WO2025178803A1 - Compositions and methods for targeted delivery of nucleic acid-binding effector polypeptides - Google Patents
Compositions and methods for targeted delivery of nucleic acid-binding effector polypeptidesInfo
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- WO2025178803A1 WO2025178803A1 PCT/US2025/015615 US2025015615W WO2025178803A1 WO 2025178803 A1 WO2025178803 A1 WO 2025178803A1 US 2025015615 W US2025015615 W US 2025015615W WO 2025178803 A1 WO2025178803 A1 WO 2025178803A1
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- 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
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- C12N2760/20211—Vesiculovirus, e.g. vesicular stomatitis Indiana virus
- C12N2760/20222—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
Definitions
- RNA-mediated adaptive immune systems in bacteria and archaea rely on Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) genomic loci and CRISPR-associated (Cas) proteins that function together to provide protection from invading viruses and plasmids.
- Genome editing can be carried out using a CRISPR/Cas system comprising a CRISPR/Cas effector polypeptide and a guide RNA.
- CRISPR/Cas systems are revolutionizing the field of gene editing and genome engineering. Efficient methods for delivering CRISPR-Cas genome editing components into target cells are needed, for both ex vivo and in vivo applications.
- the present disclosure also provides methods that use an EDV of the present disclosure, e.g., methods of delivering a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) into a eukaryotic cell, in vivo gene editing methods, and methods for modifying a target nucleic acid.
- the present disclosure also provides methods of producing an EDV of the present disclosure, e.g., using a subject collection of one of more nucleic acids.
- FIG.1 Schematic illustrating need for delivery vehicles to bypass delivery barriers and transport genome editors to target cells in vivo.
- FIG. 4 Schematic illustrating that the goal of the work described herein was to simplify EDV systems.
- FIG.5. Schematic illustrating incubation of EDVs or lentiviruses (LV) with capsid inhibitors.
- FIG.6 Data demonstrating that capsid inhibitors did not inhibit EDV mediated editing.
- FIG.7 Data demonstrating that capsid inhibitors did not inhibit EDV mediated editing.
- FIG. 9A-9G Experimental optimization to form 3 rd generation EDVs.
- the Pol polypeptide which includes integrase (Int), reverse transcriptase (Rt), and protease (Pr), was deleted without adversely affecting EDV editing activity. Following this deletion, EDVs were formed and their editing activity was evaluated using a luminescence assay in cell culture. A higher luminescence value indicates increased editing.
- the 3rd generation EDVs included a full-length matrix, capsid protein from residues 149-231, no nucleocapsid, 7 NLS on the C-terminus of Cas9, and were devoid of integrase, reverse transcriptase, and protease.
- the “Added NLS” construct represents generation 1 EDVs with 7 NLS on the C-terminus of Cas9.
- the “streamlined +PR” variant mirrors the 3rd generation EDV, with the addition of protease. Both “streamlined -NES +PR” and “streamlined -NES -PR” conditions were analogous to their respective “streamlined +PR” or “streamlined -PR” setups but lacked the NES on Cas9.
- FIG.15A-15D show delivery of homology-directed templates (HDRT) and separate delivery of Cas9 with enveloped delivery vehicles (EDVs) for knock-in at the T cell receptor ⁇ constant (TRAC) locus.
- FIG.15A shows an illustration of an HDR template targeting a chimeric antigen receptor (CAR) to TRAC delivered and an EDV carrying Cas9/sgTRAC.
- FIG.15B shows TCR expression in human T cells after transduction with EDVs carrying Cas9/sgTRAC ribonucleoproteins (RNPs).
- HDRT homology-directed templates
- EDVs enveloped delivery vehicles
- FIG.16A-16D show characterization of human T cells after transduction with EDVs carrying Cas9/sgTRAC RNP and VSVG-WT (VSVG-WT EDV), or EDVs Cas9/sgTRAC RNP and VSVGm- aCD3 (VSVGm-aCD3 EDV), in combination with HDRT, delivered separately.
- FIG.16A shows TCR and EGFR expression in human T cells after transduction with different combinations of Cas9/sgTRAC RNP EDV with VSVG-WT (VSVG-WT EDV), Cas9/sgTRAC RNP EDV with VSVGm-aCD3 (VSVGm-aCD3 EDV), and HDRT.
- FIG.16B shows knock-in efficiency of a CD19 specific CAR at the TRAC locus by combining either VSVG-WT EDV or VSVGmut-aCD3 EDV carrying Cas9/sgTRAC, combined with a TRAC-CAR HDRT.
- FIG.16C shows CD25 expression as determined by flow cytometry as a marker for T cell activation.
- UT untreated cells
- Low cells treated with 5 ⁇ l concentrated EDVs
- High cells treated with 25 ⁇ l concentrated EDVs.
- FIG.16D compares cytotoxicity of TCR knock out (KO) T cells with TRAC CD19-CAR T cells generated by transduction with VSVG-WT EDVs carrying Cas9/sgTRAC with a vector carrying a HDRT. Cytotoxicity was determined by luminescence. Results are the mean ⁇ SEM from three technical replicates.
- FIG.17A-17C show treatment of NOD scid gamma (NSD) mice and flow cytometry analysis of spleen cells isolated from the mice.
- FIG. 17A shows a treatment schedule for NSD mice engrafted with human peripheral blood mononuclear cells (PBMCs).
- PBMCs peripheral blood mononuclear cells
- FIG.18A-18G Small molecule inhibitors that disrupt the capsid core do not impact EDV editing.
- FIG.18a Schematic of small molecule inhibition experiments. EDVs or lentivirus (LV) were incubated with luciferase reporter HEK-293T cells in the presence of Lenacapavir or PF74. The luminescence of the reporter cells were recorded after incubation.
- FIG.18b Schematic showing that Lenacapavir stabilizes the capsid core.
- FIG.18c Lenacapavir did not inhibit EDVs compared to the DMSO control (0 nM).
- FIG.18d Schematic showing that PF74 destabilizes the capsid core.
- FIG.18e PF74 did not inhibit EDVs compared to the DMSO control (0 nM).
- FIG.18f Lenacapavir inhibited LVs compared to the DMSO vehicle control (0 nM).
- FIG.18g PF74 inhibited LVs compared to the DMSO vehicle control (0 nM).
- FIG.19d Schematic of photocatalytic proximity labeling experiment.
- the Lenacapavir-eosin Y (EY) conjugate or unconjugated EY and Lenacapavir were incubated with EDVs and allowed to bind. Different photo-probes were then added to enable biotinylation of proximal proteins upon blue light illumination. Biotinylated proteins were isolated using biotin enrichment (biotin-IP).
- FIG.19e Western blot demonstrating the amount of biotinylated Cas9 or mature capsid upon lenacapavir-EY-mediated photocatalytic proximity labeling.
- FIG.20a Removal of NLS on Cas9 enzymes reduced editing and luminescence. Data were normalized to the current design with two N-terminal p53 and two C-terminal SV40 NLS.
- FIG.20b The capsid core does not transport Cas9 enzymes missing nuclear localization signals (NLS) into the nucleus.
- EDVs packaging Cas9 enzymes with no NLS were incubated with luciferase reporter HEK- 293T cells in the presence of Lenacapavir (0 - 500 nM). The luminescence of the reporter cells were recorded after incubation.
- FIG.21c The matrix protein was minimized one secondary structure element at a time from the C-terminal end. An equal volume of EDVs were incubated per condition. Data were normalized to EDVs containing the full matrix.
- FIG.21d The nucleocapsid (NC) protein and the activity of the EDVs were compared to EDVs containing the full NC. Data were normalized to EDVs containing the full NC.
- FIG.21e Schematic showing the components and plasmids involved in making full and minimized EDV. The minimized structural proteins are referred to as “miniGag” (FIG.21f) Minimized EDVs had higher activity than the original full EDV design.
- FIG.24A-24F Structural characterization of EDVs and lentiviral vectors (LVs) using cryo-ET.
- FIG.24a Representative two-dimensional slices in the XY plane of the cryo-tomograms of EDVs and LVs containing different core morphologies. Scale bars are 50 nm.
- FIG.25A-25B Characterization of EDVs with more NLS.
- FIG.25a Adding additional N- terminal NLS did not improve EDV editing. To facilitate tiling of NLS, the bipartite p53 NLS (18 amino acids) was first replaced with a monopartite c-myc NLS (9 amino acids). Both NLS use the same mechanism of nuclear import.
- FIG. 25b Flow cytometry quantification shows that four and seven NLS Cas9 RNPs in EDVs decreased the number of primary activated human T cells expressing the TRAC protein in concordance with the sequencing results. The gating strategy is shown in the top panels. One representative biological replicate of three is shown. [0036] FIG.26A-26F Characterization of miniEDVs.
- FIG.26a Quantification of the physical titers of EDVs using the NanoFCM NanoAnalyzer.
- FIG.26c Two-dimensional slice of a minimized EDVs tomogram. Scale bar is 50 nm. Orange arrows point to densities underneath the lipid bilayer that potentially corresponds to the minimized Gag.
- FIG.26d Averaged 66.8 ⁇ thick slice of minimized EDV to show the protein density underneath the lipid membrane (black arrow). Scale bar is 50 nm.
- FIG.26e Quantitation of Cas9 enzymes per particle for EDVs targeting TRAC measured by ELISAs.
- FIG.28A-28B Single-chain variable fragments (scFvs) can be displayed on the surface of miniEDVs to mediate cell entry.
- VSV- G vesicular stomatitis virus glycoprotein
- PDGFR platelet-derived growth factor receptor
- FIG.31A-31B (FIG.31A) Schematic of photocatalytic proximity labeling experiment.
- EY-LEN Eosin Y - Lencapavir conjugate (500 nM) or unconjugated EY and LEN (EY & LEN, 500 nM each) were incubated with EDVs.
- NLS1 KKKYK
- NLS2 KSKKK
- FIG.34 Schematic showing the viral structural proteins in example lentiviral vectors (LV), EDVs, and minimized EDV (miniEDVs). The schematic is not drawn to scale.
- FIG.35 Expression of the Gag-Cas9 polyprotein in the producer cells decreased when too many NLS were added. Producer cells were transfected with the appropriate EDV plasmids. Cell lysates were harvested 48 h after transfection for Western blotting. Each lane indicates a separate batch of producer cells.
- FIG.36 NLS-optimized EDVs designs showed similar editing efficacy in activated human T cells from two donors.
- EDVs 100 ⁇ L were incubated with T cells from Donor 1 and editing was quantified by flow cytometry 5 d after incubation by flow cytometry. Donor 1 was used for experiments in Figure 3.
- EDVs 100 ⁇ L were incubated with T cells from Donor 2 and editing was quantified by flow cytometry 5 d after incubation by flow cytometry.
- Donor 2 was used for experiments in Figure 4. Error bars indicate standard deviation of three separate batches of EDVs. P-values were calculated using a one-way ANOVA with Dunnett’s multiple comparisons. P-values are as indicated.
- Heterologous means a nucleotide or polypeptide sequence that is not found in the native nucleic acid or protein, respectively.
- a heterologous polypeptide comprises an amino acid sequence from a protein other than the CRISPR-Cas effector polypeptide.
- a CRISPR-Cas effector protein e.g., a dead or nickase CRISPR-Cas effector protein
- a non-CRISPR-Cas effector protein e.g., a cytidine deaminase
- the sequence of the active domain could be considered a heterologous polypeptide (it is heterologous to the CRISPR-Cas effector protein).
- polynucleotide and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxynucleotides.
- this term includes, but is not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA- RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases.
- polynucleotide and nucleic acid should be understood to include, as applicable to the embodiment being described, single- stranded (such as sense or antisense) and double-stranded polynucleotides.
- polypeptide refers to a polymeric form of amino acids of any length, which can include genetically coded and non-genetically coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones.
- the term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; immunologically tagged proteins; and the like.
- nucleic acid refers to a nucleic acid, cell, protein, or organism that is found in nature.
- isolated is meant to describe a polynucleotide, a polypeptide, or a cell that is in an environment different from that in which the polynucleotide, the polypeptide, or the cell naturally occurs.
- An isolated genetically modified host cell may be present in a mixed population of genetically modified host cells.
- Heterologous refers to a nucleotide or amino acid sequence that is not found in the native nucleic acid or protein, respectively.
- a heterologous polypeptide comprises an amino acid sequence from a protein other than the Cas9 polypeptide.
- a polymerase polypeptide is heterologous to a Cas9 polypeptide.
- Recombinant means that a particular nucleic acid (DNA or RNA) is the product of various combinations of cloning, restriction, and/or ligation steps resulting in a construct having a structural coding or non-coding sequence distinguishable from endogenous nucleic acids found in natural systems.
- nucleotide sequences encoding the structural coding sequence can be assembled from cDNA fragments and short oligonucleotide linkers, or from a series of synthetic oligonucleotides, to provide a synthetic nucleic acid which is capable of being expressed from a recombinant transcriptional unit contained in a cell or in a cell-free transcription and translation system.
- sequences can be provided in the form of an open reading frame uninterrupted by internal non- translated sequences, or introns, which are typically present in eukaryotic genes.
- Genomic DNA comprising the relevant nucleotide sequences can also be used in the formation of a recombinant gene or transcriptional unit. Sequences of non-translated DNA may be present 5’ or 3’ from the open reading frame, where such sequences do not interfere with manipulation or expression of the coding regions, and may indeed act to modulate production of a desired product by various mechanisms (see “DNA regulatory sequences”, below).
- the term “recombinant” polynucleotide or “recombinant” nucleic acid refers to one which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of sequence through human intervention. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. Such artificial combination can be carried out to join together nucleic acid segments of desired functions to generate a desired combination of functions.
- DNA regulatory sequences 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 expression of a coding sequence and/or production of an encoded polypeptide in a host cell.
- transcriptional and translational control sequences such as promoters, enhancers, polyadenylation signals, terminators, protein degradation signals, and the like, that provide for and/or regulate expression of a coding sequence and/or production of an encoded polypeptide in a host cell.
- transformation is used interchangeably herein with “genetic modification” and refers to a permanent or transient genetic change induced in a cell following introduction of new nucleic acid (e.g., DNA exogenous to the cell) into the cell.
- Genetic change can be accomplished either by incorporation of the new nucleic acid into the genome of the host cell, or by transient or stable maintenance of the new nucleic acid as an episomal element.
- a permanent genetic change can be achieved by introduction of new DNA into the genome of the cell.
- permanent changes can be introduced into the chromosome or via extrachromosomal elements such as plasmids and expression vectors, which may contain one or more selectable markers to aid in their maintenance in the recombinant host cell.
- Suitable methods of genetic modification include viral infection, transfection, conjugation, protoplast fusion, electroporation, particle gun technology, calcium phosphate precipitation, direct microinjection, and the like.
- “Operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression.
- heterologous promoter and “heterologous control regions” refer to promoters and other control regions that are not normally associated with a particular nucleic acid in nature.
- a “transcriptional control region heterologous to a coding region” is a transcriptional control region that is not normally associated with the coding region in nature.
- a “host cell,” as used herein, denotes an in vivo or in vitro eukaryotic cell, a prokaryotic cell, or a cell from a multicellular organism (e.g., a cell line) cultured as a unicellular entity, which eukaryotic or prokaryotic cells can be, or have been, used as recipients for a nucleic acid (e.g., an expression vector), and include the progeny of the original cell which has been genetically modified by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation.
- a “recombinant host cell” (also referred to as a “genetically modified host cell”) is a host cell into which has been introduced a heterologous nucleic acid, e.g., an expression vector.
- a eukaryotic host cell is a genetically modified eukaryotic host cell, by virtue of introduction into a suitable eukaryotic host cell of a heterologous nucleic acid, e.g., an exogenous nucleic acid that is foreign to the eukaryotic host cell, or a recombinant nucleic acid that is not normally found in the eukaryotic host cell.
- a group of amino acids having aliphatic side chains consists of glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains consists of serine and threonine; a group of amino acids having amide- containing side chains consists of asparagine and glutamine; a group of amino acids having aromatic side chains consists of phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains consists of lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains consists of cysteine and methionine.
- Exemplary conservative amino acid substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, and asparagine- glutamine.
- a polynucleotide or polypeptide has a certain percent “sequence identity” to another polynucleotide or polypeptide, meaning that, when aligned, that percentage of bases or amino acids are the same, and in the same relative position, when comparing the two sequences. Sequence similarity can be determined in a number of different manners.
- sequences can be aligned using the methods and computer programs, including BLAST, available over the world wide web at ncbi.nlm.nih.gov/BLAST. See, e.g., Altschul et al. (1990), J. Mol. Biol.215:403-10.
- FASTA is Another alignment algorithm
- GCG Genetics Computing Group
- Other techniques for alignment are described in Methods in Enzymology, vol.266: Computer Methods for Macromolecular Sequence Analysis (1996), ed.
- antibodies and “immunoglobulin” include antibodies or immunoglobulins of any isotype, fragments of antibodies that retain specific binding to antigen (antigen binding region), including, but not limited to, Fab, Fv, scFv, and Fd fragments, chimeric antibodies, humanized antibodies, single-chain antibodies (scAb), single domain antibodies (dAb), single domain heavy chain antibodies, a single domain light chain antibodies, nanobodies, bi-specific antibodies, multi-specific antibodies, evibodies, minobodies, diabodies, and fusion proteins comprising an antigen-binding (also referred to herein as antigen binding) portion of an antibody and a non-antibody protein.
- antigen binding also referred to herein as antigen binding
- Nb refers to the smallest antigen binding fragment or single variable domain (VHH) derived from naturally occurring heavy chain antibody and is known to the person skilled in the art. They are derived from heavy chain only antibodies, seen in camelids. In the family of “camelids” immunoglobulins devoid of light polypeptide chains are found. "Camelids” comprise old world camelids (Camelus bactrianus and Camelus dromedarius) and new world camelids (for example, Llama paccos, Llama glama, Llama guanicoe and Llama vicugna).
- Treatment covers any treatment of a disease in a mammal, e.g., in a human, and includes: (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., causing regression of the disease.
- the terms "individual,” “subject,” “host,” and “patient,” used interchangeably herein, refer to an individual organism, e.g., a mammal, including, but not limited to, murines, simians, non-human primates, humans, mammalian farm animals, mammalian sport animals, and mammalian pets. [0071] Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims.
- a guide RNA includes a plurality of such guide RNAs
- reference to “a targeting polypeptide” includes a plurality of such polypeptides
- the CRISPR-Cas effector polypeptide includes reference to one or more CRISPR-Cas effector polypeptides and equivalents thereof known to those skilled in the art, and so forth.
- the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation.
- the “about” used in reference to the lower amount of the range means that the lower amount includes an amount that is 10% lower than the lower amount of the range
- “about” used in reference to the higher amount of the range means that the higher amount includes an amount 10% higher than the higher amount of the range.
- from about 100 to about 1000 means that the range extends from 90 to 1100.
- the term “and/or” as used herein a phrase such as “A and/or B” is intended to include both A and B; A or B; A (alone); and B (alone).
- EDV enveloped delivery vehicle
- VLP virus like particle
- enveloped delivery vehicles also referred to as virus like particles (VLPs)
- nucleic acids encoding them, e.g., a collection of one or more nucleic acids encoding a subject EDV.
- a subject EDV includes (a) a nucleic acid- binding effector polypeptide (e.g., a CRISPR Cas effector polypeptide such as a Cas9 or Cas12a); (b) a viral envelop protein (e.g., VSVG or a mutant thereof); (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody); (d) a matrix (MA) polypeptide (e.g., in some cases a truncated MA polypeptide); and (e) an N-terminally truncated capsid (CA) protein.
- a nucleic acid- binding effector polypeptide e.g., a CRISPR Cas effector polypeptide such as a Cas9 or Cas12a
- a viral envelop protein e.g., VSVG or a mutant thereof
- a targeting polypeptide that provides for binding to a target cell (e.g., an antibody
- the EDV lacks one or more (in some cases all) of the following proteins: a pol polypeptide protease (PR), a pol polypeptide reverse transcriptase (RT), a pol polypeptide integrase (IN), a nucleocapsid (NC) protein.
- a subject EDV includes 7 or more NLSs (e.g., at the C-terminus).
- a subject EDV includes (a) a Cas9 polypeptide comprising 4 or more NLSs (e.g., at the C-terminus); (b) a variant vesicular stomatitis virus glycoprotein (VSVG) viral envelop protein that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R354A), respectively, relative to SEQ ID NO: 153; and (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody), where the targeting polypeptide is a fusion protein comprising a PDGFR transmembrane domain fused to an antibody or antibody analog.
- a target cell e.g., an antibody
- a subject collection of one or more nucleic acids includes a nucleic acid in which a viral envelop protein and a targeting polypeptide are encoded by nucleotide sequences that are: (i) present on the same nucleic acid as part of the same transcript, and (ii) are separated by a sequence that promotes the production of two independent proteins (e.g., a 2A peptide, an intein, or an IRES, or comprises intronic splice donor/splice acceptor sequences).
- a collection of one or more nucleic acids includes: (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); (b) a viral envelop protein (e.g., VSVG); and (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody); where the viral envelop protein and the targeting polypeptide are encoded by nucleotide sequences that are: (i) present on the same nucleic acid as part of the same transcript, and (ii) are separated by a sequence that promotes the production of two independent proteins (e.g., a 2A peptide, an intein, or an IRES, or comprises intronic splice donor/splice acceptor sequences).
- a nucleic acid-binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide such as
- the present disclosure also provides methods that use an EDV of the present disclosure, e.g., methods of delivering a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) into a eukaryotic cell, in vivo gene editing methods, and methods for modifying a target nucleic acid.
- a nucleic acid-binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a
- the present disclosure also provides methods of producing an EDV of the present disclosure, e.g., using a subject collection of one of more nucleic acids.
- a subject EDV comprises a nucleic acid comprising a nucleotide sequence encoding a therapeutic polypeptide, such as a chimeric antigen receptor (CAR).
- a subject EDV comprises one or more CRISPR-Cas guide nucleic acids (e.g., guide RNA), or one or more nucleic acids comprising nucleotide sequences encoding the one or more CRISPR-Cas guide nucleic acids.
- the one or more CRISPR-Cas guide nucleic acids provide for knockout of an endogenous nucleic acid.
- a subject EDV includes a donor template nucleic acid.
- contacting a target nucleic acid e.g., chromosomal DNA
- a CRISPR-Cas effector polypeptide e.g., chromosomal DNA
- the one or more CRISPR-Cas guide nucleic acids e.g., a CRISPR-Cas guide nucleic acids
- the donor template nucleic acid comprises a nucleotide sequence encoding a therapeutic polypeptide.
- EDVs enveloped delivery vehicles
- VLPs virus like particles
- nucleic acids e.g., a collection of one or more nucleic acids encoding a subject EDV, in addition to methods of their use and production.
- EDVs enveloped delivery vehicles
- nucleic acids e.g., a collection of one or more nucleic acids encoding a subject EDV
- the EDV comprises a therapeutic polypeptide, or a nucleic acid comprising a nucleotide sequence encoding the therapeutic polypeptide, encapsidated within the EDV.
- the EDVs can be used in in vivo methods of genome editing, which methods are also provided.
- the EDVs comprise a CRISPR-Cas effector polypeptide as the nucleic acid-binding effector polypeptide. In some cases, the EDVs comprise a nucleic acid comprising a nucleotide sequence encoding a CRISPR-Cas effector polypeptide.
- an EDV of the present disclosure comprises an RNP comprising: a) a CRISPR-Cas effector polypeptide; and b) a CRISPR-Cas guide nucleic acid
- the guide nucleic acid e.g., guide RNA
- the guide nucleic acid comprises: i) a nucleotide sequence that comprises a protein-binding segment comprising a nucleotide sequence that binds to the CRISPR-Cas effector polypeptide, and a target- binding segment comprising a nucleotide sequence that is complementary to a target nucleotide sequence of a target DNA in a cell (e.g., a eukaryotic cell; e.g., a eukaryotic cell present in an individual).
- a cell e.g., a eukaryotic cell; e.g., a eukaryotic cell present in an individual.
- an EDV of the present disclosure comprises: a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding a CRISPR-Cas effector polypeptide and a nucleotide sequence encoding a CRISPR-Cas guide RNA.
- an EDV of the present disclosure comprises a donor nucleic acid.
- components of a subject EDV are produced as part of a gag polyprotein.
- the gag polyprotein is a retroviral gag polyprotein, and in some cases, the retroviral gag polyprotein is a lentiviral gag polyprotein.
- the lentiviral gag polyprotein can be selected from the group consisting of a bovine immunodeficiency virus gag polyprotein, a simian immunodeficiency virus gag polyprotein, a feline immunodeficiency virus gag polyprotein, a human immunodeficiency virus gag polyprotein, an equine infection anemia virus gag polyprotein, and a caprine arthritis encephalitis virus gag polyprotein.
- the matrix protein (MA), capsid protein (CA), and nucleocapsid protein (NC) portions of a gag polyprotein can be of any of a variety of retroviruses.
- a MA polypeptide of the gag polyprotein can comprise an amino acid sequence having 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 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following MA amino acid sequence: GARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQ PSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVS QNY (SEQ ID NO:296).
- a CA polypeptide of the gag polyprotein can comprise an amino acid sequence having 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 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following CA amino acid sequence: PIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQA AMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGE IYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQN ANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO:282).
- the retroviral gag polyprotein comprises a p1 polypeptide and a p6 polypeptide (e.g., in some cases, an MA polypeptide, a CA polypeptide, an NC polypeptide, a p1 polypeptide, and a p6 polypeptide).
- the retroviral gag polyprotein comprises a p6 polypeptide (e.g., in some cases, an MA polypeptide, a CA polypeptide, an NC polypeptide, and a p6 polypeptide).
- the NC-p1-p6 polypeptide of the gag polyprotein comprises an amino acid sequence having 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 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: IQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWP SHKGRPGNFLQSRPEPTAPPEESFRFGEETTTPSQKQEPIDKELYPLASLRSLFGSDPSSQ (SEQ ID NO:211).
- the retroviral gag polyprotein comprises a p2 polypeptide.
- the p2 polypeptide comprises an amino acid sequence having 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 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: AEAMSQVTNPATIM (SEQ ID NO:212).
- a retroviral gag polyprotein is a gag polyprotein of an alpha retrovirus, a beta retrovirus, a gamma retrovirus, a delta retrovirus, an epsilon retrovirus, or a spumavirus.
- the retroviral gag polyprotein is a gag polyprotein of a human immunodeficiency virus.
- a Gag polypeptide such as a retroviral (e.g. lentiviral) Gag polypeptide includes CA (e.g., p24), MA (e.g., p17) and NC (e.g., p7) polypeptides (in some cases CA and MA, but not NC – see Gen 3 EDVs below).
- a Gag polypeptide such as a retroviral (e.g. lentiviral) Gag polypeptide includes, in addition, a p6 polypeptide.
- a Gag polypeptide such as a retroviral (e.g. lentiviral) Gag polypeptide includes, in addition, one or more of p1, p2, and p6 polypeptides.
- Gag polypeptide includes CA, MA, NC, and p6 polypeptides (in some cases it does not include the NC – see Gen 3 EDVs below).
- a Gag polypeptide such as a retroviral (e.g. lentiviral) Gag polypeptide includes CA, MA, NC, p1, p2, and p6 polypeptides (in some cases it does not include the NC – see Gen 3 EDVs below). See, e.g., Muriaux and Darlix (2010) RNA Biol.7:744.
- a subject nucleic acid comprises a nucleotide sequence encoding a fusion polypeptide comprising: i) a lentiviral gag polyprotein (e.g., a lentiviral gag polyprotein) comprising a MA polypeptide, a CA polypeptide, and an NC polypeptide (in some cases it does not encode an NC and in some cases the CA and/or the MA is truncated – see Gen3 EDVs below); and ii) a nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a), wherein the fusion polypeptide comprises a proteolytically cleavable linker between the gag polyprotein and the nucleic acid-binding effector polypeptide.
- a lentiviral gag polyprotein e.g., a lentiviral gag polyprotein
- an NC polypeptide in some cases it does not encode an NC and in some cases the
- At least one of the nucleic acids in a subject collection comprises a nucleotide sequence encoding a protease that cleaves the proteolytically cleavable linker.
- the proteolytically cleavable linker can be one that is cleaved by a lentiviral protease.
- the proteolytically cleavable linker can be one that is cleaved by a protease other than a lentiviral protease (i.e., the protease is heterologous to the lentivirus).
- a proteolytically cleavable linker comprises a protease cleavage site.
- a proteolytically cleavable linker can comprise a matrix metalloproteinase cleavage site, e.g., a cleavage site for a MMP selected from collagenase-1, -2, and -3 (MMP-1, -8, and -13), gelatinase A and B (MMP-2 and -9), stromelysin 1, 2, and 3 (MMP-3, -10, and -11), matrilysin (MMP-7), and membrane metalloproteinases (MT1-MMP and MT2-MMP).
- MMP-1, -2, and -3 MMP-1, -8, and -13
- MMP-2 and -9 gelatinase A and B
- MMP-3, -10, and -11 stromelysin 1, 2, and 3
- MMP-7 matrilysin
- MT1-MMP and MT2-MMP membrane metalloproteinases
- the cleavage sequence of MMP-9 is Pro-X-X-Hy (wherein, X represents an arbitrary residue; Hy, a hydrophobic residue), e.g., Pro-X-X-Hy-(Ser/Thr), e.g., Pro-Leu/Gln-Gly- Met-Thr-Ser, or Pro-Leu/Gln-Gly-Met-Thr.
- a protease cleavage site is a plasminogen activator cleavage site, e.g., a uPA or a tissue plasminogen activator (tPA) cleavage site.
- the cleavage site is a furin cleavage site.
- cleavage sequences of uPA and tPA include sequences comprising Val-Gly-Arg.
- a protease cleavage site that can be included in a proteolytically cleavable linker is a tobacco etch virus (TEV) protease cleavage site, e.g., ENLYTQS (SEQ ID NO:336), where the protease cleaves between the glutamine and the serine.
- TSV tobacco etch virus
- protease cleavage site that can be included in a proteolytically cleavable linker is an enterokinase cleavage site, e.g., DDDDK (SEQ ID NO:337), where cleavage occurs after the lysine residue.
- enterokinase cleavage site e.g., DDDDK (SEQ ID NO:337)
- a protease cleavage site that can be included in a proteolytically cleavable linker
- a thrombin cleavage site e.g., LVPR (SEQ ID NO:338).
- linkers comprising protease cleavage sites include linkers comprising one or more of the following amino acid sequences: LEVLFQGP (SEQ ID NO:339), cleaved by PreScission protease (a fusion protein comprising human rhinovirus 3C protease and glutathione-S-transferase; Walker et al.
- a thrombin cleavage site e.g., CGLVPAGSGP (SEQ ID NO:340); SLLKSRMVPNFN (SEQ ID NO:341) or SLLIARRMPNFN (SEQ ID NO:342), cleaved by cathepsin B; SKLVQASASGVN (SEQ ID NO:343) or SSYLKASDAPDN (SEQ ID NO:344), cleaved by an Epstein-Barr virus protease; RPKPQQFFGLMN (SEQ ID NO:345) cleaved by MMP-3 (stromelysin); SLRPLALWRSFN (SEQ ID NO:346) cleaved by MMP-7 (matrilysin); SPQGIAGQRNFN (SEQ ID NO:347) cleaved by MMP-9; DVDERDVRGFASFL SEQ ID NO:348) cleaved by a thrombin cleavage site, e.g
- the protease cleavage site is a TEV protease cleavage site, e.g., ENLYFQS (SEQ ID NO:362), where cleavage occurs between the Gln and the Ser.
- the protease cleavage site is the TEV protease cleavage site ENLYFQP (SEQ ID NO:363).
- ENLYFQS (SEQ ID NO:362) and ENLYFQP (SEQ ID NO:363) are wildtype recognition sequences (cleavage substrates) for TEV protease (see e.g. Stols et al. (2002) Prot. Exp. Purif.25: 8-12).
- the proteolytically cleavable linker comprises an HIV-1 protease cleavage site (e.g. SQNYPIVQ (SEQ ID NO:205)), where cleavage occurs between the tyrosine and the proline.
- an HIV-1 protease cleavage site e.g. SQNYPIVQ (SEQ ID NO:205)
- the protease cleavage site is a TEV protease cleavage site, e.g., ENLYTQS (SEQ ID NO:336), where the protease cleaves between the glutamine and the serine.
- the protease cleavage site is a variant TEV-cleavage substrate, where the variant TEV cleavage site is cleaved by a TEV protease less efficiently than cleavage of ENLYTQS (SEQ ID NO:336) by the TEV protease.
- a variant TEV-cleavage site can: (1) mimic the temporal cleavage observed with wild-type gag polyprotein maturation; and/or (2) maximize packaging of a CRISPR/Cas effector polypeptide into a VLP. Suitable variant TEV cleavage sites are described in Tözsér et al. (2005) FEBS J.272:514.
- Suitable variant TEV cleavage sites include: ENAYFQS (SEQ ID NO:364), ENLRFQS (SEQ ID NO:365), ENLFFQS (SEQ ID NO:366), ETVRFQS (SEQ ID NO:367), ETLRFQS (SEQ ID NO:368), ETARFQS (SEQ ID NO:369), ETVYFQS (SEQ ID NO:370), and ENVYFQS (SEQ ID NO:371).
- a subject EDV includes (a) a Cas9 polypeptide comprising 4 or more NLSs (e.g., at the C-terminus); (b) a variant vesicular stomatitis virus glycoprotein (VSVG) viral envelop protein that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R354A), respectively, relative to SEQ ID NO: 153; and (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody), where the targeting polypeptide is a fusion protein comprising a PDGFR transmembrane domain fused to an antibody or antibody analog.
- a target cell e.g., an antibody
- the Cas9 polypeptide is a fusion polypeptide comprising: i) a Cas9 protein; and ii) one or more heterologous polypeptides.
- the Cas9 protein has nickase activity (nCas9) or is catalytically deactivated (i.e., is a ‘dead’ Cas9, i.e., dCas9).
- at least one of the one or more heterologous polypeptides includes a deaminase, a reverse transcriptase, a transcription modulator, or an epigenetic modulator.
- At least one of the one or more heterologous polypeptides is a Gag polypeptide.
- the Cas9 polypeptide is produced as part of a polyprotein (e.g., a gag-Cas9 polyprotein).
- a collection of one or more nucleic acids (e.g., in some cases two nucleic acids) that encodes a subject EDV includes nucleotide sequences that encode a pol polyprotein comprising a protease (PR), a reverse transcriptase (RT), and an integrase (INT).
- PR protease
- RT reverse transcriptase
- INT integrase
- the pol polyprotein is part of a gag-pol protein.
- a subject collection of one or more nucleic acids encodes an EDV that includes: (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); (b) a viral envelop protein or a variant thereof (e.g., VSVG or a variant thereof); and (c) a targeting polypeptide (e.g., an antibody) that provides for binding to a target cell, where the viral envelop protein and the targeting polypeptide are encoded by nucleotide sequences that are: (i) present on the same nucleic acid as part of the same transcript, and (ii) are separated by a sequence that promotes the production of two independent proteins.
- a nucleic acid-binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a
- a viral envelop protein or a variant thereof
- Sequence that promotes the production of two independent proteins include, but are not limited to: a 2A peptide (e.g., P2A, F2A, E2A, T2A, and any combination thereof), an intein, an IRES, or intronic splice donor/splice acceptor sequences.
- a 2A peptide e.g., P2A, F2A, E2A, T2A, and any combination thereof
- an intein e.g., an IRES, or intronic splice donor/splice acceptor sequences.
- a “2A peptide” it is meant a small peptide sequence (usually 18-25 amino acids although several of such sequences can be placed in tandem) that allows for expression (translation) of discrete protein products from a single RNA transcript (e.g., through a self-“cleaving” event often referred to as “ribosome skipping”—although the disclosure herein does not rely on and is not bound by the mechanism of action), even though the separate proteins are encoding as part of the same open reading frame (ORF).2A peptides are readily identifiable by their consensus motif (DXEXNPGP, sometimes described as DVEXNPGP) and their ability to promote protein cleavage/skipping.
- DXEXNPGP consensus motif
- 2A peptide sequence may be used in a subject nucleic acid.
- 2A peptides include, but are not limited to 2A peptides from a virus such as foot-and-mouth disease virus (F2A), equine Rhinitis A virus (E2A), porcine teschovirus-1 (P2A) or Thosea asigna virus (T2A). See, e.g., Szymczak-Workman, A. et al. “Design and Construction of 2A Peptide-Linked Multicistronic Vectors”. Cold Spring Harb Protoc.
- F2A foot-and-mouth disease virus
- E2A equine Rhinitis A virus
- P2A porcine teschovirus-1
- T2A Thosea asigna virus
- 2A peptide sequences include, but are not limited to (SEQ ID NOs: 372-377, respectively): P2A: ATNFSLLKQAGDVEENPGP E2A: QCTNYALLKLAGDVESNPGP F2A: VKQTLNFDLLKLAGDVESNPGP T2A: EGRGSLLTCGDVEENPGP EZA-F2A: QCTNYALLKLAGDVESNPGPVKQTLNFDLLKLAGDVESNPGP T2A-E2A-F2A: EGRGSLLTCGDVEENPGPQCTNYALLKLAGDVESNPGPVKQTLNFDLLKLAGD VESNPGP [00104] 2A peptide sequences can be used in tandem, and multiple different 2A peptide sequences can be positioned one after another, in any desired combination (see “E2A-F2A” and “T2A-E2A-F2A” above as non-limiting examples).
- a 2A peptide sequence is selected from the group consisting of: P2A, F2A, E2A, T2A, and any combination thereof.
- an “internal ribosome entry site,” or “IRES” it is meant a nucleotide sequence that allows for the initiation of protein translation in the middle of a messenger RNA (mRNA) sequence.
- mRNA messenger RNA
- Introns typically include a 5' splice site (splice donor sequence) and a 3’ splice site (spice acceptor sequence).
- the splice donor includes an almost invariant sequence GU at the 5' end of the intron.
- the splice acceptor terminates the intron with an almost invariant AG sequence.
- Gen3 EDVs can include any or all of the above-described features of Gen2 EDVs. Surprisingly, as demonstrated in the working examples below (see, e.g., Example 1), in some embodiments, a subject EDV (a Gen3 EDV) can be streamlined in the sense that it includes reduced components (e.g., a reduced number of components and/or truncated components) compared to those in the art.
- reduced components e.g., a reduced number of components and/or truncated components
- a subject collection of one or more nucleic acids that encodes a subject EDV does not include (i.e., lacks) nucleotide sequence encoding one or more of the following proteins: a pol polypeptide protease (PR), a pol polypeptide reverse transcriptase (RT), a pol polypeptide integrase (IN), a nucleocapsid (NC) protein.
- PR pol polypeptide protease
- RT pol polypeptide reverse transcriptase
- IN pol polypeptide integrase
- NC nucleocapsid
- a subject collection of one or more nucleic acids that encodes a subject EDV does not include (i.e., lacks) nucleotide sequences encoding a pol polypeptide protease (PR), a pol polypeptide reverse transcriptase (RT), a pol polypeptide integrase (IN), and a nucleocapsid (NC) protein.
- PR pol polypeptide protease
- RT pol polypeptide reverse transcriptase
- a pol polypeptide integrase a nucleocapsid
- NC nucleocapsid
- a subject EDV includes an N-terminally truncated capsid (CA) protein.
- CA N-terminally truncated capsid
- the term “N-terminally truncated capsid (CA) protein” is meant herein to mean that the CA protein is missing (via deletion) amino acids from the N-terminal half of the protein relative to the corresponding full length CA protein.
- a subject N-terminally truncated capsid (CA) protein is missing some amino acids from the C-terminal half of the protein as well.
- an N-terminally truncated capsid (CA) protein retains some amino acids (e.g., in some cases from 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, or 1) from the N-terminus of the corresponding full length CA protein, but is missing other amino acids from the N-terminal half of the protein.
- a subject N-terminally truncated capsid (CA) protein includes from 1-10 amino acids (e.g., 1-9, 1- 8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, or 1) of the first 10 amino acids of the corresponding full length CA protein.
- a subject N-terminally truncated capsid (CA) protein includes from 1-5 amino acids (e.g., 1-4, 1-3, 1-2, or 1) of the first 10 amino acids of the corresponding full length CA protein. In some cases, a subject N-terminally truncated capsid (CA) protein includes the first 5 amino acids of the corresponding full length CA protein. In some cases, a subject N-terminally truncated capsid (CA) protein includes the first 4 amino acids of the corresponding full length CA protein. In some cases, a subject N-terminally truncated capsid (CA) protein includes the first 3 amino acids of the corresponding full length CA protein.
- 1-5 amino acids e.g., 1-4, 1-3, 1-2, or 1
- a subject N-terminally truncated capsid (CA) protein includes the first 5 amino acids of the corresponding full length CA protein.
- a subject N-terminally truncated capsid (CA) protein includes the first
- a subject N-terminally truncated capsid (CA) protein includes the first 2 amino acids of the corresponding full length CA protein. In some cases, a subject N-terminally truncated capsid (CA) protein includes the amino acid of the corresponding full length CA protein. [00112] As noted above, a CA protein can be of any of a variety of retroviruses.
- a subject full length CA protein is: PIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQA AMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGE IYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQN ANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 282).
- a subject N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-148 of SEQ ID NO: 282 (i.e., the protein has a deletion of amino acids that includes those corresponding to amino acids 5-148).
- corresponding to amino acids 5-148 it is meant that the full length CA protein may have a different overall amino acid sequence than SEQ ID NO: 282, but the N- terminally truncated capsid protein derived therefrom would be lacking an equivalent region/portion of the full length CA protein (a region/portion equivalent to amino acids 5-148 of SEQ ID NO: 282).
- a subject N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-61 SEQ ID NO: 282 (i.e., the protein has a deletion of amino acids that includes those corresponding to amino acids 5-61). In some cases, a subject N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-47 SEQ ID NO: 282 (i.e., the protein has a deletion of amino acids that includes those corresponding to amino acids 5-47).
- a subject N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-34 of SEQ ID NO: 282 (i.e., the protein has a deletion of amino acids that includes those corresponding to amino acids 5-34). In some cases, a subject N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-15 of SEQ ID NO: 282 (i.e., the protein has a deletion of amino acids that includes those corresponding to amino acids 5-15). [00113] In some cases, a subject N-terminally truncated capsid protein has a deletion that removes at least those amino acids corresponding to amino acids 5-148 of SEQ ID NO: 282.
- a subject N-terminally truncated capsid protein has a deletion of amino acids corresponding to amino acids 5-148 of SEQ ID NO: 282.
- the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with PIVQSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPG ATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 290).
- the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 290. In some cases, the N- terminally truncated capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 290. In some cases, the N-terminally truncated capsid protein includes the amino acid sequence of SEQ ID NO: 290.
- the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLE EMMTACQGVGGPGHKARVL (SEQ ID NO: 331).
- a subject N-terminally truncated capsid protein has a deletion that removes at least those amino acids corresponding to amino acids 5-61 of SEQ ID NO: 282.
- a subject N-terminally truncated capsid protein has a deletion of amino acids corresponding to amino acids 5-61 of SEQ ID NO: 282.
- the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with PIVQHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH NPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWM TETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 286).
- the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 286. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 286.
- the N-terminally truncated capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 286. In some cases, the N-terminally truncated capsid protein includes the amino acid sequence of SEQ ID NO: 286.
- the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with HQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPI PVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETL LVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 332).
- a subject N-terminally truncated capsid protein has a deletion that removes at least those amino acids corresponding to amino acids 5-47 of SEQ ID NO: 282. In some cases, a subject N-terminally truncated capsid protein has a deletion of amino acids corresponding to amino acids 5-47 of SEQ ID NO: 282.
- the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with PIVQTPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAG TTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTL RAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 285).
- the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 285. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 285.
- the N-terminally truncated capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 285. In some cases, the N-terminally truncated capsid protein includes the amino acid sequence of SEQ ID NO 285.
- the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with TPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTS TLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAE QASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 333).
- a subject N-terminally truncated capsid protein has a deletion that removes at least those amino acids corresponding to amino acids 5-34 of SEQ ID NO: 282. In some cases, a subject N-terminally truncated capsid protein has a deletion of amino acids corresponding to amino acids 5-34 of SEQ ID NO: 282.
- the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with PIVQEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAP GQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKE PFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV GGPGHKARVL (SEQ ID NO: 284).
- the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 284. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 284.
- the N-terminally truncated capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 284. In some cases, the N- terminally truncated capsid protein includes the amino acid sequence of SEQ ID NO 284.
- the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with EVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQM REPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRD YVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPG HKARVL (SEQ ID NO: 334).
- a subject N-terminally truncated capsid protein has a deletion that removes at least those amino acids corresponding to amino acids 5-15 of SEQ ID NO: 282. In some cases, a subject N-terminally truncated capsid protein has a deletion of amino acids corresponding to amino acids 5-15 of SEQ ID NO: 282.
- the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with PIVQSPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETIN EEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLN KIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILK ALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 283).
- the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 283. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 283.
- the N-terminally truncated capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 283. In some cases, the N-terminally truncated capsid protein includes the amino acid sequence of SEQ ID NO 283.
- the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAA EWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVR MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGP GATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 335).
- the N-terminally truncated capsid protein has a length of 80-220 amino acids (e.g., 80-210, 80-190, 80-180, 80-185, 80-175, 80-90, 170-220, 170-210, 170-190, 170-180, 170-185, 170-175, 170-90, 180-220, 180-210, 180-190, 180-180, 180-185, 180-175, 180-90, 195-220, 195-210, 195-190, 195-180, 195-185, 195-175, 195-90, 210-220, 210-210, 210-190, 210-180, 210-185, 210-175, 210-90, 83-220, 83-210, 83-190, 83-180, 83-185, 83-175, 83-90, 87-220, 87-210, 87-190, 87-180, 87- 185, 87-175, 87-90, 174-2
- 80-220 amino acids
- the N-terminally truncated capsid protein has a length of 80-90 amino acids. In some cases, the N-terminally truncated capsid protein has a length of 83-90 amino acids. In some cases, the N-terminally truncated capsid protein has a length of 83-87 amino acids. [00119] In some cases, the N-terminally truncated capsid protein has a length of about 83, 87, 170, 174, 184, 188, 197, 201, 216, or 220 amino acids. For example, in some cases, the N-terminally truncated capsid protein has a length of about 83 amino acids.
- the N-terminally truncated capsid protein has a length of about 85 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 87 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 170 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 175 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 184 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 188 amino acids.
- the N-terminally truncated capsid protein has a length of about 197 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 201 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 216 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 220 amino acids.
- Truncated matrix (MA) protein [00120] As noted above, an MA protein can be of any of a variety of retroviruses.
- a subject MA protein is: GARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQ PSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVS QNY (SEQ ID NO:296), which is an example of a full length MA protein.
- an MA protein is a full length protein.
- an MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO:296.
- a subject MA protein is a variant (e.g., can be truncated).
- an MA polypeptide lacks amino acids (aa) corresponding to aa 72-127 of SEQ ID NO: 296 (see, e.g., SEQ ID NO: 298).
- a subject MA polypeptide has a deletion that removes at least those amino acids corresponding to amino acids 72-127 of SEQ ID NO: 296.
- a MA polypeptide has a deletion of amino acids corresponding to amino acids 72-127 of SEQ ID NO: 296.
- a truncated MA polypeptide includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 298.
- an MA polypeptide lacks amino acids (aa) corresponding to aa 30-127 of SEQ ID NO: 296 (see, e.g., SEQ ID NO: 301).
- a subject MA polypeptide has a deletion that removes at least those amino acids corresponding to amino acids 30-127 of SEQ ID NO: 296.
- a MA polypeptide has a deletion of amino acids corresponding to amino acids 30-127 of SEQ ID NO: 296.
- a truncated MA polypeptide includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 301.
- an MA polypeptide lacks amino acids (aa) corresponding to aa 53-127 of SEQ ID NO: 296 (see, e.g., SEQ ID NO: 299).
- a subject MA polypeptide has a deletion that removes at least those amino acids corresponding to amino acids 53-127 of SEQ ID NO: 296. In some cases, a MA polypeptide has a deletion of amino acids corresponding to amino acids 53-127 of SEQ ID NO: 296. In some cases, a truncated MA polypeptide includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 299.
- a subject truncated MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 298. In some cases, a subject truncated MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 299.
- a subject truncated MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 301.
- a subject MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with any one of SEQ ID NOs: 298, 299, and 301.
- a subject MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 301.
- the MA protein has a length of 30-135 amino acids (e.g., 30-131, 30-60, 30-40, 30-35, 33-135, 33-131, 33-60, 33-40, 33-35, 50-135, 50-131, 50-60, 55-57, 100-135, or 100-131).
- the MA protein has a length of 30-35 amino acids.
- the MA protein has a length of 50-60 amino acids.
- the MA protein has a length of 120-135 amino acids. In some cases, the MA protein has a length of about 33, 56, or 131 amino acids. For example, in some cases, the MA protein has a length of about 33 amino acids. In some cases, the MA protein has a length of about 56 amino acids. In some cases, the MA protein has a length of about 131 amino acids.
- a subject EDV includes (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR Cas effector polypeptide such as a Cas9 or Cas12a); (b) a viral envelop protein (e.g., VSVG or a mutant thereof); (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody); (d) a matrix (MA) polypeptide (e.g., in some cases a truncated MA polypeptide); and (e) an N-terminally truncated capsid (CA) protein.
- a nucleic acid-binding effector polypeptide e.g., a CRISPR Cas effector polypeptide such as a Cas9 or Cas12a
- a viral envelop protein e.g., VSVG or a mutant thereof
- a targeting polypeptide that provides for binding to a target cell (e.g., an
- EDVs of the present disclosure include a viral envelope protein (e.g., a viral envelope glycoprotein).
- the viral envelope protein is a variant that includes one or more amino acid substitutions that reduce binding of the viral envelope protein to its receptor.
- Suitable viral envelope proteins include, e.g., a vesicular stomatitis virus (VSV) glycoprotein (VSV-G protein or VSVG), a Measles virus hemagglutinin (HA) protein and/or a measles virus fusion glycoprotein, an Influenza virus neuraminidase (NA) protein, a Measles virus F protein, an Influenza virus HA protein, a cocal virus glycoprotein, a Moloney virus MLV-A protein, a Moloney virus MLV-E protein, a Baboon Endogenous retrovirus (BAEV) envelope protein, an Ebola virus glycoprotein, a foamy virus envelope protein, a variant of any of the above that comprises one or more amino acid substitutions that reduce binding of the viral envelope protein to its receptor, and a combination or two or more of the foregoing viral envelope proteins.
- VSV vesicular stomatitis virus
- VSV-G protein or VSVG a Meas
- the viral envelope protein is selected from: a Hepatitis B virus (HBV) glycoprotein, a Hepatitis C virus (HCV) glycoprotein, a Marburg virus glycoprotein, an Ebola virus glycoprotein, a vesicular stomatitis virus (VSV) glycoprotein, an influenza virus hemagglutinin, a SARS-CoV glycoprotein, a respiratory syncytial virus (RSV) glycoprotein, a human parainfluenza virus glycoprotein, a moloney murine leukemia virus (MMLV), a measles virus hemagglutinin and/or a measles virus fusion glycoprotein, an HTLV-1 glycoprotein, a Ross river virus glycoprotein, a rabies virus glycoprotein, a Mokola virus glycoprotein, a Semliki Forest virus glycoprotein, a Sindbis virus glycoprotein, a Venezuelan equine encephalitis virus glycoprotein, a sendai virus, a baculo
- the viral envelope protein is a VSV-G protein (VSVG). In some cases, the viral envelope protein is a measles virus hemagglutinin protein. In some cases, the viral envelope protein is a measles virus F protein. In some cases, the viral envelope protein is an influenza virus hemagglutinin protein. In some cases, the viral envelope protein is a Moloney virus MLV-A protein. In some cases, the viral envelope protein is a Moloney virus MLV-E protein. In some cases, the viral envelope protein is a moloney murine leukemia virus (MMLV). In some cases, the viral envelope protein is a baboon endogenous retrovirus envelope protein.
- VSVG VSV-G protein
- the viral envelope protein is a measles virus hemagglutinin protein. In some cases, the viral envelope protein is a measles virus F protein. In some cases, the viral envelope protein is an influenza virus hemagglutinin protein. In some cases, the viral envelope protein is
- the viral envelope protein is an Ebola virus glycoprotein. In some cases, the viral envelope protein is a foamy virus envelope protein. [00133] In some cases, the viral envelope protein is a VSV-G protein.
- a suitable VSV-G protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00134] imkcllylaflfigvnckftivfphnqkgnwknvpsnyhycpsssdlnwhndligtalqvkmpkshkaiqadgwmchaskwvttc dfrwygpkyithsirsftpsveqckesieqtkqgtwlnpgfppqscgyatvtdaeavivqvtphhvlvdeytgewvdsqfingkcsny
- a suitable VSV-G protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00136] mkcllylaflfigvnckftivfphnqkgnwknvpsnyhycpsssdlnwhndligtalqvkmpkshkaiqadgwmchaskwvttc dfrwygpkyithsirsftpsveqckesieqtkqgtwlnpgfppqscgyatvtdaeavivqvtphhvlvdeytgewvdsqfingkcsnyicptvhn sttwhsdykvkglcdsnlismditffsedgelsslgkegtgfrsnyfa
- a suitable VSV-G protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence of SEQ ID NO: 153.
- the viral envelope protein is a BAEV-G protein.
- a suitable BAEV-G protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00139] mgfttkiiflynlvlvyagfddprkaielvqkrygrpcdcsggqvseppsdrvsqvtcsgktaylmpdqrwkcksipkdtspsgplqe cpcnsyqssvhsscytsyqqcrsgnktyytatllktqtggtsdvqvlgstnkliqspcngikgqsicwsttapihvsdgggpldttriksvqrkleeih kalypelqyhplaipkvrdnlmvdaqtlnilnatynlll
- the viral envelope protein is an influenza virus H1N1 hemagglutinin glycoprotein.
- a suitable influenza hemagglutinin protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MKAILVVLLY TFATANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVETP SSDNGTCYPG DFIDYEELRE QLSSVSSFER FEIFPKTSSW PNHDSNKGVT AACPHAGAKS FYKNLIWLVK KGNSYPKLSK SYINDKGKEV LVLWGIHHPS TSADQQSLYQ NADAYVFVGS SRYSKKFKPE IAIRPKVRXX EGRMNYYWTL VEPGDKITFE ATGNLV
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and natural killer (NK) cells.
- the viral envelope protein is an influenza virus H3N2 hemagglutinin glycoprotein.
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and natural killer (NK) cells.
- the viral envelope protein is an influenza virus A H5N1 hemagglutinin glycoprotein.
- a suitable influenza hemagglutinin protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLTER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLEF SADLIIERRE GSDVCYPGKF VNEEALRQIL RESGGIDKEA MGFTYSGIRT NGATSACRRS GSSFYAEMKW LLSNTDNAAF PQMTKSYKNT RKSPALIVWG IHHSVSTAEQ TKLYGSGNKL VTVGSSNYQQ SFVPSPGARP QVNGLSGRID FHWLMLNPND TVTFSFNGAF IAPDRASFLR GKSMGIQSGV QVDANCEGDC YHSGGTIISN LPFQNIDSRA VGKCPRY
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is a Hepatitis B Virus (HBV) S glycoprotein.
- a suitable HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MENTTSGFLG PLLVLQAGFF LLTRNLTIPQ SLDSWWTSLN FLGGAPTCPG QNSQSPTSNH SPTSCPPICP GYRWMCLRRF IIFLFILLLC LIFLLVLLDY QGMLPVCPLL PGTSTTSTGP CKTCTIPAQG TSMFPSCCCT KPSDGNCTCI PIPSSWAFAR FLWEWASVRF SWLSLLVPFV QWFVGLSPTV WLSVIWMMWY WGPSLYNILS PFLPLLPIFF CLWVYI (SEQ ID NO:54; GenBank Accession No: ABV02793).
- the viral envelope protein is a Hepatitis B Virus (HBV) middle S glycoprotein.
- HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MQWNSTAFHQ ALQDPKVRGL YFPAGGSSSG TVNPAPNIAS HISSISARTG DPVTNMENIT SGFLGPLLVL QAGFFLLTRI LTIPQSLDSW WTSLNFLGGS PVCLGQNSQS PTSNHSPTSC PPICPGYRWM CLRRFIIFLF ILLLCLIFLL VLLDYQGMLP VCPLIPGSTT TSTGPCKTCT TPAQGNSMFP SCCCTKPTDG NCTCIPIPSS WAFAKYLWEW ASVRFSWLSL LVPFVQWF
- the viral envelope protein is a Hepatitis B Virus (HBV) large S glycoprotein.
- HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGLSWTVPLE WGKNHSTTNP LGFFPDHQLD PAFRANTRNP DWDHNPNKDH WTEANKVGVG AFGPGFTPPH GGLLGWSPQA QGMLKTLPAD PPPASTNRQS GRQPTPITPP LRDTHPQAMQ WNSTTFHQAL QDPKVSALYL PAGGSSSGTV NPVPTTASLI SSIFSRIGDP APNMESITSG FLGPLLVLQA GFFLLTKILT IPQSLDSWWT SLNFLGGAPV CLGQNSQSPT SSHS
- the viral envelope protein is a Hepatitis B Virus (HBV) small S glycoprotein.
- HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MENITSGFLG PLLVLQAGFF LLTRILTIPQ SLDSWWTSLN FLGGTTVCLG QNSQSPTSNH SPTSCPPTCP GYRWMCLRRF IIFLFILLLC LIFLLVLLDY QGMLPVCPLI PGSSTTSTGP CRTCTTPAQG TSMYPSCCCT KPSDGNCTCI PIPSSWAFGK FLWEWASARF SWLSLLVPFV QWFVGLSPTV WLSVIWMMWY WAPNLHNILS PFLPLLPIFL CLWVYI (SEQ ID NO:57;
- the viral envelope protein is a Hepatitis B Virus (HBV) preS2 glycoprotein.
- HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MQWNSTTFHQ TLQDPRVRGL YFPAGGSSSG TVNPVPTTVS HISSIFSRIG DPALNMENIT SGFLGPLLVL QAGFFLLTRI LTIPQSLDSW WTSLNFLGGT TVCLGQNSQS PTSNHSPTSC PPTCPGYRWM CLRRFIIFLF ILLLCLIFLL VLLDYQGMLS VCPLIPGSTT TSTGPCKTCTTPAQGTSIHP SCCCTKPSDG NCTWIPIPSS WAFGKFLWEW ASARFSWLSL LVPFVQW
- the viral envelope protein is a Rabies virus.
- a suitable Rabies virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MVPQALLFVP LLVFPLCFGK FPIYTIPDKL GPWSPIDIHH.
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to neurons, astrocytes, oligodendrocyctes, glia, and other cells of the of the central nervous system.
- the viral envelope protein is a Mokola virus glycoprotein.
- the viral envelope protein is a lymphocytic choriomeningitis virus (LCMV) glycoprotein.
- a suitable LCMV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGQIVTMFEA LPHIIDEVIN IVIIVLIIIT SIKAVYNFAT CGILALISFL LLAGRSCGLY GLDGPDIYKG IYQFKSVEFD MSHLNLTMPN ACSANNSHHY ISMGNSGLEL TFTNDSIISH NFCNLTSAFN KKTFDHTLMS IVSSLHLSIR GNSNYKAVSC DFNSGITIQY NLSFSDAQSA LSQCKTFRGR VLDMFRTAFG GKYMRSGWGW TGSDGKTTWC SQTSYQYLII QNRTWENHCR YAGPFGMARI LFAQEKTKFL TRRLAGTFTW TLSDSSGVDN PGGYCLTRWM ILAADLKCFG NTAVAKCNMN HDEEFCDMLR LIDYNKAALS
- the viral envelope protein is a lymphocytic choriomeningitis virus (LCMV) G1 glycoprotein.
- a suitable LCMV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MYGLKGPDIYKG VYQFKSVEFD MSHLNLTMPN ACSANNSHHY ISMGTSGLEL TFTNDSIISH NFCNLTSAFN KKTFDHTLMS IVSSLHLSIR GNSNYKAVSC DFNNGITIQY NLTFSDAQSA QSQCRTFRGR VLDMFRTAFG GKYMRSGWGW TGSDGKTTWC SQTSYQYLII QNRTWENHCT YAGPFGMSRI LLSQEKTKFF TRRLA (SEQ ID NO:65; GenBank Accession No: P09991).
- the viral envelope protein is a lymphocytic choriomeningitis virus (LCMV) G2 glycoprotein.
- a suitable LCMV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: GTFTW TLSDSSGVEN PGGYCLTKWM ILAAELKCFG NTAVAKCNVN HDAEFCDMLR LIDYNKAALS KFKEDVESAL HLFKTTVNSL ISDQLLMRNH LRDLMGVPYC NYSKFWYLEH AKTGETSVPK CWLVTNGSYL NETHFSDQIE QEADNMITEM LRKDYIKRQG STPLALMDLL MFSTSAYLVS IFLHLVKIPT HRHIKGGSCP KPHRLTNKGI CSCGAFKVPG VKTVWKRR (SEQ ID NO:66; GenBank Accession No: P09991).
- the viral envelope protein is a Ross River virus E1 glycoprotein.
- a suitable Ross River virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: YEHTATIPNV VGFPYKAHIE RNXFSPMTLQ LEVVXXSLEP TLNLEYITCE YKTVVPSPFI KCCGTSECSS KEQPDYQCKV YTGVYPFMWG GAYCFCDSEN TQLSEAYVDR SDVCKHDHAL AYKAHTASLK ATIRISYGTI NQTTEAFVNG EHAVNVGGSK FIFGPISTAW SPFDNKIVVY KDDVYNQDFP PYGSGQPGRF GDIQSRTVES KDLYANTALK LSRPSPGVVH VPYTQTPSGF KYWLKEKGSS LNTKAPFGCK IKTNPVRAMD CA
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to skeletal muscle, and cells that make up the joints, joint-associated connective tissue, bone, neurons, and lymphatic cells.
- the viral envelope protein is a Ross River virus E2 glycoprotein.
- a suitable Ross River virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: SVIEHFNVYK ATRPYLAXCA DCGDGYFCYS PVAIEKIRDE ASDGMLKIQV SAQIGLDKAG THAHTKMRYM AGHDVQESKR DSLRVYTSAA CSIHGTMGHF IVAHCPPGDY LKXSFEDANS HVKACKVQYK HDPLPVGREK FVVRPHFGVE LPCTSYQLTT APTDEEIDMH TPPDIPDRTL LSQTAGNVKI TAGGRTIRYN CTCGRDNVGT TSTDKTINTC KIDQCHAAVT SHDKWXFTSP FVPRADQTAR KGKVHVPFPL TNVTCRVPLA RAPDVTYGKK EVTLRLHPDH PTXFSYRSLG AVPHPYEEWV DKFSERIIP
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to skeletal muscle, and cells that make up the joints, joint-associated connective tissue, bone, neurons, and lymphatic cells.
- the viral envelope protein is a Semliki Forest virus E1 glycoprotein.
- a suitable Semliki Forest virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMWG GAYCFCDSEN TQLSEAYVDR SDVCRHDHAS AYKAHTASLK AKVRVMYGNV NQTVDVYVNG DHAVTIGGTQ FIFGPLSSAW TPFDNKIVVY KDEVFNQDFP PYGSGQPGRF GDIQSRTVES NDLYANTALK LARPSPGMVH VPYTQTPSGF KYWLKEKGTA LNTKAPFGCQ IKTNPVRAMN CAVGNIPVSM NLPDSAFTRI VEAPTIIDLT
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to muscle, pancreas, neurons, astrocytes, oligodendrocytes, glia, and other cells of the of the central nervous system.
- the viral envelope protein is a Semliki Forest virus E2 glycoprotein.
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to muscle, pancreas, neurons, astrocytes, oligodendrocyctes, glia, and other cells of the of the central nervous system.
- the viral envelope protein is a Sindbis virus E1 glycoprotein.
- a suitable Sindbis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: SVIDDFTLTS PYLGTCSYCH HTVPCFSPVK IEQVWDEADD NTIRIQTSAQ FGYDQSGAAS ANKYRYMSLK QDHTVKEGTM DDIKISTSGP CRRLSYKGYF LLAKCPPGDS VTVSIVSSNS ATSCTLARKI KPKFVGREKY DLPPVHGKKI PCTVYDRLKE TTAGYITMHR PRPHAYTSYL EESSGKVYAK PPSGKNITYE CKCGDYKTGT VSTRTEITGC TAIKQCVAYK SDQTKWVFNS PDLIRHDDHT AQGKLHLPFK LIPSTCMVPV AHAPNVIHGF KHISLQLDTD HLTLLTTRRL GANPEPTTEW I
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to skeletal muscle, and cells that make up the joints, joint-associated connective tissue, bone, neurons, and lymphatic cells.
- the viral envelope protein is an Ebola Zaire virus glycoprotein.
- a suitable Ebola Zaire virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGVTGILQLP RDRFKRTSFF LWVIILFQRT FSIPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLNL EGNGVATDVP SATKRWGFRS GVPPKVVNYE AGEWAENCYN LEIKKPDGSE CLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILPQAK KDFFSSHPLR EPVNATEDPS SGYYSTTIRY QATGFGTNET EYLFEVDNLT YVQLESRFTP QFLLQLNETI YTSGKRSNTT GKLIWKVNPE IDTTIGEWAF WETKKNLTRK IRSEELSFTV
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to hepatocytes, endothelial cells, dendritic cells, macrophages, and monocytes.
- the viral envelope protein is an Ebola Zaire virus glycoprotein.
- a suitable Ebola Zaire virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: IPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLNL EGNGVATDVP SATKRWGFRS GVPPKVVNYE AGEWAENCYN LEIKKPDGSECLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILPQAK KDFFSSHPLR EPVNATEDPS SGYYSTTIRY QATGFGTNET EYLFEVDNLT YVQLESRFTP QFLLQLNETI YTSGKRSNTT GKLIWKVNPE IDTTIGEWAF WETKKNLTRK IRSEELSFTV VSNGAKNISG QSPARTSSDP GTNTTTEDHK IMASENSSAM V
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to hepatocytes, endothelial cells, dendritic cells, macrophages, and monocytes.
- the viral envelope protein is an Ebola Reston virus glycoprotein.
- a suitable Ebola Reston virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGSGYQLLQL PRERFRKTSF LVWVIILFQR AISMPLGIVT NSTLKATEID QLVCRDKLSS TSQLKSVGLN LEGNGIATDV PSATKRWGFR SGVPPKVVSY EAGEWAENCY NLEIKKSDGS ECLPPDGV RGFPRCRYVH KVQGTGPCPG DLAFHKNGAF FLYDRLASTV IYRGTTFAEG VVAFLILSEP KKHFWKATPA HEPVNTTDDS TSYYMTLTLS YEMSNFGGNE SNTLFKVDNH TYVQLDRPHT PQFLVQLNET LRRNNRLSNS TGRLTWTLDP KIEPDVGEWA FWETKKNFSQ QLHGENLHFQ
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to hepatocytes, endothelial cells, dendritic cells, macrophages, and monocytes.
- the viral envelope protein is a Marburg virus glycoprotein.
- a suitable Marburg virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MKTTCFLISL ILIQGTKNLP ILEIASNNQP QNVDSVCSGT LQKTEDVHLM GFTLSGQKVA DSPLEASKRW AFRTGVPPKN VEYTEGEEAK TCYNISVTDP SGKSLLLDPP TNIRDYPKCK TIHHIQGQNP HAQGIALHLW GAFFLYDRIA STTMYRGKVF TEGNIAAMIV NKTVHKMIFS RQGQGYRHMN LTSTNKYWTS SNGTQTNDTG CFGALQEYNS TKNQTCAPSK IPPPLPTARP EIKLTSTPTD ATKLNTTDPS SDDEDLATSG SGSGEREPHT TSDAVTKQGL SSTMPPTPSP QPSTPQQGGN NTN
- the viral envelope protein is a murine leukemia virus (MLV) glycoprotein.
- a suitable MLV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MESTTLSKPF KNQVNPWGPL IVLLILGGVN PVALGNSPHQ VFNLTWEVTN GDRETVWAIA GNHPLWTWWP DLTPDLCMLA LHGPSYWGLE YRAPFSPPPG PPCCSGSSDS TPGCSRDCEE PLTSYTPRCN TAWNRLKLSK VTHAHNEGFY VCPGPHRPRW ARSCGGPESF YCASWGCETT GRASWKPSSS WDYITVSNNL TSDQATPVCK GNEWCNSLTI RFTSFGKQAT SWVTGHWWGL RLYVSGHDPG LIFGIRLKIT DSGPRVPIGP NPVLSDRRPP SRPRPTRSPP PSNSTPTETP LTLPEPPPAG VENRLLNLVK GAYQAL
- the viral envelope protein is an MLV glycoprotein.
- a suitable MLV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MESTTLSKPF KNQVNPWGPL IVLLILRGVN PVTLGNSPHQ VFNLTWEVTN GDRETVWAIT GNHPLWTWWP DLTPDLCMLA LHGPSYWGLE YRAPFSPPPG PPCCSGSSDS TPGCSRDCEE PLTSYTPRCN TAWNRLKLSK VTHAHNGGFY VCPGPHRPRW ARSCGGPESF YCASWGCETT GRASWKPSSS WDYITVSNNL TSDQATPVCK GNKWCNSLTI RFTSFGKQAT SWVTGHWWGL RLYVSGHDPG LIFGIRLKIT DSGPRVPIGP NPVLSDRRPP SRPRPTRSPP PSNSTPTETP
- the viral envelope protein is an MLV glycoprotein.
- a suitable MLV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MARSTLSKPP QDKINPWKPL IVMGVLLGVG MAESPHQVFN VTWRVTNLMT GRTANATSLL GTVQDAFPKL YFDLCDLVGE EWDPSDQEPY VGYGCKYPAG RQRTRTFDFY VCPGHTVKSG CGGPGEGYCG KWGCETTGQA YWKPTSSWDL ISLKRGNTPW DTGCSKVACG PCYDLSKVSN SFQGATRGGR CNPLVLEFTD AGKKANWDGP KSWGLRLYRT GTDPITMFSL TRQVLNVGPR VPIGPNPVLP DQRLPSSPIE IVPAPQPPSP LNTSYPPSTT STPSTSPTSP SVP
- the viral envelope protein is an MLV glycoprotein.
- a suitable MLV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEGPAFSKPL KDKINPWKSL MVMGVYLRVG MAESPHQVFN VTWRVTNLMT GRTANATSLL GTVQDAFPRL YFDLCDLVGE EWDPSDQEPY VGYGCKYPGG RKRTRTFDFY VCPGHTVKSG CGGPREGYCG EWGCETTGQA YWKPTSSWDL ISLKRGNTPW DTGCSKMACG PCYDLSKVSN SFQGATRGGR CNPLVLEFTD AGKKANWDGP KSWGLRLYRT GTDPITMFSL TRQVLNIGPR IPIGPNPVIT GQLPPSRPVQ IRLPRPPQPP PTGAASIVPE TAPPSQQPGT G
- the viral envelope protein is an MLV glycoprotein.
- a suitable MLV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEGSAFSKPL KDKINPWGPL IVMGILVRAG ASVQRDSPHQ IFNVTWRVTN LMTGQTANAT SLLGTMTDTF PKLYFDLCDL VGDYWDDPEP DIGDGCRTPG GRRRTRLYDF YVCPGHTVPI GCGGPGEGYC GKWGCETTGQ AYWKPSSSWD LISLKRGNTP KDQGPCYDSS VSSGVQGATP GGRCNPLVLE FTDAGRKASW DAPKVWGLRL YRSTGADPVT RFSLTRQVLN VGPRVPIGPN PVITDQLPPS QPVQIMLPRP PHPPPSGTVS MVPGAPPPSQ QPGTGDRLLN LVEGAYQ
- the viral envelope protein is a polytropic mink cell focus-forming virus glycoprotein.
- a suitable polytropic mink cell focus-forming virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: VQHDSPHQVF NVTWRVTNLM TGQTANATSL LGTMTDAFPK LYFDLCDLIG DDWDETGLGC RTPGGRKRAR TFDFYVCPGH TVPTGCGGPR EGYCGKWGCE TTGQAYWKPS SLWDLISLKR GNTPQNQGPC YDSSAVSSDI KGATPGGRCN PLVLEFTDAG KKASWDGPKV WGLRLYRSTG TDPVTRFSLT RRVLNIGPRV PIGPNPVIID QLPPSRPVQI MLPRPPQPPP PGAASIVPET APPSNQPGTG DRLLNLVDGA
- the viral envelope protein is a gibbon ape leukemia virus (GALV) glycoprotein.
- a suitable GALV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MVLLPGSMLL TSNLHHLRHQ MSPGSWKRLI ILLSCVFGGG GTSLQNKNPH QPMTLTWQVL SQTGDVVWDT KAVQPPWTWW PTLKPDVCAL AASLESWDIP GTDVSSSKRV RPPDSDYTAA YKQITWGAIG CSYPRARTRM ASSTFYVCPR DGRTLSEARR CGGLESLYCK EWDCETTGTG YWLSKSSKDL ITVKWDQNSE WTQKFQQCHQ TGWCNPLKID FTDKGKLSKD WITGKTWGLR FYVSGHPGVQ FTIRLKITNM PAVAVGPDLV
- the viral envelope protein is a GALV glycoprotein.
- a suitable GALV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: TSLQNKNPH QPMTLTWQVL SQTGDVVWDT KAVQPPWTWW PTLKPDVCAL AASLESWDIP GTDVSSSKRV RPPDSDYTAA YKQITWGAIG CSYPRARTRM ASSTFYVCPR DGRTLSEARR CGGLESLYCK EWDCETTGTG YWLSKSSKDL ITVKWDQNSE WTQKFQQCHQ TGWCNPLKID FTDKGKLSKD WITGKTWGLR FYVSGHPGVQ FTIRLKITNM PAVAVGPDLV LVEQGPPRTS LALPPPLPPR EAPPPSLPDS NSTALATSAQ TPTVRKTIVT LNTPPPTTGD RLFD
- the viral envelope protein is a GALV glycoprotein.
- a suitable GALV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: TSLQNKNPH QPMTLTWQVL SQTGDVVWDT KAVQPPWTWW PTLKPDVCAL AASLESWDIP GTDVSSSKRV RPPDSDYTAA YKQITWGAIG CSYPRARTRM ASSTFYVCPR DGRTLSEARR CGGLESLYCK EWDCETTGTG YWLSKSSKDL ITVKWDQNSE WTQKFQQCHQ TGWCNPLKID FTDKGKLSKD WITGKTWGLR FYVSGHPGVQ FTIRLKITNM PAVAVGPDLV LVEQGPPRTS LALPPPLPPR EAPPPSLPDS NSTALATSAQ TPTVRKTIVT LNTPPPTTGD RLFD
- the viral envelope protein is a GALV glycoprotein.
- a suitable GALV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: TSLQNKNPH QPMTLTWQVL SQTGDVVWDT KAVQPPWTWW PTLKPDVCAL AASLESWDIP GTDVSSSKRV RPPDSDYTAA YKQITWGAIG CSYPRARTRM ASSTFYVCPR DGRTLSEARR CGGLESLYCK EWDCETTGTG YWLSKSSKDL ITVKWDQNSE WTQKFQQCHQ TGWCNPLKID FTDKGKLSKD WITGKTWGLR FYVSGHPGVQ FTIRLKITNM PAVAVGPDLV LVEQGPPRTS LALPPPLPPR EAPPPSLPDS NSTALATSAQ TPTVRKTIVT LNTPPPTTGD RLFD
- the viral envelope protein is a GALV glycoprotein.
- a suitable GALV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: E AVSLTLAVLL GLGITAGIGT GSTALIKGPI DLQQGLTSLQ IAIDADLRAL QDSVSKLEDS LTSLSEVVLQ NRRGLDLLFL KEGGLCAALK EECCFYIDHS GAVRDSMKKL KEKLDKRQLE RQKSQNWYEG WFNNSPWFTT LLSTIAGPLL LLLLLLILGP CIINKLVQFI NDRISAVKIL (SEQ ID NO:85).
- the viral envelope protein is a RD114 retrovirus glycoprotein.
- a suitable RD114 retrovirus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MKLPTGMVIL CSLIIVRAGF DDPRKAIALV QKQHGKPCEC SGGQVSEAPP NSIQQVTCPG KTAYLMTNQK WKCRVTPKNL TPSGGELQNC PCNTFQDSMH SSCYTEYRQC RANNKTYYTA TLLKIRSGSL NEVQILQNPN QLLQSPCRGS INQPVCWSAT APIHISDGGG PLDTKRVWTV QKRLEQIHKA MHPELQYHPL ALPKVRDDLS LDARTFDILN TTFRLLQMSN FSLAQDCWLC LKLGTPTPLA IPTPSLTYSL ADSLANASCQ IIPPLLVQPM QFS
- the viral envelope protein is a Sendai virus (SeV) glycoprotein.
- a suitable SeV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MTAYIQRSQC ISTSLLVVLT TLVSCQIPRD RLSNIGVIVD EGKSLKIAGS HESRYIVLSL VPGVDFENGC GTAQVIQYKS LLNRLLIPLR DALDLQEALI TVTNDTTQNA GAPQSRFFGA VIGTIALGVA TSAQITAGIA LAEAREAKRD IALIKESMTK THKSIELLQN AVGEQILALK TLQDFVNDEI KPAISELGCE TAALRLGIKL TQHYSELLTA FGSNFGTIGE KSLTLQALSS LYSANITEIM TTIKTGQSNI YDVIYTEQIK GTVIDVDLER YMV
- the viral envelope protein is an SeV F2 glycoprotein.
- a suitable SeV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QIPRD RLSNIGVIVD EGKSLKIAGS HESRYIVLSL VPGVDFENGC GTAQVIQYKS LLNRLLIPLR DALDLQEALI TVTNDTTQNA GAPQSR (SEQ ID NO:89; GenBank Accession No: P04855).
- the viral envelope protein is an SeV F1 glycoprotein.
- a suitable SeV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: FFGA VIGTIALGVA TSAQITAGIA LAEAREAKRD IALIKESMTK THKSIELLQN AVGEQILALK TLQDFVNDEI KPAISELGCE TAALRLGIKL TQHYSELLTA FGSNFGTIGE KSLTLQALSS LYSANITEIM TTIKTGQSNI YDVIYTEQIK GTVIDVDLER YMVTLSVKIP ILSEVPGVLI HKASSISYNI DGEEWYVTVP SHILSRASFL GGADITDCVE SRLTYICPRD PAQLIPDSQQ KCILGDTTRC PVTKVVDSLI PKFAFVNGGV VANCIASTCT CGTGRRPISQ DRSKGVVFLT HDNCGLIGVN GVELYANRRG HDATWG
- the viral envelope protein is an SeV hemagglutinin-neuraminidase glycoprotein.
- a suitable SeV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MDGDRSKRDS YWSTSPGGST TKLVSDSERS GKVDTWLLIL AFTQWALSIA TVIICIVIAA RQGYSMERYS MTVEALNTSN KEVKESLTSL IRQEVITRAA NIQSSVQTGI PVLLNKNSRD VIRLIEKSCN RQELTQLCDS TIAVHHAEGI APLEPHSFWR CPAGEPYLSS DPEVSLLPGP SLLSGSTTIS GCVRLPSLSI GEAIYAYSSN LITQGCADIG KSYQVLQLGY ISLNSDMFPD LNPVVSHTYD INDNRKSCSV VATGTRGY
- the viral envelope protein is a Jaagsiekte sheep retrovirus (JSRV) glycoprotein.
- JSRV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MPKRRAGFRK GWYARQRNSL THQMQRMTLS EPTSELPTQR QIEALMRYAW NEAHVQPPVT PTNILIMLLL LLQRIQNGAA ATFWAYIPDP PMLQSLGWDK ETVPVYVNDT SLLGGKSDIH ISPQQANISF YGLTTQYPMC FSYQSQHPHC IQVSADISYP RVTISGIDEK TGMRSYRDGT GPLDIPFCDK HLSIGIGIDT PWTLCRARIA SVYNINNANT TLLWDWAPGG TPDFPEYRGQ HPPISSVNTA PIYQTELWKL
- the viral envelope protein is a baculovirus gp64 glycoprotein.
- a suitable baculovirus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MFHLLTLLLL LFINMNLYLA GEHCNVQMKN GPYRIKNLAI TPPRETLKKD VTVTIVETDY EENVLIGYKG YYQAYGYNGG SLDANTRLEE TMESLPLTKE DLLTWTYRQE CEVGEELIDR WGSDSDDCYR NKDGRGVWVK TKELVKRQNN NHFAHHTCNR SWRCGFSTAK MYSKLVCDDE TNDCKVFILD NTGKPINITT NEVLYRDGVN MMLKSKPTFT RREEKVACLL VKDELNPDKT REHCLIDSDI YDLSNNNWFC MFNKCI
- the viral envelope protein is a baculovirus gp64 glycoprotein.
- a suitable baculovirus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MLRITLLILF LVRFVSGAEH CNAQMKSGPW RIKNLPIAPP KETLQKDVDV EIVETDLDEN VIIGYKGYYQ AYAYNGGSLD PNTSVDETTQ TLNIDKDDLI TWGDRRKCEV GEELIDQWGS DSDSCFKDKL GRGVWVAGKE LVKRKNNNHF AHHTCNRSWR CGVSTAKMYT RLECDNETDD CKVTILDING TVINVTENEV LHRDGVSMIL KQKSTFTRRT EKVACLLIKD DKSDPYSITR EHCLIDNDIF DLSKNTWNCK FNRCIK
- the viral envelope protein is a Chandipura virus glycoprotein.
- a suitable Chandipura virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MTSSVTISVI LLISFIAPSY SSLSIAFPEN TKLDWKPVTK NTRYCPMGGE WFLEPGLQEE SFLSSTPIGA TPSKSDGFLC HAAKWVTTCD FRWYGPKYIT HSIHNIKPTR SDCDTALASY KSGTLVSPGF PPESCGYASV TDSEFLVIMI TPHHVGVDDY RGHWVDPLFV GGECDQSYCD TIHNSSVWIP ADQTKKNICG QSFTPLTVTV AYDKTKEIAA GAIVFKSKYH SHMEGARTCR LSYCGRNGIK FPNGEWVSLD VKTKIQEKPL LPLFKECPAG
- viral envelope protein is a Venezuelan equine encephalitis virus glycoprotein.
- a suitable Venezuelan equine encephalitis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSAKKPKKEA SQKQKGGGQG KKKKNQGKKK AKTGPPNPKA QNGNKKKTNK KPGKRQRMVM KLESDKTFPI MLEGKINGYA CVVGGKLFRP MHVEGKIDND VLAALKTKKA SKYDLEYADV PQNMRADTFK YTHEKPQGYY SWHHGAVQYE NGRFTVPKGV GAKGDSGRPI LDNQGRVVAI VLGGVNEG
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to dendritic cells, macrophages, and cells of the spleen, lymph node, thymus, pancreas, skeletal muscle, and central nervous system.
- the viral envelope protein is a Venezuelan equine encephalitis virus E2 glycoprotein.
- a suitable Venezuelan equine encephalitis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: STEELFKEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLHTSRPC HIVDGHGYFL LARCPAGDSI TMEFKKDSVT HSCSVPYEVK FNPVGRELYT HPPEHGVEQA CQVYAHDAQN RGAYVEMHLP GSEVDSSLVS LSGSSVTVTP PVGTSALVEC ECGGTKISET INKTKQFSQC TKKEQCRAYR LQNDKWVYIS DKLPKAAGAT LKGKLHVPFL LADGKCTVPL APEPMITFGF RSVSLKLHPK NPTYLTTRQL ADEPHYTHEL IS
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to dendritic cells, macrophages, and cells of the spleen, lymph node, thymus, pancreas, skeletal muscle, and central nervous system.
- the viral envelope protein is a Venezuelan equine encephalitis virus E1 glycoprotein.
- a suitable Venezuelan equine encephalitis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: Y EHATTMPSQA GISYNTIVNR AGYAPLPISI TPTKIKLIPT VNLEYVTCHY KTGMDSPAIK CCGSQECTPT YRPDEQCKVF TGVYPFMWGG AYCFCDTENT QVSKAYVMKS DDCLADHAEA YKAHTASVQA FLNITVGEHS IVTTVYVNGE TPVNFNGVKL TAGPLSTAWT PFDRKIVQYA GEIYNYDFPE YGAGQPGAFG DIQSRTVSSS DLYANTNLVL QRPKAGAIHV PYTQAPSGFE QWKKDKAPSL KSTAPFGCEI YTNPIRAENC AVGSIPLAFD IPDALFTRVS ETPTLSAAEC
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to dendritic cells, macrophages, and cells of the spleen, lymph node, thymus, pancreas, skeletal muscle, and central nervous system.
- the viral envelope protein is a Lassa virus glycoprotein.
- a suitable Lassa virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKNN SHHYIMVGNE TGLELTLTNT SIINHKFCNL SDAHKKNLYD HALMSIISTF HLSIPNFNQY EAMSCDFNGG KISVQYNLSH SYAGDAANHC GTVANGVLQT FMRMAWGGSY IALDSGRGNW DCIMTSYQYL IIQNTTWEDH CQFSRPSPIG YLGLLSQRTR DIYISRRLLG TFTWTLSDSE GKDTPGGYCL TRWMLIEAEL KCFGNTAVAK CNEKHDEEFC DMLRLFDFNK
- the viral envelope protein is an avian leukosis virus glycoprotein.
- a suitable avian leukosis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEAVIKMRRA LFLQAFLTGR PGKASKKDPK KNPLATSKKD PEKTPLLPTR VNYILIIGVL VLCEVTGVRA DVHLLEQPGN LWITWANRTG QTDFCLSTQS ATSPFQTCLI GIPSPISEGD FKGYVSDNCT TLGTDRLVSS ASITGGPDNS TTLTYRKVSC LLLKLNVSMW NEPPELQLLG SQSLPNITDI TQISGVAGGC VGFRPKGVPW YLGWSQGEAT RFLLRHPSFS NLTGPFTVVT ADRHNLFMGS EYCGAYGYRF WEIYNCSQEG Q
- the viral envelope protein is an avian leukosis virus glycoprotein.
- a suitable avian leukosis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEAVIKMRRA LFLQAFLTGH PGKVSKKDSK KKPPATGKRD PEKTPLLPTR VNYILIIGVL VLCEVTGVRA DVHLLEQPGN LWITWANRTG QTDFCLSTQS ATSPFQTCLI GIPSPISEGD FKGYVSGNCT ALGTHRLVSS GIHGGPDNST TLTYRKVSCL LLKLNVSLLD EPSELQLLGS QSLPNITNIT QIPSVAGGCI GFTPYGSPAG VYGWDRRQVT HILLTDPGSN PFFNKASNSS KPFTVVTADR HNLFMGSEYC GAYGYRFWEM YNCSQ
- the viral envelope protein is an avian leukosis virus glycoprotein.
- a suitable avian leukosis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEAVIKAFLT GHPGKVSKKD SKKKPPATSK KDPEKTPLLP SRGYFFFPTI LVCVVIISVV PGVGGVHLLR QPGNVWVTWA NKTGRTDFCL SLQSATSPFR TCLIGIPQYP LNTFKGYVTN VTACDNDADL ASQTACLIKA LNTTLPWDPQ ELDILGSQMI KNGTTRTCVT FGSVCYKENN RSRVCHNFDG NFNGTGGAEA ELRDFIAKWK SDDLLIRPYV NQSWTMVSPI NVESFSISRR YCGFTSNETR YYRGDLSNWC GSKRGKWSAG
- the viral envelope protein is a human T-lymphotropic virus 1 (HTLV-1) glycoprotein.
- a suitable HTLV-1 protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGKFLATLIL FFQFCPLILG DYSPSCCTLT VGVSSYHSKP CNPAQPVCSW TLDLLALSAD QALQPPCPNL VSYSSYHATY SLYLFPHWIK KPNRNGGGYY SASYSDPCSL KCPYLGCQSW TCPYTGAVSS PYWKFQQDVN FTQEVSHLNI NLHFSKCGFP FSLLVDAPGY DPIWFLNTEP SQLPPTAPPL LSHSNLDHIL EPSIPWKSKL LTLVQLTLQS TNYTCIVCID RASLSTWHVL YSPNVSVPSL SSTPLLYPSL
- the viral envelope protein is a human foamy virus gp130 glycoprotein.
- a suitable human foamy virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MAPPMTLQQW IIWKKMNKAH EALQNTTTVT EQQKEQIILD IQNEEVQPTR RDKFRYLLYT CCATSSRVLA WMFLVCILLI IVLVSCFVTI SRIQWNKDIQ VLGPVIDWNV TQRAVYQPLQ TRRIARSLRM QHPVPKYVEV NMTSIPQGVY YEPHPEPIVV KERVLGLSQI LMINSENIAN NANLTQEVKK LLTEMVNEEM QSLSDVMIDF EIPLGDPRDQ EQY
- the viral envelope protein is a human foamy virus glycoprotein.
- a suitable human foamy virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: SLRM QHPVPKYVEV NMTSIPQGVY YEPHPEPIVV KERVLGLSQI LMINSENIAN NANLTQEVKK LLTEMVNEEM QSLSDVMIDF EIPLGDPRDQ EQYIHRKCYQ EFANCYLVKY KEPKPWPKEG LIADQCPLPG YHAGLTYNRQ SIWDYYIKVE SIRPANWTTK SKYGQARLGS FYIPSSLRQI NVSHVLFCSD QLYSKWYNIE NTIEQNERFL LNKLNNLTSG TSVLKKRALP KDWSSQGKNA LFREINVLDI CSKPESVILL NTSYYSFSLWW
- the viral envelope protein is a human foamy virus glycoprotein.
- a suitable human foamy virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: SVDNNYAK LRSMGYALTG AVQTLSQISD INDENLQQGI YLLRDHVITL MEATLHDISV MEGMFAVQHL HTHLNHLKTM LLERRIDWTY MSSTWLQQQL QKSDDEMKVI KRIARSLVYY VKQTHSSPTA TAWEIGLYYE LVIPKHIYLN NWNVVNIGHL VKSAGQLTHV TIAHPYEIIN KECVETIYLH LEDCTRQDYV ICDVVKIVQP CGNSSDTSDC PVWAEAVKEP FVQVNPLKNG SYLVLASSTD CQIPPYVPSI VTVNETTSCF GL
- the viral envelope protein is a visna-maedi virus gp160 glycoprotein.
- a suitable visna-maedi virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MASKESKPSR TTRRGMEPPL RETWNQVLQE LVKRQQQEEE EQQGLVSGKK KSWVSIDLLG TEGKDIKKVN IWEPCEKWFA QVVWGVLWVL QIVLWGCLMW EVRKGNQCQA EEVIALVSDP GGFQRVQHVE TVPVTCVTKN FTQWGCQPEG AYPDPELEYR NISREILEEV YKQDWPWNTY HWPLWQMENM RQWMKENEKE YKERTNKTKE DIDDLVAGRI RGRFCVPYPY ALLRCEEWCW
- the viral envelope protein is a visna-maedi virus glycoprotein.
- a suitable visna- maedi virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QCQA EEVIALVSDP GGFQRVQHVE TVPVTCVTKN FTQWGCQPEG AYPDPELEYR NISREILEEV YKQDWPWNTY HWPLWQMENM RQWMKENEKE YKERTNKTKE DIDDLVAGRI RGRFCVPYPY ALLRCEEWCW YPESINQETG HAEKIKINCT KAKAVSCTEK MSLAAVQRVY WEKEDEESMK FLNIKACNIS LRCQDEGKSP GGCVQGYPIP KGAEIIPEAM KYLRGKKSRY GGIKDKNGEL KLPLSVRVWV
- the viral envelope protein is a visna-maedi virus glycoprotein.
- a suitable visna- maedi virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QCQA EEVIALVSDP GGFQRVQHVE TVPVTCVTKN FTQWGCQPEG AYPDPELEYR NISREILEEV YKQDWPWNTY HWPLWQMENM RQWMKENEKE YKERTNKTKE DIDDLVAGRI RGRFCVPYPY ALLRCEEWCW YPESINQETG HAEKIKINCT KAKAVSCTEK MSLAAVQRVY WEKEDEESMK FLNIKACNIS LRCQDEGKSP GGCVQGYPIP KGAEIIPEAM KYLRGKKSRY GGIKDKNGEL KLPLSVRVWV
- the viral envelope protein is a visna-maedi virus glycoprotein.
- a suitable visna- maedi virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QCQA EEVIALVSDP GGFQRVQHVE TVPVTCVTKN FTQWGCQPEG AYPDPELEYR NISREILEEV YKQDWPWNTY HWPLWQMENM RQWMKENEKE YKERTNKTKE DIDDLVAGRI RGRFCVPYPY ALLRCEEWCW YPESINQETG HAEKIKINCT KAKAVSCTEK MSLAAVQRVY WEKEDEESMK FLNIKACNIS LRCQDEGKSP GGCVQGYPIP KGAEIIPEAM KYLRGKKSRY GGIKDKNGEL KLPLSVRVWV
- the viral envelope protein is a visna-maedi virus glycoprotein.
