WO2018165631A1 - Cancer vaccine - Google Patents

Cancer vaccine Download PDF

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Publication number
WO2018165631A1
WO2018165631A1 PCT/US2018/021880 US2018021880W WO2018165631A1 WO 2018165631 A1 WO2018165631 A1 WO 2018165631A1 US 2018021880 W US2018021880 W US 2018021880W WO 2018165631 A1 WO2018165631 A1 WO 2018165631A1
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nucleotide sequence
target
base
domain
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PCT/US2018/021880
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English (en)
French (fr)
Inventor
Juan Pablo Maianti
David R. Liu
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Harvard University
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Harvard University
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Priority to EP18717146.7A priority Critical patent/EP3592381A1/en
Priority to US16/492,534 priority patent/US12390514B2/en
Priority to CN201880029909.6A priority patent/CN110662556A/zh
Priority to JP2019548908A priority patent/JP2020510038A/ja
Priority to KR1020197029548A priority patent/KR20190123328A/ko
Publication of WO2018165631A1 publication Critical patent/WO2018165631A1/en
Anticipated expiration legal-status Critical
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Definitions

  • Tumor- specific immune responses may be elicited by peptides generated from proteins expressed in tumor cells or on tumor cell surface (e.g., tumor- specific antigens).
  • Native peptides derived from tumor- specific antigens are tolerated as "self by the immune system and do not elicit strong immune response against the tumor- specific antigen.
  • Altered versions of the native peptides derived from tumor- specific antigens e.g., heteroclitic peptides or cryptic peptides
  • tumor specific antigens e.g., heteroclitic epitopes or cryptic epitopes
  • Targeted mutations are introduced into tumor- specific antigens using gene editing agents, e.g., a nucleobase editor comprising a programmable DNA binding domain (e.g., catalytically-inactive Cas9 or a Cas9 nickase) fused to a cytosine deaminase, to generate altered versions of peptides arising from the tumor- specific antigens (heteroclitic epitopes) or peptides arising from normally untranslated regions of the tumor- specific antigen genes (cryptic peptides).
  • gene editing agents e.g., a nucleobase editor comprising a programmable DNA binding domain (e.g., catalytically-inactive Cas9 or a Cas9 nickase) fused to a cytosine deaminase, to generate altered versions of peptides arising from the tumor- specific antigens (heteroclitic epitopes) or peptides arising
  • the heteroclitic peptides or cryptic peptides may be generated in vivo in a subject (e.g., a subject who has cancer) and presented to the adaptive immune system via the MHC class I or MHC class II pathway, which in turn induces a strong adaptive immune response, e.g. , T cell response and B cell response.
  • a strong adaptive immune response e.g. , T cell response and B cell response.
  • Such an adaptive immune response is antigen specific and is effective in reducing tumor growth and preventing metastasis.
  • Some aspects of the present disclosure provide methods of eliciting a tumor- specific immune response in a subject in need thereof, the methods including administering to the subject a therapeutically effective amount of a composition comprising: (i) a fusion protein comprising (a) a guide nucleotide sequence-programmable DNA-binding protein domain; and (b) a cytosine deaminase domain; and (ii) a guide nucleotide sequence, wherein the guide nucleotide sequence of (ii) targets the fusion protein of (i) to a polynucleotide encoding a tumor- specific antigen in a tumor cell, wherein the fusion protein changes a target cytosine (C) base to a thymine (T) base via deamination.
  • a composition comprising: (i) a fusion protein comprising (a) a guide nucleotide sequence-programmable DNA-binding protein domain; and (b) a cytosine deaminase
  • the polynucleotide comprises a coding strand and a complementary strand. In some embodiments, the polynucleotide comprises a coding region and a non-coding region. In some embodiments, the polynucleotide encoding the tumor- specific antigen is located in the genome of the tumor cell. In some embodiments, deamination of the target C base results in a C-G base-pair to thymine- adenine (T-A) base- pair change.
  • T-A thymine- adenine
  • the guide nucleotide sequence-programmable DNA binding protein domain is selected from the group consisting of: nuclease inactive Cas9 (dCas9) domains, nuclease inactive Cpfl domains, nuclease inactive Argonaute domains, and variants thereof.
  • the guide nucleotide sequence-programmable DNA-binding protein domain is a nuclease inactive Cas9 (dCas9) domain.
  • the amino acid sequence of the dCas9 domain comprises mutations corresponding to a D10A and/or H840A mutation in SEQ ID NO: 1.
  • the amino acid sequence of the dCas9 domain comprises a mutation corresponding to a D10A mutation in SEQ ID NO: 1, and wherein the dCas9 domain comprises a histidine at the position corresponding to amino acid 840 of SEQ ID NO: 1.
  • the guide nucleotide sequence-programmable DNA-binding protein domain comprises a nuclease inactive Cpfl (dCpfl) domain.
  • the dCpf 1 domain is from a species of Acidaminococcus or Lachnospiraceae.
  • the guide nucleotide sequence-programmable DNA-binding protein domain comprises a nuclease inactive Argonaute (dAgo) domain.
  • the (dAgo) domain is from Natronobacterium gregoryi (dNgAgo).
  • the cytosine deaminase domain comprises an apolipoprotein B niRNA-editing complex (APOBEC) family deaminase.
  • APOBEC apolipoprotein B niRNA-editing complex
  • the cytosine deaminase is selected from the group consisting of APOBEC 1, APOBEC2, APOBEC3A, APOBEC3B, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G deaminase,
  • the cytosine deaminase comprises an amino acid sequence of any of SEQ ID NOs: 27-292, 303, and 1072-1083.
  • the fusion protein of (a) further comprises a uracil glycosylase inhibitor (UGI) domain.
  • the cytosine deaminase domain is fused to the N-terminus of the guide nucleotide sequence-programmable DNA-binding protein domain.
  • the UGI domain is fused to the C-terminus of the guide nucleotide sequence-programmable DNA-binding protein domain.
  • the cytosine deaminase and the guide nucleotide sequence-programmable DNA-binding protein domain is fused via an optional linker.
  • the UGI domain is fused to the guide nucleotide sequence-programmable DNA-binding protein domain via an optional linker.
  • the fusion protein comprises the structure NH 2 -[cytosine deaminase domain] -[optional linker sequence] -[ guide nucleotide sequence-programmable DNA-binding protein domain] -[optional linker sequence] -[UGI domain] -COOH.
  • the optional linker comprises (GGGS) n , (SEQ ID NO: 337) (GGGGS) n (SEQ ID NO: 308), (G)n (SEQ ID NO: 783), (EAAAK) n (SEQ ID NO: 309), (GGS) compassion (SEQ ID NO: 784), SGSETPGTSESATPES (SEQ ID NO: 310), or (XP)n (SEQ ID NO: 785) motif, or a combination of any of these, wherein n is independently an integer between 1 and 30 and wherein X is any amino acid.
  • the linker comprises the amino acid sequence of SGSETPGTSESATPES (SEQ ID NO: 310).
  • the linker is (GGS) n (SEQ ID NO: 784), and wherein n is 1, 3, or 7.
  • the fusion protein comprises the amino acid sequence of any one of SEQ ID NOs: 293-302, 1071, and 1084.
  • the tumor specific antigen is selected from the group consisting of: CEA; gplOO; Pmell7; mammaglobin-A; Melan-A; MART- 1 ; NY-BR-1; ERBB2; OA1; PAP; PSA; RAB38; NY-MEL- 1; TRP-1; gp75; TRP-2; tyrosinase; WT1; CD33; BAGE-1; D393-CD20n; Cyclin-Al; GAGE-1,2,8; GAGE-3,4,5,6,7; GnTVf; HERV- K-MEL; KK-LC-1; KM-HN-1; LAGE-1; LY6K; MAGE-A1; MAGE-A2; MAGE- A3;
  • adipophilin AIM-2; ALDH1A1; BCLX(L); BING-4; CALCA; CD45; CD274; CPSF; cyclin Dl; DKKl; ENAH (hMena); EpCAM; EphA3; EZH2; FGF5; glypican-3; G250; MN; CAIX; HER-2; neu; HLA-DOB; Hepsin; IDOl; IGF2B3; IL13Ralpha2; Intestinal carboxyl esterase; alpha-foetoprotein; Kallikrein 4; KIF20A; Lengsin; M-CSF; MCSP; mdm-2; Meloe;
  • the target C base is in a target codon located in a coding region of the polynucleotide encoding the tumor- specific antigen.
  • the target codon is any one of the target codons in Tables 4 and 8.
  • the target codon is converted to a modified codon selected from any one of the modified codons in Table 4.
  • the target C base is located in a non-coding region of the polynucleotide encoding the tumor specific antigen. In some embodiments, the target C base is located in an intron in the polynucleotide encoding the tumor specific antigen.
  • the methods described herein further comprising generating an immunogenic peptide from the tumor- specific antigen.
  • the immunogenic peptide is a heteroclitic epitope.
  • the heteroclitic epitope is at least 2 fold, at least 5 fold, at least 10 fold, at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 60 fold, at least 70 fold, at least 80 fold, at least 90 fold, at least 100 fold, or more immunogenic than a native epitope from the tumor specific antigen.
  • the immunogenic peptide is a cryptic epitope.
  • the cryptic epitope is at least 2 fold, at least 5 fold, at least 10 fold, at least 20 fold, at least 30 fold, at least 40 fold, at least 50 fold, at least 60 fold, at least 70 fold, at least 80 fold, at least 90 fold, at least 100 fold, or more immunogenic than a native epitope from the tumor specific antigen.
  • the immunogenic peptide is displayed on the surface of the tumor cell via the MHC class I antigen presentation pathway. In some embodiments, the immunogenic peptide is displayed on the surface of an antigen presenting cell (APC) via the MHC class II antigen presentation pathway.
  • APC antigen presenting cell
  • the method is carried out in vivo. In some embodiments, the method is carried out ex vivo.
  • the APC is selected from the group consisting of: tumor cells, dendritic cells, mononuclear phagocytes, thymic epithelial cells, and B cells.
  • the immunogenic peptide elicits adaptive immune response against the tumor- specific antigen.
  • the adaptive immune response comprises promoting the maturation of dendritic cells, activation of CD4+T lymphocytes, activation of CD8+ T lymphocytes, activation and maturation of B lymphocytes, and/or production of tumor antigen-specific antibodies.
  • the adaptive immune response kills tumor cells, reduces tumor size, and/or prevents metastasis.
  • the guide nucleotide sequence is an RNA.
  • the RNA is chemically modified.
  • the guide nucleotide sequence is a single strand DNA (ssDNA).
  • the tumor specific antigen is gplOO.
  • the gplOO is from melanoma.
  • the deamination of the target C base in codon T210 of gplOO results in a T210I mutation.
  • a heteroclitic epitope comprising the amino acid sequence of IIDQVPFSV (SEQ ID NO: 786) is generated, and wherein the I at position 2 corresponds to the T210I mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 724 and 870-888.
  • the deamination of the target C base in codon A288 of gplOO results in a A288V mutation.
  • a heteroclitic epitope comprising the amino acid sequence of YLEPGPVTV (SEQ ID NO: 818) is generated, and wherein the V at position 7 corresponds to the A288V mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 725 and 889.
  • the deamination of the target C base in codon T155 of gplOO results in a T155I mutation.
  • a heteroclitic epitope comprising the amino acid sequence of KIWGQYWQV (SEQ ID NO: 787) is generated, and wherein the I at position 2 corresponds to the T155I mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 726 and 890-892.
  • the tumor specific antigen is melanoma antigen recognized by T cells 1 (MART-1).
  • the MART-1 antigen is from melanoma.
  • the deamination of the target C base in codon A27 of MART-1 results in a A27V mutation.
  • a heteroclitic epitope comprising the amino acid sequence of EVAGIGILTV (SEQ ID NO: 819) is generated, and wherein the V at position 2 corresponds to the A27V mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 727 and 893-896.
  • the tumor specific antigen is cancer/testis antigen IB (NY- ESO-1).
  • the NY-ESO-1 antigen is from melanoma or breast cancer.
  • the deamination of the target C base in codon C165 of NY-ESO-1 results in a C165Y mutation.
  • a heteroclitic epitope comprising the amino acid sequence of SLLMWITQY (SEQ ID NO: 788) is generated, and wherein the C at position 9 corresponds to the C165Y mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 728 and 897.
  • the tumor specific antigen is Tyrosinase (TYR).
  • the TYR antigen is from melanoma.
  • the deamination of the target C base in codon T373 of TYR results in a T373I mutation.
  • a heteroclitic epitope comprising the amino acid sequence of YMNGIMSQV (SEQ ID NO: 789) is generated, and wherein the I at position 5 corresponds to the T373I mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 729 and 898-901.
  • the tumor specific antigen is tyrosinase-related protein 1 (TyRPl).
  • TyRPl tyrosinase-related protein 1
  • the TyRPl antigen is from melanoma.
  • the deamination of the target C base in codon C244 of TyRPl results in a C244Y mutation.
  • a heteroclitic epitope comprising the amino acid sequence of DAEKYDICTDEY (SEQ ID NO: 790) is generated, and wherein the Y at position 5 corresponds to the C244Y mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 730 and 902.
  • the tumor specific antigen is Survivin.
  • the Survivin is from melanoma, breast cancer, or leukemia.
  • the deamination of the target C base in codon T97 of Survivin results in a T97I mutation.
  • a heteroclitic epitope comprising the amino acid sequence of ELILGEFLKL (SEQ ID NO: 791) is generated, and wherein the I at position 3
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 731 and 903.
  • the tumor specific antigen is telomerase reverse
  • hTERT transcriptase
  • the hTERT is from breast cancer.
  • the deamination of the target C base in codon M549 of hTERT results in a M549I mutation.
  • a heteroclitic epitope comprising the amino acid sequence of ILAKFLHWLI (SEQ ID NO: 792) is generated, and wherein the I at position 10 corresponds to the M549I mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 735 and 916-920.
  • the tumor specific antigen is human epidermal growth factor receptor 2 (HER2).
  • the HER2 is from breast cancer.
  • the deamination of the target C base in codon V658 of HER2 results in a V658M mutation.
  • a heteroclitic epitope comprising the amino acid sequence of AMVGILLVVV (SEQ ID NO: 793) is generated, and wherein the M at position 2 corresponds to the V658M mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 732 and 904-909.
  • the deamination of the target C base in codon T912 of HER2 results in a T912I mutation.
  • a heteroclitic epitope comprising the amino acid sequence of IIWELMTFGA (SEQ ID NO: 794) is generated, and wherein the
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 733 and 910-912.
  • the deamination of the target C base in codon A920 of HER2 results in a A920V mutation.
  • a heteroclitic epitope comprising the amino acid sequence of ITWELMTFGV (SEQ ID NO: 795) is generated, and wherein the
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 734 and 913-915.
  • the tumor specific antigen is CD33.
  • the CD33 is from leukemia.
  • the deamination of the target C base in codon A65 of CD33 results in a A65V mutation.
