Synthetic immune receptors and methods of use thereof
The disclosure provides synthetic immune receptors (SIRs), nucleic acids encoding the SIRs, methods of making and using the SIRs, in, for example, adoptive cell therapy.
1. An at least one recombinant polynucleotide encoding a synthetic immune receptor (SIR), wherein the SIR comprises a heterodimer of two T-cell receptor (TCR) constant chains selected from (a)(i) and (a)(ii), (a)(i) and (a)(iii), (a)(iv) and (a)(ii), (a)(iv) and (a)(iii), and (a)(v) and (a)(vi) below, wherein the TCR constant chains of the encoded SIR comprise:
(a) an amino acid sequence selected from the group consisting of:
(i) an amino acid sequence that is at least 85% identical to SEQ ID NO:3010 and has one or more mutations at positions 10, 15, 45, 48, 61, 91, 92, 93, and/or 94;
(ii) an amino acid sequence that is at least 85% identical to SEQ ID NO:3024 and has one or more mutations at positions 15, 17, 18, 22, 57, 59, 77, 79, 133, 136 and/or 139;
(iii) an amino acid sequence that is at least 85% identical to SEQ ID NO: 3025 and has one or more mutations at position 15, 17, 18, 22, 57, 59, 77, 79, 133, 136 and/or 139;
(iv) an amino acid sequence that is at least 85% identical to SEQ ID NO: 3046, 3047 or 3048;
(v) an amino acid sequence that is at least 90% identical to SEQ ID NO:3049; or
(vi) an amino acid sequence that is at least 85% identical to SEQ ID NO: 3051 or 3052; and
(b) an optional linker; and
(c) one or more non-natural TCR antigen binding domain(s) linked to (a) selected from the group consisting of:
(1) an antibody;
(2) an antibody fragment selected from the group consisting of a Fv, a Fab, and a (Fab′)2;
(3) a heavy chain variable region of an antibody (vH domain) and a light chain variable region of an antibody (vL domain) specific for a target antigen, such that one of said vH and vL domains is attached to a first of said two TCR constant chains of (a) and the other of said vH and vL domains is attached to a second of said TCR constant chains of (a);
(4) a single chain variable fragment (scFv);
(5) a single domain antibody (SDAB);
(6) a camelid VHH domain;
(7) a monomeric variable region of an antibody;
(8) a non-immunoglobulin antigen binding scaffold selected from the group consisting of a DARPIN, an affibody, an affilin, an adnectin, an affitin, an obody, a repebody, a fynomer, an alphabody, an avimer, an atrimer, a centyrin, a pronectin, an anticalin, a kunitz domain, an Armadillo repeat protein and a functional fragment thereof;
(9) a receptor or a fragment thereof;
(10) a ligand or a fragment thereof; and
(11) an autoantigen or a fragment thereof.
2. The recombinant polynucleotide of claim 1 , wherein the one or more non-natural TCR antigen binding domains are selected from the group consisting of:
two single chain variable fragments (scFv) specific for one or more target antigens, such that, when expressed, one of said scFv is attached to one of said two chains of said T-cell constant chains and the other of said scFv is attached to the other of said two chains of said T-cell constant chains;
two antibody fragments specific for one or more target antigens, such that, when expressed, one of said antibody fragments is attached to one of said two chains of said T-cell constant chains and the other of said antibody fragments is attached to the other of said two chains of said T-cell constant chains;
two single domain antibody (SDAB) fragments specific for one or more target antigens, such that, when expressed, one of said SDAB fragments is attached to one of said two chains of said T-cell constant chains and the other of SDAB fragments is attached to the other of said two chains of said T-cell constant chains;
two camelid vHH domains specific for one or more target antigens, such that, when expressed, one of said vHH domains is attached to one of said two chains of said T-cell constant chains and the other of vHH domains is attached to the other of said two chains of said T-cell constant chains;
two non-immunoglobulin antigen binding scaffolds specific for one or more-target antigens, such that, when expressed, one of said non-immunoglobulin antigen binding scaffolds is attached to one of said two chains of said T-cell constant chains and the other of said non-immunoglobulin antigen binding scaffolds domains is attached to the other of said two chains of said T-cell constant chains;
two receptors or a fragment thereof specific for one or more target antigens, such that, when expressed, one of said receptors or a fragment thereof is attached to one of said two chains of said T-cell constant chains and the other of said receptors or a fragment thereof is attached to the other of said two chains of said T-cell constant chains;
two ligands or a fragment thereof specific for one or more target antigens, such that, when expressed, one of said ligands or a fragment thereof is attached to one of said two chains of said T-cell constant chains and the other of said ligands or a fragment thereof is attached to the other of said two chains of said T-cell constant chains;
two structurally distinct antigen binding fragments specific for one or more-target antigens, such that, when expressed, one of said antigen binding fragments is attached to one of said two chains of said T-cell constant chains and the other of said antigen binding fragments is attached to the other of said two chains of said T-cell constant chains;
two autoantigens or fragments thereof, such that, when expressed, one of said autoantigens or fragments thereof is attached to one of said two chains of said T-cell constant chains and the other of said autoantigens or fragments thereof is attached to the other of said two chains of said T-cell constant chains.
3. The recombinant polynucleotide of claim 1 , wherein the polynucleotide encoding the TCR constant chain of (a) encodes a TCR constant chain(s) wherein the one or more mutations enhance the expression and/or pairing of TCR constant chains and reduce their pairing with the endogenous T cell receptor chains, wherein the one or more mutations are selected from the group consisting of:
(i) codon-optimization;
(ii) a nucleic acid sequence encoding the amino acid sequence of (a)(i), wherein said nucleic acid sequence comprises SEQ ID NO: 730 to 743 with 1-40 modifications;
(iii) a nucleic acid sequence encoding the amino acid sequence of (a)(ii) or (a)(iii), wherein said nucleic acid sequence comprises SEQ ID NO: 744 to 765 with 1-40 modifications;
(iv) a nucleic acid sequence encoding the amino acid sequence of (a)(v), wherein said nucleic acid sequence comprises SEQ ID NO: 769 to 770 with 1-40 modifications;
(v) a nucleic acid sequence encoding the amino acid sequence of (a)(vi), wherein said nucleic acid sequence comprises SEQ ID NO: 771 to 772 with 1-40 modifications; and
(vi) a nucleic acid sequence encoding the amino acid sequence of (a)(iv), wherein said nucleic acid sequence comprises SEQ ID NO: 766 to 768 with 1-40 modifications.
