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WO2024151640A1 - Lymphocytes t de récepteur antigénique chimérique générées par transposase - Google Patents

Lymphocytes t de récepteur antigénique chimérique générées par transposase Download PDF

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WO2024151640A1
WO2024151640A1 PCT/US2024/010890 US2024010890W WO2024151640A1 WO 2024151640 A1 WO2024151640 A1 WO 2024151640A1 US 2024010890 W US2024010890 W US 2024010890W WO 2024151640 A1 WO2024151640 A1 WO 2024151640A1
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seq
enzyme
cell
nucleic acid
car
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Omid F. HARANDI
Francisco Navarro
Zafira CASTANO CORSINO
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Saliogen Therapeutics Inc
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Saliogen Therapeutics Inc
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/10—Cellular immunotherapy characterised by the cell type used
    • A61K40/11—T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/30—Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/30—Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
    • A61K40/31—Chimeric antigen receptors [CAR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41—Vertebrate antigens
    • A61K40/42—Cancer antigens
    • A61K40/4202—Receptors, cell surface antigens or cell surface determinants
    • A61K40/421—Immunoglobulin superfamily
    • A61K40/4211—CD19 or B4
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41—Vertebrate antigens
    • A61K40/42—Cancer antigens
    • A61K40/4202—Receptors, cell surface antigens or cell surface determinants
    • A61K40/421—Immunoglobulin superfamily
    • A61K40/4212—CD22, BL-CAM, siglec-2 or sialic acid binding Ig-related lectin 2
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41—Vertebrate antigens
    • A61K40/42—Cancer antigens
    • A61K40/4202—Receptors, cell surface antigens or cell surface determinants
    • A61K40/4221—CD20
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1138—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 against receptors or cell surface proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90—Stable introduction of foreign DNA into chromosome
    • C12N15/902—Stable introduction of foreign DNA into chromosome using homologous recombination
    • C12N15/907—Stable introduction of foreign DNA into chromosome using homologous recombination in mammalian cells
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases [RNase]; Deoxyribonucleases [DNase]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K40/00
    • A61K2239/27—Indexing codes associated with cellular immunotherapy of group A61K40/00 characterized by targeting or presenting multiple antigens
    • A61K2239/29—Multispecific CARs
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/03—Fusion polypeptide containing a localisation/targetting motif containing a transmembrane segment
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPR]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2800/00—Nucleic acids vectors
    • C12N2800/90—Vectors containing a transposable element

Definitions

  • the present disclosure relates, in part, to a method making a chimeric antigen receptor (CAR)-immune cell or chimeric autoantibody receptor (CAAR)-immune cell, e.g., using an enzyme capable of performing targeted genomic integration, such as a mobile element enzyme.
  • CAR chimeric antigen receptor
  • CAAR chimeric autoantibody receptor
  • CARs Chimeric antigen receptors
  • T cell specificity could be redirected by fusing a targeting moiety that recognizes a cell surface protein with a T cell activation domain such as the CD3 ⁇ cytoplasmic tail.
  • the first example of this technology fused CD4 to the CD3 ⁇ chain (CD4 ⁇ CAR).
  • CD4 ⁇ CAR When expressed in effector T cells, this construct redirected T cell specificity to HIV-infected cells by taking advantage of the interaction between HIV envelope protein DB1/ 143560057.1 SAL-026PC/126933-5026 (Env) and CD42. This concept was brought to the clinic in the late 1990s; although it was shown to be safe and feasible, durable control of virus infection was not observed.
  • CAAR-T Chimeric auto-antibody receptor T
  • a method of making a chimeric antigen receptor (CAR)-immune cell comprising: obtaining an immune cell from a sample obtained from a subject, the sample comprising immune cells or immune cell progenitors; and transfecting the immune cell with a first nucleic acid encoding an enzyme capable of performing targeted genomic integration, optionally wherein the first nucleic acid is RNA, and a second, non-viral nucleic acid encoding a donor DNA comprising a chimeric CAR and flanked by ends recognized by the enzyme capable of performing targeted genomic integration, e.g., without limitation, a mobile element enzyme, to thereby create a transfected CAR-immune cell, wherein the immune cell is selected from a T cell, macrophage, and a natural killer (NK) cell.
  • CAR chimeric antigen receptor
  • a method of making a chimeric antigen receptor (CAR)-immune cell comprising: administering to a subject with a first nucleic acid encoding an enzyme capable of performing targeted genomic integration, wherein the first nucleic acid is RNA, and a second, non-viral nucleic acid encoding a donor DNA comprising a chimeric CAR and flanked by ends recognized by the enzyme capable of performing targeted genomic integration, e.g., without limitation, a mobile element enzyme, wherein the administration uses lipid nanoparticles (LNPs) capable of directing the first and second nucleic acids to an immune cell, to thereby create a CAR- immune cell, wherein the immune cell is selected from a T cell, macrophage, and a natural killer (NK) cell.
  • LNPs lipid nanoparticles
  • the administration is to the skin cell in a subject.
  • the immune cell is a T cell.
  • the transfected CAR-immune cell is a CAR-T cell, optionally selected from an allogeneic CAR-T cell or an autologous CAR-T cell.
  • the immune cell is a 2 DB1/ 143560057.1 SAL-026PC/126933-5026 macrophage.
  • the transfected CAR-immune cell is a CAR-M cell, optionally selected from an allogeneic CAR-M cell or an autologous CAR-M cell.
  • the immune cell is a natural killer (NK).
  • the transfected CAR-immune cell is a CAR-NK cell, optionally selected from an allogeneic CAR- NK cell or an autologous CAR-NK cell.
  • the donor DNA comprises or further comprises one or more of a nucleic acid sequence of a transmembrane domain, a nucleic acid sequence of an intracellular domain of a costimulatory molecule, and a nucleic acid sequence of a signaling domain.
  • the donor DNA comprises or further comprises a nucleic acid sequence of a CD8 alpha chain signal peptide.
  • the nucleic acid sequence of the transmembrane domain encodes an CD8 alpha chain hinge and a transmembrane domain.
  • the donor DNA further comprises a nucleic acid sequence of a peptide linker.
  • the nucleic acid sequence of the intracellular signaling domain comprises a nucleic acid sequence encoding a CD3 zeta signaling domain.
  • the second nucleic acid encodes an extracellular single-chain variable fragment (scFv) antibody to CD19 fused to a T cell cytoplasmic signaling domain.
  • the second nucleic acid further encodes an additional extracellular single-chain variable fragment (scFv) antibody to CD20 or CD22.
  • the CAR comprises: a) one or more extracellular domains that binds an antigen selected from alpha folate receptor, 5T4, ⁇ v ⁇ 6 integrin, BCMA, B7-H3, B7-H6, CAIX, CD19, CD20, CD22, CD30, CD33, CD44, CD44v6, CD44v7/8, CD70, CD79a, CD79b, CD123, CD138, CD171, CEA, CSPG4, EGFR, EGFR family including ErbB2 (HER2), EGFRvIII, EGP2, EGP40, EPCAM, EphA2, EpCAM, FAP, fetal AchR, GD2, GD3, Glypican-3 (GPC3), HLA- A1+MAGE1, HLA-A2+MAGE1, HLA-A3+MAGE1, HLA-A1+NY-ESO-1, HLA-A2+NY-ESO-1, HLA-A3+NY-ESO-1, IL- 11R ⁇ , IL
  • a method of making a chimeric autoantibody receptor (CAAR)-immune cell comprising: obtaining a cell from a sample obtained from a subject, the sample comprising T cells or Tcell progenitors; and transfecting the cell with a first nucleic acid encoding an enzyme capable of performing targeted genomic integration, wherein the first nucleic acid is RNA, and a second, non-viral nucleic acid encoding a donor DNA comprising a chimeric CAAR comprising an autoantigen or a fragment thereof, and flanked by ends recognized by the enzyme capable of performing targeted genomic integration, e.g., without limitation, a mobile element enzyme, to thereby create a transfected CAAR-immune cell.
  • CAAR chimeric autoantibody receptor
  • a method of making a method of making a chimeric autoantibody receptor (CAAR)-immune cell comprising: administering to a skin cell in a subject with a first nucleic acid encoding an enzyme capable of performing targeted genomic integration, wherein the first nucleic acid is RNA, and a second, non-viral nucleic acid encoding a donor DNA comprising a chimeric CAAR comprising an autoantigen or a fragment thereof, and flanked by ends recognized by the enzyme capable of performing targeted genomic integration, e.g., without limitation, a mobile element enzyme, wherein the administration is performed via intradermal or subcutaneous delivery and using lipid nanoparticles (LNPs) capable of directing the first and second nucleic acids to an immune cell, to thereby create a CAR- immune cell.
  • LNPs lipid nanoparticles
  • the immune cell is a T cell.
  • the transfected CAAR-immune cell is a CAAR -T cell, optionally selected from an allogeneic CAAR -T cell or an autologous CAAR-T cell.
  • the immune cell is a macrophage.
  • the transfected CAAR -immune cell is a CAAR -M cell, optionally selected from an allogeneic CAAR -M cell or an autologous CAAR-M cell.
  • the immune cell is a natural killer (NK).
  • the transfected CAAR -immune cell is a CAAR-NK cell, optionally selected from an allogeneic CAAR - NK cell or an autologous CAAR-NK cell.
  • the autoantigen or a fragment thereof is an extracellular domain for targeting of an autoantibody or a B-cell receptor (BCR).
  • BCR B-cell receptor
  • the extracellular domain is an AChR autoantigen.
  • the AChR autoantigen comprises domains E2-E6, and wherein the AChR autoantigen is fused to a CD8 alpha chain transmembrane domain and CD137-CD3z cytoplasmic signaling domains.
  • the extracellular domain is a Muscle Specific Kinase (MuSK) extracellular domain.
  • the extracellular domain is a desmoglein-3 (Dsg3).
  • the extracellular domain is a desmoglein-1 (Dsg1).
  • the enzyme capable of performing targeted genomic integration is a recombinase, e.g., an integrase or a mobile element enzyme.
  • the enzyme is a mobile element enzyme, e.g., derived from, or an engineered version of a mobile element enzyme of, Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Myotis lucifugus, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Molossus molossus, Pan troglodytes, or Homo sapiens, e.g., one or more of the Tn1, Tn2, Tn3, Tn5, Tn7, Tn9, Tn10, Tn552, Tn903, Tn1000/Gamma-delta, Tn/O, tnsA, tnsB, tnsC, tniQ, IS10, ISS, IS911, Minos
  • the mobile element enzyme has the amino acid sequence of SEQ ID NO: 1, or a variant thereof, e.g., having an amino acid other than serine at the position corresponding to position 2 of SEQ ID NO: 1 (e.g., selected from G, A, V, L, I and P, optionally A), not having additional residues at the C terminus relative to SEQ ID NO: 1, and/or having one or more mutations which confer hyperactivity (e.g., of TABLE 1) and/or having one or more mutations which 4 DB1/ 143560057.1 SAL-026PC/126933-5026 modulation integration (e.g., of TABLE 2A or TABLE 2B).
  • SEQ ID NO: 1 e.g., having an amino acid other than serine at the position corresponding to position 2 of SEQ ID NO: 1 (e.g., selected from G, A, V, L, I and P, optionally A), not having additional residues at the C terminus relative to SEQ ID NO: 1, and/or having one or more mutations
  • the mobile element enzyme having at least about 90% identity to the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 10, SEQ ID NO: 11, or SEQ ID NO: 430, or a variant thereof, e.g., having one or more mutations which confer hyperactivity (e.g., of TABLE 1) and/or having one or more mutations which modulation integration (e.g., of TABLE 2A or TABLE 2B).
  • the mobile element enzyme has gene cleavage activity (Exc+) and/or gene integration activity (Int+).
  • the mobile element enzyme has gene cleavage activity (Exc+) and/or lacks gene integration activity (Int-).
  • the enzyme comprises a targeting element, and an enzyme that is capable of inserting the donor DNA comprising a chimeric CAR or chimeric CAAR, optionally at a TA dinucleotide site or a TTAA (SEQ ID NO: 440) tetranucleotide site, optionally in a genomic safe harbor site (GSHS).
  • the mobile element enzyme is a chimeric mobile element enzyme.
  • the targeting element comprises one or more of a gRNA, optionally associated with a Cas enzyme, which is optionally catalytically inactive, transcription activator-like effector (TALE), Zinc finger, catalytically inactive transcription factor, nickase, a transcriptional activator, a transcriptional repressor, a recombinase, a DNA methyltransferase, a histone methyltransferase, a paternally expressed gene 10 (PEG10), and a TnsD.
  • TALE transcription activator-like effector
  • Zinc finger Zinc finger
  • catalytically inactive transcription factor nickase
  • a transcriptional activator a transcriptional repressor
  • a recombinase a DNA methyltransferase
  • histone methyltransferase a paternally expressed gene 10 (PEG10)
  • PEG10 paternally expressed gene 10
  • the GSHS is selected from adeno-associated virus site 1 (AAVS1), chemokine (C-C motif) receptor 5 (CCR5) gene, HIV-1 coreceptor, and human Rosa26 locus.
  • AAVS1 adeno-associated virus site 1
  • CCR5 chemokine receptor 5
  • HIV-1 coreceptor HIV-1 coreceptor
  • Rosa26 locus human Rosa26 locus.
  • the GSHS is located on human chromosome 2, 4, 6, 10, 11, 17, 22, or X.
  • the GSHS is selected from TALC1, TALC2, TALC3, TALC4, TALC5, TALC7, TALC8, AVS1, AVS2, AVS3, ROSA1, ROSA2, TALER1, TALER2, TALER3, TALER4, TALER5, SHCHR2-1, SHCHR2-2, SHCHR2-3, SHCHR2-4, SHCHR4-1, SHCHR4-2, SHCHR4-3, SHCHR6-1, SHCHR6-2, SHCHR6-3, SHCHR6-4, SHCHR10-1, SHCHR10-2, SHCHR10-3, SHCHR10-4, SHCHR10-5, SHCHR11-1, SHCHR11-2, SHCHR11-3, SHCHR17-1, SHCHR17-2, SHCHR17-3, and SHCHR17-4.
  • the disclosure provides a CAR-immune cell or a CAAR-immune cell generated by a method described herein. In embodiments, the disclosure provides a method of delivering a CAR-immune cell or a CAAR-immune cell therapy, comprising administering to a patient in need thereof the CAR-immune cell or a CAAR-immune cell generated by a method described herein. In embodiments, the disclosure provides a method of treating a disease or condition using a CAR-immune cell or a CAAR-immune cell therapy, comprising administering to a patient in need thereof the CAR-immune cell or a CAAR- immune cell generated by a method described herein.
  • FIGs.1A-1D depict a non-limiting representation of a system in accordance with embodiments of the present disclosure comprising a nucleic acid (e.g., helper RNA or DNA) encoding an enzyme capable of performing targeted genomic integration and a nucleic acid encoding a mobile element enzyme (donor DNA).
  • the chimeric, monomer or head-to- tail dimer mobile element enzymes are designed to target human genomic safe harbor site (GSHS) using Zinc Finger proteins (ZnF), TALE and Cas9/guide RNA DNA binders. Both DNA and RNA constructs are shown in FIGs.1A-1B.
  • FIG.1A and FIG.1C show DNA helper constructs while FIG.1B shows RNA helper constructs.
  • All DNA binding proteins are designed to target a TTAA site within 100 base pairs, 200 base pairs in either the sense or anti-sense orientation from the TTAA sites.
  • ZnF sequences are based on rational design by using structure-based (Elrod-Erickson M, Pabo C. 1999 J Biol Chem 274:19281–19285) and database-guided (Desjarlais J R, Berg J M.; 1992 Proteins 12:101–104) rules that govern these discriminating DNA binding (Choo Y, Klug A.
  • TALEs include nuclear localization signals (NLS) and an activation domain (AD) to function as transcriptional activators.
  • the DNA binding domain has approximately 16.5 repeats of 33-34 amino acids with a residual variable di-residue (RVD) at bases of the DNA leading strand are shown.
  • FIGs.1A-1B show chimeric mobile element enzyme constructs comprising a ZnF, TALE DNA- binding protein, or dCas with guide RNAs fused thereto by a linker that is greater than 23 amino acids in length or spliced internally to the N-terminus of the mobile element enzyme by an intein comprises either a DNA or RNA chimeric mobile element enzyme construct.
  • FIG.1C shows a DNA donor construct flanked by two recognition ends or ITRs that depicts a gene of interest driven by a promoter.
  • FIG.1D is a non-limiting representation of a system in accordance with embodiments of the present disclosure comprising a nucleic acid (e.g., helper RNA or DNA) encoding an enzyme capable of performing targeted genomic integration and a nucleic acid encoding a mobile element enzyme (donor DNA).
  • the helper RNA or DNA is translated into a bioengineered enzyme (e.g., integrase, recombinase, or mobile element enzyme) that recognizes specific ends and seamlessly inserts the donor DNA into the human genome in a site-specific manner without a footprint.
  • a bioengineered enzyme e.g., integrase, recombinase, or mobile element enzyme
  • Chimeric mobile element enzymes form dimers or tetramers at open chromatin to insert donor DNA at TTAA (SEQ ID NO: 440) recognition sites near DNA binding regions targeted by ZnF, dCas9/gRNA or TALEs. Binding of the ZnF, TALE, or Cas9/gRNA to genomic safe harbor site (GSHS) physically 6 DB1/ 143560057.1 SAL-026PC/126933-5026 sequesters the mobile element enzyme as a monomer or dimer to the same location and promotes transposition to the nearby TTAA (SEQ ID NO: 440) sequences near repeat variable di-residues (RVD) nucleotide sequences.
  • TTAA SEQ ID NO: 440
  • RVD near repeat variable di-residues
  • FIG.2 depicts a schematic diagram of present embodiments of the disclosure to produce CAR-immune (e.g., CAR-T) cells.
  • FIG.3 depicts a schematic diagram of chimeric autoantibody receptor (CAAR) with the autoantigen AchR as the CAAR extracellular domain.
  • a panel of AchR CAARs was designed for expression in primary human T-cells using AchR domains (E2-E6) as the extracellular domain, fused to a dimerization-competent CD8a transmembrane and CD137- CD3z cytoplasmic signaling domains which were used successfully in CD19 clinical trials.
  • FIG.4 depicts a schematic representation of the experimental design of the T cell process for generating either a GFP or CD19-CAR-T cells from three different healthy donors for ex-vivo analysis.
  • FIGs.5A-5B depict results showing that nanoplasmid donor-DNA outperforms plasmid and dbDNA backbones in T cells with >50% integration >90% viability at harvest.
  • FIG.5A depicts GFP transgene expression by flow cytometry at days 1 and 11 post-electroporation.
  • FIG.5B shows % integration efficiency and % Live for human primary T cells at Day 14.
  • FIGs.6A-6C depicts results showing that several mRNA can achieve ⁇ 50% expression, >60% integration, and 59- 75% viability in T-cells at harvest.
  • FIG.6A depicts % GFP transgene expression at day 14 post-electroporation.
  • FIG. 6B depicts % integration efficiency at day 14 post-electroporation.
  • FIG.6C depicts representative flow plots at day 14 post-electroporation for CleanCap (34A) mRNA.
  • FIGs.7A-7C depicts results showing that donor:mRNA ratio of 1:2 and 1:5 show the highest GFP+ cells at Day 11 Post EP.
  • FIG.7A depicts GFP transgene expression at day 11 post-electroporation.
  • FIG.7B depicts T cell viability at day 11 post-electroporation.
  • FIG.7C depicts GFP Mean Fluorescence Intensity (MFI) at day 11 post-electroporation. The results indicate that the highest number of GFP+ cells were in the 2 ug donor.
  • FIG.8A-8B depict results showing that 1 ug and 2 ug donor show similar % integration at higher mRNA ratios at Day 11 Post EP.
  • FIG.8A depicts representative flow plots at day 11 post-electroporation.
  • FIG.8B depicts % integration efficiency at day 11 post-electroporation. The results suggest that the next step should focus on the ratio of 1:5.
  • FIGs.9A-9C depicts results showing that efficient engineering of T cells by MLT transposase shows stable GFP and CAR expression as well demonstrating good safety profile.
  • FIG.9A depicts GFP transgene expression at days 1 and 12 post-electroporation.
  • FIG.9B depicts CD19-CAR expression at day 14 post-electroporation.
  • FIG.9C depicts number of viable cells over time.
  • FIGs. 10A-10B depict an ex vivo efficacy of CD19-CAR-T cells from three healthy donors generated by MLT transposase that efficiently kill CD19-expressing tumor target cells.
  • FIG. 10A depicts CD19- data which shows 7 DB1/ 143560057.1 SAL-026PC/126933-5026 Cytotoxicity of control and CD19-CAR T cells against CD19 negative K562 erythroleukemia cells.
  • FIG.10B depicts cytotoxicity of control and CD19-CAR T cells against CD19 positive B cell leukemia and lymphoma cells.
  • FIGs.11A-11B depict ex vivo efficacy by showing high levels of proinflammatory cytokine release by CD19 CAR-T cells upon recognition of CD19 expressing tumor targets.
  • FIG.11A depicts levels of IFNg and TNFa released into the supernatant upon co-culturing control or CD19-CAR T cells with CD19- or CD19+ leukemia cells.
  • FIG.11B depicts levels of GZMB released into the supernatant upon co-culturing control or CD19-CAR T cells with CD19- or CD19+ leukemia cells.
  • FIG.12A depicts CAR expression by flow cytometry of untransfected and CD19-CAR T cells at time of collection (D14).
  • FIG. 12B depicts viability of CD19-CAR T cells at time of collection (D14).
  • the bars on the left represent EP only and the bars on the right represent D+H.
  • FIGs.13A-13B depict results showing that CD19 CAR + T Cells exhibit a CD4:CD8 ratio similar to those of CAR- T Cells.