- a suitable visna- maedi virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: GIGL VIVLAIMAII AAAGAGLGVA NAVQQSYTRT AVQSLANATA AQQEVLEASY AMVQHIAKGI RILEARVARV EALVDRMMVY QELDCWHYQH YCVTSTRSEV ANYVNWTRFK DNCTWQQWEE EIEQHEGNLS LLLREAALQV HIAQRDARRI PDAWKAIQEA FNWSSWFSWL KYIPWIIMGI VGLMCFRILM CVISMCLQAY KQVKQIRYTQ VTVVIEAPVE LEEKQKRNGD GTNGCASLER ERRTSHRSFI QIW
- the viral envelope protein is a severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein.
- SARS-CoV severe acute respiratory syndrome-associated coronavirus
- a suitable SARS-CoV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MFIFLLFLTL TSGSDLDRCT TFDDVQAPNY TQHTSSMRGV YYPDEIFRSD TLYLTQDLFL PFYSNVTGFH TINHTFGNPV IPFKDGIYFA ATEKSNVVRG WVFGSTMNNK SQSVIIINNS TNVVIRACNF ELCDNPFFAV SKPMGTQTHT MIFDNAFNCT FEYISDAFSL DVSEKSGNFK HLREFVFKNK DGFLYVYKGY QPIDVVRDLP SGFNTLKPIF KLPLGINITN FRAILTAFSP
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is a SARS-CoV S2 glycoprotein.
- a suitable SARS- CoV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: CDI PIGAGICASY HTVSLLRSTS QKSIVAYTMS LGADSSIAYS NNTIAIPTNF SISITTEVMP VSMAKTSVDC NMYICGDSTE CANLLLQYGS FCTQLNRALS GIAAEQDRNT REVFAQVKQM YKTPTLKYFG GFNFSQILPD PLKPTKRSFI EDLLFNKVTL ADAGFMKQYG ECLGDINARD LICAQKFNGL TVLPPLLTDD MIAAYTAALV SGTATAGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLYE NQKQIANQFN KAISQIQESL TTTSTALGKL QDVVNQNAQA LNTLVKQLSS NFGAISSVLN DIL
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is a SARS-CoV spike receptor binding domain glycoprotein.
- a suitable SARS-CoV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: PNIT NLCPFGEVFN ATKFPSVYAW ERKKISNCVA DYSVLYNSTF FSTFKCYGVS ATKLNDLCFS NVYADSFVVK GDDVRQIAPG QTGVIADYNY KLPDDFMGCV LAWNTRNIDA TSTGNYNYKY RYLRHGKLRP FERDISNVPF SPDGKPCTPP ALNCYWPLND YGFYTTTGIG YQPYRVVVLS FELLNAPATV CGPKLSTDLI KNQCVNFNFN GLTGTGVLTP SSKRFQPFQQ FGRDVSDFTD SVRDPKTSE (SEQ ID NO:113; GenBank Accession No: ABD73002).
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is a respiratory syncytial virus (RSV) glycoprotein G.
- RSV respiratory syncytial virus
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is an RSV glycoprotein F.
- a suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PPTNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRRFLGF LLGVGSAIAS GVAVSKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ KKLMSNNVQI VRQQSYSIMS IIKEEVLAYV VQLPLYGVID TPCWKLHTSP LCTT
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is an RSV glycoprotein.
- a suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PPTNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRRFLGF LLGVGSAIAS GVAVSKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ KKLMSNNVQI VRQQSYSIMS IIKEEVLAYV VQLPLYGVID TPCWKLHTSP LCTTNTKEGS NICLTRTDRG WYCDNA
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is an RSV F0 glycoprotein.
- a suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PPTNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRRFLGF LLGVGSAIAS GVAVSKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ KKLMSNNVQI VRQQSYSIMS IIKEEVLAYV VQLPLYGVID TPCWKLHTSP LCTTNTKEGS NICLTRTDRG WYCDNA
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is an RSV F2 glycoprotein.
- a suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PPTNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRR (SEQ ID NO:117; GenBank Accession No: P03420).
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is an RSV F1 glycoprotein.
- a suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: FLGF LLGVGSAIAS GVAVSKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ KKLMSNNVQI VRQQSYSIMS IIKEEVLAYV VQLPLYGVID TPCWKLHTSP LCTTNTKEGS NICLTRTDRG WYCDNAGSVS FFPQAETCKV QSNRVFCDTM NSLTLPSEIN LCNVDIFNPK YDCKIMTSKT DVSSSVITSL GAIVSCYGKT KCTASNKNRG IIKTFSNGCD YVSNKGMDTV SVGNTLYYVN KQ
- the viral envelope protein is an RSV glycoprotein.
- a suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PPTNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRRFLGF LLGVGSAIAS GVAVSKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ
- the viral envelope protein is a human parainfluenza virus type 3 hemagglutinin- neuraminidase glycoprotein.
- a suitable human parainfluenza virus type 3 protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEYWKHTNHG KDAGNELETS MATHGNKLTN KITYILWTII LVLLSIVFII VLINSIKSEK AHESLLQNIN NEFMEITEKI QMASDNTNDL IQSGVNTRLL TIQSHVQNYI PISLTQQMSD LRKFISEITI RNDNQEVLPQ RITHDVGIKP LNPDDFWRCT SGLPSLMKTP KIRLMPGPGL LAMPTTVDGC IRTPSLVIND LIYAYTSNLI TRGCQDIGKS YQVLQIGIIT VNSDLVPDLN PRISHTFNIN DNRKSCSLAL LNTDVYQLCS TPKVDERSDY ASPGIEDIVL DIVNYDGSIS TTRFKNN
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is a human parainfluenza virus type 3 glycoprotein F0.
- a suitable human parainfluenza virus type 3 protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MPISILLIIT TMIMASHCQI DITKLQHVGV LVNSPKGMKI SQNFETRYLI LSLIPKIDDS NSCGDQQIKQ YKRLLDRLII PLYDGLRLQK DVIVANQESN ENTDPRTERF FGGVIGTIAL GVATSAQITA AVALVEAKQA RSDIEKLKEA IRDTNKAVQS VQSSVGNLIV AIKSVQDYVN KEIVPSIARL GCEAAGLQLG IALTQHYSEL TNIFGDNIGS LQEKGIKLQG IASLYRTNIT EIFTTSTVDK YDIYDLLFTE SIKVRVIDVD LNDYSITLQV RLPLLTRLLN TQIYKV
- Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells.
- the viral envelope protein is a Hepatitis C virus (HCV) E1 glycoprotein.
- a suitable HCV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: YQVRNSSGLY HVTNDCPNSS IVYEAADAIL HTPGCVPCVR EGNASRCWVA VTPTVATRDG KLPTTQLRRH IDLLVGSATL CSALYVGDLC GSVFLVGQLF TFSPRRHWTT QDCNCSIYPG HITGHRMAWD MMMNWSPTAA LVVAQLLRIP QAIMDMIAGA HWGVLAGIAY FSMVGNWAKV LVVLLLFAGV DA (SEQ ID NO:121; GenBank Accession No: NP_751920).
- the viral envelope protein is an HCV E2 glycoprotein.
- a suitable HCV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: ETHVTGGSAG RTTAGLVGLL TPGAKQNIQL INTNGSWHIN STALNCNESL NTGWLAGLFY QHKFNSSGCP ERLASCRRLT DFAQGWGPIS YANGSGLDER PYCWHYPPRP CGIVPAKSVC GPVYCFTPSP VVVGTTDRSG APTYSWGAND TDVFVLNNTR PPLGNWFGCT WMNSTGFTKV CGAPPCVIGG VGNNTLLCPT DCFRKHPEAT YSRCGSGPWI TPRCMVDYPY RLWHYPCTIN YTIFKVRM
- the viral envelope protein is a measles virus fusion (F) polypeptide.
- an EDV of the present disclosure includes a variant viral envelope protein that includes one or more amino acid substitutions compared to a corresponding wild-type viral envelope protein, and where the variant viral envelope protein exhibits reduced binding to its native receptor, compared to the binding of the wild-type viral envelope protein to the native receptor. In some cases, the variant viral envelope protein retains endosomal fusion activity.
- the viral envelope protein is a variant VSV-G protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%, amino acid sequence identity to the VSV-G amino acid sequence depicted in of SEQ ID NO:153; where the variant VSV-G protein exhibits comprises one or more amino acid substitutions compared to a wild- type viral envelope protein (compared to the amino acid sequence depicted in of SEQ ID NO:153), and where the variant viral envelope protein exhibits reduced binding to its native receptor, compared to the binding of a VSV-G polypeptide comprising the amino acid sequence of SEQ ID NO:153 to its native receptor.
- the native receptor for VSV-G is the low-density lipoprotein receptor (LDLR).
- LDLR low-density lipoprotein receptor
- the VSV-G polypeptide comprises one or more amino acid substitutions that reduce binding to the native receptor for VSV-G, while retaining the endosomal fusion function of the VSV-G polypeptide.
- the viral envelope protein is a VSV-G protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the VSV-G amino acid sequence of SEQ ID NO:153, where amino acid 47 is other than a Lys.
- the viral envelope protein is a VSV-G protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the VSV-G amino acid sequence of SEQ ID NO:153, where amino acid 354 is other than an Arg.
- the viral envelope protein is a VSV- G protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the VSV-G amino acid sequence of SEQ ID NO:153, where amino acid 47 is other than a Lys and amino acid 354 is other than an Arg.
- the Lys at amino acid 47 is substituted with an Ala. In some cases, the Lys at amino acid 47 is substituted with a Gln (K47Q). In some cases, the Arg at amino acid 354 is substituted with an Ala (R354A). In some cases, the Arg at amino acid 354 is substituted with a Gln.
- the viral envelope protein is a VSV-G protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the VSV-G amino acid sequence of SEQ ID NO:154, in which the VSV-G protein has a Gln at position 47 and an Ala at position 354 (K47Q/R354A) relative to SEQ ID NO:153.
- the viral envelope protein is a variant measles hemagglutinin (HA) protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%, amino acid sequence identity to the measles HA amino acid sequence of SEQ ID NO:155; where the variant measles HA protein exhibits comprises one or more amino acid substitutions compared to a wild-type viral envelope protein (compared to the amino acid sequence of SEQ ID NO:155), and where the variant viral envelope protein exhibits reduced binding to its native receptor, compared to the binding of a measles HA protein comprising the amino acid sequence of SEQ ID NO: 155 to its native receptor.
- HA hemagglutinin
- the variant measles HA protein comprises a substitution of one or more of Y481, R533, S548, and F549, based on the amino acid numbering of SEQ ID NO: 155.
- CD46 is a native receptor for measles virus HA.
- the viral envelope protein is a variant measles HA protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%, amino acid sequence identity to the measles HA amino acid sequence of SEQ ID NO:156, where amino acid 841 is other than a Tyr, amino acid 533 is other than an Arg, amino acid 548 is other than a Ser, and amino acid 549 is other than a Phe.
- the viral envelope protein is a variant measles HA protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%, amino acid sequence identity to the measles HA amino acid sequence of SEQ ID NO:156, where amino acid 841 is Ala, amino acid 533 is Ala, amino acid 548 is Leu, and amino acid 549 is Ser.
- Targeting polypeptides [00230]
- An EDV of the present disclosure includes a targeting polypeptide (i.e., one or more targeting polypeptides) that provides for binding to a target cell (e.g., target cell type).
- Targeting polypeptides include antibodies and antibody mimetics (also referred to as antibody analogs).
- Suitable antibody analogs include, e.g., an affibody, an affilin, an affimer, an affitin, an alphabody, an anticalin, an avimer, a DARPin, a Fynomer, a Kunitz domain peptide, a monobody, a repebody, a VLR, and a nanoCLAMP.
- Suitable antibodies include a single chain Fv (scFv) polypeptide, a diabody, a triabody, and a nanobody. In some cases, the antibody is a single-chain Fv polypeptide. In some cases, the antibody is a nanobody.
- the antibody is a bispecific antibody.
- an EDV of the present disclosure comprises two different antibodies (e.g., a first antibody and a second antibody), where the first antibody specifically binds to a first target polypeptide on a target cell and the second antibody specifically binds to a second target polypeptide on the same target cell.
- EDVs comprise two or more different targeting polypeptides.
- EDVs comprising a bispecific targeting polypeptide, e.g., where the bispecific targeting polypeptide binds to two different targets on the targeted cell type.
- the bispecific targeting polypeptide is a bispecific antibody or derivative thereof.
- the targeting polypeptide provides for selective binding to an organ such as kidney, liver, bone, pancreas, brain, lung, heart, and the like. In some cases, the targeting polypeptide provides for selective binding to a particular cell type. For example, in some cases, the targeting polypeptide provides for selective binding to a cell such as a skeletal muscle cell, a cardiomyocyte, an adipocyte, an epithelial cell, an endothelial cell, a macrophage, a beta islet cell, or an immune cell (e.g., a T cell, a B cell, a monocyte, a natural killer cell, a dendritic cell, etc.).
- a cell such as a skeletal muscle cell, a cardiomyocyte, an adipocyte, an epithelial cell, an endothelial cell, a macrophage, a beta islet cell, or an immune cell (e.g., a T cell, a B cell, a monocyte, a natural killer cell, a den
- the targeting polypeptide provides for selective binding to a cell such as a cancer cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue-resident stem cell, a monocyte, a macrophage, a B cell, or a T cell.
- the targeting polypeptide provides for selective binding to a diseased cell, relative to a non-diseased cell of the same cell type.
- the antibody provides for selective binding to a CAR-T cell, i.e., a T cell that is modified to express a chimeric antigen receptor (CAR) on its surface.
- Fusion polypeptides [00233]
- the antibody itself is a fusion polypeptide comprising: (i) the antibody; and (ii) a heterologous polypeptide (a “fusion partner”).
- the fusion partner can be a polypeptide that enhances accessibility of the antibody to a target cell.
- Suitable fusion partners include, but are not limited to, the stalk portion of a polypeptide; the stalk and transmembrane domain of a polypeptide; an immunoglobulin hinge polypeptide; a linker polypeptide; and the like.
- the antibody is fused to a transmembrane domain via a linker.
- the fusion partner is the stalk and transmembrane domain of a transmembrane protein.
- a “transmembrane domain” (TMD), as used herein, is a portion of a transmembrane (TM) protein that contains a hydrophobic portion that can insert into or span a cell membrane.
- Transmembrane components or domains have a three-dimensional structure that is thermodynamically stable in a cell membrane and generally range in length from about 15 amino acids to about 30 amino acids.
- the structure of a transmembrane component or domain may comprise an alpha helix, a beta barrel, a beta sheet, a beta helix, or any combination thereof.
- a transmembrane component or domain comprises or is derived from a known transmembrane protein (e.g., a CD4 transmembrane domain, a CD8 transmembrane domain, a CD27 transmembrane domain, a CD28 transmembrane domain, a PDGFR transmembrane domain or any combination thereof).
- the fusion partner includes the stalk and transmembrane domain of a CD8 ⁇ polypeptide.
- the stalk and transmembrane domain can comprise the following amino acid sequence: TTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACDIYIWAPLAGTCGVLLLSLVIT LYC (SEQ ID NO:20), where the stalk has the amino acid sequence TTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACD (SEQ ID NO:21) and the TMD has the sequence IYIWAPLAGTCGVLLLSLVITLYC (SEQ ID NO:22).
- the fusion partner includes the stalk domain of a CD8 ⁇ polypeptide (a CD8 ⁇ stalk polypeptide); e.g., the fusion partner comprises the amino acid sequence: TTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACD (SEQ ID NO:21).
- a CD8 ⁇ polypeptide includes the amino acid sequence ASAKPTTTPAPRPPTPAPTIASQPLSLRPEAARPAAGGAVHTRGLDFAK (SEQ ID NO: 23).
- the fusion partner includes the stalk and/or transmembrane domain of a platelet- derived growth factor receptor (PDGFR).
- PDGFR platelet- derived growth factor receptor
- a “hinge polypeptide,” “hinge region,” or a “hinge” refers to (a) an immunoglobulin hinge sequence (made up of, for example, upper and core regions of an immunoglobulin hinge) or a functional fragment or variant thereof, (b) a type II C-lectin interdomain (stalk) region or a functional fragment or variant thereof, or (c) a cluster of differentiation (CD) molecule stalk region or a functional variant thereof.
- the antibody is a scFv or a nanobody that binds to CD4. In some cases, the antibody is a scFv or a nanobody that binds to CD3. In some cases, the antibody is a scFv or a nanobody that binds to CD8. In some cases, the antibody is a scFv or a nanobody that binds to CD28.
- the targeting polypeptide comprises one or more antibodies, e.g., one or a combination of anti-CD3 (e.g., CD3 scFv-3), anti-CD4 (e.g., CD4 scFv-2), and anti-CD28 (e.g., CD28 scFv-2) (e.g., an anti-CD3 and an anti-CD4 antibody; an anti-CD3 and an anti- CD28 antibody; an anti-CD3, an anti-CD4, and an anti-CD28 antibody; and the like).
- anti-CD3 e.g., CD3 scFv-3
- anti-CD4 e.g., CD4 scFv-2
- anti-CD28 e.g., CD28 scFv-2
- the targeting polypeptide includes an anti-CD3 scFV having the sequence MALPVTALLLPLALLLHAARPQVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRP GQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHY CLDYWGQGTTLTVSSSGGGGSGGGGSGGGGSIVLTQSPAIMSASPGEKVTMTCSASSSVSYMN WYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTF GSGTKLEINRAA (SEQ ID NO: 125).
- a superagonistic anti-CD28 antibody is used.
- such antibodies can be used to target EDVs to T-regs, which can be useful for treating autoimmune disease.
- CD28 superagonists CD28SAs
- mAbs potent T-cell-activating monoclonal antibodies
- TGN1412 also called TAB08.
- an EDV comprises an anti-CD3 scFv and an anti-CD28 scFv. In some cases, an EDV comprises an anti- CD3 scFv and an anti-CD4 scFv.
- Cancer cell-targeting antibodies [00243] In some cases, the targeting polypeptide is an antibody that targets a cancer antigen, thereby targeting the EDV to a cancerous cell that displays the cancer antigen on its cell surface.
- Suitable antigens bound by an antibody present in an EDV of the present disclosure include, e.g., CD3, epidermal growth factor receptor (EGFR), CA-125 (highly expressed on epithelial ovarian cancer cells), CD80, CD86, glycoprotein IIb/IIIa receptor, CD51, TNF- ⁇ , epithelial adhesion molecule EpCAM (CD326), vascular endothelial growth factor receptor-2 (VEGFR-2), CD52, mesothelin, activin receptor- like kinase 1 (ALK-1), phosphatidyl serine, CD19, vascular endothelial growth factor A (VEGF-A), IL-6 receptor, CD11a, CD25, CD2, CD3 receptor, and the like.
- EGFR epidermal growth factor receptor
- CA-125 highly expressed on epithelial ovarian cancer cells
- CD80 CD86
- glycoprotein IIb/IIIa receptor CD51
- TNF- ⁇ epithelial adhesion molecule EpCAM
- Suitable antigens bound by an antibody present in an EDV of the present disclosure include, e.g., carbonic anhydrase IX, alpha-fetoprotein (AFP), ⁇ -actinin-4, A3, ART-4, B7, Ba 733, BAGE, BrE3- antigen, CA-125, CAMEL, CAP-1, CASP-8/m, CCL19, CCL21, CD1, CD1a, CD2, CD3, CD4, CD5, CD8, CD11A, CD14, CD15, CD16, CD18, CD19, CD20, CD21, CD22, CD23, CD25, CD29, CD30, CD32b, CD33, CD37, CD38, CD40, CD40L, CD44, CD45, CD46, CD52, CD54, CD55, CD59, CD64, CD66a-e, CD67, CD70, CD70L, CD74, CD79a, CD80, CD83, CD95, CD126, CD132, CD133, CD138, CD147,
- AFP
- the cancer-associated antigen is an antigen associated with a hematological cancer.
- antigens include, but are not limited to, BCMA, C5, CD19, CD20, CD22, CD25, CD30, CD33, CD38, CD40, CD45, CD52, CD56, CD66, CD74, CD79a, CD79b, CD80, CD138, CTLA-4, CXCR4, DKK, EphA3, GM2, HLA-DR beta, integrin ⁇ V ⁇ 3, IGF-R1, IL6, KIR, PD-1, PD-L1, TRAILR1, TRAILR2, transferrin receptor, and VEGF.
- the cancer-associated antigen is an antigen expressed by malignant B cells, such as CD19, CD20, CD22, CD25, CD38, CD40, CD45, CD74, CD80, CTLA-4, IGF-R1, IL6, PD-1, TRAILR2, or VEGF.
- the cancer-associated antigen is an antigen associated with a solid tumor.
- antigens include, but are not limited to, CAIX, cadherins, CEA, c-MET, CTLA-4, EGFR family members, EpCAM, EphA3, FAP, folate-binding protein, FR-alpha, gangliosides (such as GC2, GD3 and GM2), HER2, HER3, IGF-1R, integrin ⁇ V ⁇ 3, integrin ⁇ 5 ⁇ 1, Legamma, Liv1, mesothelin, mucins, NaPi2b, PD-1, PD-L1, PD-1 receptor, pgA33, PSMA, RANKL, ROR1, TAG-72, tenascin, TRAILR1, TRAILR2, VEGF, VEGFR, and others listed above.
- the cancer-associated antigen is an antigen associated with a cancer stem cell.
- antigens include, but are not limited to, SSEA3, SSEA4, TRA-1-60, TRA-1-81, CD133, CD90, CD326, Cripto-1, PODXL-1, ABCG2, CD24, CD49f, Notch2, CD146, CD10, CD117, and CD26 (Kim & Ryu (2017) BMB Rep 50(6): 285–298).
- Suitable antibodies include, e.g., abciximab (anti-glycoprotein IIb/IIIa), alemtuzumab (anti-CD52), bevacizumab (anti-VEGF), cetuximab (anti-EGFR), gemtuzumab (anti- CD33), ibritumomab (anti-CD20), panitumumab (anti-EGFR), rituximab (anti-CD20), tositumomab (anti-CD20), trastuzumab (anti-ErbB2), lambrolizumab (anti-PD-1 receptor), nivolumab (anti-PD-1 receptor), ipilimumab (anti-CTLA-4), abagovomab (anti-CA-125), adecatumumab (anti-EpCAM), atlizumab (anti-IL-6 receptor), benralizumab (anti-CD125), obinutuzumab
- VH and VL amino acid sequences of various cancer antigen-binding antibodies are known in the art, as are the light chain and heavy chain CDRs of such antibodies. See, e.g., Ling et al. (2016) Frontiers Immunol.9:469; WO 2005/012493; US 2019/0119375; US 2013/0066055.
- the following are non- limiting examples of antibodies that can be used as part of a targeting polypeptide of a subject EDV.
- an antibody includes the CDR sequences from the anti-CD19 scFv FMC63.
- an antibody includes the CDR sequences from the anti-CD4 antibody ibalizumab (IMGT/mAb-DB ID 241).
- an antibody includes the CDR sequences from the anti-CD20 antibody rituximab (IMGT/mAb-DB ID 161). In some cases, an antibody includes the CDR sequences from the anti-CD3 antibody acapatamab (IMGT/mAb-DB ID 1074). In some cases, an antibody includes the CDR sequences from the anti-CD3 antibody OKT3. In some cases, an antibody includes the CDR sequences from the anti-CD28 antibody PDB ID 1YJD. In some cases, an antibody includes the CDR sequences from the anti-CD19 antibody IMGT/mAb-DB ID 1232. In some cases, an antibody includes the CDR sequences from the anti-CD45 antibody Ab4122.
- an antibody includes the CDR sequences from the anti-CD45 antibody Ab4129. In some cases, an antibody includes the CDR sequences from the anti-CD45 antibody apamistamab (IMGT/mAb-DB ID 633). See, e.g., FIG.10 and FIG.11. The following are non-limiting examples of cancer antigen-binding antibodies.
- an anti-Her2 antibody comprises: a) a light chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00253] DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVP SRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLK SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKH KVYACEVTHQGLSSPVTKSFNRGEC (SEQ ID NO:159); and b) a heavy chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence:
- an anti-Her2 antibody can comprise a VL CDR1 having the amino acid sequence RASQDVNTAVA (SEQ ID NO:164); a VL CDR2 having the amino acid sequence SASFLY (SEQ ID NO:165); a VL CDR3 having the amino acid sequence QQHYTTPP (SEQ ID NO:166); a VH CDR1 having the amino acid sequence GFNIKDTY (SEQ ID NO:167); a VH CDR2 having the amino acid sequence IYPTNGYT (SEQ ID NO:168); and a VH CDR3 having the amino acid sequence SRWGGDGFYAMDY (SEQ ID NO:169).
- an anti-Her2 antibody comprises VL CDR1, VL CDR2, and VL CDR3 present in the light chain amino acid sequence provided above; and VH CDR1, CDR2, and CDR3 present in the heavy chain amino acid sequence provided above.
- an anti-CD19 antibody is a scFv.
- an anti-CD19 scFv comprises an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: DIQLTQSPASLAVSLGQRATISCKASQSVDYDGDSYLNWYQQIPGQPPKLLIYDASNLVSGIPPRF SGSGSGTDFTLNIHPVEKVDAATYHCQQSTEDPWTFGGGTKLEIKGGGGSGGGGSGGGGSQVQ LQQSGAELVRPGSSVKISCKASGYAFSSYWMNWVKQRPGQGLEWIGQIWPGDGDTNYNGKFK GKATLTADESSSTAYMQLSSLASEDSAVYFCARRETTTVGRYYYAMDYWGQGTTVTVS (SEQ ID NO:187).
- Anti-mesothelin antibodies are known in the art, see, e.g., U.S.2019/0000944; WO 2009/045957; WO 2014/031476; USPN 8,460,660; US 2013/0066055; and WO 2009/068204.
- an anti-mesothelin antibody comprises: a) a light chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00271] DIALtqpasvsgspgqsitisctgtssdiggynsvswyqqhpgkapklmiygvnnrpsgvsnrfsgsksgntasltisglqaedead yycssydiesatpvfgggtkltvlgqpkaapsvtlfppsseelqankatlvclisdfypgavtvawkgdsspvkagvetttpskqsnNkyaassyls ltpeqwkshrsyscqvthegstvektvaptEss (SEQ ID
- an anti-mesothelin antibody comprises VL CDR1, VL CDR2, and VL CDR3 present in the light chain amino acid sequence provided above; and VH CDR1, CDR2, and CDR3 present in the heavy chain amino acid sequence provided above.
- an anti-mesothelin antibody can comprise a VL CDR1 having the amino acid sequence tgtssdiggynsvs (SEQ ID NO:219); a VL CDR2 having the amino acid sequence Lmiygvnnrps (SEQ ID NO:220); a VL CDR3 having the amino acid sequence ssydiesatp (SEQ ID NO:221); a VH CDR1 having the amino acid sequence gysftsywig (SEQ ID NO:222); a VH CDR2 having the amino acid sequence wmgiidpgdsrtrysp (SEQ ID NO:223); and a VH CDR3 having the amino acid sequence gqlyggtymdg (SEQ ID NO:224).
- An anti-mesothelin antibody can be a scFv.
- an anti-mesothelin scFv can comprise the following amino acid sequence: QVQLQQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGRINPNSGGTNYA QKFQGRVTMTRDTSISTAYMELSRLRSEDTAVYYCARGRYYGMDVWGQGTMVTVSSGGGGS GGGGSGGGGSGGGGSEIVLTQSPATLSLSPGERATISCRASQSVSSNFAWYQQRPGQAPRLLIYD ASNRATGIPPRFSGSGSGTDFTLTISSLEPED FAAYYCHQRSNWLYTFGQGTKVDIK (SEQ ID NO:225), where VH CDR1, CDR2, and CDR3 are underlined; and VL CDR1, CDR2, and CDR3 are bolded and underlined.
- an anti-mesothelin scFv can comprise the following amino acid sequence: QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNY AQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARDLRRTVVTPRAYYGMDVWGQGTTV TVSSGGGGSGGGGSGGGGSGGSDIQLTQSPSTLSASVGDRVTITCQASQDISNSLNWYQQKA GKAPKLLIYDASTLETGVPSRFSGSGSGTDFSF TISSLQPEDIATYYCQQHDNLPLTFGQGTKVEIK (SEQ ID NO:226), where VH CDR1, CDR2, and CDR3 are underlined; and VL CDR1, CDR2, and CDR3 are bolded and underlined.
- CD22 also known as B-Lymphocyte Cell Adhesion Molecule, Sialic Acid-Binding Ig-Like Lectin 2, or SIGLEC2
- B-Lymphocyte Cell Adhesion Molecule Sialic Acid-Binding Ig-Like Lectin 2, or SIGLEC2
- SIGLEC2 Sialic Acid-Binding Ig-Like Lectin 2, or SIGLEC2
- Anti-CD22 antibodies are known in the art; and the VH and VL, or the VH and VL CDRs, of any anti-CD22 antibody can be used. See, e.g., Xiao et al. (2009) Mabs 1:297 (describing the fully human anti-CD22 m971 scFv); and U.S.
- Patent Publication No.2020/0147134 examples include epratuzumab and inotuzumab. See, e.g., Lenoard et al. (2007) Oncogene 26:3704 and U.S. Patent No.5,789,554 (describing epratuzumab); and DiJoseph et al. (2007) Leukemia 21:2240 (describing inotuzumab).
- an anti-CD22 antibody can comprise: i) a heavy chain variable region (VH) CDR1 having the amino acid sequence: GDSVSSNSAA (SEQ ID NO:227); ii) a VH CDR2 having the amino acid sequence: TYYRSKWYN (SEQ ID NO:228); iii) a VH CDR3 having the amino acid sequence: AREVTGDLEDAFDI (SEQ ID NO:229); iv) a light chain variable region (VL) CDR1 having the amino acid sequence: QTIWSY (SEQ ID NO:230); v) a VL CDR2 having the amino acid sequence: AAS (Ala- Ala-Ser); and vi) a VL CDR3 having the amino acid sequence: QQSYSIPQT (SEQ ID NO:231).
- VH heavy chain variable region
- Trophoblast cell surface antigen 2 (also known as epithelial glycoprotein-1, gastrointestinal tumor-associated antigen GA733-1, membrane component chromosome 1 surface marker-1, and tumor-associated calcium signal transducer-2) is a transmembrane glycoprotein that is upregulated in numerous cancer types and is the protein product of the TACSTD2 gene.
- Trop-2 also known as epithelial glycoprotein-1, gastrointestinal tumor-associated antigen GA733-1, membrane component chromosome 1 surface marker-1, and tumor-associated calcium signal transducer-2
- Anti-TROP-2 antibodies are known in the art; and the VH and VL, or the VH and VL CDRs, of any anti-TROP-2 antibody can be used. See, e.g., U.S. Patent No.7,238,785).
- an anti- TROP-2 antibody comprises: i) light chain CDR sequences CDR1 (KASQDVSIAVA; SEQ ID NO:232); CDR2 (SASYRYT; SEQ ID NO:233); and CDR3 (QQHYITPLT; SEQ ID NO:234); and ii) heavy chain CDR sequences CDR1 (NYGMN; SEQ ID NO:235); CDR2 (WINTYTGEPTYTDDFKG; SEQ ID NO:236); and CDR3 (GGFGSSYWYFDV; SEQ ID NO:237).
- an anti-TROP2 antibody comprises: a) VL CDR1, VL CDR2, and VL CDR3 present in a light chain variable region (VL) comprising the following amino acid sequence: DIQLTQSPSSLSASVGDRVSITCKASQDVSIAVAWYQQKPGKAPKLLIYSASYRYTGVPDRFSGS GSGTDFTLTISSLQPEDFAVYYCQQHYITPLTFGAGTKVEIK (SEQ ID NO:244); and b) VH CDR1, CDR2, and CDR3 present in a heavy chain variable region (VH) comprising the following amino acid sequence: QVQLQQSGSELKKPGASVKVSCKASGYTFTNYGMNWVKQAPGQGLKWMGWINTYTGEPTYT DDFKGRFAFSLDTSVSTAYLQISSLKADDTAVYFCARGGFGSSYWYFDVWGQGSLVTVSS (SEQ ID NO:245).
- an anti-TROP-2 antibody comprises: a) a VL region comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: DIQLTQSPSSLSASVGDRVSITCKASQDVSIAVAWYQQKPGKAPKLLIYSASYRYTGVPDRFSGS GSGTDFTLTISSLQPEDFAVYYCQQHYITPLTFGAGTKVEIK (SEQ ID NO:244); and b) a VH region comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QVQLQQSGSELKKPGASVKVSCKASGYTFTNYGMNWVKQAPGQGLKWMGWINTYTGEPTYT DDFKGRFAFSLDTSVSTAYLQISSLKADDTAVYFCARGGFGSSYWYFDVWGQ
- Anti-BCMA B-cell maturation antigen
- VH and VL or the VH and VL CDRs, of any anti-BCMA antibody can be used. See, e.g., WO 2014/089335; US 2019/0153061; and WO 2017/093942.
- an anti-BCMA antibody comprises: a) a light chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00289] qsvltqppsasgtpgqrvtiscsgsssnigsntvnwyqqlpgtapkllifnyhqrpsgvpdrfsgsksgssaslaisglqsedeadyycaa wddslngwvfgggtkltvlgqpkaapsvtlfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpdskqsnnkyaassylsltp eqwkshrsyscqvthegSTVEKTVAPTECS (SEQ ID NO
- an anti-BCMA antibody comprises a VL present in the light chain amino acid sequence provided above; and a VH present in the heavy chain amino acid sequence provided above.
- an anti-BCMA antibody can comprise: a) a VL comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: [00292] qsvltqppsasgtpgqrvtiscsgsssnigsntvnwyqqlpgtapkllifnyhqrpsgvpdrfsgsksgsslaisglqsedeadyycaa wddslngwvfgggtkltvlG (SEQ ID NO:250); and b) a VH comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid
- an anti-BCMA antibody comprises VL CDR1, VL CDR2, and VL CDR3 present in the light chain amino acid sequence provided above; and VH CDR1, CDR2, and CDR3 present in the heavy chain amino acid sequence provided above.
- an anti-BCMA antibody can comprise a VL CDR1 having the amino acid sequence ssnigsnt (SEQ ID NO:252), a VL CDR2 having the amino acid sequence NYH, a VL CDR3 having the amino acid sequence aawddslngwv (SEQ ID NO:253)), a VH CDR1 having the amino acid sequence gftfgdya (SEQ ID NO:254), a VH CDR2 having the amino acid sequence srskayggtt (SEQ ID NO:255), and a VH CDR3 having the amino acid sequence assgyssgwtpfdy (SEQ ID NO:256).
- an anti-BCMA antibody can comprise a VL CDR1 having the amino acid sequence SASQDISNYLN (SEQ ID NO:259); a VL CDR2 having the amino acid sequence YTSNLHS (SEQ ID NO:260); a VL CDR3 having the amino acid sequence QQYRKLPWT (SEQ ID NO:261); a VH CDR1 having the amino acid sequence NYWMH (SEQ ID NO:262); a VH CDR2 having the amino acid sequence ATYRGHSDTYYNQKFKG (SEQ ID NO:263); and a VH CDR3 having the amino acid sequence GAIYNGYDVLDN (SEQ ID NO:264).
- an anti-BCMA antibody comprises: a) a light chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKLLIYYTSNLHSGVPSRFSGS GSGTDFTLTISSLQPEDFATYYCQQYRKLPWTFGQGTKLEIKR (SEQ ID NO:265).
- an anti-MUC16 antibody can comprise a VH CDR1 having the amino acid sequence GFTFSNYY (SEQ ID NO:267); a VH CDR2 having the amino acid sequence ISGRGSTI (SEQ ID NO:268); a VH CDR3 having the amino acid sequence VKDRGGYSPY (SEQ ID NO:269); a VL CDR1 having the amino acid sequence QSISTY (SEQ ID NO:270); a VL CDR2 having the amino acid sequence TAS; and a VL CDR3 having the amino acid sequence QQSYSTPPIT (SEQ ID NO:271). See, e.g., US 2018/0118848.
- an antibody is specific for claudin-18 isoform 2 (“claudin-18.2”). See, e.g., WO 2013/167259.
- a claudin-18.2-specific antibody is a scFv.
- a claudin-18.2- specific antibody is a nanobody.
- an anti-claudin-18.2 antibody can comprise a VH CDR1 having the amino acid sequence GYTFTDYS (SEQ ID NO:272); a VH CDR2 having the amino acid sequence INTETGVP (SEQ ID NO:273); a VH CDR3 having the amino acid sequence ARRTGFDY (SEQ ID NO:274); a VL CDR1 having the amino acid sequence KNLLHSDGITY (SEQ ID NO:275); a VL CDR2 having the amino acid sequence RVS; and a VL CDR3 having the amino acid sequence VQVLELPFT (SEQ ID NO:276).
- an anti-claudin-18.2 antibody can comprise a VH CDR1 having the amino acid sequence GFTFSSYA (SEQ ID NO:277); a VH CDR2 having the amino acid sequence ISDGGSYS (SEQ ID NO:278); a VH CDR3 having the amino acid sequence ARDSYYDNSYVRDY (SEQ ID NO:279); a VL CDR1 having the amino acid sequence QDINTF (SEQ ID NO:280); a VL CDR2 having the amino acid sequence RTN; and a VL CDR3 having the amino acid sequence LQYDEFPLT (SEQ ID NO:281).
- antibodies include, but are not limited to: Natalizumab (Tysabri®; Biogen Idec/Elan) targeting ⁇ 4 subunit of ⁇ 4 ⁇ 1 and ⁇ 4 ⁇ 7 integrins (used in the treatment of MS and Crohn's disease); Vedolizumab (MLN2; Millennium Pharmaceuticals/Takeda) targeting ⁇ 4 ⁇ 7 integrin (as used in the treatment of UC and Crohn's disease); Belimumab (Benlysta; Human Genome Sciences/ GlaxoSmithKline) targeting BAFF (as used in the treatment of SLE); Atacicept (TACI–Ig; Merck/Serono) targeting BAFF and APRIL (as used in the treatment of SLE); Alefacept (Amevive®; Astellas) targeting CD2 (as used in the treatment of Plaque psoriasis, GVHD); Otelixizumab (TRX4; Tolerx/GlaxoSmithKline)
- the antibody whose production is induced by the intracellular domain of a synNotch polypeptide of the present disclosure is a therapeutic antibody for the treatment of cancer.
- Such antibodies include, e.g., Ipilimumab targeting CTLA-4 (as used in the treatment of Melanoma, Prostate Cancer, RCC); Tremelimumab targeting CTLA-4 (as used in the treatment of CRC, Gastric, Melanoma, NSCLC); Nivolumab targeting PD-1 (as used in the treatment of Melanoma, NSCLC, RCC); MK-3475 targeting PD-1 (as used in the treatment of Melanoma); Pidilizumab targeting PD-1 (as used in the treatment of Hematologic Malignancies); BMS-936559 targeting PD-L1 (as used in the treatment of Melanoma, NSCLC, Ovarian, RCC); MEDI4736 targeting PD-L1; MPDL33280A targeting PD-L1 (as used in the
- antibodies include, but are not limited to: Abagovomab, Abciximab, Abituzumab, Abrilumab, Actoxumab, Aducanumab, Afelimomab, Afutuzumab, Alacizumab pegol, ALD518, Alirocumab, Altumomab pentetate, Amatuximab, Anatumomab mafenatox, Anetumab ravtansine, Anifrolumab, Anrukinzumab, Apolizumab, Arcitumomab, Ascrinvacumab, Aselizumab, Atezolizumab, Atinumab, Atlizumab/ tocilizumab, Atorolimumab, Bapineuzumab, Basiliximab, Bavituximab, Bectumomab, Begelomab, Benralizuma
- an EDV of the present disclosure comprises an antibody mimetic (also referred to as an “antibody analog”).
- antibody mimetics include peptide aptamers, affimers, affilins, affibodies, affitins, alphabodies, anticalins, avimers, DARPins, fynomers, Kunitz domain peptides, nanoCLAMPs, affinity reagents, and scaffold proteins.
- Nucleic acid-binding polypeptides [00309] As noted above, the present disclosure provides EDVs comprising a nucleic acid-binding effector polypeptide, and collections of one or more nucleic acids that encode the nucleic acid-binding effector polypeptide. The present disclosure also provides methods of delivery and production of such. [00310] Suitable nucleic acid binding effector polypeptides include nucleases.
- Suitable nucleases include, but are not limited to, a homing nuclease polypeptide; a FokI polypeptide; a transcription activator-like effector nuclease (TALEN) polypeptide; a MegaTAL polypeptide; a meganuclease polypeptide; a zinc finger nuclease (ZFN); an ARCUS nuclease; a Transposon-encoded type nuclease such as TnpB or IscB (see, e.g., Meers et al., Nature.2023 Oct;622(7984):863-871 and Jiang et al., Sci Adv.2023 Sep 29;9(39):eadk0171), a serine recombinase or tyrosine recombinase (e.g., a site-specific recombinase such as Cre recombinase, Dre recombinas
- an EDV of the present disclosure comprises a CRISPR-Cas effector polypeptide (e.g., a nucleic acid-binding effector polypeptide is in some cases a CRISPR-Cas effector polypeptide).
- the CRISPR-Cas effector polypeptide can be any of a variety of CRISPR-Cas effector polypeptides. Suitable CRISPR-Cas effector polypeptides are described in detail below.
- the CRISPR-Cas effector polypeptide is a type II CRISPR-Cas effector polypeptide.
- the type II CRISPR-Cas effector polypeptide is a Cas9 polypeptide.
- the CRISPR-Cas effector polypeptide is a type V CRISPR-Cas effector polypeptide, e.g., a Cas12a, a Cas12b, a Cas12c, a Cas12d, or a Cas12e polypeptide.
- the CRISPR-Cas effector polypeptide is a type VI CRISPR-Cas effector polypeptide, e.g., a Cas13a polypeptide, a Cas13b polypeptide, a Cas13c polypeptide, or a Cas13d polypeptide.
- the CRISPR-Cas effector polypeptide is a Cas14 polypeptide. In some cases, the CRISPR-Cas effector polypeptide is a Cas14a polypeptide, a Cas14b polypeptide, or a Cas14c polypeptide. Also suitable for use is a variant CRISPR- Cas effector polypeptide, where the variant CRISPR-Cas effector polypeptide has reduced nucleic acid cleavage activity.
- CRISPR-Cas effector fusion polypeptide comprising: i) a CRISPR-Cas effector polypeptide is a variant that has reduced nucleic acid cleavage activity; and ii) a heterologous fusion polypeptide.
- the heterologous fusion polypeptide is a protein modifying enzyme.
- the heterologous fusion polypeptide is a nucleic acid modifying enzyme.
- the heterologous fusion polypeptide is a reverse transcriptase.
- the heterologous fusion polypeptide is a cytidine deaminase.
- the heterologous fusion polypeptide is an adenine deaminase. In some cases, the heterologous fusion polypeptide is a transcription factor. In some cases, the heterologous fusion polypeptide is a transcription activator. In some cases, the heterologous fusion polypeptide is a transcription repressor.
- Suitable protein-modifying enzymes and nucleic acid modifying enzymes are described in detail below.
- the nucleic acid modifying enzyme is a cytidine deaminase. In some cases, the nucleic acid modifying enzyme is an adenosine deaminase. In some cases, the nucleic acid modifying enzyme is a prime editor.
- the CRISPR-Cas effector polypeptide comprises one or more nuclear localization signals.
- CRISPR-Cas effector polypeptides are CRISPR-Cas endonucleases (e.g., class 2 CRISPR-Cas effector polypeptide such as a type II, type V, or type VI CRISPR-Cas effector polypeptide).
- CRISPR-Cas effector polypeptide has endonuclease activity
- the CRISPR-Cas effector polypeptide may also be referred to as a “CRISPR-Cas endonuclease.”
- a CRISPR-Cas effector polypeptide can also have reduced or undetectable endonuclease activity.
- a CRISPR-Cas effector polypeptide can also be a fusion CRISPR-Cas effector polypeptide comprising a heterologous fusion partner.
- a suitable CRISPR-Cas effector polypeptide is a class 2 CRISPR-Cas effector polypeptide.
- a suitable CRISPR-Cas effector polypeptide is a class 2 type II CRISPR-Cas effector polypeptide (e.g., a Cas9 protein).
- a suitable CRISPR-Cas effector polypeptide is a class 2 type V CRISPR-Cas endonuclease (e.g., a Cpf1 protein (Cas12a), a C2c1 protein, or a C2c3 protein).
- a suitable CRISPR-Cas effector polypeptide is a class 2 type VI CRISPR-Cas effector polypeptide (e.g., a C2c2 protein; also referred to as a “Cas13a” protein).
- a CasX protein also referred to as a “Cas12e” protein.
- a CasY protein also referred to as a “Cas12d” protein.
- a suitable CRISPR-Cas effector polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence of any one of SEQ ID NOs: 137-152.
- the CRISPR-Cas effector polypeptide is a Type II CRISPR-Cas effector polypeptide.
- the CRISPR-Cas effector polypeptide is a Cas9 polypeptide.
- the Cas9 protein is guided to a target site (e.g., stabilized at a target site) within a target nucleic acid sequence (e.g., a chromosomal sequence or an extrachromosomal sequence, e.g., an episomal sequence, a minicircle sequence, a mitochondrial sequence, a chloroplast sequence, etc.) by virtue of its association with the protein-binding segment of the Cas9 guide RNA.
- a target nucleic acid sequence e.g., a chromosomal sequence or an extrachromosomal sequence, e.g., an episomal sequence, a minicircle sequence, a mitochondrial sequence, a chloroplast sequence, etc.
- a Cas9 polypeptide comprises an amino acid sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, at least 99%, or more than 99%, amino acid sequence identity to the Streptococcus pyogenes Cas9 of SEQ ID NO: 137.
- the Cas9 polypeptide is a Staphylococcus aureus Cas9 (saCas9) polypeptide.
- the saCas9 polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the saCas9 amino acid sequence of SEQ ID NO: 143.
- a suitable CRISPR-Cas effector polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence of any one of SEQ ID NOs: 137-152.
- a suitable CRISPR-Cas effector polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence of any one of SEQ ID NOs: 137-143.
- a suitable Cas9 polypeptide is a high-fidelity (HF) Cas9 polypeptide. Kleinstiver et al. (2016) Nature 529:490. For example, amino acids N497, R661, Q695, and Q926 of the amino acid sequence of SEQ ID NO: 137 are substituted, e.g., with alanine.
- an HF Cas9 polypeptide can comprise an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence of SEQ ID NO:137, where amino acids N497, R661, Q695, and Q926 are substituted, e.g., with alanine.
- a suitable Cas9 polypeptide exhibits altered PAM specificity. See, e.g., Kleinstiver et al. (2015) Nature 523:481.
- a suitable CRISPR-Cas effector polypeptide is a type V CRISPR-Cas effector polypeptide.
- a type V CRISPR-Cas effector polypeptide is a Cpf1 protein (also known as Cas12a).
- a Cpf1 protein comprises an amino acid sequence having at least 30%, at least 35%, at least 40%, at least 45%, 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 95%, at least 90%, or 100%, amino acid sequence identity to the Cpf1 amino acid sequence of SEQ ID NOs: 144-146.
- a suitable CRISPR-Cas effector polypeptide is a CasX or a CasY polypeptide.
- a suitable CRISPR-Cas effector polypeptide is a fusion protein comprising a CRISPR-Cas effector polypeptide that is fused to a heterologous polypeptide (also referred to as a “fusion partner”).
- a CRISPR-Cas effector polypeptide is fused to an amino acid sequence (a fusion partner) that provides for subcellular localization, i.e., the fusion partner is a subcellular localization sequence (e.g., one or more nuclear localization signals (NLSs) for targeting to the nucleus, two or more NLSs, three or more NLSs, 4 or more NLSs, 5 or more NLSs, 6 or more NLSs, 7 or more NLSs, 8 or more NLSs, 9 or more NLSs, or 10 or more NLSs.
- a subcellular localization sequence e.g., one or more nuclear localization signals (NLSs) for targeting to the nucleus, two or more NLSs, three or more NLSs, 4 or more NLSs, 5 or more NLSs, 6 or more NLSs, 7 or more NLSs, 8 or more NLSs, 9 or more NLSs, or 10 or more NLSs.
- NLSs nuclear localization signals
- a guide RNA includes two separate nucleic acid molecules: an “activator” and a “targeter” and is referred to herein as a “dual guide RNA”, a “double-molecule guide RNA”, a “two- molecule guide RNA”, or a “dgRNA.”
- the guide RNA is one molecule (e.g., for some class 2 CRISPR-Cas proteins, the corresponding guide RNA is a single molecule; and in some cases, an activator and targeter are covalently linked to one another, e.g., via intervening nucleotides), and the guide RNA is referred to as a “single guide RNA”, a “single-molecule guide RNA,” a “one-molecule guide RNA”, or simply “sgRNA.”
- an EDV of the present disclosure comprises a CRISPR-Cas effector polypeptide, or both a CRISPR-Cas effector poly
- an EDV when said to include a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a, it is to be understood that such encompasses an EDV that includes an RNP.
- a target nucleic acid comprises a deleterious mutation in a defective allele (e.g., a deleterious mutation in a target nucleic acid)
- the CRISPR-Cas effector polypeptide/guide RNA complex together with a donor nucleic acid comprising a nucleotide sequence that corrects the deleterious mutation (e.g., a donor nucleic acid comprising a nucleotide sequence that encodes a functional copy of the protein encoded by the defective allele), can be used to correct the deleterious mutation, e.g., via homology-directed repair (HDR).
- HDR homology-directed repair
- an EDV of the present disclosure comprises: i) a CRISPR-Cas effector polypeptide; and ii) a guide RNA.
- the guide RNA is a single-molecule (or “single guide”) guide RNA (an “sgRNA”).
- the guide RNA is a dual-molecule (or “dual-guide”) guide RNA (“dgRNA”).
- an EDV of the present disclosure comprises: i) a CRISPR-Cas effector polypeptide; and ii) 2 or more gRNAs, where the two or more gRNAs can, e.g., provide for multiplexed gene knockout, e.g., each of the 2 or more guide RNAs can be targeted to a different gene (or in some cases to two different sequences of the same gene).
- the guide RNAs are sgRNAs.
- the guide RNAs are dgRNAs.
- an EDV of the present disclosure comprises: i) a CRISPR-Cas effector polypeptide; and ii) 2 separate sgRNAs, where the 2 separate sgRNAs provide for deletion (“knockout”) of a target nucleic acid via non-homologous end joining (NHEJ).
- the guide RNAs are sgRNAs.
- the guide RNAs are dgRNAs.
- an EDV of the present disclosure does not include a guide RNA.
- Class 2 CRISPR-Cas effector polypeptides [00326]
- the functions of the effector complex e.g., the cleavage of target DNA
- the functions of the effector complex are carried out by a single endonuclease (e.g., see Zetsche et al., Cell.2015 Oct 22;163(3):759-71; Makarova et al., Nat Rev Microbiol.2015 Nov;13(11):722-36; Shmakov et al., Mol Cell.2015 Nov 5;60(3):385-97); and Shmakov et al. (2017) Nature Reviews Microbiology 15:169.
- class 2 CRISPR-Cas protein is used herein to encompass the CRISPR-Cas effector polypeptide (e.g., the target nucleic acid cleaving protein) from class 2 CRISPR systems.
- class 2 CRISPR- Cas effector polypeptide as used herein encompasses type II CRISPR-Cas effector polypeptides (e.g., Cas9); type V-A CRISPR-Cas effector polypeptides (e.g., Cpf1 (also referred to a “Cas12a”)); type V-B CRISPR-Cas effector polypeptides (e.g., C2c1 (also referred to as “Cas12b”)); type V-C CRISPR-Cas effector polypeptides (e.g., C2c3 (also referred to as “Cas12c”)); type V-U1 CRISPR-Cas effector polypeptides
- class 2 CRISPR-Cas effector polypeptides encompass type II, type V, and type VI CRISPR-Cas effector polypeptides, but the term is also meant to encompass any class 2 CRISPR-Cas effector polypeptide suitable for binding to a corresponding guide RNA and forming an RNP complex.
- a nucleic acid-binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a
- a fusion polypeptide comprising: i) the nucleic acid-binding effector polypeptide; and ii) one or more heterologous fusion partners (one or more heterologous fusion polypeptides).
- a fusion nucleic acid-binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a
- Suitable localization signals include, e.g., a nuclear localization signal (NLS) for targeting to the nucleus; a sequence to keep the fusion protein out of the nucleus, e.g., a nuclear export sequence (NES); a sequence to keep the fusion protein retained in the cytoplasm; a mitochondrial localization signal for targeting to the mitochondria; a chloroplast localization signal for targeting to a chloroplast; an endoplasmic reticulum (ER) retention signal; and ER export signal; and the like.
- NLS nuclear localization signal
- NES nuclear export sequence
- mitochondrial localization signal for targeting to the mitochondria
- chloroplast localization signal for targeting to a chloroplast
- ER endoplasmic reticulum
- a fusion CRISPR-Cas effector polypeptide does not include a NLS so that the protein is not targeted to the nucleus (which can be advantageous, e.g., when the target nucleic acid is an RNA that is present in the cytosol).
- a fusion nucleic acid-binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a
- a suitable NES comprises hydrophobic amino acid residues, e.g., LXXXLXXLXL (SEQ ID NO:207), where L is a hydrophobic amino acid residue (e.g., Leu) and X is any other amino acid.
- Suitable NESs are known in the art; see, e.g., Xu et al. (2012) Mol. Biol. Cell 23:3677.
- Non-limiting examples of suitable NESs include: LPPLERLTL (SEQ ID NO:188); LALKLAGLDL (SEQ ID NO:189); LSQALASSFSV (SEQ ID NO:190); NELALKLAGLDI (SEQ ID NO:191).
- the NES comprises the amino acid sequence LPPLERLTL (SEQ ID NO:188).
- the nucleic acid-binding effector polypeptide is a Cas9 protein having multiple NESs (e.g., 3 NESs), and multiple NLSs (e.g., about 7 NLSs).
- a fusion CRISPR-Cas effector polypeptide includes (is fused to) a nuclear localization signal (NLS) (e.g., in some cases 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs).
- NLS nuclear localization signal
- a fusion polypeptide includes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs).
- one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus and/or the C-terminus.
- one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the C-terminus.
- one or more NLSs (3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) both the N-terminus and the C- terminus. In some cases, an NLS is positioned at the N-terminus and an NLS is positioned at the C- terminus.
- a fusion CRISPR-Cas effector polypeptide includes (is fused to) from 1 to 10 NLSs (e.g., 1-9, 1-8, 1-7, 1-6, 1-5, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, 4-10, 4-9, 4-8, 4-7, 5-10, 5-9, or 5-8 NLSs).
- a fusion CRISPR-Cas effector polypeptide includes (is fused to) from 2 to 5 NLSs (e.g., 2-4 NLSs, or 2-3 NLSs).
- a fusion CRISPR-Cas effector polypeptide includes (is fused to) about 4 NLSs.
- a fusion CRISPR-Cas effector polypeptide includes (is fused to) about 7 NLSs.
- a nucleic acid-binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a
- a Gag polypeptide e.g., as a Gag-Cas9 polyprotein.
- the fusion protein includes one or more heterologous protease cleavage sites between the gag polyprotein and the nucleic acid-binding effector polypeptide (e.g., the CRISPR-Cas effector polypeptide such as Cas9 or Cas12a).
- the CRISPR-Cas effector polypeptide such as Cas9 or Cas12a.
- Many protease cleavage sites will be known to one of ordinary skill in the art, and any convenient cleavage site can be used.
- a fusion CRISPR-Cas effector polypeptide comprises: i) a lentiviral Gag polypeptide; ii) a nuclear export signal peptide; iii) 2 copies of an NLS; and iv) a CRISPR-Cas effector polypeptide.
- Non-limiting examples of nucleotide sequences encoding Gag-Cas9 fusion polypeptides with NES and/or NLS are provided in FIG.14A-14D.
- FIG.14E provides an example of a Gag-Cas9 fusion polypeptide with 3 NES and 2 NLS.
- the CRISPR-Cas effector polypeptide (e.g., Cas9) has more than 2 NLSs, e.g., in some cases 3, 4, 5, 6, 7, 8, 9, or 10 NLSs.
- the CRISPR-Cas effector polypeptide (e.g., Cas9) has multiple NESs (e.g., in some cases 2, 3, 4, or 5 NESs).
- the CRISPR-Cas effector polypeptide e.g., Cas9 has 3 NESs and 7 NLSs.
- a gag polyprotein is a retroviral gag polyprotein (e.g., a lentiviral gag polyprotein).
- a lentiviral gag polyprotein is selected from a bovine immunodeficiency virus gag polyprotein, a simian immunodeficiency virus gag polyprotein, a feline immunodeficiency virus gag polyprotein, a human immunodeficiency virus gag polyprotein, an equine infection anemia virus gag polyprotein, and a caprine arthritis encephalitis virus gag polyprotein.
- the HIV gag polyprotein includes one or more heterologous protease cleavage sites between one or more of: i) the MA polypeptide and the CA polypeptide; ii) the CA polypeptide and the p2 polypeptide; iii) the p2 polypeptide and the NC polypeptide; iv) the NC polypeptide and the p1 polypeptide; and v) the p1 polypeptide and the p6 polypeptide.
- a lentiviral gag polyprotein is a human immunodeficiency virus (HIV) gag polyprotein comprising a p6 polypeptide.
- a lentiviral gag polyprotein is a human immunodeficiency virus (HIV) gag polyprotein comprising a MA polypeptide, a CA polypeptide, an NC polypeptide, and a p6 polypeptide.
- 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:1); the NLS from nucleoplasmin (e.g., the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ ID NO:2)); the c-myc NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO:3) or RQRRNELKRSP (SEQ ID NO:4); the hRNPA1 M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO:5); the sequence R
- an NLS comprises the amino acid sequence MDSLLMNRRKFLYQFKNVRWAKGRRETYLC (SEQ ID NO:17).
- NLS or multiple NLSs are of sufficient strength to drive accumulation of the fusion polypeptide in a detectable amount in the nucleus of a eukaryotic cell. Detection of accumulation in the nucleus may be performed by any suitable technique. For example, a detectable marker may be fused to the fusion polypeptide such that location within a cell may be visualized. 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.
- nucleic acid-binding effector polypeptide e.g., CRISPR-Cas effector polypeptide such as Cas9 harbors a mutation that reduces its catalytic activity compared to a wild-type CRISPR-Cas effector polypeptide.
- the mutation renders it a nickase and in some cases renders it catalytically inactive (“dead), e.g., a dCas9.
- a CRISPR-Cas effector protein e.g., Cas9 or Cas12a
- a CRISPR-Cas effector protein is catalytically inactivated (i.e.,‘dead’), which is referred to in the art as a dCas protein (e.g., dCas9, dCas12a).
- a dCas protein e.g., dCas9, dCas12a
- Such a protein will not exhibit the nuclease cleavage activity of the Cas effector protein, but if fused another protein, the fusion will exhibit the activity of the protein to which the ‘dead’ protein is fused (i.e., the fusion partner - the transcription activating protein). Examples of mutations to produce a dCas effector protein will be known to one of ordinary skill in the art.
- nucleic acid-binding effector polypeptide is a TnpB or IscB protein, and in some such cases the protein is a dead version (e.g., dTnpB, dIscB, and the like.)
- the nucleic acid-binding effector polypeptide e.g., CRISPR-Cas effector polypeptide such as Cas9
- the protein has nickase activity, e.g., in some cases the protein harbors a mutation in a catalytic domain such that the protein cleaves one strand of a double-stranded target nucleic acid.
- a CRISPR-Cas effector protein (e.g., a nickase or ‘dead’ version) is fused to a heterologous protein, e.g., one that has transcription repressor activity (e.g., includes a transcription repression domain) and thereby reduces transcription (and therefore expression) of a target gene.
- a nickase or dead version of a nucleic acid-binding effector polypeptide e.g., CRISPR-Cas effector polypeptide such as Cas9 or Cas12a
- a heterologous protein e.g., one having a catalytic activity or transcription modulation activity.
- a CRISPR-Cas effector protein e.g., a nickase or ‘dead’ version
- a heterologous protein that has transcription activating activity (e.g., includes a transcription activation domain) and thereby increases transcription (and therefore expression) of a target gene.
- a nucleic acid-binding effector polypeptide can be used to modify target nucleic acids (e.g., DNA and/or RNA) in a variety of ways without creating a double strand break (DSB) in the target DNA.
- the fusion partner is a protein (or a domain from a protein) that inhibits transcription (e.g., a transcriptional repressor, a protein that functions via recruitment of transcription inhibitor proteins, modification of target DNA such as methylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histones, and the like).
- a transcriptional repressor a protein that functions via recruitment of transcription inhibitor proteins, modification of target DNA such as methylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histones, and the like.
- the fusion partner is a protein (or a domain from a protein) that increases transcription (e.g., a transcription activator, a protein that acts via recruitment of transcription activator proteins, modification of target DNA such as demethylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histones, and the like).
- the fusion partner is a reverse transcriptase.
- the fusion partner is a base editor.
- the fusion partner is a deaminase.
- a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) includes a heterologous polypeptide that has enzymatic activity that modifies a target nucleic acid (e.g., nuclease activity, methyltransferase activity, demethylase activity, DNA repair activity, DNA damage activity, deamination activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity, transposase activity, recombinase activity, polymerase activity, ligase activity, helicase activity, photolyase activity, or glycosylase activity).
- a target nucleic acid e.g., nuclease activity, methyltransferase activity, demethylase activity, DNA repair activity, DNA damage activity, deamination activity, dismutase activity, alkylation activity,
- a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) includes a heterologous polypeptide that has enzymatic activity that modifies a polypeptide (e.g., a histone) associated with a target nucleic acid (e.g., methyltransferase activity, demethylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity or demyristoylation activity).
- a target nucleic acid e.g., methyltransferase activity, demethylase activity, acetyltransferase activity,
- proteins (or fragments thereof) that can be used in increase transcription include but are not limited to: transcriptional activators such as VP16, VP64, VP48, VP160, p65 subdomain (e.g., from NFkB), and activation domain of EDLL and/or TAL activation domain (e.g., for activity in plants); histone lysine methyltransferases such as SET1A, SET1B, MLL1 to 5, ASH1, SYMD2, NSD1, and the like; histone lysine demethylases such as JHDM2a/b, UTX, JMJD3, and the like; histone acetyltransferases such as GCN5, PCAF, CBP, p300, TAF1, TIP60/PLIP, MOZ/MYST3, MORF/MYST4, SRC1, ACTR, P160, CLOCK, and the like; and DNA demethylases such as Ten-Eleven Translocation (TET) di
- transcriptional activators
- the fusion partner has enzymatic activity that modifies the target nucleic acid (e.g., ssRNA, dsRNA, ssDNA, dsDNA).
- enzymatic activity that can be provided by the fusion partner include but are not limited to: nuclease activity such as that provided by a restriction enzyme (e.g., FokI nuclease), methyltransferase activity such as that provided by a methyltransferase (e.g., HhaI DNA m5c-methyltransferase (M.HhaI), DNA methyltransferase 1 (DNMT1), DNA methyltransferase 3a (DNMT3a), DNA methyltransferase 3b (DNMT3b), METI, DRM3 (plants), ZMET2, CMT1, CMT2 (plants), and the like); demethylase activity such as that provided by a demethylase (e.g., Ten
- enzymatic activity that modifies a protein associated with a target nucleic acid
- enzymatic activity that modifies a protein associated with a target nucleic acid
- methyltransferase activity such as that provided by a histone methyltransferase (HMT) (e.g., suppressor of variegation 3-9 homolog 1 (SUV39H1, also known as KMT1A), Vietnamese histone lysine methyltransferase 2 (G9A, also known as KMT1C and EHMT2), SUV39H2, ESET/SETDB1, and the like, SET1A, SET1B, MLL1 to 5, ASH1, SYMD2, NSD1, DOT1L, Pr-SET7/8, SUV4-20H1, EZH2, RIZ1), demethylase activity such as that provided by a histone demethylase (e.g., Lysine Demethylase 1A (KDM1A also known as LSD1), JHDM2a/
- a suitable fusion partners are dihydrofolate reductase (DHFR) destabilization domain (e.g., to generate a chemically controllable fusion polypeptide), and a chloroplast transit peptide.
- DHFR dihydrofolate reductase
- a Nucleic acid-binding effector fusion polypeptide comprises: a) a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas polypeptide such as Cas9 or Cas12a); and b) a chloroplast transit peptide.
- a ribonucleoprotein (RNP) complex comprising a CRISPR-Cas effector polypeptide of the present disclosure and a guide RNA
- RNP ribonucleoprotein
- this targeting may be achieved by the presence of an N-terminal extension, called a chloroplast transit peptide (CTP) or plastid transit peptide.
- CTP chloroplast transit peptide
- Chromosomal transgenes from bacterial sources must have a sequence encoding a CTP sequence fused to a sequence encoding an expressed polypeptide if the expressed polypeptide is to be compartmentalized in the plant plastid (e.g. chloroplast).
- localization of an exogenous polypeptide to a chloroplast is often 1 accomplished by means of operably linking a polynucleotide sequence encoding a CTP sequence to the 5' region of a polynucleotide encoding the exogenous polypeptide.
- the CTP is removed in a processing step during translocation into the plastid. Processing efficiency may, however, be affected by the amino acid sequence of the CTP and nearby sequences at the amino terminus of the peptide.
- Other options for targeting to the chloroplast which have been described are the maize cab-m7 signal sequence (U.S. Pat.
- heterologous polypeptides include, but are not limited to, a polypeptide that directly and/or indirectly provides for increased or decreased transcription and/or translation of a target nucleic acid (e.g., a transcription activator or a fragment thereof, a protein or fragment thereof that recruits a transcription activator, a small molecule/drug-responsive transcription and/or translation regulator, a translation-regulating protein, etc.).
- a target nucleic acid e.g., a transcription activator or a fragment thereof, a protein or fragment thereof that recruits a transcription activator, a small molecule/drug-responsive transcription and/or translation regulator, a translation-regulating protein, etc.
- heterologous polypeptides to accomplish increased or decreased transcription include transcription activator and transcription repressor domains.
- a CRISPR-Cas fusion polypeptide is targeted by the guide nucleic acid (guide RNA) to a specific location (i.e., sequence) in the target nucleic acid and exerts locus-specific regulation such as blocking RNA polymerase binding to a promoter (which selectively inhibits transcription activator function), and/or modifying the local chromatin status (e.g., when a fusion sequence is used that modifies the target nucleic acid or modifies a polypeptide associated with the target nucleic acid).
- the changes are transient (e.g., transcription repression or activation).
- heterologous polypeptide can include the entire protein or in some cases can include a fragment of the protein (e.g., a functional domain).
- the heterologous polypeptide can be any domain capable of interacting with ssRNA (which, for the purposes of this disclosure, includes intramolecular and/or intermolecular secondary structures, e.g., double-stranded RNA duplexes such as hairpins, stem-loops, etc.), whether transiently or irreversibly, directly or indirectly, including but not limited to an effector domain selected from the group comprising; Endonucleases (for example RNase III, the CRR22 DYW domain, Dicer, and PIN (PilT N-terminus) domains from proteins such as SMG5 and SMG6); proteins and protein domains responsible for stimulating RNA cleavage (for example CPSF, CstF, CFIm and CFIIm); Exonucleases (for example XRN-1 or Exonucle
- the hnRNP protein hnRNP Al binds to exonic splicing silencers (ESSs) through its RRM domains and inhibits exon inclusion through a C-terminal Glycine-rich domain.
- Some splicing factors can regulate alternative use of splice site (ss) by binding to regulatory sequences between the two alternative sites.
- ss splice site
- ASF/SF2 can recognize ESEs and promote the use of intron proximal sites
- hnRNP Al can bind to ESSs and shift splicing towards the use of intron distal sites.
- One application for such factors is to generate ESFs that modulate alternative splicing of endogenous genes, particularly disease associated genes.
- Bcl-x pre-mRNA produces two splicing isoforms with two alternative 5' splice sites to encode proteins of opposite functions.
- the long splicing isoform Bcl-xL is a potent apoptosis inhibitor expressed in long-lived postmitotic cells and is up-regulated in many cancer cells, protecting cells against apoptotic signals.
- the short isoform Bcl-xS is a pro-apoptotic isoform and expressed at high levels in cells with a high turnover rate (e.g., developing lymphocytes).
- a nucleic acid-binding effector fusion polypeptide comprises: i) a nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) a heterologous polypeptide (a “fusion partner”), where the heterologous polypeptide is a nuclease.
- a nucleic acid-binding effector fusion polypeptide comprises a nucleic acid binding effector polypeptide.
- Suitable nucleic acid binding effector polypeptides can be nucleases including, but not limited to, a homing nuclease polypeptide; a FokI polypeptide; a transcription activator-like effector nuclease (TALEN) polypeptide; a MegaTAL polypeptide; a meganuclease polypeptide; a zinc finger nuclease (ZFN); an ARCUS nuclease; and the like.
- the meganuclease can be engineered from an LADLIDADG homing endonuclease (LHE).
- a megaTAL polypeptide can comprise a TALE DNA binding domain and an engineered meganuclease.
- a nucleic acid-binding effector fusion polypeptide comprises: i) a Nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) a heterologous polypeptide (a “fusion partner”), where the heterologous polypeptide is a reverse transcriptase polypeptide.
- a Nucleic acid-binding effector fusion polypeptide e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a
- a heterologous polypeptide a “fusion partner”
- Suitable reverse transcriptases include, e.g., a murine leukemia virus reverse transcriptase; a Rous sarcoma virus reverse transcriptase; a human immunodeficiency virus type I reverse transcriptase; a Moloney murine leukemia virus reverse transcriptase; a transcription xenopolymerase (RTX); avian myeloblastosis virus reverse transcriptase (AMV-RT); a Eubacterium rectale maturase reverse transcriptase (Marathon®; and the like.
- the reverse transcriptase fusion partner can include one or more mutations.
- the reverse transcriptase is a M-MLV reverse transcriptase polypeptide that comprises one or more mutations selected from the group consisting of D200N, T306K, W313F, T330P and L603W.
- the reverse transcriptase is a pentamutant of M-MLV RT (e.g., comprising the following substitutions: D200N/L603W/T330P/T306K/W313F) (where D200, L603, T330, T306, and W313 correspond to D199, L602, T329, T305, and W312 of the M-MLV RT amino acid sequence of SEQ ID NO:157).
- a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises: i) a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) one or more heterologous polypeptides (a “fusion partner”), where at least one of the one or more heterologous polypeptides is a deaminase.
- a Nucleic acid-binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a
- a heterologous polypeptides a “fusion partner”
- Suitable deaminases include, e.g., an adenosine deaminase; a cytidine deaminase (e.g., an activation-induced cytidine deaminase (AID)); APOBEC3G; and the like); and the like.
- a suitable adenosine deaminase is any enzyme that is capable of deaminating adenosine in DNA.
- the deaminase is a TadA deaminase.
- a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MSEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMA LRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHP GMNHRVEITEGILADECAALLSDFFRMRRQEIKAQKKAQSSTD (SEQ ID NO:26).
- a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Staphylococcus aureus TadA amino acid sequence: MGSHMTNDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIER AAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFN HRAIVDKGVLKEACSTLLTTFFK NLRANKKSTN (SEQ ID NO:28).
- a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Salmonella typhimurium TadA: MPPAFITGVTSLSDVELDHEYWMRHALTLAKRAWDEREVPVGAVLVHNHRVIGEGWNRPIGR HDPTAHAEIMALRQGGLVLQNYRLLDTTLYVTLEPCVMCAGAMVHSRIGRVVFGARDAKTGA AGSLIDVLHHPGMNHRVEIIEGVLRDECATLLSDFFRMRRQEIKALKKADRAEGAGPAV (SEQ ID NO:30).
- a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Shewanella putrefaciens TadA amino acid sequence: MDEYWMQVAMQMAEKAEAAGEVPVGAVLVKDGQQIATGYNLSISQHDPTAHAEILCLRSAG KKLENYRLLDATLYITLEPCAMCAGAMVHSRIARVVYGARDEKTGAAGTVVNLLQHPAFNHQ VEVTSGVLAEACSAQLSRFFKRRRDEKKALKLAQRAQQGIE (SEQ ID NO:31).
- a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Haemophilus influenzae F3031 TadA amino acid sequence: MDAAKVRSEFDEKMMRYALELADKAEALGEIPVGAVLVDDARNIIGEGWNLSIVQSDPTAHAE IIALRNGAKNIQNYRLLNSTLYVTLEPCTMCAGAILHSRIKRLVFGASDYKTGAIGSRFHFFDDY KMNHTLEITSGVLAEECSQKLS TFFQKRREEKKIEKALLKSLSDK (SEQ ID NO:32).
- a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Caulobacter crescentus TadA amino acid sequence: MRTDESEDQDHRMMRLALDAARAAAEAGETPVGAVILDPSTGEVIATAGNGPIAAHDPTAHAE IAAMRAAAAKLGNYRLTDLTLVVTLEPCAMCAGAISHARIGRVVFGADDPKGGAVVHGPKFFA QPTCHWRPEVTGGVLADESADLLRGFFRARRKAKI (SEQ ID NO:33).
- a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Geobacter sulfurreducens TadA amino acid sequence: MSSLKKTPIRDDAYWMGKAIREAAKAAARDEVPIGAVIVRDGAVIGRGHNLREGSNDPSAHAE MIAIRQAARRSANWRLTGATLYVTLEPCLMCMGAIILARLERVVFGCYDPKGGAAGSLYDLSA DPRLNHQVRLSPGVCQEECGTMLSDFFRDLRRRKKAKATPALFIDERKVPPEP (SEQ ID NO:34).
- Cytidine deaminases suitable for inclusion in a nucleic acid-binding effector fusion polypeptide include any enzyme that is capable of deaminating cytidine in DNA.
- the cytidine deaminase is a deaminase from the apolipoprotein B mRNA-editing complex (APOBEC) family of deaminases.
- APOBEC apolipoprotein B mRNA-editing complex
- the transcription factor comprises a Krüppel-associated box (KRAB) polypeptide (transcriptional repression).
- the transcription factor comprises a Mad mSIN3 interaction domain (SID) polypeptide (transcriptional repression).
- the transcription factor comprises an ERF repressor domain (ERD) polypeptide (transcriptional repression).
- the transcription factor is a transcriptional activator, where the transcriptional activator is GAL4-VP16.
- a fusion polypeptide comprises: i) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) a heterologous polypeptide (a “fusion partner”), where the heterologous polypeptide is a recombinase.
- Suitable recombinases include, e.g., a Cre recombinase; a Hin recombinase; a Tre recombinase; a FLP recombinase; and the like.
- a nucleic acid-binding effector fusion polypeptide comprises: i) a nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) a heterologous polypeptide (a “fusion partner”), where the heterologous polypeptide provides for subcellular localization, i.e., the heterologous polypeptide contains a subcellular localization sequence (e.g., a nuclear localization signal (NLS) for targeting to the nucleus, a sequence to keep the fusion protein out of the nucleus, e.g., a nuclear export sequence (NES), a sequence to keep the fusion protein retained in the cytoplasm, a mitochondrial localization signal for targeting to the mitochondria, a chloroplast localization signal for targeting to a chloroplast, an endoplasmic reticulum (ER) retention signal, and the like).
- the heterologous polypeptide can provide a tag (i.e., the heterologous polypeptide is a detectable label) for ease of tracking and/or purification (e.g., a fluorescent protein, e.g., green fluorescent protein (GFP), yellow fluorescent protein (YFP), red fluorescent protein (RFP), cyan fluorescent protein (CFP), mCherry, tdTomato, and the like; a histidine tag, e.g., a 6XHis tag; a hemagglutinin (HA) tag; a FLAG tag; a Myc tag; and the like).
- a fluorescent protein e.g., green fluorescent protein (GFP), yellow fluorescent protein (YFP), red fluorescent protein (RFP), cyan fluorescent protein (CFP), mCherry, tdTomato, and the like
- a histidine tag e.g., a 6XHis tag
- HA hemagglutinin
- FLAG tag a FLAG tag
- a Nucleic acid-binding effector fusion polypeptide comprises: a) a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and b) one or more nuclear localization signals (NLSs) (e.g., in some cases 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs).
- NLSs nuclear localization signals
- a fusion polypeptide of the present disclosure includes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs).
- one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus and/or the C-terminus.
- one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more) are positioned at or near (e.g., within 50 amino acids of) the C-terminus.
- a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises: a) a Nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and b) from 2 to 5 NLSs (e.g., 2-4 NLSs, or 2-3 NLSs). In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises about 4 NLSs.
- NLS are of sufficient strength to drive accumulation of the Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) in a detectable amount in the nucleus of a eukaryotic cell. Detection of accumulation in the nucleus may be performed by any suitable technique. For example, a detectable marker may be fused to the Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) such that location within a cell may be visualized.
- a detectable marker may be fused to the Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) such that location within a cell may be visualized.
- a Nucleic acid-binding effector fusion polypeptide e.g., a CRISPR-Cas fusion polypeptide
- a Nucleic acid-binding effector fusion polypeptide includes a "Protein Transduction Domain” or PTD (also known as a CPP – cell penetrating peptide), which refers to a polypeptide, polynucleotide, carbohydrate, or organic or inorganic compound that facilitates traversing a lipid bilayer, micelle, cell membrane, organelle membrane, or vesicle membrane.
- a PTD attached to another molecule which can range from a small polar molecule to a large macromolecule and/or a nanoparticle, facilitates the molecule traversing a membrane, for example going from extracellular space to intracellular space, or cytosol to within an organelle.
- a PTD is covalently linked to the amino terminus of a Nucleic acid-binding effector polypeptide (e.g., a CRISPR- Cas effector polypeptide such as Cas9 or Cas12a).
- a PTD is covalently linked to the carboxyl terminus of a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a).
- a Nucleic acid-binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a.
- the PTD is inserted internally in a Nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) (i.e., is not at the N- or C-terminus of the Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a)) at a suitable insertion site.
- a Nucleic acid- binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a
- a Nucleic acid- binding effector fusion polypeptide includes: a) a nucleic acid- binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide); and b) one or more PTDs (e.g., two or more, three or more, four or more PTDs).
- a PTD includes a nuclear localization signal (NLS) (e.g., in some cases 2 or more, 3 or more, 4 or more, or 5 or more NLSs).
- NLS nuclear localization signal
- a CRISPR-Cas fusion polypeptide includes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, or 5 or more NLSs).
- a PTD is covalently linked to a nucleic acid (e.g., a CRISPR-Cas guide nucleic acid, a polynucleotide encoding a CRISPR-Cas guide nucleic acid, a polynucleotide encoding a fusion polypeptide, a donor polynucleotide, etc.).
- PTDs include but are not limited to a minimal undecapeptide protein transduction domain (corresponding to residues 47-57 of HIV-1 TAT comprising YGRKKRRQRRR; SEQ ID NO: 127); a polyarginine sequence comprising a number of arginines sufficient to direct entry into a cell (e.g., 3, 4, 5, 6, 7, 8, 9, 10, or 10-50 arginines); a VP22 domain (Zender et al. (2002) Cancer Gene Ther.9(6):489-96); a Drosophila Antennapedia protein transduction domain (Noguchi et al. (2003) Diabetes 52(7):1732-1737); a truncated human calcitonin peptide (Trehin et al.
- a minimal undecapeptide protein transduction domain corresponding to residues 47-57 of HIV-1 TAT comprising YGRKKRRQRRR; SEQ ID NO: 127
- a polyarginine sequence comprising a number of arginines sufficient to direct
- Exemplary PTDs include but are not limited to, YGRKKRRQRRR (SEQ ID NO: 127), RKKRRQRRR (SEQ ID NO: 132); an arginine homopolymer of from 3 arginine residues to 50 arginine residues;
- Exemplary PTD domain amino acid sequences include, but are not limited to, any of the following: YGRKKRRQRRR (SEQ ID NO: 127); RKKRRQRR (SEQ ID NO: 133); YARAAARQARA (SEQ ID NO: 134); THRLPRRRRRR (SEQ ID NO: 135); and GGRRARRRRRR (SEQ ID NO: 136).
- the PTD is an activatable CPP (ACPP) (Aguilera et al. (2009) Integr Biol (Camb) June; 1(5-6): 371-381).
- ACPPs comprise a polycationic CPP (e.g., Arg9 or “R9”) connected via a cleavable linker to a matching polyanion (e.g., Glu9 or “E9”), which reduces the net charge to nearly zero and thereby inhibits adhesion and uptake into cells.
- a polyanion e.g., Glu9 or “E9”
- Linkers (e.g., for fusion partners)
- a CRISPR-Cas polypeptide can be fused to a fusion partner via a linker polypeptide (e.g., one or more linker polypeptides).
- the linker polypeptide may have any of a variety of amino acid sequences. Proteins can be joined by a spacer peptide, generally of a flexible nature, although other chemical linkages are not excluded. Suitable linkers include polypeptides of between 4 amino acids and 40 amino acids in length, or between 4 amino acids and 25 amino acids in length.
- linkers can be produced by using synthetic, linker-encoding oligonucleotides to couple the proteins, or can be encoded by a nucleic acid sequence encoding the fusion protein.
- Peptide linkers with a degree of flexibility can be used.
- the linking peptides may have virtually any amino acid sequence, bearing in mind that the preferred linkers will have a sequence that results in a generally flexible peptide.
- small amino acids, such as glycine and alanine are of use in creating a flexible peptide. The creation of such sequences is routine to those of skill in the art.
- a variety of different linkers are commercially available and are considered suitable for use.
- linker polypeptides include glycine polymers (G)n where n is an integer of at least one; glycine-serine polymers (including, for example, (GS)n, (GSGGS)n (SEQ ID NO: 40), (GGSGGS)n (SEQ ID NO: 41), (GGGGS)n (SEQ ID NO:38), and (GGGS)n (SEQ ID NO: 42), where n is an integer of at least one; e.g., where n is an integer from 1 to 10); glycine-alanine polymers; and alanine-serine polymers.
- G glycine polymers
- glycine-serine polymers including, for example, (GS)n, (GSGGS)n (SEQ ID NO: 40), (GGSGGS)n (SEQ ID NO: 41), (GGGGS)n (SEQ ID NO:38), and (GGGS)n (SEQ ID NO: 42), where n is an integer of at least one;
- an EDV of the present disclosure comprises a CRISPR-Cas effector polypeptide guide nucleic acid (e.g., RNA) or a nucleic acid comprising a nucleotide sequence encoding a CRISPR-Cas effector polypeptide guide RNA.
- RNA CRISPR-Cas effector polypeptide guide nucleic acid
- nucleic acid comprising a nucleotide sequence encoding a CRISPR-Cas effector polypeptide guide RNA.
- a nucleic acid molecule that binds to a CRISPR-Cas effector polypeptide protein and targets the complex to a specific location within a target nucleic acid is referred to herein as a “CRISPR-Cas effector polypeptide guide RNA” or simply a “guide RNA.”
- a guide RNA can be said to include two segments, a first segment (referred to herein as a “targeting segment”); and a second segment (referred to herein as a “protein-binding segment”).
- segment it is meant a segment/section/region of a molecule, e.g., a contiguous stretch of nucleotides in a nucleic acid molecule.
- the first segment (targeting segment) of a guide RNA includes a nucleotide sequence (a guide sequence) that is complementary to (and therefore hybridizes with) a specific sequence (a target site) within a target nucleic acid (e.g., a target DNA, e.g., ssDNA, dsDNA, or a target RNA), such as the complementary strand of a double stranded target DNA, etc.
- a target nucleic acid e.g., a target DNA, e.g., ssDNA, dsDNA, or a target RNA
- the protein-binding segment (or “protein- binding sequence”) interacts with (binds to) a CRISPR-Cas effector polypeptide.
- the protein-binding segment of a guide RNA includes two complementary stretches of nucleotides that hybridize to one another to form a double stranded RNA duplex (dsRNA duplex).
- Site-specific binding and/or cleavage of a target nucleic acid can occur at locations (e.g., target sequence of a target locus) determined by base-pairing complementarity between the guide RNA (the guide sequence of the guide RNA) and the target nucleic acid.
- a guide RNA and a CRISPR-Cas effector polypeptide form a complex (e.g., bind via non- covalent interactions).
- the guide RNA provides target specificity to the complex by including a targeting segment, which includes a guide sequence (a nucleotide sequence that is complementary to a sequence of a target nucleic acid).
- the CRISPR-Cas effector polypeptide of the complex provides the site-specific activity (e.g., cleavage activity or an activity provided by the CRISPR-Cas effector polypeptide when the CRISPR-Cas effector polypeptide is a CRISPR-Cas effector polypeptide fusion polypeptide, i.e., has a fusion partner).
- the CRISPR-Cas effector polypeptide is guided to a target nucleic acid sequence (e.g.
- a target sequence in a chromosomal nucleic acid e.g., a chromosome
- a target sequence in an extrachromosomal nucleic acid e.g. an episomal nucleic acid, a minicircle, an ssRNA, an ssDNA, etc.
- a target sequence in a mitochondrial nucleic acid e.g. an episomal nucleic acid, a minicircle, an ssRNA, an ssDNA, etc.
- a target sequence in a mitochondrial nucleic acid a target sequence in a chloroplast nucleic acid
- a target sequence in a plasmid a target sequence in a viral nucleic acid; etc.
- the “guide sequence” also referred to as the “targeting sequence” of a guide RNA can be modified so that the guide RNA can target a CRISPR-Cas effector polypeptide to any desired sequence of any desired target nucleic acid, with the exception that the protospacer adjacent motif (PAM) sequence can be taken into account.
- PAM protospacer adjacent motif
- a guide RNA can have a targeting segment with a sequence (a guide sequence) that has complementarity with (e.g., can hybridize to) a sequence in a nucleic acid in a eukaryotic cell, e.g., a viral nucleic acid, a eukaryotic nucleic acid (e.g., a eukaryotic chromosome, chromosomal sequence, a eukaryotic RNA, etc.), and the like.
- a eukaryotic cell e.g., a viral nucleic acid, a eukaryotic nucleic acid (e.g., a eukaryotic chromosome, chromosomal sequence, a eukaryotic RNA, etc.), and the like.
- a guide RNA includes two separate nucleic acid molecules: an “activator” and a “targeter” and is referred to herein as a “dual guide RNA”, a “double-molecule guide RNA”, or a “two-molecule guide RNA” a “dual guide RNA”, or a “dgRNA.”
- the activator and targeter are covalently linked to one another (e.g., via intervening nucleotides) and the guide RNA is referred to as a “single guide RNA”, a “Cas9 single guide RNA”, a “single-molecule Cas9 guide RNA,” or a “one-molecule Cas9 guide RNA”, or simply “sgRNA.”
- a guide RNA comprises a crRNA-like (“CRISPR RNA”/“targeter”/“crRNA”/“crRNA repeat”) molecule and a corresponding tracrRNA-like (“trans-acting CRISPR
- a crRNA-like molecule comprises both the targeting segment (single stranded) of the guide RNA and a stretch (“duplex-forming segment”) of nucleotides that forms one half of the dsRNA duplex of the protein-binding segment of the guide RNA.
- a corresponding tracrRNA-like molecule comprises a stretch of nucleotides (duplex-forming segment) that forms the other half of the dsRNA duplex of the protein-binding segment of the guide nucleic acid.
- a stretch of nucleotides of a crRNA-like molecule are complementary to and hybridize with a stretch of nucleotides of a tracrRNA-like molecule to form the dsRNA duplex of the protein-binding domain of the guide RNA.
- each targeter molecule can be said to have a corresponding activator molecule (which has a region that hybridizes with the targeter).
- the targeter molecule additionally provides the targeting segment.
- a targeter and an activator molecule hybridize to form a guide RNA.
- the exact sequence of a given crRNA or tracrRNA molecule is characteristic of the species in which the RNA molecules are found.
- a dual guide RNA can include any corresponding activator and targeter pair.
- activator or “activator RNA” is used herein to mean a tracrRNA-like molecule (tracrRNA: “trans-acting CRISPR RNA”) of a dual guide RNA (and therefore of a single guide RNA when the “activator” and the “targeter” are linked together by, e.g., intervening nucleotides).
- a guide RNA comprises an activator sequence (e.g., a tracrRNA sequence).
- a tracr molecule is a naturally existing molecule that hybridizes with a CRISPR RNA molecule (a crRNA) to form a dual guide RNA.
- the term “activator” is used herein to encompass naturally existing tracrRNAs, but also to encompass tracrRNAs with modifications (e.g., truncations, sequence variations, base modifications, backbone modifications, linkage modifications, etc.) where the activator retains at least one function of a tracrRNA (e.g., contributes to the dsRNA duplex to which Cas9 protein binds).
- the activator provides one or more stem loops that can interact with Cas9 protein.
- an activator can be referred to as having a tracr sequence (tracrRNA sequence) and in some cases is a tracrRNA, but the term “activator” is not limited to naturally existing tracrRNAs.
- the term “targeter” or “targeter RNA” is used herein to refer to a crRNA-like molecule (crRNA: “CRISPR RNA”) of a dual guide RNA (and therefore of a single guide RNA when the “activator” and the “targeter” are linked together, e.g., by intervening nucleotides).
- a guide RNA comprises a targeting segment (which includes nucleotides that hybridize with (are complementary to) a target nucleic acid, and a duplex-forming segment (e.g., a duplex forming segment of a crRNA, which can also be referred to as a crRNA repeat).
- a targeting segment the segment that hybridizes with a target sequence of a target nucleic acid
- a crRNA repeat the sequence of a targeter will often be a non-naturally occurring sequence.
- the duplex-forming segment of a targeter (described in more detail below), which hybridizes with the duplex-forming segment of an activator, can include a naturally existing sequence (e.g., can include the sequence of a duplex-forming segment of a naturally existing crRNA, which can also be referred to as a crRNA repeat).
- targeter is used herein to distinguish from naturally occurring crRNAs, despite the fact that part of a targeter (e.g., the duplex- forming segment) often includes a naturally occurring sequence from a crRNA.
- the term “targeter” encompasses naturally occurring crRNAs.
- a guide RNA can also be said to include 3 parts: (i) a targeting sequence (a nucleotide sequence that hybridizes with a sequence of the target nucleic acid); (ii) an activator sequence (as described above)(in some cases, referred to as a tracr sequence); and (iii) a sequence that hybridizes to at least a portion of the activator sequence to form a double stranded duplex.
- a targeter has (i) and (iii); while an activator has (ii).
- a guide RNA e.g. a dual guide RNA or a single guide RNA
- a guide RNA can be comprised of any corresponding activator and targeter pair.
- the duplex forming segments can be swapped between the activator and the targeter.
- the targeter includes a sequence of nucleotides from a duplex forming segment of a tracrRNA (which sequence would normally be part of an activator) while the activator includes a sequence of nucleotides from a duplex forming segment of a crRNA (which sequence would normally be part of a targeter).
- a targeter comprises both the targeting segment (single stranded) of the guide RNA and a stretch (“duplex-forming segment”) of nucleotides that forms one half of the dsRNA duplex of the protein-binding segment of the guide RNA.
- a corresponding tracrRNA-like molecule comprises a stretch of nucleotides (a duplex-forming segment) that forms the other half of the dsRNA duplex of the protein-binding segment of the guide RNA.
- a stretch of nucleotides of the targeter is complementary to and hybridizes with a stretch of nucleotides of the activator to form the dsRNA duplex of the protein-binding segment of a guide RNA.
- each targeter can be said to have a corresponding activator (which has a region that hybridizes with the targeter).
- the targeter molecule additionally provides the targeting segment.
- a targeter and an activator hybridize to form a guide RNA.
- RNA molecules are found.
- suitable activator and targeter are well known in the art.
- Knockouts [00397]
- an EDV of the present disclosure provides for: i) delivery of a therapeutic protein; and ii) knockout of a target nucleic acid.
- an EDV of the present disclosure can both: i) provide for delivery of a therapeutic protein (such as a chimeric antigen receptor (CAR)); and ii) knock out an endogenous nucleic acid encoding a beta-2 microglobulin ( ⁇ 2M) polypeptide, where the guide RNA present in the EDV (or encoded by a nucleic acid present in the EDV) would comprise a nucleotide sequence targeting a ⁇ 2M-encoding nucleic acid in a target cell.
- a therapeutic protein such as a chimeric antigen receptor (CAR)
- ⁇ 2M beta-2 microglobulin
- an EDV would be useful for generating T cells that express a CAR (“CAR-T cells”) that do not express endogenous major histocompatibility complex (MHC) class I antigens on their cell surface and thus could be useful for delivery of allogeneic CAR-T cells.
- CAR-T cells CAR-T cells
- MHC major histocompatibility complex
- an EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding the guide RNA, where the guide RNA provides for knockout of the endogenous T-cell receptor alpha constant (TRAC) gene, such that a TRAC polypeptide is not produced in the cell.
- TRAC T-cell receptor alpha constant
- a TRAC polypeptide can comprise the following amino acid sequence: IQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVA WSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVAGF NLLMTLRLWSS (SEQ ID NO:204).
- an EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding the guide RNA, where the guide RNA provides for knockout of an endogenous gene encoding an immune checkpoint.
- Immune checkpoints include, e.g., PD-1, PD- L1, CTLA4, and TIGIT.
- Donor nucleic acid [00402]
- an EDV of the present disclosure comprises a donor nucleic acid.
- a “donor nucleic acid” or “donor sequence” or “donor polynucleotide” or “donor template” it is meant a nucleic acid sequence to be inserted at the site cleaved by a CRISPR-Cas effector protein (e.g., after dsDNA cleavage, after nicking a target DNA, after dual nicking a target DNA, and the like).
- the 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 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.
- Donor polynucleotides can be of any length, e.g.10 nucleotides or more, 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.