  • a heteroclitic epitope comprising the amino acid sequence of VIISGDSPV (SEQ ID NO: 796) is generated, and wherein the V at position 1 corresponds to the A65V mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 740 and 930-932.
  • the tumor specific antigen is Synovial Sarcoma X
  • Breakpoint 2 (SSX2).
  • the deamination of the target C base in codon A42 of SSX2 results in a A42V mutation.
  • a heteroclitic epitope comprising the amino acid sequence of KVSEKIFYV (SEQ ID NO: 797) is generated, and wherein the V at position 2 corresponds to the A42V mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 737 and 921.
  • the tumor specific antigen is Wilm's tumor 1 (WT1) protein.
  • WT1 is from leukemia.
  • the deamination of the target C base in codon C235 of WT1 results in a C235Y mutation.
  • a heteroclitic epitope comprising the amino acid sequence of
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 738 and 922-925.
  • the deamination of the target C base in codon M236 of WT1 results in a M236I mutation.
  • a heteroclitic epitope comprising the amino acid sequence of CITWNQMNL (SEQ ID NO: 799) is generated, and wherein the I at position 2 corresponds to the M236I mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 739 and 926-929.
  • the tumor specific antigen is Epithelial cell adhesion molecule precursor (EpCAM).
  • EpCAM Epithelial cell adhesion molecule precursor
  • the deamination of the target C base in codon T192 of EpCAM results in a T192I mutation.
  • a heteroclitic epitope comprising the amino acid sequence of ILYENNVII (SEQ ID NO: 800) is generated, and wherein the I at position 9 corresponds to the T192I mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 741 and 933-934.
  • the tumor specific antigen is carcinoembryonic antigen- related cell adhesion molecules (CEA-CAM).
  • CEA-CAM carcinoembryonic antigen- related cell adhesion molecules
  • the CEA-CAM is from colorectal cancer, lung cancer, or breast cancer.
  • the deamination of the target C base in codon T314 of CEA-CAM results in a T314I mutation.
  • a heteroclitic epitope comprising the amino acid sequence of LLTFWNPPI (SEQ ID NO: 801) is generated, and wherein the I at position 9 corresponds to the T314I mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 742 and 935-936.
  • the deamination of the target C base in codon T311 of CEA-CAM results in a T31 II mutation.
  • a heteroclitic epitope comprising the amino acid sequence of RITVTTITV (SEQ ID NO: 802) is generated, and wherein the V at position 2 corresponds to the T31 II mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 743 and 937-940.
  • the deamination of the target C base in codon T688 of CEA-CAM results in a T688V mutation.
  • a heteroclitic epitope comprising the amino acid sequence of AVVGIMIGV (SEQ ID NO: 803) is generated, and wherein the V at position 2 corresponds to the T688V mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 744 and 941-947.
  • the deamination of the target C base in codon V695 of CEA-CAM results in a V695M mutation.
  • a heteroclitic epitope comprising the amino acid sequence of IMIGMLVGV (SEQ ID NO: 804) is generated, and wherein the M at position 5 corresponds to the V695M mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 745 and 948-953.
  • the tumor specific antigen is melanoma-associated antigen A3 (MAGEA3).
  • MAGEA3 melanoma-associated antigen A3
  • the deamination of the target C base in codon HI 18 of MAGEA3 results in a HI 18Y mutation.
  • a heteroclitic epitope comprising the amino acid sequence of KVAELVYFL (SEQ ID NO: 805) is generated, and wherein the Y at position 7 corresponds to the HI 18Y mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 746 and 954.
  • the tumor specific antigen is melanoma-associated antigen (MAGE) common antigen A3, Al, A4, A2, or A12.
  • MAGE melanoma-associated antigen
  • a heteroclitic epitope comprising the amino acid sequence of YLGLSYDGLL (SEQ ID NO: 806) is generated, and wherein the Y at position 1 corresponds to the C181Y mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 747-750 and 955-983.
  • the tumor specific antigen is MUC-1. In some embodiments, the tumor specific antigen is MUC-1.
  • the deamination of the target C base in codon T93 of MUC-1 results in a T93I mutation.
  • a heteroclitic epitope comprising the amino acid sequence of AIWGQDVTSV (SEQ ID NO: 807) is generated, and wherein the I at position 2 corresponds to the T93I mutation.
  • the guide nucleotide sequence comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 751 and 984-985.
  • the target C base is located in intron 4 of the
  • the deamination of the target C base results in a cryptic peptide comprising the amino acid sequence of VYFFLPDHL (SEQ ID NO: 808).
  • the guide nucleotide sequence comprises a nucleotide selected from the group consisting of SEQ ID NOs: 752-753 and 986-998.
  • the target C base is located on the complementary strand of open reading frame 1 (ORF1) of TYRP1 gene. In some embodiments, the target C base is located in the complementary strain of the first start codon (ATG) of ORF1 of the TYRP1 gene. In some embodiments, the deamination of the target C base results in a cryptic peptide comprising the amino acid sequence of MSLQRQFLR (SEQ ID NO: 809).
  • the guide nucleotide sequence comprises a nucleotide selected from the group consisting of SEQ ID NOs: 754 and 999-1005.
  • the target C base is located on the complementary strand of the last base of intron 2 of the mannosyl (alpha- l,6-)-glycoprotein beta-l,6-N-acetyl glucosaminyltransferase (MGAT5) gene.
  • the deamination of the target C base results in a cryptic peptide comprising the amino acid sequence of VLPDVFIRCV (SEQ ID NO: 810).
  • the cryptic peptide is translated from exon 3 of the MGAT5 gene.
  • the guide nucleotide sequence comprises a nucleotide selected from the group consisting of SEQ ID NOs: 755 and 1006-1008.
  • the target C base is located in open reading frame 1 (ORF1) of cancer/testis antigen 2 (LAGE-1) gene.
  • the target C base is located in the complementary strand of the first start codon of ORF1 of the LAGE-1 gene.
  • the deamination of the target C base results in a cryptic peptide comprising the amino acid sequence of selected from the group consisting of: MLMAQEALAFL (SEQ ID NO: 811), LAAQERRVPR (SEQ ID NO: 812), APRGVRMAV (SEQ ID NO: 813),
  • the guide nucleotide sequence comprises a nucleotide selected from the group consisting of SEQ ID NOs: 756 and 1009-1014.
  • the target C base is located in intron 2 of tyrosinase-related protein 2 (TRP-2) gene. In some embodiments, the target C base is located on the
  • the deamination of the target C base results in a cryptic peptide comprising the amino acid sequence of EVISCKLIKR (SEQ ID NO: 816).
  • the guide nucleotide sequence comprises a nucleotide selected from the group consisting of SEQ ID NOs: 757-758 and 1015-1023.
  • the target C base is located in intron 2 of baculoviral IAP repeat containing 5 (BIRC5) gene. In some embodiments, the target C base is located on the spliceosome branch site of intron 2 of the BIRC5 gene. In some embodiments, the target C base is located in the complementary strand of the last base of intron 2 of the BIRC5 gene. In some embodiments, the deamination of the target C base results in a cryptic peptide comprising the amino acid sequence of AYACNTSTL (SEQ ID NO: 817). In some embodiments, the guide nucleotide sequence comprises a nucleotide selected from the group consisting of SEQ ID NOs: 759 and 1024-1029.
  • the target C base is located in intron 1 acceptor site of BCR/ABL fusion proteins (BCR/ABL-OOF) gene. In some embodiments, the target C base is located in intron 2 acceptor site of BCR/ABL fusion proteins (BCR/ABL-OOF) gene. In some embodiments, the deamination of the target C base results in a cryptic peptide comprising the amino acid sequence of any one of SSKALQRPV (SEQ ID NO: 603), GFKQSSKAL (SEQ ID NO: 604), and ATGFKQS S KALQRPVAS (SEQ ID NO: 605).
  • the guide nucleotide sequence comprises a nucleotide selected from the group consisting of SEQ ID NOs: 761 and 1032-1045. In some embodiments, the guide nucleotide sequence comprises a nucleotide selected from the group consisting of SEQ ID NOs: 762 and 1046-1056.
  • the methods further comprising administering to the subject a therapeutically effective amount of an immune checkpoint inhibitor.
  • the immune checkpoint inhibitor inhibits binding of CTLA-4, PD-1, PD-L1, TEVI3, LAG3, B7-H3, B7-H4, BTLA, GAL9, Chkl, or A2aR to a cognate binding partner.
  • the immune checkpoint inhibitor is an antibody or a fragment thereof.
  • the antibody is selected from anti-CTLA-4 antibodies, anti-PD-1 antibodies, anti-PD-Ll antibodies, anti-TIM3 antibodies, anti-LAG3 antibodies, anti-B7-H3 antibodies, anti-B7-H4 antibodies, anti-BTLA antibodies, anti-GAL9 antibodies, anti-Chkl antibodies, and anti-A2aR antibodies. In some embodiments, the antibody is selected from
  • pembrolizumab pembrolizumab, nivolumab, and ipilimumab.
  • the immune checkpoint inhibitor is a small molecule.
  • the immune checkpoint inhibitor is a recombinant protein.
  • the immune checkpoint inhibitor is a nucleic acid ap tamer.
  • the immune checkpoint inhibition is performed by genome editing of a gene selected from the group consisting of: CTLA-4, PD-1, PD-L1, TIM3, LAG3, B7-H3, B7-H4, BTLA, GAL9, Chkl, or A2aR.
  • compositions comprising: (i) a fusion protein comprising (a) a guide nucleotide sequence-programmable DNA-binding protein domain; and (b) a cytosine deaminase domain; and (ii) a guide nucleotide sequence; wherein the fusion protein of (i) and the guide nucleotide sequence of (ii) enters a tumor cell, and wherein the guide nucleotide sequence targets the fusion protein of (i) to a polynucleotide encoding a tumor- specific antigen, wherein the fusion protein changes a target cytosine (C) residue to a (T) residue in the polynucleotide.
  • the methods include administering to the subject a therapeutically effective amount of an immune checkpoint inhibitor.
  • a composition comprising: (i) a fusion protein comprising (a) a guide nucleotide sequence-programmable DNA-binding protein domain; and (b) a nuclease domain; and (ii) a guide nucleotide sequence; wherein the fusion protein of (i) and the guide nucleotide sequence of (ii) enters the tumor cell, and wherein the guide nucleotide sequence targets the fusion protein of (i) to a polynucleotide encoding a tumor- specific antigen, wherein the fusion protein introduces an indel in the polynucleotide.
  • the nuclease is a Fokl nuclease.
  • a composition comprising: (i) a guide nucleotide sequence-programmable nuclease; and (ii) a guide nucleotide sequence; wherein the fusion protein of (i) and the guide nucleotide sequence of (ii) enters the tumor cell, and wherein the guide nucleotide sequence targets the fusion protein of (i) to a polynucleotide encoding a tumor- specific antigen, wherein the guide nucleotide sequence-programmable nuclease introduces an indel in the polynucleotide.
  • the guide nucleotide sequence-programmable nuclease comprises a Cas9, a Cpfl, an Argonaute, or a variant thereof.
  • the indel causes a mutation or frame shift.
  • Method of inducing a tumor- specific immune response in a subject in need thereof including administering to a subject in need thereof a therapeutically effective amount of a composition comprising a fusion protein comprising (a) a programmable DNA-binding protein domain; and (b) a deaminase domain; wherein the fusion protein enters the tumor cell and changes a target base in the polynucleotide via deamination.
  • a composition comprising a fusion protein comprising (a) a programmable DNA-binding protein domain; and (b) a deaminase domain; wherein the fusion protein enters the tumor cell and changes a target base in the polynucleotide via deamination.
  • the deaminase domain comprises a cytosine deaminase and the target base is a cytosine (C) base.
  • the programmable DNA-binding domain comprises a zinc finger nuclease (ZFN).
  • the programmable DNA-binding domain comprises a transcription activator- like effector (TALE).
  • the programmable DNA-binding domain is a guide nucleotide sequence-programmable DNA binding protein domain.
  • the programmable DNA-binding domain is selected from the group consisting of: nuclease- inactive Cas9 domains, nuclease inactive Cpfl domains, nuclease inactive Argonaute domains, and variants thereof.
  • the programmable DNA-binding domain is associated with a guide nucleotide sequence. In some embodiments, the
  • deamination of the target C base results in a C to thymine (T) change.
  • the deamination of the target C base results in a C-G base pair to thymine-adenine (T-A) change in a translated codon, resulting in the incorporation of a different amino acid in an immunogenic or heteroclitic peptide.
  • the deamination of the target C base results in a C-G basepair to thymine- adenine (T-A) change in an non-coding intron region of a gene, resulting in alternative splicing and translation of immunogenic or cryptic peptide sequences.
  • the deamination of the target C base results in a C- G basepair to thymine- adenine (T-A) change in the start (Met) codon of the open reading frame of a gene, resulting in the translation of an alternative open reading frame comprising immunogenic or cryptic peptide sequences.
  • T-A thymine- adenine
  • compositions comprising: (i) a fusion protein comprising (a) a guide nucleotide sequence-programmable DNA-binding protein domain; and (b) a cytosine deaminase domain; and (ii) a guide nucleotide sequence targeting the fusion protein of (i) to a polynucleotide encoding a tumor specific antigen.
  • compositions comprising a polynucleotide encoding a fusion protein and a guide nucleotide sequence, wherein the fusion protein comprises (a) a guide nucleotide sequence-programmable DNA-binding protein domain; and (b) a cytosine deaminase domain, and wherein the guide nucleotide sequence targets the fusion protein to a polynucleotide encoding a tumor specific antigen.
  • cancer vaccines comprising: (i) a fusion protein comprising (a) a guide nucleotide sequence-programmable DNA-binding protein domain; and (b) a cytosine deaminase domain; and (ii) a guide nucleotide sequence targeting the fusion protein of (i) to a polynucleotide encoding a tumor specific antigen.
  • cancer vaccine comprising a polynucleotide encoding a fusion protein and a guide nucleotide sequence, wherein the fusion protein comprises (a) a guide nucleotide sequence-programmable DNA-binding protein domain; and (b) a cytosine deaminase domain, and wherein the guide nucleotide sequence targets the fusion protein to a polynucleotide encoding a tumor specific antigen.
  • Kits comprising the cancer vaccines described herein are also provided.
  • Figure 1 shows strategies to engineer heteroclitic and cryptic epitopes using genome base editing.
  • Figure 2A shows strategies to introduce immunogenic heteroclitic epitopes by editing conservative anchor residues to match the binding preference of the main HLA allele supertypes.
  • the example shows a base-editing reaction that turns an alanine residue at anchor position 9 of a weakly immunogenic peptide epitope into a preferred valine residue for binding HLA-A2.
  • Figure 2B shows anchor-residue binding preference and population coverage of the main HLA allele supertypes (MHC-I pathway).
  • the peptides in Figure 2B are as follows: HLA Al, A2, A3, and A24 (SEQ ID NOs: 878-881) and HLA B7, B27, B44, B58, and B62 (SEQ ID NOs: 882-886).