  • FIG.13A depicts CD4 and CD8 expression by flow cytometry of control and CD19-CAR T cells.
  • FIG.13B depicts percentages of CD4 and CD8 populations shown in FIG.13A. In FIG.13B, the bars of the graph are separated by lines as CD8+ on top and CD4+ on the bottom.
  • FIGs.14A-14B depict results showing that CD19-CAR + T Cells exhibit a favorable memory phenotype similar to CAR- T Cells. The favorable memory phenotype exhibits are mostly that of T CM and T SCM .
  • FIG.14A depicts a schematic diagram of different stages of memory T cell differentiation.
  • FIG. 14B depicts Representative flow plots and percentages of T scm , T cm , T em , and T eff populations. In FIG.14B, the bars of the graph are separated by lines in descending order of T scm , T cm , T em , and T eff populations.
  • FIGs.15A-15B depict results showing that CD19-CAR + T cells exhibit non-exhaustion phenotype with low expression of two exhaustion markers. The exhaustion markers are PD-1 and LAG-3.
  • FIG.15A depicts expression of exhaustion markers PD-1, LAG-3, and TIM-3 by flow cytometry.
  • FIG.15B depicts percentages of CD19-CAR T cells that express PD-1, LAG-3, or TIM-3.
  • the bars on the left are PD-1
  • the bars in the middle are LAG-3
  • the bars on the right are TIM-3.
  • FIGs.16A-16B depict results showing that CAR-T production generates cell therapy with approximately 60% CAR expression, 5 genomic integrations and 5000-8000 CAR copies per cell.
  • FIGs.17A-17B depict results showing that CAR-T cells show effective anti-tumor activity against human antigen and leukemia cells in vivo.
  • FIG.18 depicts results showing that CAR-T cells persist in circulation and are effective against tumor rechallenge.
  • FIGs.19A-19C depict results showing numer of CAR-T cells in peripheral blood of treated mice at different days post CAR T infusion, as analyzed by flow cytometry.
  • FIG.20 depicts the transgene integration profile of the MLT transposase engineered CD19-CAR T cells. In FIG.20, the bars of the graph are separated by lines in ascending order of Intergenic, TTS, Exon, Intron, Promoter-Tss.
  • FIG. 21 depicts a cytokine independent growth assay performed with non-engineered and MLT transposase engineered CD19-CAR T cells.
  • FIG.22 depicts a schematic overview of the process of generating single CD19, single CD20, and single CD22, and dual CD19/CD20 and dual CD19/CD22 CAR T cells from two different healthy donors.
  • FIGs.23A-23C depicts flow cytometry analysis of CAR expression in order to determine levels of CAR expression for single CAR T cells. “D315” and “D784” denote cells from two different donors.
  • FIG.24 depicts flow cytometry analysis of CAR expression in order to determine levels of CAR expression for dual- targeted CAR T cells. “D315” and “D784” denote cells from two different donors.
  • FIG.25 shows that parental CD19-expressing and CD19-Knockout (KO) Raji cells differ in their expression of CD19 antigen but have similar levels of CD20 and CD22 antigens.
  • the peak on the left represents isotype control and the peak on the right represent Ag-specific Mab
  • the peak on the left represents isotype control and the peak on the right represent Ag-specific Mab
  • the peak on the left represents isotype control and the peak on the right represent Ag-specific Mab.
  • FIG.25 shows the ability of single CD19 and dual-targeted CD19/CD20 or CD19/CD22 CAR T cells to kill tumor targets with heterogeneous CD19 expression via a mix of parental CD19-expressing and CD19-Knockout (KO) Raji cells at different ratios.
  • FIG. 27 depicts cytokine IFN ⁇ levels produced by dual CAR T cells in tumor targets with heterogeneous CD19 expression, as compared to IFN ⁇ levels produced by single CAR T cells.
  • FIG.28 depicts cytokine TNF ⁇ levels produced by dual CAR T cells in tumor targets with heterogeneous CD19 expression, as compared to TNF ⁇ levels produced by single CAR T cells.
  • “D315” and “D784” denote cells from two different donors.
  • FIG.29 depicts granule protease GZMB levels produced by dual CAR T cells in tumor targets with heterogeneous CD19 expression, as compared to granule protease GZMB levels produced by single CAR T cells.
  • “D315” and “D784” denote cells from two different donors.
  • DETAILED DESCRIPTION The present disclosure is based, in part, on the discovery that CAR-immune cell or a CAAR-immune cell generation can be made more efficient with the use of enzymatic transposition.
  • a method of making a chimeric antigen receptor (CAR)-immune cell comprising: obtaining an immune cell from a sample obtained from a subject, the sample comprising immune cells or immune cell progenitors; and transfecting the immune cell with a first nucleic acid encoding an enzyme capable of performing targeted genomic integration, optionally wherein the first nucleic acid is RNA, and a second, non-viral nucleic acid encoding a donor DNA comprising a chimeric CAR and flanked by ends recognized by the enzyme capable of performing targeted genomic integration, e.g., without limitation, a mobile element enzyme, to thereby create a transfected CAR-immune cell, wherein the immune cell is selected from a T cell, a macrophage, and an NK cell.
  • CAR chimeric antigen receptor
  • a method of making a chimeric antigen receptor (CAR)-immune cell comprising: administering to a subject with a first nucleic acid encoding an enzyme capable of performing targeted genomic integration, wherein the first nucleic acid is RNA, and a second, non-viral nucleic acid encoding a donor DNA comprising a chimeric CAR and flanked by ends recognized by the enzyme capable of performing targeted genomic integration, e.g., without limitation, a mobile element enzyme, wherein the administration uses lipid nanoparticles (LNPs) capable of directing the first and second nucleic acids to an immune cell, to thereby create a CAR- immune cell, wherein the immune cell is selected from a T cell, a macrophage, and an NK cell.
  • LNPs lipid nanoparticles
  • a method of making a chimeric autoantibody receptor (CAAR)-immune cell comprising: obtaining a cell from a sample obtained from a subject, the sample comprising T cells or T cell progenitors; and transfecting the cell with a first nucleic acid encoding an enzyme capable of performing targeted genomic integration, wherein the first nucleic acid is RNA, and a second, non-viral nucleic acid encoding a donor DNA comprising a chimeric CAAR comprising an autoantigen or a fragment thereof, and flanked by ends recognized by enzyme capable of performing targeted genomic integration, e.g., without limitation, a mobile element enzyme, to thereby create a transfected CAAR-immune cell.
  • CAAR chimeric autoantibody receptor
  • a method of making a chimeric autoantibody receptor (CAAR)-immune cell comprising: administering to a skin cell in a subject with a first nucleic acid encoding an enzyme capable of performing targeted genomic integration, wherein the first nucleic acid is RNA, and a second, non-viral nucleic acid encoding a donor DNA comprising a chimeric CAAR comprising an autoantigen or a fragment thereof, and flanked by ends 10 DB1/ 143560057.1 SAL-026PC/126933-5026 recognized by the enzyme capable of performing targeted genomic integration, e.g., without limitation, a mobile element enzyme, wherein the administration is performed via intradermal or subcutaneous delivery and using lipid nanoparticles (LNPs) capable of directing the first and second nucleic acids to an immune cell, to thereby create a CAR- immune cell.
  • LNPs lipid nanoparticles
  • the enzyme that is capable of performing targeted genomic integration inserts transgene(s) into a TCR, MHC class I, and MHC class II.
  • the enzyme is capable of performing targeted genomic integration in a T-cell receptor (TCR) (e.g., without limitation, TRAC).
  • TCR T-cell receptor
  • MHC major histocompatibility complex
  • the enzyme is capable of performing targeted genomic integration in an MHC class II (e.g., without limitation, CIITA).
  • the transgene is a T cell receptor alpha constant (TRAC) gene.
  • the transgene is a ⁇ 2 microglobulin (B2M) gene. In embodiments, the transgene is a CIITA gene. In embodiments, the transgene is a PDL gene, optionally a programmed cell death ligand-1 (PDL-1) gene. In embodiments, the enzyme is capable of targeting the genes, optionally a TRAC gene, associated with the TCR. In embodiments, the enzyme is capable of targeting the genes, optionally a B2M gene, associated with MHC class I. In embodiments, the enzyme is capable of targeting the genes, optionally a CIITA gene, associated with MHC class II.
  • the present disclosure relates to the production of CAR- immune cells and/or CAAR-immune cells via an enzyme capable of performing targeted genomic integration.
  • the methods are conducted ex vivo or in vivo.
  • the immune cell is selected from a T cell, a macrophage, and an NK cell.
  • the immune cell is a T cell.
  • the T cells comprise primary T cells.
  • the transfected CAR-immune cell is a CAR-T cell, optionally selected from an allogeneic CAR-T cell or an autologous CAR-T cell.
  • the immune cell is a macrophage. In embodiments, the macrophages comprise primary macrophages. In embodiments, the transfected CAR-immune cell is a CAR-M cell, optionally selected from an allogeneic CAR-M cell or an autologous CAR-M cell. In embodiments, the immune cell is a natural killer (NK) cell. In embodiments, the NK cells comprise primary NK cells. In embodiments, the transfected CAR-immune cell is a CAR-NK cell, optionally selected from an allogeneic CAR-NK cell or an autologous CAR-NK cell. 11 DB1/ 143560057.1 SAL-026PC/126933-5026 In embodiments, the immune cell is a T cell.
  • the T cells comprise primary T cells.
  • the transfected CAAR-immune cell is a CAAR-T cell, optionally selected from an allogeneic CAAR-T cell or an autologous CAAR-T cell.
  • the immune cell is a macrophage.
  • the macrophages comprise primary macrophages.
  • the transfected CAAR-immune cell is a CAAR-M cell, optionally selected from an allogeneic CAAR- M cell or an autologous CAAR-M cell.
  • the immune cell is a natural killer (NK) cell.
  • the NK cells comprise primary NK cells.
  • the transfected CAAR-immune cell is a CAAR-NK cell, optionally selected from an allogeneic CAAR- NK cell or an autologous CAAR-NK cell.
  • the method comprises activating the cell before transfection or administration, wherein the activation optionally comprises contacting the cell with an anti-CD3 antibody or CD3-binding fragment thereof.
  • the method comprises stimulating the cell before transfection or administration to create a population of cells, wherein the stimulation optionally comprises contacting the cell with an anti-CD28 antibody or a CD28-binding fragment thereof, B7-1 or a CD28-binding fragment thereof, or B7-2 or a CD28-binding fragment thereof.
  • the chimeric CAAR comprises an autoantigen or a fragment thereof.
  • the autoantigen or a fragment thereof is an extracellular domain for targeting of an autoantibody or a B-cell receptor (BCR).
  • BCR B-cell receptor
  • the extracellular domain is an AChR autoantigen.
  • the AChR autoantigen comprises domains E2-E6, and wherein the AChR autoantigen is fused to a CD8 alpha chain transmembrane domain and CD137- CD3z cytoplasmic signaling domains.
  • the extracellular domain is a Muscle Specific Kinase (MuSK) extracellular domain.
  • the extracellular domain is a desmoglein-3 (Dsg3).
  • the extracellular domain is a desmoglein-1 (Dsg1).
  • the autoantigen or a fragment thereof is allogeneic.
  • the autoantigen or a fragment thereof is xenogeneic.
  • the method comprises culturing the transfected CAAR-immune cells in a medium that selectively enhances proliferation of CAAR-immune cells.
  • the transfected CAAR-immune cell is created in about 1 day or about 2 days. In embodiments, the transfected CAAR-immune cell is created in less than 2 days. In embodiments, the method obviates the use of ex vivo CAAR-immune cell expansion.
  • the CAAR comprises an extracellular domain that binds an autoantibody expressed on a B cell, a transmembrane domain, and/or an intracellular signaling domain.
  • the extracellular domain that binds an autoantibody expressed on a B cell comprises Dsg1, Dsg3, or a fragment thereof.
  • the CAAR comprises a transmembrane domain, such as those disclosed elsewhere herein.
  • the CAAR comprises a transmembrane domain, such as, but not limited to, a human T cell surface glycoprotein CD8 alpha chain hinge 12 DB1/ 143560057.1 SAL-026PC/126933-5026 and/or transmembrane domain.
  • the CAAR comprises an intracellular signaling domain, such as those disclosed elsewhere herein.
  • the CAAR comprises an intracellular signaling domain such as the cytoplasmic portion of the T cell receptor (TCR) and co-receptors that act in concert to initiate signal transduction following antigen receptor engagement, as well as any derivative or variant thereof.
  • the donor DNA comprises or further comprises one or more of a nucleic acid sequence of a transmembrane domain, a nucleic acid sequence of an intracellular domain of a costimulatory molecule, and a nucleic acid sequence of a signaling domain.
  • the donor DNA comprises or further comprises a nucleic acid sequence of a CD8 alpha chain signal peptide.
  • the nucleic acid sequence of the transmembrane domain encodes a CD8 alpha chain hinge and a transmembrane domain.
  • the donor DNA further comprises a nucleic acid sequence of a peptide linker.
  • the nucleic acid sequence of the intracellular signaling domain comprises a nucleic acid sequence encoding a CD3 zeta (CD3 ⁇ ) signaling domain.
  • the second nucleic acid encodes an extracellular single-chain variable fragment (scFv) antibody to CD19 fused to a T cell cytoplasmic signaling domain.
  • the second nucleic acid further encodes an additional extracellular single-chain variable fragment (scFv) antibody to CD20 or CD22.
  • the second nucleic acid encodes a single-chain Fv domain (scFv) comprising a VL linked to a VH of a specific antibody by a flexible linker, at least a part of a transmembrane domain, at least a part of a cytoplasmic, optionally an extracellular, domain of an endogenous protein.
  • scFv domain is an scFv domain of an antibody against a tumor cell or tumor cell marker.
  • the scFv domain is an scFv domain of an antibody against a virus.
  • CD19 has a nucleotide sequence of SEQ ID NO: 818 (which is codon-optimized) and an amino acid sequence SEQ ID NO: 817, respectively.
  • CD19 has a nucleotide sequence of SEQ ID NO: 818, or a nucleotide sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto, or a codon-optimized form thereof.
  • CD19 has an amino acid sequence SEQ ID NO: 817, or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto.
  • CD20 has a nucleotide sequence of SEQ ID NO: 820, or a nucleotide sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto, or a codon-optimized form thereof.
  • CD20 has an amino acid sequence SEQ ID NO: 819, or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto.
  • CD20_HUMAN B-lymphocyte antigen amino acid sequence MTTPRNSVNGTFPAEPMKGPIAMQSGPKPLFRRMSSLVGPTQSFFMRESKTLGAVQIMNG LFHIALGGLLMIPAGIYAPICVTVWYPLWGGIMYIISGSLLAATEKNSRKCLVKGKMIMN SLSLFAAISGMILSIMDILNIKISHFLKMESLNFIRAHTPYINIYNCEPANPSEKNSPST QYCYSIQSLFLGILSVMLIFAFFQELVIAGIVENEWKRTCSRPKSNIVLLSAEEKKEQTI EIKEEVVGLTETSSQPKNEEDIEIIPIQEEEEEETETNFPEPPQDQESSPIENDSSP (SEQ ID NO: 820) CD20_HUMAN B-lymphocyte antigen nucleotide sequence 14 DB1/ 143560057.1 SAL-026PC/126933-5026 ATGACCACCCCCAGGAACAGCGTGAACGGCACCTTCCCCGCCGAGCCCATGAAG
  • CD22 has a nucleotide sequence of SEQ ID NO: 822, or a nucleotide sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto, or a codon-optimized form thereof.
  • CD22 has an amino acid sequence SEQ ID NO: 821, or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto.
  • the second nucleic acid encodes the ⁇ , ⁇ , ⁇ , or ⁇ chain of an antigen-specific T cell receptor.
  • the donor DNA comprises a nucleic acid encoding an extracellular domain, a transmembrane domain, and an intracellular domain of the CAR.
  • the intracellular domain comprises a costimulatory signaling region comprising an intracellular domain of a costimulatory molecule selected from CD27, CD28, 4-1BB, IL-2R ⁇ , OX40, CD30, GITR, TIM3, DAP10, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, and any combination thereof.
  • a costimulatory signaling region comprising an intracellular domain of a costimulatory molecule selected from CD27, CD28, 4-1BB, IL-2R ⁇ , OX40, CD30, GITR, TIM3, DAP10, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, and any combination thereof.
  • the CAR comprises one or more extracellular domains that binds an antigen selected from alpha folate receptor, 5T4, ⁇ v ⁇ 6 integrin, BCMA, B7-H3, B7-H6, CAIX, CD19, CD20, CD22, CD30, CD33, CD44, CD44v6, CD44v7/8, CD70, CD79a, CD79b, CD123, CD138, CD171, CEA, CSPG4, EGFR, EGFR family including ErbB2 (HER2), EGFRvIII, EGP2, EGP40, EPCAM, EphA2, EpCAM, FAP, fetal AchR, GD2, GD3, Glypican-3 (GPC3), HLA- A1+MAGE1, HLA-A2+MAGE1, HLA-A3+MAGE1, HLA-A1+NY-ESO-1, HLA-A2+NY-ESO-1, HLA-A3+NY-ESO-1, IL- 11R ⁇ , IL-13R ⁇ 2,
  • the CAR comprises a transmembrane domain derived from a polypeptide selected from CD8 ⁇ ; CD4, CD28, CD45, PD-1, and CD152.
  • the CAR comprises one or more intracellular costimulatory signaling domains selected from CD28, CD54 (ICAM), CD134 (OX40), CD137 (41BB), IL-2R ⁇ , CD152 (CTLA4), CD273 (PD-L2), CD274 (PD-L1), and CD278 (ICOS).
  • the CAR comprises a CD3 zeta (CD3 ⁇ ) signaling domain.
  • the CAR comprises one or more extracellular domains that binds an antigen selected from alpha folate receptor, 5T4, ⁇ v ⁇ 6 integrin, BCMA, B7-H3, B7-H6, CAIX, CD19, CD20, CD22, CD30, CD33, CD44, CD44v6, CD44v7/8, CD70, CD79a, CD79b, CD123, CD138, CD171, CEA, CSPG4, EGFR, EGFR family including ErbB2 (HER2), EGFRvIII, EGP2, EGP40, EPCAM, EphA2, EpCAM, FAP, fetal AchR, GD2, GD3, Glypican-3 (GPC3), HLA- A1+MAGE1, HLA-A2+MAGE1, HLA-A3+MAGE1, HLA-A1+NY-ESO-1, HLA-A2+NY-ESO-1, HLA-A3+NY-ESO-1, IL- 11R ⁇ , IL-13R ⁇ 2,
  • the CARs to be used in the method of the present disclosure are recombinant chimeric receptors comprising: (i) an antigen-specific targeting domain; (ii) a spacer domain; (iii) a transmembrane domain; (iv) at least one costimulatory domain; and/or (v) an intracellular signaling domain. 17 DB1/ 143560057.1 SAL-026PC/126933-5026.
  • the extracellular domain of the CAR to be used in the method of the present disclosure comprises an antigen-specific targeting domain that has the function of binding to the target antigen of interest.
  • the antigen-specific targeting domain may be any naturally occurring, synthetic, semi-synthetic, or a molecule produced recombinant technology, protein, peptide or oligo peptide that specifically binds to the target antigen.
  • examples of possible antigen-specific targeting domains include antibodies or antibody fragments or derivatives, synthetic or naturally occurring ligands of the targeted receptor including molecules, binding or extracellular domains of receptors or binding proteins.
  • the antigen-specific targeting domain is, or is derived from, an antibody.
  • An antibody is a protein, or a polypeptide sequence derived from an immunoglobulin able to bind with an antigen.
  • Antibody as herein used includes polyclonal or monoclonal, multiple or single chain antibodies as well as immunoglobulins, whether deriving from natural or recombinant source.
  • An antibody-derived targeting domain can be a fragment of an antibody or a genetically engineered product of one or more fragments of the antibody, which fragment is involved in binding with the antigen. Examples include a variable region (Fv), a complementarity determining region (CDR), a Fab, a single chain antibody (scFv), a heavy chain variable region (VFI), a light chain variable region (VL) and a camelid antibody (VHH).
  • the binding domain is a single chain antibody (scFv).
  • the scFv may be murine, human, or humanized scFv.
  • the CAR to be used in the method of the disclosure comprises an extracellular spacer domain that connects the antigen-specific targeting domain to the transmembrane domain.
  • the most common sequence used as spacer is the constant immunoglobulin IgG1 hinge-CH2-CH3 Fc domain. Mutants and or variants of this spacer may be employed, e.g., those which reduce Fc Receptor binding.
  • the CAR to be used in the method of the disclosure comprises a transmembrane domain between the spacer domain and the signaling domain.
  • the transmembrane domain may be derived either from a natural or from a synthetic source.
  • the domain deriving from natural sources may comprise the transmembrane sequence from any membrane-bound or transmembrane protein including any of the type I, type II, or type III transmembrane proteins.
  • the transmembrane regions that may be used in the CAR may be derived from the alpha, beta, or zeta chain of the T-cell receptor, CD28, CD3 epsilon, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, CD137, CD154, CD244 (2B4), DAP10, or DAP12.
  • the domain deriving from synthetic source will comprise predominantly hydrophobic sequence including residues such as leucine and valine.
  • the CAR used in the method of the present disclosure may include, e.g., in the cytoplasmic tail, one or more costimulatory domains.
  • Such domains may consist of the intracellular signaling domain of one or more costimulatory protein receptors (e.g., CD28, 41BB, ICOS).
  • the costimulatory domain provides additional signals to the cells thus enhancing cell expansion, cell survival and development of memory cells.
  • the CAR used in the method of the present disclosure may comprise one or more costimulatory domain selected from the group consisting of the intracellular domain of members of the TNFR super family, CD28, CD137 (4-1BB), CD134 (OX40), Dap10, CD27, CD2, CD5, ICAM-1, LFA-1, Lck, TNFR-1, TNFR-II, Fas, CD30, CD40, CD244 (2B4), DAP12, or combinations thereof. Further examples of costimulatory domains may be employed by the skilled in the art in the CAR.
