. and DSPE-PEG-X.
[00750] In some embodiments, the LNP comprises a PEGylated lipid disclosed in one of US 2019/0240354; US 2010/0130588; US 2021/0087135; WO 2021/204179; US 2021/0128488; US 2020/0121809; US 2017/0119904; US 2013/0108685; US 2013/0195920; US 2015/0005363; US 2014/0308304: US 2013/0053572; WO 2019/232095A1; WO 2021/077067; WO 2019/152557; US 2015/0203446; US 2017/0210697; US 2014/0200257; or WO 2019/089828A1, each of which is incorporated by reference herein in their entirety.
[00751] In some embodiments, the LNP comprises a PEGylated lipid substitute in place of the PEGylated lipid. All embodiments disclosed herein that contemplate a PEGylated lipid should be understood to also apply to PEGylated lipid substitutes. In some embodiments, the LNP comprises a polysarcosine-lipid conjugate, such as those disclosed in US 2022/0001025 Al, which is incorporated by reference herein in its entirety. In some embodiments the LNP comprises a polyoxazoline-lipid conjugate, such as those disclosed in US 2022/0249695 Al, which is incorporated by reference herein in its entirety.
[00752] In some embodiments, the LNP comprises a PEGylated lipid disclosed and described in PCT Application WO 2024/044728 Al, which is incorporated by reference herein, in its entirety. In certain embodiments, the PEGylated lipid is a lipid of any one of formulas PL-I’, PL-I”, PL-I, PL-Ia, PL-Ib, PL-Iaa, PL-Iab, PL-Iac, PL-Iad, PL-Iae, PL-Iaf, PL-Iag, PL-Iah, PL-Iba, PL-Ibb, PL-Ibc, PL-Ibd, PL-Ibe, PL-Ibf, PL- Ibg. PL-Ibh, PL-Ica, PL-Icb, PL-Icc, PL-Icd, PL-Id PL-Ie, PL-If, PL-Ig, PL-Ih, PL-Ii, PL-Iha, PL-Ihb, PL- Ihc. PL-Ihd, PL-Iia. PL-lib. PL-Iic, PL-Iid, PL-Ij. PL-Ik, L-Il, PL-Im. PL-In, PL-Io, PL-Ip, PL-Iq, PL-Ioa, PL-Iob, PL-Ioc, PL-Iod, PL-Ioe, PL-Iof, PL-Iog, PL-Ioh, PL-Ipa, PL-Ipb, PL-Ipc, PL-Ipd, PL-Ipe, PL-Ipf, PL-Ipg, PL-Iph, PL-Iqa, PL-Iqb, PL-Iqc, PL-Iqd, PL-Ir, PL-Is, PL-It, PL-Iu, PL-Iv, PL-Iw, PL-Iva, PL-Ivb, PL-Ivc, PL-Ivd, PL-Iwa, PL-Iwb, PL-Iwc, PL-Iwd, PL-Ix, PL-Ixx, PL-Iy, PL-Iyy, PL-Iyyy, PL-Iz, PL-Izz, PL-Izzz, PL-II’, PL-II”, PL-II, PL-IIc, PL-IId, PL-IIe, PL-IIf, PL-IIg, PL-IIh, PL-IIa, PL-IIb, PL-IIk, PL-IIm or PL-IIn. iv. Phospholipids
[00753] In some embodiments, an LNP of the present disclosure comprises a phospholipid. In some embodiments, an LNP of the present disclosure comprises two or more phospholipids. Phospholipids useful in the compositions and methods may be selected from the non-limiting group consisting of 1,2-distearoyl- sn-glycero-3 -phosphocholine (DSPC), l,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), 1,2- dilinoleoyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-phosphocholine (DMPC), 1.2- dioleoyl-sn-glycero-3-phosphocholine (DOPC), l,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2- diundecanoyl-sn-glycero-phosphocholine (DUPC), l-palmitoyl-2 -oleoyl -sn-glycero-3 -phosphocho line (POPC), l,2-di-O-octadecenyl-sn-glycero-3-phosphocholine (18:0 Diether PC), l-oleoyl-2- cholesterylhemisuc cinoyl-sn-glycero-3-phosphocholine (OChemsPC). l-hexadecyl-sn-glycero-3- phosphocholine (Cl 6 Lyso PC), l,2-dilinolenoyl-sn-glycero-3 -phosphocholine, 1,2-diarachidonoyl-sn- glycero-3 -phosphocholine, 1,2-didocosahexaenoyl -sn-glycero-3 -phosphocholine, 1 ,2-diphytanoylsn-glycero- 3 -phosphoethanolamine (ME 16.0 PE), l,2-distearoyl-sn-glycero-3 -phosphoethanolamine, 1,2-dilinoleoyl-sn- glycero-3 -phosphoethanolamine, l,2-dilinolenoyl-sn-glycero-3 -phosphoethanolamine, 1,2-diarachidonoyl-sn- glycero-3 -phosphoethanolamine, l,2-didocosahexaenoyl-sn-glycero-3-phosphoethanolamine, 1,2-dioleoyl- sn-glycero-3-phospho-rac-(l -glycerol) sodium salt (DOPG), sodium (S)-2-ammonio-3-((((R)-2-(oleoyloxy)- 3-(stearoyloxy)propoxy)oxidophosphoryl)oxy)propanoate (L-a-phosphatidylserine; Brain PS), dimyristoyl phosphatidylcholine (DMPC), dimyristoyl phosphoethanolamine (DMPE), dimyristoylphosphatidylglycerol (DMPG), dioleoyl -phosphatidylethanolamine4-(N-maleimidomethyl)-cyclohexane- 1 -carboxylate (DOPE- mal), dioleoylphosphatidylglycerol (DOPG), l,2-dioleoyl-sn-glycero-3-(phospho-L-serine) (DOPS), acell- fusogenicphospholipid (DPhPE), dipalmitoylphosphatidylethanolamine (DPPE), 1,2-Dielaidoyl-sn- phosphatidylethanolamine (DEPE). dipalmitoylphosphatidylglycerol (DPPG), dipalmitoy lphosphatidylserine (DPPS), distearoylphosphatidylcholine (DSPC), distearoyl-phosphatidyl-ethanolamine (DSPE), distearoyl phosphoethanolamineimidazole (DSPEI), 1,2-diundecanoyl-sn-glycero-phosphocholine (DUPC), egg phosphatidylcholine (EPC), l,2-dioleoyl-sn-glycero-3-phosphate (18: 1 PA; DOPA), ammonium bis((S)-2- hydroxy-3 -(oleoyloxy )propyl) phosphate (18: 1 DMP; LBPA), l,2-dioleoyl-sn-glycero-3-phospho-(l '-myoinositol) (DOPI; 18: 1 PI). l,2-distearoyl-sn-glycero-3-phospho-L-serine (18:0 PS), 1.2-dilinoleoyl-sn- glycero-3-phospho-L-serine (18:2 PS), l-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (16:0-18: 1 PS; POPS), l -stearoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (18:0-18: 1 PS), l -stearoyl-2-linoleoyl-sn-glycero- 3-phospho-L-serine (18:0-18:2 PS), l-oleoyl-2-hydroxy-sn-glycero-3-phospho-L-serine (18: 1 Lyso PS), 1- stearoyl-2-hydroxy-sn-glycero-3-phospho-L-serine (18:0 Lyso PS), and sphingomyelin. In some embodiments, an LNP comprises DSPC. In certain embodiments, an LNP comprises DOPE. In some embodiments, an LNP comprises both DSPC and DOPE.
[00754] In some embodiments, an LNP comprises a phospholipid selected from l-pentadecanoyl-2-oleoyl-sn- glycero-3 -phosphocholine, 1 -myristoyl -2 -palmitoyl-sn-glycero-3 -phosphocholine, 1 -myristoyl -2-stearoyl-sn- glycero-3 -phosphocholine, l-palmitoyl-2-myristoyl-sn-glycero-3-phosphocholine, l-palmitoyl-2-stearoyl-sn- glycero-3 -phosphocholine, l-palmitoyl-2-oleoyl-glycero-3-phosphocholine, l-palmitoyl-2-linoleoyl-sn- glycero-3 -phosphocholine, l-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine, l-palmitoyl-2- docosahexaenoyl-sn-glycero-3-phosphocholine, l-stearoyl-2-myristoyl-sn-glycero-3-phosphocholine, 1- stearoyl-2-palmitoyl-sn-glycero-3-phosphocholine, 1 -stearoyl -2 -oleoyl-sn-glycero-3 -phosphocholine, 1- stearoyl-2-linoleoyl-sn-glycero-3-phosphocholine, l-stearoyl-2-arachidonoyl-sn-glycero-3 -phosphocholine, l-stearoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine, l-oleoyl-2-myristoyl-sn-glycero-3- phosphocholine, 1 -oleoyl -2 -palmitoyl-sn-glycero-3 -phosphocholine, l-oleoyl-2-stearoyl-sn-glycero-3- phosphocholine, l-palmitoyl-2-acetyl-sn-glycero-3-phosphocholine, l,2-dioleoyl-sn-glycero-3-phospho-(l ’- myo-inositol-3 ’,4’ -bisphosphate), l,2-dioleoyl-sn-glycero-3-phospho-(l’-myo-inositol-3’,5’-bisphosphate),
1.2-dioleoyl-sn-glycero-3-phospho-(l’-myo-inositol-4’, 5 ’-bisphosphate), l,2-dioleoyl-sn-glycero-3-phospho- (r-myo-inositol-3',4',5'-trisphosphate), l,2-dioleoyl-sn-glycero-3-phospho-(l’-myo-inositol-3’ -phosphate),
1.2-dioleoyl-sn-glycero-3-phospho-(r-myo-inositol-4'-phosphate). l,2-dioleoyl-sn-glycero-3-phospho-(l'- myo-inositol-5'-phosphate). l,2-dioleoyl-sn-glycero-3 -phospho-) 1’ -myo-inositol), l,2-dioleoyl-sn-glycero-3- phospho-L-serine, and l-(8Z-octadecenoyl)-2-palmitoyl-sn-glycero-3-phosphocholine.
[00755] In some embodiments, the LNP comprises a phospholipid selected from DSPS (Distearoylphosphatidylserine), DSPG (l,2-distearoyl-sn-glycero-3-phospho-(l'-rac-glycerol)), DSPA (1,2- Distearoyl-sn-glycero-3-phosphate), diPhyPC (l,2-diphytanoyl-sn-glycero-3 -phosphocholine), diPhy-diether- PC (l,2-di-O-phytanyl-sn-glycero-3-phosphocholine), diPhyPE (l,2-diphytanoyl-sn-glycero-3- phosphoethanolamine), diPhy-diether-PE (l,2-di-O-phytanyl-sn-glycero-3 -phosphoethanolamine), diPhyPS ( 1 ,2-diphytanoyl-sn-glycero-3-phospho-L-serine), diPhyPG ( 1 ,2-diphytanoyl-sn-glycero-3 -phospho-) 1 '-rac- glycerol)), diPhyPA (1.2-diphytanoyl-sn-glycero-3-phosphate). Egg PA (L-a-phosphatidic acid), and Soy PA (L-a-phosphatidic acid).
[00756] In some embodiments, the LNP comprises a phospholipid selected from 18: 1 (A9-Cis) PE (DOPE), 18:0-18: 1 PE (SOPE), C16-18: 1 PE, 16:0-18: 1 PE (POPE), 18: 1 BMP (S,R), 18:0-18: 1 PC (SOPC), 16:0- 18: 1 PC (POPC), 4ME 16:0 Diether PE (4Me), 18: 1 (A9-Trans) PE (DEPE), 16: 1 PE (DPPE), and CL. In certain embodiments, the LNP comprises a phospholipid described or disclosed in Alvarcz-Bcncdicto, ct al. (Biomater. Sci.. 2022, 10, 549) and Li, et al. (Asian Journal of Phannaceutical Sciences, 2015, 10, 81-98).
[00757] In certain embodiments, the phospholipid is a sphingoid lipid or sphingolipid, such as, but not limited to sphingomyelin. As used herein, the tenns ‘‘sphingoid lipid” and “sphingolipid” are meant to refer to a class of lipids containing a backbone comprising a sphingoid base. An exemplary sphingoid base is sphingosine. In certain embodiments, the LNP comprises a sphingolipid selected from Egg Sphingomyelin (Egg SM / ESM / (2S,3R,E)-3-hydroxy-2-palmitamidooctadec-4-en-l-yl (2-(trimethylammonio)ethyl) phosphate), Brain or Porcine Sphingomyelin (Brain SM / (2S,3R,E)-3-hydroxy-2-stearamidooctadec-4-en-l- yl (2-(trimethylammonio)ethyl) phosphate). Milk or Bovine Sphingomyelin (Milk SM / (2S,3R,E)-3- hydroxy-2-tricosanamidooctadec-4-en-l-yl (2-(trimethylammonio)ethyl) phosphate), 28:0 SM (N- octacosanoyl-D-erythro-sphingosylphosphorylcholine), 14:0 SM (N-myristoyl-D-erythro- sphingosylphosphorylcholine), 16: 1 SM (N-palmitoleoyl-D-erythro-sphingosylphosphorylcholine), 12:0 Dihydro SM (N-lauroyl-D-erythro-sphinganylphosphorylcholine), Lyso SM (Sphingosylphosphorylcholine), Lyso SM (Sphingosylphosphorylcholine), Lyso SM (dihydro) (Sphinganine Phosphorylcholine), 24: 1 SM (N-nervonoyl-D-erythro-sphingosylphosphorylcholine), 24:0 SM (N-lignoceroyl-D-erythro- sphingosylphosphorylcholine), 18: 1 SM (N-oleoyl-D-erythro-sphingosylphosphoiy Icholine), 18:0 SM (N- stearoyl-D-erythro-sphingosylphosphorylcholine), 17:0 SM (N-heptadecanoyl-D-erythro- sphingosylphosphorylcholine), 16:0 SM (N-palmitoyl-D-erythro-sphingosylphosphorylcholine), 12:0 SM (N- lauroyl-D-erythro-sphingosylphosphorylcholine). 06:0 SM (N-hexanoyl-D-erythro- sphingosylphosphorylcholine), 02:0 SM (N-acetyl-D-erythro-sphingosylphosphorylcholine), 3-O-methyl Lyso SM (3-O-methyl-spingosylphosphorylcholine), 3-O-methyl-N-methyl Lyso SM (3-O-methyl-N-methyl- spingosylphosphorylcholine), and 3-N-methyl Lyso SM (3-N-methyl-spingosylphosphorylcholine).
[00758] In some embodiments, the LNP comprises a phospholipid comprising at least one constrained tail, such as those described by Gan, et al. (Bioeng Transl Med. 2020 Sep; 5(3): elO16L). In certain embodiments, the phospholipid is one selected from:
[00759] In some embodiments, the LNP comprises a phospholipid comprising a ceramide analogue having a triazole linkage, such as those described by Kim et al., Bioorg. Med. Chem. Lett., 17(16), 2007, 4584-4587.
[00760] In some embodiments, the LNP comprises a phospholipid disclosed in WO 2023/141470, which is incorporated by reference herein, in its entirety. In certain embodiments, the phospholipid is [00761] In some embodiments, the LNP comprises a phospholipid disclosed in WO 2022/040641, which is incorporated by reference herein, in its entirety.
[00762] In some embodiments, a phospholipid tail may be modified in order to promote endosomal escape as described in U.S. Application Publication 2021/0121411, which is incorporated herein by reference.
[00763] In some embodiments, the LNP comprises a phospholipid disclosed in one of US 2019/0240354; US 2010/0130588; US 2021/0087135; WO 2021/204179; US 2021/0128488; US 2020/0121809; US 2017/0119904; US 2013/0108685; US 2013/0195920; US 2015/0005363; US 2014/0308304; US 2013/0053572; WO 2019/232095A1; WO 2021/077067; WO 2019/152557; US 2017/0210697; or WO 2019/089828A1, each of which is incorporated by reference herein in their entirety.
[00764] In some embodiments, the LNP comprises a phospholipid disclosed in PCT Publication WO2023141470A2, which is incorporated by reference herein in its entirety. In certain embodiments, the LNP comprises a phospholipid of Formula (1) of PCT Publication WO2023141470A2. including but not limited to 2-ammonioethyl ((S)-3-(((S)-12-methyltetradecanoyl)oxy)-2-((13-methyltetradecanoyl)oxy)propyl) phosphate. v. Targeting moieties
[00765] In some embodiments, the lipid nanoparticle further comprises a targeting moiety. The targeting moiety may be an antibody or a fragment thereof. The targeting moiety may be capable of binding to a target antigen. In certain embodiments, the lipid nanoparticle comprises more than one targeting moiety. In certain embodiments, the lipid nanoparticle comprises more than one targeting moiety, wherein the targeting moieties target at least two different receptors, and in some embodiments, the at least two different receptors are prevalent on different types of cells or tissues.
[00766] In some embodiments, the pharmaceutical composition comprises a targeting moiety that is operably connected to a lipid nanoparticle. In some embodiments, the targeting moiety is capable of binding to a target antigen. In some embodiments, the target antigen is expressed in a target organ. In some embodiments, the target antigen is expressed more in the target organ than it is in the liver.
[00767] In some embodiments, the targeting moiety is an antibody as described in WO2016189532A1, which is incorporated herein by reference. For example, in some embodiments, the targeted particles are conjugated to a specific anti-CD38 monoclonal antibody (mAb), which allows specific delivery of the siRNAs encapsulated within the particles at a greater percentage to B-cell lymphocytes malignancies (such as MCL) than to other subtypes of leukocytes. [00768] In some embodiments, the targeting moiety targets a receptor selected from CD20, CCR7, CD3, CD4, CD5, CD8, CD16, CD19, CD20, CD21, CD22, CD25, CD28, CD35, CD40, CD45RA, CD45RO, CD52, CD62L, CD80, CD95, CD127, and CD137. In some embodiments, the targeting moiety targets a receptor selected from CD1, CD2, CD3, CD5, CD7, CD8, CD16, CD25, CD26, CD27, CD28, CD30, CD38, CD39, CD40L, CD44, CD45. CD62L, CD69, CD73, CD80, CD83. CD86, CD95, CD103, CD119, CD126. CD150. CD153, CD154, CD161. CD183. CD223, CD254, CD275. CD45RA, CXCR3. CXCR5, FasL, IL18R1, CTLA-4, 0X40, GITR, LAG3, ICOS, PD-1, leu-12, TCR, TLR1, TLR2, TLR3, TLR4, TLR6, NKG2D, CCR, CCR1, CCR2, CCR4, CCR6, and CCR7. In some embodiments, the targeting moiety targets a receptor selected from CD2, CD3, CD5 and CD7. In some embodiments, the targeting moiety targets a receptor selected from CD2, CD3, CD5, CD7, CD8, CD4, beta 7 integrin, beta 2 integrin, and Clq. In some embodiments, the targeting moiety targets CD117. In some embodiments, the targeting moiety targets CD90. In some embodiments, the targeting moiety targets a receptor selected from a mannose receptor, CD206 and C Iq. In some embodiments, the targeting moiety is selected from T-cell receptor motif antibodies, T-cell a chain antibodies, T-cell [3 chain antibodies, T-cell y chain antibodies, T-cell 5 chain antibodies, CCR7 antibodies, CD3 antibodies, CD4 antibodies, CD5 antibodies, CD7 antibodies, CD8 antibodies, CDl lb antibodies, CDl lc antibodies, CD16 antibodies, CD19 antibodies, CD20 antibodies, CD21 antibodies, CD22 antibodies, CD25 antibodies, CD28 antibodies, CD34 antibodies, CD35 antibodies. CD40 antibodies, CD45RA antibodies, CD45RO antibodies, CD52 antibodies, CD56 antibodies, CD62L antibodies, CD68 antibodies, CD80 antibodies, CD95 antibodies, CD117 antibodies, CD127 antibodies, CD133 antibodies, CD137 (4-1BB) antibodies, CD163 antibodies, F4/80 antibodies, IL-4Ra antibodies, Sca-1 antibodies, CTLA-4 antibodies, GITR antibodies GARP antibodies, LAP antibodies, granzyme B antibodies, LFA-1 antibodies, transferrin receptor antibodies, and fragments thereof. In certain embodiments, the targeting moiety is any one described or contemplated in US20230312713A1, US20230203538A1, US20230320995A1, US20160145348, and US20110038941. each of which is incorporated by reference herein in its entirety.
[00769] In some embodiments, the lipid nanoparticles may be targeted when conjugated/attached/associated with a targeting moiety such as an antibody, or a fragment thereof. vi. Zwitterionic amino lipids [00770] In some embodiments, an LNP comprises a zwitterionic lipid. In some embodiments, an LNP comprising a zwitterionic lipid does not comprise a phospholipid.
[00771] Zwitterionic amino lipids have been shown to be able to self-assemble into LNPs without phospholipids to load, stabilize, and release mRNAs intracellularly as described in U.S. Patent Application 20210121411, which is incorporated herein by reference in its entirety. Zwitterionic, ionizable cationic and permanently cationic helper lipids enable tissue-selective mRNA delivery' and CRISPR-Cas9 gene editing in spleen, liver and lungs as described in Liu et al., Membrane-destablizing ionizable phospholipids for organ- selective mRNA delivery and CRISPR-Cas gene editing, Nat Mater. (2021), which is incorporated herein by reference in its entirety.
[00772] The zwitterionic lipids may have head groups containing a cationic amine and an anionic carboxylate as described in Walsh et al., Synthesis, Characterization and Evaluation of Ionizable Lysine-Based Lipids for siRNA Delivery, Bioconjug Chem. (2013), which is incorporated herein by reference in its entirety. Ionizable lysine-based lipids containing a lysine head group linked to a long-chain dialkylamine through an amide linkage at the lysine a-amine may reduce immunogenicity as described in Walsh et al., Synthesis, Characterization and Evaluation of Ionizable Lysine-Based Lipids for siRNA Delivery, Bioconjug Chem. (2013). vii. Additional lipid components
[00773] In some embodiments, the LNP compositions of the present disclosure further comprise one or more additional lipid components capable of influencing the tropism of the LNP. In some embodiments, the LNP further comprises at least one lipid selected from DDAB, EPC, 14PA, 18BMP, DODAP, DOTAP, and Cl 2- 200 (see Cheng, et al. Nat Nanotechnol. 2020 April; 15(4): 313-320.: Dillard, et al. PNAS 2021 Vol. 118 No. 52.).
[00774] In some embodiments, an LNP of the present disclosure further comprises one or more additional ionizable lipids, such as, but not limited to those disclosed in one of US 2023/0053437; US 2019/0240354; US 2010/0130588; US 2021/0087135; WO 2021/204179; US 2021/0128488; US 2020/0121809; US 2017/0119904; US 2013/0108685; US 2013/0195920; US 2015/0005363; US 2014/0308304; US 2013/0053572; WO 2019/232095A1; WO 2021/077067; WO 2019/152557; US 2017/0210697; or WO 2019/089828A1, each of which is incorporated by reference herein in their entirety. In certain embodiments, an LNP of the present disclosure further comprises one or more additional ionizable lipids selected from those disclosed in WO2023044343A1 or WO2023044333A1, both of which are incorporated by reference herein in their entirety.
[00775] In some embodiments, the LNP compositions of the present disclosure comprise, or further comprise one or more lipids selected from l,2-di-O-octadecenyl-sn-glycero-3 -phosphocholine (18:0 Diether PC), 1,2- dilinolenoyl-sn-glycero-3-phosphocholine (18:3 PC), Acylcamosine (AC), l-hexadecyl-sn-glycero-3- phosphocholine (C16 Lyso PC), N-oleoyl-sphingomyelin (SPM) (C 18:1), N-lignoceryl SPM (C24:0), N- nervonoylshphingomyelin (C24:l), Cardiolipin (CL), l,2-bis(tricosa-10,12-diynoyl)-sn-glycero-3- phosphocholine (DC8-9PC), dicetyl phosphate (DCP), dihexadecyl phosphate (DCP1), 1,2- Dipalmitoylglycerol-3-hemisuccinate (DGSucc), short-chain bis-n-heptadecanoyl phosphatidylcholine (DHPC), dihexadecoyl-phosphoethanolamine (DHPE), l,2-dilinoleoyl-sn-glycero-3 -phosphocholine (DLPC), l,2-dilauroyl-sn-glycero-3-PE (DLPE), dimyristoyl glycerol hemisuccinate (DMGS), dimyristoyl phosphatidylcholine (DMPC), dimyristoyl phosphoethanolamine (DMPE), dimyristoylphosphatidylglycerol (DMPG). dioleyloxybenzylalcohol (DOBA), 1.2-dioleoylglyceryl-3 -hemisuccinate (DOGEIEMS), N-[2-(2- {2-[2-(2,3-Bis-octadec-9-enyloxy-propoxy)-ethoxy]-ethoxy}-ethoxy)-ethyl]-3-(3,4,5-dihydroxy-6- hydroxymethyl- 1 etrahydro-pyran-2-ylsulfanyl)-propionamide (D0GP4aMan), dioleoylphosphatidylcholine (DOPC), dioleoylphosphatidylethanolamine (DOPE), dioleoyl-phosphatidylethanolamine4-(N- maleimidomethyl)-cyclohexane-l -carboxylate (DOPE-mal), dioleoylphosphatidylglycerol (DOPG), 1,2- dioleoyl-sn-glycero-3-(phospho-L-serine) (DOPS), acell-fusogenicphospholipid (DPhPE), dipalmitoylphosphatidylethanolamine (DPPE), dipalmitoylphosphatidylglycerol (DPPG). dipalmitoylphosphatidylserine (DPPS), distearoylphosphatidylcholine (DSPC), distearoyl-phosphatidyl- ethanolamine (DSPE), distearoyl phosphoethanolamineimidazole (DSPEI), 1,2-diundecanoyl-sn-glycero- phosphocholine (DUPC), egg phosphatidylcholine (EPC), histaminedistearoylglycerol (HDSG), 1,2- Dipalmitoylglycerol-hemisuccinate-Na-Histidinyl-Hemisuccinate (HistSuccDG), N-(5'-hydroxy-3'- oxypentyl)-10-12-pentacosadiynamide (h-Pegi-PCDA). 2-[l-hexyloxyethyl]-2-devinylpyropheophorbide-a (HP PH), hydrogenatedsoybeanphosphatidylcholine (HSPC), 1.2-Dipalmitoylglycerol-O-a-histidinyl-N a- hemisuccinate (IsohistsuccDG), mannosialized dipalmitoylphosphatidylethanolamine (ManDOG), 1,2- Dioleoyl-sn-Glycero-3-Phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide] (MCC- PE), l,2-diphytanoyl-sn-glycero-3-phosphoethanolamine (ME 16:0 PE), l-myristoyl-2-hydroxy-sn-glycero- phosphocholine (MHPC). a thiol-reactive maleimide headgroup lipid e.g.l,2-dioleoyl-sn-glycero-3- phosphoethanolamine-N-[4-(p-maleimidophenyl)but-yramid (MPB-PE), Nervonic Acid (NA), sodium cholate (NaChol). 1.2-dioleoyl-sn-glycero-3-[phosphoethanolamine-N-dodecanoyl (NC12-DOPE), 1-oleoyl- 2-cholesteryl hemisuccinoyl-sn-glycero-3-phosphocholine (OChemsPC), phosphatidylethanolamine lipid (PE), PE lipid conjugated with polyethylene glycol(PEG) (e.g., polyethylene glycoldistearoylphosphatidylethanolamine lipid (PEG-PE)), phosphatidylglycerol (PG), partially hydrogenated soy phosphatidylchloline (PHSPC), phosphatidylinositol lipid (PI), pho sphotidylinositol -4 -phosphate (PIP), palmitoyloleoylphosphatidylcholine (POPC), phosphatidylethanolamine (POPE). palmitoyloleyolphosphatidylglycerol (POPG), phosphatidylserine (PS), lissamine rhodamine B- phosphatidylethanolamine lipid (Rh-PE), purified soy-derived mixture of phospholipids (SIOO), phosphatidylcholine (SM), 18-l-trans-PE,l-stearoyl-2-oleoyl-phosphatidyethanolamine (SOPE), soybean phosphatidylcholine (SPC), sphingomyelins (SPM), alpha, alpha-trehalose-6,6'-dibehenate (TDB), 1,2- dielaidoyl-sn-glycero-3-phophoethanolamine (transDOPE), ((23S,5R)-3-(bis(hexadecyloxy)methoxy)-5-(5- methyl-2,4-dioxo-3,4-dihydropyrimidin-l(2H)-yl)tetrahydrofi.iran-2-yl)methylmethylphosphate, 1,2- diarachidonoyl-sn-glycero-3-phosphocholine, l,2-diarachidonoyl-sn-glycero-3 -phosphoethanolamine, 1,2- didocosahexaenoyl-sn-glycero-3 -phosphocholine, l,2-didocosahexaenoyl-sn-glycero-3- phosphoethanolamine, l,2-dilinolenoyl-sn-glycero-3 -phosphocholine, l,2-dilinolenoyl-sn-glycero-3- phosphoethanolamine, l,2-dilinoleoyl-sn-glycero-3-phosphoethanolamine, L2-dioleyl-sn-glycero-3- phosphoethanolamine, l,2-distearoyl-sn-glycero-3-phosphoethanolamine, 16-0-monomethyl PE, 16-0- dimethyl PE, and dioleylphosphatidylethanolamine.
Exemplary LNP Compositions
[00776] In some embodiments, provided herein are LNPs comprising (a): at least one ionizable lipid; (b) at least one PEG lipid; (c) at least one structural lipid; and (d) at least one non-ionizable lipid and/or a zwitterionic lipid. In some embodiments, the LNPs further comprise an additional ionizable lipid, besides a compound disclosed herein. In some embodiments, the LNPs further comprise an additional lipid component, of any class, besides a compound disclosed herein.
[00777] In some embodiments, the PEG-lipid is selected from the group consisting of PEG-c-DOMG, PEG- DMG, PEG-DLPE. PEG-DMPE. PEG-DPPC, and PEG-DSPE.
[00778] In some embodiments, the structural lipid is selected from the group consisting of cholesterol, fecosterol, sitosterol, ergosterol, campesterol, stigmasterol, brassicasterol, tomatidine, ursolic acid, and alphatocopherol.
[00779] In some embodiments, the non-ionizable lipid is a phospholipid selected from the group consisting of l,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), l,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), l,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLPC), 1,2-dimyristoyl-sn-glycero-phosphocholine (DMPC), 1 ,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), l,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-diundecanoyl-sn-glycero-phosphocholine (DUPC), l-palmitoyl-2-oleoyl-sn-glycero-3- phosphocho line (POPC). l,2-di-O-octadecenyl-sn-glycero-3 -phosphocholine (18:0 Diether PC), l-oleoyl-2- cholesterylhemisuc cinoyl-sn-glycero-3-phosphocholine (OChemsPC), l-hexadecyl-sn-glycero-3- phosphocholine (Cl 6 Lyso PC), l,2-dilinolenoyl-sn-glycero-3 -phosphocholine, 1,2-diarachidonoyl-sn- glycero-3 -phosphocholine, l,2-didocosahexaenoyl-sn-glycero-3 -phosphocholine, 1 ,2-diphytanoylsn-glycero- 3 -phosphoethanolamine (ME 16.0 PE), l,2-distearoyl-sn-glycero-3 -phosphoethanolamine, 1,2-dilinoleoyl-sn- glycero-3 -phosphoethanolamine, l,2-dilinolenoyl-sn-glycero-3 -phosphoethanolamine, 1,2-diarachidonoyl-sn- glycero-3 -phosphoethanolamine, L2-didocosahexaenoyl-sn-glycero-3-phosphoethanolamine, 1,2-dioleoyl- sn-glycero-3-phospho-rac-(l -glycerol) sodium salt (DOPG), sodium (S)-2-ammonio-3-((((R)-2-(oleoyloxy)- 3-(stearoyloxy)propoxy)oxidophosphoryl)oxy)propanoate (L-a-phosphatidylserine; Brain PS), dimyristoyl phosphatidylcholine (DMPC), dimyristoyl phosphoethanolamine (DMPE), dimyristoylphosphatidylglycerol (DMPG), dioleoyl -phosphatidylethanolamine4-(N-maleimidomethyl)-cyclohexane- 1 -carboxylate (DOPE- mal), dioleoylphosphatidylglycerol (DOPG), l,2-dioleoyl-sn-glycero-3-(phospho-L-serine) (DOPS), acell- fusogenicphospholipid (DPhPE), dipalmitoylphosphatidylethanolamine (DPPE), dipalmitoylphosphatidylglycerol (DPPG), dipalmitoylphosphatidylserine (DPPS), distearoylphosphatidylcholine (DSPC), distearoyl-phosphatidyl-ethanolamine (DSPE), distearoyl phosphoethanolamineimidazole (DSPEI), 1,2-diundecanoyl-sn-glycero-phosphocholine (DUPC), egg phosphatidylcholine (EPC), l,2-dioleoyl-sn-glycero-3-phosphate (18: 1 PA; DOPA), ammonium bis((S)-2- hydroxy-3 -(oleoyloxy )propyl) phosphate (18: 1 DMP; LBPA), l,2-dioleoyl-sn-glycero-3-phospho-(l' -myoinositol) (DOPI; 18: 1 PI). l,2-distearoyl-sn-glycero-3-phospho-L-serine (18:0 PS), 1.2-dilinoleoyl-sn- glycero-3-phospho-L-serine (18:2 PS), 1 -palmitoyl -2 -oleoyl-sn-glycero-3-phospho-L-serine (16:0-18: 1 PS; POPS), l-stearoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (18:0-18: 1 PS), l-stearoyl-2-linoleoyl-sn-glycero- 3-phospho-L-serine (18:0-18:2 PS), l-oleoyl-2-hydroxy-sn-glycero-3-phospho-L-serine (18: 1 Lyso PS), 1- stearoyl-2-hydroxy-sn-glycero-3-phospho-L-serine (18:0 Lyso PS), and sphingomyelin.
[00780] In some embodiments, the non-ionizable lipid is a phospholipid selected from the group consisting of Egg Sphingomyelin (Egg SM / ESM / (2S,3R,E)-3-hydroxy-2-palmitamidooctadec-4-en-l-yl (2- (trimethylammonio)ethyl) phosphate), Brain or Porcine Sphingomyelin (Brain SM / (2S,3R,E)-3-hydroxy-2- stearamidooctadec-4-en-l-yl (2-(trimethylammonio)ethyl) phosphate), Milk or Bovine Sphingomyelin (Milk SM / (2S.3R.E)-3-hydroxy-2-tricosanamidooctadec-4-en-l-yl (2-(trimethylammonio)ethyl) phosphate), 28:0 SM (N-octacosanoyl-D-erythro-sphingosylphosphoiy Icholine), 14:0 SM (N-myristoyl-D-erythro- sphingosylphosphorylcholine), 16: 1 SM (N-palmitoleoyl-D-erythro-sphingosylphosphorylcholine), 12:0 Dihydro SM (N-lauroyl-D-erythro-sphinganylphosphorylcholine), Lyso SM (Sphingosylphosphorylcholine), Lyso SM (Sphingosylphosphorylcholine), Lyso SM (dihydro) (Sphinganine Phosphorylcholine), 24: 1 SM (N-nervonoyl-D-erythro-sphingosylphosphorylcholine), 24:0 SM (N-lignoceroyl-D-erythro- sphingosylphosphorylcholine), 18: 1 SM (N-oleoyl-D-erythro-sphingosylphosphorylcholine). 18:0 SM (N- stearoyl-D-erythro-sphingosylphosphorylcholine), 17:0 SM (N-heptadecanoyl-D-erythro- sphingosylphosphorylcholine), 16:0 SM (N-palmitoyl-D-erythro-sphingosylphosphorylcholine), 12:0 SM (N- lauroyl-D-crythro-sphingosylphosphorylcholinc), 06:0 SM (N-hcxanoyl-D-crythro- sphingosylphosphorylcholine), 02:0 SM (N-acetyl-D-erythro-sphingosylphosphorylcholine), 3-O-methyl Lyso SM (3-O-methyl-spingosylphosphorylcholine), 3-O-methyl-N-methyl Lyso SM (3-O-methyl-N-methyl- spingosylphosphon Icholine), and 3-N-methyl Lyso SM (3-N-methyl-spingosylphosphorylcholine). [00781] In some embodiments, (a) the PEG lipid is PEG2k-DMG or PEG2k-DSPE or a mixture thereof: (b) the structural lipid is cholesterol; and (c) the phospholipid, non-ionizable lipid or zwitterionic lipid is a sphingolipid or DSPC or a mixture thereof.
[00782] In some embodiments, the lipid component of the nanoparticle comprises: (a) about 0 mol% to about 10 mol% of PEG lipid; (b) about 0 mol% to about 30 mol% structural lipid; (c) about 20 mol% to about 45 mol% phospholipid, non-ionizable lipid or zwitterionic lipid; and (d) about 30 mol% to about 60 mol% of a Lipid of the Disclosure.
[00783] In some embodiments, the lipid component of tire nanoparticle comprises: (a) about 1 mol% to about 2 mol% of PEG lipid; (b) about 25 mol% to about 40 mol% structural lipid; (c) about 20 mol% to about 45 mol% phospholipid, non-ionizable lipid or zwitterionic lipid; and (d) about 30 mol% to about 60 mol% of a Lipid of the Disclosure.
[00784] In some embodiments, the lipid component of the nanoparticle comprises: (a) about 2 mol% of PEG lipid; (b) about 25 mol% structural lipid; (c) about 40 mol% phospholipid, non-ionizable lipid or zwitterionic lipid; and (d) about 33 mol% of a Lipid of the Disclosure.
[00785] In some embodiments, the lipid component of the nanoparticle comprises: (a) about 2.5 mol% of PEG lipid; (b) about 39 mol% structural lipid; (c) about 10 mol% phospholipid, non-ionizable lipid or zwitterionic lipid; and (d) about 48.5 mol% of a Lipid of the Disclosure.
[00786] In some embodiments, the lipid component of the nanoparticle comprises: (a) about 1.5 mol% of PEG lipid; (b) about 40 mol% structural lipid; (c) about 10 mol% phospholipid, non-ionizable lipid or zwitterionic lipid; and (d) about 48.5 mol% of a Lipid of the Disclosure.
[00787] In certain embodiments, the lipid component of tire nanoparticle composition comprises about 30 mol % to about 60 mol % ionizable lipid, about 0 mol % to about 30 mol % phospholipid, about 18.5 mol % to about 48.5 mol % structural lipid, and about 0 mol% to about 10 mol% of PEG lipid, provided that the total mol % does not exceed 100%. In certain embodiments, the lipid component of the nanoparticle composition comprises about 20 mol % to about 45 mol % ionizable lipid, about 30 mol % to about 60 mol % phospholipid, about 10 mol % to about 30 mol % structural lipid, and about 0 mol% to about 10 mol% of PEG lipid, provided that the total mol % does not exceed 100%. In some embodiments, the lipid component of the nanoparticle composition comprises about 35 mol % to about 55 mol % ionizable lipid, about 5 mol % to about 25 mol % phospholipid, about 30 mol % to about 40 mol % structural lipid, and about 0 mol % to about 10 mol % of PEG lipid, provided that the total mol % does not exceed 100%. In some embodiments, the lipid component of the nanoparticle composition comprises about 30 mol % to about 40 mol % ionizable lipid, about 35 mol % to about 45 mol % phospholipid, about 20 mol % to about 30 mol % structural lipid, and about 0.5 mol % to about 5 mol % of PEG lipid, provided that the total mol % does not exceed 100%. In certain embodiments, tire lipid component of the nanoparticle composition comprises about 25 mol % to about 45 mol % ionizable lipid, about 35 mol % to about 50 mol % phospholipid, about 10 mol % to about 25 mol % structural lipid, and about 1 mol% to about 5 mol% of PEG lipid, provided that the total mol % does not exceed 100%. In a particular embodiment, the lipid component comprises about 50 mol % ionizable lipid, about 10 mol % phospholipid, about 38.5 mol % structural lipid, and about 1.5 mol% of PEG lipid. In another particular embodiment, the lipid component comprises about 40 mol % ionizable lipid, about 20 mol % phospholipid, about 38.5 mol % structural lipid, and about 1.5 mol % of PEG lipid. In another particular embodiment, the lipid component comprises about 48.5 mol % ionizable lipid, about 10 mol % phospholipid, about 40 mol % structural lipid, and about 1.5 mol % of PEG lipid. In another particular embodiment, the lipid component comprises about 48.5 mol % ionizable lipid, about 10 mol % phospholipid, about 39 mol % structural lipid, and about 2.5 mol % of PEG lipid. In another particular embodiment, the lipid component comprises about 33 mol % ionizable lipid, about 40 mol % phospholipid, about 25 mol % structural lipid, and about 2 mol % of PEG lipid. In some embodiments, the phospholipid is DOPE or DSPC. In some embodiments, the phospholipid is DSPC. In some embodiments, the phospholipid is a sphingolipid. In some embodiments, the phospholipid is a sphingomyelin. In other embodiments, the PEG lipid is PEG-DMG (eg. PEG2K-DMG). In other embodiments, the PEG lipid is PEG-DSPE (eg. PEG2K-DSPE). In other embodiments, the PEG lipid is PEG-DMPE (eg. PEG2K-DMPE). In other embodiments, the structural lipid is cholesterol. In other embodiments, the PEG lipid is PEG-DMG and/or the structural lipid is cholesterol. In some embodiments, the PEG lipids is PEG2K-DMG, tire structural lipid is cholesterol, and the phospholipid is DSPC. In some embodiments, the PEG lipids is PEG2K-DMG, the structural lipid is cholesterol, and the phospholipid is sphingomyelin. In some embodiments, the PEG lipids is PEG-DMG, the structural lipid is cholesterol, and the phospholipid is a mixture of DSPC and sphingomyelin. In certain embodiments, the LNP comprises about 33mol% ionizable lipid (eg. at least one ionizable lipid of a Formula described herein), about 40mol% of a sphingolipid, about 25mol% cholesterol and about 2mol% PEG2K-DMG. In some embodiments, the PEG lipids is PEG2K-DSPE, the structural lipid is cholesterol, and the phospholipid is DSPC. In some embodiments, the PEG lipids is PEG2K-DSPE, the structural lipid is cholesterol, and the phospholipid is sphingomyelin. In some embodiments, the PEG lipids is PEG-DSPE. the structural lipid is cholesterol, and the phospholipid is a mixture of DSPC and sphingomyelin. In some embodiments, the PEG lipids is PEG2K-DMG, the structural lipid is cholesterol, and the phospholipid is DOPE. In some embodiments, the PEG lipids is PEG2K-DMG, the structural lipid is cholesterol, and the phospholipid is DOPC. In some embodiments, the PEG lipids is PEG2K-DMG, the structural lipid is cholesterol, and the phospholipid is DLPC. In some embodiments, the PEG lipids is PEG2K-DMG, the structural lipid is cholesterol, and the phospholipid is DOPS. In some embodiments, the PEG lipids is PEG-DMG, the structural lipid is cholesterol, and the phospholipid is a mixture of a phosphatidylcholine lipid and a sphingolipid. In some embodiments, the PEG lipids is PEG-DMG, the structural lipid is cholesterol, and the phospholipid is a mixture of a phosphatidylcholine lipid and phosphatidylserine lipid. In some embodiments, the PEG lipids is PEG-DMG. the structural lipid is cholesterol, and the phospholipid is a mixture of a phosphatidylcholine lipid and a phosphoethanolamine lipid. In some embodiments, the PEG lipids is PEG- DMG, the structural lipid is cholesterol, and the phospholipid is a mixture of a sphingolipid and phosphatidylserine lipid. In some embodiments, the PEG lipids is PEG-DMG, the structural lipid is cholesterol, and the phospholipid is a mixture of a sphingolipid and a phosphoethanolamine lipid. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 20mol% of a sphingolipid, about 20mol% of a non-sphingolipid phospholipid, about 25mol% cholesterol and about 2mol% of a PEGylated lipid. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 10mol% of a sphingolipid, about 30mol% of a non-sphingolipid phospholipid, about 25mol% cholesterol and about 2mol% of a PEGylated lipid. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 30mol% of a sphingolipid, about 10mol% of a non-sphingolipid phospholipid, about 25mol% cholesterol and about 2mol% of a PEGylated lipid. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 20mol% sphingomyelin, about 20mol% of a DSPC, about 25mol% cholesterol and about 2mol% of a PEGylated lipid. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 10mol% sphingomyelin, about 30mol% of a DSPC, about 25mol% cholesterol and about 2mol% of a PEGylated lipid. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 30mol% sphingomyelin, about 10mol% of a DSPC, about 25mol% cholesterol and about 2mol% of a PEGylated lipid. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 25mol% cholesterol, about 2mol% of a PEGylated lipid, and about 40% of a mixture of phosphatidylcholine, phosphatidylserine, phosphoethanolamine, and sphingoid lipids. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 25mol% cholesterol, about 2mol% of a PEGylated lipid, and about 40% of a mixture of phosphatidylcholine, phosphatidylserine, phosphoethanolamine, and sphingoid lipids, wherein each of the phosphatidylcholine, phosphatidylserine, phosphoethanolamine, and sphingoid lipids is present in an amount less than 30 mol% of the total lipid component of the LNP. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 25mol% cholesterol, about 2mol% of a PEGylated lipid, and about 40% of a mixture of phosphatidylcholine, phosphatidylserine, phosphoethanolamine, and sphingoid lipids, wherein each of the phosphatidylcholine, phosphatidylserine, phosphoethanolamine, and sphingoid lipids is present in an amount less than 25 mol% of the total lipid component of the LNP. In certain embodiments, LNP is any one of the aforementioned in this paragraph wherein the PEG lipid is PEG2k-DMG. In certain embodiments, LNP is any one of the aforementioned in this paragraph wherein the PEG lipid is PEG2k-DSPE.
[00788] In another particular embodiment, LNP comprises about 33 mol % ionizable lipid, about 40 mol % DSPC, about 25 mol % cholesterol, and about 2 mol % of PEG lipid. In another particular embodiment, LNP comprises about 33 mol % ionizable lipid, about 40 mol % sphingomyelin, about 25 mol % cholesterol, and about 2 mol % of PEG lipid. In another particular embodiment, LNP comprises about 33 mol % ionizable lipid, about 40 mol % DOPE, about 25 mol % cholesterol, and about 2 mol % of PEG lipid. In another particular embodiment. LNP comprises about 33 mol % ionizable lipid, about 40 mol % DOPC, about 25 mol % cholesterol, and about 2 mol % of PEG lipid. In another particular embodiment, LNP comprises about 33 mol % ionizable lipid, about 40 mol % DLPC, about 25 mol % cholesterol, and about 2 mol % of PEG lipid. In another particular embodiment, LNP comprises about 33 mol % ionizable lipid, about 40 mol % DOPS, about 25 mol % cholesterol, and about 2 mol % of PEG lipid. In another particular embodiment, LNP comprises about 33 mol % ionizable lipid, about 40 mol % phospholipid, about 25 mol % cholesterol, and about 2 mol % of PEG lipid. In another particular embodiment, LNP comprises about 33 mol % ionizable lipid, about 20 mol % sphingomyelin, about 20 mol% DSPC, about 25 mol % cholesterol, and about 2 mol % of PEG lipid. In certain embodiments, LNP is any one of the aforementioned in this paragraph wherein the PEG lipid is PEG2k-DMG. In certain embodiments, LNP is any one of the aforementioned in this paragraph wherein the PEG lipid is PEG2k-DSPE.
[00789] In certain embodiments, the LNP comprises about 43mol% ionizable lipid, about 15mol% of a sphingolipid, about 15mol% of a non-sphingolipid phospholipid, about 25mol% cholesterol and about 2mol% of a PEGylated lipid. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 25mol% of a sphingolipid, about 15mol% of a non-sphingolipid phospholipid, about 25mol% cholesterol and about 2mol% of a PEGylated lipid. In certain embodiments, the LNP comprises about 33mol% ionizable lipid, about 15mol% of a sphingolipid, about 25mol% of a non-sphingolipid phospholipid, about 25mol% cholesterol and about 2mol% of a PEGylated lipid. In some embodiments, tire PEG lipid is PEG2K-DSPE, the structural lipid is cholesterol, and the phospholipid is a mixture of DSPC and sphingomyelin. In some embodiments, the PEG lipid is PEG2K-DMG, the structural lipid is cholesterol, and the phospholipid is a mixture of DSPC and sphingomyelin. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 40mol% cholesterol and about 1 5mol% PEG2K-DSPE. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 40mol% cholesterol and about 1.5mol% PEG2K-DMG. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 39mol% cholesterol and about 2.5mol% PEG2K-DSPE.
[00790] In another particular embodiment, the lipid component includes about 48.5 mol % ionizable lipid, about 10 mol % phospholipid, about 38.5 mol % structural lipid, and about 3 mol % of PEG lipid. In another particular embodiment, the lipid component includes about 48.5 mol % ionizable lipid, about 10 mol % phospholipid, about 38 mol % structural lipid, and about 3.5 mol % of PEG lipid. In some embodiments, the PEG lipid is PEG2K-DPPE, the structural lipid is cholesterol, and the phospholipid is a DSPC or a mixture of DSPC and sphingomyelin. In some embodiments, the PEG lipid is PEG2K-DPPE, the structural lipid is cholesterol, and the phospholipid is a mixture of DSPC and sphingomyelin. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 40mol% cholesterol and about 1.5mol% PEG2K-DPPE. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 39.5 mol% cholesterol and about 2 mol% PEG2K-DPPE. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 39mol% cholesterol and about 2.5mol% PEG2K-DPPE. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 38.5 mol% cholesterol and about 3 mol% PEG2K-DPPE. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 38 mol% cholesterol and about 3.5mol% PEG2K-DPPE. In some embodiments, the PEG lipid is PEG2K-DMG, the structural lipid is cholesterol, and the phospholipid is a DSPC or a mixture of DSPC and sphingomyelin. In some embodiments, the PEG lipid is PEG2K-DMG. the structural lipid is cholesterol, and the phospholipid is a mixture of DSPC and sphingomyelin. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 40mol% cholesterol and about 1.5mol% PEG2K-DMG. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 39.5 mol% cholesterol and about 2 mol% PEG2K-DMG. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 39mol% cholesterol and about 2.5mol% PEG2K-DMG. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 38.5 mol% cholesterol and about 3 mol% PEG2K-DMG. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 38 mol% cholesterol and about 3.5mol% PEG2K-DMG. In some embodiments, the PEG lipid is PEG2K-DSPE, the structural lipid is cholesterol, and the phospholipid is a DSPC or a mixture of DSPC and sphingomyelin. In some embodiments, the PEG lipid is PEG2K-DSPE, the structural lipid is cholesterol, and the phospholipid is a mixture of DSPC and sphingomyelin. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 40mol% cholesterol and about 1.5mol% PEG2K-DSPE. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 39.5 mol% cholesterol and about 2 mol% PEG2K-DSPE. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 39mol% cholesterol and about 2.5mol% PEG2K-DSPE. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 38.5 mol% cholesterol and about 3 mol% PEG2K-DSPE. In certain embodiments, the LNP comprises about 48.5mol% ionizable lipid, about 10mol% of a phospholipid (such as DSPC), about 38 mol% cholesterol and about 3.5mol% PEG2K-DSPE.
[00791] In some embodiments, the LNP further comprises a targeting moiety. In some embodiments, the targeting moiety is an antibody or a fragment thereof.
[00792] The amount of active agent in a nanoparticle composition may depend on the size, composition, desired target and/or application, or other properties of the nanoparticle composition as well as on the properties of the active agent. For example, the amount of active agent useful in a nanoparticle composition may depend on the size, sequence, and other characteristics of tire active agent. Tire relative amounts of active agent and other elements (e.g.. lipids) in a nanoparticle composition may also vary. In some embodiments, the wt/wt ratio of the lipid component to payload in a nanoparticle composition is from about 5: 1 to about 60: 1, such as 5: 1, 6: 1, 7: 1, 8:1, 9: 1, 10: 1, 11: 1, 12: 1, 13: 1, 14: 1, 15: 1, 16: 1, 17: 1, 18: 1, 19: 1, 20: 1, 25: 1, 30: 1, 35: 1, 40: 1, 45: 1, 50: 1, and 60: 1. The amount of a payload in a nanoparticlc composition may, for example, be measured using absorption spectroscopy (e.g., ultraviolet-visible spectroscopy).
[00793] In some embodiments, a nanoparticle composition of tire present disclosure is formulated to provide a specific N:P ratio. The N:P ratio of the composition refers to the molar ratio of nitrogen atoms in one or more lipids to tire number of phosphate groups in an RNA active agent (e.g., a linear or circular mRNA payload). In general, a lower N:P ratio is preferred. The one or more enzymes, lipids, and amounts thereof is selected to provide an N:P ratio from about 2: 1 to about 30: 1, such as 2: 1, 3: 1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1, 10: 1, 12: 1, 14: 1, 16: 1, 18: 1, 20: 1, 22: 1, 24: 1, 26: 1, 28: 1, or 30:1. In certain embodiments, the N:P ratio is from about 2: 1 to about 8: 1. In other embodiments, tire N:P ratio is from about 5: 1 to about 8: 1. For example, the N:P ratio is about 5.0:1. about 5.5: 1, about 5.67: 1, about 6.0: 1, about 6.5: 1, or about 7.0: 1.
[00794] The dose of a phannaceutical composition provided herein can be measured in units of mg/kg, which refers to mg of total nucleic acid used to formulate the LNPs per kg of body weight of a subject (mg of total mRNA/kg). In some embodiments, the pharmaceutical composition is present in the dosage form at a dose of about 10, 9, 8, 7,6, 5, 4, 3, 2, 1.5, 1.0, 0.5, 0.2, 0.1, 0.05, 0.02, 0.01, .005, 0.002, or 0.001 milligram per kilogram (mg/kg, or mpk) body weight, or of a range between (inclusive) any two of the foregoing values. In some embodiments, the pharmaceutical composition is present in the dosage form at a dose of no more than about 10 milligram per kilogram (mg/kg, or mpk) body w eight. In some embodiments, the pharmaceutical composition is present in tire dosage form at a dose of no more than about 9 mg/kg, no more than about 8mg/kg , no more than about 7 mg/kg, no more than about 6 mg/kg, no more than about 5 mg/kg. no more than about 4 mg/kg, no more than about 3 mg/kg. no more than about2 mg/kg, no more than about 1 mg/kg. no more than about 0.5 mg/kg, no more than about 0.2 mg/kg, no more than about 0.1 mg/kg, no more than about 0.05 mg/kg, or no more than about 0.01 mg/kg.
[00795] In some embodiments, the pharmaceutical composition is present in the dosage form at a concentration of no more than about 5 milligram per milliliter (mg/mL). In some embodiments, the pharmaceutical composition is present in the dosage form at a concentration of about 5, 4-, 3, 2, 1, 0.5, 0.2, or 0.1 milligram per milliliter(mg/mL), or of a range between (inclusive) any two of the foregoing values.
[00796] In some embodiments, the pharmaceutical composition is present in the dosage form at a concentration of no more than about 5 milligram per milliliter (mg/mL). In some embodiments, the pharmaceutical composition is present in the dosage form at a concentration of no more than about 2 milligram per milliliter (mg/mL). In some embodiments, the pharmaceutical composition is present in the dosage form at a concentration of no more than about 1 milligram per milliliter (mg/mL). In some embodiments, the pharmaceutical composition is present in the dosage form at a concentration of no more than about 0.5 milligram per milliliter (mg/mL). In some embodiments, tire pharmaceutical composition is present in the dosage form at a concentration of no more than about 0.1 milligram per milliliter (mg/mL).
[00797] In some embodiments, the pharmaceutical composition is present in the dosage form at a concentration of about 10, 9, 8, 7. 6, 5, 4, 3. 2, 1, 0.5, 0.2, or 0. 1 microgram per milliliter (pg/mL), or of a range between (inclusive) any two of the foregoing values. In some embodiments, the pharmaceutical composition is present in the dosage form at a concentration of no more than about 10, no more than about 9, no more than about 8, no more than about 7, no more than about 6, no more than about 5, no more than about 4, no more than about 3, no more than about 2, no more than about 1, no more than about 0.5, no more than about 0.2, no more than about 0. 1 microgram per milliliter (pg/mL).
[00798] The characteristics of a nanoparticle composition may depend on the components thereof. For example, a nanoparticle composition including cholesterol as a structural lipid may have different characteristics than a nanoparticle composition that comprises a different structural lipid. Similarly, tire characteristics of a nanoparticle composition may depend on the absolute or relative amounts of its components. For instance, a nanoparticle composition including a higher molar fraction of a phospholipid may have different characteristics than a nanoparticle composition including a lower molar fraction of a phospholipid. Characteristics may also vary depending on the method and conditions of preparation of the nanoparticle composition. Nanoparticle compositions may be characterized by a variety of methods. For example, microscopy (e.g., transmission electron microscopy or scanning electron microscopy) may be used to examine the morphology and size distribution of a nanoparticle composition. Dynamic light scattering or potentiometry (e.g.. potentiometric titrations) may be used to measure Zeta potentials. Dynamic light scattering may also be utilized to determine particle sizes. Instruments such as the Zetasizer Nano ZS (Malvern Instruments Ltd, Malvern, Worcestershire, UK) may also be used to measure multiple characteristics of a nanoparticle composition, Such as particle size, polydispersity index, and Zeta potential.
[00799] In some embodiments, the mean size of a nanoparticle composition is betw een 10s of nm and 100s of nm, e.g., measured by dynamic light scattering (DLS). For example, the mean size may be from about 40 nm to about 150 nm, such as about 40 nm, 45 nm, 50 nm, 55 nm, 60 nm, 65 nm, 70 nm, 75 nm, 80 nm, 85 nm, 90 nm. 95 nm, 100 nm, 105 nm, 110 nm, 115nm, 120 nm, 125 nm, 130 nm, 135 nm. 140 nm, 145 nm, or 150 nm. In some embodiments, the mean size of a nanoparticle composition is from about 50 nm to about 100 nm, from about 50 nm to about 90 nm, from about 50 nm to about 80 nm, from about 50 nm to about 70 nm, from about 50 nm to about 60 nm, from about 60 nm to about 100 nm, from about 60 nm to about 90 nm, from about 60 nm to about 80 nm, from about 60 nm to about 70 nm, from about 70 nm to about 100 nm, from about 70 nm to about 90 nm, from about 70 nm to about 80 nm, from about 80 nm to about 100 nm, from about 80 nm to about 90 nm, or from about 90 nm to about 100 nm. In certain embodiments, the mean size of a nanoparticle composition is from about 70 nm to about 100 nm. In a particular embodiment, the mean size is about 80 nm. In other embodiments, the mean size is about 100 nm.
[00800] In some embodiments, the LNPs of the present disclosure can be characterized by their shape. In some embodiments, the LNPs are essentially spherical. In some embodiments, the LNPs are essentially rodshaped (i.e., cylindrical). In some embodiments, the LNPs are essentially disk shaped.
[00801] A nanoparticle composition may be relatively homogenous. A polydispersity index may be used to indicate tire homogeneity of a nanoparticle composition, e.g., the particle size distribution of the nanoparticle compositions. A small (e.g., less than 0.3) polydispersity index generally indicates a narrow' particle size distribution. A nanoparticle composition may have a polydispersity index from about 0 to about 0.25, such as 0.01, 0.02, 0.03, 0.04. 0.05. 0.06, 0.07, 0.08, 0.09, 0.10. 0.11. 0.12, 0.13, 0.14, 0.15, 0.16. 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24, or 0.25.
[00802] The Zeta potential of a nanoparticle composition may be used to indicate the electrokinetic potential of the composition. For example, the Zeta potential may describe the surface charge of a nanoparticle composition. Nanoparticle compositions with relatively low charges, positive or negative, are generally desirable, as more highly charged species may interact undesirably with cells, tissues, and other elements in the body. In some embodiments, the Zeta potential of a nanoparticle composition is from about -10 mV to about +20 mV, from about -10 mV to about +15 mV, from about -10 mV to about +10 mV, from about -10 mV to about +5 mV, from about -10 mV to about 0 mV, from about -10 mV to about -5 mV, from about -5 mV to about +20 mV, from about -5 mV to about +15 mV, from about -5 mV to about +10 mV, from about - 5 mV to about +5 mV, from about -5 mV to about 0 mV, from about 0 mV, to about +20 mV, from about 0 mV to about +15 mV, from about 0 mV to about +10 mV, from about 0 mV to about +5 mV, from about +5 mV to about +20 mV, from about +5 mV, to about +15 mV, or from about +5 mV to about +10 mV.
[00803] The efficiency of encapsulation of a payload describes the amount of payload that is encapsulated or otherwise associated with a nanoparticle composition after preparation, relative to the initial amount provided. Hie encapsulation efficiency is desirably high (e.g., close to 100%). The encapsulation efficiency may be measured, for example, by comparing the amount of pay load in a solution containing the nanoparticle composition before and after breaking up the nanoparticle composition with one or more organic solvents or detergents. Fluorescence may be used to measure the amount of free payload in a solution. For the nanoparticle compositions described herein, the encapsulation efficiency of a therapeutic and/or prophylactic may be at least 50%, for example 50%, 55%, 60%. 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%. In some embodiments, the encapsulation efficiency is at least 80%. In certain embodiments, the encapsulation efficiency is at least 90%.
[00804] Lipids and their method of preparation are disclosed in, e.g., U.S. Patent Nos. 8,569,256, 5,965,542 and U.S. Patent Publication Nos. 2016/0199485, 2016/0009637, 2015/0273068, 2015/0265708, 2015/0203446, 2015/0005363, 2014/0308304, 2014/0200257, 2013/086373, 2013/0338210, 2013/0323269, 2013/0245107, 2013/0195920, 2013/0123338, 2013/0022649, 2013/0017223, 2012/0295832, 2012/0183581, 2012/0172411, 2012/0027803, 2012/0058188, 2011/0311583, 2011/0311582, 2011/0262527, 2011/0216622, 2011/0117125, 2011/0091525, 2011/0076335, 2011/0060032, 2010/0130588, 2007/0042031, 2006/0240093, 2006/0083780, 2006/0008910, 2005/0175682, 2005/017054, 2005/0118253, 2005/0064595, 2004/0142025, 2007/0042031, 1999/009076 and PCT Pub. Nos. WO 99/39741, WO 2017/117528. WO 2017/004143, WO 2017/075531, WO 2015/199952, WO 2014/008334, WO 2013/086373, WO 2013/086322, WO 2013/016058, WO 2013/086373, WO2011/141705, and WO 2001/07548 and Semple et. al, Nature Biotechnology, 2010, 28, 172-176, the full disclosures of which are herein incorporated by reference in their entirety for all purposes. [00805] A nanoparticle composition may comprise any substance useful in pharmaceutical compositions. For example, the nanoparticle composition may comprise one or more pharmaceutically acceptable excipients or accessory ingredients such as, but not limited to, one or more solvents, dispersion media, diluents, dispersion aids, suspension aids, granulating aids, disintegrants, fdlers, glidants, liquid vehicles, binders, surface active agents, isotonic agents, thickening or emulsifying agents, buffering agents, lubricating agents, oils, preservatives, and other species. Excipients such as waxes, butters, coloring agents, coating agents, flavorings, and perfuming agents may also be comprised. Pharmaceutically acceptable excipients are well known in the art (see for example Remington’s The Science and Practice of Pharmacy, 21st Edition, A. R. Gennaro: Lippincott, Williams & Wilkins, Baltimore, Md., 2006).
G. LNP Payloads
[00806] The Cast 2a (or Cas Type V) gene editing systems and/or components thereof may be delivered by way of LNPs as described here. In various embodiments, the Casl2a (or Cas Type V) gene editing systems may be delivered by LNPs into cells, tissues, organs, or organisms. Depending on the chosen format, the Casl2a-based gene editing systems and/or the individual or combined components thereof may be delivered as DNA molecules (e.g., encoded on one or more plasmids), RNA molecules (e.g., guide RNAs for targeting the Cas 12a (or Cas Type V) protein or linear or circular mRNAs coding for the Cas 12a protein or accessory protein components of the Casl2a-based gene editing systems), proteins (e.g., Casl2a (or Cas Type V) polypeptides, accessory proteins having other functions (e.g., recombinases, nucleases, polymerases, ligases, deaminases, or reverse transcriptases), or protein-nucleic acid complexes (e.g., complexes between a guide RNA and a Casl2a (or Cas Type V) protein or fusion protein comprising a Casl2a protein). These DNA, RNA. protein, or nucleoprotein corresponding to and/or encoding the Casl2a (or Cas Type V) gene editing systems or components thereof comprise the LNP cargo or payloads. In various embodiments, the LNP cargo or payloads may comprise nucleic acid payloads, including coding payloads such as linear and circular mRNA for encoding the various components of the Cas 12a (or Cas Type V) editing system.
A. Nucleic acid payloads
[00807] In various embodiments, the LNP compositions described herein can be used to deliver a nucleic acid or polynucleotide pay load, e.g., a linear or circular mRNA.
[00808] In various embodiments, the Cas 12a editing compositions described herein can include a nucleic acid or polynucleotide payload, e.g., a linear or circular mRNA. For example, the Casl2a gene editing systems may comprise one or more coding mRNA (circular or linear) for encoding Cas 12a and other accessory proteins and these RNA components may be delivered by LNPs. [00809] In some embodiments, a LNP is capable of delivering a polynucleotide to a target cell, tissue, or organ. A polynucleotide, in its broadest sense of the term, includes any compound and/or substance that is or can be incorporated into an oligonucleotide chain. Exemplary polynucleotides for use in accordance with the present disclosure include, but are not limited to, one or more of deoxyribonucleic acid (DNA), ribonucleic acid (RNA) including messenger mRNA (mRNA), hybrids thereof. RNAi-inducing agents. RNAi agents, siRNAs, shRNAs, miRNAs, antisense RNAs. ribozymes, catalytic DNA. RNAs that induce triple helix formation, aptamers, vectors, etc. RNAs useful in the compositions and methods described herein can be selected from the group consisting of but are not limited to, shortimers, antagomirs, antisense, ribozy es, short interfering RNA (siRNA), asymmetrical interfering RNA (aiRNA), microRNA (miRNA), Dicer substrate RNA (dsRNA), short hairpin RNA (shRNA), transfer RNA (tRNA), messenger RNA (mRNA), and mixtures thereof. In some embodiments, a polynucleotide is mRNA. In some embodiments, a polynucleotide is circular RNA. In some embodiments, a polynucleotide encodes a protein, e.g., a nucleobase editing enzyme. A polynucleotide may encode any polypeptide of interest, including any naturally or non-naturally occurring or otherwise modified polypeptide. A polypeptide may? be of any? size and may have any secondary' structure or activity. In some embodiments, a polypeptide encoded by an mRNA may have a therapeutic effect when expressed in a cell.
[00810] In other embodiments, a polynucleotide is an siRNA. An siRNA may be capable of selectively- knocking down or down regulating expression of a gene of interest. For example, an siRNA could be selected to silence a gene associated with a particular disease, disorder, or condition upon administration to a subject in need thereof of a nanoparticle composition including the siRNA. An siRNA may comprise a sequence that is complementary' to an mRNA sequence that encodes a gene or protein of interest. In some embodiments, the siRNA may be an immunomodulatory siRNA.
[00811] In some embodiments, a polynucleotide is an shRNA or a vector or plasmid encoding the same. An shRNA may be produced inside a target cell upon delivery of an appropriate construct to the nucleus. Constructs and mechanisms relating to shRNA arc well known in tire relevant arts.
[00812] A polynucleotide may include a first region of linked nucleosides encoding a polypeptide of interest (e.g., a coding region), a first flanking region located at the 5'-terminus of the first region (e.g., a 5'-UTR), a second flanking region located at the 3'-temiinus of the first region (e.g., a 3'-UTR), at least one 5'-cap region, and a 3 '-stabilizing region. In some embodiments, a polynucleotide further includes a poly-A region or a Kozak sequence (e.g., in the 5'-UTR). In some cases, polynucleotides may contain one or more intronic nucleotide sequences capable of being excised from the polynucleotide. In some embodiments, a polynucleotide (e.g., an mRNA) may include a 5'cap structure, a chain terminating nucleotide, a stem loop, a polyA sequence, and/or a polyadenylation signal. Any one of the regions of a nucleic acid may include one or more alternative components (e.g., an alternative nucleoside). For example, the 3 '-stabilizing region may contain an alternative nucleoside such as an L-nucleoside, an inverted thymidine, or a 2'-O-methyl nucleoside and/or the coding region, 5'-UTR, 3'-UTR, or cap region may include an alternative nucleoside such as a 5- substituted uridine (e.g., 5-methoxyu ridine), a 1-substituted pseudouridine (e.g., 1 -methyl pseudouridine or 1 -ethyl -pseudouridine), and/or a 5-substituted cytidine (e.g., 5-methyl-cytidine). In some embodiments, a polynucleotide contains only naturally occurring nucleosides.
[00813] In some cases, a polynucleotide is greater than 30 nucleotides in length. In another embodiment, the poly nucleotide molecule is greater than 35 nucleotides in length. In another embodiment, the length is at least 40 nucleotides. In another embodiment, the length is at least 45 nucleotides. In another embodiment, the length is at least 55 nucleotides. In another embodiment, the length is at least 50 nucleotides. In another embodiment, the length is at least 60 nucleotides. In another embodiment, the length is at least 80 nucleotides. In another embodiment, the length is at least 90 nucleotides. In another embodiment, the length is at least 100 nucleotides. In another embodiment, the length is at least 120 nucleotides. In another embodiment, the length is at least 140 nucleotides. In another embodiment, the length is at least 160 nucleotides. In another embodiment, the length is at least 180 nucleotides. In another embodiment, the length is at least 200 nucleotides. In another embodiment, the length is at least 250 nucleotides. In another embodiment, the length is at least 300 nucleotides. In another embodiment, the length is at least 350 nucleotides. In another embodiment, the length is at least 400 nucleotides. In another embodiment, the length is at least 450 nucleotides. In another embodiment, the length is at least 500 nucleotides. In another embodiment, the length is at least 600 nucleotides. In another embodiment, the length is at least 700 nucleotides. In another embodiment, the length is at least 800 nucleotides. In another embodiment, the length is at least 900 nucleotides. In another embodiment, the length is at least 1000 nucleotides. In another embodiment, the length is at least 1100 nucleotides. In another embodiment, the length is at least 1200 nucleotides. In another embodiment, the length is at least 1300 nucleotides. In another embodiment, the length is at least 1400 nucleotides. In another embodiment, the length is at least 1500 nucleotides. In another embodiment, the length is at least 1600 nucleotides. In another embodiment, the length is at least 1800 nucleotides. In another embodiment, the length is at least 2000 nucleotides. In another embodiment, the length is at least 2500 nucleotides. In another embodiment, the length is at least 3000 nucleotides. In another embodiment, the length is at least 4000 nucleotides. In another embodiment, the length is at least 5000 nucleotides, or greater than 5000 nucleotides. [00814] In some embodiments, a polynucleotide molecule, formula, composition or method associated therewith comprises one or more polynucleotides comprising features as described in W02002/098443, W02003/051401, W02008/052770, W02009/127230, WO2006/122828, W02008/083949, WO2010/088927, WO2010/037539, W02004/004743, W02005/016376, W02006/024518, W02007/095976, W02008/014979, W02008/077592, W02009/030481, W02009/095226, WO2011/069586, WO2011/026641, WO2011/144358. W02012/019780, WO2012/013326, WO2012/089338, WO2012/113513, WO2012/116811, WO2012/116810, WO2013/113502, WO2013/113501, WO2013/113736, WO2013/143698, WO2013/143699, W02013/143700, WO2013/120626, WO2013/120627, WO2013/120628, WO2013/120629, WO2013/174409, WO2014/127917. WO2015/024669, WO2015/024668, WO2015/024667, WO2015/024665, WO2015/024666, WO2015/024664, W02015/101415, W02015/101414, WO2015/024667, WO2015/062738, W02015/101416, all of which are incorporated by reference herein.
[00815] In some embodiments, a polynucleotide comprises one or more microRNA binding sites. In some embodiments, a microRNA binding site is recognized by a microRNA in a non-target organ. In some embodiments, a microRNA binding site is recognized by a microRNA in the liver. In some embodiments, a microRNA binding site is recognized by a microRNA in hepatic cells.
