ENGINEERED T CELL RECEPTORS FUSED TO BINDING DOMAINS FROM ANTIBODIES
The present disclosure provides improved T cell receptors, polynucleotides, polypeptides, vectors, cells, and methods of using the same. Particularly, the present invention relates to T cell receptor-based constructs engineered to comprise one or more additional binding domains, and methods of using the same. In certain embodiments, the one or more binding domains are fused to one or both TCR variable domains. In particular embodiments, the one or more additional binding domains are linked to the TCR with one or more polypeptide linkers.
1 . An engineered T cell receptor (TCR) comprising:
a) a TCRα polypeptide comprising a TCRα variable domain;
b) a TCRβ polypeptide comprising a TCRβ variable domain; and
c) one or more antigen-binding domains linked to the TCRα variable domain and/or TCRβ variable domain.
2 . An engineered T cell receptor (TCR) comprising:
a) a TCRγ polypeptide comprising a TCRγ variable domain;
b) a TCRδ polypeptide comprising a TCRδ variable domain; and
c) one or more antigen-binding domains linked to the TCRγ variable domain and/or TCRδ variable domain.
3 . The engineered TCR of claim 1 , wherein the TCRα polypeptide comprises a TCRα constant domain and the TCRβ polypeptide comprises a TCRβ constant domain.
4 . The engineered TCR of claim 2 , wherein the TCRγ polypeptide comprises a TCRγ constant domain and the TCRδ polypeptide comprises a TCRδ constant domain.
5 . The engineered TCR of any one of claims 1-4 , wherein the one or more antigen-binding domains comprises a first antigen-binding domain linked to the TCRα or TCRγ variable domain.
6 . The engineered TCR of any one of claims 1-5 , wherein the one or more antigen-binding domains comprises a first antigen-binding domain linked to the TCRβ or TCRδ variable domain.
7 . The engineered TCR of any one of claims 1-6 , wherein the one or more antigen-binding domains comprise: (i) a first antigen-binding domain linked to the TCRα or TCRγ variable domain, and (ii) a first antigen-binding domain linked to the TCRβ or TCRδ variable domain.
8 . The engineered TCR of any one of claims 5-7 , wherein the first antigen-binding domains are linked to the N-terminus of the variable domains.
9 . The engineered TCR of any one of claims 5-8 , wherein the first antigen-binding domains are the same or different, and/or bind to the same or different target antigens.
10 . The engineered TCR of any one of claims 5-9 , wherein the one or more antigen-binding domains comprises a second antigen-binding domain linked to the first antigen-binding domain linked to the TCRα or TCRγ variable domain.
11 . The engineered TCR of any one of claims 5-10 , wherein the one or more antigen-binding domains comprises a second antigen-binding domain linked to the first antigen-binding domain linked to the TCRβ or TCRδ variable domain.
12 . The engineered TCR of any one of claims 5-11 , wherein the one or more antigen-binding domains comprises: (i) a second antigen-binding domain linked to the first antigen-binding domain linked to the TCRα or TCRγ variable domain, and (ii) a second antigen-binding domain linked to the first antigen-binding domain linked to the TCRβ or TCRδ variable domain.
13 . The engineered TCR of any one of claims 10-12 , wherein the second antigen-binding domains are linked to the N-terminus of the first antigen-binding domain.
14 . The engineered TCR of claim 12 or claim 13 , wherein the second antigen-binding domains are the same or different, and/or bind to the same or different target antigens.
15 . The engineered TCR of any one of claims 5-14 , wherein the first and second antigen-binding domains are the same or different, and/or bind to the same or different target antigens.
16 . The engineered TCR of any one of claims 1-15 , wherein the one or more antigen-binding domains bind a target antigen selected from the group consisting of: alpha folate receptor (FRα), α v β 6 integrin, ADGRE2, BACE2, B cell maturation antigen (BCMA), B7-H3 (CD276), B7-H4, B7-H6, CA19.9, carbonic anhydrase IX (CAIX), CCR1, CD7, CD16, CD19, CD20, CD22, CD30, CD33, CD3γ, CD38, CD44, CD44v6, CD44v7/8, CD70, CD79a, CD79b, CD123, CD133, CD138, CD171, CD244, carcinoembryonic antigen (CEA), C-type lectin-like molecule-1 (CLL-1), CD2 subset 1 (CS-1), CLDN6, cMET, chondroitin sulfate proteoglycan 4 (CSPG4), CLDN18.2, cutaneous T cell lymphoma-associated antigen 1 (CTAGE1), DLL3, epidermal growth factor receptor (EGFR), epidermal growth factor receptor variant III (EGFRvIII), EGFR806, epithelial glycoprotein 2 (EGP2), epithelial glycoprotein 40 (EGP40), EPHB2, ERBB4, epithelial cell adhesion molecule (EPCAM), ephrin type-A receptor 2 (EPHA2), fibroblast activation protein (FAP), Fc Receptor Like 5 (FCRL5), fetal acetylcholinesterase receptor (AchR), FLT3, FN, FN-EDB, FRBeta, ganglioside G2 (GD2), ganglioside G3 (GD3), Glypican-3 (GPC3), EGFR family including ErbB2 (HER2), HER2p95, EGFRv3, IL-10Rα, IL-13Rα2, Kappa, cancer/testis antigen 2 (LAGE-1A), K-Ras, K-Ras G12C, K-Ras G12D, K-Ras G12V, Lambda, Lewis-Y (LeY), L1 cell adhesion molecule (L1-CAM), LILRB2, LY6G6GD, melanoma antigen recognized by T cells 1 (MelanA or MART1), Mesothelin (MSLN), MMP10, MUC1, MUC16, MHC class I chain related proteins A (MICA), MHC class I chain related proteins B (MICB), neural cell adhesion molecule (NCAM), prostate stem cell antigen (PSCA), prostate-specific membrane antigen (PSMA), receptor tyrosine kinase-like orphan receptor 1 (ROR1), synovial sarcoma, X breakpoint 2 (SSX2), Survivin, tumor associated glycoprotein 72 (TAG72), transmembrane activator and CAML interactor (TACI), tumor endothelial marker 1 (TEM1/CD248), tumor endothelial marker 7-related (TEM7R), TIM3, trophoblast glycoprotein (TPBG), UL16-binding protein (ULBP) 1, ULBP2, ULBP3, ULBP4, ULBP5, ULBP6, and vascular endothelial growth factor receptor 2 (VEGFR2).