  • the CAR used in the method of the disclosure may also comprise an intracellular signaling domain.
  • This domain may be cytoplasmic, transmits the activation signal and direct the cell to perform its specialized function.
  • intracellular signaling domains include, but are not limited to, z chain of the T-cell receptor or any of its homologs (e.g., h chain, FcRly and b chains, MB1 (Iga) chain, B29 (IgP) chain, etc.), CD3 polypeptides (D, d and e), syk family tyrosine kinases (Syk, ZAP 70, etc.), src family tyrosine kinases (Lck, Fyn, Lyn, etc.) and other molecules involved in T-cell signal transduction, such as CD2, CD5 and CD28.
  • z chain of the T-cell receptor or any of its homologs e.g., h chain, FcRly and b chains, MB1 (Iga) chain, B29 (IgP) chain, etc.
  • the intracellular signaling domain may be human CD3 zeta chain, FcyRIII, FcsRI, cytoplasmic tails of Fc receptors, immunoreceptor tyrosine-based activation motif (ITAM) bearing cytoplasmic receptors or combinations thereof.
  • the signaling domain comprises the intracellular signaling domain of human CD3 zeta chain.
  • the method comprises culturing the transfected CAR-immune cell in a medium that selectively enhances proliferation of CAR-immune cells or CAAR-immune cells.
  • the CAR-immune cell or CAAR-immune cell is created in about 1 day or about 2 days.
  • the CAR-immune cell or CAAR-immune cell is created in less than about 2 days, or less than about 3 days, or less than about 7 days, or less than about 14 days.
  • the method obviates a use of ex vivo expansion of CAR-immune cells or CAAR-immune cells.
  • the skin cell is epidermis or dermis skin cell.
  • the extracellular domain comprises an antibody or antigen binding fragment that binds an antigen.
  • the cell is transfected by electroporation, nucleofection, hydrodynamic delivery, or calcium phosphate precipitation and/or is carried out using a lipid vehicle, optionally N-[1-(2,3-dioleoyloxy)propyl]-N,N,N- trimethylammonium chloride (DOTMA), 1,2-bis(oleoyloxy)-3-3-(trimethylammonia) propane (DOTAP), or 1,2-dioleoyl- 3-dimethylammonium-propane (DODAP), dioleoylphosphatidylethanolamine (DOPE), cholesterol, LIPOFECTIN (cationic liposome formulation), LIPOFECTAMINE (cationic liposome formulation), LIPOFECTAMINE 2000 (cationic liposome formulation), LIPOFECTAMINE 3000 (cationic liposome formulation), TRANSFECTAM (cationic liposome formulation), a lipid nanoparticle, or a liposome and combinations thereof.
  • DOTMA 1,2-bis(ole
  • the transfecting of the cell is carried out using electroporation, or calcium phosphate precipitation. 19 DB1/ 143560057.1 SAL-026PC/126933-5026 In embodiments, the transfecting of the cell is carried out using a lipid vehicle, optionally N-[1-(2,3-dioleoyloxy)propyl]- N,N,N-trimethylammonium chloride (DOTMA), 1,2-bis(oleoyloxy)-3-3-(trimethylammonia) propane (DOTAP), or 1,2- dioleoyl-3-dimethylammonium-propane (DODAP), dioleoylphosphatidylethanolamine (DOPE), cholesterol, LIPOFECTIN (cationic liposome formulation), LIPOFECTAMINE (cationic liposome formulation), LIPOFECTAMINE 2000 (cationic liposome formulation), LIPOFECTAMINE 3000 (cationic liposome formulation), TRANSFECTAM (cationic liposome formulation), a lipid vehicle,
  • the transfecting of the cell is carried out using a lipid selected from one or more of the following categories: cationic lipids; anionic lipids; neutral lipids; multi-valent charged lipids; and zwitterionic lipids.
  • a cationic lipid may be used to facilitate a charge-charge interaction with nucleic acids.
  • the lipid is a neutral lipid.
  • the neutral lipid is dioleoylphosphatidylethanolamine (DOPE), 1,2-Dioleoyl- sn-glycero-3-phosphocholine (DOPC), or cholesterol.
  • DOPE dioleoylphosphatidylethanolamine
  • DOPC 1,2-Dioleoyl- sn-glycero-3-phosphocholine
  • cholesterol is derived from plant sources.
  • cholesterol is derived from animal, fungal, bacterial or archaeal sources.
  • the lipid is a cationic lipid.
  • the cationic lipid is N-[1-(2,3-dioleoyloxy)propyl]-N,N,N-trimethylammonium chloride (DOTMA), 1,2-bis(oleoyloxy)-3-3-(trimethylammonia) propane (DOTAP), or 1,2-dioleoyl-3-dimethylammonium- propane (DODAP).
  • DOTMA 1,2-bis(oleoyloxy)-3-3-(trimethylammonia) propane
  • DODAP 1,2-dioleoyl-3-dimethylammonium- propane
  • one or more of the phospholipids 18:0 PC, 18:1 PC, 18:2 PC, DMPC, DSPE, DOPE, 18:2 PE, DMPE, or a combination thereof are used as lipids.
  • the lipid is DOTMA and DOPE, optionally in a ratio of about 1:1.
  • the lipid is DHDOS and DOPE, optionally in a ratio of about 1:1.
  • the lipid is a commercially available product (e.g., LIPOFECTIN (cationic liposome formulation), LIPOFECTAMINE (cationic liposome formulation), LIPOFECTAMINE 2000 (cationic liposome formulation), LIPOFECTAMINE 3000 (cationic liposome formulation) (Life Technologies)).
  • the transfecting of the cell is carried out using a cationic vehicle, optionally LIPOFECTIN or TRANSFECTAM.
  • the transfecting of the cell is carried out using a lipid nanoparticle, or a liposome.
  • the method is helper virus-free.
  • the second nucleic acid is included in an expression vector.
  • the expression vector comprises a plasmid. In embodiments, the expression vector includes a neomycin phosphotransferase gene.
  • the second nucleic acid is DNA, optionally cDNA. In embodiments, the second nucleic acid is a plasmid. In embodiments, the second nucleic acid has at least one chromatin element, wherein the at least one chromatin element is optionally a Matrix Attachment Region (MAR) element. 20 DB1/ 143560057.1 SAL-026PC/126933-5026 Epigenetic regulatory elements can be used to protect a transgene from unwanted epigenetic effects when placed near the transgene on a vector including the transgene.
  • MAR Matrix Attachment Region
  • MARs were shown to increase genomic integration and integration of a transgene while preventing heterochromatin silencing, as exemplified by the human MAR 1–68. See id.; see also Grandjean et al., Nucleic Acids Res.2011 Aug; 39(15):e104. MARs can also act as insulators and thereby prevent the activation of neighboring cellular genes. Gaussin et al., Gene Ther.2012 Jan; 19(1):15-24.
  • the cell is further transfected with a third nucleic acid having at least one chromatin element, wherein the at least one chromatin element is optionally a Matrix Attachment Region (MAR) element.
  • MARs are expression enhancing, epigenetic regulator elements which are used to enhance and/or facilitate transgene expression, as described, for example, in PCT/IB2010/002337 (WO2011033375) which is incorporated by reference herein in its entirety.
  • a MAR element can be located in cis or trans to the donor DNA.
  • the donor DNA has a size of about 100,000 bases or less, e.g., about 100,000 bases, or about 50,000 bases, or about 30,000 bases, or about 10,000 bases, or about 5,000 bases, or about 10,000 to about 100,000 bases, or about 30,000 to about 100,000 bases, or about 50,000 to about 100,000 bases, or about 10,000 to about 50,000 bases, or about 10,000 to about 30,000 bases, or about 30,000 to about 50,000 bases.
  • the donor DNA has a size of about 200,000 bases or less, e.g., about 200,000 bases, or about 10,000 to about 200,000 bases, or about 30,000 to about 200,000 bases, or about 50,000 to about 200,000 bases, or about 100,000 to about 200,000 bases, or about 150,000 to about 200,000 bases.
  • the enzyme and the donor DNA are transfected at a donor DNA to enzyme ratio of about 1 to about 5, or about 1 to about 4, or about 1 to about 3, or about 1 to about 2, or about 1 to about 1.
  • the amount of donor DNA transfected is about 1 ⁇ g to about 10 ⁇ g, or about 1 ⁇ g to about 8 ⁇ g, or about 1 ⁇ g to about 6 ⁇ g, or about 1 ⁇ g to about 4 ⁇ g, or about 1 ⁇ g, or about 2 ⁇ g, or about 5 ⁇ g, or about 10 ⁇ g.
  • the amount of donor DNA transfected is about 1 ⁇ g.
  • the amount of donor DNA transfected is about 2 ⁇ g.
  • the amount of donor DNA transfected is about 1 ⁇ g and the amount of an enzyme RNA transfected is about 2 ⁇ g, or about 5 ⁇ g, or about 10 ⁇ g.
  • the amount of donor DNA transfected is about 2 ⁇ g and the amount of an enzyme RNA transfected is about 4 ⁇ g, or about 8 ⁇ g, or about 10 ⁇ g, or about 20 ⁇ g. 21 DB1/ 143560057.1 SAL-026PC/126933-5026
  • the present method comprises culturing for about 10, or about 12, or about 14, or about 16 days, or about 18 days after transfection.
  • the resultant cells have a viability of at least about 90%, or at least about 95%, or at least about 99%.
  • the present method yields CAR T-cells that are cytotoxic to target, e.g., tumor, cells.
  • the present method yields CAR T-cells that cause release of cytokines upon target recognition on a tumor cell. In embodiments, the present method yields CAR T-cells that cause release of one or more of IFN gamma, TNF alpha, and granzyme B upon target recognition on a tumor cell. In embodiments, the present method yields CAR T-cells which are not exhausted. In embodiments, the present method yields CAR T-cells with low expression of PD-1 and/or LAG- 3. In embodiments, the present method yields CAR T-cells which are memory competent.
  • the present methods generate a plurality of cells with about or at least about 20%, or about or at least about 30%, or about or at least about 40%, or about or at least about 50%, or about or at least about 60% CAR expression. In embodiments, the present methods generate a plurality of cells with about or at least about 1, or about or at least about 2, or about or at least about 3, or about or at least about 4, or about or at least about 5 genomic integrations per cell.
  • the present methods generate a plurality of cells having about 1000 to about 10000, or about 5000 to about 10000, or about 5000 to about 8000, or about or at least about 5000, or about or at least about 6000, or about or at least about 7000, or about or at least about 8000, or about or at least about 9000, or about or at least about 10000 transgenic molecules expressed per cell.
  • the present methods generate a plurality of cells having about 1000 to about 10000, or about 5000 to about 10000, or about 5000 to about 8000, or about or at least about 5000, or about or at least about 6000, or about or at least about 7000, or about or at least about 8000, or about or at least about 9000, or about or at least about 10000 CAR copies per cell.
  • an enzyme capable of performing targeted genomic integration is any type of an enzyme that cause a donor DNA to be inserted from one location (e.g., without limitation, donor DNA) to a specific site and/or locus in a subject’s genome.
  • the enzyme capable of performing targeted genomic integration is a recombinase.
  • the recombinase is an integrase.
  • the enzyme is a mobile element enzyme.
  • the recombinase is an integrase or a mobile element enzyme. 22 DB1/ 143560057.1 SAL-026PC/126933-5026
  • the mobile element enzyme is an engineered mammalian mobile element enzyme.
  • the mobile element enzyme is a mammal-derived, helper RNA mobile element enzyme.
  • Messenger RNA (mRNA) is an effective alternative to DNA as a source of a mobile element enzyme for targeting somatic cells and tissues, given that RNA is a safer alternative to DNA as a source of a mobile element enzyme for somatic gene therapy applications.
  • the mobile element enzyme is a mammal-derived, DNA mobile element enzyme. In embodiments, the mobile element enzyme is a chimeric mobile element enzyme.
  • the enzyme capable of performing targeted genomic integration is a mobile element enzyme
  • the mobile element enzyme comprises (a) a targeting element which is or comprises a gene-editing system, and (b) a mobile element enzyme that is capable of inserting the donor DNA comprising a transgene, a chimeric CAR, or chimeric CAAR, optionally at a TA dinucleotide site or a TTAA (SEQ ID NO: 440) tetranucleotide site, optionally in a genomic safe harbor site (GSHS), as described elsewhere herein.
  • GSHS genomic safe harbor site
  • the enzyme is derived from Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Myotis lucifugus, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Molossus molossus, Pan troglodytes, or Homo sapiens.
  • the enzyme is an engineered version, including but not limited to hyperactive forms, of an enzyme derived from Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Myotis lucifugus, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Molossus molossus, Pan troglodytes, or Homo sapiens.
  • an enzyme derived from Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Myotis lucifugus, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Molos
  • the enzyme is a mobile element enzyme derived from Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Myotis lucifugus, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Molossus molossus, Pan troglodytes, or Homo sapiens.
  • the enzyme is an engineered version, including but not limited to hyperactive forms, of a mobile element enzyme derived from Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Myotis lucifugus, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Molossus molossus, Pan troglodytes, or Homo sapiens.
  • a mobile element enzyme derived from Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Myotis lucifugus, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuh
  • the mobile element enzyme is from one or more of the Tn1, Tn2, Tn3, Tn5, Tn7, Tn9, Tn10, Tn552, Tn903, Tn1000/Gamma-delta, Tn/O, tnsA, tnsB, tnsC, tniQ, IS10, ISS, IS911, Minos, Sleeping beauty, piggyBac, Tol2, Mos1, Himar1, Hermes, Tol2, Minos, Tel, P-element, MuA, Ty1, Chapaev, transib, Tc1/mariner, or Tc3 donor DNA system, or biologically active fragments variants thereof, inclusive of hyperactive mutants (e.g., without limitation selected from TABLE 1, or equivalents thereof).
  • the mobile element enzyme is from a MLT donor DNA system that is based on a cut-and-paste MLT element obtained from the little brown bat (Myotis lucifugus) or other bat mobile element enzymes, such as Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii, and Molossus molossus.
  • MLT donor DNA system that is based on a cut-and-paste MLT element obtained from the little brown bat (Myotis lucifugus) or other bat mobile element enzymes, such as Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii, and Molossus molossus.
  • hyperactive forms of a bat mobile element enzyme are used.
  • the MLT mobile element enzyme has been shown to be capable of transposition in bat, human, and yeast cells.
  • the hyperactive forms of the MLT mobile element enzyme enhance the transposition process.
  • chimeric MLT mobile element enzymes are capable of site-specific excision without genomic integration.
  • the mobile element enzyme is a Myotis lucifugus mobile element enzyme (MLT), which is either the wild type, monomer, dimer, tetramer (or another multimer), hyperactive, an Int-mutant, or of any other form.
  • MMT Myotis lucifugus mobile element enzyme
  • the MLT mobile element enzyme has an amino acid sequence of SEQ ID NO: 1, or a variant having at least about 80%, at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto, and one or more mutations selected from L573X, E574X, and S2X, wherein X is any amino acid or no amino acid, optionally X is A, G, or a deletion, optionally the mutations are L573del E574del, and S2A).
  • the MLT mobile element enzyme has the nucleotide sequence of SEQ ID NO: 2 (which is a codon-optimized form of MLT), or a nucleotide sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto.
  • SEQ ID NO: 1 is: MAQHSDYSDDEFCADKLSNYSCDSDLENASTSDEDSSDDEVMVRPRTLRRRRISSSSSDSESDIEGGREEWSHV DNPPVLEDFLGHQGLNTDAVINNIEDAVKLFIGDDFFEFLVEESNRYYNQNRNNFKLSKKSLKWKDITPQEMKK FLGLIVLMGQVRKDRRDDYWTTEPWTETPYFGKTMTRDRFRQIWKAWHFNNNADIVNESDRLCKVRPVLDYFVP KFINIYKPHQQLSLDEGIVPWRGRLFFRVYNAGKIVKYGILVRLLCESDTGYICNMEIYCGEGKRLLETIQTVV SPYTDSWYHIYMDNYYNSVANCEALMKNKFRICGTIRKNRGIPKDFQTISLKKGETKFIRKNDILLQVWQSKKP VYLISSIHSAEMEESQNIDRTSKKKIVKPNALIDYNKHMKGVDRADQYLS
  • the amino acid is a non-polar aliphatic amino acid, optionally a non-polar aliphatic amino acid optionally selected from G, A, V, L, I and P, optionally A.
  • the mobile element enzyme does not have additional residues at the C terminus relative to SEQ ID NO: 1.
  • the MLT mobile element enzyme has a nucleotide sequence of SEQ ID NO: 2 (which is codon- optimized) and an amino acid sequence SEQ ID NO: 1, respectively.
  • the MLT mobile element enzyme has a nucleotide sequence of SEQ ID NO: 2, or a nucleotide sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto, or a codon-optimized form thereof.
  • the MLT mobile element enzyme has an amino acid sequence SEQ ID NO: 1, or an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto.
  • the mobile element enzyme can act on an MLT left terminal end, or a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto, wherein the nucleotide sequence of the MLT left terminal end (5’ to 3’) is as follows: ttaacacttggattgcgggaaacgagttaagtcggctcgcgtgaattgcgcgcgtactccgcgggagccgtcttaactcggttcatatag atttgcggtggagtgcgggaaacgtgtaaactcgggccgattgtaactgcgtattaccaaatatttgtt (SEQ ID NO: 21)
  • the mobile element enzyme can act on an MLT right terminal end, or a sequence having at least about 90%, or at least about
  • the donor DNA is or comprises a gene encoding a compete polypeptide. In embodiments, the donor DNA is or comprises a gene which is defective or substantially absent in a disease state.
  • the enzyme e.g., without limitation, a mobile element enzyme, e.g., without limitation, MLT mobile element enzyme
  • the enzyme has one or more mutations which confer hyperactivity.
  • the enzyme e.g., without limitation, a mobile element enzyme, e.g., without limitation, MLT mobile element enzyme
  • the 25 DB1/ 143560057.1 SAL-026PC/126933-5026 enzyme (e.g., without limitation, a mobile element enzyme, e.g., without limitation, MLT mobile element enzyme) has gene cleavage activity (Exc+) and/or a lack of gene integration activity (Int-).
  • the mobile element enzyme e.g., without limitation, MLT mobile element enzyme includes a hyperactive mutation, e.g., about 1, or about 2, or about 3, or about 4, or about 5 hyperactive mutations or combinations thereof.
  • the mobile element enzyme can include any number of any of the hyperactive mutations, or equivalents thereof, described herein.
  • the MLT mobile element enzyme includes a hyperactive mutation, e.g., about 1, or about 2, or about 3, or about 4, or about 5 hyperactive mutations, or combinations thereof.
  • the mobile element enzyme can include any number of any of the hyperactive mutations, or equivalents thereof, described herein.
  • the enzyme comprises one or more mutations corresponding to TABLE 1, or positions corresponding thereto, which, without being bound by theory, provides hyperactive mutations. Numbering relative to the amino acid sequence of protein of SEQ ID NO: 1, and nucleic acid sequence of SEQ ID NO: 2.
  • the MLT mobile element enzyme has S8X1, C13X2 and N125X3 substitutions, at positions corresponding to SEQ ID NO: 1, wherein X1 is selected from G, A, V, L, I and P, X2 is selected from K, R, and H, and X3 is selected from K, R, and H, or wherein: X1 is P, X2 is R, and/or X3 is K.
  • the MLT mobile element enzyme has S8X1 and C13X2 substitutions, at positions corresponding to SEQ ID NO: 1, wherein X1 is selected from G, A, V, L, I and P, X2 is selected from K, R, and H, and X3 is selected from K, R, and H, or wherein: X1 is P, X2 is R, and/or X3 is K.
  • the MLT mobile element enzyme has S8X1 and N125X3 substitutions, at positions corresponding to SEQ ID NO: 1, wherein X1 is selected from G, A, V, L, I and P, X2 is selected from K, R, and H, and X3 is selected from K, R, and H, or wherein: X1 is P, X2 is R, and/or X3 is K.
  • the MLT mobile element enzyme has C13X2 and N125X3 substitutions, at positions corresponding to SEQ ID NO: 1, wherein X1 is selected from G, A, V, L, I and P, X2 is selected from K, R, and H, and X3 is selected from K, R, and H, or wherein: X1 is P, X2 is R, and/or X3 is K.
  • the MLT mobile element enzyme has an amino acid sequence of SEQ ID NO: 1, or a variant thereof, and S8P and C13R mutations (SEQ ID NO: 11).
  • the MLT mobile element enzyme has an amino acid sequence having mutations at positions which correspond to at least one of S8P and C13R mutations relative to the amino acid of SEQ ID NO: 1 or a functional equivalent thereof. In embodiments, the MLT mobile element enzyme has an amino acid sequence having mutations at positions which correspond to S8P and C13R mutations relative to the amino acid of SEQ ID NO: 1 or a functional equivalent thereof. In embodiments, the MLT mobile element enzyme has an amino acid sequence of SEQ ID NO: 1, or a variant thereof, and S8P, C13R, and N125K mutations (SEQ ID NO: 10).
  • a MLT mobile element enzyme comprising the amino acid sequence of SEQ ID NO: 1, or a variant thereof, and includes one or more hyperactive mutations selected from a substitution or deletion at one or more of positions S5, S8, D9, D10, E11, C13, A14, S36, S54, N125, K130, G239, T294, T300, I345, R427, D475, M481, P491, A520, and A561, or positions corresponding thereto.
  • a MLT mobile element enzyme comprising the amino acid sequence of SEQ ID NO: 1, or a variant thereof, and includes one or more hyperactive mutations selected from S5P, S8P, S8P/C13R, D9G, D10G, E11G, C13R, A14V, S36G, S54N, N125K, K130T, G239S, T294A, T300A, I345V, R427H, D475G, M481V, P491Q, A520T, and A561T, or positions corresponding thereto.