[00816] In certain embodiments, an RNA of the present disclosure comprises one or more phosphonate modifications selected from a phosphorothioate linkage (PS), phosphorodithioate linkage (PS2), mcthylphosphonatc linkage (MP), mcthoxypropylphosphonatc linkage (MOP), 5’-(E)-vinylphosphonatc linkage (5’-(E)-VP), 5’-Methyl Phosphonate linkage (5’-MP), (S)-5’-C -methyl with phosphate linkage. 5’- phosphorothioate linkage (5 ’-PS), and a peptide nucleic acid linkage (PNA). In certain embodiments, an RNA of the present disclosure comprises one or more ribose modifications selected from a 2’-O-methyl (2’- OMe), 2’-O-methoxyethyl (2’-0-M0E), 2 ’-deoxy-2’ -fluoro (2’-F), 2’-arabino-fluoro (2’-Ara-F), 2 -O- benzyl, 2’-O-methyl-4-pyridine (2’-O-CH2Py(4)), Locked nucleic acid (LNA), (S)-cET-BNA, tricyclo-DNA (tcDNA), PMO, Unlocked Nucleic Acid (UNA) and glycol nucleic acid (GNA). In certain embodiments, the RNA comprises a Locked Nucleic Acid (LNA) comprising a methyl bridge, an ethyl bridge, a propyl bridge, a butyl bridge or an optionally substituted variant of any of the aforementioned. In certain embodiments, an RNA of the present disclosure comprises one or more modified bases selected from a pseudouridine (y), 2’thiouridine (s2U), N6’-methyladenosine (nt’A). 5 ’methyl cytidine (m5C), 5 ’fluoro2’ -deoxyuridine, N- ethylpiperidine 7’-EAA triazole modified adenine, N-ethylpiperidine 6’triazole modified adenine, 6‘pheynlpyrrolo-cytosine (PhpC), 2’,4’-difluorotoluyl ribonucleoside (rF), and 5’ -nitroindole.
B. Single-stranded DNA payloads [00817] In various embodiments, the LNPs of the present disclosure may comprise a payload having at least one single stranded DNA. In certain embodiments, the single stranded DNA is a linear single stranded DNA. In certain embodiments, the single stranded DNA is a circular single stranded DNA. In certain embodiments, the payload further comprises a nucleobase editing system, such as an enzyme or polynucleotide encoding an enzyme capable of independently or co-dependently editing, modifying, or altering a target polynucleotide sequence or a target transcript comprising a nucleic acid sequence.
[00818] In certain embodiments, the circular single stranded DNA (CiSSD) payload is one described in PCT Publication W02020142730A1, which is incorporated by reference herein in its entirety. In certain embodiments, the CiSSD is a donor template for use as part of a nucleobase editing system for targeted genome modification. In certain embodiments, the CiSSD comprises a DNA insert, a 5’ homology arm, and a 3’ homology arm. In some embodiments, the DNA insert is located between the 5’ homology arm and the 3' homology ami. Homology arms as used herein refer to a series of nucleotides that are complementary to a series of nucleotides in an endogenous DNA sequence in the target region. The homology amis flanking the DNA insert allow for specific insertion of the DNA insert in the target region. A target region is a nucleic acid sequence where a desired insertion or modification occurs.
[00819] In certain embodiments, the DNA insert is at least 1 nucleotide. In certain embodiments, the DNA insert is at least about 0.5 kb, 2 kb, 2.5 kb, 5 kb, 10 kb, 20 kb, 40 kb, 80 kb, 100 kb, 150 kb, or 200 kb. In certain embodiments, the length of the DNA insert is about 0.5 kb to 5 kb, about 1 kb to 5 kb, about 1 kb to 10 kb, about 1.6 kb to 5 kb, about 1.6 kb to 10 kb, about 2 kb to 5 kb, about 2 kb to 20 kb, about 2.5 kb to 5 kb, about 2.5 kb to 10 kb, about 2.5 kb to 20 kb, and about 5kb to 100 kb. In some embodiments, the DNA insert size may range from about 1 kb to about 3 kb, about 3 kb to about 6 kb, about 6 kb to about 9 kb. about 9 kb to about 12 kb, about 12 kb to about 15 kb, about 15 kb to about 18 kb, or about 18 kb to about 21 kb.
[00820] In some embodiments, the DNA insert may comprise a nucleotide sequence that encodes a maker or a reporter, e.g., a fluorescent marker, an antibiotic marker, or any suitable marker. A ‘'marker’ or '‘reporter” as used herein means a feature that allows for identification and selection of a desired cell, e g., by fluorescence or antibiotic resistance. For example, the insert may include a nucleotide sequence encoding a reporter (e.g, GFP, RFP, or any suitable reporter) or a recombinase. For example, the reporter is an N- terminal GFP fusion reporter.
[00821] In some embodiments, the DNA insert may comprise a nucleotide sequence that encodes a transcription unit, wherein each transcription unit can produce a cellular product (e g. protein or RNA). In some embodiments, the DNA insert may comprise a nucleotide sequence that encodes a protein, e.g, an immunomodulatory protein (e.g, a cytokine), an antibody, a chimeric antigen receptor (CAR), a grow th factor, a T cell receptor, or another protein.
[00822] In certain embodiments, the CiSSD comprises a DNA insert that can be inserted at a nucleotide break in a target region of genomic DNA. In some embodiments, the break is a double stranded break (DSB). In certain embodiments, the break is a single stranded DNA break or a nick. Precision gene editing techniques, e.g, CRISPR, create a break near a desired sequence change (target sequence). CRISPR can be applied to produce deletions, disruptions, insertions, replacements, and repairs. The components of template donors for these different modifications is generally the same, consisting of three basic elements: a 5’ homology arm, a DNA insert, and a 3’ homology arm. CRISPR-based gene editing can generate gene knockouts by disrupting the gene sequence, how ever, efficiency for inserting exogenous DNA (knock-in) or replacement of genomic sequences is very poor using current methods. In certain embodiments, CiSSDs may be used with CRISPR by generating a knock-in modification. Double-stranded breaks can be introduced by any suitable mechanism, including, for example, by gene-editing systems using CRISPR, zinc finger nuclease, TALEN nuclease (Transcription Activator-Like Effector Nuclease), or meganuclease as described previously. Briefly, the CRISPR genome editing system generates a targeted DSB using the CRISPR programmable DNA endonuclease that can be targeted to a specific DNA sequence (target sequence) by a small “guide” RNA (crRNA). Guide RNAs for use in CRISPR-based modification (z.e., crRNAs and tracrRNAs) may be generated by any suitable method, hi certain embodiments, crRNAs and tracrRNAs may be chemically synthesized. In other embodiments, a single guide RNA (sgRNA) may be constructed and synthesized by in vitro transcription.
[00823] In certain embodiments, an LNP of the present disclosure comprises a CiSSD disclosed herein and further comprises a precision gene editing system component such as a CRISPR, zinc finger nuclease, TALEN nuclease (Transcription Activator-Like Effector Nuclease), or meganuclease, or any other nucleobase editing system known in the art.
[00824] In certain embodiments, the single stranded DNA (SSD) payload is one described in PCT Publication WO2020232286A1, which is incorporated by reference herein in its entirety.
[00825] In certain embodiments, the SSD comprises an engineered initiator sequence and an engineered terminator sequence from a filamentous bacteriophage, and a DNA sequence of interest, wherein the DNA sequence of interest is located 3 ’ to the engineered initiator sequence and 5 ’ to the engineered terminator sequence. In certain embodiments, the SSD comprises a selectable marker.
[00826] In certain embodiments, the single stranded DNA (SSD) payload is made by a method described in PCT Publication WO2020232286A1. In certain embodiments, the SSD is made by a method comprising: (a) culturing a host cell of claim 11 under conditions suitable for producing a ssDNA from the DNA sequence of interest in tire engineered nucleic acid and the plurality of bacteriophage proteins from the nucleic acid helper plasmid; (b) allowing the ssDNA and the plurality of bacteriophage proteins to assemble into an engineered phage; and (c) collecting the engineered phage. In certain embodiments, the method further comprises extracting the SSD from the engineered phage.
[00827] In certain embodiments, at least 90% of the SSD is the same length as the DNA sequence of interest. In certain embodiments, at least 95% of the ssDNA is the same length as the DNA sequence of interest. In certain embodiments, the SSD is between 100 and 20,000 nucleotides in length. In certain embodiments, the ssDNA is circular.
[00828] In certain embodiments, the single stranded DNA (SSD) payload is one described in PCT Publication W02022011082A1, which is incorporated by reference herein in its entirety. In certain embodiments, the SSD comprises a first sequence from a filamentous bacteriophage, the first sequence having both initiator and terminator functions; a second sequence that is identical to the first sequence; and a single-strand DNA sequence of interest that is located between the first sequence and the second sequence. In certain embodiments, the SSD further comprises a selectable marker. In certain embodiments, the SSD is circular. In certain embodiments, the SSD is linear.
[00829] In certain embodiments, the single stranded DNA (SSD) payload is made by a method described in PCT Publication W02022011082A1. In certain embodiments, the method comprises culturing a host cell under conditions suitable for producing the single-stranded DNA from the single-strand DNA sequence of interest in the isolated nucleic acid and producing the bacteriophage proteins from the nucleic acid helper plasmid; allowing the single-stranded DNA and bacteriophage proteins to assemble into an engineered phage; and collecting the engineered phage. In certain embodiments, the host cell comprises an isolated nucleic acid that includes: a first sequence from a filamentous bacteriophage, the first sequence having both initiator and terminator functions; a second sequence that is identical to the first sequence; and a single-strand DNA sequence of interest that is located between the first sequence and the second sequence, and a nucleic acid helper plasmid for expressing bacteriophage proteins capable of assembling a single-strand DNA into a bacteriophage. In certain embodiments, tire method further comprises extracting the SSD from the engineered phage.
[00830] In certain embodiments, at least 90% of the SSD is the same length as the DNA sequence of interest. In certain embodiments, at least 95% of the ssDNA is the same length as the DNA sequence of interest. In certain embodiments, the SSD is between 100 and 20,000 nucleotides in length. In certain embodiments, the SSD is circular. [00831] In certain embodiments, the single stranded DNA (SSD) payload is one described in PCT Publication WO2021055616A1, which is incorporated by reference herein in its entirety.
C. Linear mRNA payloads
[00832] In various embodiments, the LNP -based pharmaceutical compositions described herein, e.g., LNP- based gene editing systems, may include one or more linear mRNA molecules or linear mRNA payloads. In various embodiments, the mRNA payloads may encode one or more components of the herein described gene editing systems. For example, an mRNA payload may encode an amino acid sequence-programmable DNA binding domain (e.g.. TALENS and zinc finger-binding domains) or a nucleic acid sequence-programmable DNA binding domain (e.g., CRISPR Cas9, CRISPR Casl2a, CRISPR Casl2f, CRISPR Casl3a, CRISPR Cast 3b, or TnpB).
[00833] mRNA payloads may also encode, depending upon the nature of the gene editing system, one or more effector domains that provide various functionalities that facilitate changes in nucleotide sequence and/or gene expression, such as, but not limited to, single-strand DNA binding proteins, nucleases, endonucleases, exonucleases, deaminases (e.g., cytidine deaminases or adenosine deaminases), polymerases (e.g., reverse transcriptases), integrases, recombinases, etc., and fusion proteins comprising one or more functional domains linked together.
[00834] Ribonucleic acid (RNA) is a molecule that is made up of nucleotides, which are ribose sugars attached to nitrogenous bases and phosphate groups. The nitrogenous bases include adenine (A), guanine (G), uracil (U), and cytosine (C). Generally, RNA mostly exists in the single-stranded form but can also exists double -stranded in certain circumstances. The length, form and structure of RNA is diverse depending on the purpose of the RNA. For example, the length of an RNA can vary’ from a short sequence (e.g., siRNA) to a long sequences (e.g., IncRNA), can be linear (e.g., mRNA) or circular (e.g., oRNA), and can either be a coding (e.g., mRNA) or a non-coding (e.g., IncRNA) sequence.
[00835] In various embodiments, the LNP -based gene editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein can be used to deliver a mRNA payload that is a linear mRNA molecule. In embodiments, the mRNA payload may comprise one or more nucleotide sequences that encode a product of interest, such as, but not limited to a component of a gene editing system (e.g., an endonuclease, a prime editor, etc.) and/or a therapeutic protein.
[00836] In some embodiments, the RNA payload may be a linear mRNA. As used herein, the term "messenger RNA" (mRNA) refers to any polynucleotide which encodes a protein of interest and which is capable of being translated to produce the encoded protein of interest in vitro, in vivo, in situ or ex vivo. [00837] Generally, a mRNA molecule comprises at least a coding region, a 5' untranslated region (UTR), a 3' UTR, a 5' cap and a poly-A tail. In some aspects, one or more structural and/or chemical modifications or alterations may be included in the RNA which can reduce the innate immune response of a cell in which the mRNA is introduced. As used herein, a "structural" feature or modification is one in which two or more linked nucleotides are inserted, deleted, duplicated, inverted or randomized in a nucleic acid without significant chemical modification to the nucleotides themselves. Because chemical bonds will necessarily be broken and reformed to affect a structural modification, structural modifications are of a chemical nature and hence are chemical modifications. However, structural modifications will result in a different sequence of nucleotides. For example, the polynucleotide "ATCG" may be chemically modified to "AT-5meC-G".
[00838] Generally, a coding region of interest in an mRNA used herein may encode a dipeptide, a tripeptide, a tetrapeptide, a pentapeptide, a hexapeptide, a heptapeptide, an octapeptide, a nonapeptide, or a decapeptide. In another embodiment, the mRNA may encode a peptide of 2-30 amino acids, e.g. 5-30, 10-30, 2-25, 5-25, 10-25, or 10-20 amino acids. The mRNA may encode a peptide of at least 10, 11. 12. 13, 14, 15, 17, 20, 25, 26, 27, 28, 29, 30, 31. 32. 33. 34, 35, 36, 37, 38, 39, or 40 amino acids, or a peptide that is no longer than 10. 11, 12, 13, 14, 15, 17, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 ammo acids.
[00839] Generally, the length of the region of the mRNA encoding a product of interest is greater than about 30 nucleotides in length (e g., at least or greater than about 35, 40, 45, 50, 55, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1000, 1,100, 1,200, 1,300, 1,400, 1,500, 1,600, 1,700, 1,800, 1,900, 2,000, 2,500, and 3,000, 4,000, 5,000, 6,000, 7,000, 8,000, 9,000, 10,000, 20,000, 30,000, 40,000, 50,000. 60,000, 70,000, 80.000, 90,000 or up to and including 100,000 nucleotides).
[00840] In some embodiments, the mRNA has a total length that spans from about 30 to about 100,000 nucleotides (e.g., from 30 to 50, from 30 to 100, from 30 to 250, from 30 to 500, from 30 to 1,000, from 30 to 1.500, from 30 to 3,000, from 30 to 5,000, from 30 to 7,000, from 30 to 10.000, from 30 to 25,000. from 30 to 50,000, from 30 to 70,000, from 100 to 250, from 100 to 500, from 100 to 1,000, from 100 to 1,500, from 100 to 3,000, from 100 to 5,000, from 100 to 7,000, from 100 to 10,000, from 100 to 25,000, from 100 to 50,000, from 100 to 70,000, from 100 to 100,000, from 500 to 1,000, from 500 to 1,500, from 500 to 2,000, from 500 to 3,000, from 500 to 5,000, from 500 to 7,000, from 500 to 10,000, from 500 to 25,000, from 500 to 50,000, from 500 to 70,000, from 500 to 100,000, from 1,000 to 1,500, from 1,000 to 2,000, from 1,000 to 3.000, from 1,000 to 5,000. from 1.000 to 7,000, from 1,000 to 10,000, from 1 ,000 to 25,000, from 1,000 to 50,000, from 1,000 to 70,000, from 1,000 to 100,000, from 1,500 to 3,000, from 1,500 to 5,000, from 1,500 to 7,000, from 1,500 to 10,000, from 1 ,500 to 25,000, from 1,500 to 50,000, from 1,500 to 70,000, from 1,500 to 100,000, from 2,000 to 3,000, from 2,000 to 5,000, from 2,000 to 7,000, from 2,000 to 10,000, from 2,000 to 25,000, from 2,000 to 50,000, from 2,000 to 70,000, and from 2,000 to 100,000 nucleotides).
[00841] In some embodiments, the region or regions flanking the region encoding the product of interest may range independently from 15-1,000 nucleotides in length (e.g., greater than 30, 40, 45, 50, 55, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, and 900 nucleotides or at least 30, 40, 45, 50, 55, 60, 70. 80, 90, 100, 120, 140, 160, 180, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900. and 1,000 nucleotides).
[00842] In some embodiments, tire mRNA comprises a tailing sequence which can range from absent to 500 nucleotides in length (e.g., at least 60, 70. 80, 90, 120, 140, 160, 180, 200, 250, 300, 350, 400, 450. or 500 nucleotides). Where tire tailing region is a polyA tail, the length may be determined in units of or as a function of polyA Binding Protein binding. In this embodiment, the polyA (SEQ ID NO:2652) tail is long enough to bind at least 4 monomers of PolyA Binding Protein. PolyA Binding Protein monomers bind to stretches of approximately 38 nucleotides. As such, it has been observed that polyA tails of about 80 nucleotides and 160 nucleotides are functional.
[00843] In some embodiments, the mRNA comprises a capping sequence which comprises a single cap or a series of nucleotides forming the cap. Hie capping sequence may be from 1 to 10, e.g. 2-9, 3-8. 4-7, 1-5, 5- 10, or at least 2, or 10 or fewer nucleotides in length. In some embodiments, the caping sequence is absent.
[00844] In some embodiments, the mRNA comprises a region comprising a start codon. The region comprising the start codon may range from 3 to 40. e.g., 5-30, 10-20. 15, or at least 4, or 30 or fewer nucleotides in length.
[00845] In some embodiments, the mRNA comprises a region comprising a stop codon. The region comprising the stop codon may range from 3 to 40, e.g., 5-30, 10-20, 15, or at least 4, or 30 or fewer nucleotides in length.
[00846] In some embodiments, the mRNA comprises a region comprising a restriction sequence. The region comprising the restriction sequence may range from 3 to 40, e.g., 5-30, 10-20, 15, or at least 4, or 30 or fewer nucleotides in length.
Untranslated Regions (UTRs)
[00847] In various embodiments, the mRNA payloads of the LNP -based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein, may comprise at least one untranslated region (UTR) which flanks the region encoding the product of interest and/or is incorporated within the mRNA molecule. UTRs are transcribed by not translated. The mRNA payloads can include 5’ UTR sequences and 3’ UTR sequences, as well as internal UTRs.
[00848] The RNA payloads of the present disclosure may comprise one or more regions or parts which act or function as an untranslated region. Where nucleic acids are designed to encode at least one polypeptide of interest, the nucleic acid may comprise one or more of these untranslated regions (UTRs). Wild-type untranslated regions of a nucleic acid are transcribed but not translated. In mRNA, the 5' UTR starts at the transcription start site and continues to the start codon but does not include the start codon; whereas, the 3' UTR starts immediately following the stop codon and continues until the transcriptional termination signal. There is growing body of evidence about the regulatory roles played by the UTRs in terms of stability of the nucleic acid molecule and translation. The regulatory features of a UTR can be incorporated into the RNA payload molecules (e.g., linear and circular mRNA molecules) of the present disclosure to, among other things, enhance the stability of the molecule. The specific features can also be incorporated to ensure controlled down-regulation of the transcript in case they are misdirected to undesired organs sites. A variety of 5 'UTR and 3 'UTR sequences are known and available in the art.
[00849] In various embodiments, the mRNA payloads of the LNP -based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein, may comprise at least one UTR that may be selected from any UTR sequence listed in Tables 19 or 20 of U.S. Patent No. 10,709,779, which is incorporated herein by reference.
5' UTR regions
[00850] In various embodiments, the mRNA payloads of the LNP -based gene editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein, may comprise at least one 5' UTR.
[00851] A 5' UTR is region of an mRNA that is directly upstream (5') from the start codon (the first codon of an mRNA transcript translated by a ribosome). A 5' UTR does not encode a protein (is non-coding). Natural 5 'UTRs have features that play roles in translation initiation. They harbor signatures like Kozak sequences which are commonly known to be involved in the process by which the ribosome initiates translation of many genes. Kozak sequences have the consensus CCR(A/G)CCAUGG (SEQ ID NO:681), where R is a purine (adenine or guanine) three bases upstream of the start codon (AUG), which is followed by another ‘G’. 5'UTR also have been known to form secondary structures which are involved in elongation factor binding. 5 ‘ UTR sequences are also known to be important for ribosome recruitment to the mRNA and have been reported to play a role in translation (Hinnebusch A, et al., (2016) Science, 352:6292: 1413-6). In addition, 5' UTR sequences may confer increased half-life, increased expression and/or increased activity of a polypeptide encoded by the RNA payload described herein. [00852] In various embodiments, the RNA payload constructs contemplated herein may include 5’UTRs that are found in nature and those that are not. For example, the 5’UTRs can be synthetic and/or can be altered in sequence with respect to a naturally occurring 5’UTR. Such altered 5’UTRs can include one or more modifications relative to a naturally occurring 5’UTR, such as, for example, an insertion, deletion, or an altered sequence, or the substitution of one or more nucleotide analogs in place of a naturally occurring nucleotide.
[00853] Tire 5' UTR starts at the transcription start site and continues to the start codon but does not include the start codon: whereas, the 3 'UTR starts immediately following tire stop codon and continues until the transcriptional termination signal. While not wishing to be bound by theory , the UTRs may have a regulatory' role in terms of translation and stability of the nucleic acid.
[00854] Natural 5' UTRs usually include features which have a role in translation initiation as they tend to include Kozak sequences which are commonly known to be involved in the process by which the ribosome initiates translation of many genes. Kozak sequences have the consensus CCR(A/G)CCAUGG (SEQ ID NO: 1338), where R is a purine (adenine or guanine) three bases upstream of the start codon (AUG), which is followed by another 'G'. 5'UTR also have been known to form secondary structures which are involved in elongation factor binding.
[00855] In an embodiment, the 5 ’ UTR comprises a sequence provided in Table X or a sequence having at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to a 5’ UTR sequence provided in Table X (SEQ ID NO: 1339, SEQ ID NO: 1340, SEQ ID NO: 1341, SEQ ID NO: 1342, SEQ ID NO: 1343, SEQ ID NO: 1344, SEQ ID NO: 1345, SEQ ID NO: 1346, SEQ ID NO: 1347, SEQ ID NO: 1348, SEQ ID NO: 1349, SEQ ID NO: 1350, SEQ ID NO: 1351, SEQ ID NO: 1352, SEQ ID NO: 1353, SEQ ID NO: 1354, SEQ ID NO: 1355, SEQ ID NO: 1356, SEQ ID NO: 1357, SEQ ID NO: 1358, SEQ ID NO: 1359, SEQ ID NO: 1360. SEQ ID NO: 1361. SEQ ID NO: 1362. SEQ ID NO: 1363. SEQ ID NO: 1364, SEQ ID NO: 1365, or SEQ ID NO: 1366), or a variant or a fragment thereof (e.g., a fragment that lacks the first one, two, three, four, five, or six nucleotides of the 5’ UTR sequence provided in Table X). In an embodiment, the 5’ UTR comprises a sequence with at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identity to SEQ ID NO: 1339, SEQ ID NO: 1340, SEQ ID NO: 1341, SEQ ID NO: 1342, SEQ ID NO: 1343, SEQ ID NO: 1344, SEQ ID NO: 1345, SEQ ID NO: 1346, SEQ ID NO: 1347, SEQ ID NO: 1348, SEQ ID NO: 1349, SEQ ID NO: 1350, SEQ ID NO: 1351, SEQ ID NO: 1352, SEQ ID NO: 1353, SEQ ID NO: 1354, SEQ ID NO: 1355, SEQ ID NO: 1356, SEQ ID NO: 1357, SEQ ID NO: 1358, SEQ ID NO: 1359, SEQ ID NO: 1360, SEQ ID NO: 1361, SEQ ID NO: 1362, SEQ ID NO: 1363, SEQ ID NO: 1364, SEQ ID NO: 1365, or SEQ ID NO: 1366. Table X - Exemplary nucleotide sequences of 5’ UTRs
[00856] In some embodiments of the disclosure, a 5' UTR is a heterologous UTR, i.e., is a UTR found in nature associated with a different mRNA. In another embodiment, a 5' UTR is a synthetic UTR, i.e., does not occur in nature. Synthetic UTRs include UTRs that have been mutated to improve their properties, e.g., which increase gene expression as well as those which are completely synthetic. Exemplary 5' UTRs include Xenopus or human derived alpha-globin or beta-globin (e.g., US8, 278,063 and US9,012,219), human cytochrome b-245 polypeptide, and hydroxysteroid (17b) dehydrogenase, and Tobacco etch virus. CMV immediate-early 1 (IE1) gene (see US20140206753 and
WG2013/185069), the sequence GGGAUCCUACC (SEQ ID NO:2589) (WO2014144196) may also be used. In another embodiment. 5' UTR of a TOP gene is a 5' UTR of a TOP gene lacking tire 5' TOP motif (the oligopyrimidine tract) (e.g., WO/2015101414, WO2015101415, WO/2015/062738, WO2015024667, WO2015024667; 5' UTR element derived from ribosomal protein Large 32 (L32) gene (WO/2015101414, WO2015101415, WO/2015/062738)), 5' UTR element derived from the 5 'UTR of an hydroxysteroid ( 17-|3) dehydrogenase 4 gene (HSD 17B4) (W 02015024667), or a 5 ' UTR element derived from the 5' UTR of ATP5A1 (WO2015024667) can be used. In one embodiment, an internal ribosome entry site (IRES) is used as a substitute for a 5' UTR.
[00857] In some embodiments, a 5' UTR of the present disclosure comprises a sequence selected from SEQ ID NO: 2590 (GGGAAAUAAG AGAGAAAAGA AGAGUAAGAA GAAAUAUAAG AGCCACC). and SEQ ID NO:2591 (GGGAAATAAG AGAGAAAAGA AGAGTAAGAA GAAATATAAG AGCCACC).
3' UTR regions
[00858] In various embodiments, the mRNA payloads of the LNP -based base editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein, may comprise at least one 3' UTR. 3' UTRs may be heterologous or synthetic.
[00859] A 3' UTR is region of an mRNA that is directly downstream (3') from the stop codon (the codon of an mRNA transcript that signals a termination of translation). A 3' UTR does not encode a protein (is noncoding). Natural or wild type 3' UTRs are known to have stretches of adenosines and uridines embedded in them. These AU rich signatures are particularly prevalent in genes with high rates of turnover. Based on their sequence features and functional properties, the AU rich elements (AREs) can be separated into three classes (Chen et al, 1995): Class I AREs contain several dispersed copies of an AUUUA motif within U-rich regions. C-Myc and MyoD contain class I AREs. Class II AREs possess two or more overlapping UUAUUUA(U/A)(U/A) nonamers. Molecules containing this type of AREs include GM-CSF and TNF-a. Class III ARES are less well defined. These U rich regions do not contain an AUUUA motif. c-Jun and Myogenin are two well-studied examples of this class. Most proteins binding to the AREs are known to destabilize the messenger, whereas members of the ELAV family, most notably HuR, have been documented to increase the stability of mRNA. HuR binds to AREs of all the three classes. Engineering the HuR specific binding sites into the 3' UTR of nucleic acid molecules will lead to HuR binding and thus, stabilization of the message in vivo.
[00860] 3' UTRs are known to have stretches of adenosines and uridines embedded in them. These AU rich signatures are particularly prevalent in genes with high rates of turnover. Based on their sequence features and functional properties, tire AU rich elements (AREs) can be separated into three classes (Chen et al., 1995): Class I AREs contain several dispersed copies of an AUUUA motif within U-rich regions. C-Myc and MyoD contain class I AREs. Class II AREs possess two or more overlapping UUAUUUA(U/A)(U/A) nonamers. Molecules containing this type of AREs include GM-CSF and TNF-a. Class III ARES are less well defined. These U rich regions do not contain an AUUUA motif. c-Jun and Myogenin are two well- studied examples of this class. Most proteins binding to the AREs are known to destabilize the messenger, whereas members of the ELAV family, most notably HuR, have been documented to increase the stability of mRNA. HuR binds to AREs of all tire three classes. Engineering the HuR specific binding sites into the 3' UTR of nucleic acid molecules will lead to HuR binding and thus, stabilization of the message in vivo.
[00861] Introduction, removal or modification of 3' UTR AU rich elements (AREs) can be used to modulate the stability of the mRNA payloads described herein. For example, one or more copies of an ARE can be introduced to make mRNA less stable and thereby curtail translation and decrease production of the resultant protein. Alternatively, AREs can be identified and removed or mutated to increase the intracellular stability and thus increase translation and production of the resultant protein.
[00862] In some embodiments, the introduction of features often expressed in genes of target organs the stability and protein production of the mRNA can be enhanced in a specific organ and/or tissue. As a nonlimiting example, the feature can be a UTR. As another example, the feature can be introns or portions of introns sequences.
[00863] Those of ordinary skill in the art will understand that 5' UTRs that are heterologous or synthetic may be used with any desired 3' UTR sequence. For example, a heterologous 5' UTR may be used with a synthetic 3' UTR with a heterologous 3' UTR.
[00864] Non-UTR sequences may also be used as regions or subregions within an RNA payload construct. For example, introns or portions of introns sequences may be incorporated into regions of nucleic acid of the disclosure. Incorporation of intronic sequences may increase protein production as well as nucleic acid levels.
[00865] Combinations of features may be included in flanking regions and may be contained within other features. For example, the polypeptide coding region of interest in an mRNA payload may be flanked by a 5' UTR which may contain a strong Kozak translational initiation signal and/or a 3' UTR which may include an oligo(dT) sequence for templated addition of a poly-A tail. 5' UTR may comprise a first polynucleotide fragment and a second polynucleotide fragment from the same and/or different genes such as the 5 ' UTRs described in US Patent Application Publication No. 20100293625 and PCT/US2014/069155, herein incorporated by reference in its entirety
[00866] It should be understood that any UTR from any gene may be incorporated into the regions of an RNA payload molecule (e.g., a linear mRNA). Furthennore, multiple wild-type UTRs of any known gene may be utilized. It is also within the scope of the present disclosure to provide artificial UTRs which are not variants of wild type regions. These UTRs or portions thereof may be placed in the same orientation as in the transcript from which they were selected or may be altered in orientation or location. Hence a 5' or 3' UTR may be inverted, shortened, lengthened, made with one or more other 5' UTRs or 3' UTRs. As used herein, the term “altered” as it relates to a UTR sequence, means that the UTR has been changed in some way in relation to a reference sequence. For example, a 3' UTR or 5' UTR may be altered relative to a wild-type or native UTR by the change in orientation or location as taught above or may be altered by the inclusion of additional nucleotides, deletion of nucleotides, swapping or transposition of nucleotides. Any of these changes producing an “altered” UTR (whether 3' or 5') comprise a variant UTR.
[00867] In some embodiments, a double, triple or quadruple UTR such as a 5' UTR or 3' UTR may be used. As used herein, a “double” UTR is one in which two copies of the same UTR are encoded either in series or substantially in series. For example, a double beta-globin 3' UTR may be used as described in US Patent publication 20100129877, the contents of which arc incorporated herein by reference in its entirety.
[00868] It is also within the scope of the present disclosure to have patterned UTRs. As used herein “patterned UTRs” are those UTRs which reflect a repeating or alternating pattern, such as ABABAB or AABBAABBAABB or ABCABCABC or variants thereof repeated once, twice, or more than 3 times. In these patterns, each letter. A, B, or C represent a different UTR at the nucleotide level.
[00869] In some embodiments, flanking regions are selected from a family of transcripts whose proteins share a common function, structure, feature or property. For example, polypeptides of interest may belong to a family of proteins which are expressed in a particular cell, tissue or at some time during development. The UTRs from any of these genes may be swapped for any other UTR of the same or different family of proteins to create a new polynucleotide. As used herein, a “family of proteins” is used in the broadest sense to refer to a group of two or more polypeptides of interest which share at least one function, structure, feature, localization, origin, or expression pattern. [00870] The untranslated region may also include translation enhancer elements (TEE). As a non-limiting example, the TEE may include those described in US Application No. 20090226470, herein incorporated by reference in its entirety, and those known in the art.
5' Capping
[00871] In various embodiments, the mRNA payloads of the LNP -based base editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein, may comprise a 5’ cap structure.
[00872] The 5' cap structure of an mRNA is involved in nuclear export, increasing mRNA stability and binds the mRNA Cap Binding Protein (CBP). which is responsible for mRNA stability in the cell and translation competency through the association of CBP with poly(A) binding protein to form the mature cyclic mRNA species. The cap further assists the removal of 5' proximal introns removal during mRNA splicing.
[00873] Endogenous mRNA molecules may be 5'-end capped generating a 5'-ppp-5'-triphosphate linkage between a terminal guanosine cap residue and the 5'-terminal transcribed sense nucleotide of the mRNA molecule. This 5'-guanylate cap may then be methylated to generate an N7-methyl -guanylate residue. The ribose sugars of tire terminal and/or antetenninal transcribed nucleotides of the 5' end of the mRNA may optionally also be 2'-0-methylated. 5'-decapping through hydrolysis and cleavage of the guanylate cap structure may target a nucleic acid molecule, such as an mRNA molecule, for degradation.
[00874] Modifications to mRNA may generate a non-hydrolyzablc cap structure preventing dccapping and thus increasing mRNA half-life. Because cap structure hydrolysis requires cleavage of 5'-ppp-5' phosphorodiester linkages, modified nucleotides may be used during the capping reaction. For example, a Vaccinia Capping Enzyme from New England Biolabs (Ipswich, MA) may be used with a-thio-guanosine nucleotides according to the manufacturer's instructions to create a phosphorothioate linkage in the 5 '-ppp-5 ' cap.
[00875] Additional modified guanosine nucleotides may be used such as a-methyl-phosphonate and selenophosphate nucleotides.
[00876] Additional modifications include, but are not limited to, 2'-0-methylation of the ribose sugars of 5 '- terminal and/or 5 '-antetenninal nucleotides of the mRNA (as mentioned above) on the 2'-hydroxyl group of the sugar ring. Multiple distinct 5 '-cap structures can be used to generate the 5 '-cap of a nucleic acid molecule, such as an mRNA molecule.
[00877] Cap analogs, which herein are also referred to as synthetic cap analogs, chemical caps, chemical cap analogs, or structural or functional cap analogs, differ from natural (i.e. endogenous, wild-type or physiological) 5'-caps in their chemical structure, while retaining cap function. Cap analogs may be chemically (i.e. non-enzymatically) or enzymatically synthesized and/or linked to a nucleic acid molecule.
[00878] For example, the Anti-Reverse Cap Analog (ARCA) cap contains two guanines linked by a 5 '-5 '- triphosphate group, wherein one guanine contains an N7 methyl group as well as a 3'-0-methyl group (i.e., N7,3'-0-dimethyl-guanosine-5'-triphosphate-5 '-guanosine (m7G-3'mppp-G; which may equivalently be designated 3' O-Me-m7G(5')ppp(5')G). The 3'-0 atom of the other, unmodified, guanine becomes linked to the 5'-terminal nucleotide of the capped nucleic acid molecule (e.g. an mRNA). The N7- and 3'-0-methlyated guanine provides the terminal moiety of tire capped nucleic acid molecule (e.g. mRNA).
[00879] Another exemplary cap is mCAP, which is similar to ARCA but has a 2'-0-methyl group on guanosine (i.e.. N7.2'-0-dimethyl-guanosine-5'-triphosphate-5'-guanosine, m7Gm-ppp-G).
[00880] While cap analogs allow for the concomitant capping of a nucleic acid molecule in an in vitro transcription reaction, up to 20% of transcripts can remain uncapped. This, as well as the structural differences of a cap analog from an endogenous 5 '-cap structures of nucleic acids produced by the endogenous, cellular transcription machinery, may lead to reduced translational competency and reduced cellular stability.
[00881] mRNA may also be capped post-transcriptionally, using enzymes, in order to generate more authentic 5'-cap structures. As used herein, the phrase "more authentic" refers to a feature that closely mirrors or mimics, either structurally or functionally, an endogenous or wild type feature. That is, a "more authentic" feature is better representative of an endogenous, wild-type, natural or physiological cellular function and/or structure as compared to synthetic features or analogs, etc., of the prior art, or which outperforms the corresponding endogenous, wild-type, natural or physiological feature in one or more respects. Non-limiting examples of more authentic 5 'cap structures are those which, among other things, have enhanced binding of cap binding proteins, increased half-life, reduced susceptibility to 5' endonucleases and/or reduced 5'decapping, as compared to synthetic 5 'cap structures known in the art (or to a wild-type, natural or physiological 5 'cap structure). For example, recombinant Vaccinia Virus Capping Enzyme and recombinant 2'-0-methyltransferase enzyme can create a canonical 5 '-5 '-triphosphate linkage between the 5 '-terminal nucleotide of an mRNA and a guanine cap nucleotide wherein the cap guanine contains an N7 methylation and the 5 '-terminal nucleotide of the mRNA contains a 2'-0-methyl. Such a structure is termed the Capl structure. This cap results in a higher translational-competency and cellular stability’ and a reduced activation of cellular pro-inflammatory cytokines, as compared, e.g., to other 5 'cap analog structures known in the art. Cap structures include, but are not limited to. 7mG(5*)ppp(5*)N,pN2p (cap 0), 7mG(5*)ppp(5*)NlmpNp (cap 1), and 7mG(5*)-ppp(5')NlmpN2mp (cap 2). [00882] In some embodiments, the 5' terminal caps may include endogenous caps or cap analogs.
[00883] In some embodiments, a 5' terminal cap may comprise a guanine analog. Useful guanine analogs include, but are not limited to, inosine, Nl-methyl-guanosine, 2'fluoro-guanosine, 7-deaza-guanosine, 8-oxo- guanosine, 2-amino-guanosine, LNA-guanosine, and 2-azido-guanosine.
IRES Sequences
[00884] In various embodiments, the mRNA payloads of the LNP -based gene editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein, may comprise one or more IRES sequences.
[00885] In some embodiments, the mRNA may contain an internal ribosome entry site (IRES). First identified as a feature Picoma virus RNA, IRES plays an important role in initiating protein synthesis in absence of the 5' cap structure. An IRES may act as the sole ribosome binding site, or may serve as one of multiple ribosome binding sites of an mRNA. An mRNA that contains more than one functional ribosome binding site may encode several peptides or polypeptides that are translated independently by the ribosomes. Non-limiting examples of IRES sequences that can be used include without limitation, those from picomaviruses (e.g. FMDV), pest viruses (CFFV), polio viruses (PV), encephalomyocarditis viruses (ECMV), foot-and-mouth disease viruses (FMDV), hepatitis C viruses (HCV), classical swine fever viruses (CSFV), murine leukemia virus (MLV), simian immune deficiency viruses (SIV) or cricket paralysis viruses (CrPV).
[00886] In some embodiments, the IRES is from Taura syndrome virus. Triatoma virus, Theiler's encephalomyelitis virus, Simian Virus 40, Solenopsis invicta virus 1, Rhopalosiphum padi virus, Reticuloendotheliosis virus. Human poliovirus 1, Plautia stali intestine virus, Kashmir bee virus, Human rhinovirus 2, Homalodisca coagulata virus-1, Human Immunodeficiency Virus type 1, Homalodisca coagulata virus- 1, Himetobi P virus, Hepatitis C virus, Hepatitis A virus, Hepatitis GB virus, Foot and mouth disease virus, Human enterovirus 71, Equine rhinitis virus, Ectropis obliqua picoma-like virus, Encephalomyocarditis virus, Drosophila C Virus. Human coxsackievirus B3. Crucifer tobamovirus, Cricket paralysis virus, Bovine viral diarrhea vims 1, Black Queen Cell Vims, Aphid lethal paralysis vims, Avian encephalomyelitis vims. Acute bee paralysis vims, Hibiscus chlorotic ringspot vims, Classical swine fever vims, Human FGF2, Human SFTPA1, Human AML1/RUNX1, Drosophila antennapedia, Human AQP4, Human AT1R, Human BAG-1, Human BCL2, Human BiP, Human c-IAPl, Human c-myc, Human eIF4G, Mouse NDST4L, Human LEF1, Mouse HIF1 alpha, Human n.myc, Mouse Gtx, Human p27kipl, Human PDGF2/c-sis. Human p53, Human Pim-1, Mouse Rbm3, Drosophila reaper, Canine Scamper, Drosophila Ubx, Human UNR, Mouse UtrA, Human VEGF-A, Human XIAP, Drosophila hairless, S. cerevisiae TFIID, S. cerevisiae YAP1, tobacco etch virus, turnip crinkle virus, EMCV-A, EMCV-B, EMCV-Bf, EMCV-Cf, EMCV pEC9, Picobimavirus, HCV QC64, Human Cosavirus E/D, Human Cosavirus F, Human Cosavirus JMY, Rhinovirus NAT001, HRV14, HRV89, HRVC-02, HRV- A21, Salivirus A SHI, Salivirus FHB, Salivirus NG-J1, Human Parechovirus 1, Crohivirus B, Yc-3, Rosavirus M-7, Shanbavirus A, Pasivirus A, Pasivirus A 2, Echovirus El 4, Human Parecho virus 5. Aichi Virus, Hepatitis A Virus HA 16. Phopivirus, CVA10, Enterovirus C, Enterovirus D. Enterovirus J, Human Pegivirus 2, GBV-C GT110, GBV-C K1737, GBV-C Iowa, Pegivirus A 1220, Pasivirus A 3, Sapelovirus, Rosavirus B, Bakunsa Virus, Tremovirus A, Swine Pasivirus 1, PLV-CHN, Pasivirus A, Sicinivirus, Hepacivirus K, Hepacivirus A, BVDV1, Border Disease Virus, BVDV2, CSFV-PK15C, SF573 Dicistrovirus, Hubei Picoma-like Virus, CRPV, Salivirus A BNS, Salivirus A BN2, Salivirus A 02394, Salivirus A GUT, Salivirus A CH, Salivirus A SZ1, Salivirus FHB, CVB3, CVB1, Echovirus 7, CVBS. EVA71, CVA3, CVA12, EV24 or an aptamer to eIF4G.
Poly-A tails and 3 ’ stabilizing regions
[00887] In various embodiments, the mRNA payloads of the LNP-based gene editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein, may comprise a poly-A tail.
[00888] During RNA processing, a long chain of adenine nucleotides (poly-A tail) may be added to a polynucleotide such as an mRNA molecules in order to increase stability. Immediately after transcription, the 3' end of the transcript may be cleaved to free a 3' hydroxyl. Then poly-A polymerase adds a chain of adenine nucleotides to the free 3' hydroxyl end. Tire process, called polyadcnylation, adds a poly-A tail of a certain length.
[00889] In some embodiments, the length of a poly-A (SEQ ID NO:2652) tail is greater than 30 nucleotides in length. In another embodiment, the poly-A (SEQ ID NO:2652) tail is greater than 35 nucleotides in length (e.g., at least or greater than about 35, 40. 45. 50, 55, 60, 70, 80, 90, 100, 120, 140, 160, 180, 200, 250, 300, 350, 400, 450, 500, 600, 700, 800, 900, 1,000, 1,100, 1,200, 1,300, 1,400, 1,500, 1,600, 1,700, 1,800, 1,900, 2,000, 2,500, and 3,000 nucleotides) and no more than about 50, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 2000, or 3000 nucleotides in length. In some embodiments, tire mRNA includes a poly-A (SEQ ID NO:2652) tail from about 30 to about 3,000 nucleotides (e.g., from 30 to 50, from 30 to 100, from 30 to 250, from 30 to 500, from 30 to 750. from 30 to 1,000, from 30 to 1.500, from 30 to 2,000, from 30 to 2,500, from 50 to 100, from 50 to 250, from 50 to 500, from 50 to 750, from 50 to 1 ,000. from 50 to 1,500. from 50 to 2,000, from 50 to 2,500, from 50 to 3,000, from 100 to 500, from 100 to 750, from 100 to 1,000, from 100 to 1,500, from 100 to 2,000, from 100 to 2,500, from 100 to 3,000, from 500 to 750, from 500 to 1,000, from 500 to 1,500, from 500 to 2,000, from 500 to 2,500, from 500 to 3,000, from 1,000 to 1,500, from 1,000 to 2,000, from 1,000 to 2,500, from 1,000 to 3,000, from 1,500 to 2,000, from 1,500 to 2,500, from 1,500 to 3,000, from 2,000 to 3,000, from 2,000 to 2,500, and from 2,500 to 3,000).
[00890] In some embodiments, the poly-A tail is designed relative to the length of the overall mRNA. This design may be based on tire length of the region coding for a target of interest, the length of a particular feature or region (such as a flanking region), or based on the length of the ultimate product expressed from the mRNA.
[00891] In this context the poly-A tail may be 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100% greater in length than the mRNA or feature thereof. The poly-A tail may also be designed as a fraction of mRNA to which it belongs. In this context, the poly-A tail may be 10, 20, 30, 40, 50, 60. 70. 80, or 90% or more of the total length of the construct or the total length of the construct minus the poly-A tail. Further, engineered binding sites and conjugation of mRNA for poly-A binding protein may enhance expression.
[00892] Additionally, multiple distinct mRNA may be linked together to the PABP (Poly-A binding protein) through the 3'-end using modified nucleotides at the 3 '-terminus of the poly-A tail. Transfection experiments can be conducted in relevant cell lines at and protein production can be assayed by ELISA at 12hr, 24hr, 48hr, 72 hr and day 7 post-transfection.
[00893] In some embodiments, the mRNA are designed to include a polyA-G Quartet. The G-quartet is a cyclic hydrogen bonded array of four guanine nucleotides that can be formed by G-rich sequences in both DNA and RNA. In this embodiment, the G-quartet is incorporated at the end of the poly-A tail.
Stop Codons
[00894] In various embodiments, the mRNA payloads of the LNP -based gene editing systems, RNA therapeutics and phannaceutical compositions thereof described herein, may comprise one or more translation stop codons. Translational stop codons, UAA, UAG, and UGA, are an important component of the genetic code and signal the termination of translation of an mRNA. During protein synthesis, stop codons interact with protein release factors and this interaction can modulate ribosomal activity thus having an impact translation (Tate WP, et al., (2018) Biochem Soc Trans, 46(6): 1615-162).
[00895] A stop element as used herein, refers to a nucleic acid sequence comprising a stop codon. The stop codon can be selected from TGA, TAA and TAG in the case of DNA, or from UGA, UAA and UAG in the case of RNA. In an embodiment, a stop element comprises two consecutive stop codons. In an embodiment, a stop element comprises three consecutive stop codons. In an embodiment, a stop element comprises four consecutive stop codons. In an embodiment, a stop element comprises five consecutive stop codons. [00896] In some embodiments, the mRNA may include one stop codon. In some embodiments, the mRNA may include two stop codons. In some embodiments, the mRNA may include three stop codons. In some embodiments, the mRNA may include at least one stop codon. In some embodiments, the mRNA may include at least two stop codons. In some embodiments, the mRNA may include at least three stop codons. As non-limiting examples, the stop codon may be selected from TGA, TAA and TAG.
[00897] In other embodiments, the stop codon may be selected from one or more of the following stop elements of Table Y :
Table Y : Additional stop elements of linear mRNA
[00898] In some embodiments, the mRNA includes the stop codon TGA and one additional stop codon. In a further embodiment the addition stop codon may be TAA. MicroRNA binding sites and other regulatory elements
[00899] In various embodiments, the mRNA payloads of the LNP -based gene editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein, may comprise one or more regulatory elements, including, but not limited to microRNA (miRNA) binding sites, structured mRNA sequences and/or motifs, artificial binding sites to bind to endogenous nucleic acid binding molecules, and combinations thereof.
Chemically unmodified nucleotides
[00900] In some embodiments, the mRNA payloads of the LNP-based gene editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein are not chemically modified and comprises the standard ribonucleotides consisting of adenosine, guanosine, cytosine and uridine. In some embodiments, nucleotides and nucleosides of the present disclosure comprise standard nucleoside residues such as those present in transcribed RNA (e.g. A, G, C, or U). In some embodiments, nucleotides and nucleosides of the present disclosure comprise standard deoxyribonucleosides such as those present in DNA (e.g. dA, dG, dC, or dT).
Chemically modified nucleotides
[00901] In some embodiments, the mRNA payloads of the LNP-based gene editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein comprise, in some embodiments, comprises at least one chemical modification.
[00902] The terms “chemical modification” and “chemically modified” refer to modification with respect to adenosine (A), guanosine (G), uridine (U), thymidine (T) or cytidine (C) ribonucleosides or deoxyribnucleosides in at least one of their position, pattern, percent or population. Generally, these terms do not refer to the ribonucleotide modifications in naturally occurring 5 '-terminal mRNA cap moieties. With respect to a polypeptide, the tenn “modification” refers to a modification relative to the canonical set 20 amino acids. Polypeptides, as provided herein, are also considered “modified” of they contain amino acid substitutions, insertions or a combination of substitutions and insertions.
[00903]
[00904] Polynucleotides (e.g.. RNA polynucleotides, such as mRNA polynucleotides), in some embodiments, comprise various (more than one) different modifications. In some embodiments, a particular region of a polynucleotide contains one, two or more (optionally different) nucleoside or nucleotide modifications. In some embodiments, a modified RNA polynucleotide (e.g., a modified mRNA polynucleotide), introduced to a cell or organism, exhibits reduced degradation in the cell or organism, respectively, relative to an unmodified polynucleotide. In some embodiments, a modified RNA polynucleotide (e.g.. a modified mRNA polynucleotide), introduced into a cell or organism, may exhibit reduced immunogenicity in the cell or organism, respectively (e.g., a reduced innate response).
[00905] Modifications of polynucleotides include, without limitation, those described herein. Polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) may comprise modifications that are naturally- occurring, non-naturally-occurring or the polynucleotide may comprise a combination of naturally-occurring and non-naturally-occurring modifications. Polynucleotides may include any useful modification, for example, of a sugar, a nucleobase, or an intemucleoside linkage (e.g.. to a linking phosphate, to a phosphodiester linkage or to the phosphodiester backbone).
[00906]
[00907] Polynucleotides (e.g.. RNA polynucleotides, such as mRNA polynucleotides), in some embodiments, comprise non-natural modified nucleotides that are introduced during synthesis or post-synthesis of the polynucleotides to achieve desired functions or properties. The modifications may be present on an intemucleotide linkages, purine or pyrimidine bases, or sugars. The modification may be introduced with chemical synthesis or with a polymerase enzyme at the terminal of a chain or anywhere else in the chain. Any of tire regions of a polynucleotide may be chemically modified.
[00908] The present disclosure provides for modified nucleosides and nucleotides of a polynucleotide (e.g., RNA polynucleotides, such as mRNA polynucleotides). A “nucleoside'’ refers to a compound containing a sugar molecule (e.g., a pentose or ribose) or a derivative thereof in combination with an organic base (e.g., a purine or pyrimidine) or a derivative thereof (also referred to herein as “nucleobase”). A “nucleotide” refers to a nucleoside, including a phosphate group. Modified nucleotides may by synthesized by any useful method, such as, for example, chemically, enzymatically, or recombinantly, to include one or more modified or non-natural nucleosides. Polynucleotides may comprise a region or regions of linked nucleosides. Such regions may have variable backbone linkages. The linkages may be standard phosphodiester linkages, in which case the polynucleotides would comprise regions of nucleotides.
[00909]
[00910] Modified nucleotide base pairing encompasses not only the standard adenosine-thymine, adenosineuracil, or guanosine-cytosine base pairs, but also base pairs formed between nucleotides and/or modified nucleotides comprising non-standard or modified bases, wherein the arrangement of hydrogen bond donors and hydrogen bond acceptors permits hydrogen bonding between a non-standard base and a standard base or between two complementary non-standard base structures. One example of such non-standard base pairing is the base pairing between the modified nucleotide inosine and adenine, cytosine or uracil. Any combination of base/sugar or linker may be incorporated into polynucleotides of the present disclosure.
[00911] In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) include a combination of at least two (e.g., 2, 3, 4 or more) of the aforementioned modified nucleobases.
[00912] In some embodiments, modified nucleobases in polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) are selected from the group consisting of pseudouridine (y), Nl- methylpseudouridine (m'y), N1 -ethylpseudouridine, 2-thiouridine, 4'-thiouridine, 5-mcthylcytosinc. 2-thio-l- methyl-l-deaza-pseudouridine, 2-thio-l-methyl-pseudouridine, 2-thio-5 -aza-uridine, 2-thio- dihydropseudouridine, 2-thio-dihydrouridine. 2-thio-pseudouridine, 4-methoxy-2-thio-pseudouridine, 4- methoxy-pseudouridine, 4-thio-l -methyl -pseudouridine, 4-thio-pseudouridine, 5 -aza-uridine. dihydropseudouridine, 5 -methoxyuridine and 2'-O-methyl uridine. In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) include a combination of at least two (e.g., 2, 3, 4 or more) of the aforementioned modified nucleobases.
[00913] In some embodiments, modified nucleobases in polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) are selected from the group consisting of 1 -methyl -pseudouridine (m’y), 5- methoxy-uridine (mo’U), 5 -methyl -cytidine (m’C), pseudouridine (\|/), a-thio-guanosine and a-thio- adenosine. In some embodiments, polynucleotides includes a combination of at least two (e.g., 2. 3, 4 or more) of the aforementioned modified nucleobases.
[00914] In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) comprise pseudouridine (y) and 5-methyl-cytidine (m5C). In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) comprise 1 -methyl -pseudouridine (m1^). In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) comprise 1- methyl-pseudouridine (m \|/) and 5-methyl-cytidine (nr C). In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) comprise 2-thiouridine (s2U). In some embodiments, polynucleotides (e.g.. RNA polynucleotides, such as mRNA polynucleotides) comprise 2-thiouridine and 5- methyl-cytidine (nr C). In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) comprise methoxy-uridine (mo5U). In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) comprise 5 -methoxy-uridine (mo’U) and 5 -methyl -cytidine (m5C). In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) comprise 2'-O-methyl uridine. In some embodiments polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) comprise 2'-O-methyl uridine and 5-methyl-cytidine (m’C). In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) comprise N6-methyl-adenosine (mbA). In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) comprise N6-methyl-adenosine (m6A) and 5 - ethyl -cytidine (mC).
[00915] In some embodiments, polynucleotides (e.g., RNA polynucleotides, such as mRNA polynucleotides) are uniformly modified (e.g., fully modified, modified throughout the entire sequence) for a particular modification. For example, a polynucleotide can be uniformly modified with 5-mcthyl-cytidinc (m5C), meaning that all cytosine residues in the mRNA sequence are replaced with 5-methyI-cytidine (m5C).
Similarly, a polynucleotide can be uniformly modified for any type of nucleoside residue present in tire sequence by replacement with a modified residue such as those set forth above.
[00916] Exemplary nucleobases and nucleosides having a modified cytosine include N4-acetyl-cytidine (ac4C). 5 -methyl -cytidine (m5C). 5-halo-cytidinc (e.g.. 5-iodo-cytidine), 5 -hydroxymethyl -cytidine (hm5C). 1 -methyl -pseudoisocytidine, 2-thio-cytidine (s2C), and 2 -thio-5 -methyl -cytidine.
[00917] In some embodiments, a modified nucleobase is a modified uridine. Exemplary nucleobases and In some embodiments, a modified nucleobase is a modified cytosine, nucleosides having a modified uridine include 5-cyano uridine, and 4'-thio uridine.
[00918] The polynucleotides of the present disclosure may be partially or fully modified along the entire length of the molecule. For example, one or more or all or a given type of nucleotide (e.g., purine or pyrimidine, or any one or more or all of A, G, U, C) may be unifonnly modified in a polynucleotide of the invention, or in a given predetermined sequence region thereof (e.g., in the mRNA including or excluding tire polyA tail). In some embodiments, all nucleotides X in a polynucleotide of the present disclosure (or in a given sequence region thereof) are modified nucleotides, wherein X may any one of nucleotides A, G, U, C, or any one of the combinations A+G, A+U, A+C, G+U, G+C, U+C, A+G+U, A+G+C, G+U+CorA+G+C.
[00919] The polynucleotide may contain from about 1% to about 100% modified nucleotides (either in relation to overall nucleotide content, or in relation to one or more types of nucleotide, i.e., any one or more of A, G, U or C) or any intervening percentage (e.g., from 1% to 20%, from 1% to 25%, from 1% to 50%, from l% to 60%, from l% to 70%, from l% to 80%, from l% to 90%, from l% to 95%, from 10% to 20%, from 10% to 25%, from 10% to 50%. from 10% to 60%, from 10% to 70%, from 10% to 80%, from 10% to 90%, from 10% to 95%, from 10% to 100%, from 20% to 25%, from 20% to 50%, from 20% to 60%, from 20% to 70%, from 20% to 80%, from 20% to 90%, from 20% to 95%, from 20% to 100%, from 50% to 60%, from 50% to 70%, from 50% to 80%, from 50% to 90%, from 50% to 95%, from 50% to 100%, from 70% to 80%, from 70% to 90%, from 70% to 95%, from 70% to 100%, from 80% to 90%, from 80% to 95%, from 80% to 100%, from 90% to 95%, from 90% to 100%, and from 95% to 100%). It will be understood that any remaining percentage is accounted for by the presence of unmodified A, G. U, or C. [00920] The polynucleotides may contain at a minimum 1% and at maximum 100% modified nucleotides, or any intervening percentage, such as at least 5% modified nucleotides, at least 10% modified nucleotides, at least 25% modified nucleotides, at least 50% modified nucleotides, at least 80% modified nucleotides, or at least 90% modified nucleotides. For example, the polynucleotides may contain a modified pyrimidine such as a modified uracil or cytosine. In some embodiments, at least 5%, at least 10%, at least 25%, at least 50%. at least 80%, at least 90% or 100% of the uracil in the polynucleotide is replaced with a modified uracil (e.g., a 5 -substituted uracil). The modified uracil can be replaced by a compound having a single unique structure, or can be replaced by a plurality of compounds having different structures (e.g., 2, 3, 4 or more unique structures). In some embodiments, at least 5%, at least 10%, at least 25%, at least 50%, at least 80%, at least 90% or 100% of the cytosine in the polynucleotide is replaced with a modified cytosine (e.g., a 5-substituted cytosine). The modified cytosine can be replaced by a compound having a single unique structure, or can be replaced by a plurality of compounds having different structures (e.g., 2, 3, 4 or more unique structures).
D. Circular mRNA payloads
[00921] In various embodiments, the LNP -based pharmaceutical compositions described herein, e.g.. LNP- based gene editing systems, may include one or more circular mRNA molecules or ‘‘oRNAs.’’ In various embodiments, the circular mRNA payloads may encode one or more components of the herein described gene editing systems or other therapeutic protein of interest. For example, a circular mRNA payload may encode an amino acid sequence -programmable DNA binding domain (e.g., TALENS and zinc finger-binding domains) or a nucleic acid sequence-programmable DNA binding domain (e.g., CRISPR Cas9. CRISPR Casl2a. CRISPR Casl2f. CRISPR Casl3a. CRISPR Casl3b. or TnpB).
[00922] Tire circular mRNA payloads may also encode, depending upon the nature of the gene editing system, one or more effector domains that provide various functionalities that facilitate changes in nucleotide sequence and/or gene expression, such as, but not limited to, single-strand DNA binding proteins, nucleases, endonucleases, exonucleases, deaminases (e.g., cytidine deaminases or adenosine deaminases), polymerases (e.g., reverse transcriptases), integrases, recombinases, etc., and fusion proteins comprising one or more functional domains linked together.
[00923] Circular RNA described herein are polyribonucleotides that form a continuous structure through covalent or non-covalent bonds. Due to the circular structure, oRNAs have improved stability, increased halflife. reduced immunogenicity, and/or improved functionality (e.g., of a function described herein) compared to a corresponding linear RNA.
[00924] In some embodiments, an oRNA binds a target. In some embodiments, an oRNA binds a substrate. In some embodiments, an oRNA binds a target and binds a substrate of the target. In some embodiments, an oRNA binds a target and mediates modulation of a substrate of the target. In some embodiments, an oRNA brings together a target and its substrate to mediate modification of the substrate, e.g., post-translational modification. In some embodiments, an oRNA brings together a target and its substrate to mediate a cellular process (e.g., alters protein degradation or signal transduction) involving the substrate. In some embodiments, a target is a target protein and a substrate is a substrate protein.
[00925] In some embodiments, an oRNA comprises a conjugation moiety for binding to chemical compound. Hie conjugation moiety can be a modified polyribonucleotide. The chemical compound can be conjugated to the oRNA by the conjugation moiety. In some embodiments, the chemical compound binds to a target and mediates modulation of a substrate of the target. In some embodiments, an oRNA binds a substrate of a target and a chemical compound conjugated to the oRNA by the conjugation moiety binds the target to bring together the target and its substrate to mediate modification of the substrate, e.g., post-translational modification. In some embodiments, an oRNA binds a substrate of a target and a chemical compound conjugated to the oRNA by the conjugation moiety binds the target to bring together the target and its substrate to mediate modification of the substrate to mediate a cellular process (e.g., alters protein degradation or signal transduction) involving the substrate. In some embodiments, a target is a target protein and a substrate is a substrate protein.
[00926] In some embodiments, the oRNA may be non-immunogenic in a mammal (e.g., a human, non-human primate, rabbit, rat, and mouse).
[00927] In some embodiments, the oRNA may be capable of replicating or replicates in a cell from an aquaculture animal (e.g., fish, crabs, shrimp, oysters etc.), a mammalian cell, a cell from a pet or zoo animal (e.g., cats, dogs, lizards, birds, lions, tigers and bears etc.), a cell from a farm or working animal (e.g., horses, cows, pigs, chickens etc.), a human cell, cultured cells, primary cells or cell lines, stem cells, progenitor cells, differentiated cells, germ cells, cancer cells (e.g., tumorigenic, metastatic), non-tumorigenic cells (e.g., normal cells), fetal cells, embryonic cells, adult cells, mitotic cells, non-mitotic cells, or any combination thereof.
[00928] In one aspect, provided herein is a pharmaceutical composition comprising: a circular RNA comprising, in the following order, a 3 ’ group I intron fragment, an Internal Ribosome Entry Site (IRES), an expression sequence encoding a polypeptide (e.g., a nucleobase editing system or component thereof), and a 5 ' group I intron fragment, and a transfer vehicle comprising at least one of (i) an ionizable lipid, (ii) a structural lipid, and (iii) a PEG-modified lipid, wherein the transfer vehicle is capable of delivering the circular RNA polynucleotide to a cell (e.g.. a human cell, such as an immune cell present in a human subject), such that the polypeptide is translated in the cell. [00929] In some embodiments, the pharmaceutical composition is formulated for intravenous administration to the human subject in need thereof. In some embodiments, the 3’ group I intron fragment and 5’ group I intron fragment are Anabaena group I intron fragments.
[00930] In certain embodiments, the 3 ’ intron fragment and 5 ’ intron fragment are defined by the L9a-5 permutation site in the intact intron. In certain embodiments, the 3’ intron fragment and 5’ intron fragment are defined by the L8-2 permutation site in the intact intron.
[00931] In some embodiments, the IRES is from Taura syndrome virus, Tiiatoma virus, Theiler's encephalomyelitis virus, Simian Vims 40, Solenopsis invicta vims 1, Rhopalosiphum padi vims, Reticuloendotheliosis vims, Human poliovims 1, Plautia stall intestine vims, Kashmir bee vims, Human rhinovims 2, Homalodisca coagulata vims- 1. Human Immunodeficiency Vims type 1. Homalodisca coagulata vims- 1, Himetobi P vims, Hepatitis C vims, Hepatitis A vims, Hepatitis GB vims , Foot and mouth disease vims, Human enterovims 71, Equine rhinitis vims, Ectropis obliqua picoma-like vims, Encephalomyocarditis vims, Drosophila C Vims, Human coxsackievirus B3, Cmcifer tobamovims, Cricket paralysis vims, Bovine viral diarrhea vims 1, Black Queen Cell Vims, Aphid lethal paralysis vims, Avian encephalomyelitis vims, Acute bee paralysis vims, Hibiscus chlorotic ringspot vims, Classical swine fever vims. Human FGF2, Human SFTPA1, Human AML1/RUNX1, Drosophila antennapedia, Human AQP4. Human AT1R, Human BAG-1, Human BCL2, Human BiP, Human c-TAPl, Human c-myc, Human eIF4G, Mouse NDST4L, Human LEF1, Mouse HIF1 alpha, Human n.myc, Mouse Gtx, Human p27kipl, Human PDGF2/c-sis, Human p53, Human Pim-1, Mouse Rbm3, Drosophila reaper, Canine Scamper, Drosophila Ubx, Human UNR, Mouse UtrA, Human VEGF-A. Human XIAP, Drosophila hairless, S. cerevisiae TFIID, S. cerevisiae YAP1, tobacco etch vims, turnip crinkle vims, EMCV-A, EMCV-B, EMCV-Bf, EMCV-Cf, EMCV pEC9, Picobimavims, HCV QC64, Human Cosavims E/D, Human Cosavims F, Human Cosavims JMY, Rhinovims NAT001, HRV14, HRV89, HRVC-02, HRV-A21, Salivirus A SHI, Salivims FHB, Salivims NG-J1, Human Parechovims 1, Crohivims B, Yc-3, Rosavirus M-7, Shanbavims A, Pasivims A, Pasivims A 2, Echovims E14, Human Parechovims 5, Aichi Vims, Hepatitis A Vims HA 16, Phopivims, CVA10, Enterovirus C, Enterovims D, Enterovirus J, Human Pegivims 2, GBV-C GT110, GBV-C K1737. GBV-C Iowa, Pegivims A 1220, Pasivims A 3. Sapelovims, Rosavims B, Bakunsa Vims, Tremovims A, Swine Pasivims 1, PLV-CHN, Pasivims A, Sicinivims, Hepacivirus K, Hepacivims A, BVDV1, Border Disease Vims, BVDV2, CSFV- PK15C, SF573 Dicistravims, Hubei Picoma-like Vims, CRPV, Salivims A BN5, Salivims A BN2, Salivims A 02394, Salivims A GUT, Salivims A CH, Salivims A SZ1, Salivims FHB, CVB3, CVB1, Echovims 7, CVB5, EVA71, CVA3, CVA12, EV24 or an aptamer to eIF4G. [00932] In some embodiments, the IRES comprises a CVB3 IRES or a fragment or variant thereof. In some embodiments, the pharmaceutical composition comprises a first internal spacer between the 3 ’ group I intron fragment and the IRES, and a second internal spacer between the expression sequence and the 5 ’ group I intron fragment. In certain embodiments, the first and second internal spacers each have a length of about 10 to about 60 nucleotides.
[00933] In some embodiments, the circular mRNA comprises a nucleotide sequence encoding a polypeptide of interest, such as a nucleobase editing system or therapeutic protein (e.g., a CAR or TCR complex protein).
[00934] In some embodiments, the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein further comprise a targeting moiety. In certain embodiments, the targeting moiety mediates receptor-mediated endocytosis or direct fusion of the delivery vehicle (LNPs) into selected cells of a selected cell population or tissue in the absence of cell isolation or purification. In certain embodiments, the targeting moiety is capable of binding to a protein selected from the group CD3, CD4, CD8, CDS, CD7, PD-1, 4- IBB, CD28, Clq, and CD2. In certain embodiments, tire targeting moiety comprises an antibody specific for a macrophage, dendritic cell, NK cell, NKT. or T cell antigen. In certain embodiments, the targeting moiety comprises a scFv, nanobody, peptide, minibody, polynucleotide aptamer, heavy chain variable region, light chain variable region or fragment thereof.
[00935] In some embodiments, the LNP-based nucleobase editing systems. RNA therapeutics and pharmaceutical compositions described herein are administered in an amount effective to treat a disease in the human subject (e.g., wherein the disease can be cancer, muscle disorder, or CNS disorder, etc.). In some embodiments, the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions have an enhanced safety profile when compared to a pharmaceutical composition comprising T cells or vectors comprising exogenous DNA encoding the same polypeptide.
[00936] In some embodiments, the LNP-based nucleobase editing systems and pharmaceutical compositions thereof are administered in an amount effective to induce a desire precise edit in a genome. In some embodiments, tire LNP-based nucleobase editing systems and pharmaceutical compositions have an enhanced safety profile when compared to state of the art gene editing delivery compositions.
[00937] In another aspect, the present disclosure provides a circular RNA comprising, in the following order, a 3 ’ group I intron fragment, an Internal Ribosome Entry Site (IRES), an expression sequence encoding a polypeptide (e.g., a nucleobase editing system or component thereof), and a 5’ group I intron fragment.
[00938] In some embodiments, the 3 ’ group I intron fragment and 5 ’ group I intron fragment are Anabaena group I intron fragments. In certain embodiments, the 3’ intron fragment and 5’ intron fragment are defined by the L9a-5 permutation site in the intact intron. In certain embodiments, the 3’ intron fragment and 5’ intron fragment are defined by the L8-2 permutation site in the intact intron. In certain embodiments, the IRES comprises a CVB3 IRES or a fragment or variant thereof.
[00939] In some embodiments, the circular RNA comprises a first internal spacer between the 3’ group I intron fragment and tire IRES, and a second internal spacer between the expression sequence and the 5 ' group I intron fragment.
[00940] In certain embodiments, the first and second internal spacers each have a length of about 10 to about 60 nucleotides.
[00941] In some embodiments, the circular RNA payload of the LNP -based nucleobase editing systems, RNA therapeutics and phannaceutical compositions described herein consists of natural nucleotides. In some embodiments, tire circular RNA further comprises a second expression sequence encoding a therapeutic protein. In some embodiments, the therapeutic protein comprises a checkpoint inhibitor. In certain embodiments, the therapeutic protein comprises a cytokine.
[00942] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein consists of natural nucleotides.
[00943] In some embodiments, the circular RNA payload LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein comprises a nucleotide sequence that is codon optimized, either partially or fully. In some embodiments, the circular RNA is optimized to lack at least one microRNA binding site present in an equivalent pre-optimized polynucleotide. In some embodiments, the circular RNA is optimized to lack at least one endonuclease susceptible site present in an equivalent preoptimized polynucleotide. In some embodiments, the circular RNA is optimized to lack at least one RNA- editing susceptible site present in an equivalent pre-optimized polynucleotide.
[00944] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein has an in vivo functional half- life in humans greater than that of an equivalent linear RNA having the same expression sequence. In some embodiments, the circular RNA has a length of about 100 nucleotides to about 10 kilobases. In some embodiments, the circular RNA has a functional half-life of at least about 20 hours. In some embodiments, the circular RNA has a duration of therapeutic effect in a human cell of at least about 20 hours. In some embodiments, the circular RNA has a duration of therapeutic effect in a human cell greater than or equal to that of an equivalent linear RNA comprising the same expression sequence. In some embodiments, the circular RNA has a functional half-life in a human cell greater than or equal to that of an equivalent linear RNA comprising the same expression sequence.
[00945] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein has a half-life of at least that of a linear counterpart. In some embodiments, the oRNA has a half-life that is increased over that of a linear counterpart. In some embodiments, the half-life is increased by about 5%, 10%, 15%, 20%. 25%, 30%, 35%, 40%, 45%, 50%, or greater. In some embodiments, the oRNA has a half-life or persistence in a cell for at least about 1 hour to about 30 days, or at least about 2 hours, 6 hours. 12 hours. 18 hours. 24 hours (1 day). 2 days, 3, days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 22 days, 23 days, 24 days, 25 days, 26 days, 27 days, 28 days, 29 days, 30 days, 60 days, or longer or any time therebetween. In some embodiments, the oRNA has a half-life or persistence in a cell for no more than about 10 mins to about 7 days, or no more than about 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 24 hours (1 day), 36 hours (1.5 days), 48 hours (2 days), 60 hours (2.5 days), 72 hours (3 days), 4 days, 5 days, 6 days, or 7 days.
[00946] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein has a half-life or persistence in a cell while the cell is dividing. In some embodiments, the oRNA has a half-life or persistence in a cell post division.
[00947] In certain embodiments, the circular RNA payload of tire LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein has a half-life or persistence in a dividing cell for greater than about 10 minutes to about 30 days, or at least about 10 minutes, 15 minutes. 30 minutes, 45 minutes, 1 hour, 2 hours, 3 hours, 4 hours, 5 hours. 6 hours, 7 hours, 8 hours. 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 24 hours (1 day), 2 days, 3, days, 4 days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 22 days, 23 days, 24 days, 25 days, 26 days, 27 days, 28 days, 29 days, 30 days, 60 days, or longer or any time therebetween.
[00948] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein modulates a cellular function, e.g., transiently or long term. In certain embodiments, the cellular function is stably altered, such as a modulation that persists for at least about 1 hour to about 30 days, or at least about 2 hours, 6 hours. 12 hours. 18 hours. 24 hours (1 day), 2 days, 3, days, 4days, 5 days, 6 days, 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, 14 days, 15 days, 16 days, 17 days, 18 days, 19 days, 20 days, 21 days, 22 days, 23 days, 24 days, 25 days, 26 days, 27 days, 28 days, 29 days, 30 days, 60 days, or longer. In certain embodiments, the cellular function is transiently altered, e.g., such as a modulation that persists for no more than about 30 mins to about 7 days, or no more than about 30 minutes, 45 minutes, 1 hour, 2 hours, 3 hours, 4 hours, 5 hours, 6 hours, 7 hours, 8 hours, 9 hours, 10 hours, 11 hours, 12 hours, 13 hours, 14 hours, 15 hours, 16 hours, 17 hours, 18 hours, 19 hours, 20 hours, 21 hours, 22 hours, 23 hours, 24 hours (1 day). 36 hours (1.5 days), 48 hours (2 days), 60 hours (2.5 days), 72 hours(3 days), 4 days, 5 days, 6 days, or 7 days.