17 . The engineered TCR of any one of claims 1-16 , wherein the one or more antigen-binding domains bind a target polypeptide derived from a protein selected from the group consisting of: α-fetoprotein (AFP), ASCL2, B Melanoma Antigen (BAGE) family members, Brother of the regulator of imprinted sites (BORIS), Cancer-testis antigens, Cancer-testis antigen 83 (CT-83), Carbonic anhydrase IX (CAIX), Carcinoembryonic antigen (CEA), Cytomegalovirus (CMV) antigens, Cytotoxic T cell (CTL)-recognized antigen on melanoma (CAMEL), Epstein-Barr virus (EBV) antigens, EPHB2, G antigen 1 (GAGE-1), GAGE-2, GAGE-3, GAGE-4, GAGE-5, GAGE-6, GAGE-7B, GAGE-8, Glycoprotein 100 (GP100), Hepatitis B virus (HBV) antigens, Hepatitis C virus (HCV) non-structure protein 3 (NS3), Human papillomavirus (HPV)-E6, HPV-E7, Human telomerase reverse transcriptase (hTERT), IGF2BP3/A3, IGF2BP1, K-Ras, K-Ras G12C, K-Ras G12D, K-Ras G12V, Latent membrane protein 2 (LMP2), LY6G6D, Melanoma antigen family A, 1 (MAGE-A1), MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A6, MAGE-A10, MAGE-A12, Melanoma antigen recognized by T cells (MART-1), Mesothelin (MSLN), Mucin 1 (MUC1), Mucin 16 (MUC16), New York esophageal squamous cell carcinoma-1 (NYESO-1), P53,P antigen (PAGE) family members, PAP, PIK3CA, PIK3CA H1047R, Placenta-specific 1 (PLAC1), Preferentially expressed antigen in melanoma (PRAME), Prostate specific antigen PSA, Survivin, Synovial sarcoma X 1 (SSX1), Synovial sarcoma X 2 (SSX2), Synovial sarcoma X 3 (SSX3), Synovial sarcoma X 4 (SSX4), Synovial sarcoma X 5 (SSX5), Synovial sarcoma X 8 (SSX8), Thyroglobulin, TP53 R175H, Tyrosinase, Tyrosinase related protein (TRP)1, TRP2, UBD, Wilms tumor protein (WT-1), Wnt10A, X Antigen Family Member 1 (XAGE1), and X Antigen Family Member 2 (XAGE2).
18 . The engineered TCR of any one of claims 1-17 , wherein the one or more antigen-binding domains bind CD33, CLL1, CD19, CD20, CD22, CD79A, CD79B, or BCMA.
19 . The engineered TCR of any one of claims 1-17 , wherein the one or more antigen-binding domains bind CD19, CD20, CD22, CD33, CD79A, CD79B, B7H3, Muc16, Her2, EGFR, FN-EDB, CLDN18.2, DLL3, FLT3, CLL1, CD123, or BCMA.
20 . The engineered TCR of any one of claims 1-17 , wherein the one or more antigen-binding domains comprises an amino acid sequence at least 95% identical to an amino acid sequence as set forth in any one of SEQ ID NOs: 1-32.
21 . The engineered TCR of any one of claims 1-20 , wherein the one or more antigen-binding domains comprise an antibody or antigen binding fragment thereof selected from the group consisting of: a Camel Ig, a Llama Ig, an Alpaca Ig, Ig NAR, a Fab′ fragment, a F(ab′) 2 fragment, a bispecific Fab dimer (Fab2), a trispecific Fab trimer (Fab3), an Fv, an single chain Fv protein (“scFv”), a bis-scFv, (scFv) 2 , a minibody, a diabody, a triabody, a tetrabody, a disulfide stabilized Fv protein (“dsFv”), and a single-domain antibody (sdAb, a camelid VHH, Nanobody).
22 . The engineered TCR of any one of claims 1-21 , wherein the one or more antigen-binding domains comprise one or more single-chain variable fragments (scFv).
23 . The engineered TCR of any one of claims 1-22 , wherein the one or more antigen-binding domains comprise one or more single domain antibodies (sdAb).
24 . The engineered TCR of claim 23 , wherein the sdAb is a camelid VHH, nanobody, or heavy chain-only antibody (HcAb).
25 . The engineered TCR of claim 23 , wherein the sdAb is a camelid VHH.
26 . The engineered TCR of any one of claims 21-25 , wherein antibody or antigen binding fragment thereof is human or humanized.
27 . The engineered TCR of any one of claims 1-19 , wherein the one or more antigen-binding domains comprise a ligand.
28 . The engineered TCR of any one of claims 1-27 , wherein the one or more antigen-binding domain are linked to the TCR variable domains by one or more polypeptide linkers.
29 . The engineered TCR of claim 28 , wherein the one or more polypeptide linkers comprise a linker from about 2 to about 25 amino acids long.