  • the MLT mobile element enzyme comprises one or more of hyperactive mutants selected from S8X 1 , C13X 2 and/or N125X 3 (e.g., all of S8X 1 , C13X 2 and N125X 3 , S8X 1 and C13X 2 , S8X 1 and N125X 3 , and C13X 2 and N125X 3 ), where X 1 , X 2 , and X 3 is each independently any amino acid, or X 1 is a non-polar aliphatic amino acid, selected from G, A, V, L, I and P, X 2 is a positively charged amino acid selected from K, R, and H, and/or X 3 is a positively charged amino acid selected from K, R, and H.
  • S8X 1 , C13X 2 and/or N125X 3 e.g., all of S8X 1 , C13X 2 and N125X 3 , S8X 1 and C13X 2 , S8X 1 and N125X 3 , and
  • X 1 is P
  • X 2 is R
  • X 3 is K
  • the enzyme e.g., without limitation, a mobile element enzyme, e.g., without limitation, MLT mobile element enzyme
  • the enzyme has gene cleavage activity (Exc+) and/or gene integration activity (Int+).
  • the enzyme e.g., without limitation, a mobile element enzyme
  • the MLT mobile element enzyme has gene cleavage activity (Exc+) and/or gene integration activity (Int+).
  • the MLT mobile element enzyme has gene cleavage activity (Exc+) and/or a lack of gene integration activity (Int-).
  • the mobile element enzyme e.g., without limitation, MLT mobile element enzyme includes an integration reduced or deficient mutation, e.g., about 1, or about 2, or about 3, or about 4, or about 5 integration reduced or deficient mutations or combinations thereof.
  • the mobile element enzyme can include any number of any of the integration reduced or deficient mutations, or equivalents thereof, described herein.
  • the MLT mobile element enzyme includes an integration reduced or deficient mutations, e.g., about 1, or about 2, or about 3, or about 4, or about 5 integration reduced or deficient mutations, or combinations thereof.
  • the mobile element enzyme can include any number of any of the integration reduced or deficient mutations, or equivalents thereof, described herein.
  • the enzyme comprises one or more mutations corresponding to TABLE 2A, or positions corresponding thereto, which, without being bound by theory, provides integration reduced or deficient mutations. Numbering relative to the amino acid sequence of protein of SEQ ID NO: 1, and nucleic acid sequence of SEQ ID NO: 2.
  • TABLE 2A Amino Acid Change DB1/ 143560057.1 SAL-026PC/126933-5026 G283A E284A
  • the enzyme comprises one or more mutations corresponding to TABLE 2B, or positions corresponding thereto, which, without being bound by theory, provides excision positive and integration deficient mutations.
  • a MLT mobile element enzyme comprising the amino acid sequence of SEQ ID NO: 1, or a variant thereof, and includes one or more mutations selected from S8P and/or C13R and one of R164N, W168V, M278A, K286A, R287A, R333A, K334A, N335A, K349A, K350A, K368A, K369A, and D416N.
  • a MLT mobile element enzyme comprising the amino acid sequence of SEQ ID NO: 1, or a variant thereof, and includes one or more mutations selected from S8P and/or C13R and one of R164N, W168V, M278A, K286A, R287A, R333A, K334A, N335A, K349A, K350A, K368A, K369A, and D416N and/or one or more of E284A, K286A, R287A, N310A, R333A, K334A, R336A, K349A, K350A, K368A, and K369A.
  • a MLT mobile element enzyme comprising the amino acid sequence of SEQ ID NO: 1, or a variant thereof, and includes one or more mutations selected from S8P and/or C13R and one of R164N, W168V, M278A, K286A, R287A, R333A, K334A, N335A, K349A, K350A, K368A, K369A, and D416N and/or one or more of E284A, K286A, R287A, N310A, R333A, K334A, R336A, K349A, K350A, K368A, and K369A and/or one R336A.
  • the mobile element enzyme is or is derived from any of Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Myotis lucifugus, Pipistrellus kuhlii, Pteropus vampyrus, and Molossus molossus.
  • the mobile element enzyme is or is derived from any of Trichoplusia ni (SEQ ID NO: 433), Myotis myotis (SEQ ID NO: 435, SEQ ID NO: 436, SEQ ID NO: 438, or SEQ ID NO: 439), or Pteropus vampyrus (SEQ ID NO: 434).
  • the mobile element enzymes have one or more hyperactive and/or integration deficient mutations selected from TABLE 1, TABLE 2A, and/or TABLE 2B, or equivalents thereof.
  • Trichoplusia ni SEQ ID NO: 433
  • Myotis lucifugus SEQ ID NO: 437
  • Myotis myotis SEQ ID NO: 435
  • SEQ ID NO: 436 SEQ ID NO: 438
  • SEQ ID NO: 439 Pteropus vampyrus
  • Pteropus vampyrus SEQ ID NO: 434
  • Trichnoplusia ni 1 MGSSLDDEHI LSALLQSDDE LVGEDSDSEI SDHVSEDDVQ SDTEEAFIDE VHEVQPTSSG 61
  • the mobile element enzyme is an engineered version of a mobile element enzyme, including but not limited to monomers, dimers, tetramers, hyperactive, or Int-forms, derived from Bombyx mori, Xenopus tropicalis, or Trichoplusia ni. 32 DB1/ 143560057.1 SAL-026PC/126933-5026 In embodiments, the mobile element enzyme is derived from Bombyx mori, Xenopus tropicalis, Trichoplusia ni, or Myotis lucifugus.
  • the mobile element enzyme is an engineered version, including but not limited to a mobile element enzyme that is a monomer, dimer, tetramer (or another multimer), hyperactive, or has a reduced interaction with non-TTAA (SEQ ID NO: 440) recognitions sites (Int-), derived from Bombyx mori, Xenopus tropicalis, Trichoplusia ni, or Myotis lucifugus.
  • the mobile element enzymes have one or more hyperactive and/or integration deficient mutations selected from TABLE 1, TABLE 2A, and TABLE 2B, or equivalents thereof.
  • one skilled in the art can correspond such mutants to mobile element enzymes from any of Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Myotis lucifugus, Pipistrellus kuhlii, Pteropus vampyrus, Pan troglodytes, and Molossus molossus.
  • the mobile element enzyme has a nucleotide sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity to a nucleotide sequence of any of Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Myotis lucifugus, Pteropus vampyrus, Pipistrellus kuhliim, Pan troglodytes, and Molossus molossus.
  • the mobile element enzyme has an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity to an amino acid sequence of any of Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Myotis lucifugus, Pteropus vampyrus, Pipistrellus kuhlii, and Molossus molossus. See Jebb, et al. (2020).
  • the enzyme e.g., without limitation, a mobile element enzyme
  • the enzyme is derived from Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Myotis lucifugus, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Molossus molossus, Pan troglodytes, or Homo sapiens.
  • the enzyme e.g., without limitation, a mobile element enzyme
  • the enzyme is an engineered version, including but not limited to hyperactive forms, of a mobile element enzyme derived from Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Myotis lucifugus, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Molossus molossus, Pan troglodytes, or Homo sapiens.
  • the enzyme is either the wild type, monomer, dimer, tetramer, hyperactive, or an Int-mutant.
  • the mobile element enzymes have one or more hyperactive and/or integration deficient mutations selected from TABLE 1, TABLE 2A, and/or TABLE 2B, or equivalents thereof.
  • the mobile element enzyme has a nucleotide sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity to a nucleotide sequence of any of Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Molossus molossus, and Pan troglodytes.
  • the mobile element enzyme has an amino acid sequence having at least about 90%, or at least about 93%, or at least about 95%, or at 33 DB1/ 143560057.1 SAL-026PC/126933-5026 least about 97%, or at least about 98%, or at least about 99% identity to an amino acid sequence of any of Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Molossus molossus, Pan troglodytes, and Homo sapiens.
  • the mobile element enzyme is an engineered version, including but not limited to a mobile element enzyme that is a monomer, dimer, tetramer, hyperactive, or has a reduced interaction with non-TTAA (SEQ ID NO: 440) recognitions sites (Int-), derived from any of Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Myotis lucifugus, Pipistrellus kuhlii, Pteropus vampyrus, and Molossus molossus Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Pan troglodytes, Myotis lucifugus, and Homo sapiens.
  • a mobile element enzyme that is a monomer, dimer, tetramer, hyperactive, or
  • the mobile element enzyme is either the wild type, monomer, dimer, tetramer or another multimer, hyperactive, or a an Int-mutant.
  • the mobile element enzyme is from a Tc1/mariner donor DNA system. See, e.g., Plasterk et al. Trends in Genetics.1999; 15(8):326–32.
  • the mobile element enzyme is from a Sleeping Beauty donor DNA system (see, e.g., Cell.
  • a hyperactive form of Sleeping Beauty e.g., SB100X (see Gene Therapy volume 18, pages 849–856(2011), or a piggyBac (PB) donor DNA system (see, e.g., Trends Biotechnol.2015 Sep;33(9):525-33, which is incorporated herein by reference in its entirety)
  • PB piggyBac
  • a hyperactive form of PB mobile element enzyme e.g., with seven amino acid substitutions (e.g., I30V, S103P, G165S, M282V, S509G, N570S, N538K on mPB, or functional equivalents in non-mPB, see Mol Ther Nucleic Acids.2012 Oct; 1(10): e50, which is incorporated herein by reference in its entirety); see also Yusa et al., PNAS January 25, 2011108 (4) 1531-1536; Voigt et al., PNAS January 25, 2011108 (4) 1531-1536; Voig
  • the piggyBac mobile element enzymes belong to the IS4 mobile element enzyme family. De Palmenaer et al., BMC Evolutionary Biology.2008;8:18. doi: 10.1186/1471-2148-8-18.
  • the piggyBac family includes a large diversity of donor DNAs, and any of these donor DNAs can be used in embodiments of the present disclosure. See, e.g., Bouallègue et al., Genome Biol Evol.2017;9(2):323-339.
  • the founding member of the piggyBac (super)family, insect piggyBac was originally identified in the cabbage looper moth (Trichoplusiani ni) and studied both in vivo and in vitro.
  • Insect piggyBac is known to transpose by a canonical cut-and-paste mechanism promoted by an element-encoded mobile element enzyme with a catalytic site resembling the RNase H fold shared by many recombinases.
  • the insect piggyBac donor DNA system has been shown to be highly active in a wide range of animals, including Drosophila and mice, where it has been developed as a powerful tool for gene tagging and genome engineering.
  • Other donor DNAs affiliated to the piggyBac superfamily are common in arthropods and vertebrates including Xenopus and Bombyx.
  • Mammalian piggyBac donor DNAs and mobile element enzymes including hyperactive mammalian piggyBac variants, which can 34 DB1/ 143560057.1 SAL-026PC/126933-5026 be used in embodiments of the present disclosure, are described, e.g., in International Application WO2010085699, which is incorporated herein by reference in its entirety.
  • the mobile element enzyme is from a LEAP-IN 1 type or LEAP-IN donor DNA system (Biotechnol J. 2018 Oct;13(10):e1700748. doi: 10.1002/biot.201700748. Epub 2018 Jun 11).
  • the LEAPIN mobile element enzyme system includes a mobile element enzyme (e.g., without limitation, a mobile element enzyme mRNA) and a vector containing one or more genes of interest (donor DNAs), selection markers, regulatory elements, insulators, etc., flanked by the donor DNA cognate inverted terminal ends and the transposition recognition motif (TTAT).
  • a mobile element enzyme e.g., without limitation, a mobile element enzyme mRNA
  • donor DNAs genes of interest
  • selection markers e.g., selection markers, regulatory elements, insulators, etc.
  • TTAT transposition recognition motif
  • the LEAPIN mobile element enzyme generates stable transgene integrants with various advantageous characteristics, including single copy integrations at multiple genomic loci, primarily in open chromatin segments; no payload limit, so multiple independent transcriptional units may be expressed from a single construct; the integrated transgenes maintain their structural and functional integrity; and maintenance of transgene integrity ensures the desired chain ratio in every recombinant cell.
  • the mobile element enzyme is an engineered form of a mobile element enzyme reconstructed from Homo sapiens or a predecessor thereof.
  • PGBD1 and PGBD2 may resemble the PGBD3 donor DNA in which the mobile element enzyme ORF is flanked upstream by a 3′ splice site and downstream by a polyadenylation site. See Newman et al., PLoS Genet 2008;4:e1000031. PLoS Genet 4(3): e1000031.
  • the PGBD5 inactive mobile element enzyme sequence belongs to the RNase H clan of Pfam structures, while PGBD3 has sustained only a single D to N mutation in the essential catalytic triad DDD(D) and retains the ability to bind the upstream piggyBac terminal inverted repeat. Bailey et al., DNA Repair (Amst) 2012;11:488-501.
  • the PGBD5 mobile element enzyme does not retain the catalytic DDD (D) motif found in active elements, and the mobile element enzyme is not only inactive but fails to associate with either DNA or chromatin in vivo.
  • DDD catalytic DDD
  • PGBD1 and PGBD2 are thought to be present in the common ancestor of mammals, while PGBD3 and PGBD4 are restricted to primates. See Sarkar et al., Mol Genet Genomics 2003;270:173-80.
  • the Pteropus vampyrus mobile 35 DB1/ 143560057.1 SAL-026PC/126933-5026 element enzyme is closely related to PGBD4 and shares DDD catalytic domain and the C-terminal region that are involved in excision mechanisms. See Mitra et al., EMBO J 2008;27:1097-109.
  • a mammalian mobile element enzyme which has gene cleavage and/or gene integration activity, can be constructed based on alignment of the amino acid sequence of Pteropus vampyrus mobile element enzyme to PGBD1, PGBD2, PGBD3, PGBD4, and PGBD5 sequences. Also, in embodiments.
  • the mammalian mobile element enzyme has mutations that confers hyperactivity to a recombinant mammalian mobile element enzyme. Accordingly, in embodiments, the mobile element enzyme has gene cleavage activity (Exc+) and/or gene integration activity (Int+). In embodiments, the mobile element enzyme has gene cleavage activity (Exc+) and/or lacks gene integration activity (Int-). In some aspects, an enzyme capable of performing targeted genomic integration is a recombinant mammalian mobile element enzyme that was derived by, in part, aligning several inactive mobile element enzyme sequences from a human genome to Pteropus vampyrus mobile element enzyme sequence.
  • the Pteropus vampyrus mobile element enzyme has an amino acid sequence having at least 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to SEQ ID NO: 430 (or a functional equivalent thereof.
  • the Pteropus vampyrus mobile element enzyme has an amino acid sequence of SEQ ID NO: 430, or a functional equivalent thereof.
  • the Pteropus vampyrus mobile element enzyme has a nucleotide sequence having at least 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to SEQ ID NO: 429 or a codon-optimized variant thereof.
  • the mobile element enzyme is a mammalian mobile element enzyme, such as a mobile element enzyme from a bat, e.g., without limitation, Pteropus vampyrus.
  • the mobile element enzyme is an engineered form that is based on a mobile element enzyme reconstructed from Homo sapiens or a predecessor thereof.
  • the mobile element enzyme includes but is not limited to an engineered version that is a monomer, dimer, tetramer (or another multimer), hyperactive, or has a reduced interaction with non-TTAA (SEQ ID NO: 440) recognitions sites (Int-), of an engineered version of a mobile element enzyme reconstructed from Homo sapiens or a predecessor thereof.
  • the mobile element enzyme is an engineered form that is based on a mobile element enzyme reconstructed from mammalian species.
  • the mobile element enzyme includes but is not limited to an engineered that is a monomer, dimer, tetramer (or another multimer), hyperactive, or has a reduced interaction with non-TTAA (SEQ ID NO: 440) recognitions sites (Int-), of a mobile element enzyme reconstructed from mammalian species.
  • the donor DNA is included in a vector comprising left and right end sequences recognized by the enzyme capable of performing targeted genomic integration, e.g., without limitation, a mobile element enzyme.
  • the end sequences are selected from MER, MER75A, MER75B, and MER85.
  • the end sequences are selected from nucleotide sequences of SEQ ID NO: 12, SEQ ID NO: 13 , SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 441, and SEQ ID NO: 22, or a nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) thereto.
  • a nucleotide sequence having at least about 90% identity e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity
  • one or more of the end sequences are optionally flanked by a TTAA (SEQ ID NO: 440) sequence.
  • the end sequences include at least one repeat from a nucleotide sequence having at least about 90% (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) identity to the nucleotide sequence of SEQ ID NO: 12, and wherein the at least one repeat from the nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 12 is positioned at the 5’ end of the donor DNA.
  • the end sequences can further include at least one repeat from a nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity to the nucleotide sequence of SEQ ID NO: 17, and wherein the at least one repeat from the nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 17 is positioned at the 3’ end of the donor DNA.
  • a nucleotide sequence having at least about 90% identity e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least
  • the end sequences which can be from, e.g., Pteropus vampyrus, are optionally flanked by a TTAA (SEQ ID NO: 440) sequence.
  • the end sequences include at least one repeat from a nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 13, and wherein the at least one repeat from the nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 13 is positioned at the 5’ end of the donor DNA.
  • the end sequences can further include at least one repeat from a nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 18, and wherein the at least one repeat from the nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 37 DB1/ 143560057.1 SAL-026PC/126933-5026 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 18 is positioned at the 3’ end of the donor DNA.
  • a nucleotide sequence having at least about 90% identity e.g., a sequence having at least about 90%, or at least about 93%, or at least
  • the end sequences which can be, e.g., PGBD4, are optionally flanked by a TTAA (SEQ ID NO: 440) sequence.
  • the end sequences include at least one repeat from a nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 14, wherein the at least one repeat from the nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 14 is positioned at the 5’ end of the donor DNA.
  • the end sequences include at least one repeat from a nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 18, wherein the at least one repeat from the nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 19 is positioned at the 3’ end of the donor DNA.
  • a nucleotide sequence having at least about 90% identity e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about
  • the end sequences which can be, e.g., MER75, are optionally flanked by a TTAA (SEQ ID NO: 440) sequence.
  • the end sequences include at least one repeat from a nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 15, wherein the at least one repeat from the nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 15 is positioned at the 5’ end of the donor DNA.
  • the end sequences include at least one repeat from a nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 20, wherein the at least one repeat from the nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 20 is positioned at the 3’ end of the donor DNA.
  • a nucleotide sequence having at least about 90% identity e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about
  • the end sequences which can be, e.g., MER75B, are optionally flanked by a TTAA (SEQ ID NO: 440) sequence.
  • the end sequences include at least one repeat from a nucleotide sequence having at least about 90% (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) identity to the nucleotide sequence of SEQ ID NO: 16, wherein the at 38 DB1/ 143560057.1 SAL-026PC/126933-5026 least one repeat from the nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 16 is positioned at the 5’ end of the donor
  • the end sequences include at least one repeat from a nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 21 or SEQ ID NO: 441, wherein the at least one repeat from the nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) to the nucleotide sequence of SEQ ID NO: 21 or SEQ ID NO: 441 is positioned at the 3’ end of the donor DNA.
  • a nucleotide sequence having at least about 90% identity e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least
  • a donor DNA is or comprises a vector comprising a donor DNA comprising one or more end sequences recognized by an enzyme such as, for example a mobile element enzyme.
  • the end sequences are selected from Pteropus vampyrus, MER75, MER75A, and MER75B. MERs contain end sequences with similarity to piggyBac-like mobile elements and exhibit duplications of their presumed TTAA (SEQ ID NO: 440) target sites.
  • the end sequences are selected from nucleotide sequences of SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 441, and SEQ ID NO: 22, or a nucleotide sequence having at least about 90% identity (e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity) thereto.
  • a nucleotide sequence having at least about 90% identity e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity
  • the mobile element enzyme has an amino acid sequence of SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 8, or SEQ ID NO: 9, or a variant sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto, or at least about 10 mutations, or at least about 9 mutations, or at least about 8 mutations, or at least about 7 mutations, or at least about 6 mutations, or at least about 5 mutations, or at least about 4 mutations, or at least about 3 mutations, or at least about 2 mutations, or at least about 1 mutation.
  • the mobile element enzyme has an amino acid sequence having S8P, G17R, and/or K134K mutation relative to the amino acid sequence of SEQ ID NO: 4 or a functional equivalent thereof. In embodiments, the mobile element enzyme has an amino acid sequence having S8P, G17R, and/or K134K mutation relative to the amino acid sequence of SEQ ID NO: 5 or a functional equivalent thereof. In embodiments, the mobile element enzyme has an amino acid sequence having I83P and/or V118R mutation relative to the amino acid sequence of SEQ ID NO: 6 or a functional equivalent thereof.
  • the mobile element enzyme has an amino acid sequence having S20P and/or A29R mutation relative to the amino acid sequence of SEQ ID NO: 7 or a functional equivalent thereof. In embodiments, the mobile element enzyme has an amino acid sequence having T4P and/or L13R mutation relative to the amino acid sequence of SEQ ID NO: 8 or a functional equivalent thereof. In embodiments, the mobile element enzyme has an amino acid sequence having A12P and/or I28R mutation and/or R152K mutation relative to the amino acid sequence of SEQ ID NO: 9 or a functional equivalent thereof.
  • the enzyme capable of performing targeted genomic integration is in a monomeric or dimeric form. In embodiments, the enzyme capable of performing targeted genomic integration (e.g., without limitations, a mobile element enzyme) is in a multimeric form.
  • the enzyme e.g., without limitation, a mobile element enzyme
  • the enzyme is an engineered version, including but not limited to a mobile element enzyme that is a monomer, dimer, tetramer, hyperactive, or has a reduced interaction with non-TTAA (SEQ ID NO: 440) recognitions sites (Int-), and is derived from any of Bombyx mori, Xenopus tropicalis, Trichoplusia ni, Myotis lucifugus, Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pteropus vampyrus, Pipistrellus kuhlii, Pan troglodytes, Molossus molossus, or Homo sapiens.