[00949] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein is at least about 20 nucleotides, at least about 30 nucleotides, at least about 40 nucleotides, at least about 50 nucleotides, at least about 75 nucleotides, at least about 100 nucleotides, at least about 200 nucleotides, at least about 300 nucleotides, at least about 400 nucleotides, at least about 500 nucleotides, at least about 1,000 nucleotides, at least about 2,000 nucleotides, at least about 5.000 nucleotides, at least about 6,000 nucleotides, at least about 7,000 nucleotides, at least about 8.000 nucleotides, at least about 9,000 nucleotides, at least about 10,000 nucleotides, at least about 12,000 nucleotides, at least about 14,000 nucleotides, at least about 15,000 nucleotides, at least about 16,000 nucleotides, at least about 17,000 nucleotides, at least about 18,000 nucleotides, at least about 19,000 nucleotides, or at least about 20,000 nucleotides. In some embodiments, the oRNA may be of a sufficient size to accommodate a binding site for a ribosome.
[00950] In some embodiments, the maximum size of the circular RNA payload of the LNP-bascd nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein may be limited by the ability of packaging and delivering the RNA to a target. In some embodiments, the size of the oRNA is a length sufficient to encode polypeptides, and thus, lengths of at least 20,000 nucleotides, at least 15,000 nucleotides, at least 10,000 nucleotides, at least 7,500 nucleotides, or at least 5,000 nucleotides, at least 4,000 nucleotides, at least 3,000 nucleotides, at least 2,000 nucleotides, at least 1,000 nucleotides, at least 500 nucleotides, at least 400 nucleotides, at least 300 nucleotides, at least 200 nucleotides, at least 100 nucleotides may be useful.
[00951] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and phannaceutical compositions described herein comprises one or more elements described elsewhere herein. In some embodiments, the elements may be separated from one another by a spacer sequence or linker. In some embodiments, the elements may be separated from one another by 1 nucleotide, 2 nucleotides, about 5 nucleotides, about 10 nucleotides, about 15 nucleotides, about 20 nucleotides, about 30 nucleotides, about 40 nucleotides, about 50 nucleotides, about 60 nucleotides, about 80 nucleotides, about 100 nucleotides, about 150 nucleotides, about 200 nucleotides, about 250 nucleotides, about 300 nucleotides, about 400 nucleotides, about 500 nucleotides, about 600 nucleotides, about 700 nucleotides, about 800 nucleotides, about 900 nucleotides, about 1000 nucleotides, up to about 1 kb, at least about 1000 nucleotides.
[00952] In some embodiments, one or more elements are contiguous with one another, e.g., lacking a spacer element.
[00953] In some embodiments, one or more elements is conformationally flexible. In some embodiments, the conformational flexibility is due to the sequence being substantially free of a secondary structure.
[00954] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein comprises a secondary' or tertiary structure that accommodates a binding site for a ribosome, translation, or rolling circle translation.
[00955] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and phannaceutical compositions described herein comprises particular sequence characteristics. For example, the oRNA may comprise a particular nucleotide composition. In some such embodiments, the oRNA may include one or more purine rich regions (adenine or guanosine). In some such embodiments, the oRNA may include one or more purine rich regions (adenine or guanosine). In some embodiments, the oRNA may' include one or more AU rich regions or elements (AREs). In some embodiments, the oRNA may include one or more adenine rich regions.
[00956] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein comprises one or more modifications described elsewhere herein.
[00957] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and phannaceutical compositions described herein comprises one or more expression sequences and is configured for persistent expression in a cell of a subject in vivo. In some embodiments, the oRNA is configured such that expression of the one or more expression sequences in the cell at a later time point is equal to or higher than an earlier time point. In such embodiments, the expression of the one or more expression sequences can be either maintained at a relatively stable level or can increase over time. The expression of the expression sequences can be relatively stable for an extended period of time. For instance, in some cases, the expression of tire one or more expression sequences in the cell over a time period of at least 7, 8. 9, 10. 12. 14. 16, 18, 20, 22, 23 or more days does not decrease by 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, or 5%. In some cases, in some cases, the expression of the one or more expression sequences in the cell is maintained at a level that does not vary by more than 50%. 45%, 40%, 35%, 30%, 25%, 20%, 15%, 10%, or 5% for at least 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 23 or more days.
Regulatory Elements
[00958] In some embodiments, the circular RNA payload of the LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions described herein comprises one or more regulatory' elements. As used herein, a "regulatory element" is a sequence that modifies expression of an expression sequence, e.g., a nucleotide sequence encoding a nucleobase editing system or a therapeutic protein, i.e., a coding region of interest (CROI). The regulatory element may include a sequence that is located adjacent to a coding region of interest encoded on the circular RNA payload. The regulatory' element may be operatively linked to a nucleotide sequence of the circular RNA that encodes a coding region of interest (e.g., a nucleobase editing system or therapeutic polypeptide).
[00959] In some embodiments, a regulatory element may increase an amount of expression of a coding region of interest encoded on the circular RNA payload as compared to an amount expressed when no regulatory' element exists.
[00960] In some embodiments, a regulatory element may comprise a sequence to selectively initiates or activates translation of a coding sequence of interest encoded on tire circular RNA payload.
[00961] In some embodiments, a regulatory clement may comprise a sequence to initiate degradation of the oRNA or the payload or cargo. Non-limiting examples of the sequence to initiate degradation includes, but is not limited to, riboswitch aptazyme and miRNA binding sites.
[00962] In some embodiments, a regulatory element can modulate translation of a coding region of interest encoded on the oRNA. The modulation can create an increase (enhancer) or decrease (suppressor) in the expression of the coding region of interest. The regulatory element may be located adjacent to the CROI (e.g., on one side or both sides of the CROI).
Translation Initiation Sequence
[00963] In some embodiments, a translation initiation sequence functions as a regulatory element. In some embodiments, the translation initiation sequence comprises an AUG/ATG codon. In some embodiments, a translation initiation sequence comprises any eukaryotic start codon such as, but not limited to, AUG/ATG. CUG/CTG, GUG/GTG, UUG/TTG, ACG, AUC/ATC, AUU. AAG, AUA/ATA, or AGG. In some embodiments, a translation initiation sequence comprises a Kozak sequence. In some embodiments, translation begins at an alternative translation initiation sequence, e.g., translation initiation sequence other than AUG/ATG codon, under selective conditions, e.g., stress induced conditions. As a non-limiting example, the translation of the circular polyribonucleotide may begin at alternative translation initiation sequence, such as ACG. As another non-limiting example, the circular polyribonucleotide translation may begin at alternative translation initiation sequence, CUG/CTG. As another non-limiting example, the translation may begin at alternative translation initiation sequence, GUG/GTG. As yet another non-limiting example, the translation may begin at a repeat-associated non-AUG (RAN) sequence such as an alternative translation initiation sequence that includes short stretches of repetitive RNA e.g. CGG, GGGGCC, CAG, or CTG.
[00964] In some embodiments, the oRNA encodes a polypeptide or peptide and may comprise a translation initiation sequence. The translation initiation sequence may comprise, but is not limited to a start codon, a non-coding start codon, a Kozak sequence or a Shine-Dalgamo sequence. The translation initiation sequence may be located adjacent to the payload or cargo (e.g., on one side or both sides of the coding region of interest).
[00965] In some embodiments, the translation initiation sequence provides conformational flexibility to tire oRNA. In some embodiments, the translation initiation sequence is within a substantially single stranded region of the oRNA.
[00966] Tire oRNA may include more than 1 start codon such as, but not limited to. at least 2, at least 3, at least 4, at least 5, at least 6, at least 7. at least 8. at least 9, at least 10, at least 11, at least 12, at least 13. at least 14, at least 15 or more than 15 start codons. Translation may initiate on the first start codon or may initiate downstream of the first start codon.
[00967] In some embodiments, the oRNA may initiate at a codon which is not the first start codon, e.g., AUG. Translation of the circular polyribonucleotide may initiate at an alternative translation initiation sequence, such as, but not limited to, ACG, AGG, AAG, CUG/CTG, GUG/GTG, AUA/ATA, AUU/ATT, UUG/TTG. In some embodiments, translation begins at an alternative translation initiation sequence under selective conditions, e.g., stress induced conditions. As a non-limiting example, the translation of the oRNA may begin at alternative translation initiation sequence, such as ACG. As another non-limiting example, the oRNA translation may begin at alternative translation initiation sequence, CUG/CTG. As yet another nonlimiting example, the oRNA translation may begin at alternative translation initiation sequence, GTG/GUG. As yet another non-limiting example, the oRNA may begin translation at a repeat-associated non-AUG (RAN) sequence, such as an alternative translation initiation sequence that includes short stretches of repetitive RNA e g. CGG, GGGGCC, CAG, CTG. IRES Sequences
[00968] In some embodiments, the oRNA described herein comprises an internal ribosome entry site (IRES) element capable of engaging an eukaryotic ribosome. In some embodiments, the IRES element is at least about 5 nucleotides, at least about 8 nucleotides, at least about 9 nucleotides, at least about 10 nucleotides, at least about 15 nucleotides, at least about 20 nucleotides, at least about 25 nucleotides, at least about 30 nucleotides, at least about 40 nucleotides, at least about 50 nucleotides, at least about 100 nucleotides, at least about 200 nucleotides, at least about 250 nucleotides, at least about 350 nucleotides, or at least about 500 nucleotides. In one embodiment, the IRES element is derived from the DNA of an organism including, but not limited to, a virus, a mammal, and a Drosophila. Such viral DNA may be derived from, but is not limited to, picomavirus complementary DNA (cDNA), with encephalomyocarditis virus (EMCV) cDNA and poliovirus cDNA. In one embodiment, Drosophila DNA from which an IRES element is derived includes, but is not limited to, an Antennapedia gene from Drosophila melanogaster.
[00969] In some embodiments, the IRES element is at least partially derived from a virus, for instance, it can be derived from a viral IRES element, such as ABPV IGRpred, AEV, ALPV IGRpred, BQCV IGRpred, BVDV1 1-385, BVDV1 29-39I, CrPV 5NCR, CrPV IGR, crTMV IREScp, crTMV_IRESmp75, crTMV_IRESmp228, crTMV IREScp, crTMV IREScp, CSFV, CVB3, DCV IGR, EMCV-R, EoPV_5NTR, ERAV 245-961, ERBV 162-920, EV71 1-748, FeLV-Notch2, FMDV type C, GBV-A, GBV-B, GBV-C, gypsy env, gypsyD5. gypsyD2, HAV HM175, HCV type la. HiPV IGRpred, HIV-1, HoCVl IGRpred, HRV-2, lAPV IGRpred, idefix, KBV IGRpred, LINE-l_ORFl_-101_to_-l, LINE- l_ORFl-302_to_-202, LlNE-l_ORF2-138_to_-86. LINE-l_ORFl_-44to_-l, PSIVJGR, PV typel Mahoney, PV_type3_Leon, REV-A, RhPV 5NCR, RhPV IGR, SINVl IGRpred, SV40 661 -830, TMEV, TMV_UI_IRESmp228, TRV 5NTR, TrV IGR, or TSV IGR. In some embodiments, the IRES element is at least partially derived from a cellular IRES, such as AML1/RUNX1, Antp-D, Antp-DE, Antp- CDE, Apaf-1. Apaf-1, AQP4. ATIR varl, ATlR_var2, ATlR_var3, ATlR_var4, BAGl_p36delta236 nt, BAGl_p36, BCL2, BiP_-222_-3. C-IAP1 285-1399, C-IAP1 1313-1462. c-jun, c-myc. Cat-1224, CCND1, DAPS, eIF4G, eIF4GI-ext, eIF4GII, eIF4GII-long. ELG1, ELH, FGF1A.FMR1, Gtx-133-141, Gtx-1-166, Gtx-1-120, Gtx-1-196, hairless, HAP4, HIFla, hSNMl, HsplOl, hsp70, hsp70, Hsp90, IGF2_leader2, Kvl.4_1.2, L-myc, LamBl_-335_-l, LEF1, MNT_75-267, MNT 36-160, MTG8a, MYB, MYT2_997-1152, n-MYC, NDST1, NDST2, NDST3, NDST4L, NDST4S, NRF_-653_-17, NtHSFl, ODC1, p27kipl, 03 128- 269, PDGF2/c-sis, Pim-1. PITSLRE_p58, Rbm3, reaper, Scamper, TFIID, TIF4631, Ubx_l-966, Ubx_373- 961, UNR, Ure2, UtrA. VEGF-A-133-1, XIAP 5-464, XIAP 305-466. or YAP1. [00970] In another embodiment, the IRES is an IRES sequence from Coxsackievirus B3 (CVB3), the protein coding region encodes Guassia luciferase (Glue) and the spacer sequences are polyA-C.
[00971] In some embodiments, the IRES, if present, is at least about 50 nucleotides in length. In one embodiment, the vector comprises an IRES that comprises a natural sequence. In one embodiment, the vector comprises an IRES that comprises a synthetic sequence.
[00972] An IRES may act as the sole ribosome binding site, or may serve as one of multiple ribosome binding sites of an mRNA. A polynucleotide containing more than one functional ribosome binding site may encode several peptides or polypeptides that are translated independently by the ribosomes (e.g., multicistronic mRNA). When polynucleotides are provided with an IRES, further optionally provided is a second translatable region. Examples of IRES sequences that can be used according to the present disclosure include without limitation, those from picomaviruses (e.g., FMDV), pest viruses (CFFV), polio viruses (PV), encephalomyocarditis viruses (ECMV), foot-and mouth disease viruses (FMDV), hepatitis C viruses (HCV), classical Swine fever viruses (CSFV), murine leukemia virus (MLV), simian immune deficiency viruses (SIV) or cricket paralysis viruses (CrPV).
Termination Element
[00973] In some embodiments, the oRNA includes one or more coding regions of interest (i.e., also referred to as product expression sequences) which encode polypeptides of interest, including but not limited to nucleobase editing system and therapeutic proteins. In various embodiments, the product expression sequences may or may not have a termination element.
[00974] In some embodiments, the oRNA includes one or more product expression sequences that lack a termination element, such that the oRNA is continuously translated.
[00975] Exclusion of a termination element may result in rolling circle translation or continuous expression of the encoded peptides or polypeptides as tire ribosome will not stall or fall-off. In such an embodiment, rolling circle translation expresses continuously through the product expression sequence.
[00976] In some embodiments, one or more product expression sequences in the oRNA comprise a termination element.
[00977] In some embodiments, not all of the product expression sequences in the oRNA comprise a termination element. In such instances, the product expression sequence may fall off the ribosome when the ribosome encounters the termination element and terminates translation. Rolling Circle Translation
[00978] In some embodiments, once translation of the oRNA is initiated, the ribosome bound to the oRNA does not disengage from the oRNA before finishing at least one round of translation of the oRNA. In some embodiments, the oRNA as described herein is competent for rolling circle translation. In some embodiments, during rolling circle translation, once translation of tire oRNA is initiated, the ribosome bound to the oRNA does not disengage from the oRNA before finishing at least 2 rounds, at least 3 rounds, at least 4 rounds, at least 5 rounds, at least 6 rounds, at least 7 rounds, at least 8 rounds,at least 9 rounds, at least 10 rounds, at least 11 rounds, at least 12 rounds, at least 13 rounds, at least 14 rounds, at least 15 rounds, at least 20 rounds, at least 30 rounds, at least 40 rounds, at least 50 rounds, at least 60 rounds, at least 70 rounds, at least 80 rounds, at least 90 rounds, at least 100 rounds, at least 150 rounds, at least 200 rounds, at least 250 rounds, at least 500 rounds, at least 1000 rounds, at least 1500 rounds, at least 2000 rounds, at least 5000 rounds, at least 10000 rounds, at least 105 rounds, or at least 10b rounds of translation of the oRNA.
[00979] In some embodiments, the rolling circle translation of tire oRNA leads to generation of polypeptide that is translated from more than one round of translation of tire oRNA. In some embodiments, the oRNA comprises a stagger element, and rolling circle translation of the oRNA leads to generation of polypeptide product that is generated from a single round of translation or less than a single round of translation of the oRNA.
Circularization
[00980] In one embodiment, a linear RNA may be cyclized, or concatcmcrizcd. In some embodiments, the linear RNA may be cyclized in vitro prior to formulation and/or delivery. In some embodiments, the linear RNA may be cyclized within a cell.
[00981] In some embodiments, the mechanism of cyclization or concatemerization may occur through at least 3 different routes: 1) chemical, 2) enzymatic, and 3) ribozyme catalyzed. Hie newly formed 5'-/3 '-linkage may be intramolecular or intermolecular.
[00982] In the first route, the 5'-end and the 3 '-end of the nucleic acid contain chemically reactive groups that, when close together, form a new covalent linkage between the 5 '-end and the 3 '-end of the molecule. The 5 '-end may contain an NHS-ester reactive group and the 3 '-end may contain a 3'-amino-terminated nucleotide such that in an organic solvent the 3'-amino-terminated nucleotide on the 3 '-end of a synthetic mRNA molecule will undergo a nucleophilic attack on the 5 '-NHS-ester moiety forming a new 5 '-/3 '-amide bond.
[00983] In the second route. T4 RNA ligase may be used to enzymatically link a 5'-phosphorylated nucleic acid molecule to the 3'-hydroxyl group of a nucleic acid fanning a new phosphorodiester linkage. In an example reaction, Ag of a nucleic acid molecule is incubated at 37°C for 1 hour with 1-10 units of T4 RNA ligase (New England Biolabs, Ipswich, MA) according to the manufacturer's protocol. The ligation reaction may occur in the presence of a split oligonucleotide capable of base-pairing with both the 5'-and 3'-region in juxtaposition to assist tire enzymatic ligation reaction.
[00984] In the third route, either the 5 '-or 3 '-end of the cDNA template encodes a ligase ribozyme sequence such that during in vitro transcription, the resultant nucleic acid molecule can contain an active ribozyme sequence capable of ligating the 5 '-end of a nucleic acid molecule to the 3 '-end of a nucleic acid molecule. Tire ligase ribozyme may be derived from tire Group I Intron. Group I Intron. Hepatitis Delta Virus, Hairpin ribozyme or may be selected by SELEX (systematic evolution of ligands by exponential enrichment). The ribozyme ligase reaction may take 1 to 24 hours at temperatures between 0 and 37°C.
[00985] In some embodiments, the oRNA is made via circularization of a linear RNA.
[00986] In some embodiments, the following elements are operably connected to each other and, in some embodiments, arranged in the following sequence: a.) a 5' homology arm, b.) a 3' group I intron fragment containing a 3' splice site dinucleotide, c.) a protein coding or noncoding region, d.) a 5' group I intron fragment containing a 5' splice site dinucleotide, and e.) a 3' homology arm. In certain embodiments said vector allows production of a circular RNA that is translatable and/or biologically active inside eukaryotic cells. In some embodiments, the biologically active RNA is, for example, an miRNA sponge, or long noncoding RNA.
[00987] In some embodiments, the following elements are operably connected to each other and arranged in the following sequence: a.) a 5' homology arm, b.) a 3' group I intron fragment containing a 3' splice site dinucleotide, c.) optionally, a 5' spacer sequence, d.) optionally, an internal ribosome entry site (IRES), e.) a protein coding or noncoding region, f.) optionally, a 3' spacer sequence, g.) a 5' group I intron fragment containing a 5' splice site dinucleotide, and h.) a 3' homology ami. In certain embodiments, said vector allows production of a circular RNA that is translatable and/or biologically active inside eukaryotic cells.
[00988] In some embodiments, the following elements are operably connected to each other and arranged in the following sequence: a.) a 5' homology ami, b.) a 3' group I intron fragment containing a 3' splice site dinucleotide, c.) a 5' spacer sequence, d.) an internal ribosome entry site (IRES), e.) a protein coding or noncoding region, f.) a 5' group I intron fragment containing a 5' splice site dinucleotide, and g.) a 3' homology arm. In some embodiments, said vector allows production of a circular RNA that is translatable and/or biologically active inside eukaryotic cells. [00989] In some embodiments, the following elements are operably connected to each other and arranged in the following sequence: a.) a 5' homology arm, b.) a 3' group I intron fragment containing a 3' splice site dinucleotide, c.) a 5' spacer sequence, d.) a protein coding or noncoding region, e.) a 3' spacer sequence, f.) a 5' group I intron fragment containing a 5' splice site dinucleotide, and g.) a 3' homology arm. In some embodiments, said vector allows production of a circular RNA that is translatable and/or biologically active inside eukaryotic cells.
[00990] In some embodiments, the following elements are operably connected to each other and arranged in the following sequence: a.) a 5' homology arm. b.) a 3' group I intron fragment containing a 3' splice site dinucleotide, c.) an internal ribosome entry site (IRES), d.) a protein coding or noncoding region, e.) a 3' spacer sequence, f) a 5' group I intron fragment containing a 5' splice site dinucleotide, and g.) a 3' homology arm. In some embodiments, said vector allows production of a circular RNA that is translatable and/or biologically active inside eukaryotic cells.
[00991] In some embodiments, the following elements are operably connected to each other and arranged in the following sequence: a.) a 5' homology arm, b.) a 3' group I intron fragment containing a 3' splice site dinucleotide, c.) a protein coding or noncoding region, d.) a 3' spacer sequence, e.) a 5' group I intron fragment containing a 5' splice site dinucleotide, and f.) a 3’ homology arm. In some embodiments, said vector allows production of a circular RNA that is translatable and/or biologically active inside eukaryotic cells.
[00992] In some embodiments, the following elements are operably connected to each other and arranged in the following sequence: a.) a 5' homology arm, b.) a 3' group I intron fragment containing a 3' splice site dinucleotide, c.) a 5' spacer sequence, d.) a protein coding or noncoding region, e.) a 5' group I intron fragment containing a 5' splice site dinucleotide, and f.) a 3’ homology ann. In some embodiments, said vector allows production of a circular RNA that is translatable and/or biologically active inside eukaryotic cells.
[00993] In some embodiments, the following elements are operably connected to each other and arranged in the following sequence: a.) a 5' homology arm, b.) a 3' group I intron fragment containing a 3' splice site dinucleotide, c.) an internal ribosome entry site (IRES), d.) a protein coding or noncoding region, e.) a 5' group I intron fragment containing a 5' splice site dinucleotide, and f) a 3' homology arm. In some embodiments, said vector allows production of a circular RNA that is translatable and/or biologically active inside eukaryotic cells.
[00994] In some embodiments, the following elements are operably connected to each other and arranged in the following sequence: a.) a 5' homology arm, b.) a 3' group I intron fragment containing a 3' splice site dinucleotide, c.) a 5' spacer sequence, d.) an internal ribosome entry site (IRES), e.) a protein coding or noncoding region, f) a 3' spacer sequence, g.) a 5' group I intron fragment containing a 5' splice site dinucleotide, and h.) a 3' homology arm. In some embodiments, said vector allowing production of a circular RNA that is translatable and/or biologically active inside eukaryotic cells.
[00995] In one embodiment, the 3' group I intron fragment and/or tire 5' group I intron fragment is from a Cyanobacterium Anabaena sp. pre-tRNA-Leu gene or T4 phage Td gene.
[00996] In one embodiment, the 3' group I intron fragment and/or tire 5' group I intron fragment is from a Cyanobacterium Anabaena sp. pre-tRNA-Leu gene.
[00997] In one embodiment, the protein coding region encodes a protein of eukaryotic or prokaryotic origin. In another embodiment, the protein coding region encodes human protein or non-human protein. In some embodiments, the protein coding region encodes one or more antibodies. For example, in some embodiments, the protein coding region encodes human antibodies. In one embodiment, the protein coding region encodes a protein selected from hFTX, SP-B, VEGF-A, human methylmalonyl -Co A mutase (hMUT), CFTR, cancer self-antigens, and additional gene editing enzymes like Cpfl, zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). In another embodiment, the protein coding region encodes a protein for therapeutic use. In one embodiment, the human antibody encoded by the protein coding region is an anti -HIV antibody. In one embodiment, the antibody encoded by tire protein coding region is a bispecific antibody. In one embodiment, the bispecific antibody is specific for CD 19 and CD22. In another embodiment, the bispecific antibody is specific for CD3 and CLDN6. In one embodiment, the protein coding region encodes a protein for diagnostic use. In one embodiment, the protein coding region encodes Gaussia luciferase (Glue), Firefly luciferase (Flue), enhanced green fluorescent protein (eGFP), human erythropoietin (hEPO), or Cas9 endonuclease.
[00998] In one embodiment, the 5' homology ami is about 5-50 nucleotides in length. In another embodiment, the 5' homology ami is about 9-19 nucleotides in length. In some embodiments, the 5' homology ann is at least 5, 6. 7, 8, 9, 10, 11, 12, 13, 14. 15. 16. 17, 18 or 19 nucleotides in length. In some embodiments, the 5' homology ami is no more than 50, 45, 40, 35, 30, 25 or 20 nucleotides in length. In some embodiments, the 5' homology arm is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 or 19 nucleotides in length.
[00999] In one embodiment, the 3' homology arm is about 5-50 nucleotides in length. In another embodiment, the 3' homology arm is about 9-19 nucleotides in length. In some embodiments, the 3' homology arm is at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18 or 19 nucleotides in length. In some embodiments, the 3' homology ann is no more than 50, 45, 40, 35, 30, 25 or 20 nucleotides in length. In some embodiments, the 3' homology ami is 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16. 17. 18 or 19 nucleotides in length. [001000] In one embodiment, the 5' spacer sequence is at least 10 nucleotides in length. In another embodiment, the 5' spacer sequence is at least 15 nucleotides in length. In a further embodiment, the 5' spacer sequence is at least 30 nucleotides in length. In some embodiments, tire 5' spacer sequence is at least 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25 or 30 nucleotides in length. In some embodiments, tire 5' spacer sequence is no more than 100, 90, 80. 70. 60, 50, 45, 40, 35 or 30 nucleotides in length. In some embodiments the 5' spacer sequence is between 20 and 50 nucleotides in length. In certain embodiments, the 5' spacer sequence is 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 or 50 nucleotides in length. In one embodiment, the 5' spacer sequence is a polyA sequence. In another embodiment, the 5' spacer sequence is a polyA-C sequence.
[001001] In one embodiment, the 3' spacer sequence is at least 10 nucleotides in length. In another embodiment, the 3' spacer sequence is at least 15 nucleotides in length. In a further embodiment, the 3' spacer sequence is at least 30 nucleotides in length. In some embodiments, the 3’ spacer sequence is at least 7, 8, 9, 10, 11, 12, 13, 14, 15. 16. 17. 18, 19, 20, 25 or 30 nucleotides in length. In some embodiments, the 3' spacer sequence is no more than 100, 90, 80, 70, 60, 50, 45, 40, 35 or 30 nucleotides in length. In some embodiments the 3' spacer sequence is between 20 and 50 nucleotides in length. In certain embodiments, the 3' spacer sequence is 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38. 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 or 50 nucleotides in length. In one embodiment, the 3' spacer sequence is a polyA sequence. In another embodiment, the 5' spacer sequence is a polyA-C sequence.
Extracellular Circularization
[001002] In some embodiments, the linear RNA is cyclized, or concatemerized using a chemical method to form an oRNA. In some chemical methods, the 5'-end and the 3'-end of the nucleic acid (e.g., a linear RNA) includes chemically reactive groups that, when close together, may form a new covalent linkage between the 5'-cnd and the 3'-cnd of the molecule. Tire 5'-cnd may contain an NHS-cstcr reactive group and the 3'-end may contain a 3'-amino-tenninated nucleotide such that in an organic solvent the 3'-amino- terminated nucleotide on the 3'-end of a linear RNA will undergo a nucleophilic attack on the 5'-NHS-ester moiety forming a new 5'-/3'-amide bond.
[001003] In one embodiment, a DNA or RNA ligase may be used to enzymatically link a 5'- phosphorylated nucleic acid molecule (e.g., a linear RNA) to the 3'-hydroxyl group of a nucleic acid (e.g., a linear nucleic acid) forming a new phosphorodiester linkage. In an example reaction, a linear RNA is incubated at 37C for 1 hour with 1-10 units of T4 RNA ligase according to the manufacturer's protocol. The ligation reaction may occur in the presence of a linear nucleic acid capable of base-pairing with both the 5'- and 3'-region in juxtaposition to assist the enzymatic ligation reaction. In one embodiment, the ligation is splint ligation where a single stranded polynucleotide (splint), like a single stranded RNA, can be designed to hybridize with both termini of a linear RNA, so that the two termini can be juxtaposed upon hybridization with the single-stranded splint. Splint ligase can thus catalyze the ligation of the juxtaposed two tennini of the linear RNA, generating an oRNA.
[001004] In one embodiment, a DNA or RNA ligase may be used in the synthesis of the oRNA. As a non-limiting example, the ligase may be a circ ligase or circular ligase.
[001005] In one embodiment, either the 5'-or 3'-end of the linear RNA can encode a ligase ribozyme sequence such that during in vitro transcription, the resultant linear RNA includes an active ribozyme sequence capable of ligating the 5'-end of the linear RNA to the 3'-end of the linear RNA. The ligase ribozyme may be derived from the Group I Intron, Hepatitis Delta Virus, Hairpin ribozyme or may be selected by SELEX (systematic evolution of ligands by exponential enrichment).
[001006] In one embodiment, a linear RNA may be cyclized or concatemerized by using at least one non-nucleic acid moiety. In one aspect, the at least one non-nucleic acid moiety may react with regions or features near the 5' tenninus and/or near the 3' tenninus of the linear RNA in order to cyclize or concatermerize the linear RNA. In another aspect, the at least one non-nucleic acid moiety may be located in or linked to or near the 5' terminus and/or the 3' terminus of the linear RNA. The non-nucleic acid moieties contemplated may be homologous or heterologous. As a non-limiting example, the non-nucleic acid moiety may be a linkage such as a hydrophobic linkage, ionic linkage, a biodegradable linkage and/or a cleavable linkage. As another non-limiting example, the non-nucleic acid moiety is a ligation moiety. As yet another non-limiting example, the non-nucleic acid moiety may be an oligonucleotide or a peptide moiety, such as an aptamer or a non-nucleic acid linker as described herein.
[001007] In one embodiment, a linear RNA may be cyclized or concatemerized due to a non-nucleic acid moiety that causes an attraction between atoms, molecular surfaces at, near or linked to the 5' and 3' ends of the linear RNA. As a non-limiting example, one or more linear RNA may be cyclized or concatemerized by intermolecular forces or intramolecular forces. Non-limiting examples of intermolecular forces include dipole-dipole forces, dipole-induced dipole forces, induced dipole-induced dipole forces, Van der Waals forces, and London dispersion forces. Non-limiting examples of intramolecular forces include covalent bonds, metallic bonds, ionic bonds, resonant bonds, agnostic bonds, dipolar bonds, conjugation, hyperconjugation and antibonding. [001008] In one embodiment, the linear RNA may comprise a ribozyme RNA sequence near the 5' terminus and near the 3' terminus. The ribozyme RNA sequence may covalently link to a peptide when the sequence is exposed to the remainder of the ribozyme. In one aspect, the peptides covalently linked to the ribozyme RNA sequence near the 5' terminus and the 3' terminus may associate with each other causing a linear RNA to cyclize or concatemerize. In another aspect, the peptides covalently linked to tire ribozyme RNA near tire 5' tenninus and the 3' terminus may cause the linear RNA to cyclize or concatemerize after being subjected to ligated using various methods known in the art such as, but not limited to, protein ligation.
[001009] In some embodiments, the linear RNA may include a 5' triphosphate of the nucleic acid converted into a 5' monophosphate, e.g., by contacting the 5' triphosphate with RNA 5' pyrophosphohydrolase (RppH) or an ATP diphosphohydrolase (apyrase). Alternately, converting the 5' triphosphate of the linear RNA into a 5' monophosphate may occur by a two-step reaction comprising: (a) contacting the 5' nucleotide of the linear RNA with a phosphatase (e.g., Antarctic Phosphatase, Shrimp Alkaline Phosphatase, or Calf Intestinal Phosphatase) to remove all three phosphates: and (b) contacting the 5' nucleotide after step (a) witha kinase (e.g., Polynucleotide Kinase) that adds a single phosphate.
[001010] In some embodiments, RNA may be circularized using the methods described in WO2017222911 and WO2016197121, the contents of each of which are herein incorporated by reference in their entirety.
[001011] In some embodiments, RNA may be circularized, for example, by back splicing of a nonmammalian exogenous intron or splint ligation of the 5' and 3 ' ends of a linear RNA. In one embodiment, the circular RNA is produced from a recombinant nucleic acid encoding the target RNA to be made circular. As a non-limiting example, the method comprises: a) producing a recombinant nucleic acid encoding the target RNA to be made circular, wherein the recombinant nucleic acid comprises in 5' to 3 ' order: i) a 3 ' portion of an exogenous intron comprising a 3' splice site, ii) a nucleic acid sequence encoding the target RNA, and iii) a 5 ' portion of an exogenous intron comprising a 5 ' splice site: b) performing transcription, whereby RNA is produced from the recombinant nucleic acid; and c) performing splicing of the RNA, whereby the RNA circularizes to produce a oRNA.
[001012] While not wishing to be bound by theory, circular RNAs generated with exogenous introns are recognized by the immune system as "non-self ' and trigger an innate immune response. On tire other hand, circular RNAs generated with endogenous introns are recognized by the immune system as "self1 and generally do not provoke an innate immune response, even if carrying an exon comprising foreign RNA.
[001013] Accordingly, circular RNAs can be generated with either an endogenous or exogenous intron to control immunological self/non-self discrimination as desired. Numerous intron sequences from a wide variety of organisms and viruses are known and include sequences derived from genes encoding proteins, ribosomal RNA (rRNA), or transfer RNA (tRNA).
[001014] Circular RNAs can be produced from linear RNAs in a number of ways. In some embodiments, circular RNAs are produced from a linear RNA by backsplicing of a downstream 5' splice site (splice donor) to an upstream 3' splice site (splice acceptor). Circular RNAs can be generated in this manner by any nonmammalian splicing method. For example, linear RNAs containing various types of introns, including self-splicing group I introns, self-splicing group II introns, spliceosomal introns, and tRNA introns can be circularized. In particular, group I and group II introns have the advantage that they can be readily used for production of circular RNAs in vitro as well as in vivo because of their ability to undergo selfsplicing due to their autocatalytic ribozyme activity.
[001015] In some embodiments, circular RNAs can be produced in vitro from a linear RNA by chemical or enzymatic ligation of the 5' and 3' ends of the RNA. Chemical ligation can be performed, for example, using cyanogen bromide (BrCN) or ethyl-3-(3'-dimethylaminopropyl) carbodiimide (EDC) for activation of a nucleotide phosphomonoester group to allow phosphodiester bond formation. See e.g., Sokolova (1988) FEBS Lett 232: 153-155; Dolinnaya et al. (1991) Nucleic Acids Res., 19:3067-3072; Fedorova (1996) Nucleosides Nucleotides Nucleic Acids 15: 1 137-1 147; herein incorporated by reference. Alternatively, enzymatic ligation can be used to circularize RNA. Exemplary ligases that can be used include T4 DNA ligase (T4 Dnl), T4 RNA ligase 1 (T4 Rnl 1), and T4 RNA ligase 2 (T4 Rnl 2).
[001016] In some embodiments, splint ligation using an oligonucleotide splint that hybridizes with the two ends of a linear RNA can be used to bring the ends of the linear RNA together for ligation. Hybridization of tire splint, which can be either a DNA or a RNA, orientates the 5 '-phosphate and 3' -OH of the RNA ends for ligation. Subsequent ligation can be performed using either chemical or enzymatic techniques, as described above. Enzymatic ligation can be performed, for example, with T4 DNA ligase (DNA splint required), T4 RNA ligase 1 (RNA splint required) or T4 RNA ligase 2 (DNA or RNA splint). Chemical ligation, such as with BrCN or EDC, in some cases is more efficient than enzymatic ligation if the structure of tire hybridized splint-RNA complex interferes with enzymatic activity.
[001017] In some embodiments, the oRNA may further comprise an internal ribosome entry site (IRES) operably linked to an RNA sequence encoding a polypeptide. Inclusion of an IRES permits the translation of one or more open reading frames from a circular RNA. The IRES element attracts a eukaryotic ribosomal translation initiation complex and promotes translation initiation. See, e.g.. Kaufman et al., Nuc. Acids Res. (1991) 19:4485-4490: Gurtu et al., Biochem. Biophys. Res. Comm. (1996) 229:295-298; Rees et al., BioTechniques (1996) 20: 102-110; Kobayashi et al., BioTechniques (1996) 21 :399-402; and Mosser et al., BioTechniques 1997 22 150-161).
[001018] In some embodiments, the circularization efficiency of the circularization methods provided herein is at least about 10%, at least about 15%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, or 100%. In some embodiments, the circularization efficiency of the circularization methods provided herein is at least about 40%.
Splicing Element
[001019] In some embodiments, the oRNA includes at least one splicing element. The splicing element can be a complete splicing element that can mediate splicing of the oRNA or the spicing element can be a residual splicing element from a completed splicing event. For instance, in some cases, a splicing element of a linear RNA can mediate a splicing event that results in circularization of the linear RNA, thereby the resultant oRNA comprises a residual splicing element from such splicing-mediated circularization event. In some cases, the residual splicing element is not able to mediate any splicing. In other cases, the residual splicing element can still mediate splicing under certain circumstances. In some embodiments, the splicing element is adjacent to at least one expression sequence. In some embodiments, the oRNA includes a splicing element adjacent each expression sequence. In some embodiments, the splicing element is on one or both sides of each expression sequence, leading to separation of the expression products, e.g., peptide(s) and or polypcptidc(s).
[001020] In some embodiments, the oRNA includes an internal splicing element that when replicated the spliced ends are joined together. Some examples may include miniature introns (<100 nt) with splice site sequences and short inverted repeats (30-40 nt) such as AluSq2, AluJr, and AluSz, inverted sequences in flanking introns, Alu elements in flanking introns, and motifs found in (suptable4 enriched motifs) cissequence elements proximal to backsplice events such as sequences in the 200 bp preceding (upstream of) or following (downstream from) a backsplice site with flanking exons. In some embodiments, the oRNA includes at least one repetitive nucleotide sequence described elsewhere herein as an internal splicing element. In such embodiments, the repetitive nucleotide sequence may include repeated sequences from the Alu family of introns. See, e.g., US Patent No. 11,058,706.
[001021] In some embodiments, the oRNA may include canonical splice sites that flank head-to-tail junctions of the oRNA.
[001022] In some embodiments, the oRNA may include a bulge-helix-bulge motif, comprising a 4- base pair stem flanked by two 3-nucleotide bulges. Cleavage occurs at a site in the bulge region, generating characteristic fragments with terminal 5'-hydroxyl group and 2', 3'-cyclic phosphate. Circularization proceeds by nucleophilic attack of the 5'-OH group onto the 2', 3'-cyclic phosphate of the same molecule forming a 3', 5'-phosphodiester bridge.
[001023] In some embodiments, the oRNA may include a sequence that mediates self-ligation. Nonlimiting examples of sequences that can mediate self-ligation include a self-circularizing intron, e.g., a 5' and 3' slice junction, or a self-circularizing catalytic intron such as a Group I, Group II or Group III Introns. Nonlimiting examples of group I intron self-splicing sequences may includeself-splicing permuted intron-exon sequences derived from T4 bacteriophage gene td, and the intervening sequence (IVS) rRNA of Tetrahymena.
Other Circularization Methods
[001024] In some embodiments, linear RNA may include complementary sequences, including either repetitive or nonrepetitive nucleic acid sequences within individual introns or across flanking introns. In some embodiments, the oRNA includes a repetitive nucleic acid sequence. In some embodiments, the repetitive nucleotide sequence includes poly CA or poly UG sequences. In some embodiments, the oRNA includes at least one repetitive nucleic acid sequence that hybridizes to a complementary repetitive nucleic acid sequence in another segment of the oRNA. with the hybridized segment forming an internal double strand. In some embodiments, repetitive nucleic acid sequences and complementary repetitive nucleic acid sequences from two separate oRNA that hybridize to generate a single oRNA, with the hybridized segments forming internal double strands. In some embodiments, the complementary sequences arc found at the 5' and 3' ends of the linear RNA. In some embodiments, the complementary sequences include about 3, 4, 5, 6, 7, 8. 9, 10, 11. 12, 13, 14, 15, 16, 17, 18. 19. 20, 21, 22, 23, 24, 25, 26, 27. 28. 29, 30, 35, 40, 45, 50, 55, 60. 65. 70, 75, 80, 85, 90, 95, 100, or more paired nucleotides.
[001025] In some embodiments, chemical methods of circularization may be used to generate the oRNA. Such methods may include, but are not limited to click chemistry (e.g., alkyne- and azide-based methods, or clickable bases), olefin metathesis, phosphoramidate ligation, hemiaminal-imine crosslinking, base modification, and any combination thereof. In some embodiments, enzymatic methods of circularization may be used to generate the oRNA. In some embodiments, a ligation enzyme, e.g., DNA or RNA ligase, maybe used to generate a template of the oRNA or complement, a complementary strand of the oRNA, or the oRNA.
Any of the circular polynucleotides as taught in for example U.S. Provisional Application No. 61/873.010 filed Sep. 3, 2013 or U.S. Patent No. 10,709,779. may be used herein. The contents of these references are incorporated herein by reference in their entirety. In addition, any of the circular RNAs, methods for making circular RN As. circular RNA compositions that are described in the following publications are contemplated herein and are incorporated by reference in their entireties are part of the instant specification: US Patents US 11,352,640, US 11,352,641, US 11,203,767, US 10,683,498, US 5,773,244, and US 5,766,903; US Application Publications US 2022/0177540, US 2021/0371494, US 2022/0090137, US 2019/0345503, and US 2015/0299702; and PCT Application Publications WO 2021/226597. WO 2019/236673, WO 2017/222911, WO2016/187583, WO2014/082644 and WO 1997/007825.
H. Pharmaceutical Compositions
[001026] The present disclosure relates to pharmaceutical compositions comprising novel Cast 2a (or Cas Type V) editing systems. In some embodiments, the Casl2a (or Cas Type V) editing system comprising one or more polypeptides and cognate guide RNA are fonnulated as part of a lipid nanoparticle. In some embodiments, a lipid nanoparticle comprises an ionizable lipid, a structural lipid, a PEGylated lipid, and a phospholipid.
[001027] In various aspects of the invention, the Cas 12a (or Cas Type V) genome editing system is delivered as polynucleotides. For instance, in one embodiment, the Casl2a (or Cas Type V) nuclease and the gRNA are delivered as polynucleotides and encoded by one or more plasmids (Lauritsen, I., Porse, A., Sommer, M.O.A. et al. A versatile onc-stcp CRISPR-Cas9 based approach to plasmid-curing. Microb Cell Fact 16, 135 (2017). https://doi.org/10T 186/sl2934-017-0748- z; Wasels, Francois et al. “A two-plasmid inducible CRISPR/Cas9 genome editing tool for Clostridium acctobiitylicum," Journal of microbiological methods vol. 140 (2017): 5-11) doi: 10.1016/j.mimet.2017.06.010). In other embodiments, the Casl2a nuclease is encoded in a mRNA and the gRNA is encoded as an in vitro transcribed synthetic oligonucleotide (Y ang, Hui et al. “One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas- mediated genome engineering.” Cell vol. 154,6 (2013): 1370-9. doi: 10.1016/j. cell.2013.08.022). In other aspects, the Cas 12a nuclease protein and a synthetic gRNA oligonucleotide (Suresh, Bharathi et al. “Cell- Penetrating Peptide-Mediated Delivery of Cas9 Protein and Guide RNA for Genome Editing.” Methods in molecular biology (Clifton, N.J.) vol. 1507 (2017): 81-94. doi: 10. 1007/978-1-4939-6518-2 7) or alternatively as an Cas 12a nuclease protein gRNA RNP complex (Gasiunas, Giedrius et al. “Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria.” Proceedings of the National Academy of Sciences of the United States of America vol. 109,39 (2012): E2579-86. doi: 10.1073/pnas.1208507109).
[001028] The pharmaceutical compositions described herein (e.g., LNP compositions comprising a Casl2agene editing system or components thereof) may be delivered as described in PCT Publication WO2012135805, which is incorporated herein by reference in its entirety, or by another method known or described herein.
[001029] In various aspects, the present disclosure provides methods comprising administering a pharmaceutical composition (e.g., LNP formulation comprising a Cas 12a gene editing system) to a subject in need thereof. The pharmaceutical composition may be administered to a subject using any amount and any route of administration which may be effective for preventing, treating, diagnosing, or imaging a disease, disorder, and/or condition. The exact amount required will van- from subject to subject, depending on factors such as. but not limited to, the species, age. and general condition of the subject, the severity of the disease, the particular composition, its mode of administration, its mode of activity, and the like. The pharmaceutical composition may be administered to animals, such as mammals (e.g., humans, domesticated animals, cats, dogs, monkeys, mice, rats, etc.). Tire payload of the pharmaceutical composition is a polynucelotide.
[001030] In some embodiments, pharmaceutical, prophylactic, diagnostic, or imaging compositions thereof are administered to humans.
[001031] In some embodiments, the herein disclosed pharmaceutical compositions (e.g., LNPs comprising a Cas 12a (or Cas Type V) gene editing system) are administered by one or more of a variety of routes, including, but not limited to, local, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, subcutaneous, intraventricular, transdermal. interdermal, rectal, intravaginal, intraperitoneal, topical (e.g., by powders, ointments, creams, gels, lotions, and/or drops), mucosal, nasal, buccal, enteral, vitreal, intratumoral, sublingual: by intratracheal instillation, bronchial instillation, and/or inhalation; as an oral spray, nasal spray, and/or aerosol, and/or through a portal vein catheter.
[001032] In some embodiments, the herein disclosed pharmaceutical compositions (e.g., LNPs comprising a Cas 12a (or Cas Type V) gene editing system) are administered by systemic intravenous injection.
[001033] In some embodiments, the herein disclosed pharmaceutical compositions (e.g., LNPs comprising a Cas 12a (or Cas Type V) gene editing system) are administered intravenously and/or orally. Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, an active ingredient is mixed with at least one inert, pharmaceutically acceptable excipient such as sodium citrate or dicalcium phosphate and/or fillers or extenders (e.g. starches, lactose, sucrose, glucose, mannitol, and silicic acid), binders (e.g. carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia), humectants (e.g. glycerol), disintegrating agents (e.g. agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate), solution retarding agents (e.g. paraffin), absorption accelerators (e.g. quaternary ammonium compounds), wetting agents (e.g. cetyl alcohol and glycerol monostearate), absorbents (e.g. kaolin and bentonite clay), and lubricants (e.g. talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate), and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may comprise buffering agents.
[001034] In specific embodiments, tire herein disclosed pharmaceutical compositions (e.g., LNPs comprising a Cast 2a gene editing system) may be administered in a way which allows the genome editing system to cross the blood-brain barrier, vascular barrier, or other epithelial barrier.
[001035] Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing agents, wetting agents, and/or suspending agents. Sterile injectable preparations may be sterile injectable solutions, suspensions, and/or emulsions in nontoxic parenterally acceptable diluents and/or solvents, for example, as a solution in 1,3- butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer’s solution, U.S.P., and isotonic sodium chloride solution. Sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil can be employed including synthetic mono- or diglycerides. Fatty acids such as oleic acid can be used in the preparation of injectables.
[001036] Injectable formulations can be sterilized, for example, by filtration through a bacterial- retaining filter, and/or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
[001037] Dosage fonns for local, topical and/or transdermal administration of a pharmaceutical composition may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants and/or patches. Additionally, the present disclosure contemplates the use of transdermal patches, which often have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms may be prepared, for example, by dissolving and/or dispensing the compound in the proper medium. Alternatively or additionally, rate may be controlled by either providing a rate controlling membrane and/or by dispersing the compound in a polymer matrix and/or gel.
[001038] Formulations suitable for topical administration include, but are not limited to, liquid and/or semi liquid preparations such as liniments, lotions, oil in water and/or water in oil emulsions such as creams, ointments and/or pastes, and/or solutions and/or suspensions.
[001039] Topically-administrable formulations may. for example, comprise from about 1% to about 10% (w/w) active ingredient, although the concentration of active ingredient may be as high as the solubility limit of the active ingredient in the solvent. Formulations for topical administration may further comprise one or more of the additional ingredients described herein.
[001040] A pharmaceutical composition may be prepared, packaged, and/or sold in a formulation suitable for ophthalmic administration. Such formulations may, for example, be in the form of eye drops including, for example, a 0.1/1.0% (w/w) solution and/or suspension of the active ingredient in an aqueous or oily liquid excipient. Such drops may further comprise buffering agents, salts, and/or one or more other of any additional ingredients described herein. Other opthalmically-administrable formulations which are useful include those which comprise the active ingredient in microcrystalline form and/or in a liposomal preparation. Ear drops and/or eye drops are contemplated as being within the scope of this disclosure.
[001041] In general, the most appropriate route of administration will depend upon a variety of factors including the nature of the genome editing system to be delivered (e.g., its stability in the environment of the gastrointestinal tract, bloodstream, etc), the condition of the patient (e.g., whether the patient is able to tolerate particular routes of administration), etc. The present disclosure encompasses the delivery of the genome editing system by any appropriate route taking into consideration likely advances in the sciences of drug delivery. [00308] In certain embodiments, pharmaceutical compositions in accordance with the present disclosure may be administered at dosage levels sufficient to deliver from about 0.0001 mg/kg to about 100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, from about 0.1 mg/kg to about 40 mg/kg, from about 0.5 mg/kg to about 30 mg/kg, from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to about 10 mg/kg, or from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic, diagnostic or prophylactic effect. The desired dosage may be delivered three times a day, two times a day, once a day, every other day. every third day, every week, every two weeks, every three weeks, or every four weeks. In certain embodiments, the desired dosage may be delivered using multiple administrations (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or more administrations). When multiple administration is employed, split dosing regimens such as those described herein may be used.
[001042] According to the present disclosure, administration of the genome editing system in splitdose regimens may produce higher levels of proteins in mammalian subjects. As used herein, a “split dose” is the division of single unit dose or total daily dose into two or more doses. As used herein, a “single unit dose” is a dose of any therapeutic administered in one dose/at one time/single route/single point of contact, i.e., single administration event. As used herein, a “total daily dose” is an amount given or prescribed in 24 hr period. It may be administered as a single unit dose. In one embodiment, the genome editing system of the present disclosure are administered to a subject in split doses. In some embodiments, the genome editing system is formulated in buffer only or in a formulation described herein.
[001043] The herein disclosed pharmaceutical compositions (e.g., LNPs comprising a Casl2a gene editing system) of the present disclosure may be used or administered in combination with one or more other therapeutic, prophylactic, diagnostic, or imaging agents. By “in combination with,” it is not intended to imply that the agents must be administered at the same time and/or formulated for delivery together, although these methods of delivery are within the scope of the present disclosure. Pharmaceutical compositions can be administered concurrently with, prior to, or subsequent to, one or more other desired therapeutics or medical procedures. In general, each agent will be administered at a dose and/or on a time schedule determined for that agent. In some embodiments, the present disclosure encompasses the delivery of pharmaceutical, prophylactic, diagnostic, or imaging compositions in combination with agents that may improve their bioavailability, reduce and/or modify their metabolism, inhibit their excretion, and/or modify their distribution within the body.
[001044] It will further be appreciated that therapeutically, prophylactically, diagnostically, or imaging active agents utilized in combination may be administered together in a single pharmaceutical composition or administered separately in different pharmaceutical compositions. In general, it is expected that agents utilized in combination with be utilized at levels that do not exceed the levels at which they are utilized individually. In some embodiments, the levels utilized in combination will be lower than those utilized individually. In one embodiment, the combinations, each or together may be administered according to the split dosing regimens described herein.
[001045] The particular combination of therapies (therapeutics or procedures) to employ in a combination regimen will take into account compatibility of tire desired therapeutics and/or procedures and the desired therapeutic effect to be achieved. It will also be appreciated that the therapies employed may achieve a desired effect for the same disorder (for example, a pharmaceutical composition useful for treating cancer in accordance with the present disclosure may be administered concurrently with a chemotherapeutic agent), or they may achieve different effects (e.g., control of any adverse effects).
[001046] Pharmaceutical compositions containing LNPs disclosed herein are formulated for administration intramuscularly, transarterially, intraocularly, vaginally, rectally, intraperitoneally, intravenously, intranasally, subcutaneously, endoscopically, transdermally, intramuscularly, intraventricularly, intradermally, intrathecally, topically (e.g. by powders, ointments, creams, gels, lotions, and/or drops), mucosally. nasal, enterally, intratumorally. by intratracheal instillation, bronchial instillation, and/or inhalation; nasal spray and/or aerosol, and/or through a portal vein catheter. [001047] The pharmaceutical compositions may also be formulated for direct delivery to an organ or tissue in any of several ways in the art including, but not limited to, direct soaking or bathing, via a catheter, by gels, powder, ointments, creams, gels, lotions, and/or drops, by using substrates such as fabric or biodegradable materials coated or impregnated with the pharmaceutical compositions, and the like. In some embodiments, the pharmaceutical composition is formulated for extended release. In specific embodiments, the genome editing systems of the present disclosure and/or pharmaceutical, prophylactic, diagnostic, or imaging compositions thereof, may be administered in a way which allows the genome editing system to cross the blood-brain barrier, vascular barrier, or other epithelial barrier.
[001048] In some aspects of the present disclosure, the genome editing system of the present disclosure are spatially retained within or proximal to a target tissue. Provided are methods of providing a pharmaceutical composition to a target tissue of a mammalian subject by contacting tire target tissue (which contains one or more target cells) with tire pharmaceutical composition under conditions such that the pharmaceutical composition, in particular the genome editing system component(s) of the pharmaceutical composition, is substantially retained in the target tissue, meaning that at least 10, 20. 30. 40. 50, 60, 70, 80, 85, 90, 95, 96, 97, 98, 99, 99.9, 99.99 or greater than 99.99% of the pharmaceutical composition is retained in the target tissue. Advantageously, retention is determined by measuring the amount of a component of the genome editing system present in the pharmaceutical composition that enters one or more target cells. For example, at least 1, 5. 10, 20, 30, 40, 50, 60, 70, 80. 85, 90, 95, 96, 97, 98, 99, 99.9, 99.99 or greater than 99.99% of the genome editing system administered to the subject are present intracellularly at a period of time following administration.
[001049] Aspects of the present disclosure are directed to methods of providing a phannaceutical composition to a target tissue or organ of a mammalian subject, by contacting the target tissue (containing one or more target cells) or organ (containing one or more target cells) with the pharmaceutical composition under conditions such that the pharmaeutical composition is substantially retained in the target tissue or organ. The pharmaceutical composition contains an effective amount of a genome editing system of the present disclosure.
[001050] Phannaceutical compositions which may be administered intramuscularly and/or subcutaneously may include, but are not limited to, polymers, copolymers, and gels. The polymers, copolymers and/or gels may further be adjusted to modify release kinetics by adjusting factors such as, but not limited to, molecular weight, particle size, payload and/or ratio of the monomers. As a nonlimiting example, formulations administered intramuscularly and/or subcutaneously may include a copolymer such as poly(lactic-co-glycolic acid). [001051] Localized delivery of the pharmaceutical compositions described herein may be administered by methods such as, but not limited to, topical delivery, ocular delivery, transdermal delivery, and the like. The pharmaceutical composition may also be administered locally to a part of the body not normally available for localized delivery such as, but not limited to, when a subject’s body is open to the environment during treatment. Tire pharmaceutical composition may further be delivered by bathing, soaking and/or surrounding tire body part with the pharmaceutical composition.
[001052] However, the present disclosure encompasses the delivery of a genome editing system disclosed herein, and/or pharmaceutical, prophylactic, diagnostic, or imaging compositions thereof, by any appropriate route taking into consideration likely advances in the sciences of drug delivery.
[001053] In some embodiments, an LNP composition includes an ionizable lipid, a phospholipid, a PEG lipid, and a structural lipid. In certain embodiments, the lipid component of the nanoparticle composition includes about 30 mol % to about 60 mol % ionizable lipid, about 0 mol % to about 30 mol % phospholipid, about 18.5 mol % to about 48.5 mol % structural lipid, and about 0 mol% to about 10 mol% of PEG lipid, provided that the total mol% does not exceed 100%. In some embodiments, the lipid component of the nanoparticle composition includes about 35 mol % to about 55 mol % ionizable lipid, about 5 mol % to about 25 mol % phospholipid, about 30 mol % to about 40 mol % structural lipid, and about 0 mol % to about 10 mol % of PEG lipid. In a particular embodiment, the lipid component includes about 50 mol % ionizable lipid, about 10 mol % phospholipid, about 38.5 mol % structural lipid, and about 1.5 mol% of PEG lipid. In another particular embodiment, the lipid component includes about 40 mol % ionizable lipid, about 20 mol % phospholipid, about 38.5 mol % structural lipid, and about 1.5 mol % of PEG lipid. In another particular embodiment, the lipid component includes about 48.5 mol % ionizable lipid, about 10 mol % phospholipid, about 40 mol % structural lipid, and about 1.5 mol % of PEG lipid. In another particular embodiment, the lipid component includes about 48.5 mol % ionizable lipid, about 10 mol % phospholipid, about 39 mol % structural lipid, and about 2.5 mol % of PEG lipid. In some embodiments, the phospholipid may be DOPE or DSPC. In other embodiments, the PEG lipid may be PEG-DMG and/or the structural lipid may be cholesterol. Hie amount of a genome editing system payload in a nanoparticle composition may depend on the size, composition, desired target and/or application, or other properties of the nanoparticle composition as well as on the properties of the genome editing system. For example, the amount of genome editing system usefid in a nanoparticle composition may depend on the size, sequence, and other characteristics of the genome editing system. The relative amounts of genome editing system and other elements (e.g., lipids) in a nanoparticle composition may also vary. In some embodiments, the vvt/wt ratio of the lipid component to a polynucleotide or enzyme in a nanoparticle composition is about 5: 1 to about 60:1, such as 5: 1, 6: 1, 7: 1, 8: 1, 9: 1. 10: 1, 11: 1, 12: 1, 13: 1, 14: 1, 15: 1, 16: 1, 17: 1, 18: 1, 19: 1, 20: 1, 25: 1, 30: 1, 35: 1, 40: 1, 45: 1, 50: 1, and 60: 1. The amount of a polynucleotide or an enzyme in a nanoparticle composition may, for example, be measured using absorption spectroscopy (e.g., ultraviolet-visible spectroscopy).
[001054] In some embodiments, an LNP composition containing a genome editing system of the present disclosure, comprising a genome editing system is formulated to provide a specific N:P ratio. The N:P ratio of the composition refers to the molar ratio of nitrogen atoms in one or more lipids to the number of phosphate groups in an RNA. In general, a lower N:P ratio is preferred. The one or more enzymes, lipids, and amounts thereof may be selected to provide an N:P ratio from about 2: 1 to about 30: 1, such as 2: 1, 3: 1. 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1, 10: 1, 12: 1, 14: 1, 16: 1, 18: 1, 20: 1, 22: 1, 24: 1, 26: 1, 28: 1, or 30: 1. In certain embodiments, the N:P ratio is about 2: 1 to about 8: 1. In other embodiments, the N:P ratio is from about 5: 1 to about 8: 1. For example, the N:P ratio may be about 5.0: 1, about 5.5: 1, about 5.67: 1, about 6.0: 1, about 6.5:1, or about 7.0: 1.
[001055] The characteristics of an LNP (or “nanoparticles”) composition may depend on the components thereof. For example, a nanoparticle composition including cholesterol as a structural lipid may have different characteristics than a nanoparticle composition that includes a different structural lipid.
Similarly, the characteristics of a nanoparticle composition may depend on the absolute or relative amounts of its components. For instance, a nanoparticle composition including a higher molar fraction of a phospholipid may have different characteristics than a nanoparticle composition including a lower molar fraction of a phospholipid. Characteristics may also van’ depending on the method and conditions of preparation of tire nanoparticle composition. Nanoparticle compositions may be characterized by a variety of methods. For example, microscopy (e.g., transmission electron microscopy or scanning electron microscopy) may be used to examine the morphology and size distribution of a nanoparticle composition. Dynamic light scattering or potentiometry’ (e g., potentiometric titrations) may be used to measure Zeta potentials. Dynamic light scattering may also be utilized to determine particle sizes. Instruments such as the Zetasizer Nano ZS (Malvern Instruments Ltd, Malvern, Worcestershire, UK) may also be used to measure multiple characteristics of a nanoparticle composition, Such as particle size, polydispersity index, and Zeta potential.
[001056] The mean size of an LNP composition may be between 10s of nm and 100s of nm, e.g., measured by dynamic light scattering (DLS). For example, the mean size is about 40 nm to about 150 nm, such as about 40 nm, 45 nm, 50 nm, 55 nm. 60 nm. 65 nm, 70 nm, 75 nm, 80 nm. 85 nm, 90 nm, 95 nm, 100 nm, 105 nm, 110 nm, 115nm, 120 nm, 125 nm, 130 nm, 135 nm, 140 nm, 145 nm, or 150 nm. In some embodiments, the mean size of a nanoparticle composition is about 50 nm to about 100 nm, from about 50 nm to about 90 nm, from about 50 nm to about 80 nm, from about 50 nm to about 70 nm, from about 50 nm to about 60 nm, from about 60 nm to about 100 nm, from about 60 nm to about 90 nm, from about 60 nm to about 80 nm, from about 60 nm to about 70 nm, from about 70 nm to about 100 nm, from about 70 nm to about 90 nm, from about 70 nm to about 80 nm, from about 80 nm to about 100 nm, from about 80 nm to about 90 nm, or from about 90 nm to about 100 nm. In certain embodiments, the mean size of a nanoparticle composition is about 70 nm to about 100 nm. In a particular embodiment, the mean size may be about 80 nm. In other embodiments, the mean size may be about 100 nm.
[001057] A LNP composition may be relatively homogenous. A polydispersity index may be used to indicate the homogeneity of a nanoparticle composition, e.g.. the particle size distribution of the nanoparticle compositions. A small (e.g., less than 0.3) poly dispersity index generally indicates a narrow particle size distribution. A nanoparticle composition may have a polydispersity index from about 0 to about 0.25, such as 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 0.10, 0.11, 0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23. 0.24, or 0.25.
[001058] The Zeta potential of a LNP composition may be used to indicate the electrokinetic potential of the composition. For example, the Zeta potential may describe the surface charge of a nanoparticle composition. Nanoparticle compositions with relatively low charges, positive or negative, are generally desirable, as more highly charged species may interact undesirably with cells, tissues, and other elements in the body. In some embodiments, the Zeta potential of a nanoparticle composition is about -10 mV to about +20 mV, from about -10 mV to about +15 mV, from about -10 mV to about +10 mV, from about -10 mV to about +5 mV, from about -10 mV to about 0 mV, from about -10 mV to about -5 mV, from about -5 mV to about +20 mV, from about -5 mV to about +15 mV, from about -5 mV to about +10 mV, from about -5 mV to about +5 mV, from about -5 mV to about 0 mV, from about 0 mV. to about +20 mV, from about 0 mV to about +15 mV, from about 0 mV to about +10 mV, from about 0 mV to about +5 mV, from about +5 mV to about +20 mV, from about +5 mV, to about +15 mV, or from about +5 mV to about +10 mV.
[001059] The efficiency of encapsulation of an LNP payload describes the amount of payload that is encapsulated or otherwise associated with a nanoparticle composition after preparation, relative to the initial amount provided. The encapsulation efficiency is desirably high (e.g., close to 100%). The encapsulation efficiency may be measured, for example, by comparing the amount of pay load in a solution containing the nanoparticle composition before and after breaking up the nanoparticle composition with one or more organic solvents or detergents. Fluorescence may be used to measure the amount of free payload in a solution. For the nanoparticle compositions described herein, the encapsulation efficiency of a therapeutic and/or prophylactic may be at least 50%, for example 50%, 55%, 60%. 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%. In some embodiments, the encapsulation efficiency may be at least 80%. In certain embodiments, the encapsulation efficiency may be at least 90%.
[001060] Lipids and their method of preparation are disclosed in, e.g., U.S. Patent Nos. 8,569,256, 5,965,542 and U.S. Patent Publication Nos. 2016/0199485, 2016/0009637, 2015/0273068, 2015/0265708, 2015/0203446, 2015/0005363, 2014/0308304, 2014/0200257, 2013/086373, 2013/0338210, 2013/0323269, 2013/0245107, 2013/0195920, 2013/0123338, 2013/0022649, 2013/0017223, 2012/0295832, 2012/0183581, 2012/0172411, 2012/0027803, 2012/0058188, 2011/0311583, 2011/0311582, 2011/0262527. 2011/0216622, 2011/0117125, 2011/0091525, 2011/0076335, 2011/0060032, 2010/0130588. 2007/0042031. 2006/0240093, 2006/0083780, 2006/0008910, 2005/0175682, 2005/017054, 2005/0118253, 2005/0064595, 2004/0142025, 2007/0042031, 1999/009076 and PCT Pub. Nos. WO 99/39741, WO 2017/117528, WO 2017/004143, WO 2017/075531, WO 2015/199952, WO 2014/008334, WO 2013/086373, WO 2013/086322, WO 2013/016058, WO 2013/086373, WO2011/141705, and WO 2001/07548 and Semple et. al, Nature Biotechnology, 2010, 28, 172-176, the full disclosures of which are herein incorporated by reference in their entirety for all purposes.
[001061] An LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions may include any substance useful in phannaceutical compositions. For example, the nanoparticle composition may include one or more pharmaceutically acceptable excipients or accessory ingredients such as, but not limited to, one or more solvents, dispersion media, diluents, dispersion aids, suspension aids, granulating aids, disintegrants, fillers, glidants, liquid vehicles, binders, surface active agents, isotonic agents, thickening or emulsify ing agents, buffering agents, lubricating agents, oils, preservatives, and other species. Excipients such as waxes, butters, coloring agents, coating agents, flavorings, and perfuming agents may also be included. Pharmaceutically acceptable excipients are well known in the art (see for example Remington's The Science and Practice of Pharmacy, 21 Edition, A. R. Gennaro: Lippincott, Williams & Wilkins, Baltimore, Md., 2006).
[001062] The LNP-based nucleobase editing systems, RNA therapeutics and pharmaceutical compositions thereof described herein may be administered by any delivery' route which results in a therapeutically effective outcome. These include, but are not limited to, enteral (into the intestine), gastroenteral, epidural (into the dura mater), oral (by way of the mouth), transdennal. intracerebral (into the cerebrum), intracerebroventricular (into the cerebral ventricles), epicutaneous (application onto the skin), intradermal (into the skin itself), subcutaneous (under the skin), nasal administration (through the nose), intravenous (into a vein), intravenous bolus, intravenous drip, intra-arterial (into an artery ), intramuscular (into a muscle), intracardiac (into the heart), intraosseous infusion (into the bone marrow), intrathecal (into the spinal canal), intraparenchymal (into brain tissue), intraperitoneal (infusion or injection into the peritoneum), intravesical infusion, intravitreal (through the eye), intracavemous injection (into a pathologic cavity) intracavitary (into the base of the penis), intravaginal administration, intrauterine, extra-amniotic administration, transdermal (diffusion through the intact skin for systemic distribution), transmucosal (diffusion through a mucous membrane), transvaginal, insufflation (snorting), sublingual, sublabial, enema, eye drops (onto the conjunctiva), ear drops, auricular (in or by way of the ear), buccal (directed toward the cheek), conjunctival, cutaneous, dental (to a tooth or teeth), electro-osmosis, endocervical, endosinusial, endotracheal, extracorporeal, hemodialysis, infiltration, interstitial, intra-abdominal, intra-amniotic, intraarticular, mtrabiliary. intrabronchial, intrabursal, intracartilaginous (within a cartilage), intracaudal (within the cauda equine), intracistemal (within the cistema magna cerebellomedularis), intracorneal (within the cornea), dental intracoronal, intracoronary (within tire coronary arteries), intracorporus cavemosum (within the dilatable spaces of tire corporus cavernosa of the penis), intradiscal (within a disc), intraductal (within a duct of a gland), intraduodenal (within the duodenum), intradural (within or beneath the dura), intraepidermal (to the epidermis), intraesophageal (to the esophagus), intragastric (within the stomach), intragingival (within the gingivae), intraileal (within the distal portion of tire small intestine), intralesional (within or introduced directly to a localized lesion), intraluminal (within a lumen of a tube), intralymphatic (within the lymph), intramedullary (within the marrow cavity of a bone), intrameningeal (within the meninges), intramyocardial (within the myocardium), intraocular (within the eye), intraovarian (within the ovary), intrapericardial (within the pericardium), intrapleural (within the pleura), intraprostatic (within the prostate gland), intrapulmonary (within the lungs or its bronchi), intrasinal (within the nasal or periorbital sinuses), intraspinal (within the vertebral column), intrasynovial (within the synovial cavity of a joint), intratendinous (within a tendon), intratesticular (within the testicle), intrathecal (within the cerebrospinal fluid at any level of the cerebrospinal axis), intrathoracic (within the thorax), intratubular (within the tubules of an organ), intratumor (within a tumor), intratympanic (within the aurus media), intravascular (within a vessel or vessels), intraventricular (within a ventricle), iontophoresis (by means of electric current where ions of soluble salts migrate into the tissues of the body), irrigation (to bathe or flush open wounds or body cavities), laryngeal (directly upon the larynx), nasogastric (through the nose and into the stomach), occlusive dressing technique (topical route administration which is then covered by a dressing which occludes the area), ophthalmic (to the external eye), oropharyngeal (directly to the mouth and pharynx), parenteral, percutaneous, periarticular, peridural, perineural, periodontal, rectal, respiratory (within the respiratory tract by inhaling orally or nasally for local or systemic effect), retrobulbar (behind the pons or behind the eyeball), soft tissue, subarachnoid, subconjunctival, submucosal, topical, transplacental (through or across the placenta), transtracheal (through the wall of the trachea), transtympanic (across or through the tympanic cavity), ureteral (to the ureter), urethral (to the urethra), vaginal, caudal block, diagnostic, nerve block, biliary perfusion, cardiac perfusion, photopheresis, and spinal.
[001063] In some embodiments, compositions may be administered in a way which allows them to cross the blood-brain barrier, vascular barrier, or other epithelial barrier. The originator constructs, benchmark constructs, and targeting systems may be administered in any suitable form, either as a liquid solution or suspension, as a solid form suitable for liquid solution or suspension in a liquid solution. Tire originator constructs, benchmark constructs, and targeting systems may be formulated with any appropriate and pharmaceutically acceptable excipient.
[001064] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be delivered to a subject via a single route administration.
[001065] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be delivered to a subject via a multi-site route of administration. A subject may be administered at 2, 3, 4, 5, or more than 5 sites.
[001066] In some embodiments, a subject may be administered the originator constructs, benchmark constructs, and targeting systems using a bolus infusion.
[001067] In some embodiments, a subject may be administered originator constructs, benchmark constructs, and targeting systems using sustained delivery’ over a period of minutes, hours, or days. The infusion rate may be changed depending on the subject, distribution, formulation or another delivery parameter.
[001068] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be delivered by intramuscular delivery route. Non-limiting examples of intramuscular administration include an intravenous injection or a subcutaneous injection.
[001069] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be delivered by oral administration. Non-limiting examples of oral delivery include a digestive tract administration and a buccal administration.
[001070] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be delivered by intraocular delivery route. A non-limiting example of intraocular delivery include an intravitreal injection. [001071] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be delivered by intranasal delivery route. Non-limiting examples of intranasal delivery include nasal drops or nasal sprays.
[001072] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be administered to a subject by peripheral injections. Non-limiting examples of peripheral injections include intraperitoneal, intramuscular, intravenous, conjunctival, or joint injection.
[001073] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be delivered by injection into the cerebrospinal fluid. Non-limiting examples of delivery to the cerebrospinal fluid include intrathecal and intracerebroventricular administration.
[001074] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be delivered by systemic delivery. As a non-limiting example, the systemic delivery may be by intravascular administration.
[001075] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be administered to a subject by intracranial delivery.
[001076] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be administered to a subject by intraparenchymal administration.
[001077] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be administered to a subject by intramuscular administration.
[001078] In some embodiments, the originator constructs, benchmark constructs, and targeting systems are administered to a subject and transduce muscle of a subject. As a non-limiting example, the originator constructs, benchmark constructs, and targeting systems are administered by intramuscular administration.
