US20220090012A1 - Genetically engineered t cells with regnase-1 and/or tgfbrii disruption have improved functionality and persistence - Google Patents

Genetically engineered t cells with regnase-1 and/or tgfbrii disruption have improved functionality and persistence Download PDF

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US20220090012A1
US20220090012A1 US17/483,100 US202117483100A US2022090012A1 US 20220090012 A1 US20220090012 A1 US 20220090012A1 US 202117483100 A US202117483100 A US 202117483100A US 2022090012 A1 US2022090012 A1 US 2022090012A1
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cells
gene
car
seq
tgfbrii
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Mary-Lee Dequeant
Demetrios Kalaitzidis
Mohammed Ghonime
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CRISPR Therapeutics AG
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CRISPR Therapeutics AG
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Priority to US17/483,100 priority Critical patent/US20220090012A1/en
Priority to US17/493,253 priority patent/US11679130B2/en
Priority to US17/493,271 priority patent/US11679131B2/en
Priority to US17/493,280 priority patent/US11497773B2/en
Assigned to CRISPR THERAPEUTICS AG reassignment CRISPR THERAPEUTICS AG ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: Kalaitzidis, Demetrios, GHONIME, Mohammed, DEQUEANT, MARY-LEE
Publication of US20220090012A1 publication Critical patent/US20220090012A1/en
Priority to US18/054,521 priority patent/US11857574B2/en
Priority to US19/056,007 priority patent/US20250179146A1/en
Abandoned legal-status Critical Current

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    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
    • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector

Definitions

  • Chimeric antigen receptor (CAR) T-cell therapy uses genetically modified T cells to more specifically and efficiently target and kill cancer cells. After T cells have been collected from the blood, the cells are engineered to include CARs on their surface. The CARs may be introduced into the T cells using CRISPR/Cas9 gene editing technology. When these allogeneic CAR T cells are injected into a patient, the receptors enable the T cells to kill cancer cells.
  • CAR Chimeric antigen receptor
  • T cells having improved persistence in culture are desired in CAR T therapy. Such T cells live longer in both in vitro and in vivo, thereby conferring benefits in CAR T cell manufacturing and clinical applications. However, it remains challenging to improve persistence of T cells in culture.
  • the present disclosure is based, at least in part, on the development of genetically edited T cells carrying a disrupted Regnase 1 (Reg1) gene (e.g., “Reg1 Knockout T cells”), a disrupted TGFBRII gene (e.g., “TGFBRII Knockout T cells”, or genetically edited T cells carrying both a disrupted Reg1 gene and a disrupted TGFBRII gene, and effective methods of producing such genetically edited T cells via CRISPR/Cas-mediated gene editing using guide RNAs, for example, those targeting specific sites within the Reg1 gene with high on-target editing efficiency and low off-target editing efficiency, and/or those targeting specific sites within the TGFBRII gene with high on-target editing efficiency and low off-target editing efficiency.
  • a disrupted Regnase 1 (Reg1) gene e.g., “Reg1 Knockout T cells”
  • TGFBRII Knockout T cells e.g., “TGFBRII Knockout T cells
  • Such genetically engineered T cells exhibits at least one of the following advantageous features: (a) improved cell growth activity; (b) enhanced persistence; (c) reduced T cell exhaustion; (d) resistant to inhibitory effects induced by TGF- ⁇ ; (e) enhanced cell killing capacity; and (f) resistant to inhibitory effects by fibroblasts and/or inhibitory factors secreted thereby.
  • the Reg1 disrupted T cells, the TGFBRII disrupted T cells, or the Reg1/TGFBRII double disrupted T cells disclosed herein can further be genetically engineered to express a chimeric antigen receptor (CAR) targeting an antigen of interest, e.g., an antigen associated with an undesired cell such as a cancer cell, and to comprise one or more additional disrupted genes, for example, TRAC, ⁇ 2M, CD70, or a combination thereof.
  • CAR chimeric antigen receptor
  • the resultant CAR-expressing, Reg1 disrupted T cells exhibit enhanced cytotoxic activity against target cells and anti-tumor activity as compared with CAR-T cells having a wild-type Reg1 gene.
  • the current disclosure is related to the development of genetically engineered CAR T cells that comprise a disrupted Reg1 gene.
  • the genetically engineered CAR T cells are further genetically engineered to comprise a disrupted cluster of differentiation 70 (CD70) gene.
  • CD70 disrupted cluster of differentiation 70
  • the CAR T cells described herein may express anti-CD70 CAR, anti-cluster of differentiation 19 (CD19) CAR or anti-B-cell maturation antigen (anti-BCMA) CAR.
  • the genetically edited T cells disclosed herein showed enhanced cell expansion, longevity and proliferation capacity in culture, enhanced potency (e.g., enhanced cytotoxicity), and enhanced CAR-T efficacy in animal models (via, e.g., longer persistence). Further, the genetically edited T cells showed cytokine-dependent growth, indicating safety. In addition, disrupting both the Reg1 and TGFBRII genes exhibited synergistic effects in anti-tumor activity and CAR-T cell expansion and persistence as observed in animal models.
  • the present disclosure provides, in some aspects, a population of genetically engineered T cells, comprising: (i) a disrupted Regnase-1 (Reg1) gene; and/or (ii) a disrupted Transforming Growth Factor Beta Receptor II (TGFBRII) gene.
  • the population of genetically engineered T cells comprises (i).
  • population of genetically engineered T cells comprises (ii).
  • the population of genetically engineered T cells comprises both (i) and (ii). Any of the genetically engineered T cells may be further engineered to express a chimeric antigen receptor (CAR).
  • CAR chimeric antigen receptor
  • the population of genetically engineered T cells disclosed herein has one or more of the following features: (a) improved cell growth activity; (b) enhanced persistence; (c) reduced T cell exhaustion; (d) resistant to inhibitory effects induced by TGF- ⁇ ; (e) enhanced cell killing capacity; and (f) resistant to inhibitory effects by fibroblasts and/or inhibitory factors secreted thereby.
  • the disrupted Reg1 gene is genetically edited in exon 1, exone 2, exon 3, or exon 4. In some examples, the disrupted Reg1 gene is genetically edited in exon 2 and/or exon 4. Alternatively or in addition, the disrupted TGFBRII gene is genetically edited in exon 1, exon 2, exon 3, exon 4, or exon 5. In some examples, the disrupted TGFBRII gene is genetically edited in exon 4. In other examples, the disrupted TGFBRII gene is genetically edited in exon 5.
  • the disrupted Reg1 gene, the disrupted TGFBRII gene, or both can be genetically edited by a CRISPR/Cas-mediated gene editing system.
  • the CRISPR/Cas-mediated gene editing comprises a guide RNA (gRNA) targeting a site in the Reg1 gene that comprises a nucleotide sequence listed in Table 22 (with or without PAM) (e.g., SEQ ID NO: 320, 322, 323, or 327, or the corresponding ones with PAM).
  • gRNA targeting the Reg1 gene comprises a spacer that comprises the nucleotide sequence of listed in Table 22 (e.g., SEQ ID NO: 24, 32, 36, or 52).
  • the disrupted Reg1 gene comprises a nucleotide sequence selected from those listed in Tables 29-38 (e.g., Table 31, 33, 34, or 38).
  • the CRISPR/Cas-mediated gene editing system comprises a guide RNA (gRNA) targeting a site in the TGFBRII gene that comprises a nucleotide sequence listed in Table 39 (with or without PAM).
  • gRNA guide RNA
  • the gRNA targeting the TGFBRII gene comprises a spacer listed in Table 39, for example, having a nucleotide sequence of any one of SEQ ID NOs: 270, 302, 308, and 312.
  • the disrupted TGFBRII gene may comprise a nucleotide sequence selected from those listed in Tables 40-48 (e.g., Table 43).
  • any of the gRNAs disclosed herein may further comprise a scaffold sequence.
  • the gRNA targeting the Reg1 gene comprises any of the nucleotide sequences listed in Table 22. Examples include 22, 23, 30, 31, 34, 35, 50, and 51.
  • the gRNA targeting the TGFBRII gene may comprise any of the nucleotide sequences provided in Table 39. Examples include SEQ ID NOs: 270, 271, 300, 301, 306, 307, 312, and 313.
  • any of the populations of genetically engineered T cells disclosed herein may further comprise: (iii) a disrupted T cell receptor alpha chain constant region (TRAC) gene, (iv) a disrupted beta-2-microglobulin ( ⁇ 2M) gene, (v) a disrupted CD70 gene, or (vi) a combination of any of (iii)-(v).
  • the T cells comprise a disrupted T cell receptor alpha chain constant region (TRAC) gene.
  • the T cells comprise a disrupted beta-2-microglobulin ( ⁇ 2M) gene.
  • Any of the T cells disclosed herein may also comprise a disrupted CD70 gene.
  • the disrupted TRAC gene, the disrupted ⁇ 2M gene, and/or the disrupted CD70 gene is genetically edited by one or more CRISPR/Cas-mediated gene editing system
  • the genetically engineered T cells may comprise a nucleic acid encoding the CAR, and wherein the nucleic acid is inserted in the genome of the T cells.
  • the nucleic acid encoding the CAR is inserted in the disrupted Reg1 gene, the disrupted TGFBRII gene, the disrupted TRAC gene, the disrupted ⁇ 2M, or the disrupted CD70 gene.
  • the nucleic acid encoding the CAR is inserted in the disrupted TRAC gene.
  • the nucleic acid encoding the CAR may replace the deleted fragment comprising SEQ ID NO: 69 in the TRAC gene.
  • the disrupted Reg1 gene may comprise a nucleotide sequence listed in Tables 29-38 (e.g., Table 31, 33, 34, or 38).
  • the disrupted TGFBRII gene may comprise a nucleotide sequence selected from those listed in Tables 40-48 (e.g., Table 43).
  • the disrupted TRAC gene may comprise a nucleotide sequence of any one of SEQ ID NOs: 75-82 (see Table 24).
  • the disrupted ⁇ 2M may comprise a nucleotide sequence of any one of SEQ ID NOs: 83-88 (see Table 25).
  • the disrupted CD70 gene may comprise a nucleotide sequence of any one of SEQ ID NOs: 89-94 (see Table 26).
  • any of the CAR constructs disclosed herein may comprise an extracellular antigen binding domain specific to a tumor antigen, a co-stimulatory signaling domain of 4-1BB or CD28, and a cytoplasmic signaling domain of CD3 ⁇ .
  • the tumor antigen is CD19.
  • the tumor antigen is BCMA.
  • the tumor antigen is CD70.
  • the tumor antigen is CD33.
  • the tumor antigen is PTK7.
  • the CAR binds CD19 (anti-CD19 CAR).
  • the extracellular antigen binding domain in the anti-CD19 CAR can be a single chain variable fragment (scFv) that binds CD19 (anti-CD19 scFv).
  • the anti-CD19 scFv may comprise (i) a heavy chain variable region (V H ) that comprises the same heavy chain complementary determining regions (CDRs) as those in SEQ ID NO: 124; and (ii) a light chain variable region (V L ) that comprises the same light chain CDRs as those in SEQ ID NO: 125.
  • the V H comprises the amino acid sequence of SEQ ID NO: 124 and the V L comprises the amino acid sequence of SEQ ID NO: 125.
  • the anti-CD19 scFv comprises the amino acid sequence of SEQ ID NO: 120.
  • the anti-CD19 CAR comprises the amino acid sequence of SEQ ID NO: 118 (with an N-terminal signal peptide) or SEQ ID NO:353 (without N-terminal signal peptide).
  • the CAR binds CD70 (anti-CD70 CAR).
  • the extracellular antigen binding domain in the anti-CD70 CAR can be a single chain variable fragment (scFv) that binds CD70 (anti-CD70 scFv).
  • the anti-CD70 scFv comprises (i) a heavy chain variable region (V H ) that comprises the same heavy chain complementary determining regions (CDRs) as those in SEQ ID NO: 143; and (ii) a light chain variable region (V L ) that comprises the same light chain CDRs as those in SEQ ID NO: 144.
  • the V H comprises the amino acid sequence of SEQ ID NO: 143 and the V L comprises the amino acid sequence of SEQ ID NO: 144.
  • the anti-CD70 scFv comprises the amino acid sequence of SEQ ID NO: 140 or 142.
  • the anti-CD70 CAR comprises the amino acid sequence of SEQ ID NO: 138 (with an N-terminal signal peptide) or SEQ ID NO:354 (without N-terminal signal peptide).
  • the CAR binds BCMA (anti-BCMA CAR).
  • the extracellular antigen binding domain in the anti-BCMA CAR can be a single chain variable fragment (scFv) that binds BCMA (anti-BCMA CAR).
  • the anti-BCMA scFv comprises (i) a heavy chain variable region (V H ) that comprises the same heavy chain complementary determining regions (CDRs) as those in SEQ ID NO: 149; and (ii) a light chain variable region (V L ) that comprises the same light chain CDRs as those in SEQ ID NO: 150.
  • the V H comprises the amino acid sequence of SEQ ID NO: 149
  • the V L comprises the amino acid sequence of SEQ ID NO: 150.
  • the anti-BCMA scFv comprises the amino acid sequence of SEQ ID NO: 148.
  • the anti-BCMA CAR comprises the amino acid sequence of SEQ ID NO: 146 (with an N-terminal signal peptide) or SEQ ID NO:355 (without N-terminal signal peptide).
  • the genetically engineered T cells disclosed herein may be derived from primary T cells of one or more human donors. In some instances, the genetically engineered T cells show cytokine-dependent growth.
  • the present disclosure provides a method for preparing any of the populations of genetically engineered T cells disclosed herein.
  • the method may comprise: (a) providing a plurality of cells, which are T cells or precursor cells thereof; (b) genetically editing the Reg1 gene and/or the TGFBRII gene; and (c) producing the population of genetically engineered T cells having disrupted Reg1 gene and/or the TGFBRII gene.
  • the T cells of step (a) are derived from primary T cells of one or more human donors.
  • step (b) comprises genetically editing the Reg1 gene.
  • step (b) comprises genetically editing the TGFBRII gene.
  • step (b) comprises genetically editing both the Reg1 gene and the TGFBRII gene.
  • step (b) is performed by one or more CRISPR/Cas-mediated gene editing systems.
  • step (b) can be performed by delivering to the plurality of cells an RNA-guided nuclease and a gRNA targeting the Reg1 gene.
  • the gRNA targeting the Reg1 gene may be specific to an exon of the Reg1 gene, e.g., exon 2 or exon 4.
  • the gRNA targeting the Reg1 gene comprises a spacer that comprises a nucleotide sequence listed in Table 22 (e.g., SEQ ID NO: 24, 32, 36, or 52).
  • step (b) can be performed, inter alia, by delivering to the plurality of cells an RNA-guided nuclease and a gRNA targeting the TGFBRII gene.
  • the gRNA targeting the TGFBRII gene may be specific to an exon of the TGFBRII gene, e.g., exon 1, exon 2, exon 3, exon 4, and exon 5.
  • the gRNA targeting the TGFBRII gene is specific to exon 4.
  • the gRNA targeting the TGFBRII gene is specific to exon 5.
  • the gRNA targeting the TGFBRII gene comprises a spacer listed in Table 39. Examples include SEQ ID NOs: 272, 302, 308, and 314.
  • any of the gRNAs disclosed herein may further comprise a scaffold sequence.
  • the gRNA targeting the Reg1 gene may comprise any of the nucleotide sequences listed in Table 22. Examples include SEQ ID NO: 22, 23, 30, 31, 34, 35, 50, and 51.
  • the gRNA targeting the TGFBRII gene may comprise any of the nucleotide sequences provided in Table 39. Examples include SEQ ID NOs: 270, 271, 300, 301, 306, 307, 312, and 313.
  • the plurality of T cells in step (a) comprises one or more of the following genetic modifications: (i) engineered to express a chimeric antigen receptor (CAR); (ii) has a disrupted T cell receptor alpha chain constant region (TRAC) gene; (iii) has a disrupted ⁇ 2M gene; and (iv) has a disrupted CD70 gene.
  • CAR chimeric antigen receptor
  • TRAC T cell receptor alpha chain constant region
  • any of the methods disclosed herein may further comprise:
  • one or more of (i)-(iv) are performed by one or more CRISPR/Cas-mediated gene editing system comprising one or more RNA-guided nucleases and one or more gRNAs targeting the TRAC gene, the ⁇ 2M gene, and/or the CD70 gene.
  • the gRNA targeting the TRAC gene comprises a spacer that comprises the nucleotide sequence of SEQ ID NO: 61.
  • the gRNA targeting the ⁇ 2M gene comprises a spacer that comprises the nucleotide sequence of SEQ ID NO: 65.
  • the gRNA targeting the CD70 gene comprises a spacer that comprises the nucleotide sequence of SEQ ID NO: 57. See Table 23.
  • the method disclosed herein may comprise delivering to the T cells one or more ribonucleoprotein particles (RNP), which may comprise the RNA-guided nuclease, one or more of the gRNAs, and the nucleic acid encoding the CAR.
  • RNP ribonucleoprotein particles
  • the RNA-guided nuclease is a Cas9 nuclease, for example, a S. pyogenes Cas9 nuclease.
  • the nucleic acid encoding the CAR is in an AAV vector.
  • the nucleic acid encoding the CAR comprises a left homology arm and a right homology arm flanking the nucleotide sequence encoding the CAR.
  • the left homology arm and the right homology arm are homologous to a genomic locus in the T cells, allowing for insertion of the nucleic acid into the genomic locus.
  • the genomic locus is in the Reg1 gene.
  • the genomic locus is in the TGFBRII gene.
  • the genomic locus is in the TRAC gene.
  • the genomic locus is in the ⁇ 2M gene.
  • the genomic locus is in the CD70 gene.
  • the method comprising disrupting the TRAC gene by a CRISPR/Cas-mediated gene editing system comprising a gRNA comprising the nucleotide sequence of SEQ ID NO: 59 and the nucleic acid encoding the CAR is inserted at the site targeted by the gRNA.
  • the method may comprise delivering to the T cells a nucleic acid encoding a CAR, which is specific to CD70, and genetically editing the CD70 gene to disrupt its expression.
  • the present disclosure provides a method for eliminating undesired cells in a subject, the method comprising administering to a subject in need thereof any of the populations of genetically engineered T cells disclosed herein.
  • the undesired cells are cancer cells, for example, hematopoietic cancer cells or solid tumor cells.
  • the undesired cells are CD19 + .
  • the undesired cells are BCMA + .
  • the undesired cells are CD70 + .
  • the undesired cells are CD33 + .
  • the undesired cells are PTK7 + .
  • a guide RNA (gRNA) targeting a Reg1 gene comprising a nucleotide sequence specific to a fragment in exon 2 or exon 4 of the Reg1 gene.
  • the gRNA comprises a spacer listed in Table 22 (e.g., SEQ ID NO: 24, 32, 36 or 52).
  • a gRNA may further comprise a scaffold sequence.
  • the gRNA comprises one or more modified nucleotides.
  • the gRNA comprises one or more 2′-O-methyl phosphorothioate residues at the 5′ and/or 3′ terminus of the gRNA.
  • Examples of gRNAs targeting Reg1 include any of those listed in Table 22 (e.g., SEQ ID NO: 22, 23, 30, 31, 34, 35, 50, or 51; see also disclosures herein).
  • a guide RNA targeting a TGFBRII gene, comprising a nucleotide sequence specific to a fragment in exon 1, exon 2, exon 3, exon 4, or exon5 of the TGFBRII gene.
  • the gRNA comprises a nucleotide sequence specific to exon 4 of the TGFBRII gene.
  • the gRNA comprises a nucleotide sequence specific to exon 5 of the TGFBRII gene.
  • the gRNA comprises a spacer having the nucleotide sequence listed in Table 39 (e.g., SEQ ID NOs: 272, 302, 308, and 314).
  • Such a gRNA may further comprise a scaffold sequence.
  • the gRNA comprises one or more modified nucleotides.
  • the gRNA comprises one or more 2′-O-methyl phosphorothioate residues at the 5′ and/or 3′ terminus of the gRNA.
  • Examples of gRNAs targeting the TGFBRII gene include any of those listed in Table 39 (e.g., SEQ ID NOs: 270, 271, 300, 301, 306, 307, 312, and 313).
  • FIGS. 1A and 1B include diagrams showing that exemplary CAR T cells (anti-CD70 CAR T cells) with Reg1 KO exhibit superior in vitro expansion
  • FIG. 1A Proliferation of anti-CD70 CAR T cells (CAR T) with Reg1 KO using one of the 10 guides (Z01-Z10) targeting Reg1 as indicated.
  • CAR T indicates anti-CD70 CAR T cells with an unedited (wild-type) Reg1 gene.
  • FIG. 1B Proliferation of anti-CD70 CAR T cells with Reg1 KO using guide REG1-Z10 (Z10) up to 52 days post HDR.
  • Anti-CD70 CAR T cells with an unedited Reg1 gene are also shown (CAR T).
  • (A) and (B) refer to duplicative assays.
  • FIGS. 2A-2E include diagrams showing that exemplary CAR T cells (anti-CD70 CAR T cells) with Reg1 KO (+reg1 KO) exhibit superior in vitro potency against tumor cell lines relative to CAR T cells with an unedited Reg1 gene (CAR T).
  • FIG. 2A Cell lysis of ACHN cells by anti-CD70 CAR T cells with Reg1 KO, using Regnase guides Z03 or Z10, relative to CAR T cells with an unedited (wild-type) Reg1 gene (CAR T). Cell lysis was measured after 24 h co-culture at day 12 post HDR.
  • FIG. 2B Cell lysis of ACHN cells by anti-CD70 CAR T cells with Regnase 1 KO using Regnase guides Z05 or Z06 relative to CAR T cells with an unedited Reg1 gene. Cell lysis was measured after 24 h co-culture at day 12 post HDR.
  • FIG. 2C Cell lysis of ACHN cells by anti-CD70 CAR T cells with Regnase 1 KO, using Regnase guides Z03, Z05, Z06 or Z10 relative to CAR T cells with an unedited Reg1 gene. Cell lysis was measured after 24 h co-culture at day 27 post HDR.
  • FIG. 2D Cell lysis of caki-1 cells by anti-CD70 CAR T cells with Regnase 1 KO using Regnase guides Z03, Z05, Z06 or Z10 relative to CAR T cells with an unedited Reg1 gene. Cell lysis was measured after 24 h co-culture at day 27 post HDR.
  • FIG. 2E Cell lysis of 769P cells by anti-CD70 CAR T cells with Regnase 1 KO using Regnase guides Z03, Z05, Z06 or Z10 relative to CAR T cells with an unedited Reg1 gene. Cell lysis was measured after 24 h co-culture at day 27 post HDR.
  • FIGS. 3A-3D include diagrams showing that exemplary CAR T cells (anti-CD70 CAR T cells) with Reg1 KO (CAR T+Reg KO, using Z10 guide as an example) express lower levels of T cell exhaustion markers in vitro relative to Reg1 wild-type counterparts (CAR T).
  • FIG. 3A Day 13 post HDR PD1 expression in CD4+ and CD8+ anti-CD70 CAR T cells with Reg1 KO (+Reg KO) relative to wild-type counterparts.
  • FIG. 3B Day 26 post HDR PD1 expression in CD4+ and CD8+ anti-CD70 CAR T cells with Reg1 KO (+Reg KO) relative to wild-type counterparts.
  • FIG. 3A Day 13 post HDR PD1 expression in CD4+ and CD8+ anti-CD70 CAR T cells with Reg1 KO (+Reg KO) relative to wild-type counterparts.
  • FIG. 3B Day 26 post HDR PD1 expression in CD4+ and CD8+ anti-CD70 CAR T
  • FIG. 3C Day 13 post HDR Tim3 expression in CD4+ and CD8+ anti-CD70 CAR T cells with Reg1 KO (+Reg KO) relative to wild-type counterparts.
  • FIG. 3D Day 26 post HDR Tim3 expression in CD4+ and CD8+ anti-CD70 CAR T cells with Reg1 KO (+Reg KO) relative to wild-type counterparts.
  • FIG. 4 is a diagram showing that exemplary CAR T cells (anti-CD19 CAR T cells) with Reg1 KO showed enhanced expansion in the presence of cytokines in vitro and continue to depend on cytokines for in vitro expansion.
  • Anti-CD19 CAR T cells with a Reg1 KO Anti-CD19 CAR T/Reg KO
  • Anti-CD19 CAR T cells with a wild-type Reg1 gene were cultured in the presence and absence (No cytokines) of cytokines for 40 days.
  • FIGS. 5A-5D include diagrams showing that exemplary CAR T cells (anti-CD19 CAR T cells) with Reg1 KO (Anti-CD19 CAR T/Reg KO) provide superior in vivo survival and decreased tumor burden relative to Reg1 wild-type counterparts (Anti-CD19 CAR T) in the intravenous disseminated Nalm-6 human acute lymphoblastic leukemia tumor xenograft mouse model.
  • FIG. 5A Probability of survival of untreated mice, mice dosed with 4e6 anti-CD19 CAR T cells, and 4e6 anti-CD19 CAR T/Reg KO cells.
  • FIG. 5A Probability of survival of untreated mice, mice dosed with 4e6 anti-CD19 CAR T cells, and 4e6 anti-CD19 CAR T/Reg KO cells.
  • FIG. 5B Probability of survival of untreated mice, mice dosed with 8e6 anti-CD19 CAR T cells, and 8e6 anti-CD19 CAR T/Reg KO cells.
  • FIG. 5C Bioluminescence signal from bioluminescent model leukemia cells in mice treated with 4e6 anti-CD19 CAR T cells or 4e6 anti-CD19 CAR T/Reg KO cells.
  • FIG. 5D Bioluminescence signal from bioluminescent model leukemia cells in mice treated with 8e6 anti-CD19 CAR T cells or 8e6 anti-CD19 CAR T/Reg KO cells.
  • FIGS. 6A-6B include diagrams showing that exemplary CAR T cells (anti-CD70 CAR T cells) with Reg1 KO (CAR T+Reg KO) exhibit superior in vitro potency against tumor cell lines relative to Reg1 wild-type counterparts (CAR T).
  • FIG. 6A Cell lysis of ACHN cells by anti-CD70 CAR T cells with Reg1 KO using guide REG1-Z10 (CAR T+Reg KO) relative to Reg1 wild-type counterparts (CAR T). Cell lysis was measured after 24 h co-culture at day 19 and 26 post HDR.
  • FIGS. 7A and 7B include diagrams showing knock out of TGFBRII using various guide RNAs as indicated.
  • FIG. 7A Indel rates of edited TGFBRII gene by eight gRNAs that target different TGFBRII gene exons as indicated. From left to right, EX1_T1, EX1_T3, EX2_T1, EX3_T1, EX3_T2, EX4_T1, EX4_T2, and EX5_T1, the nucleotide sequence of each of which is provided in Table 32.
  • FIG. 7B immunoblot of TGFBRII expression in gene-edited T cells. GAPDH was used as a loading control. The mock sample is unedited T cells with wild-type TGFBRII.