- the donor sequence is typically not identical to the genomic sequence that it replaces.
- the donor sequence may contain at least one or more single base changes, insertions, deletions, inversions or rearrangements with respect to the 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).
- the donor sequence 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 the non- homologous sequence at the target region.
- one or more dideoxynucleotide residues can be added to the 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 internucleotide 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.
- a donor sequence can be introduced into a cell as part of a vector molecule having additional sequences such as, for example, replication origins, promoters and genes encoding antibiotic resistance.
- a CAR comprises an extracellular domain comprising an antigen-binding domain.
- the antigen-binding domain present in a CAR can be any antigen-binding polypeptide, a wide variety of which are known in the art.
- the antigen-binding domain is a single chain Fv (scFv).
- an anti-CD19 antibody includes a VH CDR1 comprising the amino acid sequence SYWMN (SEQ ID NO:184); a VH CDR2 comprising the amino acid sequence QIWPGDGDTNYNGKFKG (SEQ ID NO:185); and a VH CDR3 comprising the amino acid sequence RETTTVGRYYYAMDY (SEQ ID NO:186).
- Suitable buffers include, but are not limited to, (such as N,N-bis(2-hydroxyethyl)-2- aminoethanesulfonic acid (BES), bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS-Tris), N- (2-hydroxyethyl)piperazine-N'3-propanesulfonic acid (EPPS or HEPPS), glycylglycine, N-2- hydroxyehtylpiperazine-N'-2-ethanesulfonic acid (HEPES), 3-(N-morpholino)propane sulfonic acid (MOPS), piperazine-N,N'-bis(2-ethane-sulfonic acid) (PIPES), sodium bicarbonate, 3-(N- tris(hydroxymethyl)-methyl-amino)-2-hydroxy-propanesulfonic acid) TAPSO, (N- tris(hydroxymethyl)methyl-2-aminoethanesulfonic
- Suitable salts include, e.g., NaCl, MgCl2, KCl, MgSO4, etc.
- the composition is sterile. In some cases, the composition is suitable for administration to a human subject, e.g., where the composition is sterile and is free of detectable pyrogens and/or other toxins.
- a composition of the present disclosure comprises: i) an EDV that does not include a donor template nucleic acid; and ii) a donor template nucleic acid (provided separately from the EDV).
- a coding sequence (e.g., a nucleotide sequence encoding a CRISPR-Cas effector polypeptide; a nucleotide sequence encoding a CRISPR-Cas guide RNA; a nucleotide sequence encoding a therapeutic protein) present in an EDV of the present disclosure can be operably linked to a transcriptional control element (e.g., a promoter).
- the transcriptional control element can be a promoter. In some cases, the promoter is a constitutively active promoter.
- a promoter can be a constitutively active promoter (i.e., a promoter that is constitutively in an active/”ON” state), it may be an inducible promoter (i.e., a promoter whose state, active/”ON” or inactive/“OFF”, is controlled by an external stimulus, e.g., the presence of a particular temperature, compound, or protein.), it may be a spatially restricted promoter (i.e., transcriptional control element, enhancer, etc.)(e.g., tissue specific promoter, cell type specific promoter, etc.), and it may be a temporally restricted promoter (i.e., the promoter is in the “ON” state or “OFF” state during specific stages of embryonic development or during specific stages of a biological process, e.g., hair follicle cycle in mice).
- a constitutively active promoter i.e., a promoter that is constitutively in an active/”ON” state
- it may be an inducible promote
- Exemplary promoters include, but are not limited to the SV40 early promoter, mouse mammary tumor virus long terminal repeat (LTR) promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (HSV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), a rous sarcoma virus (RSV) promoter, a human U6 small nuclear promoter (U6) (Miyagishi et al., Nature Biotechnology 20, 497 - 500 (2002)), an enhanced U6 promoter (e.g., Xia et al., Nucleic Acids Res.2003 Sep 1;31(17)), a human H1 promoter (H1), and the like.
- LTR mouse mammary tumor virus long terminal repeat
- Ad MLP adenovirus major late promoter
- HSV herpes simplex virus
- CMV cytomegalovirus
- CMVIE C
- a nucleotide sequence encoding guide RNA is operably linked to a promoter operable in a eukaryotic cell (e.g., a CMV promoter, an EF1 ⁇ promoter, an estrogen receptor- regulated promoter, and the like).
- a promoter operable in a eukaryotic cell e.g., a CMV promoter, an EF1 ⁇ promoter, an estrogen receptor- regulated promoter, and the like.
- the promoter is a spatially restricted promoter (i.e., cell type specific promoter, tissue specific promoter, etc.) such that in a multi-cellular organism, the promoter is active (i.e., “ON”) in a subset of specific cells.
- Spatially restricted promoters may also be referred to as enhancers, transcriptional control elements, control sequences, etc. Any convenient spatially restricted promoter may be used as long as the promoter is functional in the targeted host cell (e.g., eukaryotic cell; prokaryotic cell).
- the promoter is a reversible promoter.
- the present disclosure provides methods of making an EDV of the present disclosure.
- the methods generally involve introducing into a packaging cell a system (collection of nucleic acids) of the present disclosure; and harvesting the EDVs produced by the packaging cell.
- the EDVs are harvested from the supernatant (e.g., the cell culture medium) in which the packaging cells are cultures.
- the cell culture medium is filtered (e.g., with a 0.45 ⁇ m filter).
- Any suitable permissive or packaging cell known in the art may be employed in the production of an EDV of the present disclosure.
- the cell is a mammalian cell.
- the cell is an insect cell.
- the nucleic acids present in a system (collection) of the present disclosure can be extra- chromosomal or integrated into the cell's chromosomal DNA.
- the packaging cell is a cell line with one or more packaging functions incorporated extrachromosomally or integrated into the cell's chromosomal DNA, or a cell line with helper functions incorporated extra-chromosomally or integrated into the cell's chromosomal DNA.
- the present disclosure provides methods of delivering a nucleic acid-binding effector polypeptide (e.g., CRIPSR-Cas effector polypeptide such as a Cas9 or Cas12a – including variants such as nickase versions, dead versions, fusion protein versions, etc.) to a target eukaryotic cell.
- a nucleic acid-binding effector polypeptide e.g., CRIPSR-Cas effector polypeptide such as a Cas9 or Cas12a – including variants such as nickase versions, dead versions, fusion protein versions, etc.
- the target cell is in vitro (e.g., an immortalized cell line).
- the target cell is ex vivo (e.g., a primary isolated from a patient that is not immortalized and has gone through minimal to no passages – in some cases such cells can be re-introduced into an individual).
- the target cell is in vivo and the method comprises administering the EDV to an individual.
- the present disclosure provides methods of delivering a CRISPR-Cas polypeptide (e.g., Cas9, Cas12a – including variants such as dead, nickase, and/or fusion variants) to a target eukaryotic cell.
- a CRISPR-Cas polypeptide e.g., Cas9, Cas12a – including variants such as dead, nickase, and/or fusion variants
- the methods generally involve contacting the cell with a EDV of the present disclosure or administering a EDV to an organism.
- the target cell is ex vivo (e.g., a primary isolated from a patient that is not immortalized and has gone through minimal to no passages – in some cases such cells can be re- introduced into an individual).
- the target cell is in vivo and the method comprises administering the EDV to an individual.
- a EDV of the present disclosure comprises a guide RNA
- the guide RNA provides for knockout of a nucleic acid targeted by the guide RNA.
- a EDV of the present disclosure provides for: i) delivery of a therapeutic protein; and ii) knockout of a target nucleic acid.
- a EDV of the present disclosure can both: i) provide for delivery of a therapeutic protein (such as a chimeric antigen receptor (CAR)); and ii) knock out an endogenous nucleic acid, e.g., one encoding a beta-2 microglobulin ( ⁇ 2M) polypeptide, where the guide RNA present in the EDV (or encoded by a nucleic acid present in the EDV) would comprise a nucleotide sequence targeting the endogenous nucleic acid (e.g., a ⁇ 2M-encoding nucleic acid) in a target cell.
- a therapeutic protein such as a chimeric antigen receptor (CAR)
- ⁇ 2M beta-2 microglobulin
- CAR-T cells Such a EDV would be useful for generating T cells that express a CAR (“CAR-T cells”) that do not express endogenous major histocompatibility complex (MHC) class I antigens on their cell surface and thus could be useful for delivery of allogeneic CAR-T cells.
- CAR-T cells CAR-T cells
- MHC major histocompatibility complex
- a EDV of the present disclosure can both: i) provide for delivery of a therapeutic protein (such as an antibody, e.g., a cancer-specific antibody or other therapeutic antibody); and ii) knock out an endogenous nucleic acid encoding an antibody light chain (e.g., a kappa light chain) or an immunoglobulin (Ig) Fc polypeptide (e.g., an Ig Fc polypeptide of a particular isotype such as IgG1).
- a therapeutic protein such as an antibody, e.g., a cancer-specific antibody or other therapeutic antibody
- an endogenous nucleic acid encoding an antibody light chain (e.g., a kappa light chain) or an immunoglobulin (Ig) Fc polypeptide (e.g., an Ig Fc polypeptide of a particular isotype such as IgG1).
- a therapeutic protein such as an antibody, e.g., a cancer-specific antibody or other therapeutic antibody
- a EDV of the present disclosure provides for homology directed repair (HDR) of a defective target nucleic acid (e.g., in some cases a donor/template nucleic acid is provided, either as part of the EDV, e.g., encapsidated within the EDV, and in some cases along with the EDV but as part of the EDV).
- HDR homology directed repair
- a EDV of the present disclosure provides for non-homologous end joining (NHEJ) of a target nucleic acid, e.g., to provide for a knockout of a target nucleic acid.
- NHEJ non-homologous end joining
- a cell that serves as a recipient for a EDV of the present disclosure can be any of a variety of eukaryotic cells, including, e.g., in vitro cells; in vivo cells; ex vivo cells; primary cells; cancer cells; animal cells; plant cells; algal cells; fungal cells; etc.
- a cell that serves as a recipient for a EDV of the present disclosure is referred to as a “host cell” or a “target cell.”
- the target cell is in vitro (e.g., the cells can be an immortalized cell line).
- the target cell is ex vivo, e.g., in some cases, cells are removed from an individual, contacted with a EDV of the present disclosure ex vivo, such that the cells are modified to produce the therapeutic protein encoded by a nucleic acid present in the EDV; and the modified cells can be returned to the individual from whom the cells were obtained.
- cells are removed from an individual, contacted with a EDV of the present disclosure ex vivo, such that the cells are modified to produce the therapeutic protein encoded by a nucleic acid present in the EDV; and the modified cells can be administered to an individual other than the individual from whom the cells were obtained.
- Suitable cells include a stem cell (e.g.
- an embryonic stem (ES) cell an induced pluripotent stem (iPS) cell
- a germ cell e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.
- a somatic cell e.g. a fibroblast, an oligodendrocyte, a glial cell, a hematopoietic cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell, etc.
- Suitable cells include human embryonic stem cells, fetal cardiomyocytes, myofibroblasts, mesenchymal stem cells, cardiomyocytes, adipocytes, totipotent cells, pluripotent cells, blood stem cells, myoblasts, adult stem cells, bone marrow cells, mesenchymal cells, embryonic stem cells, parenchymal cells, epithelial cells, endothelial cells, mesothelial cells, fibroblasts, osteoblasts, chondrocytes, exogenous cells, endogenous cells, stem cells, hematopoietic stem cells, bone-marrow derived progenitor cells, myocardial cells, skeletal cells, fetal cells, undifferentiated cells, multi-potent progenitor cells, unipotent progenitor cells, monocytes, cardiac myoblasts, skeletal myoblasts, macrophages, capillary endothelial cells, xenogeneic cells, allogeneic cells,
- Suitable cells include a cancer cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue-resident stem cell, a monocyte, a macrophage, a B cell, and a T cell.
- the cell is an immune cell, a neuron, an epithelial cell, and endothelial cell, or a stem cell.
- the immune cell is a T cell, a B cell, a monocyte, a natural killer cell, a dendritic cell, or a macrophage. In some cases, the immune cell is a cytotoxic T cell. In some cases, the immune cell is a helper T cell. In some cases, the immune cell is a regulatory T cell (Treg).
- the cell is a stem cell. Stem cells include adult stem cells. Adult stem cells are also referred to as somatic stem cells. In some cases, the cell is a tissue-resident stem cell.
- Adult stem cells are resident in differentiated tissue, but retain the properties of self-renewal and ability to give rise to multiple cell types, usually cell types typical of the tissue in which the stem cells are found.
- somatic stem cells include muscle stem cells; hematopoietic stem cells; epithelial stem cells; neural stem cells; mesenchymal stem cells; mammary stem cells; intestinal stem cells; mesodermal stem cells; endothelial stem cells; olfactory stem cells; neural crest stem cells; and the like.
- Stem cells of interest include mammalian stem cells, where the term “mammalian” refers to any animal classified as a mammal, including humans; non-human primates; domestic and farm animals; and zoo, laboratory, sports, or pet animals, such as dogs, horses, cats, cows, mice, rats, rabbits, etc.
- the stem cell is a human stem cell.
- the stem cell is a rodent (e.g., a mouse; a rat) stem cell.
- the stem cell is a non-human primate stem cell.
- Stem cells can express one or more stem cell markers, e.g., SOX9, KRT19, KRT7, LGR5, CA9, FXYD2, CDH6, CLDN18, TSPAN8, BPIFB1, OLFM4, CDH17, and PPARGC1A.
- the stem cell is a hematopoietic stem cell (HSC).
- HSCs are mesoderm-derived cells that can be isolated from bone marrow, blood, cord blood, fetal liver and yolk sac. HSCs are characterized as CD34+ and CD3-.
- HSCs can repopulate the erythroid, neutrophil-macrophage, megakaryocyte and lymphoid hematopoietic cell lineages in vivo.
- HSCs can be induced to undergo at least some self-renewing cell divisions and can be induced to differentiate to the same lineages as is seen in vivo.
- HSCs can be induced to differentiate into one or more of erythroid cells, megakaryocytes, neutrophils, macrophages, and lymphoid cells.
- the stem cell is a neural stem cell (NSC).
- Neural stem cells are capable of differentiating into neurons, and glia (including oligodendrocytes, and astrocytes).
- a neural stem cell is a multipotent stem cell which is capable of multiple divisions, and under specific conditions can produce daughter cells which are neural stem cells, or neural progenitor cells that can be neuroblasts or glioblasts, e.g., cells committed to become one or more types of neurons and glial cells respectively. Methods of obtaining NSCs are known in the art.
- the stem cell is a mesenchymal stem cell (MSC).
- the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA
- the guide RNA comprises a targeting sequence that targets a CFTR (cystic fibrosis transmembrane conductance regulator) gene.
- targeting a CFTR gene can treat cystic fibrosis.
- a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected.
- the target cell is a CD34+ cell.
- the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, where the guide RNA comprises a targeting sequence that targets an HbF (fetal hemoglobin) gene.
- HbF fetal hemoglobin
- targeting an HbF gene can treat sickle cell disease or beta-thalassemia.
- a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected.
- the target cell is a CD8+ T cell.
- the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA
- the guide RNA comprises a targeting sequence that targets a gene selected from PD1 (programmed cell death 1), CTLA4 (cytotoxic T-lymphocyte-associated protein 4), and TCR (T-cell receptor).
- PD1 programmed cell death 1
- CTLA4 cytotoxic T-lymphocyte-associated protein 4
- TCR T-cell receptor
- targeting a PD-1 gene, a CTLA-4 gene, or a TCR gene can be used in the generation of chimeric antigen receptor (CAR)- T cells.
- CAR chimeric antigen receptor
- the target cell is a CD4+ T cell.
- the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, where the guide RNA comprises a targeting sequence that targets a CCR5 gene, or targets an integrated and proviral HIV-1.
- Targeting a CCR5 gene can be used to enhance resistance to HIV.
- Targeting an integrated and proviral HIV-1 can be used to reduce the pool of T cells that are reservoirs for latent HIV.
- the target cell is a skeletal muscle cell.
- the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, where the guide RNA comprises a targeting sequence that targets a Duchenne muscular dystrophy (DMD) gene.
- DMD Duchenne muscular dystrophy
- Targeting a DMD gene can be used to treat Duchenne muscular dystrophy.
- the target gene comprises a defect that leads to pathology
- a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected.
- the target cell is an ocular cell (e.g., in a retinal cell, a photoreceptor cell, etc.).
- the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, and wherein the guide RNA comprises a targeting sequence that targets a CEP290 (centrosomal protein 290) gene.
- CEP290 centrosomal protein 290
- Targeting a CEP290 gene can be used to treat Leber congenital amaurosis 10 (LCA10).
- LCA10 Leber congenital amaurosis 10
- a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected.
- target cell is an auditory cell (e.g., hair cells, cochlear cells, etc.).
- the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, where the guide RNA comprises a targeting sequence that targets a USH2A (Usher syndrome 2A) gene.
- a USH2A User syndrome 2A
- Targeting a USH2A gene can be used to treat Usher Syndrome type 2A.
- a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected.
- the target cell is a central nervous system cell (e.g., neurons (e.g., excitatory and inhibitory neurons); and glial cells (e.g., oligodendrocytes, astrocytes and microglia)).
- central nervous system cell e.g., neurons (e.g., excitatory and inhibitory neurons); and glial cells (e.g., oligodendrocytes, astrocytes and microglia)).
- the EDV comprises: a) a nucleic acid comprising a nucleotide sequence encoding a CAR; and b) a guide RNA that provides for knockout of an TRAC-encoding nucleic acid in the target cell.
- the EDV comprises a nucleic acid comprising a nucleotide sequence encoding a CAR.
- the EDV comprises: a) a nucleic acid comprising a nucleotide sequence encoding a CAR; and b) a guide RNA that provides for knockout of an immune checkpoint in the target cell.
- the target cell is a CD8+ T cell.
- the targeting polypeptide comprises an anti-CD19, anti-CD20, anti-CD4, anti-CD28, or anti-CD3 antibody or antibody analog.
- the targeting polypeptide comprises: (i) an anti-CD3 and an anti-CD4 antibody or antibody analog; (ii) an anti-CD3 and an anti-CD28 antibody or antibody analog; or (iii) an anti-CD3, an anti-CD4, and an anti-CD28 antibody or antibody analog.
- the target cell is a regulatory T cell (Treg) and the targeting polypeptide comprises an anti-CD28 superagonist (CD28SA). 22.
- a method of producing an enveloped delivery vehicle comprising: a) introducing the collection of any one of 39-43 and 49-59 into a packaging cell; and b) harvesting EDVs produced by the packaging cell.
- a method of delivering a nucleic acid-binding effector polypeptide (e.g., a CRISPR- Cas effector polypeptide) to a eukaryotic cell the method comprising contacting a eukaryotic cell with the EDV of any one of 1-37 and 44-48 or the composition of 38.
- a method for modifying a target nucleic acid in a eukaryotic cell comprising contacting a eukaryotic cell with the EDV of any one of 1-37 and 44-48 or the composition of 38, wherein said contacting results in delivery of the nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide) into the cell and modification of a target nucleic acid within the cell.
- the nucleic acid- binding effector polypeptide e.g., a CRISPR-Cas effector polypeptide
- the eukaryotic cell is a cancer cell, a stem cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue-resident stem cell, a monocyte, a macrophage, a B cell, or a T cell.
- the method of 65 or 66, wherein the eukaryotic cell is in vitro or ex vivo. 68.
- 70. The method of any one of 65-68, wherein the eukaryotic cell is a regulatory T cell (Treg).
- the method of any one of 65-70, wherein the targeting polypeptide comprises an anti-CD3 and/or an anti-CD28 antibody or antibody analog. 72.
- the targeting polypeptide comprises an anti-CD19, anti-CD20, anti-CD4, anti-CD28, or anti-CD3 antibody or antibody analog.
- the targeting polypeptide comprises an antibody, antibody analog, single chain Fv, diabody, triabody, nanobody or a bi-specific antibody.
- the targeting polypeptide binds to CD19, CD20, CD4, CD28, or CD3.
- the EDV comprises a donor template nucleic acid or a nucleotide sequence encoding the donor template nucleic acid, wherein the donor template nucleic acid comprises a nucleotide sequence encoding a chimeric antigen receptor (CAR).
- CAR comprises one or more scFv or one or more nanobodies specific for a cancer-associated antigen.
- the cancer-associated antigen is a solid tumor-associated antigen selected from: EGFR, HER2, EGFR806, mesothelin, PSCA, MUC1, claudin 18.2, EpCAM, GD2, VEGFR2, AFP, Nectin4/FAP, CEA, LewisY, Glypican-3, EGFRIII, IL-13R ⁇ 2, CD171, MUC16, PSMA, AXL, CD20, CD80/86, c-MET, DLL-3, DR5, EpHA2, FR- ⁇ , gp100, MAGE-A1, MAGE-A3, MAGE-A4, and LMP1; or b) the cancer-associated antigen is an antigen associated with hematological cancer, wherein the cancer-associated antigen is selected from: BCMA, C5, CD19, CD20, CD22, CD25, CD30, CD33, CD38, CD40, CD45, CD52, CD56, CD66, CD74, CD79a,
- Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pl, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c., subcutaneous(ly); and the like.
- Gen3 EDVs [00472] Objective: To streamline the delivery of genome editors.
- FIG.9a The Pol polypeptide, which includes integrase (Int), reverse transcriptase (Rt), and protease (Pr), was deleted without adversely affecting EDV editing activity. Following this deletion, EDVs were produced and their editing activity was evaluated using a luminescence assay in cell culture. A higher luminescence value indicated increased editing.
- FIG.9e Adding C-terminal NLSs enhanced EDV activity. SV40 NLS were appended to the C-terminal end of Cas9, followed by the formation of EDVs and evaluation of their editing activity.
- FIG.9f Adding additional NLS to the N-terminal end of Cas9 did not improve editing activity. The specifics of the NLS added are noted accordingly.
- FIG.9g Integrating the above optimizations resulted in the creation of the 3rd generation EDVs. This version exhibited over 3 times the editing efficiency and contained fewer viral structural protein domains compared to earlier generations. The benchmark was the generation 1 (Hamilton et al., Nat Biotechnol.2024 Jan 11) labelled as “Baseline”.
- the 3rd generation EDVs included a full-length matrix, capsid protein from residues 149-231, no nucleocapsid, 7 NLS on the C-terminus of Cas9, and were devoid of integrase, reverse transcriptase, and protease.
- the “Added NLS” construct represents generation 1 EDVs with 7 NLS on the C-terminus of Cas9.
- the “streamlined +PR” variant mirrors the 3rd generation EDV, with the addition of protease. Both “streamlined -NES +PR” and “streamlined - NES -PR” conditions were analogous to their respective “streamlined +PR” or “streamlined -PR” setups but lacked the NES on Cas9.
- Cas9-EDVs displaying CD19 scFv targeting molecules (which should not bind T cells) did not result in editing of either population. Multiplexing the display of CD3 and CD4 scFv-targeting molecules enhanced genome editing over displaying either CD3 or CD4 scfvs alone.
- Cas9-EDVs pseudotyped with HIV-1 and VSVG are presented as controls – HIV-1 Env pseudotyped EDVs mediated genome editing specifically in CD4+ T cells, while VSVG pseudotyped EDVs mediated genome editing in CD4+ and CD8+ T cells.
- FIG.13 Multiplexing CD3 and CD28 scFv targeting molecules on Cas9-EDVs facilitated T cell activation and proliferation.
- a panel of Cas9-EDVs (packaging PDCD1-targeting Cas9 RNP complexes) were produced with various indicated pseudotypes and concentrated approximately 62.5-fold (10ml sup into 160 ⁇ l T cell media).50ul were used to treat 30k pre-stimulated primary human cells in a final well volume of 100 ⁇ l.
- FIG.11 provides a table that provides descriptions of illustrative non-limiting examples of scFv polypeptides that can be used as targeting polypeptides of subject EDVs. Sequences: (GGGGSGGGGSGGGGS, SEQ ID NO194; TGGGGSGGGGSGGGGS, SEQ ID NO:192; TGSTSGSGKPGSGEGSTKG, SEQ ID NO:193; GGGGSGGGGSGGGGSS, SEQ ID NO:203).
- EDVs leverage retroviral VLP assembly for the transient delivery of Cas9 RNP.
- Cas9-EDVs achieved targeted genome editing within in vivo-generated CAR T cells in humanized mice, with no off-target delivery to liver hepatocytes, showing that EDVs are a programmable, cell-specific delivery platform for complex genome engineering in vivo.
- Examples 3-8 Overview – In Vivo Generation of TRAC-CAR T Cells
- the Examples below relate to in vivo methods using vector-delivered HDRTs and CD3 targeting enveloped delivery vehicles (EDVs) loaded with Cas9 nuclease to precisely integrate CAR transgenes to the TRAC locus of T cells.
- In vivo generated TRAC-CAR T cells would combine T cell specific and physiological CAR expression while bypassing the ex vivo cell manufacturing and patients pre- conditioning.
- Example 3 Materials and Methods [00481] The materials and methods for Examples 4-9 below are provided here in Example 3. [00482] Enveloped delivery vehicles (EDVs).
- EDVs were used in the Examples herein to deliver Cas9/sgTRAC ribonucleoprotein (RNP) to a cell.
- a first generation EDV was used that was coated with a WT vesicular stomatitis virus glycoprotein G (WT-VSVG EDV).
- WT-VSVG EDV WT vesicular stomatitis virus glycoprotein G
- a second generation EDV was used that was coated with a mutated VSVG (K47Q and R354A) that has fusogenic activity and an anti-CD3 antibody (VSVGm-aCD3 EDV).
- the VSVGm-aCD3 EDV included a Cas9 with a 4xNLS at the C-terminus, and in addition, the VSVGm and antibody coding sequences were present on the same nucleic acid as part of the same transcript, separated by a P2A sequence.
- VSVGm-aCD3 EDV is discussed in Examples 6-9 and Figures 16A-2D and 17A-17C.
- CD-19-Targeting TRAC-CAR T Cells To generate CD19-targeting TRAC-CAR T cells, a nucleic acid sequence encoding a CD19 targeted CAR was used in certain HDRTs discussed below.
- Ex vivo transduction of human T cells was used in certain HDRTs discussed below.
- T cells were activated for 48 hours using anti-CD3/CD28 dynabeads. The cells were then transduced with various combinations of concentrated EDVs carrying Cas9/sgTRAC RNPs with separate vectors carrying an HDRTs.
- Flow cytometry Cell expression of TCRs, EGFR, and cell surface markers (e.g., CD4, CD8, CD19, CD25, and CD45) were determined by flow cytometry. Flow cytometry analysis was typically performed 72 to 96 hours after T cell transduction. [00486] Cytotoxicity assay.
- NALM6 is a CD19+ acute lymphoblastic leukemia (ALL) cell line.
- the method produces a cytotoxic activity profile of target PBMCs, e.g., transduced T cells, towards the firefly luciferase NALM6 cell line – a decrease in luciferase signal indicates toxicity of the target PBMCs towards NALM6.
- NALM6 cells were co-cultured with T cells for 24 hours with several effector to tumor cell (E:T) ratios.
- E:T effector to tumor cell
- mice Six to 8-week old immunodeficient NOD/SCID/IL2R ⁇ -/-(NSG) mice were acquired from the Jackson Laboratory (jax.org). The mice were engrafted with human PBMCs for reconstitution of T cell, NK cell, and B cell populations in the mice ( Figure 17A). Two weeks after human PBMC engraftment, the mice receive intravenous (IV) injections of mixtures of 5x10 10 particles of (1) WT-VSVG EDV or VSVGm-aCD3 EDV carrying Cas9/sgTRAC and (2) a vector providing a CD19 targeted CAR. Control mice were injected with phosphate buffer saline (PBS).
- PBS phosphate buffer saline
- the first-generation WT-VSVG EDV successfully delivered a Cas9/sgTRAC RNP in activated primary human T cells and disrupted TCR expression with the HDRT. TCR expression was knocked-down in a dose-response manner; a 60% decrease of TCR expression was achieved.
- Example 5 Transduction of T Cells using an EDV with a Fusogenic Variant and an Anti-CD3 Antibody [00490] This Example demonstrates the use of a second generation EDV which comprises two features on its surface: (1) a VSVG variant with fusogenic activity (VSVGm), and (2) a CD3-targeting antibody (aCD3).
- VSVGm-aCD3 does not have broad tropism – it preferentially targets T cells.1x10 5 human T cells were transduced with 5x10 10 particles of EDV and a separate vector delivering HDRT. Ninety-six hours after transduction, the cells were analyzed by flow cytometry. When combined with an HDRT- carrying vector for transduction of activated human primary T cells, VSVGm-aCD3 EDV achieved similar TRAC CAR knock-in rates compared to the WT-VSVG EDV ( Figures 16A-16B).
- Example 6 The Anti-CD3 Antibody on the EDV Activated Na ⁇ ve T cells
- the anti-CD3 antibody delivered by the second generation EDV (VSVGm-aCD3) was analyzed for activation of na ⁇ ve T cells.
- Na ⁇ ve T cells were treated with either 5 ⁇ l (low dose) or 25 ⁇ l (high dose) of concentrated EDVs and were compared to untransduced (UT) na ⁇ ve T cells.
- CD25 expression was used as a marker for T cell activation.
- the T cells were analyzed by flow cytometry 48 hours post transduction. As shown in Figure 16C, the VSVGm-aCD3 induced CD25 expression on T cells.
- Example 7 TRAC-CAR T Cells were Toxic against B Cells [00492] This Example demonstrates that CD19-targeting TRAC-CAR T cells were cytotoxic against the NALM6 B-ALL cell line.
- CD19 CAR T cells were generated by transducing activated T cells with WT-VSVG EDVs carrying Cas9/sgTRAC in combination with a vector carrying the CD19 CAR HDRT.
- NALM6 cells expressing luciferase were co-cultured with the transduced T cells at three effector to tumor cell (E:T) ratios: 1:1, 1:2, and 1:4. T cell cytotoxicity was determined by luminescence.
- Example 8 In vivo Editing of a T cell Genome Generates a CAR T Cell Capable of Killing Target Cells
- EDV and HDRT combinations were assessed for generation of TRAC-targeted CAR T cells in vivo.
- a humanized mouse model was used as discussed in Example 3 and shown in Figure 17A.
- the mice received IV injections of EDV and HDRT combinations or PBS (control) as shown in Table 2 below.
- PBS control
- Example 9 In vivo Editing of a T cell Genome Generates a CAR T Cell Capable of Killing Target Cells
- Enveloped Delivery Vehicles are engineered virally-derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs).
- RNPs CRISPR-Cas9 ribonucleoproteins
- the data here show that Cas9 RNP nuclear delivery is independent of the native lentiviral capsid structure. Instead, EDV- mediated genome editing activity corresponds directly to the number of nuclear localization sequences on the Cas9 enzyme. EDV structural analysis using cryo-electron tomography and small molecule inhibitors guided the removal of ⁇ 80% of viral residues, creating a minimal EDV (miniEDV) that retains full RNP delivery capability. MiniEDVs are 25% smaller yet package equivalent amounts of Cas9 RNPs relative to the original EDVs, and demonstrated increased editing in cell lines and therapeutically- relevant primary human T cells. [00497] The work here shows the determination of the components that are necessary for EDV-mediated genome editing.
- the capsid structure assembles in a subset of EDV particles, it does not transport Cas9 RNPs into the nucleus. Instead, NLS peptides engineered into the Cas9 protein confer nuclear entry and can be tuned to improve delivery efficiency. Furthermore, mechanism-guided engineering enabled simplification of the EDV design, creating miniEDV particles with only 22% of the original viral residues while achieving up to 2.5-fold higher editing potency compared to the original EDVs in primary human T cells. These results show that virally-derived particles can be efficacious genome editing delivery vehicles that simplify production and manufacturing.
- EDV capsid core does not mediate nuclear delivery of Cas9 RNPs
- Two small molecule inhibitors of the capsid core were tested, lenacapavir and PF-3450074 (PF74) (Fig.18a).
- EDVs packaging Cas9 RNPs were produced that target a prematurely truncated luciferase reporter gene (C205ATC).
- HIV-1 lentiviral vectors packaging a transgene encoding Cas9 enzymes and the same guide RNA were used as a positive control.
- the particles were incubated with HEK-293T cells expressing the truncated luciferase reporter in either the presence or absence of the inhibitors.
- Luciferase expression was specific to cleavage at the luciferase locus, proportional to the dose of EDVs and detectable 48 h after transduction (Fig.22).
- lenacapavir a clinically-approved HIV-1 inhibitor that impairs cargo delivery by stabilizing the core
- Fig.18c no decrease in EDV-mediated induction of reporter cell luminescence occurred
- Fig.18e incubation of cells with increasing concentrations of the capsid core destabilizer PF74 (Fig. 18d) also had no effect on EDV-mediated luminescence (Fig.18e).
- HEK-293T cells were incubated with EDVs and PF74 for 24 h, isolated cell nuclei and used Western blots to determine the relative amounts of Cas9 enzymes or capsid associated with the nucleus (Fig.23).
- PF74 was used in this experiment because lenacapavir has been shown to stall capsid cores on the cytosolic side of nuclear pores, leading to their co-isolation with the nuclear fraction.
- Successful nuclear isolation was confirmed by monitoring nuclear localization of EZH2 and cytosolic localization of GAPDH (Fig.23b).
- the 24 kDa mature capsid protein decreased in the nuclear fraction in the presence of 10 ⁇ M PF74, while the amount of Cas9 enzyme remained consistent across all PF74 concentrations (Fig.23b). Both the Gag- Cas9 polyprotein (220 kDa) and Cas9 (160 kDa) were present in the nuclear fractions.
- the presence of Gag-Cas9 in the nuclear fractions was surprising because it was assumed that editing enzymes needed to be liberated from viral structural proteins by viral protease cleavage to enable nuclear entry. The results suggested that the liberation of Cas9 enzymes by protease cleavage may not be necessary for nuclear association.
- Three-dimensional tomograms of the EDVs and lentiviral vectors revealed spherical particles with a lipid bilayer in each case (Fig.19a). Surface glycoproteins appeared as dark spots densely coating the lipid bilayer exterior. The proportion of mature particles (with a capsid core), immature particles (concentric rings of proteins under the lipid bilayer) and unknown particles was quantified and compared. Consistent with previous reports, both EDVs and lentiviral particles were of similar size ( ⁇ 125 nm diameter) and contained multiple morphologies of the mature capsid core (Fig. 24a-d).
- lenacapavir-eosin Y or unconjugated lenacapavir and eosin Y was incubated with EDVs, then one of three photo-probes (diazirine-biotin, aryl-azide-biotin and phenol-biotin) was added, each with a different labeling radius.
- photo-probes diazirine-biotin, aryl-azide-biotin and phenol-biotin
- proteins proximal to the photocatalyst were biotinylated and captured by biotin enrichment using NeutrAvidin beads.
- the amount of the capsid protein that became biotinylated was proportional to the concentration of the lenacapavir-eosin Y conjugate used in the experiment.
- Each sample had similar quantities of input proteins, so the differences in abundance detected by biotin immunoprecipitation were caused by different localization of the photocatalyst and not sample loading.
- Adding additional N-terminal NLSs to the Cas9 enzymes with seven C-terminal NLSs did not further improve EDV-mediated editing activity (Fig.25a).
- the TRAC locus was targeted to disrupt the native T cell receptor (TCR), a step in the creation of therapeutic TCR-T cells.
- Activated T cells were incubated with an equal number of EDVs, and editing was quantified three days post-incubation by amplicon sequencing.
- EDVs packaging Cas9 RNPs with four or seven NLSs increased editing by 79% and 73% at the TRAC locus, respectively, compared to the original two-NLS designs (Fig.20e).
- This increase in TRAC editing resulted in a corresponding reduction in the number of TCR-expressing T cells as quantified by flow cytometry (Fig.25b).
- Removing capsid core-related components created functional minimal EDVs [00505] It was next investigated whether viral proteins that form or interact with the EDV capsid core could be removed, which could simplify particle production and avoid undesirable interactions with host cell proteins.
- the capsid N-terminal domain (amino acids 5 -148) or the entire capsid protein (amino acids 5 - 227) was removed from the Gag and Gag-Pol polypeptides and the resulting EDVs were tested in luciferase reporter cells. N-terminal domain removal had no effect but removing the entire capsid protein decreased editing by ⁇ 75% (Fig.21a). Next, the removal of the Pol polyprotein, which includes viral protease, reverse transcriptase and integrase, was tested.
- the viral protease matures HIV-1 virions and may also liberate Cas9 RNPs from Gag proteins but is unnecessary in murine leukemia virus-based particles packaging base editors. Reverse transcriptase and integrase assemble with the capsid core to form the pre-integration complex for transgene integration. Removing either the viral protease (RT + INT) independently or the entire Pol polypeptide did not significantly decrease the activity of the EDVs, which shows that both Cas9 and Gag-Cas9 are functional (Fig.21b). Similar deletion or truncation of the two remaining HIV-1 structural proteins, matrix and nucleocapsid, showed that matrix is required but nucleocapsid is not (Fig.21c, 21d).
- miniEDVs could be produced with high functional titers without supplementing producer cells with plasmids encoding extra structural proteins (Fig.27), simplifying their production.
- single-chain antibodies can be displayed on their surface to mediate cell entry (Fig.28).
- the editing efficiency of the miniEDVs was compared to both the original and NLS- optimized EDV designs in primary human activated T cells at the TRAC locus by quantifying the decrease in T cell receptor expression by flow cytometry five days post-incubation (Fig.21f).
- MiniEDVs packaging four- or seven-NLS Cas9s increased editing by 107% and 53%, respectively, relative to the original EDVs and were comparable to their respective NLS-optimized EDV counterparts.
- the editing efficiency of the miniEDVs packaging four-NLS Cas9s was further benchmarked across a range of concentrations in both HEK-293T cells and activated primary human T cells at the B2M locus, whose disruption enables production of allogeneic CAR T cells. An average increase in editing per EDV particle of ⁇ 2.5-fold in both HEK-293T and activated T cells was observed.
- understanding the components inside of EDVs necessary for Cas9 delivery allowed increased editing potency while streamlining the production of delivery vehicles for genome editing.
- EDVs do not use the internal capsid core for nuclear delivery of Cas9 RNPs. Instead, EDV-mediated genome editing depended on the presence of nuclear localization signal (NLS) peptides engineered onto Cas9. Cas9 RNPs were not associated with the capsid core, paving the way for removal of the capsid structure from EDVs to create simpler and more efficacious miniEDV particles. [00510] The miniEDVs are 25% smaller than the original EDVs, yet packaged an equivalent quantity of guide RNAs and by extension Cas9 RNPs.
- NLS nuclear localization signal
- Penicillin-streptomycin 10,000 units/mL (15140122), Opti-MEMTM I reduced serum medium ( 31985062), RIPA lysis and extraction buffer (89900), HaltTM protease inhibitor cocktail (100X) (78429), PierceTM BCA protein assay kits (23225), SuperSignalTM west femto maximum sensitivity substrate (34094), PierceTM ECL Western blotting substrate (32109), RestoreTM PLUS Western blot stripping buffer (46428), NP-40 Surfact-AmpsTM detergent solution (85124), DynabeadsTM human T-activator CD3/CD28 (11161D), custom TaqManTM small RNA assays (CTRWFGP for luciferase sgRNA, CTZTEYN for CLTA sgRNA, CTCE4RX for TRAC sgRNA, and CTWCW3V for the B2M sgRNA), MicroAmpTM optical 384-well reaction plates (4309849), DAPI (4',6- diami
- coli C862003 and NuPAGETM LDS sample buffer (4X) (NP0007) were purchased from Thermo Fisher Scientific, Inc.2-mercaptoethanol (M6250), DL-dithiothreitol (DTT) (D9779), anti-HIV-1 p24 antibody produced in rabbit (SAB3500946), monoclonal anti-Flag M2 antibody produced in mouse (F1804), ethylenediaminetetraacetic acid disodium salt dihydrate (ED2SS), magnesium chloride (M4880), bovine serum albumin (A2058), copper (II) sulfate (C1297), sodium L-ascorbate (A4034), and dimethyl sulfoxide (DMSO) (D8418) were from Sigma-Aldrich.
- M6250 2-mercaptoethanol
- DTT DL-dithiothreitol
- SAB3500946 anti-HIV-1 p24 antibody produced in rabbit
- SAB3500946 monoclonal anti-
- DNA/RNA shield DirectDetectTM ZymoPURE II plasmid midiprep (D4200), ZymoPURE II plasmid maxiprep (D4202), ZymoPURE II plasmid gigaprep (D4204) and Mix & go E. coli transformation kit & buffer sets (T3002) were purchased from Zymo Research Corporation. Sucrose (S24060) was purchased from Research Products International. Primers and oligonucleotide sequences were purchased from Integrated DNA Technologies.
- Plasmids pJRH-1179 U6-reci Gag-Cas9 v2 (Add gene 201915) and pJRH-1180 U6-reci Gag-pol v2 (Addgene 201914) were a gift from Jennifer Hamilton.
- Plasmids pMD2.G (12259), psPAX2 (12260), pHAGE-CMV-Luc2-IRES-ZsGreen-W (164432), and U6-sgRNA-EFS-Cas9-P2A-Puro (211687) were ordered from Addgene.
- NEBuilder® HiFi DNA assembly master mix (E2621X), Luna® universal one-step RT-qPCR kit (E3005E), nuclease- free water (B1500L), thermolabile proteinase K (P8111S) and Q5® high-fidelity 2X master mix (M0492L) were purchased from New England Biolabs.
- EM gold tracer, 10 nm (25487), and Quantifoil R2/2, UT, 200 mesh, gold grids (Q2100AR2-2nm) were purchased from Electron Microscopy Sciences. Polyethylemimine, Linear (MW 25,000) (23966) was purchased from Polysciences. HIV1 p24 ELISA kits (ab218268) were purchased from Abcam.
- Goat anti-mouse IgG heavy and light chain cross-adsorbed antibody HRP conjugated (A90-516P) and goat anti-rabbit IgG heavy and light chain cross-adsorbed antibody HRP conjugated (A120-201P) were purchased from Fortis Life Sciences.
- Mouse anti-cas9 antibody (61758) was purchased from Active Motif, Inc.
- EZH2 (D2C9) XP® rabbit mAb #5246 (5246S) was purchased from Cell Signaling technology.
- GAPDH antibody (G-9) (sc-365062) was purchased from Santa Cruz Biotechnology.
- Lenacapavir (HY-111964), and PF74 (HY-120072) were purchased from MedChemExpress.
- N-acetyl-L- cysteine USP (VWRV0108-25G) was purchased from VWR International, LLC.
- Recombinant human IL-7 (200-07), and recombinant human IL-2 (200-02) were purchased from PeproTech, Inc.
- Silica quality control nanospheres were purchased from NanoFCM, Inc.
- Recombinant human IL-15 (247-ILB) was purchased from R&D systems.
- Cas9 ELISA kits PRB-5079 were purchased from Cell Biolabs.
- APC anti-human ⁇ 2-microglobulin antibody (316312) and APC anti-human TCR ⁇ / ⁇ antibody (306718) were purchased from BioLegend, Inc.
- a 10% SDS solution (S0288) was from Alpha Teknova, Inc.
- QIAprep spin miniprep kits (27106), QIAquick gel extraction kits (28704) and QIAquick PCR purification kits (28104) were purchased from Qiagen.
- SPRIselect beads (B23318) were purchased from Beckman Coulter Life Sciences.
- PhiX sequencing control v3 (FC-110-3001), NextSeq 500/550 mid output kit v2.5 (150 Cycles) (20024904) and HT1 hybridization buffer (20015892) was purchased from Illumina Inc.
- Isothiocyanate-EY (90091) was purchased from Biotium.
- Azide-PEG 4 -amine (BP-21615) was purchased from BroadPharm.
- BTTAA (1236-100) was purchased from Click Chemistry Tools (Vector Laboratories).
- T cells were used fresh for in vitro experiments without freezing.
- T cells were seeded (1,000,000/mL) in complete X-VIVO 15 media (5 v/v% FBS, 4 nM N-acetyl-cysteine, and 55 ⁇ M 2-mercaptoethanol) and activated with anti-human CD3/CD28 magnetic Dynabeads (1:1 beads to cells) for 24 h with IL-2 (200 units/mL) in complete X-VIVO 15 media.
- the magnetic beads were removed and the T cells were cultured in X-VIVO 15 medium with FBS (5 v/v%), IL-7 (10 ng/mL), IL-15 (5 ng/mL), and IL-2 (200 units/mL).
- CRISPR-Cas9 spacer sequences are shown in Table 3.
- the appropriate spacer sequences were cloned into U6-sgRNA-EFS-Cas9-P2A-Puro, pJRH-1179 U6-reci Gag-Cas9 v2 (referred to as Gag-Cas9) and pJRH-1180 U6-reci Gag-pol v2 (referred to as Gag-Pol) plasmids using NEBuilder® HiFi DNA assembly.
- a C205ATC mutation was generated in pHAGE-CMV-Luc2-IRES-ZsGreen-W by ordering the appropriate primers and HiFi DNA assembly.
- Deletions (nuclear localization signals or Gag-Pol domains) were made to the Gag-Cas9 and Gag-Pol plasmids using NEBuilder® HiFi DNA assembly. Nuclear localization signals were inserted into the Gag-Cas9 plasmids using NEBuilder® HiFi DNA assembly of the appropriate plasmid fragments, where the sequences of the nuclear localization signal with appropriate overhangs were purchased as double-stranded oligonucleotides from IDT. Plasmids were transformed into Mach1 E.coli cells rendered competent using the Mix & Go E. coli transformation kit following the manufacturer’s instructions. Mach1 cells were grown with the appropriate antibiotic selection.
- Plasmids were extracted and purified using mini-, midi-, maxi-, or giga- prep kits as necessary following the manufacturer’s instructions. All plasmids were sequence-verified by whole plasmid sequencing (Primordium Labs and Plasmidsaurus Inc.) before use. [00515] Table 3. Oligonucleotide sequences Note: the sequences of Table 3, from top to bottom, are SEQ ID NOs:378-384. Cryogenic electron tomography (cryo-ET) of EDVs and lentiviral vectors. HEK-293T cells (4 million) were seeded into 10-cm plates and allowed to attach overnight.
- cryo-ET Cryogenic electron tomography
- the Gag-Pol 3300 ng
- Gag-Cas9 6700 ng
- VSV-G mut 1000 ng
- Opti-MEM Opti-MEM
- PEI polyethylenimine
- the mixture was incubated for 30 min at room temperature and added dropwise ( ⁇ 400 ⁇ L total) to the HEK- 293T cells.
- Cells were incubated with the transfection mixture for at least 6 h, then swapped with Opti- MEM (10 mL).
- EDVs designed to edit luciferase were used for safety, as the spacer does not have complementary sequences in the human genome.
- the mutant VSV-G defective for binding was used for similar reasons.
- Lentiviral vectors were produced similarly using the Gag-Pol (10000 ng) and VSV-G mut (1000 ng) plasmids. No transgene encoding plasmid was included for safety. Particles were collected the following morning ( ⁇ 48 h after transfection). Cell debris was removed by centrifugation (4000 g for 10 min) and filtering through a 0.45- ⁇ m filter. Particles ( ⁇ 30 mL) were concentrated by iodixanol cushion (10 w/v% OptiPrep in 1 ⁇ PBS) ultracentrifugation (100,000g for 75 min).
- Tilt series were collected on a Titan Krios G3i 300kV cryogenic transmission electron microscope (Thermo Fisher Scientific) with a K3 direct electron detector and an energy filter (Gatan) with a pixel size of 1.67 ⁇ .
- Tilt series were acquired from -60° to 60° in 3° increments using a dose-symmetric tilt scheme, a defocus range of -2 to -4.5 ⁇ m, and a total dose of 120 electrons/ ⁇ 2 . At each tilt position the total exposure was split into 4 frames.
- Detailed imaging parameters per dataset are summarized in Table 4. Tilt images were motion-corrected (Motioncorr2) and exposure filtered based on the accumulated dose using the Alignframes function in IMOD 4.11.
- CTF contrast transfer function
- Subtomogram averaging for EDVs and lentiviral vectors was performed as previously described using a combination of Matlab scripts (MATLAB R2023B, Mathworks) based on functions from the TOM, AV3 and Dynamo packages and subTOM 1.1.6 (https://github.com/DustinMorado/subTOM). 1,6–8
- Initial subtomogram positions and orientations were determined based on the radius and the particle center and were sampled along the surface of a sphere at on the level of the particle membrane. Overlapping subtomograms with an edge length of 428 ⁇ were extracted from the 3D-CTF corrected tomograms binned 4 ⁇ times.
- An initial reference was generated by iteratively aligning subtomograms from a single tomogram using an exhaustive search. This process resulted in a low resolution average that resembled previously determined structures of the immature HIV capsid protein displaying 6-fold symmetry. The reference and corresponding subtomograms were shifted to center the 6-fold symmetry axis. Subtomograms were then re-extracted from the updated positions and 6-fold symmetry was applied during subsequent iterations of subtomogram alignment until the reference did not improve further. This average was then supplied as a reference to align the full data set from the 4 ⁇ binned tomograms. The full data set was split into two half sets by particle and both half sets were aligned independently from each other with identical parameters.
- the full data set was aligned for 5 iterations with 6-fold symmetry applied and subtomogram positions converged onto overlapping positions. Subtomograms with low cross correlation values were subsequently removed. Once the reference and resolution did not improve further, subtomograms with an edge length of 390 ⁇ were re-extracted at the aligned positions from 2 ⁇ binned tomograms. After 6 iterations of alignment, the resolution and quality of the map did not improve further. The resolution was determined by calculating the Fourier Shell Correlation (FSC) between the two independently aligned half sets.
- FSC Fourier Shell Correlation
- EDVs (1 mL) were harvested 30, 48 and 72 h after transfection and frozen at -80°C.
- the concentration of capsid domains in each sample was determined using a capsid (p24) ELISA kit and normalized across samples using RIPA buffer.
- Samples (30 ⁇ L) were mixed with 4 ⁇ LDS (10 ⁇ L with 5 v/v% 2-mercaptoethanol) and loaded into the wells of a Criterion TGX Stain-free gel.
- the SDS-PAGE gel (100 V, 1 h, room temperature) was ran, then proteins were transferred in the gel to nitrocellulose membranes (40 V, overnight, 4°C).
- Membranes were blocked (1 h, room temperature) in a blocking buffer (5% Non-fat dry milk and 0.1 v/v% Tween-20 in 1 ⁇ tris- buffered saline). Rabbit anti-p24 antibody and mouse anti-Flag antibody (1/2500 dilution in blocking buffer) were added and incubated (overnight, 4°C). Blots were washed three times with 1 ⁇ TBST (0.1 v/v% Tween-20 in 1 ⁇ tris-buffered saline). IRDye® 680RD goat anti-mouse IgG secondary antibody and IRDye® 800CW goat anti-rabbit IgG secondary antibody (1/500 dilution in blocking buffer) was added and incubated (1 h, room temperature).
- a blocking buffer 5% Non-fat dry milk and 0.1 v/v% Tween-20 in 1 ⁇ tris- buffered saline.
- Some of the cells (100 ⁇ L) were taken, pelleted by centrifugation (100 g, 2 min) and lysed in RIPA with protease inhibitors (30 min, on ice). The samples were centrifuged (20,000 g, 10 min, 4°C) and the supernatant was transferred to a new tube and stored as the “total” fraction.
- the remaining cells (900 ⁇ L) were pelleted by centrifugation and lysed in cytoplasm lysis buffer (315 ⁇ L, 10 mM Tris-HCl pH 7.4 with 1 mM DTT, 1 mM MgCl 2 , 10% sucrose, 100 mM NaCl, 0.5 v/v% NP-40 and 1 ⁇ protease inhibitors) on ice. After 10 min, the samples were centrifuged (664 g, 2 min, 4°C) and the supernatant was transferred to a new tube and stored as the “cytosolic” fraction.
- cytoplasm lysis buffer 315 ⁇ L, 10 mM Tris-HCl pH 7.4 with 1 mM DTT, 1 mM MgCl 2 , 10% sucrose, 100 mM NaCl, 0.5 v/v% NP-40 and 1 ⁇ protease inhibitors
- the pellet was washed by centrifugation (20,000 g, 10 min, 4°C) using cytoplasm lysis buffer (1 mL) three times, then resuspended in RIPA with protease inhibitors.
- the nuclei were lysed (30 min, on ice), and insoluble components were removed by centrifugation (5,200 g, 2 min, 4°C).
- the supernatant was transferred to a new tube and stored as the “nuclear” fraction.
- the protein concentration of the samples were quantified using BCA assays and normalized to 1 ⁇ g/ ⁇ L, then mixed with the appropriate amount of 5 v/v% 2-mercaptoethanol in 4 ⁇ LDS.
- Luciferase HEK-293T cells were made by transducing low passage HEK- 293T cells with a lentiviral vector packaging a mutant luciferase (C205ATC) and zsGreen transgene. Monoclonal cell lines were established by sorting the cells for zsGreen expression using a BD FACSAria Fusion cell sorter (BD Biosciences). For small molecule drug experiments, lenacapavir and PF74 were dissolved in DMSO. EDVs editing the luciferase transgene were produced as described above.
- Lentivirus were made using the Gag-Pol (10000 ng), pMD2.G (1000 ng) and transgene plasmid U6-sgRNA-EFS- Cas9-P2A-Puro with the luciferase gRNA (2500 ng).
- Luciferase HEK-293T cells (6000 cells per well) were incubated with lentivirus or EDVs (100 ⁇ L for PF74, 75 ⁇ L for lenacapavir) with the indicated concentrations of PF74 or lenacapavir in black bottom 96-well plates. An equivalent volume of DMSO was used as the vehicle control.
- the media from the luciferase HEK-293T cells incubated with EDVs was removed and replaced with a passive lysis buffer (1 ⁇ in ultrapure water, 20 ⁇ L) and incubated on a rocking shaker (room temperature, 30 min). After incubation, the luminescence of the wells were recorded on a Tecan Spark multimode microplate reader (Tecan Group Ltd.) by injecting luciferase substrate (30 ⁇ L) into each well immediately before measurement. The conditions with lentiviral vectors were quantified as above 72 h after transduction to provide sufficient time for the transgene to integrate, produce Cas9 and edit the reporter.
- EDVs were produced with the appropriate Gag-Cas9 plasmid as described above. Luciferase HEK-293T cells were transduced with EDVs (100 ⁇ L). The luminescence of the wells were measured 48 h after transduction as described above. To test whether EDVs without NLSs could use the capsid core for transport, EDVs packaging Cas9 RNPs without NLS were produced. EDVs (50 ⁇ L) were incubated with luciferase HEK-293T cells with the indicated concentrations of lenacapavir. The luminescence of the wells were recorded 48 h after transduction.
- the appropriate EDVs were produced and incubated (6.25 ⁇ L) with the luciferase HEK-293T cells. The luminescence was recorded 48 h after transduction.
- the appropriate EDVs were produced and incubated (capsid deletions 40 ⁇ L, Pol deletions 25 ⁇ L, matrix deletions 40 ⁇ L, nucleocapsid deletions 40 ⁇ L, combining deletions 10 ⁇ L) with luciferase HEK-293T cells. The luminescence was recorded 48 h after transduction.
- EDVs were quantified using a NanoAnalyzer instrument (NanoFCM) following the manufacturer’s SOP. Briefly, EDVs were diluted in Tris-HCl buffer (100 mM Tris-HCl pH 7.5 with 1 mM EDTA) at least ten-fold before analysis. Silica quality controls beads of known concentration were used as calibration standards to determine the physical titre. Particle concentrations were determined using instrument software, NanoFCM Profession V2.0.
- the particles were first purified by ultracentrifugation, then diluted in either DirectDetect buffer for reverse transcription quantitative polymerase chain reactions (RT-qPCR) or RIPA buffer for ELISA.
- RT-qPCR DirectDetect buffer for reverse transcription quantitative polymerase chain reactions
- RIPA buffer for ELISA.
- Custom TaqManTM small RNA assays were designed and ordered against the gRNA sequence. Synthetic sgRNA sequences with the appropriate spacers and no modifications were used as standards for quantification.
- Samples (4 ⁇ L) or standards (4 ⁇ L) were mixed with RT-qPCR mix (6 ⁇ L) (1 ⁇ Luna Luna® Universal One-Step RT-qPCR mix with 0.25 ⁇ RT primer and 1 ⁇ small RNA assay probes from TaqManTM small RNA assay kit in nuclease-free water). The entire sample or standard was loaded into 384-well plates. Samples and standards were prepared in duplicate.
- the cells were stained (on ice in the dark, 30 min) with APC anti-human ⁇ 2-microglobulin antibody (5 ⁇ L per sample) and DAPI as a viability stain (0.3 nmol per sample) in the staining buffer. The cells were then washed three times with the staining buffer. Flow cytometry was used to quantify B2M expression using an Attune Nxt Flow Cytometer (Thermo Fisher Scientific, Inc.). Data was analyzed in FlowJo 10.9.0 with the gates shown in Fig.29. All data was plotted and statistics calculated as indicated in GraphPad Prism v.10.1.1. [00523] Editing in primary activated T cells.
- Activated T cells (30,000 for NLS experiments, 10,000 for EDV minimization experiments) were incubated with EDVs (concentrations as indicated).
- T cells were harvested 5 d after incubation, and stained for B2M as above. Expression of the T cell receptor was stained for similarly, but using an APC anti-human TCR ⁇ / ⁇ antibody (5 ⁇ L per sample).
- Flow cytometry was used to quantify expression using an Attune Nxt Flow Cytometer (Thermo Fisher Scientific, Inc.). Data was analyzed in FlowJo 10.9.0 with the gates shown in Fig.25.
- T cells were harvested 3 d after incubation, then spun down (300 g, 3 min).
- FIG.31A-31B (FIG.31A) [Related to FIG.19] Schematic of photocatalytic proximity labeling experiment.
- EY-LEN Eosin Y - Lencapavir conjugate (500 nM) or unconjugated EY and LEN (EY & LEN, 500 nM each) were incubated with EDVs.
- FIG.34 is a schematic showing the viral structural proteins in example lentiviral vectors (LV), EDVs, and minimized EDV (miniEDVs). The schematic is not drawn to scale.
- FIG.35 [Related to FIG.25] Producer cells were transfected with the appropriate EDV plasmids. Cell lysates were harvested 48 h after transfection for Western blotting. Each lane indicates a separate batch of producer cells. The data show that expression of the Gag-Cas9 polyprotein in the producer cells decreased when too many NLS were added, thus decreasing editing efficiency.
- FIG.36 [Related to FIG.20 and FIG.21] NLS-optimized EDVs designs showed similar increases in editing efficacy in activated human T cells from two donors.
- A EDVs (100 ⁇ L) were incubated with T cells from Donor 1 and editing was quantified by flow cytometry 5 d after incubation by flow cytometry. Donor 1 was used for experiments in FIG.20.
- B EDVs (100 ⁇ L) were incubated with T cells from Donor 2 and editing was quantified by flow cytometry 5 d after incubation by flow cytometry.
- Donor 2 was used for experiments in FIG.21. Error bars indicate standard deviation of three separate batches of EDVs.
- FIG.37 [Related to FIG.21G and FIG.21H] The original and miniEDVs did not show toxicity in HEK-293T or activated human T cells (Donor 2). The indicated doses of EDVs were incubated with cells. After 5 d, cells were stained with DAPI and quantified using flow cytometry. Neither the full EDVs or the miniEDVs decreased the viability of the HEK-293T cells or primary human T cells.
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Abstract
The present disclosure provides enveloped delivery vehicles (EDVs) that include a nucleic acid-binding effector polypeptide, and provided a collection of nucleic acids encoding a subject EDV. In some cases, the EDV is streamlined, e.g., lacks certain proteins and/or includes truncated versions of proteins. The present disclosure provides methods of using and producing an EDV of the present disclosure, e.g., for delivery of a nucleic acid-binding effector polypeptide to a eukaryotic cell.
Description
COMPOSITIONS AND METHODS FOR TARGETED DELIVERY OF NUCLEIC ACID-BINDING EFFECTOR POLYPEPTIDES CROSS-REFERENCE [0001] This application claims the benefit of U.S. Provisional Patent Application Nos.63/556,238 filed February 21, 2024, and 63/674,103 filed July 22, 2024, which applications are incorporated herein by reference in their entirety. STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH [0002] This invention was made with government support under Grant Number GM127018 awarded by the National Institutes of Health and under Grant Number DE-AC52-07NA27344 awarded by the US Department of Energy. The government has certain rights in the invention. INCORPORATION BY REFERENCE OF SEQUENCE LISTING PROVIDED AS A SEQUENCE LISTING XML FILE [0003] A Sequence Listing is provided herewith as a Sequence Listing XML, “BERK- 512WO_SEQLIST.xml” created on February 4, 2025, and having a size of 462,766 bytes. The contents of the Sequence Listing XML are incorporated by reference herein in their entirety. I. INTRODUCTION [0004] RNA-mediated adaptive immune systems in bacteria and archaea rely on Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) genomic loci and CRISPR-associated (Cas) proteins that function together to provide protection from invading viruses and plasmids. Genome editing can be carried out using a CRISPR/Cas system comprising a CRISPR/Cas effector polypeptide and a guide RNA. CRISPR/Cas systems are revolutionizing the field of gene editing and genome engineering. Efficient methods for delivering CRISPR-Cas genome editing components into target cells are needed, for both ex vivo and in vivo applications. [0005] Current delivery strategies for genome editing proteins such as CRISPR have drawbacks. For example, delivery of a recombinant virus encoding a CRISPR-Cas effector polypeptide can lead to prolonged CRISPR-Cas effector polypeptide expression in target cells, thus increasing the likelihood for off-target gene editing events. Others have used a ribonucleoprotein (RNP) comprising a CRISPR-Cas effector polypeptide and guide RNA (gRNA) to deliver the genome editing components into a cell. [0006] There is a need for additional and improved strategies for delivering nucleic acid-binding effector proteins, such CRISPR-Cas effector polypeptides, into target cells. Such are provided herein.
II. SUMMARY [0007] The present disclosure provides enveloped delivery vehicles (EDVs) (also referred to as virus like particles (VLPs)) and nucleic acids encoding them (e.g., a collection of one or more nucleic acids encoding a subject EDV). In some cases, a subject EDV includes (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR Cas effector polypeptide such as a Cas9 or Cas12a); (b) a viral envelop protein (e.g., VSVG or a mutant thereof); (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody); (d) a matrix (MA) polypeptide (e.g., in some cases a truncated MA polypeptide); and (e) an N-terminally truncated capsid (CA) protein. In some such cases, the EDV lacks one or more (in some cases all) of the following proteins: a pol polypeptide protease (PR), a pol polypeptide reverse transcriptase (RT), a pol polypeptide integrase (IN), a nucleocapsid (NC) protein. In some cases, a subject EDV includes 7 or more NLSs (e.g., at the C-terminus). [0008] In some cases, a subject EDV includes (a) a Cas9 polypeptide comprising 4 or more NLSs (e.g., at the C-terminus); (b) a variant vesicular stomatitis virus glycoprotein (VSVG) viral envelop protein that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R354A), respectively, relative to SEQ ID NO: 153; and (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody), where the targeting polypeptide is a fusion protein comprising a PDGFR transmembrane domain fused to an antibody or antibody analog. [0009] In some cases, a subject collection of one or more nucleic acids includes a nucleic acid in which a viral envelop protein and a targeting polypeptide are encoded by nucleotide sequences that are: (i) present on the same nucleic acid as part of the same transcript, and (ii) are separated by a sequence that promotes the production of two independent proteins (e.g., a 2A peptide, an intein, or an IRES, or comprises intronic splice donor/splice acceptor sequences). For example, in some cases, a collection of one or more nucleic acids includes: (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); (b) a viral envelop protein (e.g., VSVG); and (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody); where the viral envelop protein and the targeting polypeptide are encoded by nucleotide sequences that are: (i) present on the same nucleic acid as part of the same transcript, and (ii) are separated by a sequence that promotes the production of two independent proteins (e.g., a 2A peptide, an intein, or an IRES, or comprises intronic splice donor/splice acceptor sequences). [0010] The present disclosure also provides methods that use an EDV of the present disclosure, e.g., methods of delivering a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) into a eukaryotic cell, in vivo gene editing methods, and methods for modifying a target nucleic acid. The present disclosure also provides methods of producing an EDV of the present disclosure, e.g., using a subject collection of one of more nucleic acids.
III. BRIEF DESCRIPTION OF THE DRAWINGS [0011] FIG.1. Schematic illustrating need for delivery vehicles to bypass delivery barriers and transport genome editors to target cells in vivo. (Adapted from Wang JY, et al. Science (2023)) [0012] FIG. 2. Schematic illustrating that viruses have evolved machinery to bypass delivery barriers. (Adapted from “scienceofhiv.” Followed by “org/wp/life-cycle/”). [0013] FIG.3. Schematic illustrating that Cas9 enzymes have been packaged into retrovirus-like particles (termed Enveloped Delivery Vehicles (EDVs)), which have been used to edit cells in vitro and in vivo (see, e.g., Mangeot PE, et al. Nat. Commun (2019) Jan 3;10(1):45; Hamilton JR, et al. Cell Rep (2021) Jun 1;35(9):109207; Banskota S, et al. Cell (2022) Jan 20;185(2):250-265.e16; and Hamilton JR, et al. Nat Biotechnol (2024) Jan 11 doi: 10.1038/s41587-023-02085-z). [0014] FIG. 4. Schematic illustrating that the goal of the work described herein was to simplify EDV systems. [0015] FIG.5. Schematic illustrating incubation of EDVs or lentiviruses (LV) with capsid inhibitors. [0016] FIG.6. Data demonstrating that capsid inhibitors did not inhibit EDV mediated editing. [0017] FIG.7. Data demonstrating that nuclear transport of Cas9 was independent of the capsid cone. [0018] FIG.8. Data demonstrating that nuclear transport of Cas9 required nuclear localization signals. [0019] FIG. 9A-9G. Experimental optimization to form 3rd generation EDVs. (FIG. 9a) The Pol polypeptide, which includes integrase (Int), reverse transcriptase (Rt), and protease (Pr), was deleted without adversely affecting EDV editing activity. Following this deletion, EDVs were formed and their editing activity was evaluated using a luminescence assay in cell culture. A higher luminescence value indicates increased editing. (FIG. 9b) Only the C-terminal (residues 149-231) of capsid were necessary for EDV activity. After shortening the capsid protein to the indicated residues, EDVs were formed and their editing activity was assessed with the same luminescence assay. (FIG.9c) The nucleocapsid protein was not essential for EDV editing activity. The nucleocapsid protein was truncated (deletions as indicated), EDVs were formed and editing activity was measured with a luminescence assay. (FIG. 9d) The matrix protein was important and could not be eliminated without compromising EDV activity. After reducing the matrix protein to specific residues, EDVs were formed and their editing activity was determined with the luminescence assay. (FIG. 9e) Adding C-terminal NLSs enhanced EDV activity. SV40 NLS were appended to the C-terminal end of Cas9, followed by the formation of EDVs and evaluation of their editing activity. (FIG.9f) Adding additional NLS to the N-terminal end of Cas9 did not improve editing activity. The specifics of the NLS added are noted accordingly. (FIG.9g) Integrating the above optimizations resulted in the creation of the 3rd generation EDVs. This version exhibited over 3 times the editing efficiency and contained fewer viral structural protein domains compared to earlier generations. The benchmark was the generation 1 (Hamilton et al., Nat Biotechnol.2024 Jan 11) labelled
as “Baseline”. The 3rd generation EDVs, labelled as “Streamlined -PR”, included a full-length matrix, capsid protein from residues 149-231, no nucleocapsid, 7 NLS on the C-terminus of Cas9, and were devoid of integrase, reverse transcriptase, and protease. The “Added NLS” construct represents generation 1 EDVs with 7 NLS on the C-terminus of Cas9. The “streamlined +PR” variant mirrors the 3rd generation EDV, with the addition of protease. Both “streamlined -NES +PR” and “streamlined -NES -PR” conditions were analogous to their respective “streamlined +PR” or “streamlined -PR” setups but lacked the NES on Cas9. EDVs with these specific modifications were synthesized and their editing efficiency was quantified using the luminescence assay. [0020] FIG. 10 provides a table that provides descriptions of illustrative non-limiting examples of scFv polypeptides that can be used as targeting polypeptides of subject EDVs. [0021] FIG. 11 provides a table that provides descriptions of illustrative non-limiting examples of scFv polypeptides that can be used as targeting polypeptides of subject EDVs. Sequences: (GGGGSGGGGSGGGGS, SEQ ID NO194; TGGGGSGGGGSGGGGS, SEQ ID NO:192; TGSTSGSGKPGSGEGSTKG, SEQ ID NO:193; GGGGSGGGGSGGGGSS, SEQ ID NO:203). Results from experiments using these antibodies with EDVs demonstrated cell-specific genome editing can be achieved both ex vivo and in vivo by pairing the display of VSVGmut with single-chain antibody fragments (scFvs) on EDVs that package Cas9 ribonucleoprotein (RNP) complexes (Cas9-EDVs). EDVs leverage retroviral VLP assembly for the transient delivery of Cas9 RNP. Cas9-EDVs achieved targeted genome editing within in vivo-generated CAR T cells in humanized mice, with no off-target delivery to liver hepatocytes, showing that EDVs are a programmable, cell-specific delivery platform for complex genome engineering in vivo. [0022] FIG. 12 depicts genome editing of primary human T cells with Cas9-EDVs comprising a guide RNA that provides for knockout of TRAC. The EDVs comprised an envelope protein comprising: i) single- chain Fv (scFv) targeting ii) CD3; iii) CD4; iv) scFv targeting CD19; v) CD3 and CD4; or vi) no scFv. Cas9-EDVs pseudotyped with HIV-1 and VSVG are presented as controls - HIV-1 Env pseudotyped EDVs mediate genome editing specifically in CD4+ T cells, while VSVG pseudotyped EDVs mediate genome editing in CD4+ and CD8+ T cells. [0023] FIG.13 depicts activation of primary human T cells with Cas9-EDV displaying anti-CD3 scFv and anti-CD28 scFv. [0024] FIG.14A-14F provide nucleotide sequences (FIG.14A-14D and FIG.14F) encoding: Gag-Cas9 (FIG.19A); Gag-Cas9 with 3x NES (FIG.19B); Gag-Cas9 with 2x p53 NLS (FIG.19C); Gag-Cas9 with 3x NES and 2x p53 NLS (FIG.19D); anti-CD19 scFv 1 (FIG.19F); and an amino acid sequence of Gag- Cas9 with 3x NES and 2x p53 NLS (FIG.19E). [0025] FIG.15A-15D show delivery of homology-directed templates (HDRT) and separate delivery of Cas9 with enveloped delivery vehicles (EDVs) for knock-in at the T cell receptor α constant (TRAC)
locus. FIG.15A shows an illustration of an HDR template targeting a chimeric antigen receptor (CAR) to TRAC delivered and an EDV carrying Cas9/sgTRAC. FIG.15B shows TCR expression in human T cells after transduction with EDVs carrying Cas9/sgTRAC ribonucleoproteins (RNPs). TCR expression was determined by flow cytometry.50 μl of EDV was used for 3x105 T cells (Low), 2x105 T cells (Med), 1x105 T cells (High) and compared to untransduced T cells (UT). FIG.15C shows enhanced green fluorescent protein (EGFR) and T cell receptor (TCR) expression after transduction with Cas9/sgTRAC RNP EDV alone (EDV), Cas9/sgTRAC RNP EDV and vector-delivered HDRT (EDV + vector) as determined by flow. FIG.15D shows knock-in efficiency determined by EGFR expression of activated T cells transduced with EDV, EDV + HDRT, each at three different multiplicities of infection (MOIs). [0026] FIG.16A-16D show characterization of human T cells after transduction with EDVs carrying Cas9/sgTRAC RNP and VSVG-WT (VSVG-WT EDV), or EDVs Cas9/sgTRAC RNP and VSVGm- aCD3 (VSVGm-aCD3 EDV), in combination with HDRT, delivered separately. FIG.16A shows TCR and EGFR expression in human T cells after transduction with different combinations of Cas9/sgTRAC RNP EDV with VSVG-WT (VSVG-WT EDV), Cas9/sgTRAC RNP EDV with VSVGm-aCD3 (VSVGm-aCD3 EDV), and HDRT. EGFR and TCR expression were determined by flow cytometry. FIG.16B shows knock-in efficiency of a CD19 specific CAR at the TRAC locus by combining either VSVG-WT EDV or VSVGmut-aCD3 EDV carrying Cas9/sgTRAC, combined with a TRAC-CAR HDRT. FIG.16C shows CD25 expression as determined by flow cytometry as a marker for T cell activation. UT = untreated cells; Low = cells treated with 5 μl concentrated EDVs; High = cells treated with 25 μl concentrated EDVs. FIG.16D compares cytotoxicity of TCR knock out (KO) T cells with TRAC CD19-CAR T cells generated by transduction with VSVG-WT EDVs carrying Cas9/sgTRAC with a vector carrying a HDRT. Cytotoxicity was determined by luminescence. Results are the mean ± SEM from three technical replicates. [0027] FIG.17A-17C show treatment of NOD scid gamma (NSD) mice and flow cytometry analysis of spleen cells isolated from the mice. FIG. 17A shows a treatment schedule for NSD mice engrafted with human peripheral blood mononuclear cells (PBMCs). Mice received intravenous (IV) injections of Cas9/sgTRAC EDVs with VSVG-WT or VSVGm-aCD3 (aCD3), in combination with HDRT targeting a CD19-CAR-2A-EGFRt construct to the TRAC locus. FIG.17B shows total B cells and CAR-T cells per spleen. FIG.17C shows CD45+/CD19+ B cells and CD45+/CAR+/EGFRT+ CAR-T cells as a percentage of CD45+ cells in each spleen. FIG.17B-17C: Results are the mean ± SEM. Significance was assessed using a repeated-measures one-way ANOVA and Dunnett’s multiple comparisons test. *p<0.05; **p<0.01. [0028] FIG.18A-18G Small molecule inhibitors that disrupt the capsid core do not impact EDV editing. (FIG.18a) Schematic of small molecule inhibition experiments. EDVs or lentivirus (LV) were incubated with luciferase reporter HEK-293T cells in the presence of Lenacapavir or PF74. The
luminescence of the reporter cells were recorded after incubation. (FIG.18b) Schematic showing that Lenacapavir stabilizes the capsid core. (FIG.18c) Lenacapavir did not inhibit EDVs compared to the DMSO control (0 nM). (FIG.18d) Schematic showing that PF74 destabilizes the capsid core. (FIG.18e) PF74 did not inhibit EDVs compared to the DMSO control (0 nM). (FIG.18f) Lenacapavir inhibited LVs compared to the DMSO vehicle control (0 nM). (FIG.18g) PF74 inhibited LVs compared to the DMSO vehicle control (0 nM). Data were normalized to the DMSO control. P-values were calculated using an ordinary one-way ANOVA with Dunnett’s multiple comparisons test. Mean ± standard deviation of n = 3 biological replicates. Significant p-values as indicated. Non significance indicated by “n.s.” [0029] FIG.19A-19E EDVs produce capsid cores that do not encapsulate Cas9. (FIG.19a) Representative two-dimensional slices in the XY plane from cryogenic-electron tomograms of EDVs and LVs that are immature, mature, or unknown. Scale bars are 50 nm. (FIG.19b) Fraction of EDVs (n = 498) and LVs (n = 374) that are mature, immature, or unknown. (FIG.19c) Western blot showing the fraction of immature capsid protein (55 kDa) compared to mature capsid protein (24 kDa) in EDVs and LVs harvested 30, 48 or 72 h after transfection (as indicated). Three independent batches of EDVs and LVs were harvested (one per lane). Partially mature forms of the capsid protein are also visible in the blot. (FIG.19d) Schematic of photocatalytic proximity labeling experiment. The Lenacapavir-eosin Y (EY) conjugate or unconjugated EY and Lenacapavir were incubated with EDVs and allowed to bind. Different photo-probes were then added to enable biotinylation of proximal proteins upon blue light illumination. Biotinylated proteins were isolated using biotin enrichment (biotin-IP). (FIG.19e) Western blot demonstrating the amount of biotinylated Cas9 or mature capsid upon lenacapavir-EY-mediated photocatalytic proximity labeling. The proximity ligation experiments were repeated twice with similar results. [0030] FIG.20A-20E EDV editing activity correlates with nuclear localization signal abundance on Cas9. (FIG.20a) Removal of NLS on Cas9 enzymes reduced editing and luminescence. Data were normalized to the current design with two N-terminal p53 and two C-terminal SV40 NLS. (FIG.20b) The capsid core does not transport Cas9 enzymes missing nuclear localization signals (NLS) into the nucleus. EDVs packaging Cas9 enzymes with no NLS were incubated with luciferase reporter HEK- 293T cells in the presence of Lenacapavir (0 - 500 nM). The luminescence of the reporter cells were recorded after incubation. (FIG.20c) Summary schematic of Cas9 RNP nuclear delivery mechanism by EDVs. Cas9 RNPs are dominantly delivered to the nucleus by the NLS (bottom) and not by the capsid core (top). Schematic not to scale. Adding SV40 NLS to the C-terminus of RNPs in EDVs increased editing. (FIG.20d) EDVs packaging Cas9 enzymes with two p53 N-terminal NLS and increasing numbers of SV40 NLS at the C-terminus were created. An equal volume of EDVs were incubated per design to capture both improvements in physical titer and per particle editing. Data were normalized to
the current design (labeled as “2”). (FIG.20e) EDV designs with four or seven NLS increased editing in activated primary human T cells as measured by amplicon sequencing at a dose of 4500 EDV per cell. The physical titers of the EDVs were determined using nanoparticle flow cytometry on a NanoFCM Nanoanalyzer instrument. P-values were calculated using an ordinary one-way ANOVA with Dunnett’s multiple comparisons test. Mean ± standard deviation of n = 3 biological replicates. Significant p-values as indicated. Non significance indicated by “n.s.” [0031] FIG.21A-21H Removing capsid core-related components created functional minimal EDVs. (FIG.21a) The N-terminal domain of the capsid protein (residues 5 - 149) or the entire capsid protein was removed and the activity of the EDVs was compared to EDVs containing the full capsid. An equal volume of EDVs were incubated per condition. Data were normalized to EDVs containing the full capsid. (FIG.21b) Domains from the Pol polyprotein were removed systematically and the activity of the EDVs were compared to EDVs containing the full Pol polyprotein. Rt: Reverse transcriptase, Pr: Protease, Int: Integrase. An equal volume of EDVs were incubated per condition. Data were normalized to EDVs containing the full Pol. (FIG.21c) The matrix protein was minimized one secondary structure element at a time from the C-terminal end. An equal volume of EDVs were incubated per condition. Data were normalized to EDVs containing the full matrix. (FIG.21d) The nucleocapsid (NC) protein and the activity of the EDVs were compared to EDVs containing the full NC. Data were normalized to EDVs containing the full NC. (FIG.21e) Schematic showing the components and plasmids involved in making full and minimized EDV. The minimized structural proteins are referred to as “miniGag” (FIG.21f) Minimized EDVs had higher activity than the original full EDV design. Full, NLS optimized (7x and 4x) and minimized designs (7x and 4x) were incubated with primary activated human T cells (12000 particles per cell). Particle numbers were determined using the NanoFCM Nanoanalyzer. Expression of the T cell receptor was quantified five days after incubation. Mean ± standard deviation of n = 3 independent replicates. P-values were calculated using a one-way ANOVA with Šídák’s multiple comparison tests between the indicated pairs. Non-significance is indicated by “n.s.” (FIG.21g) Editing at the B2M locus in HEK-293T cells was compared between minimized EDVs and full EDVs. Editing was determined five days after incubation using flow cytometry. Particle numbers were determined using the NanoFCM Nanoanalyzer. (FIG.21h) Editing at the B2M locus in activated T cells was compared between minimized EDVs and full EDVs. Editing was determined five days after incubation using flow cytometry. Particle numbers were determined using the NanoFCM Nanoanalyzer. Unless stated otherwise, Mean ± standard deviation of n = 3 independent replicates. P-values were calculated using a one-way ANOVA with Dunnett’s multiple comparisons. Non-significance is indicated by “n.s.” [0032] FIG.22 Luminescence from the reporter cell line was linear with the volume of EDVs incubated (circles). EDVs that do not edit the truncated luciferase locus do not turn on the reporter cell line (squares). Mean ± range of n = 2 biological replicates.
[0033] FIG.23A-23B Western blot showing inhibition of capsid core nuclear entry does not reduce Cas9 entry into the nucleus. (FIG.23a) HEK-293T cells were incubated with EDVs in the presence of PF74 inhibitors (0 - 10 μM). Cells were collected and fractionated into total, cytosolic and nuclear fractions 24 h of incubation. (FIG.23b) Western blot of the fractions. EZH2 and GAPDH were used as nuclear and cytosolic markers respectively. The intensity of the Cas9 and capsid protein were measured in ImageJ, normalized to the DMSO control (0 nM), and indicated in the relevant lanes. The experiment was repeated twice with similar results. [0034] FIG.24A-24F Structural characterization of EDVs and lentiviral vectors (LVs) using cryo-ET. (FIG.24a) Representative two-dimensional slices in the XY plane of the cryo-tomograms of EDVs and LVs containing different core morphologies. Scale bars are 50 nm. (FIG.24b) Fraction of mature EDVs (n = 142) and LVs (n = 189) that have conical, tubular, multilayer or multiple cores. (FIG.24c) Size distribution of EDVs (measured by the diameter of the outer lipid membrane) N = 498. (FIG.24d) Size distribution of lentivirus. N = 374. (FIG.24e) Cryo-ET 3D reconstructions of immature capsid from LVs and EDVs obtained by subtomogram averaging in gray at 10 Å resolution and 9 Å resolution, respectively. HIV-1 CA structures were fitted into the gray density maps (PDB 5L93). The density shown on the left is oriented with the CA- N-terminal domain (NTD) facing upward, the density map in the middle with CA- C-terminal domain (CTD) facing upwards. On the right, a cross section through the density at the position indicated by the dashed line in the middle panel is shown. The NTD regions of the fitted CA models are colored in blue and CTD regions of the fitted CA models are colored in orange. (FIG.24f) Number of CA hexamers per EDV or lentiviral particle. The cross indicates an outlying datapoint. [0035] FIG.25A-25B Characterization of EDVs with more NLS. (FIG.25a) Adding additional N- terminal NLS did not improve EDV editing. To facilitate tiling of NLS, the bipartite p53 NLS (18 amino acids) was first replaced with a monopartite c-myc NLS (9 amino acids). Both NLS use the same mechanism of nuclear import. EDVs were then incubated with the luciferase HEK-293T cells. (FIG. 25b) Flow cytometry quantification shows that four and seven NLS Cas9 RNPs in EDVs decreased the number of primary activated human T cells expressing the TRAC protein in concordance with the sequencing results. The gating strategy is shown in the top panels. One representative biological replicate of three is shown. [0036] FIG.26A-26F Characterization of miniEDVs. (FIG.26a) Quantification of the physical titers of EDVs using the NanoFCM NanoAnalyzer. (FIG.26b) Size distribution of miniEDVs (N = 315) compared to full EDVs (N = 498) measured as the diameter of the outer lipid membrane in cryo- tomograms. (FIG.26c) Two-dimensional slice of a minimized EDVs tomogram. Scale bar is 50 nm. Orange arrows point to densities underneath the lipid bilayer that potentially corresponds to the minimized Gag. (FIG.26d) Averaged 66.8 Å thick slice of minimized EDV to show the protein density
underneath the lipid membrane (black arrow). Scale bar is 50 nm. (FIG.26e) Quantitation of Cas9 enzymes per particle for EDVs targeting TRAC measured by ELISAs. The particle number was determined by nanoparticle flow cytometry. (FIG.26f) Quantitation of gRNA per particle for EDVs targeting TRAC measured by RT-qPCR. The particle number was determined by nanoparticle flow cytometry. [0037] FIG.27A-27F MiniEDVs could be produced without supplementing producer cells with structural plasmids encoding extra Gag-Pol structural proteins. (FIG.27a) Schematic illustrating the production of the full particles, which is efficient with a 2:1 mass ratio of Gag-Cas9 to Gag-Pol plasmids. (FIG.27b) Producing EDVs using only the Gag-Cas9 plasmids results in low functional titers. Full EDVs were produced with either a 2:1 ratio of Gag-Cas9:Gag-Pol plasmids (black) or only Gag-Cas9 (green). EDVs were incubated with HEK-293T cells and the number of edited cells was quantified by flow cytometry 5 d after incubation. (FIG.27c) Schematic illustrating the production of the miniEDVs with four NLS, which is efficient without the added miniGag-Pol plasmids. (FIG.27d) MiniEDVs could be produced using only the miniGag-Cas9 plasmids with only a small decrease in functional titer. MiniEDVs were produced with either a 2:1 ratio of Gag-Cas9:Gag-Pol plasmids (black) or only Gag- Cas9 (green). (FIG.27e) Schematic illustrating the production of the miniEDVs with seven NLS, which is efficient without the added miniGag-Pol plasmids. (FIG.27f) MiniEDVs could be produced using only the miniGag-Cas9 plasmids with only a small decrease in functional titer. MiniEDVs were produced with either a 2:1 ratio of Gag-Cas9:Gag-Pol plasmids (black) or only Gag-Cas9 (green). EDVs were incubated with HEK-293T cells and the number of edited cells was quantified by flow cytometry 5 d after incubation. Mean ± standard deviation of n = 3 independent replicates. Data points were fitted to a sigmoidal curve for visualization. [0038] FIG.28A-28B Single-chain variable fragments (scFvs) can be displayed on the surface of miniEDVs to mediate cell entry. (FIG.28a) Schematic of a vesicular stomatitis virus glycoprotein (VSV- G) pseudotyped EDV membrane and a EDV membrane displaying a scFV using a CD8a stalk and platelet-derived growth factor receptor (PDGFR) transmembrane (TM) domain. The EDV membranes displaying scFvs are supplemented with a receptor binding deficient mutant of VSV-G (VSVG-mut) that retains fusogen activity. (FIG.28b) Editing activity of a scFv miniEDV and a VSV-G miniEDV in primary activated human T cells. T cell receptor (TCR) expression was quantified with flow cytometer five d after incubation. Mean ± standard deviation of n = 3 independent replicates. [0039] FIG.29 The gating strategy for quantifying the expression of B2M in HEK-293T cells. [0040] FIG.30A-30J Raw Western blots. (FIG.30a) Blot from Figure 1c. EDVs were stained for the capsid domain. (FIG.30b) Blot from Figure 1c. Lentiviral vectors were stained for the capsid domain. (FIG.30c) Blot from Fig.24. The cell fractions were stained for Cas9. (FIG.30d) Blot from Fig.24. The cell fractions were stained for the capsid domain. (FIG.30e) Blot from Fig.24. The cell fractions were
stained for EZH2. (FIG.30f) Blot from Fig.24. The cell fractions were stained for GAPDH. (FIG.30g) Blot from Figure 2e. The biotinylated proteins were stained for Cas9 using anti-Flag antibodies. (FIG. 30h) Blot from Figure 2e. The biotinylated proteins were stained for the capsid protein. (FIG.30i) Blot from Figure 2e. The input proteins were stained for Cas9 using anti-Flag antibodies. (FIG.30j) Blot from Figure 2e. The input proteins were stained for the capsid protein. [0041] FIG.31A-31B (FIG.31A) Schematic of photocatalytic proximity labeling experiment. The Eosin Y - Lencapavir (EY-LEN) conjugate (500 nM) or unconjugated EY and LEN (EY & LEN, 500 nM each) were incubated with EDVs. Phenol biotinylation probes were then added to enable biotinylation of proximal proteins upon blue light illumination. Biotinylated proteins were isolated using biotin enrichment (biotin-IP). Schematic is not to scale. (FIG.31B) Western blot showing the amount of biotinylated Cas9, mature nucleocapsid protein, or mature capsid upon lenacapavir-EY-mediated photocatalytic proximity labeling. The proximity labeling experiments were similarly repeated twice with similar results. [0042] FIG.32 The NLS in the matrix protein accounts for the residual editing activity. The NLS in the matrix protein were mutated in EDVs packaging Cas9 RNPs without NLS. NLS1 (KKKYK) and NLS2 (KSKKK) were mutated to IIKYK and KSIIK respectively. [0043] FIG.33 The p6 protein was removed and the activity of the EDVs were compared to full EDVs. An equal volume of EDVs were incubated per condition. Data were normalized to EDVs containing the full matrix. Mean ± standard deviation of n = 3 batches of EDVs. P-values were calculated using a one- way ANOVA with Dunnett’s multiple comparisons to the EDV designs containing the full protein (“Full”). Mean ± standard deviation of n = 3 batches of EDVs. Non significance indicated by “ns”, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001 ****P ≤ 0.0001. [0044] FIG.34 Schematic showing the viral structural proteins in example lentiviral vectors (LV), EDVs, and minimized EDV (miniEDVs). The schematic is not drawn to scale. [0045] FIG.35 Expression of the Gag-Cas9 polyprotein in the producer cells decreased when too many NLS were added. Producer cells were transfected with the appropriate EDV plasmids. Cell lysates were harvested 48 h after transfection for Western blotting. Each lane indicates a separate batch of producer cells. [0046] FIG.36 NLS-optimized EDVs designs showed similar editing efficacy in activated human T cells from two donors. (A) EDVs (100 μL) were incubated with T cells from Donor 1 and editing was quantified by flow cytometry 5 d after incubation by flow cytometry. Donor 1 was used for experiments in Figure 3. (B) EDVs (100 μL) were incubated with T cells from Donor 2 and editing was quantified by flow cytometry 5 d after incubation by flow cytometry. Donor 2 was used for experiments in Figure 4. Error bars indicate standard deviation of three separate batches of EDVs. P-values were calculated using a one-way ANOVA with Dunnett’s multiple comparisons. P-values are as indicated.
[0047] FIG.37 The original and miniEDVs did not show toxicity in HEK-293T or activated human T cells (Donor 2). The indicated doses of EDVs were incubated with cells. After 5 d, cells were stained with DAPI and quantified using flow cytometry. IV. DEFINITIONS [0048] “Heterologous,” as used herein, means a nucleotide or polypeptide sequence that is not found in the native nucleic acid or protein, respectively. For example, relative to a CRISPR-Cas effector polypeptide, a heterologous polypeptide comprises an amino acid sequence from a protein other than the CRISPR-Cas effector polypeptide. As another example, a CRISPR-Cas effector protein (e.g., a dead or nickase CRISPR-Cas effector protein) can be fused to an active domain from a non-CRISPR-Cas effector protein (e.g., a cytidine deaminase), and the sequence of the active domain could be considered a heterologous polypeptide (it is heterologous to the CRISPR-Cas effector protein). [0049] The terms “polynucleotide” and “nucleic acid,” used interchangeably herein, refer to a polymeric form of nucleotides of any length, either ribonucleotides or deoxynucleotides. Thus, this term includes, but is not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA- RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases. The terms “polynucleotide” and “nucleic acid” should be understood to include, as applicable to the embodiment being described, single- stranded (such as sense or antisense) and double-stranded polynucleotides. [0050] The terms "polypeptide," "peptide," and "protein", are used interchangeably herein, refer to a polymeric form of amino acids of any length, which can include genetically coded and non-genetically coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones. The term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence, fusions with heterologous and homologous leader sequences, with or without N-terminal methionine residues; immunologically tagged proteins; and the like. [0051] The term “naturally-occurring” as used herein as applied to a nucleic acid, a protein, a cell, or an organism, refers to a nucleic acid, cell, protein, or organism that is found in nature. [0052] As used herein the term “isolated” is meant to describe a polynucleotide, a polypeptide, or a cell that is in an environment different from that in which the polynucleotide, the polypeptide, or the cell naturally occurs. An isolated genetically modified host cell may be present in a mixed population of genetically modified host cells. [0053] “Heterologous,” as used herein, refers to a nucleotide or amino acid sequence that is not found in the native nucleic acid or protein, respectively. For example, relative to a Cas9 polypeptide, a
heterologous polypeptide comprises an amino acid sequence from a protein other than the Cas9 polypeptide. Thus, for example, a polymerase polypeptide is heterologous to a Cas9 polypeptide. [0054] “Recombinant,” as used herein, means that a particular nucleic acid (DNA or RNA) is the product of various combinations of cloning, restriction, and/or ligation steps resulting in a construct having a structural coding or non-coding sequence distinguishable from endogenous nucleic acids found in natural systems. Generally, nucleotide sequences encoding the structural coding sequence can be assembled from cDNA fragments and short oligonucleotide linkers, or from a series of synthetic oligonucleotides, to provide a synthetic nucleic acid which is capable of being expressed from a recombinant transcriptional unit contained in a cell or in a cell-free transcription and translation system. Such sequences can be provided in the form of an open reading frame uninterrupted by internal non- translated sequences, or introns, which are typically present in eukaryotic genes. Genomic DNA comprising the relevant nucleotide sequences can also be used in the formation of a recombinant gene or transcriptional unit. Sequences of non-translated DNA may be present 5’ or 3’ from the open reading frame, where such sequences do not interfere with manipulation or expression of the coding regions, and may indeed act to modulate production of a desired product by various mechanisms (see “DNA regulatory sequences”, below). [0055] Thus, e.g., the term “recombinant” polynucleotide or “recombinant” nucleic acid refers to one which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of sequence through human intervention. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. Such artificial combination can be carried out to join together nucleic acid segments of desired functions to generate a desired combination of functions. [0056] Similarly, the term “recombinant” polypeptide refers to a polypeptide which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of amino acid sequence through human intervention. Thus, e.g., a polypeptide that comprises a heterologous amino acid sequence is recombinant. [0057] By “construct” or “vector” is meant a recombinant nucleic acid, generally recombinant DNA, which has been generated for the purpose of the expression and/or propagation of a specific nucleotide sequence(s), or is to be used in the construction of other recombinant nucleotide sequences. [0058] The terms “DNA regulatory sequences,” “control elements,” and “regulatory elements,” used interchangeably herein, 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 expression of a coding sequence and/or production of an encoded polypeptide in a host cell.