[001079] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be administered to a subject by intravenous administration.
[001080] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be administered to a subject by subcutaneous administration.
[001081] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be administered to a subject by topical administration.
[001082] In some embodiments, the originator constructs, benchmark constructs, and targeting systems may be delivered by more than one route of administration. [001083] The originator constructs, benchmark constructs, and targeting systems described herein may be co-administered in conjunction with one or more originator constructs, benchmark constructs, targeting systems, or therapeutic agents or moieties.
[001084] In some embodiments, pharmaceutical compositions and/or formulations described herein may be administered parenterally. Liquid dosage forms for oral and parenteral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups, and/or elixirs. In addition to active ingredients, liquid dosage fonns may comprise inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3- butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, com, germ, olive, castor, and sesame oils), glycerol, tctrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, oral compositions can include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and/or perfuming agents. In certain embodiments for parenteral administration, compositions are mixed with solubilizing agents such as CREMOPHOR®, alcohols, oils, modified oils, glycols, polysorbates, cyclodextrins, polymers, and/or combinations thereof. In other embodiments, surfactants are included such as hydroxypropylcellulose.
[001085] Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing agents, wetting agents, and/or suspending agents. Sterile injectable preparations may be sterile injectable solutions, suspensions, and/or emulsions in nontoxic parenterally acceptable diluents and/or solvents, for example, as a solution in 1,3- butanediol. Among the acceptable vehicles and solvents that may be employed are water. Ringer's solution, U.S.P., and isotonic sodium chloride solution. Sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil can be employed including synthetic mono- or diglycerides. Fatty acids such as oleic acid can be used in the preparation of injectables.
[001086] Injectable formulations may be sterilized, for example, by filtration through a bacterial- retaining filter, and/or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.
[001087] In order to prolong the effect of active ingredients, it is often desirable to slow the absorption of active ingredients from subcutaneous or intramuscular injections. This may be accomplished by the use of liquid suspensions of crystalline or amorphous material with poor water solubility. The rate of absorption of active ingredients depends upon the rate of dissolution which, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered drug form is accomplished by dissolving or suspending the drug in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the drug in biodegradable polymers such as polylactide-polyglycolide. Depending upon the ratio of drug to polymer and the nature of the particular polymer employed, the rate of drug release can be controlled. Examples of other biodegradable polymers include poly (orthoesters) and poly(anhydrides). Depot injectable formulations are prepared by entrapping tire drug in liposomes or microemulsions which are compatible with body tissues.
[001088] In some embodiments, pharmaceutical compositions and/or fonnulations described herein may be formulated for administration topically. The skin may be an ideal target site for delivery as it is readily accessible. Three routes are commonly considered to deliver pharmaceutical compositions and/or formulations described herein to the skin: (i) topical application (e.g. for local/regional treatment and/or cosmetic applications); (ii) intradermal injection (e.g. for local/regional treatment and/or cosmetic applications); and (iii) systemic delivery (e.g. for treatment of dermatologic diseases that affect both cutaneous and extracutaneous regions).
[001089] In some embodiments, pharmaceutical compositions and/or fonnulations described herein may be delivered using a variety of dressings (e.g., wound dressings) or bandages (e.g.. adhesive bandages) for conveniently and/or effectively carrying out methods described herein. Typically dressing or bandages may comprise sufficient amounts of pharmaceutical compositions and/or formulations described herein to allow users to perform multiple treatments.
[001090] Dosage forms for topical and/or transdermal administration may include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants and/or patches. Generally, active ingredients are admixed under sterile conditions with pharmaceutically acceptable excipients and/or any needed preservatives and/or buffers. Additionally, contemplated herein is the use of transdermal patches, which often have the added advantage of providing controlled delivery of pharmaceutical compositions and/or formulations described herein to the body. Such dosage forms may be prepared, for example, by dissolving and/or dispensing pharmaceutical compositions and/or formulations described herein in the proper medium. Alternatively, or additionally, rates may be controlled by either providing rate controlling membranes and/or by dispersing pharmaceutical compositions and/or formulations described herein in a polymer matrix and/or gel.
[001091] Formulations suitable for topical administration include, but are not limited to, liquid and/or semi liquid preparations such as liniments, lotions, oil in water and/or water in oil emulsions such as creams, ointments and/or pastes, and/or solutions and/or suspensions. [001092] Topically-administrable formulations may, for example, comprise from about 1% to about 10% (w/w) active ingredient, although the concentration of active ingredient may be as high as the solubility limit of the active ingredient in the solvent. Formulations for topical administration may further comprise one or more of the additional ingredients described herein.
[001093] In some embodiments, pharmaceutical compositions and/or formulations described herein may be prepared, packaged, and/or sold in formulations suitable for ophthalmic and/or otic administration. Such formulations may, for example, be in the form of eye and/or ear drops including, for example, a 0.1/1.0% (w/w) solution and/or suspension of the active ingredient in aqueous and/or oily liquid excipients. Such drops may further comprise buffering agents, salts, and/or one or more other of any additional ingredients described herein. Other ophthalmically-administrable formulations which are useful include those which comprise active ingredients in microcrystalline form and/or in liposomal preparations. Subretinal inserts may also be used as forms of administration.
[001094] In some embodiments, pharmaceutical compositions and/or formulations described herein may be administered orally. Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage fonns, an active ingredient is mixed with at least one inert, pharmaceutically acceptable excipient such as sodium citrate or dicalcium phosphate and/or fillers or extenders (e.g. starches, lactose, sucrose, glucose, mannitol, and silicic acid), binders (e.g. carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia), humectants (e.g. glycerol), disintegrating agents (e.g. agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate), solution retarding agents (e.g. paraffin), absorption accelerators (e.g. quaternary ammonium compounds), wetting agents (e.g. cetyl alcohol and glycerol monostearate), absorbents (e.g. kaolin and bentonite clay), and lubricants (e.g. talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate), and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may comprise buffering agents.
[001095] In some embodiments, pharmaceutical compositions and/or formulations described herein are formulated in depots for extended release.
[001096] In some embodiments, pharmaceutical compositions and/or formulations described herein are spatially retained within or proximal to target tissues. Provided are methods of providing pharmaceutical compositions and/or fonn illations described herein to target tissues of mammalian subjects by contacting target tissues (w hich comprise one or more target cells) with pharmaceutical compositions and/or formulations described herein under conditions such that they are substantially retained in target tissues, meaning that at least 10, 20, 30, 40, 50, 60, 70, 80, 85, 90, 95, 96, 97, 98, 99, 99.9, 99.99 or greater than 99.99% of the composition is retained in the target tissues. Advantageously, retention is determined by measuring the amount of pharmaceutical compositions and/or formulations described herein that enter one or more target cells. For example, at least 1%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 99.9%, 99.99%, or greater than 99.99% of pharmaceutical compositions and/or formulations described herein administered to subjects are present intracellularly at a period of time following administration. For example, intramuscular injection to mammalian subjects may be performed using aqueous compositions comprising an active ingredient and one or more transfection reagents, and retention is determined by measuring the amount of active ingredient present in muscle cells.
[001097] In some embodiments, provided are methods for delivering pharmaceutical compositions and/or formulations described herein to target tissues of mammalian subjects, by contacting target tissues (comprising one or more target cells) with pharmaceutical compositions and/or formulations described herein under conditions such that they are substantially retained in such target tissues. Pharmaceutical compositions and/or formulations described herein comprise enough active ingredient such that the effect of interest is produced in at least one target cell. In some embodiments, pharmaceutical compositions and/or formulations described herein generally comprise one or more cell penetration agents, although "naked" formulations (such as without cell penetration agents or other agents) are also contemplated, with or without pharmaceutically acceptable carriers.
[001098] In some embodiments, pharmaceutical compositions and/or formulations described herein may be prepared, packaged, and/or sold in formulations suitable for pulmonary administration. In some embodiments, such administration is via the buccal cavity. In some embodiments, formulations may comprise dry particles comprising active ingredients. In such embodiments, dry particles may have a diameter in the range from about 0.5 nm to about 7 nm or from about 1 nm to about 6 nm. In some embodiments, formulations may be in the form of dry powders for administration using devices comprising dry powder reservoirs to which streams of propellant may be directed to disperse such powder. In some embodiments, self-propelling solvcnt/powdcr dispensing containers may be used. In such embodiments, active ingredients may be dissolved and/or suspended in low-boiling propellant in sealed containers. Such powders may comprise particles wherein at least 98% of the particles by weight have diameters greater than 0.5 nm and at least 95% of the particles by number have diameters less than 7 nm. Alternatively, at least 95% of the particles by weight have a diameter greater than 1 nm and at least 90% of the particles by number have a diameter less than 6 nm. Dry powder compositions may include a solid fine powder diluent such as sugar and are conveniently provided in a unit dose form. [001099] Low boiling propellants generally include liquid propellants having a boiling point of below 65 °F at atmospheric pressure. Generally, propellants may constitute 50% to 99.9% (w/w) of the composition, and active ingredient may constitute 0.1% to 20% (w/w) of the composition. Propellants may further comprise additional ingredients such as liquid non-ionic and/or solid anionic surfactant and/or solid diluent (which may have particle sizes of the same order as particles comprising active ingredients).
[001100] Phannaceutical compositions formulated for pulmonary delivery may provide active ingredients in the form of droplets of solution and/or suspension. Such formulations may be prepared, packaged, and/or sold as aqueous and/or dilute alcoholic solutions and/or suspensions, optionally sterile, comprising active ingredients, and may conveniently be administered using any nebulization and/or atomization device. Such formulations may further comprise one or more additional ingredients including, but not limited to, a flavoring agent such as saccharin sodium, a volatile oil, a buffering agent, a surface active agent, and/or a preservative such as methylhydroxybenzoate. Droplets provided by this route of administration may have an average diameter in the range from about 0.1 nm to about 200 nm.
[001101] In some embodiments, pharmaceutical compositions and/or fonnulations described herein may be administered nasally and/or intranasal. In some embodiments, fonnulations described herein useful for pulmonary delivery may also be usefi.il for intranasal delivery. In some embodiments, formulations for intranasal administration comprise a coarse powder comprising the active ingredient and having an average particle from about 0.2 m to 500 m. Such formulations are administered in the manner in which snuff is taken, i.e. by rapid inhalation through the nasal passage from a container of the powder held close to the nose.
[001102] Formulations suitable for nasal administration may, for example, comprise from about as little as 0.1% (w/w) and as much as 100% (w/w) of active ingredient, and may comprise one or more of the additional ingredients described herein. A pharmaceutical composition may be prepared, packaged, and/or sold in a formulation suitable for buccal administration. Such fonnulations may, for example, be in the form of tablets and/or lozenges made using conventional methods, and may, for example, 0.1% to 20% (w/w) active ingredient, the balance comprising an orally dissolvable and/or degradable composition and, optionally, one or more of the additional ingredients described herein. Alternately, formulations suitable for buccal administration may comprise powders and/or an aerosolized and/or atomized solutions and/or suspensions comprising active ingredients. Such powdered, aerosolized, and/or aerosolized formulations, when dispersed, may comprise average particle and/or droplet sizes in the range of from about 0. 1 nm to about 200 nm, and may further comprise one or more of any additional ingredients described herein.
[001103] In some embodiments, pharmaceutical compositions and/or formulations described herein may be administered rectally and/or vaginally. Compositions for rectal or vaginal administration are typically suppositories which can be prepared by mixing compositions with suitable non-irritating excipients such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active ingredient.
I. Host Cells
[001104] One aspect of the disclosure provides an isolated host cell that includes one or more of the compositions described herein, including, but not limited to, a Casl2a (or Cas Type V) gene editing systems or any component thereof. In some embodiments, the host cell is a prokaryotic cell, an archaeal cell, or a eukaryotic host cell. In some embodiments, the eukaryotic host cell is a mammalian cell, such as a human cell, a non-human cell, or a non-human mammalian cell. In some embodiments, the host cell is an artificial cell or genetically modified cell. In some embodiments, the host cell is in vitro, such as a tissue culture cell. In some embodiments, the host cell is within a living host organism.
[001105] Cells that may contain any of the compositions described herein. The methods described herein are used to deliver a Cas 12a (or Cas Type V) gene editing system described herein into a eukaryotic cell (e.g., a mammalian cell, such as a human cell). In some embodiments, the cell is in vitro (e.g., cultured cell. In some embodiments, the cell is in vivo (e.g., in a subject such as a human subject). In some embodiments, the cell is ex vivo (e.g., isolated from a subject and may be administered back to the same or a different subject).
[001106] Hie present disclosure contemplates the use of any suitable host cell. For example, the cell host can be a mammalian cell. Mammalian cells of the present disclosure include human cells, primate cells (e.g., vero cells), rat cells (e.g., GH3 cells, OC23 cells) or mouse cells (e.g., MC3T3 cells). There are a variety of human cell lines, including, without limitation, human embry onic kidney (HEK) cells, HeLa cells, cancer cells from the National Cancer Institute's 60 cancer cell lines (NCI60), DU145 (prostate cancer) cells, Lncap (prostate cancer) cells, MCF-7 (breast cancer) cells, MDA-MB-438 (breast cancer) cells, PC3 (prostate cancer) cells, T47D (breast cancer) cells, THP-1 (acute myeloid leukemia) cells, U87 (glioblastoma) cells, SHSY5Y human neuroblastoma cells (cloned from a myeloma) and Saos-2 (bone cancer) cells. In some embodiments, the cells can be human embryonic kidney (HEK) cells (e.g., HEK 293 or HEK 293T cells). In some embodiments, the cells can be stem cells (e.g., human stem cells) such as, for example, pluripotent stem cells (e.g., human pluripotent stem cells including human induced pluripotent stem cells (hiPSCs)). A stem cell refers to a cell with the ability to divide for indefinite periods in culture and to give rise to specialized cells. A pluripotent stem cell refers to a type of stem cell that is capable of differentiating into all tissues of an organism, but not alone capable of sustaining full organismal development. A human induced pluripotent stem cell refers to a somatic (e.g., mature or adult) cell that has been reprogrammed to an embryonic stem cell-like state by being forced to express genes and factors important for maintaining the defining properties of embryonic stem cells (see, e.g., Takahashi and Yamanaka, Cell 126 (4): 663-76, 2006, incorporated by reference herein). Human induced pluripotent stem cells express stem cell markers and are capable of generating cells characteristic of all three germ layers (ectoderm, endoderm, mesoderm).
[001107] Some aspects of this disclosure provide cells comprising any of the compositions disclosed herein, including, but not limited to, Casl2a (or Cas Type V) gene editing systems and components and vector or vector systems encoding the engineered gene editing systems, and any combinations thereof. In some embodiments, a host cell is transiently or non-transiently transfected with one or more delivery systems described herein, including virus-based systems, virus-like particle systems, and non-virus-base delivery, including LNPs and liposomes. In some embodiments, a cell is transfected as it naturally occurs in a subject. In some embodiments, a cell that is transfected is taken from a subject, i.e., ex vivo transfection. In some embodiments, the cell is derived from cells taken from a subject, such as a cell line. A wide variety of cell lines for tissue culture are known in the art. Examples of cell lines include, but are not limited to, C8161, CCRF-CEM, MOLT. mIMCD- 3, NHDF, HeLa-S3, Huhl. Huh4, Huh7, HUVEC, HASMC. HEKn, HEKa, MiaPaCell, Panel, PC-3, TF1, CTLL-2, C1R, Rat6, CV1, RPTE, A10, T24, J82, A375, ARH-77, Calul, SW480, SW620, SKOV3, SK-UT, CaCo2, P388D1, SEM-K2, WEHI-231, HB56, TIB55, Jurkat, J45.01, LRMB, Bcl-I, BC-3, IC21, DLD2, Raw264.7, NRK, NRK-52E, MRC5, MEF, Hep G2, HeLa B, HeLa T4, COS, COS-1, COS-6. COS-M6A, BS-C-1 monkey kidney epithelial, BALB/3T3 mouse embryo fibroblast. 3T3 Swiss, 3T3-L1, 132-d5 human fetal fibroblasts; 10.1 mouse fibroblasts, 293-T. 3T3, 721, 9L, A2780, A2780ADR, A2780cis. A 172, A20, A253. A431, A-549. ALC, B16. B35. BCP-1 cells, BEAS-2B, bEnd.3, BHK-21, BR 293. BxPC3. C3H-10T1/2, C6/36, Cal-27, CHO, CHO-7, CHO-IR, CHO-K1 , CHO-K2, CHO- T, CHO Dhfr -/-, COR-L23, COR-L23/CPR, COR-L23/5010, COR-L23/R23, COS-7, COV-434, CML Tl, CMT, CT26, D17, DH82, DU145, DuCaP, EL4, EM2, EM3, EMT6/AR1, EMT6/AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, HEK-293, HeLa, Hepalclc7, HL-60, HMEC, HT-29, Jurkat, JY cells, K562 cells, Ku812, KCL22, KG1, KY01, LNCap, Ma-Mel 1-48. MC-38, MCF-7, MCF-10A, MDA-MB-231, MDA-MB-468. MDA-MB-435, MDCK II. MDCK 11. MOR/0.2R. MONO-MAC 6. MTD-1A. MyEnd, NCI- H69/CPR, NCI-H69/LX10, NCI-H69/LX20, NCI-H69/LX4, NIH-3T3, NALM-1, NW-145, OPCN/OPCT cell lines, Peer, PNT-1A/PNT 2, RenCa, RIN-5F, RMA/RMAS, Saos-2 cells, Sf-9, SkBr3, T2, T-47D, T84, THP1 cell line, U373, U87, U937, VCaP, Vcro cells, WM39, WT-49, X63, YAC-1, YAR, and transgenic varieties thereof.
[001108] Cell lines are available from a variety of sources known to those with skill in the art (see, e.g., the American Type Culture Collection (ATCC) (Manassus, Va.)). In some embodiments, a cell transfected with one or more retron delivery systems described herein is used to establish anew cell line comprising one or more nucleic acid molecules encoding the recombinant retron-based gene editing systems described herein, or encoding at last a component of said systems (e.g., a recombinant ncRNA or a recombinant retron RT).
[001109] It is an object of the invention to deliver the herein described genome editing system into various host cells. Preferably, each of the components of the genome editing system are delivered together. In other embodiments, one or more of tire components of the genome editing system are delivered separately. In some embodiments, the gene editing components are delivered as DNA molecule, RNA molecules, proteins, nucleoproteins, or combinations thereof.
[001110] Alternatively, provided also are delivery ofthe genome editing system using plasmids.
[001111] Suitable host cell is selected from one or more prokaryotic cells, mammalian cells, human cells or synthetic cells. Various tissue types are selected based on the delivery modality. In various embodiments, the various host cells transformed, transduced or the uptake ofthe genome editing system produces a site-specific modification of a targeted polynucleotide sequence of a host cell genome.
[001112] Exemplary host cells for the methods and compositions of the invention include but are not limited to prokaryotic cells, yeast or fungal cells, archaea cells, plant cells, animal cells or human cells.
[001113] In various other aspects, provided are fusion protein comprising an isolated polypeptide encoded by an isolated or recombinant nucleic acid sequence fused to a heterologous amino acid sequence. Preferably, the fusion protein comprises a nuclease- deficient polypeptide.
[001114] In preferred aspects, the Casl2a (or Cas Type V) gene editing systems described herein rely on the cells’ DNA repair pathways. DNA double-stranded breaks (DSBs) are repaired in cells via the error- prone non- homologous end-joining (NHEJ), or the error-free homologous recombination (HR), the most common form of homology-directed repair (HDR). The DSB repair through NHEJ creates small insertions or deletions (indels), while HDR requires a repair template, which could be a sister chromatid, another homologous region, or an exogenous repair donor. Preferably, the double-stranded breaks (DSBs) created by the Cas 12a nuclease makes deletions or insertions at a precise loci in the host cell genome. Accordingly, in some embodiments, the method of modifying a targeted polynucleotide sequence comprises homology- directed repair (HDR). In other embodiments, use of the Cas 12a complex for HDR provides an efficiency of HDR of 1, 1.5, 2. 2.5. 3, 3.5, 4, 4.5. 5, 5.5, 6, 6.5. 7, 7.5, 8, 8.5, 9. 9.5, 10 or higher-fold improvement. es non- homologous end joining (NHEJ). In certain cases, use of the Cas 12a complex for NHEJ provides an efficiency of 1, 1.5, 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10 or higher-fold improvement.
J. Methods of Use Gene Editing
[001116] In some embodiments, the Casl2a (or Cas Type V) gene editing systems described herein (including any described or contemplated format, such as a Casl2a base editor, Casl2a prime editor, or Cas 12a retron editor) are used for genome editing at a desired site. In some embodiments, the Cas 12a (or Cas Type V) systems include a DNA donor template comprising an edited sequence.
[001117] In some embodiments, the DNA donor template has 10-100 or more bp of homologous nucleic acid sequence to the genome on both sides of the desired edit. The desired edit (insertion, deletion, or mutation) is in between the homologous sequence.
[001118] In some embodiments, DNA donor template comprise a sequence comprising an intended genome edit flanked by a pair of homology arms responsible for targeting tire donor polynucleotide to the target locus to be edited in a cell. The donor polynucleotide typically comprises a 5' homology arm that hybridizes to a 5' genomic target sequence and a 3' homology arm that hybridizes to a 3' genomic target sequence. The homology arms are referred to herein as 5' and 3' (z.e., upstream and downstream) homology arms, which relate to the relative position of the homology amis to the nucleotide sequence comprising the intended edit within the donor polynucleotide. The 5' and 3' homology amis hybridize to regions within the target locus in the genomic DNA to be modified, which are referred to herein as the “5' target sequence” and ■‘3' target sequence,” respectively.
[001119] The homology arm must be sufficiently complementary for hybridization to the target sequence to mediate homologous recombination between the donor polynucleotide and genomic DNA at the target locus. For example, a homology arm may comprise a nucleotide sequence having at least about 80- 100% sequence identity to the corresponding genomic target sequence, including any percent identity within this range, such as at least 80%. 81%. 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity thereto, wherein the nucleotide sequence comprising the intended edit can be integrated into the genomic DNA by HDR at the genomic target locus recognized (z.e. , having sufficient complementary for hybridization) by the 5' and 3' homology arms.
[001120] In some embodiments, the corresponding homologous nucleotide sequences in the genomic target sequence (z.e., the ”5' target sequence” and “3' target sequence”) flank a specific site for cleavage and/or a specific site for introducing the intended edit. The distance between the specific cleavage site and the homologous nucleotide sequences (e.g., each homology arm) can be several hundred nucleotides. In some embodiments, the distance between a homology arm and the cleavage site is 200 nucleotides or less (e.g.. 0, 10, 20, 30, 50, 75, 100, 125, 150, 175, and 200 nucleotides). In most cases, a smaller distance may give rise to a higher gene targeting rate. In some embodiments, the donor polynucleotide is substantially identical to the target genomic sequence, across its entire length except for the sequence changes to be introduced to a portion of the genome that encompasses both the specific cleavage site and the portions of the genomic target sequence to be altered.
[001121] A homology arm can be of any length, e.g. 10 nucleotides or more, 15 nucleotides or more, 20 nucleotides or more, 50 nucleotides or more, 100 nucleotides or more, 250 nucleotides or more, 300 nucleotides or more, 350 nucleotides or more, 400 nucleotides or more, 450 nucleotides or more, 500 nucleotides or more, 1000 nucleotides (1 kb) or more, 5000 nucleotides (5 kb) or more. 10000 nucleotides (10 kb) or more, etc. In some instances, the 5' and 3' homology arms are substantially equal in length to one another. However, in some instances the 5' and 3' homology arms are not necessarily equal in length to one another. For example, one homology arm may be 30% shorter or less than the other homology arm, 20% shorter or less than the other homology arm, 10% shorter or less than the other homology ami, 5% shorter or less than the other homology ami, 2% shorter or less than the other homology ami, or only a few nucleotides less than the other homology ann. In other instances, the 5' and 3' homology anns are substantially different in length from one another, e.g. one may be 40% shorter or more. 50% shorter or more, sometimes 60% shorter or more, 70% shorter or more, 80% shorter or more, 90% shorter or more, or 95% shorter or more than the other homology ann.
[001122] The DNA donor template may be used in combination with an RNA-guided nuclease, which is targeted to a particular genomic sequence (z.e., genomic target sequence to be modified) by a guide RNA. A target-specific guide RNA comprises a nucleotide sequence that is complementary to a genomic target sequence, and thereby mediates binding of the nuclease-gRNA complex by hybridization at the target site. For example, the gRNA can be designed with a sequence complementary to the sequence of a minor allele to target the nuclease-gRNA complex to the site of a mutation. The mutation may comprise an insertion, a deletion, or a substitution. For example, tire mutation may include a single nucleotide variation, gene fusion, translocation, inversion, duplication, frameshift, missense, nonsense, or other mutation associated with a phenotype or disease of interest. The targeted minor allele may be a common genetic variant or a rare genetic variant. In some embodiments, the gRNA is designed to selectively bind to a minor allele with single basepair discrimination, for example, to allow binding of the nuclease-gRNA complex to a single nucleotide polymorphism (SNP). In particular, the gRNA may be designed to target disease-relevant mutations of interest for the purpose of genome editing to remove the mutation from a gene. Alternatively, the gRNA can be designed with a sequence complementary to the sequence of a major or wild-type allele to target the nuclease-gRNA complex to the allele for the purpose of genome editing to introduces a mutation into a gene in the genomic DNA of the cell, such as an insertion, deletion, or substitution. Such genetically modified cells can be used, for example, to alter phenotype, confer new properties, or produce disease models for drug screening.
[001123] In some embodiments, the Casl2a (or Cas Type V) editing systems can comprise one or more additional RNA-guided nuclease used for genome modification is a clustered regularly interspersed short palindromic repeats (CRISPR) system Cas nuclease. Any RNA-guided Cas nuclease capable of catalyzing site- directed cleavage of DNA to allow integration of donor polynucleotides by tire HDR mechanism can be used in genome editing, including CRISPR system Class 1, Type I, II, or III Cas nucleases; Class 2, Type II nuclease (such as Cas9); a Class 2, Type V nuclease (such as Cpfl). or a Class 2, Type VI nuclease (such as C2c2). Examples of Cas proteins include Cash CaslB, Cas2, Cas3, Cas4, Cas5, Cas5e (CasD), Cas6, Cas6e, Cas6f, Cas7, Cas8al, Cas8a2, Cas8b, Cas8c, Cas9 (Csnl or Csxl2), CaslO, CaslOd, CasF, CasG, CasH, Csyl, Csy2, Csy3, Csel (CasA), Cse2 (CasB), Cse3 (CasE), Cse4 (CasC), Cscl, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6. Cmrl, Cmr3, Cmr4, Cmr5, Cmr6, Csbl, Csb2, Csb3, Csxl7, Csxl4, CsxlO, Csxl6, CsaX, Csx3. Csxl, Csxl5, Csfl, Csf2, Csf3, Csf4, and Cul966, and homologs or modified versions thereof.
[001124] In some embodiments, a Class 1, type II CRISPR system Cas9 endonuclease is used. Cas9 nucleases from any species, or biologically active fragments, variants, analogs, or derivatives thereof that retain Cas9 endonuclease activity (z.e., catalyze site-directed cleavage of DNA to generate double-strand breaks) may be used to perform genome modification as described herein. The Cas9 need not be physically derived from an organism but may be synthetically or rccombinantly produced. Cas9 sequences from a number of bacterial species are well known in the art and listed in tire National Center for Biotechnology Information (NCBI) database. See, for example, NCBI entries for Cas9 from: Streptococcus pyogenes (WP 002989955, WP_038434062, WP_011528583); Campylobacter jejuni (WP_022552435, YP 002344900), Campylobacter colt (WP 060786116): Campylobacter fetus (WP 059434633); Corynebacterium ulcerans (NC_015683, NC_017317); Corynebacterium diphtheria (NC_016782, NC_016786); Enterococcus faecalis (WP 033919308); Spiroplasma syrphidicola (NC 021284); Prevotella intermedia (NC 017861); Spiroplasma taiwanense (NC 021846); Streptococcus iniae (NC 021314); Belliella baltica (NC 018010); Psychroflexus torquisl (NC O 18721); Streptococcus thermophilus (YP 820832), Streptococcus mutans (WP 061046374, WP 024786433); Listeria innocua (NP 472073); Listeria monocytogenes (WP 061665472); Legionella pneumophila (WP 062726656); Staphylococcus aureus (WP_001573634); Francisella tularensis
(WP 032729892, WP_014548420), Enterococcus faecalis (WP 033919308); Lactobacillus rhamnosus (WP 048482595, WP_032965177); and Neisseria meningitidis (WP 061704949, YP_002342100); all of which sequences (as entered by the date of filing of this application) are herein incorporated by reference in their entireties. Any of these sequences or a variant thereof comprising a sequence having at least about 70-100% sequence identity thereto, including any percent identity within this range, such as 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, can be used for genome editing, as described herein. See also Fonfara et al. (2014) Nucleic Acids Res. 42(4):2577-90; Kapitonov et al. (2015) J. Bacterid. 198(5): 797-807, Shmakov et al. (2015) Mol. Cell. 60(3):385- 397. and Chylinski et al. (2014) Nucleic Acids Res. 42( 10):6091-6105); for sequence comparisons and a discussion of genetic diversity and phylogenetic analysis of Cas9.
[001125] The genomic target site will typically comprise a nucleotide sequence that is complementary to the gRNA and may further comprise a protospacer adjacent motif (PAM). In some embodiments, the target site comprises 20-30 base pairs in addition to a 3 or more base pair PAM. Typically, the first nucleotide of a PAM can be any nucleotide, while the two or more other nucleotides will depend on the specific Cas9 protein that is chosen. Exemplary PAM sequences are known to those of skill in the art and include, without limitation, NNG, NGN. NAG, and NGG, wherein N represents any nucleotide. In some embodiments, the allele targeted by a gRNA comprises a mutation that creates a PAM within the allele, wherein the PAM promotes binding of the Cas9-gRNA complex to the allele.
[001126] In some embodiments, the gRNA is 5-50 nucleotides, 10-30 nucleotides. 15- 25 nucleotides. 18-22 nucleotides, or 19-21 nucleotides in length, or any length between the stated ranges, including, for example, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35 nucleotides in length. The guide RNA may be a single guide RNA comprising crRNA and tracrRNA sequences in a single RNA molecule, or the guide RNA may comprise two RNA molecules with crRNA and tracrRNA sequences residing in separate RNA molecules.
[001127] In another embodiment, the CRISPR nuclease from Prevotella and Francisella 1 (Cpfl, or Casl2a) is used. Cpfl is another class II CRISPR/Cas system RNA-guided nuclease with similarities to Cas9 and may be used analogously. Unlike Cas9, Cpfl does not require a tracrRNA and only depends on a crRNA in its guide RNA, which provides the advantage that shorter guide RNAs can be used with Cpfl for targeting than Cas9. Cpfl is capable of cleaving either DNA or RNA. The PAM sites recognized by Cpfl have the sequences 5'-YTN-3' (w here Y is a pyrimidine and “N" is any nucleobase) or 5'-TTN-3', in contrast to the G-rich PAM site recognized by Cas9. Cpfl cleavage of DNA produces double-stranded breaks with a sticky - ends having a 4 or 5 nucleotide overhang. For a discussion of Cpfl, see. e.g., Ledford et al. (2015) Nature. 526 (7571): 17-17, Zetsche et al. (2015) Cell. 163 (3):759-771, Murovec et al. (2017) Plant BiotechnoL J. 15(8):917-926, Zhang et al. (2017) Front. Plant Sci. 8: 177, Fernandes et al. (2016) Postepy Biochem.
62(3):315-326; herein incorporated by reference. [001128] C2cl (Casl2b) is another class II CRISPR/Cas system RNA-guided nuclease that may be used. C2cl, similarly to Cas9, depends on both a crRNA and tracrRNA for guidance to target sites. See. e.g., Shmakov et al. (2015) Mol Cell. 60(3):385-397, Zhang et al. (2017) Front Plant Sci. 8: 177; herein incorporated by reference.
[001129] In yet another embodiment, an engineered RNA-guided Fokl nuclease may be used. RNA- guided Fokl nucleases comprise fusions of inactive Cas9 (dCas9) and tire Fokl endonuclease (FokI-dCas9), wherein the dCas9 portion confers guide RNA-dependent targeting on Fokl. For a description of engineered RNA-guided Fold nucleases, see. e.g., Havlicek et al. (2017) Mol. Ther. 25(2):342-355, Pan et al. (2016) Sci Rep. 6:35794, Tsai et al. (2014) Nat Biotechnol. 32(6): 569-576; herein incorporated by reference.
[001130] In other embodiments, any other Cas enzymes and variants described in other sections of the application (all incorporated herein) can be used similarly.
[001131] In some embodiments, the RNA-guided nuclease is provided in the form of a protein, optionally where the nuclease is complexed with a gRNA to form a ribonucleoprotein (RNP) complex. In some embodiments, the RNA-guided nuclease is provided by a nucleic acid encoding the RNA-guided nuclease, such as an RNA (e.g., messenger RNA) or DNA (expression vector). In some embodiments, the RNA-guided nuclease and tire gRNA are both provided by vectors, such as the vectors and the vector system described in other parts of the application (all incorporated herein by reference). Both can be expressed by a single vector or separately on different vectors. The vectors encoding the RNA-guided nuclease and gRNA may be included in the vector system comprising the Casl2a editing system msr gene, msd gene and ret gene sequences. In some embodiments, the RNA-guided nuclease is fused to the RT and/or the msDNA.
[001132] The RNP complex may be administered to a subject or delivered into a cell by methods known in the art, such as those described in U.S. Pat. No. 11,390,884, which is incorporated by reference herein in its entirety. In some embodiments, the endonuclease/gRNA ribonucleoprotein (RNP) complexes are delivered to cells by electroporation. Direct delivery of the RNP complex to a subject or cell eliminates the need for expression from nucleic acids (e.g., transfection of plasmids encoding Cas9 and gRNA). It also eliminates unwanted integration of DNA segments derived from nucleic acid delivery (e.g., transfection of plasmids encoding Cas9 and gRNA). An endonuclease/gRNA ribonucleoprotein (RNP) complex usually is formed prior to administration.
[001133] Codon usage may be optimized to further improve production of an RNA-guided nuclease and/or reverse transcriptase (RT) in a particular cell or organism. For example, a nucleic acid encoding an RNA-guided nuclease or reverse transcriptase can be modified to substitute codons having a higher frequency of usage in a yeast cell, a bacterial cell, a human cell, a non-human cell, a mammalian cell, a rodent cell, a mouse cell, a rat cell, or any other host cell of interest, as compared to the naturally occurring polynucleotide sequence. When a nucleic acid encoding the RNA-guided nuclease or reverse transcriptase is introduced into cells, the protein can be transiently, conditionally, or constitutively expressed in the cell.
[001134] In some embodiments, the Casl2a editing system used for genome editing with nuclease genome editing systems can further include accessory' or enhancer proteins for recombination. Examples of recombination enhancers can include nonhomologous end joining (NHEJ) inhibitors (e g., inhibitor of DNA ligase IV. a KU inhibitor (e g., KU70 or KU80), a DNA-PKc inhibitor, or an artemis inhibitor) and homologous directed repair (HDR) promoters, or both, that can enhance or improve more precise genome editing and/or the efficiency of homologous recombination. In some embodiments, the recombination accessory' or enhancers can comprise C-terminal binding protein interacting protein (CtIP), cyclinB2, Rad family members (e.g. Rad50, Rad51, Rad52, etc).
[001135] CtIP is a transcription factor containing C2H2 zinc fingers that are involved in early steps of homologous recombination. Mammalian CtIP and its orthologs in other eukaryotes promote the resection of DNA double-strand breaks and are essential for meiotic recombination. HDR may be enhanced by using Cas9 nuclease associated (e.g. fused) to an N-terminal domain of CtIP, an approach that forces CtIP to the cleavage site and increases transgene integration by HDR. In some embodiments, an N-terminal fragment of CtIP, called HE for HDR enhancer, may be sufficient for HDR stimulation and requires the CtIP multimerization domain and CDK phosphory lation sites to be active. HDR stimulation by the Cas9-HE fusion depends on the guide RNA used, and therefore the guide RNA will be designed accordingly.
[001136] Using the gene editing system described herein, any target gene or sequence in a host cell can be edited or modified for a desired trait, including but not limited to: Myostatin (e.g, GDF8) to increase muscle growth; Pc POLEED to induce hairlessness; KISS 1R to induce bore taint; Dead end protein (dnd) to induce sterility; Nano2 and DDX to induce sterility; CD163 to induce PRRSV resistance; REEA to induce ASFV resilience; CD 18 to induce Mannheimia (Pasteurella) haemolytica resilience; NRAMP1 to induce tuberculosis resilience; Negative regulators of muscle mass (e.g., Myostatin) to increase muscle mass.
Epigenetic editing
[001137] In some embodiments, the Casl2a (or Cas Type V) gene editing systems described herein when including an epigenetic modifier domain can be used for genome editing at a desired site. Epigenetic modifications of DNA and histones are known for their multifaceted contributions to transcriptional regulation. As these modifications are faithfully propagated throughout DNA replication, they are considered central players in cellular memory of transcriptional states. Many efforts in the last decade have generated a vast understanding of individual epigenetic modifications and their contribution to transcriptional regulation. Epigenetic editing offers powerfill tools to selectively induce epigenetic changes in a genome without altering the sequence of a nucleotide sequence as a means to regulate gene activity. The foundation of epigenetic editing is formed by the ability to generate fusion proteins of epigenetic enzymes or their catalytic domains with programmable DNA-binding platforms such as the clustered regularly interspaced short palindromic repeat (e.g., CRISPR Cas9 or Casl2a) to target these to an endogenous locus of choice. Hie enzymatic fusion protein then dictates tire initial deposited modification while subsequent cross-talk within the local chromatin environment likely influences epigenetic and transcriptional output.
[001138] Accordingly, in one aspect, the disclosure provides an epigenetic gene editing system comprising one or more epigenetic enzymes or their catalytic domains combined with a Casl2a programmable nuclease, and an appropriate guide RNA for guiding the Cas 12a to a particular target site. In some embodiments, the Cas 12a may be fused to the epigenetic enzyme or a catalytic domain thereof. In other embodiments, the Cas 12a and the epigenetic enzyme or catalytic domain thereof are not fused but may be co-delivered. In the latter embodiment, the epigenetic enzyme or catalytic domain there may include at targeting moiety to cause it to be co-localized with the Cas 12a at the target site defined by the guide RNA.
[001139] Epigenetic enzymes include, but are not limited to DNA methyltransferases, histone methyltransferases, and histone deacetylases. In other embodiments, the epigenetic enzyme is histone deacetylase, histone deacetylase, histone methyl transferase, histone demethylase, DNA methyl transferase, DNA demethylase, DNA ligase, other ligases, ubiquitinase, ubiquitin ligase, phosphatase, or a phosphokinase.
[001140] In some embodiments, the DNA donor template has 10-100 or more bp of homologous nucleic acid sequence to the genome on both sides of the desired edit. The desired edit (insertion, deletion, or mutation) is in between the homologous sequence.
[001141] In still other embodiments, the LNPs may be used to deliver an epigenetic editing system. Epigenetic editors are generally composed of an epigenetic enzyme or their catalytic domain fused with a user-programmable DNA-binding protein, such as CRISPR Cas 12a. The user-programmable DNA-binding protein (plus a guide RNA in the case of a nucleic acid programmable DNA binding protein) guides the epigenetic enzy me (e.g., a DNA methyltransferase or DNMT) to a specific site (e.g., a CpG island in a promoter region of a gene) in order to induce a change in promoter activity.
[001142] Epigenetic modifications of DNA and histones are known for their multifaceted contributions to transcriptional regulation. As these modifications are faithfully propagated throughout DNA replication, they are considered central players in cellular memory of transcriptional states. Many efforts in tire last decade have generated a vast understanding of individual epigenetic modifications and their contribution to transcriptional regulation. Epigenetic editing offers powerful tools to selectively induce epigenetic changes in a genome without altering the sequence of a nucleotide sequence as a means to regulate gene activity. The foundation of epigenetic editing is formed by the ability to generate fusion proteins of epigenetic enzymes or their catalytic domains with programmable DNA-binding platforms such as the clustered regularly interspaced short palindromic repeat (e.g., CRISPR Cas9 or Casl2a) to target these to an endogenous locus of choice. The enzymatic fusion protein then dictates the initial deposited modification while subsequent crosstalk within the local chromatin environment likely influences epigenetic and transcriptional output.
[001143] The following published literature discussing epigenetic editing is incorporated herein by reference each in their entireties.
[001144] Gjaltema RAF. Rots MG. Advances of epigenetic editing. Curr Opin Chem Biol. 2020 Aug;57:75-81. doi: 10.1016/j.cbpa.2020.04.020. Epub 2020 Jun 30. PMID: 32619853. htps://www.sciencedirect.com/science/article/pii/S136759312030Q6367via%3Dihub
[001145] Kleinstiver BP, Sousa A A, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Homg JE, Malagon-Lopez J, Scarf'd I, Maus MV, Pinello L, Aryee MJ, Joung JK. Engineered CRISPR-Casl2a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nat Biotechnol.
2019 Mar;37(3):276-282. doi: 10.1038/s41587-018-0011-0. Epub 2019 Feb 11. Erratum in: Nat Biotechnol.
2020 Jul;38(7):901. PMID: 30742127; PMCID: PMC6401248. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6401248/
[001146] Rots MG, Jeltsch A. Editing the Epigenome: Ovendew, Open Questions, and Directions of Future Development. Methods Mol Biol. 2018;1767:3-18. doi: 10.1007/978-1-4939-7774-1 1. PMID: 29524127.
[001147] Liu XS, Jaenisch R. Editing the Epigenome to Tackle Brain Disorders. Trends Neurosci. 2019 Dec;42(12):861-870. doi: 10. 1016/j.tins.2019.10.003. Epub 2019 Nov 7. PMID: 31706628.
[001148] Waryah CB, Moses C, Arooj M, Blancafort P. Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing. Methods Mol Biol. 2018;1767: 19-63. doi: 10.1007/978-1- 4939-7774-1 2. PMID: 29524128.
[001149] Xu X, Hulshoff MS, Tan X, Zeisberg M, Zeisberg EM. CRISPR/Cas Derivatives as Novel Gene Modulating Tools: Possibilities and In Vivo Applications. Int J Mol Sci. 2020 Apr 25;21(9):3038. doi: 10.3390/ijms21093038. PMID: 32344896; PMCID: PMC7246536. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246536/ [001150] In addition, the following published patent literature relating to epigenetic editing is incorporated herein by reference each in their entireties.
Diseases and Disorders
[001151] Provided herein are methods of treating a disease or disorder, tire methods comprising administering to a subject in need thereof a pharmaceutical composition of the present disclosure. In various embodiments of the invention, target genome or epigenetic modifications include cells with monogenic diseases or disorders. Various monogenic diseases include but are not limited to: Adenosine Deaminase (ADA) Deficiency; Alpha- 1 Antitrypsin Deficiency; Cystic Fibrosis; Duchenne Muscular Dystrophy; Galactosemia; Hemochromatosis: Huntington’s Disease; Maple Syrup Urine Disease; Marfan Syndrome: Neurofibromatosis Type 1 ; Pachyonychia Congenita: Phenylkeotnuria; Severe Combined Immunodeficiency; Sickle Cell Disease: Smith-Lemli-Opitz Syndrome; Tay-Sachs Disease: hereditary tyrosinemia I; Influenza; SARS-CoV-2; Alzheimer’s disease; Parkinson’s disease.
[001152] Target sequences related to certain diseases and disorders are known in some cases. Target sequences or target editing sites include disease-associated or causative mutations for one or more of 10,000 monogenic disorders. A list of target sequences can be generated based on the monogenic disorders. Common genetic disorders that may be correctable by the Cast 2a (or Cas Type V) gene editing systems described here including but are not limited to: Adenosine Deaminase (ADA) Deficiency; Alpha- 1 Antitrypsin Deficiency; Cystic Fibrosis: Duchenne Muscular Dystrophy; Galactosemia: Hemochromatosis; Huntington’s Disease; Maple Syrup Urine Disease; Marfan Syndrome: Neurofibromatosis Type 1; Pachyonychia Congenita; Phenylkeotnuria; Severe Combined Immunodeficiency; Sickle Cell Disease; Smith-Lemli-Opitz Syndrome; and Tay-Sachs Disease. In other embodiments, the disease-associated gene can be associated with a polygenic disorder selected from the group consisting of: heart disease; high blood pressure; Alzheimer’s disease; arthritis; diabetes; cancer; and obesity.
[001153] The Casl2a (or Cas Type V) gene editing systems disclosed herein may also be used to treat the following genetic disorders by editing a defect in the disease-associated gene, as follows:
Genetic disease Disease gene
Arenoleukodystrophy (ALD) ABCD1
Agammaglobulinemia non-Bruton type IGHM
Alport syndrome COL4A5
Amyloid neuropathy - Andrade disease TTR
Angioneurotic oedema C INH
Alphal -antitrypsin deficiency SERPINEA 1
Bartter syndrome type 4 BSND
Blcpharophimosis - ptosis - epicanthus inversus syndrome (BEPS) FOXL2
Brugada sindrome - Long QT syndrome-3 SCN5A
Bruton agammaglobulinemia tyrosine kinase BTK
Ceroid lipofuscinosis neuronal type 2 CLN2
Charcot Marie Tooth type 1A (CMT1A) PMP22
Charcot Marie Tooth type X (CMTX) CMTX
Chronic granulomatous disease (CGD) CYBB
Cystic Fibrosis (CF) CFTR
Congenital adrenal hyperplasia (CAH) CYP21A2
Congenital disorder of glycosylation type la (CDG la) PMM2
Congenital fibrosis of extraocular muscles 1 (CFE0M1) KIF21A
Crigler-Najjar syndrome UGT1A1
Deafness, autosomal recessive CX26
Diamond-Blackfan anemia (DBA) RPS 19
Duchenne-Becker muscular dystrophy (DMD/DMB) DMD
Duncan disease - X-linked lymphoproliferative syndrome (XLPD) SH2D1A
Ectrodactyly ectodermal dysplasia and cleft lip/palate syndrome p63 Genetic disease Disease gene
(EEC)
Epidermolysis bullosa dystrophica/pruriginosa C0L7A1
Exostoses multiple type I (EXT1) EXT1
Exostoses multiple type II (EXT2) EXT2
Facioscapulohumeral muscular dystrophy FRG1
Factor VII deficiency F7
Familial Mediterranean Fever (FMF) MEFV
Fanconi anemia A FANCA
Fanconi anemia G FANCG
Fragile-X FRAXA
Gangliosidosis (GM1) GLB1
Gaucher disease (GD) GBA
Glanzmann thrombasthenia ITGA2B
Glucose-6-phosphate dehydrogenase deficiency G6PD
Glutaric acidemia I GCDH
Haemophilia A F8
Haemophilia B F9
Hand-foot-uterus syndrome H0XD13
Hemophagocytic lymphohistiocytosis familial, type 2 (FHL2) PR F l
Hypomagnesaemia primary CLDN16
HYPOPHOSPHATASIA ALPL
Holt-Oram Sindrome (HOS) TBX5
Homocystinuria MTHFR
Incontinentia pigmenti NEMO
Lesch-Nyhan syndrome HPRT
Limb-girdle muscular dystrophy type 2C (LGMD2C) SGCG
Long QT syndrome- 1 KCNQ1
Mannosidosis Alpha MAN2B1 Genetic disease Disease gene
Marfan syndrome FBN1
Methacrylic Aciduria, deficiency of beta-hydroxyisobutyryl-CoA HIBCH deacylase
Mevalonic aciduria MVK
Myotonic dystrophy (DM) DMPK
Myotonic dystrophy type 2 (DM2) ZNF9
Mucopolysaccharidosis Type I - Hurler syndrome IDUA
Mucopolysaccharidosis Type IIIA - Sanfilippo sindrome A SGSH (MPS3A)
Mucopolysaccharidosis Type IIIB - Sanfilippo sindrome B
NAGLU (MPS3B)
Mucopolysaccharidosis Type VI (MPS VI) - Maroteaux-Lamy
ARSB
Syndrome
Neuronal ceroid lipofuscinosis 1 - Batten's disease (CLN1) PPT1
Niemann-Pick disease SMPD1
Noonan sindrome PTPN11
Pancreatitis, hereditary (PCTT) PRSS1
Paramyotonia congenita (PMC) SCN4A
Phenylketonuria PAH
Polycystic kidney disease type 1 (PKD1) PKD1
Polycystic kidney disease type 2 (PKD2) PKD2
Polycystic kidney and hepatic disease- 1 (ARPKD) PKHD1
Schwartz-Jampel/Stuve-Wiedemann syndrome LIFR
Sickle cell anemia HBB
Synpolydactyly (SPD1) H0XA13
Smith-Lemli-Opitz syndrome DHCR7
Spastic paraplegia type 3 SPG3A
Spinal Muscular Atrophy (SMA) SMN
Spinocerebellar ataxia 3 (SCA3) ATXN3
Spinocerebellar ataxia 7 (SCA7) ATXN7 Genetic disease Disease gene
Stargardt disease ABCA4
Tay Sachs (TSD) HEXA
Thalassemia-a mental retardation syndrome ATRX
Thalassemia-p HBB
Torsion dystonia, early onset (EOTD) DYT1
Tyrosinacmia type 1 FAH
Tuberosclerosis 1 TSC1
Tuberosclerosis 2 TSC2
Wiskott-Aldrich Sindrome (WAS) WAS
[001154] In addition, tire Cas 12a gene editing systems disclosed herein may also be used to treat the following genetic disorders by editing a defect in the disease-associated gene, or in more than one gene associated with a particular disorders, as follows:
[001155] Accordingly, to treat one or more such diseases or disorders, in various aspects of the invention, one or more targeted polynucleotide sequence related to certain diseases and disorders, e.g., a genetic mutation, is contacted by a Cast 2a gene editing system disclosed herein; and a guide RNA, wherein the guide RNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
[001156] In some embodiments, the guide RNA directs the Casl2a polypeptide to the target site or the targeted polynucleotide sequence; and optionally forms a ribonucleoprotein complex with the polypeptide and the guide RNA.
[001157] Additional therapeutic applications for the Cas 12a genome editing systems disclosed herein include base editing, prime editing, gene insertions and/or deletions.
[001158] Diagnostic applications forthe Casl2a genome editing system include probes, diagnostics, theranostics.
[001159] The Casl2a editing system comprising the heterologous nucleic acid sequence can be used in a variety of applications, several non-limiting examples of which are described herein. In general, the Cas 12a editing system can be used in any suitable organism. In some embodiments, the organism is a eukaryote. [001160] In some embodiments, the organism is an animal. In some embodiments, the animal is a fish, an amphibian, a reptile, a mammal, or a bird. In some embodiments, the animal is a farm animal or agriculture animal. Non-limiting examples of farm and agriculture animals include horses, goats, sheep, swine, cattle, llamas, alpacas, and birds, e.g., chickens, turkeys, ducks, and geese. In some embodiments, the animal is a non-human primate, e g., baboons, capuchin monkeys, chimpanzees, lemurs, macaques, marmosets, tamarins, spider monkeys, squirrel monkeys, and vervet monkeys. In some embodiments, the animal is a pet. Non-limiting examples of pets include dogs, cats, horses, rabbits, ferrets, gerbils, hamsters, chinchillas, fancy rats, guinea pigs, canaries, parakeets, and parrots.
[001161] In some embodiments, the organism is a plant. Plants that may be transfected with an Casl2a editing system include monocots and dicots. Particular examples include, but are not limited to, com (maize), sorghum, wheat, sunflower, potato, cotton, rice, soybean, sugarbeet, sugarcane, tobacco, barley, and oilseed rape, Brassica sp.. alfalfa, rye. millet, safflower, peanuts, sweet potato, cassava, coffee, coconut, pineapple, citrus trees, cocoa, tea. banana, avocado, fig. guava, mango, olive, papaya, cashew, macadamia, almond, oats, vegetables, ornamentals, and conifers. Vegetables include, but are not limited to. crucifers, peppers, tomatoes, lettuce, green beans, lima beans, peas, and members of the genus Cucumis such as cucumber, cantaloupe, and musk melon. Ornamentals include, but are not limited to, azalea, hydrangea, hibiscus, roses, tulips, daffodils, petunias, carnation, poinsettia, and chrysanthemum.
[001162] In some embodiments, heterologous nucleic acid sequences can be added to the subject Cast 2a editing system to provide a cell with a heterologous nucleic acid encoding a protein or regulatory RNA of interest, a cellular barcode, a donor polynucleotide suitable for use in gene editing, e g., by homology directed repair (HDR) or recombination-mediated genetic engineering (recombineering), or a CRISPR protospacer DNA sequence for use in molecular recording, as discussed further below. In embodiments relating to Casl2a retron-based gene editing systems, uch heterologous sequences may be inserted, for example, into the msr locus or the msd locus such that the heterologous sequence is transcribed by the retron reverse transcriptase as part of the msDNA product.
[001163] In some embodiments, the Casl2a editing systems described herein may be used for research tools, such as kits, functional genomics assays, and generating engineered cell lines and animal models for research and drug screening. The kit may comprise one or more reagents in addition to the Cast 2a editing system, such as a buffer, a control reagent, a control vector, a control RNA polynucleotide, a reagent for in vitro production of the polypeptide from DNA, and adaptors for sequencing. A buffer can be, for example, a stabilization buffer, a reconstituting buffer, a diluting buffer, a wash buffer, or a buffer for introducing a polypeptide and/or polynucleotide of the kit into a cell. In some instances, a kit can comprise one or more additional reagents specific for plants. One or more additional reagents for plants can include, for example, soil, nutrients, plants, seeds, spores, Agrobacterium, a T-DNA vector, and a pBINAR vector.
Production of Protein or RNA
[001164] In some embodiments, the Casl2a (Cas Type V) gene editing systems may comprise one or more additional proteins (e.g., an accessory protein, such as a recombinase) or RNA molecules (e.g., a donor template), or a nucleotide sequence encoding die one or more additional proteins or RNA molecules.
[001165] In some embodiments, Casl2a gene editing systems may comprise a nucleic acid molecule encoding a polypeptide of interest. Hie polypeptide of interest may be any type of protein/peptide including, without limitation, an enzyme, an extracellular matrix protein, a receptor, transporter, ion channel, or other membrane protein, a hormone, a neuropeptide, an antibody, or a cytoskeletal protein, a functional fragment thereof, or a biologically active domain of interest. In some embodiments, the protein is a therapeutic protein, therapeutic antibody for use in treatment of a disease, or a template to fix a mutation or mutated exon in the genome. In other embodiments, the polypeptide of interest is a gene editing accessory' protein, e.g., recombinases, invertases, nucleases, polymerases, ligases, deaminases, reverse transcriptases, or epigenetic modifying functions. The polypeptide of interest, e.g., recombinases, invertases, nucleases, polymerases, ligases, deaminases, reverse transcriptases, or epigenetic modifying functions, could be fused to the Cas 12a gene editing system or a component thereof (e.g., fused to the Casl2a nuclease).
[001166] In other embodiments, the Cas 12a gene editing system could also be engineered to include a DNA template.
[001167] In still other embodiments, the Casl2a gene editing system could also include a least one additional nucleic acid molecule for modulating a target in the cell, e.g., without limitation, a RNA interference (RNAi) nucleic acid or regulatory' RNA such as, but not limited to, a microRNA (miRNA), a small interfering RNA (siRNA), a short hairpin RNA (shRNA), a small nuclear RNA (snRNA), a long noncoding RNA (IncRNA), an antisense nucleic acid, and the like.
Recombineering
[001168] Recombineering (recombination-mediated genetic engineering) can be used in modifying chromosomal as well as episomal replicons in cells, for example, to create gene replacements, gene knockouts, deletions, insertions, inversions, or point mutations. Recombineering can also be used to modify a plasmid or bacterial artificial chromosome (BAC), for example, to clone a gene or insert markers or tags.
[001169] The Cas 12a (Cas Type V) editing systems described herein can be used in recombineering applications to provide linear single-stranded or double-stranded DNA for recombination. Homologous recombination may be mediated by bacteriophage proteins such as RecE/RecT from Rac prophage or Redobd from bacteriophage lambda. The linear DNA should have sufficient homology at the 5' and 3' ends to a target DNA molecule present in a cell (e.g., plasmid, BAC, or chromosome) to allow recombination.
[001170] The linear double-stranded or single -stranded DNA molecule used in recombineering (i.e. donor polynucleotide) comprises a sequence having the intended edit to be inserted flanked by two homology arms that target tire linear DNA molecule to a target site for homologous recombination. Homology anns for recombineering typically range in length from 13-300 nucleotides, or 20 to 200 nucleotides, including any length within this range such as 13. 14, 15, 16, 17, 18, 19, 20. 22. 24. 26, 28, 30, 32, 34, 36, 38. 40. 42. 44, 46, 48, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, or 200 nucleotides in length. In some embodiments, a homology arm is at least 15, at least 20, at least 30, at least 40, or at least 50 or more nucleotides in length. Homology anns ranging from 40-50 nucleotides in length generally have sufficient targeting efficiency for recombination; however, longer homology anns ranging from 150 to 200 bases or more may further improve targeting efficiency. In some embodiments, the 5' homology arm and the 3' homology ann differ in length. For example, the linear DNA may have about 50 bases at the 5' end and about 20 bases at the 3' end with homology to the region to be targeted.
[001171] The bacteriophage homologous recombination proteins can be provided to a cell as proteins or by one or more vectors encoding the recombination proteins, such as tire vector or vector system. In some embodiments, one or more vectors encoding the bacteriophage recombination proteins arc included in the vector system comprising the Casl2a editing system msr gene, msd gene, and/or ret gene sequences. Additionally, a number of bacterial strains containing prophage recombination systems are available for recombineering, including, without limitation, DY380, containing a defective 1 prophage with recombination proteins exo, bet, and gam; EL250, derived from DY380, which in addition to the recombination genes found in DY380, also contains a tightly controlled arabinose-inducible flpe gene (flpe mediates recombination between two identical frt sites); EL350, also derived from DY380, which in addition to the recombination genes found in DY380, also contains a tightly controlled arabinose-inducible ere gene (ere mediates recombination between two identical loxP sites; SW102, derived from DY380, which is designed for BAC recombineering using a galK positive/negative selection; SW105, derived from EL250, which can also be used for galK positive/negative selection, but like EL250, contain an ara-inducible Flpe gene; and SW106, derived from EL350, which can be used for galK positive/negative selection, but like EL350, contains an ara- inducible Cre gene. Recombineering can be carried out by transfecting bacterial cells of such strains with an Cast 2a editing system comprising a heterologous sequence encoding a linear DNA suitable for recombineering. For a discussion of recombineering systems and protocols, see, e.g., Sharan etal. (2009) Nat Protoc. 4(2): 206-223, Zhang et al. (1998) Nature Genetics 20: 123-128, Muyrers et al. (1999) Nucleic Acids Res. 27: 1555-1557, Yu et al. (2000) Proc. Natl. Acad. Sci U.S.A. 97 (11):5978-5983; herein incorporated by reference.
Molecular Recording
[001172] In some embodiments, the Casl2a (Cas Type V) editing system comprises a synthetic CRISPR protospacer DNA sequence to allow molecular recording. Hie endogenous CRISPR Casl-Cas2 system is normally utilized by bacteria and archaea to keep track of foreign DNA sequences originating from viral infections by storing short sequences (z.e., protospacers) that confer sequence-specific resistance to invading viral nucleic acids within genome-based arrays. These arrays not only preserve the spacer sequences but also record the order in which the sequences are acquired, generating a temporal record of acquisition events.
[001173] This system can be adapted to record arbitrary' DNA sequences into a genomic CRISPR array in the form of “synthetic protospacers” that are introduced into cells using Cas 12a editing systems. Cas 12a editing systems carrying the protospacer sequences can be used for integration of synthetic CRISPR protospacer sequences at a specific genomic locus by utilizing the CRISPR system Casl-Cas2 complex. Molecular recording can be used to keep track of certain biological events by producing a stable genetic memory tracking code. See, e.g, Shipman et al. (2016) Science 353(6298): aafl 175 and International Patent Application Publication No. WO/2018/191525; herein incorporated by reference in their entireties.
[001174] In some embodiments, the CRISPR-Cas system is harnessed to record specific and arbitrary' DNA sequences into a bacterial genome. Tire DNA sequences can be produced by an Casl2a editing system within tire cell. For example, the Cas 12a editing system can be used to produce the protospacers within the cell, which are inserted into a CRISPR array within the cell. The cell may be modified to include one or more engineered returns (or vector systems encoding them) that can produce one or more synthetic protospacers in the cell, wherein the synthetic protospacers are added to the CRISPR array. A record of defined sequences, recorded over many days, and in multiple modalities can be generated.
[001175] In some embodiments, the Casl2a editing system comprises an msd protospacer nucleic acid region or an msr protospacer nucleic acid region. In the case of a msr protospacer nucleic acid region, the protospacer sequence is first incorporated into the msr RNA, which is reverse transcribed into protospacer DNA. Double stranded protospacer DNA is produced when two complementary protospacer DNA sequences having complementary sequences hybridize, or when a double -stranded structure (such as a hairpin) is formed in a single stranded protospacer DNA (e.g., a single msDNA can form an appropriate hairpin structure to provide the double stranded DNA protospacer).
[001176] In some embodiments, a single stranded DNA produced in vivo from a first Casl2a editing system may be hybridized with a complementary single-stranded DNA produced in vivo from the same retron or a second Casl2a editing system or may form a hairpin structure and then used as a protospacer sequence to be inserted into a CRISPR array as a spacer sequence. Tire Casl2a editing system(s) should provide sufficient levels of the protospacer sequence within a cell for incorporation into the CRISPR array. Hie use of protospacers generated within the cell extends the in vivo molecular recording system from only capturing information known to a user, to capturing biological or environmental information that may be previously unknown to a user. For example, an msDNA protospacer sequence in an Casl2a editing system construct may be driven by a promoter that is downstream of a sensor pathway for a biological phenomenon or environmental toxin. The capture and storage of the protospacer sequence in the CRISPR array records the event. If multiple msDNA protospacers are driven by different promoters, the activity of those promoters is recorded (along with anything that may be upstream of the promoters) as well as the relative order of promoter activity (based on the relative position of spacer sequences in the CRISPR array). At any point after the recording has taken place, the CRISPR array may be sequenced to determine whether a given biological or environmental event has taken place and the order of multiple events, given by tire presence and relative position of msDNA-derived spacers in the CRISPR array.
[001177] In some embodiments, the synthetic protospaccr further comprises an AAG PAM sequence at its 5' end. Protospacers including the 5' AAG PAM are acquired by the CRISPR array with greater efficiency than those that do not include a PAM sequence.
[001178] In some embodiments, Casl and Cas2 are provided by a vector that expresses the Casl and Cas2 at a level sufficient to allow the synthetic protospacer sequences produced by Casl2a editing systems to be acquired by a CRISPR array in a cell. Such a vector system can be used to allow molecular recording in a cell that lacks endogenous Cas proteins.
Therapeutic Applications
[001179] Also provided herein are methods of diagnosing, prognosing, treating, and/or preventing a disease, state, or condition in or of a subject, using the Cas 12a (Cas Type V) editing system of the invention.
[001180] Generally, the methods of diagnosing, prognosing, treating, and/or preventing a disease, state, or condition in or of a subject can include modifying a polynucleotide in a subject or cell thereof using a composition, system, or component thereof of the Casl2a editing system as described herein, and/or include detecting a diseased or healthy polynucleotide in a subject or cell thereof using a composition, system, or component thereof of the Casl2a editing system as described herein.
[001181] In some embodiments, the method of treatment or prevention can include using a composition, system, or component of the Casl2a editing system to modify a polynucleotide of an infectious organism (e.g. bacterial or vims) within a subject or cell thereof.
[001182] In some embodiments, the method of treatment or prevention can include using a composition, system, or component of the Casl2a editing system to modify a polynucleotide of an infectious organism or symbiotic organism within a subject.
[001183] In some embodiments, the composition, system, and components of the Casl2a editing system can be used to develop models of diseases, states, or conditions.
[001184] In some embodiments, the composition, system, and components of the Casl2a editing system can be used to detect a disease state or correction thereof, such as by a method of treatment or prevention described herein.
[001185] In some embodiments, the composition, system, and components of the Casl2a editing system can be used to screen and select cells that can be used, for example, as treatments or preventions described herein.
[001186] In some embodiments, the composition, system, and components thereof can be used to develop biologically active agents that can be used to modify one or more biologic functions or activities in a subject or a cell thereof.
[001187] In general, the method can include delivering a composition, system, and/or component of the Casl2a editing system to a subject or cell thereof, or to an infectious or symbiotic organism by a suitable delivery' technique and/or composition. Once administered, the components can operate as described elsewhere herein to elicit a nucleic acid modification event. In some embodiments, the nucleic acid modification event can occur at the genomic, epigenomic, and/or transcriptomic level. DNA and/or RNA cleavage, gene activation, and/or gene deactivation can occur.
[001188] The composition, system, and components of the Cast 2a editing system as described elsewhere herein can be used to treat and/or prevent a disease, such as a genetic and/or epigenetic disease, in a subject; to treat and/or prevent genetic infectious diseases in a subject, such as bacterial infections, viral infections, fungal infections, parasite infections, and combinations thereof; to modify the composition or profile of a microbiome in a subject, which can in turn modify the health status of the subject; to modify cells ex vivo, which can then be administered to the subject whereby the modified cells can treat or prevent a disease or symptom thereof: or to treat mitochondrial diseases, where the mitochondrial disease etiology involves a mutation in the mitochondrial DNA.
[001189] Also provided is a method of treating a subject, e.g, a subject in need thereof, comprising inducing gene editing by transforming the subject with the polynucleotide encoding one or more components of tire composition, system, or complex or any of polynucleotides or vectors described herein of the Casl2a editing system, and administering them to the subject.
[001190] Also provided is a method of treating a subject, e.g, a subject in need thereof, comprising inducing transcriptional activation or repression of multiple target gene loci by transforming the subject with the polynucleotides or vectors described herein, wherein said polynucleotide or vector encodes or comprises one or more components of composition, system, complex or component of the Cast 2a editing system, and comprising multiple Cas effectors.
[001191] Also provided is a method of treating a subject, e.g., a subject in need thereof, comprising inducing gene editing by transforming the subject with the Cas effector(s), and encoding and expressing in vivo the remaining portions of the composition, system, (e.g. , RNA, guides), complex or component of the Casl2a editing system. A suitable repair template may also be provided by the Casl2a editing system as described herein elsewhere.
[001192] Also provided is a method of treating a subject, e.g, a subject in need thereof, comprising inducing transcriptional activation or repression by transfonning the subject with the systems or compositions herein.
[001193] Also provided is a method of inducing one or more polynucleotide modifications in a eukaryotic or prokaryotic cell or component thereof (e.g. a mitochondria) of a subject, infectious organism, and/or organism of the microbiome of the subject. The modification can include the introduction, deletion, or substitution of one or more nucleotides at a target sequence of a polynucleotide of one or more cell(s). The modification can occur in vitro, ex vivo, in situ, or in vivo.
[001194] In some embodiments, the method of treating or inhibiting a condition or a disease caused by one or more mutations in a genomic locus in a eukary otic organism or a non-human organism can include manipulation of a target sequence within a coding, non-coding or regulatory element of said genomic locus in a target sequence in a subject or a non-human subject in need thereof comprising modifying tire subject or a non -human subject by manipulation of the target sequence and wherein the condition or disease is susceptible to treatment or inhibition by manipulation of the target sequence including providing treatment comprising delivering a composition comprising the particle delivery system or the delivery system or the virus particle of any one of the above embodiment or the cell of any one of the above embodiment.
[001195] Also provided herein is the use of any of the above delivery systems, e.g., LNP delivery system in ex vivo or in vivo gene or genome editing; or for use in in vitro, ex vivo or in vivo gene editing.
[001196] Also provided herein are particle delivery systems, non-viral delivery systems, and/or the virus particle of any one of the above embodiments or the cell of any one of the above embodiments used in the manufacture of a medicament for in vitro, ex vivo or in vivo gene or genome editing or for use in in vitro, ex vivo or in vivo gene therapy or for use in a method of modifying an organism or a non-human organism by manipulation of a target sequence in a genomic locus associated with a disease or in a method of treating or inhibiting a condition or disease caused by one or more mutations in a genomic locus in a eukaryotic organism or a non- human organism.
[001197] In some embodiments, target polynucleotide modification using the subject Casl2a editing system and the associated compositions, vectors, systems and methods comprise addition, deletion, or substitution of 1 nucleotide to about 10,000 nucleotides at each target sequence of said polynucleotide of said cell(s). Tire modification can include the addition, deletion, or substitution of at least 1, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20. 21, 22, 23, 24, 25, 26, 27, 28, 29. 30, 35, 40, 45, 50, 75, 100, 200, 250, 300, 500, 1000. 1500. 2000. 2500, 3000, 3500, 4000, 5000, 6000. 7000. 8000, 9000, 10,000 or more nucleotides at each target sequence.
[001198] In some embodiments, formation of system or complex results in cleavage, nicking, and/or another modification of one or both strands in or near (e.g. within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or more base pairs from) the target sequence.
[001199] In some embodiments, a method of modifying a target polynucleotide in a cell to treat or prevent a disease can include allowing a composition, system, or component of the subject Casl2a editing system to bind to the target polynucleotide, e.g., to effect cleavage, nicking, or other modification as the composition, system, is capable of said target polynucleotide, thereby modifying the target polynucleotide, wherein the composition, system, or component thereof, complex with a guide sequence, and hybridize said guide sequence to a target sequence within the target polynucleotide, wherein said guide sequence is optionally linked to atracr mate sequence, which in turn can hybridize to atracr sequence. In some embodiments, modification can include cleaving or nicking one or two strands at the location of the target sequence by one or more components of the composition, system, or component thereof. [001200] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat diseases of the circulatory system. In some embodiments, the treatment can be carried out by using an AAV or a lentiviral vector to deliver the Cas 12a editing system, composition, system, and/or vector described herein to modify hematopoietic stem cells (HSCs) or iPSCs in vivo or ex vivo. In some embodiments, the treatment can be carried out by correcting HSCs or iPSCs as to the disease using a composition, system, herein or a component thereof, wherein the composition, system, optionally includes a suitable HDR repair template (e.g., a template in the msDNA of the Cas 12a editing system).
[001201] In some embodiments, the treatment or prevention for treating a circulatory system or blood disease can include modifying a human cord blood cell. In some embodiments, the treatment or prevention for treating a circulatory system or blood disease can include modifying a granulocy te colony-stimulating factor-mobilized peripheral blood cell (mPB) with any modification described herein. In some embodiments, the human cord blood cell or mPB can be CD34+. In some embodiments, the cord blood cells or mPB cells modified are autologous. In some embodiments, the cord blood cells or mPB cells are allogenic. In addition to the modification of the disease genes, allogenic cells can be further modified using the composition, system, described herein to reduce the immunogenicity of the cells when delivered to the recipient. The modified cord blood cells or mPB cells can be optionally expanded in vitro. The modified cord blood cell(s) or mPB cells can be derived to a subject in need thereof using any suitable delivery technique.
[001202] The composition and system may be engineered to target genetic locus or loci in HSCs. In some embodiments, the components of the systems can be codon-optimized for a eukaryotic cell and especially a mammalian cell, e.g., a human cell, for instance, HSC, or iPSC and sgRNA targeting a locus or loci in HSC, such as circulatory disease, can be prepared. These may be delivered via particles, such as the lipid nanoparticle delivery system described herein. The particles may be formed by the components of the systems herein being admixed.
[001203] In some embodiments, after ex vivo modification the HSCs or iPCS can be expanded prior to administration to the subject. Expansion of HSCs can be via any suitable method such as that described by, Lee, “Improved ex vivo expansion of adult hematopoietic stem cells by overcoming CUL4-mediated degradation of H0XB4.” Blood. 2013 May 16;121(20):4082-9. doi: 10.1182/blood-2012-09-455204. Epub 2013 Mar 21.
[001204] In some embodiments, the HSCs or iPSCs modified are autologous. In some embodiments, the HSCs or iPSCs are allogenic. In addition to the modification of the disease genes, allogenic cells can be further modified using the composition, system, described herein to reduce the immunogenicity of the cells when delivered to the recipient.
[001205] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat neurological diseases. In some embodiments, the neurological diseases comprise diseases of the brain and CNS.
[001206] Delivery options for the diseases in the brain include encapsulation of the systems in the fonn of either DNA or RNA into liposomes and conjugating to molecular Trojan horses for trans-blood brain barrier (BBB) delivery. Molecular Trojan horses have been shown to be effective for delivery of B-gal expression vectors into the brain of non-human primates. Tire same approach can be used to delivery vectors or vector systems of the invention. In other embodiments, an artificial virus can be generated for CNS and/or brain delivery.