  • Figure 3 shows a proposed mechanism for anti-cancer vaccination by
  • heteroclitic/cryptic epitopes introduced by genome base-editing reactions programmed by guide-RNAs.
  • the edited tumor cells produce heteroclitic and cryptic epitopes in cancer- specific genes, which chemotactically attract immature dendritic cells (DCs) (la), inducing DC maturation (lb).
  • Edited tumor cells produce apoptotic bodies (2a) that are taken up by DCs (2b), contributing to maturation of DCs (lb) and B cells (2b').
  • Mature DCs activate CD4+ T lymphocytes (lc) and CD8+ T lymphocytes (lc').
  • Activated CD4+ T lymphocytes further stimulate B-lymphocyte activation (Id) and provide IL-2 for CD8+ T lymphocytes (Id').
  • B lymphocytes produce TAA-specific antibodies to cell-surface proteins that result in antibody-dependent cell-mediated cytotoxicity or complement-mediated tumor cell death (le).
  • Activated CD8+ T lymphocytes then kill tumor cells via recognition of MHC class I molecules in association with TAA epitopes (le').
  • Figure 4 shows comparison of cancer lineages that display high frequency of mutagenesis, which may harbor non- synonymous hitchhiker mutations and "neo-epitopes".
  • an "immunogenic peptide” or “antigenic peptide” is a peptide or epitope that can be recognized by the immune system and elicit an immune response. Immunogenic peptides or antigenic peptide may comprise a motif such that the peptide will bind an MHC molecule and induce a T cell response, or can be recognized by the B cell receptor on the B cell to induce antibody production. These terms are used interchangeably herein.
  • an "immunogenic epitope” or “antigenic epitope” refers to a part of an antigen is recognized by the immune system, e.g., by antibodies, B cells, or T cells. In some
  • the epitope is the specific piece of the antigen to which an antibody binds.
  • epitopes are usually non-self proteins, sequences derived from the host can, in some instances, be recognized.
  • Immuno response is how your body recognizes and defends itself against bacteria, viruses, and substances that appear foreign and harmful to the body.
  • the immune response begins with the sensitization of helper (TH, CD4+) and cytotoxic (CD8+) T cell subsets through their interaction with antigen presenting cells (APC) that express major histocompatibility (MHC)-class I or class II molecules associated with antigenic fragments (i.e., specific amino acid sequences derived from the antigen which bind to MHC I and/or MHC II for presentation on the cell surface).
  • APC antigen presenting cells
  • MHC major histocompatibility-class I or class II molecules associated with antigenic fragments (i.e., specific amino acid sequences derived from the antigen which bind to MHC I and/or MHC II for presentation on the cell surface).
  • MHC major histocompatibility
  • the sensitized or primed CD4+ T cells produce lymphokines that participate in the activation of B cells as well as various T cell subsets
  • the sensitized CD8+ T cells increase in numbers in response to lymphokines and are capable of destroying any cells that express the specific antigenic fragments associated with matching MHC-encoded class I molecules.
  • CTL eradicate cells expressing cancer associated or cancer specific antigens, thereby limiting the
  • the "adaptive immune system,” also known as the acquired immune system, is a subsystem of the overall immune system that is composed of highly specialized, systemic cells and processes that eliminate or prevent pathogen growth.
  • the adaptive immune system is one of the two main immunity strategies found in vertebrates (the other being the innate immune system). Adaptive immunity creates immunological memory after an initial response to a specific pathogen, and leads to an enhanced response to subsequent encounters with that pathogen. This process of acquired immunity is the basis of vaccination.
  • the adaptive system includes both humoral immunity components and cell-mediated immunity components.
  • the adaptive immune system is highly specific to a particular pathogen or antigen. Adaptive immunity can also provide long-lasting protection.
  • the adaptive system response destroys invading pathogens and any toxic molecules they produce.
  • the adaptive immune system response destroys tumor or cancer cells. Sometimes the adaptive system is unable to distinguish harmful from harmless foreign molecules.
  • the cells that carry out the adaptive immune response are white blood cells known as lymphocytes.
  • Two main broad classes— antibody responses and cell mediated immune response— are also carried by two different
  • B cells and T cells lymphocytes (B cells and T cells). In antibody responses, B cells are activated to secrete antibodies, which are proteins also known as immunoglobulins. Antibodies travel through the bloodstream and bind to the foreign antigen causing it to inactivate, which does not allow the antigen to bind to the host.
  • pathogen-specific receptors are "acquired” during the lifetime of the organism (whereas in innate immunity pathogen- specific receptors are already encoded in the germline).
  • the acquired response is called “adaptive” because it prepares the body's immune system for future challenges (though it can actually also be maladaptive when it results in autoimmunity).
  • the immune system is highly adaptable because of somatic hypermutation (a process of accelerated somatic mutations), and V(D)J recombination (an irreversible genetic recombination of antigen receptor gene segments).
  • somatic hypermutation a process of accelerated somatic mutations
  • V(D)J recombination an irreversible genetic recombination of antigen receptor gene segments.
  • This mechanism allows a small number of genes to generate a vast number of different antigen receptors, which are then uniquely expressed on each individual lymphocyte. Since the gene rearrangement leads to an irreversible change in the DNA of each cell, all progeny (offspring) of that cell inherit genes that encode the same receptor specificity, including the memory B cells and memory T cells that are the keys to long-lived specific immunity.
  • T cell or "T lymphocyte” is a type of lymphocyte (a subtype of white blood cell) that plays a central role in cell-mediated immunity.
  • T cells can be distinguished from other lymphocytes, such as B cells and natural killer cells, by the presence of a T-cell receptor on the cell surface. They are called T cells because they mature in the thymus from thymocytes. The several subsets of T cells each have a distinct function. The majority of human T cells rearrange their alpha and beta chains on the cell receptor and are termed alpha beta T cells ( ⁇ T cells) and are part of the adaptive immune system.
  • ⁇ T cells alpha beta T cells
  • T cells Specialized gamma delta T cells, (a small minority of T cells in the human body, more frequent in ruminants), have invariant T cell receptors with limited diversity, that can effectively present antigens to other T cells and are considered to be part of the innate immune system.
  • Effector T cell broadly includes various T cell types that actively respond to a stimulus, such as co- stimulation. This includes helper, killer, regulatory, and potentially other T cell types.
  • One skilled in the art is familiar with different types of T cells and their respective roles in adaptive immune response.
  • a "human leukocyte antigen (HLA) system” is a gene complex encoding the major histocompatibility complex (MHC) proteins in humans. These cell-surface proteins are responsible for the regulation of the immune system in humans.
  • MHC major histocompatibility complex
  • the HLA gene complex resides on a 3 Mbp stretch within chromosome 6p21.
  • HLA genes are highly polymorphic, which means that they have many different alleles, allowing them to fine-tune the adaptive immune system.
  • the proteins encoded by certain genes are also known as antigens, as a result of their historic discovery as factors in organ transplants. Different classes have different functions:
  • MHC class I major histocompatibility complex
  • A, B, and C major histocompatibility complex
  • MHC class I major histocompatibility complex
  • A, B, and C major histocompatibility complex
  • MHC class I major histocompatibility complex
  • MHC class I major histocompatibility complex
  • Class I MHC molecules bind peptides generated mainly from degradation of cytosolic proteins by the proteasome.
  • the MHC I peptide complex is then inserted via endoplasmic reticulum into the external plasma membrane of the cell.
  • the epitope peptide is bound on extracellular parts of the class I MHC molecule.
  • the function of the class I MHC is to display intracellular proteins to cytotoxic T cells (CTLs).
  • CTLs cytotoxic T cells
  • class I MHC can also present peptides generated from exogenous proteins, in a process known as cross- presentation.
  • a normal cell will display peptides from normal cellular protein turnover on its class I MHC, and CTLs will not be activated in response to them due to central and peripheral tolerance mechanisms.
  • CTLs specific for the MHC:peptide complex will recognize and kill presenting cells.
  • class I MHC itself can serve as an inhibitory ligand for natural killer cells (NKs). Reduction in the normal levels of surface class I MHC, a mechanism employed by some viruses during immune evasion or in certain tumors, will activate NK cell killing. Antigens or antigenic epitopes presented by MHC class II molecules are recognized by cytotoxic T cells.
  • MHC class II DP, DM, DOA, DOB, DQ, and DR molecules
  • MHC class II DP, DM, DOA, DOB, DQ, and DR molecules
  • extracellular proteins are endocytosed, digested in lysosomes, and the resulting epitopic peptide fragments are loaded onto MHC class II molecules prior to their migration to the cell surface.
  • Antigens or antigenic epitopes presented by MHC class II molecules are recognized by T helper cells and stimulate the multiplication of T-helper cells, which in turn stimulate antibody-producing B-cells to produce antibodies to that specific antigen.
  • Self-antigens are suppressed by regulatory T cells.
  • An "antigen-presenting cell (APC)” is a cell that displays antigen complexed with major histocompatibility complexes (MHCs) on their surfaces; this process is known as antigen presentation. T cells may recognize these complexes using their T cell receptors (TCRs). These cells process antigens and present them to T-cells.
  • Antigen-presenting cells fall into two categories: professional and non-professional. Those that express MHC class II molecules along with co- stimulatory molecules and pattern recognition receptors are often called professional antigen-presenting cells. The non-professional APCs express MHC class I molecules.
  • APCs specialize in presenting antigen to T cells. They are very efficient at internalizing antigens, either by phagocytosis (macrophages and dendritic cells) or by receptor-mediated endocytosis (B cells), processing the antigen into peptide fragments and then displaying those peptides, bound to a class II MHC molecule, on their membrane.
  • the T cell recognizes and interacts with the antigen-class II MHC molecule complex on the membrane of the antigen-presenting cell. An additional co-stimulatory signal is then produced by the antigen-presenting cell, leading to activation of the T cell.
  • the expression of co-stimulatory molecules and MHC class II are defining features of professional APCs.
  • APC Almost all cell types can serve as a non-professional APC. They are found in a variety of tissue types. Professional antigen-presenting cells, including dendritic cells, mononuclear phagocytes, thymic epithelial cells, and B cells, present foreign antigens to helper T cells, while other cell types can present antigens originating inside the cell to cytotoxic T cells. In addition to the MHC family of proteins, antigen presentation relies on other specialized signaling molecules on the surfaces of both APCs and T cells.
  • B lymphocyte or "B cell” is a type of white blood cell of the lymphocyte subtype.
  • B cells function in the humoral immunity component of the adaptive immune system by secreting antibodies. Additionally, B cells present antigen (they are also classified as professional antigen-presenting cells (APCs)) and secrete cytokines. In mammals, B cells mature in the bone marrow, which is at the core of most bones. B cells express B cell receptors (BCRs) on their cell membrane. BCRs allow the B cell to bind a specific antigen, against which it will initiate an antibody response.
  • BCRs B cell receptors
  • Cancer immunotherapy refers to a type of cancer treatment designed to boost the body's natural defenses to fight the cancer. It uses substances either made by the body or in a laboratory to improve or restore immune system function.
  • TSA Tumor specific antigen
  • TAA tumor specific antigen
  • TAA tumor associated antigen
  • the tumor specific antigen may be from all protein classes, e.g., enzymes, receptors, transcription factors, etc.
  • heteroclitic epitope or “heteroclitic analog” refers to an altered version of an endogenous peptide sequence ⁇ i.e., an analog) engineered to elicit potent immune reactions. Heteroclitic epitopes have increased stimulatory capacity or potency for a specific T cell, as measured by increased responses to a given dose, or by a requirement of lesser amounts to achieve the same response and therefore provide benefit as vaccine components since these epitopes induce T cell responses stronger than those induced by the native epitope.
  • a "self-antigen” refers to an antigen that originates from within the body.
  • the immune system usually does not react to self-antigens under normal homeostatic conditions.
  • Epitopes from self-antigens ⁇ i.e., self-epitopes
  • APCs Antigen-presenting cells
  • MHC major histocompatibility complex
  • APCs Antigen-presenting cells
  • MHC major histocompatibility complex
  • a "cryptic epitope” refers to an epitope derived from a self-antigen that does not necessarily undergo antigen processing/presentation and are 'hidden' from immune recognition. Cryptic epitopes usually appear in very low concentration on APC and do not delete auto-reactive T cells. Cryptic epitopes are not presented for recognition by T cells unless they are produced in unusually large concentrations or unless they are freed from the configuration of their native antigen. Cryptic epitopes derived from tumor- specific antigens may be used to break the tolerance of T cells to the tumor and induce potent immune response against the tumor. Such principles have been described in Pardoll, et al., PNAS, Vol. 96, pp. 5340-5342 (1999), the entire contents of which are incorporated herein by reference.
  • Neoepitope refers to an antigenic epitope generated via random somatic mutations occurring in tumor cells. Neoepitopes are usually derived from individually specific tumor antigens or unique antigens and is thus specific to the lineage of tumor cells it is derived from. Neoepitopes are regarded in the art to be responsible for the immunogenicity of tumors ((Srivastava et al., 1993, Duan et al., 2009; van der Bruggen et al., 2013), and mathematic modeling has predicted the existence of tens to hundreds of neoepitopes in individual human tumors (Srivastava 2009). The recent revolution in high-throughput DNA sequencing and accompanying bioinformatics approaches has finally made it possible to actually identify the individually specific neoepitopes in individual cancers.
  • Cancer vaccine refers to a composition that induces tumor- specific immunoresponse against a tumor or a tumor- specific antigen. Such immunoresponse is effective in inhibiting tumor growth and/or preventing reoccurrence of tumor.
  • an "intron” refers to any nucleotide sequence within a gene that is removed by RNA splicing during maturation of the final RNA product.
  • the term intron refers to both the DNA sequence within a gene and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation.
  • rRNA ribosomal RNA
  • tRNA transfer RNA
  • exon refers to any part of a gene that will become a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing.
  • exon refers to both the DNA sequence within a gene and to the corresponding sequence in RNA transcripts.
  • introns are removed and exons are covalently joined to one another as part of generating the mature messenger RNA.
  • RNA splicing refers to the processing of a newly synthesized messenger RNA transcript (also referred to as a primary mRNA transcript). After splicing, introns are removed and exons are joined together (ligated) for form mature mRNA molecule containing a complete open reading frame that is decoded and translated into a protein. For nuclear- encoded genes, splicing takes place within the nucleus either co-transcriptionally or immediately after transcription. The molecular mechanism of RNA splicing has been extensively described, e.g., in Pagani et al, Nature Reviews Genetics 5, 389-396, 2004;
  • Alternative splicing refers to a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed messenger RNA (mRNA) produced from that gene. Consequently, the proteins translated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions . Notably, alternative splicing allows the human genome to direct the synthesis of many more proteins than would be expected from its 20,000 protein-coding genes.
  • mRNA messenger RNA
  • Alternative splicing is sometimes also termed differential splicing.
  • Alternative splicing occurs as a normal phenomenon in eukaryotes, where it greatly increases the biodiversity of proteins that can be encoded by the genome; in humans, -95% of multi-exonic genes are alternatively spliced.