  • FIGS. 8A-8K include diagrams showing the effect of TGF- ⁇ on CAR T cell expansion.
  • Anti-CD70 CAR T cells were exposed to different concentrations of recombinant human TGF- ⁇ (10, 20, 50, 100 ng/ml) and cell number was recorded at different time points ( FIG. 8A ).
  • T cells with or without TGFBRII knock-out, generated using different TGFBRII gRNAs as indicated, were incubated with 0 or 50 ng/ml of TGFB- ⁇ and cell expansion was recorded over time ( FIGS. 8B-8K ).
  • FIG. 9 is a diagram showing the effect of TGFBRII KO on CAR T cell killing ability against A498 cells at various E:T ratios as indicated. TGFBRII KO improves cytotoxicity of CAR-T cells.
  • FIGS. 10A-10E include diagrams showing the effect of TGFBRII KO on CAR T cell kill ability against multiple tumor cell lines.
  • the cell kill capacity of anti-CD70 CAR T cells was compared to anti-CD70 CAR T cells with TGFBRII KO.
  • Cell killing activity of the CAR T cells was assessed against CAM-1 ( FIG. 10A ) H1975 ( FIG. 10B ), Hs-766T ( FIG. 10C ), 786-O ( FIG. 10D ) and SK-OV3 ( FIG. 10E ).
  • TGFBRII KO improves cytotoxicity of CAR-T cells.
  • FIG. 11 is a graph showing the effect of TGFBRII KO on CAR T cell phenotype.
  • Anti-CD70 CAR T cells with or without TGFBRII KO were exposed to 50 ng/ml recombinant human TGF- ⁇ and the expression of CD25 was assessed by flow cytometry.
  • TGFBRII KO protects CAR T from TGF- ⁇ inhibitory effect on cell phenotype.
  • FIG. 12 is a graph showing that TGFBRII KO protects CAR T cells against TGF- ⁇ inhibitory effect on cytotoxicity.
  • Anti-CD70 CAR T cells was co-cultured with target tumor cells (A498) in the presences or absence of TGF- ⁇ (0, 1, 10, 50 ng/ml)
  • TGF- ⁇ 0.01, 10, 50 ng/ml
  • the ability of anti-CD70 CAR T cells with unedited TGFBRII to kill target cells were compared to anti-CD70 CAR T with TGFBRII KO using an exemplary guide RNA as indicated.
  • FIGS. 13A-13C include diagrams showing that TGFBRII KO anti-CD70 CAR T cells are resistant to TGF- ⁇ inhibitory effects on effector function.
  • Anti-CD70 CAR T cells were co-cultured with target cells (A498) with TGF- ⁇ (50 ng/ml) or without TGF- ⁇ and compared to anti-CD70 CAR T with TGFBRII KO (e.g.: anti-CD70 CAR+TGFBRII_EX4_T1) in their ability to kill target cells.
  • FIG. 14 is a graph showing fibroblasts reduce CAR-T cell cytolytic activity.
  • Anti-CD70 CAR T was co-cultured with target cells (A498) with or without fibroblast (CCL-190) placed in a transwell plate at 0.25:1, fibroblast: anti-CD70 CAR T.
  • FIGS. 15A-15C include graphs showing that TGFBRII KO protects CAR-T cells against the inhibitory effect of fibroblasts.
  • Anti-CD70 CAR T was co-cultured with target cells (A498) at 0.1:1 (E:T) in presence of different volumes of conditioned media from CCL-190 (2.5, 5, 10 ⁇ L) and the cell kill capacity was evaluated and compared to cells with TGFBRII KO.
  • the ability of anti-CD70 CAR T cells (with or without TGFBRII KO) to kill target cells is shown in Hs-766T pancreatic tumor cells ( FIG. 15A ), A498 kidney tumor cells ( FIG. 15B ), and H1975 lung tumor cells ( FIG. 15C ).
  • FIG. 16A-16B include diagrams showing synergistic effects of TGFBRII and Regnase double disruptions with in vitro rechallenge of CAR T Cells with ACHN.
  • FIG. 16A improved potency.
  • FIG. 16B improved CAR expansion.
  • FIG. 17A-17B include diagrams showing synergistic effects of disrupting both TGFBRII and Regnase genes in cancer xenograph models.
  • FIG. 17A CAKI-1 renal cell carcinoma xenograph model with anti-CD70 CAR T cells.
  • FIG. 17B H1975 lung cancer xenograph model with anti-CD70 CAR T cells.
  • FIG. 18A-18B include diagrams showing synergistic effects of disrupting both TGFBRII and Regnase genes in an RCC rechallenge xenograph model.
  • FIG. 18A reduction in RCC (A498) tumor size.
  • FIG. 18B inhibition of RCC tumor cell growth following rechallenge with ACHN cells.
  • FIG. 19A-19B include diagrams showing impact of Reg1 and/or TGFBRII disruption on CAR-T cell differentiation and expansion in vivo.
  • FIG. 19A CAR-T cell differentiation.
  • FIG. 19B CAR-T cell expansion.
  • FIG. 20A-20B include diagrams showing synergistic effects of TGFBRII and Regnase double knock-out in a Nalm6-leukemia (B-ALL) mouse model.
  • FIG. 20A reduction in tumor size.
  • FIG. 20B survival rates.
  • FIG. 21 is a diagram showing survival advantage arising from TGFBRII and Regnase double disruptions in a NOG Mantle cell lymphoma (MCL) tumor xenograft mouse model.
  • FIGS. 22A-22B include diagrams showing increased in vivo expansion of CAR-T cells having TGFBRII and/or Regnase knock-out.
  • FIG. 22A shows CAR T cell expansion in the Jeko-1 xenograph model.
  • FIG. 22B shows CAR T cell expansion in the nalm-6 xenograph model.
  • FIGS. 23A-23D include diagrams showing consistent rates of CRISPR/Cas editing in anti-BCMA CAR-T cells with Reg-1 and/or TGFBRII disruption as determined by flowcytometry.
  • FIG. 23A levels of TCR ⁇ cells.
  • FIG. 23B levels of ⁇ 2M ⁇ cells.
  • FIG. 23C levels of CAR + cells.
  • FIG. 23D ratio of CD4 + /CD8 + cells.
  • FIGS. 24A-24B include diagrams showing consistent edit editing rates in anti-BCMA CAR-T cells with Reg-1 and/or TGFBRII disruptions.
  • FIG. 24A TGFBRII disruption efficiency.
  • FIG. 24B Reg-1 disruption efficiency.
  • FIGS. 25A-25D include diagrams showing superior cell cytotoxicity of TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ TGFBRII ⁇ anti-BCMA CAR+ T-cells.
  • FIGS. 25A-25B cytotoxicity against MM1s (multiple myeloma cell line) cells ( 25 A) relative to K562 cells ( 25 B).
  • FIGS. 25C-25D cytotoxicity against JeKo-1 cells (mantle cell lymphoma cell line) ( 25 C) relative to K562 cells ( 25 D).
  • FIGS. 26A-26C include diagrams showing that the combined disruption of Regnase-1 and TGFBRII improved anti-BCMA CAR-T activity against murine multiple myeloma in an animal model.
  • FIG. 26A tumor volume reduction.
  • FIG. 26B survival rate.
  • FIG. 26C CAR-T cell expansion in peripheral blood.
  • FIGS. 27A-27F include diagrams showing that the combined disruption of Regnase and TGFBRII improves anti-BCMA CAR-T activity against murine mantle cell lymphoma in an animal model.
  • FIG. 27A tumor volume reduction.
  • FIG. 27B survival rate.
  • FIG. 27C CAR-T cell expansion in peripheral blood.
  • FIG. 27D PD-1 and LAG-3 levels in CAR T cells.
  • FIG. 27E levels of circulating T cells at three weeks post CAR-T injection.
  • FIG. 27F levels of exhaustion markers (LAG-3 and PD-1) on circulating T cells at three weeks post CAR-T injection.
  • FIG. 28 is a diagram showing disruption of TGFBRII and Reg-1 genes increases proliferation of anti-PTK7 CAR T cells.
  • FIGS. 29A-29D include diagrams showing impact of TGFBRII disruption, optionally in combination with Reg-1 disruption, in long-term in vitro rechallenge assays.
  • FIG. 29A TGFBRII disruption alone improves anti-PTK7 CAR T-cell potency in a long-term in vitro rechallenge assay.
  • FIG. 29B TGFBRII disruption improves anti-PTK7 CAR T-cell persistence and expansion in a long-term in vitro rechallenge assay as measured by humCD45+ cells.
  • FIG. 29C TGFBRII disruption enhances cytotoxic CD8+ T cells expressing the anti-PTK7 CAR.
  • FIG. 29D CD4+ cells expressing the anti-PTK7 CAR remains consistent regardless of TGFBRII disruption.
  • FIGS. 30A-30B include diagrams showing anti-tumor activity of anti-PTK7 CAR T-cells with or without TGFBRII disruption.
  • FIG. 30A effect of treatment on tumor volume.
  • FIG. 30B effect of treatment on body weight.
  • Group 1 no treatment.
  • Group 2 anti-PTK7 CAR-T cells, 5 ⁇ 10 6 cells/mouse (iv) Day 1.
  • UTA chow was administered 9 days prior to CAR-T cell treatment to applicable groups.
  • FIGS. 31A-31B include diagrams showing T cell fractions in a pancreatic cell carcinoma (Hs766T) tumor xenograft animal model treated with anti-PTK7 CAR T cells with or without TGFBRII disruption.
  • FIG. 31A number of humCD45+ cells/ul in murine blood at Day 47 post dose.
  • FIG. 31B CAR-T cell differentiation at Day 47 post dose.
  • the present disclosure aims at establishing genetically engineered T cells having improved growth activity, persistence, reduced T cell exhaustion, and enhanced potency, a long-felt need in CAR-T therapy.
  • a T cell may use bona fide T cells as the starting material, for example, non-transformed T cells, terminally differentiated T cells, T cells having stable genome, and/or T cells that depend on cytokines and growth factors for proliferation and expansion.
  • a T cell may use T cells generated from precursor cells such as hematopoietic stem cells (e.g., iPSCs), e.g., in vitro culture.
  • iPSCs hematopoietic stem cells
  • the T cells disclosed herein may confer one or more benefits in both CAR-T cell manufacturing and clinical applications.
  • CAR T cells are produced wherein a single donor leukopak is edited in most cases so that the cells can avoid components of the patient immune system and thus do not cause GvHD.
  • the process of expanding these CAR T cells can yield 10s to 100s of vialed drug product. Patients may receive a single dose or multiple doses.
  • these CAR T cells lose potential due to various mechanisms, for example, apoptosis, exhaustion, replicative senescence, and other processes where the cells become less fit.
  • the genetically engineered T cells having a disrupted TGFBRII gene, a disrupted Reg1 gene, or a combination thereof, and optionally one or more additional genetic edits, for example, a disrupted TRAC gene, a disrupted ⁇ 2M gene, a disrupted CD70 gene, and/or an inserted nucleic acid coding for a chimeric antigen receptor (CAR), or a combination thereof.
  • a disrupted TRAC gene for example, a disrupted TRAC gene, a disrupted ⁇ 2M gene, a disrupted CD70 gene, and/or an inserted nucleic acid coding for a chimeric antigen receptor (CAR), or a combination thereof.
  • CAR chimeric antigen receptor
  • T cell-mediated cell therapy such as CAR-T therapy.
  • examples include, but are not limited to: improved cell culture growth and in vitro expansion including faster expansion, longer viability, faster proliferation and/or increased resistance to apoptosis, which are beneficial for manufacturing and production of therapeutic T-cell based products such as CAR-T cells; T cell potency advantages related to maintaining therapeutic T cells (e.g., CAR-T cells) in vitro and in vivo potency and activity (target cell killing) for a more effective and persistent T-cell based therapeutic products; production and/or retention of more central memory cells; lower expression of T cell exhaustion markers (such as, PD-1, Tim-3); improved efficacy of T cell therapeutics in vivo, related to decreasing tumor burden and increasing survival of CAR T treated subjects.
  • T cell potency advantages related to maintaining therapeutic T cells (e.g., CAR-T cells) in vitro and in vivo potency and activity (target cell killing) for a more effective and persistent T-cell based therapeutic products
  • T cells having a disrupted TGFBRII gene showed advantageous features, including improved cell growth and expansion, enhanced cytotoxicity activity, resistant to the inhibitory effect mediated by TGF ⁇ , and/or mediated by fibroblasts.
  • the genetically engineered T cells e.g., CAR-T cells
  • having a disrupted TGFBRII gene and optionally other genetic edits as disclosed herein would be expected to exhibit superior therapeutic effects, for example, superior anti-tumor effects, e.g., in TME of a solid tumor.
  • CAR-T cells having both a disrupted Reg1 gene and a disrupted TGFBRII gene showed much higher anti-tumor activities, as well as CAR-T cell expansion in animal models as relative to CAR-T cells having a disrupted Reg1 gene or a disrupted TGFBRII gene.
  • T cells disclosed herein have enhanced proliferation and expansion capacities, they can live longer in vivo. As such, a lower dose relative to standard CAR-T therapy may be used to achieve substantially similar therapeutic effects relative to a high dose of conventional CAR-T cell therapy.
  • T cells having improved persistence in culture methods of producing such T cells, and methods of using such T cells for producing therapeutic T cells such as CAR-T cells.
  • Components and processes e.g., the CRISPR approach for gene editing and components used therein are also within the scope of the present disclosure.
  • the T cells disclosed herein comprises genetically engineered T cells having enhanced persistence in culture.
  • Such genetically engineered T cells may have genetic editing of the Reg1 gene or genetic editing of the TGFBRII gene.
  • such genetically engineered T cells may have genetic editing of both the Reg1 gene and the TGFBRII gene.
  • the genetically engineered T cells may have genetic editing in one or more additional genes involved in T cell exhaustion, such as CD70.
  • additional genes involved in T cell exhaustion such as CD70.
  • such genetically engineered T cells show one or more of the following superior features as relative to the T cell counterparts having a wild-type Regnase 1 gene: enhanced expansion capacity in culture (e.g., expandable in culture for at least 4 weeks, e.g., at least 6 weeks; and/or at least 10-fold expandable, for example, at least 15-fold expandable, relative to the non-edited counterpart), enhanced longevity, enhanced proliferation capacity, greater T cell activation, enhanced potency, enhanced expression of central memory T cell markers, and reduced expression of T cell exhaustion markers.
  • enhanced expansion capacity in culture e.g., expandable in culture for at least 4 weeks, e.g., at least 6 weeks
  • 10-fold expandable for example, at least 15-fold expandable, relative to the non-edited counterpart
  • enhanced longevity enhanced proliferation capacity
  • the genetically engineered T cells may be derived from parent T cells (e.g., non-edited wild-type T cells) obtained from a suitable source, for example, one or more mammal donors.
  • the parent T cells are primary T cells (e.g., non-transformed and terminally differentiated T cells) obtained from one or more human donors.
  • the parent T cells may be differentiated from precursor T cells obtained from one or more suitable donor or stem cells such as hematopoietic stem cells or inducible pluripotent stem cells (iPSC), which may be cultured in vitro.
  • the genetically engineered T cells carry a disrupted Reg1 gene, and optionally, one or more disrupted genes involved in cell exhaustion (e.g., CD70).
  • Such genetically engineered T cells may further comprise one or more disrupted genes, for example, TRAC or ⁇ 2M.
  • Such genetically engineered T cells may further express a chimeric antigen receptor (CAR), which may be capable of binding to an antigen of interest, for example, a tumor associated antigen (e.g., CD19, BCMA, CD70, CD33, or PTK7).
  • CAR chimeric antigen receptor
  • the genetically engineered T cells carry a disrupted TGFBRII gene, and optionally, one or more disrupted genes involved in cell exhaustion (e.g., CD70).
  • Such genetically engineered T cells may further comprise one or more disrupted genes, for example, TRAC or ⁇ 2M.
  • Such genetically engineered T cells may further express a chimeric antigen receptor (CAR), which may be capable of binding to an antigen of interest, for example, a tumor associated antigen (e.g., CD19, BCMA, CD70, CD33, or PTK7).
  • the genetically engineered T cells may express an anti-PTK7 CAR such as those disclosed herein.
  • such genetically engineered T cells may have a wild-type endogenous Reg-1 gene.
  • the genetically engineered T cells carry a disrupted Reg1 gene and a disrupted TGFBRII gene, and optionally, one or more disrupted genes involved in cell exhaustion (e.g., CD70).
  • Such genetically engineered T cells may further comprise one or more disrupted genes, for example, TRAC or ⁇ 2M.
  • Such genetically engineered T cells may further express a chimeric antigen receptor (CAR), which may be capable of binding to an antigen of interest, for example, a tumor associated antigen (e.g., CD19, BCMA, CD70, CD33, or PTK7).
  • CAR chimeric antigen receptor
  • any of the genetically engineered T cells may be generated via gene editing (including genomic editing), a type of genetic engineering in which nucleotide(s)/nucleic acid(s) is/are inserted, deleted, and/or substituted in a DNA sequence, such as in the genome of a targeted cell.
  • Targeted gene editing enables insertion, deletion, and/or substitution at pre-selected sites in the genome of a targeted cell (e.g., in a targeted gene or targeted DNA sequence).
  • a sequence of an endogenous gene is edited, for example by deletion, insertion or substitution of nucleotide(s)/nucleic acid(s)
  • the endogenous gene comprising the affected sequence may be knocked-out due to the sequence alteration.
  • Targeted editing may be used to disrupt endogenous gene expression.
  • “Targeted integration” refers to a process involving insertion of one or more exogenous sequences, with or without deletion of an endogenous sequence at the insertion site. Targeted integration can result from targeted gene editing when a donor template containing an exogenous sequence is present.
  • the present disclosure provides genetically engineered T cells that may comprise a disrupted Reg1 gene, a disrupted TGFBRII gene, or a combination thereof.
  • the genetically engineered T cells provided herein comprise both a disrupted Reg1 gene and a disrupted TGFBRII gene.
  • the genetically engineered T cells disclosed herein may further comprise a disrupted CD70 gene, a disrupted ⁇ 2M gene, a disrupted TRAC gene, or a combination thereof.
  • a “disrupted gene” refers to a gene comprising an insertion, deletion or substitution relative to an endogenous gene such that expression of a functional protein from the endogenous gene is reduced or inhibited.
  • “disrupting a gene” refers to a method of inserting, deleting or substituting at least one nucleotide/nucleic acid in an endogenous gene such that expression of a functional protein from the endogenous gene is reduced or inhibited. Methods of disrupting a gene are known to those of skill in the art and described herein.
  • a cell that comprises a disrupted gene does not express (e.g., at the cell surface) a detectable level (e.g., in an immune assay using an antibody binding to the encoded protein or by flow cytometry) of the protein encoded by the gene.
  • a detectable level e.g., in an immune assay using an antibody binding to the encoded protein or by flow cytometry
  • a cell that does not express a detectable level of the protein may be referred to as a knockout cell.
  • the genetically engineered T cells may comprise a disrupted gene involved in mRNA decay.
  • a gene may be Reg1.
  • Reg1 contains a zinc finger motif, binds RNA and exhibits ribonuclease activity. Reg1 plays roles in both immune and non-immune cells and its expression can be rapidly induced under diverse conditions including microbial infections, treatment with inflammatory cytokines and chemical or mechanical stimulation.
  • Human Reg1 gene is located on chromosome 1p34.3. Additional information can be found in GenBank under Gene ID: 80149.
  • the genetically engineered T cells may comprise a disrupted Reg1 gene such that the expression of Reg1 in the T cells is substantially reduced or eliminated completely.
  • the disrupted Reg1 gene may comprise one or more genetic edits at one or more suitable target sites (e.g., in coding regions or in non-coding regulatory regions such as promoter regions) that disrupt expression of the Reg1 gene.
  • target sites may be identified based on the gene editing approach for use in making the genetically engineered T cells.
  • Exemplary target sites for the genetic edits may include exon 1, exon 2, exon 3, exon 4, exon 5, exon 6, or a combination thereof.
  • one or more genetic editing may occur in exon 2 or exon 4.
  • Such genetic editing may be induced by the CRISPR/Cas technology using a suitable guide RNA, for example, those listed in Table 22.
  • a suitable guide RNA for example, those listed in Table 22.
  • the resultant edited Reg1 gene using a gRNA listed in Table 22 may comprise one or more edited sequences provided in Tables 29-38 below.
  • the genetically engineered T cells may comprise a disrupted TGFBRII gene, which encodes Transforming Growth Factor Receptor Type II (TGFBRII).
  • TGFBRII receptors are a family of serine/threonine kinase receptors involved in the TGF ⁇ signaling pathway. These receptors bind growth factor and cytokine signaling proteins in the TGF ⁇ family, for example, TGF ⁇ s (TGF ⁇ 1, TGF ⁇ 2, and TGF ⁇ 3), bone morphogenetic proteins (BMPs), growth differentiation factors (GDFs), activin and inhibin, myostatin, anti-Müllerian hormone (AMH), and NODAL.
  • TGF ⁇ s TGF ⁇ 1, TGF ⁇ 2, and TGF ⁇ 3
  • BMPs bone morphogenetic proteins
  • GDFs growth differentiation factors
  • AH anti-Müllerian hormone
  • NODAL NODAL
  • the genetically engineered T cells may comprise a disrupted TGFBRII gene such that the expression of TGFBRII in the T cells is substantially reduced or eliminated completely.
  • the disrupted TGFBRII gene may comprise one or more genetic edits at one or more suitable target sites (e.g., in coding regions or in non-coding regulatory regions such as promoter regions) that disrupt expression of the TGFBRII gene.
  • suitable target sites e.g., in coding regions or in non-coding regulatory regions such as promoter regions
  • target sites may be identified based on the gene editing approach for use in making the genetically engineered T cells.
  • Exemplary target sites for the genetic edits may include exon 1, exon 2, exon 3, exon 4, exon 5, or a combination thereof.
  • one or more genetic editing may occur in exon 4 and/or exon 5.
  • Such genetic editing may be induced by a gene editing technology, (e.g., the CRISPR/Cas technology) using a suitable guide RNA, for example, those listed in Table 39.
  • a gene editing technology e.g., the CRISPR/Cas technology
  • a suitable guide RNA for example, those listed in Table 39.
  • the resultant edited TGFBRII gene using a gRNA listed in Table 39 may comprise one or more edited sequences provided in Tables 40-48 below.
  • T cell exhaustion is a process of stepwise and progressive loss of T cell functions, which may be induced by prolonged antigen stimulation or other factors.
  • Genes involved in T cell exhaustion refer to those that either positively regulate or negatively regulate this biological process.
  • the genetically engineered T cells disclosed herein may comprise genetic editing of a gene that positively regulates T cell exhaustion to disrupt its expression.
  • the genetically engineered T cells may comprise genetic editing of a gene that negatively regulates T cell exhaustion to enhance its expression and/or biologic activity of the gene product.
  • the genetically engineered T cells may comprise an edited gene involved in T cell exhaustion, e.g., disruption of a gene that positively regulates T cell exhaustion.
  • a gene may be a Cluster of Differentiation 70 (CD70) gene.
  • CD70 is a member of the tumor necrosis factor superfamily and its expression is restricted to activated T and B lymphocytes and mature dendritic cells.
  • CD70 is implicated in tumor cell and regulatory T cell survival through interaction with its ligand, CD27.
  • CD70 and its receptor CD27 have multiple roles in immune function in multiple cell types including T cells (activated and T reg cells), and B cells.
  • disrupting the CD70 gene in immune cells engineered to express an antigen targeting moiety enhanced anti-tumor efficacy against large tumors and induced a durable anti-cancer memory response. Specifically, the anti-cancer memory response prevented tumor growth upon re-challenge. Further, it has been demonstrated disrupting the CD70 gene results in enhanced cytotoxicity of immune cells engineered to express an antigen targeting moiety at lower ratios of engineered immune cells to target cells, indicating the potential efficacy of low doses of engineered immune cells. See, e.g., WO2019/215500, the relevant disclosures of which are incorporated by reference for the purpose and subject matter referenced herein.
  • CD70 genes Structures of CD70 genes are known in the art. For example, human CD70 gene is located on chromosome 19p13.3. The gene contains four protein encoding exons. Additional information can be found in GenBank under Gene ID: 970.
  • the genetically engineered T cells may comprise a disrupted CD70 gene such that the expression of CD70 in the T cells is substantially reduced or eliminated completely.
  • the disrupted CD70 gene may comprise one or more genetic edits at one or more suitable target sites (e.g., in coding regions or in non-coding regulatory regions such as promoter regions) that disrupt expression of the CD70 gene.
  • suitable target sites e.g., in coding regions or in non-coding regulatory regions such as promoter regions
  • target sites may be identified based on the gene editing approach for use in making the genetically engineered T cells.
  • Exemplary target sites for the genetic edits may include exon 1, exon 2, exon 3, exon 4, or a combination thereof. See also WO2019/215500, the relevant disclosures of which are incorporated by reference for the purpose and subject matter referenced herein.
  • the gRNA targeting CD70 listed in Table 23 may be used for disrupting the CD70 gene via CRISPR/Cas9 gene editing.
  • an edited CD70 gene may comprise a nucleotide sequence selected from the following sequences in Table 26.
  • the genetically engineered T cells disclosed herein may further comprise a disrupted ⁇ 2M gene.
  • ⁇ 2M is a common (invariant) component of MHC I complexes. Disrupting its expression by gene editing will prevent host versus therapeutic allogeneic T cells responses leading to increased allogeneic T cell persistence. In some embodiments, expression of the endogenous ⁇ 2M gene is eliminated to prevent a host-versus-graft response.
  • an edited ⁇ 2M gene may comprise a nucleotide sequence selected from the following sequences in Table 25. It is known to those skilled in the art that different nucleotide sequences in an edited gene such as an edited ⁇ 2M gene (e.g., those in Table 25) may be generated by a single gRNA such as the one listed in Table 23 ( ⁇ 2M-1). See also WO2019097305, the relevant disclosures of which are incorporated by reference for the subject matter and purpose referenced herein.
  • the genetically engineered T cells disclosed herein may further comprise one or more additional gene edits (e.g., gene knock-in or knock-out) to improve T cell function.
  • additional gene edits e.g., gene knock-in or knock-out
  • knock-in or knock-out genes to improve target cell lysis
  • knock-in or knock-out genes to enhance performance of therapeutic T cells such as CAR-T cells prepared from the genetically engineered T cells.
  • the genetically engineered T cells as disclosed herein may further comprise a disrupted TRAC gene.
  • This disruption leads to loss of function of the TCR and renders the engineered T cell non-alloreactive and suitable for allogeneic transplantation, minimizing the risk of graft versus host disease.
  • expression of the endogenous TRAC gene is eliminated to prevent a graft-versus-host response. See also WO2019097305, the relevant disclosures of which are incorporated by reference herein for the purpose and subject matter referenced herein.