[001207] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat hearing diseases or hearing loss in one or both ears. Deafness is often caused by lost or damaged hair cells that cannot relay signals to auditory neurons. In some embodiments, the composition, system, or modified cells can be delivered to one or both ears for treating or preventing hearing disease or loss by any suitable method or technique known in the art, such as US20120328580 (e.g., auricular administration), by intratympanic injection (e.g.. into the middle ear), and/or injections into the outer, middle, and/or inner ear; administration in situ, via a catheter or pump (U.S.
2006/0030837) and Jacobsen (U.S. Pat. No. 7,206,639). Also see US20120328580. Cells resulting from such methods can then be transplanted or implanted into a patient in need of such treatment.
[001208] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat diseases in non-dividing cells. Exemplary non-dividing cells include muscle cells or neurons. In such cells, homologous recombination (HR) is generally suppressed in the G1 cell-cycle phase, but can be turned back on using art-recognized methods, such as Orthwein et al. (Nature. 2015 Dec 17; 528(7582): 422-426).
[001209] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat diseases of the eye.
[001210] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat muscle diseases and cardiovascular diseases.
[001211] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat diseases of the liver and kidney. [001212] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat epithelial and lung diseases.
[001213] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat diseases of the skin.
[001214] In some embodiments, the Cast 2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat cancer.
[001215] In some embodiments, the Cas t 2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used in adoptive cell therapy.
[001216] In some embodiments, the Cas t 2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat infectious diseases.
[001217] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat mitochondrial diseases.
[001218] In some embodiments, the Casl2a editing system and the associated compositions, systems, vectors, uses, and methods of use, can be used to treat hemoglobinopathies. The hemoglobinopathies are a group of disorders passed down through families in which there is abnormal production or structure of the hemoglobin molecule. Sickle cell disease (SCD) is one such blood disorder caused by the abnormal hemoglobin that damages and deforms red blood cells. The abnormal red cells break down, causing anemia, and obstruct blood vessels, leading to recurrent episodes of severe pain and multi -organ ischemic damage. SCD affects millions of people throughout the world and is particularly common among people whose ancestors come from sub-Saharan Africa, regions in the Western Hemisphere (South America, the Caribbean, and Central America); Saudi Arabia; India; and Mediterranean countries such as Turkey, Greece and Italy. There is no widely available cure for SCD although some children have been successfully treated with blood stem cell, or bone marrow, transplants. However, hematopoietic stem cell transplant is not widely done for SCD, because of the difficulty in finding a matched donor. Therefore, the number of people with SCD who get transplants is low. In addition, there are several complications associated with the procedure, including death in about 5 percent of people. In SCD, clinical severity varies, ranging from mild and sometimes asymptomatic states to severe symptoms requiring hospitalization. Symptomatic treatments exist, and newborn screening (NBS) for SCD can reduce the burden of the disease on affected newborns and children.
[001219] Thalassemia is another type of blood disorder that is caused by a defect in the gene that helps control the production of the globin chains that make up the hemoglobin molecule. There are two main types of thalassemia: (a) Alpha thalassemia occurs when a gene or genes related to the alpha globin protein are missing or changed (mutated). Alpha thalassemias occur most often in persons from Southeast Asia, the Middle East, China and in those of African descent, (b) Beta thalassemia occurs when a beta globin gene is changed (mutated) so as to affect production of the beta globin protein. Beta thalassemias occur most often in persons of Mediterranean origin. To a lesser extent, Chinese, other Asians and African Americans can be affected.
[001220] The Casl2a editing system may be used to target a correction in the defective gene that causes the hemoglobinopathy.
[001221] All publications, published patent documents, and patent applications cited herein are hereby incorporated by reference to the same extent as though each individual publication, published patent document, or patent application was specifically and individually indicated as being incorporated by reference.
K. Sequences
Appendix A Sequences
[001222] Hie following sequences form part of the specification, each of which may be found in Appendix A of U.S. Provisional Application No. 63/621,975 [Ref. No. CSG018-P1], filed January 17, 2024 and U.S. Provisional Application No. 63/552,429 [Ref. No. CSG018-P2], filed February 12, 2024, each of which are incorporated herein by reference in their entireties.
Appendix B Sequences
[001223] The following sequences form part of the specification, each of which may be found in Appendix B of this application.
NUMBERED PARAGRAPHS
[001224] Without limitation, the following numbered paragraphs are contemplated by the instant specification and disclosure.
Paragraph 1. An isolated or recombinant polynucleotide comprising or consisting of a nucleic acid sequence selected from the group consisting of:
(a) a nucleic acid sequence that encodes a polypeptide having the amino acid sequence of: (Group 1) SEQ ID NO: 1-3; (Group 2) SEQ ID NO:20-21; (Group 3) SEQ ID NO:32-33; (Group 4) SEQ ID NO:45- 46; (Group 5) SEQ ID NO:57-59; (Group 6) SEQ ID NO:76-79; (Group 7) SEQ ID NO: 100-102; (Group 8) SEQ ID NO: 118-119; (Group 9) SEQ ID NO: 131-170; (Group 10) SEQ ID NO:331-340; (Group 11) SEQ ID NO:368-370; (Group 12) SEQ ID NO:386-387; (Group 13) SEQ ID NO:399-404; and (Group 14) SEQ ID NO:436-456;
(b) a nucleic acid sequence that encodes a polypeptide at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%. at least 99.8% or at least 99.9% identical to: (Group 1) SEQ ID NO: 1-3; (Group 2) SEQ ID NO:20-21; (Group 3) SEQ ID NO:32-33; (Group 4) SEQ ID NO:45-46; (Group 5) SEQ ID NO:57-59; (Group 6) SEQ ID NO:76-79; (Group 7) SEQ ID NO: 100-102; (Group 8) SEQ ID NO: 1 18-1 19; (Group 9) SEQ ID NO: 131-170; (Group 10) SEQ ID NO:331-340; (Group 11) SEQ ID NO:368-370; (Group 12) SEQ ID NO:386-387; (Group 13) SEQ ID NO:399-404; and (Group 14) SEQ ID NO:436-456;
(c) a codon optimized nucleotide sequence selected from (Group 1) SEQ ID NO:4; (Group 2) SEQ ID NO:22; (Group 3) SEQ ID NO:34; (Group 4) SEQ ID NO:47; (Group 5) SEQ ID NO:60; (Group 6) SEQ ID NO:80; (Group 7) SEQ ID NO: 103-105; (Group 8) SEQ ID NO: 120; (Group 9) SEQ ID NO: 171- 173, 180, 189, 198, 201, and 208; (Group 10) SEQ ID NO:338; (Group 11) SEQ ID NO:373; (Group 12) SEQ ID NO:388; (Group 13) SEQ ID N0:405-406; and (Group 14) SEQ ID NO:457;
(d) a nucleic acid sequence at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%. at least 99%%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%. at least 99.5%. at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to a sequence selected from (Group 1) SEQ ID NO: 17-19; (Group 2) SEQ ID NO:30; (Group 3) SEQ ID NO:43-44; (Group 4) SEQ ID NO:47; (Group 5) SEQ ID NO:73-75; (Group 6) SEQ ID NO:96- 99; (Group 7) SEQ ID N0:103-105; (Group 8) SEQ ID NO: 129-130; (Group 9) SEQ ID NO: 171-173, 180, 189, 198, 201, and 208; (Group 10) SEQ ID NO:362, 364-367; (Group 11) SEQ ID NO:373; (Group 12) SEQ ID NO:397-398; (Group 13) SEQ ID NO:430-435; and (Group 14) SEQ ID NO:482, 484-485, 487-490, and 492;
(e) a nucleic acid sequence encoding a polypeptide having a consensus amino acid sequence generated from (Group 1) SEQ ID NO: 1-3; (Group 2) SEQ ID NO:20-21; (Group 3) SEQ ID NO:32-33; (Group 4) SEQ ID NO:45-46; (Group 5) SEQ ID NO:57-59; (Group 6) SEQ ID NO:76-79; (Group 7) SEQ ID NO: 100-102; (Group 8) SEQ ID NO: 118-119; (Group 9) SEQ ID NO: 131-170; (Group 10) SEQ ID NO:331-340; (Group 11) SEQ ID NO:368-370; (Group 12) SEQ ID NO:386-387; (Group 13) SEQ ID NO:399-404; and (Group 14) SEQ ID Nos:436-456;
(f) a nucleic acid sequence that is a degenerate variant of the nucleic acid sequence in (a), (b), (c), (d) or (e); and
(g) a nucleic acid sequence that hybridizes under stringent conditions to the nucleic acid sequence in in (a), (b), (c), (d) or (e).
Paragraph 2. The isolated or recombinant nucleic acid sequence of paragraph 1, wherein the nucleic acid sequence encodes a polypeptide having at least one activity selected from endonuclease activity; endoribonuclease activity, or RNA-guided DNase activity.
Paragraph 3. The isolated or recombinant nucleic acid sequence of Paragraph 1, wherein the nucleic acid sequence comprises a. one or more a-helical recognition lobe (REC) and a nuclease lobe (NUC); b. a Wedge (WED), a-helical recognition lobe (REC), PAM-interacting (PI), RuvC nuclease, Bridge Helix (BH) and NUC domains; or c. one or more domains selected from RuvC, REC, WED, BH, PI and NUC domains. Paragraph 4. The isolated or recombinant nucleic acid sequence of Paragraph 1, wherein tire nucleic acid sequence encodes a polypeptide that recognizes or binds to a targeted polynucleotide sequence.
Paragraph 5. Hie isolated or recombinant nucleic acid sequence of Paragraph 1, wherein the nucleic acid sequence encodes a polypeptide that cleaves a targeted polynucleotide sequence.
Paragraph 6. The isolated or recombinant nucleic acid sequence of Paragraph 1, wherein the nucleic acid sequence encodes a polypeptide that recognizes or binds crRNAs.
Paragraph 7. The isolated or recombinant nucleic acid sequence of Paragraph 6, wherein the crRNA is: a. derived from one or more direct repeat sequences, or a reverse complement selected from: (Group 1) SEQ ID NO:7-12; (Group 2) SEQ ID NO:24-27; (Group 3) SEQ ID NO:36-39; (Group 4) SEQ ID NO:49-52; (Group 5) SEQ ID NO:63-68; (Group 6) SEQ ID NO:84-91; (Group 7) SEQ ID NO: 106-111; (Group 8) SEQ ID NO: 122- 125; (Group 9) SEQ ID Nos:211-290; (Group 10) SEQ ID NO:343-354; (Group 11) SEQ ID NO:374-379; (Group 12) SEQ ID NO: 390-393; (Group 13) SEQ ID NO:411-422; and (Group 14) SEQ ID N0:500-541; b. the direct repeat sequences of a. with 20 to 35 nucleotides, 12 to 40 nucleotides, or up to the length of the crRNA from tire 3? end of the direct repeat, wherein the direct repeat sequences are linked to a targeting guide linked to the 3’ end of the direct repeat sequence that is of 16-30 nucleotides in length; or c. (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563.
Paragraph 8. The isolated or recombinant nucleic acid sequence of Paragraph 1, wherein tire nucleic acid sequence encodes a polypeptide that modifies one or more genomes.
Paragraph 9. The isolated or recombinant nucleic acid sequence of Paragraph 8, wherein the modification comprises genome editing.
Paragraph 10. The isolated or recombinant nucleic acid sequence of Paragraph 1, wherein the polypeptide comprises one or more mutations. Paragraph 11. The isolated or recombinant nucleic acid sequence of Paragraph 10, wherein the mutation is selected from one or more RuvC, REC, WED, BH, PI and NUC domains.
Paragraph 12. Tire isolated or recombinant nucleic acid sequence of Paragraph 1, 10 or 11, wherein the nucleic acid sequence encodes a polypeptide comprising a nickase activity.
Paragraph 13. The isolated or recombinant nucleic acid sequence of Paragraph 1 , 10 or 11 , wherein the nucleic acid sequence encodes a nuclease-deficient polypeptide.
Paragraph 14. The isolated or recombinant nucleic acid sequence of Paragraph 12 or 13, wherein the nucleic acid sequence is operably fused to a nucleic acid encoding one or more deaminases.
Paragraph 15. The isolated or recombinant nucleic acid sequence of Paragraph 14, wherein the one or more deaminases is selected from adenine deaminase or cytosine deaminase.
Paragraph 16. The isolated or recombinant nucleic acid sequence of Paragraph 1 , wherein the deaminases modify a targeted polynucleotide sequence.
Paragraph 17. The isolated or recombinant nucleic acid sequence of Paragraph 16, wherein the modification comprises base editing.
Paragraph 18. The isolated or recombinant nucleic acid sequence of Paragraph 12 or 13, wherein a. the nucleic acid sequence encoding the polypeptide comprising a nickase activity; or b. the nucleic acid sequence encoding a nuclease-deficient polypeptide, is operably fused to a nucleic acid sequence encoding one or more reverse transcriptases.
Paragraph 19. Hie isolated or recombinant nucleic acid sequence of Paragraph 12 or 13, wherein a. the nucleic acid sequence encoding the polypeptide comprising a nickase activity; or b. the nucleic acid sequence encoding a nuclease-deficient polypeptide, is not operably fused to a nucleic acid sequence encoding one or more reverse transcriptases.
Paragraph 20. The isolated or recombinant nucleic acid sequence of Paragraph 18 or 19, further comprising a prime editing guide RNA (pegRNA).
Paragraph 21. The isolated or recombinant nucleic acid sequence of Paragraph 20, wherein the pegRNA hybridizes to a targeted polynucleotide sequence and acts as a primer to the one or more reverse transcriptases.
Paragraph 22. The isolated or recombinant nucleic acid sequence of Paragraph 20, wherein the pegRNA binds to a nicked strand for initiation of repair through one or more reverse transcriptases.
Paragraph 23. The isolated or recombinant nucleic acid sequence of Paragraph 1 , further comprising a donor polynucleotide.
Paragraph 24. The isolated or recombinant nucleic acid sequence of Paragraph 1, wherein the nucleic acid sequence is operably linked to a nucleic acid sequence encoding one or more nuclear localization signals.
Paragraph 25. The isolated or recombinant nucleic acid sequence of Paragraph 1, wherein the nucleic acid sequence is operably linked to one or more expression control sequences.
Paragraph 26. The isolated or recombinant nucleic acid sequence of Paragraph 1. wherein the expression control sequences comprise one or more transcriptional activators or repressors.
Paragraph 27. The isolated or recombinant nucleic acid sequence of any one of the above Paragraphs wherein the polypeptide comprises improved genome editing characteristics selected from efficiency, specificity, precision, intended edits:unintended edits, indels relative to Cas9.
Paragraph 28. A vector comprising the isolated or recombinant nucleic acid sequence of any one of Paragraphs 1-27.
Paragraph 29. Hie vector of Paragraph 28, wherein the vector is selected from viral vectors comprising a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector
Paragraph 30. The vector of Paragraph 28, wherein the vector is selected from a non-viral vectors comprising liposomes, lipid nanoparticles (LNPs), cationic polymers, vesicles, and gold nanoparticles. Paragraph 31. A host cell comprising the isolated or recombinant nucleic acid sequence of Paragraph 28.
Paragraph 32. The host cell of Paragraph 31, wherein the host cell is selected from one or more prokaryotic cells, mammalian cells, human cells or synthetic cells.
Paragraph 33. The host cell of Paragraph 31, wherein the host cell produces a site-specific modification of a targeted nucleic acid sequence of a host cell genome.
Paragraph 34. A polypeptide encoded by the isolated or recombinant nucleic acid sequence of any one of Paragraphs 1-34.
Paragraph 35. A fusion protein comprising an isolated polypeptide encoded by an isolated or recombinant nucleic acid sequence of Paragraph 1 fused to a heterologous amino acid sequence.
Paragraph 36. The fusion protein of Paragraph 35 wherein the fusion protein comprises a nuclease- deficient polypeptide.
Paragraph 37. An isolated or recombinant guide RNA comprising or consisting of a nucleic acid sequence selected from the group consisting of:
(a) one or more crRNA direct repeat sequences or a reverse complement selected from: (Group 1) SEQ ID NO: 7-12; (Group 2) SEQ ID NO:24-27; (Group 3) SEQ ID NO:36-39; (Group 4) SEQ ID NO:49-52; (Group 5) SEQ ID NO:63-68; (Group 6) SEQ ID NO:84-91; (Group 7) SEQ ID NO: 106-111; (Group 8) SEQ ID NO: 122-125; (Group 9) SEQ ID Nos:211-290; (Group 10) SEQ ID NO:343-354; (Group 11) SEQ ID NO:374-379; (Group 12) SEQ ID NO:390-393; (Group 13) SEQ ID NO:411-422; and (Group 14) SEQ ID N0:500-541;
(b) the direct repeat sequences of (a) with 20 to 35 nucleotides, 12 to 40 nucleotides, or up to the length of the crRNA from tire 3 ’ end of the direct repeat, wherein the direct repeat sequences are linked to a targeting guide linked to tire 3' end of the direct repeat sequence that is of 16-30 nucleotides in length;
(c) (Group 1) SEQ ID NO: 13- 15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41 ; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291- 330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563
(d) a nucleic acid sequence that is a degenerate variant of: (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO: 69-71; (Group 6) SEQ ID NO: 92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563
(e) a nucleic acid sequence at least 70%, at least 71%, at least 72%, at least 73%, at least 74%, at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81%, at least 82%, at least 83%, at least 84%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99% or at least 99.9% identical to: (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28- 29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380- 382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563; and
(f) a nucleic acid sequence that hybridizes under stringent conditions to: (Group 1) SEQ ID NO: 13- 15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355- 360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563.
Paragraph 38. A guide RNA comprising the crRNA of Paragraph 37.
Paragraph 39. The guide RNA of Paragraph 38 wherein the crRNA hybridizes to the targeted polynucleotide sequence.
Paragraph 40. A genome editing system comprising: a. one or more polypeptide sequences comprising at least 45%, 46%, 47%, 48%, 49%, 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, or 65% sequence identity to any one of sequences selected from SEQ ID NOs: 1-3; SEQ ID NO: 16; and b. one or more polynucleotide sequences comprising a guide RNA, wherein the guide RNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
Paragraph 41. The genome editing system of Paragraph 40, wherein the one or more polypeptide sequences comprise nuclease activity, endonuclease activity, endoribonuclease activity and/or RNA-guided DNase activity.
Paragraph 42. The genome editing system of Paragraph 40, wherein the guide RNA hybridizes to the targeted polynucleotide sequence.
Paragraph 43. The genome editing system of Paragraph 40, wherein the guide RNA comprises 12-40 nucleotides.
Paragraph 44. The genome editing system of Paragraph 40, wherein the targeted polynucleotide sequence comprises one or more protospacer adjacent motif (PAM) recognition domains selected from 5'-TTTN-3', 5'- TTN-3', 5'-TNN-3', 5'-TTV-3', or 5'-TTTV-3', wherein N= A, T, C or G and V = A, C or G.
Paragraph 45. The genome editing system of Paragraph 40, wherein the targeted polynucleotide sequence comprises one or more relaxed PAM recognition domains.
Paragraph 46. The genome editing system of Paragraph 40, wherein the one or more polypeptide sequences and the one or more polynucleotide sequences comprising a guide RNA form a ribonucleoprotein complex.
Paragraph 47. The genome editing system of Paragraph 40, wherein the one or more polypeptide sequences comprise a. one or more a-helical recognition lobe (REC) and a nuclease lobe (NUC); b. a Wedge (WED), a-helical recognition lobe (REC), PAM-interacting (PI), RuvC nuclease, Bridge Helix (BH) and NUC domains; or c. one or more domains selected from RuvC, REC, WED, BH, PI and NUC domains.
Paragraph 48. The genome editing system of Paragraph 47, wherein the REC lobe comprises RECI and REC2 domains.
Paragraph 49. The genome editing system of Paragraph 47, wherein the NUC lobe comprises the RuvC, PI, WED, and Bridge Helix (BH) domains. Paragraph 50. The genome editing system of Paragraph 47, wherein the one or more polypeptide sequences lack a HNH endonuclease domain.
Paragraph 51. The genome editing system of Paragraph 40, wherein the system is characterized as a Class 2, Type V Cas endonuclease.
Paragraph 52. The genome editing system of Paragraph 40, wherein the guide RNA comprises
(a) one or more crRNA direct repeat sequences or a reverse complement selected from: (Group 1) SEQ ID NO:7-I2; (Group 2) SEQ ID NO:24-27; (Group 3) SEQ ID NO:36-39; (Group 4) SEQ ID NO:49-52; (Group 5) SEQ ID NO:63-68; (Group 6) SEQ ID NO:84-91; (Group 7) SEQ ID NO: 106-1 I k (Group 8) SEQ ID NO: 122-125; (Group 9) SEQ ID Nos:211-290; (Group 10) SEQ ID NO:343-354; (Group 11) SEQ ID NO:374-379; (Group 12) SEQ ID NO:390-393; (Group 13) SEQ ID NO:411-422; and (Group 14) SEQ ID N0:500-541;
(b) the direct repeat sequences of (a) with 20 to 35 nucleotides, 12 to 40 nucleotides, or up to the length of tire crRNA from the 3 ’ end of the direct repeat, wherein the direct repeat sequences are linked to a targeting guide linked to tire 3’ end of the direct repeat sequence that is of 16-30 nucleotides in length;
(c) (Group 1) SEQ ID NO:13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291- 330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563;
(d) a nucleic acid sequence that is a degenerate variant of: (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563;
(e) a nucleic acid sequence at least 70%. at least 71%. at least 72%, at least 73%, at least 74%. at least 75%, at least 76%, at least 77%, at least 78%, at least 79%, at least 80%, at least 81 %, at least 82%, at least 83%, at least 84%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99% or at least 99.9% identical to: (Group 1) SEQ ID NO: 13-15; (Group 2) SEQ ID NO:28- 29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355-360; (Group 11) SEQ ID NO:380- 382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563; and
(f) a nucleic acid sequence that hybridizes under stringent conditions to: (Group 1) SEQ ID NO: 13- 15; (Group 2) SEQ ID NO:28-29; (Group 3) SEQ ID NO:40-41; (Group 4) SEQ ID NO:53-54; (Group 5) SEQ ID NO:69-71; (Group 6) SEQ ID NO:92-95; (Group 7) SEQ ID NO: 112-114; (Group 8) SEQ ID NO: 126-127; (Group 9) SEQ ID NO:291-330; (Group 10) SEQ ID NO:355- 360; (Group 11) SEQ ID NO:380-382; (Group 12) SEQ ID NO:394-395; (Group 13) SEQ ID NO:423-428; and (Group 14) SEQ ID NO:542-563.
Paragraph 53. The genome editing system of Paragraph 52, wherein the crRNA comprises about 15-40 nucleotides or direct repeat sequences comprising about 20-30 nucleotides.
Paragraph 54. Tire genome editing system of Paragraph 52, wherein the direct repeat is selected from: (Group 1) SEQ ID NO:7-12; (Group 2) SEQ ID NO:24-27; (Group 3) SEQ ID NO:36-39; (Group 4) SEQ ID NO:49-52;
(Group 5) SEQ ID NO:63-68; (Group 6) SEQ ID NO:84-91; (Group 7) SEQ ID NO: 106-111; (Group 8) SEQ ID NO: 122-125; (Group 9) SEQ ID Nos:211-290; (Group 10) SEQ ID NO:343-354; (Group 11) SEQ ID NO:374- 379; (Group 12) SEQ ID NO:390-393; (Group 13) SEQ ID NO:411-422; and (Group 14) SEQ ID N0:500-541.
Paragraph 55. The genome editing system of Paragraph 52, wherein the crRNA comprises a guide segment of 16- 26 nucleotides or 20-24 nucleotides.
Paragraph 56. The genome editing system of Paragraph 52 wherein the crRNA hybridizes to the targeted polynucleotide sequence.
Paragraph 57. The genome editing system of Paragraph 40, wherein the guide RNA comprises one or more chemical modifications selected from 2'-O-Me. 2'-F, and 2'F-ANA at 2’OFI; 2'F-4'-Ca-OMe and 2',4'-di-Ca-OMe at 2’ and 4' carbons; phosphodiester modifications comprising sulfide-based Phosphorothioate (PS) or acetate- based phosphonoacetate alterations: combinations of the ribose and phosphodiester modifications; locked nucleic acid (LNA), bridged nucleic acids (BNA), S-constrained ethyl (cEt), and unlocked nucleic acid (UNA); modifications to produce a phosphodiester bond between the 2' and 5' carbons (2',5'-RNA) of adjacent RNAs; and a butane 4-carbon chain link between adjacent RNAs.
Paragraph 58. Tire genome editing system of any one of Paragraphs 40-57 comprising one or more viral vectors selected from a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector.
Paragraph 59. The genome editing system of any one of Paragraphs 40-57 comprising one or more non-viral vectors selected from liposomes, lipid nanoparticles (LNPs), cationic polymers, vesicles, and gold nanoparticles.
Paragraph 60. The genome editing system of any one of Paragraphs 40-59, wherein the guide RNA modifies the targeted polynucleotide sequence of a host cell genome.
Paragraph 61. The genome editing system of Paragraph 60, wherein the targeted polynucleotide sequence is modified by an insertion, deletion or alteration of one or more base pairs at the targeted polynucleotide sequence in the host cell genome.
Paragraph 62. The genome editing system of Paragraph 40, wherein the system further comprises one or more donor nucleic acid sequences wherein the donor nucleic acid sequence comprises: one or more desired modification sequence flanked by two sequences homologous to one or more targeted polynucleotide sequence of a host cell genome, wherein the system recognizes and/or cleaves the targeted polynucleotide sequence of the host cell genome.
Paragraph 63. The genome editing system of Paragraph 62, wherein the donor nucleic acid sequence repairs the targeted polynucleotide sequence of the host cell genome cleaved by polypeptide.
Paragraph 64. The genome editing system of any one of Paragraphs 40-62, wherein the one or more polypeptide sequences comprise about 900, about 1000, about 1100, about 1200, about 1300, about 1400 or about 1500 amino acid residues.
Paragraph 65. The genome editing system of any one of Paragraphs 40-64. wherein the system is characterized in enhanced efficiency and precision of site-directed integration.
Paragraph 66. The genome editing system of Paragraph 65, wherein the efficiency and precision of site-directed integration is enhanced by staggered overhangs on the donor nucleic acid sequence.
Paragraph 67. The genome editing system of Paragraph 40, wherein the polypeptide sequences comprise at least one activity selected from endonuclease activity; endoribonuclease activity, or RNA-guided DNase activity .
Paragraph 68. The genome editing system of Paragraph 40, wherein the system is characterized in exhibiting reduced off-target effects relative to Cas9.
Paragraph 69. The genome editing system of Paragraph 40, wherein the targeted polynucleotide sequence and/or a non-target DNA strand is cleaved is cleaved by the RuvC domain of the polypeptide.
Paragraph 70. The genome editing system of Paragraph 40, wherein the system comprises multiple copies of guide RNA expressed in a host cell.
Paragraph 71. The genome editing system of Paragraph 40, wherein the polypeptide comprises one or more mutations.
Paragraph 72. The genome editing system of Paragraph 71, wherein the mutation is selected from one or more domains selected from RuvC, REC, WED, BH, PI and NUC domains.
Paragraph 73. The genome editing system of Paragraph 71, wherein the mutation in the nucleic acid sequence encodes a nuclease -deficient polypeptide.
Paragraph 74. The genome editing system of Paragraph 71, comprising a fusion of one or more deaminases to the nuclease deficient polypeptide.
Paragraph 75. The genome editing system of Paragraph 74, wherein the one or more deaminases is selected from adenine deaminase or cytosine deaminase.
Paragraph 76. The genome editing system of Paragraph 74, wherein the fusion enables base editing on DNA and/or RNA.
Paragraph 77. The genome editing system of Paragraph 76, wherein system modifies one or more nucleobase on DNA and RNA.
Paragraph 78. The genome editing system of Paragraph 40, wherein the system enables multiplexed gene editing.
Paragraph 79. The genome editing system of Paragraph 40, wherein the polynucleotide sequences comprise a single CRISPR RNA (crRNA).
Paragraph 80. The genome editing system of Paragraph 40, wherein the system enables targeting multiple genes simultaneously.
Paragraph 81. The genome editing system of Paragraph 40, wherein the polypeptide is operably linked to a nuclear localization signal (NLS).
Paragraph 82. The genome editing system of Paragraph 81, wherein the polypeptide linked NLS further comprises crRNA to form a ribonucleoprotein complex.
Paragraph 83. The genome editing system of Paragraph 40 wherein the one or more polypeptide sequences comprises a modification.
Paragraph 84. The genome editing system of Paragraph 83 wherein the modification comprises a nuclease- deficient polypeptide (dCas).
Paragraph 85. The genome editing system of Paragraph 40 wherein tire guide RNA comprises a prime editing guide RNA (pegRNA).
Paragraph 86. The genome editing system of Paragraph 85, wherein the pegRNA hybridizes to the targeted polynucleotide sequence and acts as a primer to tire one or more reverse transcriptases.
Paragraph 87. The genome editing system of Paragraph 85, wherein the pegRNA binds a nicked strand for initiation of repair through one or more reverse transcriptases. .
Paragraph 88. The genome editing system of Paragraph 87, wherein the nuclease-deficient polypeptide comprises nickase activity. Paragraph 89. The genome editing system of Paragraph 84, comprising a fusion of one or more reverse transcriptases to the nuclease deficient Cas (dCas).
Paragraph 90. The genome editing system of Paragraph 89, wherein the fusion of one or more reverse transcriptases is selected from Moloney Murine Leukemia Virus (M-MLV).
Paragraph 91. The genome editing system of Paragraph 84, wherein the polynucleotide sequences comprise a guide RNA or a pegRNA.
Paragraph 92. The genome editing system of Paragraph 91, wherein the pegRNA comprises or consists of an extended single guide RNA containing a primer binding site (PBS) and a reverse transcriptase (RT) template sequence.
Paragraph 93. The genome editing system of any one of Paragraphs 40-92, wherein the system comprises improved genome editing characteristics selected from efficiency, specificity, precision, intended edits : unintended edits, indels relative to Cas9.
Paragraph 94. The genome editing system of Paragraph 40 wherein the system is characterized in exhibiting reduced off-target effects in host cells when compared to the equivalent Cas9 endonuclease in host cells relative to SpCas9.
Paragraph 95. The genome editing system of Paragraph 40 wherein tire targeted polynucleotide sequence is contacted by
(a) a polypeptide having at least 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, or 65% sequence identity to any one of the sequences of(Group 1) SEQ ID NO: 1-3; (Group 2) SEQ ID NO:20-21; (Group 3) SEQ ID NO:32-33; (Group 4) SEQ ID NO:45-46; (Group 5) SEQ ID NO:57-59; (Group 6) SEQ ID NO:76-79; (Group 7) SEQ ID NO: 100-102; (Group 8) SEQ ID NO: 118-119; (Group 9) SEQ ID NO: 131-170; (Group 10) SEQ ID NO:331-340; (Group 11) SEQ ID NO:368- 370; (Group 12) SEQ ID NO:386-387; (Group 13) SEQ ID NO:399-404; and (Group 14) SEQ ID NO:436-456; and
(b) a guide RNA, wherein the guide RNA optionally forms a ribonucleoprotein complex with the polypeptide and the guide RNA. Paragraph 96. A vector comprising the isolated or recombinant nucleic acid sequence of any one of Paragraphs 1- 95.
Paragraph 97. Hie vector of Paragraph 96, wherein the vector is selected from viral vectors comprising a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector.
Paragraph 98. The vector of Paragraph 96, wherein the vector is selected from a non-viral vectors comprising liposomes, lipid nanoparticles (LNPs), cationic polymers, vesicles, and gold nanoparticles.
Paragraph 99. A host cell comprising the isolated or recombinant nucleic acid sequence of Paragraph 1 or 37.
Paragraph 100. The host cell of Paragraph 99, wherein the host cell is selected from one or more prokaryotic cells, mammalian cells, human cells or synthetic cells.
Paragraph 101. The host cell of Paragraph 99, wherein the host cell produces a site-specific modification of a targeted polynucleotide sequence of a host cell genome.
Paragraph 102. The host cell of Paragraph 99, wherein the host cell is modified to comprise lower off-target effects relative to SpCas9.
Paragraph 103. A polypeptide encoded by the isolated or recombinant nucleic acid sequence of any one of preceding Paragraphs.
Paragraph 104. A fusion protein comprising an isolated polypeptide encoded by an isolated or recombinant nucleic acid sequence of Paragraph 1 fused to a heterologous amino acid sequence.
Paragraph 105. The fusion protein of Paragraph 104, wherein tire fusion protein comprises a nuclease-deficient polypeptide.
Paragraph 106. A method of modifying a targeted polynucleotide sequence, said method comprising:
(a) one or more polypeptide sequences comprising at least 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, or 65% sequence identity to any one of sequences in(Group 1) SEQ ID NO: 1-3; (Group 2) SEQ ID NO:20-21; (Group 3) SEQ ID NO:32-33; (Group 4) SEQ ID NO:45-46; (Group 5) SEQ ID NO:57-59; (Group 6) SEQ ID NO:76-79; (Group 7) SEQ ID NO: 100-102; (Group 8) SEQ ID NO: 118-119; (Group 9) SEQ ID NO: 131-170: (Group 10) SEQ ID NO:331-340; (Group 11) SEQ ID NO:368-370; (Group 12) SEQ ID NO:386-387; (Group 13) SEQ ID NO:399-404; and (Group 14) SEQ ID NO:436-456;
(b) one or more polynucleotide sequences comprising a guide RNA, wherein the guide RNA comprises a com piemen tan sequence to that of a targeted polynucleotide sequence; and
(c) introducing into a host cell the one or more polypeptide sequences of (a) and the one or more polynucleotide sequences of (b) in a delivery vector; wherein the polypeptide sequence is configured to form a ribonucleoprotein complex with the guide RNA. and wherein the ribonucleoprotein complex modifies targeted polynucleotide sequence.
Paragraph 107. The method of Paragraph 106, wherein the delivery vector is selected from viral vector is selected from a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector.
Paragraph 108. The method of Paragraph 106, wherein the delivery vector comprises a non-viral vectors selected from cationic liposomes, lipid nanoparticles (LNPs), cationic polymers, vesicles, and gold nanoparticles.
Paragraph 109. A method of modifying a gene of interest comprising: culturing a host cell engineered to modify a targeted polynucleotide sequence, wherein the host cell comprises the isolated or recombinant polypeptide and the polynucleotide sequence of Paragraph 106.
Paragraph 1 10. A method for modifying a genome of a host cell comprising: contacting the host cell with the isolated or recombinant polypeptide sequence selected from (Group 1) SEQ ID NO: 1-3; (Group 2) SEQ ID NO:20-21; (Group 3) SEQ ID NO:32-33; (Group 4) SEQ ID NO:45-46; (Group 5) SEQ ID NO:57-59; (Group 6) SEQ ID NO:76-79; (Group 7) SEQ ID NO: 100-102; (Group 8) SEQ ID NO: 118- 119; (Group 9) SEQ ID NO: 131-170; (Group 10) SEQ ID NO:331-340; (Group 11) SEQ ID NO:368-370; (Group 12) SEQ ID NO:386-387: (Group 13) SEQ ID NO:399-404; and (Group 14) SEQ ID NO:436-456 and one or more guide RNA of Paragraph 37.
Paragraph 111. The method of Paragraph 110, wherein the genome editing system comprises enhanced transduction efficiency and/or low cytotoxicity.
Paragraph 112. The method of Paragraph 110, wherein the method comprises a high-throughput editing of the target region of the host cell genome.
Paragraph 113. The method of Paragraph 110, wherein the polypeptide displays about 50-fold higher affinity to crRNA in the presence of one or more divalent cations selected from Mg2+, Mn2+or Ca2+.
Paragraph 114. A pharmaceutical composition comprising: a) a lipid nanoparticle (LNP); and b) a biopolymer construct of any of the preceding Paragraphs.
Paragraph 115. The pharmaceutical composition of Paragraph 114, wherein the LNP encapsulates one or more elements of a biopolymer construct.
Paragraph 116. The pharmaceutical composition of any one of Paragraphs 114-115, wherein the lipid nanoparticle comprises: a) one or more ionizable lipids: b) one or more structural lipids; c) one or more PEGylated lipids; and d) one or more phospholipids.
Paragraph 117. The pharmaceutical composition of Paragraph 116. wherein the one or more ionizable lipids is selected from the group consisting of those in the present disclosure.
Paragraph 118. The pharmaceutical composition of any one of Paragraphs 116-117, wherein the one or more structural lipids are selected from the group consisting of cholesterol, fecosterol, beta sitosterol, sitosterol, ergosterol, campesterol, stigmasterol, brassicasterol, tomatidine, tomatine, ursolic acid, alpha-tocopherol, prednisolone, dexamethasone, prednisone, and hydrocortisone.
Paragraph 1 19. The pharmaceutical composition of any one of Paragraphs 1 16-1 18, wherein the one or more PEGylated lipids are selected from the group consisting of PEG-c-DOMG, PEG-DMG, PEG-DLPE, PEG-DMPE, PEG-DPPC, and PEG-DSPE. Paragraph 120. The pharmaceutical composition of any one of Paragraphs 116-119, wherein the one or more phospholipids are selected from the group consisting of l,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), 1,2- dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), l,2-dilinoleoyl-sn-glycero-3 -phosphocholine (DLPC), 1,2- dimyristoyl-sn-glycero-phosphocholine (DMPC). 1.2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2- dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), L2-diundecanoyl-sn-glycero-phosphocholine (DUPC), 1- palmitoyl-2-oleoyl-sn-glycero-3-phosphocho line (POPC), l,2-di-O-octadecenyl-sn-glycero-3-phosphocholine (18:0 Diether PC), 1 -oleoyl -2 -cholesterylhemisuc cinoyl-sn-glycero-3-phosphocholine (OChemsPC), 1- hexadecyl-sn-glycero-3-phosphocholine (C16 Lyso PC), l,2-dilinolenoyl-sn-glycero-3 -phosphocholine, 1,2- diarachidonoyl-sn-glycero-3-phosphocholine. l,2-didocosahexaenoyl-sn-glycero-3 -phosphocholine, 1,2- diphytanoylsn-glycero-3-phosphoethanolamine (ME 16.0 PE), l,2-distearoyl-sn-glycero-3 -phosphoethanolamine, L2-dilinoleoyl-sn-glycero-3-phosphoethanolamine. l,2-dilinolenoyl-sn-glycero-3-phosphoethanolamine. 1,2- diarachidonoyl-sn-glycero-3-phosphoethanolamine, l,2-didocosahexaenoyl-sn-glycero-3 -phosphoethanolamine, l,2-dioleoyl-sn-glycero-3-phospho-rac-(l -glycerol) sodium salt (DOPG), and sphingomyelin.
Paragraph 121. The pharmaceutical composition of any one of Paragraphs 116-120, wherein the lipid nanoparticle comprises about 48.5 mol % ionizable lipid, about 10 mol % phospholipid, about 40 mol % structural lipid, and about 1.5 mol% of PEG lipid.
Paragraph 122. The pharmaceutical composition of any one of Paragraphs 116-121, wherein the lipid nanoparticle comprises about 48.5 mol % ionizable lipid, about 10 mol % phospholipid, about 39 mol % structural lipid, and about 2.5 mol% of PEG lipid.
Paragraph 123. The pharmaceutical composition of any one of Paragraphs 116-122wherein the LNP further comprises a targeting moiety operably connected to the LNP.
Paragraph 124. Tire phannaceutical composition of any one of Paragraphs 116-123, wherein the LNP further comprises one or more additional components selected from tire group consisting of DDAB, EPC, 14PA, 18BMP, DODAP, DOTAP, and C 12-200.
Paragraph 201 . An isolated or recombinant polynucleotide comprising a nucleic acid sequence selected from the group consisting of: (a) a nucleic acid sequence that encodes a polypeptide having the amino acid sequence of SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID4I8), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), or SEQ ID NO: 445 (No. ID419);
(b) a nucleic acid sequence that encodes a polypeptide at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%. at least 80%, at least 85%, at least 90%, at least 91%. at least 92%. at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), or SEQ ID NO: 445 (No. ID419); and
(c) a nucleic acid sequence at least 50%. at least 55%, at least 60%, at least 65%, at least 70%. at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to a sequence selected from SEQ ID NO: 365 (No. ID405), SEQ ID NO: 74 (No. ID414), or SEQ ID NO: 565 (No. ID418), SEQ ID NO: 366 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 30 (No. 1D415). or SEQ ID NO: 445 (No. ID419).
Paragraph 202. The isolated or recombinant nucleic acid sequence of paragraph 201, wherein the nucleic acid sequence encodes a polypeptide having at least one activity selected from endonuclease activity; endoribonuclease activity, or RNA-guided DNase activity.
Paragraph 203. The isolated or recombinant nucleic acid sequence of paragraph 201, wherein the nucleic acid sequence comprises a. one or more a-helical recognition lobe (REC) and a nuclease lobe (NUC); b. a Wedge (WED), a-helical recognition lobe (REC), PAM-interacting (PI), RuvC nuclease. Bridge Helix (BH) and NUC domains; or c. one or more domains selected from RuvC, REC, WED, BH, PI and NUC domains.
Paragraph 204. The isolated or recombinant nucleic acid sequence of paragraph 201. wherein the nucleic acid sequence encodes a polypeptide that recognizes or binds to a targeted polynucleotide sequence.
Paragraph 205. The isolated or recombinant nucleic acid sequence of paragraph 201, wherein the nucleic acid sequence encodes a polypeptide that cleaves a targeted polynucleotide sequence.
Paragraph 206. The isolated or recombinant nucleic acid sequence of paragraph 201, wherein the nucleic acid sequence encodes a polypeptide that recognizes or binds crRNAs.
Paragraph 207. The isolated or recombinant nucleic acid sequence of paragraph 206, wherein the crRNA is any crRNA sequence from Table S15C.
Paragraph 208. Hie isolated or recombinant nucleic acid sequence of paragraph 201, wherein the nucleic acid sequence encodes a polypeptide that modifies one or more genomes.
Paragraph 209. The isolated or recombinant nucleic acid sequence of paragraph 208, wherein the modification comprises genome editing.
Paragraph 200. Hie isolated or recombinant nucleic acid sequence of paragraph 201, wherein the polypeptide comprises one or more mutations.
Paragraph 211. The isolated or recombinant nucleic acid sequence of paragraph 210, wherein the mutation is selected from one or more RuvC, REC, WED, BH, PI and NUC domains.
Paragraph 212. Hie isolated or recombinant nucleic acid sequence of paragraph 201, 210 or 211. wherein tire nucleic acid sequence encodes a polypeptide comprising a nickase activity.
Paragraph 213. The isolated or recombinant nucleic acid sequence of paragraph 201, 210 or 211, wherein the nucleic acid sequence encodes a nuclease -deficient polypeptide.
Paragraph 214. The isolated or recombinant nucleic acid sequence of paragraph 212 or 213, wherein the nucleic acid sequence is operably fused to a nucleic acid encoding one or more deaminases.
Paragraph 215. The isolated or recombinant nucleic acid sequence of paragraph 214, wherein the one or more deaminases is selected from adenine deaminase or cytosine deaminase.
Paragraph 216. The isolated or recombinant nucleic acid sequence of paragraph 215. wherein tire deaminases modify a targeted polynucleotide sequence.
Paragraph 217. The isolated or recombinant nucleic acid sequence of paragraph 216, wherein the modification comprises base editing.
Paragraph 218. The isolated or recombinant nucleic acid sequence of paragraph 212 or 213, wherein a. the nucleic acid sequence encoding the polypeptide comprising a nickase activity: or b. the nucleic acid sequence encoding a nuclease-deficient polypeptide, is operably fused to a nucleic acid sequence encoding one or more reverse transcriptases.
Paragraph 219. The isolated or recombinant nucleic acid sequence of paragraph 212 or 213, wherein a. the nucleic acid sequence encoding the polypeptide comprising a nickase activity; or b. the nucleic acid sequence encoding a nuclease-deficient polypeptide, is not operably fused to a nucleic acid sequence encoding one or more reverse transcriptases.
Paragraph 220. The isolated or recombinant nucleic acid sequence of paragraph 218 or 219, further comprising a prime editing guide RNA (pegRNA).
Paragraph 221. The isolated or recombinant nucleic acid sequence of paragraph 220, wherein the pegRNA hybridizes to a targeted polynucleotide sequence and acts as a primer to the one or more reverse transcriptases.
Paragraph 222. Hie isolated or recombinant nucleic acid sequence of paragraph 220, wherein the pegRNA binds to a nicked strand for initiation of repair through one or more reverse transcriptases.
Paragraph 223. The isolated or recombinant nucleic acid sequence of paragraph 201 , further comprising a donor polynucleotide.
Paragraph 224. Hie isolated or recombinant nucleic acid sequence of paragraph 201, wherein the nucleic acid sequence is operably linked to a nucleic acid sequence encoding one or more nuclear localization signals.
Paragraph 225. The isolated or recombinant nucleic acid sequence of paragraph 201 , wherein the nucleic acid sequence is operably linked to one or more expression control sequences. Paragraph 226. The isolated or recombinant nucleic acid sequence of paragraph 201, wherein the expression control sequences comprise one or more transcriptional activators or repressors.
Paragraph 227. The isolated or recombinant nucleic acid sequence of any one of tire above paragraphs wherein the polypeptide comprises improved genome editing characteristics selected from efficiency, specificity, precision, intended edits : unintended edits, indels relative to Cas9.
Paragraph 228. A vector comprising the isolated or recombinant nucleic acid sequence of any one of paragraphs 201-227.
Paragraph 229. The vector of paragraph 228, wherein tire vector is selected from viral vectors comprising a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector.
Paragraph 230. The vector of paragraph 228, wherein the vector is selected from a non-viral vectors comprising liposomes, lipid nanoparticles (LNPs), cationic polymers, vesicles, and gold nanoparticles.
Paragraph 231. A host cell comprising the isolated or recombinant nucleic acid sequence of paragraph 228.
Paragraph 232. The host cell of paragraph 231, wherein the host cell is selected from one or more prokaryotic cells, mammalian cells, human cells or synthetic cells.
Paragraph 233. The host cell of paragraph 231, wherein the host cell produces a site-specific modification of a targeted nucleic acid sequence of a host cell genome.
Paragraph 234. A polypeptide encoded by the isolated or recombinant nucleic acid sequence of any one of claims 1-34.
Paragraph 235. A fusion protein comprising an isolated polypeptide encoded by an isolated or recombinant nucleic acid sequence of paragraph 201 fused to a heterologous amino acid sequence.
Paragraph 236. The fusion protein of paragraph 235 wherein the fusion protein comprises a nuclease-deficient polypeptide. Paragraph 237. An isolated or recombinant guide RNA comprising or consisting of a nucleic acid sequence from
Table S15C.
Paragraph 238. A guide RNA comprising tire crRNA of paragraph 237.
Paragraph 239. The guide RNA of paragraph 238 wherein the crRNA hybridizes to the targeted polynucleotide sequence.
Paragraph 240. A genome editing system comprising: a. one or more polypeptide sequences comprising at least 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%. 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%. or 65% sequence identity to any one of sequences selected from SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No.
ID415), or SEQ ID NO: 445 (No. ID419); and b. one or more polynucleotide sequences comprising a guide RNA, wherein the guide RNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
Paragraph 241. Tire genome editing system of paragraph 240, wherein the one or more polypeptide sequences comprise nuclease activity, endonuclease activity, endoribonuclease activity and/or RNA-guided DNase activity.
Paragraph 242. The genome editing system of paragraph 240. wherein the guide RNA hybridizes to the targeted polynucleotide sequence.
Paragraph 243. Tire genome editing system of paragraph 240, wherein the guide RNA comprises 12-40 nucleotides.
Paragraph 244. The genome editing system of paragraph 240. wherein the targeted polynucleotide sequence comprises one or more protospacer adjacent motif (PAM) recognition domains selected from 5'-TTTN-3', 5'- TTN-3', 5'-TNN-3'. 5'-TTV-3'. or 5'-TTTV-3', wherein N= A, T. C or G and V = A, C or G.
Paragraph 245. Tire genome editing system of paragraph 240, wherein the targeted polynucleotide sequence comprises one or more relaxed PAM recognition domains. Paragraph 246. Tire genome editing system of paragraph 240, wherein the one or more polypeptide sequences and the one or more polynucleotide sequences comprising a guide RNA form a ribonucleoprotein complex.
Paragraph 247. The genome editing system of paragraph 240. wherein the one or more polypeptide sequences comprise a. one or more a-helical recognition lobe (REC) and a nuclease lobe (NUC); b. a Wedge (WED), a-helical recognition lobe (REC), PAM-interacting (PI), RuvC nuclease, Bridge Helix (BH) and NUC domains; or c. one or more domains selected from RuvC, REC, WED, BH, PI and NUC domains.
Paragraph 248. The genome editing system of paragraph 247. wherein the REC lobe comprises RECI and REC2 domains.
Paragraph 249. Tire genome editing system of paragraph 247, wherein the NUC lobe comprises the RuvC, PI, WED, and Bridge Helix (BH) domains.
Paragraph 250. The genome editing system of paragraph 247. wherein the one or more polypeptide sequences lack a HNH endonuclease domain.
Paragraph 251. Tire genome editing system of paragraph 240, wherein the system is characterized as a Class 2, Type V Cas endonuclease.
Paragraph 252. Tire genome editing system of paragraph 207 wherein the crRNA hybridizes to the targeted polynucleotide sequence.
Paragraph 253. The genome editing system of paragraph 240. wherein the guide RNA comprises one or more chemical modifications selected from 2'-O-Me. 2'-F, and 2'F-ANA at 2'OH; 2'F-4'-Ca-OMe and 2',4'-di-Ca-OMe at 2' and 4' carbons; phosphodiester modifications comprising sulfide-based Phosphorothioate (PS) or acetate- based phosphonoacetate alterations; combinations of the ribose and phosphodiester modifications; locked nucleic acid (LNA), bridged nucleic acids (BNA), S-constrained ethyl (cEt), and unlocked nucleic acid (UNA); modifications to produce a phosphodiester bond between the 2' and 5' carbons (2',5'-RNA) of adjacent RNAs; and a butane 4-carbon chain link between adjacent RNAs. Paragraph 254. The genome editing system of any one of claims 40-53 comprising one or more viral vectors selected from a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector.
Paragraph 255. The genome editing system of any one of claims 40-53 comprising one or more non-viral vectors selected from liposomes, lipid nanoparticles (LNPs), cationic polymers, vesicles, and gold nanoparticles.
Paragraph 256. Tire genome editing system of any one of claims 40-55, wherein the guide RNA modifies the targeted polynucleotide sequence of a host cell genome.
Paragraph 257. The genome editing system of paragraph 256. wherein the targeted polynucleotide sequence is modified by an insertion, deletion or alteration of one or more base pairs at the targeted polynucleotide sequence in the host cell genome.
Paragraph 258. Tire genome editing system of paragraph 240. wherein the system further comprises one or more donor nucleic acid sequences wherein the donor nucleic acid sequence comprises: one or more desired modification sequence flanked by two sequences homologous to one or more targeted polynucleotide sequence of a host cell genome, wherein the system recognizes and/or cleaves the targeted polynucleotide sequence of the host cell genome.
Paragraph 259. The genome editing system of paragraph 258. wherein the donor nucleic acid sequence repairs the targeted polynucleotide sequence of the host cell genome cleaved by polypeptide.
Paragraph 260. The genome editing system of any one of paragraphs 240-259, wherein the one or more polypeptide sequences comprise about 900, about 1000, about 1100, about 1200, about 1300, about 1400 or about 1500 amino acid residues.
Paragraph 261. The genome editing system of any one of paragraphs 240-260, wherein the system is characterized in enhanced efficiency and precision of site-directed integration.
Paragraph 262. Tire genome editing system of paragraph 261, wherein the efficiency and precision of site-directed integration is enhanced by staggered overhangs on the donor nucleic acid sequence. Paragraph 263. Tire genome editing system of paragraph 240, wherein the polypeptide sequences comprise at least one activity selected from endonuclease activity; endoribonuclease activity, or RNA-guided DNase activity.
Paragraph 264. The genome editing system of paragraph 240. wherein the system is characterized in exhibiting reduced off-target effects relative to Cas9.
Paragraph 265. Tire genome editing system of paragraph 240, wherein the targeted polynucleotide sequence and/or a non-target DNA strand is cleaved is cleaved by the RuvC domain of the polypeptide.
Paragraph 266. The genome editing system of paragraph 240. wherein the system comprises multiple copies of guide RNA expressed in a host cell.
Paragraph 267. Tire genome editing system of paragraph 240, wherein the polypeptide comprises one or more mutations.
Paragraph 268. The genome editing system of paragraph 267. wherein the mutation is selected from one or more domains selected from RuvC. REC. WED, BH. PI and NUC domains.
Paragraph 269. Tire genome editing system of paragraph 267, wherein the mutation in the nucleic acid sequence encodes a nuclease -deficient polypeptide.
Paragraph 270. The genome editing system of paragraph 267. comprising a fusion of one or more deaminases to the nuclease deficient polypeptide.
Paragraph 271. Tire genome editing system of paragraph 267, wherein the one or more deaminases is selected from adenine deaminase or cytosine deaminase.
Paragraph 272. The genome editing system of paragraph 267. wherein the fusion enables base editing on DNA and/or RNA.
Paragraph 273. Tire genome editing system of paragraph 272, wherein system modifies one or more nucleobase on DNA and RNA. Paragraph 274. Tire genome editing system of paragraph 240, wherein the system enables multiplexed gene editing.
Paragraph 275. The genome editing system of paragraph 240. wherein the polynucleotide sequences comprise a single CRISPR RNA (crRNA).
Paragraph 276. Tire genome editing system of paragraph 240, wherein the system enables targeting multiple genes simultaneously.
Paragraph 277. The genome editing system of paragraph 240. wherein the polypeptide is operably linked to a nuclear localization signal (NLS).
Paragraph 278. Tire genome editing system of paragraph 277, wherein the polypeptide linked NLS further comprises crRNA to form a ribonucleoprotein complex.
Paragraph 279. The genome editing system of paragraph 240 wherein the one or more polypeptide sequences comprises a modification.
Paragraph 280. Tire genome editing system of paragraph 279 wherein the modification comprises a nuclease- deficient polypeptide (dCas).
Paragraph 281. The genome editing system of paragraph 240 wherein the guide RNA comprises a prime editing guide RNA (pegRNA).
Paragraph 282. Tire genome editing system of paragraph 281, wherein the pegRNA hybridizes to the targeted polynucleotide sequence and acts as a primer to tire one or more reverse transcriptases.
Paragraph 283. The genome editing system of paragraph 282. wherein the pegRNA binds a nicked strand for initiation of repair through one or more reverse transcriptases.
Paragraph 284. Tire genome editing system of paragraph 283, wherein the nuclease-deficient polypeptide comprises nickase activity. Paragraph 285. Tire genome editing system of paragraph 280, comprising a fusion of one or more reverse transcriptases to the nuclease deficient Cas (dCas).
Paragraph 286. The genome editing system of paragraph 285. wherein the fusion of one or more reverse transcriptases is selected from Moloney Murine Leukemia Virus (M-MLV).
Paragraph 287. Tire genome editing system of paragraph 281, wherein the polynucleotide sequences comprise a guide RNA or a pegRNA.
Paragraph 288. The genome editing system of paragraph 287. wherein the pegRNA comprises or consists of an extended single guide RNA containing a primer binding site (PBS) and a reverse transcriptase (RT) template sequence.
Paragraph 289. The genome editing system of any one of claims 40-88. wherein the system comprises improved genome editing characteristics selected from efficiency, specificity, precision, intended edits: unintended edits, indels relative to Cas9.
Paragraph 290. Tire genome editing system of paragraph 240 wherein the system is characterized in exhibiting reduced off-target effects in host cells when compared to the equivalent Cas9 endonuclease in host cells relative to SpCas9.
Paragraph 291. The genome editing system of paragraph 240 wherein the targeted polynucleotide sequence is contacted by
(a) a polypeptide having at least 45%, 46%, 47%, 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, 64%, or 65% sequence identity to any one of the sequences in SEQ ID NOs: 1-3 or SEQ ID NO: 16; and
(b) a guide RNA. wherein the guide RNA optionally forms a ribonucleoprotein complex with tire polypeptide and the guide RNA.
Paragraph 292. A vector comprising the isolated or recombinant nucleic acid sequence of any one of paragraphs 201-291.
Paragraph 293. The vector of paragraph 292, wherein the vector is selected from viral vectors comprising a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector.
Paragraph 294. The vector of paragraph 292, wherein the vector is selected from a non- viral vectors comprising liposomes, lipid nanoparticles (LNPs), cationic polymers, vesicles, and gold nanoparticles.
Paragraph 295. A host cell comprising the isolated or recombinant nucleic acid sequence of paragraph 201 or 237.
Paragraph 296. The host cell of paragraph 295, wherein the host cell is selected from one or more prokaryotic cells, mammalian cells, human cells or synthetic cells.
Paragraph 297. The host cell of paragraph 295, wherein the host cell produces a site-specific modification of a targeted polynucleotide sequence of a host cell genome.
Paragraph 298. The host cell of paragraph 295, wherein the host cell is modified to comprise lower off-target effects relative to SpCas9.
Paragraph 299. A polypeptide encoded by the isolated or recombinant nucleic acid sequence of any one of preceding claims.
Paragraph 300. A fusion protein comprising an isolated polypeptide encoded by an isolated or recombinant nucleic acid sequence of paragraph 201 fused to a heterologous amino acid sequence.
Paragraph 301. The fusion protein of paragraph 300, wherein the fusion protein comprises a nuclease-deficient polypeptide.
Paragraph 302. A method of modifying a targeted polynucleotide sequence, said method comprising a. one or more polypeptide sequences comprising at least 45%. 46%. 47%. 48%, 49%, 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, or 65% sequence identity to any one of sequences in SEQ ID NOs: 1-3 or SEQ ID NO: 16; b. one or more polynucleotide sequences comprising a guide RNA, wherein the guide RNA comprises a complementary sequence to that of a targeted polynucleotide sequence: and c. introducing into a host cell the one or more polypeptide sequences of (a) and the one or more polynucleotide sequences of (b) in a delivery vector; wherein the polypeptide sequence is configured to form a ribonucleoprotein complex with the guide RNA, and wherein the ribonucleoprotein complex modifies targeted polynucleotide sequence. Paragraph 303. The method of paragraph 302, wherein the delivery vector is selected from viral vector is selected from a retroviral vector, a lentiviral vector, an adenoviral, an adeno-associated viral vector, vaccinia viral vector, poxviral vector, and herpes simplex viral vector.
Paragraph 304. The method of paragraph 302, wherein the delivery vector comprises a non-viral vectors selected from cationic liposomes, lipid nanoparticles (LNPs), cationic polymers, vesicles, and gold nanoparticles.
Paragraph 305. A method of modifying a gene of interest comprising: culturing a host cell engineered to modify a targeted polynucleotide sequence, wherein the host cell comprises the isolated or recombinant polypeptide and the polynucleotide sequence of paragraph 306.
Paragraph 306. A method for modifying a genome of a host cell comprising: contacting the host cell with the isolated or recombinant polypeptide sequence selected from SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), or SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
Paragraph 307. The method of paragraph 306, wherein the genome editing system comprises enhanced transduction efficiency and/or low cytotoxicity.
Paragraph 308. Tire method of paragraph 306, wherein the method comprises a high-throughput editing of the target region of the host cell genome.
Paragraph 309. The method of paragraph 306, wherein the polypeptide displays about 50-fold higher affinity to crRNA in the presence of one or more divalent cations selected from Mg2+. Mn3+or Ca2+.
Paragraph 310. A pharmaceutical composition comprising: a) a lipid nanoparticle (LNP); and b) a biopolymer construct of any of the preceding claims.
Paragraph 311. The phamraceutical composition of paragraph 310. wherein the LNP encapsulates one or more elements of a biopolymer construct.
Paragraph 312. Tire phannaceutical composition of any one of paragraphs 310-311, wherein the lipid nanoparticle comprises: a) one or more ionizable lipids; b) one or more structural lipids; c) one or more PEGylated lipids; and d) one or more phospholipids.
Paragraph 313. The pharmaceutical composition of paragraph 312, wherein the one or more ionizable lipids is selected from the group consisting of those in the present disclosure.
Paragraph 314. Tire phannaceutical composition of any one of paragraphs 312-313, wherein the one or more structural lipids are selected from the group consisting of cholesterol, fecosterol, beta sitosterol, sitosterol, ergosterol, campesterol, stigmasteroL brassicasterol, tomatidine, tomatine, ursolic acid, alpha-tocopherol, prednisolone, dexamethasone, prednisone, and hydrocortisone.
Paragraph 315. Tire pharmaceutical composition of any one of paragraphs 312-314, wherein the one or more PEGylated lipids are selected from the group consisting of PEG-c-DOMG, PEG-DMG. PEG-DLPE, PEG-DMPE, PEG-DPPC, and PEG-DSPE.
Paragraph 316. Tire pharmaceutical composition of any one of paragraphs 312-315, wherein the one or more phospholipids are selected from the group consisting of l,2-distearoyl-sn-glycero-3-phosphocholine (DSPC), 1,2- dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE), l,2-dilinoleoyl-sn-glycero-3 -phosphocholine (DLPC), 1,2- dimyristoyl-sn-glycero-phosphocholine (DMPC), 1.2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2- dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1,2-diundecanoyl-sn-glycero-phosphocholine (DUPC), 1- palmitoyl-2-oleoyl-sn-glycero-3-phosphocho line (POPC), 1.2-di-O-octadecenyl-sn-glycero-3-phosphocholine (18:0 Diether PC), l-oleoyl-2-cholesterylhemisuc cinoyl-sn-glycero-3-phosphocholine (OChemsPC), 1- hexadecyl-sn-glycero-3-phosphocholine (C16 Lyso PC), l,2-dilinolenoyl-sn-glycero-3 -phosphocholine, 1,2- diarachidonoyl-sn-glycero-3-phosphocholine, l,2-didocosahexaenoyl-sn-glycero-3 -phosphocholine, 1,2- diphytanoylsn-glycero-3-phosphoethanolamine (ME 16.0 PE), l,2-distearoyl-sn-glycero-3-phosphoethanolamine,
1.2-dilinoleoyl-sn-glycero-3 -phosphoethanolamine. l,2-dilinolenoyl-sn-glycero-3-phosphoethanolamine. 1,2- diarachidonoyl-sn-glycero-3-phosphoethanolamine, l,2-didocosahexaenoyl-sn-glycero-3 -phosphoethanolamine,
1.2-dioleoyl-sn-glycero-3-phospho-rac-(l -glycerol) sodium salt (DOPG), and sphingomyelin.
Paragraph 317. Tire phannaceutical composition of any one of paragraphs 312-316, wherein the lipid nanoparticle comprises about 48.5 mol % ionizable lipid, about 10 mol % phospholipid, about 40 mol % structural lipid, and about 1.5 mol% of PEG lipid.
Paragraph 318. Tire pharmaceutical composition of any one of paragraphs 312-317, wherein the lipid nanoparticle comprises about 48.5 mol % ionizable lipid, about 10 mol % phospholipid, about 39 mol % structural lipid, and about 2.5 mol% of PEG lipid.
Paragraph 319. Tire pharmaceutical composition of any one of paragraphs 312-318 wherein the LNP further comprises a targeting moiety operably connected to the LNP.
Paragraph 320. The pharmaceutical composition of any one of paragraphs 312-319, wherein the LNP further comprises one or more additional components selected from the group consisting of DDAB, EPC, 14PA. 18BMP, DODAP, DOTAP, and C 12-200.
Paragraph 321. An isolated or recombinant polynucleotide comprising or consisting of a nucleic acid sequence selected from the group consisting of:
(a) a nucleic acid sequence that encodes a polypeptide having the amino acid sequence of: SEQ ID NOs: 1570-1600, 1632-1670; 2306-2351; and 2354-2380;
(b) a nucleic acid sequence that encodes a polypeptide at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%. at least 80%. at least 85%, at least 90%, at least 91%. at least 92%. at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%, at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to: SEQ ID NOs: 1570-1600, 1632-1670; 2306-2351; and 2354- 2380;
(c) a codon optimized nucleotide sequence selected from SEQ ID NOs: 1601-1631. 1671-1709; and 2381-2407;
(d) a nucleic acid sequence at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%%, at least 99.1%, at least 99.2%, at least 99.3%, at least 99.4%. at least 99.5%, at least 99.6%, at least 99.7%, at least 99.8% or at least 99.9% identical to a sequence selected from SEQ ID NOs: 1601-1631, 1671-1709; and 2381-2407;
(e) a nucleic acid sequence encoding a polypeptide having a consensus amino acid sequence generated from any one of SEQ ID NOs: 1570-1600, 1632-1670; 2306-2351; and 2354-2380; (f) a nucleic acid sequence that is a degenerate variant of the nucleic acid sequence in (a), (b), (c), (d) or (e); and
(g) a nucleic acid sequence that hybridizes under stringent conditions to the nucleic acid sequence in in (a), (b), (c), (d) or (e).
Paragraph 322. The isolated or recombinant nucleic acid sequence of paragraph 321, wherein the nucleic acid sequence encodes a polypeptide having at least one activity selected from endonuclease activity; endoribonuclease activity, or RNA-guided DNase activity.
Group A) Cas Type V variants
Paragraph Al. A Cas Type V polypeptide comprising an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%. or 100% sequence identity to any one of the amino acid sequence sequences selected from SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein the polypeptide comprises one or more substitutions at positions selected from: Q492, T306. L748. A739, F297, N536. D8 1, N770. D675, K955, S972. N798, K298, H853, E377, V295. K852, F854, N1015, T845. E1019. K745, K292. Q565, K745, 1723, K821. K721, A810. K768, S16. 128, V312, V929. L474, H470, E402, K207, V294, R212, F79, Q299, Q465, F537, K1284, V929, DI 192, Q1203, T838, N735, 11063, K933, N1249, 197, R212, A1251, N1264, R1138, N588, 1584, V453, Q475, N76, R304, 1471, E544, V254, D231, H496, V534, D577, 128, A183, D341, K595, V501, S568, H470, V254, D231 and F197, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406). SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415). and SEQ ID NO: 445 (No. ID419).
Paragraph A2. The Cas Type V polypeptide of paragraph Al, comprising one or more substitutions selected from: Q492X. T306X, L748X, A739X, F297X, N536X, D851X, N770X, D675X, K955X, S972X, N798X. K298X, H853X. E377X, V295X, K852X. F854X. N1015X. T845X, E1019X. K745X and K292X, based on tire amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine.
Paragraph A3. The Cas Type V polypeptide of any preceding paragraph, wherein, excluding the one or more substitutions, the Cas Type V polypeptide is at least 95% identical to any one of: SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414). SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415). or SEQ ID NO: 445 (No. ID419).
Paragraph A4. The Cas Type V polypeptide of any preceding paragraph, comprising one or more substitutions selected from: K955X, F297X, T306X, E1018X, E377X, K852X, K298X, T845X, V295X, N536X, Q492X, N770X. N1015X and K292X, based on tire amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414). SEQ ID NO: 564 (No. ID418). SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine.
Paragraph A5. The Cas Type V polypeptide of any preceding paragraph, comprising one or more substitutions selected from: K292X, Q492X, N536X, N770X and N1015X, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414). SEQ ID NO: 564 (No. ID418). SEQ ID NO: 335 (No. ID406). SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine.
Paragraph A6. The Cas Type V polypeptide of any preceding paragraph, comprising the substitutions K292X and D169X. based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. 1D414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID41 1 ), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine.
Paragraph A7. The Cas Type V polypeptide of any preceding paragraph, comprising one or more combinations of substitutions selected from:
N536X and N770X;
N536X and N1015X;
K292X, N536X and N1015X;
K292X and N770X; K292X, N536X and N770X;
K292X, N770X and N1015X;
K292X and N1015X;
K292X and Q492X;
K292X, Q492X and N536X;
K292X, Q492X and N770X;
K292X, Q492X and N1015X;
N536X, N770X and N1015X;
Q492X, N536X and N770X;
Q492X, N536X and N1015X;
Q492X and N770X;
Q492X, N770X and N1015X;
Q492X and N536X;
K292X and N536X;
N770X and N1015X;
Q492X and N1015X;
K292X, Q492X, N536X, N770X and N1015X:
K292X, N536X, N770X and N 1015X;
K.292X, Q492X, N536X and N770X;
K292X, Q492X, N536X and N1015X;
K292X, Q492X, N770X and N1015X; and/or
Q492X, N536X, N770X and N1015X; based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding combinations of substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. 1D414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID41 1), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine.
Paragraph A8. The Cas Type V polypeptide of any preceding paragraph, comprising the substitution D169X, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405). or a corresponding substitution in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414). SEQ ID NO: 564 (No. ID418). SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID41 1), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine. Paragraph A9. The Cas Type V polypeptide of any preceding paragraph, wherein X is arginine.
Paragraph A 10. The Cas Type V polypeptide of any preceding paragraph, comprising a D169R substitution, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or a corresponding substitution in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
Paragraph Al l. The Cas Type V polypeptide of any preceding paragraph, comprising one or more substitutions at positions selected from: Q565, K745, 1723, K821, K721, A810, K768, S16, 128, V312, V929, L474, H470, E402, K207, V294, R212. F79, Q299. Q465, F537, K1284, V929. DI 192, Q1203, T838, N735, 11063, K933, N1249, 197. R212, A1251, N1264, R1138, N588. 1584. V453, Q475, N76, R304. 1471. E544. V254, D231. H496, V534, D577, 128, A183, D341, K595, V501, S568, H470, V254, D231 and F197, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
Paragraph A 12. The Cas Type V polypeptide of any preceding paragraph, comprising:
(a) one or more substitutions at positions selected from: Q565, K745, 1723, K821, K721, A810, K768, S16, 128, V312, V929; and/or
(b) one or more combinations of substitutions at positions:
L474, H470 and E402;
K207, V294, R212. F79 and Q299:
Q465 and F537;
KI 284, V929, DI 192 and QI 203;
T838 and N735;
11063, K933 and N1249;
197 and R212;
A1251. N1264 and R1138;
N588, 1584, V453 and Q475:
N76 and R304; 1471 and E544; V254 and D231; H496, V534 and D577;
128, A183 and D341;
K595, V501, S568 and H470;
V254, D231 and F197;
V254 and D341; and/or
V254, D341 and F197; based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions or combinations of substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
Paragraph A13. The Cas Type V polypeptide of any preceding paragraph, comprising one or more substitutions selected from: Q565K, K745M, I723V, K821I, K721M, A810V, K768M, S16T, I28F, V312E, V929I, L474Q, H470N, E402V K207N, V294M, R212Q, F79S, Q299E, Q465R, F537I, K1284R, V929D, D1192E, Q1203H, T838S, N735I, I1063N, K933M, N1249S, I97T, R212L, A125 IV, N1264I, R1138S, N588I, I584S, V453E, Q475H. N76D, R304S, I471T, E544D, V254M, D231V, H496N, V534F. D577G, I28F, A183T, D341V, K595T, V501D. S568I, H470L, V254M, D231V and F197V, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405). or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
Paragraph A14. Hie Cas Type V polypeptide of any preceding paragraph, comprising:
(a) one or more substitutions selected from: Q565K, K745M, I723V, K821I, K721M, A810V, K768M. S16T, I28F. V312E. V929I; and/or
(b) one or more combinations of substitutions selected from:
L474Q, H470N and E402V;
K207N, V294M, R212Q, F79S and Q299E;
Q465R and F537I;
K1284R, V929D. D1192E and Q1203H;
T838S and N7351;
I1063N, K933M and N 1249S;
I97T and R212L;
A1251V, N1264I and R1138S; N588I, I584S, V453E and Q475H;
N76D and R304S;
147 IT and E544D;
V254M and D231V;
H496N, V534F and D577G;
I28F. A183T and D341V;
K595T, V501D, S568I and H470L;
V254M, D231V and Fl 97V;
V254M and D341V; and/or
V254M, D341V and F197V, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions or combinations of substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
Paragraph A15. The Cas Type V polypeptide of any preceding paragraph, comprising the following substitutions: K207N. V294M, R212Q, F79S and Q299F, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405). or one or more corresponding substitutions or combinations of substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
Paragraph A 16. Hie Cas Type V polypeptide of any preceding paragraph, wherein the substitutions are based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405).
