Diverse antigen binding domains, novel platforms and other enhancements for cellular therapy
The disclosure provides diverse antigen binding domains and platforms for construction of conventional and next generation chimeric antigen receptors for adoptive cellular therapies for cancer, infection, allergic, degenerative and immune disorders, Also provided are approaches for activation and expansion of immune T cells for adoptive cellular therapies for cancer, infection, allergic, degenerative and immune disorders.
1 . At least one recombinant polynucleotide encoding a synthetic immune receptor-CD3-zeta (zSIR) heterodimer comprising two CD3-zeta (CD3z) chains,
wherein each CD3z chain comprises the transmembrane domain and cytoplasmic domain of a CD3z protein; wherein a variable light (vL) domain of an antibody is operably linked to a first of the two CD3z chains via a first linker and a variable heavy (vH) domain of the antibody is operably linked to a second of the two CD3z chains via a second linker; wherein the first linker comprises an IgCL domain and the second linker comprises an IgCH domain; and wherein the vL domain and the vH domain are from the same antibody and together bind a target antigen recognized by the antibody.
2 . The at least one recombinant polynucleotide of claim 1 , wherein one or both of the CD3z chains comprise one or more co-stimulatory domains, wherein
a) the encoded co-stimulatory domain comprises a cytosolic domain of 4-1BB, CD28, CD134, Dap10, CD27, CD2, CD5, ICAM-1, LFA-1, Lck, TNFR-I, TNFR-II, Fas, CD30, CD40 or combinations thereof; and/or
b) the encoded co-stimulatory domain comprises the amino acid sequence selected from the group consisting of SEQ ID NOs: 4067, 4068, or a sequence having at least 85% identity thereto.
3 . The at least one recombinant polynucleotide of claim 1 , wherein the CD3z chain comprises a polypeptide having the sequence selected from the group consisting of SEQ ID NOs: 4064, 4066, 4075, and 4076, or a polypeptide having an at least 85% sequence identity thereto.
4 . The at least one recombinant polynucleotide of claim 1 , further comprising a nucleic acid sequence encoding an accessory module, wherein the accessory module comprises one or more of the following: 4-1BBL, CD40L, HIV-1 Vif, vFLIP K13, MC159, cFLIP-L/MRITa, cFLIP-p22, HTLV-1 Tax, HTLV-2 Tax, FKBP×2-K13, FKBP×2-HTLV-2-Tax, FKBPx2-HTLV-2-Tax-RS, IL6R-304-vHH-Alb8-vHH, IL12f, PD-1-4H1 scFv, PD-1-5C4 scFv, PD-1-4H1-Alb8-vHH, PD-1-5C4-Alb8-vHH, CTLA-4-Ipilimumab-scFv, CTLA-4-Ipilimumab-Alb8-vHH, IL6-19A-scFv, IL6-19A-scFv-Alb8-vHH, sHVEM, sHVEM-Alb8-vHH, hTERT, Fx06, hNEMO-K277A, shRNA targeting Brd4, or a combination thereof.
5 . The at least one recombinant polynucleotide of claim 1 , wherein
the first linker comprises a polypeptide having the sequence of SEQ ID NO: 4027, or a sequence with at least 85% identity thereto, and the second linker comprises a polypeptide having the sequence selected from the group consisting of SEQ ID NOs: 4028-4035, or a sequence with at least 85% identity thereto.
6 . The at least one recombinant polynucleotide of claim 1 , wherein
the vL domain comprises the sequence of any one of SEQ ID NOs: 4159-4190, 4118-4126, 4128-4158, 9659-9660, 11460-11462, 14386-14405, or a sequence with at least 95% identity thereto and containing the three light chain complementarity determining regions (CDRs) of the foregoing; and the vH domain comprises the sequence of any one of SEQ ID NOs: 4233-4264, 4192-4200, 4202-4232, 9690-9691, 11464-11466, 14417-14436, or a sequence with at least 95% identity thereto and containing the three heavy chain complementarity determining regions (CDRs) of the foregoing.