4. The recombinant polynucleotide of claim 1 , wherein said one or more non-natural TCR antigen binding domain(s) binds to an antigen selected from a group consisting of: CD19; CDS; CD123; CD22; CD30; CD171; CS-1 (also referred to as CCD2 subset 1, CRACC, SLAMF7, CD319, and 19A24); C-type lectin-like molecule-1 (CLL-1 or CLECL1); CD33; epidermal growth factor receptor variant Ill (EGFRviii); ganglioside G2 (GD2); ganglioside GD3; TNF receptor family member B cell maturation (BCMA); Tn antigen ((Tn Ag) or (GalNAca-Ser/Thr)); prostate-specific membrane antigen (PSMA); Receptor tyrosine kinase-like orphan receptor 1 (ROR1); Fms Like Tyrosine Kinase 3 (FLT3); Tumor-associated glycoprotein 72 (TAG72); CD38; CD44v6; a glycosylated CD43 epitope expressed on acute leukemia or lymphoma but not on hematopoietic progenitors; a glycosylated CD43 epitope expressed on non-hematopoietic cancers; Carcinoembryonic antigen (CEA); Epithelial cell adhesion molecule (EPCAM); B7H3 (CD276); KIT (CD117); Interleukin-13 receptor subunit alpha-2 (IL-13Ra2 or CD213A2); Mesothelin; Interleukin 11 receptor alpha (IL-IIRa); prostate stem cell antigen (PSCA); vascular endothelial growth factor receptor 2 (VEGFR2); Lewis(Y) antigen; CD24; Platelet-derived growth factor receptor beta (PDGFR-beta); Stage-specific embryonic antigen-4 (SSEA-4); CD20; Folate receptor alpha; Receptor tyrosine-protein kinase ERBB2 (Her2/neu); Mucin 1, cell surface associated (MUC1); epidermal growth factor receptor (EGFR); neural cell adhesion molecule (NCAM); carbonic anhydrase IX (CAIX); tyrosinase; Fucosyl GM1; sialyl Lewis adhesion molecule (sLe); ganglioside GM3; transglutaminase 5 (TGS5); high molecular weight-melanoma associated antigen (HMWMAA); claudin 6 (CLDN6); thyroid stimulating hormone receptor (TSHR); G protein coupled receptor class C group 5, member D (GPRC5D); chromosome X open reading frame 61 (CXORF61); CD97; CD179a; anaplastic lymphoma kinase (ALK); mammary gland differentiation antigen (NY-BR-1); Wilms tumor protein (WT1); Cancer/testis antigen 1 (NY-ES0-1); Melanoma-associated antigen 1 (MAGE-A1); melanoma antigen recognized by T cells 1 (MelanA or MARTI); Rat sarcoma (Ras) mutant; human Telomerase reverse transcriptase (hTERT); human papilloma virus E6 (HPV E6); human papilloma virus E7 (HPV E7); CD79a; CD79b; CD72; Leukocyte-associated immunoglobulin-like receptor 1 (LAIRI); C-type lectin domain family 12 member A (CLEC12A); EGF-like module-containing mucin-like hormone receptor-like 2 (EMR2); lymphocyte antigen 75 (LY75); Glypican-3 (GPC3); Fe receptor-like 5 (FCRL5); immunoglobulin lambda-like polypeptide 1 (IGLLI); MPL; Biotin; c-MYC epitope Tag; CD34; LAMP1 TROP2; GFRalpha4; CDH17; CDH6; CDH19; CD200R; Slea (CA19.9; Sialyl Lewis Antigen) Fucosyl-GM1; PTK7; CDH1-CD324; DLL3; CD276/B7H3; IL11Ra; IL13Ra2; CD179b-1GL11; TCR gamma-delta; NKG2D; CD32 (FCGR2A); CSPG4-HMW-MAA; Tim1-/HVCR1; CSF2RA (GM-CSFR-alpha); TGFbetaR2; VEGFR2/KDR; Lewis Ag; TCR-beta1 chain; TCR-beta2 chain; TCR-gamma chain; TCR-delta chain; FITC; Luteinizing hormone receptor (LHR); Follicle stimulating hormone receptor (FSHR); Chorionic Gonadotropin Hormone receptor (CGHR); CCR4; GD3; SLAMF6; SLAMF4; HIV1 envelope glycoprotein; HTLV1-Tax; CMV pp65; EBV-EBNA3c; influenza A hemagglutinin (HA); GAD; PDL1; Guanylyl cyclase C (GCC); KSHV-K8.1 protein; KSHV-gH protein; auto antibody to desmoglein 3 (Dsg3); autoantibody to desmoglein 1 (Dsg1); HLA-A2; HLA-B; HLA-C; HLA-DP; HLA-DM; HLA-DOA; HLA-DOB; HLA-DQ; HLA-DR; HLA-G; IGE; CD99; Lym1; Lym2; RAS G12V; Tissue Factor 1 (TF1); AFP; GPRC5D; claudin18.2 (CLD18A2 OR CLDN18A.2); STEAP1; LIV1; NECTIN-4; CRIPTO; GPA33; BST1/CD157; low conductance chloride channel; and antigen recognized by TNT antibody.