[0059] The term “transformation” is used interchangeably herein with “genetic modification” and refers to a permanent or transient genetic change induced in a cell following introduction of new nucleic acid (e.g., DNA exogenous to the cell) into the cell. Genetic change (“modification”) can be accomplished either by incorporation of the new nucleic acid into the genome of the host cell, or by transient or stable maintenance of the new nucleic acid as an episomal element. Where the cell is a eukaryotic cell, a permanent genetic change can be achieved by introduction of new DNA into the genome of the cell. In prokaryotic cells, permanent changes can be introduced into the chromosome or via extrachromosomal elements such as plasmids and expression vectors, which may contain one or more selectable markers to aid in their maintenance in the recombinant host cell. Suitable methods of genetic modification include viral infection, transfection, conjugation, protoplast fusion, electroporation, particle gun technology, calcium phosphate precipitation, direct microinjection, and the like. The choice of method is generally dependent on the type of cell being transformed and the circumstances under which the transformation is taking place (i.e. 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. [0060] “Operably linked” refers to a juxtaposition wherein the components so described are in a relationship permitting them to function in their intended manner. For instance, a promoter is operably linked to a coding sequence if the promoter affects its transcription or expression. As used herein, the terms “heterologous promoter” and “heterologous control regions” refer to promoters and other control regions that are not normally associated with a particular nucleic acid in nature. For example, a “transcriptional control region heterologous to a coding region” is a transcriptional control region that is not normally associated with the coding region in nature. [0061] A “host cell,” as used herein, denotes an in vivo or in vitro eukaryotic cell, a prokaryotic cell, or a cell from a multicellular organism (e.g., a cell line) cultured as a unicellular entity, which eukaryotic or prokaryotic cells can be, or have been, used as recipients for a nucleic acid (e.g., an expression vector), and include the progeny of the original cell which has been genetically modified by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation. A “recombinant host cell” (also referred to as a “genetically modified host cell”) is a host cell into which has been introduced a heterologous nucleic acid, e.g., an expression vector. For example, a eukaryotic host cell is a genetically modified eukaryotic host cell, by virtue of introduction into a suitable eukaryotic host cell of a heterologous nucleic acid, e.g., an exogenous nucleic acid that is foreign to the eukaryotic host cell, or a recombinant nucleic acid that is not normally found in the eukaryotic host cell. [0062] The term “conservative amino acid substitution” refers to the interchangeability in proteins of amino acid residues having similar side chains. For example, a group of amino acids having aliphatic side chains consists of glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having
aliphatic-hydroxyl side chains consists of serine and threonine; a group of amino acids having amide- containing side chains consists of asparagine and glutamine; a group of amino acids having aromatic side chains consists of phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains consists of lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains consists of cysteine and methionine. Exemplary conservative amino acid substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, and asparagine- glutamine. [0063] A polynucleotide or polypeptide has a certain percent “sequence identity” to another polynucleotide or polypeptide, meaning that, when aligned, that percentage of bases or amino acids are the same, and in the same relative position, when comparing the two sequences. Sequence similarity can be determined in a number of different manners. To determine sequence identity, sequences can be aligned using the methods and computer programs, including BLAST, available over the world wide web at ncbi.nlm.nih.gov/BLAST. See, e.g., Altschul et al. (1990), J. Mol. Biol.215:403-10. Another alignment algorithm is FASTA, available in the Genetics Computing Group (GCG) package, from Madison, Wisconsin, USA, a wholly owned subsidiary of Oxford Molecular Group, Inc. Other techniques for alignment are described in Methods in Enzymology, vol.266: Computer Methods for Macromolecular Sequence Analysis (1996), ed. Doolittle, Academic Press, Inc., a division of Harcourt Brace & Co., San Diego, California, USA. Of particular interest are alignment programs that permit gaps in the sequence. The Smith-Waterman is one type of algorithm that permits gaps in sequence alignments. See Meth. Mol. Biol.70: 173-187 (1997). Also, the GAP program using the Needleman and Wunsch alignment method can be utilized to align sequences. See J. Mol. Biol.48: 443-453 (1970). [0064] The terms “chimeric antigen receptor” and “CAR”, used interchangeably herein, refer to artificial multi-module molecules capable of triggering or inhibiting the activation of an immune cell which generally but not exclusively comprise an extracellular domain (e.g., a ligand/antigen binding domain), a transmembrane domain and one or more intracellular signaling domains. The term CAR is not limited specifically to CAR molecules but also includes CAR variants. CAR variants include split CARs wherein the extracellular portion (e.g., the ligand binding portion) and the intracellular portion (e.g., the intracellular signaling portion) of a CAR are present on two separate molecules. CAR variants also include ON-switch CARs which are conditionally activatable CARs, e.g., comprising a split CAR wherein conditional hetero-dimerization of the two portions of the split CAR is pharmacologically controlled. CAR variants also include bispecific CARs, which include a secondary CAR binding domain that can either amplify or inhibit the activity of a primary CAR. CAR variants also include inhibitory chimeric antigen receptors (iCARs) which may, e.g., be used as a component of a bispecific CAR system, where binding of a secondary CAR binding domain results in inhibition of primary CAR activation. CAR molecules and derivatives thereof (i.e., CAR variants) are described, e.g., in PCT
Application No. US2014/016527; Fedorov et al. Sci Transl Med (2013) ;5(215):215ra172; Glienke et al. Front Pharmacol (2015) 6:21; Kakarla & Gottschalk 52 Cancer J (2014) 20(2):151-5; Riddell et al. Cancer J (2014) 20(2):141-4; Pegram et al. Cancer J (2014) 20(2):127-33; Cheadle et al. Immunol Rev (2014) 257(1):91-106; Barrett et al. Annu Rev Med (2014) 65:333-47; Sadelain et al. Cancer Discov (2013) 3(4):388-98; Cartellieri et al., J Biomed Biotechnol (2010) 956304; the disclosures of which are incorporated herein by reference in their entirety. [0065] The terms "antibodies" and “immunoglobulin” include antibodies or immunoglobulins of any isotype, fragments of antibodies that retain specific binding to antigen (antigen binding region), including, but not limited to, Fab, Fv, scFv, and Fd fragments, chimeric antibodies, humanized antibodies, single-chain antibodies (scAb), single domain antibodies (dAb), single domain heavy chain antibodies, a single domain light chain antibodies, nanobodies, bi-specific antibodies, multi-specific antibodies, evibodies, minobodies, diabodies, and fusion proteins comprising an antigen-binding (also referred to herein as antigen binding) portion of an antibody and a non-antibody protein. [0066] The term "nanobody" (Nb), as used herein, refers to the smallest antigen binding fragment or single variable domain (VHH) derived from naturally occurring heavy chain antibody and is known to the person skilled in the art. They are derived from heavy chain only antibodies, seen in camelids. In the family of "camelids" immunoglobulins devoid of light polypeptide chains are found. "Camelids" comprise old world camelids (Camelus bactrianus and Camelus dromedarius) and new world camelids (for example, Llama paccos, Llama glama, Llama guanicoe and Llama vicugna). A single variable domain heavy chain antibody is referred to herein as a nanobody or a VHH antibody. [0067] "Single-chain Fv" or "sFv" or “scFv” antibody fragments comprise the VH and VL domains of antibody, wherein these domains are present in a single polypeptide chain. In some embodiments, the Fv polypeptide further comprises a polypeptide linker between the VH and VL domains, which enables the sFv to form the desired structure for antigen binding. For a review of sFv, see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol.113, Rosenburg and Moore eds., Springer-Verlag, New York, pp.269-315 (1994). [0068] As used herein, the term "antibody mimetic" refers to compounds which, like antibodies, can specifically and/or selectively bind antigens or other targets, but which are not structurally related to antibodies. Antibody mimetics are usually artificial peptides or proteins, but they are not limited to such embodiments. Typically, antibody mimetics are smaller than antibodies, with a molar mass of about 3-20 kDa (whereas antibodies are generally about 150 kDa). Non-limiting examples of antibody mimetics include peptide aptamers, affimers, affilins, affibodies, affitins, alphabodies, anticalins, avimers, DARPins, fynomers, Kunitz domain peptides, nanoCLAMPs, affinity reagents and scaffold proteins. [0069] As used herein, the terms "treatment," "treating," and the like, refer to obtaining a desired pharmacologic and/or physiologic effect. The effect may be prophylactic in terms of completely or
partially preventing a disease or symptom thereof and/or may be therapeutic in terms of a partial or complete cure for a disease and/or adverse effect attributable to the disease. "Treatment," as used herein, covers any treatment of a disease in a mammal, e.g., in a human, and includes: (a) preventing the disease from occurring in a subject which may be predisposed to the disease but has not yet been diagnosed as having it; (b) inhibiting the disease, i.e., arresting its development; and (c) relieving the disease, i.e., causing regression of the disease. [0070] The terms "individual," "subject," "host," and "patient," used interchangeably herein, refer to an individual organism, e.g., a mammal, including, but not limited to, murines, simians, non-human primates, humans, mammalian farm animals, mammalian sport animals, and mammalian pets. [0071] Before the present invention is further described, it is to be understood that this invention is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting, since the scope of the present invention will be limited only by the appended claims. [0072] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention. [0073] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited. [0074] It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a guide RNA” includes a plurality of such guide RNAs; reference to “a targeting polypeptide” includes a plurality of such polypeptides; and reference to “the CRISPR-Cas effector polypeptide” includes reference to one or more CRISPR-Cas effector polypeptides and equivalents thereof known to those skilled in the art, and so forth. It is further noted that the claims may be drafted to exclude any optional element. As such, this statement is intended to serve as antecedent basis for use of such
exclusive terminology as “solely,” “only” and the like in connection with the recitation of claim elements, or use of a “negative” limitation. [0075] The use of the terms “a,” “an,” and “the,” and similar referents in the context of describing the disclosure (especially in the context of the following claims) are to be construed to cover both the singular and the plural, unless otherwise indicated herein or clearly contradicted by context. The terms “comprising,” “having,” “including,” and “containing” are to be construed as open-ended terms (i.e., meaning “including, but not limited to,”) unless otherwise noted. Recitation of ranges of values herein are merely intended to serve as a shorthand method of referring individually to each separate value falling within the range, unless otherwise indicated herein, and each separate value is incorporated into the specification as if it were individually recited herein. For example, if the range 10-15 is disclosed, then 11, 12, 13, and 14 are also disclosed. All methods described herein can be performed in any suitable order unless otherwise indicated herein or otherwise clearly contradicted by context. The use of any and all examples, or exemplary language (e.g., “such as”) provided herein, is intended merely to better illuminate the embodiments of the disclosure and does not pose a limitation on the scope of the disclosure unless otherwise claimed. [0076] As used herein, the term “about” used in connection with an amount indicates that the amount can vary by 10% of the stated amount. For example, “about 100” means an amount of from 90-110. Where about is used in the context of a range, the “about” used in reference to the lower amount of the range means that the lower amount includes an amount that is 10% lower than the lower amount of the range, and “about” used in reference to the higher amount of the range means that the higher amount includes an amount 10% higher than the higher amount of the range. For example, from about 100 to about 1000 means that the range extends from 90 to 1100. [0077] The term “and/or” as used herein a phrase such as “A and/or B” is intended to include both A and B; A or B; A (alone); and B (alone). Likewise, the term “and/or” as used herein a phrase such as “A, B, and/or C” is intended to encompass each of the following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone); B (alone); and C (alone). [0078] It is understood that aspects and embodiments of the present disclosure described herein include “comprising,” “consisting,” and “consisting essentially of” aspects and embodiments. [0079] It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. All combinations of the embodiments pertaining to the invention are specifically embraced by the present invention and are disclosed herein just as if each and every combination was individually and explicitly disclosed. In addition, all sub-combinations of the various embodiments and elements thereof are also specifically
embraced by the present invention and are disclosed herein just as if each and every such sub- combination was individually and explicitly disclosed herein. [0080] The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates which may need to be independently confirmed. V. DETAILED DESCRIPTION [0081] The terms enveloped delivery vehicle (EDV) and virus like particle (VLP) are used interchangeably herein as equivalent terms. As such, reference to one (e.g., EDV) is considered reference to the other (e.g., VLP). Therefore, all disclosures/discussions herein of EDVs are to be equally considered disclosures/discussions of VLPs and vice versa. [0082] As noted above, the present disclosure provides enveloped delivery vehicles (EDVs) (also referred to as virus like particles (VLPs)) and nucleic acids encoding them, e.g., a collection of one or more nucleic acids encoding a subject EDV. In some cases, a subject EDV includes (a) a nucleic acid- binding effector polypeptide (e.g., a CRISPR Cas effector polypeptide such as a Cas9 or Cas12a); (b) a viral envelop protein (e.g., VSVG or a mutant thereof); (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody); (d) a matrix (MA) polypeptide (e.g., in some cases a truncated MA polypeptide); and (e) an N-terminally truncated capsid (CA) protein. In some such cases, the EDV lacks one or more (in some cases all) of the following proteins: a pol polypeptide protease (PR), a pol polypeptide reverse transcriptase (RT), a pol polypeptide integrase (IN), a nucleocapsid (NC) protein. In some cases, a subject EDV includes 7 or more NLSs (e.g., at the C-terminus). [0083] In some cases, a subject EDV includes (a) a Cas9 polypeptide comprising 4 or more NLSs (e.g., at the C-terminus); (b) a variant vesicular stomatitis virus glycoprotein (VSVG) viral envelop protein that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R354A), respectively, relative to SEQ ID NO: 153; and (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody), where the targeting polypeptide is a fusion protein comprising a PDGFR transmembrane domain fused to an antibody or antibody analog. [0084] In some cases, a subject collection of one or more nucleic acids includes a nucleic acid in which a viral envelop protein and a targeting polypeptide are encoded by nucleotide sequences that are: (i) present on the same nucleic acid as part of the same transcript, and (ii) are separated by a sequence that promotes the production of two independent proteins (e.g., a 2A peptide, an intein, or an IRES, or comprises intronic splice donor/splice acceptor sequences). For example, in some cases, a collection of one or more nucleic acids includes: (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas
effector polypeptide such as Cas9 or Cas12a); (b) a viral envelop protein (e.g., VSVG); and (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody); where the viral envelop protein and the targeting polypeptide are encoded by nucleotide sequences that are: (i) present on the same nucleic acid as part of the same transcript, and (ii) are separated by a sequence that promotes the production of two independent proteins (e.g., a 2A peptide, an intein, or an IRES, or comprises intronic splice donor/splice acceptor sequences). [0085] The present disclosure also provides methods that use an EDV of the present disclosure, e.g., methods of delivering a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) into a eukaryotic cell, in vivo gene editing methods, and methods for modifying a target nucleic acid. The present disclosure also provides methods of producing an EDV of the present disclosure, e.g., using a subject collection of one of more nucleic acids. [0086] In some cases, a subject EDV comprises a nucleic acid comprising a nucleotide sequence encoding a therapeutic polypeptide, such as a chimeric antigen receptor (CAR). In some cases, a subject EDV comprises one or more CRISPR-Cas guide nucleic acids (e.g., guide RNA), or one or more nucleic acids comprising nucleotide sequences encoding the one or more CRISPR-Cas guide nucleic acids. In some cases, the one or more CRISPR-Cas guide nucleic acids provide for knockout of an endogenous nucleic acid. In some cases, a subject EDV includes a donor template nucleic acid. As such, in some embodiments, contacting a target nucleic acid (e.g., chromosomal DNA) with a CRISPR-Cas effector polypeptide, the one or more CRISPR-Cas guide nucleic acids, and the donor template nucleic acid – delivered to a cell via a subject EDV - results in insertion of sequence of the donor template nucleic acid into the target nucleic acid. In some cases, the donor template nucleic acid comprises a nucleotide sequence encoding a therapeutic polypeptide. ENVELOPED DELIVERY VEHICLES (EDVS) [0087] The present disclosure provides enveloped delivery vehicles (EDVs) (also referred to as virus like particles (VLPs)) and nucleic acids encoding them, e.g., a collection of one or more nucleic acids encoding a subject EDV, in addition to methods of their use and production. For literature related EDVs, please refer to Mangeot PE, et al. Nat. Commun (2019) Jan 3;10(1):45; Hamilton JR, et al. Cell Rep (2021) Jun 1;35(9):109207; Banskota S, et al. Cell (2022) Jan 20;185(2):250-265.e16; and Hamilton JR, et al. Nat Biotechnol (2024) Jan 11 doi: 10.1038/s41587-023-02085-z; as well as international patent application No. PCT/US23/72598, which is incorporated by reference herein in its entirety for its disclosures related to EDVs, nucleic acids encoding them, and methods of using and producing them. In some cases, the EDV comprises a therapeutic polypeptide, or a nucleic acid comprising a nucleotide sequence encoding the therapeutic polypeptide, encapsidated within the EDV. The EDVs can be used in in vivo methods of genome editing, which methods are also provided. In some cases, the EDVs comprise
a CRISPR-Cas effector polypeptide as the nucleic acid-binding effector polypeptide. In some cases, the EDVs comprise a nucleic acid comprising a nucleotide sequence encoding a CRISPR-Cas effector polypeptide. In some cases, an EDV of the present disclosure comprises an RNP comprising: a) a CRISPR-Cas effector polypeptide; and b) a CRISPR-Cas guide nucleic acid, where the guide nucleic acid (e.g., guide RNA)) comprises: i) a nucleotide sequence that comprises a protein-binding segment comprising a nucleotide sequence that binds to the CRISPR-Cas effector polypeptide, and a target- binding segment comprising a nucleotide sequence that is complementary to a target nucleotide sequence of a target DNA in a cell (e.g., a eukaryotic cell; e.g., a eukaryotic cell present in an individual). In some cases, an EDV of the present disclosure comprises: a nucleic acid (e.g., a recombinant expression vector) comprising a nucleotide sequence encoding a CRISPR-Cas effector polypeptide and a nucleotide sequence encoding a CRISPR-Cas guide RNA. In some cases, an EDV of the present disclosure comprises a donor nucleic acid. [0088] In some cases, components of a subject EDV are produced as part of a gag polyprotein. In some cases, the gag polyprotein is a retroviral gag polyprotein, and in some cases, the retroviral gag polyprotein is a lentiviral gag polyprotein. For example, the lentiviral gag polyprotein can be selected from the group consisting of a bovine immunodeficiency virus gag polyprotein, a simian immunodeficiency virus gag polyprotein, a feline immunodeficiency virus gag polyprotein, a human immunodeficiency virus gag polyprotein, an equine infection anemia virus gag polyprotein, and a caprine arthritis encephalitis virus gag polyprotein. [0089] When present, the matrix protein (MA), capsid protein (CA), and nucleocapsid protein (NC) portions of a gag polyprotein can be of any of a variety of retroviruses. For example, in some cases, a MA polypeptide of the gag polyprotein can comprise an amino acid sequence having 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 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following MA amino acid sequence: GARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQ PSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVS QNY (SEQ ID NO:296). [0090] In some cases, a CA polypeptide of the gag polyprotein can comprise an amino acid sequence having 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 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following CA amino acid sequence: PIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQA AMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGE
IYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQN ANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO:282). [0091] In some cases, the retroviral gag polyprotein comprises a p1 polypeptide and a p6 polypeptide (e.g., in some cases, an MA polypeptide, a CA polypeptide, an NC polypeptide, a p1 polypeptide, and a p6 polypeptide). In some cases, the retroviral gag polyprotein comprises a p6 polypeptide (e.g., in some cases, an MA polypeptide, a CA polypeptide, an NC polypeptide, and a p6 polypeptide). In some cases, the NC-p1-p6 polypeptide of the gag polyprotein comprises an amino acid sequence having 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 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: IQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQANFLGKIWP SHKGRPGNFLQSRPEPTAPPEESFRFGEETTTPSQKQEPIDKELYPLASLRSLFGSDPSSQ (SEQ ID NO:211). [0092] In some cases, the retroviral gag polyprotein comprises a p2 polypeptide. In some cases, the p2 polypeptide comprises an amino acid sequence having 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 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: AEAMSQVTNPATIM (SEQ ID NO:212). [0093] In some cases, a retroviral gag polyprotein is a gag polyprotein of an alpha retrovirus, a beta retrovirus, a gamma retrovirus, a delta retrovirus, an epsilon retrovirus, or a spumavirus. In some cases, the retroviral gag polyprotein is a gag polyprotein of a human immunodeficiency virus. [0094] In some cases, a Gag polypeptide such as a retroviral (e.g. lentiviral) Gag polypeptide includes CA (e.g., p24), MA (e.g., p17) and NC (e.g., p7) polypeptides (in some cases CA and MA, but not NC – see Gen 3 EDVs below). In some cases, the CA protein and/or the MA protein is truncated (see, e.g., Gen3 EDVs below). In some cases, a Gag polypeptide such as a retroviral (e.g. lentiviral) Gag polypeptide includes, in addition, a p6 polypeptide. In some cases, a Gag polypeptide such as a retroviral (e.g. lentiviral) Gag polypeptide includes, in addition, one or more of p1, p2, and p6 polypeptides. In some cases, a Gag polypeptide such as a retroviral (e.g. lentiviral) Gag polypeptide includes CA, MA, NC, and p6 polypeptides (in some cases it does not include the NC – see Gen 3 EDVs below). In some cases, a Gag polypeptide such as a retroviral (e.g. lentiviral) Gag polypeptide includes CA, MA, NC, p1, p2, and p6 polypeptides (in some cases it does not include the NC – see Gen 3 EDVs below). See, e.g., Muriaux and Darlix (2010) RNA Biol.7:744. [0095] In some embodiments, a subject nucleic acid comprises a nucleotide sequence encoding a fusion polypeptide comprising: i) a lentiviral gag polyprotein (e.g., a lentiviral gag polyprotein) comprising a MA polypeptide, a CA polypeptide, and an NC polypeptide (in some cases it does not encode an NC and
in some cases the CA and/or the MA is truncated – see Gen3 EDVs below); and ii) a nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a), wherein the fusion polypeptide comprises a proteolytically cleavable linker between the gag polyprotein and the nucleic acid-binding effector polypeptide. In some cases, at least one of the nucleic acids in a subject collection (system) comprises a nucleotide sequence encoding a protease that cleaves the proteolytically cleavable linker. The proteolytically cleavable linker can be one that is cleaved by a lentiviral protease. The proteolytically cleavable linker can be one that is cleaved by a protease other than a lentiviral protease (i.e., the protease is heterologous to the lentivirus). [0096] A proteolytically cleavable linker comprises a protease cleavage site. A proteolytically cleavable linker can comprise a matrix metalloproteinase cleavage site, e.g., a cleavage site for a MMP selected from collagenase-1, -2, and -3 (MMP-1, -8, and -13), gelatinase A and B (MMP-2 and -9), stromelysin 1, 2, and 3 (MMP-3, -10, and -11), matrilysin (MMP-7), and membrane metalloproteinases (MT1-MMP and MT2-MMP). For example, the cleavage sequence of MMP-9 is Pro-X-X-Hy (wherein, X represents an arbitrary residue; Hy, a hydrophobic residue), e.g., Pro-X-X-Hy-(Ser/Thr), e.g., Pro-Leu/Gln-Gly- Met-Thr-Ser, or Pro-Leu/Gln-Gly-Met-Thr. Another example of a protease cleavage site is a plasminogen activator cleavage site, e.g., a uPA or a tissue plasminogen activator (tPA) cleavage site. In some cases, the cleavage site is a furin cleavage site. Specific examples of cleavage sequences of uPA and tPA include sequences comprising Val-Gly-Arg. Another example of a protease cleavage site that can be included in a proteolytically cleavable linker is a tobacco etch virus (TEV) protease cleavage site, e.g., ENLYTQS (SEQ ID NO:336), where the protease cleaves between the glutamine and the serine. Another example of a protease cleavage site that can be included in a proteolytically cleavable linker is an enterokinase cleavage site, e.g., DDDDK (SEQ ID NO:337), where cleavage occurs after the lysine residue. Another example of a protease cleavage site that can be included in a proteolytically cleavable linker is a thrombin cleavage site, e.g., LVPR (SEQ ID NO:338). Additional suitable linkers comprising protease cleavage sites include linkers comprising one or more of the following amino acid sequences: LEVLFQGP (SEQ ID NO:339), cleaved by PreScission protease (a fusion protein comprising human rhinovirus 3C protease and glutathione-S-transferase; Walker et al. (1994) Biotechnol.12:601); a thrombin cleavage site, e.g., CGLVPAGSGP (SEQ ID NO:340); SLLKSRMVPNFN (SEQ ID NO:341) or SLLIARRMPNFN (SEQ ID NO:342), cleaved by cathepsin B; SKLVQASASGVN (SEQ ID NO:343) or SSYLKASDAPDN (SEQ ID NO:344), cleaved by an Epstein-Barr virus protease; RPKPQQFFGLMN (SEQ ID NO:345) cleaved by MMP-3 (stromelysin); SLRPLALWRSFN (SEQ ID NO:346) cleaved by MMP-7 (matrilysin); SPQGIAGQRNFN (SEQ ID NO:347) cleaved by MMP-9; DVDERDVRGFASFL SEQ ID NO:348) cleaved by a thermolysin-like MMP; SLPLGLWAPNFN (SEQ ID NO:349) cleaved by matrix metalloproteinase 2 (MMP-2); SLLIFRSWANFN (SEQ ID NO:350) cleaved by cathespin L; SGVVIATVIVIT (SEQ ID NO:351) cleaved by cathepsin D;
SLGPQGIWGQFN (SEQ ID NO:352) cleaved by matrix metalloproteinase 1(MMP-1); KKSPGRVVGGSV (SEQ ID NO:353) cleaved by urokinase-type plasminogen activator; PQGLLGAPGILG (SEQ ID NO:354) cleaved by membrane type 1 matrix metalloproteinase (MT- MMP); HGPEGLRVGFYESDVMGRGHARLVHVEEPHT (SEQ ID NO:355) cleaved by stromelysin 3 (or MMP-11), thermolysin, fibroblast collagenase and stromelysin-1; GPQGLAGQRGIV (SEQ ID NO:356) cleaved by matrix metalloproteinase 13 (collagenase-3); GGSGQRGRKALE (SEQ ID NO:357) cleaved by tissue-type plasminogen activator(tPA); SLSALLSSDIFN (SEQ ID NO:358) cleaved by human prostate-specific antigen; SLPRFKIIGGFN (SEQ ID NO:359) cleaved by kallikrein (hK3); SLLGIAVPGNFN (SEQ ID NO:360) cleaved by neutrophil elastase; and FFKNIVTPRTPP (SEQ ID NO:361) cleaved by calpain (calcium activated neutral protease). In some cases, the protease cleavage site is a TEV protease cleavage site, e.g., ENLYFQS (SEQ ID NO:362), where cleavage occurs between the Gln and the Ser. In some cases, the protease cleavage site is the TEV protease cleavage site ENLYFQP (SEQ ID NO:363). ENLYFQS (SEQ ID NO:362) and ENLYFQP (SEQ ID NO:363) are wildtype recognition sequences (cleavage substrates) for TEV protease (see e.g. Stols et al. (2002) Prot. Exp. Purif.25: 8-12). In some cases, the proteolytically cleavable linker comprises an HIV-1 protease cleavage site (e.g. SQNYPIVQ (SEQ ID NO:205)), where cleavage occurs between the tyrosine and the proline. In some cases, an HIV-1 protease cleavage site (e.g. SQNYPIVQ (SEQ ID NO:205)) is specifically excluded. [0097] In some cases, the protease cleavage site is a TEV protease cleavage site, e.g., ENLYTQS (SEQ ID NO:336), where the protease cleaves between the glutamine and the serine. In some cases, the protease cleavage site is a variant TEV-cleavage substrate, where the variant TEV cleavage site is cleaved by a TEV protease less efficiently than cleavage of ENLYTQS (SEQ ID NO:336) by the TEV protease. In some cases, a variant TEV-cleavage site can: (1) mimic the temporal cleavage observed with wild-type gag polyprotein maturation; and/or (2) maximize packaging of a CRISPR/Cas effector polypeptide into a VLP. Suitable variant TEV cleavage sites are described in Tözsér et al. (2005) FEBS J.272:514. Suitable variant TEV cleavage sites include: ENAYFQS (SEQ ID NO:364), ENLRFQS (SEQ ID NO:365), ENLFFQS (SEQ ID NO:366), ETVRFQS (SEQ ID NO:367), ETLRFQS (SEQ ID NO:368), ETARFQS (SEQ ID NO:369), ETVYFQS (SEQ ID NO:370), and ENVYFQS (SEQ ID NO:371). Gen2 EDVs [0098] In some embodiments, a subject EDV includes (a) a Cas9 polypeptide comprising 4 or more NLSs (e.g., at the C-terminus); (b) a variant vesicular stomatitis virus glycoprotein (VSVG) viral envelop protein that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R354A), respectively, relative to SEQ ID NO: 153; and (c) a
targeting polypeptide that provides for binding to a target cell (e.g., an antibody), where the targeting polypeptide is a fusion protein comprising a PDGFR transmembrane domain fused to an antibody or antibody analog. [0099] In some cases, the Cas9 polypeptide is a fusion polypeptide comprising: i) a Cas9 protein; and ii) one or more heterologous polypeptides. In some case, the Cas9 protein has nickase activity (nCas9) or is catalytically deactivated (i.e., is a ‘dead’ Cas9, i.e., dCas9). In some cases, at least one of the one or more heterologous polypeptides includes a deaminase, a reverse transcriptase, a transcription modulator, or an epigenetic modulator. In some cases, at least one of the one or more heterologous polypeptides is a Gag polypeptide. In some cases, the Cas9 polypeptide is produced as part of a polyprotein (e.g., a gag-Cas9 polyprotein). [00100] In some cases, a collection of one or more nucleic acids (e.g., in some cases two nucleic acids) that encodes a subject EDV includes nucleotide sequences that encode a pol polyprotein comprising a protease (PR), a reverse transcriptase (RT), and an integrase (INT). In some such cases, the pol polyprotein is part of a gag-pol protein. [00101] In some embodiments, a subject collection of one or more nucleic acids encodes an EDV that includes: (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); (b) a viral envelop protein or a variant thereof (e.g., VSVG or a variant thereof); and (c) a targeting polypeptide (e.g., an antibody) that provides for binding to a target cell, where the viral envelop protein and the targeting polypeptide are encoded by nucleotide sequences that are: (i) present on the same nucleic acid as part of the same transcript, and (ii) are separated by a sequence that promotes the production of two independent proteins. Sequence that promotes the production of two independent proteins include, but are not limited to: a 2A peptide (e.g., P2A, F2A, E2A, T2A, and any combination thereof), an intein, an IRES, or intronic splice donor/splice acceptor sequences. [00102] By a “2A peptide” it is meant a small peptide sequence (usually 18-25 amino acids although several of such sequences can be placed in tandem) that allows for expression (translation) of discrete protein products from a single RNA transcript (e.g., through a self-“cleaving” event often referred to as “ribosome skipping”—although the disclosure herein does not rely on and is not bound by the mechanism of action), even though the separate proteins are encoding as part of the same open reading frame (ORF).2A peptides are readily identifiable by their consensus motif (DXEXNPGP, sometimes described as DVEXNPGP) and their ability to promote protein cleavage/skipping. Any convenient 2A peptide sequence may be used in a subject nucleic acid. Examples of 2A peptides include, but are not limited to 2A peptides from a virus such as foot-and-mouth disease virus (F2A), equine Rhinitis A virus (E2A), porcine teschovirus-1 (P2A) or Thosea asigna virus (T2A). See, e.g., Szymczak-Workman, A. et al. “Design and Construction of 2A Peptide-Linked Multicistronic Vectors”. Cold Spring Harb Protoc. 2012 Feb.1; 2012(2):199-204; Liu et al., Sci Rep.2017; 7: 2193; Kim et al., PLOS One 6:e18556, 2011;
and U.S. Pat. Nos.10,738,325; 9,655,956; 10,577,417; the disclosures of which, as they relate to 2A peptides, are incorporated herein by reference. [00103] Examples of 2A peptide sequences include, but are not limited to (SEQ ID NOs: 372-377, respectively): P2A: ATNFSLLKQAGDVEENPGP E2A: QCTNYALLKLAGDVESNPGP F2A: VKQTLNFDLLKLAGDVESNPGP T2A: EGRGSLLTCGDVEENPGP EZA-F2A: QCTNYALLKLAGDVESNPGPVKQTLNFDLLKLAGDVESNPGP T2A-E2A-F2A: EGRGSLLTCGDVEENPGPQCTNYALLKLAGDVESNPGPVKQTLNFDLLKLAGD VESNPGP [00104] 2A peptide sequences can be used in tandem, and multiple different 2A peptide sequences can be positioned one after another, in any desired combination (see “E2A-F2A” and “T2A-E2A-F2A” above as non-limiting examples). Thus, in some cases a 2A peptide sequence is selected from the group consisting of: P2A, F2A, E2A, T2A, and any combination thereof. [00105] By an “internal ribosome entry site,” or “IRES” it is meant a nucleotide sequence that allows for the initiation of protein translation in the middle of a messenger RNA (mRNA) sequence. For example, when an IRES segment is located between two open reading frames in a bicistronic eukaryotic mRNA molecule, it can drive translation of the downstream protein-coding region independently of the 5'-cap structure bound to the 5' end of the mRNA molecule, i.e. in front of the upstream protein coding region. In such a setup both proteins are produced in the cell. The protein located in the first cistron is synthesized by the cap-dependent initiation approach, while translation initiation of the second protein is directed by the IRES segment located in the intercistronic spacer region between the two protein coding regions. IRESs have been isolated from viral genomes and cellular genomes. Artificially engineered IRESs are also known in the art. Any convenient IRES may be employed in the donor polynucleotide. [00106] By an “intein” it is meant a segment of a polypeptide that is able to excise itself and rejoin the remaining portions of the translated polypeptide sequence (the “exteins”) with a peptide bond. Inteins may be naturally occurring, i.e. inteins that spontaneously catalyze a protein splicing reaction to excise their own sequences and join the flanking extein sequences, or artificial, i.e. inteins that have been engineered to undergo controllable splicing. Mechanism by which inteins promote protein splicing and the requirements for intein splicing may be found in Liu, X-Q, “Protein Splicing Intein: Genetic Mobility, Origin, and Evolution” Annual Review of Genetics 2000, 34: 61-76 and in publicly available databases such as, for example, the InBase database on the New England Biolabs website, found on the
world wide web at “tools(dot)neb(dot)com/inbase/mech(dot)php”, the disclosures of which are incorporated herein by reference. [00107] By an “intron” it is meant any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene. Introns typically include a 5' splice site (splice donor sequence) and a 3’ splice site (spice acceptor sequence). The splice donor includes an almost invariant sequence GU at the 5' end of the intron. The splice acceptor terminates the intron with an almost invariant AG sequence. [00108] For details related to each of the individual components referred to in the above Gen2 EDV section, such are provided elsewhere below. For example, illustrative non-limiting examples of viral envelop proteins, nucleic acid-binding effector polypeptides (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a), and targeting polypeptides are provided elsewhere below. For working examples that utilize Gen2 EDVs, see Example 3. Gen3 EDVs (streamlined EDVs) [00109] As would be understood by one of ordinary skill in the art, natural Gag and Gag-pol precursors are expressed from full length viral genomic RNA as polyproteins, which are proteolytically cleaved. Gag, which is structurally conserved among the retroviruses, is composed of at least three protein units: matrix protein (MA), capsid protein (CA) and nucleocapsid protein (NC), whereas Pol is composed of the retroviral protease (PR), the retrotranscriptase (RT) and the integrase (IN). [00110] Gen3 EDVs can include any or all of the above-described features of Gen2 EDVs. Surprisingly, as demonstrated in the working examples below (see, e.g., Example 1), in some embodiments, a subject EDV (a Gen3 EDV) can be streamlined in the sense that it includes reduced components (e.g., a reduced number of components and/or truncated components) compared to those in the art. For example, in some case, a subject collection of one or more nucleic acids that encodes a subject EDV does not include (i.e., lacks) nucleotide sequence encoding one or more of the following proteins: a pol polypeptide protease (PR), a pol polypeptide reverse transcriptase (RT), a pol polypeptide integrase (IN), a nucleocapsid (NC) protein. In some cases, a subject collection of one or more nucleic acids that encodes a subject EDV does not include (i.e., lacks) nucleotide sequences encoding a pol polypeptide protease (PR), a pol polypeptide reverse transcriptase (RT), a pol polypeptide integrase (IN), and a nucleocapsid (NC) protein. In other words, in some cases, a subject collection of one or more nucleic acids that encodes a subject EDV does not encode a PR, PT, IN, or NC protein. As such, in some cases, a subject EDV does not include (i.e., lacks) an NC protein.
N-terminally truncated capsid (CA) protein [00111] In some embodiments, a subject EDV (a Gen3 EDV) includes an N-terminally truncated capsid (CA) protein. The term “N-terminally truncated capsid (CA) protein” is meant herein to mean that the CA protein is missing (via deletion) amino acids from the N-terminal half of the protein relative to the corresponding full length CA protein. In some embodiments, a subject N-terminally truncated capsid (CA) protein is missing some amino acids from the C-terminal half of the protein as well. In some cases, an N-terminally truncated capsid (CA) protein retains some amino acids (e.g., in some cases from 1-10, 1-9, 1-8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, or 1) from the N-terminus of the corresponding full length CA protein, but is missing other amino acids from the N-terminal half of the protein. For example, in some cases, a subject N-terminally truncated capsid (CA) protein includes from 1-10 amino acids (e.g., 1-9, 1- 8, 1-7, 1-6, 1-5, 1-4, 1-3, 1-2, or 1) of the first 10 amino acids of the corresponding full length CA protein. In some cases, a subject N-terminally truncated capsid (CA) protein includes from 1-5 amino acids (e.g., 1-4, 1-3, 1-2, or 1) of the first 10 amino acids of the corresponding full length CA protein. In some cases, a subject N-terminally truncated capsid (CA) protein includes the first 5 amino acids of the corresponding full length CA protein. In some cases, a subject N-terminally truncated capsid (CA) protein includes the first 4 amino acids of the corresponding full length CA protein. In some cases, a subject N-terminally truncated capsid (CA) protein includes the first 3 amino acids of the corresponding full length CA protein. In some cases, a subject N-terminally truncated capsid (CA) protein includes the first 2 amino acids of the corresponding full length CA protein. In some cases, a subject N-terminally truncated capsid (CA) protein includes the amino acid of the corresponding full length CA protein. [00112] As noted above, a CA protein can be of any of a variety of retroviruses. In some embodiments, a subject full length CA protein is: PIVQNIQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQA AMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGE IYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQN ANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 282). In some cases, a subject N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-148 of SEQ ID NO: 282 (i.e., the protein has a deletion of amino acids that includes those corresponding to amino acids 5-148). By using the phrase “corresponding to” amino acids 5-148, it is meant that the full length CA protein may have a different overall amino acid sequence than SEQ ID NO: 282, but the N- terminally truncated capsid protein derived therefrom would be lacking an equivalent region/portion of the full length CA protein (a region/portion equivalent to amino acids 5-148 of SEQ ID NO: 282). Likewise, in some cases, a subject N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-61 SEQ ID NO: 282 (i.e., the protein has a deletion of amino acids that includes those corresponding to amino acids 5-61). In some cases, a subject N-terminally truncated
capsid protein lacks amino acids corresponding to amino acids 5-47 SEQ ID NO: 282 (i.e., the protein has a deletion of amino acids that includes those corresponding to amino acids 5-47). In some cases, a subject N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-34 of SEQ ID NO: 282 (i.e., the protein has a deletion of amino acids that includes those corresponding to amino acids 5-34). In some cases, a subject N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-15 of SEQ ID NO: 282 (i.e., the protein has a deletion of amino acids that includes those corresponding to amino acids 5-15). [00113] In some cases, a subject N-terminally truncated capsid protein has a deletion that removes at least those amino acids corresponding to amino acids 5-148 of SEQ ID NO: 282. In some cases, a subject N-terminally truncated capsid protein has a deletion of amino acids corresponding to amino acids 5-148 of SEQ ID NO: 282. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with PIVQSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPG ATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 290). In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 290. In some cases, the N- terminally truncated capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 290. In some cases, the N-terminally truncated capsid protein includes the amino acid sequence of SEQ ID NO: 290. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLE EMMTACQGVGGPGHKARVL (SEQ ID NO: 331). [00114] In some cases, a subject N-terminally truncated capsid protein has a deletion that removes at least those amino acids corresponding to amino acids 5-61 of SEQ ID NO: 282. In some cases, a subject N-terminally truncated capsid protein has a deletion of amino acids corresponding to amino acids 5-61 of SEQ ID NO: 282. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with PIVQHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH NPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWM TETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 286). In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or
more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 286. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 286. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 286. In some cases, the N-terminally truncated capsid protein includes the amino acid sequence of SEQ ID NO: 286. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with HQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPI PVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETL LVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 332). [00115] In some cases, a subject N-terminally truncated capsid protein has a deletion that removes at least those amino acids corresponding to amino acids 5-47 of SEQ ID NO: 282. In some cases, a subject N-terminally truncated capsid protein has a deletion of amino acids corresponding to amino acids 5-47 of SEQ ID NO: 282. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with PIVQTPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAG TTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTL RAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 285). In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 285. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 285. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 285. In some cases, the N-terminally truncated capsid protein includes the amino acid sequence of SEQ ID NO 285. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with TPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTS TLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAE QASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 333).
[00116] In some cases, a subject N-terminally truncated capsid protein has a deletion that removes at least those amino acids corresponding to amino acids 5-34 of SEQ ID NO: 282. In some cases, a subject N-terminally truncated capsid protein has a deletion of amino acids corresponding to amino acids 5-34 of SEQ ID NO: 282. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with PIVQEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAP GQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKE PFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV GGPGHKARVL (SEQ ID NO: 284). In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 284. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 284. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 284. In some cases, the N- terminally truncated capsid protein includes the amino acid sequence of SEQ ID NO 284. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with EVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRVHPVHAGPIAPGQM REPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRD YVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPG HKARVL (SEQ ID NO: 334). [00117] In some cases, a subject N-terminally truncated capsid protein has a deletion that removes at least those amino acids corresponding to amino acids 5-15 of SEQ ID NO: 282. In some cases, a subject N-terminally truncated capsid protein has a deletion of amino acids corresponding to amino acids 5-15 of SEQ ID NO: 282. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with PIVQSPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETIN EEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLN KIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILK ALGPGATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 283). In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g.,
95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 283. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 90% or more sequence identity (e.g., 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 283. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 95% or more sequence identity (e.g., 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 283. In some cases, the N-terminally truncated capsid protein includes the amino acid sequence of SEQ ID NO 283. In some cases, the N-terminally truncated capsid protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAA EWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVR MYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGP GATLEEMMTACQGVGGPGHKARVL (SEQ ID NO: 335). [00118] In some cases, the N-terminally truncated capsid protein has a length of 80-220 amino acids (e.g., 80-210, 80-190, 80-180, 80-185, 80-175, 80-90, 170-220, 170-210, 170-190, 170-180, 170-185, 170-175, 170-90, 180-220, 180-210, 180-190, 180-180, 180-185, 180-175, 180-90, 195-220, 195-210, 195-190, 195-180, 195-185, 195-175, 195-90, 210-220, 210-210, 210-190, 210-180, 210-185, 210-175, 210-90, 83-220, 83-210, 83-190, 83-180, 83-185, 83-175, 83-90, 87-220, 87-210, 87-190, 87-180, 87- 185, 87-175, 87-90, 174-220, 174-210, 174-190, 174-180, 174-185, 174-175, 174-90, 184-220, 184-210, or 184-190). In some cases, the N-terminally truncated capsid protein has a length of 80-90 amino acids. In some cases, the N-terminally truncated capsid protein has a length of 83-90 amino acids. In some cases, the N-terminally truncated capsid protein has a length of 83-87 amino acids. [00119] In some cases, the N-terminally truncated capsid protein has a length of about 83, 87, 170, 174, 184, 188, 197, 201, 216, or 220 amino acids. For example, in some cases, the N-terminally truncated capsid protein has a length of about 83 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 85 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 87 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 170 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 175 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 184 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 188 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 197 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 201 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 216 amino acids. In some cases, the N-terminally truncated capsid protein has a length of about 220 amino acids.
Truncated matrix (MA) protein [00120] As noted above, an MA protein can be of any of a variety of retroviruses. In some embodiments, a subject MA protein is: GARASVLSGGELDRWEKIRLRPGGKKKYKLKHIVWASRELERFAVNPGLLETSEGCRQILGQLQ PSLQTGSEELRSLYNTVATLYCVHQRIEIKDTKEALDKIEEEQNKSKKKAQQAAADTGHSNQVS QNY (SEQ ID NO:296), which is an example of a full length MA protein. In some cases, an MA protein is a full length protein. [00121] In some cases, an MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO:296. In some cases, a subject MA protein is a variant (e.g., can be truncated). For example, in some cases, an MA polypeptide lacks amino acids (aa) corresponding to aa 72-127 of SEQ ID NO: 296 (see, e.g., SEQ ID NO: 298). In some cases, a subject MA polypeptide has a deletion that removes at least those amino acids corresponding to amino acids 72-127 of SEQ ID NO: 296. In some cases, a MA polypeptide has a deletion of amino acids corresponding to amino acids 72-127 of SEQ ID NO: 296. In some cases, a truncated MA polypeptide includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 298. [00122] In some cases, an MA polypeptide lacks amino acids (aa) corresponding to aa 30-127 of SEQ ID NO: 296 (see, e.g., SEQ ID NO: 301). In some cases, a subject MA polypeptide has a deletion that removes at least those amino acids corresponding to amino acids 30-127 of SEQ ID NO: 296. In some cases, a MA polypeptide has a deletion of amino acids corresponding to amino acids 30-127 of SEQ ID NO: 296. In some cases, a truncated MA polypeptide includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 301. [00123] In some cases, an MA polypeptide lacks amino acids (aa) corresponding to aa 53-127 of SEQ ID NO: 296 (see, e.g., SEQ ID NO: 299). In some cases, a subject MA polypeptide has a deletion that removes at least those amino acids corresponding to amino acids 53-127 of SEQ ID NO: 296. In some cases, a MA polypeptide has a deletion of amino acids corresponding to amino acids 53-127 of SEQ ID NO: 296. In some cases, a truncated MA polypeptide includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 299. [00124] As such, in some cases, a subject MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with any one of SEQ ID NOs: 296, 298, 299, and 301.
[00125] In some cases, a subject truncated MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with any one of SEQ ID NOs: 298, 299, and 301. In some cases, a subject truncated MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 298. In some cases, a subject truncated MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 299. In some cases, a subject truncated MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 301. [00126] In some cases, a subject MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with any one of SEQ ID NOs: 298, 299, and 301. In some cases, a subject MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 298. In some cases, a subject MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 299. In some cases, a subject MA protein includes an amino acid sequence having 80% or more sequence identity (e.g., 85% or more, 90% or more, 95% or more, 97% or more, 98% or more, 99% or more, or 100%) with SEQ ID NO: 301. [00127] In some cases, the MA protein has a length of 30-135 amino acids (e.g., 30-131, 30-60, 30-40, 30-35, 33-135, 33-131, 33-60, 33-40, 33-35, 50-135, 50-131, 50-60, 55-57, 100-135, or 100-131). In some cases, the MA protein has a length of 30-35 amino acids. In some cases, the MA protein has a length of 50-60 amino acids. In some cases, the MA protein has a length of 120-135 amino acids. In some cases, the MA protein has a length of about 33, 56, or 131 amino acids. For example, in some cases, the MA protein has a length of about 33 amino acids. In some cases, the MA protein has a length of about 56 amino acids. In some cases, the MA protein has a length of about 131 amino acids. [00128] In some cases, a subject EDV includes (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR Cas effector polypeptide such as a Cas9 or Cas12a); (b) a viral envelop protein (e.g., VSVG or a mutant thereof); (c) a targeting polypeptide that provides for binding to a target cell (e.g., an antibody); (d) a matrix (MA) polypeptide (e.g., in some cases a truncated MA polypeptide); and (e) an N-terminally truncated capsid (CA) protein. [00129] For details related to each of the individual components referred to in the above Gen3 EDV section, such are provided elsewhere below. For example, illustrative non-limiting examples of viral envelop proteins, nucleic acid-binding effector polypeptides (e.g., a CRISPR-Cas effector polypeptide
such as Cas9 or Cas12a), and targeting polypeptides are provided elsewhere below. For working examples that utilize Gen2 EDVs, see Example 1. Viral envelope proteins [00130] EDVs of the present disclosure include a viral envelope protein (e.g., a viral envelope glycoprotein). In some cases, the viral envelope protein is a variant that includes one or more amino acid substitutions that reduce binding of the viral envelope protein to its receptor. [00131] Suitable viral envelope proteins include, e.g., a vesicular stomatitis virus (VSV) glycoprotein (VSV-G protein or VSVG), a Measles virus hemagglutinin (HA) protein and/or a measles virus fusion glycoprotein, an Influenza virus neuraminidase (NA) protein, a Measles virus F protein, an Influenza virus HA protein, a cocal virus glycoprotein, a Moloney virus MLV-A protein, a Moloney virus MLV-E protein, a Baboon Endogenous retrovirus (BAEV) envelope protein, an Ebola virus glycoprotein, a foamy virus envelope protein, a variant of any of the above that comprises one or more amino acid substitutions that reduce binding of the viral envelope protein to its receptor, and a combination or two or more of the foregoing viral envelope proteins. In some cases, the viral envelope protein is selected from: a Hepatitis B virus (HBV) glycoprotein, a Hepatitis C virus (HCV) glycoprotein, a Marburg virus glycoprotein, an Ebola virus glycoprotein, a vesicular stomatitis virus (VSV) glycoprotein, an influenza virus hemagglutinin, a SARS-CoV glycoprotein, a respiratory syncytial virus (RSV) glycoprotein, a human parainfluenza virus glycoprotein, a moloney murine leukemia virus (MMLV), a measles virus hemagglutinin and/or a measles virus fusion glycoprotein, an HTLV-1 glycoprotein, a Ross river virus glycoprotein, a rabies virus glycoprotein, a Mokola virus glycoprotein, a Semliki Forest virus glycoprotein, a Sindbis virus glycoprotein, a Venezuelan equine encephalitis virus glycoprotein, a sendai virus, a baculovirus, and a variant of any of the above that comprises one or more amino acid substitutions that reduce binding of the viral envelope protein to its receptor. [00132] In some cases, the viral envelope protein is a VSV-G protein (VSVG). In some cases, the viral envelope protein is a measles virus hemagglutinin protein. In some cases, the viral envelope protein is a measles virus F protein. In some cases, the viral envelope protein is an influenza virus hemagglutinin protein. In some cases, the viral envelope protein is a Moloney virus MLV-A protein. In some cases, the viral envelope protein is a Moloney virus MLV-E protein. In some cases, the viral envelope protein is a moloney murine leukemia virus (MMLV). In some cases, the viral envelope protein is a baboon endogenous retrovirus envelope protein. In some cases, the viral envelope protein is an Ebola virus glycoprotein. In some cases, the viral envelope protein is a foamy virus envelope protein. [00133] In some cases, the viral envelope protein is a VSV-G protein. A suitable VSV-G protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence:
[00134] imkcllylaflfigvnckftivfphnqkgnwknvpsnyhycpsssdlnwhndligtalqvkmpkshkaiqadgwmchaskwvttc dfrwygpkyithsirsftpsveqckesieqtkqgtwlnpgfppqscgyatvtdaeavivqvtphhvlvdeytgewvdsqfingkcsnyicptvhn sttwhsdykvkglcdsnlismditffsedgelsslgkegtgfrsnyfayetggkackmqyckhwgvrlpsgvwfemadkdlfaaarfpecpegs sisapsqtsvdvsliqdverildyslcqetwskiraglpispvdlsylapknpgtgpaftiingtlkyfetryirvdiaapilsrmvgmisgttterelwd dwapyedveigpngvlrtssgykfplymighgmldsdlhlsskaqvfehphiqdaasqlpddeslffgdtglsknpielvegwfsswkssiasfff iigliiglflvlrvgihlciklkhtkkrqiytdiemnrlgk (SEQ ID NO:18). [00135] In some cases, a suitable VSV-G protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00136] mkcllylaflfigvnckftivfphnqkgnwknvpsnyhycpsssdlnwhndligtalqvkmpkshkaiqadgwmchaskwvttc dfrwygpkyithsirsftpsveqckesieqtkqgtwlnpgfppqscgyatvtdaeavivqvtphhvlvdeytgewvdsqfingkcsnyicptvhn sttwhsdykvkglcdsnlismditffsedgelsslgkegtgfrsnyfayetggkackmqyckhwgvrlpsgvwfemadkdlfaaarfpecpegs sisapsqtsvdvsliqdverildyslcqetwskiraglpispvdlsylapknpgtgpaftiingtlkyfetryirvdiaapilsrmvgmisgttterelwd dwapyedveigpngvlrtssgykfplymighgmldsdlhlsskaqvfehphiqdaasqlpddeslffgdtglsknpielvegwfsswkssiasfff iigliiglflvlrvgihlciklkhtkkrqiytdiemnrlgk (SEQ ID NO:19). [00137] In some cases, a suitable VSV-G protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence of SEQ ID NO: 153. [00138] In some cases, the viral envelope protein is a BAEV-G protein. A suitable BAEV-G protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00139] mgfttkiiflynlvlvyagfddprkaielvqkrygrpcdcsggqvseppsdrvsqvtcsgktaylmpdqrwkcksipkdtspsgplqe cpcnsyqssvhsscytsyqqcrsgnktyytatllktqtggtsdvqvlgstnkliqspcngikgqsicwsttapihvsdgggpldttriksvqrkleeih kalypelqyhplaipkvrdnlmvdaqtlnilnatynlllmsntslvddcwlclklgpptplaipnfllsyvtrssdniscliippllvqpmqfsnssclfs psynsteeidlghvafsnctsitnvtgpicavngsvflcgnnmaytylptnwtglcvlatllpdidiipgdepvpipaidhfiyrpkraiqfipllaglgi taafttgatglgvsvtqytklsnqlisdvqilsstiqdlqdqvdslaevvlqnrrgldlltaeqggiclalqekccfyvnksgivrdkiktlqeelerrrkdl asnplwtglqgllpyllpflgplltllllltigpcifnrltafindklniihamvltqqyqvlrtdeeaqd(SEQ ID NO:49). [00140] In some cases, the viral envelope protein is an influenza virus H1N1 hemagglutinin glycoprotein. A suitable influenza hemagglutinin protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MKAILVVLLY TFATANADTL CIGYHANNST DTVDTVLEKN VTVTHSVNLL EDKHNGKLCK LRGVAPLHLG KCNIAGWILG NPECESLSTA SSWSYIVETP SSDNGTCYPG DFIDYEELRE QLSSVSSFER FEIFPKTSSW PNHDSNKGVT AACPHAGAKS FYKNLIWLVK KGNSYPKLSK SYINDKGKEV LVLWGIHHPS TSADQQSLYQ NADAYVFVGS SRYSKKFKPE IAIRPKVRXX EGRMNYYWTL VEPGDKITFE ATGNLVVPRY
AFAMERNAGS GIIISDTPVH DCNTTCQTPK GAINTSLPFQ NIHPITIGKC PKYVKSTKLR LATGLRNIPS IQSRGLFGAI AGFIEGGWTG MVDGWYGYHH QNEQGSGYAA DLKSTQNAID EITNKVNSVI EKMNTQFTAV GKEFNHLEKR IENLNKKVDD GFLDIWTYNA ELLVLLENER TLDYHDSNVK NLYEKVRSQL KNNAKEIGNG CFEFYHKCDN TCMESVKNGT YDYPKYSEEA KLNREEIDGV KLESTRIYQI LAIYSTVASS LVLVVSLGAI SFWMCSNGSL QCRICI (SEQ ID NO:50; GenBank Accession No: ACP44189). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and natural killer (NK) cells. [00141] In some cases, the viral envelope protein is an influenza virus H3N2 hemagglutinin glycoprotein. A suitable influenza hemagglutinin protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MKTIIALSYI LCLVFAQKLP GNDNSTATLC LGHHAVPNGT IVKTITNDQI EVTNATELVQ SSSTGGICDS PHQILDGENC TLIDALLGDP QCDGFQNKKW DLFVERSKAY SNCYPYDVPD YASLRSLVAS SGTLEFNNES FNWTGVTQNG TSSACKRRSN NSFFSRLNWL THLKFKYPAL NVTMPNNEKF DKLYIWGVHH PGTDNDQISL YAQASGRITV STKRSQQTVI PSIGSRPRIR DVPSRISIYW TIVKPGDILL INSTGNLIAP RGYFKIRSGK SSIMRSDAPI GKCNSECITP NGSIPNDKPF QNVNRITYGA CPRYVKQNTL KLATGMRNVP EKQTRGIFGA IAGFIENGWE GMVDGWYGFR HQNSEGTGQA ADLKSTQAAI NQINGKLNRL IGKTNEKFHQ IEKEFSEVEG RIQDLEKYVE DTKIDLWSYN AELLVALENQ HTIDLTDSEM NKLFERTKKQ LRENAEDMGN GCFKIYHKCD NACIGSIRNG TYDHDVYRDE ALNNRFQIKG VELKSGYKDW ILWISFAISC FLLCVALLGF IMWACQKGNI RCNICI (SEQ ID NO:51; GenBank Accession No: YP_308839). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and natural killer (NK) cells. [00142] In some cases, the viral envelope protein is an influenza virus A H5N1 hemagglutinin glycoprotein. A suitable influenza hemagglutinin protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEKIVLLLAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KTHNGKLCDL NGVKPLILRD CSVAGWLLGN PMCDEFINVP EWSYIVEKAS PANDLCYPGD FNDYEELKHL LSRTNHFEKI QIIPKSSWSN HDASSGVSSA CPYHGRSSFF RNVVWLIKKN SAYPTIKRSY NNTNQEDLLV LWGIHHPNDA AEQTKLYQNP TTYISVGTST LNQRLVPEIA TRPKVNGQSG RMEFFWTILK PNDAINFESN GNFIAPEYAY KIVKKGDSAI MKSELEYGNC NTKCQTPMGA INSSMPFHNI HPLTIGECPK YVKSNRLVLA
TGLRNTPQRE RRRKKRGLFG AIAGFIEGGW QGMVDGWYGY HHSNEQGSGY AADKESTQKA IDGVTNKVNS IIDKMNTQFE AVGREFNNLE RRIENLNKQM EDGFLDVWTY NAELLVLMEN ERTLDFHDSN VKNLYDKVRL QLRDNAKELG NGCFEFYHKC DNECMESVKN GTYDYPQYSE EARLNREEIS GVKLESMGTY QILSIYSTVA SSLALAIMVA GLSLWMCSNG SLQCRICI (SEQ ID NO:52; GenBank Accession No: YP_308669). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00143] In some cases, the viral envelope protein is an influenza virus H7N9 hemagglutinin glycoprotein. A suitable influenza hemagglutinin protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MNTQILVFAL IAIIPTNADK ICLGHHAVSN GTKVNTLTER GVEVVNATET VERTNIPRIC SKGKRTVDLG QCGLLGTITG PPQCDQFLEF SADLIIERRE GSDVCYPGKF VNEEALRQIL RESGGIDKEA MGFTYSGIRT NGATSACRRS GSSFYAEMKW LLSNTDNAAF PQMTKSYKNT RKSPALIVWG IHHSVSTAEQ TKLYGSGNKL VTVGSSNYQQ SFVPSPGARP QVNGLSGRID FHWLMLNPND TVTFSFNGAF IAPDRASFLR GKSMGIQSGV QVDANCEGDC YHSGGTIISN LPFQNIDSRA VGKCPRYVKQ RSLLLATGMK NVPEIPKGRG LFGAIAGFIE NGWEGLIDGW YGFRHQNAQG EGTAADYKST QSAIDQITGK LNRLIEKTNQ QFELIDNEFN EVEKQIGNVI NWTRDSITEV WSYNAELLVA MENQHTIDLA DSEMDKLYER VKRQLRENAE EDGTGCFEIF HKCDDDCMAS IRNNTYDHSK YREEAMQNRI QIDPVKLSSG YKDVILWFSF GASCFILLAI VMGLVFICVK NGNMRCTICI (SEQ ID NO:53; GenBank Accession No: YP_009118475). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00144] In some cases, the viral envelope protein is a Hepatitis B Virus (HBV) S glycoprotein. A suitable HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MENTTSGFLG PLLVLQAGFF LLTRNLTIPQ SLDSWWTSLN FLGGAPTCPG QNSQSPTSNH SPTSCPPICP GYRWMCLRRF IIFLFILLLC LIFLLVLLDY QGMLPVCPLL PGTSTTSTGP CKTCTIPAQG TSMFPSCCCT KPSDGNCTCI PIPSSWAFAR FLWEWASVRF SWLSLLVPFV QWFVGLSPTV WLSVIWMMWY WGPSLYNILS PFLPLLPIFF CLWVYI (SEQ ID NO:54; GenBank Accession No: ABV02793). Such a heterologous glycoprotein may be useful in directing an EDV of the present disclosure to a liver cell.
[00145] In some cases, the viral envelope protein is a Hepatitis B Virus (HBV) middle S glycoprotein. A suitable HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MQWNSTAFHQ ALQDPKVRGL YFPAGGSSSG TVNPAPNIAS HISSISARTG DPVTNMENIT SGFLGPLLVL QAGFFLLTRI LTIPQSLDSW WTSLNFLGGS PVCLGQNSQS PTSNHSPTSC PPICPGYRWM CLRRFIIFLF ILLLCLIFLL VLLDYQGMLP VCPLIPGSTT TSTGPCKTCT TPAQGNSMFP SCCCTKPTDG NCTCIPIPSS WAFAKYLWEW ASVRFSWLSL LVPFVQWFVG LSPTVWLSAI WMMWYWGPSL YSIVSPFIPL LPIFFCLWVY I (SEQ ID NO:55; GenBank Accession No: ACJ66136). Such a heterologous glycoprotein may be useful in directing an EDV of the present disclosure to a liver cell. [00146] In some cases, the viral envelope protein is a Hepatitis B Virus (HBV) large S glycoprotein. A suitable HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGLSWTVPLE WGKNHSTTNP LGFFPDHQLD PAFRANTRNP DWDHNPNKDH WTEANKVGVG AFGPGFTPPH GGLLGWSPQA QGMLKTLPAD PPPASTNRQS GRQPTPITPP LRDTHPQAMQ WNSTTFHQAL QDPKVSALYL PAGGSSSGTV NPVPTTASLI SSIFSRIGDP APNMESITSG FLGPLLVLQA GFFLLTKILT IPQSLDSWWT SLNFLGGAPV CLGQNSQSPT SSHSPTSCPP ICPGYRWMCL RRFIIFLFIL LLCLIFLLVL LDYQGMLPVC PLIPGSSTTS TGPCRTCTTL AQGTSMFPSC CCSKPSDGNC TCIPIPSSWA FGKFLWEWAS ARFSWLSLLV PFVQWFAGLS PTVWLSVIWM MWYWGPSLYN ILSPFIPLLP IFFCLWVYI (SEQ ID NO:56; GenBank Accession No: AGR65633). Such a heterologous glycoprotein may be useful in directing an EDV of the present disclosure to a liver cell. [00147] In some cases, the viral envelope protein is a Hepatitis B Virus (HBV) small S glycoprotein. A suitable HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MENITSGFLG PLLVLQAGFF LLTRILTIPQ SLDSWWTSLN FLGGTTVCLG QNSQSPTSNH SPTSCPPTCP GYRWMCLRRF IIFLFILLLC LIFLLVLLDY QGMLPVCPLI PGSSTTSTGP CRTCTTPAQG TSMYPSCCCT KPSDGNCTCI PIPSSWAFGK FLWEWASARF SWLSLLVPFV QWFVGLSPTV WLSVIWMMWY WAPNLHNILS PFLPLLPIFL CLWVYI (SEQ ID NO:57; GenBank Accession No: AHC69850. Such a heterologous glycoprotein may be useful in directing an EDV of the present disclosure to a liver cell. [00148] In some cases, the viral envelope protein is a Hepatitis B Virus (HBV) pre S glycoprotein. A suitable HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGGWSSKPRK GMGTNLAVPN PLGFFPDHQL DPAFKANSDN PDWDLNTHKD
YWPDAWKVGV GAFGPGFTPP HGGLLGWSPQ AQGLLTTVPA APPPASTNRQ SGRQPTPLSP PLRDTHPQAM KWNSTTFHQT LQDPRVRALY LPAGGSSSGT VSPAQNTVSA ISSILSKTGD PVPNMESIAS GLLGPLLVLQ AGFFLLTKIL TIPQSLDSWW TSLNFLGGTP VCLGQNSQSQ ISSHSPTCCP PTCPGYRWMC LRRFIIFLCI LLLCLIFLLV LLDYQGMLPV CPLIPGSSTT STGPCKTCTA PAQGTSMFPS CCCTKPTDGN CTCIPIPSSW AFAKYLWEWA SVRFSWLSLL VPFVQWFVGL SPTVWLSVIW MMWFWGPSLY NILSPFIPLL PIFFCLWVYI (SEQ ID NO:58; GenBank Accession No: CAA66700). Such a heterologous glycoprotein may be useful in directing an EDV of the present disclosure to a liver cell. [00149] In some cases, the viral envelope protein is a Hepatitis B Virus (HBV) preS2 glycoprotein. A suitable HBV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MQWNSTTFHQ TLQDPRVRGL YFPAGGSSSG TVNPVPTTVS HISSIFSRIG DPALNMENIT SGFLGPLLVL QAGFFLLTRI LTIPQSLDSW WTSLNFLGGT TVCLGQNSQS PTSNHSPTSC PPTCPGYRWM CLRRFIIFLF ILLLCLIFLL VLLDYQGMLS VCPLIPGSTT TSTGPCKTCTTPAQGTSIHP SCCCTKPSDG NCTWIPIPSS WAFGKFLWEW ASARFSWLSL LVPFVQWFVG LSPTVWLSVI WIMWYWGPSL YSILSPFLPL LPIFFCLWVY I (SEQ ID NO:59; GenBank Accession No: AAO12662). Such a heterologous glycoprotein may be useful in directing an EDV of the present disclosure to a liver cell. [00150] In some cases, the viral envelope protein is a Rabies virus. A suitable Rabies virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MVPQALLFVP LLVFPLCFGK FPIYTIPDKL GPWSPIDIHH. [00151] LSCPNNLVVE DEGCTNLSGF SYMELKVGYI SAIKVNGFTC TGVVTEAETY TNFVGYVTTT FKRKHFRPTP DACRSAYNWK MAGDPRYEES LHNPYPDYHW LRTVKTTKES LVIISPSVAD LDPYDKSLHS RVFPSGKCSG ITVSSTYCST NHDYTIWMPE NLRLGTSCDI FINSRGKRAS KGSQTCGFID ERGLYKSLKG ACKLKLCGVL GLRLMDGTWV AMQTSDETKW CPPDQLVNLH DFRSDEIEHL VVEELVKKRE ECLDALESIM TTKSVSFRRL SHLRKLVPGF GKAYTIFNKT LMEADAHYKS VRTWNEIIPS KGCLRVGGRC HPHVNGVFFN GIILGPEGHV LIPEMQSSLL QQHMELLESS VIPLMHPLAD PSTVFKEGDE AEDFVEVHLP DVHKQVSGVN LGLPNWGKYV LLSAGALIAL MLIIFLLTCC RRVNRPESTQ HSLGGKRRKV SITSQSGKII SSWESYKSGG ETRL (SEQ ID NO:60; GenBank Accession No: AWR88358). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to neurons, astrocytes, oligodendrocyctes, glia, and other cells of the of the central nervous system. [00152] In some cases, the viral envelope protein is a Mokola virus glycoprotein. A suitable Mokola virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least
95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MNIPCFVVIL SLATTHSLGE FPLYTIPEKI EKWTPIDMIH LSCPNNLLSE EEGCNAESSF TYFELKSGYL AHQKVPGFTC TGVVNEAETY TNFVGYVTTT FKRKHFRPTV AACRDAYNWK VSGDPRYEES LHTPYPDSSW LRTVTTTKES LLIISPSIVE MDIYGRTLHS PMFPSGVCSN VYPSVPSCET NHDYTLWLPE DPSLSLVCDI FTSSNGKKAM NGSRICGFKD ERGFYRSLKG ACKLTLCGRP GIRLFDGTWV SFTKPDVHVW CTPNQLINIH NDRLDEIEHL IVEDIIKKRE ECLDTLETIL MSQSVSFRRL SHFRKLVPGY GKAYTILNGS LMETNVYYKR VDKWADILPS KGCLKVGQQC MEPVKGVLFN GIIKGPDGQI LIPEMQSEQL KQHMDLLKAA VFPLRHPLIS REAVFKKDGD ADDFVDLHMP DVHKSVSDVD LGLPHWGFWM LIGATIVAFV VLVCLLRVCC KRVRRRRSGR ATQEIPLSFP SAPVPRAKVV SSWESYKGLP GT (SEQ ID NO:61; GenBank Accession No: AAB26292). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to neurons, astrocytes, oligodendrocyctes, glia, and other cells of the of the central nervous system. [00153] In some cases, the viral envelope protein is a lymphocytic choriomeningitis virus (LCMV) glycoprotein. A suitable LCMV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGQIVTMFEA LPHIIDEVIN IVIIVLIIIT SIKAVYNFAT CGILALISFL LLAGRSCGLY GLDGPDIYKG IYQFKSVEFD MSHLNLTMPN ACSANNSHHY ISMGNSGLEL TFTNDSIISH NFCNLTSAFN KKTFDHTLMS IVSSLHLSIR GNSNYKAVSC DFNSGITIQY NLSFSDAQSA LSQCKTFRGR VLDMFRTAFG GKYMRSGWGW TGSDGKTTWC SQTSYQYLII QNRTWENHCR YAGPFGMARI LFAQEKTKFL TRRLAGTFTW TLSDSSGVDN PGGYCLTRWM ILAADLKCFG NTAVAKCNMN HDEEFCDMLR LIDYNKAALS KFKEDVESAL HLFKVTVNSL VSDQLLMRNH LRDLMGVPYC NYSRFWYLEH TKTGETSVPK CWLVTNGSYL NETHFSDQIE QEADNMITDM LRKDYIKRQG STPLALMDLL MFSTSAYLVS VFLHLVKIPT HRHIKGGSCP KPHRLTNKGI CSCGAFKVPG VKTVWKRR (SEQ ID NO:62; GenBank Accession No: AIW66623). [00154] In some cases, the viral envelope protein is a lymphocytic choriomeningitis virus (LCMV) glycoprotein C. A suitable LCMV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGQIVTMFEA LPHIIDEVIN IVIIVLIIIT SIKAVYNFAT CGILALVSFL FLAGRSCGMY GLNGPDIYKG VYQFKSVEFD MSHLNLTMPN ACSANNSHHY ISMGSSGLEL TFTNDSILNH NFCNLTSAFN KKTFDHTLMS IVSSLHLSIR GNSNHKAVSC DFNNGITIQY NLSFSDPQSA ISQCRTFRGR VLDMFRTAFG GKYMRSGWGW AGSDGKTTWC SQTSYQYLII QNRTWENHCR YAGPFGMSRI LFAQEKTKFL TRRLAGTFTW TLSDSSGVEN PGGYCLTKWM ILAAELKCFG NTAVAKCNVN HDEEFCDMLR LIDYNKAALS KFKQDVESAL
HVFKTTVNSL ISDQLLMRNH LRDLMGVPYC NYSKFWYLEH AKTGETSVPK CWLVTNGSYL NETHFSDQIE QEADNMITEM LRKDYIKRQG STPLALMDLL MFSTSAYLIS IFLHLVKIPT HRHIKGGSCP KPHRLTNKGI CSCGAFKVPG VKTIWKRR (SEQ ID NO:63; GenBank Accession No: CAC01231). [00155] In some cases, the viral envelope protein is a lymphocytic choriomeningitis virus (LCMV) glycoprotein. A suitable LCMV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGQIVTMFEA LPHIIDEVIN IVIIVLIVIT GIKAVYNFAT CGIFALISFL LLAGRSCGMY GLKGPDIYKG VYQFKSVEFD MSHLNLTMPN ACSANNSHHY ISMGTSGLEL TFTNDSIISH NFCNLTSAFN KKTFDHTLMS IVSSLHLSIR GNSNYKAVSC DFNNGITIQY NLTFSDAQSA QSQCRTFRGR VLDMFRTAFG GKYMRSGWGW TGSDGKTTWC SQTSYQYLII QNRTWENHCT YAGPFGMSRI LLSQEKTKFF TRRLAGTFTW TLSDSSGVEN PGGYCLTKWM ILAAELKCFG NTAVAKCNVN HDAEFCDMLR LIDYNKAALS KFKEDVESAL HLFKTTVNSL ISDQLLMRNH LRDLMGVPYC NYSKFWYLEH AKTGETSVPK CWLVTNGSYL NETHFSDQIE QEADNMITEM LRKDYIKRQG STPLALMDLL MFSTSAYLVS IFLHLVKIPT HRHIKGGSCP KPHRLTNKGI CSCGAFKVPG VKTVWKRR (SEQ ID NO:64; GenBank Accession No: P09991). [00156] In some cases, the viral envelope protein is a lymphocytic choriomeningitis virus (LCMV) G1 glycoprotein. A suitable LCMV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MYGLKGPDIYKG VYQFKSVEFD MSHLNLTMPN ACSANNSHHY ISMGTSGLEL TFTNDSIISH NFCNLTSAFN KKTFDHTLMS IVSSLHLSIR GNSNYKAVSC DFNNGITIQY NLTFSDAQSA QSQCRTFRGR VLDMFRTAFG GKYMRSGWGW TGSDGKTTWC SQTSYQYLII QNRTWENHCT YAGPFGMSRI LLSQEKTKFF TRRLA (SEQ ID NO:65; GenBank Accession No: P09991). [00157] In some cases, the viral envelope protein is a lymphocytic choriomeningitis virus (LCMV) G2 glycoprotein. A suitable LCMV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: GTFTW TLSDSSGVEN PGGYCLTKWM ILAAELKCFG NTAVAKCNVN HDAEFCDMLR LIDYNKAALS KFKEDVESAL HLFKTTVNSL ISDQLLMRNH LRDLMGVPYC NYSKFWYLEH AKTGETSVPK CWLVTNGSYL NETHFSDQIE QEADNMITEM LRKDYIKRQG STPLALMDLL MFSTSAYLVS IFLHLVKIPT HRHIKGGSCP KPHRLTNKGI CSCGAFKVPG VKTVWKRR (SEQ ID NO:66; GenBank Accession No: P09991). [00158] In some cases, the viral envelope protein is a Ross River virus E1 glycoprotein. A suitable Ross River virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at
least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: YEHTATIPNV VGFPYKAHIE RNXFSPMTLQ LEVVXXSLEP TLNLEYITCE YKTVVPSPFI KCCGTSECSS KEQPDYQCKV YTGVYPFMWG GAYCFCDSEN TQLSEAYVDR SDVCKHDHAL AYKAHTASLK ATIRISYGTI NQTTEAFVNG EHAVNVGGSK FIFGPISTAW SPFDNKIVVY KDDVYNQDFP PYGSGQPGRF GDIQSRTVES KDLYANTALK LSRPSPGVVH VPYTQTPSGF KYWLKEKGSS LNTKAPFGCK IKTNPVRAMD CAVGSIPVSM DIPDSAFTRV VDAPAVTDLS CQVAVCTHSS DFGXVATLSY KTDKPGKCAV HSHSNVATLQ EATVDVKEDG KVTVHFSXXS ASPAFKVSVC DAKTTCTAAC EPPKDHIVPY GASHNNQVFP DMSGTAMTWV QRMASGLGGL ALIAVVVLVL VTCITMRR (SEQ ID NO:67; GenBank Accession No: NP_740686). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to skeletal muscle, and cells that make up the joints, joint-associated connective tissue, bone, neurons, and lymphatic cells. [00159] In some cases, the viral envelope protein is a Ross River virus E2 glycoprotein. A suitable Ross River virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: SVIEHFNVYK ATRPYLAXCA DCGDGYFCYS PVAIEKIRDE ASDGMLKIQV SAQIGLDKAG THAHTKMRYM AGHDVQESKR DSLRVYTSAA CSIHGTMGHF IVAHCPPGDY LKXSFEDANS HVKACKVQYK HDPLPVGREK FVVRPHFGVE LPCTSYQLTT APTDEEIDMH TPPDIPDRTL LSQTAGNVKI TAGGRTIRYN CTCGRDNVGT TSTDKTINTC KIDQCHAAVT SHDKWXFTSP FVPRADQTAR KGKVHVPFPL TNVTCRVPLA RAPDVTYGKK EVTLRLHPDH PTXFSYRSLG AVPHPYEEWV DKFSERIIPV TEEGIEYQWG NNPPVRLWAQ LTTEGKPHGW PHEIIQYYYG LYPAATIAAV SGASLMALLT LAATCCMLAT ARRKCLTPYA LTPGAVVPLT LGLLXCAPRA NA (SEQ ID NO:68; GenBank Accession No: NP_740684). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to skeletal muscle, and cells that make up the joints, joint-associated connective tissue, bone, neurons, and lymphatic cells. [00160] In some cases, the viral envelope protein is a Semliki Forest virus E1 glycoprotein. A suitable Semliki Forest virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMWG GAYCFCDSEN TQLSEAYVDR SDVCRHDHAS AYKAHTASLK AKVRVMYGNV NQTVDVYVNG DHAVTIGGTQ FIFGPLSSAW TPFDNKIVVY KDEVFNQDFP PYGSGQPGRF GDIQSRTVES NDLYANTALK LARPSPGMVH VPYTQTPSGF KYWLKEKGTA LNTKAPFGCQ IKTNPVRAMN CAVGNIPVSM NLPDSAFTRI VEAPTIIDLT CTVATCTHSS DFGGVLTLTY KTNKNGDCSV HSHSNVATLQ EATAKVKTAG KVTLHFSTAS ASPSFVVSLC SARATCSASC EPPKDHIVPY AASHSNVVFP DMSGTALSWV QKISGGLGAF AIGAILVLVV VTCIGLRR (SEQ ID NO:69; GenBank Accession No: NP_819008).