7 . The at least one recombinant polynucleotide of claim 1 , wherein the encoded zSIR binds to one or more disease-associated antigens selected from the group consisting of: CD5, CD19, CD123, CD22, CD30, CD171, CS1, BAFF-R, C-type lectin-like molecule-1, CD33, MPL, epidermal growth factor receptor variant III, ganglioside G2, ganglioside GD3, TNF receptor family member B cell maturation antigen, Tn antigen, prostate-specific membrane antigen, receptor tyrosine kinase-like orphan receptor 1, Fms-like tyrosine kinase 3, tumor-associated glycoprotein 72, CD38, CD44v6, glycosylated CD43 epitope expressed on acute leukemia or lymphoma but not on hematopoietic progenitors, glycosylated CD43 epitope expressed on non-hematopoietic cancers, carcinoembryonic antigen, epithelial cell adhesion molecule, B7-H3, KIT, interleukin-13 receptor subunit alpha-2, mesothelin, interleukin-11 receptor alpha, prostate stem cell antigen, protease serine 21, vascular endothelial growth factor receptor 2, Lewis antigen, CD24, platelet-derived growth factor receptor beta, stage-specific embryonic antigen-4, CD20, folate receptor alpha, receptor tyrosine-protein kinase ERBB2, mucin 1, epidermal growth factor receptor, neural cell adhesion molecule, prostase, prostatic acid phosphatase, elongation factor 2 mutated, ephrin B2, fibroblast activation protein alpha, insulin-like growth factor 1 receptor, carbonic anhydrase IX, glycoprotein 100, oncogene fusion protein consisting of breakpoint cluster region and Abelson murine leukemia viral oncogene homolog 1, tyrosinase, ephrin type-A receptor 2, fucosyl GM1, sialyl Lewis adhesion molecule, ganglioside GM3, transglutaminase 5, high molecular weight melanoma-associated antigen, O-acetyl-GD2 ganglioside, tumor endothelial marker 1, tumor endothelial marker 7-related, claudin 6, thyroid-stimulating hormone receptor, G protein-coupled receptor class C group 5 member D, chromosome X open reading frame 61, CD97, CD179a, anaplastic lymphoma kinase, polysialic acid, placenta-specific 1, hexasaccharide portion of Globo H glycoceramide, mammary gland differentiation antigen, uroplakin 2, hepatitis A virus cellular receptor 1, adrenoceptor beta 3, pannexin 3, G protein-coupled receptor 20, lymphocyte antigen 6 complex locus K, olfactory receptor 51E2, TCR gamma alternate reading frame protein, Wilms tumor protein, cancer/testis antigen 1, cancer/testis antigen 2, melanoma-associated antigen 1, ETS translocation variant gene 6, sperm protein 17, X antigen family member 1A, angiopoietin-binding cell surface receptor 2, melanoma cancer-testis antigen 1, melanoma cancer-testis antigen 2, Fos-related antigen 1, tumor protein p53, mutant p53, prostein, survivin, telomerase, prostate carcinoma tumor antigen 1, melanoma antigen recognized by T cells 1, RAS mutant, human telomerase reverse transcriptase, sarcoma translocation breakpoints, melanoma inhibitor of apoptosis, ERG, N-acetylglucosaminyltransferase V, paired box protein Pax-3, androgen receptor, cyclin B1, MYCN, Ras homolog family member C, tyrosinase-related protein 2, cytochrome P450 1B1, CCCTC-binding factor-like, squamous cell carcinoma antigen recognized by T cells 3, paired box protein Pax-5, proacrosin binding protein SP32, lymphocyte-specific protein tyrosine kinase, A-kinase anchor protein 4, synovial sarcoma X breakpoint 2, receptor for advanced glycation end products, renal ubiquitous 1, renal ubiquitous 2, legumain, human papillomavirus E6, human papillomavirus E7, intestinal carboxyl esterase, mutated heat shock protein 70-2, CD79a, CD79b, CD72, leukocyte-associated immunoglobulin-like receptor 1, Fc fragment of IgA receptor, leukocyte immunoglobulin-like receptor subfamily A member 2, CD300 molecule-like family member F, C-type lectin domain family 12 member A, bone marrow stromal cell antigen 2, EGF-like module-containing mucin-like hormone receptor-like 2, lymphocyte antigen 75, glypican-3, Fc receptor-like 5, immunoglobulin lambda-like polypeptide 1, biotin, c-MYC epitope tag, LAMP1, TROP2, GFRα4, CDH17, CDH6, NY-BR1, CDH19, CD200R, sLea, PTK7, gpNMB, CDH1, DLL3, CD179b, TCR gamma-delta, NKG2D, CD32, CSF2RA, TGFβR2, TCR beta1 chain, TCR beta2 chain, TCR gamma chain, TCR delta chain, FITC, luteinizing hormone receptor, follicle-stimulating hormone receptor, chorionic gonadotropin hormone receptor, CCR4, SLAMF6, SLAMF4, HIV-1 envelope glycoprotein, HTLV-1 Tax, CMV pp65, EBV-EBNA3C, influenza A hemagglutinin, GAD, PD-L1, guanylyl cyclase C, KSHV-K8.1 protein, KSHV-gH protein, autoantibody to desmoglein 3, autoantibody to desmoglein 1, HLA-A, HLA-A2, HLA-B, HLA-C, HLA-DP, HLA-DM, HLA-DOA, HLA-DOB, HLA-DQ, HLA-DR, HLA-G, IgE, CD99, RAS G12V, tissue factor 1, alpha-fetoprotein, claudin 18.2, P-glycoprotein, STEAP1, LIV1, NECTIN-4, CRIPTO, GPA33, BST1, low-conductance chloride channel, integrin β7, MUC17, C16ORF54, VISTA, MUC5AC, FCRH5, MMP16, UPK1B, BMPR1B, LY6E, WISP1, and SLC34A2; or combinations thereof.