5. The recombinant polynucleotide of claim 4 , wherein said one or more non-natural TCR antigen binding domain(s) is selected from the group consisting of:
(i) a heavy chain variable region (vH) encoded by a polynucleotide having a sequence of SEQ ID NO: 226 to 400 or 10203 to 10321 or a sequence with at least 95% identity thereto that contains the complementarity determining regions (CDRs) of SEQ ID NO: 226 to 400 or 10203 to 10321 and which encodes a polypeptide that binds to its antigen; and a complementary a light chain variable region (vL) encoded by a polynucleotide having a sequence of SEQ ID NO: 16 to 191 or 10085 to 10202 or a sequence with at least 95% identity thereto that contains the complementarity determining regions (CDRs) of SEQ ID NO: 16 to 191 or 10085 to 10202 and which encodes a polypeptide that binds to its antigen;
(ii) a single chain variable fragment (scFv) encoded by a polynucleotide having a sequence of SEQ ID NO: 488 to 657, 10346 to 10400 or 18098 to 18160 or a sequence with at least 95% identity thereto that contains the complementarity determining regions (CDRs) of SEQ ID NO: 488 to 657, 10346 to 10400 or 18098 to 18160 and which encodes a polypeptide that binds to its antigen;
(iii) a camelid VHH domain encoded by a polynucleotide having a sequence of SEQ ID NO: 421 to 445 or 10322 to 10337 or a sequence with at least 95% identity thereto that contains the complementarity determining regions (CDRs) of SEQ ID NO: 421 to 445 or 10322 to 10337 and which encodes a polypeptide that binds to its antigen;
(iv) a non-immunoglobulin scaffold encoded by a polynucleotide having a sequence of SEQ ID NO: 439 to 443 or a sequence with at least 95% identity thereto and which encodes a polypeptide that binds to its antigen;
(v) a receptor encoded by a polynucleotide having a sequence of SEQ ID NO: 456 to 468 or a sequence with at least 95% identity thereto and which encodes a polypeptide that binds to its cognate;
(vi) a ligand encoded by a polynucleotide having a sequence of SEQ ID NO: 476 to 486 or 10402 to 10404 or a sequence with at least 95% identity thereto and which encodes a polypeptide that binds to its cognate; and
(vii) a light chain variable region (VL) that comprises three light chain complementary determining regions for a selected target antigen as set forth in-any of SEQ ID NO: 13999 to 14879 or 14880 and a complementary heavy chain variable region (VH) that comprises three heavy chain complementary determining regions for a selected target antigen as set forth SEQ ID NO: 14881 to 15761 or 15762.
6. The recombinant polynucleotide of claim 4 , wherein said one or more non-natural TCR antigen binding domain(s) bind to CD19 and comprise a polypeptide sequence selected from the group consisting of:
(i) a polypeptide comprising a sequence that is at least 95% identical to SEQ ID NO: 2318-2324, 12060-12068, 12108, 12127, or 12156 and that contains the complement determining regions (CDRs) of SEQ ID NO: 2318-2324, 12060-12068, 12108, 12127, or 12156;
(ii) a polypeptide comprising a sequence that is at least 95% identical to SEQ ID NO: 2517-2523, 12178-12186, 12227, 12246 or 12275 and that contains the complement determining regions (CDRs) of SEQ ID NO: 2517-2523, 12178-12186, 12227, 12246 or 12275;
(iii) a polypeptide comprising a sequence that is at least 95% identical to SEQ ID NO: 12288 and that contains the complementarity determining regions (CDRs) of SEQ ID NO: 12288; and
(iv) a polypeptide comprising a sequence that is at least 95% identical to SEQ ID NO: 2770-2774, 12325, 12308, 18162-18170 or 12354 and that contains the complementarity determining regions (CDRs) of SEQ ID NO: 2770-2774, 12325, 12308, 18162-18170 or 12354.
7. The recombinant polynucleotide of claim 6 , wherein the recombinant polynucleotide encodes a polypeptide comprising a sequence selected from the group consisting of SEQ ID Nos: 3135-3235, 3250-3346, 3396, 3401-3403, 3406, 3429-3432, 3435-3439, 3540, 3855-3859, 12431-12489, 12491-12493, 12495-12530, 12534, 13195-13203, 13249, 13267, 13289, 13429-13437, 13483, 13501, 13523, 3645-3647, 13312-13314, 13317-13320, 13366, 13406, 4069-4072, 13546-13549, 13553-13554, 13600, 13640, 4284-4287, 13665-13668, 13671-13673, 13719, 13759, 6044-6046, 6048, 13782-13785, 13788-13790, 13836, 13876, 7094-7097, 16595-16598, 16601-16603, 16649, 16689, 7304-7308, 17999-18002, 18005-18007, 18053, 18093, 12553-12555, 12557, 12765-12768, 12771-12773, 12819, 12859, 12865-12867, 12869, 13077-13080, 13083-13086, 13131, 13171, 16478-16481, 16484-16486, 16649, 16689, 18239-18240, 19248-19250, 19252, 19460-19463, 19466-19468, 19514 and 19554.