  • a mobile element enzyme that is a monomer, dimer, tetramer, hyperactive, or has a reduced interaction with non-TTAA (SEQ ID
  • the mobile element enzyme is either the wild type, monomer, dimer, tetramer or another multimer, hyperactive, or an Int-mutant.
  • Targeting Chimeric Constructs e.g., in embodiments, the enzyme, without limitation, a mobile element enzyme, comprises a targeting element.
  • the enzyme, without limitation, a mobile element enzyme, associated with the targeting element is capable of inserting the donor DNA comprising a chimeric CAR or chimeric CAAR, optionally at a TA dinucleotide site or a TTAA (SEQ ID NO: 440) tetranucleotide site in a genomic safe harbor site (GSHS).
  • GSHS genomic safe harbor site
  • the enzyme, without limitation, a mobile element enzyme, associated with the targeting element has one or more mutations which confer hyperactivity.
  • the enzyme, without limitation, a mobile element enzyme, associated with the targeting element has gene cleavage activity (Exc+) and/or gene integration activity (Int+).
  • the enzyme, without limitation, a mobile element enzyme, associated with the targeting element has gene cleavage activity (Exc+) and/or reduced integration activity (Int-).
  • the targeting element comprises one or more proteins or nucleic acids that are capable of binding to a nucleic acid.
  • the targeting element comprises one or more of a of a gRNA, optionally associated with a Cas enzyme, which is optionally catalytically inactive, transcription activator-like effector (TALE), Zinc finger, catalytically inactive transcription factor, nickase, a transcriptional activator, a transcriptional repressor, a recombinase, a DNA methyltransferase, a histone methyltransferase, paternally expressed gene 10 (PEG10), and TnsD.
  • TALE transcription activator-like effector
  • DBD DNA binding domain
  • the TALE DBD comprises one or more repeat sequences. In embodiments, the TALE DBD comprises about 14, or about 15, or about, 16, or about 17, or about 18, or about 18.5 repeat sequences. In embodiments, the TALE DBD repeat sequences comprise 33 or 34 amino acids. In embodiments, the TALE DBD repeat sequences comprise a repeat variable di-residue (RVD) at residue 12 or 13 of the 33 or 34 amino acids. In embodiments, the RVD recognizes one base pair in the nucleic acid molecule. In embodiments, the RVD recognizes a C residue in the nucleic acid molecule and is selected from HD, N(gap), HA, ND, and HI.
  • RVD repeat variable di-residue
  • the RVD recognizes a G residue in the nucleic acid molecule and is selected from NN, NH, NK, HN, and NA. In embodiments, the RVD recognizes an A residue in the nucleic acid molecule and is selected from NI and NS. In embodiments, the RVD recognizes a T residue in the nucleic acid molecule and is selected from NG, HG, H(gap), and IG. In embodiments, the GSHS is in an open chromatin location in a chromosome. In embodiments, the GSHS is selected from adeno-associated virus site 1 (AAVS1), chemokine (C-C motif) receptor 5 (CCR5) gene, HIV-1 coreceptor, and human Rosa26 locus.
  • AAVS1 adeno-associated virus site 1
  • C-C motif chemokine receptor 5
  • the GSHS is located on human chromosome 2, 4, 6, 10, 11, 17, 22, or X.
  • the GSHS is selected from TALC1, TALC2, TALC3, TALC4, TALC5, TALC7, TALC8, AVS1, AVS2, AVS3, ROSA1, ROSA2, TALER1, TALER2, TALER3, TALER4, TALER5, SHCHR2-1, SHCHR2-2, SHCHR2-3, SHCHR2-4, SHCHR4-1, SHCHR4-2, SHCHR4-3, SHCHR6-1, SHCHR6-2, SHCHR6-3, SHCHR6-4, SHCHR10-1, SHCHR10-2, SHCHR10-3, SHCHR10-4, SHCHR10-5, SHCHR11-1, SHCHR11-2, SHCHR11-3, SHCHR17-1, SHCHR17-2, SHCHR17-3, and SHCHR17-4.
  • the targeting element comprises a Cas9 enzyme guide RNA complex.
  • the Cas9 enzyme guide RNA complex comprises a nuclease-deficient dCas9 guide RNA complex.
  • the targeting element comprises a Cas12 enzyme guide RNA complex.
  • the targeting element comprises a nuclease-deficient dCas12 guide RNA complex, optionally dCas12j guide RNA complex or dCas12a guide RNA complex.
  • the targeting element comprises a Cas12k enzyme guide RNA complex.
  • the targeting element comprises a nuclease-deficient dCas12 guide RNA complex, optionally dCas12k guide RNA complex.
  • a targeting chimeric system or construct having a DBD fused to a mobile element enzyme, directs binding of an enzyme capable of performing targeted genomic integration (e.g., without limitation, a mobile element 41 DB1/ 143560057.1 SAL-026PC/126933-5026 enzyme) to a specific sequence (e.g., transcription activator-like effector proteins (TALE) repeat variable di-residues (RVD) or gRNA) near an enzyme recognition site.
  • TALE transcription activator-like effector proteins
  • RVD repeat variable di-residues
  • gRNA gRNA
  • dCas9 i.e., deficient for nuclease activity
  • gRNAs directed to bind at a desired sequence of DNA in GSHS.
  • TALEs described herein can physically sequester the enzyme such as, e.g., a mobile element enzyme, to GSHS and promote transposition to nearby TTAA (SEQ ID NO: 440) sequences in close proximity to the RVD TALE nucleotide sequences.
  • GSHS in open chromatin sites are specifically targeted based on the predilection for mobile element enzymes to insert into open chromatin.
  • an enzyme capable of performing targeted genomic integration e.g., without limitation, a recombinase, integrase, or a mobile element enzyme such as, without limitation, a mammalian mobile element enzyme
  • a TALE DNA binding domain DBD
  • a Cas-based gene-editing system such as, e.g., Cas9 or a variant thereof.
  • the targeting element targets the enzyme to a locus of interest.
  • the targeting element comprises CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) associated protein 9 (Cas9), or a variant thereof.
  • a CRISPR/Cas9 tool only requires Cas9 nuclease for DNA cleavage and a single-guide RNA (sgRNA) for target specificity.
  • sgRNA single-guide RNA
  • the inactivated form of Cas9 which is a nuclease-deficient (or inactive, or “catalytically dead” Cas9, is typically denoted as “dCas9,” has no substantial nuclease activity.
  • dCas9 has no substantial nuclease activity.
  • CRISPR/dCas9 binds precisely to specific genomic sequences through targeting of guide RNA (gRNA) sequences.
  • gRNA guide RNA
  • dCas9 is utilized to edit gene expression when applied to the transcription binding site of a desired site and/or locus in a genome.
  • gRNA guide RNA
  • dCas9 prevents the proliferation of repeating codons and DNA sequences that might be harmful to an organism's genome.
  • the targeting element comprises a nuclease-deficient Cas enzyme guide RNA complex.
  • the targeting element comprises a nuclease-deficient (or inactive, or “catalytically dead” Cas, e.g., Cas9, typically denoted as “dCas” or “dCas9”) guide RNA complex.
  • the dCas9/gRNA complex comprises a guide RNA selected from: GTTTAGCTCACCCGTGAGCC (SEQ ID NO: 91), CCCAATATTATTGTTCTCTG (SEQ ID NO: 92), GGGGTGGGATAGGGGATACG (SEQ ID NO: 93), GGATCCCCCTCTACATTTAA (SEQ ID NO: 94), GTGATCTTGTACAAATCATT (SEQ ID NO: 95), 42 DB1/ 143560057.1 SAL-026PC/126933-5026 CTACACAGAATCTGTTAGAA (SEQ ID NO: 96), TAAGCTAGAGAATAGATCTC (SEQ ID NO: 97), and TCAATACACTTAATGATTTA (SEQ ID NO: 98), wherein the guide RNA directs the enzyme to a chemokine (C-C motif) receptor 5 (CCR5) gene.
  • C-C motif chemokine receptor 5
  • the dCas9/gRNA complex comprises a guide RNA selected from: CACCGGGAGCCACGAAAACAGATCC (SEQ ID NO: 99);CACCGCGAAAACAGATCCAGGGACA (SEQ ID NO: 100); CACCGAGATCCAGGGACACGGTGCT (SEQ ID NO: 101); CACCGGACACGGTGCTAGGACAGTG (SEQ ID NO: 102); CACCGGAAAATGACCCAACAGCCTC (SEQ ID NO: 103); CACCGGCCTGGCCGGCCTGACCACT (SEQ ID NO: 104); CACCGCTGAGCACTGAAGGCCTGGC (SEQ ID NO: 105); CACCGTGGTTTCCACTGAGCACTGA (SEQ ID NO: 106); CACCGGATAGCCAGGAGTCCTTTCG (SEQ ID NO: 107); CACCGGCGCTTCCAGTGCTCAGACT (SEQ ID NO: 108); CACCGCAGTGCTCAGACTAGGGAAG (SEQ ID NO: 109
  • the guide RNAs are: AATCGAGAAGCGACTCGACA (SEQ ID NO: 425), and tgccctgcaggggagtgagc (SEQ ID NO: 426).
  • the guide RNAs are gaagcgactcgacatggagg (SEQ ID NO: 427) and cctgcaggggagtgagcagc (SEQ ID NO: 428).
  • guide RNAs (gRNAs) for targeting human genomic safe harbor sites using any of the gRNA-based targeting elements, e.g., without limitation dCas, in areas of open chromatin are as shown in TABLE 3A-3F.
  • guide RNAs for targeting human genomic safe harbor sites using any of the gRNA-based targeting elements, e.g., without limitation dCas, in areas of open chromatin are as shown in TABLE 3A: GSHS Identifier Sequence DB1/ 143560057.1 SAL-026PC/126933-5026 AAVS1 22F gatagccaggagtcctttcg (SEQ ID NO: 808) AAVS1 23F gcgcttccagtgctcagact (SEQ ID NO: 809) DB1/ 143560057.1 SAL-026PC/126933-5026 AAVS1 gAAVS31 GCAGAGTGGTCAGCACAGAG (SEQ ID NO: 161) AAVS1 gAAVS32 GCACAGAGTGGCTAAGCCCA (SEQ ID NO: 162) DB1/ 143560057.1 SAL-026PC/126933-5026 hROSA26 gHROSA26-16 CAC
  • a Cas-based targeting element comprises Cas12 or a variant thereof, e.g., without limitation, Cas12a (e.g., dCas12a), or Cas12j (e.g., dCas12j), or Cas12k (e.g., dCas12k).
  • the targeting element comprises a Cas12 enzyme guide RNA complex.
  • the targeting element is selected from a zinc finger (ZF), transcription activator-like effector (TALE), meganuclease, and clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein, any of which are, in embodiments, catalytically inactive.
  • CRISPR-associated protein is selected from Cas9, CasX, CasY, Cas12a (Cpf1), and gRNA complexes thereof.
  • the CRISPR-associated protein is selected from Cas9, xCas9, Cas 6, Cas7, Cas8, Cas12a (Cpf1), Cas13a, Cas14, CasX, CasY, a Class 1 Cas protein, 59 DB1/ 143560057.1 SAL-026PC/126933-5026 a Class 2 Cas protein, MAD7, MG1 nuclease, MG2 nuclease, MG3 nuclease, or catalytically inactive forms thereof, and gRNA complexes thereof.
  • the mobile element enzyme is capable of inserting a donor DNA at a TA dinucleotide site or a TTAA tetranucleotide site in a genomic safe harbor site (GSHS) of a nucleic acid molecule.
  • the mobile element enzyme is suitable for causing insertion of the donor DNA in a GSHS when contacted with a biological cell.
  • the targeting element is suitable for directing the mobile element enzyme to the GSHS sequence.
  • the targeting element comprises transcription activator-like effector (TALE) DNA binding domain (DBD).
  • TALE DBD comprises one or more repeat sequences.
  • the TALE DBD comprises about 14, or about 15, or about, 16, or about 17, or about 18, or about 18.5 repeat sequences.
  • the TALE DBD repeat sequences comprise 33 or 34 amino acids.
  • the one or more of the TALE DBD repeat sequences comprise a repeat variable di-residue (RVD) at residue 12 or 13 of the 33 or 34 amino acids.
  • the targeting element e.g., TALE or Cas (e.g., Cas9 or Cas12, or variants thereof) DBDs cause the mammalian mobile element enzyme to bind specifically to human GSHS.
  • the TALEs or Cas DBDs sequester the mobile element enzyme to GSHS and promote transposition to nearby TA dinucleotide or a TTAA tetranucleotide sites which can be located in proximity to the repeat variable di-residues (RVD) TALE or gRNA nucleotide sequences.
  • the GSHS regions are located in open chromatin sites that are susceptible to mobile element enzyme activity. Accordingly, the mammalian mobile element enzyme does not only operate based on its ability to recognize TA or TTAA sites, but it also directs a donor DNA comprising a chimeric CAR or chimeric CAAR to specific locations in proximity to a TALE or Cas DBD.
  • the chimeric mobile element enzyme in accordance with embodiments of the present disclosure has negligible risk of genotoxicity and exhibits superior features as compared to existing gene therapies.
  • a chimeric mobile element enzyme is mutated to be characterized by reduced or inhibited binding of off-target sequences and consequently reliant on a DBD fused thereto, such as a TALE or Cas DBD, for transposition.
  • a DBD fused thereto such as a TALE or Cas DBD
  • the described cells, compositions, and methods allow reducing vector and transgene insertions that increase a mutagenic risk.
  • the described cells and methods make use of a gene transfer system that reduces genotoxicity compared to viral- and nuclease-mediated gene therapies.
  • TALE or Cas DBDs are customizable, such as a TALE or Cas DBDs is selected for targeting a specific genomic location.
  • the genomic location is in proximity to a TA dinucleotide site or a TTAA (SEQ ID NO: 440) tetranucleotide site.
  • TTAA SEQ ID NO: 440
  • TALE repeat sequences e.g., modular arrays
  • gRNA e.g., gRNA which are linked together to recognize flanking DNA sequences.
  • TALE or gRNA can recognize certain base pair(s) or residue(s).
  • TALE nucleases TALENs
  • TALENs are a known tool for genome editing and introducing targeted double-stranded breaks. TALENs comprise endonucleases, such as FokI nuclease domain, fused to a customizable DBD. This DBD is composed of highly conserved repeats from TALEs, which are proteins secreted by Xanthomonas bacteria to alter transcription of genes in host plant cells.
  • the DBD includes a repeated highly conserved 33–34 amino acid sequence with divergent 12th and 13th amino acids. These two positions, referred to as the RVD, are highly variable and show a strong correlation with specific base pair or nucleotide recognition. This straightforward relationship between amino acid sequence and DNA recognition has allowed for the engineering of specific DBDs by selecting a combination of repeat segments containing the appropriate RVDs. Boch et al. Nature Biotechnology.2011; 29 (2): 135–6. Accordingly, TALENs can be readily designed using a “protein-DNA code” that relates modular DNA-binding TALE repeat domains to individual bases in a target-binding site. See Joung et al. Nat Rev Mol Cell Biol.2013;14(1):49-55.
  • the TALE DBD comprises one or more repeat sequences.
  • the TALE DBD comprises about 15, or about, 16, or about 17, or about 18, or about 18.5 repeat sequences.
  • the TALE DBD repeat sequences comprise 33 or 34 amino acids.
  • the one or more of the TALE DBD repeat sequences comprise an RVD at residue 12 or 13 of the 33 or 34 amino acids.
  • the RVD can recognize certain base pair(s) or residue(s).
  • the RVD recognizes one base pair in the nucleic acid molecule.
  • the RVD recognizes a C residue in the nucleic acid molecule and is selected from HD, N(gap), HA, ND, and HI.
  • the RVD recognizes a G residue in the nucleic acid molecule and is selected from NN, NH, NK, HN, and NA. In embodiments, the RVD recognizes an A 61 DB1/ 143560057.1 SAL-026PC/126933-5026 residue in the nucleic acid molecule and is selected from NI and NS. In embodiments, the RVD recognizes a T residue in the nucleic acid molecule and is selected from NG, HG, H(gap), and IG. In embodiments, the GSHS is in an open chromatin location in a chromosome.
  • the GSHS is selected from adeno-associated virus site 1 (AAVS1), chemokine (C-C motif) receptor 5 (CCR5) gene, HIV-1 coreceptor; and human Rosa26 locus.
  • AAVS1 adeno-associated virus site 1
  • CCR5 chemokine receptor 5
  • HIV-1 coreceptor HIV-1 coreceptor
  • human Rosa26 locus adeno-associated virus site 1 (AAVS1), chemokine (C-C motif) receptor 5 (CCR5) gene, HIV-1 coreceptor; and human Rosa26 locus.
  • the GSHS is located on human chromosome 2, 4, 6, 10, 11, 17, 22, or X.
  • the GSHS is selected from TALC1, TALC2, TALC3, TALC4, TALC5, TALC7, TALC8, AVS1, AVS2, AVS3, ROSA1, ROSA2, TALER1, TALER2, TALER3, TALER4, TALER5, SHCHR2-1, SHCHR2-2, SHCHR2-3, SHCHR2-4, SHCHR4-1, SHCHR4-2, SHCHR4-3, SHCHR6-1, SHCHR6-2, SHCHR6-3, SHCHR6-4, SHCHR10-1, SHCHR10-2, SHCHR10-3, SHCHR10-4, SHCHR10-5, SHCHR11-1, SHCHR11-2, SHCHR11-3, SHCHR17-1, SHCHR17-2, SHCHR17-3, and SHCHR17-4.
  • the GSHS comprises one or more of TGGCCGGCCTGACCACTGG (SEQ ID NO: 23), TGAAGGCCTGGCCGGCCTG (SEQ ID NO: 24), TGAGCACTGAAGGCCTGGC (SEQ ID NO: 25), TCCACTGAGCACTGAAGGC (SEQ ID NO: 26), TGGTTTCCACTGAGCACTG (SEQ ID NO: 27), TGGGGAAAATGACCCAACA (SEQ ID NO: 28), TAGGACAGTGGGGAAAATG (SEQ ID NO: 29), TCCAGGGACACGGTGCTAG (SEQ ID NO: 30), TCAGAGCCAGGAGTCCTGG (SEQ ID NO: 31), TCCTTCAGAGCCAGGAGTC (SEQ ID NO: 32), TCCTCCTTCAGAGCCAGGA (SEQ ID NO: 33), TCCAGCCCCTCCTCCTTCA (SEQ ID NO: 34), TCCGAGCTTGACCCTTGGA (SEQ ID NO: 35), TGGTTTCCGAGCTTGACCC (SEQ ID
  • the TALE DBD binds to one of TGGCCGGCCTGACCACTGG (SEQ ID NO: 23), TGAAGGCCTGGCCGGCCTG (SEQ ID NO: 24), TGAGCACTGAAGGCCTGGC (SEQ ID NO: 25), TCCACTGAGCACTGAAGGC (SEQ ID NO: 26), TGGTTTCCACTGAGCACTG (SEQ ID NO: 27), TGGGGAAAATGACCCAACA (SEQ ID NO: 28), TAGGACAGTGGGGAAAATG (SEQ ID NO: 29), TCCAGGGACACGGTGCTAG (SEQ ID NO: 30), TCAGAGCCAGGAGTCCTGG (SEQ ID NO: 31), TCCTTCAGAGCCAGGAGTC (SEQ ID NO: 32), TCCTCCTTCAGAGCCAGGA (SEQ ID NO: 33), TCCAGCCCCTCCTCCTTCA (SEQ ID NO: 34), TCCGAGCTTGACCCTTGGA (SEQ ID NO: 35), TGGTTTCCGAGCTTGACC
  • the TALE DBD comprises one or more of: NH NH HD HD NH NH HD HD NG NH NI HD HD NI HD NG NH NH, NH NI NI NH NH HD HD NG NH NH HD HD NH NH HD NG NH, NH NI NH HD NI HD NG NH NI NI NH NH HD HD NG NH NH HD, NH NI HD NG NH NI NH HD NI HD NG NH NI NI NH NH HD, NH NH NG NG NG HD HD NI HD NG NH NI NI HD NG NH, NH NH NH NH NH NI NI NI NI HD NG NH, NH NH NH NH NI NI NI NI NG NH NI HD NI HD NG NH, NH NH NH NH NI NI NI NI NG NH NI HD NI HD NG NH, NH NH
  • the TALE DBD comprises one or more of the sequences outlined herein or a variant sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto, or at least about 10 mutations, or at least about 9 mutations, or at least about 8 66 DB1/ 143560057.1 SAL-026PC/126933-5026 mutations, or at least about 7 mutations, or at least about 6 mutations, or at least about 5 mutations, or at least about 4 mutations, or at least about 3 mutations, or at least about 2 mutations, or at least about 1 mutation.
  • the GSHS and the TALE DBD sequences are selected from: TGGCCGGCCTGACCACTGG (SEQ ID NO: 23) and NH NH HD HD NH NH HD HD NG NH NI HD HD NI HD NG NH NH; TGAAGGCCTGGCCGGCCTG (SEQ ID NO: 24) and NH NI NI NH NH HD HD NG NH NH HD HD NH NH HD HD NG NH; TGAGCACTGAAGGCCTGGC (SEQ ID NO: 25) and NH NI NH HD NI HD NG NH NI NI NH NH HD HD NG NH NH HD; TCCACTGAGCACTGAAGGC (SEQ ID NO: 26) and HD HD NI HD NG NH NI NH HD NI HD NG NH NI NI NH NH HD; TGGTTTCCACTGAGCACTG (SEQ ID NO: 27) and NH NH NG NG NG HD HD NI HD NG NH NH
  • the GSHS is within about 25, or about 50, or about 100, or about 150, or about 200, or about 300, or about 500 nucleotides of the TA dinucleotide site or TTAA (SEQ ID NO: 440) tetranucleotide site.