8 . A synthetic immune receptor-CD3-zeta (zSIR) polypeptide heterodimer, encoded by the at least one recombinant polynucleotide of claim 1 .
9 . At least one vector comprising the recombinant polynucleotide of claim 1 , wherein the vector is selected from the group consisting of one or more of a DNA vector, an RNA vector, a plasmid, a lentiviral vector, an adenoviral vector, a retroviral vector, and a Sleeping Beauty transposon vector.
10 . A recombinant cell comprising at least one recombinant polynucleotide of claim 1 , wherein the cell is an autologous or allogeneic cell, optionally selected from the group consisting of a T cell, an NKT cell, an NK cell, a hematopoietic stem cell, an embryonic stem cell, and an induced pluripotent stem cell.
11 . A composition comprising a recombinant cell of claim 10 combined with a pharmaceutically acceptable excipient.
12 . A method of treating a disease associated with the expression of a disease-associated antigen in a subject comprising administering to the subject an effective amount of the composition of claim 11 , wherein the disease is selected from the group consisting of a cancer, an autoimmune disease, an infectious disease, an allergic disease, and a degenerative disease, or another disease associated with the expression of a disease-associated antigen.
13 . The composition of claim 11 , further comprising a stem cell wherein one or more target antigens of the zSIR have been deleted or mutated to a form no longer recognized by the zSIR, optionally wherein the one or more target antigens are selected from the group consisting of CD19, CD20, CD22, CD33, CD45, CD123, MPL, CS1, and BCMA.
14 . The composition of claim 13 , wherein the stem cell is an autologous or allogeneic hematopoietic stem cell.
15 . A synthetic immune receptor-CD3-zeta (zSIR) polypeptide heterodimer comprising two CD3-zeta (CD3z) chains, wherein each CD3z chain comprises the transmembrane domain and cytoplasmic domain of a CD3z protein; wherein a variable light (vL) domain of an antibody is operably linked to a first of the two CD3z chains via a first linker and a variable heavy (vH) domain of the antibody is operably linked to a second of the two CD3z chains via a second linker; wherein the first linker comprises an IgCL domain and the second linker comprises an IgCH domain; and wherein the vL domain and the vH domain are from the same antibody and together bind a target antigen recognized by the antibody.
16 . The zSIR polypeptide heterodimer of claim 15 , wherein
the first linker comprises a polypeptide having the sequence of SEQ ID NO: 4027, or a sequence having at least 85% identity thereto, and the second linker comprises a polypeptide having the sequence of any one of SEQ ID NOs: 4028-4037, or a sequence having at least 85% identity thereto.
17 . The zSIR polypeptide heterodimer of claim 15 , wherein one or both of the CD3z chains comprise one or more co-stimulatory domains.
18 . The zSIR polypeptide heterodimer of claim 15 , wherein the CD3z chain comprises a polypeptide having the sequence selected from SEQ ID NOs: 4064, 4066, 4075, 4076, or a polypeptide having an at least 85% sequence identity thereto.
19 . The zSIR polypeptide heterodimer of claim 15 , wherein the vL and vH domains bind to one or more of disease-associated antigens selected from a group consisting of: CD5, CD19, CD123, CD22, CD30, CD171, CS1, BAFF-R, C-type lectin-like molecule-1, CD33, MPL, epidermal growth factor receptor variant III, ganglioside G2, ganglioside GD3, TNF receptor family member B cell maturation antigen, Tn antigen, prostate-specific membrane antigen, receptor tyrosine kinase-like orphan receptor 1, Fms-like tyrosine kinase 3, tumor-associated glycoprotein 72, CD38, CD44v6, glycosylated CD43 epitope expressed on acute leukemia or lymphoma but not on hematopoietic progenitors, glycosylated CD43 epitope expressed on non-hematopoietic cancers, carcinoembryonic antigen, epithelial cell adhesion molecule, B7-H3, KIT, interleukin-13 receptor subunit alpha-2, mesothelin, interleukin-11 receptor alpha, prostate stem cell antigen, protease serine 21, vascular endothelial growth factor receptor 2, Lewis antigen, CD24, platelet-derived growth factor receptor beta, stage-specific embryonic antigen-4, CD20, folate