8. The recombinant polynucleotide of claim 1 , wherein said one or more non-natural TCR antigen binding domain(s) are selected from the group consisting of:
(i) a variable light (vL) domain comprising a sequence SEQ ID NO: 2307 to 2482 or 12042 to 12159 having up to 10 conservative amino acid substitutions and that contains the complementarity determining regions (CDRs) of SEQ ID NO: 2307 to 2482 or 12042 to 12159; and a complementary variable heavy (vH) domain comprising a sequence of SEQ ID NO: 2506 to 2680 or 12160 to 12278 having up to 10 conservative amino acid substitutions and that contains the complementarity determining regions (CDRs) of SEQ ID NO: 2506 to 2680 or 12160 to 12278;
(ii) one or more of camelid vHH domains as set forth in SEQ ID NO: 2701 to 2725 or 12279 to 12294 having up to 10 conservative amino acid substitutions and that contains the complementarity determining regions (CDRs) of SEQ ID NO: 2701 to 2725 or 12279 to 12294 and which binds to its antigen;
(iii) a non-immunoglobulin antigen binding domain having a sequence as set forth in SEQ ID NO: 2728-2732 or 12296 to 12301 and having up to 10 conservative amino acid substitutions and which binds to its antigen;
(iv) an scFv domain comprising three light chain complementary determining regions of a variable light (vL) domain comprising a sequence of SEQ ID NO: 2307 to 2482 or 12042 to 12159 and three heavy chain complementary determining regions of a variable heavy (vH) domain comprising a sequence of SEQ ID NO: 2506 to 2680 or 12160 to 12278;
(v) an scFv fragment having a sequence selected from the group consisting of SEQ ID NO: 2770 to 2939, 12303 to 12357 or 18162 to 18224 each having up to 10 conservative amino acid substitutions and that contains the complementarity determining regions (CDRs) of SEQ ID NO: 2770 to 2939, 12303 to 12357 or 18162 to 18224 and which binds to its antigen;
(vi) one or more receptors comprising the amino acid sequence of SEQ ID NO: 2736 to 2748 having up to 10 conservative amino acid substitutions;
(vii) one or more ligands comprising the sequence of SEQ ID NO: 2758-2768 or 12359 to 12361 having up to 10 conservative amino acid substitutions;
(viii) an extracellular domain of CD16A, NKG2D, CD4, PD1, desmoglein 3 (Dsg3), or CD4-DC-SIGN;
(ix) an extracellular domain of one or more of hTPO, mTPO, CGHα chain, CGHβ chain, FHβ chain, LHβ chain, TSHβ chain, APRIL or a combination thereof, and
(x) any combination of (i)-(ix).
9. The at least one recombinant polynucleotide of claim 1 , wherein the at least one polynucleotide further comprises a sequence encoding an accessory module and/or a therapeutic control, wherein the accessory module or therapeutic control is selected from the group consisting of 41BBL; CD40L; K13; MC159; cFLIP-L/MRITa; cFLIP-p22; HTLV1 Tax; HTLV2 Tax; HTLV2 Tax-RS mutant; FKBPx2-K13; FKBPx2-HTLV2-Tax; FKBPx2-HTLV2-Tax-RS; IL6R-304-vHH-Alb8-vHH; IL12f; PD1-4H1 scFV; PD1-5C4 scFV; PD1-4H1-Alb8-vHH; PD1-5C4-Alb8-vHH; CTLA4-Ipilimumab-scFv; CTLA4-Ipilimumab-Alb8-vHH; IL6-19A-scFV; IL6-19A-scFV-Alb8-vHH; sHVEM; sHVEM-Alb8-vHH; hTERT; Fx06; CD3z; CD3z-GGGS-41BB; CD3-BBz; CD3-CD28z; CD3-CD28-Lck fusion protein; shRNA targeting Brd4; chimeric antigen receptor (CAR); hTERT; heparinase; a costimulatory molecule; a CAR comprising an antigen binding domain, a transmembrane domain and a primary signaling domain; a CAR comprising an antigen binding domain, a transmembrane domain and a costimulatory domain; a CAR comprising an antigen binding domain, a transmembrane domain, a primary signaling domain and a costimulatory domain; a chimeric cytokine receptor (CCR); a cytokine; a chemokine; IL2; IL-7; IL-15; IL-21; an agent that increases the expression and/or activity of SIR chains, wherein optionally the agent is CD3ζ, CD3δ, CD3ε, CD3γ or combination thereof; a truncated epidermal growth factor receptor (tEGFR); a truncated epidermal growth factor receptor viii (tEGFRviii); a truncated CD30 (tCD30); a truncated BCMA (tBCMA); a truncated CD19 (tCD19); CD34, thymidine kinase; cytosine deaminase; nitroreductase; xanthine-guanine phosphoribosyl transferase; human caspase 8; human caspase 9; inducible caspase 9 (icaspase9); purine nucleoside phosphorylase; linamarase/linamarin/glucose oxidase; deoxyribonucleoside kinase; horseradish peroxidase (HRP)/indole-3-acetic (IAA); Gamma-glutamylcysteine synthetase; CD20/alphaCD20; CD34/thymidine kinase chimera; dox-dependent caspase-2; mutant thymidine kinase (HSV-TKSR39); AP1903/Fas system; selection marker; dihydroxyfolate receptor (DHFR); mutant DHFR; methylated-DNA-protein-cysteine methyltransferase; inosine monophosphate dehydrogenase II (IMDHP2); puromycin acetyle transferase (PAC); blasticidin-resistance gene; mutant calcinueurin a/b (Can/b); CNa12; CNb30; a suicide gene; an agent that inhibits an inhibitory molecule; an agent that promotes the proliferation, persistence, expansion and activation of a SIR-expressing cell; an agent that inhibits the expression of one or more target antigens of SIR; an agent that mutates one or more target antigens of SIR; and combination thereof.
10. At least one vector comprising the at least one recombinant polynucleotide of claim 1 , wherein the vector is selected from the group consisting of a DNA vector, an RNA vector, a plasmid, a lentivirus vector, adenoviral vector, a retrovirus vector, a baculovirus vector, a sleeping beauty transposon vector, and a piggyback transposon vector.
11. A recombinant immune effector cell or stem cell that can differentiate into an immune effector cell comprising at least one recombinant polynucleotide of claim 1 .