Paragraph Al 7. The Cas Type V polypeptide of any preceding paragraph, comprising or consisting of:
(a) an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% sequence identity to one or more regions of any one of SEQ ID NOs: 2306-2351 corresponding to positions: 18-23; 49-57; 100-105; 128-132; 158-182; 252-311; 359-405; 440-450; 485-499; 528-569; 609-628; 672-677; 734-750; 768-776; 790- 812; 840-864; 926-977; and 996, based on the numbering of SEQ ID NO: 334 (No. ID405); or
(b) an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, 99.5%. or 100% sequence identity to all of the following regions of any one of SEQ ID NOs: 2306-2351 corresponding to positions: 18-23; 49-57; 100-105; 128-132; 158-182; 252-311; 359-405; 440-450; 485-499; 528-569; 609-628; 672-677; 734-750; 768- 776; 790-812; 840-864; 926-977; and 996, based on the numbering of SEQ ID NO: 334 (No. ID405); or (c) an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% sequence identity to any one of SEQ ID NOs: 2306-2351, 1570-1600, 1632-1670, or 2354-2380.
Paragraph A18. The Cas Type V polypeptide of any preceding paragraph, wherein the Cas Type V polypeptide induces indel formation when contacted with a population of target sequences and a guide RNA targeting the Cas Type V polypeptide to the target sequence under conditions suitable for inducing indel formation, and wherein the contacting results in an increase in the percentage of target polynucleotide sequences comprising an indel in the population of target sequences of at least 20%, at least 30%, at least 40%, or at least 50% as compared to the percentage of target polynucleotide sequences comprising an indel in the population when the population is contacted with a reference polypeptide comprising the sequence of SEQ ID NO: 1554 (No. ID405-1) and a guide RNA that targets the reference polypeptide to the target polynucleotide sequence.
Paragraph A 19. A fusion protein comprising the Cas Type V polypeptide of any preceding paragraph fused to a heterologous amino acid sequence.
Paragraph A20. A gene editing system comprising:
(a) one or more Cas Type V polypeptides of any preceding paragraph or one or more polynucleotides encoding the Cas Type V polypcptidc(s): and
(b) one or more polynucleotide sequences comprising a guide RNA (gRNA) or one or more polynucleotides encoding the gRNA, wherein the gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
Paragraph A21. One or more polynucleotides encoding the Cas Type V polypeptide, fusion protein, or gene editing system of any preceding paragraph.
Paragraph A22. One or more vectors comprising the one or more polynucleotides of paragraph A21.
Paragraph A23. A cell comprising the one or more vectors of paragraph A22 or the one or more polynucleotides ofA21.
Paragraph A24. A pharmaceutical composition comprising the Cas Type V polypeptide, the fusion protein, the gene editing system, the one or more polynucleotides, the one or more vectors, or the cell of any preceding paragraph. Paragraph A25. A method of modifying a targeted polynucleotide sequence, the method comprising introducing into a cell a gene editing system according to paragraph A20.
B) NLS/Iinker configurations
Paragraph Bl. A polypeptide comprising: i) a Cas Type V polypeptide; ii) one, two. three or more NLS sequences; and iii) optionally one or more linker sequences.
Paragraph B2. The polypeptide of paragraph Bl, wherein the polypeptide comprises the structure:
(a) N-[Cas Type V polypeptide]-[NLS]-C; or
(b) N-[Cas Type V polypeptide]-[linker]-[NLS]-C; or
(c) N-[Cas Type V polypeptide]-[linker]-[NLS]-[linker]-[NLS]-C; or
(d) N-[Cas Type V polypeptide]-[linker]-[NLS]-[linker]-[NLS]-[linker]-[NLS]-C: or
(e) N-[NLS]-[linker]-[Cas Type V polypeptide]-[linker]-[NLS]-[linker]-[NLS]-C.
Paragraph B3. The polypeptide of any preceding paragraph, wherein the one or more NLS sequences are selected from: KRPAATKKAGQAKKKK (SEQ ID NO: 1556). PAAKRVKLD (SEQ ID NO: 2409).
RSSDDEATADSQHAAPPKKKRKV (SEQ ID NO: 1557) and GRSSDDEATADSQHAAPPKKKRKV (SEQ ID NO: 2497).
Paragraph B4. The polypeptide of any preceding paragraph, wherein the one or more linker sequences is GGGG.
Paragraph B5. The polypeptide of any preceding paragraph, wherein the polypeptide comprises a structure selected from:
(i) N-[Cas Type V polypeptide]-[SEQ ID NO: 1556J-C;
(ii) N-[Cas Type V polypeptide] -[GGGG] -[SEQ ID NO: 1556]-C;
(iii) N-[Cas Type V polypcptidc]-[GGGG]-[SEQ ID NO: 2409]-C;
(iv) N-[Cas Type V polypeptide]-[GGGG]-[SEQ ID NO: 1556]-[GGGG]-[SEQ ID NO: 2409]-C;
(v) N-[Cas Type V polypeptide] -[GGGG] -[SEQ ID NO: 2409]-[GGGG]-[SEQ ID NO: 1557]-C;
(vi) N-[Cas Type V polypeptide]-[GGGG]-[SEQ ID NO: 1556]-[GGGG]-[SEQ ID NO: 2409]-[GGGG]-[SEQ ID NO: 2409];
(vii) N-[Cas Type V polypeptide]-[GGGG]-[SEQ ID NO: 1557]-C;
(viii) N-[Cas Type V polypeptide] -[GGGG] -[SEQ ID NO: 1557]-[GGGG]-[SEQ ID NO: 1556]-C;
(ix) N-[Cas Type V polypeptide] -[GGGG] -[SEQ ID NO: 1556]-[GGGG]-[SEQ ID NO: 1557]-C; (x) N-[SEQ ID NO: 2409]-[GGGG]-[Cas Type V polypeptide] -[GGGG]-[SEQ ID NO: 1557]-[GGGG]-[SEQ ID NO: 1556]-C; or
(xi) N-[SEQ ID NO: 2409]-[GGGG]-[Cas Type V polypeptide]-[GGGG]-[SEQ ID NO: 2497]-[GGGG]-[SEQ ID NO: 1556]-C.
Paragraph B6. The polypeptide of any preceding paragraph, wherein the Cas Type V polypeptide comprises the sequence of any one of the Cas Type V polypeptides as defined in the Group A embodiments.
Paragraph B7. The polypeptide of any preceding paragraph, wherein the Cas Type V polypeptide comprises the sequence of SEQ ID NO: 1554 (No. ID405-1).
Paragraph B8. The polypeptide of any preceding paragraph, wherein the polypeptide induces indel formation in a target polynucleotide sequence when the target polynucleotide sequence is contacted with the polypeptide and a guide RNA that targets the polypeptide to tire target polynucleotide sequences, and wherein delivering the polypeptide and a guide RNA to a population of cells comprising the target sequence under conditions suitable for inducing indel fonnation results in an increase in indel fonnation of at least 50% compared to the percentage of indel formation induced by a reference polypeptide comprising the structure N-[SEQ ID NO: 1554 (ID405-1)]- |SEQ ID NO: SEQ ID NO: 1556J-C.
Paragraph B9. A fusion protein comprising the Cas Type V polypeptide of any preceding paragraph fused to a heterologous amino acid sequence.
Paragraph BIO. A gene editing system comprising:
(a) one or more polypeptides of any preceding paragraph or one or more polynucleotides encoding the polypeptide(s); and
(b) one or more polynucleotide sequences comprising a guide RNA (gRNA) or one or more polynucleotides encoding tire gRNA, wherein the gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
Paragraph B 11. One or more polynucleotides encoding the polypeptide, fusion protein, or gene editing system of any preceding paragraph.
Paragraph B 12. One or more vectors comprising the one or more polynucleotides of paragraph B 11. Paragraph B13. A cell comprising the one or more vectors of paragraph B12 or the one or more polynucleotides of paragraph B 11.
Paragraph B 14. A pharmaceutical composition comprising the polypeptide, the fusion protein, the gene editing system, the one or more polynucleotides, the one or more vectors, or the cell of any preceding paragraph.
Paragraph B15. A method of modifying a targeted polynucleotide sequence, the method comprising introducing into a cell a gene editing system according to paragraph BIO.
Group C) Chemically modified gRNAs
C 1. A guide RNA comprising one or more modified nucleotides and one or more phosphorothioate linkages, wherein the one or more modified nucleotides comprise a 2'-O-Methyl -nucleotide.
C2. The guide RNA of any preceding paragraph, wherein the guide RNA comprises at least four phosphorothioate linkages.
C3. The guide RNA of any preceding paragraph comprising:
(i) a phosphorothioate linkage between the first and second nucleotides from the 5’ end of the guide RNA, and/or
(ii) a phosphorothioate linkage between the second and third nucleotides from the 5’ end of the guide RNA, and/or
(iii) a phosphorothioate linkage between the first and second nucleotides from the 3’ end of the guide RNA, and/or
(iv) a phosphorothioate linkage between the second and third nucleotides from the 3' end of the guide RNA.
C4. The guide RNA of any preceding paragraph, comprising a direct repeat sequence and a spacer sequence contiguous with the direct repeat sequence.
C5. Tire guide RNA of any preceding paragraph, wherein the direct repeat sequence consists of 19 nucleotides. C6. The guide RNA of any preceding paragraph, wherein the direct repeat sequence consists of AAUUUCUACUGUUGUAGAU (SEQ ID NO: 2584).
C7. The guide RNA of any preceding paragraph, wherein the direct repeat sequence comprises a modified nucleotide at one or more of tire following positions: 4, 5. 6, 7, 8, 9, 11. 12, 13, 15, 16, 17 and 18, optionally wherein the modified nucleotide is a 2'-O-Methyl -nucleotide.
C8. The guide RNA of any preceding paragraph, wherein the direct repeat sequence comprises a modified nucleotide, optionally a 2'-O-Methyl-nucleotide, at all of the following positions:
(a) 4, 5, 8, 9, 11, 12, 13, 15, 16. 17 and 18; or
(b) 4, 5, 9, 11, 12, 13, 16. 17, 18; or
(c) 4. 5, 6, 7, 8. 9, 11. 12. 13. 15, 16, 17, 18.
C9. The guide RNA of any preceding paragraph, wherein the guide RNA comprises a modified nucleotide, optionally a 2'-O-Methyl-nucleotide, at one or more of the following positions: 4, 5, 8, 9, 11, 12, 13, 15, 16, 17, 18, 20, 27, 28, 29, 30. 31, 38 and 39, wherein position 1 is the first nucleotide of the direct repeat sequence.
CIO. The guide RNA of D4 or D5, wherein the guide RNA comprises a modified nucleotide, optionally a 2'-O- Methyl-nucleotide, at all of the following positions:
(a) -2, -1, 4, 5, 8, 9, 11, 12, 13, 15, 16, 17, 18, 20, 27, 28, 29, 31, 38 and 39; or
(b) -2, -1, 4, 5, 8, 9, 11, 12, 13, 15, 16, 17, 18, 20, 27, 28, 29, 31, 38, 39, 40, 41 and 42; or
(c) -4, -3, 4, 5, 9, 11, 12, 13, 16, 17, 18. 20, 27, 28, 29, 31, 38 and 39: or
(d) -4, -3. 4, 5, 9, 11, 12, 13, 16, 17, 18, 20. 27, 28, 29, 31, 38, 39, 40, 41 and 42;
(e) -2, -1. 4, 5, 6. 7. 8, 9, 11, 12, 13, 15. 16. 17. 18, 20, 21, 22, 26, 27. 28. 29. 30. 31, 33, 34, 36, 37, 38 and 39;
(f) -2, -1, 4, 5, 6, 7, 8, 9, 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 26, 27, 28, 29, 30, 31, 33, 34, 36, 37, 38, 39, 40, 41 and 42;
(g) -2, -1. 4, 5, 8, 9. 11, 12, 13, 15, 16, 17, 18, 20, 21, 22, 27, 28, 29, 31, 33, 34, 38 and 39; or
(h) -2, -1. 4, 5, 8, 9. 11. 12, 13, 15, 16, 17, 18, 20, 21. 22. 27, 28, 29, 31, 33, 34, 38, 39. 40, 41 and 42; wherein position 1 is the first position in the direct repeat region.
C 11. The guide RNA of any preceding paragraph, wherein the gRNA comprises a UG dinucleotide or UUUU immediately 5’ to tire 5’ end of the direct repeat sequence. C 12. The guide RNA of any preceding paragraph, wherein only the nucleotide(s) at the positions in the guide RNA identified as being modified are modified and all other nucleotides of the guide RNA are unmodified.
C13. The guide RNA of any preceding paragraph, comprising or consisting of:
(a) SEQ ID NO: 1767; or
(b) SEQ ID NO: 1768; or
(c) SEQ ID NO: 1769; or
(d) SEQ ID NO: 1770; or
(e) SEQ ID NO: 1748; or
(f) SEQ ID NO: 1749; or
(g) SEQ ID NO: 1750; or
(h) SEQ ID NO: 1751.
C14. Tire guide RNA of any preceding paragraph, wherein the guide RNA targets a Cas Type V polypeptide to a target sequence, optionally wherein the Cas Type V polypeptide is as defined in the Group A embodiments, wherein a complex comprising the guide RNA and the Cas Type V polypeptide induces indel fonnation when contacted with a population of the target sequences under conditions suitable for inducing indel formation, and wherein the contacting results in an increase in the percentage of target polynucleotide sequences comprising an indel in the population of target sequences of at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 110%, or at least 120% as compared to the percentage of target polynucleotide sequences comprising an indel in the population when the population is contacted with a complex comprising a reference guide RNA and the Cas Type V polypeptide, wherein the reference guide RNA consists of the same nucleotide sequence as the guide RNA and wherein the nucleotides are not modified.
C15. A gene editing system comprising:
(a) one or more Cas Type V polypeptides, optionally wherein the Cas Type V polypeptide is as defined in the Group A embodiments, or one or more polynucleotides encoding the Cas Type V polypeptide(s), or one or more polypeptides as defined in the Group B embodiments, or one or more polynucleotides encoding the polypeptide(s); and
(b) one or more polynucleotide sequences comprising a guide RNA (gRNA) of any preceding paragraph, or one or more polynucleotides encoding the gRNA, wherein tire gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
C16. One or more polynucleotides encoding the guide RNA or gene editing system of any preceding paragraph.
C17. One or more vectors comprising the one or more polynucleotides of C16.
C 18. A cell comprising the one or more vectors of C 17 or the one or more polynucleotides of C 16.
C19. A pharmaceutical composition comprising the guide RNA, the gene editing system, the one or more polynucleotides, the one or more vectors, or the cell of any preceding paragraph.
C20. A method of modifying a targeted polynucleotide sequence, the method comprising introducing into a cell a gene editing system according to C15.
Group D) Guide RNAs comprising NLS/PNA-NLS sequences
Paragraph D 1. A guide RNA, optionally wherein the guide RNA is as defined in the Group C or Group E embodiments, wherein the guide RNA comprises:
(i) one or more NLS sequences, optionally wherein the NLS is chemically conjugated to the guide RNA:
(ii) one or more RNA-NLS sequences, optionally wherein the gRNA is fused directly or indirectly to the RNA-NLS; and/or
(iii) a PNA probe comprising a polynucleotide sequence complementary with one or more portions of the gRNA and one or more NLS sequences conjugated to the polynucleotide sequence; optionally wherein the guide RNA comprises one or more linkers.
Paragraph D2. The guide RNA of any paragraph DI, wherein the PNA probe binds to the 3’ end of the gRNA.
Paragraph D3. The guide RNA of any preceding paragraph, wherein the guide RNA comprises a PNA binding sequence at the 5' end or 3' end, and wherein the PNA probe binds to the PNA binding sequence.
Paragraph D4. The guide RNA of any preceding paragraph, wherein the PNA probe consists of 2-30 nucleotides.
Paragraph D5. The guide RNA of any preceding paragraph, wherein the PNA probe consists of 9 nucleotides.
Paragraph D6. The guide RNA of any preceding paragraph, wherein the PNA probe further comprises one or more linkers between the polynucleotide sequence complementary with one or more portions of the gRNA and the one or more NLS sequences.
Paragraph D7. The guide RNA of any preceding paragraph, wherein the polynucleotide sequence complementary' with one or more portions of the gRNA is joined to one or more NLS via one or more linkers.
Paragraph D8. The guide RNA of any preceding paragraph, wherein the PNA probe further comprises a solubility enhancing group.
Paragraph D9. The guide RNA of paragraph D8, wherein the solubility enhancing group is ethylene glycol.
Paragraph DIO. Hie guide RNA of any preceding paragraph, wherein the PNA probe further comprises a fluorophore.
Paragraph Dl l. The guide RNA of paragraph DIO, wherein the fluorophore is Cy5.
Paragraph D12. Hie guide RNA of any preceding paragraph, wherein the NLS comprises the amino acid sequence PKKKRKV (SEQ ID NO: 584).
Paragraph D13. The guide RNA of any preceding paragraph, wherein the PNA comprises the nucleic acid sequence AGCCACGAAAA (SEQ ID NO: 753) and/or CCACGAAAA.
Paragraph D14. Hie guide RNA of any preceding paragraph, wherein the PNA probe comprises the structure:
(i) N-[SEQ ID NO: 1771]-[linker]-[SEQ ID NO: 584]-Q
(n) N-[ethylene glycol]-[SEQ ID NO: 1771]-C;
(iii) N-[SEQ ID NO: 177 l]-[linker]-[SEQ ID NO: 584]-[linker]-[Lys(Cy5)]-C;
(iv) N-[ethylene glycol]-[linker]-[AAAAGCACC]-C; or
(v) N-[SEQ ID NO: 584]-[linker]-[AAAAGCACC]-C.
Paragraph DI 5. A gene editing system comprising:
(a) one or more Cas Type V polypeptides, optionally wherein the Cas Type V polypeptide is as defined in the Group A embodiments, or one or more polynucleotides encoding the Cas Type V polypeptide(s), or one or more polypeptides as defined in the Group B embodiments, or one or more polynucleotides encoding the polypeptide(s); and
(b) one or more polynucleotide sequences comprising a guide RNA (gRNA) of any preceding paragraph, or one or more polynucleotides encoding the gRNA, wherein the gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
Paragraph D16. One or more polynucleotides encoding the guide RNA or gene editing system of any preceding paragraph.
Paragraph DI 7. One or more vectors comprising the one or more polynucleotides of paragraph DI 6.
Paragraph DI 8. A cell comprising the one or more vectors of paragraph D17 or tire one or more polynucleotides of paragraph DI 6. Paragraph DI 9. A pharmaceutical composition comprising the guide RNA, the gene editing system, the one or more polynucleotides, the one or more vectors, or the cell of any preceding paragraph.
Paragraph D20. A method of modifying a targeted polynucleotide sequence, the method comprising introducing into a cell a gene editing system according to paragraph D15.
Group E) Guide RNAs comprising RNA/DNA extensions + further chemical modifications
Paragraph El. A guide RNA, optionally wherein the guide RNA is as defined in the Group C or Group D embodiments, wherein the guide RNA comprises:
(i) a 5’ DNA extension sequence and/or a 5’ RNA extension sequence; and/or
(ii) a 3’ DNA extension sequence and/or a 3’ RNA extension sequence.
Paragraph E2. The guide RNA of paragraph El, wherein the 5’ DNA, 5’ RNA, 3’ DNA and/or 3’ RNA extension sequence consists of 4-25 nucleotides.
Paragraph E3. The guide RNA of any preceding paragraph, wherein the 5’ DNA, 5’ RNA, 3' DNA and/or 3' RNA extension sequence consists of 4, 9. 15 or 25 nucleotides.
Paragraph E4. The guide RNA of any preceding paragraph, wherein the 5’ DNA, 5’ RNA, 3’ DNA and/or 3’ RNA extension sequence consists of 15 nucleotides.
Paragraph E5. The guide RNA of any preceding paragraph, comprising a 5 ’ DNA or RNA extension consisting of 15 nucleotides.
Paragraph E6. The guide RNA of any preceding paragraph, comprising a 3’ DNA or RNA extension sequence, wherein the 3’ DNA or 3’ RNA extension sequence anneals to a spacer sequence in the guide RNA to form a hairpin structure, optionally wherein the 3’ DNA or 3’ RNA extension sequence anneals to the 3' end of the spacer sequence. Paragraph E7. The guide RNA of paragraph E6, wherein the last nucleotide at the 3’ end of the extension sequence anneals to the last nucleotide at the 3’ end of the spacer sequence, or within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 nucleotides of the last nucleotide at the 3’ end of the spacer sequence.
Paragraph E8. The guide RNA of any preceding paragraph, further comprising one or more linkers.
Paragraph E9. The guide RNA of any preceding paragraph, further comprising one or more linkers between the 5’ DNA and/or RNA extension sequences, and/or between the 3’ DNA and/or RNA extension sequences.
Paragraph E10. The guide RNA of any preceding paragraph, wherein tire guide RNA targets a Cas Type V polypeptide to a target sequence, optionally wherein the Cas Type V polypeptide is as defined in the Group A or a polypeptide as defined in the Group B embodiments, wherein the guide RNA induces indel formation when contacted with a population of the target sequences and the Cas Type V polypeptide under conditions suitable for inducing indel formation, and wherein the contacting results in an increase in the percentage of target polynucleotide sequences comprising an indel in the population of target sequences of at least 1.5-fold, at least 2- fold, at least 2.5-fold, at least 3-fold, at least 3.5-fold, at least 4-fold, at least 4.5-fold, at least 5-fold, at least 5.5- fold, at least 6-fold, at least 6.5-fold, at least 7-fold, at least 7.5-fold, at least 8-fold, at least 8.5-fold, at least 9- fold, at least 9.5-fold, or at least 10-fold as compared to the percentage of target polynucleotide sequences comprising an indel in the population when the population is contacted with a reference guide RNA and the Cas Type V polypeptide, wherein the reference guide RNA consists of the same nucleotide sequence as the guide RNA and wherein the guide RNA does not comprise a DNA or RNA extension sequence.
Paragraph El 1. A gene editing system comprising:
(a) one or more Cas Type V polypeptides, optionally wherein the Cas Type V polypeptide is as defined in the Group A embodiments, or one or more polynucleotides encoding the Cas Type V polypeptide(s), or one or more polypeptides as defined in the Group B embodiments, or one or more polynucleotides encoding the polypeptide(s); and
(b) one or more polynucleotide sequences comprising a guide RNA (gRNA) of any preceding paragraph, or one or more polynucleotides encoding the gRNA, wherein the gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
Paragraph E12. The gene editing system of paragraph El 1, wherein the Cas Type V polypeptide comprises or consists of a an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% sequence identity to SEQ ID NO: 334 (No. ID405) and comprises one or more substitutions selected from: D169R, E1014R and K292R.
Paragraph E13. One or more polynucleotides encoding the guide RNA or gene editing system of any preceding paragraph.
Paragraph El 4. One or more vectors comprising the one or more polynucleotides of paragraph E13.
Paragraph El 5. A cell comprising the one or more vectors of paragraph E 14 or the one or more polynucleotides of paragraph E14.
Paragraph El 6. A pharmaceutical composition comprising the guide RNA, the gene editing system, the one or more polynucleotides, the one or more vectors, or the cell of any preceding paragraph.
Paragraph El 7. A method of modifying a targeted polynucleotide sequence, the method comprising introducing into a cell a gene editing system according to paragraph El l or E12.
Group F) mRNAs comprising miRNA target sites
Paragraph F 1. An mRNA comprising a coding region and an untranslated region (UTR), wherein the UTR comprises one or more miRNA target sites.
Paragraph F2. The mRNA of any paragraph Fl, further comprising a poly A tail.
Paragraph F3. The mRNA of any preceding paragraph, wherein the one or more miRNA target sites are in a 5’ UTR and/or a 3’ UTR.
Paragraph F4. The mRNA of any preceding paragraph, wherein the mRNA comprises one or more copies of an miRNA target site in a 5’ UTR and/or a 3 ’UTR.
Paragraph F5. The mRNA of any preceding paragraph, wherein the mRNA comprises 3 copies of an miRNA target site in the 5’ UTR and/or the 3 'UTR.
Paragraph F6. The mRNA of any preceding paragraph, wherein the one or more miRNA target sites are at the 3’ end of the 3’ UTR.
Paragraph F7. Tire mRNA of any preceding paragraph, wherein the one or more miRNA target sites are at the 5’ end of the 3’ UTR.
Paragraph F8. The mRNA of any preceding paragraph, comprising one or more copies of a first miRNA target site at the 5’ end of the 3 ’UTR and one or more copies of a second miRNA target site at the 3’ end of the 3 ’UTR.
Paragraph F9. The mRNA of any preceding paragraph, comprising 3 copies of a first miRNA target site at the 5’ end of the 3 ’UTR and 3 of a second miRNA target site at the 3' end of the 3 ’UTR.
Paragraph F10. The mRNA of any preceding paragraph, wherein the miRNA target site is complementary to an endogenous miRNA sequence.
Paragraph F 11. The mRNA of any preceding paragraph, wherein tire endogenous miRNA sequence is expressed in hepatocytes, monocytes, haematopoietic cells, endothelial cells and/or epithelial cells. Paragraph Fl 2. The mRNA of any preceding paragraph, wherein the endogenous miRNA sequence comprises a sequence selected from any one of SEQ ID NOs: 2288-2302.
Paragraph F13. Hie mRNA of any preceding paragraph, wherein the miRNA target site comprises a sequence selected from any one of SEQ ID NOs: 2273-2287.
Paragraph F14. The mRNA of any preceding paragraph, wherein the coding region comprises a nucleic acid sequence encoding (i) a Type V Cas polypeptide, optionally wherein the Type V Cas polypeptide is as defined in the Group A embodiments, or (ii) a polypeptide as defined in the Group B embodiments.
Paragraph Fl 5. A lipid nanoparticle (LNP) comprising the mRNA of any preceding paragraph.
Paragraph Fl 6. A method of reducing expression of an engineered mRNA comprising a coding region and an untranslated region (UTR) in one or more off target tissues, the method comprising:
(i) identifying one or more miRNAs that is expressed in the one or more off target tissues,
(ii) incorporating into the UTR one or more target sites for the one or more miRNAs,
(iii) delivering the mRNA, or a LNP comprising the mRNA, to a subject.
Paragraph F17. A method of treating or preventing a condition in a subject or inducing an immune response in a subject, the method comprising administering to the subject an mRNA coding for a polypeptide that treats or prevents the condition or induces the desired immune response in the subject, or administering to the subject a LNP comprising the mRNA, wherein the mRNA comprises a coding region and an untranslated region (UTR) and wherein the UTR comprises an miRNA target site for an miRNA expressed in a tissue in which expression of the mRNA is undesirable.
Paragraph F18 The method of paragraph F16 or F17 wherein the mRNA is as defined in an of paragraphs F1-F14.
INCORPORATION BY REFERENCE
[001225] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. However, the citation of a reference herein should not be construed as an acknowledgement that such reference is prior art to the present disclosure. To the extent that any of the definitions or terms provided in the references incorporated by reference differ from the terms and discussion provided herein, the present terms and definitions control.
EXAMPLES
[001226] The following are examples of methods and compositions of the present disclosure. It is understood that various other embodiments may be practiced, given the general description provided herein.
Example 1: Production of nanoparticle compositions
[001227] A nanoparticle composition may be produced as described in US patent application US20170210697A1, which is incorporated herein by reference in its entirety.
[001228] In order to investigate safe and efficacious nanoparticle compositions for use in the delivery of various payloads, including but not limited to mRNA and siRNA therapeutics, a range of formulations are prepared and tested. Specifically, the particular elements and ratios thereof in the lipid component of nanoparticle compositions are optimized.
[001229] Nanoparticles can be made with mixing processes such as microfluidics and T-junction mixing of two fluid streams, one of which contains the genome editing system and the other has the lipid components.
[001230] Lipid compositions are prepared by combining an ionizable lipid, a phospholipid (such as DOPE or DSPC, obtainable from Avanti Polar Lipids, Alabaster, Ala ), a PEG lipid (such as PEG-DMG, obtainable from Avanti Polar Lipids, Alabaster. Ala.), and a structural lipid (such as cholesterol, obtainable from Sigma- Aldrich, Taufkirchen, Germany, or a cholesterol analog) in ethanol. Lipids are combined to yield desired molar ratios and diluted with water and ethanol.
[001231 ] Nanoparticle compositions may be prepared by combining a lipid solution with a solution including the genome editing system. The lipid solution is rapidly injected using, for example, a NanoAssemblr® microfluidic based system, into the genome editing system solution.
[001232] Solutions of the genome editing system in deionized water may be diluted in citrate buffer to fonn a stock solution.
[001233] Nanoparticle compositions can be processed by dialysis to remove ethanol and achieve buffer exchange. Formulations are dialyzed against a buffer such as phosphate buffered saline (PBS), Tris-HCl, or sodium citrate, using, for example, Slide-A-Lyzer cassettes (Thenno Fisher Scientific Inc., Rockford, Ill.). The resulting nanoparticle suspension is filtered through sterile filters (Sarstedt, Numbrecht, Germany) into glass vials and sealed with crimp closures. Alternatively, a Tangential Flow Filtration (TFF) system, such as a Spectrum KrosFlo system, may be used.
[001234] The method described above induces nano-precipitation and particle formation. Alternative processes including, but not limited to, T-junction and direct injection, may be used to achieve the same nanoprecipitation.
Example la: Exemplary Nanoparticle Formulation Procedure
[001235] Ionizable lipids, phospholipids, structural lipids (eg. Cholesterol or other sterols), and PEG lipids are dissolved in ethanol. The ionizable lipids mol % can be from 30- 70%, phospholipids mol % can be 5-20%, sterols mol % can be 20-60%, and PEG lipid mol % can be 0.1-10%. Tire lipid solution is mixed with an acidic buffer containing genome editing system on a mixing device, such as aNanoAssemblr® microfluidic systems, to fonn LNPs. To adjust LNP particle size, the volume ratio of lipid solution to genome editing system solution can be varied from 1: 1 to 20: 1, genome editing system concentration in aqueous buffer can be 0.01 mg/mL to 10 mg/mL, N/P ratio can be 1 to 50 and different identities of PEG lipids or other polymers can be used. After the LNP is formed from the mixing device, aqueous buffer is added to reduce the ethanol concentration. The volume of aqueous buffer can be 0.1 to 100 volume of LNP volume coming out of the mixing device. Hie LNPs are further dialyzed against aqueous and concentrated to a desired concentration. The particle size of LNPs is measured by dynamic light scattering (DLS), for example, by using a Zetasizer Ultra (Malvern Panalytical). Payload encapsulation efficiency is determined, for example, by Quant-it™ RiboGreen assay.
Example 2: Characterization of nanoparticle compositions
[001236] A nanoparticle composition may be characterized as described in US patent application US20170210697A1, which is incorporated herein by reference in its entirety.
[001237] Particle size, poh dispcrsity index (PDI), and the zeta potential of a nanoparticle composition can be determined using, for example, a Zetasizer Nano ZS (Malvern Instruments Ltd, Malvern, Worcestershire, UK), or a Wyatt DynaPro plate reader.
[001238] Ultraviolet-visible spectroscopy can be used to determine the concentration of the genome editing system in the nanoparticle compositions. The formulation may be diluted in PBS then added to a mixture of methanol and chloroform. After mixing, the absorbance spectrum of the solution is recorded, for example, between 230 nm and 330 nm on a DU 800 spectrophotometer (Beckman Coulter, Beckman Coulter, Inc., Brea, Calif). The concentration of tire genome editing system in the nanoparticle composition can be calculated based on tire extinction coefficient of the genome editing system used in the composition and on the difference between the absorbance at a wavelength of, for example, 260 nm and the baseline value at a wavelength of, for example, 330 nm.
[001239] For nanoparticle compositions including an RNA, a QUANT-IT™ RIBOGREEN® RNA assay (Invitrogen Corporation Carlsbad, Calif.) can be used to evaluate the encapsulation of an RNA by the nanoparticle composition. The samples are diluted in a TE buffer solution. Portions of the diluted samples are transferred to a polystyrene 96 well plate and either TE buffer or a 2% Triton X-100 solution is added to the wells. The plate is incubated at, for example, a temperature of 37° C for 15 minutes. The RIBOGREEN® reagent is diluted in TE buffer, and this solution is added to each well. The fluorescence intensity can be measured using a fluorescence plate reader (Wallac Victor 1420 Multilabel Counter; Perkin Elmer, Waltham, Mass.) at an excitation wavelength of, for example, about 480 nm and an emission wavelength of, for example, about 520 nm. The fluorescence values of the reagent blank are subtracted from that of each of the samples and the percentage of free RNA is determined by dividing the fluorescence intensity of the intact sample (without addition of Triton X-100) by the fluorescence value of the disrupted sample (caused by the addition of Triton X-100).
Example 3: In vivo studies including protein expression by organ
[001240] Delivery to a target organ may be assessed as described in US patent application US20170210697A1, which is incorporated herein by reference in its entirety.
[001241] In order to monitor how effectively various nanoparticle compositions deliver polynucleotides to targeted cells, different nanoparticle compositions including a particular polynucleotide are prepared and administered to rodent populations. Mice are intravenously, intramuscularly, intraarterially, or intratumorally administered a single dose of a nanoparticle composition. In some instances, mice may be made to inhale doses. Dose sizes may range from 0.001 mg/kg to 10 mg/kg, where 10 mg/kg describes a dose including 10 mg of polynucleotide in a nanoparticle composition for each 1 kg of body mass of the mouse. A control composition including PBS may also be employed.
[001242] Upon administration of nanoparticle compositions to mice, dose delivery profiles, dose responses, and toxicity of particular formulations and doses thereof can be measured by enzyme-linked immunosorbent assays (ELISA), bioluminescent imaging, or other methods. Time courses of protein expression can also be evaluated. Samples collected from the rodents for evaluation may include blood, sera, and tissue (for example, muscle tissue from the site of an intramuscular injection and internal tissue); sample collection may involve sacrifice of the animals.
[001243] For example, LNP formulations including RNA encoding a detectable protein such as luciferase may be administered intravenously to mice at a dosage of, for example, 0.5 mg/kg. A standard MC3 formulation and a PBS control may also be tested.
[001244] Bioluminescence in various organs, such as the liver, lung, spleen, and femur, may be measured after 6 hours.
[001245] Nanoparticle compositions including protein coding RNA are useful in the evaluation of tire efficacy and usefulness of various fonnulations for the delivery of polynucleotides. Higher levels of protein expression induced by administration of a composition including protein coding RNA will be indicative of higher RNA translation and/or nanoparticle composition RNA delivery efficiencies. As the non-RNA components are not thought to affect translational machineries themselves, a higher level of protein expression is likely indicative of a higher efficiency of delivery of the RNA by a given nanoparticle composition relative to other nanoparticle compositions or the absence thereof.
Example 4: Toxicity, cytokine induction, and complement activation
[001246] Toxicity of the LNP compositions of the disclosure may be analyzed as described by international patent application WO2016118724 and/or US20170210697A1, which are incorporated herein by reference in its entirety.
Example 5: Optimization of Particle Sizes
[001247] The fenestration sizes for different bodily organs often vary; for example, the kidney is known to have a smaller fenestration size than the liver. Thus, targeting delivery of a genome editing system (e.g., specifically delivering) to a particular organ or group of organs may require the administration of nanoparticle compositions with different particle sizes. In order to investigate this effect, nanoparticle compositions are prepared with a variety of particle sizes using a Nanoassemblr® instrument. Nanoparticle compositions include an RNA encoding Luc. Each differently sized nanoparticle composition is subsequently administered to mice to evaluate the effect of particle size on delivery selectivity. Luc expression in two or more organs or groups of organs can be measured using bioluminescence to evaluate the relative expression in each organ.
[001248] A number of parameters can be adjusted in order to optimize the particle size of the nanoparticles. Exemplary parameters include, but are not limited to, the identity of the PEG lipid, mol% of the PEG lipid in the LNP fonnulation, the identity of the structural lipid, mol% of the structural lipid in the LNP formulation, tire identity of the phospholipid, mol% of the phospholipid in the LNP fonnulation, the identity of the ionizable lipid. mol% of the ionizable lipid in the LNP formulation, identity of lipid components covalently bound to one or more targeting moieties, mol% of said targeting moiety- bound lipids in the LNP formulation, flow rate of the Nanoassemblr® instrument in the preparation of the formulation, concentration of the mixing solutions used in the formulation, buffers used in the preparation of the fonnulation, and duration of formulation mixing.
Example 6: Construction and Testing an Casl2a Nuclease Genome Editor
[001249] To generate an Cast 2a Nuclease Genome Editor, a human codon optimized Casl2a ORF is amplified from a vendor synthesized plasmid. In addition, the desired nuclear localization signal is encoded on the amplification primers. The amplified fragment containing the NLS and the human codon optimized Casl2a ORF are assembled using Gibson Assembly Master Mix (NEB), into the pCDNA3. 1 vector (Thermo Scientific). The cognate crRNA for the indicated Cas 12a ortholog is cloned under the control of the U6 promoter using Gibson Assembly Master Mix (NEB), into the pZ147-BvCasl2b-sgRNA- scaffold vector (Addgcnc). The crRNA may be designed such that the guide sequence is replaced to match the desired target sequence with a cognate PAM for the indicated Cas 12a ortholog, particularly the human genome in the case that the construct is to be used in a human genome editing experiment. In experiments where the Cas 12a is mutated, the desired mutation is created by amplifying the entire plasmid in a single amplicon where the primer encodes the mutation and is cloned using the KLD enzyme mix (NEB). To evaluate the efficacy of the system, lOOng of each of the Cas 12a plasmid and the crRNA plasmid are transfected using Lipo 3000 (Thermo Scientific) into HEK293FT cells into a single well of a 96-wcll plate. Tire cells arc left to incubate for 72 hours before they are harvested for sequencing. Quick Extract DNA solution is to extract gDNA from cells for subsequent NGS analysis of the targeted loci.
Example 7: Constructing and Testing an Casl2a-Deaminase Fusion
[001250] To generate an Casl2a-deaminase fusion construct, both a human codon optimized Cas 12a ORF and a desired human codon optimized deaminase are amplified from plasmids with primer overhangs containing the desired linker sequence. In addition, the desired nuclear localization signal is encoded on the amplification primers. Two amplified fragments containing the Casl2a ORF and deaminase are stitched together using Gibson Assembly Master Mix (NEB), into the pCDNA3. 1 vector (Thermo Scientific). The cognate crRNA for the indicated Casl2a ortholog is cloned under the control of the U6 promoter using Gibson Assembly Master Mix (NEB), into the pZ147-BvCasl2b-sgRNA-scaffold vector (Addgene). The crRNA may be designed such that the guide sequence is replaced to match the desired target sequence with a cognate PAM for the indicated Casl2a ortholog, particularly the human genome in the case that tire construct is to be used in a human genome editing experiment. In experiments where the Casl2a is mutated, the desired mutation is created by amplifying the entire plasmid in a single amplicon where the primer encodes the mutation and is cloned using the KLD enzyme mix (NEB). To evaluate the efficacy of the system, lOOng of each of the Casl2a-deaminase plasmid and the crRNA plasmid are transfected using Lipo 3000 (Thcnno Scientific) into HEK293FT cells into a single well of a 96-well plate. The cells are left to incubate for 72 hours before they are harvested for sequencing. Quick Extract DNA solution is used to extract gDNA from cells for subsequent NGS analysis of the targeted loci.
Example 8: Constructing and Testing an Casl2a-RT Fusion
[001251] To generate an Casl2a-RT fusion construct, both a human codon optimized Casl2a ORF and a desired human codon optimized RT are amplified from plasmids with primer overhangs containing tire desired linker sequence. In addition, the desired nuclear localization signal is encoded on tire amplification primers. Two amplified fragments containing the Casl2a ORF and RT are stitched together using Gibson Assembly Master Mix (NEB), into the pCDNA3. 1 vector (Thermo Scientific). The cognate extended and engineered crRNA for the indicated Casl2a ortholog is cloned under the control of the U6 promoter using Gibson Assembly Master Mix (NEB), into the pZ147-BvCas!2b-sgRNA- scaffold vector (Addgene). The extended crRNA is designed such that the guide sequence is replaced to match the desired target sequence with a cognate TAM for the indicated Casl2a ortholog, particularly the human genome in the case that the construct is to be used in a human genome editing experiment. In addition, a crRNA extension that contains a template for the desired edit, along with a homologous sequence designed to bind to the Cas 12a non-target strand are included in the engineered crRNA. In experiments where the Casl2a is mutated, the desired mutation is created by amplifying the entire plasmid in a single amplicon where the primer encodes the mutation and is cloned using the KLD enzyme mix (NEB). In experiments where a second Cas 12a ORF is included in the system, it may be expressed from a separate pCDNA3.1 vector. To evaluate the efficacy of the system, lOOng of each of the Casl2a-RT plasmid and the crRNA plasmid are transfected using Lipo 3000 (Thermo Scientific) into HEK293FT cells into a single well of a 96-well plate. The cells are left to incubate for 72 hours before they are harvested for sequencing. Quick Extract DNA solution is used to extract gDNA from cells for subsequent NGS analysis of the targeted loci.
Example 9: In vitro activity screening and PAM determination
[001252] To detect dsDNA cleavage and characterize the protospacer adjacent motif (PAM) requirement Casl2a orthologs were initially expressed in Human embry onic kidney (HEK) cell line 293T (ATCC-CRL-3216). HEK293T cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) with GlutaMAX (Thermo Fisher Scientific), supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) and 10,000 units/mL penicillin, and 10,000 pg/mL streptomycin (Thermo Fisher Scientific) at 37°C with 5% CO2 incubation.
[001253] HEK293T cells were seeded into 24-well plates (VWR) one day prior to transfection at a density of 100,000 cells per well. Cells were transfected using Lipofectamine 3000 (Invitrogen) following the manufacturer’s recommended protocol. For each well of a 24-well plate 800 ng of plasmid DNA (pcDNA3.1- Casl2a-EGFP) encoding Casl2a was used. One well per plate was transfected using 800 ng of plasmid DNA (pD608-SpCas9-EGFP) encoding SpCas9 to use as a control.
[001254] Cells were incubated at 37°C for 48 hours post transfection in 5 % CO2 before lysis. The cells were washed twice with 900 pl IX DPBS (Thermo Fisher Scientific) and resuspended in 100 pl 20 mM HEPES, 100 mM KC1, 5 mM MgCl2, 5 % glycerol. 0. 1 % Triton X-100, 1 mM DTT. IX Halt Protease Inhibitor Cocktail (Thermo Scientific), pH 7.5 lysis buffer. Resuspended cells were incubated on ice for 20 minutes. Cell lysates were further used for activity determination in vitro as described below.
[001255] Ribonucleoprotein complexes were assembled using cell lysates and 100 nM or 1000 nM of appropriate crRNA; total reaction volume - 10 pL. Reactions were incubated on ice for 15 minutes. 5 pL of RNP complex was used for 7N PAM library cleavage. 0.5 pg of the 7N PAM plasmid library yvas used, reaction buffer - NEBuffer 2.1 (New England Biolabs), total volume - 50 pL. To achieve library cleavage reactions were incubated at 37°C for 1 hour. Double-stranded break ends were blunted by adding 0.3 pL 10 mM dNTPs and 0.3 pL of T4 DNA polymerase and incubating at 12°C for 15 minutes and 75°C for 25 minutes. To add A-overhangs to blunt ends 0.3 pL 10 mM dNTPs and 0.3 pL of DreamTaq DNA polymerase (Thermo Scientific) yvere added to the reactions and incubated at 68°C for 30 minutes. RNA removal was performed using 0.5 pL of RNase A (Thermo Scientific), samples incubated at 37°C for 15 minutes. Cleaved DNA was purified using Monarch PCR & DNA Cleanup Kit (5 pg) (New England Biolabs). 100 ng of double stranded DNA linker yvas added to each reaction together with 2.5 pL ligation buffer (Neyv England Biolabs) and 1 pL T4 DNA Ligase (New England Biolabs) (final reaction volume - 25 pL). Reactions were incubated at 22°C for 1 hour. 2 pL of each ligation mixture was used as a PCR template. PCR products were visualized by performing gel electrophoresis (1.5 % agarose gel).
[001256] To determine PAM sequences, next generation sequencing was performed using Illumina MiSeq System. Using ligation mixtures as templates, PCR was performed to enrich for PAM-containing sequences (reaction volume - 100 pL). Samples were then purified using Monarch PCR & DNA Cleanup Kit (5 pg) (New England Biolabs). Purified DNA was then used as a template for primary PCR. Primers that extend past the end of library fragments with ‘tails' encoding Illumina sequences and sample -specific 6 nt barcodes (IDT, Metabion) were used. Phusion High-Fidelity DNA Polymerase (New England Biolabs) was used for both rounds of PCR and the reactions were set up according to the manufacturer’s instructions in a final volume of 50 pl and allowed to proceed for 10 cycles. In the case of primary PCR 20 ng of the purified product from the previous step was used as template and for the secondary PCR 2 pL of the primary PCR reaction was used as template. The primary PCR forward primer contained a sample-specific barcode sequence in addition to the necessary Illumina sequences. The rest of the primers were universal and contained Illumina sequences only (Table Ex.9.1). The following conditions were used for the primary two- step PCR: 95°C for 30s, 10 cycles of 95°C for 10s and 72°C for 5 s, and final extension at 72°C for 5 min. The secondary PCR was performed as follows: 95°C for 30s, 10 cycles of 95°C for 10s, 58°C for 15s and 72°C for 5s, and final extension at 72°C for 5min. The secondary PCR products were purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs), their concentration and quality assessed using NanoPhotometer® NP80 (IMPLEN) spectrophotometer and Qubit 4 (Thermo Fisher Scientific) fluorometer with the Qubit IX dsDNA HS Assay kit (Thermo Fisher Scientific). Samples from uncleaved PAM libraries were used as negative control and libraries cleaved with LbaCasl2a and SpyCas9 were used as positive control.
Table Ex,9, 1, Primers used in PAM sample preparation for Illumina sequencing [001257] Sample libraries were normalized and pooled in equimolar ratio for sequencing. The resulting pool was purified and size selection performed using Ampure XP magnetic beads (Beckman Coulter Inc), then quantified via qPCR using NEBNext Library Quant Kit for Illumina (New England Biolabs). Final I i bran pool was diluted and denatured for sequencing on Illumina MiSeq System (Illumina) with a 25% (v/v) spike of PhiX control v3 (Illumina). Single read deep sequencing was performed and the resulting sequences were post-processed and deconvoluted per the manufacturer's instruction.
[001258] PAM sequence recognition was identified for each protein by first generating a collection of sequences that represent all possible outcomes of double stranded DNA cleavage and adapter ligation within the target region. For all the reads that matched these sequences which correspond to cleavage events the adjacent 7nt PAM sequences which promote the double stranded nuclease activity were extracted. The position-specific nucleotide preference was examined by first counting the identical PAM sequences, calculating their frequency within total reads and then normalizing the frequencies to the original uncleaved PAM library to account for under- or over-represented PAM sequences. Top 10% of the most enriched PAM sequences were used for further analysis.After normalization, a position frequency matrix (PFM) was calculated. This was done by weighting each nucleotide at each position based on the frequency (normalized) associated with each PAM. For example, if a PAM of 5’-CGGTAGC-3’; had a normalized frequency of 0.15%, then tire C at first position would be given a frequency of 0.15% when determining the nucleotide frequency for the first PAM position. Next, the overall contribution of each nucleotide at each position in the dataset was summed and organized into a table with the most abundant nucleotides indicating Cast 2a PAM preferences (Table Ex.9.2). herein: A=Adenine, C=Cytosine. G=Guanine, T=Thymine, R=A or G. Y=C or T, S=G or C, W=A or T, D=A or G or T, H=A or C or T, K=G or T, M=A or C, N=any base, B=C or G or T, V=A or C or G) and displayed as a WebLogos organized in tire protein phylogenetic tree (FIG. 15).
Table Ex, 9,2. Position frequency matrix for Casl2a protein PAMs
Example 10. Genome editing determination by T7 endo assay
[001259] To determine gene editing efficiencies the Human embryonic kidney (HEK) cell line 293T (ATCC-CRL-3216) were transfected with plasmid encoding Casl2a and PCR fragment encoding U6 promoter, crRNA and HDV ribozyme. The activity of each protein was tested using 2 different sites (RUNX1 and SCN1A). Sequences of the targets and crRNA encoding fragments are provided in the supplementary file.
[001260] For that HEK293T cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) with GlutaMAX (Thermo Fisher Scientific), supplemented with 10 % fetal bovine serum (Thenno Fisher Scientific) and 10,000 units/mL penicillin, and 10,000 pg/mL streptomycin (Thermo Fisher Scientific) at 37°C with 5 % CO2 incubation.
[001261] HEK293T cells were seeded into 96-well plates (Thermo Fisher Scientific) one day prior to transfection at a density of 18,000 cells per well. Cells were transfected using FuGENE HD (Promega Corporation) following the manufacturer’s recommended protocol. For each well of a 96-well plate a total amount of 350 ng DNA containing 50 finol of plasmid encoding Cas 12a and 50 finol of PCR fragment with appropriate U6-crRNA-HDV template was used. [001262] Cells were incubated at 37°C for 96 hours post transfection in 5 % CO2 before genomic DNA extraction. The cells were washed twice with 200 pl IX DPBS (Thermo Fisher Scientific) and resuspended in 25 pl 50 mM Tris-HCl, 150 mM NaCl, 0.05% Tween 20, pH 7.6 (Sigma Aldrich) and 0.2 mg/ml Proteinase K (New England Biolabs) lysis buffer.
[001263] Resuspended cells were incubated at 55°C for 60 minutes and 95°C for 15 minutes. Genomic region surrounding each Casl2a target site was PCR amplified using primers defined in the Table Ex.10.1 PCR amplification was performed using Q5 Hot Start High-Fidelity 2X Master Mix (New England Biolabs) according to the manufacturer’s instructions. The reaction was set up using Ipl of the cell lysate and 0.5 pM of each primer in a final reaction volume of 25ul.
Table Ex, 10,1. Primer sequences used for target amplification in T7 Endonuclease I assay
Example 11. Genome editing frequencies were estimated using T7 Endonuclease I assays.
[001264] 25 pL of each PCR reaction was combined with 3 pL NEBuffer 2 (New England Biolabs) and 7 pL of water before denaturation at 95°C for 5 minutes and re-annealing by temperature ramping from 95-85°C at -2°C/s followed by ramping from 85-25°C at -0.1°C/s. 1 pL of T7 Endonuclease I (New England Biolabs) was added to each re-annealed sample and cleavage reactions were incubated at 37°C for 20 min. Fragments were analyzed by performing gel electrophoresis using E-Gel Precast Agarose Gel Electrophoresis system (Invitrogcn). 2 % gel with Ethidium bromide dye was used. 8 pL of each sample was mixed with 7 pL of E-Gel Sample Loading Buffer (Invitrogen) and the whole volume was loaded to the well. Genomic target cleavage percentage was calculated using EnageJ software. FIG. 16, 17, 18, 19, and 20 demonstrates the editing efficiencies of LbaCasl2a, ID405, ID406, ID41 L ID414, ID415, ID418, and ID419 orthologs. FIG. 21 summarizes data from at least 3 repeats of such experiments.
Example 12. Gene editing efficiency determination by deep-sequencing
[001265] Lysates of the transfected HEK293T cells were prepared for deep sequencing to determine the activity of Casl2a orthologs in eukary otic cells by studying the rates ofNHEJ outcomes in the genomic target sites of treated cells. Briefly, the genomic target regions were amplified and fragments extended with Illumina sequences including a unique index for each sample through two rounds of PCR. The triplicate samples from a single experiment were combined into a single tube and 4 pL of the mix was used as template in the primary' PCR reaction. For the primary PCR custom primers were used that were complementary' to the sequences surrounding the genomic targets and had non-complementary ‘tails’ with Illumina adapter sequences (Table Ex. 12.1). Q5 HotStart 2x MasterMix (New7 England Biolabs) was used for the primary7 PCR and tire reaction set up using 4 pL of cell lysate as template and 0.2 mM of each primer in a final volume of 25 pL. The cycling conditions used were: 98°C for 2min 30s. 24 cycles of 98°C for 30s, 56.5°C for 30s, 72°C for 25s. and final extension at 72°C for 2min. The primary PCR product was purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs) and used for the secondary7 PCR.
Table Ex, 12,1, Custom primers used for primary PCR of genomic DNA deep sequencing sample preparation
[001266] Secondary PCR was perfonned using PCR Add-on Kit for Illumina (Lexogen) with primers encoding Illumina sequences and a 6nt i7 index (Lexogen i7 6 nt Index Set (7001-7096)) according to the manufacturer’s instructions. Cycling conditions for secondary PCR were as follows: 98°C for 30s, 8 cycles at 98°C for 10s, 65°C for 20s and 72°C for 30s, followed by final extension at 72°C for 1 min. The secondary7 PCR products were purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs), their quantity and quality checked using spectrophotometry (NanoPhotometer® NP80, IMPLEN) and fluorimetry (Qubit IX dsDNA HS Assay and Qubit 4, Thermo Fisher Scientific). The purified samples were pooled in an equimolar ratio and size selection performed using Ampure XP (Beckman Coulter) magnetic beads. The resulting library was analyzed using Bioanalyzer (Agilent) and quantified using NEBNext Library Quant Kit for Illumina (New England Biolabs). Final library' pool was prepared for deep sequencing according to Illumina’s specifications. Paired end sequencing was performed using the MiScq Reagent Kit v2 (300-cyclcs) (Illumina) on the MiSeq System (Illumina) with 7% PhiX v.3 (Illumina). All sequencing data analysis was done using Geneious Prime 2023.0.4. Reads were trimmed and filtered using BBDuk and mapped to the reference sequence with 25nt quantification window set on each side of the predicted cleavage site. Reads that differed from the reference sequence in this window were included in genome editing efficiency calculations.
[001267] Efficiency results are presented in FIG. 22A and reads with the top 5 most common editing outcomes presented in FIG. 22B, with raw data presented in FIGs. 23A and 23B. Editing efficiency of ID405, ID414 and ID418 was comparable to that of LbaCasl2a over five genomic targets in DNMT1, FANCF, RUNX1 and SCN1A genes. For DNMT1, SCN1A, RUNX1 and FANCF site 2 targets ID405 exhibited best genome editing efficiency up to 56% of edited reads, even exceeding LbaCas 12a in the case of SCN 1 A and DNMT1 targets. ID414 and ID418 produced editing efficiencies up to 34% and 17% respectively. The majority of edited reads have small deletions in the editing window. [001268] Efficiency results for proteins that recognize CTC PAM are presented in FIG. 24 and reads with the top 5 most common editing outcomes of active proteins presented in FIG. 25. Editing efficiency of ID428 and ID433 is low (<1%) but elevated count of mutant reads can be detected with deep sequencing when compared to negative control, which suggests weak nuclease activity in eukaryotic cells. Sequences used in this example are provided in Tables Ex.l2.2-Ex. l2.5.
Table Ex, 12,2, Custom primers used for primary PCR of genomic DNA deep sequencing sample preparation
Table Ex, 12,3, Target sequences in HEK293T cells in Example 12 Table Ex, 12,4, crRNA sequences used in Example 12
Table Ex.12,5, Full cassete sequences used in Example 12
Example 13. Casl2a mutagenesis and evaluation of mutant editing performance
[001269] In this Example, three Casl2a nucleases (ID405 (SEQ ID NO: 334), ID414 (SEQ ID NO: 58), and ID418 (SEQ ID NO: 564)) were selected for mutagenesis and further testing to determine the effects of the mutations on the performance of the enzymes. It is contemplated that any of the mutations introduced herein could be introduced in other Casl2a orthologs disclosed herein at corresponding residue positions as determined by sequence and/or structural alignments. Mutagenesis
[001270] Targeted mutagenesis was used to mutagenize ID405, ID414, and ID418 nucleases in order to improve their editing efficiency in eukaryotic cells.
[001271] In order to conduct the targeted mutagenesis approach, literature analysis was performed on the topic of Casl2a mutagenesis and amino acid mutations which resulted in increased genome editing activity in reported Cast 2a family members. Protein structures were predicted using Alphafold2 and compared with experimentally determined Casl2a protein structures in complex with nucleic acids available in RCSB Protein Data Bank (PDB) database. Tire results of literature analysis and structural data analysis were used to generate a list of mutations to test in ID405, ID414 and ID418 orthologs (Table S13.1). Targeted mutagenesis was performed by inserting synthetic gene fragments (Twist Bioscience) containing the DNA sequence which codes for the mutated amino acid using NEBuilder® HiFi DNA Assembly kit (New England Biolabs) according to the manufacturer’s instructions. Tire mutated DNA and protein sequences are available in supplementary file (see tab “Mutant gene and protein sequences”).
Table S13.1. ID405, ID414 and ID418 amino acid targets for mutagenesis
*Reference list of publications used for selecting amino acids for targeted mutagenesis:
[001272] Schindele, P., & Puchta, H. (2020). Engineering CRISPR/LbCasl2a for highly efficient, temperature-tolerant plant gene editing. Plant biotechnology journal, 18(5), 1118-1120.
[001273] Huang, H., Huang, G., Tan, Z., Hu, Y., Shan, L., Zhou, J., Zhang, X., Ma, S., Lv, W., Huang, T., Liu, Y ., Wang, D., Zhao, X., Lin, Y ., & Rong, Z. (2022). Engineered Casl2a-Plus nuclease enables gene editing with enhanced activity and specificity. BMC biology, 20(1), 91.
[001274] Kleinstiver, B. P., Sousa. A. A., Walton, R. T.. Tak, Y. E., Hsu, J. Y ., Clement, K.. Welch. M. M., Homg, J. E., Malagon-Lopez, J., Scarf'd, L, Maus, M. V., Pinello, L., Aryee, M. J., & Joung, J. K. (2019). Engineered CRISPR-Cas 12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing. Nature biotechnology, 37(3), 276-282.
[001275] Zhang, L., Zuris, J. A., Viswanathan, R., Edelstein, J. N., Turk, R., Thommandru, B., Rube, H. T., Glenn, S. E., Collingwood, M. A., Bode, N. M., Beaudoin, S. F., Lele, S., Scott, S. N., Wasko, K. M., Sexton, S., Borges, C. M., Schubert, M. S., Kurgan, G. L., McNeill, M. S., Fernandez, C. A., Myer, V. E. Morgan, R. A, Behlke, M. A., Vakulskas. C. A. (2021). AsCasl2a ultra nuclease facilitates the rapid generation of therapeutic cell medicines. Nature communications, 12(1), 3908.
Measuring editing efficiency of mutant Casl2a nucleases
[001276] To determine gene editing efficiencies of mutant Cas 12a proteins of Table SI 3.1, the Human embryonic kidney (HEK) cell line 293T (ATCC-CRL-3216) was transfected with mRNA of each mutant Cas 12a nuclease of Table SI 3.1 and a corresponding crRNA of one of five targets (BCL1 la, HBG1, PCSK9. CISH, and TTR) as provided in Table S13.2. The mRNA transfection experiments, and activity determination were performed as described below.
Table SI 3.2. crRNA sequences for mutant Cas 12a nucleases of Table SI 3.1 Casl2a mRNA synthesis for transfection experiments
[001277] 2 pg of each plasmid was linearized using suitable restriction endonuclease that does not have a recognition site inside the target gene and generates either a blunt end or a 5’ protruding end. Digestion products were then purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs), concentrations measured using spectrophotometry- (NanoPhotometer® NP80. IMPLEN). Approximately 1 pg of each purified linearized plasmid was then used as a template for in vitro transcription reaction performed using HiScribe® T7 mRNA Kit with CleanCap® Reagent AG (New England Biolabs). In vitro transcription reaction was run for 2 hours at 37°C. After this step, IVT reaction product was purified using the RNeasy Micro Kit (Qiagen). Part of the purified samples were set aside to assess their quality. The whole volume of the eluate from the purification step was then used in poly(A) tail addition reaction which was performed using E. coll Poly(A) Polymerase (New England Biolabs). After poly(A) tailing, reaction products were purified using the RNeasy Micro Kit (Qiagen), sample concentrations were measured using spectrophotometry (NanoPhotometer® NP80, IMPLEN) and fluorimetry (Qubit RNA Broad Range Assay Kit and Qubit 4, Thermo Fisher Scientific). mRNA integrity was assessed by performing gel electrophoresis using E-Gel Electrophoresis System (Invitrogen). Synthesized mRNA was aliquoted and kept at -80°C until use. mRNA transfection experiments
[001278] To determine whether Casl2a orthologs can be delivered into HEK293T cells as mRNA, five targets in clinically important genes were selected. Synthetic crRNAs against each gene were designed and obtained (Table S13.2).
[001279] As controls, S. pyogenes Cas9 (SpyCas9) and Cas9 target genes (BCL1 la, CISH, HBG1, PCSK9, and TTR), along with synthetic sgRNA (Syntego) (Table S13.3) were used to measure editing efficiency. Commercially available SpCas9 mRNA (TriLink) and in vitro transcribed SpCas9 mRNA were used as positive controls. In the case of Cast 2a orthologs, in vitro transcribed mRNA was used for all experiments. mRNA sequences arc provided in Appendix A at Section P.3.
Table S13.3. Sequences of synthetic Cas9 sgRNAs used for RNA transfections as a part of SpyCas9 controls.
[001280] The transfections were conducted as follows. HEK293T cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) with GlutaMAX (Thermo Fisher Scientific), supplemented with 10 % fetal bovine serum (Thenno Fisher Scientific) and 10,000 units/mL penicillin, and 10,000 pg/mL streptomycin (Thermo Fisher Scientific) at 37°C with 5 % CO2 incubation. HEK293T cells were seeded into 96-well plates (Thermo Fisher Scientific) one day prior to transfection at a density of 18,000 cells per well. Cells were transfected using Lipofectamine MessengerMAX Transfection Reagent (Invitrogen) following the manufacturer’s recommended protocol. For each well of a 96-well plate a total amount of 100 ng RNA was used. This total amount consists of mRNA and crRNA in a ratio of 1 :5. Cells were incubated at 37°C for 72 hours post transfection in 5 % CO2 before genomic DNA extraction. The cells were washed twice with 200 pl IX DPBS (Thermo Fisher Scientific) and resuspended in 25 pl 50 mM Tris-HCl, 150 mM NaCl. 0.05% Tween 20, pH 7.6 (Sigma Aldrich) and 0.2 mg/ml Proteinase K (New England Biolabs) lysis buffer. Resuspended cells were incubated at 55°C for 60 minutes and 95°C for 15 minutes. The genomic region surrounding each Casl2a target site was PCR amplified using primers defined in Table S13.4. PCR amplification was performed using Q5 Hot Start High-Fidelity 2X Master Mix (New England Biolabs) according to the manufacturer’s instructions. The reaction was set up using Ipl of the cell lysate and 0.5 pM of each primer in a final reaction volume of 25 ul.
Table S13.4. Primer sequences used for target amplification in T7 Endonuclease I assay.
Genome editing frequency estimates
[001281] Genome editing frequencies were estimated using T7 Endonuclease I assays. 25 LLL of each PCR reaction was combined with 3 qL NEBuffer 2 (New England Biolabs) and 7 qL of water before denaturation at 95°C for 5 minutes and re-annealing by temperature ramping from 95-85°C at -2°C/s followed by ramping from 85-25°C at -0.1°C/s. 1 qL of T7 Endonuclease I (New England Biolabs) was added to each re-annealed sample and cleavage reactions were incubated at 37°C for 20 min. Fragments were analyzed by performing gel electrophoresis using E-Gel Precast Agarose Gel Electrophoresis system (Invitrogen). 2 % gel with Ethidium bromide dye was used. 8 qL of each sample was mixed with 7 qL of E-Gel Sample Loading Buffer (Invitrogen) and the whole volume was loaded to the well. Genomic target cleavage percentage was calculated using Image J software. FIG. 26 and FIG. 27 demonstrate the editing efficiencies of LbaCasl2a, ID405, ID414, and ID418 proteins as compared to SpCas9 mRNA transfection.
Editing efficiency results
[001282] FIG. 26 and FIG. 27 demonstrate the editing efficiencies of LbaCasl2a, ID405, ID414, and ID418 proteins as compared to SpCas9 mRNA transfection.
[001283] As shown in FIG. 26, endonuclease activity is compared among SpyCas9 (control), LbaCasl2a (control), ID405, and ID414. Cas9 TriLink mRNA was synthesized by TriLink; Cas9 IVT, LbaCasl2a. ID405, and ID414 mRNAs were synthesized in-house via in vitro transcription reaction. Arrows mark cleavage products of LbaCasl2a, ID405, and ID414 nucleases; arrows mark cleavage products of SpyCas9 nucleases. Percentages above each gel well show the editing number determined from the gel using Image J software. [001284] As shown in FIG. 27, endonuclease activity is compared among SpyCas9 (control), LbaCasl2a (control), and ID418. Cas9 TriLink mRNA was synthesized by TriLink; Cas9 IVT, LbaCasl2a, and ID418 mRNAs were synthesized in-house via in vitro transcription reaction. Arrows mark cleavage products of LbaCasl2a and ID418 nucleases; arrows mark cleavage products of SpyCas9 nucleases. Percentages above each gel well show the editing number detennined from the gel using Image J software.
[001285] FIGs. 28A-28O demonstrate the editing efficiencies of LbaCasl2a. ID405, ID414, and ID418 mutant variants as compared to the editing efficiencies of WT Cast 2a, LbaCasl2a and AsCasl2a Ultra nucleases.
[001286] FIG. 28A shows the cleavage products of genomic target PCSK9 visualized on 2 % agarose gel in the presence of various ID405 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID405 mutant were calculated using ImageJ software.
[001287] FIG. 28B shows the cleavage products of genomic target CISH visualized on 2 % agarose gel in the presence of various ID405 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID405 mutant were calculated using ImageJ software.
[001288] FIG. 28C shows the cleavage products of genomic target TTR visualized on 2 % agarose gel in the presence of various ID405 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID405 mutant were calculated using ImageJ software.
[001289] FIG. 28D shows the cleavage products of genomic target PCSK9 visualized on 2 % agarose gel in tire presence of various ID414 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID414 mutant were calculated using ImageJ software.
[001290] FIG. 28E shows the cleavage products of genomic target CISH visualized on 2 % agarose gel in the presence of various ID414 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID414 mutant were calculated using ImageJ software.
[001291] FIG. 28F shows the cleavage products of genomic target TTR visualized on 2 % agarose gel in the presence of various ID414 mutants. Editing efficiency values indicated above gel wells for LbaCasl2a and each ID414 mutant were calculated using ImageJ software.
[001292] FIG. 28G shows the cleavage products of genomic target BCLlla visualized on 2% agarose gel in the presence of various ID405 mutants. Editing efficiency values for LbaCasl 2a and each ID405 mutant were calculated using ImageJ software. [001293] FIG. 28H shows the cleavage products of genomic target HBG1 visualized on 2 % agarose gel in the presence of various ID405 mutants. Editing efficiency values for LbaCasl2a and each ID405 mutant were calculated using Image J software.
[001294] FIG. 281 shows the cleavage products of genomic target BCLlla visualized on 2 % agarose gel in tire presence of various ID414 mutants. Editing efficiency values for LbaCasl2a and each ID414 mutant were calculated using Image J software.
[001295] FIG. 28J shows the cleavage products of genomic target HBG1 visualized on 2 % agarose gel in the presence of various ID414 mutants. Editing efficiency values for LbaCasl2a and each ID414 mutant were calculated using Image J software.
[001296] FIG. 28K shows the cleavage products of genomic target PCSK9 visualized on 2 % agarose gel. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using Image J software.
[001297] FIG. 28L shows the cleavage products of genomic target CISH visualized on 2 % agarose gel in the presence of various ID418 mutants. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using Image J software.
[001298] FIG. 28M shows the cleavage products of genomic target CISH visualized on 2 % agarose gel in the presence of various ID418 mutants. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using Image J software.
[001299] FIG. 28N shows the cleavage products of genomic target BCLlla visualized on 2 % agarose gel in the presence of various ID418 mutants. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using Image J software.
[001300] FIG. 280 shows the cleavage products of genomic target HBG1 visualized on 2 % agarose gel in tire presence of various ID418 mutants. Editing efficiency values for LbaCasl2a and each ID418 mutant were calculated using Image J software.
[001301] FIGs. 29A-29B summarize the results from multiple experiments with ID405-1 (SEQ ID NO: 585) and ID414-1 (SEQ ID NO: 591) mutants respectively, and demonstrates the increase of activity on each of the tested targets compared to WT proteins. As seen from the bar graph in FIG. 29A. ID405-1 mutant showed an increase in editing efficiency from less than 30% (the editing efficiency of the wildtype ID405 nuclease) to over 60% at the PCSK9 target. Similary, the ID405-1 mutant showed an increase in editing efficiency from below 20% (in the wildtype ID405 protein) to nearly 40% at the CISH target. These represent an over 2-fold (2X) increase in editing efficiency at both targets for the ID405-1 mutant as compared to the wildtype ID405 ortholog. In addition, at the TTR target, the ID405 wildtype protein showed no activity, whereas the mutant ID405-1 protein showed nearly 40% editing efficiency.
[001302] As seen from the bar graph in FIG. 29B, the editing efficiency of the ID414-1 mutants (relative to the wildtype ID414 nuclease) increase from less than 40% to over 50% at the PCSK9 target, from less than 20% to over 40% at the TTR target, and from about 20% to over 50% at the CISH target.
Example 14. Computational methods to predict novel single, double, and triple mutations in Casl2a orthologs
[001303] Computations methods were used to predict novel single, double and triple mutations within three Casl2a orthologs. 3D structural models of each ortholog were obtained using AlphaFold v2.0 open source [I] and the models were subsequently relaxed with the RosettaSofwareSuite [2], The putative PAM site for each ortholog was determined by superimposing the protein atoms of native Casl2a (5b43.pdb) onto each of the three 12a ortholog proteins, and the resulting nucleic acid 5b43 nucleic acid coordinates were used as a reference PAM model (pymol align, cycles=0). Individual sites within 6A of the putative PAM were selected for substitution for each ortholog and in-silico substitutions were made at each site to either arginine or alanine. Additional sites were selected for in silico modeling based on literature review.
[001304] Hie RosettaDesign or ddG mode was used to estimate the free energy changes upon amino acid substitutions upon each backbone [2] . Single amino acid substitutions with negative (eg. favorable) or neutral (eg. <2 Rosetta Energy Units, or REU) were selected for visual examination and further follow-up.
References in the Example are as follows:
[001305] [1] Jumper, J et al. Highly accurate protein structure prediction with AlphaFold.
[001306] [2] Maguire JB, Haddox HK, Strickland D, Halabiya SF, Coventry B, Griffin JR, Pulavarti
SVSRK, Cummins M, Thicker DF, Klavins E, Szyperski T, DiMaio F, Baker D, and Kuhlman B. (2020). Perturbing the energy landscape for improved packing during computational protein design. Proteins 2021. doi: 10.1002/prot.26030.
[001307] Using the above computational approach, the following Casl2a mutant variants (based on Casl2a ID405 (SEQ ID NO: 334) as a reference Casl2a ortholog sequence) comprising novel single, double, and triple mutations were predicted.
[001308] Using the above computational approach, the following Casl2a mutant variants (based on Casl2a ID414 (SEQ ID NO: 58) as a reference Casl2a ortholog sequence) comprising novel single, double, and triple mutations were predicted.
[001309] Using the above computational approach, the following Casl2a mutant variants (based on Casl2a ID418 (SEQ ID NO: 564) as a reference Casl2a ortholog sequence) comprising novel single, double, and triple mutations were predicted.
Example 15. Determination of gene editing efficiency of ID405-1 (D169R), ID414-1 (T154R), and ID418-3 (D161R/T532R/K538R)
[001310] ID405-1 (D169R) (SEQ ID NO: 585), ID414-1 (T154R) (SEQ ID NO: 591), and ID418-3
(D161R/T532R/K538R) (SEQ ID NO: 599) were selected as objects for gene editing efficiency determination by sequencing according to T7 Endonuclease I assay results shown in the above examples. Lysates of HEK293T cells transfected with aforementioned mutants, ID405, ID414, and ID418 wild-type nuclease, LbaCasl2a. and AsCasl2a Ultra mRNAs were prepared for deep sequencing to detennine the activity of Casl2a orthologs in eukaryotic cells by studying the rates of NHEJ outcomes in the genomic HBG1 target site of treated cells. Briefly, the genomic target regions were amplified and fragments extended with Illumina sequences including a unique index for each sample through two rounds of PCR. 4 pL of each lysate sample was used as template in the primary PCR reaction. For the primary PCR custom primers were used that were complementary to the sequences surrounding the genomic targets and had non-complemcntary ‘tails ’ with Illumina adapter sequences (SEQ ID NOs: 1400 - 1460; sequences provided in Appendix A, subsection R of this specification). Q5 HotStart 2x MasterMix (New England Biolabs) was used for the primary PCR and the reaction set up using 4 pL of cell lysate as template and 0.2 pM of each primer in a final volume of 25 pL. The cycling conditions used were: 98°C for 2min 30s, 24 cycles of 98°C for 30s, 56.5°C for 30s, 72°C for 25s, and final extension at 72°C for 2min. The primary PCR product was purified using Ampure XP (Beckman Coulter) magnetic beads and used for the secondary PCR.