  • an edited TRAC gene may comprise a nucleotide sequence selected from the following sequences in Table 24. It is known to those skilled in the art that different nucleotide sequences in an edited gene such as an edited TRAC gene (e.g., those in Table 24) may be generated by a single gRNA such as the one listed in Table 23 (TA-1). It should be understood that more than one suitable target site/gRNA can be used for each target gene disclosed herein, for example, those known in the art or disclosed herein. Additional examples can be found in, e.g., WO2019097305, the relevant disclosures of which are incorporated by reference herein for the purpose and subject matter referenced herein.
  • any of the genetically engineered T cell having a disrupted Reg1 gene, and optionally one or more additional genetic edits may be expandable in culture for greater than 4 weeks, for example, greater than 5 weeks, greater than 6 weeks, greater than 8 weeks, and greater than 10 weeks.
  • the genetically engineered T cells comprise a disrupted Reg1 (optionally, disruptions in CD70) and are expandable after 6 weeks (e.g., after 7 weeks, after 8 weeks, after 9 weeks, or after 10 weeks) in culture.
  • Such genetically engineered T cells may maintain the ability to be activated after 6 weeks (e.g., after 7 weeks, after 8 weeks, after 9 weeks, or after 10 weeks) in culture. Further, such genetically engineered T cells have an increased expansion capacity, which can be at least 10-fold (e.g., at least 15-fold) higher than the non-engineered counterparts, i.e., T cells having the same genetic background as the engineered T cells disclosed herein except that the counterpart T cells have a wild-type Reg1 gene.
  • T cell persistence refers to the tendency of T cells to continue to grow, proliferate, self-renew, expand, and maintain healthy activity in culture.
  • T cell persistence can be represented by the longevity that T cells can grow and expand in vitro, which can be measured by conventional methods and/or assays described herein.
  • T cell persistence can be represented by the reduction of cell death (e.g., apoptosis) or reduction in cell states characterized by exhaustion or replicative senescence.
  • T cell persistence can be presented by the maintenance of T cell activation capacity in culture.
  • the genetically engineered T cells disclosed may grow faster and longer than the non-engineered T cells, for example, as observed in vitro cell culture.
  • the genetically engineered T cells may grow at least 50% (e.g., at least 1-fold, at least 2-fold, at least 5-fold, or more) than the non-engineered T cells in a conventional in vitro T cell culture (e.g., as described in Examples below).
  • the genetically engineered T cells may maintain a high growth rate (e.g., having substantially the same growth rate or with only a slight reduction) in vitro for at least 20 days (e.g., at least 25 days, at least 30 days, at least 35 days, at least 40 days, at least 45 days, at least 50 days, or longer).
  • a high growth rate e.g., having substantially the same growth rate or with only a slight reduction
  • at least 20 days e.g., at least 25 days, at least 30 days, at least 35 days, at least 40 days, at least 45 days, at least 50 days, or longer.
  • the genetically engineered T cells may exhibit a reduced level of cell exhaustion as relative to the non-engineered T cell counterpart. In some instances, a reduced level of cell exhaustion is reflected by a higher level of central memory T cells in the whole T cell population.
  • the population of genetically engineered T cells disclosed may comprise a higher number of central memory T cells as compared to non-engineered T cell counterparts. For example, in some instances the population of genetically engineered T cells include a higher number of central memory T cells that are characterized by enhanced expression of CD27 and/or CD45RO as compared to non-engineered T cell counterparts. In some instances, the population of genetically engineered T cells disclosed exhibit reduced T cell exhaustion, which is characterized, for example, by reduced expression of PD-1 and/or TIM3 as compared to non-engineered T cell counterparts.
  • any of the genetically engineered T cell having a disrupted TGFBRII gene, and optionally one or more additional genetic edits may have improved growth and expansion activities, both in vitro and in vivo, as compared with the non-engineered counterpart, which refers to T cells having the same genetic background except for an undisrupted TGFBRII gene.
  • such genetically engineered T cells may exhibit enhanced cytotoxicity activity, for example, against undesired cells (e.g., tumor cells) expressing an antigen targeted by the CAR expressed in the CAR-T cells, as compared with the non-engineered counterpart.
  • Such genetically engineered T cells e.g., CAR-T cells
  • the genetically engineered T cells with a disrupted TGFBRII gene may be resistant to inhibitory factors secreted by fibroblasts.
  • the genetically engineered T cells may further comprise one or more disrupted genes (e.g., CD70, Reg1, or a combination thereof) to improve T cell persistency.
  • T cell persistence refers to the tendency of T cells to continue to grow, proliferate, self-renew, expand, and maintain healthy activity in culture. In some instances, T cell persistence can be represented by the longevity that T cells can grow and expand in vitro, which can be measured by conventional methods and/or assays described herein. In other instances, T cell persistence can be represented by the reduction of cell death (e.g., apoptosis) or reduction in cell states characterized by exhaustion or replicative senescence. In yet other instances, T cell persistence can be presented by the maintenance of T cell activation capacity in culture.
  • such genetically engineered T cells may be expandable in culture for greater than 4 weeks, for example, greater than 5 weeks, greater than 6 weeks, greater than 8 weeks, and greater than 10 weeks.
  • the genetically engineered T cells comprise a disrupted TGFBRII gene, and a disrupted CD70 gene, Reg1 gene, or both may be expandable after 6 weeks (e.g., after 7 weeks, after 8 weeks, after 9 weeks, or after 10 weeks) in culture.
  • Such genetically engineered T cells may maintain the ability to be activated after 6 weeks (e.g., after 7 weeks, after 8 weeks, after 9 weeks, or after 10 weeks) in culture.
  • Such genetically engineered T cells may exhibit more improved growth and expansion capacity relative to the T cells having the same genetic background except for an undisrupted TGFBRII gene, and an undisrupted CD70 gene and/or Reg1 gene.
  • any of the genetically engineered T cell having a disrupted TGFBRII gene and a disrupted Reg1 gene, and optionally one or more additional genetic edits may have expansion advantage (e.g., in vivo) over counterpart T cells, i.e., having the disrupted TGFBRII gene or the disrupted Reg1 gene (but not both), as well as the other additional genetic edits.
  • CAR-T cells having disruptions of both the TGFBRII gene and the Reg1 gene were found to be more potent in cancer treatment than the counterpart T cells as observed in xenograft mouse models. Accordingly, CAR-T cells having disruptions of both the TGFBRII gene and the Reg1 gene would be expected to show superior cancer treatment efficacy.
  • the genetically engineered T cells disclosed herein can be prepared by genetic editing of parent T cells or precursor cells thereof via a conventional gene editing method or those described herein.
  • T cells can be derived from one or more suitable mammals, for example, one or more human donors.
  • T cells can be obtained from a number of sources, including, but not limited to, peripheral blood mononuclear cells, bone marrow, lymph nodes tissue, cord blood, thymus issue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors.
  • T cells can be obtained from a unit of blood collected from a subject using any number of techniques known to the skilled person, such as sedimentation, e.g., FICOLLTM separation.
  • T cells can be isolated from a mixture of immune cells (e.g., those described herein) to produce an isolated T cell population.
  • immune cells e.g., those described herein
  • cytotoxic and helper T lymphocytes can be sorted into naive, memory, and effector T cell subpopulations either before or after activation, expansion, and/or genetic modification.
  • a specific subpopulation of T cells expressing one or more of the following cell surface markers: TCRab, CD3, CD4, CD8, CD27 CD28, CD38 CD45RA, CD45RO, CD62L, CD127, CD122, CD95, CD197, CCR7, KLRG1, MCH-I proteins and/or MCH-II proteins, can be further isolated by positive or negative selection techniques.
  • a specific subpopulation of T cells, expressing one or more of the markers selected from the group consisting of TCRab, CD4 and/or CD8, is further isolated by positive or negative selection techniques.
  • subpopulations of T cells may be isolated by positive or negative selection prior to genetic engineering and/or post genetic engineering.
  • An isolated population of T cells may express one or more of the T cell markers, including, but not limited to a CD3+, CD4+, CD8+, or a combination thereof.
  • the T cells are isolated from a donor, or subject, and first activated and stimulated to proliferate in vitro prior to undergoing gene editing.
  • the T cell population comprises primary T cells isolated from one or more human donors.
  • T cells are terminally differentiated, not transformed, depend on cytokines and/or growth factors for growth, and/or have stable genomes.
  • the T cells may be derived from stem cells (e.g., HSCs or iPSCs) via in vitro differentiation.
  • stem cells e.g., HSCs or iPSCs
  • T cells from a suitable source can be subjected to one or more rounds of stimulation, activation and/or expansion.
  • T cells can be activated and expanded generally using methods as described, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681; 7,144,575; 7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223; 6,905,874; 6,797,514; and 6,867,041.
  • T cells can be activated and expanded for about 1 day to about 4 days, about 1 day to about 3 days, about 1 day to about 2 days, about 2 days to about 3 days, about 2 days to about 4 days, about 3 days to about 4 days, or about 1 day, about 2 days, about 3 days, or about 4 days prior to introduction of the genome editing compositions into the T cells.
  • T cells are activated and expanded for about 4 hours, about 6 hours, about 12 hours, about 18 hours, about 24 hours, about 36 hours, about 48 hours, about 60 hours, or about 72 hours prior to introduction of the gene editing compositions into the T cells.
  • T cells are activated at the same time that genome editing compositions are introduced into the T cells.
  • the T cell population can be expanded and/or activated after the genetic editing as disclosed herein. T cell populations or isolated T cells generated by any of the gene editing methods described herein are also within the scope of the present disclosure.
  • any of the genetically engineered T cells can be prepared using conventional gene editing methods or those described herein to edit one or more of the target genes disclosed herein (targeted editing).
  • Targeted editing can be achieved either through a nuclease-independent approach, or through a nuclease-dependent approach.
  • nuclease-independent targeted editing approach homologous recombination is guided by homologous sequences flanking an exogenous polynucleotide to be introduced into an endogenous sequence through the enzymatic machinery of the host cell.
  • the exogenous polynucleotide may introduce deletions, insertions or replacement of nucleotides in the endogenous sequence.
  • nuclease-dependent approach can achieve targeted editing with higher frequency through the specific introduction of double strand breaks (DSBs) by specific rare-cutting nucleases (e.g., endonucleases).
  • DSBs double strand breaks
  • nuclease-dependent targeted editing also utilizes DNA repair mechanisms, for example, non-homologous end joining (NHEJ), which occurs in response to DSBs.
  • NHEJ non-homologous end joining
  • DNA repair by NHEJ often leads to random insertions or deletions (indels) of a small number of endogenous nucleotides.
  • repair can also occur by a homology directed repair (HDR).
  • HDR homology directed repair
  • gene disruption may occur by deletion of a genomic sequence using two guide RNAs.
  • Methods of using CRISPR-Cas gene editing technology to create a genomic deletion in a cell are known (Bauer D E et al. Vis. Exp. 2015; 95:e52118).
  • Available endonucleases capable of introducing specific and targeted DSBs include, but not limited to, zinc-finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN), and RNA-guided CRISPR-Cas9 nuclease (CRISPR/Cas9; Clustered Regular Interspaced Short Palindromic Repeats Associated 9). Additionally, DICE (dual integrase cassette exchange) system utilizing phiC31 and Bxb1 integrases may also be used for targeted integration. Some exemplary approaches are disclosed in detail below.
  • the CRISPR-Cas9 system is a naturally-occurring defense mechanism in prokaryotes that has been repurposed as an RNA-guided DNA-targeting platform used for gene editing. It relies on the DNA nuclease Cas9, and two noncoding RNAs, crisprRNA (crRNA) and trans-activating RNA (tracrRNA), to target the cleavage of DNA.
  • CRISPR is an abbreviation for Clustered Regularly Interspaced Short Palindromic Repeats, a family of DNA sequences found in the genomes of bacteria and archaea that contain fragments of DNA (spacer DNA) with similarity to foreign DNA previously exposed to the cell, for example, by viruses that have infected or attacked the prokaryote.
  • CRISPR CRISPR-associated proteins
  • RNA molecules comprising the spacer sequence, which associates with and targets Cas (CRISPR-associated) proteins able to recognize and cut the foreign, exogenous DNA.
  • Cas CRISPR-associated proteins
  • Numerous types and classes of CRISPR/Cas systems have been described (see, e.g., Koonin et al., (2017) Curr Opin Microbiol 37:67-78).
  • crRNA drives sequence recognition and specificity of the CRISPR-Cas9 complex through Watson-Crick base pairing typically with a 20 nucleotide (nt) sequence in the target DNA. Changing the sequence of the 5′ 20 nt in the crRNA allows targeting of the CRISPR-Cas9 complex to specific loci.
  • the CRISPR-Cas9 complex only binds DNA sequences that contain a sequence match to the first 20 nt of the crRNA, if the target sequence is followed by a specific short DNA motif (with the sequence NGG) referred to as a protospacer adjacent motif (PAM).
  • PAM protospacer adjacent motif
  • tracrRNA hybridizes with the 3′ end of crRNA to form an RNA-duplex structure that is bound by the Cas9 endonuclease to form the catalytically active CRISPR-Cas9 complex, which can then cleave the target DNA.
  • NHEJ non-homologous end joining
  • HDR homology-directed repair
  • NHEJ is a robust repair mechanism that appears highly active in the majority of cell types, including non-dividing cells. NHEJ is error-prone and can often result in the removal or addition of between one and several hundred nucleotides at the site of the DSB, though such modifications are typically ⁇ 20 nt. The resulting insertions and deletions (indels) can disrupt coding or noncoding regions of genes.
  • HDR uses a long stretch of homologous donor DNA, provided endogenously or exogenously, to repair the DSB with high fidelity. HDR is active only in dividing cells, and occurs at a relatively low frequency in most cell types. In many embodiments of the present disclosure, NHEJ is utilized as the repair operant.
  • the Cas9 (CRISPR associated protein 9) endonuclease is used in a CRISPR method for making the genetically engineered T cells as disclosed herein.
  • the Cas9 enzyme may be one from Streptococcus pyogenes , although other Cas9 homologs may also be used. It should be understood, that wild-type Cas9 may be used or modified versions of Cas9 may be used (e.g., evolved versions of Cas9, or Cas9 orthologues or variants), as provided herein.
  • Cas9 may be substituted with another RNA-guided endonuclease, such as Cpf1 (of a class II CRISPR/Cas system).
  • the CRISPR/Cas system comprises components derived from a Type-I, Type-II, or Type-III system.
  • Updated classification schemes for CRISPR/Cas loci define Class 1 and Class 2 CRISPR/Cas systems, having Types I to V or VI (Makarova et al., (2015) Nat Rev Microbiol, 13(11):722-36; Shmakov et al., (2015) Mol Cell, 60:385-397).
  • Class 2 CRISPR/Cas systems have single protein effectors.
  • Cas proteins of Types II, V, and VI are single-protein, RNA-guided endonucleases, herein called “Class 2 Cas nucleases.”
  • Class 2 Cas nucleases include, for example, Cas9, Cpf1, C2c1, C2c2, and C2c3 proteins.
  • the Cpf1 nuclease (Zetsche et al., (2015) Cell 163:1-13) is homologous to Cas9, and contains a RuvC-like nuclease domain.
  • the Cas nuclease is from a Type-II CRISPR/Cas system (e.g., a Cas9 protein from a CRISPR/Cas9 system).
  • the Cas nuclease is from a Class 2 CRISPR/Cas system (a single-protein Cas nuclease such as a Cas9 protein or a Cpf1 protein).
  • the Cas9 and Cpf1 family of proteins are enzymes with DNA endonuclease activity, and they can be directed to cleave a desired nucleic acid target by designing an appropriate guide RNA, as described further herein.
  • a Cas nuclease may comprise more than one nuclease domain.
  • a Cas9 nuclease may comprise at least one RuvC-like nuclease domain (e.g., Cpf1) and at least one HNH-like nuclease domain (e.g., Cas9).
  • the Cas9 nuclease introduces a DSB in the target sequence.
  • the Cas9 nuclease is modified to contain only one functional nuclease domain.
  • the Cas9 nuclease is modified such that one of the nuclease domains is mutated or fully or partially deleted to reduce its nucleic acid cleavage activity.
  • the Cas9 nuclease is modified to contain no functional RuvC-like nuclease domain. In other embodiments, the Cas9 nuclease is modified to contain no functional HNH-like nuclease domain. In some embodiments in which only one of the nuclease domains is functional, the Cas9 nuclease is a nickase that is capable of introducing a single-stranded break (a “nick”) into the target sequence. In some embodiments, a conserved amino acid within a Cas9 nuclease domain is substituted to reduce or alter a nuclease activity.
  • the Cas nuclease nickase comprises an amino acid substitution in the RuvC-like nuclease domain.
  • Exemplary amino acid substitutions in the RuvC-like nuclease domain include D10A (based on the S. pyogenes Cas9 nuclease).
  • the nickase comprises an amino acid substitution in the HNH-like nuclease domain.
  • Exemplary amino acid substitutions in the HNH-like nuclease domain include E762A, H840A, N863A, H983A, and D986A (based on the S. pyogenes Cas9 nuclease).
  • Cas9 nuclease (SEQ ID NO: 1): MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGA LLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHR LEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKAD LRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENP INASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTP NFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAI LLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEI FFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKL
  • the Cas nuclease is from a Type-I CRISPR/Cas system. In some embodiments, the Cas nuclease is a component of the Cascade complex of a Type-I CRISPR/Cas system. For example, the Cas nuclease is a Cas3 nuclease. In some embodiments, the Cas nuclease is derived from a Type-III CRISPR/Cas system. In some embodiments, the Cas nuclease is derived from Type-IV CRISPR/Cas system. In some embodiments, the Cas nuclease is derived from a Type-V CRISPR/Cas system. In some embodiments, the Cas nuclease is derived from a Type-VI CRISPR/Cas system.
  • gRNAs Guide RNAs
  • the CRISPR technology involves the use of a genome-targeting nucleic acid that can direct the endonuclease to a specific target sequence within a target gene for gene editing at the specific target sequence.
  • the genome-targeting nucleic acid can be a RNA.
  • a genome-targeting RNA is referred to as a “guide RNA” or “gRNA” herein.
  • a guide RNA comprises at least a spacer sequence that hybridizes to a target nucleic acid sequence within a target gene for editing, and a CRISPR repeat sequence.
  • the gRNA also comprises a second RNA called the tracrRNA sequence.
  • the CRISPR repeat sequence and tracrRNA sequence hybridize to each other to form a duplex.
  • the crRNA forms a duplex.
  • the duplex binds a site-directed polypeptide, such that the guide RNA and site-direct polypeptide form a complex.
  • the genome-targeting nucleic acid provides target specificity to the complex by virtue of its association with the site-directed polypeptide. The genome-targeting nucleic acid thus directs the activity of the site-directed polypeptide.
  • each guide RNA is designed to include a spacer sequence complementary to its genomic target sequence. See Jinek et al., Science, 337, 816-821 (2012) and Deltcheva et al., Nature, 471, 602-607 (2011).
  • the genome-targeting nucleic acid (e.g., gRNA) is a double-molecule guide RNA. In some embodiments, the genome-targeting nucleic acid (e.g., gRNA) is a single-molecule guide RNA.
  • a double-molecule guide RNA comprises two strands of RNA molecules.
  • the first strand comprises in the 5′ to 3′ direction, an optional spacer extension sequence, a spacer sequence and a minimum CRISPR repeat sequence.
  • the second strand comprises a minimum tracrRNA sequence (complementary to the minimum CRISPR repeat sequence), a 3′ tracrRNA sequence and an optional tracrRNA extension sequence.
  • a single-molecule guide RNA (referred to as a “sgRNA”) in a Type II system comprises, in the 5′ to 3′ direction, an optional spacer extension sequence, a spacer sequence, a minimum CRISPR repeat sequence, a single-molecule guide linker, a minimum tracrRNA sequence, a 3′ tracrRNA sequence and an optional tracrRNA extension sequence.
  • the optional tracrRNA extension may comprise elements that contribute additional functionality (e.g., stability) to the guide RNA.
  • the single-molecule guide linker links the minimum CRISPR repeat and the minimum tracrRNA sequence to form a hairpin structure.
  • the optional tracrRNA extension comprises one or more hairpins.
  • a single-molecule guide RNA in a Type V system comprises, in the 5′ to 3′ direction, a minimum CRISPR repeat sequence and a spacer sequence.
  • a spacer sequence in a gRNA is a sequence (e.g., a 20 nucleotide sequence) that defines the target sequence (e.g., a DNA target sequences, such as a genomic target sequence) of a target gene of interest.
  • the spacer sequence range from 15 to 30 nucleotides.
  • the spacer sequence may contain 15, 16, 17, 18, 19, 29, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides.
  • a spacer sequence contains 20 nucleotides.
  • the “target sequence” is in a target gene that is adjacent to a PAM sequence and is the sequence to be modified by an RNA-guided nuclease (e.g., Cas9).
  • the “target sequence” is on the so-called PAM-strand in a “target nucleic acid,” which is a double-stranded molecule containing the PAM-strand and a complementary non-PAM strand.
  • target nucleic acid which is a double-stranded molecule containing the PAM-strand and a complementary non-PAM strand.
  • the gRNA spacer sequence hybridizes to the complementary sequence located in the non-PAM strand of the target nucleic acid of interest.
  • the gRNA spacer sequence is the RNA equivalent of the target sequence.
  • the gRNA spacer sequence is 5′-AGAGCAACAGUGCUGUGGCC**-3′ (SEQ ID NO: 61).
  • the spacer of a gRNA interacts with a target nucleic acid of interest in a sequence-specific manner via hybridization (i.e., base pairing).
  • the nucleotide sequence of the spacer thus varies depending on the target sequence of the target nucleic acid of interest.
  • the spacer sequence is designed to hybridize to a region of the target nucleic acid that is located 5′ of a PAM recognizable by a Cas9 enzyme used in the system.
  • the spacer may perfectly match the target sequence or may have mismatches.
  • Each Cas9 enzyme has a particular PAM sequence that it recognizes in a target DNA.
  • S. pyogenes recognizes in a target nucleic acid a PAM that comprises the sequence 5′-NRG-3′, where R comprises either A or G, where N is any nucleotide and N is immediately 3′ of the target nucleic acid sequence targeted by the spacer sequence.
  • the target nucleic acid sequence has 20 nucleotides in length. In some embodiments, the target nucleic acid has less than 20 nucleotides in length. In some embodiments, the target nucleic acid has more than 20 nucleotides in length. In some embodiments, the target nucleic acid has at least: 5, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30 or more nucleotides in length. In some embodiments, the target nucleic acid has at most: 5, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30 or more nucleotides in length. In some embodiments, the target nucleic acid sequence has 20 bases immediately 5′ of the first nucleotide of the PAM.
  • the target nucleic acid in a sequence comprising 5′-NNNNNNNNNNNNNNNNNNNN NRG -3′, can be the sequence that corresponds to the Ns, wherein N can be any nucleotide, and the underlined NRG sequence is the S. pyogenes PAM.
  • the guide RNA disclosed herein may target any sequence of interest via the spacer sequence in the crRNA.
  • the degree of complementarity between the spacer sequence of the guide RNA and the target sequence in the target gene can be about 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100%.
  • the spacer sequence of the guide RNA and the target sequence in the target gene is 100% complementary.
  • the spacer sequence of the guide RNA and the target sequence in the target gene may contain up to 10 mismatches, e.g., up to 9, up to 8, up to 7, up to 6, up to 5, up to 4, up to 3, up to 2, or up to 1 mismatch.
  • the length of the spacer sequence in any of the gRNAs disclosed herein may depend on the CRISPR/Cas9 system and components used for editing any of the target genes also disclosed herein.
  • the spacer sequence may have 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, or more than 50 nucleotides in length.
  • the spacer sequence may have 18-24 nucleotides in length.
  • the targeting sequence may have 19-21 nucleotides in length.
  • the spacer sequence may comprise 20 nucleotides in length.
  • the gRNA can be an sgRNA, which may comprise a 20 nucleotide spacer sequence at the 5′ end of the sgRNA sequence. In some embodiments, the sgRNA may comprise a less than 20 nucleotide spacer sequence at the 5′ end of the sgRNA sequence. In some embodiments, the sgRNA may comprise a more than 20 nucleotide spacer sequence at the 5′ end of the sgRNA sequence. In some embodiments, the sgRNA comprises a variable length spacer sequence with 17-30 nucleotides at the 5′ end of the sgRNA sequence. Examples are provided in Table 23 below. In these exemplary sequences, the fragment of “n” refers to the spacer sequence at the 5′ end.
  • the sgRNA comprises comprise no uracil at the 3′ end of the sgRNA sequence.
  • the sgRNA may comprise one or more uracil at the 3′ end of the sgRNA sequence.
  • the sgRNA can comprise 1-8 uracil residues, at the 3′ end of the sgRNA sequence, e.g., 1, 2, 3, 4, 5, 6, 7, or 8 uracil residues at the 3′ end of the sgRNA sequence.
  • any of the gRNAs disclosed herein, including any of the sgRNAs, may be unmodified. Alternatively, it may contain one or more modified nucleotides and/or modified backbones.
  • a modified gRNA such as an sgRNA can comprise one or more 2′-O-methyl phosphorothioate nucleotides, which may be located at either the 5′ end, the 3′ end, or both.
  • more than one guide RNAs can be used with a CRISPR/Cas nuclease system.
  • Each guide RNA may contain a different targeting sequence, such that the CRISPR/Cas system cleaves more than one target nucleic acid.
  • one or more guide RNAs may have the same or differing properties such as activity or stability within the Cas9 RNP complex.
  • each guide RNA can be encoded on the same or on different vectors. The promoters used to drive expression of the more than one guide RNA is the same or different.
  • the gRNAs disclosed herein target a Reg1 gene, for example, target a site within exon 1, exon 2, exon 3, exon 4, exon 5, or exon 6 of the Reg1 gene.
  • a gRNA may comprise a spacer sequence complementary (complete or partially) to the target sequences in exon 2 or exon 4 of a Reg1 gene, or a fragment thereof.
  • Exemplary target sequences of Reg1 and exemplary gRNA sequences are provided in Table 22 below.
  • the gRNAs disclosed herein target a TGFBRII gene, for example, target a site within exon 1, exon 2, exon 3, exon 4, exon 5, or exon 6 of the TGFBRII gene.
  • a gRNA may comprise a spacer sequence complementary (complete or partially) to the target sequences in exon 4 or exon 5 of a TGFBRII gene, or a fragment thereof.
  • Exemplary target sequences of TGFBRII and exemplary gRNA sequences are provided in Table 39 below.
  • the gRNAs disclosed herein target a CD70 gene, for example, target a site within exon 1 or exon 3 of a CD70 gene.
  • a gRNA may comprise a spacer sequence complementary (complete or partially) to the target sequences in exon 1 or exon 3 of a CD70 gene, or a fragment thereof.
  • Exemplary target sequences in a CD70 gene and exemplary gRNAs specific to the CD70 gene are provided in Table 23 below.
  • the gRNAs disclosed herein target a ⁇ 2M gene, for example, target a suitable site within a ⁇ 2M gene. See also WO2019097305, the relevant disclosures of which are incorporated by reference herein for the purpose and subject matter referenced herein.