12. The recombinant polynucleotide of claim 1 , wherein the encoded SIR comprises a heterodimer of two T-cell receptor (TCR) constant chains comprising the amino acid sequences of SEQ ID NOs: 3010 and 3024 with mutations at the following amino acid positions:
a) SEQ ID NO: 3010 with 48C and SEQ ID NO: 3024 with 57C; or
b) SEQ ID NO: 3010 with 15C and SEQ ID NO: 3024 with 15C; or
c) SEQ ID NO: 3010 with 45C and SEQ ID NO: 3024 with 59C; or
d) SEQ ID NO: 3010 with 45C and SEQ ID NO: 3024 with 77C; or
e) SEQ ID NO: 3010 with 10C and SEQ ID NO: 3024 with 17C; or
f) SEQ ID NO: 3010 with 91S, 92D, 93V and/or 94P and any of the forgoing mutations listed for SEQ ID NO: 3010 in (a)-(e), and SEQ ID NO: 3024 with 18K/R, 22A, 133I, 136A and/or 139H and any of the forgoing mutations listed for SEQ ID NO: 3024 in (a)-(e); or
g) SEQ ID NO: 3010 with 61R and SEQ ID NO: 3024 with 79G; or
h) any combination of mutations set forth in (a)-(g).
13. An isolated synthetic immune receptor (SIR) polypeptide heterodimer wherein SIR polypeptide heterodimer comprises two T-cell receptor (TCR) constant chains selected from (a)(i) and (a)(ii), (a)(i) and (a)(iii), (a)(iv) and (a)(ii), (a)(iv) and (a)(iii), and (a)(v) and (a)(vi) below, wherein the TCR constant chains comprise:
(a) an amino acid sequence selected from the group consisting of:
(i) an amino acid sequence that is at least 85% identical to SEQ ID NO:3010 and has one or more mutations at positions 10, 15, 45, 48, 61, 91, 92, 93, and/or 94;
(ii) an amino acid sequence that is at least 85% identical to SEQ ID NO:3024 and has one or more mutations at positions 15, 17, 18, 22, 57, 59, 77, 79, 133, 136 and/or 139;
(iii) an amino acid sequence that is at least 85% identical to SEQ ID NO: 3025 and has one or more mutations at position 15, 17, 18, 22, 57, 59, 77, 79, 133, 136 and/or 139;
(iv) an amino acid sequence that is at least 85% identical to SEQ ID NO: 3046, 3047 or 3048;
(v) an amino acid sequence that is at least 90% identical to SEQ ID NO:3049;
(vi) an amino acid sequence that is at least 85% identical to SEQ ID NO: 3051 or 3052; and
(b) an optional linker; and
(c) one or more non-natural TCR antigen binding domain(s) linked to (a) selected from the group consisting of:
(1) an antibody;
(2) an antibody fragment selected from the group consisting of a Fv, a Fab, and a (Fab′)2;
(3) a heavy chain variable region of an antibody (vH domain) and a light chain variable region of an antibody (vL domain) specific for a target antigen, such that one of said vH and vL domains is attached to a first of said two TCR constant chains of (a) and the other of said vH and vL domains is attached to a second of said TCR constant chains of (a);
(4) a single chain variable fragment (scFv);
(5) a single domain antibody (SDAB);
(6) a camelid VHH domain;
(7) a monomeric variable region of an antibody;
(8) a non-immunoglobulin antigen binding scaffold selected from the group consisting of a DARPIN, an affibody, an affilin, an adnectin, an affitin, an obody, a repebody, a fynomer, an alphabody, an avimer, an atrimer, a centyrin, a pronectin, an anticalin, a kunitz domain, an Armadillo repeat protein and a functional fragment thereof;
(9) a receptor or a fragment thereof;
(10) a ligand or a fragment thereof, and;
(11) an autoantigen or a fragment thereof.
14. The isolated synthetic immune receptor (SIR) polypeptide heterodimer of claim 13 , wherein the one or more non-natural TCR antigen binding domains are selected from the group consisting of:
two single chain variable fragments (scFv) specific for one or more target antigens, such that, when expressed, one of said scFv is attached to one of said two chains of said T-cell constant chains and the other of said scFv is attached to the other of said two chains of said T-cell constant chains;
two antibody fragments specific for one or more target antigens, such that, when expressed, one of said antibody fragments is attached to one of said two chains of said T-cell constant chains and the other of said antibody fragments is attached to the other of said two chains of said T-cell constant chains;
two single domain antibody (SDAB) fragments specific for one or more target antigens, such that, when expressed, one of said SDAB fragments is attached to one of said two chains of said T-cell constant chains and the other of SDAB fragments is attached to the other of said two chains of said T-cell constant chains;
two camelid vHH domains specific for one or more target antigens, such that, when expressed, one of said vHH domains is attached to one of said two chains of said T-cell constant chains and the other of vHH domains is attached to the other of said two chains of said T-cell constant chains;
two non-immunoglobulin antigen binding scaffolds specific for one or more target antigens, such that, when expressed, one of said non-immunoglobulin antigen binding scaffolds is attached to one of said two chains of said T-cell constant chains and the other of said non-immunoglobulin antigen binding scaffolds domains is attached to the other of said two chains of said T-cell constant chains;
two receptors or a fragment thereof specific for one or more target antigens, such that, when expressed, one of said receptors or a fragment thereof is attached to one of said two chains of said T-cell constant chains and the other of said receptors or a fragment thereof is attached to the other of said two chains of said T-cell constant chains;
two ligands or a fragment thereof specific for one or more target antigens, such that, when expressed, one of said ligands or a fragment thereof is attached to one of said two chains of said T-cell constant chains and the other of said ligands or a fragment thereof is attached to the other of said two chains of said T-cell constant chains;
two structurally distinct antigen binding fragments specific for one or more target antigens, such that, when expressed, one of said antigen binding fragments is attached to one of said two chains of said T-cell constant chains and the other of said antigen binding fragments is attached to the other of said two chains of said T-cell constant chains;
two autoantigens or fragments fragment thereof, such that, when expressed, one of said autoantigens or fragments thereof is attached to one of said two chains of said T-cell constant chains and the other of said autoantigens or fragments thereof is attached to the other of said two chains of said T-cell constant chains.