30 . The engineered TCR of claim 28 or claim 29 , wherein the one or more polypeptide linkers comprise a linker from about 4 to about 15 amino acids long.
31 . The engineered TCR of any one of claims 28-30 , wherein the one or more polypeptide linkers comprise a linker from about 4 to about 10 amino acids long.
32 . The engineered TCR of any one of claims 28-31 , wherein the one or more polypeptide linkers comprise a linker of about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, or about 15 amino acids long.
33 . The engineered TCR of any one of claims 28-32 , wherein the one or more polypeptide linkers comprise a linker of about 9 or about 10 amino acids long.
34 . The engineered TCR of any one of claims 28-33 wherein the one or more polypeptide linkers comprise a linker selected from the group consisting of: GG, GS, SG, SS, GSS, SSG, GSG, SGS, SGG, GGS, GGGS (SEQ ID NO: 53), (GGGGS) 1-5 polypeptide (SEQ ID NOs: 35-39), a linker from a marsupial γμTCR (e.g., LEKT; SEQ ID NO: 33), and any combination thereof.
35 . The engineered TCR of claims 28-34 , wherein the one or more polypeptide linkers comprises a linker from a marsupial YTCR, comprising an amino acid sequence as set forth in SEQ ID NO: 33.
36 . The engineered TCR of claims 28-35 , wherein the one or more polypeptide linkers comprise a GGGGS (SEQ ID NO: 35) linker (G4S).
37 . The engineered TCR of claims 28-36 , wherein the one or more polypeptide linkers comprise a marsupial γμTCR linker and a G4S linker as set forth in SEQ ID NO: 34.
38 . The engineered TCR of claims 28-37 , wherein the one or more polypeptide linkers comprise two GGGGS linkers (2×G4S) (SEQ ID NO: 36).
39 . The engineered TCR of claims 28-38 , wherein the one or more polypeptide linkers comprise three GGGGS linkers (3×G4S) (SEQ ID NO: 37).
40 . The engineered TCR of claims 28-39 , wherein the one or more polypeptide linkers comprise an amino acid sequence as set forth in any one of SEQ ID NOs: 33-53.
41 . The engineered TCR of any one of claims 10-40 , wherein the first and second antigen-binding domains are separated by a second polypeptide linker.
42 . The engineered TCR of claim 41 , wherein the second polypeptide linker is about 2 to about 25 amino acids long.
43 . The engineered TCR of claim 41 or claim 42 , wherein the second polypeptide linker is about 4 to about 15 amino acids long.
44 . The engineered TCR of any one of claims 41-43 , wherein the second polypeptide linker comprises a linker selected from the group consisting of: GG, GS, SG, SS, GSS, SSG, GSG, SGS, SGG, GGS, GGGS (SEQ ID NO: 53), (GGGGS) 1-5 polypeptide (SEQ ID NOs: 35-39), and any combination thereof.
45 . The engineered TCR of any one of claims 41-44 , wherein the second polypeptide linker comprises an amino acid sequence as set forth in any one of SEQ ID NOs: 33-53.
46 . The engineered TCR of any one of claims 1-45 , wherein the TCR variable domains bind a target polypeptide presented by an MHC complex.
47 . The engineered TCR of any one of the claims 1-46 , wherein the TCR variable domains bind a target polypeptide derived from a protein selected from the group consisting of: α-fetoprotein (AFP), ASCL2, B Melanoma Antigen (BAGE) family members, Brother of the regulator of imprinted sites (BORIS), Cancer-testis antigens, Cancer-testis antigen 83 (CT-83), Carbonic anhydrase IX (CAIX), Carcinoembryonic antigen (CEA), Cytomegalovirus (CMV) antigens, Cytotoxic T cell (CTL)-recognized antigen on melanoma (CAMEL), Epstein-Barr virus (EBV) antigens, EPHB2, G antigen 1 (GAGE-1), GAGE-2, GAGE-3, GAGE-4, GAGE-5, GAGE-6, GAGE-7B, GAGE-8, Glycoprotein 100 (GP100), Hepatitis B virus (HBV) antigens, Hepatitis C virus (HCV) non-structure protein 3 (NS3), Human papillomavirus (HPV)-E6, HPV-E7, Human telomerase reverse transcriptase (hTERT), IGF2BP3/A3, IGF2BP1, K-Ras, K-Ras G12C, K-Ras G12D, K-Ras G12V, Latent membrane protein 2 (LMP2), LY6G6D, Melanoma antigen family A, 1 (MAGE-A1), MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A6, MAGE-A10, MAGE-A12, Melanoma antigen recognized by T cells (MART-1), Mesothelin (MSLN), Mucin 1 (MUC1), Mucin 16 (MUC16), New York esophageal squamous cell carcinoma-1 (NYESO-1), P53,P antigen (PAGE) family members, PAP, PIK3CA, PIK3CA H1047R, Placenta-specific 1 (PLAC1), Preferentially expressed antigen in melanoma (PRAME), Prostate specific antigen PSA, Survivin, Synovial sarcoma X 1 (SSX1), Synovial sarcoma X 2 (SSX2), Synovial sarcoma X 3 (SSX3), Synovial sarcoma X 4 (SSX4), Synovial sarcoma X 5 (SSX5), Synovial sarcoma X 8 (SSX8), Thyroglobulin, TP53 R175H, Tyrosinase, Tyrosinase related protein (TRP)1, TRP2, UBD, Wilms tumor protein (WT-1), Wnt10A, X Antigen Family Member 1 (XAGE1), and X Antigen Family Member 2 (XAGE2).