Such a glycoprotein may be useful for targeting an EDV of the present disclosure to muscle, pancreas, neurons, astrocytes, oligodendrocytes, glia, and other cells of the of the central nervous system. [00161] In some cases, the viral envelope protein is a Semliki Forest virus E2 glycoprotein. A suitable Semliki Forest virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: SVSQHFNVYK ATRPYIAYCA DCGAGHSCHS PVAIEAVRSE ATDGMLKIQF SAQIGIDKSD NHDYTKIRYA DGHAIENAVR SSLKVATSGD CFVHGTMGHF ILAKCPPGEF LQVSIQDTRN AVRACRIQYH HDPQPVGREK FTIRPHYGKE IPCTTYQQTT AETVEEIDMH MPPDTPDRTL LSQQSGNVKI TVGGKKVKYN CTCGTGNVGT TNSDMTINTC LIEQCHVSVT DHKKWQFNSP FVPRADEPAR KGKVHIPFPL DNITCRVPMA REPTVIHGKR EVTLHLHPDH PTLFSYRTLG EDPQYHEEWV TAAVERTIPV PVDGMEYHWG NNDPVRLWSQ LTTEGKPHGW PHQIVQYYYG LYPAATVSAV VGMSLLALIS IFASCYMLVA ARSKCLTPYA LTPGAAVPWT LGILCCAPRA HA (SEQ ID NO:48; GenBank Accession No: NP_819006). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to muscle, pancreas, neurons, astrocytes, oligodendrocyctes, glia, and other cells of the of the central nervous system. [00162] In some cases, the viral envelope protein is a Sindbis virus E1 glycoprotein. A suitable Sindbis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: YEHATTVPNV PQIPYKALVE RAGYAPLNLE ITVMSSEVLP STNQEYITCK FTTVVPSPKI KCCGSLECQP AAHADYTCKV FGGVYPFMWG GAQCFCDSEN SQMSEAYVEL SADCASDHAQ AIKVHTAAMK VGLRIVYGNT TSFLDVYVNG VTPGTSKDLK VIAGPISASF TPFDHKVVIH RGLVYNYDFP EYGAMKPGAF GDIQATSLTS KDLIASTDIR LLKPSAKNVH VPYTQASSGF EMWKNNSGRP LQETAPFGCK IAVNPLRAVD CSYGNIPISI DIPNAAFIRT SDAPLVSTVK CEVSECTYSA DFGGMATLQY VSDREGQCPV HSHSSTATLQ ESTVHVLEKG AVTVHFSTAS PQANFIVSLC GKKTTCNAEC KPPADHIVST PHKNDQEFQA AISKTSWSWL FALFGGASSL LIIGLMIFAC SMMLTSTRR (SEQ ID NO:70; GenBank Accession No: NP_740677). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to muscle, pancreas, neurons, astrocytes, oligodendrocytes, glia, and other cells of the of the central nervous system. [00163] In some cases, the viral envelope protein is a Sindbis virus E2 glycoprotein. A suitable Sindbis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: SVIDDFTLTS PYLGTCSYCH HTVPCFSPVK IEQVWDEADD NTIRIQTSAQ FGYDQSGAAS ANKYRYMSLK QDHTVKEGTM DDIKISTSGP CRRLSYKGYF LLAKCPPGDS VTVSIVSSNS ATSCTLARKI KPKFVGREKY DLPPVHGKKI PCTVYDRLKE TTAGYITMHR PRPHAYTSYL EESSGKVYAK PPSGKNITYE CKCGDYKTGT VSTRTEITGC TAIKQCVAYK
SDQTKWVFNS PDLIRHDDHT AQGKLHLPFK LIPSTCMVPV AHAPNVIHGF KHISLQLDTD HLTLLTTRRL GANPEPTTEW IVGKTVRNFT VDRDGLEYIW GNHEPVRVYA QESAPGDPHG WPHEIVQHYY HRHPVYTILA VASATVAMMI GVTVAVLCAC KARRECLTPY ALAPNAVIPT SLALLCCVRS ANA (SEQ ID NO:71; GenBank Accession No: NP_740675). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to skeletal muscle, and cells that make up the joints, joint-associated connective tissue, bone, neurons, and lymphatic cells. [00164] In some cases, the viral envelope protein is an Ebola Zaire virus glycoprotein. A suitable Ebola Zaire virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGVTGILQLP RDRFKRTSFF LWVIILFQRT FSIPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLNL EGNGVATDVP SATKRWGFRS GVPPKVVNYE AGEWAENCYN LEIKKPDGSE CLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILPQAK KDFFSSHPLR EPVNATEDPS SGYYSTTIRY QATGFGTNET EYLFEVDNLT YVQLESRFTP QFLLQLNETI YTSGKRSNTT GKLIWKVNPE IDTTIGEWAF WETKKNLTRK IRSEELSFTV VSNGAKNISG QSPARTSSDP GTNTTTEDHK IMASENSSAM VQVHSQGREA AVSHLTTLAT ISTSPQSLTT KPGPDNSTHN TPVYKLDISE ATQVEQHHRR TDNDSTASDT PSATTAAGPP KAENTNTSKS TDFLDPATTT SPQNHSETAG NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REAIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYIEGLMHN QDGLICGLRQ LANETTQALQ LFLRATTELR TFSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDKTLPDQGD NDNWWTGWRQ WIPAGIGVTG VIIAVIALFC ICKFVF (SEQ ID NO:72; GenBank Accession No: AAB81004). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to hepatocytes, endothelial cells, dendritic cells, macrophages, and monocytes. [00165] In some cases, the viral envelope protein is an Ebola Zaire virus glycoprotein. A suitable Ebola Zaire virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: IPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLNL EGNGVATDVP SATKRWGFRS GVPPKVVNYE AGEWAENCYN LEIKKPDGSECLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILPQAK KDFFSSHPLR EPVNATEDPS SGYYSTTIRY QATGFGTNET EYLFEVDNLT YVQLESRFTP QFLLQLNETI YTSGKRSNTT GKLIWKVNPE IDTTIGEWAF WETKKNLTRK IRSEELSFTV VSNGAKNISG QSPARTSSDP GTNTTTEDHK IMASENSSAM VQVHSQGREA AVSHLTTLAT ISTSPQSLTT KPGPDNSTHN TPVYKLDISE ATQVEQHHRR TDNDSTASDT PSATTAAGPP KAENTNTSKS TDFLDPATTT SPQNHSETAG NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REAIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYIEGLMHN QDGLICGLRQ
LANETTQALQ LFLRATTELR TFSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDKTLPDQGD NDNWWTGWRQ WIPAGIGVTG VIIAVIALFC ICKFVF (SEQ ID NO:73). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to hepatocytes, endothelial cells, dendritic cells, macrophages, and monocytes. [00166] In some cases, the viral envelope protein is an Ebola Reston virus glycoprotein. A suitable Ebola Reston virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGSGYQLLQL PRERFRKTSF LVWVIILFQR AISMPLGIVT NSTLKATEID QLVCRDKLSS TSQLKSVGLN LEGNGIATDV PSATKRWGFR SGVPPKVVSY EAGEWAENCY NLEIKKSDGS ECLPLPPDGV RGFPRCRYVH KVQGTGPCPG DLAFHKNGAF FLYDRLASTV IYRGTTFAEG VVAFLILSEP KKHFWKATPA HEPVNTTDDS TSYYMTLTLS YEMSNFGGNE SNTLFKVDNH TYVQLDRPHT PQFLVQLNET LRRNNRLSNS TGRLTWTLDP KIEPDVGEWA FWETKKNFSQ QLHGENLHFQ IPSTHTNNSS DQSPAGTVQG KISYHPPANN SELVPTDSPP VVSVLTAGRT EEMSTQGLTN GETITGFTAN PMTTTIAPSP TMTSEVDNNV PSEQPNNTAS IEDSPPSASN ETIYHSEMDP IQGSNNSAQS PQTKTTPAPT TSPMTQDPQE TANSSKPGTS PGSAAGPSQP GLTINTVSKV ADSLSPTRKQ KRSVRQNTAN KCNPDLYYWT AVDEGAAVGL AWIPYFGPAA EGIYIEGVMH NQNGLICGLR QLANETTQAL QLFLRATTEL RTYSLLNRKA IDFLLQRWGG TCRILGPSCC IEPHDWTKNI TDEINQIKHD FIDNPLPDHG DDLNLWTGWR QWIPAGIGII GVIIAIIALL CICKILC (SEQ ID NO:74; GenBank Accession No: NP_690583). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to hepatocytes, endothelial cells, dendritic cells, macrophages, and monocytes. [00167] In some cases, the viral envelope protein is a Marburg virus glycoprotein. A suitable Marburg virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MKTTCFLISL ILIQGTKNLP ILEIASNNQP QNVDSVCSGT LQKTEDVHLM GFTLSGQKVA DSPLEASKRW AFRTGVPPKN VEYTEGEEAK TCYNISVTDP SGKSLLLDPP TNIRDYPKCK TIHHIQGQNP HAQGIALHLW GAFFLYDRIA STTMYRGKVF TEGNIAAMIV NKTVHKMIFS RQGQGYRHMN LTSTNKYWTS SNGTQTNDTG CFGALQEYNS TKNQTCAPSK IPPPLPTARP EIKLTSTPTD ATKLNTTDPS SDDEDLATSG SGSGEREPHT TSDAVTKQGL SSTMPPTPSP QPSTPQQGGN NTNHSQDAVT ELDKNNTTAQ PSMPPHNTTT ISTNNTSKHN FSTLSAPLQN TTNDNTQSTI TENEQTSAPS ITTLPPTGNP TTAKSTSSKK GPATTAPNTT NEHFTSPPPT PSSTAQHLVY FRRKRSILWR EGDMFPFLDG LINAPIDFDP VPNTKTIFDE SSSSGASAEE DQHASPNISL TLSYFPNINE NTAYSGENEN
DCDAELRIWS VQEDDLAAGL SWIPFFGPGI EGLYTAVLIK NQNNLVCRLR RLANQTAKSL ELLLRVTTEE RTFSLINRHA IDFLLTRWGG TCKVLGPDCC IGIEDLSKNI SEQIDQIKKD EQKEGTGWGL GGKWWTSDWG VLTNLGILLL LSIAVLIALS CICRIFTKYI G (SEQ ID NO:75); GenBank Accession No: CAA78117). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to hepatocytes, endothelial cells, dendritic cells, macrophages, and monocytes. [00168] In some cases, the viral envelope protein is a murine leukemia virus (MLV) glycoprotein. A suitable MLV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MESTTLSKPF KNQVNPWGPL IVLLILGGVN PVALGNSPHQ VFNLTWEVTN GDRETVWAIA GNHPLWTWWP DLTPDLCMLA LHGPSYWGLE YRAPFSPPPG PPCCSGSSDS TPGCSRDCEE PLTSYTPRCN TAWNRLKLSK VTHAHNEGFY VCPGPHRPRW ARSCGGPESF YCASWGCETT GRASWKPSSS WDYITVSNNL TSDQATPVCK GNEWCNSLTI RFTSFGKQAT SWVTGHWWGL RLYVSGHDPG LIFGIRLKIT DSGPRVPIGP NPVLSDRRPP SRPRPTRSPP PSNSTPTETP LTLPEPPPAG VENRLLNLVK GAYQALNLTS PDKTQECWLC LVSGPPYYEG VAVLGTYSNH TSAPANCSVA SQHKLTLSEV TGQGLCIGAV PKTHQVLCNT TQKTSDGSYY LAAPTGTTWA CSTGLTPCIS TTILDLTTDY CVLVELWPRV TYHSPSYVYH QFEGRAKYKR EPVSLTLALL LGGLTMGGIA AGVGTGTTAL VATQQFQQLQ AAMHDDLKEV EKSITNLEKS LTSLSEVVLQ NRRGLDLLFL KEGGLCAALK EECCFYADHT GLVRDSMAKL RERLSQRQKL FESQQGWFEG LFNKSPWFTT LISTIMGPLI ILLLILLFGP CILNRLVQFI KDRISVVQAL VLTQQYHQLK TIRDCKSRE (SEQ ID NO:76; GenBank Accession No: AAA51037). [00169] In some cases, the viral envelope protein is an MLV glycoprotein. A suitable MLV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MESTTLSKPF KNQVNPWGPL IVLLILRGVN PVTLGNSPHQ VFNLTWEVTN GDRETVWAIT GNHPLWTWWP DLTPDLCMLA LHGPSYWGLE YRAPFSPPPG PPCCSGSSDS TPGCSRDCEE PLTSYTPRCN TAWNRLKLSK VTHAHNGGFY VCPGPHRPRW ARSCGGPESF YCASWGCETT GRASWKPSSS WDYITVSNNL TSDQATPVCK GNKWCNSLTI RFTSFGKQAT SWVTGHWWGL RLYVSGHDPG LIFGIRLKIT DSGPRVPIGP NPVLSDRRPP SRPRPTRSPP PSNSTPTETP LTLPEPPPAG VENRLLNLVK GAYQALNLTS PDKTQECWLC LVSGPPYYEG VAVLGTYSNH
TSAPANCSVA SQHKLTLSEV TGQGLCIGAV PKTHQVLCNT TQKTSDGSYY LAAPTGTTWA CSTGLTPCIS TTILDLTTDY CVLVELWPRV TYHSPSYVYH QFERRAKYKR EPVSLTLALL LGGLTMGGIA AGVGTGTTAL VATQQFQQLQ AAMHDDLKEV EKSITNLEKS LTSLSEVVLQ NRRGLDLLFL KEGGLCAALK EECCFYADHT GLVRDSMAKL RERLSQRQKL FESQQGWFEG LFNKSPWFTT LISTIMGPLI ILLLILLFGP CILNRLVQFI KDRISVVQAL VLTQQYHQLK IIEDCKSRE (SEQ ID NO:77; GenBank Accession No: AID54959). [00170] In some cases, the viral envelope protein is an MLV glycoprotein. A suitable MLV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MARSTLSKPP QDKINPWKPL IVMGVLLGVG MAESPHQVFN VTWRVTNLMT GRTANATSLL GTVQDAFPKL YFDLCDLVGE EWDPSDQEPY VGYGCKYPAG RQRTRTFDFY VCPGHTVKSG CGGPGEGYCG KWGCETTGQA YWKPTSSWDL ISLKRGNTPW DTGCSKVACG PCYDLSKVSN SFQGATRGGR CNPLVLEFTD AGKKANWDGP KSWGLRLYRT GTDPITMFSL TRQVLNVGPR VPIGPNPVLP DQRLPSSPIE IVPAPQPPSP LNTSYPPSTT STPSTSPTSP SVPQPPPGTG DRLLALVKGA YQALNLTNPD KTQECWLCLV SGPPYYEGVA VVGTYTNHST APANCTATSQ HKLTLSEVTG QGLCMGAVPK THQALCNTTQ SAGSGSYYLA APAGTMWACS TGLTPCLSTT VLNLTTDYCV LVELWPRVIY HSPDYMYGQL EQRTKYKREP VSLTLALLLG GLTMGGIAAG IGTGTTALIK TQQFEQLHAA IQTDLNEVEK SITNLEKSLT SLSEVVLQNR RGLDLLFLKE GGLCAALKEE CCFYADHTGL VRDSMAKLRE RLNQRQKLFE TGQGWFEGLF NRSPWFTTLI STIMGPLIVL LLILLFGPCI LNRLVQFVKD RISVVQALVL TQQYHQLKPI EYEP (SEQ ID NO:78; GenBank Accession No: AAA46515). [00171] In some cases, the viral envelope protein is an MLV glycoprotein. A suitable MLV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEGPAFSKPL KDKINPWKSL MVMGVYLRVG MAESPHQVFN VTWRVTNLMT GRTANATSLL GTVQDAFPRL YFDLCDLVGE EWDPSDQEPY VGYGCKYPGG RKRTRTFDFY VCPGHTVKSG CGGPREGYCG EWGCETTGQA YWKPTSSWDL ISLKRGNTPW DTGCSKMACG PCYDLSKVSN SFQGATRGGR CNPLVLEFTD AGKKANWDGP KSWGLRLYRT GTDPITMFSL TRQVLNIGPR IPIGPNPVIT GQLPPSRPVQ IRLPRPPQPP PTGAASIVPE TAPPSQQPGT GDRLLNLVEG AYQALNLTNP DKTQECWLCL VSGPPYYEGV AVVGTYTNHS TAPASCTATS QHKLTLSEVT GQGLCMGALP KTHQALCNTT QSAGSGSYYL AAPAGTMWAC STGLTPCLST TMLNLTTDYC VLVELWPRII YHSPDYMYGQ LEQRTKYKRE PVSLTLALLL GGLTMGGIAA GIGTGTTALI KTQQFEQLHA AIQTDLNEVE KSITNLEKSL TSLSEVVLQN RRGLDLLFLK EGGLCAALKE
ECCFYADHTG LVRDSMAKLR ERLNQRQKLF ESGQGWFEGQ FNRSPWFTTL ISTIMGPLIV LLLILLFGPC ILNRLVQFVK DRISVVQALV LTQQYHQLKP IEYEP (SEQ ID NO:79; GenBank Accession No: AAA46514). [00172] In some cases, the viral envelope protein is an MLV glycoprotein. A suitable MLV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEGSAFSKPL KDKINPWGPL IVMGILVRAG ASVQRDSPHQ IFNVTWRVTN LMTGQTANAT SLLGTMTDTF PKLYFDLCDL VGDYWDDPEP DIGDGCRTPG GRRRTRLYDF YVCPGHTVPI GCGGPGEGYC GKWGCETTGQ AYWKPSSSWD LISLKRGNTP KDQGPCYDSS VSSGVQGATP GGRCNPLVLE FTDAGRKASW DAPKVWGLRL YRSTGADPVT RFSLTRQVLN VGPRVPIGPN PVITDQLPPS QPVQIMLPRP PHPPPSGTVS MVPGAPPPSQ QPGTGDRLLN LVEGAYQALN LTSPDKTQEC WLCLVSGPPY YEGVAVLGTY SNHTSAPANC SVASQHKLTL SEVTGQGLCV GAVPKTHQAL CNTTQKTSDG SYYLAAPAGT IWACNTGLTP CLSTTVLNLT TDYCVLVELW PKVTYHSPDY VYGQFEKKTK YKREPVSLTL ALLLGGLTMG GIAAGVGTGT TALVATKQFE QLQAAIHTDL GALEKSVSAL EKSLTSLSEV VLQNRRGLDL LFLKEGGLCA ALKEECCFYA DHTGVVRDSM AKLRERLNQR QKLFESGQGW FEGLFNRSPW FTTLISTIMG PLIVLLLILL LGPCILNRLV QFVKDRISVV QALILTQQYH QLKSIEPEEV ESRE (SEQ ID NO:80; GenBank Accession No: AAA46531). [00173] In some cases, the viral envelope protein is a polytropic mink cell focus-forming virus glycoprotein. A suitable polytropic mink cell focus-forming virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: VQHDSPHQVF NVTWRVTNLM TGQTANATSL LGTMTDAFPK LYFDLCDLIG DDWDETGLGC RTPGGRKRAR TFDFYVCPGH TVPTGCGGPR EGYCGKWGCE TTGQAYWKPS SLWDLISLKR GNTPQNQGPC YDSSAVSSDI KGATPGGRCN PLVLEFTDAG KKASWDGPKV WGLRLYRSTG TDPVTRFSLT RRVLNIGPRV PIGPNPVIID QLPPSRPVQI MLPRPPQPPP PGAASIVPET APPSNQPGTG DRLLNLVDGA YQALNLTSPD KTQECWLCLV AEPPYYEGVA VLGTYSNHTS APANCSVASQ HKLTLSEVTG RGLCIGTVPK THQALCNTTL KTNKGSYYLV APAGTTWACN TGLTPCLSAT VLNRTTDYCV LVELWPRVTY HPPSYVYSQF EKSYRHKR (SEQ ID NO:81; GenBank Accession No: 2016415A). [00174] In some cases, the viral envelope protein is a gibbon ape leukemia virus (GALV) glycoprotein. A suitable GALV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MVLLPGSMLL TSNLHHLRHQ MSPGSWKRLI ILLSCVFGGG GTSLQNKNPH QPMTLTWQVL SQTGDVVWDT KAVQPPWTWW PTLKPDVCAL
AASLESWDIP GTDVSSSKRV RPPDSDYTAA YKQITWGAIG CSYPRARTRM ASSTFYVCPR DGRTLSEARR CGGLESLYCK EWDCETTGTG YWLSKSSKDL ITVKWDQNSE WTQKFQQCHQ TGWCNPLKID FTDKGKLSKD WITGKTWGLR FYVSGHPGVQ FTIRLKITNM PAVAVGPDLV LVEQGPPRTS LALPPPLPPR EAPPPSLPDS NSTALATSAQ TPTVRKTIVT LNTPPPTTGD RLFDLVQGAF LTLNATNPGA TESCWLCLAM GPPYYEAIAS SGEVAYSTDL DRCRWGTQGK LTLTEVSGHG LCIGKVPFTH QHLCNQTLSI NSSGDHQYLL PSNHSWWACS TGLTPCLSTS VFNQTRDFCI QVQLIPRIYY YPEEVLLQAY DNSHPRTKRE AVSLTLAVLL GLGITAGIGT GSTALIKGPI DLQQGLTSLQ IAIDADLRAL QDSVSKLEDS LTSLSEVVLQ NRRGLDLLFL KEGGLCAALK EECCFYIDHS GAVRDSMKKL KEKLDKRQLE RQKSQNWYEG WFNNSPWFTT LLSTIAGPLL LLLLLLILGP CIINKLVQFI NDRISAVKIL VLRQKYQALE NEGNL (SEQ ID NO:82; GenBank Accession No: P21415). [00175] In some cases, the viral envelope protein is a GALV glycoprotein. A suitable GALV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: TSLQNKNPH QPMTLTWQVL SQTGDVVWDT KAVQPPWTWW PTLKPDVCAL AASLESWDIP GTDVSSSKRV RPPDSDYTAA YKQITWGAIG CSYPRARTRM ASSTFYVCPR DGRTLSEARR CGGLESLYCK EWDCETTGTG YWLSKSSKDL ITVKWDQNSE WTQKFQQCHQ TGWCNPLKID FTDKGKLSKD WITGKTWGLR FYVSGHPGVQ FTIRLKITNM PAVAVGPDLV LVEQGPPRTS LALPPPLPPR EAPPPSLPDS NSTALATSAQ TPTVRKTIVT LNTPPPTTGD RLFDLVQGAF LTLNATNPGA TESCWLCLAM GPPYYEAIAS SGEVAYSTDL DRCRWGTQGK LTLTEVSGHG LCIGKVPFTH QHLCNQTLSI NSSGDHQYLL PSNHSWWACS TGLTPCLSTS VFNQTRDFCI QVQLIPRIYY YPEEVLLQAY DNSHPRTKRE AVSLTLAVLL GLGITAGIGT GSTALIKGPI DLQQGLTSLQ IAIDADLRAL QDSVSKLEDS LTSLSEVVLQ NRRGLDLLFL KEGGLCAALK EECCFYIDHS GAVRDSMKKL KEKLDKRQLE RQKSQNWYEG WFNNSPWFTT LLSTIAGPLL LLLLLLILGP CIINKLVQFI NDRISAVKIL VLRQKYQALE NEGNL (SEQ ID NO:83). [00176] In some cases, the viral envelope protein is a GALV glycoprotein. A suitable GALV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: TSLQNKNPH QPMTLTWQVL SQTGDVVWDT KAVQPPWTWW PTLKPDVCAL AASLESWDIP GTDVSSSKRV RPPDSDYTAA YKQITWGAIG CSYPRARTRM ASSTFYVCPR DGRTLSEARR CGGLESLYCK EWDCETTGTG YWLSKSSKDL ITVKWDQNSE WTQKFQQCHQ TGWCNPLKID FTDKGKLSKD WITGKTWGLR FYVSGHPGVQ FTIRLKITNM PAVAVGPDLV LVEQGPPRTS LALPPPLPPR EAPPPSLPDS NSTALATSAQ TPTVRKTIVT LNTPPPTTGD RLFDLVQGAF LTLNATNPGA TESCWLCLAM GPPYYEAIAS SGEVAYSTDL DRCRWGTQGK LTLTEVSGHG LCIGKVPFTH QHLCNQTLSI NSSGDHQYLL PSNHSWWACS TGLTPCLSTS VFNQTRDFCI
QVQLIPRIYY YPEEVLLQAY DNSHPRTKRE AVSLTLAVLL GLGITAGIGT GSTALIKGPI DLQQGLTSLQ IAIDADLRAL QDSVSKLEDS LTSLSEVVLQ NRRGLDLLFL KEGGLCAALK EECCFYIDHS GAVRDSMKKL KEKLDKRQLE RQKSQNWYEG WFNNSPWFTT LLSTIAGPLL LLLLLLILGP CIINKLVQFI NDRISAVKIL VLRQKYQALE NEGNL (SEQ ID NO:83). [00177] In some cases, the viral envelope protein is a GALV glycoprotein. A suitable GALV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: TSLQNKNPH QPMTLTWQVL SQTGDVVWDT KAVQPPWTWW PTLKPDVCAL AASLESWDIP GTDVSSSKRV RPPDSDYTAA YKQITWGAIG CSYPRARTRM ASSTFYVCPR DGRTLSEARR CGGLESLYCK EWDCETTGTG YWLSKSSKDL ITVKWDQNSE WTQKFQQCHQ TGWCNPLKID FTDKGKLSKD WITGKTWGLR FYVSGHPGVQ FTIRLKITNM PAVAVGPDLV LVEQGPPRTS LALPPPLPPR EAPPPSLPDS NSTALATSAQ TPTVRKTIVT LNTPPPTTGD RLFDLVQGAF LTLNATNPGA TESCWLCLAM GPPYYEAIAS SGEVAYSTDL DRCRWGTQGK LTLTEVSGHG LCIGKVPFTH QHLCNQTLSI NSSGDHQYLL PSNHSWWACS TGLTPCLSTS VFNQTRDFCI QVQLIPRIYY YPEEVLLQAY DNSHPRTKR (SEQ ID NO:84). [00178] In some cases, the viral envelope protein is a GALV glycoprotein. A suitable GALV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: E AVSLTLAVLL GLGITAGIGT GSTALIKGPI DLQQGLTSLQ IAIDADLRAL QDSVSKLEDS LTSLSEVVLQ NRRGLDLLFL KEGGLCAALK EECCFYIDHS GAVRDSMKKL KEKLDKRQLE RQKSQNWYEG WFNNSPWFTT LLSTIAGPLL LLLLLLILGP CIINKLVQFI NDRISAVKIL (SEQ ID NO:85). [00179] In some cases, the viral envelope protein is a RD114 retrovirus glycoprotein. A suitable RD114 retrovirus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MKLPTGMVIL CSLIIVRAGF DDPRKAIALV QKQHGKPCEC SGGQVSEAPP NSIQQVTCPG KTAYLMTNQK WKCRVTPKNL TPSGGELQNC PCNTFQDSMH SSCYTEYRQC RANNKTYYTA TLLKIRSGSL NEVQILQNPN QLLQSPCRGS INQPVCWSAT APIHISDGGG PLDTKRVWTV QKRLEQIHKA MHPELQYHPL ALPKVRDDLS LDARTFDILN TTFRLLQMSN FSLAQDCWLC LKLGTPTPLA IPTPSLTYSL ADSLANASCQ IIPPLLVQPM QFSNSSCLSS PFINDTEQID LGAVTFTNCT SVANVSSPLC ALNGSVFLCG NNMAYTYLPQ NWTGLCVQAS LLPDIDIIPG DEPVPIPAID HYIHRPKRAV QFIPLLAGLG ITAAFTTGAT GLGVSVTQYT KLSHQLISDV QVLSGTIQDL QDQVDSLAEV VLQNRRGLDL LTAEQGGICL ALQEKCCFYA NKSGIVRNKI RTLQEELQKR RESLASNPLW TGLQGFLPYL LPLLGPLLTL LLILTIGPCV
FSRLMAFIND RLNVVHAMVL AQQYQALKAE EEAQD (SEQ ID NO:86; GenBank Accession No: YP_001497149). [00180] In some cases, the viral envelope protein is a Sendai virus (SeV) glycoprotein. A suitable SeV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MTAYIQRSQC ISTSLLVVLT TLVSCQIPRD RLSNIGVIVD EGKSLKIAGS HESRYIVLSL VPGVDFENGC GTAQVIQYKS LLNRLLIPLR DALDLQEALI TVTNDTTQNA GAPQSRFFGA VIGTIALGVA TSAQITAGIA LAEAREAKRD IALIKESMTK THKSIELLQN AVGEQILALK TLQDFVNDEI KPAISELGCE TAALRLGIKL TQHYSELLTA FGSNFGTIGE KSLTLQALSS LYSANITEIM TTIKTGQSNI YDVIYTEQIK GTVIDVDLER YMVTLSVKIP ILSEVPGVLI HKASSISYNI DGEEWYVTVP SHILSRASFL GGADITDCVE SRLTYICPRD PAQLIPDSQQ KCILGDTTRC PVTKVVDSLI PKFAFVNGGV VANCIASTCT CGTGRRPISQ DRSKGVVFLT HDNCGLIGVN GVELYANRRG HDATWGVQNL TVGPAIAIRP IDISLNLADA TNFLQDSKAE LEKARKILSE VGRWYNSRET VITIIVVMVV ILVVIIVIII VLYRLRRSML MGNPDDRIPR DTYTLEPKIR HMYTNGGFDA MAKER (SEQ ID NO:87; GenBank Accession No: P04855). [00181] In some cases, the viral envelope protein is an SeV F0 glycoprotein. A suitable SeV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QIPRD RLSNIGVIVD EGKSLKIAGS HESRYIVLSL VPGVDFENGC GTAQVIQYKS LLNRLLIPLR DALDLQEALI TVTNDTTQNA GAPQSRFFGA VIGTIALGVA TSAQITAGIA LAEAREAKRD IALIKESMTK THKSIELLQN AVGEQILALK TLQDFVNDEI KPAISELGCE TAALRLGIKL TQHYSELLTA FGSNFGTIGE KSLTLQALSS LYSANITEIM TTIKTGQSNI YDVIYTEQIK GTVIDVDLER YMVTLSVKIP ILSEVPGVLI HKASSISYNI DGEEWYVTVP SHILSRASFL GGADITDCVE SRLTYICPRD PAQLIPDSQQ KCILGDTTRC PVTKVVDSLI PKFAFVNGGV VANCIASTCT CGTGRRPISQ DRSKGVVFLT HDNCGLIGVN GVELYANRRG HDATWGVQNL TVGPAIAIRP IDISLNLADA TNFLQDSKAE LEKARKILSE VGRWYNSRET VITIIVVMVV ILVVIIVIII VLYRLRRSML MGNPDDRIPR DTYTLEPKIR HMYTNGGFDA MAEKR (SEQ ID NO:88; GenBank Accession No: P04855). [00182] In some cases, the viral envelope protein is an SeV F2 glycoprotein. A suitable SeV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QIPRD RLSNIGVIVD EGKSLKIAGS HESRYIVLSL VPGVDFENGC GTAQVIQYKS LLNRLLIPLR DALDLQEALI TVTNDTTQNA GAPQSR (SEQ ID NO:89; GenBank Accession No: P04855).
[00183] In some cases, the viral envelope protein is an SeV F1 glycoprotein. A suitable SeV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: FFGA VIGTIALGVA TSAQITAGIA LAEAREAKRD IALIKESMTK THKSIELLQN AVGEQILALK TLQDFVNDEI KPAISELGCE TAALRLGIKL TQHYSELLTA FGSNFGTIGE KSLTLQALSS LYSANITEIM TTIKTGQSNI YDVIYTEQIK GTVIDVDLER YMVTLSVKIP ILSEVPGVLI HKASSISYNI DGEEWYVTVP SHILSRASFL GGADITDCVE SRLTYICPRD PAQLIPDSQQ KCILGDTTRC PVTKVVDSLI PKFAFVNGGV VANCIASTCT CGTGRRPISQ DRSKGVVFLT HDNCGLIGVN GVELYANRRG HDATWGVQNL TVGPAIAIRP IDISLNLADA TNFLQDSKAE LEKARKILSE VGRWYNSRET VITIIVVMVV ILVVIIVIII VLYRLRRSML MGNPDDRIPR DTYTLEPKIR HMYTNGGFDA MAKER (SEQ ID NO:90; GenBank Accession No: P04855). [00184] In some cases, the viral envelope protein is an SeV hemagglutinin-neuraminidase glycoprotein. A suitable SeV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MDGDRSKRDS YWSTSPGGST TKLVSDSERS GKVDTWLLIL AFTQWALSIA TVIICIVIAA RQGYSMERYS MTVEALNTSN KEVKESLTSL IRQEVITRAA NIQSSVQTGI PVLLNKNSRD VIRLIEKSCN RQELTQLCDS TIAVHHAEGI APLEPHSFWR CPAGEPYLSS DPEVSLLPGP SLLSGSTTIS GCVRLPSLSI GEAIYAYSSN LITQGCADIG KSYQVLQLGY ISLNSDMFPD LNPVVSHTYD INDNRKSCSV VATGTRGYQL CSMPIVDERT DYSSDGIEDL VLDILDLKGR TKSHRYSNSE IDLDHPFSAL YPSVGSGIAT EGSLIFLGYG GLTTPLQGDT KCRIQGCQQV SQDTCNEALK ITWLGGKQVV SVLIQVNDYL SERPRIRVTT IPITQNYLGA EGRLLKLGDQ VYIYTRSSGW HSQLQIGVLD VSHPLTISWT PHEALSRPGN EDCNWYNTCP KECISGVYTD AYPLSPDAAN VATVTLYANT SRVNPTIMYS NTTNIINMLR IKDVQLEAAY TTTSCITHFG KGYCFHIIEI NQKSLNTLQP MLFKTSIPKL CKAES (SEQ ID NO:91; GenBank Accession No: BAA24391). [00185] In some cases, the viral envelope protein is a Jaagsiekte sheep retrovirus (JSRV) glycoprotein. A suitable JSRV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MPKRRAGFRK GWYARQRNSL THQMQRMTLS EPTSELPTQR QIEALMRYAW NEAHVQPPVT PTNILIMLLL LLQRIQNGAA ATFWAYIPDP PMLQSLGWDK ETVPVYVNDT SLLGGKSDIH ISPQQANISF YGLTTQYPMC FSYQSQHPHC IQVSADISYP RVTISGIDEK TGMRSYRDGT GPLDIPFCDK HLSIGIGIDT PWTLCRARIA SVYNINNANT TLLWDWAPGG TPDFPEYRGQ HPPISSVNTA PIYQTELWKL LAAFGHGNSL YLQPNISGSK YGDVGVTGFL YPRACVPYPF MVIQGHMEIT PSLNIYYLNC SNCILTNCIR GVAKGEQVII VKQPAFVMLP VEITEEWYDE TALELLQRIN TALSRPKRGL SLIILGIVSL ITLIATAVTA SVSLAQSIQV
AHTVDSLSSN VTKVMGTQEN IDKKIEDRLP ALYDVVRVLG EQVQSINFRM KIQCHANYKW ICVTKKPYNT SDFPWDKVKK HLQGIWFNTT VSLDLLQLHN EILDIENSPK ATLNIADTVD NFLQNLFSNF PSLHSLWRSI IAMGAVLTFV LIIICLAPCL IRSIVKEFLH MRVLIHKNML QHQHLMELLN NKERGAAGDD P (SEQ ID NO:92; GenBank Accession No: ABI50237). [00186] In some cases, the viral envelope protein is a baculovirus gp64 glycoprotein. A suitable baculovirus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MFHLLTLLLL LFINMNLYLA GEHCNVQMKN GPYRIKNLAI TPPRETLKKD VTVTIVETDY EENVLIGYKG YYQAYGYNGG SLDANTRLEE TMESLPLTKE DLLTWTYRQE CEVGEELIDR WGSDSDDCYR NKDGRGVWVK TKELVKRQNN NHFAHHTCNR SWRCGFSTAK MYSKLVCDDE TNDCKVFILD NTGKPINITT NEVLYRDGVN MMLKSKPTFT RREEKVACLL VKDELNPDKT REHCLIDSDI YDLSNNNWFC MFNKCIKRNV DSVVKKRPNK WMHNLAPKYS EGATATKGDM MHIQEELMYE NDLLKMNIEL VHAHMNKLNN IIHDLIVSIA KVDERLIGNL MNISVSSVFL SDDTFLLMPC TNPPQHTSNC YNNSIYREGR WVFNEDTSEC IDFNNYRELS IDDDIEFWIP TIGNTTYHDS WKDASGWSFV AQQKSNLIMT MENTKFGGVG TSLSDITSMS EGELTAKLTT FVFSHIVTFI LIIILIILCI CLLKK (SEQ ID NO:93; GenBank Accession No: YP_009182316). [00187] In some cases, the viral envelope protein is a baculovirus gp64 glycoprotein. A suitable baculovirus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MLRITLLILF LVRFVSGAEH CNAQMKSGPW RIKNLPIAPP KETLQKDVDV EIVETDLDEN VIIGYKGYYQ AYAYNGGSLD PNTSVDETTQ TLNIDKDDLI TWGDRRKCEV GEELIDQWGS DSDSCFKDKL GRGVWVAGKE LVKRKNNNHF AHHTCNRSWR CGVSTAKMYT RLECDNETDD CKVTILDING TVINVTENEV LHRDGVSMIL KQKSTFTRRT EKVACLLIKD DKSDPYSITR EHCLIDNDIF DLSKNTWNCK FNRCIKRRSE NVVKKRPPTW RHNEPPKHSE GTTATKGDLM HIQEELMYEN DLLRMNLELL HAHINKLNNM MHDLIVSVAK VDERLIGNLM NNSVSSTFLS DDTFLLMPCT NPPPHTSNCY NNSIYKEGRW VANTDSSQCI DFRNYKELAI DDDIEFWIPT IGNTSYHESW KDASGWSFIA QQKSNLISTM ENTKFGGHTT SLSDIGDMAK GELNATLYSF MLGHGFSFFL IIGVIVFLIC MVRSRVRAF (SEQ ID NO:94; GenBank Accession No: YP_473216). [00188] In some cases, the viral envelope protein is a Chandipura virus glycoprotein. A suitable Chandipura virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MTSSVTISVI LLISFIAPSY SSLSIAFPEN TKLDWKPVTK NTRYCPMGGE WFLEPGLQEE SFLSSTPIGA TPSKSDGFLC HAAKWVTTCD FRWYGPKYIT HSIHNIKPTR
SDCDTALASY KSGTLVSPGF PPESCGYASV TDSEFLVIMI TPHHVGVDDY RGHWVDPLFV GGECDQSYCD TIHNSSVWIP ADQTKKNICG QSFTPLTVTV AYDKTKEIAA GAIVFKSKYH SHMEGARTCR LSYCGRNGIK FPNGEWVSLD VKTKIQEKPL LPLFKECPAG TEVRSTLQSD GAQVLTSEIQ RILDYSLCQN TWDKVERKEP LSPLDLSYLA SKSPGKGLAY TVINGTLSFA HTRYVRMWID GPVLKEMKGK RESPSGISSD IWTQWFKYGD MEIGPNGLLK TAGGYKFPWH LIGMGIVDNE LHELSEANPL DHPQLPHAQS IADDSEEIFF GDTGVSKNPV ELVTGWFTSW KESLAAGVVL ILVVVLIYGV LRCFPVLCTT CRKPKWKKGV ERSDSFEMRI FKPNNMRARV (SEQ ID NO:95; GenBank Accession No: YP_007641380). [00189] In some cases, viral envelope protein is a Venezuelan equine encephalitis virus glycoprotein. A suitable Venezuelan equine encephalitis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MFPFQPMYPM QPMPYRNPFA APRRPWFPRT DPFLAMQVQE LTRSMANLTF KQRRDAPPEG PSAKKPKKEA SQKQKGGGQG KKKKNQGKKK AKTGPPNPKA QNGNKKKTNK KPGKRQRMVM KLESDKTFPI MLEGKINGYA CVVGGKLFRP MHVEGKIDND VLAALKTKKA SKYDLEYADV PQNMRADTFK YTHEKPQGYY SWHHGAVQYE NGRFTVPKGV GAKGDSGRPI LDNQGRVVAI VLGGVNEGSR TALSVVMWNE KGVTVKYTPE NCEQWSLVTT MCLLANVTFP CAQPPICYDR KPAETLAMLS VNVDNPGYDE LLEAAVKCPG STEELFKEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLHTSRPC HIVDGHGYFL LARCPAGDSI TMEFKKDSVT HSCSVPYEVK FNPVGRELYT HPPEHGVEQA CQVYAHDAQN RGAYVEMHLP GSEVDSSLVS LSGSSVTVTP PVGTSALVEC ECGGTKISET INKTKQFSQC TKKEQCRAYR LQNDKWVYIS DKLPKAAGAT LKGKLHVPFL LADGKCTVPL APEPMITFGF RSVSLKLHPK NPTYLTTRQL ADEPHYTHEL ISEPAVRNFT VTGKGWEFVW GNHPPKRFWA QETAPGNPHG LPHEVITHYY HRYPMSTILG LSICAAIATV SVAASTWLFC RSRVACLTPY RLTPNARIPF CLAVLCCART ARAETTWESL DHLWNNNQQM FWIQLLIPLA ALIVVTRLLR CVCCVVPFLV MAGAAGAGAY EHATTMPSQA GISYNTIVNR AGYAPLPISI TPTKIKLIPT VNLEYVTCHY KTGMDSPAIK CCGSQECTPT YRPDEQCKVF TGVYPFMWGG AYCFCDTENT QVSKAYVMKS DDCLADHAEA YKAHTASVQA FLNITVGEHS IVTTVYVNGE TPVNFNGVKL TAGPLSTAWT PFDRKIVQYA GEIYNYDFPE YGAGQPGAFG DIQSRTVSSS DLYANTNLVL QRPKAGAIHV PYTQAPSGFE QWKKDKAPSL KSTAPFGCEI YTNPIRAENC AVGSIPLAFD IPDALFTRVS ETPTLSAAEC TLNECVYSSD FGGIATVKYS ASKSGKCAVH VPSGTATLKE AAVELTEQGS ATIHFSTANI HPEFRLQICT SYVTCKGDCH PPKDHIVTHP QYHAQTFTAA VSKTAWTWLT SLLGGSAVII IIGLVLATIV AMYVLTNQKH N (SEQ ID NO:96; GenBank Accession No: AAU89534). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to
dendritic cells, macrophages, and cells of the spleen, lymph node, thymus, pancreas, skeletal muscle, and central nervous system. [00190] In some cases, the viral envelope protein is a Venezuelan equine encephalitis virus E2 glycoprotein. A suitable Venezuelan equine encephalitis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: STEELFKEYK LTRPYMARCI RCAVGSCHSP IAIEAVKSDG HDGYVRLQTS SQYGLDSSGN LKGRTMRYDM HGTIKEIPLH QVSLHTSRPC HIVDGHGYFL LARCPAGDSI TMEFKKDSVT HSCSVPYEVK FNPVGRELYT HPPEHGVEQA CQVYAHDAQN RGAYVEMHLP GSEVDSSLVS LSGSSVTVTP PVGTSALVEC ECGGTKISET INKTKQFSQC TKKEQCRAYR LQNDKWVYIS DKLPKAAGAT LKGKLHVPFL LADGKCTVPL APEPMITFGF RSVSLKLHPK NPTYLTTRQL ADEPHYTHEL ISEPAVRNFT VTGKGWEFVW GNHPPKRFWA QETAPGNPHG LPHEVITHYY HRYPMSTILG LSICAAIATV SVAASTWLFC RSRVACLTPY RLTPNARIPF CLAVLCCART ARA (SEQ ID NO:97; GenBank Accession No: AAU89534). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to dendritic cells, macrophages, and cells of the spleen, lymph node, thymus, pancreas, skeletal muscle, and central nervous system. [00191] In some cases, the viral envelope protein is a Venezuelan equine encephalitis virus E1 glycoprotein. A suitable Venezuelan equine encephalitis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: Y EHATTMPSQA GISYNTIVNR AGYAPLPISI TPTKIKLIPT VNLEYVTCHY KTGMDSPAIK CCGSQECTPT YRPDEQCKVF TGVYPFMWGG AYCFCDTENT QVSKAYVMKS DDCLADHAEA YKAHTASVQA FLNITVGEHS IVTTVYVNGE TPVNFNGVKL TAGPLSTAWT PFDRKIVQYA GEIYNYDFPE YGAGQPGAFG DIQSRTVSSS DLYANTNLVL QRPKAGAIHV PYTQAPSGFE QWKKDKAPSL KSTAPFGCEI YTNPIRAENC AVGSIPLAFD IPDALFTRVS ETPTLSAAEC TLNECVYSSD FGGIATVKYS ASKSGKCAVH VPSGTATLKE AAVELTEQGS ATIHFSTANI HPEFRLQICT SYVTCKGDCH PPKDHIVTHP QYHAQTFTAA VSKTAWTWLT SLLGGSAVII IIGLVLATIV AMYVLTNQKH N (SEQ ID NO:98; GenBank Accession No: AAU89534). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to dendritic cells, macrophages, and cells of the spleen, lymph node, thymus, pancreas, skeletal muscle, and central nervous system. [00192] In some cases, the viral envelope protein is a Lassa virus glycoprotein. A suitable Lassa virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGQIVTFFQE VPHVIEEVMN IVLIALSVLA VLKGLYNFAT CGLVGLVTFL LLCGRSCTTS LYKGVYELQT LELNMETLNM TMPLSCTKNN SHHYIMVGNE TGLELTLTNT SIINHKFCNL
SDAHKKNLYD HALMSIISTF HLSIPNFNQY EAMSCDFNGG KISVQYNLSH SYAGDAANHC GTVANGVLQT FMRMAWGGSY IALDSGRGNW DCIMTSYQYL IIQNTTWEDH CQFSRPSPIG YLGLLSQRTR DIYISRRLLG TFTWTLSDSE GKDTPGGYCL TRWMLIEAEL KCFGNTAVAK CNEKHDEEFC DMLRLFDFNK QAIQRLKAEA QMSIQLINKA VNALINDQLI MKNHLRDIMG IPYCNYSKYW YLNHTTTGRT SLPKCWLVSN GSYLNETHFS DDIEQQADNM ITEMLQKEYM ERQGKTPLGL VDLFVFSTSF YLISIFLHLV KIPTHRHIVG KSCPKPHRLN HMGICSCGLY KQPGVPVKWK R (SEQ ID NO:99; GenBank Accession No: ADY11070). [00193] In some cases, the viral envelope protein is an avian leukosis virus glycoprotein. A suitable avian leukosis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEAVIKMRRA LFLQAFLTGR PGKASKKDPK KNPLATSKKD PEKTPLLPTR VNYILIIGVL VLCEVTGVRA DVHLLEQPGN LWITWANRTG QTDFCLSTQS ATSPFQTCLI GIPSPISEGD FKGYVSDNCT TLGTDRLVSS ASITGGPDNS TTLTYRKVSC LLLKLNVSMW NEPPELQLLG SQSLPNITDI TQISGVAGGC VGFRPKGVPW YLGWSQGEAT RFLLRHPSFS NLTGPFTVVT ADRHNLFMGS EYCGAYGYRF WEIYNCSQEG QQYRCGKARR PRPQSPETQC TRQGGIWVNR SKEINETEPF SFTVNCTASN LGNASGCCGK AGTILPGIWV DSTQGNFTKP KALPPAIFLI CGDRAWQGIP SRPVGGPCYL GKLTMLAPNH TDILKILANS SRTGIRRRRS VSHLDDTCSD EVQLWGPTAR IFASILAPGV AAAQALREIE RLACWSVKQA NLTTSLLGDL LDDVTSIRHA VLQNRAAIDF LLLAHGHGCE DIAGMCCFNL SDHSESIQKK FQLMKEHVNK IGVDSDPIGS WLRGLFGGIG GWAVHLLKGL LLGLVVILLL VVCLPCFLQF VSSSIRKMIN NSVSYHTEYR KMQGGAV (SEQ ID NO:100; GenBank Accession No: ADO34853). [00194] In some cases, the viral envelope protein is an avian leukosis virus glycoprotein. A suitable avian leukosis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEAVIKMRRA LFLQAFLTGH PGKVSKKDSK KKPPATGKRD PEKTPLLPTR VNYILIIGVL VLCEVTGVRA DVHLLEQPGN LWITWANRTG QTDFCLSTQS ATSPFQTCLI GIPSPISEGD FKGYVSGNCT ALGTHRLVSS GIHGGPDNST TLTYRKVSCL LLKLNVSLLD EPSELQLLGS QSLPNITNIT QIPSVAGGCI GFTPYGSPAG VYGWDRRQVT HILLTDPGSN PFFNKASNSS KPFTVVTADR HNLFMGSEYC GAYGYRFWEM YNCSQMRQNW SICMDVWGRG LPESWCTSTG GIWVNQSKEI NETEPFSFTA NCTGSNLGNV SGCCGESITI LPPGAWVDST QGSFTKPKAL PPGIFLICGD RAWQGIPSRP VGGPCYLGKL TMLAPNHTDI LKILANSSQT GVRHKRSVTH LDDTCSDEVQ LWGPTARIFA SILAPGVAAA QALREIERLA CWSVKQANLT TSLLGDLLDD VTSIRHAVLQ NRAAIDFLLL AHGHGCEDIA GMCCFNLSDH SESIQKKFQL MKEHVNKIGV DSDPIGSWLR GLFGGIGEWA VHLLKGLLLG LVVILLLVVC
LPCFLQFVSS SIRKMINNSI SYHTEYRKMQ GGAV (SEQ ID NO:101; GenBank Accession No: AEF97639). [00195] In some cases, the viral envelope protein is an avian leukosis virus glycoprotein. A suitable avian leukosis virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEAVIKAFLT GHPGKVSKKD SKKKPPATSK KDPEKTPLLP SRGYFFFPTI LVCVVIISVV PGVGGVHLLR QPGNVWVTWA NKTGRTDFCL SLQSATSPFR TCLIGIPQYP LNTFKGYVTN VTACDNDADL ASQTACLIKA LNTTLPWDPQ ELDILGSQMI KNGTTRTCVT FGSVCYKENN RSRVCHNFDG NFNGTGGAEA ELRDFIAKWK SDDLLIRPYV NQSWTMVSPI NVESFSISRR YCGFTSNETR YYRGDLSNWC GSKRGKWSAG YSNRTKCSSN TTGCGGNCTT EWNYYAYGFT FGKQPEVLWN NGTAKALPPG IFLICGDRAW QGIPRNALGG PCYLGQLTML SPNFTTWITY GPNITGHRRS RRAIRGLSPD CSDEVQLWSA TARIFASFFA PGVAAAQALK EIERLACWSV KQANLTSLIL NAMLEDMNSI RHAVLQNRAA IDFLLLAQGH GCQDVEGMCC FNLSDHSESI HKALQAMKEH TEKIQVEDDP IGDWFTRTFG DLGRWLAKGV KTLLFALLVI VCLLAIIPCI IKCFQDCLSR TMNQFMDERI RYHRIREQL (SEQ ID NO:102; GenBank Accession No: AWM62167). [00196] In some cases, the viral envelope protein is a human T-lymphotropic virus 1 (HTLV-1) glycoprotein. A suitable HTLV-1 protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MGKFLATLIL FFQFCPLILG DYSPSCCTLT VGVSSYHSKP CNPAQPVCSW TLDLLALSAD QALQPPCPNL VSYSSYHATY SLYLFPHWIK KPNRNGGGYY SASYSDPCSL KCPYLGCQSW TCPYTGAVSS PYWKFQQDVN FTQEVSHLNI NLHFSKCGFP FSLLVDAPGY DPIWFLNTEP SQLPPTAPPL LSHSNLDHIL EPSIPWKSKL LTLVQLTLQS TNYTCIVCID RASLSTWHVL YSPNVSVPSL SSTPLLYPSL ALPAPHLTLP FNWTHCFDPQ IQAIVSSPCH NSLILPPFSL SPVPTLGSRS RRAVPVAVWL VSALAMGAGV AGGITGSMSL ASGKSLLHEV DKDISQLTQA IVKNHKNLLK IAQYAAQNRR GLDLLFWEQG GLCKALQEQC CFLNITNSHV SILQERPPLE NRVLTGWGLN WDLGLSQWAR EALQTGITLV ALLLLVILAG PCILRQLRHL PSRVRYPHYS LINPESSL (SEQ ID NO:103; GenBank Accession No: AAU04884). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to CD4+ and CD8+ T cells. [00197] In some cases, the viral envelope protein is a human foamy virus gp130 glycoprotein. A suitable human foamy virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MAPPMTLQQW IIWKKMNKAH EALQNTTTVT EQQKEQIILD IQNEEVQPTR RDKFRYLLYT CCATSSRVLA WMFLVCILLI IVLVSCFVTI SRIQWNKDIQ
VLGPVIDWNV TQRAVYQPLQ TRRIARSLRM QHPVPKYVEV NMTSIPQGVY YEPHPEPIVV KERVLGLSQI LMINSENIAN NANLTQEVKK LLTEMVNEEM QSLSDVMIDF EIPLGDPRDQ EQYIHRKCYQ EFANCYLVKY KEPKPWPKEG LIADQCPLPG YHAGLTYNRQ SIWDYYIKVE SIRPANWTTK SKYGQARLGS FYIPSSLRQI NVSHVLFCSD QLYSKWYNIE NTIEQNERFL LNKLNNLTSG TSVLKKRALP KDWSSQGKNA LFREINVLDI CSKPESVILL NTSYYSFSLW EGDCNFTKDM ISQLVPECDG FYNNSKWMHM HPYACRFWRS KKNEKEETKC RDGETKRCLY YPLWDSPEST YDFGYLAYQK NFPSPICIEQ QKIRDQDYEV YSLYQERKIA SKAYGIDTVL FSLKNFLNYT GTPVNEMPNA RAFVGLIDPK FPPSYPNVTR EHYTSCNNRK RRSVDNNYAK LRSMGYALTG AVQTLSQISD INDENLQQGI YLLRDHVITL MEATLHDISV MEGMFAVQHL HTHLNHLKTM LLERRIDWTY MSSTWLQQQL QKSDDEMKVI KRIARSLVYY VKQTHSSPTA TAWEIGLYYE LVIPKHIYLN NWNVVNIGHL VKSAGQLTHV TIAHPYEIIN KECVETIYLH LEDCTRQDYV ICDVVKIVQP CGNSSDTSDC PVWAEAVKEP FVQVNPLKNG SYLVLASSTD CQIPPYVPSI VTVNETTSCF GLDFKRPLVA EERLSFEPRL PNLQLRLPHL VGIIAKIKGI KIEVTSSGES IKEQIERAKA ELLRLDIHEG DTPAWIQQLA AATKDVWPAA ASALQGIGNF LSGTAQGIFG TAFSLLGYLK PILIGVGVIL LVILIFKIVS WIPTKKKNQ (SEQ ID NO:104; GenBank Accession No: P14351). [00198] In some cases, the viral envelope protein is a human foamy virus glycoprotein. A suitable human foamy virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: SLRM QHPVPKYVEV NMTSIPQGVY YEPHPEPIVV KERVLGLSQI LMINSENIAN NANLTQEVKK LLTEMVNEEM QSLSDVMIDF EIPLGDPRDQ EQYIHRKCYQ EFANCYLVKY KEPKPWPKEG LIADQCPLPG YHAGLTYNRQ SIWDYYIKVE SIRPANWTTK SKYGQARLGS FYIPSSLRQI NVSHVLFCSD QLYSKWYNIE NTIEQNERFL LNKLNNLTSG TSVLKKRALP KDWSSQGKNA LFREINVLDI CSKPESVILL NTSYYSFSLW EGDCNFTKDM ISQLVPECDG FYNNSKWMHM HPYACRFWRS KKNEKEETKC RDGETKRCLY YPLWDSPEST YDFGYLAYQK NFPSPICIEQ QKIRDQDYEV YSLYQERKIA SKAYGIDTVL FSLKNFLNYT GTPVNEMPNA RAFVGLIDPK FPPSYPNVTR EHYTSCNNRK RR (SEQ ID NO:105). [00199] In some cases, the viral envelope protein is a human foamy virus glycoprotein. A suitable human foamy virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: SVDNNYAK LRSMGYALTG AVQTLSQISD INDENLQQGI YLLRDHVITL MEATLHDISV MEGMFAVQHL HTHLNHLKTM LLERRIDWTY MSSTWLQQQL QKSDDEMKVI KRIARSLVYY VKQTHSSPTA TAWEIGLYYE LVIPKHIYLN NWNVVNIGHL VKSAGQLTHV TIAHPYEIIN KECVETIYLH LEDCTRQDYV ICDVVKIVQP CGNSSDTSDC PVWAEAVKEP FVQVNPLKNG SYLVLASSTD CQIPPYVPSI VTVNETTSCF GLDFKRPLVA EERLSFEPRL
PNLQLRLPHL VGIIAKIKGI KIEVTSSGES IKEQIERAKA ELLRLDIHEG DTPAWIQQLA AATKDVWPAA ASALQGIGNF LSGTAQGIFG TAFSLLGYLK PILIGVGVIL LVILIFKIVS WIPTKKKNQ (SEQ ID NO:106). [00200] In some cases, the viral envelope protein is a visna-maedi virus gp160 glycoprotein. A suitable visna-maedi virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MASKESKPSR TTRRGMEPPL RETWNQVLQE LVKRQQQEEE EQQGLVSGKK KSWVSIDLLG TEGKDIKKVN IWEPCEKWFA QVVWGVLWVL QIVLWGCLMW EVRKGNQCQA EEVIALVSDP GGFQRVQHVE TVPVTCVTKN FTQWGCQPEG AYPDPELEYR NISREILEEV YKQDWPWNTY HWPLWQMENM RQWMKENEKE YKERTNKTKE DIDDLVAGRI RGRFCVPYPY ALLRCEEWCW YPESINQETG HAEKIKINCT KAKAVSCTEK MSLAAVQRVY WEKEDEESMK FLNIKACNIS LRCQDEGKSP GGCVQGYPIP KGAEIIPEAM KYLRGKKSRY GGIKDKNGEL KLPLSVRVWV RMANLSGWVN GTPPYWSARI NGSTGINGTR WYGIGTLHHL GCNISSNPER GICNFTGELW IGGDKFPYYY TPSWNCSQNW TGHPVWHVFR YLDMTEHMTS RCIQRPKRHN ITVGNGTITG NCSVTNWDGC NCTRSGNHLY NSTSGGLLVI ICRQNSTITG IMGTNTNWTT MWNIYQNCSR CNNSSLDRTG SGTLGTVNNL KCSLPHRNES NKWTCKSQRD SYIAGRDFWG KVKAKYSCES NLGGLDSMMH QQMLLQRYQV IRVRAYTYGV VEMPQSYMEA QGENKRSRRN LQRKKRGIGL VIVLAIMAII AAAGAGLGVA NAVQQSYTRT AVQSLANATA AQQEVLEASY AMVQHIAKGI RILEARVARV EALVDRMMVY QELDCWHYQH YCVTSTRSEV ANYVNWTRFK DNCTWQQWEE EIEQHEGNLS LLLREAALQV HIAQRDARRI PDAWKAIQEA FNWSSWFSWL KYIPWIIMGI VGLMCFRILM CVISMCLQAY KQVKQIRYTQ VTVVIEAPVE LEEKQKRNGD GTNGCASLER ERRTSHRSFI QIWRATWWAW KTSPWRHNWR TMPYITLLPI LVIWQWMEEN GWNGENQHKK KKERVDCQDR EQMPTLENDY VEL (SEQ ID NO:107; GenBank Accession No: P35954). [00201] In some cases, the viral envelope protein is a visna-maedi virus glycoprotein. A suitable visna- maedi virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QCQA EEVIALVSDP GGFQRVQHVE TVPVTCVTKN FTQWGCQPEG AYPDPELEYR NISREILEEV YKQDWPWNTY HWPLWQMENM RQWMKENEKE YKERTNKTKE DIDDLVAGRI RGRFCVPYPY ALLRCEEWCW YPESINQETG HAEKIKINCT KAKAVSCTEK MSLAAVQRVY WEKEDEESMK FLNIKACNIS LRCQDEGKSP GGCVQGYPIP KGAEIIPEAM KYLRGKKSRY GGIKDKNGEL KLPLSVRVWV RMANLSGWVN GTPPYWSARI NGSTGINGTR WYGIGTLHHL GCNISSNPER GICNFTGELW IGGDKFPYYY TPSWNCSQNW TGHPVWHVFR YLDMTEHMTS RCIQRPKRHN ITVGNGTITG NCSVTNWDGC NCTRSGNHLY NSTSGGLLVI ICRQNSTITG IMGTNTNWTT MWNIYQNCSR CNNSSLDRTG SGTLGTVNNL KCSLPHRNES
NKWTCKSQRD SYIAGRDFWG KVKAKYSCES NLGGLDSMMH QQMLLQRYQV IRVRAYTYGV VEMPQSYMEA QGENKRSRRN LQRKKRGIGL VIVLAIMAII AAAGAGLGVA NAVQQSYTRT AVQSLANATA AQQEVLEASY AMVQHIAKGI RILEARVARV EALVDRMMVY QELDCWHYQH YCVTSTRSEV ANYVNWTRFK DNCTWQQWEE EIEQHEGNLS LLLREAALQV HIAQRDARRI PDAWKAIQEA FNWSSWFSWL KYIPWIIMGI VGLMCFRILM CVISMCLQAY KQVKQIRYTQ VTVVIEAPVE LEEKQKRNGD GTNGCASLER ERRTSHRSFI QIWRATWWAW KTSPWRHNWR TMPYITLLPI LVIWQWMEEN GWNGENQHKK KKERVDCQDR EQMPTLENDY VEL (SEQ ID NO:108). [00202] In some cases, the viral envelope protein is a visna-maedi virus glycoprotein. A suitable visna- maedi virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QCQA EEVIALVSDP GGFQRVQHVE TVPVTCVTKN FTQWGCQPEG AYPDPELEYR NISREILEEV YKQDWPWNTY HWPLWQMENM RQWMKENEKE YKERTNKTKE DIDDLVAGRI RGRFCVPYPY ALLRCEEWCW YPESINQETG HAEKIKINCT KAKAVSCTEK MSLAAVQRVY WEKEDEESMK FLNIKACNIS LRCQDEGKSP GGCVQGYPIP KGAEIIPEAM KYLRGKKSRY GGIKDKNGEL KLPLSVRVWV RMANLSGWVN GTPPYWSARI NGSTGINGTR WYGIGTLHHL GCNISSNPER GICNFTGELW IGGDKFPYYY TPSWNCSQNW TGHPVWHVFR YLDMTEHMTS RCIQRPKRHN ITVGNGTITG NCSVTNWDGC NCTRSGNHLY NSTSGGLLVI ICRQNSTITG IMGTNTNWTT MWNIYQNCSR CNNSSLDRTG SGTLGTVNNL KCSLPHRNES NKWTCKSQRD SYIAGRDFWG KVKAKYSCES NLGGLDSMMH QQMLLQRYQV IRVRAYTYGV VEMPQSYMEA QGENKRSRRN LQRKKRGIGL VIVLAIMAII AAAGAGLGVA NAVQQSYTRT AVQSLANATA AQQEVLEASY AMVQHIAKGI RILEARVARV EALVDRMMVY QELDCWHYQH YCVTSTRSEV ANYVNWTRFK DNCTWQQWEE EIEQHEGNLS LLLREAALQV HIAQRDARRI PDAWKAIQEA FNWSSWFSWL KYIPWIIMGI VGLMCFRILM CVISMCLQAY KQVKQIRYTQ VTVVIEAPVE LEEKQKRNGD GTNGCASLER ERRTSHRSFI QIWRATWWAW KTSPWRHNWR TMPYITLLPI LVIWQWMEEN GWNGENQHKK KKERVDCQDR EQMPTLENDY VEL (SEQ ID NO:108). [00203] In some cases, the viral envelope protein is a visna-maedi virus glycoprotein. A suitable visna- maedi virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QCQA EEVIALVSDP GGFQRVQHVE TVPVTCVTKN FTQWGCQPEG AYPDPELEYR NISREILEEV YKQDWPWNTY HWPLWQMENM RQWMKENEKE YKERTNKTKE DIDDLVAGRI RGRFCVPYPY ALLRCEEWCW YPESINQETG HAEKIKINCT KAKAVSCTEK MSLAAVQRVY WEKEDEESMK FLNIKACNIS LRCQDEGKSP GGCVQGYPIP KGAEIIPEAM KYLRGKKSRY GGIKDKNGEL KLPLSVRVWV RMANLSGWVN GTPPYWSARI NGSTGINGTR
WYGIGTLHHL GCNISSNPER GICNFTGELW IGGDKFPYYY TPSWNCSQNW TGHPVWHVFR YLDMTEHMTS RCIQRPKRHN ITVGNGTITG NCSVTNWDGC NCTRSGNHLY NSTSGGLLVI ICRQNSTITG IMGTNTNWTT MWNIYQNCSR CNNSSLDRTG SGTLGTVNNL KCSLPHRNES NKWTCKSQRD SYIAGRDFWG KVKAKYSCES NLGGLDSMMH QQMLLQRYQV IRVRAYTYGV VEMPQSYMEA QGENKRSRRN LQRKKR (SEQ ID NO:109). [00204] In some cases, the viral envelope protein is a visna-maedi virus glycoprotein. A suitable visna- maedi virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: GIGL VIVLAIMAII AAAGAGLGVA NAVQQSYTRT AVQSLANATA AQQEVLEASY AMVQHIAKGI RILEARVARV EALVDRMMVY QELDCWHYQH YCVTSTRSEV ANYVNWTRFK DNCTWQQWEE EIEQHEGNLS LLLREAALQV HIAQRDARRI PDAWKAIQEA FNWSSWFSWL KYIPWIIMGI VGLMCFRILM CVISMCLQAY KQVKQIRYTQ VTVVIEAPVE LEEKQKRNGD GTNGCASLER ERRTSHRSFI QIWRATWWAW KTSPWRHNWR TMPYITLLPI LVIWQWMEEN GWNGENQHKK KKERVDCQDR EQMPTLENDY VEL (SEQ ID NO:110). [00205] In some cases, the viral envelope protein is a severe acute respiratory syndrome-associated coronavirus (SARS-CoV) spike glycoprotein. A suitable SARS-CoV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MFIFLLFLTL TSGSDLDRCT TFDDVQAPNY TQHTSSMRGV YYPDEIFRSD TLYLTQDLFL PFYSNVTGFH TINHTFGNPV IPFKDGIYFA ATEKSNVVRG WVFGSTMNNK SQSVIIINNS TNVVIRACNF ELCDNPFFAV SKPMGTQTHT MIFDNAFNCT FEYISDAFSL DVSEKSGNFK HLREFVFKNK DGFLYVYKGY QPIDVVRDLP SGFNTLKPIF KLPLGINITN FRAILTAFSP AQDIWGTSAA AYFVGYLKPT TFMLKYDENG TITDAVDCSQ NPLAELKCSV KSFEIDKGIY QTSNFRVVPS GDVVRFPNIT NLCPFGEVFN ATKFPSVYAW ERKKISNCVA DYSVLYNSTF FSTFKCYGVS ATKLNDLCFS NVYADSFVVK GDDVRQIAPG QTGVIADYNY KLPDDFMGCV LAWNTRNIDA TSTGNYNYKY RYLRHGKLRP FERDISNVPF SPDGKPCTPP ALNCYWPLND YGFYTTTGIG YQPYRVVVLS FELLNAPATV CGPKLSTDLI KNQCVNFNFN GLTGTGVLTP SSKRFQPFQQ FGRDVSDFTD SVRDPKTSEI LDISPCSFGG VSVITPGTNA SSEVAVLYQD VNCTDVSTAI HADQLTPAWR IYSTGNNVFQ TQAGCLIGAE HVDTSYECDI PIGAGICASY HTVSLLRSTS QKSIVAYTMS LGADSSIAYS NNTIAIPTNF SISITTEVMP VSMAKTSVDC NMYICGDSTE CANLLLQYGS FCTQLNRALS GIAAEQDRNT REVFAQVKQM YKTPTLKYFG GFNFSQILPD PLKPTKRSFI EDLLFNKVTL ADAGFMKQYG ECLGDINARD LICAQKFNGL TVLPPLLTDD MIAAYTAALV SGTATAGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLYE NQKQIANQFN KAISQIQESL TTTSTALGKL QDVVNQNAQA LNTLVKQLSS NFGAISSVLN DILSRLDKVE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RVDFCGKGYH
LMSFPQAAPH GVVFLHVTYV PSQERNFTTA PAICHEGKAY FPREGVFVFN GTSWFITQRN FFSPQIITTD NTFVSGNCDV VIGIINNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ YIKWPWYVWL GFIAGLIAIV MVTILLCCMT SCCSCLKGAC SCGSCCKFDE DDSEPVLKGV KLHYT (SEQ ID NO:111; GenBank Accession No: ABA02260). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00206] In some cases, the viral envelope protein is a SARS-CoV S2 glycoprotein. A suitable SARS- CoV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: CDI PIGAGICASY HTVSLLRSTS QKSIVAYTMS LGADSSIAYS NNTIAIPTNF SISITTEVMP VSMAKTSVDC NMYICGDSTE CANLLLQYGS FCTQLNRALS GIAAEQDRNT REVFAQVKQM YKTPTLKYFG GFNFSQILPD PLKPTKRSFI EDLLFNKVTL ADAGFMKQYG ECLGDINARD LICAQKFNGL TVLPPLLTDD MIAAYTAALV SGTATAGWTF GAGAALQIPF AMQMAYRFNG IGVTQNVLYE NQKQIANQFN KAISQIQESL TTTSTALGKL QDVVNQNAQA LNTLVKQLSS NFGAISSVLN DILSRLDKVE AEVQIDRLIT GRLQSLQTYV TQQLIRAAEI RASANLAATK MSECVLGQSK RVDFCGKGYH LMSFPQAAPH GVVFLHVTYV PSQERNFTTA PAICHEGKAY FPREGVFVFN GTSWFITQRN FFSPQIITTD NTFVSGNCDV VIGIINNTVY DPLQPELDSF KEELDKYFKN HTSPDVDLGD ISGINASVVN IQKEIDRLNE VAKNLNESLI DLQELGKYEQ YIKWPWYVWL GFIAGLIVIV MVTILLCCMT SCCSCLKGAC SCGSCCKFDE DDSEPVLKGV KL (SEQ ID NO:112; GenBank Accession No: ABD73002). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00207] In some cases, the viral envelope protein is a SARS-CoV spike receptor binding domain glycoprotein. A suitable SARS-CoV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: PNIT NLCPFGEVFN ATKFPSVYAW ERKKISNCVA DYSVLYNSTF FSTFKCYGVS ATKLNDLCFS NVYADSFVVK GDDVRQIAPG QTGVIADYNY KLPDDFMGCV LAWNTRNIDA TSTGNYNYKY RYLRHGKLRP FERDISNVPF SPDGKPCTPP ALNCYWPLND YGFYTTTGIG YQPYRVVVLS FELLNAPATV CGPKLSTDLI KNQCVNFNFN GLTGTGVLTP SSKRFQPFQQ FGRDVSDFTD SVRDPKTSE (SEQ ID NO:113; GenBank Accession No: ABD73002). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet
cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00208] In some cases, the viral envelope protein is a respiratory syncytial virus (RSV) glycoprotein G. A suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MSKNKDQRTA KTLERTWDTL NHLLFISSCL YKLNLKSVAQ ITLSILAMII STSLIIAAII FIASANHKVT PTTAIIQDAT SQIKNTTPTY LTQNPQLGIS PSNPSEITSQ ITTILASTTP GVKSTLQSTT VKTKNTTTTQ TQPSKPTTKQRQNKPPSKPN NDFHFEVFNF VPCSICSNNP TCWAICKRIP NKKPGKKTTTKPTKKPTLKT TKKDPKPQTT KSKEVPTTKP TEEPTINTTK TNIITTLLTS NTTGNPELTS QMETFHSTSS EGNPSPSQVS TTSEYPSQPS SPPNTPRQ (SEQ ID NO:114; UniProtKB: P03423-1). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00209] In some cases, the viral envelope protein is an RSV glycoprotein F. A suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PPTNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRRFLGF LLGVGSAIAS GVAVSKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ KKLMSNNVQI VRQQSYSIMS IIKEEVLAYV VQLPLYGVID TPCWKLHTSP LCTTNTKEGS NICLTRTDRG WYCDNAGSVS FFPQAETCKV QSNRVFCDTM NSLTLPSEIN LCNVDIFNPK YDCKIMTSKT DVSSSVITSL GAIVSCYGKT KCTASNKNRG IIKTFSNGCD YVSNKGMDTV SVGNTLYYVN KQEGKSLYVK GEPIINFYDP LVFPSDEFDA SISQVNEKIN QSLAFIRKSD ELLHNVNAGK STTNIMITTI IIVIIVILLS LIAVGLLLYC KARSTPVTLS KDQLSGINNI AFSN (SEQ ID NO:115; GenBank Accession No: P03420). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00210] In some cases, the viral envelope protein is an RSV glycoprotein. A suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV
TELQLLMQST PPTNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRRFLGF LLGVGSAIAS GVAVSKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ KKLMSNNVQI VRQQSYSIMS IIKEEVLAYV VQLPLYGVID TPCWKLHTSP LCTTNTKEGS NICLTRTDRG WYCDNAGSVS FFPQAETCKV QSNRVFCDTM NSLTLPSEIN LCNVDIFNPK YDCKIMTSKT DVSSSVITSL GAIVSCYGKT KCTASNKNRG IIKTFSNGCD YVSNKGMDTV SVGNTLYYVN KQEGKSLYVK GEPIINFYDP LVFPSDEFDA SISQVNEKIN QSLAFIRKSD ELLHNVNAGK STTNIMITTI IIVIIVILLS LIAVGLLLYC KARSTPVTLS KDQLSGINNI AFSN (SEQ ID NO:116). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00211] In some cases, the viral envelope protein is an RSV F0 glycoprotein. A suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PPTNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRRFLGF LLGVGSAIAS GVAVSKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ KKLMSNNVQI VRQQSYSIMS IIKEEVLAYV VQLPLYGVID TPCWKLHTSP LCTTNTKEGS NICLTRTDRG WYCDNAGSVS FFPQAETCKV QSNRVFCDTM NSLTLPSEIN LCNVDIFNPK YDCKIMTSKT DVSSSVITSL GAIVSCYGKT KCTASNKNRG IIKTFSNGCD YVSNKGMDTV SVGNTLYYVN KQEGKSLYVK GEPIINFYDP LVFPSDEFDA SISQVNEKIN QSLAFIRKSD ELLHNVNAGK STTNIMITTI IIVIIVILLS LIAVGLLLYC KARSTPVTLS KDQLSGINNI AFSN (SEQ ID NO:116; GenBank Accession No: P03420). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00212] In some cases, the viral envelope protein is an RSV F2 glycoprotein. A suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PPTNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRR (SEQ ID NO:117; GenBank Accession No: P03420). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g.,
epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00213] In some cases, the viral envelope protein is an RSV F1 glycoprotein. A suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: FLGF LLGVGSAIAS GVAVSKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ KKLMSNNVQI VRQQSYSIMS IIKEEVLAYV VQLPLYGVID TPCWKLHTSP LCTTNTKEGS NICLTRTDRG WYCDNAGSVS FFPQAETCKV QSNRVFCDTM NSLTLPSEIN LCNVDIFNPK YDCKIMTSKT DVSSSVITSL GAIVSCYGKT KCTASNKNRG IIKTFSNGCD YVSNKGMDTV SVGNTLYYVN KQEGKSLYVK GEPIINFYDP LVFPSDEFDA SISQVNEKIN QSLAFIRKSD ELLHNVNAGK STTNIMITTI IIVIIVILLS LIAVGLLLYC KARSTPVTLS KDQLSGINNI AFSN (SEQ ID NO:118; GenBank Accession No: P03420). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the lung/respiratory tract. [00214] In some cases, the viral envelope protein is an RSV glycoprotein. A suitable RSV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNAV TELQLLMQST PPTNNRARRE LPRFMNYTLN NAKKTNVTLS KKRKRRFLGF LLGVGSAIAS GVAVSKVLHL EGEVNKIKSA LLSTNKAVVS LSNGVSVLTS KVLDLKNYID KQLLPIVNKQ SCSISNIETV IEFQQKNNRL LEITREFSVN AGVTTPVSTY MLTNSELLSL INDMPITNDQ KKLMSNNVQI VRQQSYSIMS IIKEEVLAYV VQLPLYGVID TPCWKLHTSP LCTTNTKEGS NICLTRTDRG WYCDNAGSVS FFPQAETCKV QSNRVFCDTM NSLTLPSEIN LCNVDIFNPK YDCKIMTSKT DVSSSVITSL GAIVSCYGKT KCTASNKNRG IIKTFSNGCD YVSNKGMDTV SVGNTLYYVN KQEGKSLYVK GEPIINFYDP LVFPSDEFDA SISQVNEKIN QSLAFIRKSD ELLHNVNAGK STTNIMITTI IIVIIVILLS LIAVGLLLYC KARSTPVTLS KDQLSGINNI AFSN (SEQ ID NO:116). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the lung/respiratory tract. [00215] In some cases, the viral envelope protein is a human parainfluenza virus type 3 hemagglutinin- neuraminidase glycoprotein. A suitable human parainfluenza virus type 3 protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MEYWKHTNHG KDAGNELETS MATHGNKLTN KITYILWTII LVLLSIVFII VLINSIKSEK AHESLLQNIN NEFMEITEKI QMASDNTNDL IQSGVNTRLL TIQSHVQNYI PISLTQQMSD LRKFISEITI RNDNQEVLPQ RITHDVGIKP LNPDDFWRCT SGLPSLMKTP KIRLMPGPGL LAMPTTVDGC
IRTPSLVIND LIYAYTSNLI TRGCQDIGKS YQVLQIGIIT VNSDLVPDLN PRISHTFNIN DNRKSCSLAL LNTDVYQLCS TPKVDERSDY ASPGIEDIVL DIVNYDGSIS TTRFKNNNIS FDQPYAALYP SVGPGIYYKG KIIFLGYGGL EHPINENVIC NTTGCPGKTQ RDCNQASHSP WFSDRRMVNS IIVVDKGLNS IPKLKVWTIS MRQNYWGSEG RLLLLGNKIY IYTRSTSWHS KLQLGIIDIT DYSDIRIKWT WHNVLSRPGN NECPWGHSCP DGCITGVYTD AYPLNPTGSI VSSVILDSQK SRVNPVITYS TATERVNELA ILNRTLSAGY TTTSCITHYN KGYCFHIVEI NHKSLNTLQP MLFKTEIPKS CS (SEQ ID NO:119; GenBank Accession No: AAP35240). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00216] In some cases, the viral envelope protein is a human parainfluenza virus type 3 glycoprotein F0. A suitable human parainfluenza virus type 3 protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MPISILLIIT TMIMASHCQI DITKLQHVGV LVNSPKGMKI SQNFETRYLI LSLIPKIDDS NSCGDQQIKQ YKRLLDRLII PLYDGLRLQK DVIVANQESN ENTDPRTERF FGGVIGTIAL GVATSAQITA AVALVEAKQA RSDIEKLKEA IRDTNKAVQS VQSSVGNLIV AIKSVQDYVN KEIVPSIARL GCEAAGLQLG IALTQHYSEL TNIFGDNIGS LQEKGIKLQG IASLYRTNIT EIFTTSTVDK YDIYDLLFTE SIKVRVIDVD LNDYSITLQV RLPLLTRLLN TQIYKVDSIS YNIQNREWYI PLPSHIMTKG AFLGGADVKE CIEAFSSYIC PSDPGFVLNH EMESCLSGNI SQCPRTTVTS DIVPRYAFVN GGVVANCITT TCTCNGIGNR INQPPDQGVK IITHKECNTI GINGMLFNTN KEGTLAFYTP ADITLNNSVA LDPIDISIEL NKAKSDLEES KEWIRRSNQK LDSIGSWHQS STTIIVILIM MIILFIINIT IITIAIKYYR IQKRNRVDQN DKPYVLTNK (SEQ ID NO:120; GenBank Accession No: AXA52708). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to cells of the respiratory tract (e.g., cells of the lung), where such cells include, e.g., epithelial cells, goblet cells, club cells, type I pneumocytes, type II pneumocytes, monocytes, macrophages, dendritic cells, neutrophils, and NK cells. [00217] In some cases, the viral envelope protein is a Hepatitis C virus (HCV) E1 glycoprotein. A suitable HCV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: YQVRNSSGLY HVTNDCPNSS IVYEAADAIL HTPGCVPCVR EGNASRCWVA VTPTVATRDG KLPTTQLRRH IDLLVGSATL CSALYVGDLC GSVFLVGQLF TFSPRRHWTT QDCNCSIYPG HITGHRMAWD MMMNWSPTAA LVVAQLLRIP QAIMDMIAGA HWGVLAGIAY FSMVGNWAKV LVVLLLFAGV DA (SEQ ID NO:121; GenBank Accession No: NP_751920). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to a liver cell.
[00218] In some cases, the viral envelope protein is an HCV E2 glycoprotein. A suitable HCV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: ETHVTGGSAG RTTAGLVGLL TPGAKQNIQL INTNGSWHIN STALNCNESL NTGWLAGLFY QHKFNSSGCP ERLASCRRLT DFAQGWGPIS YANGSGLDER PYCWHYPPRP CGIVPAKSVC GPVYCFTPSP VVVGTTDRSG APTYSWGAND TDVFVLNNTR PPLGNWFGCT WMNSTGFTKV CGAPPCVIGG VGNNTLLCPT DCFRKHPEAT YSRCGSGPWI TPRCMVDYPY RLWHYPCTIN YTIFKVRMYV GGVEHRLEAA CNWTRGERCD LEDRDRSELS PLLLSTTQWQ VLPCSFTTLP ALSTGLIHLH QNIVDVQYLY GVGSSIASWA IKWEYVVLLF LLLADARVCS CLWMMLLISQ AEA (SEQ ID NO:122; GenBank Accession No: NP_751921). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to a liver cell. [00219] In some cases, the viral envelope protein is a fowl plague virus glycoprotein. A suitable fowl plague virus protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MNTQILVFAL VAVIPTNADK ICLGHHAVSN GTKVNTLTER GVEVVNATET VERTNIPKIC SKGKRTTDLG QCGLLGTITG PPQCDQFLEF SADLIIERRE GNDVCYPGKF VNEEALRQIL RGSGGIDKET MGFTYSGIRT NGTTSACRRS GSSFYAEMEW LLSNTDNASF PQMTKSYKNT RRESALIVWG IHHSGSTTEQ TKLYGSGNKL ITVGSSKYHQ SFVPSPGTRP QINGQSGRID FHWLILDPND TVTFSFNGAF IAPNRASFLR GKSMGIQSDV QVDANCEGEC YHSGGTITSR LPFQNINSRA VGKCPRYVKQ ESLLLATGMK NVPEPSKKRE KRGLFGAIAG FIENGWEGLV DGWYGFRHQN AQGEGTAADY KSTQSAIDQI TGKLNRLIEK TNQQFELIDN EFTEVEKQIG NLINWTKDFI TEVWSYNAEL LVAMENQHTI DLADSEMNKL YERVRKQLRE NAEEDGTGCF EIFHKCDDDC MASIRNNTYD HSKYREEAMQ NRIQIDPVKL SSGYKDVILW FSFGASCFLL LAIAVGLVFI CVKNGNMRCT ICI (SEQ ID NO:123; GenBank Accession No: 0601245A). [00220] In some cases, the viral envelope protein is an autographa californica nuclear polyhedrosis virus (AcMNPV) major envelope glycoprotein gp64. A suitable AcMNPV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MVSAIVLYVL LAAAAHSAFA AEHCNAQMKT GPYKIKNLDI TPPKETLQKD VEITIVETDY NENVIIGYKG YYQAYAYNGG SLDPNTRVEE TMKTLNVGKE DLLMWSIRQQ CEVGEELIDR WGSDSDDCFR DNEGRGQWVK GKELVKRQNN NHFAHHTCNK SWRCGISTSK MYSRLECQDD TDECQVYILD AEGNPINVTV DTVLHRDGVS MILKQKSTFT TRQIKAACLL IKDDKNNPES VTREHCLIDN DIYDLSKNTW NCKFNRCIKR KVEHRVKKRP PTWRHNVRAK YTEGDTATKG DLMHIQEELM YENDLLKMNI ELMHAHINKL NNMLHDLIVS VAKVDERLIG NLMNNSVSST FLSDDTFLLM
PCTNPPAHTS NCYNNSIYKE GRWVANTDSS QCIDFSNYKE LAIDDDVEFW IPTIGNTTYH DSWKDASGWS FIAQQKSNLI TTMENTKFGG VGTSLSDITS MAEGELAAKL TSFMFGHVVN FVIILIVILF LYCMIRNRNR QY (SEQ ID NO:158; UniProt Accession No: P17501-1). [00221] In some cases, the viral envelope protein is an AcMNPV glycoprotein. A suitable AcMNPV protein comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: AEHCNAQMKT GPYKIKNLDI TPPKETLQKD VEITIVETDY NENVIIGYKG YYQAYAYNGG SLDPNTRVEE TMKTLNVGKE DLLMWSIRQQ CEVGEELIDR WGSDSDDCFR DNEGRGQWVK GKELVKRQNN NHFAHHTCNK SWRCGISTSK MYSRLECQDD TDECQVYILD AEGNPINVTV DTVLHRDGVS MILKQKSTFT TRQIKAACLL IKDDKNNPES VTREHCLIDN DIYDLSKNTW NCKFNRCIKR KVEHRVKKRP PTWRHNVRAK YTEGDTATKG DLMHIQEELM YENDLLKMNI ELMHAHINKL NNMLHDLIVS VAKVDERLIG NLMNNSVSST FLSDDTFLLM PCTNPPAHTS NCYNNSIYKE GRWVANTDSS QCIDFSNYKE LAIDDDVEFW IPTIGNTTYH DSWKDASGWS FIAQQKSNLI TTMENTKFGG VGTSLSDITS MAEGELAAKL TSFMFGHVVN FVIILIVILF LYCMIRNRNR QY (SEQ ID NO:124). [00222] In some cases, the viral envelope protein is a measles virus hemagglutinin (H) polypeptide. See, e.g., Levy et al. (2017) Blood Adv.1:2088. A suitable measles virus H polypeptide comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MSPQRDRINA FYKDNPHPKG SRIVINREHL MIDRPYVLLA VLFVMFLSLI GLLAIAGIRL HRAAIYTAEI HKSLSTNLDV TNSIEHQVKD VLTPLFKIIG DEVGLRTPQR FTDLVKFISD KIKFLNPDRE YDFRDLTWCI NPPERIKLDY DQYCADVAAE ELMNALVNST LLETRTTNQF LAVSKGNCSG PTTIRGQFSN MSLSLLDLYL SRGYNVSSIV TMTSQGMYGG TYLVEKPNLS SKGSELSQLS MYRVFEVGVI RNPGLGAPVF HMTNYFEQPV SNDLSNCMVA LGELKLAALC HGGDSITIPY QGSGKGVSFQ LVKLGVWKSP TDMQSWVPLS TDDPVIDRLY LSSHRGVIAD NQAKWAVPTT RTDDKLRMET CFQQACKGKI QALCENPEWA PLKDNRIPSY GVLSVDLSLT VELKIKIASG FGPLITHGSG MDLYKSNHNN VYWLTIPPMK NLALGVINTL EWIPRFKVSP YLFTVPIKEA GEDCHAPTYL PAEVDGDVKL SSNLVILPGQ DLQYVLATYD TSRVEHAVVY YVYSPSRSFS YFYPFRLPIK GIPIELQVEC FTWDQKLWCR HFCVLADSES GGHITHSGMV GMGVSCTVTR EDGTNSR (SEQ ID NO:155). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to T cells, B cells, monocytes, macrophages, dendritic cells, and hematopoietic stem cells (e.g., CD34+ cells). [00223] In some cases, the viral envelope protein is a measles virus fusion (F) polypeptide. A suitable measles virus F polypeptide comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following
amino acid sequence: MSIMGLKVNV SAIFMAVLLT LQTPTGQIHW GNLSKIGVVG IGSASYKVMT RSSHQSLVIK LMPNITLLNN CTRVEIAEYR RLLRTVLEPI RDALNAMTQN IRPVQSVASS RRHKRFAGVV LAGAALGVAT AAQITAGIAL HQSMLNSQAI DNLRASLETT NQAIETIRQA GQEMILAVQG VQDYINNELI PSMNQLSCDL IGQKLGLKLL RYYTEILSLF GPSLRDPISA EISIQALSYA LGGDINKVLE KLGYSGGDLL GILESGGIKA RITHVDTESY FIVLSIAYPT LSEIKGVIVH RLEGVSYNIG SQEWYTTVPK YVATQGYLIS NFDESSCTFM PEGTVCSQNA LYPMSPLLQE CLRGYTKSCA RTLVSGSFGN RFILSQGNLI ANCASILCKC YTTGTIINQD PDKILTYIAA DHCPVVEVNG VTIQVGSRRY PDAVYLHRID LGPPISLERL DVGTNLGNAI AKLEDAKELL ESSDQILRSM KGLSSTSIVY ILIAVCLGGL IGIPALICCC RGRCNKKGEQ VGMSRPGLKP DLTGTSKSYV RSL (SEQ ID NO:126). Such a glycoprotein may be useful for targeting an EDV of the present disclosure to T cells, B cells, monocytes, macrophages, dendritic cells, and hematopoietic stem cells (e.g., CD34+ cells). Variant viral envelope proteins [00224] In some cases, an EDV of the present disclosure includes a variant viral envelope protein that includes one or more amino acid substitutions compared to a corresponding wild-type viral envelope protein, and where the variant viral envelope protein exhibits reduced binding to its native receptor, compared to the binding of the wild-type viral envelope protein to the native receptor. In some cases, the variant viral envelope protein retains endosomal fusion activity. [00225] In some cases, the viral envelope protein is a variant VSV-G protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%, amino acid sequence identity to the VSV-G amino acid sequence depicted in of SEQ ID NO:153; where the variant VSV-G protein exhibits comprises one or more amino acid substitutions compared to a wild- type viral envelope protein (compared to the amino acid sequence depicted in of SEQ ID NO:153), and where the variant viral envelope protein exhibits reduced binding to its native receptor, compared to the binding of a VSV-G polypeptide comprising the amino acid sequence of SEQ ID NO:153 to its native receptor. The native receptor for VSV-G is the low-density lipoprotein receptor (LDLR). [00226] In some cases, the VSV-G polypeptide comprises one or more amino acid substitutions that reduce binding to the native receptor for VSV-G, while retaining the endosomal fusion function of the VSV-G polypeptide. In some cases, the viral envelope protein is a VSV-G protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the VSV-G amino acid sequence of SEQ ID NO:153, where amino acid 47 is other than a Lys. In some cases, the viral envelope protein is a VSV-G protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the VSV-G amino acid sequence of SEQ ID
NO:153, where amino acid 354 is other than an Arg. In some cases, the viral envelope protein is a VSV- G protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the VSV-G amino acid sequence of SEQ ID NO:153, where amino acid 47 is other than a Lys and amino acid 354 is other than an Arg. In some cases, the Lys at amino acid 47 is substituted with an Ala. In some cases, the Lys at amino acid 47 is substituted with a Gln (K47Q). In some cases, the Arg at amino acid 354 is substituted with an Ala (R354A). In some cases, the Arg at amino acid 354 is substituted with a Gln. [00227] In some cases, the viral envelope protein is a VSV-G protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the VSV-G amino acid sequence of SEQ ID NO:154, in which the VSV-G protein has a Gln at position 47 and an Ala at position 354 (K47Q/R354A) relative to SEQ ID NO:153. [00228] In some cases, the viral envelope protein is a variant measles hemagglutinin (HA) protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%, amino acid sequence identity to the measles HA amino acid sequence of SEQ ID NO:155; where the variant measles HA protein exhibits comprises one or more amino acid substitutions compared to a wild-type viral envelope protein (compared to the amino acid sequence of SEQ ID NO:155), and where the variant viral envelope protein exhibits reduced binding to its native receptor, compared to the binding of a measles HA protein comprising the amino acid sequence of SEQ ID NO: 155 to its native receptor. In some cases, the variant measles HA protein comprises a substitution of one or more of Y481, R533, S548, and F549, based on the amino acid numbering of SEQ ID NO: 155. CD46 is a native receptor for measles virus HA. [00229] In some cases, the viral envelope protein is a variant measles HA protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%, amino acid sequence identity to the measles HA amino acid sequence of SEQ ID NO:156, where amino acid 841 is other than a Tyr, amino acid 533 is other than an Arg, amino acid 548 is other than a Ser, and amino acid 549 is other than a Phe. In some cases, the viral envelope protein is a variant measles HA protein comprising an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, or at least 99%, amino acid sequence identity to the measles HA amino acid sequence of SEQ ID NO:156, where amino acid 841 is Ala, amino acid 533 is Ala, amino acid 548 is Leu, and amino acid 549 is Ser. Targeting polypeptides [00230] An EDV of the present disclosure includes a targeting polypeptide (i.e., one or more targeting polypeptides) that provides for binding to a target cell (e.g., target cell type). Targeting polypeptides include antibodies and antibody mimetics (also referred to as antibody analogs). Suitable antibody
analogs include, e.g., an affibody, an affilin, an affimer, an affitin, an alphabody, an anticalin, an avimer, a DARPin, a Fynomer, a Kunitz domain peptide, a monobody, a repebody, a VLR, and a nanoCLAMP. Suitable antibodies include a single chain Fv (scFv) polypeptide, a diabody, a triabody, and a nanobody. In some cases, the antibody is a single-chain Fv polypeptide. In some cases, the antibody is a nanobody. In some cases, the antibody is a bispecific antibody. In some cases, an EDV of the present disclosure comprises two different antibodies (e.g., a first antibody and a second antibody), where the first antibody specifically binds to a first target polypeptide on a target cell and the second antibody specifically binds to a second target polypeptide on the same target cell. [00231] In some instances, EDVs comprise two or more different targeting polypeptides. In some cases, EDVs comprising a bispecific targeting polypeptide, e.g., where the bispecific targeting polypeptide binds to two different targets on the targeted cell type. In some cases, the bispecific targeting polypeptide is a bispecific antibody or derivative thereof. [00232] In some cases, the targeting polypeptide provides for selective binding to an organ such as kidney, liver, bone, pancreas, brain, lung, heart, and the like. In some cases, the targeting polypeptide provides for selective binding to a particular cell type. For example, in some cases, the targeting polypeptide provides for selective binding to a cell such as a skeletal muscle cell, a cardiomyocyte, an adipocyte, an epithelial cell, an endothelial cell, a macrophage, a beta islet cell, or an immune cell (e.g., a T cell, a B cell, a monocyte, a natural killer cell, a dendritic cell, etc.). In some cases, the targeting polypeptide provides for selective binding to a cell such as a cancer cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue-resident stem cell, a monocyte, a macrophage, a B cell, or a T cell. In some cases, the targeting polypeptide provides for selective binding to a diseased cell, relative to a non-diseased cell of the same cell type. In some cases, the antibody provides for selective binding to a CAR-T cell, i.e., a T cell that is modified to express a chimeric antigen receptor (CAR) on its surface. Fusion polypeptides [00233] In some cases (e.g., in some cases where the antibody is a scFv or a nanobody), the antibody itself is a fusion polypeptide comprising: (i) the antibody; and (ii) a heterologous polypeptide (a “fusion partner”). The fusion partner can be a polypeptide that enhances accessibility of the antibody to a target cell. Suitable fusion partners include, but are not limited to, the stalk portion of a polypeptide; the stalk and transmembrane domain of a polypeptide; an immunoglobulin hinge polypeptide; a linker polypeptide; and the like. In some cases, the antibody is fused to a transmembrane domain via a linker. [00234] In some cases, the fusion partner is the stalk and transmembrane domain of a transmembrane protein. A “transmembrane domain” (TMD), as used herein, is a portion of a transmembrane (TM)
protein that contains a hydrophobic portion that can insert into or span a cell membrane. Transmembrane components or domains have a three-dimensional structure that is thermodynamically stable in a cell membrane and generally range in length from about 15 amino acids to about 30 amino acids. The structure of a transmembrane component or domain may comprise an alpha helix, a beta barrel, a beta sheet, a beta helix, or any combination thereof. In certain embodiments, a transmembrane component or domain comprises or is derived from a known transmembrane protein (e.g., a CD4 transmembrane domain, a CD8 transmembrane domain, a CD27 transmembrane domain, a CD28 transmembrane domain, a PDGFR transmembrane domain or any combination thereof). [00235] In some cases, the fusion partner includes the stalk and transmembrane domain of a CD8α polypeptide. As an example, the stalk and transmembrane domain can comprise the following amino acid sequence: TTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACDIYIWAPLAGTCGVLLLSLVIT LYC (SEQ ID NO:20), where the stalk has the amino acid sequence TTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACD (SEQ ID NO:21) and the TMD has the sequence IYIWAPLAGTCGVLLLSLVITLYC (SEQ ID NO:22). As another example, the fusion partner includes the stalk domain of a CD8α polypeptide (a CD8α stalk polypeptide); e.g., the fusion partner comprises the amino acid sequence: TTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACD (SEQ ID NO:21). In some cases, a CD8α polypeptide includes the amino acid sequence ASAKPTTTPAPRPPTPAPTIASQPLSLRPEAARPAAGGAVHTRGLDFAK (SEQ ID NO: 23). [00236] In some cases, the fusion partner includes the stalk and/or transmembrane domain of a platelet- derived growth factor receptor (PDGFR). An example of a PDFGR transmembrane domain is VVVISAILALVVLTIISLIILIMLWQKKPRYE (SEQ ID NO: 37). In some cases, the fusion partner includes a PDFGR transmembrane domain (e.g., VVVISAILALVVLTIISLIILIMLWQKKPRYE (SEQ ID NO: 37)) and a CD8α stalk polypeptide (e.g., ASAKPTTTPAPRPPTPAPTIASQPLSLRPEAARPAAGGAVHTRGLDFAK (SEQ ID NO: 23)). [00237] In some cases, the fusion partner includes a glycine-rich polypeptide having a length of from 5 amino acids to about 50 amino acids; e.g., where the fusion partner comprises the sequence (GGGGS)n (SEQ ID NO:38), where n is an integer from 1 to 10, e.g., where n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10, e.g., where n is 3. [00238] In some cases, the fusion partner includes an immunoglobulin (Ig) hinge polypeptide. As used herein, a “hinge polypeptide,” “hinge region,” or a “hinge” refers to (a) an immunoglobulin hinge sequence (made up of, for example, upper and core regions of an immunoglobulin hinge) or a functional fragment or variant thereof, (b) a type II C-lectin interdomain (stalk) region or a functional fragment or variant thereof, or (c) a cluster of differentiation (CD) molecule stalk region or a functional variant
thereof. As used herein, a "wild-type immunoglobulin hinge region" refers to a naturally occurring upper and middle hinge amino acid sequences interposed between and connecting the CH1 and CH2 domains (for IgG, IgA, and IgD) or interposed between and connecting the CH1 and CH3 domains (for IgE and IgM) found in the heavy chain of an antibody. cell-targeting antibodies [00239] In some cases, the targeting polypeptide is an antibody that targets (binds specifically to) an antigen expressed on the surface of a T cell, thereby targeting the EDV to the T cell. In some cases, the T cell is a CD4+ T cell. In some cases, the T cell is a CD8+ T cell. In some cases, the antibody is a scFv or a nanobody that binds to CD4. In some cases, the antibody is a scFv or a nanobody that binds to CD3. In some cases, the antibody is a scFv or a nanobody that binds to CD8. In some cases, the antibody is a scFv or a nanobody that binds to CD28. In some cases, the targeting polypeptide comprises one or more antibodies, e.g., one or a combination of anti-CD3 (e.g., CD3 scFv-3), anti-CD4 (e.g., CD4 scFv-2), and anti-CD28 (e.g., CD28 scFv-2) (e.g., an anti-CD3 and an anti-CD4 antibody; an anti-CD3 and an anti- CD28 antibody; an anti-CD3, an anti-CD4, and an anti-CD28 antibody; and the like). [00240] In some cases, the targeting polypeptide includes an anti-CD3 scFV having the sequence MALPVTALLLPLALLLHAARPQVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRP GQGLEWIGYINPSRGYTNYNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHY CLDYWGQGTTLTVSSSGGGGSGGGGSGGGGSIVLTQSPAIMSASPGEKVTMTCSASSSVSYMN WYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTF GSGTKLEINRAA (SEQ ID NO: 125). [00241] In some cases, a superagonistic anti-CD28 antibody is used. For example, such antibodies can be used to target EDVs to T-regs, which can be useful for treating autoimmune disease. CD28 superagonists (CD28SAs) are potent T-cell-activating monoclonal antibodies (mAbs) and are known in the art. See, e.g., Tabares et al., Eur J Immunol.2014 Apr;44(4):1225-36 as well as US patent No.8,709,414, which are incorporated herein by reference for their teachings related to CD28 superagonists. One such example is TGN1412, also called TAB08. [00242] In some cases, an EDV comprises an anti-CD3 antibody and an anti-CD8 antibody. In some cases, an EDV comprises an anti-CD3 antibody and an anti-CD28 antibody. In some cases, an EDV comprises an anti-CD3 antibody and an anti-CD4 antibody. In some cases, an EDV comprises an anti- CD3 nanobody and an anti-CD8 nanobody. In some cases, an EDV comprises an anti-CD3 nanobody and an anti-CD28 nanobody. In some cases, an EDV comprises an anti-CD3 nanobody and an anti-CD4 nanobody.In some cases, an EDV comprises an anti-CD3 scFv and an anti-CD8 scFv. In some cases, an EDV comprises an anti-CD3 scFv and an anti-CD28 scFv. In some cases, an EDV comprises an anti- CD3 scFv and an anti-CD4 scFv.
Cancer cell-targeting antibodies [00243] In some cases, the targeting polypeptide is an antibody that targets a cancer antigen, thereby targeting the EDV to a cancerous cell that displays the cancer antigen on its cell surface. [00244] Suitable antigens bound by an antibody present in an EDV of the present disclosure include, e.g., CD3, epidermal growth factor receptor (EGFR), CA-125 (highly expressed on epithelial ovarian cancer cells), CD80, CD86, glycoprotein IIb/IIIa receptor, CD51, TNF-α, epithelial adhesion molecule EpCAM (CD326), vascular endothelial growth factor receptor-2 (VEGFR-2), CD52, mesothelin, activin receptor- like kinase 1 (ALK-1), phosphatidyl serine, CD19, vascular endothelial growth factor A (VEGF-A), IL-6 receptor, CD11a, CD25, CD2, CD3 receptor, and the like. [00245] Suitable antigens bound by an antibody present in an EDV of the present disclosure include, e.g., carbonic anhydrase IX, alpha-fetoprotein (AFP), α-actinin-4, A3, ART-4, B7, Ba 733, BAGE, BrE3- antigen, CA-125, CAMEL, CAP-1, CASP-8/m, CCL19, CCL21, CD1, CD1a, CD2, CD3, CD4, CD5, CD8, CD11A, CD14, CD15, CD16, CD18, CD19, CD20, CD21, CD22, CD23, CD25, CD29, CD30, CD32b, CD33, CD37, CD38, CD40, CD40L, CD44, CD45, CD46, CD52, CD54, CD55, CD59, CD64, CD66a-e, CD67, CD70, CD70L, CD74, CD79a, CD80, CD83, CD95, CD126, CD132, CD133, CD138, CD147, CD154, CDC27, CDK-4/m, CDKN2A, CTLA-4, CXCR4, CXCR7, CXCL12, HIF-1α, colon- specific antigen-p (CSAp), CEACAM5, CEACAM6, c-Met, DAM, epidermal growth factor receptor (EGFR), EGFRvIII, EGP-1 (TROP-2), EGP-2, ELF2-M, Ep-CAM, fibroblast growth factor (FGF), Flt-1, Flt-3, folate receptor, G250 antigen, GAGE, gp100, GRO-β, HLA-DR, HM1.24, human chorionic gonadotropin (HCG) and its subunits, HER2/neu, histone H2B, histone H3, histone H4, HMGB-1, hypoxia inducible factor (HIF-1), HSP70-2M, HST-2, insulin-like growth factor-1 receptor (IGF-1R), IFN-γ IFN-α, IFN-β, IFN-λ, IL-4R, IL-6R, IL-13R, IL-15R, IL-17R, IL-18R, IL-2, IL-6, IL-8, IL-12, IL- 15, IL-17, IL-18, IL-23, IL-25, insulin-like growth factor-1 (IGF-1), KC4-antigen, KS-1-antigen, KS1-4, Le-Y, LDR/FUT, macrophage migration inhibitory factor (MIF), MAGE, MAGE-3, MART-1, MART-2, NY-ESO-1, TRAG-3, mCRP, MCP-1, MIP-1A, MIP-1B, MIF, MUC1, MUC2, MUC3, MUC4, MUC5ac, MUC13, MUC16, MUM-1/2, MUM-3, NCA66, NCA95, NCA90, PAM4 antigen, PD-1, PD- L1, PD-1 receptor, placental growth factor, p53, PLAGL2, prostatic acid phosphatase, PSA, PRAME, PSMA, P1GF, ILGF, ILGF-1R, IL-6, IL-25, RS5, RANTES, T101, SAGE, 5100, survivin, survivin-2B, TAC, TAG-72, tenascin, TRAIL receptors, TNF-α, Tn antigen, tumor necrosis antigens, VEGFR, ED-B fibronectin, WT-1, 17-1A-antigen, complement factors C3, C3a, C3b, C5a, C5; and the like. [00246] In some cases, the cancer-associated antigen is an antigen associated with a hematological cancer. Examples of such antigens include, but are not limited to, BCMA, C5, CD19, CD20, CD22, CD25, CD30, CD33, CD38, CD40, CD45, CD52, CD56, CD66, CD74, CD79a, CD79b, CD80, CD138, CTLA-4, CXCR4, DKK, EphA3, GM2, HLA-DR beta, integrin αVβ3, IGF-R1, IL6, KIR, PD-1, PD-L1,
TRAILR1, TRAILR2, transferrin receptor, and VEGF. In some cases, the cancer-associated antigen is an antigen expressed by malignant B cells, such as CD19, CD20, CD22, CD25, CD38, CD40, CD45, CD74, CD80, CTLA-4, IGF-R1, IL6, PD-1, TRAILR2, or VEGF. [00247] In some cases, the cancer-associated antigen is an antigen associated with a solid tumor. Examples of such antigens include, but are not limited to, CAIX, cadherins, CEA, c-MET, CTLA-4, EGFR family members, EpCAM, EphA3, FAP, folate-binding protein, FR-alpha, gangliosides (such as GC2, GD3 and GM2), HER2, HER3, IGF-1R, integrin αVβ3, integrin α5β1, Legamma, Liv1, mesothelin, mucins, NaPi2b, PD-1, PD-L1, PD-1 receptor, pgA33, PSMA, RANKL, ROR1, TAG-72, tenascin, TRAILR1, TRAILR2, VEGF, VEGFR, and others listed above. [00248] In some cases, the cancer-associated antigen is an antigen associated with a cancer stem cell. Examples of such antigens include, but are not limited to, SSEA3, SSEA4, TRA-1-60, TRA-1-81, CD133, CD90, CD326, Cripto-1, PODXL-1, ABCG2, CD24, CD49f, Notch2, CD146, CD10, CD117, and CD26 (Kim & Ryu (2017) BMB Rep 50(6): 285–298). [00249] Examples of suitable antibodies include, e.g., abciximab (anti-glycoprotein IIb/IIIa), alemtuzumab (anti-CD52), bevacizumab (anti-VEGF), cetuximab (anti-EGFR), gemtuzumab (anti- CD33), ibritumomab (anti-CD20), panitumumab (anti-EGFR), rituximab (anti-CD20), tositumomab (anti-CD20), trastuzumab (anti-ErbB2), lambrolizumab (anti-PD-1 receptor), nivolumab (anti-PD-1 receptor), ipilimumab (anti-CTLA-4), abagovomab (anti-CA-125), adecatumumab (anti-EpCAM), atlizumab (anti-IL-6 receptor), benralizumab (anti-CD125), obinutuzumab (GA101, anti-CD20), CC49 (anti-TAG-72), tocilizumab (anti-IL-6 receptor), basiliximab (anti-CD25), daclizumab (anti-CD25), efalizumab (anti-CD11a), GA101 (anti-CD20; Glycart Roche), muromonab-CD3 (anti-CD3 receptor), natalizumab (anti-α-4 integrin), and the like. [00250] Non-limiting examples of cancer-associated antigen-targeted antibodies that can be targeted include, but are not limited to, abituzumab (anti-CD51), LL1 (anti-CD74), LL2 or RFB4 (anti-CD22), veltuzumab (hA20, anti-CD20), rituxumab (anti-CD20), obinutuzumab (GA101, anti-CD20), ibalizumab (anti-CD4), daratumumab (anti-CD38), lambrolizumab (anti-PD-1 receptor), nivolumab (anti-PD-1 receptor), ipilimumab (anti-CTLA-4), RS7 (anti-TROP-2), PAM4 or KC4 (both anti-mucin), MN-14 (anti-CEA), MN-15 or MN-3 (anti-CEACAM6), Mu-9 (anti-colon-specific antigen-p), Immu 31 (anti- alpha-fetoprotein), R1 (anti-IGF-1R), A19 (anti-CD19), TAG-72 (e.g., CC49), Tn, J591 or HuJ591 (anti- PSMA), AB-PG1-XG1-026 (anti-PSMA dimer), D2/B (anti-PSMA), G250 (anti-carbonic anhydrase IX), L243 (anti-HLA-DR) alemtuzumab (anti-CD52), oportuzumab (anti-EpCAM), bevacizumab (anti- VEGF), cetuximab (anti-EGFR), gemtuzumab (anti-CD33), ibritumomab tiuxetan (anti-CD20); panitumumab (anti-EGFR); tositumomab (anti-CD20); PAM4 (also known as clivatuzumab; anti-mucin), trastuzumab (anti-HER2), pertuzumab (anti-HER2), polatuzumab (anti-CD79b), and anetumab (anti- mesothelin).