[001311] Secondary PCR was performed using PCR Add-on Kit for Illumina (Lexogen) with primers encoding Illumina sequences and a 6 nt i7 index (Lexogen i7 6 nt Index Set (7001-7096)) according to the manufacturer’s instructions. Cycling conditions for secondary PCR were as follows: 98°C for 30s, 8 cycles at 98°C for 10s. 65°C for 20s and 72°C for 30s. followed by final extension at 72°C for 1 min. The secondary PCR products were purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs), their quantity and quality checked using spectrophotometry (NanoPhotometer® NP80, IMPLEN) and fluorimetry (Qubit IX dsDNA HS Assay and Qubit 4, Thermo Fisher Scientific). The purified samples were pooled in an equimolar ratio and size selection performed using Ampure XP (Beckman Coulter) magnetic beads. The resulting library quantified using NEBNext Library Quant Kit for Illumina (New England Biolabs). Final library pool was prepared for deep sequencing according to Illumina’s specifications. Paired end sequencing was performed using the MiSeq Reagent Kit v2 (300-cycles) (Illumina) on the MiSeq System (Illumina) with 25% PhiX v.3 (Illumina). All sequencing data analysis was done using Geneious Prime 2023.0.4. Reads were trimmed and filtered using BBDuk and mapped to the reference sequence with a 50 nt quantification window set around the target site. Reads that had differences from the reference sequence in this window were included in genome editing efficiency calculations.
[001312] Efficiency results are presented in Figure 32 and reads with the top 5 most common editing outcomes presented in Figure 33. Sequencing results show that in all cases mutant nucleases demonstrate significantly higher editing efficiency compared to wild-type proteins. Editing efficiencies by ID405-1 mutant is comparable to that of AsCasl2a Ultra.
Targeted mutagenesis
[001313] Hie aim of Example 14 was to predict novel mutations in Casl2a orthologs. In this example, those mutations were tested to determine their effect on further improving ID405, ID414 and ID418 editing efficiency in eukaryotic cells by combining mutations from the first mutagenesis round (Example 13) with newly identified possible mutations (Example 14 - computational predictions of possible mutations), in silica analysis was first performed in accordance with Example 14. Targeted mutagenesis was then performed by inserting synthetic gene fragments (Twist Bioscience) containing the DNA sequence which codes for the desired mutated amino acid using NEBuilder® HiFi DNA Assembly kit (New England Biolabs) according to the manufacturer’s instructions. The mutation list is available in Table 1 below. Mutated protein and DNA sequences are provided in Appendix A (subsection R) of this specification - SEQ ID NOs: 1461-1490 for protein sequences: SEQ ID NOs: 1491- 1520 for nucleotide sequences).
Table 1. ID405, ID414 and ID418 amino acid targets for mutagenesis. Additional mutations beyond vaseline variants are underlined.
Mutant mRNA synthesis
[001314] Once the intended round of mutant Cast 2a design was completed and mutant plasmids were constructed, mRNA was synthesized for use in RNA transfection experiments.
[001315] After verification by sequencing of mutant plasmids, 2 pg of each plasmid was linearized using suitable restriction endonuclease that did not have a recognition site inside the target gene and generated either a blunt end or a 5’ protruding end. Digestion products were then purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs), concentrations measured using spectrophotometry (NanoPhotometer® NP80, IMPLEN). Approximately 1 pg of each purified linearized plasmid was then used as a template for in vitro transcription performed using HiScribe® T7 mRNA Kit with CleanCap® Reagent AG (New England Biolabs). In vitro transcription (IVT) reaction was run for 2 hours at 37°C. After this step, IVT reaction product was purified using the RNeasy Micro Kit (Qiagen). Part of the purified samples were set aside to assess their quality. Whole volume of the eluate from the purification step was then used in poly(A) tail addition reaction which was performed using E. coli Poly(A) Polymerase (New England Biolabs). After poly(A) tailing, reaction products were purified using the RNeasy Micro Kit (Qiagen), sample concentrations were measured using spectrophotometry (NanoPhotometer® NP80, IMPLEN) and fluorimetry (Qubit RNA Broad Range Assay Kit and Qubit 4, Thermo Fisher Scientific). mRNA integrity was assessed by performing gel electrophoresis using E-Gel Electrophoresis System (Invitrogen). Synthesized mRNA was aliquoted and kept at -80°C until use.
Activity of mutant Casl2a proteins
[001316] To determine gene editing efficiencies of mutant Casl2a proteins in the human embryonic kidney (HEK) cell line 293T (ATCC-CRL-3216), cells were transfected with mRNA of each Casl2a nuclease and crRNA of one of two genomic targets (HBG1 and TTR). The mRNA transfection experiments and activity determination were performed as described below.
[001317] Two targets in clinically important genes were selected and synthetic crRNA for them was ordered (Protein ID 122-129) (Table 2, see below).
Table 2, Sequences of crRNAs used for RNA transfections.
[001318] HEK293T cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) with GlutaMAX (Thermo Fisher Scientific), supplemented with 10 % fetal bovine serum (Thermo Fisher Scientific) and 10,000 units/mL penicillin, and 10,000 pg/mL streptomycin (Thenno Fisher Scientific) at 37°C with 5 % CO2 incubation.
[001319] HEK293T cells were seeded into 96-well plates (Thermo Fisher Scientific) one day prior to transfection at a density of 18,000 cells per well. Cells were transfected using Lipofectamine MessengerMAX Transfection Reagent (Invitrogen) following the manufacturer’s recommended protocol. For each well of a 96-well plate a total amount of 100 ng RNA was used. This total amount consists of mRNA and crRNA in a ratio of 1 :4. Cells were incubated at 37°C for 72 hours post transfection in 5 % CO2 before genomic DNA extraction. Tire cells were washed twice with 200 pl IX DPBS (Thenno Fisher Scientific) and resuspended in 25 pl 50 mM Tris-HCl, 150 mM NaCl, 0.05% Tween 20, pH 7.6 (Sigma Aldrich) and 0.2 mg/ml Proteinase K (New England Biolabs) lysis buffer. Resuspended cells were incubated at 55°C for 60 minutes and 95°C for 15 minutes. Genomic region surrounding each Casl2a target site was PCR amplified using primers defined in the Table 3 (Protein ID130 - ID133). PCR amplification was performed using Q5 Hot Start High-Fidelity 2X Master Mix (New England Biolabs) according to the manufacturer’s instructions. The reaction was set up using Ipl of the cell lysate and 0.5 pM of each primer in a final reaction volume of 25 pl.
Table 3, Primer sequences used for target amplification in T7 Endonuclease I assay
[001320] Genome editing frequencies were estimated using T7 Endonuclease I assays. 20 qL of each PCR reaction was combined with 3 qL NEBuffer 2 (New England Biolabs) and 7 qL of water before denaturation at 95°C for 5 minutes and re-annealing by temperature ramping from 95-85°C at -2°C/s followed by ramping from 85-25°C at -0.1°C/s. 1 qL of T7 Endonuclease I (New England Biolabs) was added to each re-annealed sample and cleavage reactions were incubated at 37°C for 20 min. Fragments were analyzed by performing gel electrophoresis using E-Gel Precast Agarose Gel Electrophoresis system (Invitrogen). 2 % gel with Ethidium bromide dye was used. 8 qL of each sample was mixed with 7 qL of E-Gel Sample Loading Buffer (Invitrogen) and tire whole volume was loaded to the well. Genomic target cleavage percentage was calculated using Image J software.
Gene editing efficiency determination by deep-sequencing
[001321] ID405-2-1, ID405-2-2, ID405-2-4, ID405-2-5, ID405-2-7, ID405-2-8, and ID405-2-9 were selected as objects for gene editing efficiency determination by sequencing according to T7 Endonuclease I assay results. Lysates of HEK293T cells transfected with aforementioned mutants, AsCasI2a Ultra, and ID405-1 (ID405-D169R from Example 13, SEQ ID NO: 585) mRNAs were prepared for deep sequencing to determine the activity of Casl2a orthologs in eukaryotic cells by studying the rates of NHEJ outcomes in the genomic target sites of treated cells. Briefly, the genomic target regions were amplified and fragments extended with Illumina sequences including a unique index for each sample through two rounds of PCR. 4 qL of each lysate sample was used as template in the primary PCR reaction. For the primary PCR custom primers were used that were complementary to the sequences surrounding the genomic targets and had non- complementary ‘tails’ with Illumina adapter sequences (SEQ ID NOs: 1400-1460; see Appendix A, subsection R). Q5 HotStart 2x MasterMix (New England Biolabs) was used for the primary PCR and the reaction set up using 4 qL of cell lysate as template and 0.2 qM of each primer in a final volume of 25 qL. The cycling conditions used were: 98°C for 2 min 30 s, 24 cycles of 98°C for 30 s, 56.5°C for 30 s. 72°C for 25 s, and final extension at 72°C for 2 min. The primary PCR product was purified using Ampure XP (Beckman Coulter) magnetic beads and used for the secondary PCR.
[001322] Secondary PCR was performed using PCR Add-on Kit for Illumina (Lexogen) with primers encoding Illumina sequences and a 6 nt i7 index (Lexogen i7 6 nt Index Set (7001-7096)) according to the manufacturer’s instructions. Cycling conditions for secondary PCR were as follows: 98°C for 30 s, 8 cycles at 98°C for 10 s, 65°C for 20 s and 72°C for 30 s, followed by final extension at 72°C for 1 min. The secondary- PCR products were purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs), their quantity and quality checked using spectrophotometry (NanoPhotometer® NP80, IMPLEN) and fluorimetry (Qubit IX dsDNA HS Assay and Qubit 4, Thermo Fisher Scientific). The purified samples were pooled in an equimolar ratio and size selection performed using Ampure XP (Beckman Coulter) magnetic beads. The resulting library quantified using NEBNext Library Quant Kit for Illumina (New England Biolabs). Final library pool was prepared for deep sequencing according to Illumina’s specifications. Paired end sequencing was performed using the MiSeq Reagent Kit v2 (300-cycles) (Illumina) on the MiSeq System (Illumina) with 20% PhiX v.3 (Illumina). All sequencing data analysis was done using Geneious Prime 2023.0.4. Reads were trimmed and filtered using BBDuk and mapped to the reference sequence with a 50nt quantification window set around the target site. Reads that had differences from the reference sequence in this window were included in genome editing efficiency calculations.
[001323] Efficiency results are presented in FIG. 41 and reads with the top 5 most common editing outcomes presented in FIG. 42. sequencing results show that in all cases mutant nucleases demonstrate significantly higher editing efficiency compared to wild-type proteins. Editing by ID405-2-1, ID405-2-2, ID405-2-5, and ID405-2-8 mutants is comparable to that of AsCasl2a Ultra.
Expression and purification of Cast 2a orthologs
[001324] E. coll codon-optimized Casl2a mutant ortholog genes (ID405-1, ID414-1, ID418-3 and AsCasl2a Ultra) (sequences provided in Appendix A, subsection R; SEQ ID NOs: 1521-1524 for protein sequences; SEQ ID NOs: 1525-1528 for nucleotide sequences), containing a 6xHis (SEQ ID NO:2661) affinity tag at the C-tenninus, were cloned into pET21(+) vectors and expressed in E. coll strain T7 Express (New England Biolabs) at 23°C for 16 h in the presence of 0.5 mM IPTG. The cells were pelleted bycentrifugation and resuspended in Lysis buffer (20 mM Tris-HCl pH=7.5, 300 mM NaCl, 5% (v/v) glycerol, 0.2% (v/v) Tween® 20. 0.1 mM TCEP. 1 mM EDTA, lx Halt™ Protease Inhibitor Cocktail (Thermo Fisher Scientific)) and disrupted by sonication. The resulting lysate was clarified by centrifugation and the supernatant filtered through a 0.22 pm pore size filter and loaded onto a 5 ml HisTrap™ HP (Cityva) column. The target protein was eluted with a linear gradient of increasing imidazole concentration (40 mM to 700 mM) in 20 mM Tris-HCl pH=7.5, 300 mM NaCl buffer. The fractions containing the Cas 12a protein were pooled and loaded onto a 5 ml HiTrap™ Heparin HP (Cityva) column. Tire target protein was eluted with a linear gradient of increasing NaCl concentration (300 mM to 2 M) in 20 mM Tris-HCl pH=7.5 buffer. The fractions containing the Cas 12a protein were pooled and dialyzed against 20 mM Tris-HCl pH=7.4, 300 mM NaCl. 0.1 mM EDTA, 1 mM DTT, 50% (v/v) glycerol buffer. The dialyzed sample was then diluted to reduce the glycerol concentration to 10% and loaded onto a HiLoad™ 16/600 Superdex™ 200 pg (Cityva) column. The protein was eluted with 20 mM Tris-HCl pH=7.4, 300 mM NaCl, 0. 1 mM EDTA, 1 mM DTT, 10% glycerol buffer. Fractions containing the Cas 12a protein were pooled and dialyzed against 20 mM Tris- HCl pH=7.4, 300 mM NaCl, 0.1 mM EDTA, 1 mM DTT, 50% (v/v) glycerol buffer. The resulting sample was then concentrated using Pierce™ Protein Concentrators PES. 10K MWCO (Thermo Fisher Scientific) and stored in -20°C.
Electroporation of purified Cas 12a orthologs
[001325] To determine whether the purified Cas 12a orthologs were functional in living cells, electroporation of HEK293T cells with RNPs of purified Cas 12a orthologs and synthetic crRNAs was performed; Alt-R A.s. Casl2a (Cpfl) (Integrated DNA Technologies) was used as a control. In order to do this, HEK293T cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) with GlutaMAX (Thermo Fisher Scientific), supplemented with 10 % fetal bovine serum (Thermo Fisher Scientific) and 10,000 units/mL penicillin, and 10,000 pg/mL streptomycin (Thermo Fisher Scientific) at 37°C with 5 % CO2 incubation. Two days before the electroporation, cells were split and maintained as described above. On the day of the experiment, cells were washed using Dulbecco’s Phosphate Saline Buffer (DPBS) (Thermo Fisher Scientific) and trypsinized using TrypLE Express Enzyme (IX) (Thermo Fisher Scientific). Collected cells resuspended in DPBS were diluted using SF Cell Line Nucleofector Solution (Lonza) supplemented with Supplement 1 (Lonza). RNPs were assembled in Nucleofector solution supplemented with Supplement 1 using 126 pmol of each purified nuclease (ID405. ID414, ID418, AsCasl2a Ultra); control reaction was assembled using Alt-R A.s. Casl2a (Cpfl) (Integrated DNA Technologies), and 160 pmol of crRNA (genomic targets - HBG1 and TTR). RNP assembly reactions were incubated at room temperature for 20 minutes, then kept at +4°C until nucleofection. 2 x 10’ cells per sample were added into the RNP assembly reaction and whole volume was transferred to 16-well Nucleocuvette Strips (Lonza). Cells were electroporated using preprogrammed protocol CM- 130 using 4D-Nuclcofcctor (Lonza). After electroporation, contents of each well were split and seeded into 4 w ells containing pre-wanned Dulbecco’s modified Eagle’s Medium (DMEM) with GlutaMAX (Thermo Fisher Scientific), supplemented with 10 % fetal bovine serum (Thermo Fisher Scientific) in 96-well plate (Thenno Fisher Scientific). Cells were then grown for 48 h at 37°C in 5 % CO2 before genomic DNA extraction. The cells were washed twice with 200 pl IX DPBS (Thermo Fisher Scientific) and resuspended in 25 pl 50 mM Tris-HCl, 150 mM NaCl, 0.05% Tween 20, pH 7.6 (Sigma Aldrich) and 0.2 mg/ml Proteinase K (New England Biolabs) lysis buffer. Resuspended cells were incubated at 55°C for 60 minutes and 95°C for 15 minutes. Genomic region surrounding each Casl2a target site was PCR amplified using primers SEQ ID NOs: 2356-2359. PCR amplification was performed using Q5 Hot Start High-Fidelity 2X Master Mix (New England Biolabs) according to the manufacturer's instructions. Tire reaction was set up using I l of the cell lysate and 0.5 pM of each primer in a final reaction volume of 25 pl.
[001326] Genome editing frequencies were estimated using T7 Endonuclease I assays. 20 pL of each PCR reaction was combined with 3 pL NEBuffer 2 (New England Biolabs) and 7 pL of water before denaturation at 95°C for 5 minutes and re-annealing by temperature ramping from 95-85°C at -2°C/s followed by ramping from 85-25°C at -0.1°C/s. 1 pL of T7 Endonuclease I (New England Biolabs) was added to each re-annealed sample and cleavage reactions were incubated at 37°C for 20 min. Fragments were analyzed by performing gel electrophoresis using E-Gel Precast Agarose Gel Electrophoresis system (Invitrogen). 2 % gel with Ethidium bromide dye was used. 8 pL of each sample was mixed with 7 pL of E-Gel Sample Loading Buffer (Invitrogen) and the whole volume was loaded to the well. Genomic target cleavage percentage was calculated using Image J software.
EXAMPLE 16: Arginine scanning mutagenesis results in type V editor variants with improved function [001327] Site-directed scanning mutagenesis is a useful tool applied in studying protein function and designing proteins with new properties, such as increased stability or enzymatic activity. In this experiment, a computational approach (‘‘computational arginine scanning”) was used to develop a prioritized list of amino acid residues in the type V ortholog referred to herein as ID405 (SEQ ID NO: 334) which are predicted to have a meaningful interaction with a type V guide RNA. The identified positions were then engineered to be replaced with an arginine residue to create a series of arginine-containing variants. Without being bound by theory, the arginine residues (which carry a positive charge) are drought to provide a stronger interaction with the guide RNA at the substituted positions. The arginine-containing variants were tiren tested in an editing assay to determine whether editing efficiency was improved.
Step 1. Computational arginine scanning
[001328] Alpha Fold (open access Al based protein fold prediction software) was used to generate a three dimensional model of ID405. A tertiary complex of ID405, including both RNA and DNA was then created by superimposing the protein atoms of a homologous Casl2a (example 5b43.pdb) with AlphaFold- ID405 model and directly taking the nucleotide (eg “DNA” and “RNA”) atomic coordinates from the homolog.
[001329] The entire ID405 ribonucleic complex was minimized with standard modeling software (eg MOE, PyMoL, Rosetta) using the default energy function and vary ing dielectrics (examples D=2,3,4). A set of atoms ("DNA or RNA") was created from the two bound nucleotide chains and a list of all contacts between the protein atoms and bound nucleotide atoms was created for a given distance threshold (examples distances could include 3 A. 3.5A, 4A 4.5A). Individual atom contact energies for each amino acid within the distance threshold were summed and saved as the native nucleotide (NT) binding affinity score. For each residue within the threshold, standard modeling software (such as, but not limited to Rosetta, Schordinger, and Molecular Operating Environment (MOE)) was used to mutate each individual selected ID405 site in- silico to Arginine. Surrounding residues to the mutated site were repacked and additional minimization steps were performed if a large clash resulted. Resulting protein contacts and energetic scores between atoms of the site mutated to Arginine and any nucleotide were summed and recorded as the arginine nucleotide (NT) binding affinity score. The change in score between the starting wild ty pe amino acid contacts and the mutated arginine amino acid were calculated and recorded as a '‘interchain ddG” or nucleotide binding affinity.
[001330] Independently, the delta in energetic contribution of each native amino acid within the distance threshold to the protein fold was also calculated before and after in silico mutation to arginine using standard modeling software and repacking neighboring residues (examples of standard software is as above). This score was recorded as the “intrachain ddG”.
[001331] Sites were sorted by magnitude of predicted interchain ddG (large negative values were favorable) and filtered such that the intra-chain ddG was less than a suitable threshold (values considered included <0, <1, <2, <3, <4 and <5). Residues that were native Arginine were ignored. Based on this criteria, 24 sites were prioritized for experimental validation, one of which (D169R) was already incorporated into ID405 as ID405-1 (SEQ ID NO: 585).
[001332] For illustrative purposes, FIG. 48 shows K292 amino acid native residue that is overlayed with the R292 substitution in the context of the three-dimensional structure of ID405-1 bound to a guide RNA. As can be inspected, the Arg292 residue provides for greater contacts (two dotted lines, versus a single dotted line) with the guide RNA.
[001333] In another example, FIG. 49 shows Q492 amino acid native residue that is overlayed with tire R492 substitution in the context of the three-dimensional structure of ID405-1 bound to a guide RNA. As can be inspected, the Arg492 residue provides for greater contacts (two dotted lines, versus a no dotted line) with the guide RNA.
[001334] In yet another example, FIG. 50 shows N770 amino acid native residue that is overlayed with the R770 substitution in the context of the three-dimensional structure of ID405-1 bound to a guide RNA. As can be inspected, the Arg770 residue provides for greater contacts (two dotted lines, versus a no dotted line) with the guide RNA.
Step 2, Experimental testing of select ID405-1 arginine substitution mutants leads to improved editing in primary cells
[001335] As described above in Step 1, a computational approach was undertaken to identify residues in ID405-1 that make contact sites with nucleic acid and which represent good candidates for site-specific substitution with arginine (positively charged) for enhancing said contact. It was reasoned that mutating these residues to arginine (R) could increase the affinity for guide RNAs and improve editing. The goal of this Example was to design a variant ID405-1 variant with improved editing through systematic mutational analysis and to, in general, identify a strategy for improving the editing efficiency of any Cas nuclease, such as any Type V Cas nuclease, including those disclosed herein.
RESULTS AND DISCUSSION
[001336] FIG. 51 show s the editing efficiency of the arginine variants constructed in Step 1 as measured in primary HSPCs. Each of these variants comprise both D169R replacement as well as the designated additional arginine replacement. Cells were electroporated with RNA using the protocol detailed in the Materials and Methods section below and 72 hours later samples were harvested for next generation sequencing (NGS) analysis. The benchmark control ID405-1 (base sequence SEQ ID NO: 585; tested variant with NLS/Linker SEQ ID NO: 1532 )was termed “WT” for the purposes of this experiment, despite being a modified nuclease, as compared to true wild-type ID405. This WT nuclease (ID405-1) edited the B2M locus at 63.4%. Arginine substitution mutants identified in Step 1 that demonstrated editing efficiency below the dotted line perfonned w ith lower editing efficiency than WT and those above performed with higher editing efficiency than WT. For example, ID405-1 (K292R) (SEQ ID NO: 1549) performed with the highest editing efficiency at 83.4%.
[001337] This example demonstrates that arginine scanning — particularly where computation prediction is used first to predict the optimal residue for arginine replacement — can be used to improve the editing efficiency of a type V nuclease. This approach can also be used to improve the editing efficiency of other type V nucleases disclosed herein, as well as type II nucleases, or any nucleic acid programmable nuclease which fomis a complex with a guide RNA.
[001338] Thus, in the context of type V ortholog ID405, this example demonstrates editing efficiency can be improved for nearly all of the arginine replacement variants tested, which are designated as follows: ID405 (Q492R); ID405 (T306R): ID405 (L748R); ID405 (A739R); ID405 (F297R); ID405 (D169R) [which is also designated herein as ID405-1]; ID405 (N536R); ID405 (D85IR); ID405 (N770R); ID405 (D675R); ID405 (K955R); ID405 (S972R); ID405 (N798R); ID405 (K298R); ID405 (H853R); ID405 (E377R); ID405 (V295R); ID405 (K852R); ID405 (F854R); ID405 (N1015R); ID405 (T845R); ID405 (E1019R); ID405 (K745R); and ID405 (K292R).
Table of Representative ID405 Arginine Replacement Variants
[001339] In addition, this specification is not limited to arginine replacement variants of ID405, but contemplates arginine replacement variants of any type V nuclease ortholog disclosed herein wherein the replacements are at residue positions that correspond to the positions of Q492R; T306R: L748R; A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R; N1015R; T845R; E1019R; K745R; and K292R, as determined by a BLAST alignment between ID405 and tire type V nuclease ortholog in which the substitutions are being made.
[001340] In addition, this specification contemplates variant type V orthologs that are engineered to contain two or more arginine replacements selected from the group consisting of: Q492R; T306R; L748R; A739R: F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R: N798R; K298R; H853R; E377R: V295R: K852R; F854R; N1015R; T845R; E1019R; K745R; and K292R. relative to the amino acid sequence of ID405, or at a corresponding residue positions in a type V ortholog of ID405 as determined by a BLAST alignment.
[001341] In certain embodiments, the specification contemplates a type V variant having a Q492R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: T306R; L748R; A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R;
N1015R; T845R; E1019R; K745R: and K292R.
[001342] In certain embodiments, tire specification contemplates a type V variant having a T306R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; L748R; A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R;
N1015R; T845R; E1019R; K745R; and K292R.
[001343] In certain embodiments, the specification contemplates a type V variant having a L748R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; A739R; F297R; D169R; N536R; D85 I R; N770R; D675R; K955R; S972R: N798R; K298R; H853R; E377R: V295R; K852R; F854R;
N1015R; T845R: E1019R; K745R: and K292R.
[001344] In certain embodiments, the specification contemplates a type V variant having a A739R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R: F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R;
N1015R; T845R; E1019R; K745R; and K292R. [001345] In certain embodiments, the specification contemplates a type V variant having a F297R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R; N1015R; T845R; E1019R; K745R; and K292R.
[001346] In certain embodiments, the specification contemplates a type V variant having a D 169R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R: F297R: N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R; N1015R; T845R; E1019R; K745R; and K292R.
[001347] In certain embodiments, the specification contemplates a type V variant having aN536R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R; N1015R; T845R; E1019R; K745R: and K292R.
[001348] In certain embodiments, tire specification contemplates a type V variant having a D851R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R; N1015R; T845R; E1019R; K745R; and K292R.
[001349] In certain embodiments, the specification contemplates a type V variant having aN770R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R: D851R; D675R; K955R; S972R: N798R; K298R; H853R; E377R: V295R; K852R; F854R; N1015R; T845R: E1019R; K745R: and K292R.
[001350] In certain embodiments, the specification contemplates a type V variant having a D675R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R: A739R; F297R; D169R; N536R; D851R; N770R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R; N1015R; T845R; E1019R; K745R; and K292R. [001351] In certain embodiments, the specification contemplates a type V variant having a K955R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R; D851R; N770R; D675R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R;
N1015R; T845R; E1019R; K745R; and K292R.
[001352] In certain embodiments, the specification contemplates a type V variant having a S972R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R: F297R: D169R; N536R; D851R; N770R; D675R; K955R; N798R; K298R; H853R; E377R; V295R; K852R; F854R;
N1015R; T845R; E1019R; K745R; and K292R.
[001353] In certain embodiments, the specification contemplates a type V variant having aN798R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; K298R; H853R; E377R: V295R; K852R; F854R;
N1015R; T845R; E1019R; K745R: and K292R.
[001354] In certain embodiments, tire specification contemplates a type V variant having a K298R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; H853R; E377R; V295R; K852R; F854R;
N1015R; T845R; E1019R; K745R; and K292R.
[001355] In certain embodiments, the specification contemplates a type V variant having a H853R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R: D851R; N770R; D675R; K955R; S972R; N798R; K298R; E377R: V295R; K852R; F854R;
N1015R; T845R: E1019R; K745R: and K292R.
[001356] In certain embodiments, the specification contemplates a type V variant having a Q492R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R: A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R;
N1015R; T845R; E1019R; K745R; and K292R. [001357] In certain embodiments, the specification contemplates a type V variant having a E377R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; V295R; K852R; F854R;
N1015R; T845R; E1019R; K745R; and K292R.
[001358] In certain embodiments, the specification contemplates a type V variant having a V295R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R: F297R: D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; K852R; F854R;
N1015R; T845R; E1019R; K745R; and K292R.
[001359] In certain embodiments, the specification contemplates a type V variant having a K852R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; F854R;
N1015R; T845R; E1019R; K745R: and K292R.
[001360] In certain embodiments, tire specification contemplates a type V variant having a F854R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R;
N1015R; T845R; E1019R; K745R; and K292R.
[001361] In certain embodiments, the specification contemplates a type V variant having aN1015R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R: D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R; T845R: E1019R; K745R: and K292R.
[001362] In certain embodiments, the specification contemplates a type V variant having a K745R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R: A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R; T845R; E1019R; and K292R. [001363] In certain embodiments, the specification contemplates a type V variant having a K292R substitution (or equivalent substitution based on a BLAST alignment with ID405), optionally further comprising one or more of the following substitutions: Q492R; T306R; L748R; A739R; F297R; D169R; N536R; D851R; N770R; D675R; K955R; S972R; N798R; K298R; H853R; E377R; V295R; K852R; F854R; T845R; E1019R; and K745R.
[001364] As to any of the type V variants contemplated by the method of this Example, this specification also contemplates type V proteins having at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 99%, or up to 100% sequence identity with any of the type V variants contemplated in this Example. In certain embodiments, the present disclosure contemplates a type V protein, or a polynucleotide encoding the same, having at least 80%, or at least 85%, or at least 90%, or at least 95%, or at least 99%, or up to 100% sequence identity with any of SEQ ID NOs: 2306-2351 and 1532-1555.
MATERIALS AND METHODS:
Mammalian cell culture
[001365] Primary human CD34+ HSPCs were cultured in X-Vivo 15 medium (Lonza Catalog #: 02- 053Q) supplemented with 100 ng/rnL SCF (RnD Systems Inc. 11010-SC-100), 100 ng/uL FLT-3L (RnD Systems Inc. 308-FKHB-250), and 100 ng/uL recombinant human thrombopoetin (RnD Systems Inc. 288- TPN-100/CF). HSPCs were thawed and cultured for three days before electroporation.
Electroporation
[001366] HSPCs were electroporated using a Lonza 4D 96-well electroporator and a Lonza P3 Primary cell kit (Catalog #: V4SP-3096). Briefly, 100,000 HSPCs were resuspended in Lonza P3 buffer and combined with 6 ug RNA to a total volume of 20 uL unless otherwise noted. The samples were electroporated using the DS-130 program, 80 uL of pre-warmed cell culture medium was added to the cells immediately after electroporation, and the entire mixture transferred to a pre-wanned 96-well plate containing 100 pL of cell culture medium. Samples were allowed to grow at 37°C 5% CO? for three days before harvesting genomic DNA (gDNA) using prepGEM (MicroGem PUN 1000) according to the manufacturer’s instructions.
Genomic DNA extraction
[001367] After incubation, the media was removed from tire cells and genomic DNA was extracted by the addition of prepGEM reagent (Thomas Scientific: PUN0050) directly into each well of the tissue culture plate. Lysed cells were transferred to a 96 well PCR plate and incubated at 75°C for 10 minutes, followed by 95 °C enzyme inactivation step for 5 minutes. Next Generation Sequencing and Analysis
[001368] Using prepGEM lysates as template, the edited B2M site was amplified by PCR and prepared for Illumina sequencing. Tire resulting data was analyzed using CRISPREsso2. Editing outcome (InDels%) was calculated as the number of modified reads divided by total aligned reads.
In vitro transcription (IVT) reaction
[001369] Plasmids for IVT were made with gBlocks from IDT and NEB assembly. In vitro transcription performed using NEB HiScribe according to manufacturer’s protocol using nl methyl pseudouridine supplementation. NEB is New England Biolabs. IDT is Integrated DNA Technologies.
Primers used for NGS
Human B2M fwd: CCTGAATTGCTATGTGTCTGGG (SEQ ID NO: 1529)
Human B2m rev: CTCATACACAACTTTCAGCAGC (SEQ ID NO: 1530)
405-1 targeting spacer used to target human B2M (gRNA procured from IDT):
AGTGGGGGTGAATTCAGTGT (SEQ ID NO: 1531)
Protein sequences of type V arginine substitution variants described in this Example
[001370] ID405-1 (arginine replacement locations in following sequences are relative to this sequence after the NLS/glycine linker shown in underlined text)) (SEQ ID NO: 1532); ID405-1 (A739R) (SEQ ID NO: 1533); ID405-1 (V295R) (SEQ ID NO: 1534); ID405-1 (T845R) (SEQ ID NO: 1535); ID405-1 (T306R) (SEQ ID NO: 1536); ID405-1 (S972R) (SEQ ID NO: 1537); ID405-1 (Q675R) (SEQ ID NO: 1538); ID405-1 (Q492R) (SEQ ID NO: 1539); ID405-1 (N1015R) (SEQ ID NO: 1540); ID405-1 (N798R) (SEQ ID NO: 1541); ID405-1 (N770R) (SEQ ID NO: 1542); ID405-1 (N536R) (SEQ ID NO: 1543); ID405-1 (L748R) (SEQ ID NO: 1544); ID405-1 (K955R) (SEQ ID NO: 1545); ID405-1 (K852R) (SEQ ID NO: 1546); ID405- 1 (K745R) (SEQ ID NO: 1547); ID405-1 (K298R) (SEQ ID NO: 1548); ID405-1 (K292R) (SEQ ID NO: 1549); ID405-1 (H853R) (SEQ ID NO: 1550); ID405-1 (F854R) (SEQ ID NO: 1551); ID405-1 (F297R) (SEQ ID NO: 1552); ID405-1 (E1019R) (SEQ ID NO: 1553); ID405-1 (E377R) (SEQ ID NO: 1554); ID405- 1 (D851R) (SEQ ID NO: 1555).
EXAMPLE 16B: Arginine scanning mutagenesis; Continued
[001371] Without intending to be limited to any particular theory , in view of the distal location of the top five mutations discovered in Example 16 along the protein’s structure, it is hypothesized that these mutations can be combined synergistically, or at least harmoniously. Tire five most effective mutation points are combined to generate double, triple, quadruple and quintuple mutants. These mutants are generated based on a 405-1 construct containing 3x NLS in the format:
NLS 1 -Linker-Type V Sequence-Linker-NLS2-Linker-NL3 wherein NLS1 is cMyc NLS (SEQ ID NOs: 2492 and 2496), NLS2 is SV40 NLS (SEQ ID NOs: 2493 and 2497), NLS3 is Nucleoplasmin NLS (SEQ ID NOs: 2494 and 2498), and linker is a 4x glycine linker (SEQ ID NOs: 2490 and 2495).
[001372] Method and Materials - Mobilized Human Peripheral Blood CD34+ Cells (AllCells, Donor ID# 888824822) are thawed on Day 0. The following media is used for thawing and activation: c-XVIVO Media (Complete X-VIVO) = X-VIVO + O.lug/mL SCF + O.lug/mL FLT3L + O. lug/mL TPO [X-VIVO 15 (Lonza; Cat# 04-418Q), Recombinant Human SCF Protein. CF (R&D; Cat# 11010-SC-050), Recombinant Human Thrombopoietin (NSO-expressed) Protein, CF (R&D; Cat# 288-TPN/CF), Recombinant Human Flt-3 Ligand/ FLT3L (HEK293) Protein), CF (R&D; Cat# 308-FKHB-010)]. The cells are thawed into a T75 flask (Coming; Cat# 430641U or equivalent). RNA is electroporated into 100K cells in Buffer P3 (Lonza; Cat# V4SP-3096) using Lonza 4d Nucleofector on Day 2 using 2 ug total RNA (at a ratio of 1 : 1) using pulse code DS 130 according to the manufacturer’s protocol. The cells are recovered in c-XVIVO Media. 72 hours later genomic DNA is extracted on a KingFisher Apex using Mag -Bind® Blood & Tissue DNA HDQ 96 Kit (Omega Bio-tek; Cat# M6399) according to the manufacturer’s protocol. NGS is performed on Illumina Nextseq and analysis in CRISPResso. mRNA encoding mutant nuclease sequences SEQ ID NOs: 2465- 2490, comprising triple NLS and glycine linkers according to the format described in the preceding paragraph, are produced in a small-scale IVT reaction and modified gRNA is manufactured by IDT. The IVT mRNA is produced using T7 RNA Polymerase (TriLink; Cat# ON-004) with full N I -methyl pseudo uridines' -Tri phosphate substitution (Hongene Biotech; Cat# R5-064) and co-transcriptionally capped with CleanCap M6 (TriLink; Cat# N-7453). The resulting mRNA is purified using Monarch RNA Purification Columns (NEB; Cat# T2007L).
[001373] In certain embodiments, a Type V editor of the present disclosure comprises a construct of the general formula:
NLS 1 -Linker-Type V Sequence-Linker-NLS2-Linker-NL3
[001374] In certain embodiments, NLS1, NSL2 and NLS3 are NLS sequences of the present disclosure. In certain embodiments, NLS1 is cMyc NLS (SEQ ID NOs: 2492 and 2496). In certain embodiments, NLS2 is SV40 NLS (SEQ ID NOs: 2493 and 2497). In certain embodiments, NLS3 is Nucleoplasmin NLS (SEQ ID NOs: 2494 and 2498). In certain embodiments, the linker is a 4x glycine linker (SEQ ID NOs: 2490 and 2495). In certain embodiments, the Type V Sequence is any Type V sequence described and disclosed herein. In certain embodiments, the Type V Sequence is or comprises one described in any one of SEQ ID NOs: 1570-1600; 1601-1631:1632-1670; 1671-1709; 2306-2351; 2354-2380; 2381- 2407; 2410-2411; 2439-2464; and 2465-2490 or any sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity therewith. In certain embodiments, the Type V Sequence is or comprises one described in any one of SEQ ID NOs: 2465-2490 or any sequence having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity therewith.
EXAMPLE 17: Modulation of NLS and linker configurations in a type V nuclease improve gene editing in primary cells
BACKGROUND
[001375] Recent advances in gene editing technologies have enabled the development of powerful tools for precise genome engineering. One such tool, Type V endonuclease, has garnered interest due to its smaller gRNA length and fewer off target indels. Editing using Type V endonuclease (and optimization thereof) has historically been done in the context of ribonucleoprotein (RNP). To the inventors’ knowledge, Type V endonucleases have not previously been optimized in the context of an all-RNA system (mRNA nuclease and RNA guide), in particular, for in vivo delivery and editing. Protein activity, localization, and folding may be influenced by linkers, tags and NLS components attached the N- or C-terminus (Refs 1-3). In this example, 10 different construct configurations (see FIG. 52) of ID405-1 nuclease comprising various combinations of nuclear localization signals (NLSs) and linkers have been tested in primary cells. This example demonstrates that a type V nuclease, such as ID405-1, may be engineered with improved editing efficiency by introducing one or more NLS in various configurations.
RESULTS AND DISCUSSION
[001376] FIG. 52 illustrates the general structure of the ID405-1 variants constructed with one or more NLS and linkers. The figures shows the arrangement of the linkers and NLS used. The term “nucleoplasmin” refers to the nucleoplasmin NLS having the following sequence: KRPAATKKAGQAKKKK (SEQ ID NO: 1556). The term “cMyc” refers to the cMyc NLS having the following sequence: PAAKRVKLD (SEQ ID NO: 2409). The term “SV40” refers to the SV40 NLS having the following amino acid sequence: RSSDDEATADSQHAAPPKKKRKV (SEQ ID NO: 1557). Construct 1 comprises a ID405-1 sequence fused directly to a nucleoplasmin NLS without a linker. The linker in all cases is 4 glycine (GGGG)(SEQ ID NO:2495). Full sequences for all constructs are provided below. Plasmids used for IVT production of mRNA were synthesized by a DNA sequence vendor (c.g.. Twist Biosciences) and IVT details are below.
[001377] Each of the constructs (mRNA encoding the recombinant ID405-1 variants and a guide RNA) were delivered by electroporation to primary HSPCs (AllCell). The nuclease mRNA is produced by IVT reaction and the guide RNA (spacer targeting hB2M) is synthetically manufactured by IDT. After transfection, cells were harvested 72 hours later in lysis buffer (as detailed in methods). Cells were analyzed by next-generation sequencing (NGS) and tire editing efficiency was calculated.
[001378] FIG. 53 shows the editing efficiency of the ID405-1 variants as % of sequencing reads showing an indel in the B2M locus. Construct 1 (405-1) edits the B2M locus at 8.9%. The data show that additional linkers and NLS significantly improve editing efficiency. Construct 10 performed best with 3 NLS (“3xNLS”) which edited at 47%, a more than 5 -fold increase over baseline Construct 1.
[001379] The constructs engineered and tested in this Example are not intended to be limiting on this specification. The specification contemplates additional variant configurations and/or combinations of these modifications with other modifications, such as the arginine scan substitutions of Example 16.
MATERIALSAND METHODS:
Mammalian cell culture
[001380] Primary human CD34-!- HSPCs were cultured in X-Vivo 15 medium (Lonza Catalog 02- 053Q) supplemented with 100 ng/mL SCF (RnD Systems Inc. 11010-SC-100). 100 ng/uL FLT-3L (RnD Systems Inc. 308-FKHB-250), and 100 ng/uL recombinant human thrombopoetin (RnD Systems Inc. 288- TPN-100/CF). HSPCs were thawed and cultured for three days before electroporation.
Electroporation
[001381] HSPCs were electroporated using a Lonza 4D 96-well electroporator and a Lonza P3 Primary cell kit (Catalog #: V4SP-3096). Briefly, 100,000 HSPCs were resuspended in Lonza P3 buffer and combined with 6 pg RNA to a total volume of 20 pL unless otherwise noted. The samples were electroporated using tire DS-130 program, 80 pL of pre-warmed cell culture medium was added to the cells immediately after electroporation, and the entire mixture transferred to a pre-warmed 96-well plate containing 100 pL of cell culture medium. Samples were allowed to grow at 37°C 5% CO2 for three days before harvesting genomic DNA (gDNA) using prepGEM (MicroGem PUN 1000) according to the manufacturer’s instructions. [001382] Genomic DNA extraction After incubation, the media was removed from the cells and genomic DNA was extracted by the addition ofprepGEM reagent (Thomas Scientific: PUN0050) directly into each well of the tissue culture plate. Lysed cells were transferred to a 96 well PCR plate and incubated at 75 °C for 10 minutes, followed by 95 °C enzyme inactivation step for 5 minutes.
Next Generation Sequencing and Analysis
[001383] Using prepGEM lysates as template, tire edited B2M site was amplified by PCR and prepared for Illumina sequencing. Hie resulting data was analyzed using CRISPREsso2. Editing outcome (InDels%) was calculated as the number of modified reads divided by total aligned reads.
IVT reaction
[001384] Plasmids for IVT were made with gBlocks from IDT and NEB assembly. In vitro transcription performed using NEB HiScribe according to manufacturer’s protocol.
Primers used for NGS
[001385] Human B2M fivd: CCTGAATTGCTATGTGTCTGGG (SEQ ID NO: 1529)
[001386] Human B2m rev: CTCATACACAACTTTCAGCAGC (SEQ ID NO: 1530)
405-1 targeting spacer used to target human B2M
[001387] AGTGGGGGTGAATTCAGTGT (SEQ ID NO: 1531)
Protein sequences of FIG. 52 and FIG. 53
[001388] Below are the amino acid sequences constructed in this example and as illustrated in FIG. 15.
Each construct comprises (a) the ID405-1 amino acid sequence, (b) at least one NLS, and (c) optionally one or more linkers. For each construct below, NLS moieties are indicated with bold text and linkers, if present, are indicated in italicized text.
Construct 1 (RNA0465) (SEQ ID NO: 1558); Construct 2 (RNA0821) (SEQ ID NO: 1559); Construct 3 (RNA0824) (SEQ ID NO: 1560); Construct 4 (RNA0823) (SEQ ID NO: 1561); Construct 5 (RNA0825) (SEQ ID NO: 1562); Construct 6 (RNA0827) (SEQ ID NO: 1563); Construct 7 (RNA0819) (SEQ ID NO: 1564); Construct 8 (RNA0820) (SEQ ID NO: 1565); Construct 9 (RNA0822) (SEQ ID NO: 1566); Construct 10 (RNA0826) (SEQ ID NO: 1567).
EXAMPLE 18: Improved type V variants obtained by directed evolution approach
[001389] To increase the functional activity of ID405 on the HBG1 target in human cells, a strategy was contemplated whereby the activity of mutant Cas protein was linked to the survival of a E. coli host carrying plasmid with an L-arabinose inducible toxin gene as well as target sequence for Cas protein (similar to the model described in Zhang et al. 2021). The cleavage and disruption of ccdB plasmid allows cell survival after addition of L-arabinose. The selection strategy can be iterated many times by repeated extraction and transformation of mutant plasmids (selection rounds) thereby allowing the enrichment of the most efficient Cas variants (FIG. 54A).
[001390] Firstly, toxin ccdB gene was cloned with a modified ribosome binding sequence (RBS) under the L-arabinose inducible pBAD promoter (Chen and Zhao 2005) resulting in plasmid pBAD-*RBS_ccdB- lacY. Synthetic DNA fragments encoding ccdB and lacY genes were ordered from Twist Bioscience and cloned into a pBAD plasmid vector via Ncol and Kpnl (both New England Biolabs) for ccdB, and Esp3I (New England Biolabs) for lacY. The ccdB gene encodes a protein that targets and inhibits DNA gyrase which is lethal for its bacterial host. The modified RBS allows for a more stringent control of ccdB gene expression (see Chen and Zhao 2005). Therefore, tire default RBS sequence found in the pBAD vector was modified to GATTGA by Gibson assembly cloning using a NEBuilder Hi Fi DNA Assembly kit (New England Biolabs).
[001391] Downstream of the ccdB gene in separate plasmids, tire ID405 target site HBG1 with two cloned with different PAM sequences: TCTT, TTGG denoting intermediate, and poor preference, respectively (Table 15A). Targets were cloned as annealed and phosphorylated oligo duplexes CZ-4734/CZ- 4735, CZ-5082/CZ-5083 via Kpnl/ Hindlll resulting in plasmids PBAD-*RBS-ccdB-TTGG-HBGl-lacY and pBAD-*RBS-ccdB-TCTT-HBGl-lacY, respectively. Each plasmid was transformed into T7 Express Competent E. colt (High Efficiency) (New England Biolabs) according to manufacturer’s protocol and plated onto LB media with 100 pg/mL carbenicillin. Tire transformants were grown in 300 mL of LB media supplemented with 100 pg/mL carbenicillin until mid-log, split into 6 x 50 mL falcons, washed three times with ice-cold 10 % glycerol before concentrating 300-fold to prepare electrocompetent cells, and stored at - 80°C.
[001392] To generate ID405 containing plasmids, DNA fragments encoding the ID405 protein with the J23119 promoter sequence downstream were cloned into pACY C vectors via Ncol and PacI (both New England Biolabs) restriction enzymes. Both fragments were E. coli codon optimized and synthesized by Twist Bioscience. Subsequently, the HDV ribozyme sequence was added downstream of the crRNA cloning site by ligating via Hindlll and PacI (both New England Biolabs) sites resulting in plasmid pACYCDuet_ID405-HDV. TTR fragment encoding crRNA was then cloned downstream J23119 promoter via Bsal using annealed and phosphorylated CZ-515 l/CZ-5152 oligo duplex resulting in plasmid pACYCDuet_ID405- crRNA-TTR-HDV. The plasmid was amplified with primer pair CZ-5138/CZ-5086 and cloned via Gibson assembly using NEBuilder Hi Fi DNA Assembly kit (New England Biolabs) with HBG1 fragment amplified with CZ-4415/CZ-3621 resulting in plasmid pACYCDuet_ID405-HBGl-crRNA- TTR-HDV (FIG. 54B). As a control, a construct encoding LbaCasl2a protein was constructed. Cloning scheme was the same except primer pair CZ-4402/CZ-4403 was used to generate pACY CDuet Lba- crRNA- TTR-HDV, and primer pairs CZ-5085/CZ-5086, CZ-4417/CZ-3621 were used to generate plasmid p ACYCDuet Lba-HBG 1 -crRNA-TTR-HDV .
[001393] Hie TTR target, which is not present in bacteria, was chosen to titrate the activity of ID405 as in preliminary analysis the presence of unrelated crRNA reduces the activity against intended targets. The efficiency of ID405 to cut target sequences was tested by transforming this plasmid into T7 Express strains containing ccdB encoding plasmids with target sequences and plating onto LB medium containing 20 pg/mL chloramphenicol and 0.1 % L-arabinose as described below.
[001394] To create an ID405 library with random mutations, domain structure of the protein (FIG. 54C) was inspected. A model was created using SWISS-MODEL workspace using default parameters (Guex, Pcitsch, and Schwcdc 2009; Waterhouse ct al. 2018). A PDB90 search was pcrfomicd using DALI protein structure comparison server (Holm et al. 2023) and Acidami nococcus sp. BV3L6 Cpfl (PDB accession numbers 5XH7 and 5XH6) was identified as the most similar characterized protein (Z-score = 47) (Nishimasu et al. 2017). From structural alignment against the Cpfl (PDB accession number 5XH6) the domain structure of ID405 (FIG. 54C) was inferred.
[001395] Having identified domains in ID405, the protein sequence was then split into 4 regions omitting PAM-interacting (PI) domains resulting the following fragments: N-terminus, C-terminus, N-2, C-2, each spanning 1072 base-pairs (bp), 1310 bp, 698bp, 420bp, respectively (FIG. 54C). Table 15B indicates the exact selected positions in the ID405 sequence that were mutagenized. Hie omittance of PI domain in the assay should allow the selection of more active protein variants against less preferred PAM sequences rather than versions with changed PAM recognition.
[001396] In the assay, the less preferred PAM sequences TCTT and TTGG were chosen, to create a stronger selection pressure for ID405 variants. Testing reactions were performed by electroporating E. coll cells containing pBAD-*RBS-ccdB-TCTT-HBGl-lacY or pBAD-*RBS-ccdB-TTGG-HBGl-lacY with lOOng ID405 plasmid with or without HBG1 spacer. Transformed bacteria were recovered in SOC medium for 1 h and 30 min with vigorous shaking at 37°C. Then, bacteria were plated on 3 separated LB medium plates containing 20 pg/rnL chloramphenicol; 20 pg/mL chloramphenicol, 0.1 % L-arabinose; and 20 pg/mL chloramphenicol, 0.1 % L-arabinose, 0.1 mM IPTG. As a control, LbaCasl2a protein was used, cloned in tire same manner as ID405.
[001397] Plates were incubated overnight at 37°C before inspecting bacterial growth. FIG. 55 shows that ID405 cuts toxin plasmid with target downstream TCTT PAM only in the presence of IPTG (i.e. higher protein concentration), while target downstream TTGG PAM is not cut. This shows that TCTT and TTGG can be considered as intermediate, and poor preference PAM sequences, respectively, and that can create a variable selection pressure for ID405 variants. Therefore, library selections with TCTT PAM were performed without IPTG, while library selections with TTGG PAM were performed either without IPTG or in the presence of 0.1 mM IPTG.
[001398] The target for all mutagenesis reactions was amplified from pACYCDuet_ID405- crRNA- TTR-HDV using primer pair CZ-1824/CZ-4750. Q5 2x MasterMix (New England Biolabs) was used for the PCR and the reaction set up using 100 ng plasmid as template and 0.5 pM of each primer in a final volume of 50 pL. The cycling conditions used were: 98°C for 30 s, 30 cycles of 98°C for 10 s, 70°C for 10 s, 72°C for 1 min, and final extension at 72°C for 2 min. Tire amplicon was purified using GeneJET PCR Purification Kit according to manufacturer’s recommendations. The number of total reactions were dependent on the required final quantity of the fragment required per mutagenesis reaction.
[001399] N-tcrminus library with random mutations was created by amplifying wild-type target gene sequence with error-prone GeneMorph II random mutagenesis kit (Agilent) using primer pair CZ-5248/CZ- 5239. 50 pL reaction contained 5 pL 5x reaction buffer, 1 pL 40mM dNTP mix, 2.5 ng/pL of each primer, 2 pg target, 1 pL Mutazyme II DNA polymerase. The cycling conditions used were: 95°C for 2 min, 30 cycles of 95°C for 30 s, 58°C for 30 s, 72°C for 1 min 30 s, and final extension at 72°C for 10 min. The PCR product was size-selected and recovered from a 1 % agarose gel using Monarch® DNA Gel Extraction Kit (New England Biolabs). Tire purified fragment along with pACYCDuet_ID405- crRNA-TTR-HDV plasmid was digested using FD Ncol and FD BamHI (Thermo fisher Scientific) in a total volume of 20 uL that contained 1 pg of DNA, 2 pL FD buffer, 0.5 pL each enzyme, water up to 20 pL. The prepared reactions were incubated at 37°C for 1 h. The cut plasmid was size-selected and recovered from a 1% agarose gel using Monarch® DNA Gel Extraction Kit (New England Biolabs), while the fragment was purified with Monarch® PCR & DNA Cleanup Kit. The plasmid and insert were ligated using 1 pL T4 ligase (New England Biolabs), 2 pL lOx T4 ligase buffer, 50 ng plasmid, 25 ng insert, in a total volume of 20 pL. The reaction conditions used were 16°C for 16 h, 65°C for 10 minutes. Reactions were scaled 100-fold to increase the size of resulting library. Ligations were purified and concentrated using Monarch® PCR & DNA Cleanup Kit (New England Biolabs) into 15 pL.
[001400] Libraries were delivered into NEB® 10-beta Electrocompetent E. coli (New England Biolabs) by MicroPulser Electroporator (biorad) using cold 0.1 cm electrode gap cuvettes and under 1.8 kV voltage. Transformed cells were pooled and recovered for 1 h and 10 min with vigorous shaking at 37°C. After which 100 pL of 10/100/1000/10000-fold dilutions were plated on LB medium containing 20 pg/mL chloramphenicol plates for enumeration, while the remaining transfonnation mix with library was amplified by adding lOx volume of fresh LB medium containing 20 pg/mL chloramphenicol and continuing shaking for additional 11 hours at 37°C followed by incubation at 4°C until collection by centrifugation at 2500 x g for 15 min. Tire plasmid library was extracted using ZymoPURE II Plasmid Midiprep Kit (Zymo).
[001401] All other libraries were created by Golden Gate assembly. Firstly, new ID405 plasmids were constructed by replacing C-terminus, N-2, C-2 regions in pACYCDuet_ID405- crRNA-TTR-HDV with Bsal restriction sites by amplifying plasmid with primer pairs CZ-5240/CZ-5249, CZ-5669/ CZ-5670, CZ-5673/ CZ-5674, respectively. Tire amplicons were ligated onto themselves using KLD Enzyme Mix (New England Biolabs) and transformed into NEB® 5-alpha Competent E. coli (New England Biolabs) according to manufacturer's recommendations. The plasmids were extracted using ZymoPURE II Plasmid Midiprep Kit (Zymo). Fragments with random mutations were created by amplifying wild-type target gene sequence with error-prone GeneMorph II random mutagenesis kit using primer pairs CZ-5250/ CZ-5251, CZ-5672/ CZ- 5760, CZ-5675/ CZ-5676 for C-terminus, N-2, C-2 regions, respectively. Composition and cycling conditions of PCR reactions were the same as described above, except target quantity in C-terminus, N-2, C-2 reactions were 2 pg, 100 ng, 10 ng, respectively. This was determined empirically after tire transformation of constructed library into E. coli, by nanopore sequencing of 10 random plasmids or PCR fragments, amplified from randomly picked colonies using primer pair CZ-1824/CZ-4750, to achieve ~2-3 average nucleotide mutations per sequence. The PCR products were size-selected and recovered from a 1 % agarose gel using Monarch® DNA Gel Extraction Kit (New England Biolabs). The assembly of libraries were conducted as follows: 20 pL reaction contained 100 ng plasmid DNA, insert quantity were varied to keep molar ratio of 1:3 plasmid to insert, 2 pL T4 ligation buffer. 0.5 pl T4 ligase (New England Biolabs), 0.5 pl BsaI-HFv2 (New England Biolabs), H2O up-to 20 pL. The cycling conditions used were: 50 cycles of 37°C for 5 min of 16°C for 5 min, 1 cycle of 50°C for 5 min, 1 cycle of 65°C for 5 min. Reactions for the final libraries were scaled 100-fold to increase the size of the resulting libraries. The final reactions were pooled, purified, transformed, and amplified as described above. The summary of resulting libraries is given in Table 15C.
[001402] ID405 mutant libraries were enriched for enhanced activity over 2 to 5 rounds of selections.
Approximately 5 to 10 -fold larger number of E. coli cells containing pBAD-*RBS-ccdB-TCTT-HBGl-lacY or pBAD-*RBS-ccdB-TTGG-HBGl-lacY than estimated plasmid library was transformed by electroporation of each library. Bacteria were recovered in SOC medium for 1 h and 30 min with vigorous shaking at 37°C. Then, bacteria were plated on LB medium containing 20 pg/mL chloramphenicol and 0.1 % L-arabinose. The surviving cells were collected by adding 4 mL of sterile LB medium and scraping them with cell spreader. Plasmids from pooled fractions were extracted by Monarch® Plasmid Miniprep Kit (New England Biolabs) and used for the next round of selection. 2 rounds of selection were performed with TCTT PAM, 5 rounds of selection were performed with TTGG PAM. Additionally, selection with TTGG PAM was performed using either medium without IPTG or in the presence of 0.1 mM IPTG.
Deep sequencing of the libraries
[001403] The mutagenized regions of libraries were amplified using primer pairs CZ-5165/ CZ-5167, CZ-5672/CZ-5760, CZ-5675/CZ-5676, CZ-5170/CZ-5171 for N-terminus, N-2, C-2, C-terminus libraries, respectively. Q5 2x MasterMix (New England Biolabs) was used for the PCR and tire reaction set up using 300 ng plasmid as template and 0.5 pM of each primer in a final volume of 60 pL over 2 vials. Tire cycling conditions used were 98°C for 30 s, 16 cycles of 98°C for 10 s, 66°C for 10 s, 72°C for 1 min, and final extension at 72°C for 2 min. After PCR, 1 pL of Dpnl was added to the samples and incubated at 37°C for 30 min. Illumina libraries were prepared with NEBNext® Ultra™ II FS DNA Library Prep with Sample Purification Beads kit (New England Biolabs), using the protocol for inputs < 100 ng and fragmentation time of 20 min.
[001404] Sample libraries were checked using Tapestation DI 000 DNA ScreenTape Analysis kit (Agilent), quantified with Qubit fluorometer (Thermo Fisher Scientific) and pooled in equimolar ratio. Final library pool was quantified via qPCR using NEBNext®1 Ultra™ II DNA Library Prep Kit for Illumina®) (New England Biolabs). Paired-end sequencing (2 x 150 cycles) was performed on Illumina MiSeq system with 1 % PhiX spike-in. Sequencing data analysis was performed using Geneious Prime (version 2024.0.4, GraphPad Software LLC d.b.a Geneious). Reads were merged, trimmed and filtered using BBDuk and mapped to the reference sequence of wild type ID405 using Bowtie2. Geneious variant finder was used to call SNPs with detection limit set to 0.001 %. A threshold of 5 % for the frequency of SNP was established when determining enriched sequences/positions.
Analysis of sequencing results
[001405] Hie results of the deep sequencing are summarized in Table 15D. The enrichment of more than 5% of variant frequency was observed only in the 5th round of libraries where TTGG PAM was used, while with TCTT PAM enrichment after the 2nd round of iteration was observed. Note, that 2 rounds of enrichment were chosen for the latter. An unintentional selection of plasmids with deletion in the region encoding crRNA was observed, which resulted in PAM shift and reinstation of WT PAM. This resulted in no selective pressure for enrichment of mutant ID405 sequences.
N-terminus libraries
[001406] 82 variants in round 2 were detected in the N-temrinus library under the selection with TCTT
PAM (FIG. 56A). From these, three variants exhibited frequency above or equal 5% (Table 15E). The protein (SEQ ID NOs: 1570-1600, 1632-1670) and coding DNA sequences (SEQ ID NOs: 1601-1631, 1671-1709) of the selected ID405 type V variants with mutations in N terminus are presented in the SEQ Listing Appendix. Bold letters in the SEQ indicate the mutant amino acid. round 3 and 42 were detected variants in round 5 (FIG. 19B). From these, five variants exhibited frequency above or equal to 5% (Tabic 15F).
[001408] In N-terminus library under the selection with TTGG PAM under the presence of 0. 1 mM IPTG, 572 variants in round 3 and 109 variants in round 5 (FIG. 56C) were detected. From these, twelve variants exhibited frequency above or equal to 5 % (Table 15G).
C-terminus libraries
[001409] In the C-terminus library under the selection with TCTT PAM, 681 variants in round 2 were detected (FIG. 56D). From these, 0 variants exhibited frequency above or equal to 5%. Tire protein and coding DNA sequences of the selected ID405 Type V variants with mutations in C terminus are presented in the SEQ Listing Appendix.
[001410] In C-terminus library under the selection with TTGG PAM, 801 variants were detected in round 3 and 165 variants in round 5 (FIG. 56E). From these, three variants exhibited frequency above or equal to 5 % (Table 15H). [001411] In C-terminus library under the selection with TTGG PAM under the presence of 0. 1 mM IPTG, 1001 variants in round 3 were detected and 41 variants in round 5 (FIG. 56F). From these, 10 variants were with frequency above or equal 5 % (Table 151). [001412] In C-terminus library under the selection with TTGG PAM under the presence of 0. ImM IPTG resulted in the highest enrichment frequencies of ID405 variants. It w as then evaluated whether these mutations are linked (meaning they are found on the same sequence) by randomly sequencing several Round 5 transformants. It was determined that V929D; D1192E; Q1203H; K1284R mutations are found on the same sequence.
N-2 libraries
[001413] In the N-2 library under selection w ith TCTT PAM, 476 variants w ere detected in round 2 (FIG. 56G). From these, five variants were detected with frequency above or equal 5% (Table 151). Tire protein (SEQ ID NOs: 1632-1659) and coding DNA sequences (SEQ ID NOs: 1671-1698) of the selected ID405 Casl2a variants with mutations are presented in the SEQ Listing Appendix.
[001414] In the N-2 library under selection with TTGG PAM, 496 variants were detected in round 3 and 27 variants in round 5 (FIG. 56H). From these, three variants were detected with frequency above or equal 5% (Table 15K). Note that during the selection of this library, only 3.06E+07 E. coll cells were transformed in round, i.e. library was underrepresented as initial library size was ~ 8.50E+07 plasmids (Table 15C).
[001415] In the N-2 library under selection with TTGG PAM under the presence of 0.1 mM IPTG, 549 variants were detected in round 3 and 155 variants in round 5 (FIG. 561). From these, 15 variants were detected with frequency above or equal 5 % (Table 15L). Note that during the selection of this library’, only 3.06E+07 E. coli cells were transformed in the round, i.e. the library was underrepresented as the initial library size was ~ 8.50E+07 plasmids (Table 15C).
C-2 libraries
[001416] In the C-2 library under the selection with TCTT PAM, 400 variants were detected in round 2 (FIG. 56J). From these, a single variant was detected with frequency above or equal 5% (Table 15M). The protein (SEQ ID NOs: 782-792) and coding DNA sequences (SEQ ID NOs: 1699-1709) of the selected ID405 Type V variants with mutations are presented in the SEQ Listing Appendix.
[001417] In C-2 library under the selection with TTGG PAM, 612 variants were detected in round 3 and 432 variants in round 5 (FIG. 56K). From these, five variants were detected with frequency above or equal 5% (Table 15N). [001418] In C-2 library under the selection with TTGG PAM under the presence of 0. 1 mM IPTG, 574 variants were detected in round 3 and 275 variants in round 5 (FIG. 56U). From these, 5 variants were with detected frequency above or equal 5 % (Table 150)
N-2 libraries (repetition)
[001419] To fully represent N-2 libraries under the selection with TTGG PAM, transformations were repeated using larger numbers of initial E. coli transformants in round 1 and earn ing selections up to round 4.
[001420] Under the selection with TTGG PAM, 842 variants were detected in round 3 and 813 variants were detected in round 4 (FIG. 56M). From these, no variants were with frequency above or equal 5%. Under the selection with TTGG PAM under the presence of 0.1 mM IPTG, 490 variants in round 3 were detected and 68 variants in round 4 (FIG. 56N). From these, 5 variants were with frequency above or equal 5 % (Table 15P).
Analysis of linkage status of ID405 mutants selected by directed evolutions and selection rules for testing in mammalian cell system
[001421] Hie linkages of mutations after evolution experiments were inferred from illumina results as follows: if the calculated frequency of mutations were within 1.5 % they were considered as linked. All mutations were also evaluated for the possible linkage with frameshift and/or truncation. If the similar frequency of either of the latter two (compared to the substitution) was observed, the mutation was rejected. All hit with a mutation in the active site (D1247G) were also rejected as well as K127R mutants as the latter had been previously tested. In total, for activity testing in a mammalian system, 27 mutants were selected: 11 single amino acid mutants and 16 multiple amino acid mutants (Table 15Q). Mutations based on available information in literature were also analyzed. All inferences provided are not be considered limiting theories, and are only provided herein for the purpose of discussion.
[001422] Table 15Q
Construction of ID405 mutants for testing in mammalian cell system
[001423] Single amino acid mutants were introduced into the baseline 405-1 sequence via Gibson assembly using NEBuilder® HiFi DNA Assembly Master Mix (NEB) as follows. Two overlapping fragments with the required mutation in the overlap were amplified from the 405-1 sequence . These fragments also contain overlaps with a third fragment containing PolyA sequence that is cut out of the baseline 405-1 sequence using Smal + Spel restriction endonucleases. Then, three fragments are assembled using manufacturer’s recommendations and transformed into E. coli NEB Stable competent cells. All amplicons after PCR were digested with Dpnl (NEB) for 30 min at 37 C before purification with Monarch® PCR & DNA Cleanup Kit (NEB). Multiple amino acid mutants were constructed by assembling three to four parts: DNA fragment synthesized with required mutations; PCR amplified plasmid backbone from the baseline 405-1 sequence around the fragment: and a fragment containing polyA sequence that is cut out using Smal + Spel restriction endonucleases. The assemblies were performed with NEBuilder® HiFi DNA Assembly Master Mix (NEB) using manufacturer’s recommendations and transformed into E. coli NEB S competent cells. All amplicons after PCR were digested with Dpnl (NEB) for 30 min at 37 C before purification with Monarch® PCR & DNA Cleanup Kit (NEB). All constructed plasmids were confinned by whole plasmid nanopore sequencing (to confirm mutations) and Sanger sequencing (to confinn the length of polyA sequence).
Mutant mRNA synthesis
[001424] After directed evolution of Casl2a was completed and mutant plasmids constructed, mRNA was synthesized for use in RNA transfection experiments. After verification by Sanger sequencing of mutant plasmids, 3 pg of each plasmid was linearized using suitable restriction endonuclease (SapI) that does not have a recognition site inside the target gene and generates blunt ends. Digestion products were then purified using Monarch PCR & DNA Cleanup Kit (New England Biolabs), concentrations measured using spectrophotometry (NanoPhotometer® NP80, IMPLEN). Approximately 1 pg of each purified linearized plasmid was then used as a template for in vitro transcription reaction performed using HiScribe® T7 mRNA Kit with CleanCap® Reagent AG (New England Biolabs); kit-provided UTP was not used, instead, Nl- Methylspeudouridine (TriLink Biotechnologies or Thermo Fisher Scientific) was added to a final concentration of 5 mM. In vitro transcription reaction was run for 1 hour at 37°C after which DNasel and nuclease-free water was added to the reaction and incubated for 30 min at 37°C to remove template DNA. After this step, IVT reaction product was purified using the Monarch RNA Cleanup Kit (500 pg). Part of the purified samples were set aside to assess their quality. Sample concentrations were measured using spectrophotometry (NanoPhotometer® NP80, IMPLEN) and fluorimetry (Qubit RNA Broad Range Assay Kit and Qubit 4, Thermo Fisher Scientific). mRNA integrity was assessed by performing capillary electrophoresis using 4150 TapeStation System together with RNA Screen Tape reagents (Agilent). Synthesized mRNA was aliquoted and kept at -80°C until use.
Testing activity of mutant Casl2a proteins in HEK293T cells
[001425] To determine gene editing efficiencies of mutant Type Venzymes and compare it to the baseline ID405-1 variant, mRNA transfection into human cells was performed. Human embryonic kidney (HEK) cell line 293T (ATCC-CRL-3216) cells were transfected with mRNA of each Type V nuclease and crRNA of one of two genomic targets (HBG1 and B2M). Tire mRNA transfection experiments and activity determination were perforated as described below.
[001426] Two targets in clinically important genes were selected and synthetic crRNA for them was generated:
[001427] HEK293T cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) with GlutaMAX (Thermo Fisher Scientific), supplemented with 10 % fetal bovine serum (Thermo Fisher Scientific) and 10,000 units/mL penicillin, and 10,000 pg/mL streptomycin (Thermo Fisher Scientific) at 37°C with 5 % CO2 incubation.
[001428] HEK293T cells were seeded into 96-well plates (Thermo Fisher Scientific) one day prior to transfection at a density of 18,000 cells per well. Cells were transfected using Lipofectamine MessengerMAX Transfection Reagent (Invitrogen) following the manufacturer’s recommended protocol. For each well of a 96-well plate a total amount of 100 ng RNA was used. This total amount consists of mRNA and crRNA in a ratio of 1 :4. Cells were incubated at 37°C for 72 hours post transfection in 5 % CO2 before genomic DNA extraction. The cells were washed twice with 200 pl IX DPBS (Thermo Fisher Scientific) and resuspended in 25 pl 50 mM Tris-HCl, 150 mM NaCl, 0.05% Tween 20, pH 7.6 (Sigma Aldrich) and 0.2 mg/ml Proteinase K (New England Biolabs) lysis buffer. Resuspended cells were incubated at 55°C for 60 minutes and 95°C for 15 minutes. Genomic region surrounding each Casl2a target site was PCR amplified using primers defined below (SEQ ID NOs: 752, 753, 2352, and 2353). PCR amplification was performed using Q5 Hot Start High-Fidelity 2X Master Mix (New England Biolabs) according to the manufacturer’s instructions. The reaction was set up using Ipl of the cell lysate and 0.5 pM of each primer in a final reaction volume of 25 pl.
[001429] Genome editing frequencies were estimated using T7 Endonuclease I assays. 20 pL of each PCR reaction was combined with 3 pL NEBuffer 2 (New England Biolabs) and 7 pL of water before denaturation at 95°C for 5 minutes and re-annealing by temperature ramping from 95-85°C at -2°C/s followed by ramping from 85-25°C at -0.1°C/s. 1 pL of T7 Endonuclease I (New England Biolabs) was added to each re-annealed sample and cleavage reactions were incubated at 37°C for 20 min. Fragments were analyzed by performing gel electrophoresis using either E-Gel Precast Agarose Gel Electrophoresis system (Invitrogen) or simple agarose gel. As for E-Gel Precast Agarose Gel Electrophoresis system (Invitrogen) 2 % gel with Ethidium bromide dye was used and 8 pL of each sample was mixed with 7 pL of E-Gel Sample Loading Buffer (Invitrogen), then the whole volume was loaded to the well. For fragment analysis in a simple agarose gel, 2% agarose gel in IX TAE buffer was prepared and 10 pl of sample was mixed with 2 pl of Gel Loading Dye, Purple (6X) (New England Biolabs) with added GelRed Nucleic Acid Gel Stain (Biotium). As an additional measure, genome editing efficiencies of mutants performing better than ID405-1 control (ID405-1 (D169R) mutant, selected during the first mutation round) on hB2M target were evaluated by analysing T7 Endonuclease I assay samples using 4150 TapeStation System together with DNA ScreenTape reagents (Agilent) (FIGs. 83, 84 and 85). Target cleavage percentage was calculated using ImageJ software.
EXAMPLE 19: Method for engineering guide RNAs with modifications at select ranked positions by computational means
[001430] Type V nuclease -guide RNA co-complexes within the protein data bank (PDB) were examined in order to determine key structural interactions of guide backbone atoms (e.g. 02' or phosphate hydrogen bonds). Type V nuclease-guide RNA co-complexes considered included AsCasl2 (Ternary: 5b43, 5kk5), lbCasl2 (Ternary: 5XUS, 5XUT, 5XUU, 5XUZ; Binary, 51D6, 6NM) and FnCasl2 (Ternary: 5MGA. 611 L, 611 K, 5NFV; Binary: 5NG6).
[001431] Identification of key interactions within each co-complex were determined by using the protein contacts panel within Molecular Operating Environment (MOE), a computer aided molecular design software developed by Chemical Computing Group (CCG). The AMBER10 force field for proteins and nucleic acids (ffl 0) was used to calculate energetics over six types of contacts: Hydrogen bonds (Hbond), Metal, Ionic, Arene, Covalent, and Van der Waals distance interactions. The solvation model was R-field, the dialectric was set to 1, and Group II ion and Group VIII parameters were from OPLS-AA. Contacts were calculated for both intrachain (within RNA) and interchain (between RNA and protein) by selecting SetA: ChainA (eg protein) and SetB: Full Complex. The sequence separation was set to 2, the distance threshold was set to 4.5, and no energy threshold was used. Calculations were not aggregated (e.g. Aggregate :None) and the text output was saved and used subsequently for filtering by atom interaction type.