48 . The engineered TCR of any one of the claims 1-47 , wherein the TCR variable domains bind a target polypeptide derived from MAGE-A4, PRAME, K-Ras, TP53R175H, PSA, or IGF2BP3.
49 . The engineered TCR of any one of the claims 1-48 , wherein the TCR variable domains bind a target polypeptide derived from MAGE-A4.
50 . The engineered TCR of any one of claims 1-49 , wherein the TCRα constant domain comprises an amino acid sequence at least 90% identical to an amino acid sequence as set forth in SEQ ID NOs: 82 or 88, and/or the TCRβ constant domain comprises an amino acid sequence at least 90% identical to an amino acid sequence as set forth in any one of SEQ ID NOs: 80, 81, 86, or 87.
51 . The engineered TCR of any one of claims 1-49 , wherein the TCRγ constant domain comprises an amino acid sequence at least 90% identical to an amino acid sequence as set forth in SEQ ID NO: 83 or 84, and/or the TCRδ constant domain comprises an amino acid sequence at least 90% identical to an amino acid sequence as set forth in any one of SEQ ID NO: 85.
52 . The engineered TCR of any one of claims 1-51 , wherein the TCRα or TCRγ polypeptide comprises (i) an amino acid sequence as set forth in any one of SEQ ID NOs: 105-111, or (ii) a TCRα or TCRγ variable domain comprising an amino acid sequence as set forth in any one of SEQ ID NOs: 62, 64, 66, 68, 70, 72, 74, 76, and 78.
53 . The engineered TCR of any one of claims 1-52 , wherein the TCRβ or TCRδ polypeptide comprises (i) an amino acid sequence as set forth in SEQ ID NO: 103 or 104, or (ii) a TCRβ or TCRδ variable domain comprising an amino acid sequence as set forth in any one of SEQ ID NOs: 63, 65, 67, 69, 71, 73, 75, 77, and 79.
54 . A fusion polypeptide comprising:
a) a TCRβ polypeptide comprising a TCRβ variable domain;
b) a polypeptide cleavage signal; and
c) a TCRα polypeptide comprising one or more antigen-binding domains, a polypeptide linker, and a TCRα variable domain.
55 . A fusion polypeptide comprising:
a) a TCRβ polypeptide comprising one or more antigen-binding domains, a polypeptide linker, and a TCRβ variable domain;
b) a polypeptide cleavage signal; and
c) a TCRα polypeptide comprising a TCRα variable domain.
56 . A fusion polypeptide comprising:
a) a TCRβ polypeptide comprising one or more antigen-binding domains, a polypeptide linker, and a TCRβ variable domain;
b) a polypeptide cleavage signal; and
c) a TCRα polypeptide comprising one or more antigen-binding domains, a polypeptide linker, and a TCRα variable domain.
57 . A fusion polypeptide comprising:
a) a TCRγ polypeptide comprising a TCRγ variable domain;
b) a polypeptide cleavage signal; and
c) a TCRδ polypeptide comprising one or more antigen-binding domains, a polypeptide linker, and a TCRδ variable domain.
58 . A fusion polypeptide comprising:
a) a TCRγ polypeptide comprising one or more antigen-binding domains, a polypeptide linker, and a TCRγ variable domain;
b) a polypeptide cleavage signal; and
c) a TCRδ polypeptide comprising a TCRδ variable domain.
59 . A fusion polypeptide comprising:
a) a TCRγ polypeptide comprising one or more antigen-binding domains, a polypeptide linker, and a TCRγ variable domain;
b) a polypeptide cleavage signal; and
c) a TCRδ polypeptide comprising one or more antigen-binding domains, a polypeptide linker, and a TCRδ variable domain.
60 . The fusion polypeptide of any one of claims 54-56 , wherein the TCRβ polypeptide comprises TCRβ constant domain, and the TCRα polypeptide comprises a TCRα constant domain.
61 . The fusion polypeptide of any one of claims 57-59 , wherein the TCRγ polypeptide comprises TCRγ constant domain, and the TCRδ polypeptide comprises a TCRδ constant domain.
62 . The fusion polypeptide of any one of claims 54-61 , wherein the one or more antigen-binding domains comprises a first antigen-binding domain linked to the TCRα or TCRγ variable domain.
63 . The fusion polypeptide of any one of claims 54-62 , wherein the one or more antigen-binding domains comprises a first antigen-binding domain linked to the TCRβ or TCRδ variable domain.
64 . The fusion polypeptide of any one of claims 54-63 , wherein the one or more antigen-binding domains comprise: (i) a first antigen-binding domain linked to the TCRα or TCRγ variable domain, and (ii) a first antigen-binding domain linked to the TCRβ or TCRδ variable domain.
65 . The fusion polypeptide of any one of claims 62-64 , wherein the first antigen-binding domains are linked to the N-terminus of the variable domains.
66 . The fusion polypeptide of any one of claims 62-65 , wherein the first antigen-binding domains are the same or different, and/or bind to the same or different target antigens.
67 . The fusion polypeptide of any one of claims 62-66 , wherein the one or more antigen-binding domains comprises a second antigen-binding domain linked to the first antigen-binding domain linked to the TCRα or TCRγ variable domain.
68 . The fusion polypeptide of any one of claims 62-67 , wherein the one or more antigen-binding domains comprises a second antigen-binding domain is linked to the first antigen-binding domain linked to the TCRβ or TCRδ variable domain.
69 . The fusion polypeptide of any one of claims 62-68 , wherein the one or more antigen-binding domains comprises: (i) a second antigen-binding domain linked to the first antigen-binding domain linked to the TCRα or TCRγ variable domain, and (ii) a second antigen-binding domain linked to the first antigen-binding domain linked to the TCRβ or TCRδ variable domain.