  • Abnormal variations in splicing are also implicated in disease; a large proportion of human genetic disorders result from splicing variants.
  • a "coding frame” or "open reading frame” refers to a streich of codons that encodes a polypeptide. Since DNA is interpreted in groups of three nucleotides (codons), a DNA strand has three distinct reading frames. The double helix of a DNA molecule has two anti- parallel strands so, with the two strands having three reading frames each, there are six possible frame translations. A functional protein may be produced when translation proceeds in the correct coding frame. An insertion or a deletion of one or two bases in the open reading frame causes a shift in the coding frame that is also referred to as a "frameshift mutation.” A frameshift mutation typical results in premature translation termination and/or truncated or non-functional protein.
  • proteome refers to the entire set of proteins expressed by a genome, cell, tissue, or organism at a certain time. More specifically, it is the set of expressed proteins in a given type of cell or organism, at a given time, under certain conditions. The term is a blend of proteins and genome. "Proteome-wide” refers to each and every protein in the proteome without any bias.
  • the term "genome” refers to the genetic material of a cell or organism. It typically includes DNA (or RNA in the case of RNA viruses). The genome includes both the genes, the coding regions, the noncoding DNA, and the genomes of the mitochondria and chloroplasts. A genome does not typically include genetic material that is artificially introduced into a cell or organism, e.g., a plasmid that is transformed into a bacteria is not a part of the bacterial genome.
  • a "programmable DNA-binding protein,” as used herein, refers to DNA binding proteins that can be programmed to navigate to any desired target nucleotide sequence within the genome.
  • the DNA binding protein may be modified to change its binding specificity, e.g., zinc finger nuclease (ZFN) or transcription activator-like effector proteins (TALE).
  • ZFNs are artificial restriction enzymes generated by fusing a zinc finger DNA-binding domain to a DNA- cleavage domain.
  • Zinc finger domains can be engineered to target specific desired DNA sequences and this enables zinc-finger nucleases to target unique sequences within complex genomes.
  • Transcription activator- like effector nucleases are restriction enzymes that can be engineered to cut specific sequences of DNA. They are made by fusing a TAL effector DNA-binding domain to a DNA cleavage domain (a nuclease which cuts DNA strands). Transcription activator-like effectors (TALEs) can be engineered to bind practically any desired DNA sequence, so when combined with a nuclease, DNA can be cut at specific locations.
  • TALEs Transcription activator-like effectors
  • the restriction enzymes can be introduced into cells, for use in gene editing or for genome editing in situ, Methods of programming ZFNs and TALEs are familiar to one skilled in the art. For example, such methods are described in Maeder, et al, Mol.
  • a "guide nucleotide sequence-programmable DNA-binding protein,” as used herein, refers to a protein, a polypeptide, or a domain that is able to bind DNA, and the binding to its target DNA sequence is mediated by a guide nucleotide sequence.
  • the guide nucleotide sequence-programmable DNA-binding protein binds to a guide nucleotide sequence.
  • the "guide nucleotide” may be a RNA molecule or a DNA molecule ⁇ e.g., a single- stranded DNA or ssDNA molecule) that is complementary to the target sequence and can guide the DNA binding protein to the target sequence.
  • the guide nucleotide sequence is an oligonucleotide sequence.
  • a guide nucleotide sequence-programmable DNA-binding protein may be a RNA-programmable DNA-binding protein ⁇ e.g., a Cas9 protein), or an ssDNA-programmable DNA-binding protein ⁇ e.g., an Argonaute protein).
  • "Programmable” means the DNA-binding protein may be programmed to bind any DNA sequence that the guide nucleotide targets.
  • the guide nucleotide sequence exists as a single nucleotide molecule and comprises comprise two domains: (1) a domain that shares homology to a target nucleic acid ⁇ e.g., and directs binding of a guide nucleotide sequence-programmable DNA-binding protein to the target); and (2) a domain that binds a guide nucleotide sequence- programmable DNA-binding protein.
  • the guide nucleotide is a guide RNA (gRNA).
  • domain (2) of the gRNA corresponds to a sequence known as a tracrRNA, and comprises a stem-loop structure.
  • domain (2) is identical or homologous to a tracrRNA as provided in Jinek et al, Science 337:816-821(2012), the entire contents of which is incorporated herein by reference.
  • gRNAs ⁇ e.g., those including domain 2 can be found in U.S. Provisional Patent Application, U.S.S.N. 61/874,682, filed September 6, 2013, entitled “Switchable Cas9 Nucleases And Uses Thereof," and U.S. Provisional Patent Application, U.S.S.N. 61/874,746, filed September 6, 2013, entitled “Delivery System For Functional Nucleases," the entire contents of each are hereby incorporated by reference in their entirety.
  • the guide nucleotide sequence-programmable DNA-binding proteins are able to be targeted, in principle, to any sequence specified by the guide nucleotide sequence.
  • Methods of using guide nucleotide sequence-programmable DNA-binding protein, such as Cas9, for site- specific cleavage are known in the art (see e.g., Cong, L. et al. Science 339, 819-823 (2013); Mali, P. et al. Science 339, 823-826 (2013); Hwang, W.Y. et al. Nature biotechnology 31, 227-229 (2013); Jinek, M. et al. eLife 2, e00471 (2013);
  • the guide nucleotide sequence-programmable DNA binding protein may be a Cas9 protein, or a variant thereof.
  • Cas9 As the guide nucleotide sequence- programmable DNA binding protein, but that other DNA binding proteins that adopt similar mechanism of target sequence binding may also be used.
  • Cas9 or “Cas9 nuclease” refers to an RNA-guided nuclease comprising a Cas9 protein, a fragment, or a variant thereof.
  • a Cas9 nuclease is also referred to sometimes as a casnl nuclease or a CRISPR (clustered regularly interspaced short palindromic repeat)-associated nuclease.
  • CRISPR is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids).
  • CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids.
  • CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).
  • crRNA CRISPR RNA
  • type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and a Cas9 protein.
  • the tracrRNA serves as a guide for ribonuclease 3- aided processing of pre-crRNA.
  • Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer.
  • the target strand not complementary to crRNA is first cut endonucleolytically, then trimmed 3 '-5'
  • RNA-binding and cleavage typically requires protein and both RNAs.
  • single guide RNAs sgRNA, or simply “gNRA”
  • sgRNA single guide RNAs
  • gNRA single guide RNAs
  • Cas9 nuclease sequences and structures are well known to those of skill in the art (see, e.g., Ferretti et al, Proc. Natl. Acad. Sci. 98:4658-4663(2001); Deltcheva E.
  • Cas9 orthologs have been described in various species, including, but not limited to, S. pyogenes and S. thermophilus . Additional suitable Cas9 nucleases and sequences will be apparent to those of skill in the art based on this disclosure, and such Cas9 nucleases and sequences include Cas9 sequences from the organisms and loci disclosed in Chylinski et ah, (2013) RNA Biology 10:5, 726-737; the entire contents of which are incorporated herein by reference.
  • wild type Cas9 corresponds to Cas9 from Streptococcus pyogenes (NCBI Reference Sequence: NC_002737.2, SEQ ID NO: 4 (nucleotide); and Uniport Reference Sequence: Q99ZW2, SEQ ID NO: 1 (amino acid).
  • wild type Cas9 corresponds to Cas9 from Streptococcus aureus.
  • S. aureus Cas9 wild type (SEQ ID NO: 6)
  • wild type Cas9 corresponds to Cas9 from Streptococcus thermophilus.
  • VLGNQHIIKNEGDKPKLDF (SEQ ID NO: 8)
  • the Cas9 domain of any of the fusion proteins provided herein is a Cas9 from archaea (e.g. nanoarchaea), which constitute a domain and kingdom of single-celled prokaryotic microbes.
  • the Cas9 domain is CasX or CasY, which have been described in, for example, Burstein et al., "New CRISPR-Cas systems from uncultivated microbes.” Cell Res. 2017 Feb 21. doi: 10.1038/cr.2017.21, which is incorporated herein by reference. Using genome-resolved metagenomics, a number of CRISPR-Cas systems were identified, including the first reported Cas9 in the archaeal domain of life.
  • Cas9 refers to CasX, or a variant of CasX. In some embodiments, Cas9 refers to a CasY, or a variant of CasY. It should be appreciated that other RNA-guided DNA binding proteins may be used as a nucleic acid programmable DNA binding protein (napDNAbp) and are within the scope of this disclosure.
  • napDNAbp nucleic acid programmable DNA binding protein
  • the Cas9 domain comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a naturally- occurring CasX or CasY protein.
  • the Cas9 domain is a naturally- occurring CasX or CasY protein.
  • the Cas9 domain comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of SEQ ID NOs: 336-337 or 3000.
  • the Cas9 domain comprises an amino acid sequence of any one SEQ ID NOs: 336-337 or 3000. It should be appreciated that CasX and CasY from other bacterial species may also be used in accordance with the present disclosure.
  • wild-type Cas9 refers to CasX from Sulfolobus islandicus (strain REY15A). MEVPLYNIFGDNYIIQVATEAENSTIYNNKVEIDDEELRNVLNLAYKIAKNNEDAAAE
  • wild-type Cas9 refers to CasX from Sulfolobus islandicus (strain REY15A).
  • wild-type Cas9 refers to CasY from a Parcubacteria group bacterium.
  • Cas9 refers to Cas9 from: Corynebacterium ulcerans (NCBI Refs: NC_015683.1, NC_017317.1); Corynebacterium diphtheria (NCBI Refs:
  • NCBI Ref NC_017861.1
  • Spiroplasma taiwanense NCBI Ref: NC_021846.1
  • Streptococcus iniae NCBI Ref: NC_021314.1
  • Belliella baltica NCBI Ref: NC_018010.1
  • Psychroflexus torquisl NCBI Ref: NC_018721.1
  • Listeria innocua NCBI Ref: NP_472073.1
  • Campylobacter jejuni NCBI Ref: YP_002344900.1
  • Neisseria, meningitidis NCBI Ref: YP_002342100.1
  • Cas9 from any of the organisms listed in Example 1 (SEQ ID NOs: 11-260).
  • a Cas9 protein needs to be nuclease inactive.
  • a nuclease-inactive Cas9 protein may interchangeably be referred to as a "dCas9" protein (for nuclease-"dead” Cas9).
  • Methods for generating a Cas9 protein (or a fragment thereof) having an inactive DNA cleavage domain are known (See, e.g., Jinek et ah, Science. 337:816-821(2012); Qi et al, (2013) Cell.
  • the DNA cleavage domain of Cas9 is known to include two subdomains, the HNH nuclease subdomain and the RuvCl subdomain.
  • the HNH subdomain cleaves the strand complementary to the gRNA, whereas the RuvCl subdomain cleaves the non-complementary strand. Mutations within these subdomains can silence the nuclease activity of Cas9.
  • the mutations D10A and H840A completely inactivate the nuclease activity of S. pyogenes Cas9 (Jinek et ah, Science. 337:816-821(2012); Qi et al, Cell. 28;152(5): 1173-83 (2013)).
  • dCas9 D10A and H840A
  • the dCas9 of the present disclosure encompasses completely inactive Cas9 or partially inactive Cas9.
  • the dCas9 may have one of the two nuclease domain inactivated, while the other nuclease domain remains active.
  • Such a partially active Cas9 may also be referred to as a Cas9 nickase, due to its ability to cleave one strand of the targeted DNA sequence.
  • the Cas9 nickase suitable for use in accordance with the present disclosure has an active HNH domain and an inactive RuvC domain and is able to cleave only the strand of the target DNA that is bound by the sgRNA.
  • the Cas9 nickase of the present disclosure may comprise mutations that inactivate the RuvC domain, e.g. , a D10A mutation. It is to be understood that any mutation that inactivates the RuvC domain may be included in a Cas9 nickase, e.g., insertion, deletion, or single or multiple amino acid substitution in the RuvC domain.
  • a Cas9 nickase described herein while the RuvC domain is inactivated, the HNH domain remains activate.
  • the Cas9 nickase may comprise mutations other than those that inactivate the RuvC domain (e.g., D10A), those mutations do not affect the activity of the HNH domain.
  • the histidine at position 840 remains unchanged.
  • the sequence of an exemplary Cas9 nickase suitable for the present disclosure is provided below.
  • VKSKKHPQiiKKG (SEQ ID NO: 5)
  • dCas9 or “nuclease-inactive Cas9” refers to Cas9 variants that are inactive in both HNH and RuvC domains as well as Cas9 nickases.
  • the dCas9 used in the present disclosure may include the amino acid sequence set forth in SEQ ID NO: 2 or SEQ ID NO: 3.
  • the dCas9 may comprise other mutations that inactivate RuvC or HNH domain. Additional suitable mutations that inactivate Cas9 will be apparent to those of skill in the art based on this disclosure and knowledge in the field, and are within the scope of this disclosure.
  • nuclease-inactive Cas9 domains include, but are not limited to, D839A and/or N863A (See, e.g., Prashant et al, Nature Biotechnology. 2013; 31(9): 833- 838, the entire contents of which are incorporated herein by reference), or K603R ⁇ See, e.g., Chavez et ah, Nature Methods 12, 326-328, 2015, the entire contents of which is
  • Cas9, dCas9, or Cas9 variant also encompasses Cas9, dCas9, or Cas9 variant from any organism. Also appreciated is that dCas9, Cas9 nickase, or other appropriate Cas9 variants from any organisms may be used in accordance with the present disclosure.
  • a “deaminase” refers to an enzyme that catalyzes the removal of an amine group from a molecule, or deamination.
  • the deaminase is a cytidine deaminase, catalyzing the hydrolytic deamination of cytidine or deoxycytidine to uridine or deoxyuridine, respectively.
  • the deaminase is a cytosine deaminase, catalyzing the hydrolytic deamination of cytosine to uracil ⁇ e.g., in RNA) or thymine ⁇ e.g., in DNA).
  • the deaminase is a naturally-occurring deaminase from an organism, such as a human, chimpanzee, gorilla, monkey, cow, dog, rat, or mouse. In some embodiments, the deaminase is a variant of a naturally-occurring deaminase from an organism, that does not occur in nature.
  • the deaminase or deaminase domain is at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75% at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a naturally-occurring deaminase from an organism.
  • a "cytosine deaminase” refers to an enzyme that catalyzes the chemical reaction "cytosine + H 2 0 ->uracil + NH 3 " or "5-methyl-cytosine + H20 -> thymine + NH3.”
  • cytosine deaminase refers to an enzyme that catalyzes the chemical reaction "cytosine + H 2 0 ->uracil + NH 3 " or "5-methyl-cytosine + H20 -> thymine + NH3.”
  • nucleotide change, or mutation may in turn lead to an amino acid residue change in the protein, which may affect the protein function, e.g., loss-of-function or gain-of-function.
  • cytosine deaminases are the apolipoprotein B mRNA-editing complex (APOBEC) family of cytosine deaminases encompassing eleven proteins that serve to initiate mutagenesis in a controlled and beneficial manner.