[001432] Energetic calculations saved from the MOE contacts panel for each co-complex were filtered by atom interaction type (e.g. 02’ or phosphate/OP) and hydrogen bond energies were summed on a pernucleotide basis. Summed energies for each guide nucleotide were then averaged across each Type V family member and the resulting scores were used as input for a script to calculate optimal sites for guide backbone modifications.
[001433] In brief, the guide modification script uses the per-nucleotide scores calculated from MOE and assumes that making a backbone modification to a given nucleotide atom would completely abolish the native intra- or inter-hydrogen bonding interaction calculated for that atom. Using this assumption, the script iterates combinatorically and scores any potential loss in energetics for guides with one, two, three, etc. modifications, outputting in each case a single guide that best retains maximal interactions.
[001434] Selection of optimal sites for modification were calculated independently for the scaffold guide regions (FIGs. 57A, 57B, and 57C) and spacer regions (see FIG. 58A and 58B).
[001435] MOE analysis was performed with Casl2a guide bound protein structure. Based on MOE structural protocol, nucleotide positions were identified where the 2 ’-OH of gRNA nucleotide is making contact with Casl2 protein (FIGs. 59, 60, and 61). Without intending to be limited to any particular theory’, Cast 2a 02' protein/gRNA interaction energy can provide rationale for site-specific chemical modification of Casl2 gRNA.
[001436] In FIG. 62, seven different chemical modification patterns were designed for gRNA of three different targets (target 1= PCSK9 gene; target 2 = B2M gene; target 3 = BCL11A gene). The BCL11A target is the BCL11A binding site in the HBG1/2 promoters. Targeting this site with a CRISPR-Cas editor and guide RNA can inactivate the binding site of the BCL11A transcriptional repressor, thereby increasing transcription of HBG1/2 genes, which results in increased production of HBG1/2 subunits, and consequently, increased production of HbF. Each of these three guides have same direct repeat sequence (UGAAUUUCUACUGUUGUAGAU; SEQ ID NO: 1744) but have different spacer length for unique DNA targets. In every guide, the first two and last two phosphates have been converted to phosphorothioate.
According to MOE, position 3 may not be suitable for phosphorothioate modification (FIGs. 63 and 64) and hence were kept unmodified. This work involved working with 405-1 gRNA (UGAAUUUCUACUGUUGUAGAU; SEQ ID NO: 1744) which had the UG dinucleotide (shown in bold and underlined) added before the Cast 2 guide sequence. For this work, these two nucleotides were assigned with -2 and -1 number. Following nucleotide sequences were identical with Casl2a gRNA guide sequence (AAUUUCUA....) and they were assigned with 1, 2, 3....as nucleotide identification numbers.
[001437] Initially, every nucleotide was modified with 2’ -OMe in the first sequence. This is the maximum modification possible in this gRNA. Tire second sequence had the direct repeat part completely modified, leaving the rest unmodified. The third sequence had spacer region completely modified. These two modified sequences can tell tire importance of modification of a specific portion of gRNA. Using MOE protocol, positions 1,2,3,10,14,19,23,24,25.32 and 35 were shown to have maximum interaction with Casl2 protein. These positions were left unmodified in sequence four. In sequence five, all unmodified positions of sequence four were maintained. As such, additional unmodified positions (1,2,3,6,7,10,14,19,23,24,25,26,30,32,35,36,37) were added based on MOE protocol. This set included positions which have moderate interaction with the protein. Sequence six included less strong nucleotide interactions with tire protein and included more unmodified positions (1, 2, 3, 6, 7, 10, 14, 19, 21, 22, 23, 24, 25, 26, 30, 32, 33, 34. 35. 36, 37). The first two nucleotides (position -2 and -1) were not part of Casl2 protein bound gRNA sequence and hence their interaction with protein could not be measured using MOE protocol. To test whether these positions can accommodate chemical modification, a UU dinucleotide with 2’-0Me and PS was added (position -4 and -3) in sequence 7 making position -2 and -1 unmodified. Without intending to be limited to any particular theory, this modification pattern would address the ability to accommodate chemical modification of the first two nucleotides in 405-1 sequence.
[001438] This same strategy that was applied for PCSK9 (sequences 1-7 of FIG. 65) was applied to two other gRNA targeting B2M and BCL11A with different spacer lengths. This generated 14 more gRNAs with similar chemical modification pattern (sequences 8-21 of FIG. 65). Evaluation of efficacy for these guides under in-vitro and in-vivo conditions provides insight for chemical modification of 405-1 gRNA.
[001439] MOE citation: Molecular Operating Environment (MOE), 2022.02 Chemical Computing Group ULC, 910-1010 Sherbrooke St. W„ Montreal, QC H3A 2R7, Canada, 2024.
EXAMPLE 20: Evaluation of modified guides under in vivo conditions demonstrates improved editing efficiency compared to unmodified guides
[001440] To evaluate whether the modified guides discussed in Example 19 resulted in improved editing efficiency, five (5) exemplary guides for B2M were tested (SEQ ID NOs: 1766-1770). These selected guides are shown as “boxed” regions in FIG. 65. Additionally, seven (7) guides for BCL11A were also tested (SEQ ID NOs: 1745-1751). Variants of these selected BCL11A guides are shown in the “boxed” region in FIG. 65 (SEQ ID NOs: 1759-1765). illustrating the “mod patterns” utilized. [001441] For purposes of this example, the following nomenclature is used for the above modified guide RNAs of FIG. 65:
[001442] Hie modified guides Modi, Mod2, Mod3, Mod4, Mod5, Mod6, and Mod7 were tested in accordance with tire methodology depicted in FIG. 66.
[001443] As shown in FIG. 66, two different cells lines were transfected each with an mRNA encoding Casl2a ortholog variant 405-1 (NT SEQ ID NO: 566 // AA SEQ ID NO: 585) along with either a benchmark guide RNA (AltR guide) or one of the tested modified guides. Modi, Mod2, Mod3, Mod4, Mod5, Mod6, or Mod7. In addition, the cells were transfected with a benchmark control combination of AsCasl2a Ultra and the AltR guide. The transfections were as follows:
Results
[001444] Results are shown in FIGs. 67A and 67B. The results demonstrate that:
• Mod6 outperformed AltR control in primary’ HSCs with the B2M spacer guide
• Cell type dependent differences were observed with guide performance
• In primary’ HSCs, the guide modifications provided significant advantages over standard AltR guides
• Max editing achieved in HSCs with Type V variant 405-1 was 77%
• Next steps including formulating modified guides in LNPs for in vivo studies
Methods and materials
High Editing Rates in HEK293Ts at a clinically relevant locus
[001445] HEK293Ts (ATCC; Cat# CRL-3216) were cultured in DMEM, high glucose, GlutaMAX Supplement pyruvate (ThermoFisher; Cat# 10569010) with 10% FBS (ThermoFisher; Cat# A5209501) and 1% Pen-Strep (ThermoFisher; Cat# 15140-122). One day’ prior to transfection, 2e4cells were seeded in a 96 well plate and allowed to grow overnight to a confluency of 70-90%. For each reaction, 0.6uL of Lipofectamine MessangerMAX (ThermoFisher; Cat# LMRNA001) reagent was mixed with Opti-MEM (ThermoFisher; Cat# 31985062). Nuclease mRNA and gRNAs were mixed in Opti-MEM at a 1: 1 ratio by mass. A two-fold serial dilution was performed with atop dose of 600ng. Incubation times were performed according to the manufacturer’s recommendations. 72 hours later genomic DNA was extracted using prepGEM MicroGEM (Cat# PUN1000) according to the manufacturer’s protocol. NGS was performed on Illumina Nextseq and analysis by? CRISPResso. mRNA encoding nuclease was manufactured by? Vernal Biosciences and modified gRNA was manufactured by IDT. Tire gRNAs of SEQ ID NOs: 1766-1770 were used. Results are shown in FIG. 67A, left panel.
High Editing Rates in primary HSCs at a clinically relevant locus
[001446] Mobilized Human Peripheral Blood CD34+ Cells (AllCells, Donor ID# 888824822) were thawed on Day 0. The following media was used: - X-VIVO 15 (Lonza; Cat# 04-418Q), Recombinant Human SCF Protein, CF (R&D; Cat# 11010-SC-050), Recombinant Human Thrombopoietin (NS0- expressed) Protein, CF (R&D; Cat# 288-TPN/CF), Recombinant Human Flt-3 Ligand/ FLT3L (HEK293) Protein. CF (R&D; Cat# 308-FKHB-010), c-XVIVO Media (Complete X-VIVO) = X-VIVO + O.lug/mL SCF + 0. lug/mL FLT3L + 0. lug/mL TPO, lx PBS (THERMOFISHER; Cat# 10010049 or equivalent), 6 well plate (Coming; Cat# 3516 or equivalent). RNA was electroporated into 100K cells using Lonza 4d Nucleofector on Day 2 using 8 ug total RNA (at a ratio of 1: 1) using pulse code DS130 according to the manufacturer’s protocol. 48 hours later genomic DNA was extracted using prepGEM MicroGEM (Cat# PUN 1000) according to the manufacturer’s protocol. NGS was performed on Illumina Nextseq and analysis by CRISPResso. mRNA encoding nuclease was manufactured by Vernal Biosciences and modified gRNA was manufactured by IDT. The gRNAs of SEQ ID NOs: 1745-1751 , and 1766- 1770 were used. Results are shown in FIG. 67A, right panel and FIG. 67B.
EXAMPLE 21: Targeting guides to the nucleus via a PNA-NLS localization agent
[001447] When delivering LNP -mediated CRISPR-based gene editing systems (e.g., which in various embodiments include mRNA and a gRNA), the mRNA needs to express a Cas nuclease in the cytoplasm, complex with its cognate guide RNA (to form the editing RNP - ribonucleoprotein - as depicted in FIG. 68). and then translocate into the nucleus to perform its editing function. In various embodiments, the Cas nuclease is engineered with one or more NLS sequences encoded thereon which direct the protein and/or complex to reach the nucleus. Guide RNA are unable to cross the nuclear membrane on their own and so the RNP complex must form in the cytoplasm prior to nuclear transport. Typically, to encourage RNP formation in the cytoplasm, a higher molar equivalence (10-150 fold) of guide RNA to Cas-encoding mRNA is encapsulated in the LNP. In addition, RNAs are more fragile than other genetic materials. This lack of stability leads to premature degradation while waiting for complexation with Cas protein. Selective sitespecific chemical modification may increase stability and half of gRNA facilitating RNP formation, increasing gRNA potency. Without intending to be limited to any particular theory , if guide RNA are modified such that it may translocate to the nucleus, editing efficiency may be increased as the RNP complex could form inside the nucleus.
[001448] As addressed in this Example, the problem of gRNA not being able to shuttle to the nucleus can be overcome by adding an NLS sequence directly to the guide RNA. By having an NLS sequence attached, the guide can cross the nuclear membrane and find and complex with a Cas protein which will have independently translocated into the nucleus. This is thought to significantly increase chances of RNP fomration leading to improved gRNA potency. NLS sequence can be introduced to gRNA in multiple ways. Some non-limiting examples are stated below.
(A) By conjugating one or multiple peptide NLS sequences with a PNA probe having complementary sequence with portions of gRNA.
(B) By adding RNA-NLS sequence.
(C) By chemical conjugation of peptide NLS with gRNA.
[001449] Each of these approaches has unique advantages associated with them. PNA-NLS have a charge-free backbone and can fonn a stable duplex with short sequence overlap. Tracer sequence is conserved in all Cas9 gRNA sequences and the same PNA probe can be used in any guide for nuclear delivery of gRNA. This makes NLS-PNA probes a great choice for universal purposes. After binding with guide, the PNA will form a stable duplex on 3 ’-end of gRNA, this will enhance overall gRNA stability. The concept of using a PNA-NLS probe is depicted in FIG. 69.
[001450] Various embodiments are embraced by these concepts and certain attributes may be optimized to increase performance. For example, length of the PNA probe may be adjusted to regulate PNA- gRNA duplex stability. In certain embodiments, the PNA portion may range from 2-30 nucleotides, e.g. FIG. 69 which shows a 9-residue PNA linked to an NLS. The NLS sequence can be conjugated to either N- terminus or C-terminus of the PNA. In addition, the PNA probe may be conjugated to more than one NLS. It can also be conjugated internally with PNA probes. A few examples of the PNA-NLS probe are given below.
• (SEQ ID NO: 1771)-[linker]-(SEQ ID NO: 584)
• OO-(SEQ ID NO: 1771)
• (SEQ ID NO: 1771)-[linker]-(SEQ ID NO: 584)-[linker]-Lys(Cy5)
• OO-[linker]-AAAAGCACC
• (SEQ ID NO: 584)-[linker]-AAAAGCACC
SEQ ID NO: 584 = PKKKRKV
SEQ ID NO: 1771 = AAAAGCACCGA [001451] In these examples, the PNA peptide component may be coupled to one or more NLS. The coupling can optionally take place through a linker.
[001452] In another embodiment, PNA probes may be modified to enhance solubility. PNA probes may in some embodiments be poorly soluble, either on their own or when complexed with a target guide RNA. To address this potential issue, solubility enhancing groups such as (but not limited to) ethylene glycol can be added to the PNA-NLS probe (shown by ‘OO‘ in the sequences above). The addition of a fluorophore (Cy5) can help to determine presence of gRNA in nucleus and cytoplasm. This will aid in identification of gRNA trafficking through nuclear membrane.
[001453] In various other embodiments, the PNA-NLS probes may also anneal to the 5' end of a guide RNA at a specialized additional sequence that is added to the guide RNA at the 5' or 3' end names the “PNA binding sequence" or “PNA binder”. See FIG. 70.
[001454] Exemplary additional embodiments of type V guides are shown in FIGs. 71A, 71B, and 71C.
EXAMPLE 22: Structurally modified guides result in improved editing efficiency (e.g., 3’ and 5’ RNA and/or DNA extensions on type V guides improves editing efficiency)
Background:
[001455] Genome-editing has come to the forefront of gene-therapy since the initial discovery of CRISPR/Cas9, a type II CRISPR nuclease. Despite the effectiveness of Cas9 for genome editing, several hurdles exist that make the CRISPR/Cas9 system difficult to work with for therapeutic development. Guide RNAs (gRNAs) for type II systems are typically 90-125 nts in length, w hich makes high-purity chemical RNA synthesis difficult. Furthermore, type II gRNAs must be heavily modified to ensure stability and efficacy when delivered in-vivo One solution to this problem is to use Cas proteins from a different family of nucleases which have different guide RNAs. Type V CRISPR/Cas systems are roughly the same size as Cas9 but leverage gRNAs that are only 30-50 nt in length, something that most RNA chemical synthesis platforms can accommodate.2,3 Furthermore, this shorter length means fewer residues need to be chemically modified, potentially stabilizing the gRNA at decreased cost. The present Example demonstrates that a variety of chemical and structural modifications to 405-1 gRNAs lead to more robust editing than simple chemical end modifications. Furthermore, these modifications are capable of rescuing “spacer dependent activity” often seen with type V gRNAs.2
Results:
[001456] The extension of type V gRNAs at the 5’ end enhances editing at endogenous genomic sites as well as plasmid targets.3 Here chemically end-modified 405-1 nuclease gRNA were appended with RNA and DNA sequences of 4. 9, 15, and 25 bp, and introduced along with 405-1 mRNA into primary human CD34+ HSPCs. Two days after electroporation, cells were harvested for NGS, and it was noted that appending RNA extensions increases editing 2-3 fold at the HBG locus above gRNAs containing the baseline 405-1 gRNA with chemical modifications in various positions (mod6/gRNA260) (FIG. 72).
[001457] This effect was length dependent as longer RNA sequences tended to increase editing levels. Interestingly, appending the same sequences as DNA resulted in editing levels 4-10 fold above the baseline mod6 gRNA. The baseline mod6 gRNA has the following sequence: gRNA0260: u*g*AAUuuCUacUguuGuagaUcCUUGUCaagGcUAUUGGU*c*a (SEQ ID NO: 2232) (aka ‘"mod 6” guide), wherein A, G. U, C = unmodified RNA nucleotide; a. g, u, c = 2'-O-Methyl-nucleotide; * = Phosphorothioate linkage.
[001458] These results were also somewhat length dependent but optimal editing occurred with an extension of 15 bp, rather than an extension of 25 bp. These effects were not observed with a type V gRNA targeting B2M in HSPCs, potentially because the gRNA caused robust editing at baseline (FIG. 73). These results suggest that the incorporation of 5’ extensions into type V gRNAs can increase editing levels and that DNA extensions tend to increase editing more than RNA extensions using spacers with initial poor activity. It will be interesting to determine if these results are due to increases in gRNA stability or improved affinity for the 405-1 nuclease.
[001459] Next, the mod6 schema were combined with RNA extensions to determine if further improvements in editing could be observed in HSPCs. It was observed that most RNA extensions, except for a 25bp extension (gRNA0372), decreased editing below the levels observed with mod6 alone (gRNA0260) at both HBG and B2M loci (FIGs. 73 and 74). The 25bp extension boosted editing frequencies -1.5-2 fold. This effect could be due to an extended stretch of polyuracil in the extension sequence that could be acting as a linker, separating the gRNA direct repeat from the flanking extension sequence.
[001460] Conversely, it was noted that modification scheme 7 (mod7), which was less effective in HSPCs than mod6, could be modified with RNA extensions (gRNA0373-0376) and improved editing 3-fold at the HBG locus, with an optimal extension length of 15bp (gRNA0375). Adding DNA extensions on mod7 gRNAs may further improve editing effects. Mod7 has the sequence and modification schema, as follows: u*u*UGAAUuuCUAcUguuGUagaUcCUUGUCaagGcUAUUGGu*c*a, A, G, U, C = unmodified RNA nucleotide; a, g, u, c = 2'-O-Methyl-nucleotide; * = Phosphorothioate linkage; SEQ ID NO: 1765.
[001461] As gRNA0260 originally improved editing in HSPCs, it was tested whether derivatives of gRNA0260 could improve activity. Three derivatives were chosen based on the overall level of modification in the gRNA, gRNA0390 (mod6-6; SEQ ID NO: 2233), gRNA0391 (mod6-8; SEQ ID NO: 2234), and gRNA0392 (mod6-10; SEQ ID NO: 2235), and electroporated in human HSPCs (FIG. 75). It was noted that editing levels increased as gRNAs were less modified and approached a 10-fold improvement, gRNA0392, over the initial design using gRNA0260 (FIG. 76). This suggests that some modifications are impacting the gRNA folding and/or gRNA nuclease interactions and impairing editing in some ways.
[001462] Additionally, it has been reported that fold-back gRNAs can promote proper folding of type V gRNAs which could rescue spacers with poor editing activity.2 Five different fold-back gRNAs were designed with 3’ extensions pairing with the 3’ end of the spacer sequence and introduced them into human HSPCs. It was noted that the editing frequencies with fold-back RNAs improved the editing more than mod6 (gRNA260) but had significant variability (FIG. 77).
[001463] To confirm that these results were not HSPC donor specific, these experiments were repeated in multiple HSPC donors and it was found that DNA extensions, mod6-10, and foldback increased editing across all three donors (FIG. 78). Notably, the foldback designs generated editing results there were more consistent than the prior experiment and better than the mod6 benchmark. These RNA modifications were also combined with 405-1 nuclease that contained an optimized NLS configuration and either E1014R or K292R point mutants. It was noted that editing was generally increased in the presence of optimized NLSs and increased further when combined with K292R (FIG. 79). Addition of E1014R substitution to 405-1 with optimized NLSs did not improve editing and. in most cases, decreased editing by two-fold.
[001464] Independently, internal guide modifications, extensions and fold-backs provided boosts in editing outcome. Guides combining these approaches were designed, ordered and tested in HSPCs to investigate the possibility of compounding benefits to editing efficiency. Combinations of the 15bp DNA extensions with the best performing fold-back sequence were made in the context of the internal modifications end-mods only, mod6-10, and mod7 (SEQ ID NOs: 2424-2435 and 2438). Having both structural modifications further improved editing for the end-mods only guide but decreased editing for the mod6-10 and mod7 guides (FIG 86). This boost in the context of the end-mods only internal mod pattern was further confirmed in guides with 5 ’ DNA extensions of different lengths combined with the best perfonning fold-back sequence (FIG. 86). The best performing gRNA (gRNA0648: SEQ ID NO: 2433) had an editing rate of 79.2% in the primary HSPCs.
Discussion:
[001465] Here, multiple structural modifications have been incorporated into type V gRNAs to improve editing rates in primary human HSPCs. The addition of 5’ DNA extensions. 5? RNA extensions, reduced chemical modification (mod6-10), and hairpins around the spacer region (backfolds) all led to twofold or greater improvements over the benchmark mod6 gRNA in multiple HSPC donors. While structural modifications all lead to increases in editing with chemical end modifications, some were not compatible with the mod6 schema. A different modification scheme (mod7) could support RNA extensions that improved editing. DNA extensions, RNA extensions, foldbacks, and mod6-10 gRNAs were also augmented with NLS and point mutant improvements in the 405-1 nuclease showing that these elements can be combined to augment editing. Combining these gRNA modifications yielded more robust editing than seen with a single modification alone. Without intending to be limited to any particular theory, additional increases may be achieved by including a linker sequence between the structural extensions.
Materials and Methods:
[001466] Mobilized CD34+ HSPCs were ordered from AllCells. All guide RNAs were ordered from Integrated DNA Technologies™ (IDT). Guide RNA schemas tested included the following:
• AltR modification pattemi
• 2’0-Me modifications and phosphothiorate linkages at the first and last two nucleotides (end-mods only)
• 2’0-Mc modifications and phosphothiorate linkages at the first and last two nucleotides, with 2’0- Me modifications interspersed along the guide length
• Chimeric guides including DNA extensions at the 5’ end
• RNA extensions at the 5 ’ end
• Fold-back sequences appended to the 3’ end
• Various combinations of the above tested concepts
[001467] 405-1 was manufactured through Vernal Biosciences. N1015R+3xNLS (SEQ ID NO: 2410) and K292R+3xNLS (SEQ ID NO: 2411) 405-1 nuclease variants were produced by the applicant’s scientists using literature established methodologies.
Cell Culture:
[001468] Primary human CD34+ HSPCs were cultured in X-Vivo 15 medium (Lonza Catalog #: 04-418Q) supplemented with 100 ng/mL SCF (RnD Systems Inc. 11010-SC-050), 100 ng/uL FLT-3L (RnD Systems Inc. 308-FKHB-010), and 100 ng/uL recombinant human thrombopoietin (RnD Systems Inc. 288-TPN/CF). HSPCs were thawed and cultured for two days before electroporation.
Electroporations:
[001469] Mobilized primary human CD34 HSPCs were electroporated using a Lonza 4D 96-well electroporator and a Lonza P3 Primary cell kit (Catalog #: V4SP-3096). Briefly, 100,000 HSPCs were resuspended in Lonza P3 buffer and combined with 4000 ng of guide and 4000 ng of nuclease mRNA to a total volume of 20 pL per replicate, per condition. Tire samples were electroporated using the DS- 130 program, 100 pL of pre-wamred cell culture medium was added to the cells immediately after electroporation, and tire entire mixture transferred to a pre-warmed 96-well plate containing 100 pL of cell culture medium. Samples were allowed to grow at 37°C 5% CO2 for two days before they were centrifuged, and stored as frozen pellets for genomic DNA (gDNA) isolation using the Mag-Bind® Blood & Tissue DNA HDQ 96 Kit (Omega Bio-tek Cat#: M6399) according to the manufacturer’s instructions.
Next Generation Sequencing and Analysis
[001470] Using extracted gDNA as template, the respective samples containing either HBG or B2M sites of interest were amplified by PCR and prepared for Illumina sequencing. The resulting data was analyzed using CRISPREsso2.
References
1. Yin, H., Song, CQ., Suresh, S. et al. Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing. Nat Bioteclmol 35, 1179-1187 (2017). https://doi.oru/10.1038/nbt.4005
2. Creutzburg SCA. Wu WY, Mohanraju P. Swartjes T. Alkan F, Gorodkin J. Staals RHJ, van der Oost J. Good guide, bad guide: spacer sequence-dependent cleavage efficiency of Casl2a. Nucleic Acids Res. 2020 Apr 6;48(6):3228-3243. doi: 10.1093/nar/gkzl240. PMID: 31989168; PMCID: PMC7102956.
3. Park HM. et. al. Extension of the crRNA enhances Cpfl gene editing in vitro and in vivo. Nature Comm. (2018)
EXAMPLE 23: Cell-specific regulation of mRNA expression may be controlled by miR sites Introduction
[001471] Lipid nanoparticles (LNPs) can effectively protect mRNA from degradation and facilitate its efficient delivery in vivo, as demonstrated in the development of COVID-19 vaccines. Following intravenous (IV) administration, the majority of mRNA-LNP complexes tend to accumulate in the liver, leading to the expression of cargo proteins by hepatocytes or sinusoidal endothelial cells. Additionally, myeloid cells in the liver or spleen often engulf these complexes and express cargo proteins as part of their physiological function. While efforts are ongoing to improve the precision of mRNA-loaded LNP delivery to specific tissues beyond the liver, another approach involves engineering the mRNA cargo sequence to mitigate expression in off-target tissues. Such a strategy could be implemented to ensure more specific delivery to a desired target cell or tissue, such as HSCs in bone marrow.
[001472] MicroRNAs (miRNAs) are short, non-coding single-stranded RNAs. typically 18-24 nucleotides in length, that regulate gene expression by binding to target RNA sequences. A perfect match between a miRNA and its target sequence controls mRNA stability, while an imperfect match leads to inhibition of translation for protein-coding mRNAs. By selecting miRNAs that are highly expressed in off- target tissues but not in the desired tissues and incorporating target sequences for these miRNAs into the untranslated regions (UTRs) of the cargo mRNA, the tissue-specificity of therapeutic protein expression can be modulated.
Suppression of cargo mRNA expression by endogenous miRNA and miRNA target site in the UTR of cargo mRNA
[001473] This example establishes a platform for miR-mediated suppression of mRNA expression in a tissue culture model (FIG. 82). In FIG. 82(A), a schematic representation of luciferase mRNA with microRNA (miRNA) target sites (“ts") inserted in the 3 ’UTR is shown. Luciferase mRNA consists of 5’ cap, 5’UTR. luciferase coding sequence, 3’UTR followed by a poly A tail. A single copy (xl) orthree copies (x3) of perfectly matched miRNA target sequences were inserted at the 3’ end of the 3’ UTR. An alternative (alt) insertion site is located at the 5’ end of the 3’UTR, near the luciferase coding sequence. When combining two miRNA target sites in the same UTR, the first miRNA target site is inserted at the ‘alt’ location, and the second miRNA target site is inserted at the 3’ end of UTR. In FIG. 82(B), the incorporation of miR-122 ts into the 3’ UTR of luciferase mRNA results in the suppression of encoded protein in the Huh7 hepatocyte cell line, where miR-122 is expressed. A single copy ofthe target site at tire end of3’ UTR near poly A tail is sufficient to suppress luciferase expression by 5-fold compared to the control. Increasing the number of copies to three does not further enhance suppression. However, when the target site is inserted at the 5’ end of UTR, near the coding sequence, suppression is enhanced to 10-fold. In contrast, insertion of the target site of miR-142, which is not expressed in the hepatocyte cell line, has no impact on luciferase expression by itself and does not influence miR-122 mediated suppression when both target sites are inserted together on the same UTR.
[001474] Uris data demonstrates that endogenously expressed miRNAs, along with the incorporation of miRNA target sites in cargo mRNA, can effectively suppress cargo expression in the tissue where the respective miRNA is expressed.
Tissue-specific expression of cargo mRNA is achieved through the incorporation of specific miR target sites in the cargo mRNA
[001475] To investigate whether tissue-specific expression of cargo mRNA could be achieved by miRNAs. cell lines were utilized that specifically express certain miRNAs. Huh-7 hepatocyte cell line was selected, which expresses miR-122, and the THP-1 monocyte cell line, which expresses miR-142, in a cell type-specific manner. In the experimental setup, three copies of miRNA target site were inserted at the 5’ end of 3’ UTR, near the luciferase coding sequence (FIG. 83A). When combining two miRNA target sites in the same UTR, the first miRNA target site was inserted near the luciferase coding sequence and the second miRNA target site was inserted at the 3’ end of UTR. The insertion of miR-122 ts into the 3’ UTR of luciferase mRNA led to the suppression of protein expression in the hepatocyte cell line, where miR-122 is expressed (FIG. 83B, left), but not in the monocyte cell line, where miR-122 is not expressed (right). Conversely, miR-142 ts suppressed luciferase expression only in the monocyte cell line, where miR-142 is expressed (FIG. 83B, right). Inserting both miR-122 and miR-142 target sites into the same UTR inhibited luciferase expression in both the hepatocyte and monocyte cell line. This suggests the potential use of multiple miRNA target sites to suppress expression in various off-target tissues.
Testing miRNA-mediated suppression across various immune cells and hematopoietic stem cells [001476] Table 22 lists miRNAs expressed in liver, myeloid cells and other immune cells, hematopoietic stem cells, epithelial, and endothelial cells. All fifteen variants of firefly luciferase or VHH mRNA were synthesized, each containing three copies of a unique miRNA target site. These target sites were inserted at the 'alt' location of the 3 'UTR, near the coding sequences. In FIG. 84, the miRNA target-site mediated suppression was assessed in various immune cell lines and human long-term hematopoietic stem cells (LT-HSCs). The LT-HSCs were identified as CD34+CD38-CD90+CD45RA-Lineage- by surface expression of those markers among bone marrow-derived CD34+ cells. While the insertion of liver specific miR-122 or epithelial-specific miR-200b, 200c, 203a and 205 target sites in the 3’ UTR of cargo does not affect its expression in immune cells, hematopoietic miRNAs suppress cargo expression in one or more cell types. miR-142 and let7e effectively suppress cargo expression in all cell lines. miR-223 exhibits mild activity in all cell lines, with the least effect observed in long-term hematopoietic cells. miR-155 demonstrates suppression in the monocyte cell line and in long-term hematopoietic cells, albeit weaker in the latter. miR-342 suppresses expression in both monocyte and T-cell lines. Both mir-126 5p and 3p, which are abundantly expressed in endothelial cells, show a substantial suppressive effect in long-term hematopoietic stem cells.
[001477] This data suggests that incorporating both miR-122 and miR-223 target sites into the cargo sequence could be beneficial for hematopoietic stem cell (HSC) targeting therapy, as it helps suppress expression in off-target tissues such as the liver and myeloid cells, mitigating potential liver toxicity or innate immune activation.
Methods and Materials
Mammalian cell culture
[001478] Huh-7 cells (ATCC CRF-3216) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) plus GlutaMAX (Thermo Fisher Scientific), supplemented with 10% (v/v) fetal bovine serum (Gibco). JAWSII murine DCs (ATCC: CRL-11904) were cultured in a-MEM, supplemented with 20 % (v/v) fetal bovine serum (Gibco), 2 mM GlutaMAX (Gibco), and 5 ng/mL murine GM-CSF (Sigma). THP1 dual cells (InvivoGen) were cultured in RPMI 1640, supplemented with 10% (v/v) fetal bovine serum (Gibco), 2 mM Glutamine (Gibco), 10 pg/mL of Blasticidin (InvivoGen), and 100 pg/mL of Zeocin (InvivoGen). Jurkat cells (ATCC #TIN-152) were cultured in RPMI 1640, supplemented with 10 % (v/v) fetal bovine serum (Gibco), 2 mM GlutaMAX (Gibco) and HEPES (Gibco). Human Bone Marrow derived CD34+ cells (StemCell Technologies) were cultured in X-VIVO 15 media (Lonza) supplemented with 100 ng/mL of SCF, FLG-3L, and TPO (Peprotech). Cells were maintained at 37°C with 5% CO2.
In vitro transcription
[001479] Plasmid templates were synthesized by Twist Bioscience. T7 promoter was inserted upstream of RT or ncRNA sequences. Plasmid was linearized by Sapl enzyme (NEB, R0569L) for 30 minutes at 37°C and the complete linearization was checked by agarose gel electrophoresis. Linearized template was purified by Gene JET PCR purification kit (K0701, Thermo Fisher Scientific) and quantified by NANODROP. mRNA was synthesized for 2 hours at 37°C using HiScribe T7 mRNA kit with CleanCap Reagent AG (NEB, E2080S) following manufacturer’s protocol. After DNAse 1 treatment, RNA was purified using Qiagen RNeasy midi kit (Qiagen, 75144). RNA concentration was measured by NANODROP (Thermo Fisher) and purity and size were evaluated by RNA ScreenTape analysis on Tape station (Agilent). RT mRNA was further poly (A) tailed by E.coli Poly(A) polymerase (NEB, M0276) and purified by Qiagen RNeasy midi kit. Tail length was estimated by RNA ScreenTape analysis by comparing before and after poly (A) adenylation.
RNA Transfection by messengerMax, TransIT, and jetMESSENGER reagents
[001480] 15,000-30,000 cells of Huh-7 hepatocytes, JAWSII murine DCs, Jurkat T-cells, and THP1 dual cells were seeded in 96 well plates. 16-24 hours post-seeding, cells were transfected with appropriate amount of RNA mixture complexed with Lipofectamine MessengerMax (Thermo Fisher Scientific) for Huh- 7. or TransIT (Minis Bio) for JAWSII or jetMESSENGER (polypus) for THP-1. Cells were cultured for 24 hours before measuring protein expression.
RNA Transfection by Neon Electroporation system
[001481] Human CD34+ cells were harvested and resuspended in T buffer. 50,000 cells with 1 pl of RNA mixture were electroporated by 10 pl Neon tip at 1600 voltage, 10 pulse width, 3 pulses. Electroporated cells were gently transferred to 96 well plate (VWR) containing prewarmed culture media and cultured for 24 hours before analyzing by flow cytometry .
Measurement of luciferase expression
[001482] Amount of luciferase protein was measured by ONE-Glo™ EX luciferase assay system (Promega E8120). After equilibrating the reagent and cells to room temperature, equal volume of reagent and cells were mixed and incubated for 3 minutes on an orbital shaker at 300-600 rpm. Tire luminescence was read on Varioskan LUX (Thermo Fisher Scientific) at 200 msec integration time. Luminescence from Firefly luciferase was normalized by that from Renilla luciferase.
Flow cytometry analysis of VHH expression in human long-term hematopoietic stem cells [001483] Culture media was removed by centrifuging the culture plate. Cells were washed with PBS and incubated with Live Dead Aqua (INVITROGEN) for 15 minutes at room temperature. Cells were washed with cell staining buffer (BIOLEGEND, 420201) and incubated with Human Fc Block (BIOLEGEND.
422302) for 10 minutes on ice. Antibody cocktail comprising anti-CD38 (FITC, StemCell Technologies), anti CD45 (APC-Fire750, BIOLEGEND), anti-CD34 (BV421, BIOLEGEND), anti-CD45RA (BV605, BD biosciences), anti-CD90 (PE-Cy7, BIOLEGEND), anti-CD3 (AF700, BD biosciences), anti-CD8 (AF700, BIOLEGEND), anti-CDl lb (AF700, BIOLEGEND), anti-CDl lc (AF700, BIOLEGEND), anti-CD14 (AF700, BIOLEGEND), anti-CD19 (AF700, BIOLEGEND), anti-CD56 (AF700, BIOLEGEND), and anti- CD235a (AF700, BIOLEGEND) was added to the cells and incubated for 30 minutes on ice in the dark. After incubation, cells were washed twice with cell staining buffer and acquired on Attune NxT flow cytometer (Thermo Fisher Scientific).
Table 22 - Select miRNA Sequences
EXAMPLE 24: Combining guide modification approaches, internal chemical modifications, extensions and backfolds results in improved on-target editing.
[001484] Mobilized Human Peripheral Blood CD34+ Cells (AllCells, Donor ID# 888824822) are thawed on Day 0. The following media is used for thawing and activation: c-XVIVO Media (Complete X- VIVO) = X-VIVO + O. lug/mL SCF + O.lug/mL FLT3L + O.lug/mL TPO [X-VIVO 15 (Lonza; Cat# 04- 418Q), Recombinant Human SCF Protein, CF (R&D; Cat# 11010-SC-050), Recombinant Human Thrombopoietin (NSO-expressed) Protein, CF (R&D; Cat# 288-TPN/CF), Recombinant Human Flt-3 Ligand/ FLT3L (HEK293) Protein), CF (R&D; Cat# 308-FKHB-010)]. The cells are thawed into a T75 flask (Coming; Cat# 430641U or equivalent). RNA is electroporated into 100K cells in Buffer P3 (Lonza; Cat# V4SP-3096) using Lonza 4d Nucleofector on Day 2 using 2 ug total RNA (at a ratio of 1 : 1) using pulse code DS 130 according to the manufacturer’s protocol. mRNA encoding nuclease is manufactured by Oma Therapeutics and modified gRNA is manufactured by SynOligo Biotechnologies. The cells are recovered in c-XVIVO Media. 72 hours later genomic DNA is extracted on a KingFisher Apex using Mag-Bind® Blood & Tissue DNA HDQ 96 Kit (Omega Bio-tek; Cat# M6399) according to the manufacturer’s protocol. NGS is performed on Illumina Nextseq and analysis in CRISPResso. Guide constricts tested according to the present Example comprise SEQ ID NOs: 2499-2564. Any Type V nuclease of the present disclosure can be utilized in this procedure. In certain embodiments, the above experiment is carried out utilizing the K292R 405-1 mutant variant Type V nuclease of the present disclosure (SEQ ID NO: 2322) or a variant thereof, such as SEQ ID NO: 2411.
EXAMPLE 25: Demonstration of on-target editing activity in vivo using liver PoC model
[001485] B2M, Beta-2 microglobulin, is a therapeutically relevant target that can used as a proof-of- concept locus to interrogate editing activity in a wild-type mouse. To evaluate the on-targeting editing activity of the K292R 405-1 mutant (SEQ ID: 2322) in vivo, guides for mouse B2M and nuclease mRNA were co-encapsulated and dosed in wild-type mice. The editing outcome was measured using amplicon sequencing. Guides for mouse B2M were first screened in vitro to nominate three target sites to funnel into the in vivo model. Three regions of the locus were tiled with gRNAs leveraging the TTTV PAM site.
List of gRNA sequences screened with AltR modification pattern
* each sequence comprised Integrated DNA Technologies Alt-R modifications
[001486] Methods and Materials - Hepal-6 Cells (ATCC; Cat# CRL-1830) were cultured in DMEM, high glucose. GlutaMAX Supplement pyruvate (ThermoFisher: Cat# 10569010) with 10% FBS (ThermoFisher; Cat# A5209501) and 1% Pen-Strep (ThermoFisher; Cat# 15140-122). One day prior to transfection, 2e4cells were seeded in a 96 well plate and allowed to grow overnight to a confluency of 70- 90%. For each reaction, 0.6uL of Lipofectamine MessangerMAX (ThermoFisher; Cat# LMRNA001) reagent was mixed with Opti-MEM (ThermoFisher; Cat# 31985062). Nuclease mRNA and gRNAs were mixed in Opti-MEM at a 1 : 1 ratio by mass. The gRNAs of SEQ ID NOs: 2565-2580 were used. A two-fold serial dilution was performed with atop dose of 600ng. Incubation times were performed according to the manufacturer's recommendations. 72 hours later genomic DNA was extracted on a KingFisher Apex using Mag -Bind® Blood & Tissue DNA HDQ 96 Kit (Omega Bio-tek; Cat# M6399) according to the manufacturer's protocol. NGS was performed on Illumina Nextseq and analysis in CRISPResso. Results - At the higher dose (150 ng), 7 of the screened gRNA s performed comparable to the Cas9 benchmark at 70% +/- 5%. Three gRNAs: Guide 1, Guide2, and Guide 3, were elected to move forward into the in vivo experiment based on their potency at the lower dose (9.375 ng). The maximal editing achieved by these three gRNAs were Guidel = 76.58%, Guide2 = 74.25%, Guide3 = 65.37%, which was comparable to the Cas9 benchmark (70.78%). See FIGs. 87A and 87B.
[001487] To evaluate tire on-targeting editing activity of the K292R 405-1 mutant (SEQ ID NO: 2322) in vivo, wild type mice were dosed with LNPs encapsulating nuclease mRNA and one of each of the top three gRNAs evaluated in the initial experiment comprising the Mod6 modification pattern (see Example 20) (SEQ ID NOs: 2581, 2582 and 2583).
List of gRNA sequences screened with Mod6 modification pattern
Legend: A, G, U, C: RNA nucleotide; a, g, u. c: 2'-O-Methyl-nucleotide; *: Phosphorothioate linkage
[001488] Methods and Materials - The editing cargo was formulated into LNPs comprising Ionizable lipid (48.5%) - DSPC (10%) - Cholesterol (39.5%) - DMG-PEG (2%) at a 1: 1 ratio by mass. C57BL/6 wildtype mice, aged 12-16 weeks (The Jackson Laboratory), were dosed in a single IV dose in a volume of 5ml/kg. Each LNP was dosed at 2mg/kg and 0.5mg/kg. A PBS control group was dosed and treated equally. Additionally, a Cas9 control group with guide also targeting mB2M was dosed. 7 days post-treatment, the mice were euthanized for the collection of the liver. Snap-frozen liver was homogenized using tire Spex Genomax 2050 Tissue Homogenizer (Lab Spex), and gDNA was extracted on a KingFisher Apex using Mag- Bind® Blood & Tissue DNA HDQ 96 Kit (Omega Bio-tek; Cat# M6399) according to the manufacturer’s protocol. NGS was performed on Illumina Nextseq and analysis in CRISPResso. Results - The
K292R 405-1 mutant (SEQ ID NO: 2322) had robust activity in the mouse liver. All the gRNAs used in the study showed on-target editing activity in vivo. The highest editing observed with 405-1 was 57% (Guide 1, 2mg/kg). For all gRNAs the 2mg/kg dose resulted in higher editing than the 0.5mg/kg dose. See FIG. 88.
Supplementary Sequences for Examples
[001489] The following sequences are referenced in the herein Examples.
Table SI: crRNA for PAM determination:
Table S2: Target sequences HEK293T
Table S3: crRNA cassete sequences HEK293T
Table S4: crRNA sequences HEK293T
Table S5: Primer sequences T7 Endo I
Table S6: Amplicon sequences
Table S7: Sequences referenced in Examples 16-25
[001490] The following sequences form part of the specification, each of which are part of the instant
Specification and can be found in Appendix B (which itself is part of the Specification) which accompanies and forms part of this disclosure as originally filed.
Section K of Specification
APPENDIX A - SEQUENCES
In various embodiments, the (Cas Type V) polypeptide is a polypeptide selected from any one of the polypeptide sequences listed in any of Groups 1-15, or a polypeptide having at least 70%, 75%. 80%, 85%, 90%. 95%, 99%, or 100% sequence identity with a polypeptide from any one of the polypeptide sequences listed in any of Groups 1-15. In various other embodiments, the (Cas Type V) polypeptide is encoded by a polynucleotide sequence selected from any one of Tables SIB - S15A, or a polynucleotide having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a polynucleotide of any one of Tables SIB - S15A. In various other embodiments, the Casl2a (Cas Type V) guide RNA is selected from any Cas 12a (Cas Type V) guide sequence disclosed in the following tables, including Table S15C, or a nucleic acid molecule having at least 70%, 75%, 80%, 85%, 90%, 95%, 99%, or 100% sequence identity with a Casl2a (Cas Type V) guide sequence of any of the following relevant tables, including Table S15C.
A. GROUP 1 Type V nuclease and associated sequences (SEQ ID Nos: 1-19)
Table SI A - Enzyme Sequences Group 1
Table SIB - Human Codon Optimized Nucleotide Sequences Group 1
Table SIC - Direct Repeat Group 1
Table SID - crRNA Sequences Group 1
Table S1E - Consensus Sequence Group 1
Wherein: each X is independently selected from any naturally occurring amino acid; and each Z is independently selected from absent and any naturally occurring amino acid.
Table S1F - Native Nucleotide sequences Group 1
B. GROUP 2 Type V nuclease and associated sequences (SEQ ID Nos: 20-31)
Table S2A - Enzyme sequences Group 2
Table S2B - Human Codon Optimized Nucleotide Sequences Group 2
Table S2C - Direct Repeat Group 2
Table S2D - crRNA Sequences Group 2
Table S2E - Native Nucleotide Sequences Group 2
C. GROUP 3 Type V nuclease and associated sequences (SEQ ID Nos: 32-44)
Table S3A - Enzyme Sequences Group 3
Table S3B - Human Codon Optimized Nucleotide Sequences Group 3
Table S3C - Direct Repeat Group 3 Table S3D - crRNA Sequences Group 3
Table S3E - Consensus Sequence Group 3
Wherein: each X is independently selected from any naturally occurring amino acid.
Table S3F - Native Nucleotide Sequences Group 3
D. GROUP 4 Type V nuclease and associated sequences (SEQ ID Nos: 45-56)
Table S4A - Enzyme Sequences Group 4
Table S4B - Human Codon Optimized Nucleotide Sequences Group 4
Table S4C - Direct Repeat Group 4
Table S4D - crRNA Sequences Group 4
E. GROUP 5 Type V nuclease and associated sequences (SEQ ID Nos: 57-72) Table S5A - Enzyme Sequences Group 5
Table S5B - Human Codon Optimized Nucleotide Sequences Group 5
Table S5C - Direct Repeat Group 5
Table S5D - crRNA Sequences Group 5
| SEQ ID NO | Sequence
Table S5E - Consensus Sequence Group 5
Wherein: each X is independently selected from any naturally occurring amino acid; and each Z is independently selected from absent and any naturally occurring amino acid.
Table S5F - Native Nucleotide Sequences Group 5
F. GROUP 6 Type V nuclease and associated sequences (SEQ ID Nos: 76-99)
Table S6A - Enzyme Sequences Group 6
Table S6B - Human Codon Optimized Nucleotide Sequences Group 6 Table S6C - Direct Repeat Group 6
Table S6D - crRNA Sequences Group 6
G. GROUP 7 Type V nuclease and associated sequences (SEQ ID Nos: 100-117)
Table S7A - Enzyme Sequences Group 7
Table S7B - Human Codon Optimized Nucleotide Sequences Group 7
Table S7C - Direct Repeat Group 7
Table S7D - crRNA Sequences Group 7
H. GROUP 8 Type V nuclease and associated sequences (SEQ ID Nos: 118-130)
Table S8A - Enzyme Sequences Group 8 Table S8B - Human Codon Optimized Nucleotide Sequences Group 8
Table S8C - Direct Repeat Group 8
Table S8D - crRNA Sequences Group 8
Table S8E - Consensus Sequence Group 8
Wherein: each X is independently selected from any naturally occurring amino acid. Table S8F - Native Nucleotide Sequences Group 8
I. GROUP 9 Type V nuclease and associated sequences (SEQ ID Nos: 131-330)
Table S9A - Enzyme Sequences Group 9 (SEQ ID Nos: 131-170)
Table S9B - Human Codon Optimized Nucleotide Sequences Group 9
Table S9C - Direct Repeat Group 9
Table S9D - crRNA Sequences Group 9
J. GROUP 10 Type V nuclease and associated sequences (SEQ ID Nos: 331-367)
Table S10A - Enzy me Sequences Group 10 (SEQ ID Nos: 331-336)
Table S10B - Human Codon Optimized Nucleotide Sequences Group 10
Table S10C - Direct Repeat Group 10
Table S10D - crRNA Sequences Group 10
Table S10E - Consensus Sequence Group 10
Wherein: each X is independently selected from any naturally occurring amino acid; and each Z is independently selected from absent and any naturally occurring amino acid.
Table S10F - Native Nucleotide Sequences Group 10
K. GROUP 11 Type V nuclease and associated sequences (SEQ ID Nos: 368-385)
Table Sil A - Enzyme Sequences Group 11
Table SI IB - Human Codon Optimized Nucleotide Sequences Group 11 Table S 11 C - Direct Repeat Group 11
Table SI ID - crRNA Sequences Group 11
L. GROUP 12 Type V nuclease and associated sequences (SEQ ID Nos: 386-398)
Table S12A - Enzyme Sequences Group 12
Table S12B - Human Codon Optimized Nucleotide Sequences Group 12
Table S12C - Direct Repeat Group 12
Table S12D - crRNA Sequences Group 12 Table S12E - Consensus Sequence Group 12
Wherein: each X is independently selected from any naturally occurring amino acid.
Table S12F - Native Nucleotide Sequences Group 12
IM
M. GROUP 13 Type V nuclease and associated sequences (SEQ ID Nos: 399-435)
Table S13A - Enzyme Sequences Group 13
Table S13B - Human Codon Optimized Nucleotide Sequences Group 13
Table S13 - Direct Repeat Group 13
Table S13D - crRNA Sequences Group 13
Table S13E - Consensus Sequence Group 13
Wherein: each X is independently selected from any naturally occurring amino acid; and each Z is independently selected from absent and any naturally occurring amino acid.
Table S13F - Native Nucleotide Sequences Group 13
N. GROUP 14 Type V nuclease and associated sequences (SEQ ID Nos: 436-563)
Table S14A - Enzyme Sequences Group 14 (SEQ ID Nos: 436-456)
Table SUB - Human Codon Optimized Nucleotide Sequences Group X
Table SMC - Native Nucleotide Sequences Group X
Table S14D - Direct Repeat Group 14
Table S 14. E - crRNA Sequences Group 14
O. GROUP 15 Select Type V nucleases from Groups 1-14
Table S15A - Enzyme Sequences Group 15
Table S15B - Nucleotide Sequences Group 15
Table S15C - Corresponding Guide Sequences Group 15
Table S15D - Enzyme and PAM Sequences of Table Ex. 9.2
As described in Example 9, PAM sequence recognition was identified for each protein in Table Ex. 9.2. In the table, tire following lettering refers to the following: A= Adenine, C=Cytosine, G=Guanine, T= Thymine, R=A or G, Y=C or T, S=G or C, W=A or T. D=A or G or T, H=A or C or T, K=G or T, M=A or C, N=any base, B=C or G or T, V=A or C or G).
P. Mutant Type V nuclease and associated sequences
The following are protein coding sequences (i.e., nucleotide sequences) and the corresponding protein sequences for various mutant Type V nucleases, and in particular, those based on making a variety of substitutions in ID405 (SEQ ID NO: 334), ID414 (SEQ ID NO: 58), and ID418 (SEQ ID NO: 564) as described in Table S8 of the Examples.
1. Protein coding sequences (SEQ ID Nos: 566-583)
2. Protein sequences (SEQ ID Nos: 585-602)
3. Full mRNA sequences of ID405, ID414, and ID418 Type V nucleases (wildlype) (SEQ ID Nos: 603-607)
Q. Canonical LbCasl2a (SEQ ID NO: 1382)
Source: Lachnospiraceae bacterium. As published in: Peng et al.. “Structural insight into multistage inhibition of CRISPR- Casl2a by AcrVA4,’‘ PNAS, 2019, Vol. 116(38), pp. 18928-18936 (incorporated herein by reference)
MSKLEKFTNCYSLSKTLRFKAIPVGKTQEN1DNKRLLVEDEKRAEDYKGVKKLLDRYYLSF1NDVLHSIKLKNLNN
YISLFRKKTRTEKENKELENLEINLRKE1AKAFKGNEGYKSLFKKDI1ETILPEFLDDKDE1ALVNSFNGFTTAFTGFFD
NRENMFSEEAKSTSIAFRCINENLTRYISNMDIFEKVDAIFDKHEVQEIKEKILNSDYDVEDFFEGEFFNFVLTOEGID
VYNAIIGGFVTESGEKIKGLNEYINLYNQKTKQKLPKFKPLYKQVLSDRESLSFYGEGYTSDEEVLEVFRNTLNKNSE
IFSSIKKLEKLFKNFDEYSSAGIFVKNGPAISTISKDIFGEWNVIRDKWNAEYDDIHLKKKAVVTEKYEDDRRKSFKKI
GSFSLEQLQEYADADLSWEKLKEIIIQKVDEIYKVYGSSEKLFDADFVLEKSLKKNDAWAIMKDLLDSVKSFENYI
KAFFGEGKETNRDESFYGDFVLAYDILLKVDHIYDAIRNYVTQKPYSKDKFKLYFQNPQFMGGWDKDKETDYRAT
ILRYGSKYYLAIMDKKYAKCLQKIDKDDVNGNYEKINYKELPGPNKMLPKVFFSKKWMAYYNPSEDIQKIYKNGT
FKKGDMFNLNDCHKLIDFFKDSISRYPKWSNAYDFNFSETEKYKDIAGFYREVEEQGYKVSFESASKKEVDKLVEE
GKLYMFQIYNKDFSDKSHGTPNLHTMYFKLLFDENNHGQIRLSGGAELFMRRASLKKEELWHPANSPIANKNPDN
PKKTTTLSYDVYKDKRFSEDQYELHIPIAINKCPKNIFKINTEVRVLLKHDDNPYVIGIDRGERNLLYIVVVDGKGNI
VEOYSLNEIINNFNGIRIKTDYHSLLDKKEKERFEARQNWTSIENIKELKAGYISOWHKICELVEKYDAVIALEDLN
SGFKNSRVKVEKOVYOKFEKMLIDKLNYMVDKKSNPCATGGALKGYOITNKFESFKSMSTQNGFIFYIPAWLTSKI
DPSTGFVNLLKTKYTSIADSKKFISSFDRIMYVPEEDLFEFALDYKNFSRTDADYIKKWKLYSYGNRIRIFRNPKKNN
VFDWEEVCLTSAYKELFNKYGINYQQGDIRALLCEQSDKAFYSSFMALMSLMLQMRNSITGRTDVDFLIS
PVKNSDGIFYDSRNYEAQENAILPKNADANGAYNIARKVLWAIGOFKKAEDEKLDKVKIAISNKEWLEYAQTSVK
H
The bold/underlined residues are conserved amino acids as compared to each of the Casl2a orthologs of Table S15A as determined by way of a multi-sequence aligmnent using Clustal Omega multi-sequence aligmnent tool available online at the European Molecular Biology Laboratory (EMBL). The following amino acids appearing in the canonical LbCasl2a amino acid sequence of SEQ ID ON: 1382 are conserved among each of the Table S15A enzymes at corresponding residues as determined by the alignment of FIG. 31 (as shown by an asterisk beneath each conserved residue in the alignment). The conserved amino acids are:
In addition, the multiple sequence alignment of FIG. 31 also identifies the above-underlined regions as containing (a) at least one fully conserved residue (as marked with an asterisk “*”) throughout all the aligned sequences, and (b) at least one highly similar conserved residue (as marked with a colon or moderately conserved resided (as marked with a period The wholly conserved residues are identical in all the aligned sequences. The highly similar conserved residues are those where the substitutions among the sequences have strongly similar properties. The moderately conserved residues are those where the substitutions among tire sequence have weakly similar properties. The underlined regions are referred to as “highly conserved regions.”
In certain embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length.
In certain other embodiments, the percent identity' variation between reference ortholog (e.g., any ortholog in Table S15A) and a variant of said ortholog is with respect only to the variable regions of the reference protein as detennined by an alignment of multiple related sequences (e g., as shown in the alignment of FIG. 31). The variable regions, for purposes of this application, can be considered to be those regions of the alignment of FIG. 31 that are not identified as a highly conserved region (underlined regions shown above), i.e., the non-underlined regions above.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%. 55%, 60%, 65%. 70%, 75%, 80%. 85%, 90%, 95%. 99%, or up to 100% sequence identity with any reference sequence (e.g.. the orthologs of Table S15A) over their full length, but which also must comprise at least one conserved amino acid corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk which includes at least one of tire following conserved amino acids
(relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length, but which also must comprise at least two conserved amino acids corresponding to tire conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk which includes at least two of the following conserved amino acids
(relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; SI 166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%. 55%, 60%, 65%. 70%, 75%, 80%. 85%, 90%, 95%. 99%, or up to 100% sequence identity with any reference sequence (e.g., the orthologs of Table SI 5 A) over their full length, but which also must comprise at least three conserved amino acids corresponding to the conserved amino acids identified in tire alignment of FIG. 31 (those residues marked with an asterisk “*”), which includes at least three of the following conserv ed amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; SI 166; P1167; D1180; G1183; Al 184; 11187; Al 188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%. 55%, 60%, 65%. 70%, 75%, 80%. 85%, 90%, 95%. 99%, or up to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length, but which also must comprise at least four conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk “*”). which includes at least four of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; Al 184; 11187; Al 188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%. 55%, 60%, 65%. 70%, 75%, 80%. 85%, 90%, 95%. 99%, orup to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length, but which also must comprise at least five conserved amino acids corresponding to the conserved amino acids identified in tire alignment of FIG. 31 (those residues marked with an asterisk “*”), which includes at least five of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218. In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, orup to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length, but which also must comprise at least six conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk which includes at least six of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; KI 190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with any reference sequence (e.g.. the orthologs of Table S15A) over their full length, but which also must comprise at least seven conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk “*”), which includes at least seven of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51 ; Fl 44; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length, but which also must comprise at least eight conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk “*”), which includes at least eight of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; SI 166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S 15 A) ov er their full length, but which also must comprise at least nine conserved amino acids corresponding to the conserved amino acids identified in the aligmnent of FIG. 31 (those residues marked with an asterisk “*”), which includes at least nine of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; SI 166; P1167; D1180; G1183; Al 184; 11187; Al 188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%. 55%, 60%, 65%. 70%, 75%, 80%. 85%, 90%, 95%. 99%, or up to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S 15 A) over their full length, but which also must comprise at least ten conserved amino acids corresponding to the conserv ed amino acids identified in the aligmnent of FIG. 31 (those residues marked with an asterisk “*”). which includes at least ten of the following conserved amino acids (relativ e to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009;
W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%. 65%, 70%, 75%. 80%, 85%, 90%. 95%, 99%, orup to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length, but w hich also must comprise at least eleven conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk which includes at least eleven of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%. 65%, 70%, 75%. 80%, 85%, 90%. 95%, 99%, orup to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length, but which also must comprise at least twelve conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk which includes at least twelve of tire following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991 ; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, orup to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length, but which also must comprise at least thirteen conserv ed amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk “*’'), which includes at least thirteen of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with any reference sequence (e.g.. the orthologs of Table S15A) over their full length, but which also must comprise at least fourteen conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk “*"), which includes at least fourteen of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832: R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009: W1063; R1152; N1153; S 1154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Cast 2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with any reference sequence (e.g.. the orthologs of Table S15A) over their full length, but which also must comprise between 1-10 conserved amino acids corresponding to tire conserv ed amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk “*”), which includes between 1-10 of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, orup to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length, but which also must comprise between 5-15 conserv ed amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk “*”), which includes between 5-15 of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; KI 190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with any reference sequence (e.g.. the orthologs of Table S15A) over their full length, but which also must comprise between 15-25 conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk “*”), which includes between 15-25 of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or up to 100% sequence identity with any reference sequence (e.g., the orthologs of Table S15A) over their full length, but which also must comprise between 25-35 conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk "*”), which includes between 25-35 of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179: Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; SI 166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%, 55%, 60%, 65%. 70%, 75%, 80%, 85%, 90%, 95%. 99%, or up to 100% sequence identity with any reference sequence (e g., the orthologs of Table S15A) ov er their full length, but which also must comprise between 30-60 conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk “*”), which includes between 30-60 of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; SI 166; P1167; D1180; G1183; Al 184; 11187; Al 188; K1190; or W1218.
In still other embodiments, the Casl2a orthologs disclosed herein (e.g., including, but not limited to those sequences of Table S15A) include variants thereof that may have at least 50%. 55%, 60%, 65%. 70%, 75%, 80%. 85%, 90%, 95%. 99%, or up to 100% sequence identity with any reference sequence (e.g.. the orthologs of Table S15A) over their full length, but which also must comprise between 40-75 conserved amino acids corresponding to the conserved amino acids identified in the alignment of FIG. 31 (those residues marked with an asterisk which includes between 40-75 of the following conserved amino acids (relative to the amino acid numbering of canonical LbCasl2a sequence): T16; P23; T27; D40; K51; F144; R158; N160; T169; R174; N179; Q231; 1234; N238; L276; Q279; Y504; R508; T512; F525; L555; F702; K707; D708; F745; R747; H797; 1829; G830; D832; R833; G834; E835; L838; Y840; L876; W890; K900; G902; S905; A920; E925; L927; N928; E939; Y943; E947; L950; K953; L954; K960; Q975; Q989; G991; Y995; A998; T1001; D1005; P1006; T1008; G1009; W1063; R1152; N1153; SI 154; S1166; P1167; D1180; G1183; A1184; 11187; A1188; K1190; or W1218.
R. Sequences referenced in Example 15
A. Indel sequencing primers
B. Mutant sequences - amino acid sequence KSIPEAIYQEIYQLKNKMADSISDEAKRLLESGTWCKVATHDIVKDKHF TENTYLFHCPITMNFI<AI<DRTNI<EFNNHVLEVLNI<NPDIKVIGLDRGER HLLYLSLINQKGEIECQKTLNLVEQVRNDKTVSVNYHEKLVHKEGSRDA
ARKNWQT1GN1KELKEGYLSAVVHE1ASLMVKHNA1VVMEDLNFGFKRG
RFAVERQIYQKFENMLIEKLNYLVFKDRKVTEPGGVLNAYQLANKSAKV
TDVYKQCGWLFYIPAAYTSKIDPRTGFANLFITKGLTNVEKKKEFFGKFD
SIRYDATESCFVFSFDYAKICDNADYKKKWDVYTRGTRLVYNKTERKN
VSVNPTEELQCVFDEFG1KWNTGEDLIESISLIPAEKSNAKFFDVLLRMFN
ATLQMRNSVPNTDTDYLVSPVKAEDGSFFDSREEFKKGGDARLPIDCDA NGAYHIALKGLYLLLNDFNRDNKGVIQNISNKDWFKFVQEKVYKD C. Mutant sequences - nucleotide sequences D. Variant mutants for expression in coli - amino acid sequences
E. Variant mutants for expression in E. coli - nucleotide sequences
Section K of Specification
APPENDIX B - SEQUENCES
The following sequences form part of the specification. In addition, any nucleotide or amino acid sequence having at least 70%, 75%, 80%.
85%, 90%, 95%, 99%, or 100% sequence identity with any of the following sequences also are contemplated.
1196
DM2\20736808. 1
Key: A, G, U, C, S = unmodified RNA nucleotide; a, g, u, c, s = 2'-O-Methyl -nucleotide; * = Phosphorothioate linkage
SEQ ID NO: 50 - All ’U” = N-l-Methylpsuedouridine
SEQ ID NOs: 350-352 - 5’ FAM tag present
SEQ ID NOs: 353-355 - 3’ FAM tag present
SEQ ID NOs: 432-521, 535, 536 and 537 - 2'-O-Methyl at first 3 and last 3 bases, 3' phosphorothioate bonds between first 3 and last 2 bases
SEQ ID NOs: 2354-2380 - All “U'’ = N-l-Methylpsuedouridine

Claims

1. A Cas Type V polypeptide comprising an amino acid sequence having at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% sequence identity to any one of the amino acid sequence sequences selected from SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein the polypeptide comprises one or more substitutions at positions selected from: K292, Q492, T306. L748, A739. F297. N536, D851. N770, D675, K955. S972, N798, K298, H853, E377. V295, K852, F854. N1015, T845, E1019, K745, Q565, K745, 1723, K821, K721, A810, K768, S16, 128, V312, V929, L474, H470, E402, K207, V294, R212, F79, Q299, Q465, F537, K1284, V929, DI 192, Q1203, T838, N735, 11063, K933, N1249, 197, R212, A1251, N1264, R1138, N588, 1584, V453, Q475, N76, R304, 1471, E544, V254, D231, H496, V534, D577, 128, A183, D341, K595, V501, S568, H470, V254, D231 and F197, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID4L5), and SEQ ID NO: 445 (No. ID419).
2. Hie Cas Type V polypeptide of claim 1, comprising one or more substitutions selected from: Q492X, I L748X. A739X, F297X, N536X, D851X. N770X, D675X, K955X. S972X, N798X, K298X, H853X, E37 V295X, K852X, F854X, N1015X, T845X, E1019X, K745X and K292X, based on the ammo acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No.
D406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein < is arginine, histidine or lysine. i . The Cas Type V polypeptide of claim 1 or 2, wherein, excluding the one or more substitutions, the Cas Type V polypeptide is at least 95% identical to any one of: SEQ ID NO: 334 (No. ID405), SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), or SEQ ID NO: 445 (No. ID419).
4. The Cas Type V polypeptide of any preceding claim, comprising one or more substitutions selected from: K955X, F297X, T306X, E1018X, E377X, K852X, K298X, T845X, V295X, N536X, Q492X, N770X, N101 and K292X, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine.
5. The Cas Type V polypeptide of any preceding claim, comprising one or more substitutions selected from: K292X. Q492X, N536X, N770X and N 1015X. based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID4I8), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine.
6. The Cas Type V polypeptide of any preceding claim, comprising the substitutions K292X and D169X. based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine.
7. The Cas Type V polypeptide of any preceding claim, comprising one or more combinations of substitut selected from:
N536X and N770X;
N536X and N1015X;
K292X, N536X and NI015X;
K292X and N770X;
K292X, N536X and N770X;
K292X, N770X and N1015X;
K292X and N1015X;
K292X and Q492X;
K292X, Q492X and N536X;
K292X, Q492X and N770X;
K292X, Q492X and NI0I5X;
N536X, N770X and N1015X;
Q492X, N536X and N770X;
Q492X, N536X and N1015X; Q492X and N770X;
Q492X, N770X and N1015X;
Q492X and N536X;
K292X and N536X;
N770X and N1015X:
Q492X and N1015X:
K292X, Q492X, N536X, N770X and N1015X;
K292X, N536X, N770X and N1015X;
K292X, Q492X, N536X and N770X;
K292X, Q492X, N536X and N1015X;
K292X, Q492X, N770X and N1015X; and/or
Q492X, N536X, N770X and N1015X; based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding combinations of substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine.
8. The Cas Type V polypeptide of any preceding claim, comprising the substitution D169X, based on the acid sequence provided in SEQ ID NO: 334 (No. ID405), or a corresponding substitution in any of the am sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419), wherein X is arginine, histidine or lysine.
>. The Cas Type V polypeptide of any preceding claim, wherein X is arginine.
0. Tire Cas Type V polypeptide of any preceding claim, comprising a D169R substitution, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or a corresponding substitution in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406). SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
1 1 . The Cas Type V polypeptide of any preceding claim, comprising one or more substitutions at positions selected from: Q565, K745, 1723, K821, K721, A810, K768, S16, 128, V312, V929, L474, H470, E402, K2i V294, R212, F79, Q299, Q465, F537, K1284, V929, DI 192, Q1203, T838, N735, 11063, K933, N1249, 197 R212, A1251, N1264, R1138, N588, 1584, V453, Q475, N76, R304, 1471, E544, V254, D231, H496, V534, D577, 128, A183, D341, K595, V501, S568, H470, V254, D231 and F197, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406). SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
12. The Cas Type V polypeptide of any preceding claim, comprising:
(a) one or more substitutions at positions selected from: Q565, K745, 1723, K821, K721, A810, K768, S16, 128, V312, V929; and/or
(b) one or more combinations of substitutions at positions:
L474, H470 and E402;
K207, V294, R212. F79 and Q299;
Q465 and F537;
K1284, V929, DI 192 and Q1203;
T838 and N735;
11063, K933 and N1249;
197 and R212;
A1251. N1264 and R1138;
N588, 1584, V453 and Q475;
N76 and R304;
1471 and E544;
V254 and D231;
H496, V534 and D577;
128, A183 and D341;
K595, V501, S568 and H470;
V254, D231 and Fl 97;
V254 and D341; and/or
V254, D341 and F197; based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions or combinations of substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID41 1), SEO ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
13. The Cas Type V polypeptide of any preceding claim, wherein comprising one or more substitutions selected from: Q565K, K745M, I723V, K821I, K721M, A810V, K768M, S16T, I28F, V312E, V929I, L474Q, H470N, E402V K207N, V294M, R212Q, F79S, Q299E, Q465R, F537I, K1284R, V929D, D1192E, Q1203H, T838S, N735I, I1063N, K933M, N1249S, I97T, R212L, A1251V, N1264I, R1138S, N588I, I584S, V453E, Q475H, N76D, R304S, I471T, E544D, V254M, D231V, H496N, V534F, D577G. I28F. A183T, D341V, K595T, V501D, S568I, H470L, V254M, D23 IV and F197V, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
14. The Cas Type V polypeptide of any preceding claim, comprising:
(a) one or more substitutions selected from: Q565K, K745M. I723V, K821I, K721M, A810V, K768M. S16T, I28F, V312E, V929I; and/or
(b) one or more combinations of substitutions selected from:
L474Q, H470N and E402V;
K207N, V294M, R212Q, F79S and Q299E;
Q465R and F537I;
K1284R. V929D. DI 192E and Q1203H;
T838S and N735I;
I1063N, K933M and N1249S;
I97T and R212L;
A1251V, N1264I and R1138S;
N588I, I584S, V453E and Q475H;
N76D and R304S;
147 IT and E544D;
V254M and D231V;
H496N, V534F and D577G;
I28F, A183T and D341V;
K595T. V501D, S568I and H470L:
V254M, D231V and F197V:
V254M and D341V; and/or
V254M, D341V and Fl 97V, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions or combinations of substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
15. The Cas Type V polypeptide of any preceding claim, comprising the following substitutions: K207N. V294M, R212Q. F79S and Q299F, based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405), or one or more corresponding substitutions or combinations of substitutions in any of the amino acid sequences selected from: SEQ ID NO: 58 (No. ID414), SEQ ID NO: 564 (No. ID418), SEQ ID NO: 335 (No. ID406), SEQ ID NO: 331 (No. ID411), SEQ ID NO: 20 (No. ID415), and SEQ ID NO: 445 (No. ID419).
16. The Cas Type V polypeptide of any preceding claim, wherein the substitutions are based on the amino acid sequence provided in SEQ ID NO: 334 (No. ID405).
17. Tire Cas Type V polypeptide of any preceding claim, comprising or consisting of:
(a) an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% sequence identity to one or more regions of any one of SEQ ID NOs: 2306-2351 corresponding to positions: 18-23; 49-57; 100-105; 128-132; 158-182; 252-311; 359-405; 440-450; 485-499; 528-569; 609-628; 672-677; 734-750; 768-776;
812; 840-864; 926-977; and 996, based on the numbering of SEQ ID NO: 334 (No. 1D405); or
(b) an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, 99.5%, or 100% sequence to all of the following regions of any one of SEQ ID NOs: 2306-2351 corresponding to positions: 18-23; 49-57; 100-105; 128-132; 158-182; 252-311; 359-405; 440-450; 485-499; 528-569; 609-628; 672-677; 734-750; 768- 776; 790-812; 840-864; 926-977; and 996, based on the numbering of SEQ ID NO: 334 (No. ID405); or
(c) an amino acid sequence having at least 95%, 96%, 97%, 98%, 99%, 99.5%. or 100% sequence identity o any one of SEQ ID NOs: 2306-2351. 1570-1600, 1632-1670, or 2354-2380.
8. Tire Cas Type V polypeptide of any preceding claim, wherein the Cas Type V polypeptide induces indel rbnnation when contacted with a population of target sequences and a guide RNA targeting the Cas Type V polypeptide to the target sequence under conditions suitable for inducing indel formation, and wherein the contacting results in an increase in the percentage of target polynucleotide sequences comprising an indel in the population of target sequences of at least 20%, at least 30%, at least 40%. or at least 50% as compared to the percentage of target polynucleotide sequences comprising an indel in the population when the population is contacted with a reference polypeptide comprising the sequence of SEQ ID NO: 1554 (No. ID405-1) and a j RNA that targets the reference polypeptide to the target polynucleotide sequence.
19. A fusion protein comprising the Cas Type V polypeptide of any preceding claim fused to a heterologous amino acid sequence.
20. A gene editing system comprising:
(a) one or more Cas Type V polypeptides of any preceding claim or one or more polynucleotides encoding the Cas Type V polypeptide (s); and
(b) one or more polynucleotide sequences comprising a guide RNA (gRNA) or one or more polynucleotides encoding tire gRNA, wherein the gRNA comprises a complementary sequence to that of a targeted polynucleotide sequence.
21. One or more polynucleotides encoding the Cas Type V polypeptide, fusion protein, or gene editing system of any preceding claim.
22. One or more vectors comprising the one or more polynucleotides of claim 21.
23. A cell comprising the one or more vectors of claim 22 or the one or more polynucleotides of claim 21.
24. A pharmaceutical composition comprising the Cas Type V polypeptide of any one of claims 1-18, the protein of claim 19, the gene editing system of claim 20, the one or more polynucleotides of claim 21, the one or more vectors of claim 22, or the cell of claim 23.
15. A method of modifying a targeted polynucleotide sequence, the method comprising introducing into a cell a ;cnc editing system according to claim 20.
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