  • Other gRNA sequences may be designed using the ⁇ 2M gene sequence located on Chromosome 15 (GRCh38 coordinates: Chromosome 15: 44, 711, 477-44, 718, 877; Ensembl: ENSG00000166710).
  • gRNAs targeting the ⁇ 2M genomic region and RNA-guided nuclease create breaks in the ⁇ 2M genomic region resulting in Indels in the ⁇ 2M gene disrupting expression of the mRNA or protein.
  • the gRNAs disclosed herein target a TRAC gene. See also WO2019097305, the relevant disclosures of which are incorporated by reference herein for the subject matter and purpose referenced herein.
  • Other gRNA sequences may be designed using the TRAC gene sequence located on chromosome 14 (GRCh38: chromosome 14: 22, 547, 506-22, 552, 154; Ensembl; ENSG00000277734).
  • gRNAs targeting the TRAC genomic region and RNA-guided nuclease create breaks in the TRAC genomic region resulting Indels in the TRAC gene disrupting expression of the mRNA or protein.
  • spacer sequences and gRNAs targeting a ⁇ 2M gene or TRAC gene are provided in Table 23 below.
  • guide RNAs used in the CRISPR/Cas/Cpf1 system can be readily synthesized by chemical means, as illustrated below and described in the art. While chemical synthetic procedures are continually expanding, purifications of such RNAs by procedures such as high performance liquid chromatography (HPLC, which avoids the use of gels such as PAGE) tends to become more challenging as polynucleotide lengths increase significantly beyond a hundred or so nucleotides.
  • HPLC high performance liquid chromatography
  • One approach used for generating RNAs of greater length is to produce two or more molecules that are ligated together. Much longer RNAs, such as those encoding a Cas9 or Cpf1 endonuclease, are more readily generated enzymatically.
  • RNA modifications can be introduced during or after chemical synthesis and/or enzymatic generation of RNAs, e.g., modifications that enhance stability, reduce the likelihood or degree of innate immune response, and/or enhance other attributes, as described in the art.
  • the gRNAs of the present disclosure can be are produced in vitro transcription (IVT), synthetic and/or chemical synthesis methods, or a combination thereof. Enzymatic (IVT), solid-phase, liquid-phase, combined synthetic methods, small region synthesis, and ligation methods are utilized. In one embodiment, the gRNAs are made using IVT enzymatic synthesis methods. Methods of making polynucleotides by IVT are known in the art and are described in WO2013/151666. Accordingly, the present disclosure also includes polynucleotides, e.g., DNA, constructs and vectors are used to in vitro transcribe a gRNA described herein.
  • RNA modifications can be introduced during or after chemical synthesis and/or enzymatic generation of RNAs, e.g., modifications that enhance stability, reduce the likelihood or degree of innate immune response, and/or enhance other attributes, as described in the art.
  • non-natural modified nucleobases can be introduced into any of the gRNAs disclosed herein during synthesis or post-synthesis.
  • modifications are on internucleoside linkages, purine or pyrimidine bases, or sugar.
  • a modification is introduced at the terminal of a gRNA with chemical synthesis or with a polymerase enzyme. Examples of modified nucleic acids and their synthesis are disclosed in WO2013/052523. Synthesis of modified polynucleotides is also described in Verma and Eckstein, Annual Review of Biochemistry, vol. 76, 99-134 (1998).
  • enzymatic or chemical ligation methods can be used to conjugate polynucleotides or their regions with different functional moieties, such as targeting or delivery agents, fluorescent labels, liquids, nanoparticles, etc.
  • Conjugates of polynucleotides and modified polynucleotides are reviewed in Goodchild, Bioconjugate Chemistry, vol. 1(3), 165-187 (1990).
  • a CRISPR/Cas nuclease system for use in genetically editing any of the target genes disclosed here may include at least one guide RNA.
  • the CRISPR/Cas nuclease system may contain multiple gRNAs, for example, 2, 3, or 4 gRNAs. Such multiple gRNAs may target different sites in a same target gene. Alternatively, the multiple gRNAs may target different genes.
  • the guide RNA(s) and the Cas protein may form a ribonucleoprotein (RNP), e.g., a CRISPR/Cas complex.
  • RNP ribonucleoprotein
  • the guide RNA(s) may guide the Cas protein to a target sequence(s) on one or more target genes as those disclosed herein, where the Cas protein cleaves the target gene at the target site.
  • the CRISPR/Cas complex is a Cpf1/guide RNA complex.
  • the CRISPR complex is a Type-II CRISPR/Cas9 complex.
  • the Cas protein is a Cas9 protein.
  • the CRISPR/Cas9 complex is a Cas9/guide RNA complex.
  • the indel frequency (editing frequency) of a particular CRISPR/Cas nuclease system, comprising one or more specific gRNAs may be determined using a TIDE analysis, which can be used to identify highly efficient gRNA molecules for editing a target gene.
  • a highly efficient gRNA yields a gene editing frequency of higher than 80%.
  • a gRNA is considered to be highly efficient if it yields a gene editing frequency of at least 80%, at least 85%, at least 90%, at least 95%, or 100%.
  • the CRISPR/Cas nuclease system disclosed herein comprising one or more gRNAs and at least one RNA-guided nuclease, optionally a donor template as disclosed below, can be delivered to a target cell (e.g., a T cell) for genetic editing of a target gene, via a conventional method.
  • a target cell e.g., a T cell
  • components of a CRISPR/Cas nuclease system as disclosed herein may be delivered to a target cell separately, either simultaneously or sequentially.
  • the components of the CRISPR/Cas nuclease system may be delivered into a target together, for example, as a complex.
  • gRNA and a RNA-guided nuclease can be pre-complexed together to form a ribonucleoprotein (RNP), which can be delivered into a target cell.
  • RNP ribonucleoprotein
  • RNPs are useful for gene editing, at least because they minimize the risk of promiscuous interactions in a nucleic acid-rich cellular environment and protect the RNA from degradation.
  • Methods for forming RNPs are known in the art.
  • an RNP containing an RNA-guided nuclease e.g., a Cas nuclease, such as a Cas9 nuclease
  • one or more gRNAs targeting one or more genes of interest can be delivered a cell (e.g., a T cell).
  • an RNP can be delivered to a T cell by electroporation.
  • an RNA-guided nuclease can be delivered to a cell in a DNA vector that expresses the RNA-guided nuclease in the cell.
  • an RNA-guided nuclease can be delivered to a cell in an RNA that encodes the RNA-guided nuclease and expresses the nuclease in the cell.
  • a gRNA targeting a gene can be delivered to a cell as a RNA, or a DNA vector that expresses the gRNA in the cell.
  • RNA-guided nuclease may be through direct injection or cell transfection using known methods, for example, electroporation or chemical transfection. Other cell transfection methods may be used.
  • gene editing approaching involve zinc finger nuclease (ZFN), transcription activator-like effector nucleases (TALEN), restriction endonucleases, meganucleases homing endonucleases, and the like.
  • ZFN zinc finger nuclease
  • TALEN transcription activator-like effector nucleases
  • restriction endonucleases meganucleases homing endonucleases, and the like.
  • ZFNs are targeted nucleases comprising a nuclease fused to a zinc finger DNA binding domain (ZFBD), which is a polypeptide domain that binds DNA in a sequence-specific manner through one or more zinc fingers.
  • ZFBD zinc finger DNA binding domain
  • a zinc finger is a domain of about 30 amino acids within the zinc finger binding domain whose structure is stabilized through coordination of a zinc ion. Examples of zinc fingers include, but not limited to, C2H2 zinc fingers, C3H zinc fingers, and C4 zinc fingers.
  • a designed zinc finger domain is a domain not occurring in nature whose design/composition results principally from rational criteria, e.g., application of substitution rules and computerized algorithms for processing information in a database storing information of existing ZFP designs and binding data. See, for example, U.S.
  • a selected zinc finger domain is a domain not found in nature whose production results primarily from an empirical process such as phage display, interaction trap or hybrid selection.
  • ZFNs are described in greater detail in U.S. Pat. Nos. 7,888,121 and 7,972,854. The most recognized example of a ZFN is a fusion of the Fold nuclease with a zinc finger DNA binding domain.
  • a TALEN is a targeted nuclease comprising a nuclease fused to a TAL effector DNA binding domain.
  • a “transcription activator-like effector DNA binding domain”, “TAL effector DNA binding domain”, or “TALE DNA binding domain” is a polypeptide domain of TAL effector proteins that is responsible for binding of the TAL effector protein to DNA. TAL effector proteins are secreted by plant pathogens of the genus Xanthomonas during infection. These proteins enter the nucleus of the plant cell, bind effector-specific DNA sequences via their DNA binding domain, and activate gene transcription at these sequences via their transactivation domains.
  • TAL effector DNA binding domain specificity depends on an effector-variable number of imperfect 34 amino acid repeats, which comprise polymorphisms at select repeat positions called repeat variable-diresidues (RVD).
  • RVD repeat variable-diresidues
  • TALENs are described in greater detail in US Patent Application No. 2011/0145940. The most recognized example of a TALEN in the art is a fusion polypeptide of the FokI nuclease to a TAL effector DNA binding domain.
  • targeted nucleases suitable for use as provided herein include, but are not limited to, Bxb1, phiC31, R4, PhiBT1, and W ⁇ /SPBc/TP901-1, whether used individually or in combination.
  • nucleases disclosed herein may be delivered using a vector system, including, but not limited to, plasmid vectors, DNA minicircles, retroviral vectors, lentiviral vectors, adenovirus vectors, poxvirus vectors; herpesvirus vectors and adeno-associated virus vectors, and combinations thereof.
  • a vector system including, but not limited to, plasmid vectors, DNA minicircles, retroviral vectors, lentiviral vectors, adenovirus vectors, poxvirus vectors; herpesvirus vectors and adeno-associated virus vectors, and combinations thereof.
  • Non-viral vector delivery systems include DNA plasmids, DNA minicircles, naked nucleic acid, and nucleic acid complexed with a delivery vehicle such as a liposome or poloxamer.
  • Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell.
  • Methods of non-viral delivery of nucleic acids include electroporation, lipofection, microinjection, biolistics, virosomes, liposomes, immunoliposomes, polycation or lipid:nucleic acid conjugates, naked DNA, naked RNA, capped RNA, artificial virions, and agent-enhanced uptake of DNA.
  • Sonoporation using, e.g., the Sonitron 2000 system (Rich-Mar) can also be used for delivery of nucleic acids.
  • the genetically engineered T cells having a disrupted Reg1 gene, a disrupted TGFBRII gene, or a combination of disrupted Reg1 gene and disrupted TGFBRII gene may comprise one or more of additional disrupted genes, e.g., ⁇ 2M, TRAC, CD70, or a combination thereof as disclosed herein, may further express a chimeric antigen receptor (CAR) targeting an antigen of interest or cells expressing such an antigen.
  • CAR chimeric antigen receptor
  • a chimeric antigen receptor refers to an artificial immune cell receptor that is engineered to recognize and bind to an antigen expressed by undesired cells, for example, disease cells such as cancer cells.
  • a T cell that expresses a CAR polypeptide is referred to as a CAR T cell.
  • CARs have the ability to redirect T-cell specificity and reactivity toward a selected target in a non-MHC-restricted manner. The non-MHC-restricted antigen recognition gives CAR-T cells the ability to recognize an antigen independent of antigen processing, thus bypassing a major mechanism of tumor escape.
  • CARs advantageously do not dimerize with endogenous T-cell receptor (TCR) alpha and beta chains.
  • First generation CARs join an antibody-derived scFv to the CD3zeta ( ⁇ or z) intracellular signaling domain of the T-cell receptor through hinge and transmembrane domains.
  • Second generation CARs incorporate an additional co-stimulatory domain, e.g., CD28, 4-1BB (41BB), or ICOS, to supply a costimulatory signal.
  • Third-generation CARs contain two costimulatory domains (e.g., a combination of CD27, CD28, 4-1BB, ICOS, or OX40) fused with the TCR CD3 ⁇ chain.
  • a CAR is a fusion polypeptide comprising an extracellular domain that recognizes a target antigen (e.g., a single chain fragment (scFv) of an antibody or other antibody fragment) and an intracellular domain comprising a signaling domain of the T-cell receptor (TCR) complex (e.g., CD3 ⁇ ) and, in most cases, a co-stimulatory domain.
  • a target antigen e.g., a single chain fragment (scFv) of an antibody or other antibody fragment
  • TCR T-cell receptor
  • a CAR construct may further comprise a hinge and transmembrane domain between the extracellular domain and the intracellular domain, as well as a signal peptide at the N-terminus for surface expression. Examples of signal peptides include SEQ ID NO: 95 and SEQ ID NO: 96 as provided in Table 27 below. Other signal peptides may be used.
  • the antigen-binding extracellular domain is the region of a CAR polypeptide that is exposed to the extracellular fluid when the CAR is expressed on cell surface.
  • a signal peptide may be located at the N-terminus to facilitate cell surface expression.
  • the antigen binding domain can be a single-chain variable fragment (scFv, which may include an antibody heavy chain variable region (V H ) and an antibody light chain variable region (V L ) (in either orientation).
  • V H and V L fragment may be linked via a peptide linker.
  • the linker in some embodiments, includes hydrophilic residues with stretches of glycine and serine for flexibility as well as stretches of glutamate and lysine for added solubility.
  • the scFv fragment retains the antigen-binding specificity of the parent antibody, from which the scFv fragment is derived.
  • the scFv may comprise humanized V H and/or V L domains. In other embodiments, the V H and/or V L domains of the scFv are fully human.
  • the antigen-binding extracellular domain may be specific to a target antigen of interest, for example, a pathologic antigen such as a tumor antigen.
  • a tumor antigen is a “tumor associated antigen,” referring to an immunogenic molecule, such as a protein, that is generally expressed at a higher level in tumor cells than in non-tumor cells, in which it may not be expressed at all, or only at low levels.
  • tumor-associated structures which are recognized by the immune system of the tumor-harboring host, are referred to as tumor-associated antigens.
  • a tumor-associated antigen is a universal tumor antigen, if it is broadly expressed by most types of tumors.
  • tumor-associated antigens are differentiation antigens, mutational antigens, overexpressed cellular antigens or viral antigens.
  • a tumor antigen is a “tumor specific antigen” or “TSA,” referring to an immunogenic molecule, such as a protein, that is unique to a tumor cell. Tumor specific antigens are exclusively expressed in tumor cells, for example, in a specific type of tumor cells.
  • the antigen-binding extracellular domain can be a single-chain variable fragment (scFv) that binds a tumor antigen as disclosed herein.
  • the scFv may comprise an antibody heavy chain variable region (V H ) and an antibody light chain variable region (V L ), which optionally may be connected via a flexible peptide linker.
  • V H antibody heavy chain variable region
  • V L antibody light chain variable region
  • the scFv may have the V H to V L orientation (from N-terminus to C-terminus).
  • the scFv may have the V L to V H orientation (from N-terminus to C-terminus).
  • Exemplary tumor antigens include, but are not limited to, CD19, BCMA, CD70, CD33, and PTK7. Any known antibodies specific to such tumor antigens, for example, those approved for marketing and those in clinical trials, can be used for making the CAR constructs disclosed herein.
  • Non-limiting examples of CAR constructs are provided in WO2019097305 and WO2019215500, WO2020/095107, and International Patent Application No. PCT/IB2021/053849, the relevant disclosures of which are herein incorporated by reference for the purposes and subject matter referenced herein.
  • the antigen-binding extracellular domain can be a single-chain variable fragment (scFv) that binds human CD19.
  • the anti-CD19 scFv may comprises (i) a heavy chain variable region (V H ) that comprises the same heavy chain complementary determining regions (CDRs) as those in SEQ ID NO: 124; and (ii) a light chain variable region (V L ) that comprises the same light chain CDRs as those in SEQ ID NO: 125.
  • the anti-CD19 antibody discloses herein may comprise the heavy chain CDR1, heavy chain CDR2, and heavy chain CDR3 set forth as SEQ ID NOs: 108-110, respectively as determined by the Kabat method.
  • the anti-CD19 antibody discloses herein may comprise the light chain CDR1, light chain CDR2, and light chain CDR3 set forth as SEQ ID NOs:105-107 as determined by the Kabat method.
  • the anti-CD19 antibody discloses herein may comprise the heavy chain CDR1, heavy chain CDR2, and heavy chain CDR3 set forth as SEQ ID NOs: 114-116, respectively as determined by the Chothia method.
  • the anti-CD19 antibody discloses herein may comprise the light chain CDR1, light chain CDR2, and light chain CDR3 set forth as SEQ ID NOs:111-113 as determined by the Chothia method.
  • the anti-CD19 scFv may comprise a V H comprising the amino acid sequence of SEQ ID NO: 124 and a V L comprises the amino acid sequence of SEQ ID NO: 125. See Sequence Table 27 below.
  • the antigen-binding extracellular domain can be a single-chain variable fragment (scFv) that binds human CD70.
  • the anti-CD70 scFv may comprises (i) a heavy chain variable region (V H ) that comprises the same heavy chain complementary determining regions (CDRs) as those in SEQ ID NO: 143; and (ii) a light chain variable region (V L ) that comprises the same light chain CDRs as those in SEQ ID NO: 144.
  • the anti-CD70 antibody discloses herein may comprise the heavy chain CDR1, heavy chain CDR2, and heavy chain CDR3 set forth as SEQ ID NOs: 132, 134, and 136, respectively as determined by the Kabat method.
  • the anti-CD70 antibody discloses herein may comprise the light chain CDR1, light chain CDR2, and light chain CDR3 set forth as SEQ ID NOs:127, 129, and 130, respectively as determined by the Kabat method.
  • the anti-CD70 antibody discloses herein may comprise the heavy chain CDR1, heavy chain CDR2, and heavy chain CDR3 set forth as SEQ ID NOs: 133, 135, and 137, respectively as determined by the Chothia method.
  • the anti-CD70 antibody discloses herein may comprise the light chain CDR1, light chain CDR2, and light chain CDR3 set forth as SEQ ID NO:128, LAS, and SEQ ID NO:131, respectively as determined by the Chothia method.
  • the anti-CD70 scFv may comprise a V H comprising the amino acid sequence of SEQ ID NO: 143 and a V L comprises the amino acid sequence of SEQ ID NO: 144. See Sequence Table 27 below.
  • the antigen-binding extracellular domain can be a single-chain variable fragment (scFv) that binds human BCMA.
  • the anti-BCMA scFv may comprises (i) a heavy chain variable region (V H ) that comprises the same heavy chain complementary determining regions (CDRs) as those in SEQ ID NO: 149; and (ii) a light chain variable region (V L ) that comprises the same light chain CDRs as those in SEQ ID NO: 150.
  • the anti-BCMA antibody discloses herein may comprise the heavy chain CDR1, heavy chain CDR2, and heavy chain CDR3 set forth as SEQ ID NOs: 155, 157, and 159, respectively as determined by the Kabat method.
  • the anti-BCMA antibody discloses herein may comprise the light chain CDR1, light chain CDR2, and light chain CDR3 set forth as SEQ ID NOs:151, 152, and 153, respectively as determined by the Kabat method.
  • the anti-BCMA antibody discloses herein may comprise the heavy chain CDR1, heavy chain CDR2, and heavy chain CDR3 set forth as SEQ ID NOs: 156, 158, and 160, respectively as determined by the Chothia method.
  • the anti-BCMA antibody discloses herein may comprise the light chain CDR1, light chain CDR2, and light chain CDR3 set forth as SEQ ID NOs:151, 152, and 154, respectively as determined by the Chothia method.
  • the anti-BCMA scFv may comprise a V H comprising the amino acid sequence of SEQ ID NO: 149 and a V L comprises the amino acid sequence of SEQ ID NO: 150. See Sequence Table 27 below.
  • the antigen-binding extracellular domain can be a single-chain variable fragment (scFv) that binds human CD33.
  • scFv single-chain variable fragment
  • Exemplary anti-CD33 scFv and anti-CD33 CAR constructs can be found, for example, in Sequence Table 27 below and in WO2020/095107, the relevant disclosures of which are incorporated by reference for the subject matter and purpose noted herein.
  • the antigen-binding extracellular domain can be a single-chain variable fragment (scFv) that binds human CD33.
  • the anti-CD33 scFv may comprises (i) a heavy chain variable region (V H ) that comprises the same heavy chain complementary determining regions (CDRs) as those in SEQ ID NO: 334; and (ii) a light chain variable region (V L ) that comprises the same light chain CDRs as those in SEQ ID NO: 335.
  • the anti-CD33 antibody discloses herein may comprise the heavy chain CDR1, heavy chain CDR2, and heavy chain CDR3 set forth as SEQ ID NOs: 328-330, respectively as determined by the Kabat method.
  • the anti-CD33 antibody discloses herein may comprise the light chain CDR1, light chain CDR2, and light chain CDR3 set forth as SEQ ID NOs:331-333, respectively as determined by the Kabat method.
  • the anti-BCMA scFv may comprise a V H comprising the amino acid sequence of SEQ ID NO: 149 and a V L comprises the amino acid sequence of SEQ ID NO: 150. See Sequence Table 27 below.
  • the antigen-binding extracellular domain can be a single-chain variable fragment (scFv) that binds human PTK7.
  • the anti-PTK7 scFv may comprises (i) a heavy chain variable region (V H ) that comprises the same heavy chain complementary determining regions (CDRs) as those in SEQ ID NO: 346; and (ii) a light chain variable region (V L ) that comprises the same light chain CDRs as those in SEQ ID NO: 347.
  • the anti-PTK7 antibody discloses herein may comprise the heavy chain CDR1, heavy chain CDR2, and heavy chain CDR3 set forth as SEQ ID NOs: 340-342, respectively as determined by the Kabat method.
  • the anti-PTK7 antibody discloses herein may comprise the light chain CDR1, light chain CDR2, and light chain CDR3 set forth as SEQ ID NOs:343-345, respectively as determined by the Kabat method.
  • the anti-BCMA scFv may comprise a V H comprising the amino acid sequence of SEQ ID NO: 346 and a V L comprises the amino acid sequence of SEQ ID NO: 347. See Sequence Table 27 below.
  • Two antibodies having the same V H and/or V L CDRs means that their CDRs are identical when determined by the same approach (e.g., the Kabat approach, the Chothia approach, the AbM approach, the Contact approach, or the IMGT approach as known in the art. See, e.g., bioinf.org.uk/abs/ or abysis.org/abysis/sequence_input).
  • the CAR polypeptide disclosed herein may contain a transmembrane domain, which can be a hydrophobic alpha helix that spans the membrane.
  • a “transmembrane domain” refers to any protein structure that is thermodynamically stable in a cell membrane, preferably a eukaryotic cell membrane. The transmembrane domain can provide stability of the CAR containing such.
  • the transmembrane domain of a CAR as provided herein can be a CD8 transmembrane domain.
  • the transmembrane domain can be a CD28 transmembrane domain.
  • the transmembrane domain is a chimera of a CD8 and CD28 transmembrane domain.
  • Other transmembrane domains may be used as provided herein.
  • the transmembrane domain is a CD8a transmembrane domain containing the sequence of SEQ ID NO: 97 as provided below in Table 27. Other transmembrane domains may be used.
  • a hinge domain may be located between an extracellular domain (comprising the antigen binding domain) and a transmembrane domain of a CAR, or between a cytoplasmic domain and a transmembrane domain of the CAR.
  • a hinge domain can be any oligopeptide or polypeptide that functions to link the transmembrane domain to the extracellular domain and/or the cytoplasmic domain in the polypeptide chain.
  • a hinge domain may function to provide flexibility to the CAR, or domains thereof, or to prevent steric hindrance of the CAR, or domains thereof.
  • a hinge domain may comprise up to 300 amino acids (e.g., 10 to 100 amino acids, or 5 to 20 amino acids). In some embodiments, one or more hinge domain(s) may be included in other regions of a CAR. In some embodiments, the hinge domain may be a CD8 hinge domain. Other hinge domains may be used.
  • any of the CAR constructs contain one or more intracellular signaling domains (e.g., CD3 ⁇ , and optionally one or more co-stimulatory domains), which are the functional end of the receptor. Following antigen recognition, receptors cluster and a signal is transmitted to the cell.
  • intracellular signaling domains e.g., CD3 ⁇ , and optionally one or more co-stimulatory domains
  • CD3 ⁇ is the cytoplasmic signaling domain of the T cell receptor complex.
  • CD3 ⁇ contains three (3) immunoreceptor tyrosine-based activation motif (ITAM)s, which transmit an activation signal to the T cell after the T cell is engaged with a cognate antigen.
  • ITAM immunoreceptor tyrosine-based activation motif
  • CD3 ⁇ provides a primary T cell activation signal but not a fully competent activation signal, which requires a co-stimulatory signaling.
  • the CAR polypeptides disclosed herein may further comprise one or more co-stimulatory signaling domains.
  • the co-stimulatory domains of CD28 and/or 4-1BB may be used to transmit a full proliferative/survival signal, together with the primary signaling mediated by CD3 ⁇ .
  • the CAR disclosed herein comprises a CD28 co-stimulatory molecule.
  • the CAR disclosed herein comprises a 4-1BB co-stimulatory molecule.
  • a CAR includes a CD3 ⁇ signaling domain and a CD28 co-stimulatory domain.
  • a CAR includes a CD3 ⁇ signaling domain and 4-1BB co-stimulatory domain.
  • a CAR includes a CD3 ⁇ signaling domain, a CD28 co-stimulatory domain, and a 4-1BB co-stimulatory domain.
  • Table 27 provides examples of signaling domains derived from 4-1BB, CD28 and CD3-zeta that may be used herein.
  • the anti-CD19 CAR disclosed herein may comprise the amino acid sequence of SEQ ID NO: 118, which may be encoded by the nucleotide sequence of SEQ ID NO: 117.
  • the anti-CD19 CAR may be a mature form without the N-terminal signal peptide, e.g., comprising the amino acid sequence of SEQ ID NO:353.
  • the anti-BCMA CAR disclosed herein may comprise the amino acid sequence of SEQ ID NO: 146, which may be encoded by the nucleotide sequence of SEQ ID NO: 145.
  • the anti-CDBCMA CAR may be a mature form without the N-terminal signal peptide, e.g., comprising the amino acid sequence of SEQ ID NO:355.
  • the anti-CD70 CAR disclosed herein may comprise the amino acid sequence of SEQ ID NO: 138, which may be encoded by the nucleotide sequence of SEQ ID NO: 141.
  • the anti-CD70 CAR may be a mature form without the N-terminal signal peptide, e.g., comprising the amino acid sequence of SEQ ID NO:354.
  • the anti-CD33 CAR disclosed herein may comprise the amino acid sequence of SEQ ID NO: 338 or 339.
  • the anti-CD33 CAR may be a mature form without the N-terminal signal peptide, e.g., comprising the amino acid sequence of SEQ ID NO:356 or 357.
  • the anti-PTK7 CAR disclosed herein may comprise the amino acid sequence of SEQ ID NO: 349 or 350.
  • the anti-PTK7 CAR may be a mature form without the N-terminal signal peptide, e.g., comprising the amino acid sequence of SEQ ID NO:358 or 359.