  • Illustrative DNA binding codes for human genomic safe harbor in areas of open chromatin via TALEs, encompassed by various embodiments are provided in TABLE 4A-4F.
  • TALEs encompassed by various embodiments are provided in TABLE 4A-4F, e.g., having a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity to any of the sequences in TABLE 4A-4F.
  • GSHS ID Sequence TALE (DNA binding code) DB1/ 143560057.1 SAL-026PC/126933-5026 A AVS1 2 TGAAGGCCTGGCCGGCCTG NH NI NI NH NH HD HD NG NH NH ( SEQ ID NO: 24) HD HD NH NH HD HD NG NH D I H I 71 DB1/ 143560057.1 SAL-026PC/126933-5026 h ROSA26 2F TCAAATCTTACAGCTGCTC HD NI NI NI NG HD NG NI HD ( SEQ ID NO: 44) NI NH HD NG NH HD NG HD H D H I G I D 72 DB1/ 143560057.1 SAL-026PC/126933-5026 C CR5 TALC4 GCTGCATCAACCCC (SEQ ID NN HD NG
  • the mobile element enzyme is capable of inserting a donor DNA at a TTAA (SEQ ID NO: 440) tetranucleotide site.
  • TTAA SEQ ID NO: 440
  • Illustrative DNA binding codes for human genomic safe harbor in areas of open chromatin via ZNFs encompassed by various embodiments are provided in TABLE 5A-5E.
  • there is provided a variant of the ZNFs, encompassed by various embodiments are provided in TABLE 5A-5E, e.g., having a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity to any of the sequences in TABLE 5A-5E.
  • ZNFs for targeting human genomic safe harbor sites using any of the ZNF-based targeting elements to the TTAA site in hROSA26 are shown in TABLE 5A: hROSA NAME TARGET (SEQ ID SCO ZFP AMINO ACID CODE (SEQ ID NO: _) 26 NO: _) RE TTAA Q H Q H R Q H E Q H E Q H E Q H R DB1/ 143560057.1 SAL-026PC/126933-5026 5’ ZnF5 AAC GCC CAG 54.
  • ZNFs for targeting human genomic safe harbor sites using any of the ZNF-based targeting elements to the AAVS1 are shown in TABLE 5B: AAVS1 NAME TARGET (SEQ ID NO:_) SCO ZFP AMINO ACID CODE (SEQ ID NO:_) TTAA RE 5’ ZnF1 TAG GAC AGT GGG G
  • ZNFs for targeting human genomic safe harbor sites using any of the ZNF-based targeting elements to Chromosome 4 e.g., hg38 chr4:30,793,534-30,875,476 or hg38 chr4:30,793,533-30,793,537 (9677); chr4:30,875,472-30,875,476 (
  • ZNFs for targeting human genomic safe harbor sites using any of the ZNF-based targeting elements to Chromosome X are shown in TABLE 5E: ChrX NAME TARGET (SEQ ID NO:_) SCO ZFP AMINO ACID CODE (SEQ ID NO:_) TTAA RE 5’ ZnF4 GTAGAAACTCGCCTTATG (784) 54.
  • the mobile element enzyme is capable of inserting a donor DNA at a TTAA (SEQ ID NO: 440) tetranucleotide site.
  • the present disclosure relates to a system having nucleic acids encoding the enzyme and the donor DNA, respectively.
  • FIGs.1A-1D show examples of a system in accordance with embodiments of the present disclosure.
  • the targeting element comprises a nucleic acid binding component of the gene-editing system.
  • the enzyme capable of performing targeted genomic integration e.g., without limitation, a chimeric mobile element enzyme
  • the targeting element e.g., nucleic acid binding component of the gene-editing system are fused or linked to one another.
  • the mobile element enzyme and the targeting element e.g., nucleic acid binding component of the gene-editing system are fused or linked to one another.
  • the mobile element enzyme and the targeting element are connected via a linker.
  • the linker is a flexible linker.
  • the flexible linker is substantially comprised of glycine and serine residues, optionally wherein the flexible linker comprises (Gly 4 Ser) n , where n is from about 1 to about 12.
  • the flexible linker is of about 20, or about 30, or about 40, or about 50, or about 60 amino acid residues.
  • the flexible linker is about 50, or about 100, or about 150, or about 200 amino acid residues in length.
  • the flexible linker comprises at least about 150 nucleotides (nt), or at least about 200 nt, or at least about 250 nt, or at least about 300 nt, or at least about 350 nt, or at least about 400 nt, or at least about 450 nt, or at least about 500 nt, or at least about 500 nt, or at least about 600 nt. In embodiments, the flexible linker comprises from about 450 nt to about 500 nt.
  • the mobile element enzyme and the targeting element e.g., nucleic acid binding component of the gene-editing system are encoded on a single polypeptide.
  • Inteins are mobile genetic elements that are protein domains, found in nature, with the capability to carry out the process of protein splicing. See Sarmiento & Camarero (2019) Current Protein & Peptide Science, 20(5), 408–424, which is incorporated by reference herein in its entirety. Protein spicing is a post-translation 84 DB1/ 143560057.1 SAL-026PC/126933-5026 biochemical modification which results in the cleavage and formation of peptide bonds between precursor polypeptide segments flanking the intein. Id. Inteins apply standard enzymatic strategies to excise themselves post-translationally from a precursor protein via protein splicing.
  • intein can splice its flanking N- and C-terminal domains to become a mature protein and excise itself from a sequence.
  • split inteins have been used to control the delivery of heterologous genes into transgenic organisms. See Wood & Camarero (2014) J Biol Chem.289(21):14512-14519. This approach relies on splitting the target protein into two segments, which are then post-translationally reconstituted in vivo by protein trans-splicing (PTS). See Aboye & Camarero (2012) J. Biol.
  • intein-mediated incorporation of DNA binders such as, without limitation, dCas9, dCas12j, or TALEs
  • a split-enzyme system such as, without limitation, split-MLT mobile element enzyme system, that permits reconstitution of the full-length enzyme, e.g., MLT mobile element enzyme, from two smaller fragments. This allows avoiding the need to express DNA binders at the N- or C-terminus of an enzyme, e.g., MLT mobile element enzyme.
  • a nucleic acid encoding the enzyme capable of performing targeted genomic integration comprises an intein.
  • the nucleic acid encodes the enzyme in the form of first and second portions with the intein encoded between the first and second portions, such that the first and second portions are fused into a functional enzyme upon post-translational excision of the intein from the enzyme.
  • an intein is a suitable ligand-dependent intein, for example, an intein selected from those described in U.S. Patent No.9,200,045; Mootz et al., J. Am. Chem. Soc.2002; 124, 9044-9045; Mootz et al., J. Am. Chem. Soc. 2003; 125, 10561-10569; Buskirk et al., Proc. Natl. Acad. Sci. USA.2004; 101, 10505-10510; Skretas & Wood. Protein Sci.2005; 14, 523-532; Schwartz, et al., Nat. Chem.
  • the intein is NpuN (Intein-N) (SEQ ID NO: 423) and/or NpuC (Intein-C) (SEQ ID NO: 424), or a variant thereof, e.g., a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto.
  • SEQ ID NO: 423 nucleotide sequence of NpuN (Intein-N) 85 DB1/ 143560057.1 SAL-026PC/126933-5026 GGCGGATCTGGCGGTAGTGCTGAGTATTGTCTGAGTTACGAAACGGAAATACTCACGGTTGAGTATGGGCTTCTTCC AATTGGCAAAATCGTTGAAAAGCGCATAGAGTGTACGGTGTATTCCGTCGATAACAACGGTAATATCTACACCCAGC CGGTAGCTCAGTGGCACGACCGAGGCGAACAGGAAGTGTTCGAGTATTGCTTGGAAGATGGCTCCCTTATCCGCGCC ACTAAAGACCATAAGTTTATGACGGTTGACGGGCAGATGCTGCCTATAGACGAAATATTTGAGAGAGCTGGACTT GATGAGAGTCGATAATCTGCCAAAT SEQ ID NO: 424: nucleotide sequence of NpuC (Intein-C) GGCGGATCTGGCGGTAGTGGGGGTTCCGGATCCATAAAGATAG
  • a nucleic acid encoding the donor DNA is DNA.
  • the donor DNA comprises a gene encoding a complete polypeptide.
  • the donor DNA comprises a gene which is defective or substantially absent in a disease state.
  • the enzyme e.g., without limitation, the mobile element enzyme
  • the nucleic acid is RNA, optionally a helper RNA.
  • the nucleic acid is RNA that has a 5’-m7G cap (cap0, or cap1, or cap2), optionally with pseudouridine substitution (e.g., without limitation n-methyl-pseudouridine) and/or a 5-methoxy substitution (e.g., without limitation, 5-methoxy-U) and optionally a poly-A tail of about 30, or about 34, or about 50, or about 55, or about 70, or about 80, or about 100, of about 150 nucleotides in length.
  • the poly-A tail is of about 30 nucleotides in length, optionally 34 nucleotides in length.
  • a nuclear localization signal is placed before the enzyme start codon at the N-terminus, optionally at the C-terminus.
  • the first nucleic acid RNA comprises one or more uridine modifications.
  • the first nucleic acid RNA comprises N1-methyl-psuedo U and/or 5-methoxy-U.
  • the first nucleic acid RNA comprises a poly-A tail of about 80 nucleotides in length.
  • the nucleic acid that is RNA has a 5’-m7G cap (cap 0, or cap 1, or cap 2).
  • the nucleic acid comprises a 5’ cap structure, a 5’-UTR comprising a Kozak consensus sequence, a 5’-UTR comprising a sequence that increases RNA stability in vivo, a 3′-UTR comprising a sequence that increases RNA stability in vivo, and/or a 3’ poly(A) tail.
  • the enzyme e.g., without limitation, a mobile element enzyme
  • the vector is a non-viral vector.
  • a construct comprising a donor DNA is any suitable genetic construct, such as a nucleic acid construct, a plasmid, or a vector.
  • the construct is DNA, which is referred to herein as a donor DNA.
  • sequences of a nucleic acid encoding the donor DNA is codon optimized to provide improved mRNA stability and protein expression in mammalian systems.
  • the enzyme and the donor DNA are included in different vectors. In embodiments, the enzyme and the donor DNA are included in the same vector.
  • a nucleic acid encoding the enzyme capable of performing targeted genomic integration is RNA (e.g., helper RNA), and a nucleic acid encoding a donor DNA is DNA.
  • RNA e.g., helper RNA
  • DNA DNA
  • a donor DNA often includes an open reading frame that encodes a transgene at the middle of donor DNA and terminal repeat sequences at the 5’ and 3’ end of the donor DNA.
  • the translated mobile element enzyme binds to the 5’ and 3’ sequence of the donor DNA and carries out the transposition function.
  • mobile elements which are used to refer to polynucleotides capable of inserting copies of themselves into other polynucleotides.
  • mobile element is well known to those skilled in the art and includes classes of mobile element that can be distinguished on the basis of sequence organization, for example inverted terminal sequences at each end, and/or directly repeated long terminal repeats (LTRs) at the ends.
  • LTRs long terminal repeats
  • the mobile element as described herein may be described as a piggyBac like element, e.g., a mobile element that is characterized by its traceless excision, which recognizes TTAA (SEQ ID NO: 440) sequence and restores the sequence at the insert site back to the original TTAA (SEQ ID NO: 440) sequence.
  • donor DNA or transgene are used interchangeably with mobile elements.
  • the donor DNA is flanked by one or more end sequences or terminal ends.
  • the donor DNA is or comprises a gene encoding a complete polypeptide.
  • the donor DNA is or comprises a gene which is defective or substantially absent in a disease state.
  • the mobile element includes a MLT mobile element enzyme (e.g., without limitation, a MLT mobile element enzyme having at least about 90% identity to the amino acid sequence of SEQ ID NO: 1, SEQ ID NO: 10, or SEQ ID NO: 11).
  • the mobile element enzyme can act on a left terminal end having a nucleotide sequence of SEQ ID NO: 431 or a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto.
  • the enzyme can act on a right terminal end having a nucleotide sequence of SEQ ID NO: 432 or a sequence having at least about 90%, or at 87 DB1/ 143560057.1 SAL-026PC/126933-5026 least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto.
  • the enzyme acts on both MLT left end and MLT right end, having nucleotide sequences of SEQ ID NO: 431 and of SEQ ID NO: 432 respectively, or a sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto.
  • a MLT left end is as follows: TTAACACTTGGATTGCGGGAAACGAGTTAAGTCGGCTCGCGTGAATTGCGCGTACTCCGCGGGAGCCGTC TTAACTCGGTTCATATAGATTTGCGGTGGAGTGCGGGAAACGTGTAAACTCGGGCCGATTGTAACTGCGT ATTACCAAATATTTGTT (SEQ ID NO: 431)
  • a MLT right end is as follows: AATTATTTATGTACTGAATAGATAAAAAAATGTCTGTGATTGAATAAATTTTCATTTTACACAAGAAA CCGAAAATTTCATTTCAATCGAACCCATACTTCAAAAGATATAGGCATTTTAAACTAACTCTGATTTTGC GCGGGAAACCTAAATAATTGCCCGCGCCATCTTATATTTTGGCGGGAAATTCACCCGACACCGTGGTGTT AA (SEQ ID NO: 432)
  • a transgene of the donor DNA e.g., chi
  • a transgene is encoded by a non-viral vector (e.g., without limitation, a DNA plasmid) that can comprise one or more insulator sequences that prevent or mitigate activation or inactivation of nearby genes.
  • the insulators flank the donor DNA (transgene cassette) to reduce transcriptional silencing and position effects imparted by chromosomal sequences.
  • the insulators can eliminate functional interactions of the transgene enhancer and promoter sequences with neighboring chromosomal sequences.
  • the one or more insulator sequences comprise an HS4 insulator (1.2-kb 5’-HS4 chicken ⁇ -globin (cHS4) insulator element) and an D4Z4 insulator (tandem macrosatellite repeats linked to Facio-Scapulo-Humeral Dystrophy (FSHD).
  • HS4 insulator 1.2-kb 5’-HS4 chicken ⁇ -globin (cHS4) insulator element
  • D4Z4 insulator tandem macrosatellite repeats linked to Facio-Scapulo-Humeral Dystrophy
  • the sequences of the HS4 insulator and the D4Z4 insulator are as described in Rival-Gervier et al. Mol Ther.2013 Aug; 21(8):1536-50, which is incorporated herein by reference in its entirety.
  • the donor DNA e.g., chimeric CAR or chimeric CAAR is inserted into a GSHS location in a host genome.
  • GSHSs is defined as loci well-suited for gene transfer, as integrations within these sites are not associated with adverse effects such as proto-oncogene activation, tumor suppressor inactivation, or insertional mutagenesis.
  • GSHSs can defined by the following criteria: (1) distance of at least 50 kb from the 5’ end of any gene, (2) distance of at least 300 kb from any cancer-related gene, (3) distance of at least 300 kb from any microRNA (miRNA), (4) location outside a transcription unit, and (5) location outside ultra-conserved regions (UCRs) of the human genome.
  • miRNA microRNA
  • CCR5 chemokine C-C motif receptor 5
  • the donor DNA is under control of a tissue-specific promoter.
  • the tissue-specific promoter is, e.g., without limitation, a liver-specific promoter.
  • the liver-specific promoter is an LP1 promoter that, in embodiments, is a human LP1 promoter.
  • the LP1 promoter is described, e.g., in Nathwani et al. Blood vol. 2006;107(7):2653-61, and it is constructed, without limitation, as described in Nathawani et al. It should be appreciated however that a variety of promoters can be used, including other tissue-specific promoters, inducible promoters, constitutive promoters, etc.
  • the present nucleic acids include polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides, or analogs or derivatives thereof.
  • transcriptionally- activated polynucleotides such as methylated or capped polynucleotides are provided.
  • the present compositions are mRNA or DNA.
  • the present non-viral vectors are linear or circular DNA molecules that comprise a polynucleotide encoding a polypeptide and is operably linked to control sequences, wherein the control sequences provide for expression of the polynucleotide encoding the polypeptide.
  • the non-viral vector comprises a promoter sequence, and transcriptional and translational stop signal sequences.
  • Such vectors may include, among others, chromosomal and episomal vectors, e.g., vectors bacterial plasmids, from donor DNAs, from yeast episomes, from insertion elements, from yeast chromosomal elements, and vectors from combinations thereof.
  • the present constructs may contain control regions that regulate as well as engender expression.
  • the construct comprising the enzyme and/or donor DNA is codon optimized.
  • Donor DNA codon optimization is used to optimize therapeutic potential of the donor DNA and its expression in the host organism. Codon optimization is performed to match the codon usage in the donor DNA with the abundance of transfer RNA (tRNA) for each codon in a host organism or cell.
  • Codon optimization methods are known in the art and described in, for example, WO 2007/142954, which is incorporated by reference herein in its entirety. Optimization strategies can include, for example, the modification of translation initiation regions, alteration of mRNA structural elements, and the use of different codon biases.
  • 89 DB1/ 143560057.1 SAL-026PC/126933-5026 the construct comprising the enzyme and/or donor DNA includes several other regulatory elements that are selected to ensure stable expression of the construct.
  • the non-viral vector is a DNA plasmid that can comprise one or more insulator sequences that prevent or mitigate activation or inactivation of nearby genes.
  • the one or more insulator sequences comprise an HS4 insulator (1.2-kb 5′-HS4 chicken ⁇ - globin (cHS4) insulator element) and an D4Z4 insulator (tandem macrosatellite repeats linked to Facio-Scapulo- Humeral Dystrophy (FSHD).
  • HS4 insulator 1.2-kb 5′-HS4 chicken ⁇ - globin (cHS4) insulator element
  • D4Z4 insulator tandem macrosatellite repeats linked to Facio-Scapulo- Humeral Dystrophy
  • the sequences of the HS4 insulator and the D4Z4 insulator are as described in Rival-Gervier et al. Mol Ther.2013 Aug; 21(8):1536-50, which is incorporated herein by reference in its entirety.
  • the gene of the construct comprising the enzyme and/or donor DNA is capable of transposition in the presence of a mobile element enzyme.
  • the non-viral vector in accordance with embodiments of the present disclosure comprises a nucleic acid construct encoding a mobile element enzyme.
  • the mobile element enzyme is an RNA mobile element enzyme plasmid.
  • the non-viral vector further comprises a nucleic acid construct encoding a DNA mobile element enzyme plasmid.
  • the mobile element enzyme is an in vitro-transcribed mRNA mobile element enzyme.
  • the mobile element enzyme is capable of excising and/or transposing the gene from the construct comprising the enzyme and/or donor DNA to site- or locus- specific genomic regions.
  • the enzyme and the donor DNA are included in the same vector.
  • the enzyme is disposed on the same (cis) or different vector (trans) than a donor DNA with a transgene, e.g., chimeric CAR or chimeric CAAR.
  • the enzyme and the donor DNA encompassing a transgene, e.g., chimeric CAR or chimeric CAAR are in cis configuration such that they are included in the same vector.
  • the enzyme and the donor DNA encompassing a transgene, e.g., chimeric CAR or chimeric CAAR are in trans configuration such that they are included in different vectors.
  • the vector is any non-viral vector in accordance with the present disclosure.
  • a nucleic acid encoding the enzyme capable of performing targeted genomic integration in accordance with embodiments of the present disclosure is provided.
  • the nucleic acid is or comprises DNA or RNA.
  • the nucleic acid encoding the enzyme is DNA.
  • the nucleic acid encoding the enzyme capable of performing targeted genomic integration is RNA such as, e.g., helper RNA.
  • the chimeric mobile element enzyme is incorporated into a vector.
  • the vector is a non-viral vector.
  • a nucleic acid encoding the transgene e.g., chimeric CAR or chimeric CAAR, in accordance with embodiments of the present disclosure is provided.
  • the nucleic acid is or comprises DNA or RNA.
  • the nucleic acid encoding the t transgene, e.g., chimeric CAR or chimeric CAAR is DNA.
  • the nucleic 90 DB1/ 143560057.1 SAL-026PC/126933-5026 acid encoding the transgene, e.g., chimeric CAR or chimeric CAAR is RNA such as, e.g., helper RNA.
  • the transgene is incorporated into a vector.
  • the vector is a non-viral vector.
  • the present enzyme can be in the form or an RNA or DNA and have one or two N-terminus nuclear localization signal (NLS) to shuttle the protein more efficiently into the nucleus.
  • NLS nuclear localization signal
  • the present enzyme further comprises one, two, three, four, five, or more NLSs. Examples of NLS are provided in Kosugi et al. (J. Biol. Chem. (2009) 284:478-485; incorporated by reference herein).
  • the NLS comprises the consensus sequence K(K/R)X(K/R) (SEQ ID NO: 348).
  • the NLS comprises the consensus sequence (K/R)(K/R)X 10-12 (K/R) 3/5 (SEQ ID NO: 349), where (K/R) 3/5 represents at least three of the five amino acids is either lysine or arginine.
  • the NLS comprises the c-myc NLS.
  • the c-myc NLS comprises the sequence PAAKRVKLD (SEQ ID NO: 350).
  • the NLS is the nucleoplasmin NLS.
  • the nucleoplasmin NLS comprises the sequence KRPAATKKAGQAKKKK (SEQ ID NO: 351).
  • the NLS comprises the SV40 Large T-antigen NLS.
  • the SV40 Large T-antigen NLS comprises the sequence PKKKRKV (SEQ ID NO: 352).
  • the NLS comprises three SV40 Large T-antigen NLSs (e.g., DPKKKRKVDPKKKRKVDPKKKRKV (SEQ ID NO: 353).
  • the NLS may comprise mutations/variations in the above sequences such that they contain 1 or more substitutions, additions or deletions (e.g., about 1, or about 2, or about 3, or about 4, or about 5, or about 10 substitutions, additions, or deletions).
  • a host cell comprising the nucleic acid in accordance with embodiments of the present disclosure is provided.
  • At least one of the first nucleic acid and the second nucleic acid is in the form of a lipid nanoparticle (LNP).
  • a composition comprising the first and second nucleic acids is in the form of an LNP.
  • a nucleic acid encoding the enzyme and a nucleic acid encoding the transgene are contained within the same lipid nanoparticle (LNP).
  • the nucleic acid encoding the enzyme and the nucleic acid encoding the donor DNA are a mixture incorporated into or associated with the same LNP.
  • the nucleic acid encoding the enzyme and the nucleic acid encoding the donor DNA are in the form of a co-formulation incorporated into or associated with the same LNP.
  • the LNP is selected from 1,2-dioleoyl-3-trimethylammonium propane (DOTAP), a cationic cholesterol derivative mixed with dimethylaminoethane-carbamoyl (DC-Chol), phosphatidylcholine (PC), triolein (glyceryl trioleate), and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[carboxy(polyethylene glycol)-2000] (DSPE-PEG), 1,2- dimyristoyl-rac-glycero-3-methoxypolyethyleneglycol – 2000 (DMG-PEG 2K), and 1,2 distearol -sn-glycerol- 91 DB1/ 143560057.1 SAL-026PC/126933-5026 3phospho
  • DOTAP
  • an LNP is as described, e.g., in Patel et al., J Control Release 2019; 303:91-100.
  • the LNP can comprise one or more of a structural lipid (e.g., DSPC), a PEG-conjugated lipid (CDM-PEG), a cationic lipid (MC3), cholesterol, and a targeting ligand (e.g., GalNAc).
  • a nanoparticle is a particle having a diameter of less than about 1000 nm.
  • nanoparticles of the present disclosure have a greatest dimension (e.g., diameter) of about 500 nm or less, or about 400 nm or less, or about 300 nm or less, or about 200 nm or less, or about 100 nm or less. In embodiments, nanoparticles of the present subject matter have a greatest dimension ranging between about 50 nm and about 150 nm, or between about 70 nm and about 130 nm, or between about 80 nm and about 120 nm, or between about 90 nm and about 110 nm. In embodiments, the nanoparticles of the present disclosure have a greatest dimension (e.g., a diameter) of about 100 nm.
  • the cell in accordance with the present disclosure is prepared via an in vivo genetic modification method.
  • a genetic modification in accordance with the present disclosure is performed via an ex vivo method.
  • the cell in accordance with the present disclosure is prepared by contacting a cell with an enzyme capable of performing targeted genomic integration (e.g., without limitation, a mammalian mobile element enzyme) in vivo.
  • the cell is contacted with the enzyme ex vivo.
  • the present method provides reduced insertional mutagenesis or oncogenesis as compared to a method with a non-chimeric mobile element enzyme.
  • the disclosure provides a CAR-immune cell or CAAR-immune cell generated by a method described herein.
  • the disclosure provides a method of delivering a CAR-immune cell or CAAR-immune cell, comprising administering to a patient in need thereof the CAR-immune cell generated by a method described herein.
  • the disclosure provides a method of treating a disease or condition using a CAR-immune cell or CAAR-immune cell therapy, comprising administering to a patient in need thereof the CAR-immune cell generated by a method described herein.
  • the disease or condition is or comprises cancer.
  • the cancer is or comprises an adrenal cancer, a biliary track cancer, a bladder cancer, a bone/bone marrow cancer, a brain cancer, a breast cancer, 92 DB1/ 143560057.1 SAL-026PC/126933-5026 a cervical cancer, a colorectal cancer, a cancer of the esophagus, a gastric cancer, a head/neck cancer, a hepatobiliary cancer, a kidney cancer, a liver cancer, a lung cancer, an ovarian cancer, a pancreatic cancer, a pelvis cancer, a pleura cancer, a prostate cancer, a renal cancer, a skin cancer, a stomach cancer, a testis cancer, a thymus cancer, a thyroid cancer, a uterine cancer, a lymphoma, a melanoma, a multiple myeloma, or a leukemia.
  • an adrenal cancer a biliary track cancer
  • a bladder cancer a bone
  • the cancer is selected from one or more of the basal cell carcinoma, biliary tract cancer; bladder cancer; bone cancer; brain and central nervous system cancer; breast cancer; cancer of the peritoneum; cervical cancer; choriocarcinoma; colon and rectum cancer; connective tissue cancer; cancer of the digestive system; endometrial cancer; esophageal cancer; eye cancer; cancer of the head and neck; gastric cancer; glioblastoma; hepatic carcinoma; hepatoma; intra-epithelial neoplasm; kidney or renal cancer; larynx cancer; leukemia; liver cancer; lung cancer; melanoma; myeloma; neuroblastoma; oral cavity cancer; ovarian cancer; pancreatic cancer; prostate cancer; retinoblastoma; rhabdomyosarcoma; rectal cancer; cancer of the respiratory system; salivary gland carcinoma; sarcoma; skin cancer; squamous cell cancer; stomach cancer; testicular
  • the cancer is selected from one or more of basal cell carcinoma, biliary tract cancer; bladder cancer; bone cancer; brain and central nervous system cancer; breast cancer; cancer of the peritoneum; cervical cancer; choriocarcinoma; colon and rectum cancer; connective tissue cancer; cancer of the digestive system; endometrial cancer; esophageal cancer; eye cancer; cancer of the head and neck; gastric cancer (including gastrointestinal cancer); glioblastoma; hepatic carcinoma; hepatoma; intra-epithelial neoplasm; kidney or renal cancer; larynx cancer; leukemia; liver cancer; lung cancer (e.g., small-cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, and squamous carcinoma of the lung); melanoma; myeloma; neuroblastoma; oral cavity cancer (lip, tongue, mouth, and pharynx); ovarian cancer; pancreatic cancer; prostate cancer;
  • the disease or condition is or comprises cancer, optionally selected from acute lymphoblastic leukemia, chronic lymphocytic leukemia, non-Hodgkin lymphoma (NHL), and/or multiple myeloma.
  • the cancer is relapsed or refractory acute lymphoblastic leukemia (ALL), a chronic lymphocytic leukemia (CLL), a chronic myelogenous leukemia (CML), a multiple myeloma (MM), an acute myeloid leukemia (AML), diffuse large B-cell lymphoma, primary mediastinal B-cell lymphoma, high grade B-cell lymphoma, transformed follicular lymphoma, and/or Mantle cell lymphoma.
  • ALL acute lymphoblastic leukemia
  • CLL chronic lymphocytic leukemia
  • CML chronic myelogenous leukemia
  • MM multiple myeloma
  • AML acute myeloid leukemia
  • the disease or condition is or comprises cancer, optionally a solid tumor, optionally selected from a small cell lung cancer (SCLC), large cell neuroendocrine carcinoma (LCNEC), a gastric cancer, a colon cancer, a renal cell carcinoma, a hepatocellular carcinoma, a bladder urothelial carcinoma, a metastatic melanoma, a breast cancer, an ovarian cancer, a cervical cancer, a head and neck cancer, a pancreatic cancer, a glioma, and/or a glioblastoma.
  • SCLC small cell lung cancer
  • LNEC large cell neuroendocrine carcinoma
  • a gastric cancer optionally selected from a small cell lung cancer (SCLC), large cell neuroendocrine carcinoma (LCNEC), a gastric cancer, a colon cancer, a renal cell carcinoma, a hepatocellular carcinoma, a bladder urothelial carcinoma, a metastatic melanoma, a breast cancer, an ovarian cancer, a cervical cancer,
  • the autoimmune disease is or comprises multiple sclerosis, diabetes mellitus, lupus, celiac disease, Crohn's disease, ulcerative colitis, Guillain-Barre syndrome, sclerodermas, Goodpasture's syndrome, Wegener's granulomatosis, autoimmune epilepsy, Rasmussen's encephalitis, Primary biliary sclerosis, Sclerosing cholangitis, Autoimmune hepatitis, Addison's disease, Hashimoto's thyroiditis, Fibromyalgia, Meniere’s syndrome; transplantation rejection (e.g., prevention of allograft rejection) pernicious anemia, rheumatoid arthritis, systemic lupus erythematosus, dermatomyositis, Sjogren's syndrome, lupus erythematosus, multiple sclerosis, myasthenia gravis, Reiter's syndrome, Grave's disease,
  • the disease or condition is pemphigus vulgaris, paraneoplastic pemphigus, myasthenia gravis, and pemphigus foliaceus.
  • the cell expresses the CAAR and has high affinity to autoantibodies expressed on B cells.
  • the cell expresses the CAAR and induces targeted killing of B cells expressing autoantibodies.
  • the cell expresses the CAAR and has low affinity to antibodies bound to a Fc receptor.
  • the method of delivering a gene therapy is non-immunogenic, optionally free of cytokine release syndrome. In embodiments, the method of delivering a gene therapy reduces or avoids off-target effects.
  • the method of comprises delivery via two or more doses. In embodiments, the method has reversible, inducible- or kill-switch capabilities. In embodiments, the CAR-immune cell is administered by injection or infusion. 94 DB1/ 143560057.1 SAL-026PC/126933-5026 In embodiments, the method of delivering a CAR-immune cell comprises delivery via two or more doses. In embodiments, the method of delivering a CAR-immune cell comprises creating a high copy number of the CAR- immune cell in a subject. In embodiments, the method requires a single administration. In embodiments, the method requires a plurality of administrations.
  • the CAR-immune cells of the present disclosure persist in circulation about 10 days, or about 20 days, or about 30 days, or about 40 days, or about 50 days, or about 60 days, or about 70 days, or about 80 days, or about 90 days after administration.
  • the CAR-immune cells of the present disclosure are tumor responsive and can reexpand upon interaction with a tumor antigen.
  • the targeted genomic integration substantially occurs in intronic and intergenic regions of T cells and not substantially in exons.
  • the present disclosure provides methods for generating a dual-targeted CAR T cell (e.g., a CD19/CD20 CAR T cell or a CD19/CD22 CAR T cell) that exhibits efficacy when administered to treat a tumor (e.g., a tumor in one or more hematological cancers) that does not express a CD19 antigen.
  • a dual-targeted CAR T cell e.g., a CD19/CD20 CAR T cell or a CD19/CD22 CAR T cell
  • a tumor e.g., a tumor in one or more hematological cancers
  • the present disclosure provides methods for generating a dual-targeted CAR T cell (e.g., a CD19/CD20 CAR T cell or a CD19/CD22 CAR T cell) that produces cytokine levels (e.g., IFNy or TNFa) and/or levels of granule protease GZMB in a tumor having lost CD19 antigen similar to levels produced in a tumor that did not lose CD19 antigen.
  • the dual-targeted CAR T cell is a CD19/CD20 CAR T cell or a CD19/CD22 CAR T cell.
  • the present disclosure provides methods for generating a dual-targeted CAR T cell (e.g., a CD19/CD20 CAR T cell or a CD19/CD22 CAR T cell) that exhibits efficacy when administered to treat a tumor (e.g., a tumor in one or more hematological cancers) that substantially devoid of, reduced, or ablated CD19 expression.
  • a dual-targeted CAR T cell e.g., a CD19/CD20 CAR T cell or a CD19/CD22 CAR T cell
  • a tumor e.g., a tumor in one or more hematological cancers
  • the present disclosure provides methods for generating a dual-targeted CAR T cell (e.g., a CD19/CD20 CAR T cell or a CD19/CD22 CAR T cell) that produces cytokine levels (e.g., IFNy or TNFa) and/or levels of granule protease GZMB in a tumor substantially devoid of, reduced or ablated CD19 expression similar to levels produced in a tumor which expresses CD19.
  • cytokine levels e.g., IFNy or TNFa
  • GZMB granule protease GZMB
  • an isolated CAR-immune cell is provided.
  • an isolated CAR-immune cell is provided that comprises the transfected cell in accordance with embodiments of the present disclosure.
  • the present disclosure provides an ex vivo gene therapy approach.
  • the method that is used to treat an inherited or acquired disease in a patient in need thereof comprises (a) contacting a cell obtained from a patient (autologous) or another individual (allogeneic) with a transfected cell in accordance with embodiments of the present disclosure; and (b) administering the cell to a patient in need thereof.
  • One of the advantages of ex vivo gene therapy is the ability to “sample” the transduced cells before patient administration. This facilitates efficacy and allows performing safety checks before introducing the cell(s) to the patient.
  • a composition comprising transfected cells in accordance with the present disclosure comprises a pharmaceutically acceptable carrier, excipient or diluent.
  • compositions suitable for injectable use can include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion.
  • suitable carriers include physiological saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, N.J.) or phosphate buffered saline (PBS).
  • the composition must be sterile, and the fluid should be easy to draw up by a syringe. It should be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms such as bacteria and fungi.
  • the carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof.
  • the proper fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants.
  • Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars, polyalcohols such as mannitol, sorbitol, and sodium chloride in the composition.
  • Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent that delays absorption, for example, aluminum monostearate and gelatin.
  • Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization.
  • dispersions are prepared by incorporating the active compound into a sterile vehicle, which contains a basic dispersion medium and the required other ingredients from those enumerated above.
  • sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying, which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
  • Therapeutic compounds can be prepared with carriers that will protect the therapeutic compounds against rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems.
  • Biodegradable, biocompatible polymers can be used, such as collagen, ethylene vinyl acetate, polyanhydrides (e.g., poly[1,3-bis(carboxyphenoxy)propane-co-sebacic-acid] (PCPP-SA) matrix, fatty acid dimer- sebacic acid (FAD-SA) copolymer, poly(lactide-co-glycolide)), polyglycolic acid, collagen, polyorthoesters, polyethyleneglycol-coated liposomes, and polylactic acid.
  • PCPP-SA poly[1,3-bis(carboxyphenoxy)propane-co-sebacic-acid]
  • FAD-SA fatty acid dimer- sebacic acid
  • polyglycolic acid collagen
  • polyorthoesters polyethyleneglycol-coated liposomes
  • polylactic acid polylactic acid
  • transgenic organism that may comprise cells which have been transformed by the methods of the present disclosure.
  • the organism may be a mammal or an insect.
  • the organism When the organism is a mammal, the organism may include, but is not limited to, a mouse, a rat, a monkey, a dog, a rabbit, a panda and the like. When the organism is an insect, the organism may include, but is not limited to, a fruit fly, a mosquito, a bollworm and the like.
  • the cells produced in accordance with embodiments of the present disclosure, and/or components for generating cells is included in a container, kit, pack, or dispenser together with instructions for administration. Also provided herein are kits comprising: one or more genetic constructs encoding the present enzyme and donor DNA and instructions and/or reagents for the use of the same.
  • kits comprising: i) a transfected cell in accordance with embodiments of the present disclosure, ii) instructions for the use of the transfected cell.
  • a kit is provided for creating a CAR-immune cell or a CAAR-immune cell, and instructions for creating the same, and. optionally, reagents for the same (e.g., media, factors, and the like).
  • a kit is provided that comprises an enzyme (e.g., without limitation, a recombinant mammalian mobile element enzyme) or a nucleic acid in accordance with embodiments of the present disclosure, and instructions for introducing DNA and/or RNA into a cell using the enzyme.
  • an “effective amount,” when used in connection with medical uses is an amount that is effective for providing a measurable treatment, prevention, or reduction in the rate of pathogenesis of a disease of interest.
  • the term “in vivo” refers to an event that takes place in a subject’s body.
  • the term “ex vivo” refers to an event which involves treating or performing a procedure on a cell, tissue and/or organ which has been removed from a subject’s body. Aptly, the cell, tissue and/or organ may be returned to the subject’s body in a method of treatment or surgery.
  • variant encompasses but is not limited to nucleic acids or proteins which comprise a nucleic acid or amino acid sequence which differs from the nucleic acid or amino acid sequence of a reference by way of one or more substitutions, deletions and/or additions at certain positions.
  • the variant may comprise one or more conservative substitutions. Conservative substitutions may involve, e.g., the substitution of similarly charged or uncharged amino acids.
  • Carrier or “vehicle” as used herein refer to carrier materials suitable for drug administration.
  • Carriers and vehicles useful herein include any such materials known in the art, e.g., any liquid, gel, solvent, liquid diluent, solubilizer, surfactant, lipid or the like, which is nontoxic and which does not interact with other components of the composition in a deleterious manner.
  • pharmaceutically acceptable refers to those compounds, materials, compositions, and/or dosage forms that are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problems or complications commensurate with a reasonable benefit/risk ratio.
  • pharmaceutically acceptable carrier or “pharmaceutically acceptable excipient” are intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and inert ingredients.
  • pharmaceutically acceptable carriers or pharmaceutically acceptable 98 DB1/ 143560057.1 SAL-026PC/126933-5026 excipients for active pharmaceutical ingredients is well known in the art. Except insofar as any conventional pharmaceutically acceptable carrier or pharmaceutically acceptable excipient is incompatible with the active pharmaceutical ingredient, its use in the therapeutic compositions of the disclosure is contemplated. Additional active pharmaceutical ingredients, such as other drugs, can also be incorporated into the described compositions and methods.
  • compositional percentages are by weight of the total composition, unless otherwise specified.
  • the word “include,” and its variants is intended to be non-limiting, such that recitation of items in a list is not to the exclusion of other like items that may also be useful in the compositions and methods of this technology.
  • the terms “can” and “may” and their variants are intended to be non-limiting, such that recitation that an embodiment can or may comprise certain elements or features does not exclude other embodiments of the present technology that do not contain those elements or features.
  • the therapeutic agents are given at a pharmacologically effective dose.
  • a “pharmacologically effective amount,” “pharmacologically effective dose,” “therapeutically effective amount,” or “effective amount” refers to an amount sufficient to produce the desired physiological effect or amount capable of achieving the desired result, particularly for treating the disorder or disease.
  • An effective amount as used herein would include an amount sufficient to, for example, delay the development of a symptom of the disorder or disease, alter the course of a symptom of the disorder or disease (e.g., slow the progression of a symptom of the disease), reduce or eliminate one or more symptoms or manifestations of the disorder or disease, and reverse a symptom of a disorder or disease.
  • Therapeutic benefit also includes halting or slowing the progression of the underlying disease or disorder, regardless of whether improvement is realized.
  • Effective amounts, toxicity, and therapeutic efficacy can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD 50 (the dose lethal to about 50% of the population) and the ED 50 (the dose therapeutically effective in about 50% of the population).
  • the dosage can vary depending upon the 99 DB1/ 143560057.1 SAL-026PC/126933-5026 dosage form employed and the route of administration utilized.
  • the dose ratio between toxic and therapeutic effects is the therapeutic index and can be expressed as the ratio LD 50 /ED 50 .
  • compositions and methods that exhibit large therapeutic indices are preferred.
  • a therapeutically effective dose can be estimated initially from in vitro assays, including, for example, cell culture assays. Also, a dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC 50 as determined in cell culture, or in an appropriate animal model. Levels of the described compositions in plasma can be measured, for example, by high performance liquid chromatography. The effects of any particular dosage can be monitored by a suitable bioassay. The dosage can be determined by a physician and adjusted, as necessary, to suit observed effects of the treatment. As used herein, “methods of treatment” are equally applicable to use of a composition for treating the diseases or disorders described herein and/or compositions for use and/or uses in the manufacture of a medicaments for treating the diseases or disorders described herein.
  • the present disclosure provides for any of the sequence provided herein, including the below, and a variant sequence having at least about 90%, or at least about 93%, or at least about 95%, or at least about 97%, or at least about 98%, or at least about 99% identity thereto, or at least about 10 mutations, or at least about 9 mutations, or at least about 8 mutations, or at least about 7 mutations, or at least about 6 mutations, or at least about 5 mutations, or at least about 4 mutations, or at least about 3 mutations, or at least about 2 mutations, or at least about 1 mutation.
  • FIGs.1A-1D and FIG.2 depict schematic diagrams of the process to produce CAR-immune (e.g., CAR-T) cells.
  • a sample e.g., blood
  • PBMCs peripheral blood mononuclear cells
  • PBMCs peripheral blood mononuclear cells
  • the present enzyme e.g., the enzyme of SEQ ID NO: 2, or a variant thereof
  • the present donor DNA are introduced into donor cells, e.g., by electroporation, nucleofection, or fluid dynamics.
  • Cells are washed and formulated into infusion buffer (1 days) and then infused into the patient without the need for further expansion.
  • processing 3 x 10 9 PBMCs generates 1.5 x 10 8 CAR-immune cells, equivalent to 2.1 x 10 6 CAR- immune cells/kg for a 70 kg patient.
  • production time is approximately 1 - 2 days.
  • An illustrative process for making CAAR-T cells is shown in FIG.3.
  • Example 2 Engineering of human primary T cells with donor DNA and MLT transposase enzyme Methods for FIG.4, FIGs.5A-5B, FIGs.6A-6C, FIGs.7A-7C, and FIGs.8A-8B.
  • PBMCs Peripheral Blood Mononuclear Cells
  • Leukopaks obtained from healthy donors (HemaCare) using standard ficoll gradient purification.
  • PBMC cells were grown at 37°C in TexMACS medium (Miltenyi, cat # 130-097-196) supplemented with 5% Human AB serum (Valley Biomedical, cat # HP1022HI) plus 100 IU/mL of IL-2 (Miltenyi, cat # 130-097-748) and 50 ng/mL of soluble anti-CD3 (Miltenyi, cat # 130-093-387) and anti-CD28 antibodies (Miltenyi, cat # 130-093-375) for 3 days. After activation, T cells were collected and electroporated using Lonza’s 4D-nucleofector device following manufacturer’s protocol.
  • PBMC peripheral blood mononuclear cells
  • PBMC peripheral blood mononuclear cells
  • IL-2 soluble Abs against CD3 and CD28.