70 . The fusion polypeptide of any one of claims 67-69 , wherein the second antigen-binding domains are linked to the N-terminus of the first antigen-binding domain.
71 . The fusion polypeptide of claim 69 or claim 70 , wherein the second antigen-binding domains are the same or different, and/or bind to the same or different target antigens.
72 . The fusion polypeptide of any one of claims 67-71 , wherein the first and second antigen-binding domains are the same or different, and/or bind to the same or different target antigens.
73 . The fusion polypeptide of any one of claims 54-72 , wherein the one or more antigen-binding domains bind a target antigen selected from the group consisting of: alpha folate receptor (FRα), α v β 6 integrin, ADGRE2, BACE2, B cell maturation antigen (BCMA), B7-H3 (CD276), B7-H4, B7-H6, CA19.9, carbonic anhydrase IX (CAIX), CCR1, CD7, CD16, CD19, CD20, CD22, CD30, CD33, CD37, CD38, CD44, CD44v6, CD44v7/8, CD70, CD79a, CD79b, CD123, CD133, CD138, CD171, CD244, carcinoembryonic antigen (CEA), C-type lectin-like molecule-1 (CLL-1), CD2 subset 1 (CS-1), CLDN6, cMET, chondroitin sulfate proteoglycan 4 (CSPG4), CLDN18.2, cutaneous T cell lymphoma-associated antigen 1 (CTAGE1), DLL3, epidermal growth factor receptor (EGFR), epidermal growth factor receptor variant III (EGFRvIII), EGFR806, epithelial glycoprotein 2 (EGP2), epithelial glycoprotein 40 (EGP40), EPHB2, ERBB4, epithelial cell adhesion molecule (EPCAM), ephrin type-A receptor 2 (EPHA2), fibroblast activation protein (FAP), Fc Receptor Like 5 (FCRL5), fetal acetylcholinesterase receptor (AchR), FLT3, FN, FN-EDB, FRBeta, ganglioside G2 (GD2), ganglioside G3 (GD3), Glypican-3 (GPC3), EGFR family including ErbB2 (HER2), HER2p95, EGFRv3, IL-10Rα, IL-13Rα2, Kappa, cancer/testis antigen 2 (LAGE-1A), K-Ras, K-Ras G12C, K-Ras G12D, K-Ras G12V, Lambda, Lewis-Y (LeY), L1 cell adhesion molecule (L1-CAM), LILRB2, LY6G6GD, melanoma antigen recognized by T cells 1 (MelanA or MART1), Mesothelin (MSLN), MMP10, MUC1, MUC16, MHC class I chain related proteins A (MICA), MHC class I chain related proteins B (MICB), neural cell adhesion molecule (NCAM), prostate stem cell antigen (PSCA), prostate-specific membrane antigen (PSMA), receptor tyrosine kinase-like orphan receptor 1 (ROR1), synovial sarcoma, X breakpoint 2 (SSX2), Survivin, tumor associated glycoprotein 72 (TAG72), transmembrane activator and CAML interactor (TACI), tumor endothelial marker 1 (TEM1/CD248), tumor endothelial marker 7-related (TEM7R), TIM3, trophoblast glycoprotein (TPBG), UL16-binding protein (ULBP) 1, ULBP2, ULBP3, ULBP4, ULBP5, ULBP6, and vascular endothelial growth factor receptor 2 (VEGFR2).
74 . The fusion polypeptide of any one of claims 54-73 , wherein the one or more antigen-binding domains bind a target polypeptide derived from a protein selected from the group consisting of: α-fetoprotein (AFP), ASCL2, B Melanoma Antigen (BAGE) family members, Brother of the regulator of imprinted sites (BORIS), Cancer-testis antigens, Cancer-testis antigen 83 (CT-83), Carbonic anhydrase IX (CAIX), Carcinoembryonic antigen (CEA), Cytomegalovirus (CMV) antigens, Cytotoxic T cell (CTL)-recognized antigen on melanoma (CAMEL), Epstein-Barr virus (EBV) antigens, EPHB2, G antigen 1 (GAGE-1), GAGE-2, GAGE-3, GAGE-4, GAGE-5, GAGE-6, GAGE-7B, GAGE-8, Glycoprotein 100 (GP100), Hepatitis B virus (HBV) antigens, Hepatitis C virus (HCV) non-structure protein 3 (NS3), Human papillomavirus (HPV)-E6, HPV-E7, Human telomerase reverse transcriptase (hTERT), IGF2BP3/A3, IGF2BP1, K-Ras, K-Ras G12C, K-Ras G12D, K-Ras G12V, Latent membrane protein 2 (LMP2), LY6G6D, Melanoma antigen family A, 1 (MAGE-A1), MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A6, MAGE-A10, MAGE-A12, Melanoma antigen recognized by T cells (MART-1), Mesothelin (MSLN), Mucin 1 (MUC1), Mucin 16 (MUC16), New York esophageal squamous cell carcinoma-1 (NYESO-1), P53,P antigen (PAGE) family members, PAP, PIK3CA, PIK3CA H1047R, Placenta-specific 1 (PLAC1), Preferentially expressed antigen in melanoma (PRAME), Prostate specific antigen PSA, Survivin, Synovial sarcoma X 1 (SSX1), Synovial sarcoma X 2 (SSX2), Synovial sarcoma X 3 (SSX3), Synovial sarcoma X 4 (SSX4), Synovial sarcoma X 5 (SSX5), Synovial sarcoma X 8 (SSX8), Thyroglobulin, TP53 R175H, Tyrosinase, Tyrosinase related protein (TRP)1, TRP2, UBD, Wilms tumor protein (WT-1), Wnt10A, X Antigen Family Member 1 (XAGE1), and X Antigen Family Member 2 (XAGE2).