  • a nucleic acid encoding a CAR can be introduced into any of the genetically engineered T cells disclosed herein by methods known to those of skill in the art.
  • a coding sequence of the CAR may be cloned into a vector, which may be introduced into the genetically engineered T cells for expression of the CAR.
  • a variety of different methods known in the art can be used to introduce any of the nucleic acids or expression vectors disclosed herein into an immune effector cell.
  • Non-limiting examples of methods for introducing nucleic acid into a cell include: lipofection, transfection (e.g., calcium phosphate transfection, transfection using highly branched organic compounds, transfection using cationic polymers, dendrimer-based transfection, optical transfection, particle-based transfection (e.g., nanoparticle transfection), or transfection using liposomes (e.g., cationic liposomes)), microinjection, electroporation, cell squeezing, sonoporation, protoplast fusion, impalefection, hydrodynamic delivery, gene gun, magnetofection, viral transfection, and nucleofection.
  • transfection e.g., calcium phosphate transfection, transfection using highly branched organic compounds, transfection using cationic polymers, dendrimer-based transfection, optical transfection, particle-based transfection (e.g., nanoparticle transfection), or transfection using liposomes (e.g., cationic liposomes)
  • a nucleic acid encoding a CAR construct can be delivered to a cell using an adeno-associated virus (AAV).
  • AAVs are small viruses which integrate site-specifically into the host genome and can therefore deliver a transgene, such as CAR.
  • ITRs Inverted terminal repeats
  • rep and cap proteins are present flanking the AAV genome and/or the transgene of interest and serve as origins of replication.
  • rep and cap proteins which, when transcribed, form capsids which encapsulate the AAV genome for delivery into target cells.
  • Surface receptors on these capsids which confer AAV serotype, which determines which target organs the capsids will primarily bind and thus what cells the AAV will most efficiently infect.
  • the AAV for use in delivering the CAR-coding nucleic acid is AAV serotype 6 (AAV6).
  • Adeno-associated viruses are among the most frequently used viruses for gene therapy for several reasons.
  • AAVs do not provoke an immune response upon administration to mammals, including humans
  • AAVs are effectively delivered to target cells, particularly when consideration is given to selecting the appropriate AAV serotype.
  • AAVs have the ability to infect both dividing and non-dividing cells because the genome can persist in the host cell without integration. This trait makes them an ideal candidate for gene therapy.
  • a nucleic acid encoding a CAR can be designed to insert into a genomic site of interest in the host T cells.
  • the target genomic site can be in a safe harbor locus.
  • a nucleic acid encoding a CAR (e.g., via a donor template, which can be carried by a viral vector such as an adeno-associated viral (AAV) vector) can be designed such that it can insert into a location within a TRAC gene to disrupt the TRAC gene in the genetically engineered T cells and express the CAR polypeptide. Disruption of TRAC leads to loss of function of the endogenous TCR.
  • a disruption in the TRAC gene can be created with an endonuclease such as those described herein and one or more gRNAs targeting one or more TRAC genomic regions. Any of the gRNAs specific to a TRAC gene and the target regions disclosed herein can be used for this purpose.
  • a genomic deletion in the TRAC gene and replacement by a CAR coding segment can be created by homology directed repair or HDR (e.g., using a donor template, which may be part of a viral vector such as an adeno-associated viral (AAV) vector).
  • a disruption in the TRAC gene can be created with an endonuclease as those disclosed herein and one or more gRNAs targeting one or more TRAC genomic regions, and inserting a CAR coding segment into the TRAC gene.
  • a nucleic acid encoding a CAR (e.g., via a donor template, which can be carried by a viral vector such as an adeno-associated viral (AAV) vector) can be designed such that it can insert into a location within a ⁇ 2M gene to disrupt the ⁇ 2M gene in the genetically engineered T cells and express the CAR polypeptide. Disruption of ⁇ 2M leads to loss of function of the endogenous MHC Class I complexes. For example, a disruption in the ⁇ 2M gene can be created with an endonuclease such as those described herein and one or more gRNAs targeting one or more ⁇ 2M genomic regions. Any of the gRNAs specific to a ⁇ 2M gene and the target regions disclosed herein can be used for this purpose.
  • AAV adeno-associated viral
  • a genomic deletion in the ⁇ 2M gene and replacement by a CAR coding segment can be created by homology directed repair or HDR (e.g., using a donor template, which may be part of a viral vector such as an adeno-associated viral (AAV) vector).
  • a disruption in the ⁇ 2M gene can be created with an endonuclease as those disclosed herein and one or more gRNAs targeting one or more ⁇ 2M genomic regions, and inserting a CAR coding segment into the ⁇ 2M gene.
  • a nucleic acid encoding a CAR (e.g., via a donor template, which can be carried by a viral vector such as an adeno-associated viral (AAV) vector) can be designed such that it can insert into a location within a CD70 gene to disrupt the CD70 gene in the genetically engineered T cells and express the CAR polypeptide. Disruption of CD70 leads to loss of function of the endogenous CD70 protein.
  • a disruption in the CD70 gene can be created with an endonuclease such as those described herein and one or more gRNAs targeting one or more CD70 genomic regions. Any of the gRNAs specific to a CD70 gene and the target regions disclosed herein can be used for this purpose.
  • a genomic deletion in the CD70 gene and replacement by a CAR coding segment can be created by homology directed repair or HDR (e.g., using a donor template, which may be part of a viral vector such as an adeno-associated viral (AAV) vector).
  • a disruption in the CD70 gene can be created with an endonuclease as those disclosed herein and one or more gRNAs targeting one or more CD70 genomic regions, and inserting a CAR coding segment into the CD70 gene.
  • a nucleic acid encoding a CAR (e.g., via a donor template, which can be carried by a viral vector such as an adeno-associated viral (AAV) vector) can be designed such that it can insert into a location within a Reg1 gene to disrupt the Reg1 gene in the genetically engineered T cells and express the CAR polypeptide. Disruption of Reg1 leads to loss of function of the endogenous Reg1 protein.
  • a disruption in the Reg1 gene can be created with an endonuclease such as those described herein and one or more gRNAs targeting one or more Reg1 genomic regions. Any of the gRNAs specific to a Reg1 gene and the target regions disclosed herein can be used for this purpose.
  • a genomic deletion in the Reg1 gene and replacement by a CAR coding segment can be created by homology directed repair or HDR (e.g., using a donor template, which may be part of a viral vector such as an adeno-associated viral (AAV) vector).
  • a disruption in the Reg1 gene can be created with an endonuclease as those disclosed herein and one or more gRNAs targeting one or more Reg1 genomic regions, and inserting a CAR coding segment into the Reg1 gene.
  • a nucleic acid encoding a CAR (e.g., via a donor template, which can be carried by a viral vector such as an adeno-associated viral (AAV) vector) can be designed such that it can insert into a location within a TGFBRII gene to disrupt the TGFBRII gene in the genetically engineered T cells and express the CAR polypeptide. Disruption of Reg1 leads to loss of function of the endogenous TGFBRII receptor.
  • a disruption in the TGFBRII gene can be created with an endonuclease such as those described herein and one or more gRNAs targeting one or more TGFBRII genomic regions. Any of the gRNAs specific to a TGFBRII gene and the target regions disclosed herein can be used for this purpose.
  • a genomic deletion in the TGFBRII gene and replacement by a CAR coding segment can be created by homology directed repair or HDR (e.g., using a donor template, which may be part of a viral vector such as an adeno-associated viral (AAV) vector).
  • a disruption in the TGFBRII gene can be created with an endonuclease as those disclosed herein and one or more gRNAs targeting one or more TGFBRII genomic regions, and inserting a CAR coding segment into the TGFBRII gene.
  • a donor template as disclosed herein can contain a coding sequence for a CAR.
  • the CAR-coding sequence may be flanked by two regions of homology to allow for efficient HDR at a genomic location of interest, for example, at a TRAC gene using a gene editing method known in the art.
  • a CRISPR-based method can be used. In this case, both strands of the DNA at the target locus can be cut by a CRISPR Cas9 enzyme guided by gRNAs specific to the target locus. HDR then occurs to repair the double-strand break (DSB) and insert the donor DNA coding for the CAR.
  • DSB double-strand break
  • the donor sequence is designed with flanking residues which are complementary to the sequence surrounding the DSB site in the target gene (hereinafter “homology arms”), such as the TRAC gene.
  • homology arms serve as the template for DSB repair and allow HDR to be an essentially error-free mechanism.
  • the rate of homology directed repair (HDR) is a function of the distance between the mutation and the cut site so choosing overlapping or nearby target sites is important. Templates can include extra sequences flanked by the homologous regions or can contain a sequence that differs from the genomic sequence, thus allowing sequence editing.
  • a donor template may have no regions of homology to the targeted location in the DNA and may be integrated by NHEJ-dependent end joining following cleavage at the target site.
  • a donor template can be DNA or RNA, single-stranded and/or double-stranded, and can be introduced into a cell in linear or circular form. If introduced in linear form, the ends of the donor sequence can be protected (e.g., from exonucleolytic degradation) by methods known to those of skill in the art. For example, one or more dideoxynucleotide residues are added to the 3′ terminus of a linear molecule and/or self-complementary oligonucleotides are ligated to one or both ends. See, for example, Chang et al., (1987) Proc. Natl. Acad. Sci.
  • Additional methods for protecting exogenous polynucleotides from degradation include, but are not limited to, addition of terminal amino group(s) and the use of modified internucleotide linkages such as, for example, phosphorothioates, phosphoramidates, and O-methyl ribose or deoxyribose residues.
  • a donor template can be introduced into a cell as part of a vector molecule having additional sequences such as, for example, replication origins, promoters and genes encoding antibiotic resistance.
  • a donor template can be introduced into a cell as naked nucleic acid, as nucleic acid complexed with an agent such as a liposome or poloxamer, or can be delivered by viruses (e.g., adenovirus, AAV, herpesvirus, retrovirus, lentivirus and integrase defective lentivirus (IDLY)).
  • viruses e.g., adenovirus, AAV, herpesvirus, retrovirus, lentivirus and integrase defective lentivirus (IDLY)
  • a donor template in some embodiments, can be inserted at a site nearby an endogenous prompter (e.g., downstream or upstream) so that its expression can be driven by the endogenous promoter.
  • the donor template may comprise an exogenous promoter and/or enhancer, for example, a constitutive promoter, an inducible promoter, or tissue-specific promoter to control the expression of the CAR gene.
  • the exogenous promoter is an EF1 ⁇ promoter, see, e.g., SEQ ID NO: 167 provided in Table 28 below. Other promoters may be used.
  • exogenous sequences may also include transcriptional or translational regulatory sequences, for example, promoters, enhancers, insulators, internal ribosome entry sites, sequences encoding 2A peptides and/or polyadenylation signals.
  • additional gene editing e.g., gene knock-in or knock-out
  • gene knock-in or knock-out can be introduced into therapeutic T cells as disclosed herein to improve T cell function and therapeutic efficacy.
  • additional gene editing e.g., gene knock-in or knock-out
  • ⁇ 2M disruption can be performed to reduce the risk of or prevent a host-versus-graft response.
  • Other examples include knock-in or knock-out genes to improve target cell lysis, knock-in or knock-out genes to enhance performance of therapeutic T cells such as CAR-T cells.
  • a donor template for delivering an anti-CD19 CAR may be an AAV vector inserted with a nucleic acid fragment comprising the coding sequence of the anti-CD19 CAR, and optionally regulatory sequences for expression of the anti-CD19 CAR (e.g., a promoter such as the EF1a promoter provided in the sequence Table), which can be flanked by homologous arms for inserting the coding sequence and the regulatory sequences into a genomic locus of interest.
  • the nucleic acid fragment is inserted in the endogenous TRAC gene locus, thereby disrupting expression of the TRAC gene.
  • the nucleic acid may replace a fragment in the TRAC gene, for example, a fragment comprising the nucleotide sequence of SEQ ID NO: 69.
  • the donor template for delivering the anti-CD19 CAR may comprise a nucleotide sequence of SEQ ID NO: 117, which can be inserted into a disrupted TRAC gene, for example, replacing the fragment of SEQ ID NO: 69.
  • a donor template for delivering an anti-BCMA CAR may be an AAV vector inserted with a nucleic acid fragment comprising the coding sequence of the anti-BCMA CAR, and optionally regulatory sequences for expression of the anti-BCMA CAR (e.g., a promoter such as the EF1a promoter provided in the sequence Table), which can be flanked by homologous arms for inserting the coding sequence and the regulatory sequences into a genomic locus of interest.
  • the nucleic acid fragment is inserted in the endogenous TRAC gene locus, thereby disrupting expression of the TRAC gene.
  • the nucleic acid may replace a fragment in the TRAC gene, for example, a fragment comprising the nucleotide sequence of SEQ ID NO: 69.
  • the donor template for delivering the anti-BCMA CAR may comprise a nucleotide sequence of SEQ ID NO: 145, which can be inserted into a disrupted TRAC gene, for example, replacing the fragment of SEQ ID NO: 69.
  • a donor template for delivering an anti-CD70 CAR may be an AAV vector inserted with a nucleic acid fragment comprising the coding sequence of the anti-CD70 CAR, and optionally regulatory sequences for expression of the anti-CD70 CAR (e.g., a promoter such as the EF1a promoter provided in the sequence Table), which can be flanked by homologous arms for inserting the coding sequence and the regulatory sequences into a genomic locus of interest.
  • the nucleic acid fragment is inserted in the endogenous TRAC gene locus, thereby disrupting expression of the TRAC gene.
  • the nucleic acid may replace a fragment in the TRAC gene, for example, a fragment comprising the nucleotide sequence of SEQ ID NO: 69.
  • the donor template for delivering the anti-CD70 CAR may comprise a nucleotide sequence of SEQ ID NO: 139, which can be inserted into a disrupted TRAC gene, for example, replacing the fragment of SEQ ID NO: 69.
  • the genetically engineered T cells having a disrupted Reg1 gene, additional disrupted genes, e.g., ⁇ 2M, TRAC, CD70, and further expressing a chimeric antigen receptor (CAR) can be produced by sequential targeting of the genes of interest.
  • the Reg1 gene may be disrupted first, followed by disruption of TRAC and ⁇ 2M genes and CAR insertion.
  • TRAC and ⁇ 2M genes may be disrupted first, followed by CAR insertion and disruption of the Reg1 gene.
  • the genetically engineered T cells disclosed herein may be produced by multiple, sequential electroporation events with multiple RNPs targeting the genes of interest, e.g., Reg1, ⁇ 2M, TRAC, CD70, etc.
  • the genetically engineered CAR T cells disclosed herein may be produced by a single electroporation event with an RNP complex comprising an RNA-guided nuclease and multiple gRNAs targeting the genes of interest, e.g., Reg1, ⁇ 2M, TRAC, CD70, etc.
  • gene disruption encompasses gene modification through gene editing (e.g., using CRISPR/Cas gene editing to insert or delete one or more nucleotides).
  • a disrupted gene may contain one or more mutations (e.g., insertion, deletion, or nucleotide substitution, etc.) relative to the wild-type counterpart so as to substantially reduce or completely eliminate the activity of the encoded gene product.
  • the one or more mutations may be located in a non-coding region, for example, a promoter region, a regulatory region that regulates transcription or translation; or an intron region.
  • the one or more mutations may be located in a coding region (e.g., in an exon).
  • the disrupted gene does not express or expresses a substantially reduced level of the encoded protein. In other instances, the disrupted gene expresses the encoded protein in a mutated form, which is either not functional or has substantially reduced activity.
  • a disrupted gene is a gene that does not encode functional protein.
  • a cell that comprises a disrupted gene does not express (e.g., at the cell surface) a detectable level (e.g. by antibody, e.g., by flow cytometry) of the protein encoded by the gene.
  • a cell that does not express a detectable level of the protein may be referred to as a knockout cell.
  • a cell having a ⁇ 2M gene edit may be considered a ⁇ 2M knockout cell if ⁇ 2M protein cannot be detected at the cell surface using an antibody that specifically binds ⁇ 2M protein.
  • a population of genetically engineered T cells disclosed herein express a CAR (e.g., anti-CD19, anti-BCMA, or anti-CD70 CAR), a disrupted Reg1 gene, a disrupted TGFBRII gene, a disrupted TRAC gene, and optionally a disrupted ⁇ 2M gene, and optionally a disrupted CD70 gene.
  • the nucleotide sequence encoding the CAR may be inserted in the disrupted TRAC gene (e.g., replacing the site targeted by a sgRNA such as TA-1).
  • such a population of genetically engineered T cells may comprise about 70-99% Reg1 ⁇ cells, for example about 90-97% Reg1 ⁇ cells, about 70-99% TGFBRII ⁇ cells, e.g., for example about 80-89% TGFBRII ⁇ cells, about 70-99% TCR ⁇ cells, for example about 90-99% TCR ⁇ cells, and/or optionally about 60-99% ⁇ 2M ⁇ cells, for example about 60-82% ⁇ 2M ⁇ cells, and/or optionally about 70-99% CD70 ⁇ cells, for example about 90-99% CD70 ⁇ cells.
  • the cell population may also contain at least about 30%-50% (e.g., at least 60%) cells expressing the CAR.
  • Also provided herein is population of genetically engineered immune cells e.g., T cells such as human T cells
  • a disrupted Reg1 gene e.g., a disrupted TGFBRII gene, or a combination thereof
  • an anti-CD19 CAR e.g., those disclosed herein.
  • the population of genetically engineered immune cells e.g., T cells such as human T cells
  • the population of genetically engineered immune cells comprising both a disrupted Reg1 gene and a disrupted TGFBRII gene, and expressing an anti-CD19 CAR, e.g., those disclosed herein.
  • the anti-CD19 CAR-T cells disclosed herein which express any of the anti-CD19 CAR disclosed herein (e.g., the anti-CD19 CAR comprising the amino acid sequence of SEQ ID NO: 106), may also comprise a disrupted TRAC gene and/or a disrupted ⁇ 2M gene as also disclosed herein.
  • the population of genetically engineered T cells are anti-CD19 CAR cells that further comprise a disrupted Regnanse-1 gene.
  • anti-CD19 CAR cells are CD19-directed T cells having disrupted TRAC gene and ⁇ 2M gene.
  • the nucleic acid encoding the anti-CD19 CAR can be inserted in the disrupted TRAC gene at the site of SEQ ID NO: 69, which is replaced by the nucleic acid encoding the anti-CD19 CAR, thereby disrupting expression of the TRAC gene.
  • the disrupted TRAC gene in the anti-CD19 CAR cells may comprise the nucleotide sequence of SEQ ID NO: 119.
  • Anti-CD19 CAR T cells that comprise a disrupted Reg1 gene can be produced via ex vivo genetic modification using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) technology to disrupt targeted genes (Reg1, optionally TRAC and/or ⁇ 2M genes), and adeno-associated virus (AAV) transduction to deliver the anti-CD19 CAR construct.
  • CRISPR/Cas9 Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9
  • Reg1 optionally TRAC and/or ⁇ 2M genes
  • AAV adeno-associated virus
  • CRISPR-Cas9-mediated gene editing involves at least a sgRNA targeting Reg1 (e.g., REG1-Z03 (SEQ ID NO: 22), REG1-Z05 (SEQ ID NO: 30), REG1-Z06 (SEQ ID NO: 34) or REG1-Z10 (SEQ ID NO: 50)), and optionally TA-1 sgRNA (SEQ ID NO: 59), which targets the TRAC locus, and ⁇ 2M-1 sgRNA (SEQ ID NO: 63), which targets the ⁇ 2M locus.
  • Reg1 e.g., REG1-Z03 (SEQ ID NO: 22), REG1-Z05 (SEQ ID NO: 30), REG1-Z06 (SEQ ID NO: 34) or REG1-Z10 (SEQ ID NO: 50
  • TA-1 sgRNA SEQ ID NO: 59
  • ⁇ 2M-1 sgRNA SEQ ID NO: 63
  • Anti-CD19 CAR T cells that comprise a disrupted TGFBRII gene can be produced via ex vivo genetic modification using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) technology to disrupt targeted genes (TGFBRII, optionally TRAC and/or ⁇ 2M genes), and adeno-associated virus (AAV) transduction to deliver the anti-CD19 CAR construct.
  • CRISPR/Cas9 Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9
  • TGFBRII optionally TRAC and/or ⁇ 2M genes
  • AAV adeno-associated virus
  • CRISPR-Cas9-mediated gene editing involves at least a sgRNA targeting TGFBRII (e.g., those listed in Table 39, for example, TGFBRII_EX1_T2, TGFBRII_EX4_T1, TGFBRII_EX4_T2, TGFBRII_EX5_T1), and optionally TA-1 sgRNA (SEQ ID NO: 59), which targets the TRAC locus, and ⁇ 2M-1 sgRNA (SEQ ID NO: 63), which targets the ⁇ 2M locus.
  • TGFBRII e.g., those listed in Table 39, for example, TGFBRII_EX1_T2, TGFBRII_EX4_T1, TGFBRII_EX4_T2, TGFBRII_EX5_T1
  • TA-1 sgRNA SEQ ID NO: 59
  • ⁇ 2M-1 sgRNA SEQ ID NO: 63
  • Anti-CD19 CAR T cells that comprise both a disrupted TGFBRII gene and a disrupted Reg1 gene can be produced via ex vivo genetic modification using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) technology to disrupt targeted genes (TGFBRII and Reg1, optionally TRAC and/or ⁇ 2M genes), and adeno-associated virus (AAV) transduction to deliver the anti-CD19 CAR construct.
  • CRISPR/Cas9 Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9
  • TGFBRII and Reg1 optionally TRAC and/or ⁇ 2M genes
  • AAV adeno-associated virus
  • CRISPR-Cas9-mediated gene editing involves at least a sgRNA targeting TGFBRII (e.g., those listed in Table 39) and a sgRNA targeting Reg1 (e.g., those listed in Table 22), optionally TA-1 sgRNA (SEQ ID NO: 59), which targets the TRAC locus, and ⁇ 2M-1 sgRNA (SEQ ID NO: 63), which targets the ⁇ 2M locus.
  • TGFBRII e.g., those listed in Table 39
  • a sgRNA targeting Reg1 e.g., those listed in Table 22
  • optionally TA-1 sgRNA SEQ ID NO: 59
  • ⁇ 2M-1 sgRNA SEQ ID NO: 63
  • the anti-CD19 CAR T cells are composed of an anti-CD19 single-chain antibody fragment (scFv, which may comprise the amino acid sequence of SEQ ID NO: 120), followed by a CD8 hinge and transmembrane domain (e.g., comprising the amino acid sequence of SEQ ID NO: 97) that is fused to an intracellular co-signaling domain of CD28 (e.g., SEQ ID NO: 101) and a CD3 ⁇ signaling domain (e.g., SEQ ID NO: 103).
  • the anti-CD19 CAR T cells comprises the amino acid sequence of SEQ ID NO: 118.
  • At least 30% of a population of anti-CD19 CAR T cells express a detectable level of the anti-CD19 CAR.
  • at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the anti-CD19 CAR T cells express a detectable level of the anti-CD19 CAR.
  • At least 50% of a population of anti-CD19 CAR T cells may not express a detectable level of ⁇ 2M surface protein.
  • at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the anti-CD19 CAR T cells may not express a detectable level of ⁇ 2M surface protein.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, or 90%-100% of the engineered T cells of a population does not express a detectable level of ⁇ 2M surface protein.
  • At least 50% of a population of anti-CD19 CAR T cells may not express a detectable level of TRAC surface protein.
  • at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the anti-CD19 CAR T cells may not express a detectable level of TRAC surface protein.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, or 90%-100% of the engineered T cells of a population does not express a detectable level of TRAC surface protein.
  • more than 90% (e.g., more than 99.5%) of the anti-CD19 CAR T cells do not express a detectable TRAC surface protein.
  • a substantial percentage of the population of anti-CD19 CAR T cells may comprise more than one gene edit, which results in a certain percentage of cells not expressing more than one gene and/or protein.
  • At least 50% of a population of anti-CD19 CAR T cells may not express a detectable level of two surface proteins, e.g., does not express a detectable level of ⁇ 2M and TRAC proteins.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, or 90%-100% of the anti-CD19 CAR T cells do not express a detectable level of TRAC and ⁇ 2M surface proteins.
  • at least 50% of a population of the anti-CD19 CAR T cells do not express a detectable level of TRAC and ⁇ 2M surface proteins.
  • the population of anti-CD19 CAR T cells may comprise more than one gene edit (e.g., in more than one gene), which may be an edit described herein.
  • the population of anti-CD19 CAR T cells may comprise a disrupted TRAC gene via the CRISPR/Cas technology using the TA-1 TRAC gRNA.
  • the anti-CD19 CAR T cells may comprise a deletion in the TRAC gene relative to unmodified T cells.
  • the anti-CD19 CAR T cells may comprise a deletion of the fragment AGAGCAACAGTGCTGTGGCC (SEQ ID NO: 69) in the TRAC gene.
  • anti-CD19 CAR T cells may comprise a disrupted ⁇ 2M gene via CRISPR/Cas9 technology using the gRNA of ⁇ 2M-1.
  • anti-CD19 CAR T cells may comprise Indels in the ⁇ 2M gene, which comprise one or more of the nucleotide sequences of SEQ ID NOs: 83-88.
  • anti-CD19 CAR T cells comprise ⁇ 30% CAR + T cells, ⁇ 50% ⁇ 2M + cells, and ⁇ 30% TCR ⁇ + cells.
  • anti-CD19 CAR T cells comprise ⁇ 30% CAR + T cells, ⁇ 30% ⁇ 2M + cells, and ⁇ 0.5% TCR ⁇ + cells.
  • the genetically engineered T cell population may be the anti-CD19 CAR T cells disclosed herein that further comprise a disrupted Reg1 gene.
  • the disrupted Reg1 gene may comprise any of the sequences provided in Tables 29-38 below.
  • the anti-CD19 CAR T cells may comprise at least 80% Reg1 ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above Reg1 ⁇ cells.
  • the genetically engineered T cell population may be the anti-CD19 CAR T cells disclosed herein that further comprise a disrupted TGFBRII gene.
  • the disrupted TGFBRII gene may comprise a nucleotide sequence selected from those listed in Tables 40-48 below.
  • the anti-CD19 CAR T cells may comprise at least 80% TGFBRII ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above TGFBRII ⁇ cells.
  • the genetically engineered T cell population may be the anti-CD19 CAR T cells disclosed herein that further comprise a disrupted TGFBRII gene and a disrupted Reg1 gene.
  • the disrupted Reg1 gene may comprise any of the sequences provided in Tables 29-38 below.
  • the disrupted TGFBRII gene may comprise a nucleotide sequence selected from those listed in Tables 40-48 below.
  • the anti-CD19 CAR T cells may comprise at least 80% TGFBRII ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above TGFBRII ⁇ cells.
  • the anti-CD19 CAR T cells may comprise at least 80% Reg1 ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above Reg1 ⁇ cells.
  • the anti-CD19 CAR T cells may comprise at least 60% Reg1 ⁇ /TGPBRII ⁇ cells, for example, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or above Reg1 ⁇ /TGFBRII ⁇ cells.