[00251] VH and VL amino acid sequences of various cancer antigen-binding antibodies are known in the art, as are the light chain and heavy chain CDRs of such antibodies. See, e.g., Ling et al. (2018) Frontiers Immunol.9:469; WO 2005/012493; US 2019/0119375; US 2013/0066055. The following are non- limiting examples of antibodies that can be used as part of a targeting polypeptide of a subject EDV. In some cases, an antibody includes the CDR sequences from the anti-CD19 scFv FMC63. In some cases, an antibody includes the CDR sequences from the anti-CD4 antibody ibalizumab (IMGT/mAb-DB ID 241). In some cases, an antibody includes the CDR sequences from the anti-CD20 antibody rituximab (IMGT/mAb-DB ID 161). In some cases, an antibody includes the CDR sequences from the anti-CD3 antibody acapatamab (IMGT/mAb-DB ID 1074). In some cases, an antibody includes the CDR sequences from the anti-CD3 antibody OKT3. In some cases, an antibody includes the CDR sequences from the anti-CD28 antibody PDB ID 1YJD. In some cases, an antibody includes the CDR sequences from the anti-CD19 antibody IMGT/mAb-DB ID 1232. In some cases, an antibody includes the CDR sequences from the anti-CD45 antibody Ab4122. In some cases, an antibody includes the CDR sequences from the anti-CD45 antibody Ab4129. In some cases, an antibody includes the CDR sequences from the anti-CD45 antibody apamistamab (IMGT/mAb-DB ID 633). See, e.g., FIG.10 and FIG.11. The following are non-limiting examples of cancer antigen-binding antibodies. Anti-Her2 [00252] In some cases, an anti-Her2 antibody comprises: a) a light chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00253] DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVP SRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIKRTVAAPSVFIFPPSDEQLK SGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKH KVYACEVTHQGLSSPVTKSFNRGEC (SEQ ID NO:159); and b) a heavy chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00254] EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYT RYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVS SASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYS LSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKP KDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVL HQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGF YPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNH YTQKSLSLSPGK (SEQ ID NO:160).
[00255] In some cases, an anti-Her2 antibody comprises a light chain variable region (VL) present in the light chain amino acid sequence provided above; and a heavy chain variable region (VH) present in the heavy chain amino acid sequence provided above. For example, an anti-Her2 antibody can comprise: a) a VL comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGS RSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK (SEQ ID NO:161); and b) a VH comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADS VKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS (SEQ ID NO:162). In some cases, an anti-Her2 antibody comprises, in order from N-terminus to C-terminus: a) a VH comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADS VKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS (SEQ ID NO:162); b) a linker; and c) a VL comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGS RSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK (SEQ ID NO:161). Suitable linkers are described elsewhere herein and include, e.g., (GGGGS)n (SEQ ID NO: 38), where n is an integer from 1 to 10 (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10). [00256] In some cases, an anti-Her2 antibody comprises VL CDR1, VL CDR2, and VL CDR3 present in the light chain amino acid sequence provided above; and VH CDR1, CDR2, and CDR3 present in the heavy chain amino acid sequence provided above. [00257] For example, an anti-Her2 antibody can comprise a VL CDR1 having the amino acid sequence RASQDVNTAVA (SEQ ID NO:164); a VL CDR2 having the amino acid sequence SASFLY (SEQ ID NO:165); a VL CDR3 having the amino acid sequence QQHYTTPP (SEQ ID NO:166); a VH CDR1 having the amino acid sequence GFNIKDTY (SEQ ID NO:167); a VH CDR2 having the amino acid sequence IYPTNGYT (SEQ ID NO:168); and a VH CDR3 having the amino acid sequence SRWGGDGFYAMDY (SEQ ID NO:169). [00258] In some cases, an anti-Her2 antibody is a scFv antibody. For example, an anti-Her2 scFv can comprise an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: evqlvesggglvqpggslrlscaasgfnikdtyihwvrqapgkglewvariyptngytryadsvkgrftisadtskntaylqmnslraedtavyycs
rwggdgfyamdywgqgtlvtvssggggsggggsggggsdiqmtqspsslsasvgdrvtitcrasqdvntavawyqqkpgkapklliysasfly sgvpsrfsgsrsgtdftltisslqpedfatyycqqhyttpptfgqgtkveik (SEQ ID NO:170). [00259] As another example, in some cases, an anti-Her2 antibody comprises: a) a light chain variable region (VL) comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00260] DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQQKPGKAPKLLIYSASYRYTGVPS RFSGSGSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKS GTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHK VYACEVTHQGLSSPVTKSFNRGEC (SEQ ID NO:171); and b) a heavy chain variable region (VH) comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00261] EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRQAPGKGLEWVADVNPNSGG SIYNQRFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSSA STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLS SVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPK DTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLH QDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYP SDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYT QKSLSLSPG (SEQ ID NO:172). [00262] In some cases, an anti-Her2 antibody comprises a VL present in the light chain amino acid sequence provided above; and a VH present in the heavy chain amino acid sequence provided above. For example, an anti-Her2 antibody can comprise: a) a VL comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: DIQMTQSPSSLSASVGDRVTITCKASQDVSIGVAWYQQKPGKAPKLLIYSASYRYTGVPSRFSGS GSGTDFTLTISSLQPEDFATYYCQQYYIYPYTFGQGTKVEIK (SEQ ID NO:173); and b) a VH comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: EVQLVESGGGLVQPGGSLRLSCAASGFTFTDYTMDWVRQAPGKGLEWVADVNPNSGGSIYNQ RFKGRFTLSVDRSKNTLYLQMNSLRAEDTAVYYCARNLGPSFYFDYWGQGTLVTVSS (SEQ ID NO:174). [00263] In some cases, an anti-Her2 antibody comprises VL CDR1, VL CDR2, and VL CDR3 present in the light chain amino acid sequence provided above; and VH CDR1, CDR2, and CDR3 present in the heavy chain amino acid sequence provided above. For example, an anti-HER2 antibody can comprise a VL CDR1 having the amino acid sequence KASQDVSIGVA (SEQ ID NO:175); a VL CDR2 having the
amino acid sequence SASYRY (SEQ ID NO:176); a VL CDR3 having the amino acid sequence QQYYIYPY (SEQ ID NO:177); a VH CDR1 having the amino acid sequence GFTFTDYTMD (SEQ ID NO:178); a VH CDR2 having the amino acid sequence ADVNPNSGGSIYNQRFKG (SEQ ID NO:179); and a VH CDR3 having the amino acid sequence ARNLGPSFYFDY (SEQ ID NO:180). [00264] In some cases, an anti-Her2 antibody is a scFv. For example, in some cases, an anti-Her2 scFv comprises an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00265] EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYT RYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVS SGGGGSGGGGSGGGGSDIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLL IYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK (SEQ ID NO:170). Anti-CD19 [00266] Anti-CD19 antibodies are known in the art; and the VH and VL, or the VH and VL CDRs, of any anti-CD19 antibody can be used. See e.g., WO 2005/012493. [00267] In some cases, an anti-CD19 antibody includes a VL CDR1 comprising the amino acid sequence KASQSVDYDGDSYLN (SEQ ID NO:181); a VL CDR2 comprising the amino acid sequence DASNLVS (SEQ ID NO:182); and a VL CDR3 comprising the amino acid sequence QQSTEDPWT (SEQ ID NO:183). In some cases, an anti-CD19 antibody includes a VH CDR1 comprising the amino acid sequence SYWMN (SEQ ID NO:184); a VH CDR2 comprising the amino acid sequence QIWPGDGDTNYNGKFKG (SEQ ID NO:185); and a VH CDR3 comprising the amino acid sequence RETTTVGRYYYAMDY (SEQ ID NO:186). In some cases, an anti-CD19 antibody includes a VL CDR1 comprising the amino acid sequence KASQSVDYDGDSYLN (SEQ ID NO:181); a VL CDR2 comprising the amino acid sequence DASNLVS (SEQ ID NO:182); a VL CDR3 comprising the amino acid sequence QQSTEDPWT (SEQ ID NO:183); a VH CDR1 comprising the amino acid sequence SYWMN (SEQ ID NO:184); a VH CDR2 comprising the amino acid sequence QIWPGDGDTNYNGKFKG (SEQ ID NO:185); and a VH CDR3 comprising the amino acid sequence RETTTVGRYYYAMDY (SEQ ID NO:186). [00268] In some cases, an anti-CD19 antibody is a scFv. For example, in some cases, an anti-CD19 scFv comprises an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: DIQLTQSPASLAVSLGQRATISCKASQSVDYDGDSYLNWYQQIPGQPPKLLIYDASNLVSGIPPRF SGSGSGTDFTLNIHPVEKVDAATYHCQQSTEDPWTFGGGTKLEIKGGGGSGGGGSGGGGSQVQ LQQSGAELVRPGSSVKISCKASGYAFSSYWMNWVKQRPGQGLEWIGQIWPGDGDTNYNGKFK
GKATLTADESSSTAYMQLSSLASEDSAVYFCARRETTTVGRYYYAMDYWGQGTTVTVS (SEQ ID NO:187). Anti-mesothelin [00269] Anti-mesothelin antibodies are known in the art, see, e.g., U.S.2019/0000944; WO 2009/045957; WO 2014/031476; USPN 8,460,660; US 2013/0066055; and WO 2009/068204. [00270] In some cases, an anti-mesothelin antibody comprises: a) a light chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00271] DIALtqpasvsgspgqsitisctgtssdiggynsvswyqqhpgkapklmiygvnnrpsgvsnrfsgsksgntasltisglqaedead yycssydiesatpvfgggtkltvlgqpkaapsvtlfppsseelqankatlvclisdfypgavtvawkgdsspvkagvetttpskqsnNkyaassyls ltpeqwkshrsyscqvthegstvektvaptEss (SEQ ID NO:215); and [00272] b) a heavy chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00273] qvelvqsgaevkkpgeslkisckgsgysftsywigwvrqapgkglewmgiidpgdsrtryspsfqgqvtisadksistaylqwsslka sdtamyycargqlyggtymdgwgqgtlvTvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsGvhtfpavlqssgl yslssvvtvpssslgtqtyicnvnhkpsntkvdkkvepkscdkthtcppcpapellggpsvflfppkpkdtlmisrtpevtcvvvdvshedpevkf nwyvdgvevhnaktkpreeqynstyrvvsvltvlhqdwlngkeykckvsnkalpApiektiskakgqprepqvytlppsrdeltknqvsltclv kgfypsdiavEwesngqpennykttppvldsdgsfflyskltvdksrwqqgnvfscsvmhealhnhytqkslslspgk (SEQ ID NO:216). [00274] In some cases, an anti-mesothelin antibody comprises a VL present in the light chain amino acid sequence provided above; and a VH present in the heavy chain amino acid sequence provided above. For example, an anti-mesothelin antibody can comprise: a) a VL comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: DIALtqpasvsgspgqsitisctgtssdiggynsvswyqqhpgkapklmiygvnnrpsgvsnrfsgsksgntasltisglqaedeadyycssydi esatpvfgggtk (seq id no:217); and b) a VH comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: qvelvqsgaevkkpgeslkisckgsgysftsywigwvrqapgkglewmgiidpgdsrtryspsfqgqvtisadksistaylqwsslkasdtamy ycargqlyggtymdgwgqgtlvTvss (seq id no:218). [00275] In some cases, an anti-mesothelin antibody comprises VL CDR1, VL CDR2, and VL CDR3 present in the light chain amino acid sequence provided above; and VH CDR1, CDR2, and CDR3 present in the heavy chain amino acid sequence provided above. [00276] For example, an anti-mesothelin antibody can comprise a VL CDR1 having the amino acid sequence tgtssdiggynsvs (SEQ ID NO:219); a VL CDR2 having the amino acid sequence Lmiygvnnrps
(SEQ ID NO:220); a VL CDR3 having the amino acid sequence ssydiesatp (SEQ ID NO:221); a VH CDR1 having the amino acid sequence gysftsywig (SEQ ID NO:222); a VH CDR2 having the amino acid sequence wmgiidpgdsrtrysp (SEQ ID NO:223); and a VH CDR3 having the amino acid sequence gqlyggtymdg (SEQ ID NO:224). [00277] An anti-mesothelin antibody can be a scFv. As one non-limiting example, an anti-mesothelin scFv can comprise the following amino acid sequence: QVQLQQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGRINPNSGGTNYA QKFQGRVTMTRDTSISTAYMELSRLRSEDTAVYYCARGRYYGMDVWGQGTMVTVSSGGGGS GGGGSGGGGSGGGGSEIVLTQSPATLSLSPGERATISCRASQSVSSNFAWYQQRPGQAPRLLIYD ASNRATGIPPRFSGSGSGTDFTLTISSLEPED FAAYYCHQRSNWLYTFGQGTKVDIK (SEQ ID NO:225), where VH CDR1, CDR2, and CDR3 are underlined; and VL CDR1, CDR2, and CDR3 are bolded and underlined. [00278] As one non-limiting example, an anti-mesothelin scFv can comprise the following amino acid sequence: QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNY AQKFQGRVTMTRDTSISTAYMELSRLRSDDTAVYYCARDLRRTVVTPRAYYGMDVWGQGTTV TVSSGGGGSGGGGSGGGGSGGGGSDIQLTQSPSTLSASVGDRVTITCQASQDISNSLNWYQQKA GKAPKLLIYDASTLETGVPSRFSGSGSGTDFSF TISSLQPEDIATYYCQQHDNLPLTFGQGTKVEIK (SEQ ID NO:226), where VH CDR1, CDR2, and CDR3 are underlined; and VL CDR1, CDR2, and CDR3 are bolded and underlined. Anti-CD22 [00279] CD22 (also known as B-Lymphocyte Cell Adhesion Molecule, Sialic Acid-Binding Ig-Like Lectin 2, or SIGLEC2) is a sialic acid-binding adhesion molecule largely restricted to the B cell lineage and expressed on most B-lineage malignancies. [00280] Anti-CD22 antibodies are known in the art; and the VH and VL, or the VH and VL CDRs, of any anti-CD22 antibody can be used. See, e.g., Xiao et al. (2009) Mabs 1:297 (describing the fully human anti-CD22 m971 scFv); and U.S. Patent Publication No.2020/0147134. Examples of anti-CD22 antibodies include epratuzumab and inotuzumab. See, e.g., Lenoard et al. (2007) Oncogene 26:3704 and U.S. Patent No.5,789,554 (describing epratuzumab); and DiJoseph et al. (2007) Leukemia 21:2240 (describing inotuzumab). [00281] For example, an anti-CD22 antibody can comprise: i) a heavy chain variable region (VH) CDR1 having the amino acid sequence: GDSVSSNSAA (SEQ ID NO:227); ii) a VH CDR2 having the amino acid sequence: TYYRSKWYN (SEQ ID NO:228); iii) a VH CDR3 having the amino acid sequence: AREVTGDLEDAFDI (SEQ ID NO:229); iv) a light chain variable region (VL) CDR1 having the amino
acid sequence: QTIWSY (SEQ ID NO:230); v) a VL CDR2 having the amino acid sequence: AAS (Ala- Ala-Ser); and vi) a VL CDR3 having the amino acid sequence: QQSYSIPQT (SEQ ID NO:231). Anti-TROP-2 [00282] Trophoblast cell surface antigen 2 (Trop-2) (also known as epithelial glycoprotein-1, gastrointestinal tumor-associated antigen GA733-1, membrane component chromosome 1 surface marker-1, and tumor-associated calcium signal transducer-2) is a transmembrane glycoprotein that is upregulated in numerous cancer types and is the protein product of the TACSTD2 gene. [00283] Anti-TROP-2 antibodies are known in the art; and the VH and VL, or the VH and VL CDRs, of any anti-TROP-2 antibody can be used. See, e.g., U.S. Patent No.7,238,785). In some cases, an anti- TROP-2 antibody comprises: i) light chain CDR sequences CDR1 (KASQDVSIAVA; SEQ ID NO:232); CDR2 (SASYRYT; SEQ ID NO:233); and CDR3 (QQHYITPLT; SEQ ID NO:234); and ii) heavy chain CDR sequences CDR1 (NYGMN; SEQ ID NO:235); CDR2 (WINTYTGEPTYTDDFKG; SEQ ID NO:236); and CDR3 (GGFGSSYWYFDV; SEQ ID NO:237). [00284] In some cases, an anti-TROP-2 antibody comprises: i) heavy chain CDR sequences CDR1 (TAGMQ; SEQ ID NO:238); CDR2 (WINTHSGVPKYAEDFKG (SEQ ID NO:239); and CDR3 (SGFGSSYWYFDV; SEQ ID NO:240); and ii) light chain CDR sequences CDR1 (KASQDVSTAVA; SEQ ID NO:241); CDR2 (SASYRYT; SEQ ID NO:233); and CDR3 (QQHYITPLT; SEQ ID NO:234). [00285] In some cases, an anti-TROP2 antibody comprises: a) VL CDR1, VL CDR2, and VL CDR3 present in a light chain variable region (VL) comprising the following amino acid sequence: DIQLTQSPSSLSASVGDRVSITCKASQDVSIAVAWYQQKPGKAPKLLIYSASYRYTGVPDRFSGS GSGTDFTLTISSLQPEDFAVYYCQQHYITPLTFGAGTKVEIK (SEQ ID NO:244); and b) VH CDR1, CDR2, and CDR3 present in a heavy chain variable region (VH) comprising the following amino acid sequence: QVQLQQSGSELKKPGASVKVSCKASGYTFTNYGMNWVKQAPGQGLKWMGWINTYTGEPTYT DDFKGRFAFSLDTSVSTAYLQISSLKADDTAVYFCARGGFGSSYWYFDVWGQGSLVTVSS (SEQ ID NO:245). [00286] In some cases, an anti-TROP-2 antibody comprises: a) a VL region comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: DIQLTQSPSSLSASVGDRVSITCKASQDVSIAVAWYQQKPGKAPKLLIYSASYRYTGVPDRFSGS GSGTDFTLTISSLQPEDFAVYYCQQHYITPLTFGAGTKVEIK (SEQ ID NO:244); and b) a VH region comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QVQLQQSGSELKKPGASVKVSCKASGYTFTNYGMNWVKQAPGQGLKWMGWINTYTGEPTYT
DDFKGRFAFSLDTSVSTAYLQISSLKADDTAVYFCARGGFGSSYWYFDVWGQGSLVTVSS (SEQ ID NO:245). Anti-BCMA [00287] Anti-BCMA (B-cell maturation antigen) antibodies are known in the art; and the VH and VL, or the VH and VL CDRs, of any anti-BCMA antibody can be used. See, e.g., WO 2014/089335; US 2019/0153061; and WO 2017/093942. [00288] In some cases, an anti-BCMA antibody comprises: a) a light chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00289] qsvltqppsasgtpgqrvtiscsgsssnigsntvnwyqqlpgtapkllifnyhqrpsgvpdrfsgsksgssaslaisglqsedeadyycaa wddslngwvfgggtkltvlgqpkaapsvtlfppsseelqankatlvclisdfypgavtvawkadsspvkagvetttpdskqsnnkyaassylsltp eqwkshrsyscqvthegSTVEKTVAPTECS (SEQ ID NO:248); and [00290] b) a heavy chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: evqlvesggglvkpggslrlscaasgftfgdyalswfrqapgkglewvgvsrskayggttdyaasvkgrftisrddskstaylqmnslktedtavyy cassgyssgwtpfdywgqgtlvtvssastkgpsvfplapsskstsggtaalgclvkdyfpepvtvswnsgaltsgvhtfpavlqssglyslssvvtv pssslgtqtyicnvnhkpsntkvdkkvepkscdkthtcppcpapellggpsvflfppkpkdtlmisrtpevtcvvvdvshedpevkfnwyvdgv evhnaktkpreeqynstyrvvsvltvlhqdwlngkeykckvsnkalpapiektiskakgqprepqvytlppsreemtknqvsltclvkgfypsdi avewesngqpennykttppvldsdgsfflyskltvdksrwqqgnvfscsvmhealhnhytqkslslspgk (SEQ ID NO:249). [00291] In some cases, an anti-BCMA antibody comprises a VL present in the light chain amino acid sequence provided above; and a VH present in the heavy chain amino acid sequence provided above. For example, an anti-BCMA antibody can comprise: a) a VL comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: [00292] qsvltqppsasgtpgqrvtiscsgsssnigsntvnwyqqlpgtapkllifnyhqrpsgvpdrfsgsksgssaslaisglqsedeadyycaa wddslngwvfgggtkltvlG (SEQ ID NO:250); and b) a VH comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence: [00293] evqlvesggglvkpggslrlscaasgftfgdyalswfrqapgkglewvgvsrskayggttdyaasvkgrftisrddskstaylqmnslkt edtavyycassgyssgwtpfdywgqgtlvtvssastkgpsv (SEQ ID NO:251). [00294] In some cases, an anti-BCMA antibody comprises VL CDR1, VL CDR2, and VL CDR3 present in the light chain amino acid sequence provided above; and VH CDR1, CDR2, and CDR3 present in the heavy chain amino acid sequence provided above.
[00295] For example, an anti-BCMA antibody can comprise a VL CDR1 having the amino acid sequence ssnigsnt (SEQ ID NO:252), a VL CDR2 having the amino acid sequence NYH, a VL CDR3 having the amino acid sequence aawddslngwv (SEQ ID NO:253)), a VH CDR1 having the amino acid sequence gftfgdya (SEQ ID NO:254), a VH CDR2 having the amino acid sequence srskayggtt (SEQ ID NO:255), and a VH CDR3 having the amino acid sequence assgyssgwtpfdy (SEQ ID NO:256). [00296] An anti-BCMA antibody can be a scFv. As one non-limiting example, an anti-BCMA scFv can comprise the following amino acid sequence: QVQLVQSGAEVKKPGSSVKVSCKASGGTFSNYWMHWVRQAPGQGLEWMGATYRGHSDTYY NQKFKGRVTITADKSTSTAYMELSSLRSEDTAVYYCARGAIYNGYDVLDNWGQGTLVTVSSGG GGSGGGGSGGGGSGGGGSDIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKL LIYYTSNLHSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYRKLPWTFGQGTKLEIKR (SEQ ID NO:257). [00297] As another example, an anti-BCMA scFv can comprise the following amino acid sequence: DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKLLIYYTSNLHSGVPSRFSGS GSGTDFTLTISSLQPEDFATYYCQQYRKLPWTFGQGTKLEIKRGGGGSGGGGSGGGGSGGGGSQ VQLVQSGAEVKKPGSSVKVSCKASGGTFSNYWMHWVRQAPGQGLEWMGATYRGHSDTYYN QKFKGRVTITADKSTSTAYMELSSLRSEDTAVYYCARGAIYNGYDVLDNWGQGTLVTVSS (SEQ ID NO:258). [00298] In some cases, an anti-BCMA antibody can comprise a VL CDR1 having the amino acid sequence SASQDISNYLN (SEQ ID NO:259); a VL CDR2 having the amino acid sequence YTSNLHS (SEQ ID NO:260); a VL CDR3 having the amino acid sequence QQYRKLPWT (SEQ ID NO:261); a VH CDR1 having the amino acid sequence NYWMH (SEQ ID NO:262); a VH CDR2 having the amino acid sequence ATYRGHSDTYYNQKFKG (SEQ ID NO:263); and a VH CDR3 having the amino acid sequence GAIYNGYDVLDN (SEQ ID NO:264). [00299] In some cases, an anti-BCMA antibody comprises: a) a light chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKLLIYYTSNLHSGVPSRFSGS GSGTDFTLTISSLQPEDFATYYCQQYRKLPWTFGQGTKLEIKR (SEQ ID NO:265). [00300] In some cases, an anti-BCMA antibody comprises: a) a heavy chain comprising an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: QVQLVQSGAEVKKPGSSVKVSCKASGGTFSNYWMHWVRQAPGQGLEWMGATYRGHSDTYY NQKFKGRVTITADKSTSTAYMELSSLRSEDTAVYYCARGAIYDGYDVLDNWGQGTLVTVSS (SEQ ID NO:266).
Anti-MUC16 [00301] In some cases, an antibody is specific for MUC16 (also known as CA125). See, e.g., Yin et al. (2002) Int. J. Cancer 98:737. For example, an antibody can be specific for a MUC16 polypeptide present on a cancer cell. See, e.g., US 2018/0118848; and US 2018/0112008. In some cases, a MUC16-specific antibody is a scFv. In some cases, a MUC16-specific antibody is a nanobody. [00302] As one example, an anti-MUC16 antibody can comprise a VH CDR1 having the amino acid sequence GFTFSNYY (SEQ ID NO:267); a VH CDR2 having the amino acid sequence ISGRGSTI (SEQ ID NO:268); a VH CDR3 having the amino acid sequence VKDRGGYSPY (SEQ ID NO:269); a VL CDR1 having the amino acid sequence QSISTY (SEQ ID NO:270); a VL CDR2 having the amino acid sequence TAS; and a VL CDR3 having the amino acid sequence QQSYSTPPIT (SEQ ID NO:271). See, e.g., US 2018/0118848. Anti-Claudin-18.2 [00303] In some cases, an antibody is specific for claudin-18 isoform 2 (“claudin-18.2”). See, e.g., WO 2013/167259. In some cases, a claudin-18.2-specific antibody is a scFv. In some cases, a claudin-18.2- specific antibody is a nanobody. [00304] As one example, an anti-claudin-18.2 antibody can comprise a VH CDR1 having the amino acid sequence GYTFTDYS (SEQ ID NO:272); a VH CDR2 having the amino acid sequence INTETGVP (SEQ ID NO:273); a VH CDR3 having the amino acid sequence ARRTGFDY (SEQ ID NO:274); a VL CDR1 having the amino acid sequence KNLLHSDGITY (SEQ ID NO:275); a VL CDR2 having the amino acid sequence RVS; and a VL CDR3 having the amino acid sequence VQVLELPFT (SEQ ID NO:276). [00305] As another example, an anti-claudin-18.2 antibody can comprise a VH CDR1 having the amino acid sequence GFTFSSYA (SEQ ID NO:277); a VH CDR2 having the amino acid sequence ISDGGSYS (SEQ ID NO:278); a VH CDR3 having the amino acid sequence ARDSYYDNSYVRDY (SEQ ID NO:279); a VL CDR1 having the amino acid sequence QDINTF (SEQ ID NO:280); a VL CDR2 having the amino acid sequence RTN; and a VL CDR3 having the amino acid sequence LQYDEFPLT (SEQ ID NO:281). [00306] Examples of antibodies include, but are not limited to: Natalizumab (Tysabri®; Biogen Idec/Elan) targeting α4 subunit of α4β1 andα4β7 integrins (used in the treatment of MS and Crohn's disease); Vedolizumab (MLN2; Millennium Pharmaceuticals/Takeda) targeting α4β7 integrin (as used in the treatment of UC and Crohn's disease); Belimumab (Benlysta; Human Genome Sciences/ GlaxoSmithKline) targeting BAFF (as used in the treatment of SLE); Atacicept (TACI–Ig; Merck/Serono) targeting BAFF and APRIL (as used in the treatment of SLE); Alefacept (Amevive®;
Astellas) targeting CD2 (as used in the treatment of Plaque psoriasis, GVHD); Otelixizumab (TRX4; Tolerx/GlaxoSmithKline) targeting CD3 (as used in the treatment of T1D); Teplizumab (MGA031; MacroGenics/Eli Lilly) targeting CD3 (as used in the treatment of T1D); Rituximab (Rituxan®/Mabthera; Genentech/Roche/Biogen Idec) targeting CD20 (as used in the treatment of Non- Hodgkin's lymphoma, RA (in patients with inadequate responses to TNF blockade) and CLL); Ofatumumab (Arzerra®; Genmab/GlaxoSmithKline) targeting CD20 (as used in the treatment of CLL, RA); Ocrelizumab (2H7; Genentech/Roche/Biogen Idec) targeting CD20 (as used in the treatment of RA and SLE); Epratuzumab (hLL2; Immunomedics/UCB) targeting CD22 (as used in the treatment of SLE and non-Hodgkin's lymphoma); Alemtuzumab (Campath®/MabCampath; Genzyme/Bayer) targeting CD52 (as used in the treatment of CLL, MS); Abatacept (Orencia®; Bristol-Myers Squibb) targeting CD80 and CD86 (as used in the treatment of RA and JIA, UC and Crohn's disease, SLE); Eculizumab (Soliris®; Alexion pharmaceuticals) targeting C5 complement protein (as used in the treatment of Paroxysmal nocturnal haemoglobinuria); Omalizumab (Xolair®; Genentech/Roche/Novartis) targeting IgE (as used in the treatment of Moderate to severe persistent allergic asthma); Canakinumab (Ilaris®; Novartis) targeting IL-1β (as used in the treatment of Cryopyrin-associated periodic syndromes, Systemic JIA, neonatal-onset multisystem inflammatory disease and acute gout); Mepolizumab (Bosatria; GlaxoSmithKline) targeting IL-5 (as used in the treatment of Hyper-eosinophilic syndrome); Reslizumab (SCH55700; Ception Therapeutics) targeting IL-5 (as used in the treatment of Eosinophilic oesophagitis); Tocilizumab (Actemra®/RoActemra®; Chugai/Roche) targeting IL-6R (as used in the treatment of RA, JIA); Ustekinumab (Stelara®; Centocor) targeting IL-12 and IL-23 (as used in the treatment of Plaque psoriasis, Psoriatic arthritis, Crohn's disease); Briakinumab (ABT-874; Abbott) targeting IL-12 and IL-23 (as used in the treatment of Psoriasis and plaque psoriasis); Etanercept (Enbrel®; Amgen/Pfizer) targeting TNF (as used in the treatment of RA, JIA, psoriatic arthritis, AS and plaque psoriasis); Infliximab (Remicade®; Centocor/Merck) targeting TNF (as used in the treatment of Crohn's disease, RA, psoriatic arthritis, UC, AS and plaque psoriasis); Adalimumab (Humira®/Trudexa; Abbott) targeting TNF (as used in the treatment of RA, JIA, psoriatic arthritis, Crohn's disease, AS and plaque psoriasis); Certolizumab pegol (Cimzia®; UCB) targeting TNF (as used in the treatment of Crohn's disease and RA); Golimumab (Simponi®; Centocor) targeting TNF (as used in the treatment of RA, psoriatic arthritis and AS); and the like. In some cases, the antibody whose production is induced by the intracellular domain of a synNotch polypeptide of the present disclosure is a therapeutic antibody for the treatment of cancer. Such antibodies include, e.g., Ipilimumab targeting CTLA-4 (as used in the treatment of Melanoma, Prostate Cancer, RCC); Tremelimumab targeting CTLA-4 (as used in the treatment of CRC, Gastric, Melanoma, NSCLC); Nivolumab targeting PD-1 (as used in the treatment of Melanoma, NSCLC, RCC); MK-3475 targeting PD-1 (as used in the treatment of Melanoma); Pidilizumab targeting PD-1 (as used in the treatment of Hematologic Malignancies); BMS-936559
targeting PD-L1 (as used in the treatment of Melanoma, NSCLC, Ovarian, RCC); MEDI4736 targeting PD-L1; MPDL33280A targeting PD-L1 (as used in the treatment of Melanoma); Rituximab targeting CD20 (as used in the treatment of Non-Hodgkin's lymphoma); Ibritumomab tiuxetan and tositumomab (as used in the treatment of Lymphoma); Brentuximab vedotin targeting CD30 (as used in the treatment of Hodgkin's lymphoma); Gemtuzumab ozogamicin targeting CD33 (as used in the treatment of Acute myelogenous leukaemia); Alemtuzumab targeting CD52 (as used in the treatment of Chronic lymphocytic leukaemia); IGN101 and adecatumumab targeting EpCAM (as used in the treatment of Epithelial tumors (breast, colon and lung)); Labetuzumab targeting CEA (as used in the treatment of Breast, colon and lung tumors); huA33 targeting gpA33 (as used in the treatment of Colorectal carcinoma); Pemtumomab and oregovomab targeting Mucins (as used in the treatment of Breast, colon, lung and ovarian tumors); CC49 (minretumomab) targeting TAG-72 (as used in the treatment of Breast, colon and lung tumors); cG250 targeting CAIX (as used in the treatment of Renal cell carcinoma); J591 targeting PSMA (as used in the treatment of Prostate carcinoma); MOv18 and MORAb-003 (farletuzumab) targeting Folate-binding protein (as used in the treatment of Ovarian tumors); 3F8, ch14.18 and KW-2871 targeting Gangliosides (such as GD2, GD3 and GM2) (as used in the treatment of Neuroectodermal tumors and some epithelial tumors); hu3S193 and IgN311 targeting Le y (as used in the treatment of Breast, colon, lung and prostate tumors); Bevacizumab targeting VEGF (as used in the treatment of Tumor vasculature); IM-2C6 and CDP791 targeting VEGFR (as used in the treatment of Epithelium-derived solid tumors); Etaracizumab targeting Integrin alpha(v)beta(3) (as used in the treatment of Tumor vasculature); Volociximab targeting Integrin alpha(v)beta(1) (as used in the treatment of Tumor vasculature); Cetuximab, panitumumab, nimotuzumab and 806 targeting EGFR (as used in the treatment of Glioma, lung, breast, colon, and head and neck tumors); Trastuzumab and pertuzumab targeting ERBB2 (as used in the treatment of Breast, colon, lung, ovarian and prostate tumors); MM-121 targeting ERBB3 (as used in the treatment of Breast, colon, lung, ovarian and prostate, tumors); AMG 102, METMAB and SCH 900105 targeting MET (as used in the treatment of Breast, ovary and lung tumors); AVE1642, IMC-A12, MK-0646, R1507 and CP 751871 targeting IGF1R (as used in the treatment of Glioma, lung, breast, head and neck, prostate and thyroid cancer); KB004 and IIIA4 targeting EPHA3 (as used in the treatment of Lung, kidney and colon tumors, melanoma, glioma and haematological malignancies); Mapatumumab (HGS-ETR1) targeting TRAILR1 (as used in the treatment of Colon, lung and pancreas tumors and haematological malignancies); HGS-ETR2 and CS- 1008 targeting TRAILR2; Denosumab targeting RANKL (as used in the treatment of Prostate cancer and bone metastases); Sibrotuzumab and F19 targeting FAP (as used in the treatment of Colon, breast, lung, pancreas, and head and neck tumors); 81C6 targeting Tenascin (as used in the treatment of Glioma, breast and prostate tumors); Blinatumomab (Blincyto; Amgen) targeting CD3 (as used in the treatment of
ALL); pembrolizumab targeting PD-1 as used in cancer immunotherapy; 9E10 antibody targeting c-Myc; and the like. [00307] Examples of antibodies include, but are not limited to: Abagovomab, Abciximab, Abituzumab, Abrilumab, Actoxumab, Aducanumab, Afelimomab, Afutuzumab, Alacizumab pegol, ALD518, Alirocumab, Altumomab pentetate, Amatuximab, Anatumomab mafenatox, Anetumab ravtansine, Anifrolumab, Anrukinzumab, Apolizumab, Arcitumomab, Ascrinvacumab, Aselizumab, Atezolizumab, Atinumab, Atlizumab/ tocilizumab, Atorolimumab, Bapineuzumab, Basiliximab, Bavituximab, Bectumomab, Begelomab, Benralizumab, Bertilimumab, Besilesomab, Bevacizumab/Ranibizumab, Bezlotoxumab, Biciromab, Bimagrumab, Bimekizumab, Bivatuzumab mertansine, Blosozumab, Bococizumab, Brentuximabvedotin, Brodalumab, Brolucizumab, Brontictuzumab, Cantuzumab mertansine, Cantuzumab ravtansine, Caplacizumab, Capromab pendetide, Carlumab, Catumaxomab, cBR96-doxorubicin immunoconjugate, Cedelizumab, Ch.14.18, Citatuzumab bogatox, Cixutumumab, Clazakizumab, Clenoliximab, Clivatuzumab tetraxetan, Codrituzumab, Coltuximab ravtansine, Conatumumab, Concizumab, CR6261, Crenezumab, Dacetuzumab, Daclizumab, Dalotuzumab, Dapirolizumab pegol, Daratumumab, Dectrekumab, Demcizumab, Denintuzumab mafodotin, Derlotuximab biotin, Detumomab, Dinutuximab, Diridavumab, Dorlimomab aritox, Drozitumab, Duligotumab, Dupilumab, Durvalumab, Dusigitumab, Ecromeximab, Edobacomab, Edrecolomab, Efalizumab, Efungumab, Eldelumab, Elgemtumab, Elotuzumab, Elsilimomab, Emactuzumab, Emibetuzumab, Enavatuzumab, Enfortumab vedotin, Enlimomab pegol, Enoblituzumab, Enokizumab, Enoticumab, Ensituximab, Epitumomab cituxetan, Erlizumab, Ertumaxomab, Etrolizumab, Evinacumab, Evolocumab, Exbivirumab, Fanolesomab, Faralimomab, Farletuzumab, Fasinumab, FBTA05, Felvizumab, Fezakinumab, Ficlatuzumab, Figitumumab, Firivumab, Flanvotumab, Fletikumab, Fontolizumab, Foralumab, Foravirumab, Fresolimumab, Fulranumab, Futuximab, Galiximab, Ganitumab, Gantenerumab, Gavilimomab, Gevokizumab, Girentuximab, Glembatumumab vedotin, Gomiliximab, Guselkumab, Ibalizumab, Ibalizumab , Icrucumab, Idarucizumab, Igovomab, IMAB362, Imalumab, Imciromab, Imgatuzumab, Inclacumab, Indatuximab ravtansine, Indusatumab vedotin, Inolimomab, Inotuzumab ozogamicin, Intetumumab, Iratumumab, Isatuximab, Itolizumab, Ixekizumab, Keliximab, Lambrolizumab, Lampalizumab, Lebrikizumab, Lemalesomab, Lenzilumab, Lerdelimumab, Lexatumumab, Libivirumab, Lifastuzumab vedotin, Ligelizumab, Lilotomab satetraxetan, Lintuzumab, Lirilumab, Lodelcizumab, Lokivetmab, Lorvotuzumab mertansine, Lucatumumab, Lulizumab pegol, Lumiliximab, Lumretuzumab, Margetuximab, Maslimomab, Matuzumab, Mavrilimumab, Metelimumab, Milatuzumab, Minretumomab, Mirvetuximab soravtansine, Mitumomab, Mogamulizumab, Morolimumab, Morolimumab immune, Motavizumab, Moxetumomab pasudotox, Muromonab-CD3, Nacolomab tafenatox, Namilumab, Naptumomab estafenatox, Narnatumab, Nebacumab, Necitumumab, Nemolizumab, Nerelimomab, Nesvacumab, Nofetumomab merpentan, Obiltoxaximab, Obinutuzumab,
Ocaratuzumab, Odulimomab, Olaratumab, Olokizumab, Onartuzumab, Ontuxizumab, Opicinumab, Oportuzumab monatox, Orticumab, Otlertuzumab, Oxelumab, Ozanezumab, Ozoralizumab, Pagibaximab, Palivizumab, Pankomab, Panobacumab, Parsatuzumab, Pascolizumab, Pasotuxizumab, Pateclizumab, Patritumab, Perakizumab, Pexelizumab, Pinatuzumab vedotin, Pintumomab, Placulumab, Polatuzumab vedotin, Ponezumab, Priliximab, Pritoxaximab, Pritumumab, PRO 140, Quilizumab, Racotumomab, Radretumab, Rafivirumab, Ralpancizumab, Ramucirumab, Ranibizumab, Raxibacumab, Refanezumab, Regavirumab, Rilotumumab, Rinucumab, Robatumumab, Roledumab, Romosozumab, Rontalizumab, Rovelizumab, Ruplizumab, Sacituzumab govitecan, Samalizumab, Sarilumab, Satumomab pendetide, Secukinumab, Seribantumab, Setoxaximab, Sevirumab, SGN-CD19A, SGN- CD33A, Sifalimumab, Siltuximab, Simtuzumab, Siplizumab, Sirukumab, Sofituzumab vedotin, Solanezumab, Solitomab, Sonepcizumab, Sontuzumab, Stamulumab, Sulesomab, Suvizumab, Tabalumab, Tacatuzumab tetraxetan, Tadocizumab, Talizumab, Tanezumab, Taplitumomab paptox, Tarextumab, Tefibazumab, Telimomab aritox, Tenatumomab, Teneliximab, Teprotumumab, Tesidolumab, Tetulomab, TGN1412, Ticilimumab/tremelimumab, Tigatuzumab, Tildrakizumab, TNX- 650, Toralizumab, Tosatoxumab, Tovetumab, Tralokinumab, TRBS07, Tregalizumab, Trevogrumab, Tucotuzumab celmoleukin, Tuvirumab, Ublituximab, Ulocuplumab, Urelumab, Urtoxazumab, Vandortuzumab vedotin, Vantictumab, Vanucizumab, Vapaliximab, Varlilumab, Vatelizumab, Veltuzumab, Vepalimomab, Vesencumab, Visilizumab, Vorsetuzumab mafodotin, Votumumab, Zalutumumab, Zanolimumab, Zatuximab, Ziralimumab, Zolimomab aritox, and the like. Antibody mimetics [00308] In some cases, an EDV of the present disclosure comprises an antibody mimetic (also referred to as an “antibody analog”). Non-limiting examples of antibody mimetics include peptide aptamers, affimers, affilins, affibodies, affitins, alphabodies, anticalins, avimers, DARPins, fynomers, Kunitz domain peptides, nanoCLAMPs, affinity reagents, and scaffold proteins. Nucleic acid-binding polypeptides [00309] As noted above, the present disclosure provides EDVs comprising a nucleic acid-binding effector polypeptide, and collections of one or more nucleic acids that encode the nucleic acid-binding effector polypeptide. The present disclosure also provides methods of delivery and production of such. [00310] Suitable nucleic acid binding effector polypeptides include nucleases. Suitable nucleases include, but are not limited to, a homing nuclease polypeptide; a FokI polypeptide; a transcription activator-like effector nuclease (TALEN) polypeptide; a MegaTAL polypeptide; a meganuclease polypeptide; a zinc finger nuclease (ZFN); an ARCUS nuclease; a Transposon-encoded type nuclease such as TnpB or IscB (see, e.g., Meers et al., Nature.2023 Oct;622(7984):863-871 and Jiang et al., Sci Adv.2023 Sep
29;9(39):eadk0171), a serine recombinase or tyrosine recombinase (e.g., a site-specific recombinase such as Cre recombinase, Dre recombinase, Flp recombinase, KD recombinase, B2 recombinase, B3 recombinase, R recombinase, Hin recombinase, Tre recombinase, PhiC31 integrase, Bxb1 integrase, R4 integrase, lambda integrase, HK022 integrase, HP1 integrase, etc.) and the like. A meganuclease can be engineered from an LADLIDADG homing endonuclease (LHE). A megaTAL polypeptide can comprise a TALE DNA binding domain and an engineered meganuclease. See, e.g., WO 2004/067736 (homing endonuclease); Urnov et al. (2005) Nature 435:646 (ZFN); Mussolino et al. (2011) Nucle. Acids Res. 39:9283 (TALE nuclease); Boissel et al. (2013) Nucl. Acids Res.42:2591 (MegaTAL). CRISPR-Cas effector polypeptides [00311] As noted above, in some cases, an EDV of the present disclosure comprises a CRISPR-Cas effector polypeptide (e.g., a nucleic acid-binding effector polypeptide is in some cases a CRISPR-Cas effector polypeptide). The CRISPR-Cas effector polypeptide can be any of a variety of CRISPR-Cas effector polypeptides. Suitable CRISPR-Cas effector polypeptides are described in detail below. For example, in some cases, the CRISPR-Cas effector polypeptide is a type II CRISPR-Cas effector polypeptide. In some cases, the type II CRISPR-Cas effector polypeptide is a Cas9 polypeptide. In some cases, the CRISPR-Cas effector polypeptide is a type V CRISPR-Cas effector polypeptide, e.g., a Cas12a, a Cas12b, a Cas12c, a Cas12d, or a Cas12e polypeptide. In some cases, the CRISPR-Cas effector polypeptide is a type VI CRISPR-Cas effector polypeptide, e.g., a Cas13a polypeptide, a Cas13b polypeptide, a Cas13c polypeptide, or a Cas13d polypeptide. In some cases, the CRISPR-Cas effector polypeptide is a Cas14 polypeptide. In some cases, the CRISPR-Cas effector polypeptide is a Cas14a polypeptide, a Cas14b polypeptide, or a Cas14c polypeptide. Also suitable for use is a variant CRISPR- Cas effector polypeptide, where the variant CRISPR-Cas effector polypeptide has reduced nucleic acid cleavage activity. Also suitable for use is a CRISPR-Cas effector fusion polypeptide comprising: i) a CRISPR-Cas effector polypeptide is a variant that has reduced nucleic acid cleavage activity; and ii) a heterologous fusion polypeptide. In some cases, the heterologous fusion polypeptide is a protein modifying enzyme. In some cases, the heterologous fusion polypeptide is a nucleic acid modifying enzyme. In some cases, the heterologous fusion polypeptide is a reverse transcriptase. In some cases, the heterologous fusion polypeptide is a cytidine deaminase. In some cases, the heterologous fusion polypeptide is an adenine deaminase. In some cases, the heterologous fusion polypeptide is a transcription factor. In some cases, the heterologous fusion polypeptide is a transcription activator. In some cases, the heterologous fusion polypeptide is a transcription repressor. Suitable protein-modifying enzymes and nucleic acid modifying enzymes are described in detail below. For example, in some cases, the nucleic acid modifying enzyme is a cytidine deaminase. In some cases, the nucleic acid modifying enzyme is an adenosine deaminase. In some cases, the nucleic acid modifying enzyme is a prime editor.
As described in more detail below, in some cases, the CRISPR-Cas effector polypeptide comprises one or more nuclear localization signals. [00312] Examples of CRISPR-Cas effector polypeptides are CRISPR-Cas endonucleases (e.g., class 2 CRISPR-Cas effector polypeptide such as a type II, type V, or type VI CRISPR-Cas effector polypeptide). Where a CRISPR-Cas effector polypeptide has endonuclease activity, the CRISPR-Cas effector polypeptide may also be referred to as a “CRISPR-Cas endonuclease.” A CRISPR-Cas effector polypeptide can also have reduced or undetectable endonuclease activity. A CRISPR-Cas effector polypeptide can also be a fusion CRISPR-Cas effector polypeptide comprising a heterologous fusion partner. In some cases, a suitable CRISPR-Cas effector polypeptide is a class 2 CRISPR-Cas effector polypeptide. In some cases, a suitable CRISPR-Cas effector polypeptide is a class 2 type II CRISPR-Cas effector polypeptide (e.g., a Cas9 protein). In some cases, a suitable CRISPR-Cas effector polypeptide is a class 2 type V CRISPR-Cas endonuclease (e.g., a Cpf1 protein (Cas12a), a C2c1 protein, or a C2c3 protein). In some cases, a suitable CRISPR-Cas effector polypeptide is a class 2 type VI CRISPR-Cas effector polypeptide (e.g., a C2c2 protein; also referred to as a “Cas13a” protein). Also suitable for use is a CasX protein (also referred to as a “Cas12e” protein). Also suitable for use is a CasY protein (also referred to as a “Cas12d” protein). [00313] In some cases, a suitable CRISPR-Cas effector polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence of any one of SEQ ID NOs: 137-152. [00314] In some cases, the CRISPR-Cas effector polypeptide is a Type II CRISPR-Cas effector polypeptide. In some cases, the CRISPR-Cas effector polypeptide is a Cas9 polypeptide. The Cas9 protein is guided to a target site (e.g., stabilized at a target site) within a target nucleic acid sequence (e.g., a chromosomal sequence or an extrachromosomal sequence, e.g., an episomal sequence, a minicircle sequence, a mitochondrial sequence, a chloroplast sequence, etc.) by virtue of its association with the protein-binding segment of the Cas9 guide RNA. In some cases, a Cas9 polypeptide comprises an amino acid sequence having at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 98%, at least 99%, or more than 99%, amino acid sequence identity to the Streptococcus pyogenes Cas9 of SEQ ID NO: 137. [00315] In some cases, the Cas9 polypeptide is a Staphylococcus aureus Cas9 (saCas9) polypeptide. In some cases, the saCas9 polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the saCas9 amino acid sequence of SEQ ID NO: 143. In some cases, a suitable CRISPR-Cas effector polypeptide comprises an amino acid sequence having at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence of any one of SEQ ID NOs: 137-152. In some cases, a suitable CRISPR-Cas effector polypeptide comprises an amino acid sequence having at least
85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence of any one of SEQ ID NOs: 137-143. [00316] In some cases, a suitable Cas9 polypeptide is a high-fidelity (HF) Cas9 polypeptide. Kleinstiver et al. (2016) Nature 529:490. For example, amino acids N497, R661, Q695, and Q926 of the amino acid sequence of SEQ ID NO: 137 are substituted, e.g., with alanine. For example, an HF Cas9 polypeptide can comprise an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the amino acid sequence of SEQ ID NO:137, where amino acids N497, R661, Q695, and Q926 are substituted, e.g., with alanine. In some cases, a suitable Cas9 polypeptide exhibits altered PAM specificity. See, e.g., Kleinstiver et al. (2015) Nature 523:481. [00317] In some cases, a suitable CRISPR-Cas effector polypeptide is a type V CRISPR-Cas effector polypeptide. In some cases, a type V CRISPR-Cas effector polypeptide is a Cpf1 protein (also known as Cas12a). In some cases, a Cpf1 protein comprises an amino acid sequence having at least 30%, at least 35%, at least 40%, at least 45%, 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 95%, at least 90%, or 100%, amino acid sequence identity to the Cpf1 amino acid sequence of SEQ ID NOs: 144-146. [00318] In some cases, a suitable CRISPR-Cas effector polypeptide is a CasX or a CasY polypeptide. CasX and CasY polypeptides are described in Burstein et al. (2017) Nature 542:237. [00319] In some cases, a suitable CRISPR-Cas effector polypeptide is a fusion protein comprising a CRISPR-Cas effector polypeptide that is fused to a heterologous polypeptide (also referred to as a “fusion partner”). In some cases, a CRISPR-Cas effector polypeptide is fused to an amino acid sequence (a fusion partner) that provides for subcellular localization, i.e., the fusion partner is a subcellular localization sequence (e.g., one or more nuclear localization signals (NLSs) for targeting to the nucleus, two or more NLSs, three or more NLSs, 4 or more NLSs, 5 or more NLSs, 6 or more NLSs, 7 or more NLSs, 8 or more NLSs, 9 or more NLSs, or 10 or more NLSs. [00320] A nucleic acid that binds to a class 2 CRISPR-Cas effector polypeptide (e.g., a Cas9 protein; a type V or type VI CRISPR-Cas protein; a Cpf1 protein; etc.) and targets the complex to a specific location within a target nucleic acid is referred to herein as a “guide RNA” or “CRISPR-Cas guide nucleic acid” or “CRISPR-Cas guide RNA.” A guide RNA provides target specificity to the complex (the ribonucleoprotein complex, also referred to as an RNP) by including a targeting segment, which includes a guide sequence (also referred to herein as a targeting sequence), which is a nucleotide sequence that is complementary to a sequence of a target nucleic acid. [00321] In some cases, a guide RNA includes two separate nucleic acid molecules: an “activator” and a “targeter” and is referred to herein as a “dual guide RNA”, a “double-molecule guide RNA”, a “two- molecule guide RNA”, or a “dgRNA.” In some cases, the guide RNA is one molecule (e.g., for some class 2 CRISPR-Cas proteins, the corresponding guide RNA is a single molecule; and in some cases, an
activator and targeter are covalently linked to one another, e.g., via intervening nucleotides), and the guide RNA is referred to as a “single guide RNA”, a “single-molecule guide RNA,” a “one-molecule guide RNA”, or simply “sgRNA.” [00322] In some cases, an EDV of the present disclosure comprises a CRISPR-Cas effector polypeptide, or both a CRISPR-Cas effector polypeptide and a guide RNA, e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a in the form of an RNP (i.e., complexed with a guide RNA). As such, when an EDV is said to include a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a, it is to be understood that such encompasses an EDV that includes an RNP. In some cases, e.g., where a target nucleic acid comprises a deleterious mutation in a defective allele (e.g., a deleterious mutation in a target nucleic acid), the CRISPR-Cas effector polypeptide/guide RNA complex, together with a donor nucleic acid comprising a nucleotide sequence that corrects the deleterious mutation (e.g., a donor nucleic acid comprising a nucleotide sequence that encodes a functional copy of the protein encoded by the defective allele), can be used to correct the deleterious mutation, e.g., via homology-directed repair (HDR). [00323] In some cases, an EDV of the present disclosure comprises: i) a CRISPR-Cas effector polypeptide; and ii) a guide RNA. In some cases, the guide RNA is a single-molecule (or “single guide”) guide RNA (an “sgRNA”). In some cases, the guide RNA is a dual-molecule (or “dual-guide”) guide RNA (“dgRNA”). [00324] In some cases, an EDV of the present disclosure comprises: i) a CRISPR-Cas effector polypeptide; and ii) 2 or more gRNAs, where the two or more gRNAs can, e.g., provide for multiplexed gene knockout, e.g., each of the 2 or more guide RNAs can be targeted to a different gene (or in some cases to two different sequences of the same gene). In some cases, the guide RNAs are sgRNAs. In some cases, the guide RNAs are dgRNAs. [00325] In some cases, an EDV of the present disclosure comprises: i) a CRISPR-Cas effector polypeptide; and ii) 2 separate sgRNAs, where the 2 separate sgRNAs provide for deletion (“knockout”) of a target nucleic acid via non-homologous end joining (NHEJ). In some cases, the guide RNAs are sgRNAs. In some cases, the guide RNAs are dgRNAs. In some cases, an EDV of the present disclosure does not include a guide RNA. Class 2 CRISPR-Cas effector polypeptides [00326] In class 2 CRISPR systems, the functions of the effector complex (e.g., the cleavage of target DNA) are carried out by a single endonuclease (e.g., see Zetsche et al., Cell.2015 Oct 22;163(3):759-71; Makarova et al., Nat Rev Microbiol.2015 Nov;13(11):722-36; Shmakov et al., Mol Cell.2015 Nov 5;60(3):385-97); and Shmakov et al. (2017) Nature Reviews Microbiology 15:169. As such, the term “class 2 CRISPR-Cas protein” is used herein to encompass the CRISPR-Cas effector polypeptide (e.g., the target nucleic acid cleaving protein) from class 2 CRISPR systems. Thus, the term “class 2 CRISPR-
Cas effector polypeptide” as used herein encompasses type II CRISPR-Cas effector polypeptides (e.g., Cas9); type V-A CRISPR-Cas effector polypeptides (e.g., Cpf1 (also referred to a “Cas12a”)); type V-B CRISPR-Cas effector polypeptides (e.g., C2c1 (also referred to as “Cas12b”)); type V-C CRISPR-Cas effector polypeptides (e.g., C2c3 (also referred to as “Cas12c”)); type V-U1 CRISPR-Cas effector polypeptides (e.g., C2c4); type V-U2 CRISPR-Cas effector polypeptides (e.g., C2c8); type V-U5 CRISPR-Cas effector polypeptides (e.g., C2c5); type V-U4 CRISPR-Cas proteins (e.g., C2c9); type V- U3 CRISPR-Cas effector polypeptides (e.g., C2c10); type VI-A CRISPR-Cas effector polypeptides (e.g., C2c2 (also known as “Cas13a”)); type VI-B CRISPR-Cas effector polypeptides (e.g., Cas13b (also known as C2c4)); and type VI-C CRISPR-Cas effector polypeptides (e.g., Cas13c (also known as C2c7)). To date, class 2 CRISPR-Cas effector polypeptides encompass type II, type V, and type VI CRISPR-Cas effector polypeptides, but the term is also meant to encompass any class 2 CRISPR-Cas effector polypeptide suitable for binding to a corresponding guide RNA and forming an RNP complex. [00327] In some cases, a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) is a fusion polypeptide comprising: i) the nucleic acid-binding effector polypeptide; and ii) one or more heterologous fusion partners (one or more heterologous fusion polypeptides). In some cases, a fusion nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) comprises one or more localization signal peptides. Suitable localization signals (“subcellular localization signals”) include, e.g., a nuclear localization signal (NLS) for targeting to the nucleus; a sequence to keep the fusion protein out of the nucleus, e.g., a nuclear export sequence (NES); a sequence to keep the fusion protein retained in the cytoplasm; a mitochondrial localization signal for targeting to the mitochondria; a chloroplast localization signal for targeting to a chloroplast; an endoplasmic reticulum (ER) retention signal; and ER export signal; and the like. In some cases, a fusion CRISPR-Cas effector polypeptide does not include a NLS so that the protein is not targeted to the nucleus (which can be advantageous, e.g., when the target nucleic acid is an RNA that is present in the cytosol). [00328] In some cases, a fusion nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) comprises both an NES and one or more NLSs (e.g., in some cases about 3 NESs and about 7 NLSs). A suitable NES comprises hydrophobic amino acid residues, e.g., LXXXLXXLXL (SEQ ID NO:207), where L is a hydrophobic amino acid residue (e.g., Leu) and X is any other amino acid. Suitable NESs are known in the art; see, e.g., Xu et al. (2012) Mol. Biol. Cell 23:3677. Non-limiting examples of suitable NESs include: LPPLERLTL (SEQ ID NO:188); LALKLAGLDL (SEQ ID NO:189); LSQALASSFSV (SEQ ID NO:190); NELALKLAGLDI (SEQ ID NO:191). In some cases, the NES comprises the amino acid sequence LPPLERLTL (SEQ ID NO:188). In some cases, the nucleic acid-binding effector polypeptide is a Cas9 protein having multiple NESs (e.g., 3 NESs), and multiple NLSs (e.g., about 7 NLSs).
[00329] In some cases, a fusion CRISPR-Cas effector polypeptide includes (is fused to) a nuclear localization signal (NLS) (e.g., in some cases 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs). Thus, in some cases, a fusion polypeptide includes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs). In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus and/or the C-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the C-terminus. In some cases, one or more NLSs (3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) both the N-terminus and the C- terminus. In some cases, an NLS is positioned at the N-terminus and an NLS is positioned at the C- terminus. [00330] In some cases, a fusion CRISPR-Cas effector polypeptide includes (is fused to) from 1 to 10 NLSs (e.g., 1-9, 1-8, 1-7, 1-6, 1-5, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, 4-10, 4-9, 4-8, 4-7, 5-10, 5-9, or 5-8 NLSs). In some cases, a fusion CRISPR-Cas effector polypeptide includes (is fused to) from 2 to 5 NLSs (e.g., 2-4 NLSs, or 2-3 NLSs). In some cases, a fusion CRISPR-Cas effector polypeptide includes (is fused to) about 4 NLSs. In some cases, a fusion CRISPR-Cas effector polypeptide includes (is fused to) about 7 NLSs. [00331] In some cases, a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) is produced as a fusion with a Gag polypeptide, e.g., as a Gag-Cas9 polyprotein. In some cases, the fusion protein includes one or more heterologous protease cleavage sites between the gag polyprotein and the nucleic acid-binding effector polypeptide (e.g., the CRISPR-Cas effector polypeptide such as Cas9 or Cas12a). Many protease cleavage sites will be known to one of ordinary skill in the art, and any convenient cleavage site can be used. Examples of such sties include, but are not necessarily limited to: a TEV cleavage site, a PreScission cleavage site, a human rhinovirus 3C protease cleavage site, an enterokinase cleavage site, an Epstein-Barr virus protease cleavage site, a cathepsin D cleavage site, and a thrombin cleavage site (and any combination thereof). Thus, in some cases, the heterologous protease cleavage site is a TEV cleavage site, a PreScission cleavage site, a human rhinovirus 3C protease cleavage site, an enterokinase cleavage site, an Epstein-Barr virus protease cleavage site, a cathepsin D cleavage site, and/or a thrombin cleavage site, or any combination thereof.
[00332] In some cases, a fusion CRISPR-Cas effector polypeptide comprises: i) a lentiviral Gag polypeptide; ii) a nuclear export signal peptide; iii) 2 copies of an NLS; and iv) a CRISPR-Cas effector polypeptide. Non-limiting examples of nucleotide sequences encoding Gag-Cas9 fusion polypeptides with NES and/or NLS are provided in FIG.14A-14D. FIG.14E provides an example of a Gag-Cas9 fusion polypeptide with 3 NES and 2 NLS. As noted elsewhere herein, in some cases, the CRISPR-Cas effector polypeptide (e.g., Cas9) has more than 2 NLSs, e.g., in some cases 3, 4, 5, 6, 7, 8, 9, or 10 NLSs. Also as noted elsewhere herein, in some cases, the CRISPR-Cas effector polypeptide (e.g., Cas9) has multiple NESs (e.g., in some cases 2, 3, 4, or 5 NESs). in some cases, the CRISPR-Cas effector polypeptide (e.g., Cas9) has 3 NESs and 7 NLSs. [00333] In some embodiments, a gag polyprotein is a retroviral gag polyprotein (e.g., a lentiviral gag polyprotein). In some cases, a lentiviral gag polyprotein is selected from a bovine immunodeficiency virus gag polyprotein, a simian immunodeficiency virus gag polyprotein, a feline immunodeficiency virus gag polyprotein, a human immunodeficiency virus gag polyprotein, an equine infection anemia virus gag polyprotein, and a caprine arthritis encephalitis virus gag polyprotein. In some cases, a lentiviral gag polyprotein is a human immunodeficiency virus (HIV) gag polyprotein comprising a MA polypeptide, a CA polypeptide, a p2 polypeptide, an NC polypeptide, a p1 polypeptide, and a p6 polypeptide. In some cases, the HIV gag polyprotein includes one or more heterologous protease cleavage sites between one or more of: i) the MA polypeptide and the CA polypeptide; ii) the CA polypeptide and the p2 polypeptide; iii) the p2 polypeptide and the NC polypeptide; iv) the NC polypeptide and the p1 polypeptide; and v) the p1 polypeptide and the p6 polypeptide. [00334] In some cases, a lentiviral gag polyprotein is a human immunodeficiency virus (HIV) gag polyprotein comprising a p6 polypeptide. In some cases, a lentiviral gag polyprotein is a human immunodeficiency virus (HIV) gag polyprotein comprising a MA polypeptide, a CA polypeptide, an NC polypeptide, and a p6 polypeptide. [00335] Non-limiting 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:1); the NLS from nucleoplasmin (e.g., the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ ID NO:2)); the c-myc NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO:3) or RQRRNELKRSP (SEQ ID NO:4); the hRNPA1 M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO:5); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO:6) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO:7) and PPKKARED (SEQ ID NO:8) of the myoma T protein; the sequence PQPKKKPL (SEQ ID NO:9) of human p53; the sequence KRALPNNTSSSPQPKKKP (SEQ ID NO:206) of human p53; the sequence SALIKKKKKMAP (SEQ ID NO:10) of mouse c-abl IV; the sequences DRLRR (SEQ ID NO:11) and PKQKKRK (SEQ ID
NO:16) of the influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO:12) of the Hepatitis virus delta antigen; the sequence REKKKFLKRR (SEQ ID NO:13) of the mouse Mx1 protein; the sequence KRKGDEVDGVDEVAKKKSKK (SEQ ID NO:14) of the human poly(ADP-ribose) polymerase; and the sequence RKCLQAGMNLEARKTKK (SEQ ID NO:15) of the steroid hormone receptors (human) glucocorticoid. In some cases, an NLS comprises the amino acid sequence MDSLLMNRRKFLYQFKNVRWAKGRRETYLC (SEQ ID NO:17). In general, NLS (or multiple NLSs) are of sufficient strength to drive accumulation of the fusion polypeptide in a detectable amount in the nucleus of a eukaryotic cell. Detection of accumulation in the nucleus may be performed by any suitable technique. For example, a detectable marker may be fused to the fusion polypeptide such that location within a cell may be visualized. 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. Fusion polypeptides [00336] In some cases, the nucleic acid-binding effector polypeptide (e.g., CRISPR-Cas effector polypeptide such as Cas9) harbors a mutation that reduces its catalytic activity compared to a wild-type CRISPR-Cas effector polypeptide. In some cases, the mutation renders it a nickase and in some cases renders it catalytically inactive (“dead), e.g., a dCas9. In some cases, a CRISPR-Cas effector protein (e.g., Cas9 or Cas12a) is catalytically inactivated (i.e.,‘dead’), which is referred to in the art as a dCas protein (e.g., dCas9, dCas12a). Such a protein will not exhibit the nuclease cleavage activity of the Cas effector protein, but if fused another protein, the fusion will exhibit the activity of the protein to which the ‘dead’ protein is fused (i.e., the fusion partner - the transcription activating protein). Examples of mutations to produce a dCas effector protein will be known to one of ordinary skill in the art. For example, D10A/H840A of SpyCas9 as well as D908A and E993A of Cas12a have been employed. Similarly, in some cases a nucleic acid-binding effector polypeptide is a TnpB or IscB protein, and in some such cases the protein is a dead version (e.g., dTnpB, dIscB, and the like.) [00337] In some cases, the nucleic acid-binding effector polypeptide (e.g., CRISPR-Cas effector polypeptide such as Cas9) has nickase activity, e.g., in some cases the protein harbors a mutation in a catalytic domain such that the protein cleaves one strand of a double-stranded target nucleic acid. In some cases, a CRISPR-Cas effector protein (e.g., a nickase or ‘dead’ version) is fused to a heterologous protein, e.g., one that has transcription repressor activity (e.g., includes a transcription repression domain) and thereby reduces transcription (and therefore expression) of a target gene. In some cases, a nickase or dead version of a nucleic acid-binding effector polypeptide (e.g., CRISPR-Cas effector
polypeptide such as Cas9 or Cas12a) is not fused to a heterologous protein (e.g., one having a catalytic activity or transcription modulation activity). [00338] In some cases, a CRISPR-Cas effector protein (e.g., a nickase or ‘dead’ version) is fused to a heterologous protein that has transcription activating activity (e.g., includes a transcription activation domain) and thereby increases transcription (and therefore expression) of a target gene. [00339] It is well recognized that a nucleic acid-binding effector polypeptide can be used to modify target nucleic acids (e.g., DNA and/or RNA) in a variety of ways without creating a double strand break (DSB) in the target DNA. For example, in some cases a double stranded target DNA is nicked (one strand is cleaved), and in some cases (e.g., in some cases where the nucleic acid-binding effector polypeptide is devoid of nuclease activity, e.g., a CRISPR-Cas RNA-guided polypeptide may harbor mutations in the catalytic nuclease domains), the target nucleic acid is not cleaved at all. For example, in some cases a nucleic acid-binding effector polypeptide (e.g., CRISPR-Cas effector polypeptide such as Cas9, CasX, CasY, Cpf1) with or without nuclease activity (e.g., nickase activity or dead), is fused to a heterologous protein domain. The heterologous protein domain can provide an activity to the fusion protein such as (i) a DNA-modifying activity (e.g., nuclease activity, methyltransferase activity, demethylase activity, DNA repair activity, DNA damage activity, deamination activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity, transposase activity, recombinase activity, polymerase activity, ligase activity, helicase activity, photolyase activity or glycosylase activity), (ii) a transcription modulation activity (e.g., fusion to a transcriptional repressor or activator), or (iii) an activity that modifies a protein (e.g., a histone) that is associated with target DNA (e.g., methyltransferase activity, demethylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity or demyristoylation activity). As such, a gene editing system can be used in applications that modify a target nucleic acid in way that do not cleave the target nucleic acid, and can also be used in applications that modulate transcription from a target DNA. [00340] As noted above, in some embodiments, an EDV of the present disclosure comprises a fusion polypeptide comprising: (i) a nucleic acid-binding effector polypeptide (e.g., CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and (ii) one or more heterologous polypeptides. A heterologous polypeptide is also referred to herein as a “fusion partner.” In some cases, a nucleic acid-binding effector polypeptide (e.g., CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) is fused to one or more heterologous polypeptides that has/have an activity of interest (e.g., a catalytic activity of interest, subcellular localization activity, etc.) to form a fusion protein.
[00341] In some cases, the fusion partner can modulate transcription (e.g., inhibit transcription, increase transcription) of a target DNA. For example, in some cases the fusion partner is a protein (or a domain from a protein) that inhibits transcription (e.g., a transcriptional repressor, a protein that functions via recruitment of transcription inhibitor proteins, modification of target DNA such as methylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histones, and the like). In some cases, the fusion partner is a protein (or a domain from a protein) that increases transcription (e.g., a transcription activator, a protein that acts via recruitment of transcription activator proteins, modification of target DNA such as demethylation, recruitment of a DNA modifier, modulation of histones associated with target DNA, recruitment of a histone modifier such as those that modify acetylation and/or methylation of histones, and the like). In some cases, the fusion partner is a reverse transcriptase. In some cases, the fusion partner is a base editor. In some cases, the fusion partner is a deaminase. [00342] In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) includes a heterologous polypeptide that has enzymatic activity that modifies a target nucleic acid (e.g., nuclease activity, methyltransferase activity, demethylase activity, DNA repair activity, DNA damage activity, deamination activity, dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity, transposase activity, recombinase activity, polymerase activity, ligase activity, helicase activity, photolyase activity, or glycosylase activity). [00343] In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) includes a heterologous polypeptide that has enzymatic activity that modifies a polypeptide (e.g., a histone) associated with a target nucleic acid (e.g., methyltransferase activity, demethylase activity, acetyltransferase activity, deacetylase activity, kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity or demyristoylation activity). [00344] Examples of proteins (or fragments thereof) that can be used in increase transcription include but are not limited to: transcriptional activators such as VP16, VP64, VP48, VP160, p65 subdomain (e.g., from NFkB), and activation domain of EDLL and/or TAL activation domain (e.g., for activity in plants); histone lysine methyltransferases such as SET1A, SET1B, MLL1 to 5, ASH1, SYMD2, NSD1, and the like; histone lysine demethylases such as JHDM2a/b, UTX, JMJD3, and the like; histone acetyltransferases such as GCN5, PCAF, CBP, p300, TAF1, TIP60/PLIP, MOZ/MYST3, MORF/MYST4, SRC1, ACTR, P160, CLOCK, and the like; and DNA demethylases such as Ten-Eleven Translocation (TET) dioxygenase 1 (TET1CD), TET1, DME, DML1, DML2, ROS1, and the like.
[00345] Examples of proteins (or fragments thereof) that can be used in decrease transcription include but are not limited to: transcriptional repressors such as the Krüppel associated box (KRAB or SKD); KOX1 repression domain; the Mad mSIN3 interaction domain (SID); the ERF repressor domain (ERD), the SRDX repression domain (e.g., for repression in plants), and the like; histone lysine methyltransferases such as Pr-SET7/8, SUV4-20H1, RIZ1, and the like; histone lysine demethylases such as JMJD2A/JHDM3A, JMJD2B, JMJD2C/GASC1, JMJD2D, JARID1A/RBP2, JARID1B/PLU-1, JARID1C/SMCX, JARID1D/SMCY, and the like; histone lysine deacetylases such as HDAC1, HDAC2, HDAC3, HDAC8, HDAC4, HDAC5, HDAC7, HDAC9, SIRT1, SIRT2, HDAC11, and the like; DNA methylases such as HhaI DNA m5c-methyltransferase (M.HhaI), DNA methyltransferase 1 (DNMT1), DNA methyltransferase 3a (DNMT3a), DNA methyltransferase 3b (DNMT3b), METI, DRM3 (plants), ZMET2, CMT1, CMT2 (plants), and the like; and periphery recruitment elements such as Lamin A, Lamin B, and the like. [00346] In some cases, the fusion partner has enzymatic activity that modifies the target nucleic acid (e.g., ssRNA, dsRNA, ssDNA, dsDNA). Examples of enzymatic activity that can be provided by the fusion partner include but are not limited to: nuclease activity such as that provided by a restriction enzyme (e.g., FokI nuclease), methyltransferase activity such as that provided by a methyltransferase (e.g., HhaI DNA m5c-methyltransferase (M.HhaI), DNA methyltransferase 1 (DNMT1), DNA methyltransferase 3a (DNMT3a), DNA methyltransferase 3b (DNMT3b), METI, DRM3 (plants), ZMET2, CMT1, CMT2 (plants), and the like); demethylase activity such as that provided by a demethylase (e.g., Ten-Eleven Translocation (TET) dioxygenase 1 (TET1CD), TET1, DME, DML1, DML2, ROS1, and the like) , DNA repair activity, DNA damage activity, deamination activity such as that provided by a deaminase (e.g., a cytosine deaminase enzyme such as rat APOBEC1), dismutase activity, alkylation activity, depurination activity, oxidation activity, pyrimidine dimer forming activity, integrase activity such as that provided by an integrase and/or resolvase (e.g., Gin invertase such as the hyperactive mutant of the Gin invertase, GinH106Y; human immunodeficiency virus type 1 integrase (IN); Tn3 resolvase; and the like), transposase activity, recombinase activity such as that provided by a recombinase (e.g., catalytic domain of Gin recombinase), polymerase activity, ligase activity, helicase activity, photolyase activity, and glycosylase activity). [00347] In some cases, the fusion partner has enzymatic activity that modifies a protein associated with the target nucleic acid (e.g., ssRNA, dsRNA, ssDNA, dsDNA) (e.g., a histone, an RNA binding protein, a DNA binding protein, and the like). Examples of enzymatic activity (that modifies a protein associated with a target nucleic acid) that can be provided by the fusion partner include but are not limited to: methyltransferase activity such as that provided by a histone methyltransferase (HMT) (e.g., suppressor of variegation 3-9 homolog 1 (SUV39H1, also known as KMT1A), euchromatic histone lysine methyltransferase 2 (G9A, also known as KMT1C and EHMT2), SUV39H2, ESET/SETDB1, and the
like, SET1A, SET1B, MLL1 to 5, ASH1, SYMD2, NSD1, DOT1L, Pr-SET7/8, SUV4-20H1, EZH2, RIZ1), demethylase activity such as that provided by a histone demethylase (e.g., Lysine Demethylase 1A (KDM1A also known as LSD1), JHDM2a/b, JMJD2A/JHDM3A, JMJD2B, JMJD2C/GASC1, JMJD2D, JARID1A/RBP2, JARID1B/PLU-1, JARID1C/SMCX, JARID1D/SMCY, UTX, JMJD3, and the like), acetyltransferase activity such as that provided by a histone acetylase transferase (e.g., catalytic core/fragment of the human acetyltransferase p300, GCN5, PCAF, CBP, TAF1, TIP60/PLIP, MOZ/MYST3, MORF/MYST4, HBO1/MYST2, HMOF/MYST1, SRC1, ACTR, P160, CLOCK, and the like), deacetylase activity such as that provided by a histone deacetylase (e.g., HDAC1, HDAC2, HDAC3, HDAC8, HDAC4, HDAC5, HDAC7, HDAC9, SIRT1, SIRT2, HDAC11, and the like), kinase activity, phosphatase activity, ubiquitin ligase activity, deubiquitinating activity, adenylation activity, deadenylation activity, SUMOylating activity, deSUMOylating activity, ribosylation activity, deribosylation activity, myristoylation activity, and demyristoylation activity. [00348] Additional examples of a suitable fusion partners are dihydrofolate reductase (DHFR) destabilization domain (e.g., to generate a chemically controllable fusion polypeptide), and a chloroplast transit peptide. [00349] In some case, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises: a) a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas polypeptide such as Cas9 or Cas12a); and b) a chloroplast transit peptide. Thus, for example, a ribonucleoprotein (RNP) complex, comprising a CRISPR-Cas effector polypeptide of the present disclosure and a guide RNA, can be targeted to the chloroplast. In some cases, this targeting may be achieved by the presence of an N-terminal extension, called a chloroplast transit peptide (CTP) or plastid transit peptide. Chromosomal transgenes from bacterial sources must have a sequence encoding a CTP sequence fused to a sequence encoding an expressed polypeptide if the expressed polypeptide is to be compartmentalized in the plant plastid (e.g. chloroplast). Accordingly, localization of an exogenous polypeptide to a chloroplast is often 1 accomplished by means of operably linking a polynucleotide sequence encoding a CTP sequence to the 5' region of a polynucleotide encoding the exogenous polypeptide. The CTP is removed in a processing step during translocation into the plastid. Processing efficiency may, however, be affected by the amino acid sequence of the CTP and nearby sequences at the amino terminus of the peptide. Other options for targeting to the chloroplast which have been described are the maize cab-m7 signal sequence (U.S. Pat. No.7,022,896, WO 97/41228) a pea glutathione reductase signal sequence (WO 97/41228) and the CTP described in US2009029861. [00350] In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises: a) a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas polypeptide such as Cas9 or Cas12a) of the present disclosure; and b) an endosomal escape peptide. In some cases, an endosomal escape polypeptide comprises the amino acid sequence GLFXALLXLLXSLWXLLLXA
(SEQ ID NO:24), wherein each X is independently selected from lysine, histidine, and arginine. In some cases, an endosomal escape polypeptide comprises the amino acid sequence GLFHALLHLLHSLWHLLLHA (SEQ ID NO:25). [00351] Additional suitable heterologous polypeptides include, but are not limited to, a polypeptide that directly and/or indirectly provides for increased or decreased transcription and/or translation of a target nucleic acid (e.g., a transcription activator or a fragment thereof, a protein or fragment thereof that recruits a transcription activator, a small molecule/drug-responsive transcription and/or translation regulator, a translation-regulating protein, etc.). Non-limiting examples of heterologous polypeptides to accomplish increased or decreased transcription include transcription activator and transcription repressor domains. In some such cases, a CRISPR-Cas fusion polypeptide is targeted by the guide nucleic acid (guide RNA) to a specific location (i.e., sequence) in the target nucleic acid and exerts locus-specific regulation such as blocking RNA polymerase binding to a promoter (which selectively inhibits transcription activator function), and/or modifying the local chromatin status (e.g., when a fusion sequence is used that modifies the target nucleic acid or modifies a polypeptide associated with the target nucleic acid). In some cases, the changes are transient (e.g., transcription repression or activation). In some cases, the changes are inheritable (e.g., when epigenetic modifications are made to the target nucleic acid or to proteins associated with the target nucleic acid, e.g., nucleosomal histones). [00352] Non-limiting examples of heterologous polypeptides for use when targeting ssRNA target nucleic acids include (but are not limited to): splicing factors (e.g., RS domains); protein translation components (e.g., translation initiation, elongation, and/or release factors; e.g., eIF4G); RNA methylases; RNA editing enzymes (e.g., RNA deaminases, e.g., adenosine deaminase acting on RNA (ADAR), including A to I and/or C to U editing enzymes); helicases; RNA-binding proteins; and the like. It is understood that a heterologous polypeptide can include the entire protein or in some cases can include a fragment of the protein (e.g., a functional domain). [00353] The heterologous polypeptide can be any domain capable of interacting with ssRNA (which, for the purposes of this disclosure, includes intramolecular and/or intermolecular secondary structures, e.g., double-stranded RNA duplexes such as hairpins, stem-loops, etc.), whether transiently or irreversibly, directly or indirectly, including but not limited to an effector domain selected from the group comprising; Endonucleases (for example RNase III, the CRR22 DYW domain, Dicer, and PIN (PilT N-terminus) domains from proteins such as SMG5 and SMG6); proteins and protein domains responsible for stimulating RNA cleavage (for example CPSF, CstF, CFIm and CFIIm); Exonucleases (for example XRN-1 or Exonuclease T) ; Deadenylases (for example HNT3); proteins and protein domains responsible for nonsense mediated RNA decay (for example UPF1, UPF2, UPF3, UPF3b, RNP S1, Y14, DEK, REF2, and SRm160); proteins and protein domains responsible for stabilizing RNA (for example PABP); proteins and protein domains responsible for repressing translation (for example Ago2 and
Ago4); proteins and protein domains responsible for stimulating translation (for example Staufen); proteins and protein domains responsible for (e.g., capable of) modulating translation (e.g., translation factors such as initiation factors, elongation factors, release factors, etc., e.g., eIF4G); proteins and protein domains responsible for polyadenylation of RNA (for example PAP1, GLD-2, and Star- PAP) ; proteins and protein domains responsible for polyuridinylation of RNA (for example CI D1 and terminal uridylate transferase) ; proteins and protein domains responsible for RNA localization (for example from IMP1, ZBP1, She2p, She3p, and Bicaudal-D); proteins and protein domains responsible for nuclear retention of RNA (for example Rrp6); proteins and protein domains responsible for nuclear export of RNA (for example TAP, NXF1, THO, TREX, REF, and Aly) ; proteins and protein domains responsible for repression of RNA splicing (for example PTB, Sam68, and hnRNP A1) ; proteins and protein domains responsible for stimulation of RNA splicing (for example Serine/Arginine-rich (SR) domains) ; proteins and protein domains responsible for reducing the efficiency of transcription (for example FUS (TLS)); and proteins and protein domains responsible for stimulating transcription (for example CDK7 and HIV Tat). Alternatively, the effector domain may be selected from the group comprising Endonucleases; proteins and protein domains capable of stimulating RNA cleavage; Exonucleases; Deadenylases; proteins and protein domains having nonsense mediated RNA decay activity; proteins and protein domains capable of stabilizing RNA; proteins and protein domains capable of repressing translation; proteins and protein domains capable of stimulating translation; proteins and protein domains capable of modulating translation (e.g., translation factors such as initiation factors, elongation factors, release factors, etc., e.g., eIF4G); proteins and protein domains capable of polyadenylation of RNA; proteins and protein domains capable of polyuridinylation of RNA; proteins and protein domains having RNA localization activity; proteins and protein domains capable of nuclear retention of RNA; proteins and protein domains having RNA nuclear export activity; proteins and protein domains capable of repression of RNA splicing; proteins and protein domains capable of stimulation of RNA splicing; proteins and protein domains capable of reducing the efficiency of transcription ; and proteins and protein domains capable of stimulating transcription. Another suitable heterologous polypeptide is a PUF RNA-binding domain, which is described in more detail in WO2012068627, which is hereby incorporated by reference in its entirety. [00354] Some RNA splicing factors that can be used (in whole or as fragments thereof) as heterologous polypeptides for a fusion polypeptide of the present disclosure have modular organization, with separate sequence-specific RNA binding modules and splicing effector domains. For example, members of the Serine/ Arginine-rich (SR) protein family contain N-terminal RNA recognition motifs (RRMs) that bind to exonic splicing enhancers (ESEs) in pre-mRNAs and C-terminal RS domains that promote exon inclusion. As another example, the hnRNP protein hnRNP Al binds to exonic splicing silencers (ESSs) through its RRM domains and inhibits exon inclusion through a C-terminal Glycine-rich domain. Some
splicing factors can regulate alternative use of splice site (ss) by binding to regulatory sequences between the two alternative sites. For example, ASF/SF2 can recognize ESEs and promote the use of intron proximal sites, whereas hnRNP Al can bind to ESSs and shift splicing towards the use of intron distal sites. One application for such factors is to generate ESFs that modulate alternative splicing of endogenous genes, particularly disease associated genes. For example, Bcl-x pre-mRNA produces two splicing isoforms with two alternative 5' splice sites to encode proteins of opposite functions. The long splicing isoform Bcl-xL is a potent apoptosis inhibitor expressed in long-lived postmitotic cells and is up-regulated in many cancer cells, protecting cells against apoptotic signals. The short isoform Bcl-xS is a pro-apoptotic isoform and expressed at high levels in cells with a high turnover rate (e.g., developing lymphocytes). The ratio of the two Bcl-x splicing isoforms is regulated by multiple cώ-elements that are located in either the core exon region or the exon extension region (i.e., between the two alternative 5' splice sites). For more examples, see WO2010075303, which is hereby incorporated by reference in its entirety. [00355] Further suitable fusion partners include, but are not limited to, proteins (or fragments thereof) that are boundary elements (e.g., CTCF), proteins and fragments thereof that provide periphery recruitment (e.g., Lamin A, Lamin B, etc.), protein docking elements (e.g., FKBP/FRB, Pil1/Aby1, etc.). Nucleases [00356] In some cases, a nucleic acid-binding effector fusion polypeptide comprises: i) a nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) a heterologous polypeptide (a “fusion partner”), where the heterologous polypeptide is a nuclease. In some cases, a nucleic acid-binding effector fusion polypeptide comprises a nucleic acid binding effector polypeptide. Suitable nucleic acid binding effector polypeptides can be nucleases including, but not limited to, a homing nuclease polypeptide; a FokI polypeptide; a transcription activator-like effector nuclease (TALEN) polypeptide; a MegaTAL polypeptide; a meganuclease polypeptide; a zinc finger nuclease (ZFN); an ARCUS nuclease; and the like. The meganuclease can be engineered from an LADLIDADG homing endonuclease (LHE). A megaTAL polypeptide can comprise a TALE DNA binding domain and an engineered meganuclease. See, e.g., WO 2004/067736 (homing endonuclease); Urnov et al. (2005) Nature 435:646 (ZFN); Mussolino et al. (2011) Nucle. Acids Res.39:9283 (TALE nuclease); Boissel et al. (2013) Nucl. Acids Res.42:2591 (MegaTAL). Reverse transcriptases [00357] In some cases, a nucleic acid-binding effector fusion polypeptide comprises: i) a Nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) a heterologous polypeptide (a “fusion partner”), where the heterologous polypeptide is a reverse
transcriptase polypeptide. Reverse transcriptases are known in the art; see, e.g., Coté and Roth (2008) Virus Res.134:186. Suitable reverse transcriptases include, e.g., a murine leukemia virus reverse transcriptase; a Rous sarcoma virus reverse transcriptase; a human immunodeficiency virus type I reverse transcriptase; a Moloney murine leukemia virus reverse transcriptase; a transcription xenopolymerase (RTX); avian myeloblastosis virus reverse transcriptase (AMV-RT); a Eubacterium rectale maturase reverse transcriptase (Marathon®; and the like. The reverse transcriptase fusion partner can include one or more mutations. For example, in some cases, the reverse transcriptase is a M-MLV reverse transcriptase polypeptide that comprises one or more mutations selected from the group consisting of D200N, T306K, W313F, T330P and L603W. In some cases, the reverse transcriptase is a pentamutant of M-MLV RT (e.g., comprising the following substitutions: D200N/L603W/T330P/T306K/W313F) (where D200, L603, T330, T306, and W313 correspond to D199, L602, T329, T305, and W312 of the M-MLV RT amino acid sequence of SEQ ID NO:157). Base editors [00358] In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises: i) a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) one or more heterologous polypeptides (a “fusion partner”), where at least one of the one or more heterologous polypeptides is a deaminase. Suitable deaminases include, e.g., an adenosine deaminase; a cytidine deaminase (e.g., an activation-induced cytidine deaminase (AID)); APOBEC3G; and the like); and the like. [00359] A suitable adenosine deaminase is any enzyme that is capable of deaminating adenosine in DNA. In some cases, the deaminase is a TadA deaminase. [00360] In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MSEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMA LRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHP GMNHRVEITEGILADECAALLSDFFRMRRQEIKAQKKAQSSTD (SEQ ID NO:26). [00361] In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MRRAFITGVFFLSEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGR HDPTAHAEIMALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGA AGSLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIKAQKKAQSSTD (SEQ ID NO:27).