75 . The fusion polypeptide of claims 54-74 , wherein the one or more antigen-binding domains bind CD33, CLL1, CD19, CD20, CD22, CD79A, CD79B, or BCMA.
76 . The engineered TCR of any one of claims 54-74 , wherein the one or more antigen-binding domains bind CD19, CD20, CD22, CD33, CD79A, CD79B, B7H3, Muc16, Her2, EGFR, FN-EDB, CLDN18.2, DLL3, FLT3, CLL1, CD123, or BCMA.
77 . The engineered TCR of any one of claims 54-74 , wherein the one or more antigen-binding domains comprises an amino acid sequence at least 95% identical to an amino acid sequence as set forth in any one of SEQ ID NOs: 1-32.
78 . The fusion polypeptide of any one of claims 54-77 , wherein the one or more antigen-binding domains comprise an antibody or antigen binding fragment thereof selected from the group consisting of: a Camel Ig, a Llama Ig, an Alpaca Ig, Ig NAR, a Fab′ fragment, a F(ab′) 2 fragment, a bispecific Fab dimer (Fab2), a trispecific Fab trimer (Fab3), an Fv, an single chain Fv protein (“scFv”), a bis-scFv, (scFv) 2 , a minibody, a diabody, a triabody, a tetrabody, a disulfide stabilized Fv protein (“dsFv”), and a single-domain antibody (sdAb, a camelid VHH, Nanobody).
79 . The fusion polypeptide of any one of claims 54-78 , wherein the one or more antigen-binding domains comprise one or more single-chain variable fragments (scFv).
80 . The fusion polypeptide of any one of claims 54-79 , wherein the one or more antigen-binding domains comprise one or more single domain antibodies (sdAb).
81 . The fusion polypeptide of claim 80 , wherein the sdAb is a camelid VHH, nanobody, or heavy chain-only antibody (HcAb).
82 . The fusion polypeptide of claim 80 , wherein the sdAb is a camelid VHH.
83 . The fusion polypeptide of any one of claims 74-82 , wherein the antibody or antigen binding fragment thereof is human or humanized.
84 . The fusion polypeptide of any one of claims 54-76 , wherein the one or more antigen-binding domains comprise a ligand.
85 . The fusion polypeptide of any one of claims 54-84 , wherein the one or more antigen-binding domains are linked to the TCR variable domains by one or more polypeptide linkers.
86 . The fusion polypeptide of claim 85 , wherein the one or more polypeptide linkers comprise a linker from about 2 to about 25 amino acids long.
87 . The fusion polypeptide of claim 85 or claim 86 , wherein the one or more polypeptide linkers comprise a linker from about 4 to about 15 amino acids long.
88 . The fusion polypeptide of any one of claims 85-87 , wherein the one or more polypeptide linkers comprise a linker from about 4 to about 10 amino acids long.
89 . The fusion polypeptide of any one of claims 85-88 , wherein the one or more polypeptide linkers comprise a linker of about 4, about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, or about 15 amino acids long.
90 . The fusion polypeptide of any one of claims 85-89 , wherein the one or more polypeptide linkers comprise a linker of about 9 or about 10 amino acids long.
91 . The fusion polypeptide of any one of claims 85-90 wherein the one or more polypeptide linkers comprise a linker selected from the group consisting of: GG, GS, SG, SS, GSS, SSG, GSG, SGS, SGG, GGS, GGGS (SEQ ID NO: 53), (GGGGS) 1-5 polypeptide (SEQ ID NOs: 35-39), a linker from a marsupial γμTCR (e.g., LEKT; SEQ ID NO: 33), and any combination thereof.
92 . The fusion polypeptide of claims 85-91 , wherein the one or more polypeptide linkers comprises a linker from a marsupial YTCR, comprising an amino acid sequence as set forth in SEQ ID NO: 33.
93 . The fusion polypeptide of claims 85-92 , wherein the one or more polypeptide linkers comprise a GGGGS (SEQ ID NO: 35) linker (G4S).
94 . The fusion polypeptide of claims 85-93 , wherein the one or more polypeptide linkers comprise a marsupial γμTCR linker and a G4S linker as set forth in SEQ ID NO: 34.
95 . The fusion polypeptide of claims 85-94 , wherein the one or more polypeptide linkers comprise two GGGGS linkers (2×G4S) (SEQ ID NO: 36).
96 . The fusion polypeptide of claims 85-95 , wherein the one or more polypeptide linkers comprise three GGGGS linkers (3×G4S) (SEQ ID NO: 37).
97 . The fusion polypeptide of claims 85-96 , wherein the one or more polypeptide linkers comprise an amino acid sequence as set forth in any one of SEQ ID NOs: 33-53.
98 . The fusion polypeptide of any one of claims 67-97 , wherein the first and second antigen-binding domains are separated by a second polypeptide linker.
99 . The fusion polypeptide of claim 98 , wherein the second polypeptide linker is about 2 to about 25 amino acids long.
100 . The fusion polypeptide of claim 98 or claim 99 , wherein the one or more polypeptide linkers comprise a linker from about 4 to about 15 amino acids long.
101 . The fusion polypeptide of any one of claims 98-100 , wherein the second polypeptide linker comprises a linker selected from the group consisting of: GG, GS, SG, SS, GSS, SSG, GSG, SGS, SGG, GGS, GGGS (SEQ ID NO: 53), (GGGGS) 1-5 polypeptide (SEQ ID NOs: 35-39), and any combination thereof.
102 . The fusion polypeptide of any one of claims 98-101 , wherein the second polypeptide linker comprises an amino acid sequence as set forth in any one of SEQ ID NOs: 33-53.