15. The isolated synthetic immune receptor (SIR) polypeptide heterodimer of claim 13 , comprising:
a TCR constant domain of (i), (ii), (iii), (iv), (v), or (vi) wherein the one or more non-natural TCR binding domains are selected from the group consisting of:
a variable region of the heavy chain (vH) of an antibody specific for a target antigen and a variable region of the light chain (vL) of an antibody specific for a target antigen;
a single chain variable fragment (scFv) specific for a target antigen;
an antibody fragment selected from the group consisting of Fv, a Fab, and a (Fab′)2 specific for a target antigen;
a single domain antibody (SDAB) fragment specific for a target antigen;
a camelid vHH domain specific for a target antigen;
a non-immunoglobulin antigen binding scaffold specific for a target antigen;
a receptor specific for a target antigen or fragments thereof;
a ligand specific for a target antigen or fragments thereof, and
an autoantigen or a fragment thereof.
16. The isolated synthetic immune receptor (SIR) polypeptide heterodimer of claim 13 , wherein the one or more mutations in the TCR constant chains of (a)(i) to (a)(iii) enhance the expression and/or pairing of TCR constant chains and reduce their pairing with endogenous T cell receptor chains.
17. The isolated synthetic immune receptor (SIR) polypeptide heterodimer of claim 13 , wherein said one or more non-natural TCR antigen binding domain(s) binds to an antigen selected from the group consisting of: CD19; CD5; CD123; CD22; CD30; CD171; CS-1 (also referred to as CD2 subset 1, CRACC, SLAMF7, CD319, and 19A24); C-type lectin-like molecule-1 (CLL-1 or CLECL1); CD33; epidermal growth factor receptor variant III (EGFRviii); ganglioside G2 (GD2); ganglioside GD3; TNF receptor family member B cell maturation (BCMA); Tn antigen ((Tn Ag) or (GalNAca-Ser/Thr)); prostate-specific membrane antigen (PSMA); Receptor tyrosine kinase-like orphan receptor 1 (ROR1); Fms Like Tyrosine Kinase 3 (FLT3); Tumor-associated glycoprotein 72 (TAG72); CD38; CD44v6; a glycosylated CD43 epitope expressed on acute leukemia or lymphoma but not on hematopoietic progenitors; a glycosylated CD43 epitope expressed on non-hematopoietic cancers; Carcinoembryonic antigen (CEA); Epithelial cell adhesion molecule (EPCAM); B7H3 (CD276); KIT (CD117); Interleukin-13 receptor subunit alpha-2 (IL-13Ra2 or CD213A2); Mesothelin; Interleukin 11 receptor alpha (IL-11Ra); prostate stem cell antigen (PSCA); vascular endothelial growth factor receptor 2 (VEGFR2); Lewis (Y) antigen; CD24; Platelet-derived growth factor receptor beta (PDGFR-beta); Stage-specific embryonic antigen-4 (SSEA-4); CD20; Folate receptor alpha; Receptor tyrosine-protein kinase ERBB2 (Her2/neu); Mucin 1, cell surface associated (MUC1); epidermal growth factor receptor (EGFR); neural cell adhesion molecule (NCAM); carbonic anhydrase IX (CAIX); tyrosinase; Fucosyl GM1; sialyl Lewis adhesion molecule (sLe); ganglioside GM3; transglutaminase 5 (TGS5); high molecular weight-melanoma associated antigen (HMWMAA); claudin 6 (CLDN6); thyroid stimulating hormone receptor (TSHR); G protein coupled receptor class C group 5, member D (GPRC5D); chromosome X open reading frame 61 (CXORF61); CD97; CD179a; anaplastic lymphoma kinase (ALK); mammary gland differentiation antigen (NY-BR-1); Wilms tumor protein (WT1); Cancer/testis antigen 1 (NY-ES0-1); Melanoma-associated antigen 1 (MAGE-A1); melanoma antigen recognized by T cells 1 (MelanA or MARTI); Rat sarcoma (Ras) mutant; human Telomerase reverse transcriptase (hTERT); human papilloma virus E6 (HPV E6); human papilloma virus E7 (HPV E7); CD79a; CD79b; CD72; Leukocyte-associated immunoglobulin-like receptor 1 (LAIRI); C-type lectin domain family 12 member A (CLEC12A); EGF-like module-containing mucin-like hormone receptor-like 2 (EMR2); lymphocyte antigen 75 (LY75); Glypican-3 (GPC3); Fc receptor-like 5 (FCRL5); immunoglobulin lambda-like polypeptide 1 (IGLLI); MPL; Biotin; c-MYC epitope Tag; CD34; LAMP1 TROP2; GFRalpha4; CDH17; CDH6; CDH19; CD200R; Slea (CA19.9; Sialyl Lewis Antigen) Fucosyl-GM1; PTK7; CDH1-CD324; DLL3; CD276/B7H3; IL11Ra; IL13Ra2; CD179b-IGLI1; TCR gamma-delta; NKG2D; CD32 (FCGR2A); CSPG4-HMW-MAA; Tim1-/HVCR1; CSF2RA (GM-CSFR-alpha); TGFbetaR2; VEGFR2/KDR; Lewis Ag; TCR-beta1 chain; TCR-beta2 chain; TCR-gamma chain; TCR-delta chain; FITC; hormone receptor (LHR); Follicle stimulating hormone receptor (FSHR); Chorionic Gonadotropin Hormone receptor (CGHR); CCR4; GD3; SLAMF6; SLAMF4; HIV1 envelope glycoprotein; HTLV1-Tax; CMV pp65; EBV-EBNA3c; influenza A hemagglutinin (HA); GAD; PDL1; Guanylyl cyclase C (GCC); KSHV-K8.1 protein; KSHV-gH protein; auto antibody to desmoglein 3 (Dsg3); autoantibody to desmoglein 1 (Dsg1); HLA-A2; HLA-B; HLA-C; HLA-DP; HLA-DM; HLA-DOA; HLA-DOB; HLA-DQ; HLA-DR; HLA-G; IGE; CD99; Lym1; Lym2; RAS G12V; Tissue Factor 1 (TF1); AFP; GPRC5D; claudin18.2 (CLD18A2 OR CLDN18A.2); STEAP1; LIV1; NECTIN-4; CRIPTO; GPA33; BST1/CD157; low conductance chloride channel; and antigen recognized by TNT antibody.