receptor alpha, receptor tyrosine-protein kinase ERBB2, mucin 1, epidermal growth factor receptor, neural cell adhesion molecule, prostase, prostatic acid phosphatase, elongation factor 2 mutated, ephrin B2, fibroblast activation protein alpha, insulin-like growth factor 1 receptor, carbonic anhydrase IX, glycoprotein 100, oncogene fusion protein consisting of breakpoint cluster region and Abelson murine leukemia viral oncogene homolog 1, tyrosinase, ephrin type-A receptor 2, fucosyl GM1, sialyl Lewis adhesion molecule, ganglioside GM3, transglutaminase 5, high molecular weight melanoma-associated antigen, O-acetyl-GD2 ganglioside, tumor endothelial marker 1, tumor endothelial marker 7-related, claudin 6, thyroid-stimulating hormone receptor, G protein-coupled receptor class C group 5 member D, chromosome X open reading frame 61, CD97, CD179a, anaplastic lymphoma kinase, polysialic acid, placenta-specific 1, hexasaccharide portion of Globo H glycoceramide, mammary gland differentiation antigen, uroplakin 2, hepatitis A virus cellular receptor 1, adrenoceptor beta 3, pannexin 3, G protein-coupled receptor 20, lymphocyte antigen 6 complex locus K, olfactory receptor 51E2, TCR gamma alternate reading frame protein, Wilms tumor protein, cancer/testis antigen 1, cancer/testis antigen 2, melanoma-associated antigen 1, ETS translocation variant gene 6, sperm protein 17, X antigen family member 1A, angiopoietin-binding cell surface receptor 2, melanoma cancer-testis antigen 1, melanoma cancer-testis antigen 2, Fos-related antigen 1, tumor protein p53, mutant p53, prostein, survivin, telomerase, prostate carcinoma tumor antigen 1, melanoma antigen recognized by T cells 1, RAS mutant, human telomerase reverse transcriptase, sarcoma translocation breakpoints, melanoma inhibitor of apoptosis, ERG, N-acetylglucosaminyltransferase V, paired box protein Pax-3, androgen receptor, cyclin B1, MYCN, Ras homolog family member C, tyrosinase-related protein 2, cytochrome P450 1B1, CCCTC-binding factor-like, squamous cell carcinoma antigen recognized by T cells 3, paired box protein Pax-5, proacrosin binding protein SP32, lymphocyte-specific protein tyrosine kinase, A-kinase anchor protein 4, synovial sarcoma X breakpoint 2, receptor for advanced glycation end products, renal ubiquitous 1, renal ubiquitous 2, legumain, human papillomavirus E6, human papillomavirus E7, intestinal carboxyl esterase, mutated heat shock protein 70-2, CD79a, CD79b, CD72, leukocyte-associated immunoglobulin-like receptor 1, Fc fragment of IgA receptor, leukocyte immunoglobulin-like receptor subfamily A member 2, CD300 molecule-like family member F, C-type lectin domain family 12 member A, bone marrow stromal cell antigen 2, EGF-like module-containing mucin-like hormone receptor-like 2, lymphocyte antigen 75, glypican-3, Fc receptor-like 5, immunoglobulin lambda-like polypeptide 1, biotin, c-MYC epitope tag, LAMP1, TROP2, GFRα4, CDH17, CDH6, NY-BR1, CDH19, CD200R, sLea, PTK7, gpNMB, CDH1, DLL3, CD179b, TCR gamma-delta, NKG2D, CD32, CSF2RA, TGFβR2, TCR beta1 chain, TCR beta2 chain, TCR gamma chain, TCR delta chain, FITC, luteinizing hormone receptor, follicle-stimulating hormone receptor, chorionic gonadotropin hormone receptor, CCR4, SLAMF6, SLAMF4, HIV-1 envelope glycoprotein, HTLV-1 Tax, CMV pp65, EBV-EBNA3C, influenza A hemagglutinin, GAD, PD-L1, guanylyl cyclase C, KSHV-K8.1 protein, KSHV-gH protein, autoantibody to desmoglein 3, autoantibody to desmoglein 1, HLA-A, HLA-A2, HLA-B, HLA-C, HLA-DP, HLA-DM, HLA-DOA, HLA-DOB, HLA-DQ, HLA-DR, HLA-G, IgE, CD99, RAS G12V, tissue factor 1, alpha-fetoprotein, claudin 18.2, P-glycoprotein, STEAP1, LIV1, NECTIN-4, CRIPTO, GPA33, BST1, low-conductance chloride channel, integrin β7, MUC17, C16ORF54, VISTA, MUC5AC, FCRH5, MMP16, UPK1B, BMPR1B, LY6E, WISP1, and SLC34A2; or any combination thereof.
20 . The zSIR polypeptide heterodimer of claim 15 , wherein the vH and the vL domains comprise:
a vH domain of an antibody having the sequence selected from SEQ ID NOs: 4192-4264, 9662-9691, 11464-11466, and 14417-14446; and
a complementary vL domain of the antibody having the sequence selected from SEQ ID NOs: 4118-4190, 9631-9660, 11460-11462, and 14386-14415; wherein the vH domain and the vL domain are derived from the same antibody.