  • cells were collected and electroporated with plasmid DNA encoding the CD19-CAR and mRNA encoding MLT transposase using Lonza’s 4D-Nucleofector. Cells were allowed to recover for 4 days, after which they were further expanded for 7 days in TexMACS medium supplemented with IL-7, IL-15, and IL-21 in the presence of mitomycin C treated feeder cells. Expanded CD19-CAR T cells were collected at D14 and cryopreserved.
  • Example 4 Evaluation of different MLT transposase helper mRNA designs for effective engineering of human primary T cells To determine an effective mRNA design for engineering T cells using MLT transposase, seven different MLT transposase-encoding mRNAs containing different CAP, nucleotide modifications, and poly(A) tail length were evaluated (TABLE 6).
  • CleanCap MLT transposase mRNA with N1-Methyl-Pseudo-U modified nucleotides provided the highest GFP expression and integration efficiency at D14, with those of longer poly(A) tail providing the best results (FIGs.6A-C). TABLE 6.
  • Cytokine independent growth assay 110 DB1/ 143560057.1 SAL-026PC/126933-5026 Activated T cells were generated from healthy donor PBMC cells grown at 37°C in TexMACS medium (Miltenyi, cat # 130-097-196) supplemented with 5% Human AB serum (Valley Biomedical, cat # HP1022HI) plus 100 IU/mL of IL-2 and 50 ng/mL of soluble anti-CD3 (Miltenyi, cat # 130-093-387) and anti-CD28 antibodies (Miltenyi, cat # 130-093-375) for 3 days. After activation, T cells were collected and electroporated using Lonza’s 4D-nucleofector device following manufacturer’s protocol.
  • PBMCs Peripheral Blood Mononuclear Cells
  • Leukopaks obtained from healthy donors (HemaCare) using standard ficoll gradient purification.
  • PBMC cells were grown at 37°C in TexMACS medium (Miltenyi, cat # 130-097-196) supplemented with 5% Human AB serum serum (Valley Biomedical, cat # HP1022HI) plus 100 IU/mL of IL-2 (Miltenyi, cat # 130-097-748) and 50 ng/mL of soluble anti-CD3 (Miltenyi, cat # 130- 093-387) and anti-CD28 antibodies (Miltenyi, cat # 130-093-375) for 3 days.
  • T cells were collected and electroporated using Lonza’s 4D-nucleofector device following manufacturer’s protocol. Briefly, 5e 6 activated T cells were electroporated using 100 ⁇ L cuvettes (Lonza, cat # V4XP-3024) with 4 ⁇ g of CD19-CAR Donor DNA nanoplasmid (Nature Technology Corporation) plus 6 ⁇ g of MLT transposase Helper mRNA (TriLink). As controls, cells were either not electroporated or electroporated with Donor DNA only or no nucleic acid.
  • Luciferase based cytotoxicity assays The killing ability of CD19-CAR T cells was evaluated using a bioluminescence-based assay with luciferase-expressing tumor targets (TABLE 8). Co-cultures of CD19-CAR T cells and luciferase-expressing targets were set up in flat-bottom 96 well plates (Corning, cat # 353296). Briefly, 100 ⁇ L of luciferase expressing targets at a concentration of 1e 5 cells/mL were added per well in triplicates. Effector cells were added in a volume of 100 ⁇ L at 10:1, 5:1 and 2.5:1 effector-to- target ratios.
  • Target cells incubated without effector cells or with 1% Triton X-100 were used as a measure of spontaneous and maximum lysis, respectively. Plates were incubated at 37°C for 6 or 16 111 DB1/ 143560057.1 SAL-026PC/126933-5026 hours, and luciferase activity was determined by adding 100 ⁇ L of Bright-GloTM Luciferase Assay Substrate (Promega, cat # E2620) and measuring the luminescence signal in an Infinite ® 200 PRO plate reader (Tecan).
  • % Cytotoxicity 100 - [(test counts - Tx100 counts)/(No T cells counts - Tx100 counts)) x 100].
  • CL 159 Cytokine release assay CD19-CAR T cells or control untransfected T cells were co-culture with tumor targets at a 1:1 ratio in flat-bottom 96w plates, 5e 5 cells/well in triplicates, for 24 hours and the amount of proinflammatory cytokines IFN ⁇ and TNF ⁇ , and lytic granule protease granzyme B released into the supernatant was measured by ELISA (R&D systems) following manufacturer’s instructions.
  • CD19-CAR expression was evaluated by flow cytometry using human recombinant CD19 protein conjugated to atto647N (R&D Systems, cat # ATM9269).
  • CD4/CD8 ratio, and expression of memory and exhaustion markers were evaluated by flow cytometry analysis with one or several of the antibodies shown in TABLE 9. Stained samples were acquired in a CytoFLEX flow cytometer (Beckman Coulter). TABLE 9.
  • Antibodies used for immunophenotype of CAR T cells Antibody Clone Fluorophore Vendor Cat # DB1/ 143560057.1 SAL-026PC/126933-5026 CD45RA HI100 PerCP BioLegend 304156 PD-1 EH12.2H7 PE BioLegend 329906
  • Example 7 Ef g g y p pression and good safety profile Primary activated T cells were electroporated with a donor DNA encoding a reporter GFP or a CD19-CAR receptor plus or minus MLT transposase-expressing helper mRNA. Engineered T cells were expanded in vitro and sustained GFP or CAR expression was evaluated by flow cytometry at day 12 or 14 post-electroporation, respectively.
  • transgene expression was lost in cells transfected with donor DNA only, while sustained GFP (approximately 40%) or CD19-CAR (20-25%) expression was observed in cells transfected with donor plus MLT transposase mRNA helper, consistent with stable MLT transposase-mediated genomic integration of the DNA donor.
  • GFP approximately 40%
  • CD19-CAR 20-25% expression was observed in cells transfected with donor plus MLT transposase mRNA helper, consistent with stable MLT transposase-mediated genomic integration of the DNA donor.
  • primary activated T cells were electroporated with Donor DNA only, Helper mRNA only or Donor DNA plus Helper mRNA, and their tumorigenic potential was evaluated assessing their growth in the presence or absence of IL-2 (FIGs.9A-C). As control, non-engineered T cells (No EP) were tested in parallel.
  • non-engineered T cells in the presence of IL-2, can proliferate during the first 10 days, reach a plateau at D15 and then their growth declines steadily until D25.
  • T cells engineered with Helper mRNA only follow a very similar pattern, while the growth of T cells engineered with Donor only or Donor plus Helper plateau earlier due to the higher toxicity of the DNA during electroporation.
  • the growth of engineered and non-engineered T cells declines steadily shortly after electroporation with most of the cells dying off by D16 (FIGs.9A-C).
  • FIGs.12A-B depict CD19-CAR expression of 21-26% at Day 14 (without enrichment) and >95% viability.
  • FIG.12A depicts CAR expression by flow cytometry of untransfected and CD19-CAR T cells at time of collection (D14).
  • FIG. 12B depicts viability of CD19-CAR T cells at time of collection (D14).
  • Example 8 Ex vivo efficacy - CD19-CAR-T cells from 3 healthy donors generated by MLT transposase efficiently kill CD19-expressing tumor target cells
  • the cytotoxicity potential of MLT transposase-engineered CD19-CAR T cells was evaluated in co-cultures with CD19- positive leukemia (Nalm6) or lymphoma cells (Daudi, Raji) ex vivo.
  • CD19-negative erythroleukemia K562 cells were used as control.
  • FIGs.10A-B CD19-CAR T cells from all three donors very efficiently kill CD19-positive tumor targets, at both time points evaluated 6 and 16 hours, compared to non-engineered T cells.
  • 113 DB1/ 143560057.1 SAL-026PC/126933-5026 cytotoxicity is highly specific since CD19-negative K562 cells are not killed by CD19-CAR T cells.
  • donor D154 seems to react against K562 cells. This reactivity is likely due to an alloresponse since both non-engineered and CD19- CAR T cells equally well kill K562 cells, indicating that the cytotoxic response is CD19 independent.
  • MLT transposase-engineered CD19-CAR T cells are highly cytotoxic, and their cytotoxicity is highly specific of the expression of the CD19 tumor antigen by the target cells.
  • Example 9 Ex vivo efficacy - high levels of proinflammatory cytokine release by CD19 CAR-T cells upon recognition of CD19 expressing tumor targets
  • the ability of MLT transposase engineered CD19-CAR T cells to release cytokines upon recognition of CD19- expressing tumor targets was evaluated in tumor co-cultures, ex vivo, with CD19-positive or negative tumor targets.
  • FIGs.11A-B after overnight incubation with CD19-positive B-cell leukemia or lymphoma targets, CD19- CAR T cells from all three donors released high levels of proinflammatory cytokines (i.e., INF ⁇ , TNF ⁇ ) and lytic granule protease granzyme B.
  • proinflammatory cytokines i.e., INF ⁇ , TNF ⁇
  • Example 10 Immunophenotype of MLT transposase engineered CD19-CAR T cells To determine the cellular immunophenotype of MLT transposase engineered CD19-CAR T cells, the expression of different cell surface markers was evaluated by flow cytometry (TABLE 9).
  • CD19-CAR T cells from all donors had a balanced CD4:CD8 ratio (FIGs.13A-B), and their ratio was similar to that of non-engineered T cells.
  • the CD19-CAR T cells had a high percentage of cells with a central memory or effector memory phenotype, and a low percentage of fully differentiated effector cells (FIGs.14A-B). This is consistent with a favorable memory phenotype since it has been shown that CAR-T products enriched in less differentiated T cells are associated with better clinical performance and persist longer in vivo.
  • the expression of the exhaustion markers PD-1, LAG-3, and TIM-3 was evaluated.
  • FIGs. 16A-B depict results showing that CAR-T production generates cell therapy with approximately 60% CAR expression, 5 genomic integrations and 5000-8000 CAR copies per cell.
  • FIG.16A shows CD19 CAR expression in two human donors, as assessed by flow cytometry.
  • FIG.16B shows integration, surface receptor expression and viability in the cells of the two human donor.
  • FIGs.17A-B depict results showing that CAR-T cells show effective anti-tumor activity against human antigen and leukemia cells in vivo.
  • FIG.17A shows a dramatic lack of luciferase activity in the two CAR-T treated mouse groups, demonstrating little tumor activity (as opposed to the tumor alone controls or donor untransduced controls).
  • FIG.17B shows tumor growth kinetics being notably slower in the CAR-T treated groups.
  • Example 12 MLT transposase engineered CAR T cells persist in circulation and are effective against tumor rechallenge
  • FIG.18 depicts day 42 tumor-free mice were rechallenged with Nalm-6 tumor cells (1E6 cells, i.v.) and tumor growth was followed an additional four weeks measuring luminescence once per week by IVIS imaging. As control, five na ⁇ ve mice were also injected with tumor cells. The number of CAR T cells in peripheral blood of treated mice at different days post CAR T infusion was analyzed by flow cytometry (FIGs.19A-C). Without being bound to a particular theory, the results of these analysis showed that CAR T cells persist for 42 days and can re-expand upon tumor rechallenged.
  • Example 13 MLT transposase engineered CAR T cells provide a safety profile with favorable transgene integration distribution
  • Transgene integration profile of MLT transposase engineered CD19-CAR T cells was determined by LAM-PCR from at least 2 replicates from three different donors (FIG.20). Results from these analysis revealed that most of the integration events occur in intronic and intergenic regions, with very low frequency of integration sites in exons. Cytokine independent growth assay performed with non-engineered and CD19-CAR T cells (FIG.21). Without being bound to a particular theory, genomic analysis revealed that MLT transposase engineered CAR T cells are safe, with integration sites mostly in intergenic and intronic regions, and no more than five integration events per cell.
  • Example 14 Dual-targeting CAR T cells prevent relapse upon loss of expression of one target Despite high complete response (CR) rates (70-90%) in r/rB-ALL with current CD19 CAR T cell therapies, 40-60% of responders experience relapse. Importantly, up to 60% of relapses are caused by CD19 antigen loss. A purpose of this experiment was to determine whether therapies using dual-targeting CAR T cells could help prevent relapses due to CD19 antigen loss.
  • single CD19, CD20, and CD22 and dual CD19/CD20 and CD19/CD22 CAR T cells from two different healthy donors were generated using the herein disclosed technology and then analyzed for their ability to overcome tumor antigen loss in hematological cancers.
  • Illustrative method of engineering human primary T cells with Donor DNA and Helper enzyme mRNA PBMC (Peripheral Blood Mononuclear Cells) were purified from Leukopaks obtained from healthy donors (HemaCare) using standard ficoll gradient purification.
  • PBMC cells were grown at 37°C in TexMACS medium (Miltenyi, cat # 130-097-196) supplemented with 5% Human AB serum (Valley Biomedical, cat # HP1022HI) plus 100 IU/mL of IL-2 (Miltenyi, cat # 130-097-748) and 50 ng/mL of soluble anti-CD3 (Miltenyi, cat # 130-093-387) 115 DB1/ 143560057.1 SAL-026PC/126933-5026 and anti-CD28 antibodies (Miltenyi, cat # 130-093-375) for 3 days.
  • T cells were collected and electroporated using Lonza’s 4D-nucleofector device following manufacturer’s protocol. Briefly, 15x10 6 activated T cells were electroporated using 100 ⁇ L cuvettes (Lonza, cat # V4XP-3024) with 10 ⁇ g of Donor DNA and 20 ⁇ g of Helper enzyme mRNA using program EN-138. Donor DNA constructs were generated as Nanoplasmids (Nature Technology Corporation, NTC) or GenCircles (GenScript), as listed in TABLE 10. Helper enzyme mRNA was obtained from TriLink. As control, cells were either not electroporated or electroporated with Donor DNA only.
  • CAR T cells Construct ID Name Backbone Vendor Size (bp) Illustrative phenotypic analysis of CAR T cells. CAR expression was evaluated by flow cytometry using the reagents listed in TABLE 11. Stained samples were acquired in a CytoFLEX flow cytometer (Beckman Coulter). TABLE 11: CAR detection reagents. CAR Reagent Vendor Catalog # His Tag Star Staining 200 tests SAL-026PC/126933-5026 CD22 FITC-Labeled Human Siglec-2 / CD22 Protein, AcroBiosystems CD2-HF254- Fc Tag 200 ug 20 .
  • Knockout (KO) of the CD19 gene in Raji-Fluc-EmGFP cells was performed using CRISPR/Cas9 tools.
  • the sgRNA sequence (5’CTAGGTCCGAAACATTCCACCGG3’) (SEQ ID NO: 816) was designed using IDT’s “Predesigned Alt-RTM CRISPR-Cas9 guide RNA” webtool.
  • B cell antigens CD20 and CD22 in parental and KO cells were evaluated by flow cytometry using anti-CD20 (BioLegend, catalog # 375506) and anti-CD22 MAbs (BioLegend, catalog # 302510).
  • Illustrative luciferase-based cytotoxicity assays The killing ability of single or dual CAR T cells was evaluated using a bioluminescence-based assay with luciferase- expressing tumor targets. Co-cultures of CAR T cells and luciferase-expressing targets were set up using 96-well solid white flat bottom (Corning, catalog # 3917).
  • luciferase expressing targets 100 ⁇ L of luciferase expressing targets at a concentration of 1e5 cells/mL were added per well in triplicates. Effector cells were added in a volume of 100 ⁇ L at 5:1, 2.5:1, and 1.25:1 effector-to-target ratios. Target cells incubated without effector cells or with 1% Triton X-100 (Fisher Scientific, cat # ICN19485450) were used as a measure of spontaneous and maximum lysis, respectively.
  • CAR T cells or control untransfected T cells were co-cultured with tumor targets at a 1:1 ratio in flat-bottom 96w plates, 5e5 cells/well in triplicates for 24 hours, and the amount of proinflammatory cytokines IFN ⁇ and TNF ⁇ , and lytic granule 117 DB1/ 143560057.1 SAL-026PC/126933-5026 protease granzyme B released into the supernatant was measured by MSD using the U-PLEX assay and a MESO QuickPlex SQ 120MM plate reader (Meso Scale Diagnostics) following manufacturer’s instructions. Analysis of CAR expression in engineered single and dual CAR T cells.
  • Single CD19, single CD20, and single CD22, and dual CD19/CD20 and dual CD19/CD22 CAR T cells were generated from two different healthy donors (D315 and D784) using the herein disclosed technology, as depicted in Fig.22.
  • Analysis of CAR expression by flow cytometry revealed high levels of CAR expression for single (40-86% CAR+) (Figs. 23A-23C) and dual (34-57% double positives) (Fig.24) CAR T cells.
  • This data demonstrates that the herein disclosed technology can be used for efficiently generating dual targeting CAR T cells that could help overcome tumor antigen loss in hematological cancers.
  • Dual CAR T Cells efficiently kill tumor targets that have lost CD19 expression.
  • CD19 CAR T cells progressively decreases as the percentage of CD19-expressing tumor targets diminishes (mixes WT(50)/KO(50) and WT(25)/KO(75)), becoming completely inefficient against CD19-KO Raji cells.
  • dual CD19/CD20 and CD19/CD22 CAR T cells can efficiently kill all tumor targets regardless of the degree of CD19 antigen loss.
  • Cytokine production and GZMB secretion by dual CAR T cells are not affected by tumor targets that have lost CD19 expression.
  • levels of proinflammatory cytokines IFN ⁇ and TNF ⁇ and granule protease GZMB were evaluated in the supernatants of tumor co-cultures using targets with heterogeneous CD19 expression.
  • CD19 CAR T cells produced high levels of IFN ⁇ (Fig.27) and TNF ⁇ (Fig.28) and GZMB (Fig.29) when co-cultured with CD19-expressing Raji cells.
  • the levels of proinflammatory cytokines IFN ⁇ and TNF ⁇ , and GZMB decreased substantially as the percentage of CD19-expressing tumor targets diminished (mixes WT(50)/KO(50) and WT(25)/KO(75)), becoming undetectable in tumor co-cultures with CD19-KO Raji cells.
  • the levels of proinflammatory cytokines and 118 DB1/ 143560057.1 SAL-026PC/126933-5026 GZMB produced by dual CD19/CD20, and CD19/CD22 CAR T cells were not affected by the degree of CD19 antigen loss.

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Abstract

L'invention concerne des méthodes de fabrication d'une cellule immunitaire de récepteur antigénique chimérique (CAR) ou de récepteur auto-anticorps chimérique (CAAR), par exemple, avec une enzyme pouvant effectuer une intégration génomique ciblée.
PCT/US2024/010890 2023-01-09 2024-01-09 Lymphocytes t de récepteur antigénique chimérique générées par transposase Ceased WO2024151640A1 (fr)

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Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20220298221A1 (en) * 2019-06-05 2022-09-22 Deutsches Zentrum Für Neurodegenerative Erkrankungen E. V. (Dzne) Chimeric autoantibody receptor (caar) that binds autoantibodies targeting the central nervous system in neurological autoimmune disease
WO2023279121A2 (fr) * 2020-08-03 2023-01-05 Swartz Roger EXPRESSION D'IMMUNOGLOBULINE A DIMÈRE ET D'IMMUNOGLOBULINE A POLYMÈRE PAR VECTEUR À ARNm LENTIVIRAL ET GAMMARÉTROVIRAL À INTÉGRATION ÉPISOMIQUE ET GÉNOMIQUE POUR PERMETTRE UNE IMMUNITÉ/PROTECTION MUQUEUSE ET HÉMATOLOGIQUE PAR THÉRAPIE GÉNIQUE CONTRE DES ALLERGÈNES, DES VIRUS, LE VIH, DES BACTÉRIES, LA PNEUMONIE, DES INFECTIONS, DES PROTÉINES ASSOCIÉES À UNE PATHOLOGIE, DES PATHOLOGIES SYSTÉMIQUES, LE CANCER, LES TOXINES ET DES VIRUS NON NATURELS. EXPRESSION D'IMMUNOGLOBULINE DIMÈRE A ET D'IMMUNOGLOBULINE POLYMÈRE A PAR DES CELLULES IMMUNITAIRES MODIFIÉES PAR CAR ET NON MODIFIÉES PAR CAR
WO2023081811A1 (fr) * 2021-11-04 2023-05-11 Saliogen Therapeutics, Inc. Cellules immunitaires comprenant récepteurs antigéniques chimériques ou récepteurs auto-anticorps chimériques

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20220298221A1 (en) * 2019-06-05 2022-09-22 Deutsches Zentrum Für Neurodegenerative Erkrankungen E. V. (Dzne) Chimeric autoantibody receptor (caar) that binds autoantibodies targeting the central nervous system in neurological autoimmune disease
WO2023279121A2 (fr) * 2020-08-03 2023-01-05 Swartz Roger EXPRESSION D'IMMUNOGLOBULINE A DIMÈRE ET D'IMMUNOGLOBULINE A POLYMÈRE PAR VECTEUR À ARNm LENTIVIRAL ET GAMMARÉTROVIRAL À INTÉGRATION ÉPISOMIQUE ET GÉNOMIQUE POUR PERMETTRE UNE IMMUNITÉ/PROTECTION MUQUEUSE ET HÉMATOLOGIQUE PAR THÉRAPIE GÉNIQUE CONTRE DES ALLERGÈNES, DES VIRUS, LE VIH, DES BACTÉRIES, LA PNEUMONIE, DES INFECTIONS, DES PROTÉINES ASSOCIÉES À UNE PATHOLOGIE, DES PATHOLOGIES SYSTÉMIQUES, LE CANCER, LES TOXINES ET DES VIRUS NON NATURELS. EXPRESSION D'IMMUNOGLOBULINE DIMÈRE A ET D'IMMUNOGLOBULINE POLYMÈRE A PAR DES CELLULES IMMUNITAIRES MODIFIÉES PAR CAR ET NON MODIFIÉES PAR CAR
WO2023081811A1 (fr) * 2021-11-04 2023-05-11 Saliogen Therapeutics, Inc. Cellules immunitaires comprenant récepteurs antigéniques chimériques ou récepteurs auto-anticorps chimériques

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