18. The isolated synthetic immune receptor (SIR) polypeptide heterodimer of claim 17 , wherein said one or more non-natural TCR antigen binding domain(s) is selected from the group consisting of:
(i) a heavy chain variable region (vH) comprising a sequence as set forth in SEQ ID NO: 2506 to 2680 or 12160 to 12278 or a sequence with at least 95% identity thereto that contains the CDRs of SEQ ID NO: 2506 to 2680 or 12160 to 12278 and which binds to its antigen; and a complementary light chain variable region (vL) comprising a sequence as set forth SEQ ID NO: 2307 to 2482 or 12042 to 12159 or a sequence with at least 95% identity thereto that contains the CDRs of SEQ ID NO: 2307 to 2482 or 12042 to 12159 and which binds to its antigen;
(ii) a single chain variable fragment (scFv) comprising a sequence as set forth in SEQ ID NO: 2770 to 2939, 12303 to 12357, or 18162 to 18224 or a sequence with at least 95% identity thereto that contains the CDRs of SEQ ID NO: 2770 to 2939, 12303 to 12357, or 18162 to 18224 and which binds to its antigen;
(iii) a camelid VHH domain comprising a sequence as set forth in SEQ ID NO: 2701 to 2725 or 12279 to 12294 or a sequence with at least 95% identity thereto that contains the CDRs of SEQ ID NO: 2701 to 2725 or 12279 to 12294 and which binds to its antigen;
(iv) a non-immunoglobulin scaffold encoded by a polynucleotide of SEQ ID NO: 439 to 443 or a sequence with at least 95% identity thereto that contains the CDRs of SEQ ID NO: 439 to 443 and which binds to its antigen;
(v) a receptor comprising a sequence as set forth in SEQ ID NO: 2736 to 2748 or a sequence with at least 95% identity thereto and which binds to its cognate;
(vi) a ligand comprising a sequence as set forth in SEQ ID NO: 2758 to 2768 or 12359 to 12361 or a sequence with at least 95% identity thereto that contains the CDRs of SEQ ID NO: 2758 to 2768 or 12359 to 12361 and which binds to its cognate; and
(vii) a light chain variable region (vL) comprising three light chain complementary determining regions for a selected target antigen as set forth in SEQ ID NO: 13999 to 14879 or 14880 and a complementary heavy chain variable region (VH) comprising three heavy chain complementary determining regions for a selected target antigen as set forth in SEQ ID NO: 14881 to 15761 or 15762.
19. The isolated synthetic immune receptor (SIR) polypeptide heterodimer of claim 13 , wherein said one or more non-natural TCR antigen binding domain(s) are selected from the group consisting of:
(i) a variable light (vL) domain comprising a sequence of SEQ ID NO: 2307 to 2482 or 12042 to 12159 having up to 10 conservative amino acid substitutions that contains the CDRs of SEQ ID NO: 2307 to 2482 or 12042 to 12159; and a complementary variable heavy (vH) domain comprising a sequence SEQ ID NO: 2506 to 2680 or 12160 to 12278 having up to 10 conservative amino acid substitutions that contains the CDRs of SEQ ID NO: 2506 to 2680 or 12160 to 12278;
(ii) one or more of camelid vHH domains as set forth in SEQ ID NO: 2701 to 2725 or 12279 to 12294 having up to 10 conservative amino acid substitutions that contains the CDRs of SEQ ID NO: 2701 to 2725 or 12279 to 12294;
(iii) a non-immunoglobulin antigen binding domain having a sequence as set forth in SEQ ID NO: 2728-2732 or 12296 to 12301 and having up to 10 conservative amino acid substitutions;
(iv) an scFv domain comprising three light chain complementary determining regions of a variable light (vL) domain comprising a sequence of SEQ ID NO: 2307 to 2482 or 12042 to 12159 and three heavy chain complementary determining regions of a variable heavy (vH) domain comprising a sequence of SEQ ID NO: 2506 to 2680 or 12160 to 12278;
(v) an scFv fragment having a sequence selected from the group consisting of SEQ ID NO: 2770 to 2939, 12303 to 12357 or 18162 to 18224 each having up to 10 conservative amino acid substitutions and containing the CDRs of SEQ ID NO: 2770 to 2939, 12303 to 12357 or 18162 to 18224;
(vi) one or more receptors comprising the amino acid sequence of SEQ ID NO: 2736 to 2748 having up to 10 conservative amino acid substitutions;
(vii) one or more ligands comprising the sequence of SEQ ID NO: 2758-2768 or 12359 to 12361 having up to 10 conservative amino acid substitutions;
(viii) an extracellular domain of CD16A, NKG2D, CD4, PD1, desmoglein 3 (Dsg3), or CD4-DC-SIGN;
(ix) an extracellular domain of one or more of hTPO, mTPO, CGHα chain, CGHβ chain, FHβ chain, LHβ chain, TSHβ chain, APRIL or a combination thereof; and
(x) any combination of (i)-(ix).
20. A recombinant immune effector cell or stem cell that can differentiate into an immune effector cell comprising at least one polypeptide heterodimer of claim 13 .
21. The recombinant immune effector cell or stem cell that can differentiate into an immune effector cell of claim 20 or 11 , wherein (a) the immune effector cell is selected from the group consisting of an alpha/beta T cell, a gamma/delta T cell, regulatory T cell (TREG), CD8+ T cell, a CD4+ T cell, B cell, natural killer (NK) cell, natural killer T (NKT) cell, synthetic T cell, and a myeloid-derived phagocyte; (b) the stem cell is selected from the group consisting of a hematopoietic stem cell, a peripheral blood stem cell, a bone marrow derived stem cell, an immune stem cell, a lymphoid stem cell, embryonic stem cell, and an induced pluripotent stem cell (iPSC); or (c) the immune effector cell of (a) or stem cell of (b) is autologous, allogeneic, syngeneic or xenogeneic.
22. The recombinant immune effector cell or stem cell that can differentiate into an immune effector cell of claim 20 , wherein the immune effector cell further comprises:
(a) at least one chimeric antigen receptor (CAR) polypeptide, wherein the CAR comprises:
(i) an antigen binding domain, a transmembrane domain and an intracellular domain of an inhibitory molecule,
(ii) an antigen binding domain, a transmembrane domain, and a primary signaling domain,
(iii) an antigen binding domain, a transmembrane domain, a costimulatory signaling domain but no primary signaling domain, or
(iv) an antigen binding domain, a transmembrane domain, a primary signaling domain and a costimulatory domain;
(b) reduced or eliminated expression of an endogenous TCR;
(c) reduced or eliminated expression of one or more subunits that comprise a functional endogenous TCR;
(d) lacks expression of one or more TCR chains selected from the group consisting of TCRa, TCRB1, TCRB2, TCRY, TCR8 and pre-TCRa;
(e) a impaired endogenous TCR;
(f) loss of expression or decreased expression of a functional HLA;
(g) loss of expression or decreased expression of β2 microglobulin;
(h) a deletion or mutation in one or more target antigens to a form that is no longer recognized by the SIR;
(i) deletion of diaglycerol kinase (DGK) or ikaros;
(j) an agent that increases the expression and/or activity of the SIR, wherein the agent is selected from CD3ζ, CD3δ, CD3ε, CD3γ or combination thereof;
(k) an agent that enhances the activity of SIR-expressing cell;
(l) an agent that inhibits an inhibitory molecule;
(m) an agent that inhibits the expression of one or more target antigens;
(n) an agent that provides co-stimulation to a SIR-expressing cell;
(o) a cytokine and/or a chemokine;
(p) an agent that that promotes the proliferation, persistence, expansion and activation of a SIR-expressing cell;
(q) a soluble receptor;
(r) a second SIR;
(s) an accessory module selected from the group consisting of 41BBL, CD40L, K13, MC159, cFLIP-L/MRITa, cFLIP-p22, HTLV1 Tax, HTLV2 Tax, HTLV2, Tax-RS mutant, FKBPx2-K13, FKBPx2-HTLV2-Tax, FKBPx2-HTLV2-Tax-RS, IL6R-304-vHH-Alb8-vHH, IL12f, PD1-4H1 scFV, PD1-5C4 scFV, PD1-4H1-Alb8-vHH, PD1-5C4-Alb8-vHH, CTLA4-Ipilimumab-scFv, CTLA4-Ipilimumab-Alb8-vHH, IL6-19A-scFV, IL6-19A-scFV-Alb8-vHH, sHVEM, sHVEM-Alb8-vHH, hTERT, Fx06, CD3z, CD3z-GGGS-41 BB, CD3-BBz, CD3-CD28z, CD3-CD28-Lck fusion protein, shRNA targeting Brd4, hTERT, heparinase, cytokine, chemokine, IL2, IL-7, IL-15, IL12f, IL-21, a costimulatory agent, soluble receptor, and any combination thereof; or
(t) a therapeutic control, wherein the therapeutic control is optionally selected from the group consisting of a truncated epidermal growth factor receptor (tEGFR), truncated epidermal growth factor receptor viii (tEGFRviii), truncated CD30 (tCD30), truncated BCMA (tBCMA), truncated CD19 (tCD19), CD34, thymidine kinase, cytosine deaminase, nitroreductase, xanthine-guanine phosphoribosyl transferase, human caspase 8, human caspase 9, inducible caspase 9 (icaspase9), purine nucleoside phosphorylase, linamarase/linamarin/glucose oxidase, deoxyribonucleoside kinase, horseradish peroxidase (HRP)/indole-3-acetic (IAA), Gamma-glutamylcysteine synthetase, CD20/alphaCD20, CD34/thymidine kinase chimera, dox-dependent caspase-2, mutant thymidine kinase (HSV-TKSR39), AP1903/Fas system, a chimeric cytokine receptor (CCR), a selection marker, dihydroxyfolate receptor (DHFR), mutant DHFR, methylated-DNA-protein-cysteine methyltransferase, inosine monophosphate dehydrogenase II (IMDHP2), puromycin acetyle transferase (PAC), blasticidin-resistance gene, mutant calcinueurin a/b (Can/b), CNa12, CNb30, a suicide gene and combinations thereof.
23. The isolated synthetic immune receptor (SIR) polypeptide heterodimer of claim 13 comprising a heterodimer of two T-cell receptor (TCR) constant chains comprising the amino acid sequences of SEQ ID NOs: 3010 and 3024 with mutations at the following amino acid positions:
a) SEQ ID NO: 3010 with 48C and SEQ ID NO: 3024 with 57C; or
b) SEQ ID NO: 3010 with 15C and SEQ ID NO: 3024 with 15C; or
c) SEQ ID NO: 3010 with 45C and SEQ ID NO: 3024 with 59C; or
d) SEQ ID NO: 3010 with 45C and SEQ ID NO: 3024 with 77C; or
e) SEQ ID NO: 3010 with 10C and SEQ ID NO: 3024 with 17C; or
f) SEQ ID NO: 3010 with 91S, 92D, 93V and/or 94P and any of the forgoing mutations listed for SEQ ID NO: 3010 in (a)-(e), and SEQ ID NO: 3024 with 18K/R, 22A, 133I, 136A and/or 139H and any of the forgoing mutations listed for SEQ ID NO: 3024 in (a)-(e); or
g) SEQ ID NO: 3010 with 61R and SEQ ID NO: 3024 with 79G; or
h) any combination of mutations set forth in (a)-(g).