  • APOBEC3 apolipoprotein B editing complex 3
  • cytosine deaminases all require a Zn 2+ -coordinating motif (His-X-Glu-X 23 _ 2 6- Pro-Cys-X 2 _ 4 -Cys; SEQ ID NO: 820) and bound water molecule for catalytic activity.
  • the Glu residue acts to activate the water molecule to a zinc hydroxide for nucleophilic attack in the deamination reaction.
  • Each family member preferentially deaminates at its own particular "hotspot", ranging from WRC (W is A or T, R is A or G) for hAID, to TTC for hAPOBEC3F.
  • a recent crystal structure of the catalytic domain of APOBEC3G revealed a secondary structure comprised of a five-stranded ⁇ -sheet core flanked by six a-helices, which is believed to be conserved across the entire family.
  • the active center loops have been shown to be responsible for both ssDNA binding and in determining "hotspot" identity.
  • cytosine deaminase is the activation-induced cytidine deaminase (AID), which is responsible for the maturation of antibodies by converting cytosines in ssDNA to uracils in a transcription- dependent, strand-biased fashion.
  • AID activation-induced cytidine deaminase
  • nucleobase editor refers to to a protein that edits a nucleotide base.
  • Edit refers to the conversion of one nucleotide base to another. For example, the
  • nucleobase may target C bases in a nucleic acid sequence and convert the C to T base.
  • the C to T editing is carried out by a deaminase, e.g., a cytosine deaminase. Other types of base conversions are also contemplated.
  • the nucleobase editor comprises a DNA binding domain that directs it to a target sequence.
  • a base editor may be a cytosine deaminase-dCas9 fusion protein.
  • the base editor may be a deaminase-dCas9-UGI fusion protein.
  • the base editor may be a APOBECl-dCas9-UGI fusion protein.
  • the base editor may be APOBECl-Cas9 nickase-UGI fusion protein.
  • the base editor may be APOBECl-dCpfl-UGI fusion protein.
  • the base editor may be APOBECl-dNgAgo-UGI fusion protein.
  • the base editor may be a pmCDAl-Cas9 nickase-UGI fusion protein. In some embodiments, the base editor may be a human APOBEC3G-Cas9 nickase UGI fusion protein. In some embodiments, the base editor may comprise a second UGI domain.
  • Non- limiting exemplary sequences of the nucleobase editors described herein are provided in Example 1, SEQ ID NOs: 293-302, 1071, and 1084.
  • nucleobase editors and methods of using them for genome editing have been described in the art, e.g., in US Patent 9,068,179, US Patent Application Publications US 2015/0166980, US 2015/0166981, US 2015/0166982, US20150166984, and US20150165054, and US Provisional Applications, U.S.S.N.
  • target site refers to a sequence within a nucleic acid molecule (e.g. , a DNA molecule) that is deaminated by the fusion protein provided herein.
  • the target sequence is a polynucleotide (e.g., a DNA), wherein the polynucleotide comprises a coding strand and a complementary strand.
  • the meaning of a "coding strand” and “complementary strand” is the common meaning of the terms in the art.
  • the target sequence is a sequence in the genome of a mammal. In some embodiments, the target sequence is a sequence in the genome of a human.
  • target codon refers to the amino acid codon that is edited by the base editor and converted to a different codon via deamination of C base. In some embodiments, the target codon is edited in the coding strand. In some embodiments, the target codon is edited in the complementary strand.
  • linker refers to a chemical group or a molecule linking two molecules or moieties, e.g., two domains of a fusion protein, such as, for example, a nuclease-inactive Cas9 domain and a nucleic acid editing domain (e.g., a deaminase domain).
  • the linker is positioned between, or flanked by, two groups, molecules, or other moieties and connected to each one via a covalent bond, thus connecting the two.
  • the linker is an amino acid or a plurality of amino acids (e.g. , a peptide or protein).
  • the linker is an organic molecule, group, polymer, or chemical moiety.
  • the linker is 2- 100 amino acids in length, for example, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 30-35, 35-40, 40-45, 45-50, 50-60, 60-70, 70-80, 80-90, 90- 100, 100-150, or 150-200 amino acids in length. Longer or shorter linkers are also contemplated.
  • mutation refers to a substitution of a residue within a sequence, e.g. , a nucleic acid or amino acid sequence, with another residue, or a deletion or insertion of one or more residues within a sequence. Mutations are typically described herein by identifying the original residue followed by the position of the residue within the sequence and by the identity of the newly substituted residue. Various methods for making the amino acid substitutions (mutations) provided herein are well known in the art, and are provided by, for example, Green and Sambrook, Molecular Cloning: A Laboratory Manual (4 ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2012)).
  • nucleic acid and “nucleic acid molecule,” as used herein, refer to a compound comprising a nucleobase and an acidic moiety, e.g., a nucleoside, a nucleotide, or a polymer of nucleotides.
  • polymeric nucleic acids e.g., nucleic acid molecules comprising three or more nucleotides are linear molecules, in which adjacent nucleotides are linked to each other via a phosphodiester linkage.
  • nucleic acid refers to individual nucleic acid residues (e.g. nucleotides and/or nucleosides).
  • nucleic acid refers to an oligonucleotide chain comprising three or more individual nucleotide residues.
  • oligonucleotide and
  • nucleic acid can be used interchangeably to refer to a polymer of nucleotides (e.g., a string of at least three nucleotides).
  • nucleic acid encompasses RNA as well as single and/or double-stranded DNA.
  • Nucleic acids may be naturally occurring, for example, in the context of a genome, a transcript, an mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, cosmid, chromosome, chromatid, or other naturally occurring nucleic acid molecule.
  • a nucleic acid molecule may be a non-naturally occurring molecule, e.g.
  • nucleic acid a recombinant DNA or RNA, an artificial chromosome, an engineered genome, or fragment thereof, or a synthetic DNA, RNA, DNA/RNA hybrid, or including non-naturally occurring nucleotides or nucleosides.
  • nucleic acid DNA
  • RNA and/or similar terms include nucleic acid analogs, e.g., analogs having other than a phosphodiester backbone. Nucleic acids can be purified from natural sources, produced using recombinant expression systems and optionally purified, chemically synthesized, etc.
  • nucleic acids can comprise nucleoside analogs such as analogs having chemically modified bases or sugars, and backbone modifications.
  • a nucleic acid sequence is presented in the 5' to 3 ' direction unless otherwise indicated.
  • a nucleic acid is or comprises natural nucleosides (e.g.
  • nucleoside analogs e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7- deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, 0(6)-methylguanine, and 2-thiocyt
  • methylated bases e.g., methylated bases
  • intercalated bases e.g., modified sugars (e.g., 2'-fluororibose, ribose, 2'-deoxyribose, arabinose, and hexose); and/or modified phosphate groups (e.g., phosphorothioates and 5'-N- phosphoramidite linkages).
  • modified sugars e.g., 2'-fluororibose, ribose, 2'-deoxyribose, arabinose, and hexose
  • modified phosphate groups e.g., phosphorothioates and 5'-N- phosphoramidite linkages.
  • protein refers to a polymer of amino acid residues linked together by peptide (amide) bonds.
  • the terms refer to a protein, peptide, or polypeptide of any size, structure, or function. Typically, a protein, peptide, or polypeptide will be at least three amino acids long.
  • a protein, peptide, or polypeptide may refer to an individual protein or a collection of proteins.
  • One or more of the amino acids in a protein, peptide, or polypeptide may be modified, for example, by the addition of a chemical entity such as a carbohydrate group, a hydroxyl group, a phosphate group, a farnesyl group, an isofarnesyl group, a fatty acid group, a linker for conjugation, functionalization, or other modification, etc.
  • a protein, peptide, or polypeptide may also be a single molecule or may be a multi-molecular complex.
  • a protein, peptide, or polypeptide may be just a fragment of a naturally occurring protein or peptide.
  • a protein, peptide, or polypeptide may be naturally occurring, recombinant, or synthetic, or any combination thereof.
  • fusion protein refers to a hybrid polypeptide which comprises protein domains from at least two different proteins.
  • One protein may be located at the amino-terminal (N-terminal) portion of the fusion protein or at the carboxy-terminal (C-terminal) protein thus forming an "amino-terminal fusion protein” or a "carboxy-terminal fusion protein,” respectively.
  • a protein may comprise different domains, for example, a nucleic acid binding domain (e.g., the gRNA binding domain of Cas9 that directs the binding of the protein to a target site) and a nucleic acid cleavage domain or a catalytic domain of a nucleic-acid editing protein.
  • a protein comprises a proteinaceous part, e.g., an amino acid sequence constituting a nucleic acid binding domain, and an organic compound, e.g., a compound that can act as a nucleic acid cleavage agent.
  • a protein is in a complex with, or is in association with, a nucleic acid, e.g., RNA.
  • Any of the proteins provided herein may be produced by any method known in the art.
  • the proteins provided herein may be produced via recombinant protein expression and purification, which is especially suited for fusion proteins comprising a peptide linker.
  • the term "subject,” as used herein, refers to an individual organism, for example, an individual mammal.
  • the subject is a human.
  • the subject is a non-human mammal.
  • the subject is a non-human primate.
  • the subject is a rodent.
  • the subject is a sheep, a goat, a cattle, a cat, or a dog.
  • the subject is a vertebrate, an amphibian, a reptile, a fish, an insect, a fly, or a nematode.
  • the subject is a research animal.
  • the subject is genetically engineered, e.g., a genetically engineered non-human subject. The subject may be of either sex and at any stage of development.
  • recombinant protein or nucleic acid molecule comprises an amino acid or nucleotide sequence that comprises at least one, at least two, at least three, at least four, at least five, at least six, or at least seven mutations as compared to any naturally occurring sequence.
  • the immune system is critical in preventing the outgrowth of cancers.
  • the evasion of cancer cells from immunosurveillance occurs via various well- characterized mechanisms, including induction of T-cell tolerance by autochthonous tumors (e.g., as described in Willimsky et ah, Nature 2005; 437: 141-146, incorporated herein by reference), cancer immunoediting (e.g., as described in Dunn et ah, Nat Immunol 2002; 3: 991-998, incorporated herein by reference), and development of an immune suppressive cancer microenvironment (e.g., as described in Zou et ah, Nat Rev Cancer 2005; 5: 263-274, incorporated herein by reference).
  • Therapeutic cancer vaccines or adoptive immunotherapy are being developed and tested as potential approaches to strengthen the immune responses after tumor arise in order to slow their progression and prevent their recurrence.
  • Immunotherapeutic approaches e.g., cancer vaccines have been described but are only partially successful (e.g., as described in Finn et ah, Nat Rev Immunol 2003; 3: 630-641, incorporated herein by reference).
  • tumor specific antigens e.g., heteroclitic epitopes or cryptic epitopes
  • Targeted mutations are introduced into tumor- specific antigens using a gene editing agent, e.g., a nucleobase editor comprising a programmable DNA binding domain (e.g., a catalytically-inactive Cas9 or Cas9 nickase) fused to a cytosine deaminase, to generate altered versions of peptides arising from the tumor- specific antigens (heteroclitic epitopes) or peptides arising from normally untranslated regions of the tumor- specific antigen genes (cryptic peptides).
  • a gene editing agent e.g., a nucleobase editor comprising a programmable DNA binding domain (e.g., a catalytically-inactive Cas9 or Cas9 nickase) fused to a cytosine deaminase, to generate altered versions of peptides arising from the tumor- specific antigens (heteroclitic epitopes) or peptid
  • the heteroclitic peptides or cryptic peptides may be generated in vivo in a subject (e.g., a subject who has cancer) and presented to the adaptive immune system via the MHC class I or MHC class II pathway, which in turn induces a strong adaptive immune response, e.g., T cell response and B cell response.
  • a strong adaptive immune response e.g., T cell response and B cell response.
  • Such an adaptive immune response is antigen specific and is effective in reducing tumor growth and preventing metastasis.
  • the advantage of the cancer vaccines of the present disclosure is that the vaccine (e.g., antigenic peptides derived from tumor- specific antigens) is generated from the genome and the proteome of the malignant cells in vivo and is highly personalized.
  • the cancer vaccines described herein are also highly cancer- specific and do not induce unwanted immune response against "self," since the immunogenic epitopes are derived from tumor- specific antigens.
  • the adaptive immune response induced by the cancer vaccine described herein confer "memory" to the immune system, promoting the immune system to efficiently recognize "neoepitopes" generated due to the highly mutagenic nature of the cancer genome, thus preventing metastasis and facilitate remission.
  • combination therapies using an immune checkpoint inhibitor in conjunction with the cancer vaccine is also contemplated, aiming to enhance the tumor antigen specific immune response.
  • nucleobase editing technology described herein.
  • base editing technology is described in the art, e.g., in US Patent 9,068,179, US Patent Application Publications US 2015/0166980, US 2015/0166981, US 2015/0166982, US20150166984, and
  • Some aspects of the present disclosure provide immunogenic peptides or epitopes derived from tumor- specific antigens and how these peptides or epitopes elicit tumor- specific immune response.
  • a large number of proteins that specifically express in tumor cells or are upregulated in tumor cells have been identified (Hassane et al., Holland-Frei Cancer
  • the known tumor specific antigens are classified into different classes.
  • CT antigens The first TAAs ever identified that can be recognized by T cells belong to this class, which was originally called cancer-testis (CT) antigens because of the expression of its members in histologically different human tumors and, among normal tissues, only in spermatocytes/spermatogonia of testis and, occasionally, in placenta. Since the cells of testis do not express class I and II HLA molecules, these antigens cannot be recognized by T cells in normal tissues and can therefore be considered as immunologically tumor- specific.
  • CT antigens are the MAGE family members or NY- ESO-1.
  • TAAs Differentiation antigens: These TAAs are shared between tumors and normal tissue from which the tumor arose; most are found in melanomas and normal melanocytes. Many of these melanocyte lineage-related proteins are involved in the biosynthesis of melanin and are therefore not tumor specific but nevertheless are widely used for cancer immunotherapy. Examples include, but are not limited to, tyrosinase and Melan- A/MART- 1 for melanoma, and PSA for prostate cancer.
  • TAAs Overexpressed TAAs: Genes encoding widely expressed TSAs have been detected in histologically different types of tumors as well as in many normal tissues, generally with lower expression levels. It is possible that many of the epitopes processed and potentially presented by normal tissues are below the threshold level for T-cell recognition, while their overexpression in tumor cells can trigger an anticancer response by breaking previously established tolerance. Examples of this class of TAAs are Her-2/neu, Survivin, Telomerase and WT1.
  • Tumor specific antigens These unique TAAs arise from mutations of normal genes (such as ⁇ -catenin, CDK4, etc.). Some of these molecular changes are associated with neoplastic transformation and/or progression. Tumor specific antigens are generally able to induce strong immune responses without bearing the risk for autoimmune reactions against normal tissues. On the other hand, these TAAs are in most cases only relevant to the exact tumor on which they were identified and are usually not shared between many individual tumors.