[00362] In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Staphylococcus aureus TadA amino acid sequence: MGSHMTNDIYFMTLAIEEAKKAAQLGEVPIGAIITKDDEVIARAHNLRETLQQPTAHAEHIAIER AAKVLGSWRLEGCTLYVTLEPCVMCAGTIVMSRIPRVVYGADDPKGGCSGSLMNLLQQSNFN HRAIVDKGVLKEACSTLLTTFFK NLRANKKSTN (SEQ ID NO:28). [00363] In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Bacillus subtilis TadA amino acid sequence: MTQDELYMKEAIKEAKKAEEKGEVPIGAVLVINGEIIARAHNLRETEQRSIAHAEMLVIDEACK ALGTWRLEGATLYVTLEPCPMCAGAVVLSRVEKVVFGAFDPKGGCSGTLMNLLQEERFNHQA EVVSGVLEEECGGMLSAFFRELRKKKKAARKNLSE (SEQ ID NO:29). [00364] In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Salmonella typhimurium TadA: MPPAFITGVTSLSDVELDHEYWMRHALTLAKRAWDEREVPVGAVLVHNHRVIGEGWNRPIGR HDPTAHAEIMALRQGGLVLQNYRLLDTTLYVTLEPCVMCAGAMVHSRIGRVVFGARDAKTGA AGSLIDVLHHPGMNHRVEIIEGVLRDECATLLSDFFRMRRQEIKALKKADRAEGAGPAV (SEQ ID NO:30). [00365] In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Shewanella putrefaciens TadA amino acid sequence: MDEYWMQVAMQMAEKAEAAGEVPVGAVLVKDGQQIATGYNLSISQHDPTAHAEILCLRSAG KKLENYRLLDATLYITLEPCAMCAGAMVHSRIARVVYGARDEKTGAAGTVVNLLQHPAFNHQ VEVTSGVLAEACSAQLSRFFKRRRDEKKALKLAQRAQQGIE (SEQ ID NO:31). [00366] In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Haemophilus influenzae F3031 TadA amino acid sequence: MDAAKVRSEFDEKMMRYALELADKAEALGEIPVGAVLVDDARNIIGEGWNLSIVQSDPTAHAE IIALRNGAKNIQNYRLLNSTLYVTLEPCTMCAGAILHSRIKRLVFGASDYKTGAIGSRFHFFDDY KMNHTLEITSGVLAEECSQKLS TFFQKRREEKKIEKALLKSLSDK (SEQ ID NO:32). [00367] In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Caulobacter crescentus TadA amino acid sequence: MRTDESEDQDHRMMRLALDAARAAAEAGETPVGAVILDPSTGEVIATAGNGPIAAHDPTAHAE
IAAMRAAAAKLGNYRLTDLTLVVTLEPCAMCAGAISHARIGRVVFGADDPKGGAVVHGPKFFA QPTCHWRPEVTGGVLADESADLLRGFFRARRKAKI (SEQ ID NO:33). [00368] In some cases, a suitable adenosine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following Geobacter sulfurreducens TadA amino acid sequence: MSSLKKTPIRDDAYWMGKAIREAAKAAARDEVPIGAVIVRDGAVIGRGHNLREGSNDPSAHAE MIAIRQAARRSANWRLTGATLYVTLEPCLMCMGAIILARLERVVFGCYDPKGGAAGSLYDLSA DPRLNHQVRLSPGVCQEECGTMLSDFFRDLRRRKKAKATPALFIDERKVPPEP (SEQ ID NO:34). [00369] Cytidine deaminases suitable for inclusion in a nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas effector fusion polypeptide) of the present disclosure include any enzyme that is capable of deaminating cytidine in DNA. [00370] In some cases, the cytidine deaminase is a deaminase from the apolipoprotein B mRNA-editing complex (APOBEC) family of deaminases. In some cases, the APOBEC family deaminase is selected from the group consisting of APOBEC1 deaminase, APOBEC2 deaminase, APOBEC3A deaminase, APOBEC3B deaminase, APOBEC3C deaminase, APOBEC3D deaminase, APOBEC3F deaminase, APOBEC3G deaminase, and APOBEC3H deaminase. In some cases, the cytidine deaminase is an activation induced deaminase (AID). [00371] In some cases, a suitable cytidine deaminase comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: [00372] MDSLLMNRRKFLYQFKNVRWAKGRRETYLCYVVKRRDSATSFSLDFGYLRNKNGCHV ELLFLRYISDWDLDPGRCYRVTWFTSWSPCYDCARHVADFLRGNPNLSLRIFTARLYFCEDRKA EPEGLRRLHRAGVQIAIMTFKDYFYCWNTFVENHERTFKAWEGLHENSVRLSRQLRRILLPLYE VDDLRDAFRTLGL (SEQ ID NO:35) [00373] In some cases, a suitable cytidine deaminase is an AID and comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MDSLLMNRRK FLYQFKNVRW AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK AEPEGLRRLH RAGVQIAIMT FKENHERTFK AWEGLHENSV RLSRQLRRIL LPLYEVDDLR DAFRTLGL (SEQ ID NO:36). [00374] In some cases, a suitable cytidine deaminase is an AID and comprises an amino acid sequence having at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: MDSLLMNRRK FLYQFKNVRW AKGRRETYLC YVVKRRDSAT SFSLDFGYLR NKNGCHVELL FLRYISDWDL DPGRCYRVTW FTSWSPCYDC ARHVADFLRG NPNLSLRIFT ARLYFCEDRK AEPEGLRRLH RAGVQIAIMT
FKDYFYCWNT FVENHERTFK AWEGLHENSV RLSRQLRRIL LPLYEVDDLR DAFRTLGL (SEQ ID NO:35). Transcription factors [00375] In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises: i) a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) a heterologous polypeptide (a “fusion partner”), where the heterologous polypeptide is a transcription factor. A transcription factor can include: i) a DNA binding domain; and ii) a transcription activator. A transcription factor can include: i) a DNA binding domain; and ii) a transcription repressor. Suitable transcription factors include polypeptides that include a transcription activator or a transcription repressor domain (e.g., the Kruppel associated box (KRAB or SKD); the Mad mSIN3 interaction domain (SID); the ERF repressor domain (ERD), etc.); zinc-finger-based artificial transcription factors (see, e.g., Sera (2009) Adv. Drug Deliv.61:513); TALE- based artificial transcription factors (see, e.g., Liu et al. (2013) Nat. Rev. Genetics 14:781); and the like. In some cases, the transcription factor comprises a VP64 polypeptide (transcriptional activation). In some cases, the transcription factor comprises a Krüppel-associated box (KRAB) polypeptide (transcriptional repression). In some cases, the transcription factor comprises a Mad mSIN3 interaction domain (SID) polypeptide (transcriptional repression). In some cases, the transcription factor comprises an ERF repressor domain (ERD) polypeptide (transcriptional repression). For example, in some cases, the transcription factor is a transcriptional activator, where the transcriptional activator is GAL4-VP16. Recombinases [00376] In some cases, a fusion polypeptide comprises: i) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) a heterologous polypeptide (a “fusion partner”), where the heterologous polypeptide is a recombinase. Suitable recombinases include, e.g., a Cre recombinase; a Hin recombinase; a Tre recombinase; a FLP recombinase; and the like. NLS [00377] In some cases, a nucleic acid-binding effector fusion polypeptide comprises: i) a nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and ii) a heterologous polypeptide (a “fusion partner”), where the heterologous polypeptide provides for subcellular localization, i.e., the heterologous polypeptide contains a subcellular localization sequence (e.g., a nuclear localization signal (NLS) for targeting to the nucleus, a sequence to keep the fusion
protein out of the nucleus, e.g., a nuclear export sequence (NES), a sequence to keep the fusion protein retained in the cytoplasm, a mitochondrial localization signal for targeting to the mitochondria, a chloroplast localization signal for targeting to a chloroplast, an endoplasmic reticulum (ER) retention signal, and the like). In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR- Cas fusion polypeptide) does not include an NLS (which can be advantageous, e.g., when the target nucleic acid is an RNA that is present in the cytosol). In some cases, the heterologous polypeptide can provide a tag (i.e., the heterologous polypeptide is a detectable label) for ease of tracking and/or purification (e.g., a fluorescent protein, e.g., green fluorescent protein (GFP), yellow fluorescent protein (YFP), red fluorescent protein (RFP), cyan fluorescent protein (CFP), mCherry, tdTomato, and the like; a histidine tag, e.g., a 6XHis tag; a hemagglutinin (HA) tag; a FLAG tag; a Myc tag; and the like). [00378] In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises: a) a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and b) one or more nuclear localization signals (NLSs) (e.g., in some cases 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs). Thus, in some cases, a fusion polypeptide of the present disclosure includes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs). In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus and/or the C-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more) are positioned at or near (e.g., within 50 amino acids of) the C-terminus. In some cases, one or more NLSs (3 or more, 4 or more, , 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, or 10 or more) are positioned at or near (e.g., within 50 amino acids of) both the N-terminus and the C-terminus. In some cases, an NLS is positioned at the N-terminus and an NLS is positioned at the C-terminus. [00379] In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises: a) a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and b) from 1 to 10 NLSs (e.g., 1-9, 1-8, 1-7, 1-6, 1-5, 2-10, 2-9, 2-8, 2-7, 2-6, 2-5, 4-10, 4-9, 4-8, 4-7, 5-10, 5-9, or 5-8 NLSs). In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises: a) a Nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a); and b) from 2 to 5 NLSs (e.g., 2-4 NLSs, or 2-3 NLSs). In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises about 4 NLSs. In some cases, a Nucleic
acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) comprises about 7 NLSs. [00380] Non-limiting 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:1); the NLS from nucleoplasmin (e.g., the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ ID NO:2)); the c-myc NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO:3) or RQRRNELKRSP (SEQ ID NO:4); the hRNPA1 M9 NLS having the sequence NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY (SEQ ID NO:5); the sequence RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV (SEQ ID NO:6) of the IBB domain from importin-alpha; the sequences VSRKRPRP (SEQ ID NO:7) and PPKKARED (SEQ ID NO: 8) of the myoma T protein; the sequence PQPKKKPL (SEQ ID NO:9) of human p53; the sequence SALIKKKKKMAP (SEQ ID NO:10) of mouse c-abl IV; the sequences DRLRR (SEQ ID NO:11) and PKQKKRK (SEQ ID NO:16) of the influenza virus NS1; the sequence RKLKKKIKKL (SEQ ID NO:12) of the Hepatitis virus delta antigen; the sequence REKKKFLKRR (SEQ ID NO:13) of the mouse Mx1 protein; the sequence KRKGDEVDGVDEVAKKKSKK (SEQ ID NO:14) of the human poly(ADP- ribose) polymerase; and the sequence RKCLQAGMNLEARKTKK (SEQ ID NO:15) of the steroid hormone receptors (human) glucocorticoid. In general, NLS (or multiple NLSs) are of sufficient strength to drive accumulation of the Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) in a detectable amount in the nucleus of a eukaryotic cell. Detection of accumulation in the nucleus may be performed by any suitable technique. For example, a detectable marker may be fused to the Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) such that location within a cell may be visualized. 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. PTD [00381] In some cases, a Nucleic acid-binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) includes a "Protein Transduction Domain" or PTD (also known as a CPP – cell penetrating peptide), which refers to a polypeptide, polynucleotide, carbohydrate, or organic or inorganic compound that facilitates traversing a lipid bilayer, micelle, cell membrane, organelle membrane, or vesicle membrane. A PTD attached to another molecule, which can range from a small polar molecule to a large macromolecule and/or a nanoparticle, facilitates the molecule traversing a membrane, for example going from extracellular space to intracellular space, or cytosol to within an organelle. In some cases, a PTD is covalently linked to the amino terminus of a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-
Cas effector polypeptide such as Cas9 or Cas12a). In some cases, a PTD is covalently linked to the carboxyl terminus of a Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a). In some cases, the PTD is inserted internally in a Nucleic acid- binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a) (i.e., is not at the N- or C-terminus of the Nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide such as Cas9 or Cas12a)) at a suitable insertion site. In some cases, a Nucleic acid- binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide) includes: a) a nucleic acid- binding effector fusion polypeptide (e.g., a CRISPR-Cas fusion polypeptide); and b) one or more PTDs (e.g., two or more, three or more, four or more PTDs). In some cases, a PTD includes a nuclear localization signal (NLS) (e.g., in some cases 2 or more, 3 or more, 4 or more, or 5 or more NLSs). Thus, in some cases, a CRISPR-Cas fusion polypeptide includes one or more NLSs (e.g., 2 or more, 3 or more, 4 or more, or 5 or more NLSs). In some cases, a PTD is covalently linked to a nucleic acid (e.g., a CRISPR-Cas guide nucleic acid, a polynucleotide encoding a CRISPR-Cas guide nucleic acid, a polynucleotide encoding a fusion polypeptide, a donor polynucleotide, etc.). Examples of PTDs include but are not limited to a minimal undecapeptide protein transduction domain (corresponding to residues 47-57 of HIV-1 TAT comprising YGRKKRRQRRR; SEQ ID NO: 127); a polyarginine sequence comprising a number of arginines sufficient to direct entry into a cell (e.g., 3, 4, 5, 6, 7, 8, 9, 10, or 10-50 arginines); a VP22 domain (Zender et al. (2002) Cancer Gene Ther.9(6):489-96); a Drosophila Antennapedia protein transduction domain (Noguchi et al. (2003) Diabetes 52(7):1732-1737); a truncated human calcitonin peptide (Trehin et al. (2004) Pharm. Research 21:1248-1256); polylysine (Wender et al. (2000) Proc. Natl. Acad. Sci. USA 97:13003-13008); RRQRRTSKLMKR (SEQ ID NO: 128); Transportan GWTLNSAGYLLGKINLKALAALAKKIL (SEQ ID NO: 129); KALAWEAKLAKALAKALAKHLAKALAKALKCEA (SEQ ID NO: 130); and RQIKIWFQNRRMKWKK (SEQ ID NO: 131). Exemplary PTDs include but are not limited to, YGRKKRRQRRR (SEQ ID NO: 127), RKKRRQRRR (SEQ ID NO: 132); an arginine homopolymer of from 3 arginine residues to 50 arginine residues; Exemplary PTD domain amino acid sequences include, but are not limited to, any of the following: YGRKKRRQRRR (SEQ ID NO: 127); RKKRRQRR (SEQ ID NO: 133); YARAAARQARA (SEQ ID NO: 134); THRLPRRRRRR (SEQ ID NO: 135); and GGRRARRRRRR (SEQ ID NO: 136). In some cases, the PTD is an activatable CPP (ACPP) (Aguilera et al. (2009) Integr Biol (Camb) June; 1(5-6): 371-381). ACPPs comprise a polycationic CPP (e.g., Arg9 or “R9”) connected via a cleavable linker to a matching polyanion (e.g., Glu9 or “E9”), which reduces the net charge to nearly zero and thereby inhibits adhesion and uptake into cells. Upon cleavage of the linker, the polyanion is released, locally unmasking the polyarginine and its inherent adhesiveness, thus “activating” the ACPP to traverse the membrane.
Linkers (e.g., for fusion partners) [00382] In some cases, a CRISPR-Cas polypeptide can be fused to a fusion partner via a linker polypeptide (e.g., one or more linker polypeptides). The linker polypeptide may have any of a variety of amino acid sequences. Proteins can be joined by a spacer peptide, generally of a flexible nature, although other chemical linkages are not excluded. Suitable linkers include polypeptides of between 4 amino acids and 40 amino acids in length, or between 4 amino acids and 25 amino acids in length. These linkers can be produced by using synthetic, linker-encoding oligonucleotides to couple the proteins, or can be encoded by a nucleic acid sequence encoding the fusion protein. Peptide linkers with a degree of flexibility can be used. The linking peptides may have virtually any amino acid sequence, bearing in mind that the preferred linkers will have a sequence that results in a generally flexible peptide. The use of small amino acids, such as glycine and alanine, are of use in creating a flexible peptide. The creation of such sequences is routine to those of skill in the art. A variety of different linkers are commercially available and are considered suitable for use. [00383] Examples of linker polypeptides include glycine polymers (G)n where n is an integer of at least one; glycine-serine polymers (including, for example, (GS)n, (GSGGS)n (SEQ ID NO: 40), (GGSGGS)n (SEQ ID NO: 41), (GGGGS)n (SEQ ID NO:38), and (GGGS)n (SEQ ID NO: 42), where n is an integer of at least one; e.g., where n is an integer from 1 to 10); glycine-alanine polymers; and alanine-serine polymers. Exemplary linkers can comprise amino acid sequences including, but not limited to, GGSG (SEQ ID NO: 39), GGSGG (SEQ ID NO: 43), GSGSG (SEQ ID NO: 44), GSGGG (SEQ ID NO: 45), GGGSG (SEQ ID NO: 46), GSSSG (SEQ ID NO: 47), GGGGS (SEQ ID NO:38), GGGGSGGGGSGGGGS (SEQ ID NO194), and the like. The ordinarily skilled artisan will recognize that design of a peptide conjugated to any desired element can include linkers that are all or partially flexible, such that the linker can include a flexible linker as well as one or more portions that confer less flexible structure. Guide nucleic acid [00384] As noted above, in some cases an EDV of the present disclosure comprises a CRISPR-Cas effector polypeptide guide nucleic acid (e.g., RNA) or a nucleic acid comprising a nucleotide sequence encoding a CRISPR-Cas effector polypeptide guide RNA. [00385] A nucleic acid molecule that binds to a CRISPR-Cas effector polypeptide protein and targets the complex to a specific location within a target nucleic acid is referred to herein as a “CRISPR-Cas effector polypeptide guide RNA” or simply a “guide RNA.” [00386] A guide RNA (can be said to include two segments, a first segment (referred to herein as a “targeting segment”); and a second segment (referred to herein as a “protein-binding segment”). By “segment” it is meant a segment/section/region of a molecule, e.g., a contiguous stretch of nucleotides in
a nucleic acid molecule. A segment can also mean a region/section of a complex such that a segment may comprise regions of more than one molecule. The “targeting segment” is also referred to herein as a “variable region” of a guide RNA. The “protein-binding segment” is also referred to herein as a “constant region” of a guide RNA. In some cases, the guide RNA is a Cas9 guide RNA. [00387] The first segment (targeting segment) of a guide RNA includes a nucleotide sequence (a guide sequence) that is complementary to (and therefore hybridizes with) a specific sequence (a target site) within a target nucleic acid (e.g., a target DNA, e.g., ssDNA, dsDNA, or a target RNA), such as the complementary strand of a double stranded target DNA, etc. The protein-binding segment (or “protein- binding sequence”) interacts with (binds to) a CRISPR-Cas effector polypeptide. The protein-binding segment of a guide RNA includes two complementary stretches of nucleotides that hybridize to one another to form a double stranded RNA duplex (dsRNA duplex). Site-specific binding and/or cleavage of a target nucleic acid (e.g., genomic DNA) can occur at locations (e.g., target sequence of a target locus) determined by base-pairing complementarity between the guide RNA (the guide sequence of the guide RNA) and the target nucleic acid. [00388] A guide RNA and a CRISPR-Cas effector polypeptide form a complex (e.g., bind via non- covalent interactions). The guide RNA provides target specificity to the complex by including a targeting segment, which includes a guide sequence (a nucleotide sequence that is complementary to a sequence of a target nucleic acid). The CRISPR-Cas effector polypeptide of the complex provides the site-specific activity (e.g., cleavage activity or an activity provided by the CRISPR-Cas effector polypeptide when the CRISPR-Cas effector polypeptide is a CRISPR-Cas effector polypeptide fusion polypeptide, i.e., has a fusion partner). In other words, the CRISPR-Cas effector polypeptide is guided to a target nucleic acid sequence (e.g. a target sequence in a chromosomal nucleic acid, e.g., a chromosome; a target sequence in an extrachromosomal nucleic acid, e.g. an episomal nucleic acid, a minicircle, an ssRNA, an ssDNA, etc.; a target sequence in a mitochondrial nucleic acid; a target sequence in a chloroplast nucleic acid; a target sequence in a plasmid; a target sequence in a viral nucleic acid; etc.) by virtue of its association with the guide RNA. [00389] The “guide sequence” also referred to as the “targeting sequence” of a guide RNA can be modified so that the guide RNA can target a CRISPR-Cas effector polypeptide to any desired sequence of any desired target nucleic acid, with the exception that the protospacer adjacent motif (PAM) sequence can be taken into account. Thus, for example, a guide RNA can have a targeting segment with a sequence (a guide sequence) that has complementarity with (e.g., can hybridize to) a sequence in a nucleic acid in a eukaryotic cell, e.g., a viral nucleic acid, a eukaryotic nucleic acid (e.g., a eukaryotic chromosome, chromosomal sequence, a eukaryotic RNA, etc.), and the like. [00390] In some embodiments, a guide RNA includes two separate nucleic acid molecules: an “activator” and a “targeter” and is referred to herein as a “dual guide RNA”, a “double-molecule guide RNA”, or a
“two-molecule guide RNA” a “dual guide RNA”, or a “dgRNA.” In some embodiments, the activator and targeter are covalently linked to one another (e.g., via intervening nucleotides) and the guide RNA is referred to as a “single guide RNA”, a “Cas9 single guide RNA”, a “single-molecule Cas9 guide RNA,” or a “one-molecule Cas9 guide RNA”, or simply “sgRNA.” [00391] A guide RNA comprises a crRNA-like (“CRISPR RNA”/“targeter”/“crRNA”/“crRNA repeat”) molecule and a corresponding tracrRNA-like (“trans-acting CRISPR RNA”/“activator”/“tracrRNA”) molecule. A crRNA-like molecule (targeter) comprises both the targeting segment (single stranded) of the guide RNA and a stretch (“duplex-forming segment”) of nucleotides that forms one half of the dsRNA duplex of the protein-binding segment of the guide RNA. A corresponding tracrRNA-like molecule (activator / tracrRNA) comprises a stretch of nucleotides (duplex-forming segment) that forms the other half of the dsRNA duplex of the protein-binding segment of the guide nucleic acid. In other words, a stretch of nucleotides of a crRNA-like molecule are complementary to and hybridize with a stretch of nucleotides of a tracrRNA-like molecule to form the dsRNA duplex of the protein-binding domain of the guide RNA. As such, each targeter molecule can be said to have a corresponding activator molecule (which has a region that hybridizes with the targeter). The targeter molecule additionally provides the targeting segment. Thus, a targeter and an activator molecule (as a corresponding pair) hybridize to form a guide RNA. The exact sequence of a given crRNA or tracrRNA molecule is characteristic of the species in which the RNA molecules are found. A dual guide RNA can include any corresponding activator and targeter pair. [00392] The term “activator” or “activator RNA” is used herein to mean a tracrRNA-like molecule (tracrRNA: “trans-acting CRISPR RNA”) of a dual guide RNA (and therefore of a single guide RNA when the “activator” and the “targeter” are linked together by, e.g., intervening nucleotides). Thus, for example, a guide RNA (dgRNA or sgRNA) comprises an activator sequence (e.g., a tracrRNA sequence). A tracr molecule (a tracrRNA) is a naturally existing molecule that hybridizes with a CRISPR RNA molecule (a crRNA) to form a dual guide RNA. The term “activator” is used herein to encompass naturally existing tracrRNAs, but also to encompass tracrRNAs with modifications (e.g., truncations, sequence variations, base modifications, backbone modifications, linkage modifications, etc.) where the activator retains at least one function of a tracrRNA (e.g., contributes to the dsRNA duplex to which Cas9 protein binds). In some cases, the activator provides one or more stem loops that can interact with Cas9 protein. An activator can be referred to as having a tracr sequence (tracrRNA sequence) and in some cases is a tracrRNA, but the term “activator” is not limited to naturally existing tracrRNAs. [00393] The term “targeter” or “targeter RNA” is used herein to refer to a crRNA-like molecule (crRNA: “CRISPR RNA”) of a dual guide RNA (and therefore of a single guide RNA when the “activator” and the “targeter” are linked together, e.g., by intervening nucleotides). Thus, for example, a guide RNA (dgRNA or sgRNA) comprises a targeting segment (which includes nucleotides that hybridize with (are
complementary to) a target nucleic acid, and a duplex-forming segment (e.g., a duplex forming segment of a crRNA, which can also be referred to as a crRNA repeat). Because the sequence of a targeting segment (the segment that hybridizes with a target sequence of a target nucleic acid) of a targeter is modified by a user to hybridize with a desired target nucleic acid, the sequence of a targeter will often be a non-naturally occurring sequence. However, the duplex-forming segment of a targeter (described in more detail below), which hybridizes with the duplex-forming segment of an activator, can include a naturally existing sequence (e.g., can include the sequence of a duplex-forming segment of a naturally existing crRNA, which can also be referred to as a crRNA repeat). Thus, the term targeter is used herein to distinguish from naturally occurring crRNAs, despite the fact that part of a targeter (e.g., the duplex- forming segment) often includes a naturally occurring sequence from a crRNA. However, the term “targeter” encompasses naturally occurring crRNAs. [00394] A guide RNA can also be said to include 3 parts: (i) a targeting sequence (a nucleotide sequence that hybridizes with a sequence of the target nucleic acid); (ii) an activator sequence (as described above)(in some cases, referred to as a tracr sequence); and (iii) a sequence that hybridizes to at least a portion of the activator sequence to form a double stranded duplex. A targeter has (i) and (iii); while an activator has (ii). [00395] A guide RNA (e.g. a dual guide RNA or a single guide RNA) can be comprised of any corresponding activator and targeter pair. In some cases, the duplex forming segments can be swapped between the activator and the targeter. In other words, in some cases, the targeter includes a sequence of nucleotides from a duplex forming segment of a tracrRNA (which sequence would normally be part of an activator) while the activator includes a sequence of nucleotides from a duplex forming segment of a crRNA (which sequence would normally be part of a targeter). [00396] As noted above, a targeter comprises both the targeting segment (single stranded) of the guide RNA and a stretch (“duplex-forming segment”) of nucleotides that forms one half of the dsRNA duplex of the protein-binding segment of the guide RNA. A corresponding tracrRNA-like molecule (activator) comprises a stretch of nucleotides (a duplex-forming segment) that forms the other half of the dsRNA duplex of the protein-binding segment of the guide RNA. In other words, a stretch of nucleotides of the targeter is complementary to and hybridizes with a stretch of nucleotides of the activator to form the dsRNA duplex of the protein-binding segment of a guide RNA. As such, each targeter can be said to have a corresponding activator (which has a region that hybridizes with the targeter). The targeter molecule additionally provides the targeting segment. Thus, a targeter and an activator (as a corresponding pair) hybridize to form a guide RNA. The particular sequence of a given naturally existing crRNA or tracrRNA molecule is characteristic of the species in which the RNA molecules are found. Examples of suitable activator and targeter are well known in the art.
Knockouts [00397] In some cases, as noted above, a guide RNA present in an EDV of the present disclosure, or a guide RNA encoded by a guide RNA-encoded nucleic acid present in an EDV of the present disclosure, provides for deletion (“knockout”) of a target nucleic acid. [00398] For example, in some cases, an EDV of the present disclosure provides for: i) delivery of a therapeutic protein; and ii) knockout of a target nucleic acid. As one non-limiting example, an EDV of the present disclosure can both: i) provide for delivery of a therapeutic protein (such as a chimeric antigen receptor (CAR)); and ii) knock out an endogenous nucleic acid encoding a beta-2 microglobulin (β2M) polypeptide, where the guide RNA present in the EDV (or encoded by a nucleic acid present in the EDV) would comprise a nucleotide sequence targeting a β2M-encoding nucleic acid in a target cell. Such an EDV would be useful for generating T cells that express a CAR (“CAR-T cells”) that do not express endogenous major histocompatibility complex (MHC) class I antigens on their cell surface and thus could be useful for delivery of allogeneic CAR-T cells. [00399] As another example, in some cases, an EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding the guide RNA, where the guide RNA provides for knockout of the endogenous T-cell receptor alpha constant (TRAC) gene, such that a TRAC polypeptide is not produced in the cell. [00400] A TRAC polypeptide can comprise the following amino acid sequence: IQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVA WSNKSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVAGF NLLMTLRLWSS (SEQ ID NO:204). [00401] As another example, in some cases, an EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding the guide RNA, where the guide RNA provides for knockout of an endogenous gene encoding an immune checkpoint. Immune checkpoints include, e.g., PD-1, PD- L1, CTLA4, and TIGIT. Donor nucleic acid [00402] In some cases, an EDV of the present disclosure comprises a donor nucleic acid. By a “donor nucleic acid” or “donor sequence” or “donor polynucleotide” or “donor template” it is meant a nucleic acid sequence to be inserted at the site cleaved by a CRISPR-Cas effector protein (e.g., after dsDNA cleavage, after nicking a target DNA, after dual nicking a target DNA, and the like). The 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 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. Approximately 25, 50, 100, or 200 nucleotides, or more than 200 nucleotides, of sequence homology between a donor and a genomic sequence (or any integral value between 10 and 200 nucleotides, or more) can support homology- directed repair. Donor polynucleotides can be of any length, e.g.10 nucleotides or more, 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. [00403] The donor sequence is typically not identical to the genomic sequence that it replaces. Rather, the donor sequence may contain at least one or more single base changes, insertions, deletions, inversions or rearrangements with respect to the 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 embodiments, the donor sequence 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 the non- homologous sequence at the target region. Donor sequences may also comprise a vector backbone containing sequences that are not homologous to the DNA region of interest and that are not intended for insertion into the DNA region of interest. Generally, the homologous region(s) of a donor sequence will have at least 50% sequence identity to a genomic sequence with which recombination is desired. In certain embodiments, 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. [00404] The donor sequence may comprise certain sequence differences as compared to the genomic sequence, 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 sequence 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. [00405] In some cases, the donor sequence is provided to the cell as single-stranded DNA. In some cases, the donor sequence is provided to the cell as double-stranded DNA. It may be introduced into a cell in linear or circular form. If introduced in linear form, the ends of the donor sequence may be 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
the 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 internucleotide 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 sequence, additional lengths of sequence may be included outside of the regions of homology that can be degraded without impacting recombination. A donor sequence can be introduced into a cell as part of a vector molecule having additional sequences such as, for example, replication origins, promoters and genes encoding antibiotic resistance. Therapeutic proteins [00406] As noted above, in some cases, an EDV of the present disclosure comprises a nucleic acid comprising a nucleotide sequence encoding a therapeutic polypeptide. [00407] A therapeutic polypeptide encoded by a nucleic acid present in a EDV of the present disclosure can have a length of from about 250 amino acids to about 3000 amino acids. For example, in some cases, a therapeutic polypeptide encoded by a nucleic acid present in a EDV of the present disclosure has a length of from about 250 amino acids to about 500 amino acids, from about 500 amino acids to about 1000 amino acids, from about 500 amino acids to about 750 amino acids, from about 750 amino acids to about 1500 amino acids, from about 750 amino acids to about 1000 amino acids, from about 1000 amino acids to about 1250 amino acids, from about 1000 amino acids to about 1500 amino acids, from about 1250 amino acids to about 1500 amino acids, from about 1250 amino acids to about 1750 amino acids, from about 1500 amino acids to about 1750 amino acids, from about 1500 amino acids to about 2000 amino acids, from about 1500 amino acids to about 2500 amino acids, from about 2000 amino acids to about 2500 amino acids, from about 2000 amino acids to about 3000 amino acids, or from about 2500 amino acids to about 3000 amino acids. [00408] Suitable therapeutic proteins include, but are not limited to, a chimeric antigen receptor (CAR), a T cell receptor (TCR), a natural killer cell receptor (NKR), a synNotch polypeptide, an antibody, a Modular Extracellular Sensor Architecture (MESA) receptor, and the like. In some cases, a therapeutic protein is a functional version of a protein, e.g., a cystic fibrosis transmembrane conductance (CFTR) protein, a globin polypeptide (e.g., β-globin), and the like.
Antibodies [00409] In some cases, the therapeutic protein is an antibody. Suitable antibodies include, e.g., therapeutic antibodies. In some cases, the antibody is a single-chain Fv (scFv). In some cases, the antibody is a nanobody. [00410] Suitable antibodies include, e.g., Natalizumab (Tysabri®; Biogen Idec/Elan) targeting α4 subunit of α4β1 andα4β7 integrins (as used in the treatment of MS and Crohn's disease); Vedolizumab (MLN2; Millennium Pharmaceuticals/Takeda) targeting α4β7 integrin (as used in the treatment of UC and Crohn's disease); Belimumab (Benlysta; Human Genome Sciences/ GlaxoSmithKline) targeting BAFF (as used in the treatment of SLE); Atacicept (TACI–Ig; Merck/Serono) targeting BAFF and APRIL (as used in the treatment of SLE); Alefacept (Amevive®; Astellas) targeting CD2 (as used in the treatment of Plaque psoriasis, GVHD); Otelixizumab (TRX4; Tolerx/GlaxoSmithKline) targeting CD3 (as used in the treatment of T1D); Teplizumab (MGA031; MacroGenics/Eli Lilly) targeting CD3 (as used in the treatment of T1D); Rituximab (Rituxan®/Mabthera; Genentech/Roche/Biogen Idec) targeting CD20 (as used in the treatment of Non-Hodgkin's lymphoma, RA (in patients with inadequate responses to TNF blockade) and CLL); Ofatumumab (Arzerra®; Genmab/GlaxoSmithKline) targeting CD20 (as used in the treatment of CLL, RA); Ocrelizumab (2H7; Genentech/Roche/Biogen Idec) targeting CD20 (as used in the treatment of RA and SLE); Epratuzumab (hLL2; Immunomedics/UCB) targeting CD22 (as used in the treatment of SLE and non-Hodgkin's lymphoma); Alemtuzumab (Campath®/MabCampath; Genzyme/Bayer) targeting CD52 (as used in the treatment of CLL, MS); Abatacept (Orencia®; Bristol- Myers Squibb) targeting CD80 and CD86 (as used in the treatment of RA and JIA, UC and Crohn's disease, SLE); Eculizumab (Soliris®; Alexion pharmaceuticals) targeting C5 complement protein (as used in the treatment of Paroxysmal nocturnal haemoglobinuria); Omalizumab (Xolair®; Genentech/Roche/Novartis) targeting IgE (as used in the treatment of Moderate to severe persistent allergic asthma); Canakinumab (Ilaris®; Novartis) targeting IL-1β (as used in the treatment of Cryopyrin-associated periodic syndromes, Systemic JIA, neonatal-onset multisystem inflammatory disease and acute gout); Mepolizumab (Bosatria; GlaxoSmithKline) targeting IL-5 (as used in the treatment of Hyper-eosinophilic syndrome); Reslizumab (SCH55700; Ception Therapeutics) targeting IL-5 (as used in the treatment of Eosinophilic oesophagitis); Tocilizumab (Actemra®/RoActemra®; Chugai/Roche) targeting IL-6R (as used in the treatment of RA, JIA); Ustekinumab (Stelara®; Centocor) targeting IL-12 and IL-23 (as used in the treatment of Plaque psoriasis, Psoriatic arthritis, Crohn's disease); Briakinumab (ABT-874; Abbott) targeting IL-12 and IL-23 (as used in the treatment of Psoriasis and plaque psoriasis); Etanercept (Enbrel®; Amgen/Pfizer) targeting TNF (as used in the treatment of RA, JIA, psoriatic arthritis, AS and plaque psoriasis); Infliximab (Remicade®; Centocor/Merck) targeting TNF (as used in the treatment of Crohn's disease, RA, psoriatic arthritis, UC,
AS and plaque psoriasis); Adalimumab (Humira®/Trudexa®; Abbott) targeting TNF (as used in the treatment of RA, JIA, psoriatic arthritis, Crohn's disease, AS and plaque psoriasis); Certolizumab pegol (Cimzia®; UCB) targeting TNF (as used in the treatment of Crohn's disease and RA); Golimumab (Simponi®; Centocor) targeting TNF (as used in the treatment of RA, psoriatic arthritis and AS); and the like. In some cases, the antibody whose production is induced by the intracellular domain of a synNotch polypeptide of the present disclosure is a therapeutic antibody for the treatment of cancer. Such antibodies include, e.g., Ipilimumab targeting CTLA-4 (as used in the treatment of Melanoma, Prostate Cancer, RCC); Tremelimumab targeting CTLA-4 (as used in the treatment of CRC, Gastric, Melanoma, NSCLC); Nivolumab targeting PD-1 (as used in the treatment of Melanoma, NSCLC, RCC); MK-3475 targeting PD-1 (as used in the treatment of Melanoma); Pidilizumab targeting PD-1 (as used in the treatment of Hematologic Malignancies); BMS-936559 targeting PD-L1 (as used in the treatment of Melanoma, NSCLC, Ovarian, RCC); MEDI4736 targeting PD-L1; MPDL33280A targeting PD-L1 (as used in the treatment of Melanoma); Rituximab targeting CD20 (as used in the treatment of Non- Hodgkin's lymphoma); Ibritumomab tiuxetan and tositumomab (as used in the treatment of Lymphoma); Brentuximab vedotin targeting CD30 (as used in the treatment of Hodgkin's lymphoma); Gemtuzumab ozogamicin targeting CD33 (as used in the treatment of Acute myelogenous leukaemia); Alemtuzumab targeting CD52 (as used in the treatment of Chronic lymphocytic leukaemia); IGN101 and adecatumumab targeting EpCAM (as used in the treatment of Epithelial tumors (breast, colon and lung)); Labetuzumab targeting CEA (as used in the treatment of Breast, colon and lung tumors); huA33 targeting gpA33 (as used in the treatment of Colorectal carcinoma); Pemtumomab and oregovomab targeting Mucins (as used in the treatment of Breast, colon, lung and ovarian tumors); CC49 (minretumomab) targeting TAG-72 (as used in the treatment of Breast, colon and lung tumors); cG250 targeting CAIX (as used in the treatment of Renal cell carcinoma); J591 targeting PSMA (as used in the treatment of Prostate carcinoma); MOv18 and MORAb-003 (farletuzumab) targeting Folate-binding protein (as used in the treatment of Ovarian tumors); 3F8, ch14.18 and KW-2871 targeting Gangliosides (such as GD2, GD3 and GM2) (as used in the treatment of Neuroectodermal tumors and some epithelial tumors); hu3S193 and IgN311 targeting Le y (as used in the treatment of Breast, colon, lung and prostate tumors); Bevacizumab targeting VEGF (as used in the treatment of Tumor vasculature); IM-2C6 and CDP791 targeting VEGFR (as used in the treatment of Epithelium-derived solid tumors); Etaracizumab targeting Integrin alpha(v)beta(3) (as used in the treatment of Tumor vasculature); Volociximab targeting Integrin alpha(v)beta(1) (as used in the treatment of Tumor vasculature); Cetuximab, panitumumab, nimotuzumab and 806 targeting EGFR (as used in the treatment of Glioma, lung, breast, colon, and head and neck tumors); Trastuzumab and pertuzumab targeting ERBB2 (as used in the treatment of Breast, colon, lung, ovarian and prostate tumors); MM-121 targeting ERBB3 (as used in the treatment of Breast, colon, lung, ovarian and prostate, tumors); AMG 102, METMAB and SCH 900105 targeting MET (as
used in the treatment of Breast, ovary and lung tumors); AVE1642, IMC-A12, MK-0646, R1507 and CP 751871 targeting IGF1R (as used in the treatment of Glioma, lung, breast, head and neck, prostate and thyroid cancer); KB004 and IIIA4 targeting EPHA3 (as used in the treatment of Lung, kidney and colon tumors, melanoma, glioma and haematological malignancies); Mapatumumab (HGS-ETR1) targeting TRAILR1 (as used in the treatment of Colon, lung and pancreas tumors and haematological malignancies); HGS-ETR2 and CS-1008 targeting TRAILR2; Denosumab targeting RANKL (as used in the treatment of Prostate cancer and bone metastases); Sibrotuzumab and F19 targeting FAP (as used in the treatment of Colon, breast, lung, pancreas, and head and neck tumors); 81C6 targeting Tenascin (as used in the treatment of Glioma, breast and prostate tumors); Blinatumomab (Blincyto; Amgen) targeting CD3 (as used in the treatment of ALL); pembrolizumab targeting PD-1 as used in cancer immunotherapy; 9E10 antibody targeting c-Myc; and the like. [00411] Suitable antibodies include, e.g., Abagovomab, Abciximab, Abituzumab, Abrilumab, Actoxumab, Aducanumab, Afelimomab, Afutuzumab, Alacizumab pegol, ALD518, Alirocumab, Altumomab pentetate, Amatuximab, Anatumomab mafenatox, Anetumab ravtansine, Anifrolumab, Anrukinzumab, Apolizumab, Arcitumomab, Ascrinvacumab, Aselizumab, Atezolizumab, Atinumab, Atlizumab/ tocilizumab, Atorolimumab, Bapineuzumab, Basiliximab, Bavituximab, Bectumomab, Begelomab, Benralizumab, Bertilimumab, Besilesomab, Bevacizumab/Ranibizumab, Bezlotoxumab, Biciromab, Bimagrumab, Bimekizumab, Bivatuzumab mertansine, Blosozumab, Bococizumab, Brentuximabvedotin, Brodalumab, Brolucizumab, Brontictuzumab, Cantuzumab mertansine, Cantuzumab ravtansine, Caplacizumab, Capromab pendetide, Carlumab, Catumaxomab, cBR96- doxorubicin immunoconjugate, Cedelizumab, Ch.14.18, Citatuzumab bogatox, Cixutumumab, Clazakizumab, Clenoliximab, Clivatuzumab tetraxetan, Codrituzumab, Coltuximab ravtansine, Conatumumab, Concizumab, CR6261, Crenezumab, Dacetuzumab, Daclizumab, Dalotuzumab, Dapirolizumab pegol, Daratumumab, Dectrekumab, Demcizumab, Denintuzumab mafodotin, Derlotuximab biotin, Detumomab, Dinutuximab, Diridavumab, Dorlimomab aritox, Drozitumab, Duligotumab, Dupilumab, Durvalumab, Dusigitumab, Ecromeximab, Edobacomab, Edrecolomab, Efalizumab, Efungumab, Eldelumab, Elgemtumab, Elotuzumab, Elsilimomab, Emactuzumab, Emibetuzumab, Enavatuzumab, Enfortumab vedotin, Enlimomab pegol, Enoblituzumab, Enokizumab, Enoticumab, Ensituximab, Epitumomab cituxetan, Erlizumab, Ertumaxomab, Etrolizumab, Evinacumab, Evolocumab, Exbivirumab, Fanolesomab, Faralimomab, Farletuzumab, Fasinumab, FBTA05, Felvizumab, Fezakinumab, Ficlatuzumab, Figitumumab, Firivumab, Flanvotumab, Fletikumab, Fontolizumab, Foralumab, Foravirumab, Fresolimumab, Fulranumab, Futuximab, Galiximab, Ganitumab, Gantenerumab, Gavilimomab, Gevokizumab, Girentuximab, Glembatumumab vedotin, Gomiliximab, Guselkumab, Ibalizumab, Ibalizumab , Icrucumab, Idarucizumab, Igovomab, IMAB362, Imalumab, Imciromab, Imgatuzumab, Inclacumab, Indatuximab ravtansine, Indusatumab vedotin,
Inolimomab, Inotuzumab ozogamicin, Intetumumab, Iratumumab, Isatuximab, Itolizumab, Ixekizumab, Keliximab, Lambrolizumab, Lampalizumab, Lebrikizumab, Lemalesomab, Lenzilumab, Lerdelimumab, Lexatumumab, Libivirumab, Lifastuzumab vedotin, Ligelizumab, Lilotomab satetraxetan, Lintuzumab, Lirilumab, Lodelcizumab, Lokivetmab, Lorvotuzumab mertansine, Lucatumumab, Lulizumab pegol, Lumiliximab, Lumretuzumab, Margetuximab, Maslimomab, Matuzumab, Mavrilimumab, Metelimumab, Milatuzumab, Minretumomab, Mirvetuximab soravtansine, Mitumomab, Mogamulizumab, Morolimumab, Morolimumab immune, Motavizumab, Moxetumomab pasudotox, Muromonab-CD3, Nacolomab tafenatox, Namilumab, Naptumomab estafenatox, Narnatumab, Nebacumab, Necitumumab, Nemolizumab, Nerelimomab, Nesvacumab, Nofetumomab merpentan, Obiltoxaximab, Obinutuzumab, Ocaratuzumab, Odulimomab, Olaratumab, Olokizumab, Onartuzumab, Ontuxizumab, Opicinumab, Oportuzumab monatox, Orticumab, Otlertuzumab, Oxelumab, Ozanezumab, Ozoralizumab, Pagibaximab, Palivizumab, Pankomab, Panobacumab, Parsatuzumab, Pascolizumab, Pasotuxizumab, Pateclizumab, Patritumab, Perakizumab, Pexelizumab, Pinatuzumab vedotin, Pintumomab, Placulumab, Polatuzumab vedotin, Ponezumab, Priliximab, Pritoxaximab, Pritumumab, PRO 140, Quilizumab, Racotumomab, Radretumab, Rafivirumab, Ralpancizumab, Ramucirumab, Ranibizumab, Raxibacumab, Refanezumab, Regavirumab, Rilotumumab, Rinucumab, Robatumumab, Roledumab, Romosozumab, Rontalizumab, Rovelizumab, Ruplizumab, Sacituzumab govitecan, Samalizumab, Sarilumab, Satumomab pendetide, Secukinumab, Seribantumab, Setoxaximab, Sevirumab, SGN-CD19A, SGN- CD33A, Sifalimumab, Siltuximab, Simtuzumab, Siplizumab, Sirukumab, Sofituzumab vedotin, Solanezumab, Solitomab, Sonepcizumab, Sontuzumab, Stamulumab, Sulesomab, Suvizumab, Tabalumab, Tacatuzumab tetraxetan, Tadocizumab, Talizumab, Tanezumab, Taplitumomab paptox, Tarextumab, Tefibazumab, Telimomab aritox, Tenatumomab, Teneliximab, Teprotumumab, Tesidolumab, Tetulomab, TGN1412, Ticilimumab/tremelimumab, Tigatuzumab, Tildrakizumab, TNX- 650, Toralizumab, Tosatoxumab, Tovetumab, Tralokinumab, TRBS07, Tregalizumab, Trevogrumab, Tucotuzumab celmoleukin, Tuvirumab, Ublituximab, Ulocuplumab, Urelumab, Urtoxazumab, Vandortuzumab vedotin, Vantictumab, Vanucizumab, Vapaliximab, Varlilumab, Vatelizumab, Veltuzumab, Vepalimomab, Vesencumab, Visilizumab, Vorsetuzumab mafodotin, Votumumab, Zalutumumab, Zanolimumab, Zatuximab, Ziralimumab, Zolimomab aritox, and the like. Chimeric antigen receptors (CARs) [00412] A CAR generally comprises: a) an extracellular domain comprising an antigen-binding domain (antigen-binding polypeptide); b) a transmembrane region; and c) a cytoplasmic domain comprising an intracellular signaling domain (intracellular signaling polypeptide). In some cases, a CAR comprises: a) an extracellular domain comprising the antigen-binding domain; b) a transmembrane region; and c) a cytoplasmic domain comprising: i) one or more co-stimulatory polypeptides; and ii) an intracellular
signaling domain. In some cases, a CAR comprises hinge region between the extracellular antigen- binding domain and the transmembrane domain. Thus, in some cases, a CAR comprises: a) an extracellular domain comprising the antigen-binding domain; b) a hinge region; c) a transmembrane region; and d) a cytoplasmic domain comprising an intracellular signaling domain. In some cases, a CAR comprises: a) an extracellular domain comprising the antigen-binding domain; b) a hinge region; c) a transmembrane region; and d) a cytoplasmic domain comprising: i) one or more co-stimulatory polypeptides; and ii) an intracellular signaling domain. [00413] Exemplary CAR structures are known in the art (See e.g., WO 2009/091826; US 20130287748; WO 2015/142675; WO 2014/055657; WO 2015/090229; and U.S. Patent No.9,587,020. In some cases, a CAR is a single polypeptide chain. In some cases, a CAR comprises two polypeptide chains. Generally, any CAR structure known to those skilled in the art can be used. [00414] CARs specific for a variety of tumor antigens are known in the art; for example CD171-specific CARs (Park et al., Mol Ther (2007) 15(4):825-833), EGFRvIII-specific CARs (Morgan et al., Hum Gene Ther (2012) 23(10):1043-1053), EGF-R-specific CARs (Kobold et al., J. Natl Cancer Inst (2014) 107(1):364), carbonic anhydrase IX-specific CARs (Lamers et al., Biochem Soc Trans (2016) 44(3):951- 959), folate receptor-α (FR-α)-specific CARs (Kershaw et al., Clin Cancer Res (2006) 12(20):6106- 6015), HER2-specific CARs (Ahmed et al., J Clin Oncol (2015) 33(15)1688-1696; Nakazawa et al., Mol Ther (2011) 19(12):2133-2143; Ahmed et al., Mol Ther (2009) 17(10):1779-1787; Luo et al., Cell Res (2016) 26(7):850-853; Morgan et al., Mol Ther (2010) 18(4):843-851; Grada et al., Mol Ther Nucleic Acids (2013) 9(2):32), CEA-specific CARs (Katz et al., Clin Cancer Res (2015) 21(14):3149-3159), IL- 13Rα2-specific CARs (Brown et al., Clin Cancer Res (2015) 21(18):4062-4072), ganglioside GD2- specific CARs (Louis et al., Blood (2011) 118(23):6050-6056; Caruana et al., Nat Med (2015) 21(5):524-529; Yu et al. (2018) J. Hematol. Oncol.11:1), ErbB2-specific CARs (Wilkie et al., J Clin Immunol (2012) 32(5):1059-1070), VEGF-R-specific CARs (Chinnasamy et al., Cancer Res (2016) 22(2):436-447), FAP-specific CARs (Wang et al., Cancer Immunol Res (2014) 2(2): 154-166), mesothelin (MSLN)-specific CARs (Moon et al, Clin Cancer Res (2011) 17(14):4719-30), NKG2D- specific CARs (VanSeggelen et al., Mol Ther (2015) 23(10):1600-1610), CD19-specific CARs (Axicabtagene ciloleucel (Yescarta™) and Tisagenlecleucel (Kymriah™). See also, Li et al., J Hematol and Oncol (2018) 11:22, reviewing clinical trials of tumor-specific CARs; Heyman and Yan (2019) Cancers 11:pii:E191; Baybutt et al. (2019) Clin. Pharmacol. Ther.105:71. [00415] As noted above, a CAR comprises an extracellular domain comprising an antigen-binding domain. The antigen-binding domain present in a CAR can be any antigen-binding polypeptide, a wide variety of which are known in the art. In some instances, the antigen-binding domain is a single chain Fv (scFv). Other antibody-based recognition domains (cAb VHH (camelid antibody variable domains) and humanized versions, IgNAR VH (shark antibody variable domains) and humanized versions, sdAb VH
(single domain antibody variable domains) and “camelized” antibody variable domains are suitable. In some cases, the antigen-binding domain is a nanobody. [00416] In some cases, the antigen bound by the antigen-binding domain of a CAR is selected from: a MUC1 polypeptide, an LMP2 polypeptide, an epidermal growth factor receptor (EGFR) vIII polypeptide, a HER-2/neu polypeptide, a melanoma antigen family A, 3 (MAGE A3) polypeptide, a p53 polypeptide, a mutant p53 polypeptide, an NY-ESO-1 polypeptide, a folate hydrolase (prostate-specific membrane antigen; PSMA) polypeptide, a carcinoembryonic antigen (CEA) polypeptide, a melanoma antigen recognized by T-cells (melanA/MART1) polypeptide, a Ras polypeptide, a gp100 polypeptide, a proteinase3 (PR1) polypeptide, a bcr-abl polypeptide, a tyrosinase polypeptide, a survivin polypeptide, a prostate specific antigen (PSA) polypeptide, an hTERT polypeptide, a sarcoma translocation breakpoints polypeptide, a synovial sarcoma X (SSX) breakpoint polypeptide, an EphA2 polypeptide, an acid phosphatase, prostate (PAP) polypeptide, a melanoma inhibitor of apoptosis (ML-IAP) polypeptide, an epithelial cell adhesion molecule (EpCAM) polypeptide, an ERG (TMPRSS2 ETS fusion) polypeptide, a NA17 polypeptide, a paired-box-3 (PAX3) polypeptide, an anaplastic lymphoma kinase (ALK) polypeptide, an androgen receptor polypeptide, a cyclin B1 polypeptide, an N-myc proto-oncogene (MYCN) polypeptide, a Ras homolog gene family member C (RhoC) polypeptide, a tyrosinase-related protein-2 (TRP-2) polypeptide, a mesothelin polypeptide, a prostate stem cell antigen (PSCA) polypeptide, a melanoma associated antigen-1 (MAGE A1) polypeptide, a cytochrome P4501B1 (CYP1B1) polypeptide, a placenta-specific protein 1 (PLAC1) polypeptide, a BORIS polypeptide (also known as CCCTC-binding factor or CTCF), an ETV6-AML polypeptide, a breast cancer antigen NY- BR-1 polypeptide (also referred to as ankyrin repeat domain-containing protein 30A), a regulator of G- protein signaling (RGS5) polypeptide, a squamous cell carcinoma antigen recognized by T-cells (SART3) polypeptide, a carbonic anhydrase IX polypeptide, a paired box-5 (PAX5) polypeptide, an OY- TES1 (testis antigen; also known as acrosin binding protein) polypeptide, a sperm protein 17 polypeptide, a lymphocyte cell-specific protein-tyrosine kinase (LCK) polypeptide, a high molecular weight melanoma associated antigen (HMW-MAA), an A-kinase anchoring protein-4 (AKAP-4), a synovial sarcoma X breakpoint 2 (SSX2) polypeptide, an X antigen family member 1 (XAGE1) polypeptide, a B7 homolog 3 (B7H3; also known as CD276) polypeptide, a legumain polypeptide (LGMN1; also known as asparaginyl endopeptidase), a tyrosine kinase with Ig and EGF homology domains-2 (Tie-2; also known as angiopoietin-1 receptor) polypeptide, a P antigen family member 4 (PAGE4) polypeptide, a vascular endothelial growth factor receptor 2 (VEGF2) polypeptide, a MAD- CT-1 polypeptide, a fibroblast activation protein (FAP) polypeptide, a platelet derived growth factor receptor beta (PDGFβ) polypeptide, a MAD-CT-2 polypeptide, or a Fos-related antigen-1 (FOSL) polypeptide.
[00417] The antigen-binding polypeptide of a CAR can bind any of a variety of cancer-associated antigens, including, e.g., CD19, CD20, CD38, CD30, Her2/neu, ERBB2, CA125, MUC-1, prostate- specific membrane antigen (PSMA), CD44 surface adhesion molecule, mesothelin, carcinoembryonic antigen (CEA), epidermal growth factor receptor (EGFR), EGFRvIII, vascular endothelial growth factor receptor-2 (VEGFR2), B-cell maturation antigen (BCMA), high molecular weight-melanoma associated antigen (HMW-MAA), MAGE-A1, IL-13R-a2, GD2, and the like. Cancer-associated antigens also include, e.g., 4-1BB, 5T4, adenocarcinoma antigen, alpha-fetoprotein (AFP), BAFF, B-lymphoma cell, C242 antigen, CA-125, carbonic anhydrase 9 (CA-IX), C-MET, CCR4, CD152, CD19, CD20, CD200, CD22, CD221, CD23 (IgE receptor), CD28, CD30 (TNFRSF8), CD33, CD4, CD40, CD44 v6, CD51, CD52, CD56, CD74, CD80, CEA, CNTO888, CTLA-4, DRS, EGFR, EpCAM, CD3, FAP, fibronectin extra domain-B, folate receptor 1, GD2, GD3 ganglioside, glycoprotein 75, GPNMB, HER2/neu, HGF, human scatter factor receptor kinase, IGF-1 receptor, IGF-I, IgG1, L1-CAM, IL-13, IL-6, insulin-like growth factor I receptor, integrin α5β1, integrin αvβ3, MORAb-009, MS4A1, MUC1, mucin CanAg, N- glycolylneuraminic acid, NPC-1C, PDGF-R α, PDL192, phosphatidylserine, prostatic carcinoma cells, RANKL, RON, ROR1, SCH 900105, SDC1, SLAMF7, TAG-72, tenascin C, TGF beta 2, TGF-β, TRAIL-R1, TRAIL-R2, tumor antigen CTAA16.88, VEGF-A, VEGFR-1, VEGFR2, and vimentin. [00418] VH and VL amino acid sequences of various cancer-associated antigen-binding antibodies are known in the art, as are the light chain and heavy chain CDRs of such antibodies. See, e.g., Ling et al. (2018) Frontiers Immunol.9:469; WO 2005/012493; US 2019/0119375; US 2013/0066055. The following are non-limiting examples of antibodies that bind cancer-associated antigens. [00419] As one non-limiting example, in some cases, a CAR comprises an anti-CD19 antibody (e.g., an anti-CD19 scFv or an anti-CD19 nanobody). Anti-CD19 antibodies are known in the art; and the VH and VL, or the VH and VL CDRs, of any anti-CD19 antibody can be included in a CAR. See e.g., WO 2005/012493. [00420] In some cases, an anti-CD19 antibody includes a VL CDR1 comprising the amino acid sequence KASQSVDYDGDSYLN (SEQ ID NO:181); a VL CDR2 comprising the amino acid sequence DASNLVS (SEQ ID NO:182); and a VL CDR3 comprising the amino acid sequence QQSTEDPWT (SEQ ID NO:183). In some cases, an anti-CD19 antibody includes a VH CDR1 comprising the amino acid sequence SYWMN (SEQ ID NO:184); a VH CDR2 comprising the amino acid sequence QIWPGDGDTNYNGKFKG (SEQ ID NO:185); and a VH CDR3 comprising the amino acid sequence RETTTVGRYYYAMDY (SEQ ID NO:186). In some cases, an anti-CD19 antibody includes a VL CDR1 comprising the amino acid sequence KASQSVDYDGDSYLN (SEQ ID NO:181); a VL CDR2 comprising the amino acid sequence DASNLVS (SEQ ID NO:182); and a VL CDR3 comprising the amino acid sequence QQSTEDPWT (SEQ ID NO:183); a VH CDR1 comprising the amino acid sequence SYWMN (SEQ ID NO:184); a VH CDR2 comprising the amino acid sequence
QIWPGDGDTNYNGKFKG (SEQ ID NO:185); and a VH CDR3 comprising the amino acid sequence RETTTVGRYYYAMDY (SEQ ID NO:186). [00421] In some cases, an anti-CD19 antibody is a scFv. For example, in some cases, an anti-CD19 scFv comprises an amino acid sequence having at least 90%, at least 95%, at least 98%, at least 99%, or 100%, amino acid sequence identity to the following amino acid sequence: DIQLTQSPASLAVSLGQRATISCKASQSVDYDGDSYLNWYQQIPGQPPKLLIYDASNLVSGIPPRF SGSGSGTDFTLNIHPVEKVDAATYHCQQSTEDPWTFGGGTKLEIKGGGGSGGGGSGGGGSQVQ LQQSGAELVRPGSSVKISCKASGYAFSSYWMNWVKQRPGQGLEWIGQIWPGDGDTNYNGKFK GKATLTADESSSTAYMQLSSLASEDSAVYFCARRETTTVGRYYYAMDYWGQGTTVTVS (SEQ ID NO:187). COMPOSITIONS COMPRISING AN EDV [00422] The present disclosure provides compositions, including pharmaceutical compositions, comprising an EDV of the present disclosure. The composition may comprise a pharmaceutically acceptable excipient, a variety of which are known in the art and need not be discussed in detail herein. Pharmaceutically acceptable excipients have been amply described in a variety of publications, including, for example, “Remington: The Science and Practice of Pharmacy”, 19th Ed. (1995), or latest edition, Mack Publishing Co; A. Gennaro (2000) "Remington: The Science and Practice of Pharmacy", 20th edition, Lippincott, Williams, & Wilkins; Pharmaceutical Dosage Forms and Drug Delivery Systems (1999) H.C. Ansel et al., eds 7th ed., Lippincott, Williams, & Wilkins; and Handbook of Pharmaceutical Excipients (2000) A.H. Kibbe et al., eds., 3rd ed. Amer. Pharmaceutical Assoc. [00423] A composition of the present disclosure can include: a) an EDV of the present disclosure; and b) one or more of: a buffer, a surfactant, an antioxidant, a hydrophilic polymer, a dextrin, a chelating agent, a suspending agent, a solubilizer, a thickening agent, a stabilizer, a bacteriostatic agent, a wetting agent, and a preservative. Suitable buffers include, but are not limited to, (such as N,N-bis(2-hydroxyethyl)-2- aminoethanesulfonic acid (BES), bis(2-hydroxyethyl)amino-tris(hydroxymethyl)methane (BIS-Tris), N- (2-hydroxyethyl)piperazine-N'3-propanesulfonic acid (EPPS or HEPPS), glycylglycine, N-2- hydroxyehtylpiperazine-N'-2-ethanesulfonic acid (HEPES), 3-(N-morpholino)propane sulfonic acid (MOPS), piperazine-N,N'-bis(2-ethane-sulfonic acid) (PIPES), sodium bicarbonate, 3-(N- tris(hydroxymethyl)-methyl-amino)-2-hydroxy-propanesulfonic acid) TAPSO, (N- tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES), N-tris(hydroxymethyl)methyl-glycine (Tricine), tris(hydroxymethyl)-aminomethane (Tris), etc.), phosphate buffered saline (PBS). Suitable salts include, e.g., NaCl, MgCl2, KCl, MgSO4, etc.
[00424] In some cases, the composition is sterile. In some cases, the composition is suitable for administration to a human subject, e.g., where the composition is sterile and is free of detectable pyrogens and/or other toxins. [00425] In some cases, a composition of the present disclosure comprises: i) an EDV that does not include a donor template nucleic acid; and ii) a donor template nucleic acid (provided separately from the EDV). Nucleic Acids [00426] As noted above, provided are nucleic acids encoding a subject EDV (i.e., encoding the components of a subject EDV). Provided, for example, is a collection of one or more nucleic acids (e.g., 2 or more, 3 or more, or 4 or more) encoding a subject EDV. In some such cases, the EDV is encoding by one nucleic acid (e.g., one nucleic acid encoding a Gag-Cas9 fusion polyprotein, where the collection does not include coding sequences for pol polyproteins such as PR, RT, or INT). In some cases, a collection can include two or more nucleic acids (e.g., 3 or more, or 4 or more) (e.g., one encoding a Gag-Cas9 fusion polyprotein and another encoding a Gag-pol polyprotein). In some cases, a nucleic acid of a subject collection can include donor sequences. In some cases, a nucleic acid of a subject collection can include sequences encoding a therapeutic protein, e.g., in some cases such sequences are flanked by LTR sequences. In some cases, a nucleic acid of a subject collection can include sequences encoding a CRISPR-Cas guide RNA, e.g., in some cases operably linked a promoter such as a PolIII promoter such as U6 or H1, e.g., in some cases the guide RNA or guide RNA plus operably linked promoter are flanked by LTR sequences. In some cases, a sequence encoding a CRISPR-Cas guide RNA is present on the same nucleic acid as the sequence encoding the CRISPR-Cas protein (e.g., Gag-Cas9) and in some cases, it is present on a different nucleic acid. In some cases, a collection includes only one nucleic acid. In some cases, a collection includes two nucleic acids. In some cases, a collection includes three nucleic acids. In some cases, a collection includes four nucleic acids. [00427] A coding sequence (e.g., a nucleotide sequence encoding a CRISPR-Cas effector polypeptide; a nucleotide sequence encoding a CRISPR-Cas guide RNA; a nucleotide sequence encoding a therapeutic protein) present in an EDV of the present disclosure can be operably linked to a transcriptional control element (e.g., a promoter). The transcriptional control element can be a promoter. In some cases, the promoter is a constitutively active promoter. In some cases, the promoter is a regulatable promoter. In some cases, the promoter is an inducible promoter. In some cases, the promoter is a tissue-specific promoter. In some cases, the promoter is a cell type-specific promoter. In some cases, the transcriptional control element (e.g., the promoter) is functional in a targeted cell type or targeted cell population. A promoter can be a constitutively active promoter (i.e., a promoter that is constitutively in an active/”ON” state), it may be an inducible promoter (i.e., a promoter whose state, active/”ON” or inactive/“OFF”, is
controlled by an external stimulus, e.g., the presence of a particular temperature, compound, or protein.), it may be a spatially restricted promoter (i.e., transcriptional control element, enhancer, etc.)(e.g., tissue specific promoter, cell type specific promoter, etc.), and it may be a temporally restricted promoter (i.e., the promoter is in the “ON” state or “OFF” state during specific stages of embryonic development or during specific stages of a biological process, e.g., hair follicle cycle in mice). [00428] Suitable promoters can be derived from viruses and can therefore be referred to as viral promoters, or they can be derived from any organism, including prokaryotic or eukaryotic organisms. Suitable promoters can be used to drive expression by any RNA polymerase (e.g., pol I, pol II, pol III). Exemplary promoters include, but are not limited to the SV40 early promoter, mouse mammary tumor virus long terminal repeat (LTR) promoter; adenovirus major late promoter (Ad MLP); a herpes simplex virus (HSV) promoter, a cytomegalovirus (CMV) promoter such as the CMV immediate early promoter region (CMVIE), a rous sarcoma virus (RSV) promoter, a human U6 small nuclear promoter (U6) (Miyagishi et al., Nature Biotechnology 20, 497 - 500 (2002)), an enhanced U6 promoter (e.g., Xia et al., Nucleic Acids Res.2003 Sep 1;31(17)), a human H1 promoter (H1), and the like. [00429] In some cases, a coding nucleotide sequence is operably linked to (under the control of) a promoter operable in a eukaryotic cell (e.g., a U6 promoter, an enhanced U6 promoter, an H1 promoter, and the like). As would be understood by one of ordinary skill in the art, when expressing an RNA (e.g., a guide RNA) from a nucleic acid (e.g., an expression vector) using a U6 promoter (e.g., in a eukaryotic cell), or another PolIII promoter such as H1, the RNA may need to be mutated if there are several Ts in a row (coding for Us in the RNA). This is because a string of Ts (e.g., 5 Ts) in DNA can act as a terminator for polymerase III (PolIII). Thus, in order to ensure transcription of a guide RNA in a eukaryotic cell it may sometimes be necessary to modify the sequence encoding the guide RNA to eliminate runs of Ts. In some cases, a nucleotide sequence encoding guide RNA is operably linked to a promoter operable in a eukaryotic cell (e.g., a CMV promoter, an EF1α promoter, an estrogen receptor- regulated promoter, and the like). [00430] Examples of inducible promoters include, but are not limited to T7 RNA polymerase promoter, T3 RNA polymerase promoter, Isopropyl-beta-D-thiogalactopyranoside (IPTG)-regulated promoter, lactose induced promoter, heat shock promoter, Tetracycline-regulated promoter, Steroid-regulated promoter, Metal-regulated promoter, estrogen receptor-regulated promoter, etc. Inducible promoters can therefore be regulated by molecules including, but not limited to, doxycycline; estrogen and/or an estrogen analog; IPTG; etc. [00431] Inducible promoters suitable for use include any inducible promoter described herein or known to one of ordinary skill in the art. Examples of inducible promoters include, without limitation, chemically/biochemically-regulated and physically-regulated promoters such as alcohol-regulated promoters, tetracycline-regulated promoters (e.g., anhydrotetracycline (aTc)-responsive promoters and
other tetracycline-responsive promoter systems, which include a tetracycline repressor protein (tetR), a tetracycline operator sequence (tetO) and a tetracycline transactivator fusion protein (tTA)), steroid- regulated promoters (e.g., promoters based on the rat glucocorticoid receptor, human estrogen receptor, moth ecdysone receptors, and promoters from the steroid/retinoid/thyroid receptor superfamily), metal- regulated promoters (e.g., promoters derived from metallothionein (proteins that bind and sequester metal ions) genes from yeast, mouse and human), pathogenesis-regulated promoters (e.g., induced by salicylic acid, ethylene or benzothiadiazole (BTH)), temperature/heat-inducible promoters (e.g., heat shock promoters), and light-regulated promoters (e.g., light responsive promoters from plant cells). [00432] In some cases, the promoter is a spatially restricted promoter (i.e., cell type specific promoter, tissue specific promoter, etc.) such that in a multi-cellular organism, the promoter is active (i.e., “ON”) in a subset of specific cells. Spatially restricted promoters may also be referred to as enhancers, transcriptional control elements, control sequences, etc. Any convenient spatially restricted promoter may be used as long as the promoter is functional in the targeted host cell (e.g., eukaryotic cell; prokaryotic cell). [00433] In some cases, the promoter is a reversible promoter. Suitable reversible promoters, including reversible inducible promoters are known in the art. Such reversible promoters may be isolated and derived from many organisms, e.g., eukaryotes and prokaryotes. Modification of reversible promoters derived from a first organism for use in a second organism, e.g., a first prokaryote and a second a eukaryote, a first eukaryote and a second a prokaryote, etc., is well known in the art. Such reversible promoters, and systems based on such reversible promoters but also comprising additional control proteins, include, but are not limited to, alcohol regulated promoters (e.g., alcohol dehydrogenase I (alcA) gene promoter, promoters responsive to alcohol transactivator proteins (AlcR), etc.), tetracycline regulated promoters, (e.g., promoter systems including TetActivators, TetON, TetOFF, etc.), steroid regulated promoters (e.g., rat glucocorticoid receptor promoter systems, human estrogen receptor promoter systems, retinoid promoter systems, thyroid promoter systems, ecdysone promoter systems, mifepristone promoter systems, etc.), metal regulated promoters (e.g., metallothionein promoter systems, etc.), pathogenesis-related regulated promoters (e.g., salicylic acid regulated promoters, ethylene regulated promoters, benzothiadiazole regulated promoters, etc.), temperature regulated promoters (e.g., heat shock inducible promoters (e.g., HSP-70, HSP-90, soybean heat shock promoter, etc.), light regulated promoters, synthetic inducible promoters, and the like. Methods of Making/Producing an EDV [00434] The present disclosure provides methods of making an EDV of the present disclosure. The methods generally involve introducing into a packaging cell a system (collection of nucleic acids) of the present disclosure; and harvesting the EDVs produced by the packaging cell. In some cases, the EDVs
are harvested from the supernatant (e.g., the cell culture medium) in which the packaging cells are cultures. In some cases, the cell culture medium is filtered (e.g., with a 0.45 μm filter). [00435] Any suitable permissive or packaging cell known in the art may be employed in the production of an EDV of the present disclosure. In some cases, the cell is a mammalian cell. In some cases, the cell is an insect cell. Examples of cells suitable for production of an EDV of the present disclosure include, e.g., human cell lines, such as VERO, WI38, MRC5, A549, HEK293, HEK293T, B-50 or any other HeLa cells, HepG2, Saos-2, HuH7, Chinese Hamster Ovary (CHO) cells, and HT1080 cell lines. [00436] Also suitable for use as packaging cells are insect cell lines. Any insect cell that allows for production of an EDV of the present disclosure and which can be maintained in culture can be used. Examples include Spodoptera frugiperda, such as the Sf9 or Sf21 cell lines, Drosophila spp. cell lines, or mosquito cell lines, e.g., Aedes albopictus derived cell lines. [00437] The nucleic acids present in a system (collection) of the present disclosure can be extra- chromosomal or integrated into the cell's chromosomal DNA. In some cases, the packaging cell is a cell line with one or more packaging functions incorporated extrachromosomally or integrated into the cell's chromosomal DNA, or a cell line with helper functions incorporated extra-chromosomally or integrated into the cell's chromosomal DNA. Methods of Delivering a Nucleic Acid-Binding Effector Polypeptide [00438] The present disclosure provides methods of delivering a nucleic acid-binding effector polypeptide (e.g., CRIPSR-Cas effector polypeptide such as a Cas9 or Cas12a – including variants such as nickase versions, dead versions, fusion protein versions, etc.) to a target eukaryotic cell. In some cases, such delivery results in modification of a target nucleic acid in the cell – and as such, methods of modifying a target nucleic in a eukaryotic cell are also disclosed herein. The methods generally involve contacting the cell with a EDV of the present disclosure or administering an EDV to an organism. In some cases, the target cell is in vitro (e.g., an immortalized cell line). In some cases, the target cell is ex vivo (e.g., a primary isolated from a patient that is not immortalized and has gone through minimal to no passages – in some cases such cells can be re-introduced into an individual). In some cases, the target cell is in vivo and the method comprises administering the EDV to an individual. [00439] The present disclosure provides methods of delivering a CRISPR-Cas polypeptide (e.g., Cas9, Cas12a – including variants such as dead, nickase, and/or fusion variants) to a target eukaryotic cell. The methods generally involve contacting the cell with a EDV of the present disclosure or administering a EDV to an organism. In some cases, the target cell is ex vivo (e.g., a primary isolated from a patient that is not immortalized and has gone through minimal to no passages – in some cases such cells can be re- introduced into an individual). In some cases, the target cell is in vivo and the method comprises administering the EDV to an individual.
[00440] Where a EDV of the present disclosure comprises a guide RNA, in some instances, the guide RNA provides for knockout of a nucleic acid targeted by the guide RNA. Thus, in some cases, a EDV of the present disclosure provides for: i) delivery of a therapeutic protein; and ii) knockout of a target nucleic acid. As one non-limiting example, a EDV of the present disclosure can both: i) provide for delivery of a therapeutic protein (such as a chimeric antigen receptor (CAR)); and ii) knock out an endogenous nucleic acid, e.g., one encoding a beta-2 microglobulin (β2M) polypeptide, where the guide RNA present in the EDV (or encoded by a nucleic acid present in the EDV) would comprise a nucleotide sequence targeting the endogenous nucleic acid (e.g., a β2M-encoding nucleic acid) in a target cell. Such a EDV would be useful for generating T cells that express a CAR (“CAR-T cells”) that do not express endogenous major histocompatibility complex (MHC) class I antigens on their cell surface and thus could be useful for delivery of allogeneic CAR-T cells. As another non-limiting example, a EDV of the present disclosure can both: i) provide for delivery of a therapeutic protein (such as an antibody, e.g., a cancer-specific antibody or other therapeutic antibody); and ii) knock out an endogenous nucleic acid encoding an antibody light chain (e.g., a kappa light chain) or an immunoglobulin (Ig) Fc polypeptide (e.g., an Ig Fc polypeptide of a particular isotype such as IgG1). Such a EDV would be useful for generating B cells that produce a therapeutic antibody. [00441] In some cases, a EDV of the present disclosure provides for homology directed repair (HDR) of a defective target nucleic acid (e.g., in some cases a donor/template nucleic acid is provided, either as part of the EDV, e.g., encapsidated within the EDV, and in some cases along with the EDV but as part of the EDV). In some cases, a EDV of the present disclosure provides for non-homologous end joining (NHEJ) of a target nucleic acid, e.g., to provide for a knockout of a target nucleic acid. [00442] A cell that serves as a recipient for a EDV of the present disclosure can be any of a variety of eukaryotic cells, including, e.g., in vitro cells; in vivo cells; ex vivo cells; primary cells; cancer cells; animal cells; plant cells; algal cells; fungal cells; etc. A cell that serves as a recipient for a EDV of the present disclosure is referred to as a “host cell” or a “target cell.” [00443] In some cases, the target cell is in vitro (e.g., the cells can be an immortalized cell line). In some cases, the target cell is ex vivo, e.g., in some cases, cells are removed from an individual, contacted with a EDV of the present disclosure ex vivo, such that the cells are modified to produce the therapeutic protein encoded by a nucleic acid present in the EDV; and the modified cells can be returned to the individual from whom the cells were obtained. In some cases, cells are removed from an individual, contacted with a EDV of the present disclosure ex vivo, such that the cells are modified to produce the therapeutic protein encoded by a nucleic acid present in the EDV; and the modified cells can be administered to an individual other than the individual from whom the cells were obtained. [00444] Suitable cells include a stem cell (e.g. an embryonic stem (ES) cell, an induced pluripotent stem (iPS) cell; a germ cell (e.g., an oocyte, a sperm, an oogonia, a spermatogonia, etc.); a somatic cell, e.g. a
fibroblast, an oligodendrocyte, a glial cell, a hematopoietic cell, a neuron, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell, etc. [00445] Suitable cells include human embryonic stem cells, fetal cardiomyocytes, myofibroblasts, mesenchymal stem cells, cardiomyocytes, adipocytes, totipotent cells, pluripotent cells, blood stem cells, myoblasts, adult stem cells, bone marrow cells, mesenchymal cells, embryonic stem cells, parenchymal cells, epithelial cells, endothelial cells, mesothelial cells, fibroblasts, osteoblasts, chondrocytes, exogenous cells, endogenous cells, stem cells, hematopoietic stem cells, bone-marrow derived progenitor cells, myocardial cells, skeletal cells, fetal cells, undifferentiated cells, multi-potent progenitor cells, unipotent progenitor cells, monocytes, cardiac myoblasts, skeletal myoblasts, macrophages, capillary endothelial cells, xenogeneic cells, allogeneic cells, and post-natal stem cells. [00446] Suitable cells include a cancer cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue-resident stem cell, a monocyte, a macrophage, a B cell, and a T cell. [00447] In some cases, the cell is an immune cell, a neuron, an epithelial cell, and endothelial cell, or a stem cell. In some cases, the immune cell is a T cell, a B cell, a monocyte, a natural killer cell, a dendritic cell, or a macrophage. In some cases, the immune cell is a cytotoxic T cell. In some cases, the immune cell is a helper T cell. In some cases, the immune cell is a regulatory T cell (Treg). [00448] In some cases, the cell is a stem cell. Stem cells include adult stem cells. Adult stem cells are also referred to as somatic stem cells. In some cases, the cell is a tissue-resident stem cell. [00449] Adult stem cells are resident in differentiated tissue, but retain the properties of self-renewal and ability to give rise to multiple cell types, usually cell types typical of the tissue in which the stem cells are found. Numerous examples of somatic stem cells are known to those of skill in the art, including muscle stem cells; hematopoietic stem cells; epithelial stem cells; neural stem cells; mesenchymal stem cells; mammary stem cells; intestinal stem cells; mesodermal stem cells; endothelial stem cells; olfactory stem cells; neural crest stem cells; and the like. [00450] Stem cells of interest include mammalian stem cells, where the term “mammalian” refers to any animal classified as a mammal, including humans; non-human primates; domestic and farm animals; and zoo, laboratory, sports, or pet animals, such as dogs, horses, cats, cows, mice, rats, rabbits, etc. In some cases, the stem cell is a human stem cell. In some cases, the stem cell is a rodent (e.g., a mouse; a rat) stem cell. In some cases, the stem cell is a non-human primate stem cell. [00451] Stem cells can express one or more stem cell markers, e.g., SOX9, KRT19, KRT7, LGR5, CA9, FXYD2, CDH6, CLDN18, TSPAN8, BPIFB1, OLFM4, CDH17, and PPARGC1A. [00452] In some cases, the stem cell is a hematopoietic stem cell (HSC). HSCs are mesoderm-derived cells that can be isolated from bone marrow, blood, cord blood, fetal liver and yolk sac. HSCs are characterized as CD34+ and CD3-. HSCs can repopulate the erythroid, neutrophil-macrophage,
megakaryocyte and lymphoid hematopoietic cell lineages in vivo. In vitro, HSCs can be induced to undergo at least some self-renewing cell divisions and can be induced to differentiate to the same lineages as is seen in vivo. As such, HSCs can be induced to differentiate into one or more of erythroid cells, megakaryocytes, neutrophils, macrophages, and lymphoid cells. [00453] In other instances, the stem cell is a neural stem cell (NSC). Neural stem cells (NSCs) are capable of differentiating into neurons, and glia (including oligodendrocytes, and astrocytes). A neural stem cell is a multipotent stem cell which is capable of multiple divisions, and under specific conditions can produce daughter cells which are neural stem cells, or neural progenitor cells that can be neuroblasts or glioblasts, e.g., cells committed to become one or more types of neurons and glial cells respectively. Methods of obtaining NSCs are known in the art. [00454] In other instances, the stem cell is a mesenchymal stem cell (MSC). MSCs originally derived from the embryonal mesoderm and isolated from adult bone marrow, can differentiate to form muscle, bone, cartilage, fat, marrow stroma, and tendon. Methods of isolating MSC are known in the art; and any known method can be used to obtain MSC. See, e.g., U.S. Pat. No.5,736,396, which describes isolation of human MSC. [00455] In some cases, the target cell is a lung cell. In some cases, the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, where the guide RNA comprises a targeting sequence that targets a CFTR (cystic fibrosis transmembrane conductance regulator) gene. For example, targeting a CFTR gene can treat cystic fibrosis. Where the target gene comprises a defect that leads to pathology, a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected. [00456] In some cases, the target cell is a CD34+ cell. In some cases, the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, where the guide RNA comprises a targeting sequence that targets an HbF (fetal hemoglobin) gene. For example, targeting an HbF gene can treat sickle cell disease or beta-thalassemia. Where the target gene comprises a defect that leads to pathology, a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected. [00457] In some cases, the target cell is a CD8+ T cell. In some cases, the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, where the guide RNA comprises a targeting sequence that targets a gene selected from PD1 (programmed cell death 1), CTLA4 (cytotoxic T-lymphocyte-associated protein 4), and TCR (T-cell receptor). For example, targeting a PD-1 gene, a CTLA-4 gene, or a TCR gene, can be used in the generation of chimeric antigen receptor (CAR)- T cells. [00458] In some cases, the target cell is a CD4+ T cell. In some cases, the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, where the guide RNA
comprises a targeting sequence that targets a CCR5 gene, or targets an integrated and proviral HIV-1. Targeting a CCR5 gene can be used to enhance resistance to HIV. Targeting an integrated and proviral HIV-1 can be used to reduce the pool of T cells that are reservoirs for latent HIV. [00459] In some cases, the target cell is a skeletal muscle cell. In some cases, the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, where the guide RNA comprises a targeting sequence that targets a Duchenne muscular dystrophy (DMD) gene. Targeting a DMD gene can be used to treat Duchenne muscular dystrophy. Where the target gene comprises a defect that leads to pathology, a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected. [00460] In some cases, the target cell is an ocular cell (e.g., in a retinal cell, a photoreceptor cell, etc.). In some cases, the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, and wherein the guide RNA comprises a targeting sequence that targets a CEP290 (centrosomal protein 290) gene. Targeting a CEP290 gene can be used to treat Leber congenital amaurosis 10 (LCA10). Where the target gene comprises a defect that leads to pathology, a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected. [00461] In some cases, target cell is an auditory cell (e.g., hair cells, cochlear cells, etc.). In some cases, the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, where the guide RNA comprises a targeting sequence that targets a USH2A (Usher syndrome 2A) gene. Targeting a USH2A gene can be used to treat Usher Syndrome type 2A. Where the target gene comprises a defect that leads to pathology, a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected. [00462] In some cases, the target cell is a central nervous system cell (e.g., neurons (e.g., excitatory and inhibitory neurons); and glial cells (e.g., oligodendrocytes, astrocytes and microglia)). In some cases, the EDV comprises a guide RNA, or a nucleic acid comprising a nucleotide sequence encoding a guide RNA, and wherein the guide RNA comprises a targeting sequence that targets a gene selected from Tau/MAPT-1, HTT (Huntingtin), SOD1 (superoxide dismutase 1), SOCS3 (suppressor of cytokine signaling 3), USP8 (ubiquitin specific peptidase 8), DOT1L (DOT1-like histone lysine methyltransferase), UFM1 (ufmylation; ubiquitin fold modifier 1), SOCS2 (suppressor of cytokine signaling 2), SOCS9 (suppressor of cytokine signaling 9), SOCS13 (suppressor of cytokine signaling 13), SOCS11 (suppressor of cytokine signaling 11), and SOCS5 (suppressor of cytokine signaling 5). For example, targeting a Tau gene can treat Alzheimer’s disease. As another example, targeting an HTT gene can treat Huntington Disease. As another example, targeting a SOD1 gene can treat amyotrophic lateral sclerosis. As another example, targeting a Ufmylation, USP8, DOT1L, SOCS2, SOCS3, SOCS9, SOCS13, SOCS11, or SOCS5 gene can treat glioblastoma. Where the target gene comprises a defect that
leads to pathology, a donor nucleic acid comprising a nucleotide sequence without the defect can be included in the EDV, such that the defect is corrected. [00463] In some cases, a single dose of a composition comprising a EDV of the present disclosure comprises from about 102 EDVs to about 1012 EDVs. For example, a single dose of a composition comprising a EDV of the present disclosure comprises from about 102 EDVs to about 103 EDVs, from about 103 EDVs to about 104 EDVs, from about 104 EDVs to about 105 EDVs, from about 105 EDVs to about 106 EDVs, from about 106 EDVs to about 107 EDVs, from about 107 EDVs to about 108 EDVs, from about 108 EDVs to about 109 EDVs, from about 109 EDVs to about 1010 EDVs, from about 1010 EDVs to about 1011 EDVs, or from about 1011 EDVs to about 1012 EDVs. A composition comprising a EDV of the present disclosure can be administered via any of a variety of parenteral and non-parenteral routes of administration. For example, a composition comprising a EDV of the present disclosure can be administered intravenously, intramuscularly, intratumorally, peritumorally, subcutaneously, intraperitoneally, and the like. A EDV of the present disclosure can be administered via convection enhanced delivery (CED) injection. METHODS OF IN VIVO GENOME EDITING [00464] The present disclosure provides a method of modifying a target nucleic acid in a target eukaryotic cell in vivo, the method comprising administering to an individual in need thereof an effective amount of an EDV of the present disclosure, or a composition comprising an EDV of the present disclosure. The EDV enters the target eukaryotic cell in the individual and modifies the target nucleic acid in the target eukaryotic cell. In some cases, the target cell is a CD4+ T cell. In some cases, the target cell is a CD8+ T cell. [00465] In some cases, the target cell is an immune cell. In some cases, the immune cell is a T cell, a B cell, a monocyte, a natural killer cell, a dendritic cell, or a macrophage. In some cases, the immune cell is a cytotoxic T cell. In some cases, the immune cell is a helper T cell. In some cases, the immune cell is a regulatory T cell (Treg). In some cases, the target cell is a CD4+ T cell. In some cases, the target cell is a CD8+ T cell. [00466] In some cases, the EDV comprises one or more guide RNAs (or one or more nucleic acids comprising nucleotide sequences encoding the one or more guide RNAs) that provide for one or more of: a) insertion of a nucleic acid comprising a nucleotide sequence encoding a therapeutic polypeptide into the genome of the target cell; b) deletion of one or more endogenous nucleic acids in the target cell. [00467] In some cases, the EDV comprises a nucleic acid comprising a nucleotide sequence encoding a CAR. In some cases, the EDV comprises: a) a nucleic acid comprising a nucleotide sequence encoding a CAR; and b) a guide RNA that provides for knockout of an TRAC-encoding nucleic acid in the target cell. In some cases, the EDV comprises a nucleic acid comprising a nucleotide sequence encoding a
CAR. In some cases, the EDV comprises: a) a nucleic acid comprising a nucleotide sequence encoding a CAR; and b) a guide RNA that provides for knockout of an immune checkpoint in the target cell. In some of these embodiments, the target cell is a CD8+ T cell. [00468] In some cases, a single dose of a composition comprising an EDV of the present disclosure comprises from about 102 EDVs to about 1012 EDVs. For example, a single dose of a composition comprising a EDV of the present disclosure comprises from about 102 EDVs to about 103 EDVs, from about 103 EDVs to about 104 EDVs, from about 104 EDVs to about 105 EDVs, from about 105 EDVs to about 106 EDVs, from about 106 EDVs to about 107 EDVs, from about 107 EDVs to about 108 EDVs, from about 108 EDVs to about 109 EDVs, from about 109 EDVs to about 1010 EDVs, from about 1010 EDVs to about 1011 EDVs, or from about 1011 EDVs to about 1012 EDVs. [00469] A composition comprising an EDV of the present disclosure can be administered via any of a variety of parenteral and non-parenteral routes of administration. For example, a composition comprising an EDV of the present disclosure can be administered intravenously, intramuscularly, intratumorally, peritumorally, subcutaneously, intraperitoneally, and the like. An EDV of the present disclosure can be administered via convection enhanced delivery (CED) injection. VI. EXAMPLES OF NON-LIMITING ASPECTS OF THE DISCLOSURE [00470] Aspects, including embodiments, of the present subject matter described above may be beneficial alone or in combination, with one or more other aspects or embodiments. Without limiting the foregoing description, certain non-limiting aspects of the disclosure are provided below. As will be apparent to those of skill in the art upon reading this disclosure, each of the individually numbered aspects may be used or combined with any of the preceding or following individually numbered aspects. This is intended to provide support for all such combinations of aspects and is not limited to combinations of aspects explicitly provided below: 1. An enveloped delivery vehicle (EDV), comprising: (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide); (b) a viral envelop protein (e.g., VSVG or a mutant thereof); (c) a targeting polypeptide that provides for binding to a target cell; (d) a matrix (MA) polypeptide; and (e) an N-terminally truncated capsid (CA) protein. 2. The EDV of 1, wherein the EDV lacks one or more of the following proteins: a pol polypeptide protease (PR), a pol polypeptide reverse transcriptase (RT), a pol polypeptide integrase (IN), a nucleocapsid (NC) protein.
3. The EDV of 1 or 2, wherein the viral envelope protein is selected from: a Hepatitis B virus (HBV) glycoprotein, a Hepatitis C virus (HCV) glycoprotein, a Marburg virus glycoprotein, an Ebola virus glycoprotein, a vesicular stomatitis virus (VSV) glycoprotein, an influenza virus hemagglutinin, a SARS-CoV glycoprotein, a respiratory syncytial virus (RSV) glycoprotein, a human parainfluenza virus glycoprotein, a moloney murine leukemia virus (MMLV), a measles virus hemagglutinin and/or a measles virus fusion glycoprotein, an HTLV-1 glycoprotein, a Ross river virus glycoprotein, a rabies virus glycoprotein, a Mokola virus glycoprotein, a Semliki Forest virus glycoprotein, a Sindbis virus glycoprotein, a Venezuelan equine encephalitis virus glycoprotein, a sendai virus, a baculovirus, and a variant of any of the above that comprises one or more amino acid substitutions that reduce binding of the viral envelope protein to its receptor. 4. The EDV of 1 or 2, wherein the viral envelop protein is a variant vesicular stomatitis virus glycoprotein (VSVG) that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R354A), respectively, relative to SEQ ID NO: 153. 5. The EDV of any one of 1-4, wherein the N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-15 of the capsid protein set forth as SEQ ID NO: 282. 6. The EDV of any one of 1-4, wherein the N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-34 of the capsid protein set forth as SEQ ID NO: 282. 7. The EDV of any one of 1-4, wherein the N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-47 of the capsid protein set forth as SEQ ID NO: 282. 8. The EDV of any one of 1-4, wherein the N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-148 of the capsid protein set forth as SEQ ID NO: 282. 9. The EDV of any one of 5-8, wherein the N-terminally truncated capsid protein comprises an amino acid sequence having 80% or more sequence identity with any one of SEQ ID NOs: 283-286 and 290. 10. The EDV of any one of 1-9, wherein the MA polypeptide lacks amino acids corresponding to amino acids 72-127 of the protein set forth as SEQ ID NO: 296. 11. The EDV of any one of 1-9, wherein the MA polypeptide lacks amino acids corresponding to amino acids 30-127 of the protein set forth as SEQ ID NO: 296.
12. The EDV of any one of 1-9, wherein the MA polypeptide comprises an amino acid sequence having 80% or more amino acid sequence identity with the protein set forth as SEQ ID NO: 296. 13. The EDV of any one of 1-12, wherein the targeting polypeptide comprises one or more antibodies or antibody analogs. 14. The EDV of 13, wherein the one or more antibody analogs is an affibody, an affilin, an affimer, an affitin, an alphabody, an anticalin, an avimer, a DARPin, a Fynomer, a Kunitz domain peptide, a monobody, a repebody, a VLR, or a nanoCLAMP. 15. The EDV of 13, wherein the one or more antibodies is a single chain Fv (scFv) polypeptide, a diabody, a bispecific antibody, a triabody, or a nanobody. 16. The EDV of any one of 1-15, wherein the target cell is a cancer cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue- resident stem cell, a monocyte, a macrophage, a B cell, or a T cell. 17. The EDV of any one of 1-15, wherein the target cell is a cancer cell. 18. The EDV of any one of 1-15, wherein the target cell is a CD8+ T cell or a CD4+ T cell. 19. The EDV of any one of 1-15, wherein the targeting polypeptide comprises an anti-CD19, anti-CD20, anti-CD4, anti-CD28, or anti-CD3 antibody or antibody analog. 20. The EDV of any one of 1-15, wherein the targeting polypeptide comprises: (i) an anti-CD3 and an anti-CD4 antibody or antibody analog; (ii) an anti-CD3 and an anti-CD28 antibody or antibody analog; or (iii) an anti-CD3, an anti-CD4, and an anti-CD28 antibody or antibody analog. 21. The EDV of any one of 1-15, wherein the target cell is a regulatory T cell (Treg) and the targeting polypeptide comprises an anti-CD28 superagonist (CD28SA). 22. The EDV of any one of 13-21, wherein the targeting polypeptide is a fusion polypeptide comprising: (i) the one or more antibodies or antibody analogs; and (ii) one or more heterologous polypeptides. 23. The EDV of 22, wherein said one of more heterologous polypeptides comprises a transmembrane polypeptide. 24. The EDV of 23, wherein the transmembrane polypeptide is a CD8α chain polypeptide or a platelet-derived growth factor receptor (PDGFR) polypeptide. 25. The EDV of any one of 1-24, wherein the nucleic acid-binding effector polypeptide is a CRISPR-Cas effector polypeptide (e.g., Cas9 or Cas12a), a Zinc Finger Nuclease
(ZFN), a Transcription activator-like effector nuclease (TALEN), a meganuclease, a TnpB, an IscB, a serine recombinase, or a tyrosine recombinase. 26. The EDV of any one of 1-25, wherein the nucleic acid-binding effector polypeptide is fused (e.g., at the C-terminus) to 7 or more nuclear localization signals (NLSs). 27. The EDV of any one of 1-26, wherein the nucleic acid-binding effector polypeptide is fused to 3 or more nuclear export signals (NESs). 28. The EDV of any one of 1-27, wherein the nucleic acid-binding effector polypeptide is a fusion polypeptide comprising: i) a CRISPR-Cas effector polypeptide; and ii) one or more heterologous polypeptides. 29. The EDV of 28, wherein the CRISPR-Cas effector polypeptide has nickase activity or is catalytically deactivated. 30. The EDV of 29, wherein at least one of the one or more heterologous polypeptides comprises a deaminase, a reverse transcriptase, a transcription modulator, or an epigenetic modulator. 31. The EDV of any one of 28-30, wherein at least one of the one or more heterologous polypeptides is a Gag polypeptide. 32. The EDV of any one of 1-31, wherein the EDV comprises a CRISPR-Cas guide RNA or a nucleic acid encoding the CRISPR-Cas guide RNA. 33. The EDV of any one of 1-32, wherein the EDV comprises a donor template nucleic acid, or a nucleotide sequence encoding the donor template nucleic acid. 34. The EDV of any one of 1-33, further comprising a therapeutic polypeptide, or a nucleic acid comprising a nucleotide sequence encoding a therapeutic polypeptide. 35. The EDV of 34, wherein the therapeutic polypeptide is a chimeric antigen receptor (CAR). 36. The EDV of 35, wherein the CAR comprises one or more scFv or one or more nanobodies specific for a cancer-associated antigen. 37. The EDV of 36, wherein: a) the cancer-associated antigen is a solid tumor-associated antigen selected from: EGFR, HER2, EGFR806, mesothelin, PSCA, MUC1, claudin 18.2, EpCAM, GD2, VEGFR2, AFP, Nectin4/FAP, CEA, LewisY, Glypican-3, EGFRIII, IL-13Rα2, CD171, MUC16, PSMA, AXL, CD20, CD80/86, c-MET, DLL-3, DR5, EpHA2, FR-α, gp100, MAGE-A1, MAGE-A3, MAGE-A4, and LMP1; or b) the cancer-associated antigen is an antigen associated with hematological cancer, wherein the cancer-associated antigen is selected from: BCMA, C5, CD19, CD20, CD22, CD25, CD30, CD33, CD38, CD40, CD45, CD52, CD56, CD66, CD74,
CD79a, CD79b, CD80, CD138, CTLA-4, CXCR4, DKK, EphA3, GM2, HLA-DR beta, integrin αVβ3, IGF-R1, IL6, KIR, PD-1, PD-L1, TRAILR1, TRAILR2, transferrin receptor, and VEGF. 38. A composition comprising the EDV of any one of 1-37 and a pharmaceutically acceptable excipient. 39. A collection of one or more nucleic acids, wherein said one or more nucleic acids encode the EDV of any one of 1-37. 40. The collection of 39, wherein at least one of said one or more nucleic acids encodes the MA polypeptide, the N-terminally truncated capsid (CA) protein, and the nucleic acid-binding effector polypeptide. 41. The collection of any one of 39-40, wherein at least one of said one or more nucleic acids encodes a gag polyprotein comprising the MA polypeptide, the N-terminally truncated capsid (CA) protein, and the nucleic acid-binding effector polypeptide (e.g., CRISPR-Cas effector polypeptide), but does not encode the NC protein. 42. The collection of any one of 39-41, wherein at least one of said one or more nucleic acids encodes a CRISPR-Cas guide RNA. 43. The collection of any one of 39-42, wherein said one or more nucleic acids is two or more nucleic acids. 44. An enveloped delivery vehicle (EDV), comprising: (a) a Cas9 polypeptide comprising 4 or more NLSs; (b) a variant vesicular stomatitis virus glycoprotein (VSVG) viral envelop protein that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R354A), respectively, relative to SEQ ID NO: 153; and (c) a targeting polypeptide that provides for binding to a target cell, wherein the targeting polypeptide is a fusion protein comprising a PDGFR transmembrane domain fused to an antibody or antibody analog. 45. The EDV of 44, wherein the Cas9 polypeptide is a fusion polypeptide comprising: i) a Cas9 protein; and ii) one or more heterologous polypeptides. 46. The EDV of 45, wherein the Cas9 protein has nickase activity or is catalytically deactivated. 47. The EDV of 45 or 46, wherein at least one of said one or more heterologous polypeptides comprises a deaminase, a reverse transcriptase, a transcription modulator, or an epigenetic modulator.