  • such a population of genetically engineered T cells may comprise about 90-97% Reg1 ⁇ cells, about 80-89% TGFBRII ⁇ cells, about 90-99% TCR ⁇ cells, and/or about 60-82% ⁇ 2M ⁇ cells.
  • the cell population may also contain at least 50% (e.g., at least 60%) cells expressing the anti-CD19 CAR.
  • the anti-BCMA CAR T cells disclosed herein which express any of the anti-BCMA CAR disclosed herein (e.g., the anti-BCMA CAR comprising the amino acid sequence of SEQ ID NO: 146), may also comprise a disrupted TRAC gene and/or a disrupted ⁇ 2M gene as also disclosed herein.
  • the population of genetically engineered T cells are anti-BCMA CAR T cells that further comprise a disrupted Reg1 gene, a disrupted TGFBRII gene, or a combination thereof.
  • the population of genetically engineered immune cells e.g., T cells such as human T cells
  • anti-BCMA CAR T cells are anti-BCMA CAR T cells having disrupted TRAC gene and ⁇ 2M gene.
  • the nucleic acid encoding the anti-BCMA CAR can be inserted in the disrupted TRAC gene at the site of SEQ ID NO: 69, which is replaced by the nucleic acid encoding the anti-BCMA CAR, thereby disrupting expression of the TRAC gene.
  • the disrupted TRAC gene in the anti-BCMA CAR T cells may comprise the nucleotide sequence of SEQ ID NO: 145.
  • Anti-BCMA CAR T cells that comprise a disrupted Reg1 gene can be produced via ex vivo genetic modification using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) technology to disrupt targeted genes (Reg1, and optionally TRAC and ⁇ 2M genes), and adeno-associated virus (AAV) transduction to deliver the anti-BCMA CAR construct.
  • CRISPR-Cas9-mediated gene editing involves at least three guide RNAs (sgRNAs), as described above for anti-CD19 CAR T cells.
  • Anti-BCMA CAR T cells that comprise a disrupted TGFBRII gene can be produced via ex vivo genetic modification using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) technology to disrupt targeted genes (TGFBRII, and optionally TRAC and ⁇ 2M genes), and adeno-associated virus (AAV) transduction to deliver the anti-BCMA CAR construct.
  • CRISPR-Cas9-mediated gene editing involves at least three guide RNAs (sgRNAs), as described above for anti-BCMA CAR T cells.
  • Anti-BCMA CAR T cells that comprise a disrupted Reg1 gene and a disrupted TGFBRII gene can be produced via ex vivo genetic modification using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) technology to disrupt targeted genes (TGFBRII and Reg1, and optionally TRAC and ⁇ 2M genes), and adeno-associated virus (AAV) transduction to deliver the anti-BCMA CAR construct.
  • CRISPR-Cas9-mediated gene editing involves at least three guide RNAs (sgRNAs), as described above for anti-BCMA CAR T cells.
  • the anti-BCMA CAR T cells are composed of an anti-BCMA single-chain antibody fragment (scFv, which may comprise the amino acid sequence of SEQ ID NO: 148), followed by a CD8 hinge and transmembrane domain (e.g., comprising the amino acid sequence of SEQ ID NO: 97) that is fused to an intracellular co-signaling domain of CD28 (e.g., SEQ ID NO: 101) and a CD3 ⁇ signaling domain (e.g., SEQ ID NO: 103).
  • the anti-BCMA CAR T cells comprises the amino acid sequence of SEQ ID NO: 146.
  • At least 30% of a population of anti-BCMA CAR T cells express a detectable level of the anti-BCMA CAR.
  • at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the anti-BCMA CAR T cells express a detectable level of the anti-BCMA CAR.
  • At least 50% of a population of anti-BCMA CAR T cells may not express a detectable level of ⁇ 2M surface protein.
  • at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the anti-BCMA CAR T cells may not express a detectable level of ⁇ 2M surface protein.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, or 90%-100% of the engineered T cells of a population does not express a detectable level of ⁇ 2M surface protein.
  • At least 50% of a population of anti-BCMA CAR T cells may not express a detectable level of TRAC surface protein.
  • at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the anti-BCMA CAR T cells may not express a detectable level of TRAC surface protein.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, or 90%-100% of the engineered T cells of a population does not express a detectable level of TRAC surface protein.
  • more than 90% (e.g., more than 99.5%) of the anti-BCMA CAR T cells do not express a detectable TRAC surface protein.
  • a substantial percentage of the population of anti-BCMA CAR T cells may comprise more than one gene edit, which results in a certain percentage of cells not expressing more than one gene and/or protein.
  • At least 50% of a population of anti-BCMA CAR T cells may not express a detectable level of two surface proteins, e.g., does not express a detectable level of ⁇ 2M and TRAC proteins.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, or 90%-100% of the anti-BCMA CAR T cells do not express a detectable level of TRAC and ⁇ 2M surface proteins.
  • at least 50% of a population of anti-BCMA CAR T cells do not express a detectable level of TRAC and ⁇ 2M surface proteins.
  • the population of anti-BCMA CAR T cells may comprise more than one gene edit (e.g., in more than one gene), which may be an edit described herein.
  • the population of anti-BCMA CAR T cells may comprise a disrupted TRAC gene via the CRISPR/Cas technology using the TA-1 TRAC gRNA.
  • the anti-BCMA CAR T cells may comprise a deletion in the TRAC gene relative to unmodified T cells.
  • the anti-CD19 CAR T cells may comprise a deletion of the fragment AGAGCAACAGTGCTGTGGCC (SEQ ID NO: 69) in the TRAC gene.
  • anti-BCMA CAR T cells may comprise a disrupted ⁇ 2M gene via CRISPR/Cas9 technology using the gRNA of ⁇ 2M-1.
  • Such anti-BCMA CAR T cells may comprise Indels in the ⁇ 2M gene, which comprise one or more of the nucleotide sequences of SEQ ID NOs: 83-88.
  • anti-BCMA CAR T cells comprise ⁇ 30% CAR + T cells, ⁇ 50% ⁇ 2M + cells, and ⁇ 30% TCR ⁇ + cells.
  • anti-BCMA CAR T cells comprise ⁇ 30% CAR + T cells, ⁇ 30% ⁇ 2M + cells, and ⁇ 0.5% TCR ⁇ + cells.
  • the genetically engineered T cell population may be the anti-BCMA CAR T cells disclosed herein that further comprise a disrupted Reg1 gene.
  • the disrupted Regnase 1 (Reg1) gene may comprise any of the sequences provided in Tables 29-38 below.
  • the anti-BCMA CAR T cells may comprise at least 80% Reg1 ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above Reg1 ⁇ cells.
  • the genetically engineered T cell population may be the anti-BCMA CAR T cells disclosed herein that further comprise a disrupted TGFBRII gene.
  • the disrupted TGFBRII gene may comprise a nucleotide sequence selected from those listed in Tables 40-48 below.
  • the anti-BCMA CAR T cells may comprise at least 80% TGFBRII ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above TGFBRII ⁇ cells.
  • the genetically engineered T cell population may be the anti-BCMA CAR T cells disclosed herein that further comprise a disrupted TGFBRII gene and a disrupted Reg1 gene.
  • the disrupted Reg1 gene may comprise any of the sequences provided in Tables 29-38 below.
  • the disrupted TGFBRII gene may comprise a nucleotide sequence selected from those listed in Tables 40-48 below.
  • the anti-BCMA CAR T cells may comprise at least 80% TGFBRII ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above TGFBRII ⁇ cells.
  • the anti-BCMA CAR T cells may comprise at least 80% Reg1 ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above Reg1 ⁇ cells.
  • the anti-BCMA CAR T cells may comprise at least 60% Reg1 ⁇ /TGBBRII ⁇ cells, for example, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or above Reg1 ⁇ /TGFBRII ⁇ cells.
  • Also provided herein is population of genetically engineered immune cells e.g., T cells such as human T cells
  • a disrupted Reg1 gene e.g., a disrupted TRFBRII gene, or a combination thereof
  • anti-CD70 CAR e.g., those disclosed herein.
  • the population of genetically engineered immune cells e.g., T cells such as human T cells
  • the population of genetically engineered immune cells comprising both a disrupted Reg1 gene and a disrupted TGFBRII gene, and expressing an anti-CD70 CAR, e.g., those disclosed herein.
  • the anti-CD70 CART cells disclosed herein which express any of the anti-CD70 CAR disclosed herein (e.g., the anti-CD70 CAR comprising the amino acid sequence of SEQ ID NO: 138), may also comprise a disrupted TRAC gene, a disrupted ⁇ 2M gene, and/or a disrupted CD70 gene as also disclosed herein.
  • anti-CD70 CAR T cells are anti-CD70 CAR T cells having disrupted TRAC gene, a disrupted ⁇ 2M gene, and a disrupted CD70 gene.
  • the nucleic acid encoding the anti-CD70 CAR can be inserted in the disrupted TRAC gene at the site of SEQ ID NO: 69, which is replaced by the nucleic acid encoding the anti-CD70 CAR, thereby disrupting expression of the TRAC gene.
  • the disrupted TRAC gene in the anti-CD70 CAR T cells may comprise the nucleotide sequence of SEQ ID NO: 139.
  • Anti-CD70 CAR T cells that comprise a disrupted Reg1 gene can be produced via ex vivo genetic modification using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) technology to disrupt targeted genes (Reg1, and optionally TRAC, ⁇ 2M and/or CD70 genes), and adeno-associated virus (AAV) transduction to deliver the anti-CD70 CAR construct.
  • CRISPR/Cas9 Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9
  • Regular1, and optionally TRAC, ⁇ 2M and/or CD70 genes adeno-associated virus (AAV) transduction to deliver the anti-CD70 CAR construct.
  • AAV adeno-associated virus
  • CRISPR-Cas9-mediated gene editing involves at least an sgRNA targeting the Reg1 gene as those disclosed herein (see, e.g., Table 22), and optionally an sgRNA (SEQ ID NO: 55) which targets the CD70 locus, TA-1 sgRNA (SEQ ID NO: 59) which targets the TRAC locus, and ⁇ 2M-1 sgRNA (SEQ ID NO: 63) which targets the ⁇ 2M locus.
  • SEQ ID NO: 55 which targets the CD70 locus
  • TA-1 sgRNA SEQ ID NO: 59
  • ⁇ 2M-1 sgRNA SEQ ID NO: 63
  • Anti-CD70 CAR T cells that comprise a disrupted TGFBRII gene can be produced via ex vivo genetic modification using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) technology to disrupt targeted genes (TGFBRII, and optionally, TRAC, ⁇ 2M, and/or CD70 genes), and adeno-associated virus (AAV) transduction to deliver the anti-CD70 CAR construct.
  • CRISPR/Cas9 Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9
  • TGFBRII and optionally, TRAC, ⁇ 2M, and/or CD70 genes
  • AAV adeno-associated virus
  • CRISPR-Cas9-mediated gene editing involves at least an sgRNA targeting the TGFBRII gene as those disclosed herein (see, e.g., Table 39), and optionally an sgRNA (SEQ ID NO: 43) which targets the CD70 locus, TA-1 sgRNA (SEQ ID NO: 59) which targets the TRAC locus, and ⁇ 2M-1 sgRNA (SEQ ID NO: 63) which targets the ⁇ 2M locus.
  • SEQ ID NO: 43 which targets the CD70 locus
  • TA-1 sgRNA SEQ ID NO: 59
  • ⁇ 2M-1 sgRNA SEQ ID NO: 63
  • Anti-CD70 CAR T cells that comprise a disrupted TGFBRII gene and a disrupted Reg1 gene can be produced via ex vivo genetic modification using the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9) technology to disrupt targeted genes (TGFBRII and Reg1, and optionally, TRAC, ⁇ 2M, and/or CD70 genes), and adeno-associated virus (AAV) transduction to deliver the anti-CD70 CAR construct.
  • CRISPR/Cas9 Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated protein 9
  • AAV adeno-associated virus
  • CRISPR-Cas9-mediated gene editing involves at least an sgRNA targeting the TGFBRII gene as those disclosed herein (see, e.g., Table 39), and an sgRNA targeting the Reg1 gene as those disclosed herein (see, e.g., Table 22), and optionally an sgRNA (SEQ ID NO: 55) which targets the CD70 locus, TA-1 sgRNA (SEQ ID NO: 59) which targets the TRAC locus, and ⁇ 2M-1 sgRNA (SEQ ID NO: 63) which targets the ⁇ 2M locus.
  • SEQ ID NO: 55 which targets the CD70 locus
  • TA-1 sgRNA SEQ ID NO: 59
  • ⁇ 2M-1 sgRNA SEQ ID NO: 63
  • the anti-CD70 CAR T cells are composed of an anti-CD70 CAR single-chain antibody fragment (scFv, which may comprise the amino acid sequence of SEQ ID NO: 138), followed by a CD8 hinge and transmembrane domain (e.g., comprising the amino acid sequence of SEQ ID NO: 97) that is fused to an intracellular co-signaling domain of CD28 (e.g., SEQ ID NO: 101) and a CD3 ⁇ signaling domain (e.g., SEQ ID NO: 103).
  • the anti-CD70 CAR T cells comprise the amino acid sequence of SEQ ID NO: 138.
  • At least 30% of a population of anti-CD70 CAR T cells express a detectable level of the anti-CD70 CAR.
  • at least 40%, at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the anti-CD70 CAR T cells express a detectable level of the anti-CD70 CAR.
  • At least 50% of a population of anti-CD70 CAR T cells may not express a detectable level of ⁇ 2M surface protein.
  • at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the anti-CD70 CAR T cells may not express a detectable level of ⁇ 2M surface protein.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, or 90%-100% of the engineered T cells of a population does not express a detectable level of ⁇ 2M surface protein.
  • At least 50% of a population of anti-CD70 CAR T cells may not express a detectable level of TRAC surface protein.
  • at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, or at least 95% of the anti-CD70 CAR T cells may not express a detectable level of TRAC surface protein.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, or 90%-100% of the engineered T cells of a population does not express a detectable level of TRAC surface protein.
  • more than 90% (e.g., more than 99.5%) of the anti-CD70 CAR T cells do not express a detectable TRAC surface protein.
  • At least 50% of a population of the anti-CD70 CAR T cells may not express a detectable level of CD70 surface protein.
  • at least 55%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, or at least 98% of the engineered T cells of a population may not express a detectable level of CD70 surface protein.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, 90%-100%, or 95%-100% of the engineered T cells of a population does not express a detectable level of CD70 surface protein.
  • a substantial percentage of the population of anti-CD70 CAR T cells may comprise more than one gene edit, which results in a certain percentage of cells not expressing more than one gene and/or protein.
  • At least 50% of a population of anti-CD70 CAR T cells may not express a detectable level of two surface proteins, e.g., does not express a detectable level of ⁇ 2M and TRAC proteins, ⁇ 2M and CD70 proteins, or TRAC and CD70 proteins.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, or 90%-100% of the engineered T cells of a population does not express a detectable level of two surface proteins.
  • At least 50% of a population of the CTX130 cells may not express a detectable level of all of the three target surface proteins ⁇ 2M, TRAC, and CD70 proteins.
  • 50%-100%, 50%-90%, 50%-80%, 50%-70%, 50%-60%, 60%-100%, 60%-90%, 60%-80%, 60%-70%, 70%-100%, 70%-90%, 70%-80%, 80%-100%, 80%-90%, or 90%-100% of the engineered T cells of a population does not express a detectable level of ⁇ 2M, TRAC, and CD70 surface proteins.
  • the population of anti-CD70 CAR T cells may comprise more than one gene edit (e.g., in more than one gene), which may be an edit described herein.
  • the population of anti-CD70 CAR T cells may comprise a disrupted TRAC gene via the CRISPR/Cas technology using the TA-1 TRAC gRNA.
  • the anti-CD70 CAR T cells may comprise a deletion in the TRAC gene relative to unmodified T cells.
  • the anti-CD70 CAR T cells may comprise a deletion of the fragment AGAGCAACAGTGCTGTGGCC (SEQ ID NO: 69) in the TRAC gene.
  • anti-CD70 CAR T cells may comprise a disrupted ⁇ 2M gene via CRISPR/Cas9 technology using the gRNA of ⁇ 2M-1.
  • Such anti-CD70 CAR T cells may comprise indels in the ⁇ 2M gene, which comprise one or more of the nucleotide sequences of SEQ ID NOs: 83-88.
  • anti-CD70 CAR T cells comprise ⁇ 30% CAR + T cells, ⁇ 50% ⁇ 2M + cells, and ⁇ 30% TCR ⁇ + cells.
  • anti-CD70 CAR T cells comprise ⁇ 30% CAR + T cells, ⁇ 30% ⁇ 2M + cells, and ⁇ 0.5% TCR ⁇ + cells.
  • the genetically engineered T cell population may be the anti-CD70 CAR T cells disclosed herein that further comprise a disrupted Reg1 gene.
  • the disrupted Regnase 1 gene may comprise any of the sequences provided in Tables 22-31 below.
  • Such a genetically engineered T cells may have ⁇ 30% CAR+ T cells, ⁇ 0.4% TCR + T cells, ⁇ 30% ⁇ 2M + T cells, and ⁇ 2% CD70 + T cells.
  • the anti-CD70 CAR T cells may comprise at least 80% Reg1 ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above Reg1 ⁇ cells.
  • the genetically engineered T cell population may be the anti-CD70 CAR T cells disclosed herein that further comprise a disrupted TGFBRII gene.
  • a genetically engineered T cells may have ⁇ 30% CAR+ T cells, ⁇ 0.4% TCR + T cells, ⁇ 30% ⁇ 2M + T cells, and ⁇ 2% CD70 + T cells.
  • the anti-CD70 CAR T cells may comprise at least 80% TGFBRII ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above TGFBRII ⁇ cells.
  • the genetically engineered T cell population may be the anti-CD70 CAR T cells disclosed herein that further comprise a disrupted TGFBRII gene and a disrupted Reg1 gene.
  • the disrupted Regnase 1 gene may comprise any of the sequences provided in Tables 29-38 below.
  • the disrupted TGFBRII gene may comprise a nucleotide sequence selected from those listed in Tables 40-48 below.
  • Such a genetically engineered T cells may have ⁇ 30% CAR+ T cells, ⁇ 0.4% TCR + T cells, ⁇ 30% ⁇ 2M + T cells, and ⁇ 2% CD70+ T cells.
  • the anti-CD70 CAR T cells may comprise at least 80% TGFBRII ⁇ cells, for example, at least 85%, at least 90%, at least 95%, at least 98% or above TGFBRII ⁇ cells.
  • the anti-CD70 CAR T cells may comprise at least 60% Reg1 ⁇ /TGFBRII ⁇ cells, for example, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or above Reg1 ⁇ /TGFBRII ⁇ cells.
  • the therapeutic T cells generated using the genetically engineered T cells disclosed herein would be expected to maintain T cell health enabled by the disruption of the Reg1 gene, the disruption of the TGFBRII gene, the disruption of the CD70 gene, or a combination thereof.
  • maintaining T cell health may extend expansion during manufacturing, thereby increasing yield and consistency.
  • maintaining T cell health may rescue exhausted/unhealthy T cells, thereby enabling potentially lower doses in patients and more robust responses.
  • the disruption of the Reg1 gene and the TGFBRII gene showed synergistic effects in enhancing CAR-T cell potency and in vivo expansion.
  • the therapeutic T cells disclosed herein can be administered to a subject for therapeutic purposes, for example, treatment of a solid tumor targeted by the CAR construct expressed by the therapeutic T cells.
  • the step of administering may include the placement (e.g., transplantation) of the therapeutic T cells into a subject by a method or route that results in at least partial localization of the therapeutic T cells at a desired site, such as a tumor site, such that a desired effect(s) can be produced.
  • Therapeutic T cells can be administered by any appropriate route that results in delivery to a desired location in the subject where at least a portion of the implanted cells or components of the cells remain viable.
  • the period of viability of the cells after administration to a subject can be as short as a few hours, e.g., twenty-four hours, to a few days, to as long as several years, or even the life time of the subject, i.e., long-term engraftment.
  • an effective amount of the therapeutic T cells can be administered via a systemic route of administration, such as an intraperitoneal or intravenous route.
  • the therapeutic T cells are administered systemically, which refers to the administration of a population of cells other than directly into a target site, tissue, or organ, such that it enters, instead, the subject's circulatory system and, thus, is subject to metabolism and other like processes.
  • Suitable modes of administration include injection, infusion, instillation, or ingestion.
  • Injection includes, without limitation, intravenous, intramuscular, intra-arterial, intrathecal, intraventricular, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, sub capsular, subarachnoid, intraspinal, intracerebro spinal, and intrasternal injection and infusion.
  • the route is intravenous.
  • a subject may be any subject for whom diagnosis, treatment, or therapy is desired.
  • the subject is a mammal. In some embodiments, the subject is a human.
  • the therapeutic T cells may be autologous (“self”) to the subject, i.e., the cells are from the same subject.
  • the therapeutic T cells can be non-autologous (“non-self,” e.g., allogeneic, syngeneic or xenogeneic) to the subject.
  • “Allogeneic” means that the therapeutic T cells are not derived from the subject who receives the treatment but from different individuals (donors) of the same species as the subject.
  • a donor is an individual who is not the subject being treated.
  • a donor is an individual who is not the patient.
  • a donor is an individual who does not have or is not suspected of having the cancer being treated.
  • multiple donors e.g., two or more donors, are used.
  • an engineered T cell population being administered according to the methods described herein comprises allogeneic T cells obtained from one or more donors.
  • Allogeneic refers to a cell, cell population, or biological samples comprising cells, obtained from one or more different donors of the same species, where the genes at one or more loci are not identical to the recipient (e.g., subject).
  • an engineered T cell population, being administered to a subject can be derived from one or more unrelated donors, or from one or more non-identical siblings.
  • syngeneic cell populations may be used, such as those obtained from genetically identical donors, (e.g., identical twins).
  • the cells are autologous cells; that is, the engineered T cells are obtained or isolated from a subject and administered to the same subject, i.e., the donor and recipient are the same.
  • An effective amount refers to the amount of a population of engineered T cells needed to prevent or alleviate at least one or more signs or symptoms of a medical condition (e.g., cancer), and relates to a sufficient amount of a composition to provide the desired effect, e.g., to treat a subject having a medical condition.
  • An effective amount also includes an amount sufficient to prevent or delay the development of a symptom of the disease, alter the course of a symptom of the disease (for example but not limited to, slow the progression of a symptom of the disease), or reverse a symptom of the disease. It is understood that for any given case, an appropriate effective amount can be determined by one of ordinary skill in the art using routine experimentation.
  • the dose of the therapeutic T cells provided herein would be lower than the standard dose of CAR-T cells prepared by conventional approaches (e.g., using T cells that do not have one or more of the genetic editing events disclosed herein, including a disrupted Reg1 gene and/or a disrupted CD70 gene).
  • the effective amount of the therapeutic T cells disclosed herein may be at least 2-fold lower, at least 5-fold lower, at least 10-fold lower, at least 20-fold lower, at least 50-fold lower, or at least 100-fold lower than a standard dose of a CAR-T therapy.
  • an effective amount of the therapeutic T cells disclosed herein may be less than 10 6 cells, e.g., 10 5 cells, 5 ⁇ 10 4 cells, 10 4 cells, 5 ⁇ 10 3 cells, or 10 3 cells.
  • the cells are expanded in culture prior to administration to a subject in need thereof.
  • the efficacy of a treatment using the therapeutic T cells disclosed herein can be determined by the skilled clinician.
  • a treatment is considered “effective”, if any one or all of the signs or symptoms of, as but one example, levels of functional target are altered in a beneficial manner (e.g., increased by at least 10%), or other clinically accepted symptoms or markers of disease (e.g., cancer) are improved or ameliorated.
  • Efficacy can also be measured by failure of a subject to worsen as assessed by hospitalization or need for medical interventions (e.g., progression of the disease is halted or at least slowed). Methods of measuring these indicators are known to those of skill in the art and/or described herein.
  • Treatment includes any treatment of a disease in subject and includes: (1) inhibiting the disease, e.g., arresting, or slowing the progression of symptoms; or (2) relieving the disease, e.g., causing regression of symptoms; and (3) preventing or reducing the likelihood of the development of symptoms.
  • Combination therapies are also encompassed by the present disclosure.
  • the therapeutic T cells disclosed herein may be co-used with other therapeutic agents, for treating the same indication, or for enhancing efficacy of the therapeutic T cells and/or reducing side effects of the therapeutic T cells.
  • kits for use in producing the genetically engineered T cells, the therapeutic T cells, and for therapeutic uses are provided.
  • kits provided herein may comprise components for performing genetic edit of one or more of Reg1 gene, TGFBRII gene, and CD70 gene, and optionally a population of immune cells to which the genetic editing will be performed (e.g., a leukopak).
  • a leukopak sample may be an enriched leukapheresis product collected from peripheral blood. It typically contains a variety of blood cells including monocytes, lymphocytes, platelets, plasma, and red cells.
  • the components for genetically editing one or more of the target genes may comprise a suitable endonuclease such as an RNA-guided endonuclease and one or more nucleic acid guides, which direct cleavage of one or more suitable genomic sites by the endonuclease.
  • the kit may comprise a Cas enzyme such as Cas 9 and one or more gRNAs targeting a Reg1 gene, a TGFBRII gene, and/or a CD70 gene. Any of the gRNAs specific to these target genes can be included in the kit.
  • Such a kit may further comprise components for further gene editing, for example, gRNAs and optionally additional endonucleases for editing other target genes such as ⁇ 2M and/or TRAC.
  • a kit provided herein may comprise a population of genetically engineered T cells as disclosed herein, and one or more components for producing the therapeutic T cells as also disclosed herein.
  • Such components may comprise an endonuclease suitable for gene editing and a nucleic acid coding for a CAR construct of interest.
  • the CAR-coding nucleic acid may be part of a donor template as disclosed herein, which may contain homologous arms flanking the CAR-coding sequence.
  • the donor template may be carried by a viral vector such as an AAV vector.
  • the kit may further comprise gRNAs specific to a TRAC gene for inserting the CAR-coding sequence into the TRAC gene.
  • the kit may further comprise gRNAs specific to a ⁇ 2M gene for inserting the CAR-coding sequence into the ⁇ 2M gene.
  • the kit may further comprise gRNAs specific to a CD70 gene for inserting the CAR-coding sequence into the CD70 gene.
  • the kit may further comprise gRNAs specific to a Reg1 gene for inserting the CAR-coding sequence into the Reg1 gene.
  • the kit may further comprise gRNAs specific to a TGFBRII gene for inserting the CAR-coding sequence into the TGFBRII gene.
  • the kit disclosed herein may comprise a population of therapeutic T cells as disclosed for the intended therapeutic purposes.
  • kit disclosed herein may further comprise instructions for making the therapeutic T cells, or therapeutic applications of the therapeutic T cells.
  • the included instructions may comprise a description of using the gene editing components to genetically engineer one or more of the target genes (e.g., Reg1, TGFBRII, CD70, or a combination thereof).