  • TAAs arising from abnormal post-translational modifications may arise from proteins which are neither specific nor overexpressed in tumors but nevertheless become tumor associated by posttranslational processes primarily active in tumors. Examples for this class arise from altered glycosylation patterns leading to novel epitopes in tumors (e.g., MUC1).
  • TSAs are viral proteins that may play a critical role in the oncogenic process, and because they are foreign (not of human origin), they can evoke a T-cell response.
  • examples of such proteins are the human papilloma type 16 virus proteins, E6 and E7, which are expressed in cervical carcinoma.
  • TAAs are a starting point for the development of a tumor vaccine.
  • the methods for identifying and characterizing the TAAs are based on the use of cytoxic T lymphocytes (CTL) that can be isolated from patients or healthy subjects, or they are based on the generation of differential transcription profiles or differential peptide expression patterns between tumors and normal tissues.
  • CTL cytoxic T lymphocytes
  • the tumor- specific antigen is expressed in a broad range of different types of cancers. In some embodiments, the tumor- specific antigen is expressed only in one or a few types of cancers.
  • the anti-cancer immune response described herein is antigen-specific. As such, an immune response induced by a tumor- specific antigen is specific to cancer types where the said antigen is expressed.
  • Non-limiting, exemplary tumor- specific antigens that may be edited to generate immunogenic epitopes are provided in Tables 1-3. It is appreciated that the examples are for illustration purpose only, and the methods described herein may be applied to any tumor- specific antigen.
  • the immunogenic peptide or epitope is a portion of the tumor- specific antigen.
  • the immunogenic peptide or epitope may be a portion of the tumor- specific antigen that is 5-40 amino acids long.
  • the immunogenic peptide or epitope is 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 amino acids long.
  • the immunogenic peptide or epitope comprises modifications, e.g., amino acid substitutions (also termed "heteroclitic epitopes"), as compared to the native sequence in the tumor specific antigen.
  • the immunogenic peptide or epitope comprises more than one amino acid substitutions (e.g. , 2, 3, 4, 5, or more) compared to the native sequence of the tumor- specific antigen it is derived from.
  • a heteroclitic peptide or epitope may be at least 60%, at least 70%, at least 80%, at least 90%, at least 98%, or at least 99% identical to the native sequence that it is derived from.
  • a heteroclitic peptide or epitope is 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, or 99% identical to the native sequence that it is derived from.
  • a heteroclitic peptide or epitope is more immunogenic than a peptide of its native sequence.
  • a heteroclitic epitope may be at least 30% more immunogenic (i.e., induces a stronger immune response) than its corresponding native peptide.
  • a heteroclitic epitope may be at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 20-fold, at least 30-fold, at least 40-fold, at least 50-fold, at least 60-fold, at least 70-fold, at least 80-fold, at least 90-fold, at least 100-fold, or more immunogenic than its corresponding native peptide.
  • the immunogenic peptide or epitope is a cryptic peptide or epitope, e.g. , generated from translation of a non-coding region of the tumor specific antigen gene or translation of a different reading frame of a coding region of the tumor specific antigen.
  • a cryptic peptide or epitope may be more immunogenic (i.e., induces a stronger immune response) than any native peptide derived from the tumor associated antigen.
  • a cryptic peptide or epitope may be at least 30% more immunogenic than any native peptide derived from the tumor associated antigen.
  • a cryptic peptide or epitope may be at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 100%, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 20-fold, at least 30-fold, at least 40-fold, at least 50-fold, at least 60-fold, at least 70-fold, at least 80- fold, at least 90-fold, at least 100-fold, or more immunogenic than any native peptide derived from the tumor associated antigen.
  • Tumor specific antigens from which antigenic epitopes e.g., heteroclitic epitopes and cryptic epitopes
  • Tables 1-3 HLA - human leukocyte antigen type
  • heteroclitic epitopes were fortuitously identified by eluting naturally occurring mutant peptides from melanoma cells, or by systematically screening a large number of epitopes consisting of substitutions at almost every position in the epitope (Zaremba, et ah, Cancer Research, 57:4570 (1997), Loftus, et al, Cancer Research 58:2433 (1998), Blake, et al, J. Exp. Med. 18: 121 (1996), the entire contents of each of which are incorporated herein by reference).
  • heteroclitic epitopes were identified by screening random combinatorial peptide libraries which also has required the arduous synthesis and screening of large numbers of peptides (Pinilla, et ah, Current Opinion in Immunology 11: 193-202 (1999), the entire contents of each of which are incorporated herein by reference).
  • Genetic approaches, such as screening of DNA expression libraries, have provided another method for generating CTL epitopes and analogs (Boon, et al., Annu. Rev. Immunol. 12:337-65 (1994), Gavin, et al, Eur. J. Immunol. 24(9):2124-33 (1994), the entire contents of each of which are incorporated herein by reference).
  • Some aspects of the present disclosure provide systems, compositions, and methods of editing genes encoding tumor specific antigens in vivo (e.g., in tumor cells in a subject) or ex vivo (e.g., in isolated tumor cells) to introduce mutations in the genes encoding tumor specific antigens.
  • such mutations lead to the production of heteroclitic peptides that are more immunogenic than native peptides of the tumor-specific antigen.
  • such mutations lead to the translation of a non-coding region of the tumor specific antigen, which results in cryptic peptides that are more immunogenic than any native peptides from the tumor specific antigen.
  • the nucleobase editors are highly efficient at precisely editing a target base in any of the tumor associated antigen genes described herein, and a DNA double stand break is not necessary for the gene editing, thus reducing genome instability and preventing possible oncogenic modifications that may be caused by other genome editing methods.
  • the nucleobase editors described herein may be programmed to target and modify a single base.
  • the target base is a cytosine (C) base and may be converted to a thymine (T) base via deamination by the nucleobase editor.
  • the polynucleotide is contacted with a nucleobase editor as described herein.
  • the tumor- associated antigen encoding polynucleotide is contacted with a nucleobase editor and a guide nucleotide sequence, wherein the guide nucleotide sequence targets the nucleobase editor the target base (e.g. , a C base) in the tumor-associated antigen encoding polynucleotide.
  • the tumor-associated antigen encoding polynucleotide is the tumor-associated antigen gene locus in the genomic DNA of a cell (e.g., a tumor cell).
  • the tumor cell is a cultured cell.
  • the tumor cell is in vivo.
  • the tumor cell is ex vivo.
  • the tumor cell is from a mammal.
  • the mammal is a human.
  • the mammal is a rodent.
  • the rodent is a mouse.
  • the rodent is a rat.
  • the tumor-associated antigen encoding polynucleotide may be a DNA molecule comprising a coding strand and a complementary strand, e.g., the tumor- associated antigen gene locus in the genome of a tumor cell.
  • the tumor-associated antigen encoding polynucleotide may also include coding regions (e.g., exons) and non-coding regions (e.g., introns or splicing sites).
  • the target base e.g. , a C base
  • the target base is located in the coding region (e.g. , an exon) of the tumor- associated antigen encoding polynucleotide.
  • the conversion of a base in the coding region may result in an amino acid change in the tumor-associated antigen protein sequence, i.e. , a mutation.
  • Tumor associated antigens comprising the desired mutation(s) once degraded (e.g. , via any of the protein degradation pathways, such as degradation by the proteasome) results in immunogenic heteroclitic epitopes.
  • the target base is located in a non-coding region of the tumor-associated antigen gene, e.g. , in an intron or a splice site.
  • a target base is located in a splice site, and the editing of such target base causes alternative splicing of the tumor-associated antigen mRNA.
  • the alternative splicing leads to translation of a non-coding region of the tumor-associated antigen gene, generating cryptic epitopes.
  • the immunogenic epitopes e.g.
  • heteroclitic epitopes or cryptic epitopes may be presented by the tumor cell, or a professional antigen presenting cell, and be recognized by the immune system, thus eliciting a tumor-specific immune response (e.g. , T- cell response or B-cell response).
  • a tumor-specific immune response e.g. , T- cell response or B-cell response.
  • the tumor-associated antigen gene (a polynucleotide molecule) may be contacted with the nucleobase editor, wherein the nucleobase editor binds to its target sequence and edits the desired base.
  • the nucleobase editor may be expressed in a cell where editing is desired (e.g., a tumor), allowing editing of the tumor-associated antigen gene by the nucleobase editor.
  • the binding of the nucleobase editor to its target sequence in the tumor-associated antigen gene is mediated by a guide nucleotide sequence, e.g., a nucleotide molecule comprising a nucleotide sequence that is complementary to one of the strands of the target sequence in the tumor-associated antigen gene.
  • a guide nucleotide sequence e.g., a nucleotide molecule comprising a nucleotide sequence that is complementary to one of the strands of the target sequence in the tumor-associated antigen gene.
  • the guide nucleotide sequence may be programmed to edit any target base in any tumor associated antigen gene.
  • the guide nucleotide sequence is co-expressed with the nucleobase editor in a tumor cell where editing is desired.
  • a nucleobase editor/gRNA complex is delivered to the cell where editing is desired (e.g., a tumor cell).
  • heteroclitic epitopes and cryptic epitopes that may be produced via base editing and strategies for making them.
  • cytosine (C) base is converted to a thymine (T) base via deamination by a nucleobase editor comprising a cytosine deaminase domain (e.g. ,
  • a C to T change via deamination e.g., by a cytosine deaminase such as APOBEC 1 or AID
  • the cytosine is first converted to a uridine (U), leading to a G:U mismatch.
  • the G:U mismatch is then converted by DNA repair and replication pathways to T:A pair, thus introducing the thymine at the position of the original cytosine.
  • deamination of a C base results in a C-G base pair being replaced by a T-A base pair.
  • Cytosine deaminases are capable of converting a cytosine (C) base to a thymine (T) base via deamination.
  • C cytosine
  • T thymine
  • the C base may be directly converted to T.
  • codon for leucine (CTC) may be changed to a TTC
  • nucleobase editor to bind to its target sequence and edit the desired base, the nucleobase editor depends on its guide nucleotide sequence (e.g., a guide RNA).
  • the guide nucleotide sequence is a gRNA sequence.
  • a gRNA typically comprises a tracrRNA framework allowing for Cas9 binding, and a guide sequence, which confers sequence specificity to fusion proteins disclosed herein.
  • the guide RNA comprises the structure 5 '-[guide sequence] - guuuuagagcuagaaauagcaaguuaaaauaaggcuaguccguuaucaacuugaaaaaguggcaccgagucggugcuu uuu-3 ' (SEQ ID NO: 336), wherein the guide sequence comprises a sequence that is complementary to the target sequence.
  • Other suitable tracrRNA framework sequences are provided in Table 11.
  • the guide sequence is typically about 20 nucleotides long. In certain embodiments, the guide sequence may be 15-25 nucleotides long. In some embodiments, the guide sequence is 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 nucleotides long.
  • Such suitable guide RNA sequences typically comprise guide sequences that are complementary to a nucleic sequence within 50 (e.g., within 50, 45, 40, 35, 30, 35, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, or 10) nucleotides upstream or downstream of the target nucleotide to be edited.
  • Some aspects of the present disclosure provide strategies for generating cryptic epitopes in tumor cells.
  • such strategies involve alterations of splicing sites in a tumor associated antigen gene.
  • Altered splicing site may lead to altered splicing of an mRNA that encodes a tumor associated antigen.
  • One outcome of altered splicing is the translation of an otherwise non-coding region of the gene, leading to otherwise "hidden peptides," i.e., cryptic epitopes.
  • the splicing site typically comprises an intron donor site, a Lariat branch point, and an intron acceptor site. The mechanism of splicing are familiar to those skilled in the art.
  • the intron donor site has a consensus sequence of GGGTRAGT, and the C bases paired with the G bases in the intron donor site consensus sequence may be targeted by a nucleobase editor, thereby altering the intron donor site.
  • the Lariat branch point also has a consensus sequence, e.g., YTRAC, wherein Y is a pyrimidine, and R is a purine.
  • the C base in the Lariat branch point consensus sequence may be targeted by the nucleobase editors described herein, leading to skipping of the following exon.
  • the intron acceptor site has a consensus sequence of YNCAGG, wherein Y is a pyrimidine, and N is any nucleotide.
  • the C base of the consensus sequence of the intron acceptor site, and the C base paired with the G bases in the consensus sequence of the intron acceptor site may be targeted by the nucleobase editors described herein, thereby altering the intron acceptor site, in turn leading to skipping of an exon.
  • General strategies of altering the splicing sites are described in Table 6.
  • Non-limiting, exemplary cryptic epitopes that may be produced using the base editing methods described herein are provided in Table 7.
  • the nucleobase editor may be used to introduce a premature stop codon (a stop codon that occurs upstream of the normal stop codon) into a tumor specific antigen gene (e.g. , TAA, TAG, and TGA).
  • a premature stop codon a stop codon that occurs upstream of the normal stop codon
  • introduction of a premature stop codon destabilizes the tumor specific antigen.
  • destabilization of the tumor specific antigen leads to enhanced presentation of immunogenic epitopes (e.g. , heteroclitic epitopes or cryptic epitopes).
  • Premature stop codons are introduced by changing one or more bases in a target codon that encodes a target residue.
  • nucleobase editors including a cytosine deaminase domain are capable of converting a cytosine (C) base to a thymine (T) base via deamination.
  • C cytosine
  • T thymine
  • the C base may be converted to T.
  • a CAG (Gln/Q) codon may be changed to a TAG (amber) codon via the deamination of the first C on the coding strand.
  • a C base is present on the complementary strand; and the G base may be converted to an adenosine (A) via the deamination of the C on the complementary strand.
  • a TGG (Trp/W) codon may be converted to a TAG (amber) codon via the deamination of the second C on the complementary strand.
  • two C to T changes are required to convert a codon to a nonsense codon.
  • a CGG (R) codon is converted to a TAG (amber) codon via the deamination of the first C on the coding strand and the deamination of the second C on the complementary strand.
  • the target residue is located in a flexible loop region of the tumor specific antigen.
  • tandem premature stop codons are introduced. Non-limiting examples of codons that may be changed to stop codons via base editing are provided in Table 8.
  • cryptic epitopes are generated by shifting the coding frame of a tumor specific antigen gene.
  • the coding frame is shifted by changing a start codon (ATG) to a sense codon that cannot be used as a start codon.
  • ATG start codon
  • a normal sense codon may be edited to generate a start codon to allow translation to start at the newly generated start codon, which may also lead to shifting of the coding frame.
  • start codons and the resulting shift in the coding frame generate peptides that would not otherwise be generated from the tumor specific antigen gene (i.e., cryptic epitopes).
  • Non-limiting, exemplary start codon alterations that may be achieved by the nucleobase editors described herein are provided in Table 9.
  • cancer vaccines containing immunogenic peptides from tumor specific antigens are generated in vivo (e.g., in tumor cells in a subject) or ex vivo (e.g., in tumor cells isolated from a subject).
  • the tumor cells are treated with the nucleobase editors to generate the immunogenic peptides and are irradiated and administered to the subject as whole-cell cancer vaccines.