48. The EDV of any one of 45-47, wherein at least one of the one or more heterologous polypeptides is a Gag polypeptide. 49. A collection of one or more nucleic acids, wherein said one or more nucleic acids encode the EDV of any one of 44-48. 50. A collection of one or more nucleic acids, wherein said one or more nucleic acids encode an enveloped delivery vehicle (EDV), the EDV comprising: (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide); (b) a viral envelop protein; and (c) a targeting polypeptide that provides for binding to a target cell, wherein the viral envelop protein and the targeting polypeptide are encoded by nucleotide sequences that are: (i) present on the same nucleic acid as part of the same transcript, and (ii) are separated by a sequence that promotes the production of two independent proteins. 51. The collection of 50, wherein the viral envelope protein is selected from: a Hepatitis B virus (HBV) glycoprotein, a Hepatitis C virus (HCV) glycoprotein, a Marburg virus glycoprotein, an Ebola virus glycoprotein, a vesicular stomatitis virus (VSV) glycoprotein, an influenza virus hemagglutinin, a SARS-CoV glycoprotein, a respiratory syncytial virus (RSV) glycoprotein, a human parainfluenza virus glycoprotein, a moloney murine leukemia virus (MMLV), a measles virus hemagglutinin and/or a measles virus fusion glycoprotein, an HTLV-1 glycoprotein, a Ross river virus glycoprotein, a rabies virus glycoprotein, a Mokola virus glycoprotein, a Semliki Forest virus glycoprotein, a Sindbis virus glycoprotein, a Venezuelan equine encephalitis virus glycoprotein, a sendai virus, a baculovirus, and a variant of any of the above that comprises one or more amino acid substitutions that reduce binding of the viral envelope protein to its receptor. 52. The collection of 50, wherein the viral envelop protein is a variant vesicular stomatitis virus glycoprotein (VSVG) that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R35A), respectively, relative to SEQ ID NO: 153. 53. The collection of any one of 50-52, wherein the sequence that promotes the production of two independent proteins encodes a 2A peptide, an intein, or an IRES, or comprises intronic splice donor/splice acceptor sequences.
54. The collection of any one of 50-53, wherein said two or more nucleic acids encode a pol polyprotein comprising a protease (PR), a reverse transcriptase (RT), and an integrase (INT). 55. The collection of any one of 50-54, wherein said two or more nucleic acids encode a guide RNA. 56. The collection of any one of 50-55, wherein the nucleic acid-binding effector polypeptide is a CRISPR-Cas effector polypeptide (e.g., Cas9). 57. The collection of any one of 50-56, wherein the nucleic acid-binding effector polypeptide is a fusion polypeptide comprising: i) a CRISPR-Cas effector polypeptide; and ii) one or more heterologous polypeptides. 58. The collection of 57, wherein at least one of the one or more heterologous polypeptides is a Gag polypeptide. 59. The collection of any one of 50-58, wherein the targeting polypeptide is a fusion protein comprising a PDGFR transmembrane domain fused to an antibody or antibody analog. 60. A method of producing an enveloped delivery vehicle (EDV), the method comprising: a) introducing the collection of any one of 39-43 and 49-59 into a packaging cell; and b) harvesting EDVs produced by the packaging cell. 61. A method of delivering a nucleic acid-binding effector polypeptide (e.g., a CRISPR- Cas effector polypeptide) to a eukaryotic cell, the method comprising contacting a eukaryotic cell with the EDV of any one of 1-37 and 44-48 or the composition of 38. 62. The method of 61, wherein the eukaryotic cell is in vivo. 63. The method of 61, wherein the eukaryotic cell is in vitro or ex vivo. 64. The method of any one of 61-63, wherein the eukaryotic cell is a cancer cell, a stem cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue-resident stem cell, a monocyte, a macrophage, a B cell, or a T cell. 65. A method for modifying a target nucleic acid in a eukaryotic cell, the method comprising contacting a eukaryotic cell with the EDV of any one of 1-37 and 44-48 or the composition of 38, wherein said contacting results in delivery of the nucleic acid-
binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide) into the cell and modification of a target nucleic acid within the cell. 66. The method of 65, wherein the eukaryotic cell is a cancer cell, a stem cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue-resident stem cell, a monocyte, a macrophage, a B cell, or a T cell. 67. The method of 65 or 66, wherein the eukaryotic cell is in vitro or ex vivo. 68. The method of 65 or 66, wherein the eukaryotic cell is in vivo and the method comprises administering the EDV to an individual, wherein the EDV enters the eukaryotic cell in the individual and modifies the target nucleic acid in the eukaryotic cell. 69. The method of any one of 65-68, wherein the eukaryotic cell is a CD4+ T cell or a CD8+ T cell. 70. The method of any one of 65-68, wherein the eukaryotic cell is a regulatory T cell (Treg). 71. The method of any one of 65-70, wherein the targeting polypeptide comprises an anti-CD3 and/or an anti-CD28 antibody or antibody analog. 72. The method of any one of 65-70, wherein the targeting polypeptide comprises an anti-CD19, anti-CD20, anti-CD4, anti-CD28, or anti-CD3 antibody or antibody analog. 73. The method of any one of 65-70, wherein the targeting polypeptide comprises an antibody, antibody analog, single chain Fv, diabody, triabody, nanobody or a bi-specific antibody. 74. The method of 73, wherein the targeting polypeptide binds to CD19, CD20, CD4, CD28, or CD3. 75. The method of any one of 65-74, wherein the EDV comprises a donor template nucleic acid or a nucleotide sequence encoding the donor template nucleic acid, wherein the donor template nucleic acid comprises a nucleotide sequence encoding a chimeric antigen receptor (CAR). 76. The method of 75, wherein the CAR comprises one or more scFv or one or more nanobodies specific for a cancer-associated antigen. 77. The method of 76, wherein: a) the cancer-associated antigen is a solid tumor-associated antigen selected from: EGFR, HER2, EGFR806, mesothelin, PSCA, MUC1, claudin 18.2, EpCAM, GD2, VEGFR2, AFP, Nectin4/FAP, CEA, LewisY, Glypican-3, EGFRIII, IL-13Rα2,
CD171, MUC16, PSMA, AXL, CD20, CD80/86, c-MET, DLL-3, DR5, EpHA2, FR-α, gp100, MAGE-A1, MAGE-A3, MAGE-A4, and LMP1; or b) the cancer-associated antigen is an antigen associated with hematological cancer, wherein the cancer-associated antigen is selected from: BCMA, C5, CD19, CD20, CD22, CD25, CD30, CD33, CD38, CD40, CD45, CD52, CD56, CD66, CD74, CD79a, CD79b, CD80, CD138, CTLA-4, CXCR4, DKK, EphA3, GM2, HLA-DR beta, integrin αVβ3, IGF-R1, IL6, KIR, PD-1, PD-L1, TRAILR1, TRAILR2, transferrin receptor, and VEGF. 78. The method of any one of 65-77, wherein the EDV comprises: a) a CRISPR-Cas effector polypeptide; and b) one or more CRISPR-Cas guide RNAs, or one or more nucleic acids encoding the one or more CRISPR-Cas guide RNAs. 79. The method of any one of 68-78, wherein said administering comprises intravenous administration. VII. EXAMPLES [00471] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how to make and use the present invention, and are not intended to limit the scope of what the inventors regard as their invention nor are they intended to represent that the experiments below are all or the only experiments performed. Efforts have been made to ensure accuracy with respect to numbers used (e.g. amounts, temperature, etc.) but some experimental errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, molecular weight is weight average molecular weight, temperature is in degrees Celsius, and pressure is at or near atmospheric. Standard abbreviations may be used, e.g., bp, base pair(s); kb, kilobase(s); pl, picoliter(s); s or sec, second(s); min, minute(s); h or hr, hour(s); aa, amino acid(s); kb, kilobase(s); bp, base pair(s); nt, nucleotide(s); i.m., intramuscular(ly); i.p., intraperitoneal(ly); s.c., subcutaneous(ly); and the like. Example 1 – Development and use of Gen3 EDVs [00472] Objective: To streamline the delivery of genome editors. Rationale: Viral proteins were evolved to deliver an RNA cargo, it is unclear if they are necessary to deliver genome editors. Significance: Understanding the role of these proteins allows us to design EDVs with higher editing activity and fewer viral components – simplified EDV systems (FIG.4). [00473] It was first tested whether the capsid cone was necessary for the nuclear delivery of Cas9 enzymes. There are two possible mechanisms: Capsid cone and Nuclear localization signals. EDVs or
lentiviruses (LV) were incubated with capsid inhibitors (FIG.5). The data demonstrated that while capsid inhibitors inhibited lentivirus mediated editing, they did not inhibit EDV mediated editing (FIG. 6). Additional data demonstrated that nuclear transport of Cas9 was independent of the capsid cone (FIG. 7). Further data demonstrated that nuclear transport of Cas9 required nuclear localization signals in this context (FIG.8). Additional experiments were performed and are summarized in the following paragraph. [00474] FIG.9. Experimental optimization to form 3rd generation EDVs. (FIG.9a) The Pol polypeptide, which includes integrase (Int), reverse transcriptase (Rt), and protease (Pr), was deleted without adversely affecting EDV editing activity. Following this deletion, EDVs were produced and their editing activity was evaluated using a luminescence assay in cell culture. A higher luminescence value indicated increased editing. (FIG.9b) The C-terminal (residues 149-231) of capsid were necessary for EDV activity. After shortening the capsid protein to the indicated residues, EDVs were formed and their editing activity was assessed with the same luminescence assay. (FIG.9c) The nucleocapsid protein was not essential for EDV editing activity. The nucleocapsid protein was truncated (deletions as indicated), EDVs were formed and editing activity was measured with a luminescence assay. (FIG.9d) The matrix protein was important and could not be eliminated without compromising EDV activity. After reducing the matrix protein to specific residues, EDVs were formed and their editing activity was determined with the luminescence assay. (FIG.9e) Adding C-terminal NLSs enhanced EDV activity. SV40 NLS were appended to the C-terminal end of Cas9, followed by the formation of EDVs and evaluation of their editing activity. (FIG.9f) Adding additional NLS to the N-terminal end of Cas9 did not improve editing activity. The specifics of the NLS added are noted accordingly. (FIG.9g) Integrating the above optimizations resulted in the creation of the 3rd generation EDVs. This version exhibited over 3 times the editing efficiency and contained fewer viral structural protein domains compared to earlier generations. The benchmark was the generation 1 (Hamilton et al., Nat Biotechnol.2024 Jan 11) labelled as “Baseline”. The 3rd generation EDVs, labelled as “Streamlined -PR”, included a full-length matrix, capsid protein from residues 149-231, no nucleocapsid, 7 NLS on the C-terminus of Cas9, and were devoid of integrase, reverse transcriptase, and protease. The “Added NLS” construct represents generation 1 EDVs with 7 NLS on the C-terminus of Cas9. The “streamlined +PR” variant mirrors the 3rd generation EDV, with the addition of protease. Both “streamlined -NES +PR” and “streamlined - NES -PR” conditions were analogous to their respective “streamlined +PR” or “streamlined -PR” setups but lacked the NES on Cas9. EDVs with these specific modifications were synthesized and their editing efficiency was quantified using the luminescence assay. [00475] Thus, the data demonstrated that NLSs are important and that nuclear delivery of editing enzymes did not depend on viral (e.g., lentiviral) proteins.
[00476] Table 1. Sequences of proteins tested in the experiments (see FIG. 9A-9G). For Gag-Pol, nucleotide sequences are provided. Fi L l E ID
Example 2: Demonstration that multiple different antibodies can be used to target EDVs to desired cell types [00477] FIG.12: Cas9-EDV genome editing activity can be directed to specific primary human cells using scFv-targeting molecules. A panel of optimized Cas9-EDVs (packaging TRAC-targeting Cas9 RNP complexes) were produced with various indicated pseudotypes and concentrated approximately 200-fold (30ml supernatant (sup) into 150 μl T cell media).50 μl Cas9-EDVs were used to treat 15k pre- stimulated primary human cells in a final well volume of 100ul. Flow cytometry was performed at five days post treatment to assess the loss of T cell receptor (TCR) expression in CD4+ and CD8+ cells. CD4 scFv-targeted Cas9-EDVs mediated TCR knockout in CD4+ cells but not in co-cultured CD8+ bystander cells. CD3 scFv-targeted Cas9-EDVs mediated editing in both CD4+ and CD8+. Cas9-EDVs displaying CD19 scFv targeting molecules (which should not bind T cells) did not result in editing of either population. Multiplexing the display of CD3 and CD4 scFv-targeting molecules enhanced genome
editing over displaying either CD3 or CD4 scfvs alone. Cas9-EDVs pseudotyped with HIV-1 and VSVG are presented as controls – HIV-1 Env pseudotyped EDVs mediated genome editing specifically in CD4+ T cells, while VSVG pseudotyped EDVs mediated genome editing in CD4+ and CD8+ T cells. [00478] FIG.13: Multiplexing CD3 and CD28 scFv targeting molecules on Cas9-EDVs facilitated T cell activation and proliferation. A panel of Cas9-EDVs (packaging PDCD1-targeting Cas9 RNP complexes) were produced with various indicated pseudotypes and concentrated approximately 62.5-fold (10ml sup into 160 μl T cell media).50ul were used to treat 30k pre-stimulated primary human cells in a final well volume of 100 μl. Three days post treatment, cell count and expression of CD25 (a marker of T cell activation) was analyzed by flow cytometry. Cell count was used to calculate a fold expansion, normalized to untreated “no tx” cells. Additionally, DNA was extracted and genome editing at the PDCD1 locus was assessed by next-generation amplicon sequencing. [00479] FIG.11 provides a table that provides descriptions of illustrative non-limiting examples of scFv polypeptides that can be used as targeting polypeptides of subject EDVs. Sequences: (GGGGSGGGGSGGGGS, SEQ ID NO194; TGGGGSGGGGSGGGGS, SEQ ID NO:192; TGSTSGSGKPGSGEGSTKG, SEQ ID NO:193; GGGGSGGGGSGGGGSS, SEQ ID NO:203). Results from experiments using these antibodies with EDVs demonstrated cell-specific genome editing can be achieved both ex vivo and in vivo by pairing the display of VSVGmut with single-chain antibody fragments (scFvs) on EDVs that package Cas9 ribonucleoprotein (RNP) complexes (Cas9-EDVs). EDVs leverage retroviral VLP assembly for the transient delivery of Cas9 RNP. Cas9-EDVs achieved targeted genome editing within in vivo-generated CAR T cells in humanized mice, with no off-target delivery to liver hepatocytes, showing that EDVs are a programmable, cell-specific delivery platform for complex genome engineering in vivo. Examples 3-8 Overview – In Vivo Generation of TRAC-CAR T Cells [00480] The Examples below relate to in vivo methods using vector-delivered HDRTs and CD3 targeting enveloped delivery vehicles (EDVs) loaded with Cas9 nuclease to precisely integrate CAR transgenes to the TRAC locus of T cells. In vivo generated TRAC-CAR T cells would combine T cell specific and physiological CAR expression while bypassing the ex vivo cell manufacturing and patients pre- conditioning. Example 3: Materials and Methods [00481] The materials and methods for Examples 4-9 below are provided here in Example 3. [00482] Enveloped delivery vehicles (EDVs). The following EDVs were used in the Examples herein to deliver Cas9/sgTRAC ribonucleoprotein (RNP) to a cell. A first generation EDV was used that was
coated with a WT vesicular stomatitis virus glycoprotein G (WT-VSVG EDV). A second generation EDV was used that was coated with a mutated VSVG (K47Q and R354A) that has fusogenic activity and an anti-CD3 antibody (VSVGm-aCD3 EDV). The VSVGm-aCD3 EDV included a Cas9 with a 4xNLS at the C-terminus, and in addition, the VSVGm and antibody coding sequences were present on the same nucleic acid as part of the same transcript, separated by a P2A sequence. VSVGm-aCD3 EDV is discussed in Examples 6-9 and Figures 16A-2D and 17A-17C. [00483] CD-19-Targeting TRAC-CAR T Cells. To generate CD19-targeting TRAC-CAR T cells, a nucleic acid sequence encoding a CD19 targeted CAR was used in certain HDRTs discussed below. [00484] Ex vivo transduction of human T cells. In general, human T cells were activated for 48 hours using anti-CD3/CD28 dynabeads. The cells were then transduced with various combinations of concentrated EDVs carrying Cas9/sgTRAC RNPs with separate vectors carrying an HDRTs. [00485] Flow cytometry. Cell expression of TCRs, EGFR, and cell surface markers (e.g., CD4, CD8, CD19, CD25, and CD45) were determined by flow cytometry. Flow cytometry analysis was typically performed 72 to 96 hours after T cell transduction. [00486] Cytotoxicity assay. Cell cytotoxicity was measured using a peripheral blood mononuclear cell (PBMC) cytotoxicity luciferase assay kit for toxicity towards a NALM6 cell line. NALM6 is a CD19+ acute lymphoblastic leukemia (ALL) cell line. In general, the method produces a cytotoxic activity profile of target PBMCs, e.g., transduced T cells, towards the firefly luciferase NALM6 cell line – a decrease in luciferase signal indicates toxicity of the target PBMCs towards NALM6. NALM6 cells were co-cultured with T cells for 24 hours with several effector to tumor cell (E:T) ratios. [00487] A humanized mouse model. Six to 8-week old immunodeficient NOD/SCID/IL2Rγ-/-(NSG) mice were acquired from the Jackson Laboratory (jax.org). The mice were engrafted with human PBMCs for reconstitution of T cell, NK cell, and B cell populations in the mice (Figure 17A). Two weeks after human PBMC engraftment, the mice receive intravenous (IV) injections of mixtures of 5x1010 particles of (1) WT-VSVG EDV or VSVGm-aCD3 EDV carrying Cas9/sgTRAC and (2) a vector providing a CD19 targeted CAR. Control mice were injected with phosphate buffer saline (PBS). Two weeks later, the mice were euthanized and the organs, including the spleen, were harvested. Mice spleens were analyzed by flow cytometry: B cells were determined as CD45+/CD19+ and CAR-T cells were determined as CD45+/CAR+/EGFRT+. Example 4: Transduction of T Cells with a WT-VSVG EDV Carrying a TRAC-Targeting Cas9 RNP [00488] This Example demonstrates the use of the first generation EDVs to deliver a TRAC-targeting Cas9 RNP (Cas9/sgTRAC RNP) to T cells. The first generation EDV was coated with WT-VSVG (WT- VSVG EDV; labeled “Cas9-sgTRAC” in Figure 15A). Human T cells were transduced in vitro with 50 μl of EDVs at different MOIs: (1) 3x105 T cells (low MOI), (2) 2x105 T cells (medium MOI), and (3) 1x105
T cells (high MOI). The cells were transduced with EDVs in combination with a separately delivered HDRT (labeled “TRAC-CAR-sgTRAC” in Figure 15A). Seventy-two hours after transduction, the cells were analyzed by flow cytometry. [00489] As shown in Figure 15B, the first-generation WT-VSVG EDV successfully delivered a Cas9/sgTRAC RNP in activated primary human T cells and disrupted TCR expression with the HDRT. TCR expression was knocked-down in a dose-response manner; a 60% decrease of TCR expression was achieved. Example 5: Transduction of T Cells using an EDV with a Fusogenic Variant and an Anti-CD3 Antibody [00490] This Example demonstrates the use of a second generation EDV which comprises two features on its surface: (1) a VSVG variant with fusogenic activity (VSVGm), and (2) a CD3-targeting antibody (aCD3). In contrast with the WT-VSVG used in the first generation EDV (as discussed in the Examples above), VSVGm-aCD3 does not have broad tropism – it preferentially targets T cells.1x105 human T cells were transduced with 5x1010 particles of EDV and a separate vector delivering HDRT. Ninety-six hours after transduction, the cells were analyzed by flow cytometry. When combined with an HDRT- carrying vector for transduction of activated human primary T cells, VSVGm-aCD3 EDV achieved similar TRAC CAR knock-in rates compared to the WT-VSVG EDV (Figures 16A-16B). Example 6: The Anti-CD3 Antibody on the EDV Activated Naïve T cells [00491] The anti-CD3 antibody delivered by the second generation EDV (VSVGm-aCD3) was analyzed for activation of naïve T cells. Naïve T cells were treated with either 5 μl (low dose) or 25 μl (high dose) of concentrated EDVs and were compared to untransduced (UT) naïve T cells. CD25 expression was used as a marker for T cell activation. The T cells were analyzed by flow cytometry 48 hours post transduction. As shown in Figure 16C, the VSVGm-aCD3 induced CD25 expression on T cells. Example 7: TRAC-CAR T Cells were Toxic Against B Cells [00492] This Example demonstrates that CD19-targeting TRAC-CAR T cells were cytotoxic against the NALM6 B-ALL cell line. First, CD19 CAR T cells were generated by transducing activated T cells with WT-VSVG EDVs carrying Cas9/sgTRAC in combination with a vector carrying the CD19 CAR HDRT. Then, NALM6 cells expressing luciferase were co-cultured with the transduced T cells at three effector to tumor cell (E:T) ratios: 1:1, 1:2, and 1:4. T cell cytotoxicity was determined by luminescence. As shown in Figure 16D, the CD19 CAR T cells caused toxicity in NALM6 cells. Example 8: In vivo Editing of a T cell Genome Generates a CAR T Cell Capable of Killing Target Cells
[00493] Next, the EDV and HDRT combinations were assessed for generation of TRAC-targeted CAR T cells in vivo. A humanized mouse model was used as discussed in Example 3 and shown in Figure 17A. Fourteen days after human PBMC engraftment, the mice received IV injections of EDV and HDRT combinations or PBS (control) as shown in Table 2 below. Two weeks after the mice received the EDV and HDRT vector injections, the spleens of treated mice were harvested and analyzed by flow cytometry. Table 2: EDV and HDRT vector Combinations Administered to Mice
[00494] CAR+ T cells were detected with all combinations of EDVs and HDRTs. WT-VSVG EDV and HDRT-carrying vector produced about 2x105 CAR T cells and VSVGm-aCD3 EDV and a different HDRT-carrying vector produced about 3x106 CAR T cells (Figure 17B). All combinations of EDVs and HDRT-carrying vector resulted in B cell aplasia (Figures 17B-17C). These results demonstrate in vivo editing of a T cell genome to generate a CAR T cell capable of killing target cells, which in this case, are B cells. Example 9: In vivo Editing of a T cell Genome Generates a CAR T Cell Capable of Killing Target Cells [00495] This example includes some information from the above examples, but also includes additional information. [00496] The widespread application of genome editing to treat or even cure disease requires the delivery of genome editors into the nucleus of target cells. Enveloped Delivery Vehicles (EDVs) are engineered virally-derived particles capable of packaging and delivering CRISPR-Cas9 ribonucleoproteins (RNPs). However, the presence of lentiviral genome encapsulation and replication components in EDVs has obscured the underlying delivery mechanism and precluded particle optimization. The data here show that Cas9 RNP nuclear delivery is independent of the native lentiviral capsid structure. Instead, EDV- mediated genome editing activity corresponds directly to the number of nuclear localization sequences on the Cas9 enzyme. EDV structural analysis using cryo-electron tomography and small molecule
inhibitors guided the removal of ~80% of viral residues, creating a minimal EDV (miniEDV) that retains full RNP delivery capability. MiniEDVs are 25% smaller yet package equivalent amounts of Cas9 RNPs relative to the original EDVs, and demonstrated increased editing in cell lines and therapeutically- relevant primary human T cells. [00497] The work here shows the determination of the components that are necessary for EDV-mediated genome editing. Although the capsid structure assembles in a subset of EDV particles, it does not transport Cas9 RNPs into the nucleus. Instead, NLS peptides engineered into the Cas9 protein confer nuclear entry and can be tuned to improve delivery efficiency. Furthermore, mechanism-guided engineering enabled simplification of the EDV design, creating miniEDV particles with only 22% of the original viral residues while achieving up to 2.5-fold higher editing potency compared to the original EDVs in primary human T cells. These results show that virally-derived particles can be efficacious genome editing delivery vehicles that simplify production and manufacturing. Results The EDV capsid core does not mediate nuclear delivery of Cas9 RNPs [00498] Two small molecule inhibitors of the capsid core were tested, lenacapavir and PF-3450074 (PF74) (Fig.18a). EDVs packaging Cas9 RNPs were produced that target a prematurely truncated luciferase reporter gene (C205ATC). HIV-1 lentiviral vectors packaging a transgene encoding Cas9 enzymes and the same guide RNA were used as a positive control. The particles were incubated with HEK-293T cells expressing the truncated luciferase reporter in either the presence or absence of the inhibitors. Editing leads to insertions and deletions that can restore the luciferase reporter reading frame. Luciferase expression was specific to cleavage at the luciferase locus, proportional to the dose of EDVs and detectable 48 h after transduction (Fig.22). In the presence of increasing concentrations of lenacapavir, a clinically-approved HIV-1 inhibitor that impairs cargo delivery by stabilizing the core (Fig.18b), no decrease in EDV-mediated induction of reporter cell luminescence occurred (Fig.18c). Similarly, incubation of cells with increasing concentrations of the capsid core destabilizer PF74 (Fig. 18d) also had no effect on EDV-mediated luminescence (Fig.18e). Parallel experiments with lentiviral vectors encoding analogous components (Cas9 and sgRNA against the luciferase reporter gene) showed dose-dependent loss of reporter cell luminescence, consistent with inhibitor prevention of lentivirus- mediated nuclear delivery (Fig.18f-18g). Together these results support the conclusion that the capsid core is not needed for Cas9 RNP delivery by EDVs. [00499] As the luminescence produced by the reporter cells depends on both nuclear entry and Cas9 editing, it was directly tested whether Cas9 nuclear entry required the capsid core. HEK-293T cells were incubated with EDVs and PF74 for 24 h, isolated cell nuclei and used Western blots to determine the relative amounts of Cas9 enzymes or capsid associated with the nucleus (Fig.23). PF74 was used in this
experiment because lenacapavir has been shown to stall capsid cores on the cytosolic side of nuclear pores, leading to their co-isolation with the nuclear fraction. Successful nuclear isolation was confirmed by monitoring nuclear localization of EZH2 and cytosolic localization of GAPDH (Fig.23b). The 24 kDa mature capsid protein decreased in the nuclear fraction in the presence of 10 µM PF74, while the amount of Cas9 enzyme remained consistent across all PF74 concentrations (Fig.23b). Both the Gag- Cas9 polyprotein (220 kDa) and Cas9 (160 kDa) were present in the nuclear fractions. The presence of Gag-Cas9 in the nuclear fractions was surprising because it was assumed that editing enzymes needed to be liberated from viral structural proteins by viral protease cleavage to enable nuclear entry. The results suggested that the liberation of Cas9 enzymes by protease cleavage may not be necessary for nuclear association. These results show that Cas9 RNP delivery into the nucleus is independent of the EDV capsid core. EDVs form capsid cores that do not encapsulate Cas9 [00500] It was next wondered why Cas9 RNP nuclear entry was independent of the capsid core. It was tested whether EDVs contain mature capsid cores as observed in lentivirus. After purification by iodixanol cushion ultracentrifugation to remove contaminating proteins, EDVs and lentiviral vectors were visualized in their native hydrated states using cryogenic electron tomography. Three-dimensional tomograms of the EDVs and lentiviral vectors (Supplementary movies 1 and 2) revealed spherical particles with a lipid bilayer in each case (Fig.19a). Surface glycoproteins appeared as dark spots densely coating the lipid bilayer exterior. The proportion of mature particles (with a capsid core), immature particles (concentric rings of proteins under the lipid bilayer) and unknown particles was quantified and compared. Consistent with previous reports, both EDVs and lentiviral particles were of similar size (~125 nm diameter) and contained multiple morphologies of the mature capsid core (Fig. 24a-d). A fraction of EDVs (29%) and lentiviral vectors (51%) were mature with a capsid core (Fig. 19b). Immature EDVs (36%) and lentiviral vectors (18%) were also visible (Fig.19b). The remaining particles (~30%) could not be categorized and were presumed to be other types of vesicles or broken particles (Fig.19b). The higher proportion of immature EDVs compared to lentiviral vectors was confirmed in Western blots. Western blots showed that in lentiviral vectors harvested at 30, 48 or 72 h after transfection, the mature 24 kDa capsid protein was more abundant than the uncleaved (55 kDa) Gag polyprotein (Fig.19c). In contrast, a similar analysis of EDVs showed the 55 kDa Gag polyprotein to be more abundant than the 24 kDa capsid species at all time points (Fig.19c). [00501] Based on this observation it was next examined whether Gag protein maturation differences resulted from structural differences between immature EDVs and lentiviral vectors. Subtomogram averaging and alignment was used to compare the immature capsid domains of EDVs and lentiviral vectors to those of published HIV-1 structures. This analysis revealed that the immature capsid domains
of both EDVs and lentiviral vectors matched the HIV-1 structure (PDB: 5L93) with root mean square deviations of 1.2 Å and 1.7 Å respectively (Fig.24e-f). Together, these data show that immature capsid domains in EDVs were structurally indistinguishable from lentiviral vectors. [00502] It was next tested whether EDV editing activity is independent of the capsid core because it does not encapsulate Cas9. To test this, photocatalytic proximity labeling was used with a lenacapavir-eosin Y conjugate to map proteins located near the capsid core components (Fig.19d). Examination of the published co-structures of lenacapavir and capsid (PDB: 7RJ4) suggested that the alkyne group on lenacapavir is not involved in binding and could potentially be used for small molecule conjugation. The lenacapavir-eosin Y or unconjugated lenacapavir and eosin Y was incubated with EDVs, then one of three photo-probes (diazirine-biotin, aryl-azide-biotin and phenol-biotin) was added, each with a different labeling radius. Upon illumination with blue light, proteins proximal to the photocatalyst were biotinylated and captured by biotin enrichment using NeutrAvidin beads. Control samples with unconjugated lenacapavir and eosin Y showed that Gag-Cas9 (220 kDa), Cas9 (160 kDa), and mature capsid proteins were biotinylated and detected with all probes (Fig.19e), because the eosin Y could diffuse throughout the particle. When eosin Y was conjugated to lenacapavir, preventing it from diffusing throughout the particle due to binding and localization at the capsid core, only the mature capsid protein, but not Cas9, was biotinylated regardless of the biotin probe used. The amount of the capsid protein that became biotinylated was proportional to the concentration of the lenacapavir-eosin Y conjugate used in the experiment. Each sample had similar quantities of input proteins, so the differences in abundance detected by biotin immunoprecipitation were caused by different localization of the photocatalyst and not sample loading. These results are consistent with observations of uncleaved Gag- Cas9 in the EDVs, where the Gag-Cas9 polyproteins are bound to the inner membrane of the EDVs and localized away from the capsid core. The prevalence of immature EDVs (Fig.19c) also means that the majority of particles do not form a capsid core. Altogether, the data shows that it is unlikely that Cas9 associates with the core. The amount of Cas9 associated with the mature EDV capsid core was undetectable. EDV editing activity correlates with nuclear localization signal abundance on Cas9 [00503] Since the capsid core does not transport Cas9 RNPs to the cell nucleus, it was reasoned that engineered NLSs on the Cas9 enzyme might be essential for nuclear entry and editing activity. To test this, both the heterologous N-terminal p53 and C-terminal SV40 NLSs were systematically removed from the packaged Cas9 enzymes (Fig.20a). A corresponding decrease in the luminescence of reporter cells treated with these EDVs was observed, consistent with a requirement for NLS-mediated Cas9 nuclear transport. Removing the C-terminal SV40 NLS had a larger effect on reporter luminescence than removing the N-terminal p53 NLS. Removing all NLSs reduced the luminescence of EDV-treated
reporter cells by more than 95%. It was further tested whether the residual editing activity of the Cas9 RNPs without NLSs could be due to nuclear transport by the capsid core. Lenacapavir did not significantly decrease the luminescence of reporter cells incubated with EDVs packaging Cas9 RNPs lacking NLSs, indicating that the residual editing activity was not due to capsid core transport (Fig.20b). These results show that the dominant route of nuclear delivery by EDVs is by NLSs rather than capsid core (Fig.20c). [00504] It was also found that adding additional NLSs to Cas9 enhances EDV-mediated Cas9 RNP editing efficiency. EDVs packaging Cas9 RNPs containing two to ten SV40 NLSs at the C-terminus of the Cas9 enzyme were created (Fig.20d), because the C-terminal NLS had a larger effect on editing (Fig. 20a). Cas9s with four to nine NLSs showed ~2-fold higher activity compared to the original two-NLS design, with seven NLSs being the best. Adding additional N-terminal NLSs to the Cas9 enzymes with seven C-terminal NLSs did not further improve EDV-mediated editing activity (Fig.25a). To confirm that the improvements in EDV editing were not specific to the luciferase reporter cells, the four- and seven-NLS Cas9 designs were tested in primary human T cells. The TRAC locus was targeted to disrupt the native T cell receptor (TCR), a step in the creation of therapeutic TCR-T cells. Activated T cells were incubated with an equal number of EDVs, and editing was quantified three days post-incubation by amplicon sequencing. EDVs packaging Cas9 RNPs with four or seven NLSs increased editing by 79% and 73% at the TRAC locus, respectively, compared to the original two-NLS designs (Fig.20e). This increase in TRAC editing resulted in a corresponding reduction in the number of TCR-expressing T cells as quantified by flow cytometry (Fig.25b). Removing capsid core-related components created functional minimal EDVs [00505] It was next wondered whether viral proteins that form or interact with the EDV capsid core could be removed, which could simplify particle production and avoid undesirable interactions with host cell proteins. Based on data showing that the C-terminal domain of the capsid protein was sufficient for Gag and Gag-pol proteins to assemble into immature HIV-1 virions, the capsid N-terminal domain (amino acids 5 -148) or the entire capsid protein (amino acids 5 - 227) was removed from the Gag and Gag-Pol polypeptides and the resulting EDVs were tested in luciferase reporter cells. N-terminal domain removal had no effect but removing the entire capsid protein decreased editing by ~75% (Fig.21a). Next, the removal of the Pol polyprotein, which includes viral protease, reverse transcriptase and integrase, was tested. The viral protease matures HIV-1 virions and may also liberate Cas9 RNPs from Gag proteins but is unnecessary in murine leukemia virus-based particles packaging base editors. Reverse transcriptase and integrase assemble with the capsid core to form the pre-integration complex for transgene integration. Removing either the viral protease (RT + INT) independently or the entire Pol polypeptide did not significantly decrease the activity of the EDVs, which shows that both Cas9 and Gag-Cas9 are
functional (Fig.21b). Similar deletion or truncation of the two remaining HIV-1 structural proteins, matrix and nucleocapsid, showed that matrix is required but nucleocapsid is not (Fig.21c, 21d). Removing the nucleocapsid protein increased EDV-mediated editing by 43%. Altogether, these data show that most viral proteins related to the capsid core (N-terminal of the capsid, nucleocapsid, protease, integrase, and reverse transcriptase) are not necessary in EDVs. [00506] These deletions were combined to create minimal EDVs (miniEDVs) from both the four- and seven-NLS Cas9 designs due to their similar editing potency (Fig.20). Although miniEDVs contain only 22% of the viral protein residues present in the original EDVs, they were produced with similar physical titers to the original particles (Fig.21e; Fig.26a). Cryogenic electron tomograms showed these particles to be 25% smaller than the original EDVs (Fig.26b), with visible lipid envelopes and glycoproteins but lacking capsid cores (Fig.26c). Patches of protein density underneath the membrane may correspond to the minimized Gag protein (Fig.26d). The number of packaged Cas9 enzymes dropped from 391 ± 34 to 265 ± 16 per particle in original versus miniEDVs (Fig.26e), roughly consistent with the reduction in volume from ~1.0×106 nm3 to ~4.3×105 nm3 per particle. Notably the number of sgRNAs per particle remained consistent at ~200 per particle (Fig.26f), suggesting that both original and miniEDVs package a similar number of Cas9 RNPs. It was further found that miniEDVs could be produced with high functional titers without supplementing producer cells with plasmids encoding extra structural proteins (Fig.27), simplifying their production. In addition, single-chain antibodies can be displayed on their surface to mediate cell entry (Fig.28). [00507] Lastly, the editing efficiency of the miniEDVs was compared to both the original and NLS- optimized EDV designs in primary human activated T cells at the TRAC locus by quantifying the decrease in T cell receptor expression by flow cytometry five days post-incubation (Fig.21f). MiniEDVs packaging four- or seven-NLS Cas9s increased editing by 107% and 53%, respectively, relative to the original EDVs and were comparable to their respective NLS-optimized EDV counterparts. The editing efficiency of the miniEDVs packaging four-NLS Cas9s was further benchmarked across a range of concentrations in both HEK-293T cells and activated primary human T cells at the B2M locus, whose disruption enables production of allogeneic CAR T cells. An average increase in editing per EDV particle of ~2.5-fold in both HEK-293T and activated T cells was observed. Thus, understanding the components inside of EDVs necessary for Cas9 delivery allowed increased editing potency while streamlining the production of delivery vehicles for genome editing. Discussion [00508] The data here show that EDV-mediated Cas9 RNP editing activity is independent of the viral capsid core and instead depends on Cas9 nuclear localization signals (NLSs). Based on this finding and data from EDVs lacking additional viral proteins, miniEDVs were developed that showed 2.5-fold higher
editing potency, relative to original EDVs, in both cell lines and primary cells. If desired, miniEDVs can be produced in cells transformed with two plasmids, compared to three or more plasmids required for original EDVs. [00509] Cryo-electron tomography showed that EDVs and lentiviral vectors share similar morphology and capsid structures. However, unlike lentivirus, EDVs do not use the internal capsid core for nuclear delivery of Cas9 RNPs. Instead, EDV-mediated genome editing depended on the presence of nuclear localization signal (NLS) peptides engineered onto Cas9. Cas9 RNPs were not associated with the capsid core, paving the way for removal of the capsid structure from EDVs to create simpler and more efficacious miniEDV particles. [00510] The miniEDVs are 25% smaller than the original EDVs, yet packaged an equivalent quantity of guide RNAs and by extension Cas9 RNPs. The miniEDVs do not contain functional viral enzymes (protease, reverse transcriptase or integrase) or viral nucleic acid-binding domains (nucleocapsid), reducing the possibility of unwanted interactions with target cells. [00511] While the experiments here focused on an HIV-1-derived particle system, other virally-derived particles, including those based on related retroviruses, likely contain unnecessary proteins and can be simplified. The finding that miniEDVs require fewer plasmids to be produced while exhibiting higher editing activity and programmable cell entry, underscores the value of a mechanism-based approach to development. These results help make genome editing therapies simpler, easier to produce and more efficacious. MATERIALS [00512] HEK-293T cells were a gift from Melanie Ott.15-cm plates (FB012925), 24-well plates (353047) and 10-cm plates (353003) were from Fisher Scientific. DMEM (10-013-CV), fetal bovine serum (97068-085) and 0.45-μm filters (76479-020) were purchased from VWR.1×PBS (21-040-CM), and trypsin (25-053-Cl) were from Corning. Penicillin-streptomycin (10,000 units/mL) (15140122), Opti-MEM™ I reduced serum medium ( 31985062), RIPA lysis and extraction buffer (89900), Halt™ protease inhibitor cocktail (100X) (78429), Pierce™ BCA protein assay kits (23225), SuperSignal™ west femto maximum sensitivity substrate (34094), Pierce™ ECL Western blotting substrate (32109), Restore™ PLUS Western blot stripping buffer (46428), NP-40 Surfact-Amps™ detergent solution (85124), Dynabeads™ human T-activator CD3/CD28 (11161D), custom TaqMan™ small RNA assays (CTRWFGP for luciferase sgRNA, CTZTEYN for CLTA sgRNA, CTCE4RX for TRAC sgRNA, and CTWCW3V for the B2M sgRNA), MicroAmp™ optical 384-well reaction plates (4309849), DAPI (4',6- diamidino-2-phenylindole, dilactate) (D3571), NeutrAvidin agarose beads (29200), One Shot™ Mach1™ T1 phage-resistant chemically competent E. coli (C862003) and NuPAGE™ LDS sample buffer (4X) (NP0007) were purchased from Thermo Fisher Scientific, Inc.2-mercaptoethanol (M6250),
DL-dithiothreitol (DTT) (D9779), anti-HIV-1 p24 antibody produced in rabbit (SAB3500946), monoclonal anti-Flag M2 antibody produced in mouse (F1804), ethylenediaminetetraacetic acid disodium salt dihydrate (ED2SS), magnesium chloride (M4880), bovine serum albumin (A2058), copper (II) sulfate (C1297), sodium L-ascorbate (A4034), and dimethyl sulfoxide (DMSO) (D8418) were from Sigma-Aldrich. DNA/RNA shield DirectDetect™, ZymoPURE II plasmid midiprep (D4200), ZymoPURE II plasmid maxiprep (D4202), ZymoPURE II plasmid gigaprep (D4204) and Mix & go E. coli transformation kit & buffer sets (T3002) were purchased from Zymo Research Corporation. Sucrose (S24060) was purchased from Research Products International. Primers and oligonucleotide sequences were purchased from Integrated DNA Technologies. Plasmids pJRH-1179 U6-reci Gag-Cas9 v2 (Add gene 201915) and pJRH-1180 U6-reci Gag-pol v2 (Addgene 201914) were a gift from Jennifer Hamilton. Plasmids pMD2.G (12259), psPAX2 (12260), pHAGE-CMV-Luc2-IRES-ZsGreen-W (164432), and U6-sgRNA-EFS-Cas9-P2A-Puro (211687) were ordered from Addgene. NEBuilder® HiFi DNA assembly master mix (E2621X), Luna® universal one-step RT-qPCR kit (E3005E), nuclease- free water (B1500L), thermolabile proteinase K (P8111S) and Q5® high-fidelity 2X master mix (M0492L) were purchased from New England Biolabs. EM gold tracer, 10 nm (25487), and Quantifoil R2/2, UT, 200 mesh, gold grids (Q2100AR2-2nm) were purchased from Electron Microscopy Sciences. Polyethylemimine, Linear (MW 25,000) (23966) was purchased from Polysciences. HIV1 p24 ELISA kits (ab218268) were purchased from Abcam. Criterion TGX stain-free gel 4-20% (5678094), precision plus protein kaleidoscope standards (1610375), mini bio-spin columns (7326207), and nitrocellulose membranes, 0.2 µm (1620112) were purchased from Bio-Rad Laboratories, Inc. IRDye® 800CW goat anti-rabbit IgG secondary antibody (926-68070), IRDye® 800RD goat anti-mouse IgG secondary antibody (926-32210) and IRDye® 680RD goat anti-mouse IgG secondary antibody (926-32211) were purchased from Li-COR Biosciences. Goat anti-mouse IgG heavy and light chain cross-adsorbed antibody HRP conjugated (A90-516P) and goat anti-rabbit IgG heavy and light chain cross-adsorbed antibody HRP conjugated (A120-201P) were purchased from Fortis Life Sciences. Mouse anti-cas9 antibody (61758) was purchased from Active Motif, Inc. EZH2 (D2C9) XP® rabbit mAb #5246 (5246S) was purchased from Cell Signaling technology. GAPDH antibody (G-9) (sc-365062) was purchased from Santa Cruz Biotechnology. Lenacapavir (HY-111964), and PF74 (HY-120072) were purchased from MedChemExpress. Passive lysis buffer (E1941), and CellTiter-Glo 2.0 cell viability assays (G9242) were purchased from Promega Corporation. CulturPlate-96 black plates (6005660) were purchased from PerkinElmer. Illumination™ lyophilized firefly luciferase enhanced assay kit (I-935- 1000) was purchased from Gold Biotechnology. Human peripheral blood leukopak (200-0092), and EasySep™ human T cell isolation kits (100-069) were purchased from STEMCELL Technologies. X- VIVO 15 serum-free hematopoietic cell medium (04-418Q) was purchased from Lonza. N-acetyl-L- cysteine USP (VWRV0108-25G) was purchased from VWR International, LLC. Recombinant human
IL-7 (200-07), and recombinant human IL-2 (200-02) were purchased from PeproTech, Inc. Silica quality control nanospheres were purchased from NanoFCM, Inc. Recombinant human IL-15 (247-ILB) was purchased from R&D systems. Cas9 ELISA kits (PRB-5079) were purchased from Cell Biolabs. APC anti-human β2-microglobulin antibody (316312) and APC anti-human TCR α/β antibody (306718) were purchased from BioLegend, Inc. A 10% SDS solution (S0288) was from Alpha Teknova, Inc. QIAprep spin miniprep kits (27106), QIAquick gel extraction kits (28704) and QIAquick PCR purification kits (28104) were purchased from Qiagen. SPRIselect beads (B23318) were purchased from Beckman Coulter Life Sciences. PhiX sequencing control v3 (FC-110-3001), NextSeq 500/550 mid output kit v2.5 (150 Cycles) (20024904) and HT1 hybridization buffer (20015892) was purchased from Illumina Inc. Isothiocyanate-EY (90091) was purchased from Biotium. Azide-PEG4-amine (BP-21615) was purchased from BroadPharm. BTTAA (1236-100) was purchased from Click Chemistry Tools (Vector Laboratories). METHODS [00513] Cell culture. HEK-293T cells (1.6 million) were seeded into 15-cm plates in complete DMEM media (DMEM with 10 v/v% FBS and 1 v/v% penicillin/streptomycin, 20 mL). Cells were incubated at 37°C and 5% CO2 for 72 h and passaged as required. HEK-293T cells were routinely checked for mycoplasma infection (Stem Cell Core, Gladstone Institutes). T cells were isolated from human peripheral blood Leukopaks using the EasySep™ isolation kit following the manufacturer’s instructions. Deidentified donors (< 60 years old, non-smoking) were chosen without regard to sex, gender, ethnicity and race. T cells were used fresh for in vitro experiments without freezing. For activation, T cells were seeded (1,000,000/mL) in complete X-VIVO 15 media (5 v/v% FBS, 4 nM N-acetyl-cysteine, and 55 μM 2-mercaptoethanol) and activated with anti-human CD3/CD28 magnetic Dynabeads (1:1 beads to cells) for 24 h with IL-2 (200 units/mL) in complete X-VIVO 15 media. After activation the magnetic beads were removed and the T cells were cultured in X-VIVO 15 medium with FBS (5 v/v%), IL-7 (10 ng/mL), IL-15 (5 ng/mL), and IL-2 (200 units/mL). [00514] Plasmids. CRISPR-Cas9 spacer sequences are shown in Table 3. The appropriate spacer sequences were cloned into U6-sgRNA-EFS-Cas9-P2A-Puro, pJRH-1179 U6-reci Gag-Cas9 v2 (referred to as Gag-Cas9) and pJRH-1180 U6-reci Gag-pol v2 (referred to as Gag-Pol) plasmids using NEBuilder® HiFi DNA assembly. For constructing the luciferase reporter cell lines, a C205ATC mutation was generated in pHAGE-CMV-Luc2-IRES-ZsGreen-W by ordering the appropriate primers and HiFi DNA assembly. Deletions (nuclear localization signals or Gag-Pol domains) were made to the Gag-Cas9 and Gag-Pol plasmids using NEBuilder® HiFi DNA assembly. Nuclear localization signals were inserted into the Gag-Cas9 plasmids using NEBuilder® HiFi DNA assembly of the appropriate plasmid fragments, where the sequences of the nuclear localization signal with appropriate overhangs
were purchased as double-stranded oligonucleotides from IDT. Plasmids were transformed into Mach1 E.coli cells rendered competent using the Mix & Go E. coli transformation kit following the manufacturer’s instructions. Mach1 cells were grown with the appropriate antibiotic selection. Plasmids were extracted and purified using mini-, midi-, maxi-, or giga- prep kits as necessary following the manufacturer’s instructions. All plasmids were sequence-verified by whole plasmid sequencing (Primordium Labs and Plasmidsaurus Inc.) before use. [00515] Table 3. Oligonucleotide sequences
Note: the sequences of Table 3, from top to bottom, are SEQ ID NOs:378-384. Cryogenic electron tomography (cryo-ET) of EDVs and lentiviral vectors. HEK-293T cells (4 million) were seeded into 10-cm plates and allowed to attach overnight. For Enveloped Delivery Vehicle (EDV) production, the Gag-Pol (3300 ng), Gag-Cas9 (6700 ng), and VSV-G mut (1000 ng) plasmids were diluted in Opti-MEM and mixed with polyethylenimine (PEI) (3:1 PEI: plasmid ratio by mass). The mixture was incubated for 30 min at room temperature and added dropwise (~400 μL total) to the HEK- 293T cells. Cells were incubated with the transfection mixture for at least 6 h, then swapped with Opti- MEM (10 mL). EDVs designed to edit luciferase were used for safety, as the spacer does not have complementary sequences in the human genome. The mutant VSV-G defective for binding was used for similar reasons. Lentiviral vectors were produced similarly using the Gag-Pol (10000 ng) and VSV-G mut (1000 ng) plasmids. No transgene encoding plasmid was included for safety. Particles were collected the following morning (~48 h after transfection). Cell debris was removed by centrifugation (4000 g for 10 min) and filtering through a 0.45-μm filter. Particles (~30 mL) were concentrated by iodixanol cushion (10 w/v% OptiPrep in 1× PBS) ultracentrifugation (100,000g for 75 min). The supernatant was removed and the pellets were resuspended in 1× PBS (0.1 mL). Samples were kept on ice and used freshed. EM grids (QF AU200 R 2/2, Quantifoil) were plasma-treated using a Tergeo-EM plasma cleaner (Pie Scientific). The purified particles (2 μL) were mixed with 10-nm gold fiducials (1 μL) and applied to EM grids at 4°C and 90% humidity inside a Vitrobot Mark IV (Thermo Fisher Scientific) and allowed to adsorb for 30 sec. Samples were blotted (3 - 5 sec, blot force 5) then plunge frozen in liquid ethane. Collection of cryo-ET data was performed as previously published.1 Tilt series were collected on a Titan
Krios G3i 300kV cryogenic transmission electron microscope (Thermo Fisher Scientific) with a K3 direct electron detector and an energy filter (Gatan) with a pixel size of 1.67 Å. Tilt series were acquired from -60° to 60° in 3° increments using a dose-symmetric tilt scheme, a defocus range of -2 to -4.5 μm, and a total dose of 120 electrons/Å2. At each tilt position the total exposure was split into 4 frames. Detailed imaging parameters per dataset are summarized in Table 4. Tilt images were motion-corrected (Motioncorr2) and exposure filtered based on the accumulated dose using the Alignframes function in IMOD 4.11.2 The contrast transfer function (CTF) for each tilt image was determined on non-exposure filtered tilt images using CTFFIND4.3 Tilt series were subsequently aligned using the gold fiducials using Etomo in IMOD 4.11. For visualization, tomograms were reconstructed by weighted back projection and isotropically binned by a factor of four, then three dimensionally gaussian filtered by 1 - 2.5 standard deviations in Matlab (Mathworks). Tomograms were visualized in either IMOD 4.11 or UCSF Chimera 1.18. The particles were manually annotated as immature (concentric densities underneath the bilayer), mature (internal core structure), and unknown. Slices through tomograms were exported using IMOD 4.11 and cropped using Adobe Illustrator 2024. The diameters of the particles were measured in IMOD 4.11 across the vertical and horizontal central axes and averaged to determine the particle size. Graphs were plotted in GraphPad Prism v.10.1.1 (270).
[00516] Table 4. Cryo-EM data collection and processing parameters [00517] Subtomogram averaging. For subtomogram averaging, unbinned tilt series were 3D-CTF corrected based on the determined defocus values and subsequently reconstructed by weighted projection using NovaCTF.4 Particle centers and radii were manually determined for immature particles using the volume tracer function and the Pick Particle plug in UCSF Chimera 1.18 or UCSF Chimera 1.15.5 Subtomogram averaging for EDVs and lentiviral vectors was performed as previously described using a combination of Matlab scripts (MATLAB R2023B, Mathworks) based on functions from the TOM, AV3 and Dynamo packages and subTOM 1.1.6 (https://github.com/DustinMorado/subTOM).1,6–8 Initial subtomogram positions and orientations were determined based on the radius and the particle center and
were sampled along the surface of a sphere at on the level of the particle membrane. Overlapping subtomograms with an edge length of 428 Å were extracted from the 3D-CTF corrected tomograms binned 4× times. An initial reference was generated by iteratively aligning subtomograms from a single tomogram using an exhaustive search. This process resulted in a low resolution average that resembled previously determined structures of the immature HIV capsid protein displaying 6-fold symmetry. The reference and corresponding subtomograms were shifted to center the 6-fold symmetry axis. Subtomograms were then re-extracted from the updated positions and 6-fold symmetry was applied during subsequent iterations of subtomogram alignment until the reference did not improve further. This average was then supplied as a reference to align the full data set from the 4× binned tomograms. The full data set was split into two half sets by particle and both half sets were aligned independently from each other with identical parameters. The full data set was aligned for 5 iterations with 6-fold symmetry applied and subtomogram positions converged onto overlapping positions. Subtomograms with low cross correlation values were subsequently removed. Once the reference and resolution did not improve further, subtomograms with an edge length of 390 Å were re-extracted at the aligned positions from 2× binned tomograms. After 6 iterations of alignment, the resolution and quality of the map did not improve further. The resolution was determined by calculating the Fourier Shell Correlation (FSC) between the two independently aligned half sets. Existing models of HIV-1 immature capsid (PDB: 5L93) were fitted by rigid body fitting into the final, sharpened and filtered map using the fit-in-map functionality in UCSF chimera 1.15. For lattice map analysis and visualization, the 3D positions and orientations of each subtomogram (corresponding to each aligned CA hexamer) were displayed back into the original tomogram using the “Place Object” plug-in9 in UCSF Chimera 1.15 and quantified per EDV or lentiviral vector in Matlab. [00518] Western blot analysis of EDVs and lentiviral vectors. For comparing the amount of Gag to capsid, EDVs and lentiviral vectors were produced as above. EDVs (1 mL) were harvested 30, 48 and 72 h after transfection and frozen at -80°C. The concentration of capsid domains in each sample was determined using a capsid (p24) ELISA kit and normalized across samples using RIPA buffer. Samples (30 μL) were mixed with 4× LDS (10 μL with 5 v/v% 2-mercaptoethanol) and loaded into the wells of a Criterion TGX Stain-free gel. The SDS-PAGE gel (100 V, 1 h, room temperature) was ran, then proteins were transferred in the gel to nitrocellulose membranes (40 V, overnight, 4°C). Membranes were blocked (1 h, room temperature) in a blocking buffer (5% Non-fat dry milk and 0.1 v/v% Tween-20 in 1× tris- buffered saline). Rabbit anti-p24 antibody and mouse anti-Flag antibody (1/2500 dilution in blocking buffer) were added and incubated (overnight, 4°C). Blots were washed three times with 1× TBST (0.1 v/v% Tween-20 in 1× tris-buffered saline). IRDye® 680RD goat anti-mouse IgG secondary antibody and IRDye® 800CW goat anti-rabbit IgG secondary antibody (1/500 dilution in blocking buffer) was added and incubated (1 h, room temperature). Blots were imaged using a ChemiDoc™ MP Imaging System
(Bio-Rad Laboratories, Inc.) after washing three times with 1× TBST. Images were inverted and processed in ImageJ2 V.2.14.0 and cropped in Adobe Illustrator 2024 for presentation. For determining the nuclear association of the Cas9 enzymes and the capsid proteins, EDVs were made as described above and incubated (7 mL) with HEK-293T cells in 15-cm dishes with PF74 at the indicated concentrations. DMSO was used as a vehicle control. After 24 h, the cells were trypsinized, washed with 1×PBS, then re-suspended in 1×PBS (1 mL). Some of the cells (100 μL) were taken, pelleted by centrifugation (100 g, 2 min) and lysed in RIPA with protease inhibitors (30 min, on ice). The samples were centrifuged (20,000 g, 10 min, 4°C) and the supernatant was transferred to a new tube and stored as the “total” fraction. The remaining cells (900 μL) were pelleted by centrifugation and lysed in cytoplasm lysis buffer (315 μL, 10 mM Tris-HCl pH 7.4 with 1 mM DTT, 1 mM MgCl2, 10% sucrose, 100 mM NaCl, 0.5 v/v% NP-40 and 1× protease inhibitors) on ice. After 10 min, the samples were centrifuged (664 g, 2 min, 4°C) and the supernatant was transferred to a new tube and stored as the “cytosolic” fraction. The pellet was washed by centrifugation (20,000 g, 10 min, 4°C) using cytoplasm lysis buffer (1 mL) three times, then resuspended in RIPA with protease inhibitors. The nuclei were lysed (30 min, on ice), and insoluble components were removed by centrifugation (5,200 g, 2 min, 4°C). The supernatant was transferred to a new tube and stored as the “nuclear” fraction. The protein concentration of the samples were quantified using BCA assays and normalized to 1 μg/μL, then mixed with the appropriate amount of 5 v/v% 2-mercaptoethanol in 4× LDS. Samples were heated (5 min, 90°C) then loaded (30 μL) into a 4-12% PAGE gel. SDS-PAGE gels were run, then transferred and blocked as described above. The blots were first stained with either mouse anti-cas9 antibodies (1/100 in blocking buffer) or mouse 1/100 anti-Flag antibodies for 48 h at 4°C. Blots were washed three times with 1× TBST then incubated with HRP-conjugated goat anti-mouse secondary antibodies (1/5000 in blocking buffer) for 1 h at room temperature. Blots were washed three times with 1× TBST. SuperSignal™ West femto maximum sensitivity substrate was subsequently added and the blots were imaged using a ChemiDoc™ MP Imaging System (Bio-Rad Laboratories, Inc.). After imaging, blots were stripped using a stripping buffer following the manufacturer’s manual, then blocked as described above. Blots were then stained for capsid protein using a rabbit anti-p24 antibody (1/1000) for 2 h at room temperature, washed three times with 1× TBST, the stained with HRP-conjugated goat anti-rabbit secondary antibodies (1/5000 in blocking buffer). Blots were washed and imaged as described above using Pierce™ ECL Western Blotting Substrate. The procedure was repeated to stain for EZH2 (1/2000 rabbit anti- EZH2 in blocking buffer) and GAPDH (1/5000 mouse anti-GAPDH in blocking buffer). Band intensities were quantified using the measure function in ImageJ2 V.2.14.0, then normalized to the band intensity of DMSO conditions. Images were processed as above for presentation. The raw images of the blots are shown in Fig.30.
[00519] Proximity ligation experiments. EDVs (30 mL) were produced and concentrated by ultracentrifugation using a sucrose cushion (20 w/v%, 2 mL). Prior to bioconjugation, the structure of lenacapavir bound to capsid was examined - the alkyne group was not necessary for drug binding.10 Lenacapavir-eosin Y (EY) was made using a two-step bioconjugation procedure. Isothiocyanate-eosin Y (SCN-EY, 1.0 equiv.) was coupled with azide-PEG4-amine (N3-amine, 1.1 equiv.) in freshly made sodium bicarbonate (10 mM) for 2 h at room temperature in the dark to generate azide-eosin Y (azide- EY). A mixture of BTTAA (100 μM), copper sulfate (80 μM) and lenacapavir (1.2 equiv., 400 μM) was mixed in sodium ascorbate acid (200 μM) and then immediately added to the azide-EY mixture. The reaction was incubated at 37°C for 3 h to generate lenacapavir-EY. EDVs were incubated (room temperature, 15 min) with lenacapavir-EY at a range of concentration (50 - 500 nM). For the control experiments, EDVs were incubated with unconjugated lenacapavir and unconjugated eosin Y (500 nM each). The appropriate photo-probes (diazirine-biotin, aryl-azide-biotin or phenol-biotin) were added to the EDVs (100 μM final concentration) and incubated at room temperature for 5 min. The samples were then illuminated (100% intensity, 10 min) using a Penn PhD Photoreactor M2 (Sigma Aldrich, Z744035) with a 450 nm blue light source module (Sigma Aldrich, Z744033). Fan speed was set at 6800 rpm under manual control with 100 r/min stirring. The EDVs were then lysed in 1× RIPA buffer with protease inhibitors on ice for 30 min. The samples were centrifuged (20,000 g, 10 min, 4°C) and the supernatant was transferred to a new tube with 10% of the sample saved as “input” samples. LDS sample buffer (1× final) was added to the “input” samples. Biotin immunoprecipitation was performed on the remainder of the samples. In brief, NeutrAvidin agarose beads (50 μL) were washed three times (0.5 mL, 1× PBS) then added to the EDV lysates and incubated (4°C, 16 h). The samples were loaded on mini bio-spin columns and the flowthrough was discarded. The beads were washed three times with 1× RIPA lysis buffer (0.5 mL), three times with NaCl solution (1M NaCl in 1× PBS, 0.5 mL), then three times with urea solution (2M urea freshly dissolved in 50 mM ammonium bicarbonate, 0.5 mL). The beads were subsequently suspended in LDS sample buffer (2×, 40 μL) and boiled (95°C, 5 min). For immunoblotting, proteins were run on 4-12% gels, then transferred from SDS-PAGE gels to PVDF membranes using an iBlot-2 dry blotting system (Thermo Scientific, IB21001). Membranes washed with Tris buffered saline (TBST, 37mM sodium chloride, 20mM Tris, 2.7mM potassium chloride, 0.05% Tween 20; pH=7.4) and blocked with BSA solution (TBST containing 0.1% Tween-20 and 5% BSA) before the antibodies (1/1000) were added as indicated. Immunoblot images were captured by an infrared LI-COR imager (LI-COR Biosciences, Odyssey CLx). Data were analyzed and visualized using ImageStudioLite (v5.2.5) and Adobe Illustrator (v22.1). [00520] Luciferase assays. Luciferase HEK-293T cells were made by transducing low passage HEK- 293T cells with a lentiviral vector packaging a mutant luciferase (C205ATC) and zsGreen transgene. Monoclonal cell lines were established by sorting the cells for zsGreen expression using a BD FACSAria
Fusion cell sorter (BD Biosciences). For small molecule drug experiments, lenacapavir and PF74 were dissolved in DMSO. EDVs editing the luciferase transgene were produced as described above. Lentivirus were made using the Gag-Pol (10000 ng), pMD2.G (1000 ng) and transgene plasmid U6-sgRNA-EFS- Cas9-P2A-Puro with the luciferase gRNA (2500 ng). Luciferase HEK-293T cells (6000 cells per well) were incubated with lentivirus or EDVs (100 μL for PF74, 75 μL for lenacapavir) with the indicated concentrations of PF74 or lenacapavir in black bottom 96-well plates. An equivalent volume of DMSO was used as the vehicle control. After 48 h, the media from the luciferase HEK-293T cells incubated with EDVs was removed and replaced with a passive lysis buffer (1× in ultrapure water, 20 μL) and incubated on a rocking shaker (room temperature, 30 min). After incubation, the luminescence of the wells were recorded on a Tecan Spark multimode microplate reader (Tecan Group Ltd.) by injecting luciferase substrate (30 μL) into each well immediately before measurement. The conditions with lentiviral vectors were quantified as above 72 h after transduction to provide sufficient time for the transgene to integrate, produce Cas9 and edit the reporter. For experiments using EDVs without nuclear localization sequences, EDVs were produced with the appropriate Gag-Cas9 plasmid as described above. Luciferase HEK-293T cells were transduced with EDVs (100 μL). The luminescence of the wells were measured 48 h after transduction as described above. To test whether EDVs without NLSs could use the capsid core for transport, EDVs packaging Cas9 RNPs without NLS were produced. EDVs (50 μL) were incubated with luciferase HEK-293T cells with the indicated concentrations of lenacapavir. The luminescence of the wells were recorded 48 h after transduction. For experiments using EDVs with more NLSs, the appropriate EDVs were produced and incubated (6.25 μL) with the luciferase HEK-293T cells. The luminescence was recorded 48 h after transduction. For experiments using EDVs with deletions in the Gag-Pol polypeptide, the appropriate EDVs were produced and incubated (capsid deletions 40 μL, Pol deletions 25 μL, matrix deletions 40 μL, nucleocapsid deletions 40 μL, combining deletions 10 μL) with luciferase HEK-293T cells. The luminescence was recorded 48 h after transduction. In all experiments, the luminescence signal was normalized by the vehicle control conditions or positive control conditions and plotted in GraphPad Prism v.10.1.1. Statistics as indicated were calculated in GraphPad Prism v.10.1.1. [00521] Characterization of EDVs. The physical titers of the EDVs were quantified using a NanoAnalyzer instrument (NanoFCM) following the manufacturer’s SOP. Briefly, EDVs were diluted in Tris-HCl buffer (100 mM Tris-HCl pH 7.5 with 1 mM EDTA) at least ten-fold before analysis. Silica quality controls beads of known concentration were used as calibration standards to determine the physical titre. Particle concentrations were determined using instrument software, NanoFCM Profession V2.0. For quantifying the sgRNA or Cas9 quantity inside the particles, the particles were first purified by ultracentrifugation, then diluted in either DirectDetect buffer for reverse transcription quantitative polymerase chain reactions (RT-qPCR) or RIPA buffer for ELISA. For RT-qPCR, Custom TaqMan™
small RNA assays were designed and ordered against the gRNA sequence. Synthetic sgRNA sequences with the appropriate spacers and no modifications were used as standards for quantification. Samples (4 μL) or standards (4 μL) were mixed with RT-qPCR mix (6 μL) (1× Luna Luna® Universal One-Step RT-qPCR mix with 0.25× RT primer and 1× small RNA assay probes from TaqMan™ small RNA assay kit in nuclease-free water). The entire sample or standard was loaded into 384-well plates. Samples and standards were prepared in duplicate. RT-qPCR was performed on a QuantStudio™ 5 Real-Time PCR System (Thermo Fisher Scientific, Inc.) with the following parameters: carryover prevention (25°C, 30 sec), reverse transcription (55°C, 15 min), initial denaturation (95°C, 1 min), and 45 cycles of denaturation (95°C, 10 sec), extension (60°C, 60 sec) with a plate read. Data was processed in Microsoft Excel Version 16.83. For Cas9 or p24 enzyme-linked immunosorbent assays, samples and standards were diluted in RIPA as appropriate. The manufacturer’s instructions were followed. Data was processed in Microsoft Excel Version 16.83. All data was plotted and statistics calculated as indicated in GraphPad Prism v.10.1.1. [00522] Editing in HEK-293T cells. The appropriate EDVs editing B2M were produced as described above. The physical titers of the particles were determined using the NanoAnalyzer instrument as above. HEK-293T cells (2000 cells per well) were incubated with EDVs at the indicated concentrations in 24- well plates and incubated at 37°C. The cells were trypsinized 5 d after transduction and washed with a staining buffer (1× PBS with 2 w/v% bovine serum albumin). The cells were stained (on ice in the dark, 30 min) with APC anti-human β2-microglobulin antibody (5 μL per sample) and DAPI as a viability stain (0.3 nmol per sample) in the staining buffer. The cells were then washed three times with the staining buffer. Flow cytometry was used to quantify B2M expression using an Attune Nxt Flow Cytometer (Thermo Fisher Scientific, Inc.). Data was analyzed in FlowJo 10.9.0 with the gates shown in Fig.29. All data was plotted and statistics calculated as indicated in GraphPad Prism v.10.1.1. [00523] Editing in primary activated T cells. Activated T cells (30,000 for NLS experiments, 10,000 for EDV minimization experiments) were incubated with EDVs (concentrations as indicated). For flow cytometry, T cells were harvested 5 d after incubation, and stained for B2M as above. Expression of the T cell receptor was stained for similarly, but using an APC anti-human TCR α/β antibody (5 μL per sample). Flow cytometry was used to quantify expression using an Attune Nxt Flow Cytometer (Thermo Fisher Scientific, Inc.). Data was analyzed in FlowJo 10.9.0 with the gates shown in Fig.25. For next generation sequencing, T cells were harvested 3 d after incubation, then spun down (300 g, 3 min). The cell media was removed and the cells were lysed in lysis buffer (10 mM Tris-HCl pH 7.5 with 0.05 w/v% SDS and 0.72 U/mL of thermolabile proteinase K, 200 μL). The proteinase K was subsequently deactivated by incubation at 55°C for 20 min. Extracted DNA was stored at -80°C until use. The TRAC loci was amplified from gDNA (1 ng) by TRAC-ngs.fwd and TRAC-ngs.rev primers (0.5 μM each) (Table 3) using NEB Q5 PCR mastermix (1×). PCR was performed using the Applied Biosystems
ProFlex PCR system (Thermo Fisher Scientific, Inc.) with the following parameters: initial denaturation (95°C, 3 min), 25 cycles of denaturation (95°C, 10 sec), annealing (65°C, 20 sec) and extension (72°C, 30 sec), and a final extension (72°C, 60 sec). This first PCR product was purified using SPRIselect beads (0.8×) following the manufacturer’s protocol. A second PCR was performed to ligate illumina P5 and P7 adapter and indexing sequences for sequencing (Table 3). The product of the first PCR (1 ng) was mixed with forward and reverse primers (0.5 μM each) and NEB Q5 PCR mastermix (1×). PCR was performed using the Applied Biosystems ProFlex PCR system (Thermo Fisher Scientific, Inc.) with the following parameters: initial denaturation (95°C, 3 min), 10 cycles of denaturation (95°C, 15 sec), annealing (60°C, 20 sec) and extension (72°C, 30 sec), and a final extension (72°C, 60 sec). The product of the second PCR was gel purified using the QIAquick gel extraction kit following the manufacturer’s protocol. PCR products were checked for purity and the correct size using the 2100 Bioanalyzer (Agilent Technologies, Inc.). The second PCR products were pooled to create a library (1 nM of each product). PhiX was added (30 v/v% of 1 nM). The library was denatured with sodium hydroxide (0.1N final concentration) for 5 min at room temperature, then TRIS-HCl (pH 7, 67 mM final concentration) was added. The library was diluted (1.5 pM final concentration) in HT1 Hybridization Buffer before loading onto a NextSeq 500/550 Mid Output Kit v2.5. Sequencing was performed on a Illumina NextSeq 500 sequencer (Illumina, Inc.). To quantify editing efficiency from the NGS experiments CRISPResso2 was used using default parameters for an NHEJ run as previously published (github.com/pinellolab/CRISPResso).11 For batch characterization standard parameters were followed for quantification of editing efficiency by CRISPResso2 as outlined at the github link above. Editing rates were reported as the maximum indel frequency as determined by CRISPResso2. Example 10: Additional data related to the above previous examples [00524] FIG.31A-31B (FIG.31A) [Related to FIG.19] Schematic of photocatalytic proximity labeling experiment. The Eosin Y - Lencapavir (EY-LEN) conjugate (500 nM) or unconjugated EY and LEN (EY & LEN, 500 nM each) were incubated with EDVs. Phenol biotinylation probes were then added to enable biotinylation of proximal proteins upon blue light illumination. Biotinylated proteins were isolated using biotin enrichment (biotin-IP). Schematic is not to scale. (FIG.31B) Western blot showing the amount of biotinylated Cas9, mature nucleocapsid protein, or mature capsid upon lenacapavir-EY- mediated photocatalytic proximity labeling. The proximity labeling experiments were similarly repeated twice with similar results. [00525] FIG.32 [Related to FIG.20] It was found that matrix protein contains NLSs that contribute to the nuclear delivery of the Cas9 RNP. The NLS in the matrix protein accounts for the residual editing activity. The NLS in the matrix protein were mutated in EDVs packaging Cas9 RNPs without NLS. NLS1 (KKKYK) and NLS2 (KSKKK) were mutated to IIKYK and KSIIK respectively.
[00526] FIG.33 [Related to FIG.21] Removing the p6 protein from EDVs was tested. The p6 protein recruits the producer cell endosomal sorting complexes required for transport (ESCRT) machinery for particle budding. The p6 protein was removed and the activity of the EDVs were compared to full EDVs. An equal volume of EDVs were incubated per condition. Data were normalized to EDVs containing the full matrix. Mean ± standard deviation of n = 3 batches of EDVs. P-values were calculated using a one- way ANOVA with Dunnett’s multiple comparisons to the EDV designs containing the full protein (“Full”). Mean ± standard deviation of n = 3 batches of EDVs. Non significance indicated by “ns”, *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001 ****P ≤ 0.0001. That data show that removing the p6 signal ablated the activity of the EDVs. [00527] FIG.34 [Related to FIG.21] The core-related deletions and NLS optimizations were combined together to create minimal EDVs (miniEDVs) using only 22% of the viral residues of the original EDVs. FIG.34 is a schematic showing the viral structural proteins in example lentiviral vectors (LV), EDVs, and minimized EDV (miniEDVs). The schematic is not drawn to scale. [00528] FIG.35 [Related to FIG.25] Producer cells were transfected with the appropriate EDV plasmids. Cell lysates were harvested 48 h after transfection for Western blotting. Each lane indicates a separate batch of producer cells. The data show that expression of the Gag-Cas9 polyprotein in the producer cells decreased when too many NLS were added, thus decreasing editing efficiency. [00529] FIG.36 [Related to FIG.20 and FIG.21] NLS-optimized EDVs designs showed similar increases in editing efficacy in activated human T cells from two donors. (A) EDVs (100 μL) were incubated with T cells from Donor 1 and editing was quantified by flow cytometry 5 d after incubation by flow cytometry. Donor 1 was used for experiments in FIG.20. (B) EDVs (100 μL) were incubated with T cells from Donor 2 and editing was quantified by flow cytometry 5 d after incubation by flow cytometry. Donor 2 was used for experiments in FIG.21. Error bars indicate standard deviation of three separate batches of EDVs. P-values were calculated using a one-way ANOVA with Dunnett’s multiple comparisons. P-values are as indicated. [00530] FIG.37 [Related to FIG.21G and FIG.21H] The original and miniEDVs did not show toxicity in HEK-293T or activated human T cells (Donor 2). The indicated doses of EDVs were incubated with cells. After 5 d, cells were stained with DAPI and quantified using flow cytometry. Neither the full EDVs or the miniEDVs decreased the viability of the HEK-293T cells or primary human T cells. [00531] While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto.
Claims
CLAIMS What is claimed is: 1. An enveloped delivery vehicle (EDV), comprising: (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide); (b) a viral envelop protein (e.g., VSVG or a mutant thereof); (c) a targeting polypeptide that provides for binding to a target cell; (d) a matrix (MA) polypeptide; and (e) an N-terminally truncated capsid (CA) protein.
2. The EDV of claim 1, wherein the EDV lacks one or more of the following proteins: a pol polypeptide protease (PR), a pol polypeptide reverse transcriptase (RT), a pol polypeptide integrase (IN), a nucleocapsid (NC) protein.
3. The EDV of claim 1 or claim 2, wherein the viral envelope protein is selected from: a Hepatitis B virus (HBV) glycoprotein, a Hepatitis C virus (HCV) glycoprotein, a Marburg virus glycoprotein, an Ebola virus glycoprotein, a vesicular stomatitis virus (VSV) glycoprotein, an influenza virus hemagglutinin, a SARS-CoV glycoprotein, a respiratory syncytial virus (RSV) glycoprotein, a human parainfluenza virus glycoprotein, a moloney murine leukemia virus (MMLV), a measles virus hemagglutinin and/or a measles virus fusion glycoprotein, an HTLV-1 glycoprotein, a Ross river virus glycoprotein, a rabies virus glycoprotein, a Mokola virus glycoprotein, a Semliki Forest virus glycoprotein, a Sindbis virus glycoprotein, a Venezuelan equine encephalitis virus glycoprotein, a sendai virus, a baculovirus, and a variant of any of the above that comprises one or more amino acid substitutions that reduce binding of the viral envelope protein to its receptor.
4. The EDV of claim 1 or claim 2, wherein the viral envelop protein is a variant vesicular stomatitis virus glycoprotein (VSVG) that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R354A), respectively, relative to SEQ ID NO: 153.
5. The EDV of any one of claims 1-4, wherein the N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-15 of the capsid protein set forth as SEQ ID NO: 282.
6. The EDV of any one of claims 1-4, wherein the N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-34 of the capsid protein set forth as SEQ ID NO: 282.
7. The EDV of any one of claims 1-4, wherein the N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-47 of the capsid protein set forth as SEQ ID NO: 282.
8. The EDV of any one of claims 1-4, wherein the N-terminally truncated capsid protein lacks amino acids corresponding to amino acids 5-148 of the capsid protein set forth as SEQ ID NO: 282.
9. The EDV of any one of claims 5-8, wherein the N-terminally truncated capsid protein comprises an amino acid sequence having 80% or more sequence identity with any one of SEQ ID NOs: 283-286 and 290.
10. The EDV of any one of claims 1-9, wherein the MA polypeptide lacks amino acids corresponding to amino acids 72-127 of the protein set forth as SEQ ID NO: 296.
11. The EDV of any one of claims 1-9, wherein the MA polypeptide lacks amino acids corresponding to amino acids 30-127 of the protein set forth as SEQ ID NO: 296.
12. The EDV of any one of claims 1-9, wherein the MA polypeptide comprises an amino acid sequence having 80% or more amino acid sequence identity with the protein set forth as SEQ ID NO: 296.
13. The EDV of any one of claims 1-12, wherein the targeting polypeptide comprises one or more antibodies or antibody analogs.
14. The EDV of claim 13, wherein the one or more antibody analogs is an affibody, an affilin, an affimer, an affitin, an alphabody, an anticalin, an avimer, a DARPin, a Fynomer, a Kunitz domain peptide, a monobody, a repebody, a VLR, or a nanoCLAMP.
15. The EDV of claim 13, wherein the one or more antibodies is a single chain Fv (scFv) polypeptide, a diabody, a bispecific antibody, a triabody, or a nanobody.
16. The EDV of any one of claim 1-15, wherein the target cell is a cancer cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue-resident stem cell, a monocyte, a macrophage, a B cell, or a T cell.
17. The EDV of any one of claims 1-15, wherein the target cell is a cancer cell.
18. The EDV of any one of claims 1-15, wherein the target cell is a CD8+ T cell or a CD4+ T cell.
19. The EDV of any one of claims 1-15, wherein the targeting polypeptide comprises an anti-CD19, anti- CD20, anti-CD4, anti-CD28, or anti-CD3 antibody or antibody analog.
20. The EDV of any one of claims 1-15, wherein the targeting polypeptide comprises: (i) an anti-CD3 and an anti-CD4 antibody or antibody analog; (ii) an anti-CD3 and an anti-CD28 antibody or antibody analog; or (iii) an anti-CD3, an anti-CD4, and an anti-CD28 antibody or antibody analog.
21. The EDV of any one of claims 1-15, wherein the target cell is a regulatory T cell (Treg) and the targeting polypeptide comprises an anti-CD28 superagonist (CD28SA).
22. The EDV of any one of claims 13-21, wherein the targeting polypeptide is a fusion polypeptide comprising: (i) the one or more antibodies or antibody analogs; and (ii) one or more heterologous polypeptides.
23. The EDV of claim 22, wherein said one of more heterologous polypeptides comprises a transmembrane polypeptide.
24. The EDV of claim 23, wherein the transmembrane polypeptide is a CD8α chain polypeptide or a platelet-derived growth factor receptor (PDGFR) polypeptide.
25. The EDV of any one of claims 1-24, wherein the nucleic acid-binding effector polypeptide is a CRISPR-Cas effector polypeptide (e.g., Cas9 or Cas12a), a Zinc Finger Nuclease (ZFN), a Transcription activator-like effector nuclease (TALEN), a meganuclease, a TnpB, an IscB, a serine recombinase, or a tyrosine recombinase.
26. The EDV of any one of claims 1-25, wherein the nucleic acid-binding effector polypeptide is fused (e.g., at the C-terminus) to 7 or more nuclear localization signals (NLSs).
27. The EDV of any one of claims 1-26, wherein the nucleic acid-binding effector polypeptide is fused to 3 or more nuclear export signals (NESs).
28. The EDV of any one of claims 1-27, wherein the nucleic acid-binding effector polypeptide is a fusion polypeptide comprising: i) a CRISPR-Cas effector polypeptide; and ii) one or more heterologous polypeptides.
29. The EDV of claim 28, wherein the CRISPR-Cas effector polypeptide has nickase activity or is catalytically deactivated.
30. The EDV of claim 29, wherein at least one of the one or more heterologous polypeptides comprises a deaminase, a reverse transcriptase, a transcription modulator, or an epigenetic modulator.
31. The EDV of any one of claims 28-30, wherein at least one of the one or more heterologous polypeptides is a Gag polypeptide.
32. The EDV of any one of claims 1-31, wherein the EDV comprises a CRISPR-Cas guide RNA or a nucleic acid encoding the CRISPR-Cas guide RNA.
33. The EDV of any one of claims 1-32, wherein the EDV comprises a donor template nucleic acid, or a nucleotide sequence encoding the donor template nucleic acid.
34. The EDV of any one of claims 1-33, further comprising a therapeutic polypeptide, or a nucleic acid comprising a nucleotide sequence encoding a therapeutic polypeptide.
35. The EDV of claim 34, wherein the therapeutic polypeptide is a chimeric antigen receptor (CAR).
36. The EDV of claim 35, wherein the CAR comprises one or more scFv or one or more nanobodies specific for a cancer-associated antigen.
37. The EDV of claim 36, wherein: a) the cancer-associated antigen is a solid tumor-associated antigen selected from: EGFR, HER2, EGFR806, mesothelin, PSCA, MUC1, claudin 18.2, EpCAM, GD2, VEGFR2, AFP, Nectin4/FAP, CEA, LewisY, Glypican-3, EGFRIII, IL-13Rα2, CD171, MUC16, PSMA, AXL, CD20, CD80/86, c-MET, DLL-3, DR5, EpHA2, FR-α, gp100, MAGE-A1, MAGE-A3, MAGE-A4, and LMP1; or b) the cancer-associated antigen is an antigen associated with hematological cancer, wherein the cancer-associated antigen is selected from: BCMA, C5, CD19, CD20, CD22, CD25, CD30, CD33, CD38, CD40, CD45, CD52, CD56, CD66, CD74, CD79a, CD79b, CD80, CD138, CTLA-4, CXCR4, DKK, EphA3, GM2, HLA-DR beta, integrin αVβ3, IGF-R1, IL6, KIR, PD-1, PD-L1, TRAILR1, TRAILR2, transferrin receptor, and VEGF.
38. A composition comprising the EDV of any one of claims 1-37 and a pharmaceutically acceptable excipient.
39. A collection of one or more nucleic acids, wherein said one or more nucleic acids encode the EDV of any one of claims 1-37.
40. The collection of claim 39, wherein at least one of said one or more nucleic acids encodes the MA polypeptide, the N-terminally truncated capsid (CA) protein, and the nucleic acid-binding effector polypeptide.
41. The collection of any one of claims 39-40, wherein at least one of said one or more nucleic acids encodes a gag polyprotein comprising the MA polypeptide, the N-terminally truncated capsid (CA) protein, and the nucleic acid-binding effector polypeptide (e.g., CRISPR-Cas effector polypeptide), but does not encode the NC protein.
42. The collection of any one of claims 39-41, wherein at least one of said one or more nucleic acids encodes a CRISPR-Cas guide RNA.
43. The collection of any one of claims 39-42, wherein said one or more nucleic acids is two or more nucleic acids.
44. An enveloped delivery vehicle (EDV), comprising: (a) a Cas9 polypeptide comprising 4 or more NLSs; (b) a variant vesicular stomatitis virus glycoprotein (VSVG) viral envelop protein that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R354A), respectively, relative to SEQ ID NO: 153; and (c) a targeting polypeptide that provides for binding to a target cell, wherein the targeting polypeptide is a fusion protein comprising a PDGFR transmembrane domain fused to an antibody or antibody analog.
45. The EDV of claim 44, wherein the Cas9 polypeptide is a fusion polypeptide comprising: i) a Cas9 protein; and ii) one or more heterologous polypeptides.
46. The EDV of claim 45, wherein the Cas9 protein has nickase activity or is catalytically deactivated.
47. The EDV of claim 45 or claim 46, wherein at least one of said one or more heterologous polypeptides comprises a deaminase, a reverse transcriptase, a transcription modulator, or an epigenetic modulator.
48. The EDV of any one of claims 45-47, wherein at least one of the one or more heterologous polypeptides is a Gag polypeptide.
49. A collection of one or more nucleic acids, wherein said one or more nucleic acids encode the EDV of any one of claims 44-48.
50. A collection of one or more nucleic acids, wherein said one or more nucleic acids encode an enveloped delivery vehicle (EDV), the EDV comprising: (a) a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide); (b) a viral envelop protein; and (c) a targeting polypeptide that provides for binding to a target cell, wherein the viral envelop protein and the targeting polypeptide are encoded by nucleotide sequences that are: (i) present on the same nucleic acid as part of the same transcript, and (ii) are separated by a sequence that promotes the production of two independent proteins.
51. The collection of claim 50, wherein the viral envelope protein is selected from: a Hepatitis B virus (HBV) glycoprotein, a Hepatitis C virus (HCV) glycoprotein, a Marburg virus glycoprotein, an Ebola virus glycoprotein, a vesicular stomatitis virus (VSV) glycoprotein, an influenza virus hemagglutinin, a SARS-CoV glycoprotein, a respiratory syncytial virus (RSV) glycoprotein, a human parainfluenza virus glycoprotein, a moloney murine leukemia virus (MMLV), a measles virus hemagglutinin and/or a measles virus fusion glycoprotein, an HTLV-1 glycoprotein, a Ross river virus glycoprotein, a rabies virus glycoprotein, a Mokola virus glycoprotein, a Semliki Forest virus glycoprotein, a Sindbis virus glycoprotein, a Venezuelan equine encephalitis virus glycoprotein, a sendai virus, a baculovirus, and a variant of any of the above that comprises one or more amino acid substitutions that reduce binding of the viral envelope protein to its receptor.
52. The collection of claim 50, wherein the viral envelop protein is a variant vesicular stomatitis virus glycoprotein (VSVG) that comprises a K to Q substitution and an R to A substitution at amino acid positions corresponding to K47 (K47Q) and R354 (R35A), respectively, relative to SEQ ID NO: 153.
53. The collection of any one of claims 50-52, wherein the sequence that promotes the production of two independent proteins encodes a 2A peptide, an intein, or an IRES, or comprises intronic splice donor/splice acceptor sequences.
54. The collection of any one of claims 50-53, wherein said two or more nucleic acids encode a pol polyprotein comprising a protease (PR), a reverse transcriptase (RT), and an integrase (INT).
55. The collection of any one of claims 50-54, wherein said two or more nucleic acids encode a guide RNA.
56. The collection of any one of claims 50-55, wherein the nucleic acid-binding effector polypeptide is a CRISPR-Cas effector polypeptide (e.g., Cas9).
57. The collection of any one of claims 50-56, wherein the nucleic acid-binding effector polypeptide is a fusion polypeptide comprising: i) a CRISPR-Cas effector polypeptide; and ii) one or more heterologous polypeptides.
58. The collection of claim 57, wherein at least one of the one or more heterologous polypeptides is a Gag polypeptide.
59. The collection of any one of claims 50-58, wherein the targeting polypeptide is a fusion protein comprising a PDGFR transmembrane domain fused to an antibody or antibody analog.
60. A method of producing an enveloped delivery vehicle (EDV), the method comprising: a) introducing the collection of any one of claims 39-43 and 49-59 into a packaging cell; and b) harvesting EDVs produced by the packaging cell.
61. A method of delivering a nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide) to a eukaryotic cell, the method comprising contacting a eukaryotic cell with the EDV of any one of claims 1-37 and 44-48 or the composition of claim 38.
62. The method of claim 61, wherein the eukaryotic cell is in vivo.
63. The method of claim 61, wherein the eukaryotic cell is in vitro or ex vivo.
64. The method of any one of claims 61-63, wherein the eukaryotic cell is a cancer cell, a stem cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue-resident stem cell, a monocyte, a macrophage, a B cell, or a T cell.
65. A method for modifying a target nucleic acid in a eukaryotic cell, the method comprising contacting a eukaryotic cell with the EDV of any one of claims 1-37 and 44-48 or the composition of claim 38, wherein said contacting results in delivery of the nucleic acid-binding effector polypeptide (e.g., a CRISPR-Cas effector polypeptide) into the cell and modification of a target nucleic acid within the cell.
66. The method of claim 65, wherein the eukaryotic cell is a cancer cell, a stem cell, a hematopoietic stem cell, a lung cell, a neuron, an astrocyte, an islet cell, a kidney cell, an adipocyte, a hepatocyte, an endothelial cell, a muscle cell, a cardiomyocyte, a retinal cell, a tissue-resident stem cell, a monocyte, a macrophage, a B cell, or a T cell.
67. The method of claim 65 or claim 66, wherein the eukaryotic cell is in vitro or ex vivo.
68. The method of claim 65 or claim 66, wherein the eukaryotic cell is in vivo and the method comprises administering the EDV to an individual, wherein the EDV enters the eukaryotic cell in the individual and modifies the target nucleic acid in the eukaryotic cell.
69. The method of any one of claims 65-68, wherein the eukaryotic cell is a CD4+ T cell or a CD8+ T cell.
70. The method of any one of claims 65-68, wherein the eukaryotic cell is a regulatory T cell (Treg).
71. The method of any one of claims 65-70, wherein the targeting polypeptide comprises an anti-CD3 and/or an anti-CD28 antibody or antibody analog.
72. The method of any one of claims 65-70, wherein the targeting polypeptide comprises an anti-CD19, anti-CD20, anti-CD4, anti-CD28, or anti-CD3 antibody or antibody analog.
73. The method of any one of claims 65-70, wherein the targeting polypeptide comprises an antibody, antibody analog, single chain Fv, diabody, triabody, nanobody or a bi-specific antibody.
74. The method of claim 73, wherein the targeting polypeptide binds to CD19, CD20, CD4, CD28, or CD3.
75. The method of any one of claims 65-74, wherein the EDV comprises a donor template nucleic acid or a nucleotide sequence encoding the donor template nucleic acid, wherein the donor template nucleic acid comprises a nucleotide sequence encoding a chimeric antigen receptor (CAR).
76. The method of claim 75, wherein the CAR comprises one or more scFv or one or more nanobodies specific for a cancer-associated antigen.
77. The method of claim 76, wherein: a) the cancer-associated antigen is a solid tumor-associated antigen selected from: EGFR, HER2, EGFR806, mesothelin, PSCA, MUC1, claudin 18.2, EpCAM, GD2, VEGFR2, AFP, Nectin4/FAP, CEA, LewisY, Glypican-3, EGFRIII, IL-13Rα2, CD171, MUC16, PSMA, AXL, CD20, CD80/86, c-MET, DLL-3, DR5, EpHA2, FR-α, gp100, MAGE-A1, MAGE-A3, MAGE-A4, and LMP1; or b) the cancer-associated antigen is an antigen associated with hematological cancer, wherein the cancer-associated antigen is selected from: BCMA, C5, CD19, CD20, CD22, CD25, CD30, CD33,
CD38, CD40, CD45, CD52, CD56, CD66, CD74, CD79a, CD79b, CD80, CD138, CTLA-4, CXCR4, DKK, EphA3, GM2, HLA-DR beta, integrin αVβ3, IGF-R1, IL6, KIR, PD-1, PD-L1, TRAILR1, TRAILR2, transferrin receptor, and VEGF.
78. The method of any one of claims 65-77, wherein the EDV comprises: a) a CRISPR-Cas effector polypeptide; and b) one or more CRISPR-Cas guide RNAs, or one or more nucleic acids encoding the one or more CRISPR-Cas guide RNAs.
79. The method of any one of claims 68-78, wherein said administering comprises intravenous administration.
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| WO2022183072A1 (en) * | 2021-02-26 | 2022-09-01 | Kelonia Therapeutics, Inc. | Lymphocyte targeted lentiviral vectors |
| US20220403379A1 (en) * | 2021-05-28 | 2022-12-22 | The Regents Of The University Of California | Compositions and methods for targeted delivery of crispr-cas effector polypeptides and transgenes |
| WO2024015605A1 (en) * | 2022-07-14 | 2024-01-18 | Innovative Cellular Therapeutics Holdings, Ltd. | Recombinant viral particle for gene and/or cellular therapy |
| WO2024044557A1 (en) * | 2022-08-23 | 2024-02-29 | The Regents Of The University Of California | Compositions and methods for targeted delivery of crispr-cas effector polypeptides |
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| WO2022183072A1 (en) * | 2021-02-26 | 2022-09-01 | Kelonia Therapeutics, Inc. | Lymphocyte targeted lentiviral vectors |
| US20220403379A1 (en) * | 2021-05-28 | 2022-12-22 | The Regents Of The University Of California | Compositions and methods for targeted delivery of crispr-cas effector polypeptides and transgenes |
| WO2024015605A1 (en) * | 2022-07-14 | 2024-01-18 | Innovative Cellular Therapeutics Holdings, Ltd. | Recombinant viral particle for gene and/or cellular therapy |
| WO2024044557A1 (en) * | 2022-08-23 | 2024-02-29 | The Regents Of The University Of California | Compositions and methods for targeted delivery of crispr-cas effector polypeptides |
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