103 . The fusion polypeptide of any one of claims 54-102 , wherein the TCR variable domains bind a target polypeptide presented by an MHC complex.
104 . The fusion polypeptide of any one of the claims 54-103 , wherein the TCR variable domains bind a target polypeptide derived from a protein selected from the group consisting of: α-fetoprotein (AFP), ASCL2, B Melanoma Antigen (BAGE) family members, Brother of the regulator of imprinted sites (BORIS), Cancer-testis antigens, Cancer-testis antigen 83 (CT-83), Carbonic anhydrase IX (CAIX), Carcinoembryonic antigen (CEA), Cytomegalovirus (CMV) antigens, Cytotoxic T cell (CTL)-recognized antigen on melanoma (CAMEL), Epstein-Barr virus (EBV) antigens, EPHB2, G antigen 1 (GAGE-1), GAGE-2, GAGE-3, GAGE-4, GAGE-5, GAGE-6, GAGE-7B, GAGE-8, Glycoprotein 100 (GP100), Hepatitis B virus (HBV) antigens, Hepatitis C virus (HCV) non-structure protein 3 (NS3), Human papillomavirus (HPV)-E6, HPV-E7, Human telomerase reverse transcriptase (hTERT), IGF2BP3/A3, IGF2BP1, K-Ras, K-Ras G12C, K-Ras G12D, K-Ras G12V, Latent membrane protein 2 (LMP2), LY6G6D, Melanoma antigen family A, 1 (MAGE-A1), MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A6, MAGE-A10, MAGE-A12, Melanoma antigen recognized by T cells (MART-1), Mesothelin (MSLN), Mucin 1 (MUC1), Mucin 16 (MUC16), New York esophageal squamous cell carcinoma-1 (NYESO-1), P53,P antigen (PAGE) family members, PAP, PIK3CA, PIK3CA H1047R, Placenta-specific 1 (PLAC1), Preferentially expressed antigen in melanoma (PRAME), Prostate specific antigen PSA, Survivin, Synovial sarcoma X 1 (SSX1), Synovial sarcoma X 2 (SSX2), Synovial sarcoma X 3 (SSX3), Synovial sarcoma X 4 (SSX4), Synovial sarcoma X 5 (SSX5), Synovial sarcoma X 8 (SSX8), Thyroglobulin, TP53 R175H, Tyrosinase, Tyrosinase related protein (TRP)1, TRP2, UBD, Wilms tumor protein (WT-1), Wnt10A, X Antigen Family Member 1 (XAGE1), and X Antigen Family Member 2 (XAGE2).
105 . The fusion polypeptide of any one of the claims 54-104 , wherein the TCR variable domains bind a target polypeptide derived from MAGE-A4, PRAME, K-Ras, TP53R175H, PSA, or IGF2BP3.
106 . The fusion polypeptide of any one of the claims 54-105 , wherein the TCR variable domains bind a target polypeptide derived from MAGE-A4.
107 . The engineered TCR of any one of claims 54-106 , wherein the TCRα constant domain comprises an amino acid sequence at least 90% identical to an amino acid sequence as set forth in SEQ ID NOs: 82 or 88, and/or the TCRβ constant domain comprises an amino acid sequence at least 90% identical to an amino acid sequence as set forth in any one of SEQ ID NOs: 80, 81, 86, or 87.
108 . The engineered TCR of any one of claims 54-106 , wherein the TCRγ constant domain comprises an amino acid sequence at least 90% identical to an amino acid sequence as set forth in SEQ ID NO: 83 or 84, and/or the TCRδ constant domain comprises an amino acid sequence at least 90% identical to an amino acid sequence as set forth in any one of SEQ ID NO: 85.
109 . The fusion polypeptide of any one of claims 54-108 , wherein the TCRα or TCRγ polypeptide comprises (i) an amino acid sequence as set forth in any one of SEQ ID NOs: 105-111, or (ii) a TCRα or TCRγ variable domain comprising an amino acid sequence as set forth in any one of SEQ ID NOs: 62, 64, 66, 68, 70, 72, 74, 76, and 78.
110 . The fusion polypeptide of any one of claims 54-109 , wherein the TCRβ or TCRδ polypeptide comprises an amino acid sequence as set forth in any one of SEQ ID NOs: 103 or 104, or (ii) a TCRβ or TCRδ variable domain comprising an amino acid sequence as set forth in any one of SEQ ID NOs: 63, 65, 67, 69, 71, 73, 75, 77, and 79.
111 . The fusion polypeptide of any one of claims 54-110 , wherein the polypeptide cleavage signal is a viral self-cleaving peptide or ribosomal skipping sequence.
112 . The fusion polypeptide of any one of claims 54-111 , wherein the polypeptide cleavage signal is a viral 2A peptide.
113 . The fusion polypeptide of any one of claims 54-112 , wherein the polypeptide cleavage signal is an aphthovirus 2A peptide, a potyvirus 2A peptide, or a cardiovirus 2A peptide.
114 . The fusion polypeptide of any one of claims 54-113 , wherein the polypeptide cleavage signal is a viral 2A peptide selected from the group consisting of: a foot-and-mouth disease virus (FMDV) 2A peptide, an equine rhinitis A virus (ERAV) 2A peptide, a Thosea asigna virus (TaV) 2A peptide, a porcine teschovirus-1 (PTV-1) 2A peptide, a Theilovirus 2A peptide, and an encephalomyocarditis virus 2A peptide.
115 . The fusion polypeptide of any one of claims 111-114 , wherein the polypeptide cleavage signal comprises a furin recognition site upstream of the self-cleaving peptide, optionally wherein the furin recognition site comprises the amino acid sequence as set forth in SEQ ID NO: 112.