  • nucleobase editor and/or the guide nucleotide sequence is introduced into the cell (e.g., a tumor cell) where the editing occurs.
  • nucleic acid molecules e.g., expression vectors
  • nucleobase editors and/or the guide nucleotide sequences are delivered into the cell, resulting in co-expression of nucleobase editors and/or the guide nucleotide sequences in the cell.
  • the nucleic acid molecules encoding the nucleobase editors and/or the guide nucleotide sequences may be delivered into the cell using any known methods in the art, e.g., transfection (e.g., transfection mediated by cationic liposomes), transduction (e.g., via viral infection) and electroporation.
  • transfection e.g., transfection mediated by cationic liposomes
  • transduction e.g., via viral infection
  • electroporation e.g., electroporation.
  • an isolated nucleobase editor/gRNA complex is delivered. Methods of delivering an isolated protein to a cell is familiar to those skilled in the art.
  • the isolated nucleobase editor in complex with a gRNA be associated with a supercharged, cell-penetrating protein or peptide, which facilitates its entry into a cell (e.g., as described in PCT Application Publication WO2010129023 and US Patent Application Publication US20150071906, incorporated herein by reference).
  • the isolated nucleobase editor in complex with a gRNA may be delivered by a cationic transfection reagent, e.g., the Lipofectamine CRISPRMAX Cas9 Transfection Reagent from Thermofisher Scientific.
  • the nucleobase editor and the gRNA may be delivered separately.
  • AAV mediated gene transfer Other suitable delivery methods may also be used, e.g., AAV mediated gene transfer.
  • AAV mediated gene transfer e.g., AAV mediated gene transfer.
  • Strategies for delivery a Cas9-based genome editing agent (e.g., the nucleobase editor described herein) using AAV have been described, e.g., in Zetsche et al., Nature Biotechnology 33, 139-142 (2015), incorporated herein by reference.
  • the immunogenic peptide is displayed on the surface of the tumor cell via the MHC class I antigen presentation pathway. In some embodiments, the immunogenic peptide is displayed on the surface of an antigen presenting cell (APC) via the MHC class II antigen presentation pathway. In some embodiments, the APC is selected from the group consisting of: tumor cells, dendritic cells, mononuclear phagocytes, thymic epithelial cells, and B cells. In some embodiments, the immunogenic peptide elicits an adaptive immune response against the tumor- specific antigen where the peptide is derived from. In some embodiments, the immunogenic peptide elicits an adaptive immune response against the tumor.
  • the adaptive immune response comprises promoting the maturation of dendritic cells, activation of CD4+T lymphocytes, (T helper cells) activation of CD8+ T lymphocytes (cytotoxic T cells), activation and maturation of B lymphocytes, and/or production of tumor antigen-specific antibodies.
  • T helper cells assist other white blood cells in immunologic processes, including maturation of B cells into plasma cells and memory B cells, and activation of cytotoxic T cells and macrophages. These cells are also known as CD4+ T cells because they express the CD4 glycoprotein on their surfaces. Helper T cells become activated when they are presented with peptide antigens by MHC class II molecules, which are expressed on the surface of antigen-presenting cells (APCs). Once activated, they divide rapidly and secrete small proteins called cytokines that regulate or assist in the active immune response.
  • APCs antigen-presenting cells
  • T cells can differentiate into one of several subtypes, including THl, TH2, TH3, TH17, TH9, or TFH, which secrete different cytokines to facilitate different types of immune responses. Signaling from the APC directs T cells into particular subtypes.
  • Cytotoxic T cells e.g., TC cells, CTLs, T-killer cells, killer T cells
  • TC cells e.g., TC cells, CTLs, T-killer cells, killer T cells
  • CD8+ T cells e.g., CD8+ T cells since they express the CD8 glycoprotein at their surfaces. These cells recognize their targets by binding to antigen associated with MHC class I molecules, which are present on the surface of all nucleated cells.
  • MHC class I molecules which are present on the surface of all nucleated cells.
  • IL-10 adenosine, and other molecules secreted by regulatory T cells, the CD8+ cells can be inactivated to an anergic state, which prevents autoimmune diseases.
  • TCRs T-cell receptors
  • Antigens inside a cell are bound to class I MHC molecules, and brought to the surface of the cell by the class I MHC molecule, where they can be recognized by the T cell. If the TCR is specific for that antigen, it binds to the complex of the class I MHC molecule and the antigen, and the T cell destroys the cell, e.g., via inducing apoptosis.
  • the TCR In order for the TCR to bind to the class I MHC molecule, the former must be accompanied by a glycoprotein called CD8, which binds to the constant portion of the class I MHC molecule. Therefore, these T cells are called CD8+ T cells.
  • Natural killer T cells (NKT cells - not to be confused with natural killer cells of the innate immune system) bridge the adaptive immune system with the innate immune system. Unlike conventional T cells that recognize peptide antigens presented by major
  • NKT cells recognize glycolipid antigen presented by a molecule called CD Id. Once activated, these cells can perform functions ascribed to both Th and Tc cells (i.e., cytokine production and release of cytolytic/cell killing molecules). They are also able to recognize and eliminate some tumor cells and cells infected with microorganisms, e.g., bacteria or virus.
  • MHC histocompatibility complex
  • Memory T cells are a subset of antigen- specific T cells that persist long-term after an initial T cell response. They quickly expand to large numbers of effector T cells upon re-expo to their cognate antigen, thus providing the immune system with "memory” against past antigens.
  • the cancer vaccine described herein provides the immune system with
  • Regulatory T cells are crucial for the maintenance of immunological tolerance. Their major role is to shut down T cell-mediated immunity toward the end of an immune reaction and to suppress autoreactive T cells that escaped the process of negative selection in the thymus. Suppressor T cells along with Helper T cells can collectively be called Regulatory T cells due to their regulatory functions.
  • B cell activation occurs in the secondary lymphoid organs (SLOs), such as the spleen and lymph nodes. After B cells mature in the bone marrow, they migrate through the blood to SLOs, which receive a constant supply of antigen through circulating lymph. At the SLO, B cell activation begins when the B cell binds to an antigen via its BCR.
  • SLOs secondary lymphoid organs
  • the antigen can either be free-floating or presented by APCs such as macrophages or dendritic cells (DCs), and include proteins, glycoproteins, polysaccharides, whole virus particles, and whole bacterial cells. Some subtypes of B cell preferentially undergo T cell-dependent activation while other subtypes of cells preferentially undergo T cell-independent activation.
  • APCs such as macrophages or dendritic cells (DCs)
  • DCs dendritic cells
  • T cell-dependent (TD) antigens Antigens that activate B cells with the help of T-cell are known as T cell-dependent (TD) antigens and include foreign proteins. They are named as such because they are unable to induce a humoral response in organisms that lack T cells. B cell response to these antigens takes multiple days, though antibodies generated have a higher affinity and are more functionally versatile than those generated from T cell-independent activation.
  • T helper (TH) cells typically follicular T helper (TFH) cells, that were activated with the same antigen recognize and bind these MHC-II-peptide complexes through their T cell receptor (TCR).
  • TCR T cell receptor
  • T cells express the surface protein CD40L as well as cytokines such as IL- 4 and IL-21.
  • CD40L serves as a necessary co- stimulatory factor for B cell activation by binding the B cell surface receptor CD40, which promotes B cell proliferation,
  • T cell-derived cytokines bound by B cell cytokine receptors also promote B cell proliferation, immunoglobulin class switching, and somatic hypermutation as well as guide differentiation. After B cells receive these signals, they are considered activated.
  • Activated B cells participate in a two-step differentiation process that yields both short-lived plasmablasts for immediate protection and long-lived plasma cells and memory B cells for persistent protection.
  • the first step known as the extrafollicular response, occurs outside of lymphoid follicles but still in the SLO. During this step activated B cells proliferate, may undergo immunoglobulin class switching, and differentiate into plasmablasts that produce early, weak antibodies mostly of class IgM.
  • the second step consists of activated B cells entering a lymphoid follicle and forming a germinal center (GC), which is a specialized microenvironment where B cells undergo extensive proliferation,
  • immunoglobulin class switching, and affinity maturation directed by somatic hypermutation are facilitated by TFH cells within the GC and generate both high-affinity memory B cells and long-lived plasma cells. Resultant plasma cells secrete large amounts of antibody and either stay within the SLO or, more preferentially, migrate to bone marrow.
  • T cell-independent (TI) antigens include foreign polysaccharides and unmethylated CpG DNA. They are named as such because they are able to induce a humoral response in organisms that lack T cells. B cell response to these antigens is rapid, though antibodies generated tend to have lower affinity and are less functionally versatile than those generated from T cell-dependent activation.
  • B cells activated by TI antigens need additional signals to complete activation, but instead of receiving them from T cells, they are provided either by recognition and binding of a common microbial constituent to toll-like receptors (TLRs) or by extensive crosslinking of BCRs to repeated epitopes on a bacterial cell.
  • TLRs toll-like receptors
  • B cells activated by TI antigens go on to proliferate outside of lymphoid follicles but still in SLOs (GCs do not form), possibly undergo immunoglobulin class switching, and differentiate into short-lived plasmablasts that produce early, weak antibodies mostly of class IgM, but also some populations of long-lived plasma cells.
  • Memory B cell activation begins with the detection and binding of their target antigen, which is shared by their parent B cell.
  • Some memory B cells can be activated without T cell help, such as certain virus -specific memory B cells, but others need T cell help.
  • T cell helper typically memory follicular T helper (TFH) cells, that were derived from T cells activated with the same antigen recognize and bind these MHC-II-peptide complexes through their TCR.
  • the memory B cell is activated and differentiates either into plasmablasts and plasma cells via an extrafollicular response or enter a germinal center reaction where they generate plasma cells and more memory B cells.
  • the adaptive immune response results in the killing tumor cells, reducing tumor burden, reducing tumor size, and/or preventing metastasis.
  • the adaptive immune response is active against neo-epitopes associated with spontaneous somatic mutations.
  • the neo-epitope is specific to the lineage of tumor cells.
  • the adaptive immune response elicited by the heteroclitic or cryptic epitopes is cross-reactive with the native tumor- specific antigen.
  • the adaptive immune response elicited by the heteroclitic or cryptic epitopes is cross-reactive with neoepitopes arising from spontaneous mutations occurring in the tumor specific antigen.
  • heteroclitic epitopes have the ability to break/overcome tolerance by reversing a state of T cell anergy, activating non-tolerized cross -reactive clones of T cells, or by mediating "immune deviation," i.e., the type of CTL produced, such as Thl or Th2.
  • heteroclitic epitopes or cryptic epitopes modulate cytokine production from T cells (Pfeiffer, et al., J. Exp. Med., 181: 1569 (1995), Tao, et al., J.
  • heteroclitic epitopes offer an advantage in drug development since significantly smaller amounts of peptide are needed for treatment doses, due to their strong biological potency. This feature overcomes certain manufacturing and toxicity concerns.
  • a heteroclitic analog of a MART-1 peptide (Rivoltini, et ah, Cancer Research 59:301 (1999), the entire contents of which are incorporated herein by reference), which generated antigen specific T cells in melanoma patients, was active at much lower concentrations than the native epitope. Similar results were reported by Schlom and colleagues (Zaremba, et ah, Cancer Research 57:4570 (1997), the entire contents of which are incorporated herein by reference) regarding heteroclitic analog of the CEA derived CAP1 epitope.
  • nucleobase editor is a fusion protein comprising: (i) a programmable DNA binding protein domain; and (ii) a deaminase domain. It is to be understood that any programmable DNA binding domain may be used in the based editors.
  • the programmable DNA binding protein domain comprises the DNA binding domain of a zinc finger nuclease (ZFN) or a transcription activator-like effector domain (TALE).
  • ZFN zinc finger nuclease
  • TALE transcription activator-like effector domain
  • the programmable DNA binding protein domain may be programmed by a guide nucleotide sequence, and is thus referred as a "guide nucleotide sequence-programmable DNA binding-protein domain.”
  • the guide nucleotide sequence-programmable DNA binding protein is a nuclease inactive Cas9, or dCas9.
  • a dCas9 encompasses a Cas9 that is completely inactive in its nuclease activity, or partially inactive in its nuclease activity ⁇ e.g., a Cas9 nickase).
  • the guide nucleotide sequence-programmable DNA binding protein is a Cas9 nickase.
  • the guide nucleotide sequence-programmable DNA binding protein is a nuclease inactive Cpfl.
  • the guide nucleotide sequence-programmable DNA binding protein is a nuclease inactive Argonaute.
  • the guide nucleotide sequence-programmable DNA binding protein is a nuclease inactive CasX or CasY, e.g., as described in Burstein et al., New CRISPR-Cas systems from uncultivated microbes, Nature 542, 237-241, 2017, incorporated herein by reference.
  • the guide nucleotide sequence-programmable DNA binding protein is a dCas9 domain.
  • the guide nucleotide sequence- programmable DNA binding protein is a Cas9 nickase.
  • the dCas9 domain comprises the amino acid sequence of SEQ ID NO: 2 or SEQ ID NO: 3.
  • the dCas9 domain comprises an amino acid sequence that is at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of the Cas9 domains provided herein (e.g., SEQ ID NOs: 11-260), and comprises mutations corresponding to D10X (X is any amino acid except for D) and/or H840X (X is any amino acid except for H) in SEQ ID NO: 1.
  • the dCas9 domain comprises an amino acid sequence that is at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of the Cas9 domains provided herein (e.g. , SEQ ID NOs: 11-260), and comprises mutations corresponding to D10A and/or H840A in SEQ ID NO: 1.
  • the Cas9 nickase comprises an amino acid sequence that is at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of the Cas9 domains provided herein (e.g. , SEQ ID NOs: 11-260), and comprises mutations
  • the Cas9 nickase comprises an amino acid sequence that is at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of the Cas9 domains provided herein (e.g., SEQ ID NOs: 11-260), and comprises mutations corresponding to D10A in SEQ ID NO: 1 and a histidine at a position correspond to position 840 in SEQ ID NO: 1.
  • variants or homologues of dCas9 or Cas9 nickase are provided which are at least about 70% identical, at least about 80% identical, at least about 90% identical, at least about 95% identical, at least about 98% identical, at least about 99% identical, at least about 99.5% identical, or at least about 99.9% to SEQ ID NO: 2 or SEQ ID NO: 3, respectively, and comprises mutations corresponding to D10A and/or H840A in SEQ ID NO: 1.
  • variants of Cas9 are provided having amino acid sequences which are shorter, or longer than SEQ ID NO: 2, by about 5 amino acids, by about 10 amino acids, by about 15 amino acids, by about 20 amino acids, by about 25 amino acids, by about 30 amino acids, by about 40 amino acids, by about 50 amino acids, by about 75 amino acids, by about 100 amino acids, or more, provided that the dCas9 variants comprise mutations corresponding to DIOA and/or H840A in SEQ ID NO: 1.
  • variants of Cas9 nickase are provided having amino acid sequences which are shorter, or longer than SEQ ID NO: 3, by about 5 amino acids, by about 10 amino acids, by about 15 amino acids, by about 20 amino acids, by about 25 amino acids, by about 30 amino acids, by about 40 amino acids, by about 50 amino acids, by about 75 amino acids, by about 100 amino acids, or more, provided that the dCas9 variants comprise mutations corresponding to DIOA and comprises a histidine at a position corresponding to position 840 in SEQ ID NO: 1.
  • nuclease-inactive dCas9 domains will be apparent to those of skill in the art based on this disclosure and knowledge in the field, and are within the scope of this disclosure.
  • Such additional exemplary suitable nuclease-inactive Cas9 domains include, but are not limited to, D10A/H840A, D10A/D839A/H840A, D10A/D839A/H840A/N863A mutant domains (See, e.g., Prashant et ah , Nature Biotechnology. 2013; 31(9): 833-838, which are incorporated herein by reference), or K603R (See, e.g. , Chavez et ah , Nature Methods 12, 326-328, 2015, which is incorporated herein by reference.
  • the nucleobase editors utilized in the present invention comprise a Cas9 domain with decreased electrostatic interactions between the Cas9 domain and a sugar-phosphate backbone of a DNA, as compared to a wild-type Cas9 domain.
  • a Cas9 domain comprises one or more mutations that decreases the association between the Cas9 domain and a sugar-phosphate backbone of a DNA.
  • the nucleobase editors described herein comprises a dCas9 (e.g., with DIOA and H840A mutations) or a Cas9 nickase (e.g.
  • the dCas9 or the Cas9 nickase further comprises one or more of a N497X, R661X, Q695X, and/or Q926X mutation of the amino acid sequence provided in SEQ ID NO: 1, or a corresponding mutation in any of the amino acid sequences provided in SEQ ID NOs: 11-260, wherein X is any amino acid.
  • the nucleobase editors described herein comprises a dCas9 (e.g.
  • the dCas9 or the Cas9 nickase further comprises one or more of a N497A, R661A, Q695A, and/or Q926A mutation of the amino acid sequence provided in SEQ ID NO: 1, or a corresponding mutation in any of the amino acid sequences provided in SEQ ID NOs: 11- 260.
  • the dCas9 domain (e.g. , of any of the nucleobase editors provided herein) comprises the amino acid sequence as set forth in any one of SEQ ID NOs: 2-9.
  • the nucleobase editor comprises the amino acid sequence as set forth in any one of SEQ ID NOs: 293-302 and 321.
  • the guide nucleotide sequence-programmable DNA binding protein is a single effector of a microbial CRISPR-Cas system.
  • Single effectors of microbial CRISPR-Cas systems include, without limitation, Cas9, Cpfl, C2cl, C2c2, and C2c3.
  • microbial CRISPR-Cas systems are divided into Class 1 and Class 2 systems.
  • Class 1 systems have multisubunit effector complexes, while Class 2 systems have a single protein effector.
  • Cas9 and Cpfl are Class 2 effectors.
  • three distinct Class 2 CRISPR-Cas systems (C2cl, C2c2, and C2c3) have been described by Shmakov et al., "Discovery and Functional Characterization of Diverse Class 2 CRISPR Cas Systems", Mol. Cell, 2015 Nov 5; 60(3): 385-397, the entire contents of which are herein incorporated by reference.
  • C2cl and C2c3 contain RuvC- like endonuclease domains related to Cpfl .
  • a third system, C2c2 contains an effector with two predicted HEPN RNase domains.
  • Production of mature CRISPR RNA is tracrRNA- independent, unlike production of CRISPR RNA by C2cl.
  • C2cl depends on both CRISPR RNA and tracrRNA for DNA cleavage.
  • Bacterial C2c2 has been shown to possess a unique RNase activity for CRISPR RNA maturation distinct from its RNA-activated single- stranded RNA degradation activity. These RNase functions are different from each other and from the CRISPR RNA-processing behavior of Cpfl.
  • C2c2 is guided by a single CRISPR RNA and can be programmed to cleave ssRNA targets carrying complementary protospacers.
  • Catalytic residues in the two conserved HEPN domains mediate cleavage. Mutations in the catalytic residues generate catalytically inactive RNA-binding proteins. See e.g., Abudayyeh et al., "C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector," Science, 2016 Aug 5;
  • the nucleobase editors described herein comprise a C2cl, a C2c2, or a C2c3 protein.
  • the guide nucleotide sequence-programmable DNA binding protein is a C2cl protein.
  • the guide nucleotide sequence-programmable DNA binding protein is a C2c2 protein.
  • the guide nucleotide sequence-programmable DNA binding protein is a C2c3 protein.
  • the guide nucleotide sequence-programmable DNA binding protein comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to a naturally-occurring C2cl, C2c2, or C2c3 protein.
  • the guide nucleotide sequence-programmable DNA binding protein is a naturally-occurring C2cl, C2c2, or C2c3 protein.
  • the guide nucleotide sequence-programmable DNA binding protein comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99.5% identical to any one of SEQ ID NOs: 1057-1059.
  • the guide nucleotide sequence- programmable DNA binding protein comprises an amino acid sequence of any one SEQ ID NOs: 1057-1059. It should be appreciated that C2cl, C2c2, or C2c3 from other bacterial species may also be used in accordance with the present disclosure.
  • C2c 1 (uniprot.org/uniprot/T0D7 A2#) splT0D7 A2IC2C 1_ALIAG
  • C2c2 (uniprot.org/uniprot/P0DOC6) >splP0DOC6IC2C2_LEPSD
  • TARA_037_MES_0.1-0.22 contig TARA_037_MES_0.1-0.22_scaffold22115_l, whole genome shotgun sequence.
  • Cas9 recognizes a short motif (PAM motif) in the CRISPR repeat sequences in the target DNA sequence.
  • a "PAM motif,” or “protospacer adjacent motif,” as used herein, refers a DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system.
  • PAM is a component of the invading virus or plasmid, but is not a component of the bacterial CRISPR locus.
  • Cas9 will not successfully bind to or cleave the target DNA sequence if it is not followed by the PAM sequence.
  • PAM is an essential targeting component (not found in the bacterial genome) which distinguishes bacterial self from non-self DNA, thereby preventing the CRISPR locus from being targeted and destroyed by nuclease.
  • Wild-type Streptococcus pyogenes Cas9 recognizes a canonical PAM sequence (5'- NGG-3')- Other Cas9 nucleases (e.g., Cas9 from Streptococcus thermophiles, Staphylococcus aureus, Neisseria meningitidis, or Treponema denticolaor) and Cas9 variants thereof have been described in the art to have different, or more relaxed PAM requirements.
  • Cas9 nucleases e.g., Cas9 from Streptococcus thermophiles, Staphylococcus aureus, Neisseria meningitidis, or Treponema denticolaor
  • Cas9 variants thereof have been described in the art to have different, or more relaxed PAM requirements.
  • Kleinstiver et al Nature 523, 481-485, 2015; Klenstiver et al, Nature 529, 490-495, 2016; Ran et al, Nature, Apr 9; 520(7546): 186-191, 2015; Kleinstiver et al, Nat
  • the guide nucleotide sequence-programmable DNA-binding protein of the present disclosure may recognize a variety of PAM sequences including, without limitation: NGG, NGAN, NGNG, NGAG, NGCG, NNGRRT, NGRRN, NNNRRT, NNNGATT, NNAGAAW, NAAAC, TTN, TTTN, and YTN, wherein Y is a pyrimidine, and N is any nucleobase.
  • the PAM is located 5' of the target base. In some embodiments, the PAM is located 3 ' of the target base.
  • RNA-programmable DNA-binding protein that has different PAM specificity is Clustered Regularly Interspaced Short Palindromic Repeats from
  • Cpfl Prevotella and Francisella 1
  • Cpfl is also a class 2 CRISPR effector. It has been shown that Cpflmediates robust DNA interference with features distinct from Cas9.
  • Cpfl is a single RNA-guided endonuclease lacking tracrRNA, and it utilizes a T-rich protospacer-adjacent motif (TTN, TTTN, or YTN).
  • TTN T-rich protospacer-adjacent motif
  • YTN T-rich protospacer-adjacent motif
  • Cpfl cleaves DNA via a staggered DNA double- stranded break.
  • two enzymes from Acidaminococcus and Lachnospiraceae are shown to have efficient genome-editing activity in human cells.
  • nuclease-inactive Cpfl (dCpfl) variants that may be used as a guide nucleotide sequence-programmable DNA-binding protein domain.
  • the Cpfl protein has a RuvC-like endonuclease domain that is similar to the RuvC domain of Cas9 but does not have a HNH endonuclease domain, and the N-terminal of Cpfl does not have the alfa-helical recognition lobe of Cas9.
  • the RuvC-like domain of Cpfl is responsible for cleaving both DNA strands and inactivation of the RuvC-like domain inactivates Cpfl nuclease activity.
  • mutations corresponding to D917A, E1006A, or D1255A in Francisella novicida Cpfl inactivates Cpfl nuclease activity.
  • the dCpfl of the present disclosure comprises mutations corresponding to D917A, E1006A, D1255A, D917A/E1006A, D917A/D1255A, E1006A/D1255A, or D917A/E1006A/D1255A in SEQ ID NO: 10. It is to be understood that any mutations, e.g., substitution mutations, deletions, or insertions that inactivates the RuvC domain of Cpfl may be used in accordance with the present disclosure.
  • the guide nucleotide sequence-programmable DNA binding protein is a nuclease inactive Cpfl (dCpfl).
  • the dCpfl comprises the amino acid sequence of any one SEQ ID NOs: 261-267.
  • the dCpfl comprises an amino acid sequence that is at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at ease 99.5% identical to SEQ ID NO: 10, and comprises mutations corresponding to D917A, E1006A, D1255A, D917A/E1006A, D917A/D1255A,
  • E1006A/D1255A or D917A/ E1006A/D1255A in SEQ ID NO: 10.
  • Cpfl from other bacterial species may also be used in accordance with the present disclosure.
  • Wild type Francisella novicida Cpfl (SEQ ID NO: 10) (D917, E1006, and D1255 are bolded and underlined)
  • Francisella novicida Cpfl E1006A (SEQ ID NO: 262) (D917, A1006, and D1255 are bolded and underlined)
  • Francisella novicida Cpfl D1255A (SEQ ID NO: 263) (D917, E1006, and A1255 are bolded and underlined)
  • Francisella novicida Cpfl D917A/E1006A (SEQ ID NO: 264) (A917, A1006, and D1255 are bolded and underlined)
  • Francisella novicida Cpfl D917A/D1255A (SEQ ID NO: 265) (A917, E1006, and A1255 are bolded and underlined)
  • Francisella novicida Cpfl E1006A/D1255A (SEQ ID NO: 266) (D917, A1006, and A1255 are bolded and underlined)
  • Francisella novicida Cpfl D917A/E1006A/D1255A (SEQ ID NO: 267) (A917, A1006, and A 1255 are bolded and underlined)
  • the guide nucleotide sequence-programmable DNA binding protein is a Cpfl protein from a Acidaminococcus species (AsCpfl).
  • Cpfl proteins form Acidaminococcus species have been described previously and would be apparent to the skilled artisan.
  • Exemplary Acidaminococcus Cpfl proteins (AsCpfl) include, without limitation, any of the AsCpfl proteins provided herein.
  • Wild-type AsCpfl- Residue R912 is indicated in bold underlining and residues 661-667 are indicated in italics and underlining.
  • the nucleic acid programmable DNA binding protein is a Cpfl protein from a Lachnospiraceae species (LbCpfl).
  • Cpfl proteins form Lachnospiraceae species have been described previously have been described previously and would be apparent to the skilled artisan.
  • Exemplary Lachnospiraceae Cpfl proteins include, without limitation, any of the LbCpfl proteins provided herein.
  • the Cpfl protein is a crippled Cpfl protein.
  • a "crippled Cpfl" protein is a Cpfl protein having diminished nuclease activity as compared to a wild-type Cpfl protein.
  • the crippled Cpfl protein preferentially cuts the target strand more efficiently than the non-target strand.
  • the Cpfl protein preferentially cuts the strand of a duplexed nucleic acid molecule in which a nucleotide to be edited resides.
  • the crippled Cpfl protein is a crippled Cpfl protein.
  • the Cpfl protein preferentially cuts the strand of a duplexed nucleic acid molecule in which a nucleotide to be edited does not reside.
  • the crippled Cpfl protein preferentially cuts the target strand at least 5% more efficiently than it cuts the non-target strand.
  • the crippled Cpfl protein preferentially cuts the target strand at least 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 50%, 60%, 70%, 80%, 90%, or at least 100% more efficiently than it cuts the non-target strand.
  • a crippled Cpfl protein is a non-naturally occurring Cpfl protein.
  • the crippled Cpfl protein comprises one or more mutations relative to a wild-type Cpfl protein.
  • the crippled Cpfl protein comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 mutations relative to a wild-type Cpfl protein.
  • the crippled Cpfl protein comprises an R836A mutation mutation as set forth in SEQ ID NO: 763, or in a
  • the crippled Cpfl protein comprises a Rl 138A mutation as set forth in SEQ ID NO: 763, or in a corresponding amino acid in another Cpfl protein.
  • the crippled Cpfl protein comprises an R912A mutation mutation as set forth in SEQ ID NO: 762, or in a corresponding amino acid in another Cpfl protein.
  • residue R838 of SEQ ID NO: 763 (LbCpfl) and residue R912 of SEQ ID NO: 762 (AsCpfl) are examples of corresponding (e.g., homologous) residues.
  • a portion of the alignment between SEQ ID NO: 762 and 763 shows that R912 and R838 are corresponding residues.
  • any of the Cpfl proteins provided herein comprises one or more amino acid deletions. In some embodiments, any of the Cpfl proteins provided herein comprises 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 amino acid deletions.
  • there is a helical region in Cpfl which includes residues 661-667 of AsCpfl (SEQ ID NO: 762), that may obstruct the function of a deaminase (e.g., APOBEC) that is fused to the Cpfl. This region comprises the amino acid sequence KKTGDQK.
  • aspects of the disclosure provide Cpfl proteins comprising mutations (e.g., deletions) that disrupt this helical region in Cpfl.
  • the Cpfl protein comprises one or more deletions of the following residues in SEQ ID NO: 762, or one or more corresponding deletions in another Cpfl protein: K661, K662, T663, G664, D665, Q666, and K667.
  • the Cpfl protein comprises a T663 and a D665 deletion in SEQ ID NO: 762, or corresponding deletions in another Cpfl protein.
  • the Cpfl protein comprises a K662,T663, D665, and Q666 deletion in SEQ ID NO: 762, or corresponding deletions in another Cpfl protein.
  • the Cpfl protein comprises a K661, K662, T663, D665, Q666 and K667 deletion in SEQ ID NO: 762, or corresponding deletions in another Cpfl protein.
  • AsCpfl (deleted K662, T663, D665, and Q666) TQFEGFTNLYQVSKTLRFELIPQGKTLKHIQEQGFIEEDKARNDHYKELKPIIDRIYKTYADQCLQLVQL

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