  • the included instructions may comprise a description of how to introduce a nucleic acid encoding a CAR construction into the T cells for making therapeutic T cells.
  • the kit may further comprise instructions for administration of the therapeutic T cells as disclosed herein to achieve the intended activity, e.g., eliminating disease cells targeted by the CAR expressed on the therapeutic T cells.
  • the kit may further comprise a description of selecting a subject suitable for treatment based on identifying whether the subject is in need of the treatment.
  • the instructions relating to the use of the therapeutic T cells described herein generally include information as to dosage, dosing schedule, and route of administration for the intended treatment.
  • the containers may be unit doses, bulk packages (e.g., multi-dose packages) or sub-unit doses. Instructions supplied in the kits of the disclosure are typically written instructions on a label or package insert.
  • the label or package insert indicates that the therapeutic T cells are used for treating, delaying the onset, and/or alleviating a disease or disorder in a subject.
  • kits provided herein are in suitable packaging.
  • suitable packaging includes, but is not limited to, vials, bottles, jars, flexible packaging, and the like.
  • packages for use in combination with a specific device such as an infusion device for administration of the therapeutic T cells.
  • a kit may have a sterile access port (for example, the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • the container may also have a sterile access port.
  • Kits optionally may provide additional components such as buffers and interpretive information.
  • the kit comprises a container and a label or package insert(s) on or associated with the container.
  • the disclosure provides articles of manufacture comprising contents of the kits described above.
  • the Reg1 gene was efficiently edited in primary human T cells ex vivo using CRISPR/Cas9 gene editing. Genomic segments of the Reg1 gene containing the six (6) protein coding exons were used as input in gRNA design software. Desired gRNAs were those that would lead to insertions or deletions in the coding sequence, disrupting the amino acid sequence of Reg1, leading to out of frame/loss of function allele(s) (referred to as “Reg1 knockout (KO)” alleles or “Reg1 disrupted alleles”). All ten (10) in silico-identified gRNA spacer sequences targeting the Reg1 gene were synthesized, and the gRNAs were specifically modified, as indicated in Table 1.
  • gRNAs used in this example were modified with 2′-O-methyl phosphorothioate modifications, unmodified gRNAs, or gRNAs with other modifications, may be used.
  • the target sequences and gRNA sequences of the Reg1 guides Z01-Z10 are provided in Table 22 below.
  • gRNAs yielded measurable data by TIDE analysis, as indicated in Table 1.
  • Eight (8) gRNA sequences yielded indel percentages (editing frequencies) above 90%, indicating highly efficient gene editing.
  • On-target and off-target editing efficiencies of various REG1-targeting gRNAs noted above were examined following the method disclosed in the above section. Briefly, activated T cells were transfected (electroporated) with a ribonucleoprotein particle (RNP) containing Cas9 nuclease and a synthetic modified sgRNA targeting the Reg1 gene (sequences in Table 22 below) or controls (no Cas9, no gRNA).
  • RNP ribonucleoprotein particle
  • NHEJ on-target non-homologous end joining
  • Table 2 shows the on and off target editing results (from two donors) of exemplary Reg1 gRNAs obtained by the hybrid capture assay disclosed herein.
  • On-target gene edited sequences by the exemplary Reg1 gRNAs are presented in Tables 29-38 below, with the frequencies of these sequences representing the percent of all sequences spanning the on-target site within 20 bp upstream and downstream of each cut site.
  • the indels for each guide are shown relative to an on-target reference sequence in Tables 29-38.
  • the reference sequence is centered on the cleavage site with 10 bp in either direction, ending 4 bp 3′ of the PAM.
  • Allogeneic human T cells that lack expression of the TRAC gene, ⁇ 2M gene, CD70 gene, and Regnase-1 gene, and express a chimeric antigen receptor (CAR) targeting CD70 were produced. Briefly, activated human T cells were first isolated and then Cas9:sgRNA RNPs (1 ⁇ M Cas9, 5 ⁇ M gRNA) were delivered to the activated human T cells by electroporation, followed by incubation with recombinant adeno-associated adenoviral vectors (AAVs), serotype 6 (AAV6) (MOI 50,000).
  • AAVs adeno-associated adenoviral vectors
  • AAV6 serotype 6
  • the nucleofection mix contained the NucleofectorTM Solution, 5 ⁇ 10 6 cells, 1 ⁇ M Cas9, and 5 ⁇ M gRNA (as described in Hendel et al., Nat Biotechnol. 2015; 33(9):985-989, PMID: 26121415).
  • the RNP complex comprised Cas9 and sgRNA targeting the TRAC, B2M, and CD70 (shown in Table 23) and optionally Regnase-1 genes (using the REG1-Z01 to REG1-Z10 sgRNAs shown in Table 22).
  • the rAAV vector included the nucleotide sequence encoding an anti-CD70 CAR (the donor template in SEQ ID NO: 169, encoding an anti-CD70 CAR amino acid sequence of SEQ ID NO: 138).
  • anti-CD70 CAR T cells were utilized. Specifically, 2.5 to 3.8 ⁇ 10 6 total anti-CD70 CAR T cells comprising a quadruple disruption (TRAC ⁇ / ⁇ 2M ⁇ /CD70 ⁇ /Reg1 ⁇ ) were generated and compared to anti-CD70 CAR T cells with unedited Reg1 (TRAC ⁇ / ⁇ 2M ⁇ /CD70 ⁇ ).
  • Reg1 guides REG1-Z01, REG1-Z03, REG1-Z07, REG1-Z09, and REG1-Z10 appear to have a greater effect on cell expansion than cells made using Reg1 guides REG1-Z02 or REG1-Z08.
  • Reg1 guide REG1-Z10 was used in CAR T cells made from a different T cell donor in replicates by two operators (labelled A and B). The effect of increased cell culture expansion was demonstrated again. The increase in cell expansion can be seen as early as day 13 and continues throughout the experiment to day 52 ( FIG. 1B ). Furthermore, anti-CD70 CAR-T cells containing a Reg1 disruption are maintained over a longer time in culture (at least up to day 52) as compared to anti-CD70 CAR-T cells with an unedited Regnase 1 gene, one of which was no longer viable on day 26. Collectively, these data show that disruption of the Reg1 gene results in greater cell culture yields and longer cell maintenance in culture as compared to CAR T cells with an unedited Reg1 gene.
  • Allogeneic human T cells that lack expression of the TRAC gene, ⁇ 2M gene and CD70 gene, and express a chimeric antigen receptor (CAR) targeting CD70 were produced.
  • the edited CAR T cells further comprised knock out of Reg1 gene.
  • activated human T cells we electroporated with Cas9:sgRNA RNPs (1 ⁇ M Cas9, 5 ⁇ M gRNA), followed by incubation with a recombinant adeno-associated adenoviral vectors, serotype 6 (AAV6) (MOI 50,000).
  • Recombinant AAV comprised the nucleotide sequence of SEQ ID NO: 169 (encoding anti-CD70 CAR comprising the amino acid sequence of SEQ ID NO: 138).
  • the following sgRNAs were used: TRAC (SEQ ID NO: 58), ⁇ 2M (SEQ ID NO: 62), CD70 (SEQ ID NO: 54), and optionally Reg1 (e.g., REG1-Z03, Z05, Z06, and Z10; see Table 22 and FIGS. 2A to 2E ).
  • T cells were checked for CAR expression by flow cytometry. Both anti-CD70 CAR T cells and anti-CD70 CAR T cells that lack Reg1 (using four gRNAs REG1-Z03, Z05, Z06, Z10) expressed nearly equivalent amount of CAR on their surface at day 7 (85.6% and 81.8%, 80%, 84.4%, 85.6%) and day 32 (97.6% and 90.7%, 91.5%, 92.6%, 93.2%) post HDR.
  • Reg1 using four gRNAs REG1-Z03, Z05, Z06, Z10
  • a cell killing assay was used to assess the ability of the TRAC ⁇ / ⁇ 2M ⁇ /CD70 ⁇ /Reg1 ⁇ /anti-CD70 CAR+ cells to kill CD70+ adherent renal cell carcinoma (RCC)-derived cell lines (ACHN, Caki-1, and/or 769P cell lines).
  • RCC adherent renal cell carcinoma
  • Adherent cells were seeded in 96-well plates at 50,000 cells per well and incubated overnight at 37° C. The next day edited anti-CD70 CAR T cells (cultured until day 12 post HDR or day 27 post HDR) were added to the wells containing target cells at 1:1, 2:1 or 1.5:1 CAR T:Target cell ratios.
  • CART cells were removed from the culture by aspiration and 100 ⁇ L Cell titer-Glo (Promega) was added to each well of the plate to assess the number of remaining viable target cells. The amount of light emitted per well was then quantified using a plate reader.
  • CD70 CAR+ T cells with Reg1 disruption using gRNAs REG1-Z03, REG1-Z05, REG1-Z10 gave a higher persistent potency than when using gRNA REG1-Z06.
  • CAR-T cells with Reg1 disruption demonstrated a visible increased in potency after 24 h co-culture with caki-1 ( FIGS. 2A, 2B, and 2C ) and ACHN ( FIG. 2D ), and after 6 hours co-culture with 769P (difference not visible anymore after 24 h) ( FIG. 2E ).
  • CD4+ and CD8+ T cells were assessed for PD-1 expression ( FIGS. 3A and 3B ) and TIM3 expression ( FIGS. 3C and 3D ) by flow cytometry at Day 13 ( FIGS. 3A and 3C ) and Day 26 ( FIGS. 3B and 3D ) post HDR.
  • T SCM T stem cell memory
  • T CM T central memory cell
  • TEM T effector memory cell
  • T EFF T effector cell
  • Exemplary surface markers of T cells at different differentiation stages are provided below.
  • T CM cells have been associated with T cell long term persistence in vivo: CD8+ clones isolated from T CM cells were shown to persist long term in vivo during adoptive T cell transfer in non-human primates while clones isolated from effector cells did not. (Berger et al., J. Clin. Investig. (2008) 118:294-305). Representative cell surface markers of the various types of T cells are provided in Table 3 below.
  • CD27 and CD45 RO T central memory T cell markers were assessed on TRAC ⁇ / ⁇ 2M ⁇ /CD70 ⁇ /anti-CD70 CAR+ and TRAC ⁇ / ⁇ 2M ⁇ /CD70 ⁇ /Reg1 ⁇ /anti-CD70 CAR+ cells.
  • Cells were stained using commercial antibodies for CD27 (Biolegend, clone M-T271) and CD45 RO (Biolegend, clone UCHL1) and analyzed by flow cytometry.
  • CAR-T cells with Reg1 knock out were more likely to exhibit central memory T cell identity (double positive for CD27 and CD45 RO) and less likely to exhibit effector memory cell identity (identified as CD27- and CD45 RO+), as shown in Table 4.
  • TRAC ⁇ / ⁇ 2M ⁇ /anti-CD19 CAR+ and TRAC ⁇ / ⁇ 2M ⁇ /Reg1 ⁇ /anti-CD19 CAR+ cells were assessed. 5 ⁇ 10 6 cells were plated approximately 2 weeks post cell production (Day 0) in 10 mL of full media containing IL2, IL7 and human serum, or in serum-containing media lacking cytokines (IL-2 and IL-7). Fresh full media or media lacking cytokines were added to the respective cultures once per week. The volume of media added allowed for the cultures to maintain a density of approximately 1-2 million cells/mL.
  • TRAC ⁇ / ⁇ 2M ⁇ /anti-CD19 CAR+ or TRAC ⁇ / ⁇ 2M ⁇ /Reg1 ⁇ /anti-CD19 CAR+ were no longer detectable at 40 days in the cultures that lacked cytokines, indicating that any potential off-target effects due to genome editing did not induce growth factor independent growth/proliferation to the cells ( FIG. 4 ).
  • the cells only proliferated in the presence of cytokines (full media that contains cytokines) and did not proliferate in the presence of serum alone. Thus, genome editing did not induce any adverse events that allow the cells to grow in the absence of cytokine, growth factor or antigen stimulation.
  • a disseminated mouse model was utilized to further assess the in vivo efficacy of allogeneic CAR T cells lacking ⁇ 2M and TRAC, as well as Reg1.
  • the intravenous disseminated model utilized CD19+B-ALL derived Nalm-6 Human Acute Lymphoblastic Leukemia tumor cell line in NOG mice to demonstrate the efficacy of TRAC ⁇ / ⁇ 2M ⁇ /anti-CD19 CAR+ T cells (anti-CD19 CAR T cells) with or without editing of the Reg1 locus.
  • the Reg1 gene was edited via CRISPR/Cas-mediated gene editing using REG1-Z10 guide RNA (see Table 22).
  • the anti-CD19 CAR T cells express an anti-CD19 CAR comprising the amino acid sequence of SEQ ID NO: 118. See also the sequence Tables 27 and 28 below, and WO2019/097305, the relevant disclosures of which are incorporated by reference for the subject matter and purpose referenced herein.
  • mice were individually housed in ventilated microisolator cages, maintained under pathogen-free conditions, 5-7 days prior to the start of the study. At the start of the study, the mice were divided into 5 treatment groups as shown in Table 5.
  • mice were inoculated with Nalm6-Fluc-GFP (Nalm6-Fluc-Neo/eGFP—Puro) cells intravenously to model disseminated disease.
  • Nalm6-Fluc-GFP Nalm6-Fluc-Neo/eGFP—Puro cells
  • mice received an intravenous injection of 0.5 ⁇ 10 6 Nalm6 cells/mouse.
  • Groups 2-5 received an intravenous injection of CAR T cells (4 ⁇ 10 6 CAR+ cells/mouse) as indicated in Table 5.
  • CAR T cells i.v.
  • mice were monitored daily and body weight was measured two times weekly. Bioluminescence (BLI; total ROI, photon/s) was measured twice weekly beginning on Day 4 of the study. A significant endpoint was the time to peri-morbidity and the effect of T-cell engraftment was also assessed. The percentage of animal mortality and time to death were recorded for every group in the study. Mice were euthanized prior to reaching a moribund state. Mice may be defined as moribund and sacrificed if one or more of the following criteria were met:
  • mice in groups receiving TRAC ⁇ / ⁇ 2M ⁇ /anti-CD19 CAR+ T cells with or without an additional Reg1 disruption exhibited an increase in survival relative to mice in the untreated group (Group 1).
  • Mice receiving either dose of TRAC ⁇ / ⁇ 2M ⁇ /Reg1 ⁇ /anti-CD19 CAR+ T cells exhibited increased survival in comparison to TRAC ⁇ / ⁇ 2M ⁇ /anti-CD19 CAR+ T cells at each respective dose ( FIGS. 5A and 5B ).
  • mice receiving either dose of TRAC ⁇ / ⁇ 2M ⁇ /Reg1 ⁇ /anti-CD19 CAR+ T cells had reduced leukemia burdens as indicated by diminished bioluminescence signal in comparison to TRAC ⁇ / ⁇ 2M ⁇ /anti-CD19 CAR+ T cells at each respective dose ( FIGS. 5C and 5D ).
  • This example describes efficient editing of the TGFBRII gene in primary human T cells ex vivo using CRISPR/Cas9 gene editing.
  • Genomic segments of the TGFBRII gene containing the first five (5) protein coding exons were used as input in gRNA design software.
  • the genomic segments also included flanking splice site acceptor/donor sequences. Desired gRNAs were those that would lead to insertions or deletions in the coding sequence, disrupting the amino acid sequence of TFBRII, leading to out of frame/loss of function allele(s) (referred to as “TGFBRII knockout alleles” or “TGFBRII disrupted alleles”).
  • gRNA spacer sequences targeting the CD70 gene were synthesized, and the gRNAs were specifically modified, as indicated in Table 39 and FIGS. 7A and 7B . While the modified gRNAs in Table 39 were modified with 2′-O-methyl phosphorothioate modifications, unmodified gRNAs, or gRNAs with other modifications, can be used.
  • gRNAs yielded measurable data by TIDE analysis, as indicated in FIG. 7A .
  • Seven (7) gRNA sequences yielded indel percentages (editing frequencies) above 80% indicating highly efficient gene editing ( FIG. 7A ).
  • the level of TGFBRII protein expression was assessed by western blot to confirm the TIDE analysis data and GAPDH was used as a loading control.
  • Seven (7) of the gRNAs showed nearly complete knock out of TGFBRII on the T cells ( FIG. 7B ).
  • TGFBRII-targeting gRNAs On-target and off-target editing efficiencies of various TGFBRII-targeting gRNAs noted above were examined following the method disclosed in the above section. Briefly, activated T cells were transfected (electroporated) with a ribonucleoprotein particle (RNP) containing Cas9 nuclease and a synthetic modified sgRNA targeting the TGFBRII gene (sequences in Table 39 below) or controls (no Cas9, no gRNA).
  • RNP ribonucleoprotein particle
  • gRNAs showed no off-target effect with an on-target editing rate greater than 85%, which includes TGFBRII_Ex1_T1, TGFBRII-Ex1-T2, TGFBRII_Ex1_T3, TGFBRII_Ex2_T1 and TGBBRII_Ex5_T1 as shown in Table 6 below.
  • Tables 29-38 list potential indel sequences that may be generated by the gRNAs disclosed herein (deletions as dashes and insertions in bold).
  • Example 9 Generation of Genetically Modified T Cells that Lack TGFBRII Expression and are Resistant to TGF- ⁇
  • This example describes the production of CAR T cells that lack expression of TGFBRII and the assessment of the effect of TGF- ⁇ on CAR T cell expansion with TGFBRII KO cells grown in complete media (X-Vivo 15 supplemented with IL-2 and IL-7).
  • Cas9:sgRNA RNPs (1 ⁇ M Cas9, 5 ⁇ M gRNA) were delivered to activated human T cells by electroporation, followed by incubation with the recombinant adeno-associated adenoviral vectors (AAVs), serotype 6 (AAV6) (MOI 50,000).
  • the nucleofection mix contained the NucleofectorTM Solution, 5 ⁇ 10 6 cells, 1 ⁇ M Cas9, and 5 ⁇ M gRNA (as described in Hendel et al., Nat Biotechnol. 2015; 33(9):985-989, PMID: 26121415).
  • the RNP complex comprised Cas9 and sgRNA targeting the TRAC, B2M, CD70, and optionally TGFBRII genes (sgRNA sequences are shown in Table 23 and Tables 39, SEQ ID NOs: 58, 62, 54, and 301, respectively).
  • the rAAV vector included the nucleotide sequence encoding an anti-CD70 CAR (the donor template in SEQ ID NO: 169 and the anti-CD70 CAR amino acid sequence of SEQ ID NO: 138.
  • CAR T cells with an intact (i.e.: wild-type or non-engineered counterpart) TGFBRII gene were exposed to varying amounts recombinant human TGF- ⁇ (10, 20, 50 and 100 ng/ml) and cell expansion was recorded over time.
  • TGF- ⁇ significantly inhibited CAR T expansion, a concentration as low as 10 ng/ml was sufficient to reduce CAR T expansion in cells with an intact TGFBRII gene ( FIG. 8A ).
  • anti-CD70 CAR T cells with TGFBRII disruption were incubated with or without 50 ng/ml of recombinant human TGF- ⁇ , and the T cell expansion was monitored at day 2 and day 8 post-incubation with TGF- ⁇ and compared to mock cells.
  • Mock cells FIG. 8B
  • FIGS. 8C-8K T cells with TGFBRII knocked-out were protected against the inhibitory effect of TGF- ⁇ on T cell expansion. The extent of protection varied with the sgRNA used to disrupt the TGFBRII gene.
  • T cells that were transfected with gRNA targeting exon 1, 4 and 5 (TGFBRII_EX1_T2, TGFBRII_EX4_T1, TGFBRII_EX4_T2, TGFBRII_EX5_T1) showed the most resistance against a TGF- ⁇ inhibitory effect. Sequences of these gRNAs are provided in Table 39 below.
  • This example describes the production of allogeneic human T cells that lack expression of the TRAC gene, ⁇ 2M gene and CD70 gene, and express a chimeric antigen receptor (CAR) targeting CD70.
  • the edited CAR T cells further comprised knock out of the TGFBRII gene.
  • activated human T cells were electroporated with Cas9:sgRNA RNPs (1 ⁇ M Cas9, 5 ⁇ M gRNA), followed by incubation with a recombinant adeno-associated adenoviral vectors, serotype 6 (AAV6) (MOI 50,000).
  • Recombinant AAV comprised the nucleotide sequence of SEQ ID NO: 169 (encoding anti-CD70 CAR comprising the amino acid sequence of SEQ ID NO: 138).
  • the following sgRNAs were used: TRAC (SEQ ID NO: 58), ⁇ 2M (SEQ ID NO: 62), CD70 (SEQ ID NO: 54) and TGFBRII (SEQ ID NO: 301).
  • T cells were checked for CAR expression by flow cytometry. Both anti-CD70 CAR T cells and anti-CD70 CAR T cells lacking TGFBRII expressed nearly equivalent amount of CAR on their surface (71.5% CAR + cells versus 73.7% CARP cells).
  • a cell killing assay was used to assess the ability of the TRAC ⁇ / ⁇ 2M ⁇ /CD70 ⁇ /TGFBRII ⁇ /anti-CD70 CAR+ cells to kill a CD70+ adherent renal cell carcinoma (RCC)-derived cell line (A498 cells).
  • RCC adherent renal cell carcinoma
  • Adherent cells were seeded in 96-well plates at 50,000 cells per well and left overnight at 37° C.
  • the next day edited anti-CD70 CAR T cells were added to the wells containing target cells at 0.05:1 or 0.1:1 CAR T:T cell (E:T) ratios.
  • CAR T cells were removed from the culture by aspiration and 100 ⁇ L Cell titer-Glo (Promega) was added to each well of the plate to assess the number of remaining viable cells. The amount of light emitted per well was then quantified using a plate reader. Cells with TGFBRII knock out exhibited a more potent cell killing of RCC-derived cells following 24-hour co-incubation. The anti-CD70 CAR T cells demonstrated higher potency when TGFBRII was knocked out, which is clearly visible at two T cell: A498 ratios (0.05:1 and 0.1:1) ( FIG. 9 ).
  • anti-CD70 CAR T was incubated with 50 ng/ml of recombinant human TGF- ⁇ for 24 hours and the expression of CD25 (IL-2R) on cell surface was assessed by flow cytometry.
  • IL-2R recombinant human TGF- ⁇
  • FIG. 11 anti-CD70 CAR T cells are susceptible to the inhibitory effect of TGF- ⁇ that causes downregulation of CD25.
  • CD25 is an activation marker and involved in T cell proliferation. When the TGFBRII gene was knocked out, these cells become resistant to TGF- ⁇ and the CAR T cells retain activity and CD25 expression.
  • This example describes the production of allogeneic human T cells that lack expression of the TRAC gene, ⁇ 2M gene and CD70 gene, and express a chimeric antigen receptor (CAR) targeting CD70 and how they are susceptible to the inhibitory effect of fibroblasts, which are a major component of solid tumor microenvironment (TME).
  • the edited CAR T cells further comprised knock out of the TGFBRII gene.
  • activated human T cells we electroporated with a recombinant adeno-associated adenoviral vectors, serotype 6 (AAV6) (MOI 50,000), and Cas9:sgRNA RNPs (1 ⁇ M Cas9, 5 ⁇ M gRNA).
  • Recombinant AAV comprised the nucleotide sequence of SEQ ID NO: 169 (encoding anti-CD70 CAR comprising the amino acid sequence of SEQ ID NO: 138).
  • the following sgRNAs were used: TRAC (SEQ ID NO: 58), ⁇ 2M (SEQ ID NO: 62), CD70 (SEQ ID NO: 54) and TGFBRII (SEQ ID NO: 301).
  • a cell killing assay was used to assess the inhibitory effect of fibroblast on anti-CD70 CAR T cells to kill CD70+ adherent tumor cell lines: H1975 (Non-small cell lung cancer), Hs-766T (Pancreatic carcinoma), or SK-OV3 (Ovarian cancer).
  • the cell kill assay was performed as described in example 3. Briefly, Adherent cells were seeded in 96-well plates at 50,000 cells per well and left overnight at 37° C. and the fibroblast cells (LL 86 (LeSa) ATCC® CCL-190TM) were added to the top chamber of a transwell plate without direct contact with target cells. The next day edited anti-CD70 CAR T cells were added to the wells containing target cells.
  • CAR T cells were removed from the culture by aspiration and 100 ⁇ L Cell titer-Glo (Promega) was added to each well of the plate to assess the number of remaining viable cells. The amount of light emitted per well was then quantified using a plate reader. As shown in FIG. 14 , the presence of the fibroblast cells on the top chamber led to a decrease of the cell kill capacity of anti-CD70 CAR T cells against the target cells which might suggest that these fibroblast secreted a factor that decrease anti-CD70 CAR T killing effect.
  • TGFBRII KO improved the cell killing ability of anti-CD70 CAR T cells against pancreatic tumor cells, Hs-766T ( FIG. 15A ), kidney tumor cells, A498 ( FIG. 15B ), and lung tumor cells, H1975 ( FIG. 15C ) in the presence of fibroblasts.
  • Allogeneic human T cells that lack expression of the TRAC gene, ⁇ 2M gene, CD70 gene, TGFBRII gene and Regnase-1 gene, and express a chimeric antigen receptor (CAR) targeting CD70 were produced.
  • Activated human T cells were electroporated with Cas9:sgRNA RNPs (1 ⁇ M Cas9, 5 ⁇ M gRNA), followed by incubation with a recombinant adeno-associated adenoviral vectors, serotype 6 (AAV6) (MOI 50,000).
  • Recombinant AAV comprised the nucleotide sequence of SEQ ID NO: 169 (encoding anti-CD70 CAR comprising the amino acid sequence of SEQ ID NO: 138).
  • the following sgRNAs were used: TRAC (SEQ ID NO: 58), ⁇ 2M (SEQ ID NO: 62), CD70 (SEQ ID NO:54), TGFBRII (SEQ ID NO: 313) and REG-1 (SEQ ID NO: 51).
  • the sgRNAs which form RNPs with the Cas9 enzyme, can be introduced into the T cells in a single electroporation event to produce the resulting modified cell populations shown in Table 7 below. Alternatively, they can be introduced into the T cells in two sequential electroporation events to produce the resulting cell populations. After the electroporation, the cells were transduced with the recombinant AAVs to introduce the donor template encoding for the anti-CD70 CAR.
  • T cells were checked for CAR expression by flow cytometry. Both anti-CD70 CAR T cells and anti-CD70 CAR T cells that lack Regnase expressed nearly equivalent amount of CAR on their surface at day 7 post HDR. The results are provided in Table 7A below.
  • Example 13 Disruption of Regnase-1 and TGFBRII Increases CAR T Cell Killing Upon Serial Rechallenge In Vitro
  • the anti-CD70 CARP T cells generated above were serially rechallenged with CD70+ kidney cancer cell line, ACHN, and evaluated for their ability to kill the CD70+ kidney cancer cell line ACHN.
  • the anti-CD70 CAR + T cells used in this experiment contained the following edits:
  • CAR T cells were first co-cultured with ACHN cells (4,000 CAR T cells, 16,000 tumor cells) on D0 and re-challenged with tumor cells as follows: 16,000 tumor cells on D2 and D4; 40,000 cells on D7; 50,000 cells on D9; 50,000 cells on D11).
  • Example 14 Treatment Efficacy of Anti-CD70 CART Cells with Multiple Gene Disruptions in the Subcutaneous Renal Cell Carcinoma Tumor Xenograft Model
  • T cells expressing a CD70 CAR with TGFBRII and/or Regnase gene edits to eliminate renal cell carcinoma cells that express medium levels of CD70 was evaluated in vivo using a subcutaneous renal cell carcinoma (CAKI-1) tumor xenograft mouse model.
  • Anti-CD70 CAR+ T cells were produced as described above. See, e.g., Example 13.
  • mice were individually housed in ventilated microisolator cages, maintained under pathogen-free conditions, 5-7 days prior to the start of the study.
  • Mice received a subcutaneous inoculation of 5 ⁇ 10 6 Caki-1 renal cell carcinoma cells/mouse in the right hind flank.
  • mean tumor size reached target of ⁇ 70 mm 3
  • the mice were further divided into 5 treatment groups as shown in Table 9.
  • treatment four groups received a single 200 ⁇ l intravenous dose of 1 ⁇ 10 7 anti-CD70 CAR+ T cells according to Table 9.
  • tumor volume was measured 2 times weekly ( ⁇ every 3-4 days) from day of treatment initiation.
  • anti-CD70 CAR T cells with both TGFBRII and Regnase genes KO began to show a significant effect on reducing tumor volume compared to other treatment groups.
  • the anti-CD70 CAR T+Reg KO+TGFBRII KO cells had completely eliminated tumor growth in the subcutaneous CAM-1 model ( FIG. 17A ).
  • NSCLC Non-Small Cell Lung Carcinoma
  • T cells expressing a CD70 CAR with TGFBRII and/or Regnase gene edits to eliminate lung adenocarcinoma cells that express moderate levels of CD70 was evaluated in vivo using a subcutaneous lung carcinoma (NCI-H1975) tumor xenograft mouse model.
  • Anti-CD70 CAR+ T cells were produced as described herein. See, e.g., Example 13.
  • mice were individually housed in ventilated microisolator cages, maintained under pathogen-free conditions, 5-7 days prior to the start of the study.
  • Mice received a subcutaneous inoculation of 5 ⁇ 10 6 NCI-H1975 lung carcinoma cells/mouse in the right hind flank.
  • mean tumor size reached target of ⁇ 85 mm 3
  • the mice were further divided into 5 treatment groups as shown in Table 10. On Day 1, treatment four groups received a single 200 ⁇ l intravenous dose of 1 ⁇ 10 7 anti-CD70 CAR+ T cells according to Table 10.
  • Tumor volume was measured 2 times weekly from day of treatment initiation.
  • animal treated with anti-CD70 CAR T cells having the TGFBRII edit exhibited attenuated tumor growth.
  • Tumors treated with anti-CAR T cells with both TGFBRII and Regnase genes disrupted began to show a decrease in tumor volume by day 8 post-injection and cleared tumors by day 29 in 4 mice out of 4. This complete regression of tumors in treated animals continued through day 53 post injection.
  • Treatment with anti-CD70 CAR+/TRAC ⁇ /B2M ⁇ /CD70 ⁇ /Reg ⁇ /TGFBRII ⁇ T cells resulted in potent activity against established H1975 lung cancer xenografts through 53 days post injection ( FIG. 17B ).
  • Example 15 Tumor Re-Challenge Model Renal Cell Carcinoma Large Tumor Xenograft Model
  • the efficacy of anti-CD70 CAR T cells having TGFBRII and/or Regnase-1 genes disrupted were tested in a subcutaneous A498 xenograft model with an ACHN re-challenge.
  • mice treated with all CAR T cell populations having a disrupted TGFBRII and/or Regnase gene showed complete clearance of the A498 tumor by day 50.
  • mice were rechallenged with a new RCC tumor cell (ACHN) only CAR T Cells with both Regnase and TGFBRII edits were able to clear the tumor compared to cells with either Regnase-1 or TGFBRII disruptions alone ( FIG. 18B ).
  • Example 17 Assessment of Anti-CD19 CAR-T Cells Having TGFBRII and/or Regnase-1 Gene Disruptions in an Intravenous Disseminated Models in NOG Mice
  • the Intravenous Disseminated Model (Disseminated Model) using the Nalm-6 Human Acute Lymphoblastic Leukemia tumor cell line in NOG mice was used to further demonstrate the efficacy of anti-CD19 CAR T cells with TGFBRII and/or Regnase-1 gene edits. Efficacy of various anti-CD19 CAR T populations were evaluated in the Disseminated Model using methods employed by Translations Drug Development, LLC (Scottsdale, Ariz.) and described herein.
  • mice were individually housed in ventilated microisolator cages, maintained under pathogen-free conditions, 5-7 days prior to the start of the study.
  • the mice were divided into 5 treatment groups as shown in Table 12.
  • mice in Groups 2-4 received an intravenous injection of 0.5 ⁇ 10 6 Nalm6 cells/mouse.
  • the mice were inoculated intravenously to model disseminated disease.
  • treatment Groups 2-4 received a single 200 ⁇ l intravenous dose of CAR+ T cells per Table 12.
  • Anti-CD19 CAR T Nalm6 Cells Treatment Group CAR T (i.v.) (i.v.) N 1 Untreated 0.5 ⁇ 10 6 None 5 cells/mouse 2 Anti-CD19 CAR T cells: 0.5 ⁇ 10 6 4 ⁇ 10 6 5 anti-CD19 CAR+/TRAC ⁇ / cells/mouse CAR-T B2M ⁇ positive cells/mouse 3 Anti-CD19 CAR T + Reg 0.5 ⁇ 10 6 4 ⁇ 10 6 5 KO cells: anti-CD19 CAR+/ cells/mouse CAR-T TRAC ⁇ /B2M ⁇ /Reg ⁇ positive cells/mouse 4 Anti-CD19 CAR T + 0.5 ⁇ 10 6 4 ⁇ 10 6 5 TGFBRII KO cells: cells/mouse CAR-T anti-CD19 CAR+/TRAC ⁇ / positive B2M ⁇ /TGFBRII ⁇ cells/mouse 5 Anti-CD19 CAR T + Reg 0.5 ⁇ 10 6 4 ⁇ 10 6 5
  • mice were monitored daily and body weight was measured two times weekly as described above.
  • TGFBRII gene editing combined with Regnase editing induced a maintained NALM6 tumor regression at an early time point (day 18) post tumor inoculation, compared to either edit alone. This reduction in tumor size was maintain ( FIG. 20A ).
  • the sharp decline in tumor size in the TGFBRII KO group at day 74 post tumor inoculation represents only 5 of 15 mince. Ten of the 15 mice in TGFBRIIKO group had already reached the tumor BLI endpoint.
  • the Intravenous Disseminated Model (Disseminated Model) using the JeKo-1 Human Mantle cell lymphoma (MCL) tumor cell line in NOG mice was used to further demonstrate the efficacy of anti-CD19 CAR T cells with TGFBRII and/or Regnase gene edits. Efficacy of various anti-CD19 CAR T populations were evaluated in the Disseminated Model using methods employed by Translations Drug Development, LLC (Scottsdale, Ariz.) and described herein.
  • mice were individually housed in ventilated microisolator cages, maintained under pathogen-free conditions, 5-7 days prior to the start of the study.
  • the mice were divided into 5 treatment groups as shown in Table 13.
  • mice in Groups 2-4 received an intravenous injection of 0.5 ⁇ 10 6 JeKo-1 cells/mouse.
  • the mice were inoculated intravenously to model disseminated disease.
  • treatment Groups 2-4 received a single 200 ⁇ l intravenous dose of CAR T cells per Table 13.
  • mice were monitored daily and body weight was measured two times weekly as described above.
  • mice treated with anti-CD19 CAR+ cells having both TGFBRII and Regnase gene edits exhibited the greatest survival advantage FIG. 21 .
  • CAR T cell expansion was assessed by measuring the CAR copy number by ddPCR of DNA isolated from blood samples collected throughout the Jeko-1 and Nalm-6 studies as described above.
  • ddPCR droplet digital PCR
  • ddPCR was performed using the Bio-Rad Automated Droplet Generator, Bio-Rad T100 Thermal Cycler, and Bio-Rad QX200 Droplet Reader machine(s) (Bio-rad Laboratories, Hercules, Calif.). QuantaSoft Version 1.7.4.0917 (Bio-rad Laboratories) software was used to calculate the absolute number of integrated CAR copies per sample. Finally, the number of detected CAR alleles was divided by the input total DNA amount to compute the absolute number of CAR copies per mass of input sample.
  • the ddPCR assay detects the number of copies of integrated CAR transgene per mass of genomic DNA (gDNA) by amplifying an 866 bp amplicon spanning endogenous TRAC sequence and the CAR expression cassette promotor (EF-1 ⁇ ).
  • qualification of the assay yielded linear data (R 2 >0.95) within the range tested (2 to 300,000 copies per ug of gDNA) as well as generated a % relative error (% RE) and % coefficient of variation (% CV) within normal ranges (% RE ⁇ 100% and % CV ⁇ 20%) for conditions ⁇ LLOQ.
  • the LLOD and LLOQ were calculated based on the available data and the LLOD was set to 5 copies per 0.2 ⁇ g of gDNA and the LLOQ was set to 40 copies per 0.2
  • Activated primary human T cells were electroporated with Cas9/sgRNA RNP complexes (200 pmol Cas9, 1000 pmol gRNA) to generate cells edited for TRAC ⁇ / ⁇ 2M ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /Regnase-1 ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII ⁇ and TRAC ⁇ / ⁇ 2M ⁇ /Regnase-1 ⁇ /TGFBRII ⁇ .
  • Sequence encoding anti-BCMA CAR was inserted into the TRAC locus using recombinant AAV6 carrying the DNA sequence for anti-BCMA CAR (SEQ ID NO: 170).
  • TRAC SEQ ID NO: 58
  • ⁇ 2M SEQ ID NO: 62
  • Reg-1 SEQ ID NO: 51; REG1-Z10
  • TGFBRII SEQ ID NO: 313
  • Flowcytometry was used to verify the editing for TRAC, ⁇ 2M and the insertion and expression of anti-BCMA CAR. Briefly, about one week post electroporation, cells were stained with anti-human TCR, anti-human ⁇ 2M and recombinant biotinylated human BCMA/streptavidin-APC to assess the levels of editing for TRAC and ⁇ 2M, and insertion of the nucleotide sequence encoding anti-BCMA CAR.
  • TRAC ⁇ / ⁇ 2M ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII ⁇ and TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ /TGFBRII ⁇ anti-BCMA CAR+ T-cells show consistent rates of TCR and ⁇ 2M disruptions at >90% and >60% rates, respectively as determined by flow cytometry ( FIGS. 23A and 23B ).
  • Anti-BCMA CAR expression was measured flow cytometrically by determining the percentage of cells that bound recombinant biotinylated BCMA/streptavidin-APC conjugate.
  • TRAC ⁇ / ⁇ 2M ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII ⁇ and TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ /TGFBRII ⁇ anti-BCMA CAR+ T-cells show consistent rates of CAR insertion (>70%), while the unedited RNP ⁇ T-cells have no detectable staining for anti-BCMA CAR ( FIG. 23C ).
  • the ratio of CD4/CD8 T cells as assessed by flow cytometry in the TRAC ⁇ / ⁇ 2M ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII ⁇ and TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ /TGFBRII ⁇ anti-BCMA CAR+ T-cells were found to be consistent in the range of 55-60%/40-45% across all the samples ( FIG. 23D ).
  • TIDE analysis was performed for the verification of editing rates for Reg-1 and TGFBRII genes. Briefly, about one week post electroporation, two million cells from TRAC ⁇ / ⁇ 2M ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII ⁇ and TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ /TGFBRII ⁇ anti-BCMA CAR+ T-cells and two million unedited T-cells from the same donor were removed from culture and transferred to 1.5 mL microcentrifuge tubes. Cells were spun down in a tabletop microcentrifuge at 300 g for 10 minutes and the resulting supernatant was discarded.
  • the cells were washed twice with 1000 uL 1 ⁇ PBS and the cell pellets were frozen at ⁇ 80° C. The frozen cell pellets were then used for the extraction of genomic DNA using QIAamp DNA Blood Mini Kit (Qiagen, catalog #51106). Gene-specific primers were used to amplify the region flanking the cut sites of Reg-1 and TGFBRII (InvitrogenTM PlatinumTM SuperFiTM II Green PCR Master Mix; catalog #12369050) and the PCR amplicons derived were subsequently sequenced and analyzed by TIDE to determine the indel patterns/frequencies (editing frequencies).
  • Reg-1 and TGFBRII InvitrogenTM PlatinumTM SuperFiTM II Green PCR Master Mix
  • the analyzed indel frequencies were found to be within the expected range of 65-80% for TGF sgRNA and >80% for the Regnase-1 sgRNA, respectively ( FIGS. 24A and 24B ).
  • a cytotoxicity (cell kill) assay was used to assess the ability of the TRAC ⁇ / ⁇ 2M ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII ⁇ and TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ /TGFBRII ⁇ anti-BCMA CAR+ T-cells (produced by the methods disclosed herein, see, e.g., Example 18) to cause cell lysis in two target cell lines, MM.1S (multiple myeloma cell line) and JeKo-1 (mantle cell lymphoma cell line). Unedited RNP ⁇ cells without CAR were used as a negative control to determine the specific lysis by CAR+ T cells.
  • the target cell lines were stained with eBioscienceTM Cell Proliferation Dye eFluorTM 670 (Thermofisher Scientific; catalog #65-0840-85) per manufacturer's instructions and seeded into 96-well plates at 50,000 cells per well.
  • CAR T-cells or RNP ⁇ T cells were added to the wells containing target cells at ratios of 0, 0.5:1, 1:1, 2:1, or 4:1 (T cell: target cell) and incubated further for approximately 4 hours for MM.1S and 24 hours for JeKo-1. After the respective incubation period, the 96-well plates were spun down at 300 g for 10 minutes and 100 ⁇ L of supernatant was removed for cytokine quantification.
  • DAPI Invitrogen; catalog #D3571
  • cells were then washed once with 1 ⁇ PBS and stained with 150 ul of 1 ⁇ PBS supplemented with 0.5% BSA and 5 ⁇ g/mL DAPI (Invitrogen; catalog #D3571) and incubated for 15 minutes in dark. Post-incubation, cells were washed-off DAPI, resuspended in 150 ⁇ l of 1 ⁇ PBS supplemented with 0.5% BSA, and acquired and analyzed using a flow cytometer. Target cells were identified via eFluor-based fluorescence and then divided into live and dead cells based on their DAPI fluorescence.
  • the TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ /TGFBRII ⁇ anti-BCMA CAR+ T-cells exhibited greater cytotoxicity towards the MM.1S ( FIG. 25A ) and JeKo-1 cell lines ( FIG. 25C ) compared to TRAC ⁇ / ⁇ 2M ⁇ , TRAC ⁇ / ⁇ 2M ⁇ /Regnase-1 ⁇ or TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII ⁇ anti-BCMA CAR+ T-cells. Comparative data from K562 cells (as controls) are provided in FIG. 25B and FIG. 25D .
  • a subcutaneous tumor mouse model was utilized to assess the in vivo efficacy of allogeneic anti-BCMA CARs with the following gene disruptions: 1) ⁇ 2M and TRAC, 2) ⁇ 2M, TRAC, and TGFBRII, 3) ⁇ 2M, TRAC, and Reg-1, and 4) ⁇ 2M, TRAC, TGFBRII, and Reg-1.
  • the subcutaneous tumor mouse model utilized the BCMA+ multiple myeloma derived RPMI-8226 tumor cell line in NSG mice.
  • the TGFBRII gene was edited via CRISPR/Cas-mediated gene editing using the TGFBRII Ex5_T1 guide (SEQ ID NO. 313).
  • the Reg-1 gene was edited via CRISPR/Cas-mediated gene editing using the Z10 guide (SEQ ID NO. 51).
  • the anti-BCMA CAR T cells express an anti-BCMA CAR comprising the amino acid sequence of SEQ ID NO: 146). See also the sequence Tables 22, 23, 27, and 39 below.
  • mice were individually housed in ventilated microisolator cages, maintained under pathogen-free conditions, 5-7 days prior to the start of the study.
  • mice received a subcutaneous inoculation of 1 ⁇ 10 7 RPMI-8226 cells/mouse in the right hind flank.
  • the tumor inoculation sites were inspected to determine if the tumors were palpable.
  • mice were further divided into 5 treatment groups as shown in Table 1. All treatment groups received a single 200 ul intravenous dose of 1e6 anti-BCMA CAR+ T cells.
  • mice were subjected to gross observations daily, while tumor volume and body weight were measured twice weekly ( ⁇ every 3-4 days) starting on Day 10. A significant endpoint was the time to peri-morbidity and the effect of T-cell engraftment was also assessed. The percentage of animal mortality and time to death were recorded for every group in the study. Mice were euthanized prior to reaching a moribund state. Mice may be defined as moribund and sacrificed if one or more of the following criteria were met:
  • mice in groups receiving TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII ⁇ /Reg-1 ⁇ anti-BCMA CAR+ T-cells saw an increase in survival relative to untreated mice; mice treated TRAC ⁇ / ⁇ 2M ⁇ anti-BCMA CAR+ T-cells, TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII anti-BCMA CAR+ T-cells, or TRAC ⁇ / ⁇ 2M ⁇ /Reg-1 ⁇ anti-BCMA CAR+ T-cells ( FIG. 26B ).
  • Mice receiving TRAC ⁇ /B2M ⁇ /TGFBRII ⁇ /Regnase ⁇ anti-BCMA CAR+ T cells showed significant tumor regression, while none of the other conditions tested showed significant inhibition of tumor growth ( FIG. 26A ).
  • a subcutaneous tumor mouse model was utilized to further assess the in vivo efficacy of TRAC ⁇ / ⁇ 2M ⁇ anti-BCMA CAR+ T-cells and TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII ⁇ /Reg-1/anti-BCMA CAR+ T-cells.
  • the subcutaneous tumor mouse model utilized the low BCMA expressing mantle cell lymphoma derived JeKo-1 tumor cell line in NSG mice.
  • the TGFBRII gene was edited via CRISPR/Cas-mediated gene editing using TGFBRII Ex5_T1 guide (SEQ ID NO: 313).
  • the Reg-1 gene was edited via CRISPR/Cas-mediated gene editing using the Z10 guide (SEQ ID NO: 51).
  • the anti-BCMA CAR T cells express an anti-BCMA CAR comprising the amino acid sequence of SEQ ID NO: 146. See also the sequence Tables 22, 23, 27, and 39 below.
  • mice were individually housed in ventilated microisolator cages, maintained under pathogen-free conditions, 5-7 days prior to the start of the study.
  • mice received a subcutaneous inoculation of 5 ⁇ 10 6 JeKo-1 cells/mouse in the right hind flank. Tumors were then periodically sized in via calipers. Once average tumor size reached an average of 150 mm 3 (with an acceptable range of 125-175 mm 3 ), the mice were further divided into 3 treatment groups as shown in Table 1. All treatment groups received a single 200 ul intravenous dose of 10e6 anti-BCMA CAR+ T cells. The day of T-cell injection was marked as Day 1.
  • mice were subjected to gross observations daily, while tumor volume and body weight were measured twice weekly (every 3-4 days) starting on Day 1. A significant endpoint was the time to peri-morbidity and the effect of T-cell engraftment was also assessed. The percentage of animal mortality and time to death were recorded for every group in the study. Mice were euthanized prior to reaching a moribund state. Mice may be defined as moribund and sacrificed if one or more of the following criteria were met:
  • mice in groups receiving TRAC ⁇ / ⁇ 2M ⁇ /TGFBRII ⁇ /Reg-1 ⁇ anti-BCMA CAR+ T-cells saw a significant increase in survival relative to both untreated mice and mice treated TRAC ⁇ / ⁇ 2M ⁇ anti-BCMA CAR+ T-cells ( FIG. 27B ).
  • the TRAC ⁇ / ⁇ 2M ⁇ TGFBRII ⁇ /Reg-1 ⁇ anti-BCMA CAR+ T-cells showed lower expression of the T-cell exhaustion markers Lag3 and PD1 relative to the TRAC ⁇ / ⁇ 2M ⁇ anti-BCMA CAR+ T-cells ( FIG. 27D ).
  • the overall level of hCD45+ cells in circulation had equalized between groups ( FIG. 27E ), but the expression of Lag3 and PD1 remained lower in mice treated with TRAC ⁇ / ⁇ 2M ⁇ TGFBRII ⁇ /Reg-1 ⁇ anti-BCMA CAR+ T-cells ( FIG. 27F ).
  • CAR-T cells containing the TGFBRII and Regnase knockouts have a superior ability to expand when compared to CAR-T cells lacking those edits while also reducing the expression of T-cell exhaustion markers PD-1 and Lag3.
  • Allogeneic human T cells that lack expression of the TRAC gene, ⁇ 2M gene, TGFBRII gene and Reg-1 gene, and express a chimeric antigen receptor (CAR) targeting PTK7 were produced.
  • Activated human T cells were electroporated with Cas9:sgRNA RNPs (1 ⁇ M Cas9, 5 ⁇ M gRNA), followed by incubation with a recombinant adeno-associated adenoviral vectors, serotype 6 (AAV6) (MOI 50,000).
  • Recombinant AAV comprised a nucleotide sequence encoding an anti-PTK7 CAR comprising the amino acid sequence of SEQ ID NO: 349.
  • the following sgRNAs were used: TRAC (SEQ ID NO: 58), ⁇ 2M (SEQ ID NO: 62), TGFBRII (SEQ ID NO: 313) and REGNASE-1 (SEQ ID NO: 51).
  • the sgRNAs which form RNPs with the Cas9 enzyme, can be introduced into the T cells in a single electroporation event to produce the resulting modified cell populations shown in Table 17 below. After the electroporation, the cells were transduced with the recombinant AAV to introduce the donor template encoding for the anti-PTK7 CAR.
  • T cells were checked for CAR expression by flow cytometry. Both anti-PTK7 CAR T cells and anti-PTK7 CAR T cells that lack TGFBRII and anti-PTK7 CAR T cells that lack TGFBRII and Regnase expressed nearly equivalent amount of CAR on their surface at day 7 post HDR. The results are provided in Table 18 below.
  • TGFBRII and/or Reg-1 disruption in anti-Ptk7 CAR T cells can increase cell proliferation, while not affecting cell viability or CD4/CD8 cell ratios.
  • Example 23 Disruption of TGFBRII Alone Increases CAR T Cell Killing Upon Serial Rechallenge In Vitro
  • the anti-PTK7 CAR+ T cells generated above were serially rechallenged with PTK7+ osteosarcoma cancer cell line, Saos2, and evaluated for their ability to kill the PTK7+ osteosarcoma cancer cell line Saos2.
  • the anti-PTK7 CAR+ T cells used in this experiment contained the following edits:
  • CAR T cells were first co-cultured with Saos2 cells (6,250 CAR T cells, 50,000 tumor cells) on D0 and re-challenged with 50,000 tumor cells on D2, D4, D6, D8, D10, D12 and D14.
  • Example 24 Treatment Efficacy of Anti-PTK7 CART Cells with Multiple Gene Disruptions in the Subcutaneous Pancreatic Cell Carcinoma Tumor Xenograft Model
  • T cells expressing a PTK7 CAR with TGFBRII and/or Reg-1 gene edits to eliminate pancreatic cell carcinoma cells that express medium levels of PTK7 was evaluated in vivo using a subcutaneous renal cell carcinoma (Hs766T) tumor xenograft mouse model.
  • Anti-PTK7 CAR+ T cells were produced as described above. See, e.g., Example 22.
  • mice were individually housed in ventilated microisolator cages, maintained under pathogen-free conditions, 5-7 days prior to the start of the study.
  • Mice received a subcutaneous inoculation of 5 ⁇ 10 6 Hs766T pancreatic cell carcinoma cells/mouse in the right hind flank.
  • mean tumor size reached target of ⁇ 50 mm 3
  • the mice were further divided into 3 treatment groups as shown in Table 21.
  • treatment four groups received a single 200 ⁇ l intravenous dose of 0.5 ⁇ 10 7 anti-PTK7 CAR+ T cells according to Table 21.
  • tumor volume was measured 2 times weekly ( ⁇ every 3-4 days) from day of treatment initiation.
  • anti-PTK7 CAR T cells with and without TGFBRII gene KO began to show a significant effect on reducing tumor volume compared to no treatment group 1.
  • the anti-PTK7CAR T with and without TGFBRII KO cells had completely eliminated tumor growth in the subcutaneous Hs766T model ( FIG. 30A ).
  • Blood samples were taken from mice with Hs766T tumors, 47 days after CAR T administration. Briefly, 100 ul of mouse whole blood was collected via submandibular vein. Red blood cell lysis buffer was used to achieve optimal lysis of erythrocytes with minimal effect on lymphocytes. Human CD45 and mouse CD45 were used as a biomarker to separate human and mouse cells by FACS. The blood samples were evaluated by flow cytometry looking for absolute human CD45+ counts as well as memory T cell subsets. Staining for CD45RO+CD27+ was used to define central memory T cells.
  • Reference On-target sequence a TTCTGGTTGTCAC (AGG) TGGA (SEQ ID NO: 448) SEQ Donor Donor Std. ID 1 2 Mean Dev.
  • inventive embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto, inventive embodiments may be practiced otherwise than as specifically described and claimed.
  • inventive embodiments of the present disclosure are directed to each individual feature, system, article, material, kit, and/or method described herein.
  • a reference to “A and/or B”, when used in conjunction with open-ended language such as “comprising” can refer, in one embodiment, to A only (optionally including elements other than B); in another embodiment, to B only (optionally including elements other than A); in yet another embodiment, to both A and B (optionally including other elements); etc.
  • the term “about” as used herein means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, “about” can mean within an acceptable standard deviation, per the practice in the art. Alternatively, “about” can mean a range of up to ⁇ 20%, preferably up to ⁇ 10%, more preferably up to ⁇ 5%, and more preferably still up to ⁇ 1% of a given value. Where particular values are described in the application and claims, unless otherwise stated, the term “about” is implicit and in this context means within an acceptable error range for the particular value.
  • the phrase “at least one,” in reference to a list of one or more elements, should be understood to mean at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each and every element specifically listed within the list of elements and not excluding any combinations of elements in the list of elements.
  • This definition also allows that elements may optionally be present other than the elements specifically identified within the list of elements to which the phrase “at least one” refers, whether related or unrelated to those elements specifically identified.
  • “at least one of A and B” can refer, in one embodiment, to at least one, optionally including more than one, A, with no B present (and optionally including elements other than B); in another embodiment, to at least one, optionally including more than one, B, with no A present (and optionally including elements other than A); in yet another embodiment, to at least one, optionally including more than one, A, and at least one, optionally including more than one, B (and optionally including other elements); etc.

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