116 . The fusion polypeptide of any one of claims 54-115 , wherein the polypeptide cleavage signal comprises an amino acid sequence as set forth in any one of SEQ ID NOs: 113-137.
117 . The fusion polypeptide of any one of claims 54-116 , wherein the TCRβ or TCRδ polypeptide is N-terminal of the TCRα or TCRγ polypeptide.
118 . The fusion polypeptide of any one of claims 54-116 , wherein the TCRα or TCRγ polypeptide is N-terminal of the TCRβ or TCRδ polypeptide.
119 . The fusion polypeptide of any one of claims 54-118 , wherein the TCRα and TCRβ polypeptides each comprise an N-terminal signal sequence.
120 . The fusion polypeptide of any one of claims 54-119 , wherein the TCRγ and TCRδ polypeptides each comprises an N-terminal signal sequence.
121 . The fusion polypeptide of claim 119 or claim 120 , wherein the signal sequences are the same or different.
122 . The fusion polypeptide of any one of claims 119-121 , wherein the signal sequence is an IgK or TCRα signal sequence.
123 . The fusion polypeptide of any one of claims 54-122 , wherein the fusion polypeptide comprises an amino acid sequence at least 90% identical to an amino acid sequence as set forth in any one of SEQ ID NOs: 91-97, 100, and 102.
124 . A polynucleotide encoding the TCR polypeptides of the engineered TCR according to any one of claims 1-51 , or the fusion polypeptide of any one of claims 54-123 .
125 . A vector comprising the polynucleotide of claim 124 .
126 . The vector of claim 125 , wherein the vector is an expression vector, retroviral vector, or a lentiviral vector.
127 . A cell comprising the engineered TCR according to any one of claims 1-53 , the fusion polypeptide of any one of claims 54-123 , the polynucleotide of claim 124 , or the vector of claim 125 or claim 126 .
128 . The cell of claim 127 , wherein the cell is a hematopoietic cell.
129 . The cell of claim 127 or claim 128 , wherein the cell is a T cell, an αβ-T cell, or a γδ-T cell.
130 . The cell of any one of claims 127-129 , wherein the cell is a CD3 + , CD4 + , and/or CD8 + cell.
131 . The cell of any one of claims 127-130 , wherein the cell is an immune effector cell.
132 . The cell of any one of claims 127-131 , wherein the cell is a cytotoxic T lymphocytes (CTLs), a tumor infiltrating lymphocytes (TILs), or a helper T cell.
133 . The cell of any one of claims 127-132 , wherein the cell is a T cell, a natural killer (NK) cell, or a natural killer T (NKT) cell.
134 . The cell of any one of claims 127-133 , wherein the source of the cell is peripheral blood mononuclear cells, bone marrow, lymph nodes tissue, cord blood, thymus issue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, or tumors.
135 . The cell of any one of claims 127-134 , wherein the cell is an isolated non-natural cell.
136 . The cell of any one of claims 127-135 , wherein the cell is obtained from a subject.
137 . The cell of any one of claims 127-136 , wherein the cell is a human cell.
138 . A composition comprising the engineered TCR according to any one of claims 1-53 , the fusion polypeptide of any one of claims 54-123 , the polynucleotide of claim 124 , or the vector of claim 125 or claim 126 , or the cell of any one of claims 127-137 .
139 . A pharmaceutical composition comprising a pharmaceutically acceptable carrier and the engineered TCR according to any one of claims 1-53 , the fusion polypeptide of any one of claims 54-123 , the polynucleotide of claim 124 , or the vector of claim 125 or claim 126 , or the cell of any one of claims 127-137 .
140 . A method of treating a subject in need thereof comprising administering the subject an effective amount of the cell of any one of claims 127-137 , the composition of claim 138 , or the pharmaceutical composition of claim 139 .
141 . A method of treating, preventing, or ameliorating at least one symptom of a cancer, infectious disease, autoimmune disease, inflammatory disease, and immunodeficiency, or condition associated therewith, comprising administering to the subject an effective amount of the cell of any one of claims 127-137 , the composition of claim 138 , or the pharmaceutical composition of claim 139 .
142 . A method of treating a solid cancer comprising administering to the subject an effective amount of the cell of any one of claims 127-137 , the composition of claim 138 , or the pharmaceutical composition of claim 139 .
143 . The method of claim 142 , wherein the solid cancer is selected from the group consisting of: lung cancer, squamous cell carcinoma, colorectal cancer, pancreatic cancer, breast cancer, thyroid cancer, bladder cancer, cervical cancer, esophageal cancer, ovarian cancer, gastric cancer endometrial cancer, brain cancer, or sarcoma.
144 . The method of claim 142 , wherein the solid cancer is a non-small cell lung carcinoma (NSCLC), small cell lung cancer (SCLC), head and neck squamous cell carcinoma, colorectal cancer, pancreatic cancer, breast cancer, thyroid cancer, bladder cancer, cervical cancer, esophageal cancer, ovarian cancer, gastric cancer endometrial cancer, gliomas, glioblastomas, oligodendroglioma, sarcoma, or osteosarcoma.
145 . A method of treating a hematological malignancy comprising administering to the subject an effective amount of the cell of any one of claims 127-137 , the composition of claim 138 , or the pharmaceutical composition of claim 139 .
146 . The method of claim 145 , wherein the hematological malignancy is a leukemia, lymphoma, or multiple myeloma.
147 . The method of claim 145 or claim 146 , wherein the hematological malignancy is selected from the group consisting of non-Hodgkin's lymphoma, acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL).