T cell receptor constructs and uses thereof
Recombinant TCRs with tailored CDR sequences are developed to enhance antigen specificity and affinity, addressing the need for effective cancer therapies by targeting peptide-MHC complexes.
Patent Information
- Application Number
- PCT/US2025/022094
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2024-03-29
- Filing Date
- 2025-03-28
- Publication Date
- 2025-10-02
AI Technical Summary
There is a need for T cell receptors (TCRs) that can effectively target peptide-MHC complexes for the development of new therapeutic approaches, particularly for treating cancer, as existing TCRs may not be sufficiently sensitive to antigen-specific interactions.
Development of recombinant nucleic acids encoding TCRs with specific CDR3 sequences, optionally accompanied by CDR1 and CDR2 sequences, which are designed to recognize and bind to epitopes from human GATA3, especially those with frameshift mutations, enhancing antigen specificity and affinity.
The designed TCRs demonstrate enhanced binding affinity to peptide-MHC complexes, particularly with KD or IC50 values less than 500 nM, making them suitable for targeted immunotherapy in cancer treatment.
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Figure US2025022094_02102025_PF_FP_ABST
Abstract
Description
WSGR Docket No. 50401-775.601 T CELL RECEPTOR CONSTRUCTS AND USES THEREOF CROSS REFERENCE
[0001] This application claims the benefit of U.S. Provisional Application No. 63 / 571,935, filed onMarch 29, 2024, which is hereby incorporated by reference in their entirety. BACKGROUND
[0002] T cell receptors (TCRs) are members of the immunoglobulin superfamily and usually consist- -subunits. These possess one N-terminal immunoglobulin (Ig)-variable (V) domain, one Ig-constant (C) domain, a transmembrane / cell membrane-spanning region,and a short cytoplasmic tail at the C- -chain and-chain have three hypervariable or complementarity determining regions (CDRs), whereas the -chain has an additional area of hypervariability (HV4) that does not normally contact antigen and therefore is not considered a CDR.
[0003] CDR3 is the principal CDR responsible for recognizing processed antigen, although CDR1 ofthe alpha chain has also been shown to interact with the N-terminal part of the antigenic peptide, -chain interacts with the C-terminal part of the peptide. CDR2 is thought to recognize the MHC. The constant domain of the TCR domain consists of short connecting sequencesin which a cysteine residue forms disulfide bonds, which forms a link between the two chains. Theaffinity of TCRs for a specific antigen makes them valuable for several therapeutic approaches. For example, cancer patients, such as melanoma patients, can be effectively treated by using adoptiveimmunotherapy as TCRs are exquisitely sensitive for their antigen and can direct immune responsesat tumor cells expressing their cognate antigen. Accordingly, there is a need for TCRs against peptide- MHC complexes for development of new and effective therapeutics. SUMMARY
[0004] The instant application is based on development of TCRs against peptide-MHC complexesand effective therapeutics comprising the TCRs. Provided herein, isolated nucleic acid molecules encoding TCRs against peptide-MHC complexes, T cells expressing TCRs against peptide-MHCcomplexes, and pharmaceutical compositions for use in the treatment of diseases.
[0005] In one aspect, provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR)comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CATSDRGDSQETQYF (SEQ ID NO: 21). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and aWSGR Docket No. 50401-775.601 complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 19; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 20. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence set forth in SEQ ID NO: 27. In some embodiments, the TCR beta chain construct comprises a variable region having at least 90% sequence identity to an amino acid sequence set forth in SEQ ID NO: 27. In some embodiments, the TCR beta chain constructcomprises a variable region having at least 95%, 96%, 97%, 98% or 99% sequence identity to an a minoacid sequence set forth in SEQ ID NO: 27. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 27. In some embodiments, the recombinant nucleic acid encoding a T cell receptor (TCR) further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 16; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 17; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 18. In some embodiments, the recombinant nucleic acid encoding the TCR comprises (a) a sequence having at least 80% sequence identity with SEQ ID NOs: 25 or 26, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 21; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 22 or 23, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 18. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence set forth in SEQ ID NO: 24. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 90% sequence identity to an amino acid sequence set forth in SEQ ID NO: 24. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 24. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 24. In some embodiments, the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 29, or SEQ ID NO: 126, or SEQ ID NO: 127, or SEQ ID NO: 128 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 29; or SEQ ID NO: 126, or SEQ ID NO: 127, or SEQ ID NO: 128; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 28, or SEQ ID NO: 125, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 28 or at least 80% identical to SEQ ID NO: 125. In some embodiments, the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 110, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 110; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 109, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 109. In some embodiments, the recombinant nucleic acid encodesWSGR Docket No. 50401-775.601 a TCR that binds to an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 30.
[0006] In one aspect, provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR)comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASQDREGGNQPQHF (SEQ ID NO: 66). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 64; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 65. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence set forth in SEQ ID NO: 72. In some embodiments, the TCR beta chain construct comprises a variable region having at least 90% sequence identity to an amino acid sequence set forth in SEQ ID NO: 72. In some embodiments, the TCR beta chain construct comprises a variable region having at least 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 72. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 72. In some embodiments, the TCR further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 61; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 62; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 63. In some embodiments, the recombinant nucleic acid encoding the TCR, comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NOs: 70 or 71, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 66; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 67 or 68, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 63. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence set forth in SEQ ID NO: 69. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 90% sequence identity to an amino acid sequence set forth in SEQ ID NO: 69. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 69. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 69. In some embodiments, the recombinant nucleic acid encoding the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 74, or SEQ ID NO: 138, or SEQ ID NO: 139, or SEQ ID NO: 140; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 74 or SEQ ID NO: 138, or SEQ ID NO: 139, or SEQ ID NO: 140; (b)WSGR Docket No. 50401-775.601 an alpha chain having an amino acid sequence set forth in SEQ ID NO: 73, or SEQ ID NO: 137; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 73 or SEQ ID NO: 137. In some embodiments, the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 116, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 116; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 115, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 115. In some embodiments, the TCR binds to an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 75.
[0007] In one aspect, provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR)comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSSDIFYEQYF (SEQ ID NO: 6). In some embodiments, TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 4; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 5. In some embodiments, TCR beta chain construct comprises a variable region having at least 80%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 12. In some embodiments, TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 12. In some embodiments, TCR further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 1; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 2; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 3. In some embodiments, the recombinant nucleic acid described above comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NOs: 10 or 11, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 6; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 7 or 8, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 3. In some embodiments, the recombinant nucleic acid encoding a T cell receptor (TCR) having the TCR alpha chain construct comprises a variable region having at least 80% , 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 9. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 9. In some embodiments, the TCR comprises:(a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 14, or SEQ ID NO: 122, or SEQ ID NO: 123 or SEQ ID NO: 124, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 14, SEQ ID NO: 122, SEQ ID NO: 123 or SEQ ID NO: 124; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 13, or SEQ ID NO: 121 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13, or SEQ IDWSGR Docket No. 50401-775.601 NO: 121. In some embodiments, the TCR comprises:(a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 108, or an amino acid sequence that is at least 80% identical to SEQ ID NO:108; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 107, or an amino acidsequence that is at least 80% identical to SEQ ID NO: 107. In some embodiments, the recombinant nucleic acid encodes the TCR as described above, wherein the TCR binds to an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 15.
[0008] In one aspect, provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR)comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSLISLGAGEDTEAFF (SEQ ID NO: 96). In some embodiments, the recombinant nucleic acid encodes the TCR, wherein the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 94; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 95. In some embodiments, the recombinant nucleic acid encodes a T cell receptor (TCR) wherein the TCR beta chain construct comprises a variable region having at least 80%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 102. In some embodiments, the TCR comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 91; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 92; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 93. In some embodiments, the recombinant nucleic acid comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 100 or 101, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 96; and (b) a sequence having at least 80% sequence identity with SEQ ID NOs: 97 or 98, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 93. In some embodiments, the recombinant nucleic acid encodes a T cell receptor (TCR) wherein the TCR alpha chain construct comprises a variable region having at least 80% , 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 99. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 99. In some embodiments, the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 104, or SEQ ID NO: 146, or SEQ ID NO: 147, or SEQ ID NO: 148; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 104, SEQ ID NO: 146, or SEQ ID NO: 147, or SEQ ID NO: 148; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 103, or SEQ ID NO: 145; or an amino acid sequence that is at least 80% identical to SEQ IDWSGR Docket No. 50401-775.601 NO: 103 or SEQ ID NO: 145. In some embodiments, the recombinant nucleic acid encodes a TCR, wherein the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 120, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 120; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 119, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 119. In some embodiments, the recombinant nucleic acid encodes a TCR, wherein the TCR binds to an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 105.
[0009] In one aspect, provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR)comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASQGPYSLDTQYF (SEQ ID NO: 36). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 34; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 35. Insome embodiments, the TCR beta chain construct comprises a variable region having at least 80%,90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 42. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 42. In some embodiments, the recombinant nucleic acid encodes a TCR that further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein: the CDR1 has an amino acid sequence set forth in SEQ ID NO: 31; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 32; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 33. In some embodiments, the recombinant nucleic acid described herein comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 40 or 41, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 36; and (b) a sequence having at least 80% sequence identity with SEQ ID NOs: 37 or 38, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 33. In some embodiments, the recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 53-58, wherein the TCR alpha chain construct comprises a variable region having at least 80% , 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 39. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 39. In some embodiments, the recombinant nucleic acid encodes the TCR, wherein the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 44, or SEQ ID NO: 130, or SEQ ID NO: 131, or SEQ ID NO: 132, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 44; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 43, or SEQ ID NO: 129, or an aminoWSGR Docket No. 50401-775.601 acid sequence that is at least 80% identical to SEQ ID NO: 43 or SEQ ID NO: 129. In some embodiments, the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 112, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 112; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 111, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 111. In some embodiments, the recombinant nucleic acid encoding a TCR described herein, wherein the TCR binds to an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 45.
[0010] In one aspect, provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR)comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSLSETQYF (SEQ ID NO: 51). In some embodiments, the recombinant nucleic acid encodes a T cell receptor (TCR) wherein the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 49; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 50. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to an amino acid sequence set forth in SEQ ID NO: 57. In some embodiments, the TCR further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 46; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 47; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 48. In some embodiments, the recombinant nucleic acid comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 55 or 56, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 51; and (b) a sequence having at least 80% sequence identity with SEQ ID NOs: 52 or 53, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 48. In some embodiments, the recombinant nucleic acid encodes a T cell receptor (TCR) wherein the TCR alpha chain construct comprises a variable region having at least 80% , 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to an amino acid sequence set forth in SEQ ID NO: 54. In some embodiments, the recombinant nucleic acid encodes the TCR as described herein, wherein the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 59, or SEQ ID NO: 134, or SEQ ID NO: 135, or SEQ ID NO: 136 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 59, or SEQ ID NO: 134, or SEQ ID NO: 135, or SEQ ID NO: 136; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 58, or SEQ ID NO: 133, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 58 or SEQ ID NO: 133. In some embodiments, the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ IDWSGR Docket No. 50401-775.601 NO: 114, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 114; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 113, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 113. In some embodiments, the recombinant nucleic acid encoding a TCR, wherein the TCR binds to an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 60.
[0011] In one aspect, provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR)comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSTLTISTDTQYF (SEQ ID NO: 81). he recombinant nucleic acid encoding a T cell receptor (TCR) of claim 73, wherein the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 79; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 80. In some embodiments, the recombinant nucleic acid encodes a TCR, wherein the TCR beta chain construct comprises a variable region having at least 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to an amino acid sequence set forth in SEQ ID NO: 87. In some embodiments, the recombinant nucleic acid encodes a TCR, that further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 76; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 77; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 78. In some embodiments, the recombinant nucleic acid described herein, comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 85 or 86, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 81; and (b) a sequence having at least 80% sequence identity with SEQ ID NOs: 82 or 83, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 78. In some embodiments, the recombinant nucleic acid encoding a TCR as described herein, wherein the TCR alpha chain construct comprises a variable region having at least 80% , 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to an amino acid sequence set forth in SEQ ID NO: 84. In some embodiments, the recombinant nucleic acid encodes the TCR wherein the TCR comprises: (a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 89, or SEQ ID NO: 142, or SEQ ID NO: 143, or SEQ ID NO: 144; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 89, or SEQ ID NO: 142, or SEQ ID NO: 143, or SEQ ID NO: 144; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 88, or SEQ ID NO: 141; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 88 or SEQ ID NO: 141. In some embodiments, the recombinantnucleic acid encodes the TCR comprising: (a) a beta chain having an amino acid sequence set f orth inSEQ ID NO: 118, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 118; (b) anWSGR Docket No. 50401-775.601 alpha chain having an amino acid sequence set forth in SEQ ID NO: 117, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 117. In some embodiments, the recombinant nucleic acid encodes the TCR as described in this paragraph, wherein the TCR binds to an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 90.
[0012] In one aspect, provided herein is a recombinant nucleic acid encoding soluble TCR,comprising at least a TCR variable domain, comprising a sequence selected from the group : CATSDRGDSQETQYF (SEQ ID NO: 21); CASQDREGGNQPQHF (SEQ ID NO: 66); CASSSDIFYEQYF (SEQ ID NO: 6); CASSLISLGAGEDTEAFF (SEQ ID NO: 96); CASQGPYSLDTQYF (SEQ ID NO: 36); CASSLSETQYF (SEQ ID NO: 51); and CASSTLTISTDTQYF (SEQ ID NO: 81).
[0013] In one aspect, provided herein is a vector comprising the recombinant nucleic acid of any oneof the TCR constructs described in the embodiments above.
[0014] In one aspect, provided herein is a cell comprising the recombinant nucleic acid of any one ofthe embodiments described above, or the vector as described.
[0015] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR constructcomprising: (a) a TCR beta chain construct, and (b) a TCR alpha chain construct; wherein the TCR recognizes and binds to an epitope from human GATA3 comprising a frameshift mutation, the epitope being in a human MHC-protein complex, wherein the human MHC-protein is an HLA antigen encoded by the HLA-A*02:01 allele. In some embodiments the recombinant nucleic acid as described herein, wherein the TCR beta chain construct comprises a CDR3 having an amino acid sequence selected from the group set forth in SEQ ID NOs: 6, 21, 36, 51, 66, 81, and 96.
[0016] In some embodiments, the epitope has a length of from 8-50 amino acids. In someembodiments, the epitope binds to the human MHC with a greater affinity than a wild-type GATA3 epitope. In some embodiments, the epitope binds to the human MHC with a KD or an IC50 less than 500 nM, 250 nM, 150 nM, 100 nM, 50 nM, 25 nM, 10 nM or less than 10 nM. In some embodiments, the mutation is not present in non-cancer cells of a subject. In some embodiments, the TCR binds to a MHC-peptide complex with a KD or an IC50 of less than 500 nM, 250 nM, 150 nM, 100 nM, 50 nM, 25 nM, 10 nM or less than 10 nM.WSGR Docket No. 50401-775.601
[0017] In some embodiments, the vector is a lentiviral vector.
[0018] In some embodiments, the cell is a CD4+ T cell. In some embodiments, the cell is a CD8+ Tcell. In some embodiments, the cell is isolated from a subject having a GATA3 mutation.
[0019] In some embodiments, the TCR binds to a complex comprising (i) an epitope from humanGATA3 and (ii) an MHC protein, wherein the MHC protein is encoded by HLA-A*02:01 allele. In some embodiments the TCR comprises a sequence provided in Table 2. In some embodiments, the TCR may be a TCR described in Table 3. In some embodiments, the vector is a lentiviral vector. In some embodiments, the cell is a CD4+ T cell. In some embodiments, the cell is a CD8+ T cell. In some embodiments, the cell is isolated from a subject having a GATA3 mutation.
[0020] In one aspect, provided herein is a pharmaceutical composition comprising: (a) the nucleicacid encoding a TCR are described above; or, the vector described herein; or, the cell as described herein; and (b) a pharmaceutically acceptable excipient or diluent.
[0021] In some embodiments, the pharmaceutical composition is for use in treating an immunedisease or cancer. In one aspect, provided herein is use of the pharmaceutical composition, for treating an immune disease or cancer.
[0022] In one aspect, provided herein is a method of treating a subject having a disease or condition,comprising administering to the subject in need thereof the pharmaceutical composition described herein. In one aspect, provided herein is a method of identifying a subject with cancer as a candidate for a therapeutic, the method comprising determining the subject as a subject that expresses a protein encoded by an HLA-A*02:01 allele wherein therapeutic is the pharmaceutical composition described herein.
[0023] In one aspect, provided herein is a soluble TCR, comprising at least a TCR variable domain,comprising a sequence selected from the group : CATSDRGDSQETQYF (SEQ ID NO: 21); CASQDREGGNQPQHF (SEQ ID NO: 66); CASSSDIFYEQYF (SEQ ID NO: 6); CASSLISLGAGEDTEAFF (SEQ ID NO: 96); CASQGPYSLDTQYF (SEQ ID NO: 36); CASSLSETQYF (SEQ ID NO: 51); and CASSTLTISTDTQYF (SEQ ID NO: 81).
[0024] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSQGVGESPEAFF (SEQ ID NO: 206). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 204; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 205. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%,WSGR Docket No. 50401-775.601 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 210. In some embodiments, the TCR beta chain construct comprises a variable region having anamino acid sequence set forth in SEQ ID NO: 210. In some embodiments, the recombinan t nucleicacid encoding a TCR described herein, further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 201; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 202; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 203. In some embodiments, the recombinant nucleic acid comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 209, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 206; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 207, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 203. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 208. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 208.
[0025] In one aspect, provided herein is a TCR having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 203; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 206, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200) and (ii) an MHC protein.
[0026] In one aspect provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSFPGTGYGNTEAFF (SEQ ID NO: 296). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 294; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 295. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 300. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 300. In some embodiments, the recombinant nucleic acid encoding a TCR further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 291; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 292; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 293. In some embodiments, the recombinant nucleic acid comprise: (a) aWSGR Docket No. 50401-775.601 sequence having at least 80% sequence identity with SEQ ID NO: 299, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 296; and (b) a sequence having at least 80%sequence identity with SEQ ID NO: 297, wherein the sequence comprises a sequence encoding at leastSEQ ID NO: 293. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 298. In some embodiments, the TCR alpha chain constructcomprises a variable region having an amino acid sequence set forth in SEQ ID NO: 298.
[0027] In one aspect, provided herein is a TCR having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 293; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 296, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO:15), or an epitope SMLTGPPARV (SEQ ID NO: 200) and (ii) an MHC protein.
[0028] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSFTLGVSETQYF (SEQ ID NO: 326). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 324; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 325. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 330. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 330. In some embodiments, the recombinant nucleic acid, further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 321; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 322; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 323. In some embodiments, the recombinant nucleic acid comprises (a) a sequence having at least 80% sequence identity with SEQ ID NO: 329, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 326; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 327, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 323. In some embodiments, the recombinant nucleic acid encoding a TCR, wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 328.WSGR Docket No. 50401-775.601
[0029] In some embodiments, the TCR alpha chain construct comprises a variable region having anamino acid sequence set forth in SEQ ID NO: 328.
[0030] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 323; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 326, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and(ii) an MHC protein.
[0031] In one aspect provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASRPEGGLYEQYF (SEQ ID NO: 336). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 334; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 335. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 340. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 340.
[0032] In some embodiments, the recombinant nucleic acid encoding a TCR further comprising aTCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 331; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 332; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 333. In some embodiments, the recombinant nucleic acid comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 339, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 336; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 337, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 333. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 338. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 338.
[0033] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 333; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 336, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO:WSGR Docket No. 50401-775.601 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein. In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising a TCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASRPEGGLYEQYF (SEQ ID NO: 346). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 344; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 345. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 350. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 350. In some embodiments, the recombinant nucleic acid encoding a TCR further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 341; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 342; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 343. In some embodiments, the recombinant nucleic acid comprises (a) a sequence having at least 80% sequence identity with SEQ ID NO: 349, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 346; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 347, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 343. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 348. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 348.
[0034] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 343; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 346, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.
[0035] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSSVATGTIYEKLFF (SEQ ID NO: 366). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 364; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 365. InWSGR Docket No. 50401-775.601 some embodiments, TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 370. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 370. In some embodiments, the TCR further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 361; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 362; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 363. In some embodiments, the recombinant nucleic acid comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 369, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 366; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 367, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 363. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 368. In some embodiments, TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 368.
[0036] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 363; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 366, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.
[0037] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSPDSGQGWVNEQFF (SEQ ID NO: 386). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 384; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 385. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 390. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 390. In some embodiments, the TCR further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 381; the CDR2 has an amino acid sequence set forth in SEQID NO: 382; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 383.WSGR Docket No. 50401-775.601
[0038] In some embodiments, the recombinant nucleic acid comprising: (a) a sequence having at least80% sequence identity with SEQ ID NO: 389, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 386; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 387, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 383. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 388. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 388.
[0039] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 383; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 386, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.
[0040] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSQDGIDLSGNTIYF (SEQ ID NO: 396). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 394; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 395. In some embodiments, TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 400. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 400.
[0041] In some embodiments, the TCR further comprising a TCR alpha chain construct having aCDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 391; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 392; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 393. In some embodiments, the recombinant nucleic acid encoding the TCR comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 399, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 396; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 397, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 393. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 398. In some embodiments, theWSGR Docket No. 50401-775.601 TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 398.
[0042] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 393; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 396, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.
[0043] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from CASSVDGRDADTQYF (SEQ ID NO: 216), CASSVDGRDADTQYF (SEQ ID NO: 226), CASSQGVGESPEAFF (SEQ ID NO: 236), CASRTNYGYTF (SEQ ID NO: 246), CASRTNYGYTF (SEQ ID NO: 256), CSARDWTGGYNGTEAFF (SEQ ID NO: 266), CASSFTLGVSETQYF (SEQ ID NO: 276), CASSFTLGVSETQYF (SEQ ID NO: 286), CASSFPGTGYGNTEAFF (SEQ ID NO: 306), CASSFTLGVSETQYF (SEQ ID NO: 316), CASSPPEGGNEQFF (SEQ ID NO: 356), CASSPDSGQGWVNEQFF (SEQ ID NO: 376), and CASSPPEGGNEQFF (SEQ ID NO: 406); wherein the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 214, a CDR2having a sequence of SEQ ID NO: 215, and a CDR3 having a sequence of SEQ ID NO: 216; and (b)an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 211, a CDR2 having a sequence of SEQ ID NO: 212 and a CDR3 having a sequence of SEQ ID NO: 213. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 220; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 218. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 224, a CDR2 having a sequence of SEQ ID NO: 225, and a CDR3 having a sequence of SEQ ID NO: 226; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 221, a CDR2 having a sequence of SEQ ID NO: 222 and a CDR3 having a sequence of SEQ ID NO: 223. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 230; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 228. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 234, a CDR2 having a sequence of SEQ ID NO: 235, and a CDR3 having a sequence of SEQ IDWSGR Docket No. 50401-775.601 NO: 236; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 231, a CDR2 having a sequence of SEQ ID NO: 232 and a CDR3 having a sequence of SEQ ID NO: 233. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 240; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 238. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 244, a CDR2 having a sequence of SEQ ID NO: 245, and a CDR3 having a sequence of SEQ ID NO: 246; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 241, a CDR2 having a sequence of SEQ ID NO: 242 and a CDR3 having a sequence of SEQ ID NO: 243. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 250; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 248. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 254, a CDR2 having a sequence of SEQ ID NO: 255, and a CDR3 having a sequence of SEQ ID NO: 256; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 251, a CDR2 having a sequence of SEQ ID NO: 252 and a CDR3 having a sequence of SEQ ID NO: 253. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 260; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 258. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 264, a CDR2 having a sequence of SEQ ID NO: 265, and a CDR3 having a sequence of SEQ ID NO: 266; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 261, a CDR2 having a sequence of SEQ ID NO: 262 and a CDR3 having a sequence of SEQ ID NO: 263. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 270; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 268. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 274, a CDR2 having a sequence of SEQ ID NO: 275, and a CDR3 having a sequence of SEQ ID NO: 276; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 271, a CDR2 having a sequence of SEQ ID NO: 272 and a CDR3 having a sequence of SEQ ID NO: 273. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 280; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 278. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 284, a CDR2 having a sequence of SEQ ID NO: 285, and a CDR3 having a sequence of SEQ IDWSGR Docket No. 50401-775.601 NO: 286; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 281, a CDR2 having a sequence of SEQ ID NO: 282 and a CDR3 having a sequence of SEQ ID NO: 283. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 290; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 288. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 304, a CDR2 having a sequence of SEQ ID NO: 305, and a CDR3 having a sequence of SEQ ID NO: 306; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 301, a CDR2 having a sequence of SEQ ID NO: 302 and a CDR3 having a sequence of SEQ ID NO: 303. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 310; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 308. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 314, a CDR2 having a sequence of SEQ ID NO: 315, and a CDR3 having a sequence of SEQ ID NO: 316; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 311, a CDR2 having a sequence of SEQ ID NO: 312 and a CDR3 having a sequence of SEQID NO: 313. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable regionhaving at least 80% sequence identity to SEQ ID NO: 320; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 318. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 354, a CDR2 having a sequence of SEQ ID NO: 355, and a CDR3 having a sequence of SEQ ID NO: 356; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 351, a CDR2 having a sequence of SEQ ID NO: 352 and a CDR3 having a sequence of SEQ ID NO: 353. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 360; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 358. In some embodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ ID NO: 374, a CDR2 having a sequence of SEQ ID NO: 375, and a CDR3 having a sequence of SEQ ID NO: 376; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 371, a CDR2 having a sequence of SEQ ID NO: 372 and a CDR3 having a sequence of SEQ ID NO: 373. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 380; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 378. In someembodiments, the TCR comprises: (a) a beta chain, comprising a CDR1 having a sequence of SEQ IDNO: 404, a CDR2 having a sequence of SEQ ID NO: 405, and a CDR3 having a sequence of SEQ IDWSGR Docket No. 50401-775.601 NO: 406; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 401, a CDR2 having a sequence of SEQ ID NO: 402 and a CDR3 having a sequence of SEQ ID NO: 403. In some embodiments, the TCR comprises: (a) a beta chain comprising a variable region having at least 80% sequence identity to SEQ ID NO: 410; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 408. In some embodiments, the TCR binds to a complex comprising (i) a peptide MHC complex comprising an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein. In some embodiments, the MHC protein is encoded by HLA-A*A02:01In some embodiments, the TCR comprises a sequence provided in Table 4A. In some embodiments, the TCR is a TCR described Table 4B.
[0044] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASNVGQGYTDTQYF (SEQ ID NO: 426). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 424; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 425. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 430. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 430. In some embodiments, the TCR further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 421; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 422; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 423. In some embodiments, the TCR comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 429, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 426; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 427, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 423. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 428. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 428.
[0045] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 423; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO:WSGR Docket No. 50401-775.601 426, and where in the TCR binds to a complex comprising (i) an epitope KPKRDGYMF, or an epitope KPKRDGYMFL, and (ii) an MHC protein.
[0046] In some embodiments, the MHC is encoded by HLA-B*07:02 allele.
[0047] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSPTSGISYEQYF (SEQ ID NO: 516). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 514; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 515. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 520. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 520. In some embodiments, the TCR further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 511; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 512; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 513. In some embodiments, the recombinant nucleic acid comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 519, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 516; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 517, whereinthe sequence comprises a sequence encoding at least SEQ ID NO: 513. In some embodiments, theTCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 518. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 518.
[0048] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 513; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 516, and where in the TCR binds to a complex comprising (i) an epitope KPKRDGYMF, or an epitopeKPKRDGYMFL, and (ii) an MHC protein.
[0049] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSSQGWGTEAFF (SEQ ID NO: 526). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and aWSGR Docket No. 50401-775.601 complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 524; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 525. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 530. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 530. In some embodiments, the TCR comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 521; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 522; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 523. In some embodiments, the TCR comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 529, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 526; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 527, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 523. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 528. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 528.
[0050] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 523; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 526, and where in the TCR binds to a complex comprising (i) an epitope KPKRDGYMF, or an epitope KPKRDGYMFL, and (ii) an MHC protein.
[0051] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSVGVSLTNEKLFF (SEQ ID NO: 596). In some embodiments, providedherein is a the TCR beta chain construct further comprises a complementarity determining region 1(CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 594; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 595. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 600. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 600. In some embodiments, the TCR comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1WSGR Docket No. 50401-775.601 has an amino acid sequence set forth in SEQ ID NO: 591; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 592; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 593. In some embodiments, the recombinant nucleic acid comprises: (a) a sequence having at least 80% sequence identity with SEQ ID NO: 599, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 596; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 597, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 593. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 598. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 598.
[0052] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 593; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 596, and where in the TCR binds to a complex comprising (i) an epitope KPKRDGYMF, or an epitope KPKRDGYMFL, and (ii) an MHC protein.
[0053] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from CASSSEIVGPSQYF (SEQ ID NO: 416), CASSPGAGPGQPQHF (SEQ ID NO: 436), CASTTGGRGYTF (SEQ ID NO: 456), CASTTGGRGYTF (SEQ ID NO: 466), CASTQYKDEQFF (SEQ ID NO: 476), CASSLDRTSGSYNEQFF (SEQ ID NO: 486), CASSLDRTSGSYNEQFF (SEQ ID NO: 496), CASSPTSGISYEQYF (SEQ ID NO: 506), CASTPAGGNTGELFF (SEQ ID NO: 536), CSARDGQGSSYEQYF (SEQ ID NO: 546), CASWGEGAYEQYF (SEQ ID NO: 556), CASSPRLAQFSRNEQFF (SEQ ID NO: 566), CASMTGGLDEQFF (SEQ ID NO: 576), CASWGEGAYEQYF (SEQ ID NO: 586), CASMTGGLDEQFF (SEQ ID NO: 606), CASSPGQGWDSPLHF (SEQ ID NO: 616) and CASSLHHPTVYGYTF (SEQ ID NO: 626); wherein the TCR binds to a complex comprising (i) an epitope KPKRDGYMF, or an epitope KPKRDGYMFL. In some embodiments, the TCR comprises a sequence provided in Table 5A. In some embodiments, the TCR is a TCR described Table 5B. In some embodiments, the TCR binds to a complex comprising (i) a peptide-MHC complex comprising an epitope KPKRDGYMF, or an epitope KPKRDGYMFL, and (ii) an MHC protein. In some embodiments, the MHC protein is encoded by HLA-B*07:02 allele.
[0054] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having anWSGR Docket No. 50401-775.601 amino acid sequence CASGSTGTAYEQYF (SEQ ID NO: 676). In some embodiments, the TCR beta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 674; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 675. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 680. In some embodiments, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 680. In some embodiments, the recombinant nucleic acid encoding a TCR that further comprises a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 671; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 672; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 673. In some embodiments, the TCR comprises (a) a sequence having at least 80% sequence identity with SEQ ID NO: 679, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 676; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 677, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 673. In someembodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%,90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 678. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 678.
[0055] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 673; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 676, and where in the TCR binds to a complex comprising (i) an epitope ESKIMFATL, and (ii) an MHC protein.
[0056] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having anamino acid sequence CASSPDPGSYGYTF (SEQ ID NO: 686). In some embodiments, the TCR betachain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 684; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 685. In some embodiments, the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 690. In some embodiments, the TCR beta chain construct comprises a variable region having anWSGR Docket No. 50401-775.601 amino acid sequence set forth in SEQ ID NO: 690. In some embodiments, the TCR further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 681; the CDR2 has an amino acid sequence set forth in SEQID NO: 682; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 683.
[0057] In some embodiments, the recombinant nucleic acid of comprises: (a) a sequence having atleast 80% sequence identity with SEQ ID NO: 689, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 686; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 687, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 683. In some embodiments, the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 688. In some embodiments, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 688.
[0058] In one aspect, provided herein is a TCR, having a TCR alpha chain and a TCR beta chain,wherein the TCR alpha chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 683; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 686, and where in the TCR binds to a complex comprising (i) an epitope ESKIMFATL and (ii) an MHC protein.
[0059] In one aspect, provided herein is a recombinant nucleic acid encoding a TCR comprising aTCR beta chain construct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from CASSPSGVFNEQYF (SEQ ID NO: 636), CASSQEGQGVVKLFF (SEQ ID NO: 646), CASSLSLGRIAYEQYF (SEQ ID NO: 656), and CASGSTGTAYEQYF (SEQ ID NO: 666), wherein the TCR binds to an epitope ESKIMFATL in complex with an MHC protein. In some embodiments, the TCR binds to a complex comprising (i) an epitope ESKIMFATL and (ii) an MHC protein. In some embodiments, the MHC protein is encoded by HLA-B*08:01 allele.
[0060] In one aspect, provided herein is an engineered cell, comprising any one of the recombinantnucleic acids described herein. In some embodiments, the cell is a T cell.
[0061] In one aspect, provided herein is a method of treating a disease in a subject in need thereof,comprising administering to the subject a composition comprising an engineered cell described herein.
[0062] In one aspect, provided herein is a method of treating a disease in subject in need thereof,comprising administering to the subject a composition comprising a recombinant nucleic acid of described herein in a formulation suitable for expressing in a cell in vivo. In some embodiments, the disease is cancer. In some embodiments, the cancer is a breast cancer.WSGR Docket No. 50401-775.601
[0063] In one aspect, provided herein is a pharmaceutical composition comprising the recombinantnucleic acid; the TCR; or the engineered described herein.
[0064] Additional aspects and advantages of the present disclosure will become readily apparent tothose skilled in this art from the following detailed description, wherein only illustrative embodiments of the present disclosure are shown and described. As will be realized, the present disclosure is capable of other and different embodiments, and its several details are capable of modifications in various obvious respects, all without departing from the disclosure. Accordingly, the drawings and description are to be regarded as illustrative in nature, and not as restrictive. INCORPORATION BY REFERENCE
[0065] All publications, patents, and patent applications mentioned in this specification are hereinincorporated by reference to the same extent as if each individual publication, patent, or patentapplication was specifically and individually indicated to be incorporated by reference.BRIEF DESCRIPTION OF THE DRAWINGS
[0066] The novel features of the invention are set forth with particularity in the appended claims. Abetter understanding of the features and advantages of the present invention will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the invention are utilized, and the accompanying drawings of which:
[0067] FIG. 1 depicts an example schematic of an antigen-specific CD8+ T cell expansion. PBMCscan be stimulated with the antigen of interest and cytokines. After expansion antigen-specific CD8+T cells can be identified with peptide-MHC multimers.
[0068] FIG.2 depicts experimental results of a TCR functional avidity assay (peptide titration). Thegraph shows percentage of CD69+ T cells after co-culturing TCR-transduced Jurkat cells with K562 cells expressing HLA-A*02:01 loaded with increasing amounts of GATA3neoORF peptide.
[0069] FIG.3 depicts experimental EC50 results of a TCR functional avidity assay. A graph showingpercentage of CD69+ T cells after co-culturing TCR-transduced Jurkat cells with K562 cells expressing HLA-A*02:01 loaded with increasing amounts of GATA3neoORF peptide. TCR2 and TCR5 showed the lowest EC50 values.
[0070] FIG. 4A depicts an exemplary flow cytometry analysis of TCR recognition of engineeredK562 cell lines restricted to GATA3neoORF and HLA-A02:01. K562 lines express the mutated GATA3 (neoORF) and HLA-A*02:01.WSGR Docket No. 50401-775.601
[0071] FIG.4B depicts an exemplary data showing primary T cells transduced with TCR-2 or TCR-5 can recognize MCF-7 breast cancer cells expressing GATA3neoORF peptide complexed with HLA- A02:01.
[0072] FIG.5 depicts exemplary data demonstrating that multiple TCRs generated and presented inTables 5A and 5B are functional. GATA3neoORF specific TCR expressing T cells successfullyrecognize target cells with the GATA3 neoORF mutation. T cells were transduced with nucleic acidencoding sample mutation-specific TCRs (TCRs-B7-2, B74, B7-11, B7-12, and B7-19 respectively) (Table 5A-5B). These T cells can recognize naturally processed / presented peptide-MHC on K562 cells expressing full-length GATA3neoORF and HLA-B*07:02, without external peptide pulsing. This data indicate that the TCRs thus tested were functional, exhibiting binding to target epitope, as indicated by expression of the marker 4-1BB on a high percentage of T cells expressing the TCRs when co- cultured with the K562 cells expressing the GATA3 neoORF, and HLA-B*07:02.
[0073] FIG.6 depicts exemplary data demonstrating that multiple TCRs generated and presented inTables 6A and 6B are functional. The data show that T cells transduced with mutation-specific TCRs generated herein can recognize naturally processed / presented peptide-MHC on K562 cells expressingfull-length GATA3neoORF and HLA-B*08:01, without external peptide pulsing. TCR recognition ofengineered K562 lines is specific to the GATA3neoORF and HLA-B*08:01.
[0074] FIG. 7 depicts exemplary data demonstrating functional avidities of GATA3neoORF specificTCRs that bind to a complex of (i) the epitope sequence ESKIMFATL and (ii) HLA-B*08:01.
[0075] FIG.8 depicts exemplary data demonstrating functional avidities of GATA3neoORF specificTCRs that bind to the 10-mer or 9-mer epitope -HLA-B*07:0201complexes respectively.
[0076] FIG. 9 depicts exemplary data demonstrating T cells successfully recognize target cells withthe GATA3 neoORF mutation. The data show that T cells transduced with mutation-specific TCRs generated herein can recognize naturally processed / presented peptide-MHC on MCF-7 cells expressing full-length GATA3neoORF and HLA-A*02:01, without external peptide pulsing. DETAILED DESCRIPTION
[0077] value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measur mean a range of up to 20%, up to 10%, up to 5%, or up to 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, preferably within 5-fold, and more preferably within 2-fold, of a value. Where particularWSGR Docket No. 50401-775.601values are described in the application and claims, unless otherwise statedwithin an acceptable error range for the particular value should be assumed.
[0078] Unless defined otherwise, all technical and scientific terms used herein have the same meaningas commonly understood by one of ordinary skill in the art to which this disclosure belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present disclosure, the preferred methods and materials are now described.The details of one or more particular embodiments are set forth in the description below.
[0079] can be understood to encompass full TCRs as well asantigen-binding portions or antigen-binding fragments (also called MHC-peptide binding fragments) thereof. In some embodiments, the TCR may be an intact or full-length TCR. In some embodiments, the TCR may be an antigen-binding portion that may be less than a full-length TCR but that binds to a specific antigenic peptide bound to (i.e., in the context of) an MHC molecule, i.e., an MHC-peptide complex. In some cases, an antigen-binding portion or fragment of a TCR can contain only a portion of the structural domains of a full-length or intact TCR, but yet may be able to bind the epitope (e.g., MHC-peptide complex) to which the full TCR binds. In some cases, an antigen-binding portion or chain of a TCR, sufficient to form a binding site for binding to a specific MHC-peptide complex, such as generally where each chain contains three complementarity determining regions. Polypeptides or proteins having a binding domain which is an antigen-binding domain or is homologous to an antigen- binding domain are included. Complementarity determining region (CDR) grafted TCRs and other humanized TCRs (including CDR modifications and framework region modifications) are also contemplated by these terms. It should be noted that while reference may be made only to immunoglobulin chains (e.g., heavy chains and lights chains), the disclosed invention can be applied to multiple other different types of paired sequences, e.g., T cell
[0080] -contiguous sequences of amino acids within TCR variable regions, which confer specificity and / or binding affinity to an MHC-peptide complex. In general, there are three CDRs in each alpha chain variable region (CDR-H1, CDR-H2, CDR-H3) and three CDRs in each beta chain variable region (CDR-L1, CDR-L2, CDR-L3). -CDR portions of the variable regions of the alpha and beta chains. In general, there are four FRs in each full-length alpha chainWSGR Docket No. 50401-775.601 variable region (FR-H1, FR-H2, FR-H3, and FR-H4), and four FRs in each full-length beta chain variable region (FR-L1, FR-L2, FR-L3, and FR-L4).
[0081] gamma or delta chain, that may be involved in binding the TCR to antigen-MHC complexes. The ures, with each -MHC complex.
[0082] Also provided herein are TCR fragments, including antigen-binding fragments. In someembodiments, the TCR may be an antigen-binding portion thereof, such as a variant of a full-length TCR not containing the transmembrane and / or cytoplasmic region(s) thereof, which may be referred to as a full soluble TCR. In some embodiments, the TCR may be a dimeric TCR (dTCR). In some embodiments, the TCR may be a single-chain TCR (scTCR), such as a scTCR having a structure as described in PCT patent publication numbers WO2003 / 020763, WO2004 / 033685, orWO2011 / 044186. In certain embodiments, the TCR may be a single-chain TCR fragment comprisingan alpha chain variable region linked to a beta chain variable region, such as a scTv. In some embodiments, a scTv may be also referred to as a scFv. A single-chain Tv or scTv refers in some aspects to polypeptide chain. Generally, the Tv polypeptide further comprises a polypeptide linker between the antigen binding. A diabody refers in some aspects to TCR fragments with two antigen-binding sites,which frag -- pairing between the two domains on the same chain, the domains are forced to pair with the complementary domains of another chain and create two antigen-binding sites. Exemplary diabodies are described more fully in, for example, EP404097 and WO93111161. Fv refers in some aspects to a TCR fragment which contains a complete peptide-MHC complex recognition and peptide-MHC -covalent association. It is in this configuration that the three CDRs of each variable domain interact to define a peptide-MHC complex binding site on the --WSGR Docket No. 50401-775.601 -- -MHC complex binding specificity to- -ecipient selected TCR or antigen-binding fragment thereof andthis combination of CDRs can be tested for binding, affinity, etc. Furthermore, although the two joined using recombinant methods by a synthetic linker that enables them to be made as a single protein as single chain Tv (scTv). Such scTvs are also intended to be encompassed within the peptide-MHC complex binding portion of a TCR.
[0083] A bispecific TCR refers in some aspects to a TCR that shows specificities to two differentpeptide-MHC complexes or two different types of peptide-MHC complexes. The terms as used herein specifically include, without limitation, TCRs which show binding specificity for a target peptide- MHC complex and to another peptide-MHC complex that facilitates delivery to a particular tissue. Similarly, multi-specific TCRs have two or more binding specificities. A linear TCR refers in someaspects to a pair of tandem Fd segments (e.g. - 1- - 1) which form a pair of antigen bindingregions. Linear TCRs can be bispecific or monospecific.
[0084] An antigen-binding domain refers in some aspects to one or more fragments of a TCR thatretain the ability to specifically bind to a peptide-MHC complex. Non-limiting examples of TCR fragments included within such terms include, but are not limited to, (i) a Tab fragment, a monovalent 2 fragment, a bivalent fragment containing two Tab fragments linked by a disulfide bridge at the hinge region; (iii) a Td fragment 1 domains; (iv) a Tv fragm single arm of a TCR, including scTvs, (v) a dAb fragment (Ward et al., (1989) Nature 341:544546), single alpha chain or a single beta chain.
[0085] may be aTCR in which all or substantially all CDR amino acid residues are derived from non-human CDRs and all or substantially all FR amino acid residues are derived from human FRs. A humanized TCR optionally may include at least a portion of a TCR constant region derived from a human TCR. A -human TCR, refers to a variant of the non-human TCR that has undergone humanization, typically to reduce immunogenicity to humans, while retaining the specificity and affinity of the parental non-human TCR. In some embodiments, some FR residues in a humanizedWSGR Docket No. 50401-775.601 TCR are substituted with corresponding residues from a non-human TCR (e.g., the TCR from which may be a TCR with an amino acid sequence corresponding to that of a TCR produced by a human or a human cell, or non-human source that utilizes human TCR repertoires or other human TCR-encoding sequences, including human TCR libraries. The term excludes humanized forms of non-human TCRs comprising non-human peptide-MHC complex binding regions, such as those in which all or substantially all CDRs are non-human. Human TCRs may be prepared by administering an immunogen to a transgenic animal that has been modified to produce intact human TCRs or intact TCRs with human variable regions in response to antigenic challenge. Such animals typically contain all or a portion of the human TCR loci, which replace the endogenous TCR loci, or which are present animals, the endogenous TCR loci have generally been inactivated. Human TCRs also may be derived from human TCR libraries, including phage display and cell-free libraries, containing TCR-encoding sequences derived from a human repertoire.
[0086] at arenot encoded in a normal, non-mutated host genome. A neoantigen can relate to an antigen including one or more amino acid modifications compared to the parental antigen. For example, a neoantigen may be a tumor-associated neoantigen, wherein the term - peptide or protein including amino acid modifications due to tumor-specific mutations. In some instances, a neoantigen represents either oncogenic viral proteins or abnormal proteins that arise as a consequence of somatic mutations. For example, a neoantigen can arise by the disruption of cellular mechanisms through the activity of viral proteins. Another example can be an exposure of a carcinogenic compound, which in some cases can lead to a somatic mutation. This somatic mutation can ultimately lead to the formation of a tumor / cancer. A neoantigen can be a class of tumor antigens which arise from tumor-specific changes in proteins. Neoantigens encompass, but are not limited to, tumor antigens which arise from, for example, a substitution in a protein sequence, a frame shift mutation, a fusion polypeptide, an in-frame deletion, an insertion, and expression of an endogenous retroviral polypeptide. A neoepitope can be an epitope that is not present in a reference, such as a non- diseased cell, e.g., a non-cancerous cell or a germline cell, but is found in a diseased cell, e.g., a cancer cell. This includes situations where a corresponding epitope is found in a normal non-diseased cell or a germline cell but, due to one or more mutations in a diseased cell, e.g., a cancer cell, the sequence of the epitope is changed so as to result in the neoepitope.WSGR Docket No. 50401-775.601
[0087] of forming a binding interaction with the variable region binding pocket of a TCR. In some aspects, an epitope refers to a portion of a peptide-MHC complex capable of forming a binding interaction withthe variable region binding pocket of a TCR. Such binding interactions can be man ifested as anintermolecular contact with one or more amino acid residues of one or more CDRs. Peptide -MHCcomplex binding can involve, for example, a CDR3, a CDR3 pair, or in some instances, interactionssequence (e.g. e.g.,. Therefore, an epitope can define more than one distinct amino acid sequence. In some aspects, a TCR can recognize one or more amino acid sequences or epitopes in the context of an MHC. Epitopesrecognized by TCRs can be determined by peptide mapping and sequence analysis tech niques wellknown to one of skill in the art. Binding interactions are manifested as intermolecular contacts with one or more amino acid residues of a CDR. An epitope can refer to an antigenic determinant in a molecule such as an antigen, i.e., to a part in or fragment of the molecule that is recognized by the immune system, for example, that is recognized by a T cell, in particular when presented in the context of MHC molecules. An epitope of a protein such as a tumor antigen can comprise a continuous or discontinuous portion of the protein and can be between 5 and 100, 5 and 50, 8 and 30, or 10 and 25 amino acids in length, for example, the epitope may be 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids in length.
[0088] covalent, electrostatic, hydrophobic, and ionic and / or hydrogen-bond interactions under physiological conditions, and includes interactions such as salt bridges and water bridges, as well as any other conventional means of binding.
[0089] In some embodiments, reference to a TCR with specific binding refers to a situation inwhich a TCR will not show any significant binding to molecules other than the peptide-MHC complex containing the epitope recognized by the TCR. The term may be also applicable where for example, an antigen binding domain may be specific for a particular epitope which is carried by a number of peptide-MHC complexes, in which case the selected TCR or peptide-MHC complex binding fragment thereof carrying the peptide-MHC complex binding domain will be able to bind to the various peptide- MHC complexes carrying the epitope. that the TCRs or fragments thereof bind to an epitope with greater affinity than it binds unrelated amino acid sequences, and if cross-reactive to other polypeptides containing the epitope, are not toxicWSGR Docket No. 50401-775.601at the levels at which they are formulated for administration to human use. In one aspect, such affinitymay be at least 1-fold greater, at least 2-fold greater, at least 3-fold greater, at least 4-fold greater, at least 5-fold greater, at least 6-fold greater, at least 7-fold greater, at least 8-fold greater, at least 9-fold greater, 10-fold greater, at least 20-fold greater, at least 30-fold greater, at least 40-fold greater, at least 50-fold greater, at least 60-fold greater, at least 70-fold greater, at least 80-fold greater, at least 90-fold greater, at least 100-fold greater, or at least 1000-fold greater than the affinity of the TCR or fragment thereof for unrelated amino acid sequences.
[0090] binding pair (e.g., a human leukocyte antigen (HLA)-binding peptide and a class I or II HLA, or a peptide-HLA complex and a T cell receptor (TCR)). Affinity can be expressed as an equilibriumconstant of the reversible binding of two agents and can be expressed as KD, KA, Koff or Kon. KD refersto the dissociation constant between two members of a binding pair and has units of molarity. KArefers to the affinity constant between two members of a binding pair is the inverse of the dissociation constant. Affinity may be determined experimentally, for example by surface plasmon resonance (SPR) using commercially available Biacore SPR units. Koffrefers to the off-rate constant of two members ofa binding pair, (e.g., the off -rate constant of an HLA-binding peptide and a class I or II HLA, or apeptide-HLA complex and a TCR). Konrefers to the on-rate constant of two members of a binding pair, (e.g., the on-rate constant of an HLA-binding peptide and a class I or II HLA, or a peptide-HLA complex and a TCR). Affinity of a binding protein to a ligand such as affinity of a TCR for an epitope can be, for example, from about 100 nanomolar (nM) to about 0.1 nM, from about 100 nM to about 1resistance of a complex of two or more agents to dissociation after dilution.
[0091] 50Affinity may also be expressed as the inhibitory concentration 50 (IC50), or the concentration at which 50% of a first member of a binding pair (e.g., a peptide) is displaced. Likewise, ln(IC50) refers to the natural log of the IC50. For example, an IC50may be the concentration of a tested peptide in a binding assay at which 50% inhibition of binding of a labeled reference peptide is observed. Given the conditions in which the assays are run (e.g., limiting HLA protein concentrations and / or labeled reference peptide concentrations), these values can approximate KDvalues. Assays for determining binding are well known in the art and are described in detail, for example, in PCT publications WO 94 / 20127 and WO 94 / 03205, and other publications such as Sidney et al., Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J. Immunol.154:247 (1995); and Sette, et al., Mol. Immunol.31:813 (1994). Alternatively, binding can be expressed relative to binding by a referenceWSGR Docket No. 50401-775.601 standard peptide. Binding can also be determined using other assay systems including those using: live cells (e.g., Ceppellini et al., Nature 339:392 (1989); Christnick et al., Nature 352:67 (1991); Busch et al., Int. Immunol.2:443 (1990); Hill et al., J. Immunol.147:189 (1991); del Guercio et al., J. Immunol. 154:685 (1995)), cell free systems using detergent lysates (e.g., Cerundolo et al., J. Immunol.21:2069 (1991)), immobilized purified MHC (e.g., Hill et al., J. Immunol.152, 2890 (1994); Marshall et al., J. Immunol.152:4946 (1994)), ELISA systems (e.g., Reay et al., EMBO J. 11:2829 (1992)), surface plasmon resonance (e.g., Khilko et al., J. Biol. Chem.268:15425 (1993)); high flux soluble phase assays (Hammer et al., J. Exp. Med.180:2353 (1994)), and measurement of class I MHC stabilization or assembly (e.g., Ljunggren et al., Nature 346:476 (1990); Schumacher et al., Cell 62:563 (1990); Townsend et al., Cell 62:285 (1990); Parker et al., J. Immunol.149:1896 (1992)).
[0092] class I and MHC class II molecules and relate to a complex of genes which occurs in all vertebrates. MHC proteins or molecules can be important for signaling between lymphocytes and antigen presenting cells or diseased cells in immune reactions, wherein the MHC proteins or molecules bind peptides and present them for recognition by T cell receptors. The proteins encoded by the MHC canbe expressed on the surface of cells, and display both self -antigens (peptide fragments from the cellitself) and non-self-antigens (e.g., fragments of invading microorganisms) to a T cell. The MHC region can be divided into three subgroups, class I, class II, and class III. MHC class I proteins can contain --microglobulin (not part of the MHC encoded by chromosome 15). They can presentantigen fragments to cytotoxic T cell - -chains and they canpresent antigen fragments to T-helper cells. MHC class III region can encode for other immune components, such as complement components and cytokines. The MHC can be both polygenic (there are several MHC class I and MHC class II genes) and polymorphic (there are multiple alleles of each gene).
[0093] HLA) alleles found on onechromosome and the proteins encoded thereby. Haplotype may also refer to the allele present at any one locus within the MHC. Each class of MHC may be represented by several loci: e.g., HLA-A (Human Leukocyte Antigen-A). HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, HLA-H, HLA-J, HLA- K, HLA-L, HLA-P and HLA-V for class I and HLA-DRA, HLA-DRB1-9, HLA-DQA1, HLA-DQB1, HLA-DPA1, HLA-DPB1, HLA-DPB2, HLA-DMA, HLA-DMB, HLA-DOA, and HLA-DOB for d interchangeably herein.
[0094] WSGR Docket No. 50401-775.601 length, either deoxyribonucleotides or ribonucleotides, or analogs thereof. Polynucleotides may have any three-dimensional structure, and may perform any function, known or unknown. The following are non-limiting examples of polynucleotides: coding or non-coding regions of a gene or gene fragment, loci (locus) defined from linkage analysis, exons, introns, messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), short interfering RNA (siRNA), short-hairpin RNA (shRNA), micro-RNA (miRNA), ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes, and primers. A polynucleotide may comprise one or more modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure may be imparted before or after assembly of the polymer. Polynucleotides can include nonstandard nucleotides, such as nucleotide analogs or modified nucleotides. In some embodiments, nonstandard nucleotides can stabilize hybrid formation. In some embodiments, nonstandard nucleotides can destabilize hybrid formation. In some embodiments, nonstandard nucleotides can enhance hybridization specificity. In some embodiments, nonstandard nucleotides can reduce hybridizationspecificity. Example - - -- -alkyl- deoxyguanosine, 5-halo-substituted pyrimidine, alkyl-substituted purine, halo-substituted purine, -molecules, LNA-like molecules, diaminopurine, S2T, 5-fluorouracil, 5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine, xantine, 4- acetylcytosine, 5-(carboxyhydroxylmethyl)uracil, 5-carboxymethylaminomethyl-2-thiouridine, 5- carboxymethylaminomethyluracil, dihydrouracil, beta-D-galactosylqueosine, inosine, N6- isopentenyladenine, 1-methylguanine, 1-methylinosine, 2,2-dimethylguanine, 2-methyladenine, 2- methylguanine, 3-methylcytosine, 5-methylcytosine, N6-adenine, 7-methyl guanine, 5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil, beta-D- -methoxycarboxymethyluracil, 5-methoxyuracil, 2-methylthio-D46-isopentenyladenine, uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine, 2 -thiocytosine, 5- methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester, uracil-5-oxy acetic acid(v), 5-methyl-2-thiouracil, 3-(3-amino-3-N-2- carboxypropyl) uracil, (acp3)w, 2,6-diaminopurine, andderivatives thereof. The sequence of nucleotides may be interrupted by non-nucleotide components. A polynucleotide may be further modified after polymerization, such as by conjugation with a labeling component.WSGR Docket No. 50401-775.601
[0095] another nucleic acid sequence by either traditional Watson-Crick or other non-traditional types. A percent complementarity can indicate the percentage of residues in a nucleic acid molecule which can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary, respectively). hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence. to a degree of complementarity that may be at least 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% over a region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, or more nucleotides, or can refer to two nucleic acids that hybridize under stringent conditions. Sequence identity, such as for the purpose of assessing percent complementarity, may be measured by any suitable alignment algorithm, including but not limited to the Needleman-Wunsch algorithm (e.g., the EMBOSS Needle aligner available at www.ebi.ac.uk / Tools / psa / emboss_needle / nucleotide.html, optionally with default settings), the BLAST algorithm (see e.g., the BLAST alignment tool available at blast.ncbi.nlm.nih.gov / Blast.cgi,optionally with default settings), or the Smith-Waterman algorithm. Optimal alignment may beassessed using any suitable parameters of a chosen algorithm, including default parameters.
[0096] and may refer to a polymerof amino acid residues, and are not limited to a minimum length. For example, a polypeptide can comprise at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 1000 peptides or amino acids. Examples of polypeptides include, but are not limited to, amino acid chains, proteins, peptides, hormones,polypeptide saccharides, lipids, glycolipids, phospholipids, antibodies, enzymes, kinases, receptors,transcription factors, and ligands. Polypeptides, including the provided TCRs and TCR chains and other peptides, e.g., linkers and binding peptides, may include amino acid residues including natural and / or non-natural amino acid residues. The terms also include post-expression modifications of the polypeptide, for example, glycosylation, sialylation, acetylation, phosphorylation, and the like. In some aspects, the polypeptides may contain modifications with respect to a native or natural sequence, as long as the protein maintains the desired activity. These modifications may be deliberate, as through site-directed mutagenesis, or may be accidental, such as through mutations of hosts which produce the proteins or errors due to PCR amplification.
[0097] As used herein, the twenty conventional amino acids and their abbreviations known to oneskilled in the art follow conventional usage. Stereoisomers (e.g., D-amino acids) of the twentyWSGR Docket No. 50401-775.601 --disubstituted amino acids, N-alkylamino acids, lactic acid, and other unconventional amino acids may also be suitable components forpolypeptides of the present invention. Examples of unconventional amino acids include: 4 -- -N,N,N-trimethyll -N-acetyllysine, O-phosphoserine, N-acetylserine, N-formylmethionine, 3-methylhistidine, 5- -N-methylarginine, and othersimilar amino acids and imino acids (e.g., 4-hydroxyproline). In the polypeptide notation used herein, the left hand direction is the amino terminal direction and the right hand direction is the carboxy- terminal direction, in accordance with standard usage and convention. Percent (%) sequence identity with respect to a reference polypeptide sequence (or nucleic acid sequence) may be the percentage of amino acid residues (or nucleotides in case of nucleic acid sequence) in a candidate sequence that are identical with the amino acid residues (or nucleotides) in the reference polypeptide sequence (or nucleic acid sequence), after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or Megalign (DNASTAR) software. Those skilled in the art can determine appropriate parameters for aligning sequences, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared. For purposes herein, however, % amino acid sequence identity values are generated using the sequence comparison computer program ALIGN-2. The ALIGN-2 sequence comparison computer program was authored by Genentech, Inc., and the source code has been filed with user documentation in the U.S. Copyright Office, Washington D.C., 20559, where it is registered under U.S. Copyright Registration No. TXU510087. The ALIGN-2 program is publicly available from Genentech, Inc., South San Francisco, Calif., or may be compiled from the source code. The ALIGN-2 program should be compiled for use on a UNIX operating system, including digital UNIX V4.0D. All sequence comparison parameters are set by the ALIGN-2 program and do not vary. In situations where ALIGN- 2 is employed for amino acid sequence comparisons, the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain % amino acid sequence identity to, with, or against a given amino acid sequence B) is calculated as follows: 100 times the fraction X / Y, where X is the number of amino acid residues scored as identical matches by the sequence alignment program ALIGN-2 in that program's alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acidWSGR Docket No. 50401-775.601 sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A. Unless specifically stated otherwise, all % amino acid sequence identity values used herein are obtained as described in the immediately preceding paragraph using the ALIGN-2 computer program.
[0098] idcells from which they are formed. Germline DNA contains multiple gene segments that encode a single cells but cannot be transcribed and translated until they are arranged into functional genes. During T cell differentiation in the bone marrow, these gene segments are randomly shuffled by a dynamic genetic system capable of generating more than 108specificities.
[0099] interchangeably and refer to, for example, stasisof symptoms, prolongation of survival, partial or full amelioration of symptoms, and partial or full eradication of a condition, disease or disorder associated with excess levels of protein or correlated with protein activity. For example, treatment of cancer includes, but is not limited to, stasis, partial or total elimination of a cancerous growth or tumor. Treatment or partial elimination includes, for example, a fold reduction in growth or tumor size and / or volume such as about 2-fold, about 3-fold, about 4-fold, about 5-fold, about 10-fold, about 20-fold, about 50-fold, or any fold reduction in between. Similarly, treatment or partial elimination can include a percent reduction in growth or tumor size and / or volume of about 1%, 2%, 3%, 4%, 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or any percentage reduction in between. Prevention refers to prophylaxis, prevention of onset of symptoms, prevention of progression of a disease or disorder associated with excess levels of protein or correlated with protein activity.
[0100] Examples of subjects and hosts include, but are not limited to, horses, cows, camels, sheep, p igs, goats,dogs, cats, rabbits, guinea pigs, rats, mice (e.g., humanized mice), gerbils, non-human primates (e.g., macaques), humans and the like, non-mammals, including, e.g., non-mammalian vertebrates, such as birds (e.g., chickens or ducks) fish (e.g., sharks) or frogs (e.g., Xenopus), and non-mammalian invertebrates, as well as transgenic species thereof. In certain aspects, a subject refers to a single organism (e.g., human). In certain aspects, or a group of individuals composing a small cohort having either a common immune factor to study and / or disease, and / or a cohort of individuals without the disease (e.g., negative / normal control) are provided. A subject from whom samples are obtained can either be inflicted with a disease and / or disorder (e.g., one or more allergies, infections, cancers orWSGR Docket No. 50401-775.601 autoimmune disorders or the like) and can be compared against a negative control subject which is not affected by the disease.
[0101] ing out amethod disclosed herein. In some embodiments, kits include systems that allow for the storage, transport, or delivery of reaction reagents (e.g., probes, enzymes, etc. in the appropriate containers) and / or supporting materials (e.g., buffers, written instructions for performing the assay etc.) from one location to another. For example, kits include one or more enclosures (e.g., boxes) containing the relevant reaction reagents and / or supporting materials. Such contents may be delivered to the intended recipient together or separately. For example, a first container may contain an enzyme for use in an assay, while a second container contains a plurality of primers. A packaging material refers to a physical structure housing the components of the kit. The packaging material can maintain the components sterilely and can be made of material commonly used for such purposes (e.g., paper, corrugated fiber, glass, plastic, foil, ampules, etc.). The label or packaging insert can include appropriate written instructions. Kits, therefore, can additionally include labels or instructions for using the kit components in any method of the invention. A kit can include a compound in a pack, ordispenser together with instructions for administering the compound in a method described herein.
[0102] gene or the hostcell containing the gene to become resistant to treatment with a drug. For example, BTK C481Smutation is a resistance mutation which can confer ibrutinib resistance.Overview
[0103] The present disclosure provides T cell receptors (TCRs) against neoantigens, isolated nucleicacid molecules encoding TCRs against neoantigens, T cells expressing said TCRs, and pharmaceutical compositions for use in the treatment of diseases involving malignant cells expressing said neoantigens.
[0104] Provided herein is an isolated nucleic acid or a cell comprising a recombinant nucleic acid,wherein the nucleic acid encodes at least one T cell receptor (TCR) comprising a TCR alpha chain construct and / or a TCR beta chain construct, wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A*02:01 allele.
[0105] In some embodiments, the TCR alpha chain construct comprises a variable region having atleast 80% sequence identity to an amino acid sequence selected from SEQ ID NOs: 9, 24, 39, 54, 69, 84, and 99. In some embodiments, the TCR alpha chain construct comprises a variable region having at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at leastWSGR Docket No. 50401-775.601about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at leastabout 98%, at least about 99%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 9, 24, 39, 54, 69, 84, and 99. In some embodiments, the TCR beta chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence selected from SEQ ID NOs: 12, 27, 42, 57, 72, 87, 102. In some embodiments, the TCR beta chain construct comprises a variable region have at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 12, 27, 42, 57, 72, 87, 102.
[0106] In some embodiments, the TCR alpha chain construct comprises a complementaritydetermining region 1 (CDR1) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to an amino acid sequence selected from SEQ ID NOs: 1, 16, 31, 46, 61, 76, and 91. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.9%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 1, 16, 31, 46, 61, 76, and 91.
[0107] In some embodiments, the TCR beta chain construct comprises a complement aritydetermining region 1 (CDR1) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to an amino acid sequence selected from SEQ ID NOs: 4, 19, 34, 49, 64, 79, and 94. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.9%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 4, 19, 34, 49, 64, 79, and 94.
[0108] In some embodiments, the TCR alpha chain construct comprises a complementaritydetermining region 2 (CDR2) having at least 90% sequence identity to an amino acid sequence selectedfrom SEQ ID NOs: 2, 17, 32, 47, 62, 77, and 92. In some embodiments, the TCR alpha chain constructWSGR Docket No. 50401-775.601 comprises a complementarity determining region 2 (CDR2) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.9% or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 2, 17, 32, 47, 62, 77, and 92.
[0109] In some embodiments, the TCR beta chain construct comprises a complementaritydetermining region 2 (CDR2) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to an amino acid sequence selected from SEQ ID NOs: 5, 20, 35, 50, 65, 80, and 95. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, at least about 99.9%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 5, 20, 35, 50, 65, 80, and 95.
[0110] In some embodiments, the TCR alpha chain construct comprises a complementaritydetermining region 3 (CDR3) as set forth in SEQ ID NOs: 3, 18, 33, 48, 63, 78, or 93. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 3 (CDR3) as set forth in SEQ ID NOs: 6, 21, 36, 51, 66, 81, or 96.
[0111] In some embodiments, the TCR alpha chain construct comprises a variable region having atleast 80% sequence identity to SEQ ID NO: 24; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 27. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 16, a CDR2 of SEQ ID NO: 17, and a CDR3 of SEQ ID NO: 18; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 19, a CDR2 of SEQ ID NO: 20, and a CDR3 of SEQ ID NO: 21. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 69; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 72. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 61, a CDR2 of SEQ ID NO: 62, and a CDR3 of SEQ ID NO: 63; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 64, a CDR2 of SEQ ID NO: 65, and a CDR3 of SEQ ID NO: 66. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 9; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 12. In some embodiments, the TCR alpha chain constructWSGR Docket No. 50401-775.601 comprises a CDR1 of SEQ ID NO: 1, a CDR2 of SEQ ID NO: 2, and a CDR3 of SEQ ID NO: 3; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 4, a CDR2 of SEQ ID NO: 5, and a CDR3 of SEQ ID NO: 6. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 99; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 102. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 91, a CDR2 of SEQ ID NO: 92, and a CDR3 of SEQ ID NO: 93; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 94, a CDR2 of SEQ ID NO: 95, and a CDR3 of SEQ ID NO: 96. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 39; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 42. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 31, a CDR2 of SEQ ID NO: 32, and a CDR3 of SEQ ID NO: 33; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 34, a CDR2 of SEQ ID NO: 35, and a CDR3 of SEQ ID NO: 36. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 54; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 57. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 46, a CDR2 of SEQ ID NO: 47, and a CDR3 of SEQ ID NO: 48; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 49, a CDR2 of SEQ ID NO: 50, and a CDR3 of SEQ ID NO: 51. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 84; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 87. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 76, a CDR2 of SEQ ID NO: 77, and a CDR3 of SEQ ID NO: 78; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 79, a CDR2 of SEQ ID NO: 80, and a CDR3 of SEQ ID NO: 81.
[0112] In yet another aspect, the present disclosure provides a host cell comprising the nucleic acidencoding a TCR against a neoantigen provided herein, a vector containing the nucleic acid sequence, or a protein encoded by the nucleic acid provided herein. In some embodiments, the host cell is a CD4+T cell. In some embodiments, the host cell is a CD8+ T cell. The host cell may be a natural killer (NK)cell or a B cell. The host cell may be an immortalized cell line.
[0113] In yet another aspect, the present disclosure provides pharmaceutical compositions comprisingthe nucleic acid encoding a TCR against a neoantigen provided herein, a host cell comprising thenucleic acid encoding a TCR against a neoantigen provided herein, a vector containing the nucleic acidWSGR Docket No. 50401-775.601 sequence, or a protein encoded by the nucleic acid provided herein. In some embodiments, providedherein also comprises a method of using the pharmaceutical compositions disclosed herein.
[0114] Also provided herein in an additional aspect is a method of treating a subject with a diseaseor condition, comprising administering to the subject a pharmaceutical composition disclosed herein. In some embodiments, the subject has cancer. Also provided herein in an additional aspect is a method of identifying a subject with cancer as a candidate for a therapeutic comprising determining the subject expresses a protein encoded by an HLA-A*02:01 allele. T Cell Receptors (TCRs)
[0115] The ability of T cells to recognize antigens associated with various cancers or infectiouswhich employs a unique mechanism for generating the tremendous diversity of the TCR. This multi- subunit immune recognition receptor associates with the CD3 complex and binds peptides presented by the MHC class I and II proteins on the surface of antigen-presenting cells (APCs). Binding of a TCR to the antigenic peptide on the APC is a central event in T cell activation, which occurs at animmunological synapse at the point of contact between the T cell and the APC.
[0116] Each TCR contains variable complementarity determining regions (CDRs), as well asframework regions (FRs) and a constant region. The amino acid sequence of the third complementarity- T cells arising from recom i allows for a large number of distinct CDR3 sequences to be encoded. -- -process of TCR gene rearrangement further increases CDR3 sequence diversity. In this respect, early in development, has specialized anatomical distribution, has unique pathogen and small-molecule specificities, and has a broad spectrum of innate and adaptive cellular interactions. Early in ontogeny, V and J segment expression is established.WSGR Docket No. 50401-775.601
[0117] The TCRs provided herein target may be engineered TCRs, for example, chimeric antigenreceptors (CARs). CARs can be composed of three regions: an ectodomain, a transmembrane domain and an endodomain.
[0118] An ectodomain can be the region of the receptor that is exposed to the extracellular fluidand can consist of an antigen recognition region. In some embodiments, an ectodomain further comprises and a spacer. In some embodiments, an ectodomain further comprises and a signal peptide. A signal peptide can direct the nascent protein into the endoplasmic reticulum. A signal protein in a CAR may be a single-chain variable fragment (scFv). A fusion protein may be a protein that is formed by merging two or more genes that code originally for different proteins but when they are translated in the cell, the translation produces one or more polypeptides with functional properties derived for each of the original genes. A scFv is a chimeric protein made up of a light chain domain and heavychain variable domain connected with a short linker peptide. The linker may comprise hydrophilicresidues with stretches of glycine and / or serine residues. The linker may comprise stretches of glutamate and lysine residues, which can improve solubility.
[0119] A transmembrane domain can be a hydrophobic domain that spans the membrane. In someembodiments, a transmembrane domain comprises an alpha-helical domain. A transmembrane domain may be functional for the stability of the receptor as a whole. In some embodiments, a transmembrane domain comprises a transmembrane domain from the most membrane proximal component of an endodomain. In some embodiments, a transmembrane domain comprises a CD3-zeta transmembrane domain. In some embodiments, a transmembrane domain allows for incorporation of an artificial TCR into a native TCR complex. In some embodiments, a transmembrane domain comprises a CD28 transmembrane domain.
[0120] An endodomain can be a functional intracellular portion of a receptor, such as a TCR orCAR. After antigen recognition, receptors cluster and a signal may be transmitted to the cell. In some embodiments, an endodomain comprises aCD3-zeta intracellular domain. In some embodiments, an endodomain comprises at least one ITAM. In some embodiments, an endodomain comprises at least3 or at least 3 ITAMs. In some embodiments, an endodomain comprises a CD28 intracellular domain.In some embodiments, an endodomain comprises an OX40 intracellular domain. In some embodiments, an endodomain comprises a chimeric intracellular domain. For example, an endodomain can comprises aCD28 intracellular domain, an OX40 intracellular domain and a CD3-zeta intracellular domain. T cellsWSGR Docket No. 50401-775.601
[0121] T cells belong to a group of white blood cells known as lymphocytes, and play a central rolein cell-mediated immunity. T cells include CD4+T cells (helper T cells) and CD8+T cells (cytotoxic T cells). CD4+T cells can assist other white blood cells in immunologic processes, including maturation of B-cells and activation of cytotoxic T cells and macrophages. CD4+T cells are activated when presented with peptide antigens by MHC class II molecules expressed on the surface of antigen presenting cells (APCs). Once activated, the T cells can divide rapidly and secrete cytokines that regulate the active immune response. CD8+T cells can destroy virally infected cells and tumor cells, and can also be implicated in transplant rejection. CD8+T cells can recognize their targets by binding to antigen associated with MHC class I, which is present on the surface of nearly every cell of the body. Most T cells have a T cell receptor (TCR). The ability of T cells to recognize antigens associated with various cancers or infectious organisms is conferred by its TCR, which is made up of both an these chains are encoded by DNA, which employs a unique mechanism for generating the diversity of the TCR. This multi-subunit immune recognition receptor can associate with the CD3 complex andbind peptides presented by the MHC class I and II proteins on the surface of antigen -presenting cells(APCs). The first signal in activation of T cells can be provided by binding of the T cell receptor to ashort peptide presented by the MHC on another cell. This ensures that only a T cell with a TCR specific to (binds specifically to) that peptide is activated. The partner cell is usually an antigen presenting cell such as a professional antigen presenting cell, usually a dendritic cell in the case of naive responses, although B-cells and macrophages can be important APCs. Binding of a TCR to the antigenic peptide on the APC can be a central event in T cell activation, which occurs at an immunological synapse at the point of contact between the T cell and the APC.
[0122] T cells can be prepared according to methods known in the art. T cells can be an enriched Tcell preparation, an APC-depleted cell preparation, or a substantially purified T cell preparation. T cells can be a mixed T cell population or a purified T cell subset. T cells can be an enriched T cell preparation containing a number or percentage of T cells that is increased with respect to an isolated population of T cells.
[0123] T cells, or a subset of T cells, can be obtained from various lymphoid tissues. T cells can beobtained from a number of sources, including peripheral blood mononuclear cells (PBMCs), bonemarrow, thymus, tissue biopsy, tumor, lymph node tissue, gut associated lymphoid tissue, mucosa l circulate in the blood (e.g., peripheral blood). Peripheral blood lymphocytes can refer to lymphocytesWSGR Docket No. 50401-775.601 that are not localized to organs. Peripheral blood lymphocytes can comprise T cells, NK cells, B cell, or any combinations thereof.
[0124] The method can comprise isolating T cells from a subject. The method can comprise obtainingT cells isolated from a subject. T cells can be obtained from T cell lines. T cells can be obtained from autologous sources. T cells can be obtained from allogeneic sources. T cells may also be obtained from a xenogeneic source, for example, from mouse, rat, non-human primate, and pig.
[0125] T cells can be an APC-depleted cell preparation. T cells can be substantially free of APCs.For example, T cells can comprise T cells separated from over 75% of APCs. In an exemplary embodiment, peripheral blood mononuclear cells (PBMCs) can be obtained from blood, e.g., in heparinized vials. PBMCs can be separated from red blood cells by centrifugation and PBMCsrecovered from the interface. The recovered PBMCs optionally can be washed (e.g., with PBS).
[0126] T cell purification can be achieved, for example, by positive or negative selection including,but not limited to, the use of antibodies directed to CD2, CD3, CD4, CD5, CD8, CD14, CD19, and / or MHC class II molecules. A specific T cell subset, such as CD28+, CD4+, CD8+, CD45RA+, and / or CD45RO+T cells, can be isolated by positive or negative selection techniques. For example, CD3+, CD28+T cells can be positively selected using CD3 / CD28 conjugated magnetic beads. In one aspect of the present invention, enrichment of a T cell population by negative selection can be accomplished with a combination of antibodies directed to surface markers unique to the negatively selected cells.
[0127] For example, a T cellobtained by apheresis or leukapheresis. A T cell sample may contain lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and / or platelets. Undesirable components of the T cell sample can be removed and the remaining T cells can besuspended in culture media. For example, cells can be washed to remove the plasma fraction. Forexample, T cells can be isolated from peripheral blood lymphocytes by lysing the red blood cells andby centrifugation through a PERCOLL gradient.
[0128] In some embodiments, T cells can be obtained by positive selection and / or negative selection.In positive selection, an affinity agent (such as an antibody, an antibody fragment, and aptamer) can be used to bind a cell surface marker expressed on the population of cells, for example, CD3 for T cells. Using the affinity agent, the T cells can be labeled. The labeled T cells can then be enriched using various methods that are well-known in the art. Non-limiting examples of those methods include fluorescent-activated cell sorting (FACS) and (para)magnetic particle-based cell separation (e.g. MACS cell separation kits from Miltenyi Biotec).WSGR Docket No. 50401-775.601
[0129] In negative selection, affinity agents can be used to bind cell surface markers expressed onblood cells other than the desired population. For example, when attempting to isolate T cells, a cocktail of affinity agents can be used to label B cells, NK cells, monocytes, platelets, dendritic cells,granulocytes and erythrocytes. The labeled cells can then be depleted, leaving the T cells enriched.The exemplary methods to deplete labeled cells include FACS and (para)magnetic particle-based cell separation.
[0130] In addition to labeling-based isolation, special growth condition may be used to promote thegrowth of one particular cell population. For example, the special growth condition can be obtained using special cytokines or growth factors. For another example, in culture media containing phytohemagglutinin (PHA), IL-2, and / or IL-15, T cells may preferentially proliferate.
[0131] In some situations, non-functional markers may be used to isolate T cells since binding offunctional markers such as binding of CD3 by anti-CD3 antibody (alone or conjugated to magnetic particles) may trigger unwanted signaling events on T cells. Therefore, a cocktail of antibodies against CD14, CD15, CD16, CD19, CD34, CD36, CD56, CD123, and CD235a (glycophorin A) can be used to isolate T cells.
[0132] Detailed protocol can be found in published literatures (e.g. see Lefort et al. , J Vis Exp.2010;(40): 2017) which are incorporated by reference herein. T cell isolation kits can be obtained from, for example, STEMCELL Technologies, Thermofisher, and Miltenyi Biotec.
[0133] The T cell described herein may be an allogeneic T cell.
[0134] In some embodiments, the T cell may be a genetically-modified cell comprising in its genomea modified human T cell receptor (TCR) alpha chain gene and / or a modified human TCR beta chain gene, wherein the cell has reduced cell-surface expression of the endogenous TCR.
[0135] Gene-editing nucleases may be employed in order to disrupt components of the TCR. The
[0136] Various methods may be used to disrupt endogen For example,four classes of gene editing proteins exist that share a common mode of action in binding a user defined sequence of DNA and mediating a double stranded DNA break (DSB). Zinc finger nucleases (ZFN) are heterodimeric arrays that co-localize at a target DNA site. ZFNs include individual finger subunits that bind DNA and are tethered to the Fokl nuclease domain that cleaves DNA. Transcription activator- like effector nucleases (TALEN) include repeating units that bind DNA by virtue of a hypervariable two amino acid sequence (repeat variable diresidue; RVD) that governs DNA base recognition. SimilarWSGR Docket No. 50401-775.601 to ZFNS, TALENs function as dimeric proteins that are fused to the Fokl endonuclease domain for DSB generation. Meganucleases (MN) are monomeric proteins with innate nuclease activity that are derived from bacterial homing endonucleases and engineered for a unique target site. The clustered regularly interspaced short palindromic repeats (CRISPR) and associated Cas9 nuclease platform involves a small guide RNA (gRNA) transcript that contacts a target DNA sequence via Watson-Crick base pairing and the Cas9 nuclease that cleaves the DNA.
[0137] In some embodiments, introducing the genome-editing nuclease into the T cell includesintroducing into the T cell a polynucleotide that encodes the genome-editing nuclease.
[0138] In some embodiments, introducing the genome-editing nuclease into the T cell includesintroducing into the T cell a Cas9 polypeptide. In some embodiments, the genome-editing nucleaseincludes a TALEN nuclease, a CRISPR / Cas9 nuclease, or a megaTAL nuclease.
[0139] In some embodiments, the CRISPR / Cas9 nuclease is derived from either Streptococcuspyogenes or Staphylococcus aureus. In some of these embodiments, the CRISPR / Cas9 nuclease includes a nuclease-resistant gRNA such as, for example, at least one 2'-OMe-phosphorothioate modified base, at least one 2'-O-methyl modified base, or at least one 2'-O-methyl 3' thioPACE modified base.
[0140] In some embodiments, the TALEN nuclease or the megaTAL nuclease is encoded by an RNAthat has an exogenous polyadenylation signal.
[0141] In some embodiments, the method described herein may further include culturing the T cellunder conditions effective for expanding the population of genome-modified T cells.
[0142] In some embodiments, disrupting expression of further disrupts. In some embodiment further disruptsformation of a complex between TCR and CD3. In some embodiments, disrupting expreinvolves fur .
[0143] In some embodiments, a genetically-modified T cell comprises a disrupted TCR alpha chainand / or beta chain and an inactivated gene encoding immune checkpoint protein such as PD1 and CTLA-4. This may be made possible by gene inactivation using specific TALE-nucleases directed against TCR alpha or TCR beta coupled with inactivation of genes encoding immune checkpoint protein such as PD1 and CTLA-4.
[0144] In some embodiments, the genetic modification relies on the inactivation of one gene, or twogenes selected from the group consisting of PD1, CTLA-4, LAG3, Tim3, BTLA, BY55, TIGIT, B7H5, LAIR1, SIGLEC10, 2B4, TCR alpha and TCR beta. In some embodiments, the genetic modification relies on the inactivation of two genes selected from the group consisting of PD1 and TCR alpha, PD1WSGR Docket No. 50401-775.601 and TCR beta, CTLA-4 and TCR alpha, CTLA-4 and TCR beta, LAG 3 and TCR alpha, LAG 3 and TCR beta, Tim3 and TCR alpha, Tim3 and TCR beta, BTLA and TCR alpha, BTLA and TCR beta, BY55 and TCR alpha, BY55 and TCR beta, TIGIT and TCR alpha, TIGIT and TCR beta, B7H5 and TCR alpha, B7H5 and TCR beta, LAIRl and TCR alpha, LAIR1 and TCR beta, SIGLEC10 and TCR alpha, SIGLEC10 and TCR beta, 2B4 and TCR alpha, 2B4 and TCR beta. In some embodiments, the genetic modification relies on the inactivation of more than two genes. The genetic modification may be operated ex-vivo. TCRs Specific to GATA3 peptide-MHC complexes
[0145] GATA3 is frequently mutated in breast cancer and appears to regulate b reast cancer vianumerous molecular mechanisms. GATA3 distal deletion mutations also cause HDR syndrome (hypoparathyroidism, sensorineural deafness, and renal dysplasia) and DiGeorge syndrome. GATA3 gene is on chromosome 10p15. It consists of six exons and encodes a transcription factor and two transactivating domains and two zinc finger domains on exons 2-6. Tumor suppressor functions of GATA3 have been demonstrated primarily in basal-like breast cancers and luminal breast cancers. In ER- (ER negative) basal-like breast cancer (BLBC) GATA3 function is largely attributed to negative regulation of genes associated with invasion and dedifferentiation, and loss of GATA3 expression is involved in aggressiveness of BLBC. In luminal breast cancer, GATA3 directly upregulated proto- oncogenes.
[0146] Several frameshift mutations in GATA3 gene in various cancers result in neoORFs, whichcan translate to generate mutated GATA3 protein containing segments encoded by the neoORFs, and which in turn may comprise neoantigens. Nearly 39 / 66 frameshift mutations in GATA3 result in aprotein with extended C-terminus. These extension mutations predominantly occur in exon 6 and mayaffect the amino acids following the frameshift, resulting in mutant proteins starting from different residues between alanine 395 and glycine 444, with a hotspot (11 / 39) at proline 409. The mutations are strongly biased toward the +1 frame. This is surprising, as -1 frameshifts in this position wouldresult in a shortened and aberrant C-terminus. The alternative +1 frame alters up to 49 amino acids ofthe original C-terminus and extends the protein by 63 novel amino acids.
[0147] Provided below in Table 3 are GATA3 sequences encoded by three most common neoORFs.Underlined amino acids (AAs) represent non-native AAs.
[0148] Table 3: GATA3 frameshifted mutated sequencesWSGR Docket No. 50401-775.601
[0149] The frameshift mutations described herein are highly prevalent in estrogen positive (ER+)breast cancers. T cells having TCRs that can bind to epitopes that are thus mutated by the frameshift, can target specifically those cancer cells presenting the mutated epitopes. ER positive breast cancer is a common type of breast cancer, and may account for nearly 80% of all breast cancers. ER+ breast However, these mutations could also occur in hormone receptor negative (HR-) breast cancer as well. T cell therapy can be an efficient and innovative therapeutic approach in breast cancer, wherein the T cell is engineered to express a TCR that specifically binds to a HLA-peptide complex comprising (i) an epitope from the frameshift mutation of GATA3, and (ii) an MHC protein encoded by an HLA allele that is known to bind to the epitope, and is expressed by the subject with the cancer. Additional immunotherapeutic modalities are described herein, including but not limited to vaccines, e.g., peptide vaccines, dendritic cell (or APC cell) vaccines, TCR vaccines, each of which may be generated based on the disclosure provided herein.
[0150] Accordingly, in one aspect, a GATA3 neoantigen from a GATA mutated segment thatgenerates a novel peptide and that is encoded by the neoORF may be used in the preparation of a vaccine for use in treating a GATA3 cancer, e.g. a breast cancer, wherein the vaccine comprises one or more neoantigenic epitopes, or a polynucleic acid encoding the one or more neoantigenic epitopes. In some embodiments, a vaccine may comprise one or more polypeptides comprising one or more neoepitopes encoded by a GATA3 neoORF.
[0151] In some embodiments, a therapeutic composition, e.g., a vaccine may comprise a GATA3polypeptide, or a polynucleic acid encoding the GATA3 polypeptide. In one embodiment, theWSGR Docket No. 50401-775.601 GATA3 polypeptide may comprise a sequence, PGRPLQTHVLPEPHLALQPLQPHADHAHADAPAIQPVLWTTPPLQHGHRHGLEPCSMLTGP PARVPAVPFDLHFCRSSIMKPKRDGYMFLKAESKIMFATLQRSSLWCLCSNH.
[0152] In one embodiment, a therapeutic composition, e.g., a vaccine may comprise a polynucleicacid sequence encoding the polypeptide PGRPLQTHVLPEPHLALQPLQPHADHAHADAPAIQPVLWTTPPLQHGHRHGLEPCSMLTGP PARVPAVPFDLHFCRSSIMKPKRDGYMFLKAESKIMFATLQRSSLWCLCSNH. For example, the vaccine may comprise an mRNA encoding the polypeptide, having the neoORF encoded sequence provided above. In some embodiments, the vaccine is a dendritic cell vaccine or an APC cell therapeutic. In some embodiments, a polynucleic acid (e.g. mRNA) having a sequence encoding the polypeptide as provided above is incorporated into antigen presenting cells (e.g., via electroporation) to generate an APC cell therapeutic. The APCs of the APC cell therapeutic express the polynucleotide and present the neoepitopes in combination with an MHC molecule encoded by an HLA on the surface, wherein the combination with an MHC molecule encoded by an HLA and the neoepitope presented on the APCs can activate T cells and may generate antigen responsive T cells. In some embodiments, antigen presenting cells expressing the polynucleic acid (e.g. mRNA) having a sequence encoding the polypeptide as provided above may be used to stimulate T cells ex vivo.
[0153] In some embodiments, a therapeutic composition, e.g., a vaccine may comprise a GATA3polypeptide, or a polynucleic acid encoding the GATA3 polypeptide. In one embodiment, a GATA3 peptide may comprise a sequence, PRPRRCTRHPACPLDHTTPPAWSPPWVRALLDAHRAPSESPCSPFRLAFLQEQYHEA.
[0154] In one embodiment, a therapeutic composition, e.g., a vaccine may comprise a polynucleicacid sequence encoding the polypeptide PRPRRCTRHPACPLDHTTPPAWSPPWVRALLDAHRAPSESPCSPFRLAFLQEQYHEA. For example, the vaccine may comprise an mRNA encoding the polypeptide having the neoORF encoded sequence provided above. In some embodiments, the vaccine is a dendritic cell vaccine or an APC cell therapeutic. In some embodiments, a polynucleic acid (e.g. mRNA) having a sequence encoding the polypeptide as provided above is incorporated antigen presenting cells (e.g., via electroporation) to generate an APC cell therapeutic. The APCs of the APC cell therapeutic express the polynucleotide and present the neoepitopes in combination with an MHC molecule encoded by an HLA. In some embodiments, antigen presenting cells expressing the polynucleic acid (e.g.WSGR Docket No. 50401-775.601 mRNA) having a sequence encoding the polypeptide as provided above may be used to stimulate T cells ex vivo.
[0155] In some embodiments, a therapeutic composition, e.g., a vaccine may comprise a GATA3polypeptide, or a polynucleic acid encoding the GATA3 polypeptide. In one embodiment, the GATA3 polypeptide may comprise a sequence: AQAKAVCSQESRDVLCELSDHHNHTLEEECQWGPCLQCLWALLQASQY.
[0156] In one embodiment, a therapeutic composition, e.g., a vaccine may comprise a polynucleicacid sequence encoding the polypeptide AQAKAVCSQESRDVLCELSDHHNHTLEEECQWGPCLQCLWALLQASQY. For example, the vaccine may comprise an mRNA encoding the polypeptide having the neoORF encoded sequence provided above. In some embodiments, the vaccine is a dendritic cell vaccine or an APC cell therapeutic. In some embodiments, a polynucleic acid (e.g. mRNA) having a sequence encoding the polypeptide as provided above is incorporated antigen presenting cells (e.g., via electroporation) to generate an APC cell therapeutic. The APCs of the APC cell therapeutic express the polynucleotideand present the neoepitopes in combination with an MHC molecule encoded by an HLA. In so meembodiments, antigen presenting cells expressing the polynucleic acid (e.g. mRNA) having asequence encoding the polypeptide as provided above may be used to stimulate T cells ex vivo.
[0157] In one aspect, TCRs may be generated that are capable of binding to a neoantigen, e.g. aGATA3 neoantigen resulting from a frame-shift mutation leading to formation of a neoORF. The advantage for such TCRs, as is known for all neoantigen-specific TCRs is that T cells comprising the TCR will selectively attack and destroy cells that express the mutated GATA3 gene expressing the neoantigens. In an aspect, therefore, provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chain construct capable of specifically binding to an epitope from human GATA3 in complex with a human MHC, wherein the TCR beta chain construct comprises a complementarity determining region 3 (CDR3) having an amino acid sequence selected from SEQ ID NOs: 6, 21, 36, 51, 66, 81, and 96.
[0158] In some embodiments, the TCR beta chain construct comprises a complementaritydetermining region 1 (CDR1) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to an amino acid sequence selected from SEQ ID NOs: 4, 19, 34, 49, 64, 79, and 94. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) comprising an amino acid sequence of SEQ ID NOs: 4, 19, 34, 49, 64, 79, or 94, or a variant thereof comprisingWSGR Docket No. 50401-775.601 1-3 amino acid modifications. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) having 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 4, 19, 34, 49, 64, 79, and 94. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to an amino acid sequence selected from SEQ ID NOs: 5, 20, 35, 50, 65, 80, and 95. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) comprising an amino acid sequence of SEQ ID NOs: 5, 20, 35, 50, 65, 80, or 95, or a variant thereof comprising 1-3 amino acid modifications. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 2 (CDR2) having 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 5, 20, 35, 50, 65, 80, and 95.
[0159] In some embodiments, the recombinant nucleic acid encoding a T cell receptor (TCR)comprises a TCR alpha chain construct capable of specifically binding to an epitope from human GATA3 in complex with a human MHC, wherein the TCR alpha chain construct comprises a complementarity determining region 3 (CDR3) having an amino acid sequence selected from SEQ ID NOs: 3, 18, 33, 48, 63, 78, and 93.
[0160] In some embodiments, the TCR alpha chain construct comprises a complementaritydetermining region 1 (CDR1) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to an amino acid sequence selected from SEQ ID NOs: 1, 16, 31, 46, 61, 76, and 91. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 1 (CDR1) comprising an amino acid sequence of SEQ ID NOs: 1, 16, 31, 46, 61, 76, or 91, or a variant thereof comprising 1-3 amino acid modifications. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 1 (CDR1) having 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 1, 16, 31, 46, 61, 76, and 91. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) having at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, at least about 99.5%, or at least about 99.9% sequence identity to an amino acid sequence selected from SEQ ID NOs: 2, 17, 32, 47, 62, 77, and 92. In some embodiments, the TCR beta chain construct comprises aWSGR Docket No. 50401-775.601 complementarity determining region 2 (CDR2) comprising an amino acid sequence of SEQ ID NOs:2, 17, 32, 47, 62, 77, or 92, or a variant thereof comprising 1 -3 amino acid modifications. In someembodiments, the TCR alpha chain construct comprises a complementarity determining region 2(CDR2) having 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 2, 17, 32, 47, 62, 77, and 92.
[0161] In some embodiments, the recombinant nucleic acid encoding a T cell receptor (TCR)comprises a TCR beta chain construct; wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the TCR beta chain construct comprises a variable region having at least 70%, 75%, 80%, or 85% sequence identity to an amino acid sequence selected from SEQ ID NOs: 12, 27, 42, 57, 72, 87, 102. In some embodiments, the TCR beta chain construct comprises a variable region having at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 12, 27, 42, 57, 72, 87, 102. In some embodiments, the nucleic acid encoding at least one T cell receptor (TCR) comprises a TCR alpha chain construct; wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 70%, 75%, 80%, or 85% sequence identity to an amino acid sequence selected from SEQ ID NOs: 9, 24, 39, 54, 69, 84, and 99. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 9, 24, 39, 54, 69, 84, and 99.
[0162] In some embodiments, the recombinant nucleic acid encoding a T cell receptor (TCR)comprises a TCR beta chain construct; wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the TCR beta chain construct comprises a variable region having at least 70%, 75%, 80%, or 85% sequence identity to an amino acid sequence selected from SEQ ID NOs: 108, 110, 112, 114, 116, 118, and 120. In some embodiments, the TCR beta chain construct comprises a variable region having at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 108, 110, 112, 114, 116, 118, and 120. In some embodiments, the nucleic acid encoding at least one T cell receptor (TCR) comprises a TCR alpha chain construct; wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 70%, 75%, 80%, or 85% sequence identity to an amino acid sequence selected from SEQ ID NOs: 107, 109, 111, 113, 115, 117, and 119. In some embodiments, the TCR alpha chain construct comprises aWSGR Docket No. 50401-775.601 variable region having at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 107, 109, 111, 113, 115, 117, and 119.
[0163] In some embodiments, the TCR comprises a beta chain construct having at least 70%, 75%,80%, or 85% sequence identity to an amino acid sequence selected from SEQ ID NOs: 14, 29, 44, 59, 74, 89, and 104. In some embodiments, the TCR comprises a beta chain construct having at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 14, 29, 44, 59, 74, 89, and 104. In some embodiments, the TCR comprises an alpha chain construct having at least 70%, 75%, 80%, or 85% sequence identity to an amino acid sequence selected from SEQ ID NOs: 13, 28, 43, 58, 73, 88, and 103. In some embodiments, the TCR comprises an alpha chain construct having at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 13, 28, 43, 58, 73, 88, and 103.
[0164] In some embodiments, the epitope from human GATA3 comprises a region having at least70%, 75%, 80%, 85%, 90%, 95%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NO: 15.
[0165] Provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR) comprising aTCR beta chain construct, wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the beta chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence selected from SEQ ID NOs: 27 and 72 wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence selected from SEQ ID NOs: 24 and 69, wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele.
[0166] In some embodiments, the TCR alpha chain construct as described above comprises acomplementarity determining region 1 (CDR1) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 16 and 61. In some embodiments, the TCR beta chain construct as described above comprises a complementarity determining region 1 (CDR1) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 19 and 64. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 17 and 62. In some embodiments TCR beta chain construct comprises a complementarity determining region 2 (CDR2) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 20 and 65. In some embodiments, the TCR alpha chain construct comprises aWSGR Docket No. 50401-775.601 complementarity determining region 3 (CDR3) having an amino acid sequence selected from SEQ ID NOs: 18 and 63. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 3 (CDR3) having an amino acid sequence selected from SEQ ID NOs: 21 and 66.
[0167] Provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR) comprising aTCR beta chain construct, wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the beta chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence selected from SEQ ID NOs: 12 and 102 wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence selected from SEQ ID NOs: 9 and 99, wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele.
[0168] In some embodiments, the TCR alpha chain construct as described above comprises acomplementarity determining region 1 (CDR1) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 1 and 91. In some embodiments, the TCR beta chain construct as described above comprises a complementarity determining region 1 (CDR1) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 4 and 94. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 2 and 92. In some embodiments TCR beta chain construct comprises a complementarity determining region 2 (CDR2) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 5 and 95. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 3 (CDR3) having an amino acid sequence selected from SEQ ID NOs: 3 and 93. In some embodiments, the TCR beta chain construct comprises a complementarity determining region3 (CDR3) having an amino acid sequence selected from SEQ ID NOs: 6 and 96.
[0169] Provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR) comprising aTCR beta chain construct, wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the beta chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence selected from SEQ ID NOs: 42 and 57 wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to an amino acidWSGR Docket No. 50401-775.601 sequence selected from SEQ ID NOs: 39 and 54, wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele.
[0170] In some embodiments, the TCR alpha chain construct as described above comprises acomplementarity determining region 1 (CDR1) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 31 and 46. In some embodiments, the TCR beta chain construct as described above comprises a complementarity determining region 1 (CDR1) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 34 and 49. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 32 and 47. In some embodiments TCR beta chain construct comprises a complementarity determining region 2 (CDR2) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 35 and 50. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 3 (CDR3) having an amino acid sequence selected from SEQ ID NOs: 33 and 48. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 3 (CDR3) having an amino acid sequence selected from SEQ ID NOs: 36 and 51.
[0171] Provided herein is a recombinant nucleic acid encoding a T cell receptor (TCR) comprising aTCR beta chain construct, wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the beta chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence selected from SEQ ID NO: 87 wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence selected from SEQ ID NO: 84, wherein the TCR specifically binds to an epitope from GATA3 in complex with a human MHC encoded by an HLA-A02:01 allele.
[0172] In some embodiments, the TCR alpha chain construct as described above comprises acomplementarity determining region 1 (CDR1) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 76. In some embodiments, the TCR beta chain construct as described above comprises a complementarity determining region 1 (CDR1) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 79. In some embodiments, the TCR alpha chain construct comprises a complementarity determining region 2 (CDR2) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 77. In some embodiments TCR beta chain construct comprises a complementarity determining region 2 (CDR2) having at least 90% sequence identity to an amino acid sequence selected from SEQ ID NOs: 80. InWSGR Docket No. 50401-775.601 some embodiments, the TCR alpha chain construct comprises a complementarity determining region 3 (CDR3) having an amino acid sequence selected from SEQ ID NOs: 78. In some embodiments, the TCR beta chain construct comprises a complementarity determining region 3 (CDR3) having an amino acid sequence selected from SEQ ID NOs: 81.
[0173] In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 16,a CDR2 of SEQ ID NO: 17, and a CDR3 of SEQ ID NO: 18; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 19, a CDR2 of SEQ ID NO: 20, and a CDR3 of SEQ ID NO: 21. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 24; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 27. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 61, a CDR2 of SEQ ID NO: 62, and a CDR3 of SEQ ID NO: 63; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 64, a CDR2 of SEQ ID NO: 65, and a CDR3 of SEQ ID NO: 66. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 69; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 72. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 1, a CDR2 of SEQ ID NO: 2, and a CDR3 of SEQ ID NO: 3; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 4, a CDR2 of SEQ ID NO: 5, and a CDR3 of SEQ ID NO: 6. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 9; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 12. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 91, a CDR2 of SEQ ID NO: 92, and a CDR3 of SEQ ID NO: 93; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 94, a CDR2 of SEQ ID NO: 95, and a CDR3 of SEQ ID NO: 96. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 99; and the TCR beta chainconstruct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 102. Insome embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 31, a CDR2 of SEQ ID NO: 32, and a CDR3 of SEQ ID NO: 33; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 34, a CDR2 of SEQ ID NO: 35, and a CDR3 of SEQ ID NO: 36. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 39; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 42. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 46, a CDR2 of SEQ ID NO: 47, and a CDR3 of SEQ ID NO: 48; and the TCRWSGR Docket No. 50401-775.601 beta chain construct comprises a CDR1 of SEQ ID NO: 49, a CDR2 of SEQ ID NO: 50, and a CDR3 of SEQ ID NO: 51. In some embodiments, the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 54; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 57. In some embodiments, the TCR alpha chain construct comprises a CDR1 of SEQ ID NO: 76, a CDR2 of SEQ ID NO: 77, and a CDR3 of SEQ ID NO: 78; and the TCR beta chain construct comprises a CDR1 of SEQ ID NO: 79, aCDR2 of SEQ ID NO: 80, and a CDR3 of SEQ ID NO: 81. In some embodiments, the TCR alphachain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 84; and the TCR beta chain construct comprises a variable region having at least 80% sequence identity to SEQ ID NO: 87.
[0174] In an aspect, provided herein is a soluble T cell receptor (TCR), comprising at least a TCRvariable domain, comprising a CDR3 having at least 90%, 95%, 96%, 97%, 98%, 99%, or 100% sequence identity to an amino acid sequence selected from SEQ ID NOs: 6, 21, 36, 51, 66, 81, and 96.
[0175] In various embodiments, the nucleic acid sequence encoding a TCR is codon optimized.Codon optimization is a technique that may maximize protein expression by increasing the translational efficiency of the encoding gene. Codon optimization may enhance translational efficiency through modification of the nucleic acid sequence. In some embodiments, codon optimization may further enhance vector yield. In some embodiments, a TCR alpha chain variable domain may be codon optimized. In some embodiments, the TCR alpha chain construct comprises a variable region having at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% sequence identity to a codon optimized sequence as set forth in SEQ ID NOs: 8, 23, 38, 53, 68, 83, 98. In some embodiments, a TCR alpha chain variable domain may not be t. In some embodiments, the TCR alpha chain construct comprises a variable region having at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at leastabout 98%, at least about 99%, or 100% sequence identity to a nucleotide sequence as set forth in SEQID NOs: 7, 22, 37, 67, 82, 97.
[0176] In some embodiments, a TCR beta chain variable domain may be codon optimized. In someembodiments, the TCR beta chain construct comprises a variable region having at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at leastWSGR Docket No. 50401-775.601 about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% sequence identity to a codon optimized sequence as set forth in SEQ ID NOs: 11, 26, 41, 56, 71, 86, 101. In some embodiments, a TCR beta chain variable domain may not be codon optimized. In some embodiments, the TCR beta chain construct comprises a variable region having at least about 75%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% sequence identity to a nucleotide sequence as set forth in SEQ ID NOs: 10, 25, 40, 55, 70, 85, 100.
[0177] T cells can combine through V(D)J recombination to generate diverse and functional TCRScapable of proper expression and MHC recognition. A TCR is composed of an alpha and beta chain which can be generated through V(D)J recombination. In some embodiments, the TCR alpha chain comprises a complementarity determining region 3 (CDR3) as set forth in SEQ ID NO: 18. In some embodiments, the TCR alpha chain comprises a CDR3 generated from TRAV9-2*02 and / or TRAJ48*01. In some embodiments, the TCR beta chain comprises a complementarity determining region 3 (CDR3) as set forth in SEQ ID NO: 21. In some embodiments, the TCR beta chain comprises a CDR3 generated from TRBV24-1*01, TRBJ2-5*01, and / or TRBD1*01.
[0178] In some embodiments, the TCR alpha chain comprises a complementarity determining region3 (CDR3) as set forth in SEQ ID NO: 63. In some embodiments, the TCR alpha chain comprises a CDR3 generated from TRAV29 / DV5*04 and / or TRAJ28*01. In some embodiments, the TCR beta chain comprises a complementarity determining region 3 (CDR3) as set forth in SEQ ID NO: 66. In some embodiments, the TCR beta chain comprises a CDR3 generated from TRBV27*01, TRBJ1- 5*01, and / or TRBD1*01.
[0179] In some embodiments, the TCR alpha chain comprises a complementarity determining region3 (CDR3) as set forth in SEQ ID NO: 3. In some embodiments, the TCR alpha chain CDR3 may be generated from TRAV19*01 and / or TRAJ42*01. In some embodiments, the TCR beta chain comprises a complementarity determining region 3 (CDR3) as set forth in SEQ ID NO: 6. In some embodiments, the TCR beta chain comprises a CDR3 generated from TRBV28*01, TRBJ2-7*01, and / or TRBD1*01.
[0180] In some embodiments, the TCR alpha chain comprises a complementarity determining region3 (CDR3) as set forth in SEQ ID NO: 93. In some embodiments, the TCR alpha chain comprises a CDR3 generated from TRAV8-1*01 and / or TRAJ6*01. In some embodiments, the TCR beta chainWSGR Docket No. 50401-775.601 comprises a complementarity determining region 3 (CDR3) as set forth in SEQ ID NO: 96. In some embodiments, the TCR beta chain comprises a CDR3 generated from TRBV28*01, TRBJ1-1*01, TRBD1*01.
[0181] In some embodiments, the TCR alpha chain comprises a complementarity determining region3 (CDR3) as set forth in SEQ ID NO: 33. In some embodiments, the TCR alpha chain comprises a CDR3 generated from TRAV41*01 and / or TRAJ45*01. In some embodiments, the TCR beta chain comprises a complementarity determining region 3 (CDR3) as set forth in SEQ ID NO: 36. In some embodiments, the TCR beta chain comprises a CDR3 generated from TRBV28*01, TRBJ2-3*01, and / or TRBD1*01.
[0182] In some embodiments, the TCR alpha chain comprises a complementarity determining region3 (CDR3) as set forth in SEQ ID NO: 48. In some embodiments, the TCR alpha chain comprises a CDR3 generated from TRAV8-1*01 and / or TRAJ45*01. In some embodiments, the TCR beta chain comprises a complementarity determining region 3 (CDR3) as set forth in SEQ ID NO: 51. In some embodiments, the TCR beta chain comprises a CDR3 generated from TRBV7-8*01 and / or TRBJ2- 5*01.
[0183] In some embodiments, the TCR alpha chain comprises a complementarity determining region3 (CDR3) as set forth in SEQ ID NO: 78. In some embodiments, the TCR alpha chain comprises a CDR3 generated from TRAV13-1*01 and / or TRAJ37*02. In some embodiments, the TCR beta chain comprises a complementarity determining region 3 (CDR3) as set forth in SEQ ID NO: 81. In some embodiments, the TCR beta chain comprises a CDR3 generated from TRBV6-5*01, TRBJ2-3*01, and / or TRBD2*01.
[0184] In some embodiments, the TCR alpha chain comprises a complementarity determining region3 (CDR3) as set forth in SEQ ID NO: 78. In some embodiments, the TCR alpha chain comprises a CDR3 generated from TRAV13-1*01 and / or TRAJ37*02. In some embodiments, the TCR beta chain comprises a complementarity determining region 3 (CDR3) as set forth in SEQ ID NO: 81. In some embodiments, the TCR beta chain comprises a CDR3 generated from TRBV6-5*01, TRBJ2-3*01, and / or TRBD2*01.
[0185] In various embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein theGATA peptide comprises at least one amino acid encoded by a GATA3 neoORF sequence. In variousembodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein the GATA peptidecomprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids encoded by a GATA3 neoORF sequence. In various embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein the GATA peptide comprises at least one amino acidWSGR Docket No. 50401-775.601 encoded by a GATA3 neoORF sequence and at least one amino acid encoded by a GATA3 wild type sequence. In various embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein the GATA peptide comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids encoded by a GATA3 neoORF sequence and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids encoded by a GATA3 wild type sequence. In various embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein the GATA peptide comprises at least one amino acid encoded by a GATA3 neoORF sequence and at least one amino acid not encoded by a GATA3 neoORF sequence. In various embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein the GATA peptide comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids encoded by a GATA3 neoORF sequence and at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 amino acids not encoded by a GATA3 neoORF sequence. In various embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein each amino acid of the GATA peptide is an amino acid encoded by a GATA3 neoORF sequence. In some embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein the GATA3 peptide comprises a sequence of MLTGPPARV (SEQ ID NO: 15).
[0186] In various embodiments, the human MHC is encoded by an HLA-A02:01, HLA-B07:02 orHLA-B08:01 allele. In various embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein the human MHC is encoded by an HLA-A02:01 allele. In various embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein the human MHC is encoded by an HLA-B07:02 allele. In various embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein the human MHC is encoded by an HLA-B08:01 allele.
[0187] In various embodiments, the TCR binds to an MHC:GATA3 peptide complex, wherein thehuman MHC is encoded by an HLA-B08:01 allele and wherein the GATA3 peptide comprises a sequence of MLTGPPARV (SEQ ID NO: 15). Delivery of Nucleic Acid or Vector
[0188] Nucleic acids encoding TCRs or vectors containing such nucleic acids can be delivered to hostcells for expression and processing.
[0189] and relate to the introduction of nucleic acids, in particular exogenous or heterologous nucleic acids, into a cell.
[0190] Cells can be transfected with any carriers with which nucleic acid can be associated, e.g., byforming complexes with the nucleic acid or forming vesicles in which the nucleic acid is enclosed orWSGR Docket No. 50401-775.601 encapsulated, resulting in increased stability of the nucleic acid compared to naked nucleic acid. Carriers useful according to the present disclosure include, for example, lipid-containing carriers such as cationic lipids, liposomes, in particular cationic liposomes, and micelles, and nanoparticles. Cationic lipids may form complexes with negatively charged nucleic acids. Any cationic lipid may be used according to the present disclosure.
[0191] In various embodiments, a nucleic acid encoding a TCR disclosed herein is operably linkedto a promoter. Furthermore, the present disclosure provides a vector, e.g. a plasmid, shuttle vector, phagemid, cosmid, expression vector, retroviral vector, adenoviral vector or particle and / or vector tobe used in gene therapy, which comprises one or more of the nucleic acids as disclosed above. AThe vector comprises the nucleic acid insert, which encodes the polypeptide or protein desired for expression in a cell, such as a host cell. For the purposes of the disclosure, an insert may be a nucleic acid encoding a TCR; an alpha chain or a beta chain or both of a TCR. sequence in a vector may mean preparing a suitable expression vector with a insert comprising said nucleic acid sequence. encoded by one or more genes carried by the vector when it is present in the appropriate environment.retroviridae family. Exemplary gammaretroviruses include, but are not limited to, mouse stem cellvirus, murine leukemia virus, feline leukemia virus, feline sarcoma virus, and avian reticuloendotheliosis viruses. dividing and non-dividing cells. Several examples of lentiviruses include HIV (human immunodeficiency virus: including HIV type 1, and HIV type 2); equine infectious anemia virus; feline immunodeficiency virus (FIV); bovine immune deficiency virus (BIV); and simian immunodeficiency virus (SIV). A number of available viral vectors that are suitable for use with the invention, including those identified for human gene therapy applications, such as those described by Pfeifer and Verma (Pfeifer, A. and I. M. Verma.2001. Ann. Rev. Genomics Hum. Genet.2:177-211). Suitable viral vectors include vectors based on RNA viruses, such as retrovirus-derived vectors, e.g., Moloney murine leukemia virus (MLV)-derived vectors, and include more complex retrovirus-derived vectors, e.g., lentivirus-derived vectors. HIV-1-derived vectors belong to this category. Other examples include lentivirus vectors derived from HIV-2, FIV, equine infectious anemia virus, SIV, and maedi / visna virus. Methods of using retroviral and lentiviral viral vectors and packaging cells for transducing mammalian target cells with viral particles containing TCRs transgenes are well known in the art and have been previousWSGR Docket No. 50401-775.601 described, for example, in U.S. Pat. No.8,119,772; Walchli et al., 2011, PLoS One 6:327930; Zhao et al., J. Immunol., 2005, 174:4415-4423; Engels et al., 2003, Hum. Gene Ther.14:1155-68; Frecha et al., 2010, Mol. Ther.18:1748-57; Verhoeyen et al., 2009, Methods Mol. Biol.506:97-114. Retroviraland lentiviral vector constructs and expression systems are also commercially available. In someembodiments, a viral vector is used to introduce the non-endogenous nucleic acid sequence encoding hematopoietic progenitor cells. The viral vector may be a retroviral vector or a lentiviral vector. The viral vector may also include a nucleic acid sequence encoding a marker for transduction. Transduction markers for viral vectors are known in the art and include selection markers, which may confer drug resistance, or detectable markers, such as fluorescent markers or cell surface proteins that can be detected by methods such as flow cytometry. Where the viral vector genome comprises more than one nucleic acid sequence to be expressed in the host cell as separate transcripts, the viral vector may also comprise additional sequence between the two (or more) transcripts allowing bicistronic or multicistronic expression. Examples of such sequences used in viral vectors include internal ribosome entry sites (IRES), furin cleavage sites, viral 2A peptide. Other vectors also can be used for polynucleotide delivery including DNA viral vectors, including, for example adenovirus-based vectors and adeno-associated virus (AAV)-based vectors; vectors derived from herpes simplex viruses (HSVs), including amplicon vectors, replication-defectiveHSV and attenuated HSV (Krisky et al., 1998, Gene Ther. 5: 1517-30). Other vectors include thosederived from baculoviruses and alpha-viruses. (Jolly D J.1999. Emerging viral vectors. pp 209-40 in Friedmann T. ed.1999. The development of human gene therapy. New York: Cold Spring Harbor Lab).
[0192] A vector may include nucleic acid sequences that permit the nucleic acid to replicate in a hostcell, such as an origin of replication. A vector may also include one or more selectable marker genes and other genetic elements known to those of ordinary skill in the art. A vector preferably is an expression vector that includes a nucleic acid according to the present invention operably linked tosequences allowing for the expression of said nucleic acid.
[0193] In some embodiments, provided herein is a vector comprising a nucleic acid encoding aTCR disclosed herein. In some embodiments, the vector is a self-amplifying RNA replicon, plasmid, phage, transposon, cosmid, virus, or virion. In some embodiments, the vector is a viral vector. In some embodiments, the vector is derived from a retrovirus, lentivirus, adenovirus, adeno-associated virus, herpes virus, pox virus, alpha virus, vaccina virus, hepatitis B virus, human papillomavirus or a pseudotype thereof. In some embodiments, the vector is a non-viral vector. In some embodiments, theWSGR Docket No. 50401-775.601 non-viral vector is a nanoparticle, a cationic lipid, a cationic polymer, a metallic nanopolymer, a nanorod, a liposome, a micelle, a microbubble, a cell-penetrating peptide, or a liposphere.
[0194] Presented herein are constructs, for example, nucleic acid constructs that encode an alphachain and a beta chain of a TCR for expression in a cell. In some embodiments, the constructs comprise one or more polynucleotides encoding a TCR alpha chain and a TCR beta chain. In some embodiments, the polynucleotides are incorporated in a suitable vector. In some embodiments, the polynucleotides encoding the alpha chain and the beta chain are incorporated in the same vector. In some embodiments, the polynucleotides encoding the alpha chain and the beta chain are incorporated in different vectors,and both vectors are delivered for expression in the single cell.
[0195] In some embodiments, a cell may be transduced or transfected with a nucleic acid encodinga TCR, wherein the cell is capable of expressing the TCR and the cell is used as a therapeutic. In some embodiments the cell is derived from a subject or a host, wherein the subject or the host is a human. In some embodiments, the subject or the host comprises a cell having a mutation in an epitope, and the TCR expressed in the cell is capable of binding specifically to the epitope having the mutation. In some embodiments, the cell is a lymphocyte cell. In some embodiments, the T-lymphocyte. In someembodiments, the cell is a lymphocytic precursor cell. In some embodiments, the cell is a T lymphocyteprecursor cell. In some embodiments, the cell is a T lymphocyte progenitor cell. In some embodiments the cell is a thymocyte.
[0196] In some embodiments, the T cells are immature T cells. In some embodiments, the T cellsare antigen naive T cells. The host cell may be cultured ex vivo for 1, 2, 3, 4, 5 or more days for monitoring and recover after transfectionor transduction with the polynucleotide(s) encoding the TCR. Neoantigens
[0197] The TCRs disclosed herein are specific to immunogenic neoantigens. In some embodiments,the neoantigen peptide is from RAS. In some embodiments, the neoantigen peptide is from GATA3. In some embodiments, the neoantigen peptide is from BTK. In some embodiments, the neoantigen peptide is from TMPRSS2:ERG. In some embodiments, one or more neoantigen peptides are loaded on to APCs, wherein the peptide loaded APCs are then used to stimulate T cells to produce antigen specific T cells. In some embodiments, the APCs used for peptide loading are dendritic cells. Immunogenic neoantigen sequences can be identified by any suitable method known in the art.
[0198] In various embodiments, the neoantigen comprises an epitope. In both animals and humans,mutated epitopes can be potentially effective in inducing an immune response or activating T cells. In some embodiments, the epitope comprises a mutation. In some embodiments, the mutation is selectedWSGR Docket No. 50401-775.601 from the group consisting of a point mutation, a splice-site mutation, a frameshift mutation, a read-through mutation, a gene fusion mutation and any combination thereof.
[0199] In some embodiments, the epitope has a length of at least 8 amino acids. In someembodiments, the epitope has a length of at least 16 amino acids. In some embodiments, the epitope has a length of from 8-25 amino acids. In some embodiments, the epitope has a length of from 8-12 amino acids. In some embodiments, the epitope has a length of from 16-25 amino acids. In some embodiments, the epitope has a length of 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 amino acids.
[0200] In certain embodiments, a neoantigen or epitope thereof can comprise, but is not limited to,about 5, about 6, about 7, about 8, about 9, about 10, about 11, about 12, about 13, about 14, about 15, about 16, about 17, about 18, about 19, about 20, about 21, about 22, about 23, about 24, about 25, about 26, about 27, about 28, about 29, about 30, about 31, about 32, about 33, about 34, about 35, about 36, about 37, about 38, about 39, about 40, about 41, about 42, about 43, about 44, about 45, about 46, about 47, about 48, about 49, about 50, about 60, about 70, about 80, about 90, about 100, about 110, about 120 or greater amino acid residues, and any range derivable therein. In specific embodiments, a neoantigen or epitope thereof is equal to or less than 100 amino acids.
[0201] In some embodiments, a neoantigen or epitope thereof for MHC Class I is 13 residues or lessin length and usually consists of between about 8 and about 11 residues, particularly 9 or 10 residues.In some embodiments, a neoantigen or epitope thereof for MHC Class II is 9 -24 residues in length.
[0202] In some embodiments, neoantigens bind an HLA protein (e.g., HLA class I or HLA class II).In specific embodiments neoantigens bind an HLA protein with greater affinity than a corresponding wild-type peptide. In specific embodiments, the neoantigenic peptide or polypeptide has an IC50 of at least less than 5000 nM, at least less than 500 nM, at least less than 100 nM, at least less than 50 nM or less.
[0203] In some embodiments, the epitope binds to the human MHC with a greater affinity than acorresponding wild-type epitope. In some embodiments, the epitope binds to the human MHC with a KDor an IC50less than 500 nM, 250 nM, 150 nM, 100 nM, 50 nM, 25 nM or 10 nM. In someembodiments, the epitope comprises a mutation, wherein the mutation is not present in non -cancercells of a subject. In some embodiments, the epitope is encoded by a gene or an expressed gene of a -peptide complex with a KDor an IC50of less than 500 nM, 250 nM, 150 nM, 100 nM, 50 nM, 25 nM or 10 nM.
[0204] In some embodiments, the neoantigenic peptide can be from about 8 and about 50 amino acidresidues in length, or from about 8 and about 30, from about 8 and about 20, from about 8 and aboutWSGR Docket No. 50401-775.601 18, from about 8 and about 15, or from about 8 and about 12 amino acid residues in length. In some embodiments, the neoantigenic peptide can be from about 8 and about 500 amino acid residues in length, or from about 8 and about 450, from about 8 and about 400, from about 8 and about 350, from about 8 and about 300, from about 8 and about 250, from about 8 and about 200, from about 8 and about 150, from about 8 and about 100, from about 8 and about 50, or from about 8 and about 30 amino acid residues in length.
[0205] In some embodiments, the neoantigenic peptide can be at least 8, 9, 10, 11, 12, 13, 14, 15, 16,17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or more amino acid residues in length. In some embodiments, the neoantigenic peptide can be at least 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400, 450, 500 or more amino acid residues in length. In some embodiments, the neoantigenic peptide can be at most 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, or less amino acid residues in length. In some embodiments, the neoantigenic peptide can be at most 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 55, 60, 70, 80, 90, 100, 150, 200,250, 300, 350, 400, 450, 500, or less amino acid residues in length.
[0206] In some embodiments, the neoantigenic peptide has a total length of at least 8, at least 9, atleast 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, at least 21, at least 22, at least 23, at least 24, at least 25, at least 26, at least 27, at least 28, at least 29, at least 30, at least 40, at least 50, at least 60, at least 70, at least 80, at least 90, at least 100, at least 150, at least 200, at least 250, at least 300, at least 350, at least 400, at least 450, or at least 500 amino acids.
[0207] In some embodiments, the neoantigenic peptide has a total length of at most 8, at most 9, atmost 10, at most 11, at most 12, at most 13, at most 14, at most 15, at most 16, at most 17, at most 18, at most 19, at most 20, at most 21, at most 22, at most 23, at most 24, at most 25, at most 26, at most 27, at most 28, at most 29, at most 30, at most 40, at most 50, at most 60, at most 70, at most 80, at most 90, at most 100, at most 150, at most 200, at most 250, at most 300, at most 350, at most 400, at most 450, or at most 500 amino acids.
[0208] In some embodiments, the neoantigenic peptide can have a pI value of about 0.5 and about12, about 2 and about 10, or about 4 and about 8. In some embodiments, the neoantigenic peptide canWSGR Docket No. 50401-775.601have a pI value of at least 4.5, 5, 5.5, 6, 6.5, 7, 7.5, or more. In some embodiments, th e neoantigenicpeptide can have a pI value of at most 4.5, 5, 5.5, 6, 6.5, 7, 7.5, or less.
[0209] In some embodiments, the neoantigenic peptide can have an HLA binding affinity of betweenabout 1pM and about 1mM, about 100pM and about 500µM, about 500pM and abou t 10µM, about1nM and about 1µM, or about 10nM and about 1µM. In some embodiments, the neoantigenic peptide can have an HLA binding affinity of at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 700, 800, 900 µM, or more. In some embodiments, the neoantigenic peptide can have an HLA binding affinity of atmost 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150,200, 250, 300, 350, 400, 450, 500, 550, 600, 700, 800, 900 µM.
[0210] In some embodiments, a neoantigenic peptide described herein can comprise carriers such asthose well known in the art, e.g., thyroglobulin, albumins such as human serum albumin , tetanustoxoid, polyamino acid residues such as poly L-lysine, poly L-glutamic acid, influenza virus proteins, hepatitis B virus core protein, and the like.
[0211] In some embodiments, a neoantigenic peptide described herein can be modified by terminal-NH2 acylation, e.g., by alkanoyl (C1-C20) or thioglycolyl acetylation, terminal-carboxyl amidation, e.g., ammonia, methylamine, etc. In some embodiments, these modifications can provide sites for linking to a support or other molecule.
[0212] In some embodiments, a neoantigenic peptide described herein can contain modifications suchas but not limited to glycosylation, side chain oxidation, biotinylation, phosphorylation, addition of a surface active material, e.g. a lipid, or can be chemically modified, e.g., acetylation, etc. Moreover, bonds in the peptide can be other than peptide bonds, e.g., covalent bonds, ester or ether bonds, disulfide bonds, hydrogen bonds, ionic bonds, etc.
[0213] In some embodiments, a neoantigenic peptide described herein can contain substitutions tomodify a physical property (e.g., stability or solubility) of the resulting peptide. For example, -amino butyric acid ropensity to form disulfide bridges and sufficiently -amino butyric acid for C not only alleviates this problem, but actually improves binding and cross-binding capability in certain -amino butyric acid can occur at any residue of a neoantigenic peptide, e.g., at either anchor or non-anchor positions of an epitope or analog within a peptide, or at other positions of a peptide.WSGR Docket No. 50401-775.601
[0214] In some embodiments, a neoantigenic peptide described herein can comprise amino acidmimetics or unnatural amino acid residues, e.g. D- or L-naphylalanine; D- or L-phenylglycine; D- or L-2-thieneylalanine; D- or L-1, -2, 3-, or 4-pyreneylalanine; D- or L-3 thieneylalanine; D- or L-(2- pyridinyl)-alanine; D- or L-(3-pyridinyl)-alanine; D- or L-(2-pyrazinyl)-alanine; D- or L-(4- isopropyl)-phenylglycine; D-(trifluoromethyl)-phenylglycine; D-(trifluoro-methyl)-phenylalanine; D- .rho.-fluorophenylalanine; D- or L-.rho.-biphenyl-phenylalanine; D- or L-.rho.- methoxybiphenylphenylalanine; D- or L-2-indole(allyl)alanines; and D- or L-alkylalanines, where the alkyl group can be a substituted or unsubstituted methyl, ethyl, propyl, hexyl, butyl, pentyl, isopropyl, iso-butyl, sec-isotyl, iso-pentyl, or a non-acidic amino acid residues. Aromatic rings of a non-natural amino acid include, e.g., thiazolyl, thiophenyl, pyrazolyl, benzimidazolyl, naphthyl, furanyl, pyrrolyl, and pyridyl aromatic rings. Modified peptides that have various amino acid mimetics or unnatural amino acid residues are particularly useful, as they tend to manifest increased stability in vivo. Suchpeptides can also possess improved shelf -life or manufacturing properties.
[0215] Peptide stability can be assayed in a number of ways. For instance, peptidases and variousbiological media, such as human plasma and serum, have been used to test stability. See, e.g., Verhoef, et al., Eur. J. Drug Metab. Pharmacokinetics 11:291 (1986). Half-life of the peptides described herein is conveniently determined using a 25% human serum (v / v) assay. The protocol is as follows: pooled human serum (Type AB, non-heat inactivated) is dilapidated by centrifugation before use. The serum is then diluted to 25% with RPMI-1640 or another suitable tissue culture medium. At predetermined time intervals, a small amount of reaction solution is removed and added to either 6% aqueoustrichloroacetic acid (TCA) or ethanol. The cloudy reaction sample is cooled (4 oC) for 15 minutes andthen spun to pellet the precipitated serum proteins. The presence of the peptides is then determined by reversed-phase HPLC using stability-specific chromatography conditions.
[0216] In some embodiments, a neoantigenic peptide described herein can be prepared synthetically,by recombinant DNA technology or chemical synthesis, or can be isolated from natural sources such as native tumors or pathogenic organisms. Epitopes can be synthesized individually or joined directly or indirectly in a peptide. Although a neoantigenic peptide described herein will be substantially free of other naturally occurring host cell proteins and fragments thereof, in some embodiments, the peptide can be synthetically conjugated to be joined to native fragments or particles.
[0217] In some embodiments, a neoantigenic peptide described herein can be prepared in a widevariety of ways. In some embodiments, the peptides can be synthesized in solution or on a solid support according to conventional techniques. Various automatic synthesizers are commercially available and can be used according to known protocols. (See, for example, Stewart & Young, SOLID PHASEWSGR Docket No. 50401-775.601 PEPTIDE SYNTHESIS, 2D. ED., Pierce Chemical Co., 1984). Further, individual peptides can be joined using chemical ligation to produce larger peptides that are still within the bounds of the invention.
[0218] Alternatively, recombinant DNA technology can be employed wherein a nucleotide sequencewhich encodes a peptide inserted into an expression vector, transformed or transfected into an appropriate host cell and cultivated under conditions suitable for expression. These procedures are generally known in the art, as described generally in Sambrook et al., MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Press, Cold Spring Harbor, N.Y. (1989). Thus, recombinant peptides, which comprise or consist of one or more epitopes described herein, can be used to present the appropriate T cell epitope. Pharmaceutical Compositions
[0219] Pharmaceutical compositions can be formulated using one or more physiologically acceptablecarriers including excipients and auxiliaries which facilitate processing of the active agents into preparations which can be used pharmaceutically. Proper formulation can be dependent upon the route of administration chosen. Any of the well-known techniques, carriers, and excipients can be used as suitable and as understood in the art.
[0220] In some cases, a pharmaceutical composition is formulated as cell based therapeutic, e.g., a Tcell therapeutics. In some embodiments, a pharmaceutical composition comprises a peptide-based therapy, a nucleic acid-based therapy, an antibody-based therapy, and / or a cell-based therapy. In some embodiments, a pharmaceutical composition comprises a peptide-based therapeutic, or nucleic acid based therapeutic in which the nucleic acid encodes the polypeptides. A composition can comprise T cells specific for two or more immunogenic antigen or neoantigen peptides. In some embodiments, theT cell specific therapeutic may be supplemented by one or more additional therapies.
[0221] In some embodiments, a pharmaceutical composition comprising: a nucleic acid encoding aTCR targeting a neoantigen disclosed herein, a vector containing the nucleic acid, the protein encodedby the nucleic acid, or a host cell comprising the nucleic acid, the protein or the vector; and apharmaceutically acceptable excipient or diluent. In some embodiments, the pharmaceutical composition further comprises an immunomodulatory agent or an adjuvant. In some embodiments, the immunomodulatory agent is a cytokine. In some embodiments, the adjuvant is poly I:C.
[0222] Also provided herein is the use of the pharmaceutical compositions in treating an immunedisease or cancer.
[0223] Pharmaceutical compositions can include, in addition to active ingredient, a pharmaceuticallyacceptable excipient, carrier, buffer, stabilizer or other materials well known to those skilled in the art.WSGR Docket No. 50401-775.601 Such materials should be non-toxic and should not interfere with the efficacy of the active ingredient. The precise nature of the carrier or other material will depend on the route of administration. Acceptable carriers, excipients, or stabilizers are those that are non-toxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates including glucose, mannose, or dextrins; chelating agents such as EDTA; sugars such as sucrose, mannitol, trehalose or sorbitol; salt- forming counter-ions such as sodium; metal complexes (e.g., Zn-protein complexes); and / or non-ionic surfactants such as TWEEN®, PLURONICS® or polyethylene glycol (PEG).
[0224] Acceptable carriers are physiologically acceptable to the administered patient and retaintherapeutic properties of the compounds with / in which it is administered. Acceptable carriers and their s Pharmaceutical Sciences (18th ed. A. Gennaro, Mack Publishing Co., Easton, PA 1990). One example of carrier is physiological saline. A pharmaceutically acceptable carrier is a pharmaceutically acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in carrying or transporting the subject compounds from the administration site of one organ, or portion of the body, to another organ, or portion of the body, or in an in vitro assay system. Acceptable carriers are compatible with the other ingredients of the formulation and not injurious to a subject to whom it is administered. Nor should an acceptable carrier alter the specific activity of the other ingredients.
[0225] In one aspect, provided herein are pharmaceutically acceptable or physiologically acceptablecompositions including solvents (aqueous or non-aqueous), solutions, emulsions, dispersion media, coatings, isotonic and absorption promoting or delaying agents, compatible with pharmaceutical administration. Pharmaceutical compositions or pharmaceutical formulations therefore refer to a composition suitable for pharmaceutical use in a subject. Compositions can be formulated to be compatible with a particular route of administration (i.e., systemic or local). Thus, compositions include carriers, diluents, or excipients suitable for administration by various routes.
[0226] In some embodiments, a pharmaceutical composition can further comprise an acceptableadditive in order to improve the stability of the composition. Acceptable additives may not alter theWSGR Docket No. 50401-775.601 specific activity of the active agent, e.g. immune cells. Examples of acceptable additives include, but are not limited to, a sugar such as mannitol, sorbitol, glucose, xylitol, trehalose, sorbose, sucrose, galactose, dextran, dextrose, fructose, lactose and mixtures thereof. Acceptable additives can be combined with acceptable carriers and / or excipients such as dextrose. Alternatively, examples of acceptable additives include, but are not limited to, a surfactant such as polysorbate 20 or polysorbate 80 to increase stability of the peptide and decrease gelling of the solution. The surfactant can be added to the composition in an amount of 0.01% to 5% of the solution. Addition of such acceptable additivesincreases the stability and half -life of the composition in storage.
[0227] In some embodiments the pharmaceutical composition comprises a therapeutic which is a Tcell expressing one or more polynucleotides, encoding a T cell receptor. In some embodiments, the pharmaceutical composition comprises physiologically acceptable carrier suitable for a cell suspension.
[0228] The pharmaceutical composition can be administered, for example, by injection.Pharmaceutical compositions for injection include aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersion. For intravenous administration, suitable carriers include physiological saline, bacteriostatic water, or phosphate buffered saline (PBS). The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. Fluidity can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Antibacterial and antifungal agents include, for example, parabens, chlorobutanol, phenol, ascorbic acid and thimerosal. Isotonic agents, for example, sugars, polyalcohols such as mannitol, sorbitol, and sodium chloride can be included in the composition. The resulting solutions can be packaged for use as is, or lyophilized; the lyophilized preparation can later be combined with a sterile solution prior to administration. For intravenous, injection, or injection at the site of affliction, the active ingredient will be in the form of a parenterally acceptable aqueous solution which is pyrogen-free and has suitable pH, isotonicity and stability. Those of relevant skill in the art are well able to prepare suitable solutions using, for example, isotonic Preservatives, stabilizers, buffers, antioxidants and / or other additives can be included, as needed. Sterile injectable solutions can be prepared by incorporating an active ingredient in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating theWSGR Docket No. 50401-775.601 active ingredient into a sterile vehicle which contains a basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation can be vacuum drying and freeze drying which yields a powder of the active ingredient plus any additional desired ingredient from a previouslysterile-filtered solution thereof .
[0229] Pharmaceutical compositions can be conventionally administered intravenously, such as byinjection of a unit dose, for example. For injection, an active ingredient can be in the form of a parenterally acceptable aqueous solution which is substantially pyrogen-free and has suitable pH, isotonicity and stability. One can prepare suitable solutions using, for example, isotonic vehicles such stabilizers, buffers, antioxidants and / or other additives can be included, as required. Additionally, compositions can be administered via aerosolization.
[0230] When the pharmaceutical compositions are considered for use in medicaments or any of themethods provided herein, it is contemplated that the composition can be substantially free of pyrogens such that the composition will not cause an inflammatory reaction or an unsafe allergic reaction when administered to a human patient. Testing compositions for pyrogens and preparing compositions substantially free of pyrogens are well understood to one or ordinary skill of the art and can be accomplished using commercially available kits.
[0231] Acceptable carriers can contain a compound that stabilizes, increases or delays absorption, orincreases or delays clearance. Such compounds include, for example, carbohydrates, such as glucose, sucrose, or dextrans; low molecular weight proteins; compositions that reduce the clearance orhydrolysis of peptides; or excipients or other stabilizers and / or buff ers. Agents that delay absorptioninclude, for example, aluminum monostearate and gelatin. Detergents can also be used to stabilize or to increase or decrease the absorption of the pharmaceutical composition, including liposomal carriers. To protect from digestion the compound can be complexed with a composition to render it resistant to acidic and enzymatic hydrolysis, or the compound can be complexed in an appropriately resistant carrier such as a liposome. Means of protecting compounds from digestion are known in the art (e.g., Fix (1996) Pharm Res.13:17601764; Samanen (1996) J. Pharm. Pharmacol.48:119135; and U.S. Pat. No.5,391,377).
[0232] The pharmaceutical compositions can be administered in a manner compatible with the dosageformulation, and in a therapeutically effective amount. The quantity to be administered depends on thedegree of binding capacity desired. Precise amounts of active ingredient requ ired to be administeredWSGR Docket No. 50401-775.601 depend on the judgment of the practitioner and are peculiar to each individual. Suitable regimes for initial administration and booster shots are also variable, but, are typified by an initial administration followed by repeated doses at one or more hour intervals by a subsequent injection or other administration. Alternatively, continuous intravenous infusions sufficient to maintain concentrations in the blood are contemplated.
[0233] In some embodiments, the present disclosure is directed to an immunogenic composition, e.g.,a pharmaceutical composition capable of raising a neoantigen-specific response (e.g., a humoral or cell-mediated immune response). In some embodiments, the immunogenic composition comprises neoantigen therapeutics (e.g., peptides, polynucleotides, TCR, CAR, cells containing TCR or CAR, dendritic cell containing polypeptide, dendritic cell containing polynucleotide, antibody, etc.) described herein corresponding to a tumor specific antigen or neoantigen.
[0234] In some embodiments, a pharmaceutical composition described herein is capable of raising aspecific cytotoxic T cells response, specific helper T cell response, or a B cell response.
[0235] In some embodiments, antigen polypeptides or polynucleotides can be provided as antigenpresenting cells (e.g., dendritic cells) containing such polypeptides or polynucleotides. In otherembodiments, such antigen presenting cells are used to stimulate T cells for use in patien ts. In someembodiments, the antigen presenting cells are dendritic cells. In related embodiments, the dendritic cells are autologous dendritic cells that are pulsed with the neoantigen peptide or nucleic acid. The neoantigen peptide can be any suitable peptide that gives rise to an appropriate T cell response. In some embodiments, the T cell is a CTL. In some embodiments, the T cell is an HTL. Thus, one embodiment of the present disclosure is an immunogenic composition containing at least one antigen presenting cell (e.g., a dendritic cell) that is pulsed or loaded with one or more neoantigen polypeptides or polynucleotides described herein. In some embodiments, such APCs are autologous (e.g., autologous dendritic cells). Alternatively, peripheral blood mononuclear cells (PBMCs) isolated from a patient can be loaded with neoantigen peptides or polynucleotides ex vivo. In related embodiments, such APCs or PBMCs are injected back into the patient. The polynucleotide can be any suitable polynucleotide that is capable of transducing the dendritic cell, thus resulting in the presentation of a neoantigen peptide and induction of immunity. In some embodiments, such antigen presenting cells (APCs) (e.g., dendritic cells) or peripheral blood mononuclear cells (PBMCs) are used to stimulate a T cell (e.g., an autologous T cell, or an allogeneic T cell). In related embodiments, the T cell is a CTL.In other related embodiments, the T cell is an HTL. In some embodiments, the T cells are CD8 + Tcells. In some embodiments, the T cells are CD4+T cells. Such T cells are then injected into the patient. In some embodiments, CTL is injected into the patient. In some embodiments, HTL is injected intoWSGR Docket No. 50401-775.601the patient. In some embodiments, both CTL and HTL are injected into the patient. Administration ofeither therapeutic can be performed simultaneously or sequentially and in any order.
[0236] In some embodiments, pharmaceutical compositions (e.g., immunogenic compositions)described herein for therapeutic treatment can be formulated for parenteral, topical, nasal, oral or local administration. In some embodiments, the pharmaceutical compositions described herein are administered parenterally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. In some embodiments, the composition can be administered intratumorally. The compositions can be administered at the site of surgical excision to induce a local immune response to the tumor. In someembodiments, described herein are compositions for parenteral administration which comp rise asolution of the neoantigen peptides and immunogenic compositions are dissolved or suspended in an acceptable carrier, for example, an aqueous carrier. A variety of aqueous carriers can be used, e.g., water, buffered water, 0.9% saline, 0.3% glycine, hyaluronic acid and the like. These compositions can be sterilized by conventional, well known sterilization techniques, or can be sterile filtered. The resulting aqueous solutions can be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions can contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.
[0237] The ability of an adjuvant to increase the immune response to an antigen is typicallymanifested by a significant increase in immune-mediated reaction, or reduction in disease symptoms. For example, an increase in humoral immunity can be manifested by a significant increase in the titer of antibodies raised to the antigen, and an increase in T cell activity can be manifested in increased cell proliferation, or cellular cytotoxicity, or cytokine secretion. An adjuvant can also alter an immuneresponse, for example, by changing a primarily humoral or T helper 2 response in to a primarilycellular, or T helper 1 response.
[0238] Suitable adjuvants are known in the art (see, WO 2015 / 095811) and include, but are notlimited to poly(I:C), poly-ICLC, STING agonist, 1018 ISS, aluminum salts, Amplivax, AS15, BCG, CP-870,893, CpG7909, CyaA, dSLIM, GM-CSF, IC30, IC31, Imiquimod, ImuFact IMP321, IS Patch, ISS, ISCOMATRIX, JuvImmune, LipoVac, MF59, monophosphoryl lipid A, Montanide IMS 1312, Montanide ISA 206, Montanide ISA 50V, Montanide ISA-51, OK-432, OM-174, OM-197-MP-EC, ONTAK, PepTel® vector system, PLG microparticles, resiquimod, SRL172, virosomes and othervirus-like particles, YF- -WSGR Docket No. 50401-775.601 stimulon (Aquila Biotech, Worcester, Mass., USA) which is derived from saponin, mycobacterial Quil or Superfos. Several immunological adjuvants (e.g., MF59) specific for dendritic cells and their preparation have been described (Dupuis M, et al., Cell Immunol.1998; 186(1):18-27; Allison A C; Dev Biol Stand. 1998; 92:3-11) (Mosca et al. Frontiers in Bioscience, 2007; 12:4050-4060) (Gamvrellis et al. Immunol & Cell Biol. 2004; 82: 506-516). Also cytokines can be used. Several cytokines have been directly linked to influencing dendritic cell migration to lymphoid tissues (e.g.,TNF- -presenting cells for T-lymphocytes (e.g., GM-CSF, PGE1, PGE2, IL-1, IL- -4, IL-6 and CD40L) (U.S. Pat. No.5,849,589 incorporated herein by reference in its entirety) and acting as immunoadjuvants (e.g., IL- 12) (Gabrilovich D I, et al., J Immunother Emphasis Tumor Immunol.1996 (6):414-418).
[0239] CpG immunostimulatory oligonucleotides have also been reported to enhance the effects ofadjuvants in a therapeutic setting. Without being bound by theory, CpG oligonucleotides act by activating the innate (non-adaptive) immune system via Toll-like receptors (TLR), mainly TLR9. CpG triggered TLR9 activation enhances antigen-specific humoral and cellular responses to a wide variety of antigens, including peptide or protein antigens, live or killed viruses, dendritic cell immunogenic pharmaceutical compositions, autologous cellular immunogenic pharmaceutical compositions and polysaccharide conjugates in both prophylactic and therapeutic immunogenic pharmaceutical compositions. Importantly, it enhances dendritic cell maturation and differentiation, resulting in enhanced activation of TH1 cells and strong cytotoxic T-lymphocyte (CTL) generation, even in the absence of CD4+ T cell help. The TH1 bias induced by TLR9 stimulation is maintained even in theTH2 bias. CpG oligonucleotides show even greater adjuvant activity when formulated or co -administered with other adjuvants or in formulations such as microparticles, nanoparticles, lipid emulsions or similar formulations, which are especially useful for inducing a strong response when the antigen is relatively weak. They can also accelerate the immune response and enabled the antigen doses to be reduced with comparable antibody responses to the full-dose immunogenic pharmaceutical composition without CpG in some experiments (Arthur M. Krieg, Nature Reviews, Drug Discovery, 5, June 2006, 471-484). U.S. Pat. No.6,406,705 describes the combined use of CpG oligonucleotides, non-nucleic acid adjuvants and an antigen to induce an antigen-specific immune response. A commercially available CpG TLR9 antagonist is dSLIM (double Stem Loop Immunomodulator) by Mologen (Berlin, DE), which is a component of the pharmaceutical composition described herein.Other TLR binding molecules such as RNA binding TLR7, TLR8 and / or TLR9 can also be u sed.WSGR Docket No. 50401-775.601
[0240] Other examples of useful adjuvants include, but are not limited to, chemically modified CpGs(e.g. CpR, Idera), Poly(I:C)(e.g., polyI:CI2U), polyIC:LC, non-CpG bacterial DNA or RNA, ssRNA40 for TLR8, as well as immunoactive small molecules and antibodies such as cyclophosphamide, sunitinib, bevacizumab, celebrex, NCX-4016, sildenafil, tadalafil, vardenafil, sorafinib, XL-999, CP- 547632, pazopanib, ZD2171, AZD2171, ipilimumab, tremelimumab, and SC58175, which can act therapeutically and / or as an adjuvant. The amounts and concentrations of adjuvants and additives useful in the context of the present invention can readily be determined by the skilled artisan without undue experimentation. Additional adjuvants include colony-stimulating factors, such as Granulocyte Macrophage Colony Stimulating Factor (GM-CSF, sargramostim).
[0241] In some embodiments, an immunogenic composition according to the present disclosure cancomprise more than one different adjuvant. Furthermore, the invention encompasses a pharmaceutical composition comprising any adjuvant substance including any of the above or combinations thereof. In some embodiments, the immunogenic composition comprises neoantigen therapeutics (e.g., peptides, polynucleotides, TCR, CAR, cells containing TCR or CAR, dendritic cell containing polypeptide, dendritic cell containing polynucleotide, antibody, etc.) and the adjuvant can be administered separately in any appropriate sequence.
[0242] Lipidation can be classified into several different types, such as N-myristoylation,palmitoylation, GPI-anchor addition, prenylation, and several additional types of modifications. N- myristoylation is the covalent attachment of myristate, a C14 saturated acid, to a glycine residue. Palmitoylation is thioester linkage of long-chain fatty acids (C16) to cysteine residues. GPI-anchor addition is glycosyl-phosphatidylinositol (GPI) linkage via amide bond. Prenylation is the thioether linkage of an isoprenoid lipid (e.g. farnesyl (C-15), geranylgeranyl (C-20)) to cysteine residues. Additional types of modifications can include attachment of S-diacylglycerol by a sulfur atom of cysteines, O-octanoyl conjugation via serine or threonine residues, S-archaeol conjugation to cysteine residues, and cholesterol attachment.
[0243] Fatty acids for generating a lipidated peptides can include C2 to C30 saturated,monounsaturated, or polyunsaturated fatty acyl groups. Exemplary fatty acids can include palmitoyl, myristoyl, stearoyl and decanoyl groups. In some instances, a lipid moiety that has adjuvant property is attached to a polypeptide of interest to elicit or enhance immunogenicity in the absence of anextrinsic adjuvant. A lipidated peptide or lipopeptide can be referred to as a self -adjuvant lipopeptide.Any of the fatty acids described above and elsewhere herein can elicit or enhance immunogenicity of a polypeptide of interest. A fatty acid that can elicit or enhance immunogenicity can include palmitoyl, myristoyl, stearoyl, lauroyl, octanoyl, and decanoyl groups.WSGR Docket No. 50401-775.601
[0244] Polypeptides such as naked peptides or lipidated peptides can be incorporated into a liposome.Sometimes, lipidated peptides can be incorporated into a liposome. For example, the lipid portion of the lipidated peptide can spontaneously integrate into the lipid bilayer of a liposome. Thus, a li
[0245] Liposome can also be used to deliver nucleic acids into a cell. The nucleic acid of interestcomprises one or more sequences encoding a T cell receptor. Liposomes may be used to deliver a DNA or an RNA. Liposomes may be used to deliver a nucleic acid incorporated in a vector. The nucleic acid may be 50-200,000 nucleotides long, or may be 100-500,000 nucleotides long, or may be 20-500,000 nucleotides long. Exemplary liposomes suitable for incorporation in the formulations include, and are not limited to, multilamellar vesicles (MLV), oligolamellar vesicles (OLV), unilamellar vesicles (UV), small unilamellar vesicles (SUV), medium-sized unilamellar vesicles (MUV), large unilamellar vesicles (LUV), giant unilamellar vesicles (GUV), multivesicular vesicles (MVV), single or oligolamellar vesicles made by reverse-phase evaporation method (REV), multilamellar vesicles made by the reverse-phase evaporation method (MLV-REV), stable plurilamellar vesicles (SPLV), frozen and thawed MLV (FATMLV), vesicles prepared by extrusion methods (VET), vesicles prepared by French press (FPV), vesicles prepared by fusion (FUV), dehydration-rehydration vesicles (DRV), and bubblesomes (BSV).
[0246] Depending on the method of preparation, liposomes can be unilamellar or multilamellar, andcan adsorb many types of cells and then release an incorporated agent (e.g., a peptide described herein). In some cases, the liposomes fuse with the target cell, whereby the contents of the liposome then empty into the target cell. A liposome can be endocytosed by cells that are phagocytic. Endocytosis can be followed by intralysosomal degradation of liposomal lipids and release of the encapsulated agents.
[0247] The liposomes provided herein can also comprise carrier lipids. In some embodiments, thecarrier lipids are phospholipids. Carrier lipids capable of forming liposomes include, but are not limited to dipalmitoylphosphatidylcholine (DPPC), phosphatidylcholine (PC; lecithin), phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylserine (PS). Other suitable phospholipids further include distearoylphosphatidylcholine (DSPC), dimyristoylphosphatidylcholine (DMPC), dipalmitoylphosphatidyglycerol (DPPG), distearoylphosphatidyglycerol (DSPG), dimyristoylphosphatidylglycerol (DMPG), dipalmitoylphosphatidic acid (DPPA); dimyristoylphosphatidic acid (DMPA), distearoylphosphatidic acid (DSPA), dipalmitoylphosphatidylserine (DPPS), dimyristoylphosphatidylserine (DMPS), distearoylphosphatidylserine (DSPS), dipalmitoylphosphatidyethanolamine (DPPE),WSGR Docket No. 50401-775.601 dimyristoylphosphatidylethanolamine (DMPE), distearoylphosphatidylethanolamine (DSPE) and the like, or combinations thereof. In some embodiments, the liposomes further comprise a sterol (e.g., cholesterol) which modulates liposome formation. The carrier lipids can be any known non-phosphate polar lipids.
[0248] A pharmaceutical composition can be encapsulated within liposomes using well-knowntechnology. Biodegradable microspheres can also be employed as carriers for the pharmaceutical compositions of this invention.
[0249] The pharmaceutical composition can be administered in liposomes or microspheres (ormicroparticles). Methods for preparing liposomes and microspheres for administration to a patient are well known to those of skill in the art. Essentially, material is dissolved in an aqueous solution, the appropriate phospholipids and lipids added, along with surfactants if required, and the material dialyzed or sonicated, as necessary.
[0250] Microspheres formed of polymers or proteins are well known to those skilled in the art, andcan be tailored for passage through the gastrointestinal tract directly into the blood stream. Alternatively, the compound can be incorporated and the microspheres, or composite of microspheres, implanted for slow release over a period of time ranging from days to months.
[0251] Cell-based immunogenic pharmaceutical compositions can also be administered to a subject.For example, an antigen presenting cell (APC) based immunogenic pharmaceutical composition can be formulated using any of the well-known techniques, carriers, and excipients as suitable and as understood in the art. APCs include monocytes, monocyte-derived cells, macrophages, and dendriticcells. Sometimes, an APC based immunogenic pharmaceutical composition can be a dendritic cell-based immunogenic pharmaceutical composition.
[0252] A dendritic cell-based immunogenic pharmaceutical composition can be prepared by anymethods well known in the art. In some cases, dendritic cell-based immunogenic pharmaceutical compositions can be prepared through an ex vivo or in vivo method. The ex vivo method can comprise the use of autologous DCs pulsed ex vivo with the polypeptides described herein, to activate or load the DCs prior to administration into the patient. The in vivo method can comprise targeting specific DC receptors using antibodies coupled with the polypeptides described herein. The DC-based immunogenic pharmaceutical composition can further comprise DC activators such as TLR3, TLR-7- 8, and CD40 agonists. The DC-based immunogenic pharmaceutical composition can further comprise adjuvants, and a pharmaceutically acceptable carrier.
[0253] An adjuvant can be used to enhance the immune response (humoral and / or cellular) elicitedin a patient receiving the immunogenic pharmaceutical composition. Sometimes, adjuvants can elicitWSGR Docket No. 50401-775.601 a Th1-type response. Other times, adjuvants can elicit a Th2-type response. A Th1-type response canbe characterized by the production of cytokines such as IFN- -type response whichcan be characterized by the production of cytokines such as IL-4, IL-5 and IL-10.
[0254] In some aspects, lipid-based adjuvants, such as MPLA and MDP, can be used with theimmunogenic pharmaceutical compositions disclosed herein. Monophosphoryl lipid A (MPLA), for example, is an adjuvant that causes increased presentation of liposomal antigen to specific T Lymphocytes. In addition, a muramyl dipeptide (MDP) can also be used as a suitable adjuvant in conjunction with the immunogenic pharmaceutical formulations described herein.
[0255] Adjuvant can also comprise stimulatory molecules such as cytokines. Non-limiting examplesof cytokines in - - --CSF, epidermal growth factor (EGF), cutaneous T cell- attracting chemokine (CTACK), epithelial thymus-expressed chemokine (TECK), mucosae-associated epithelial chemokine (MEC), IL-12, IL-15, IL-28, MHC, CD80, CD86, IL-1, IL-2, IL-4, IL-5, IL-6, IL-10, IL-18, MCP-1, MIP-la, MIP-1-, IL-8, L- selectin, P-selectin, E-selectin, CD34, GlyCAM-1, MadCAM-1, LFA-1, VLA-1, Mac-1, pl50.95, PECAM, ICAM-1, ICAM-2, ICAM-3, CD2, LFA-3, M-CSF, G-CSF, mutant forms of IL-18, CD40, CD40L, vascular growth factor, fibroblast growth factor, IL-7, nerve growth factor, vascular endothelial growth factor, Fas, TNF receptor, Fit, Apo-1, p55, WSL-1, DR3, TRAMP, Apo-3, AIR, LARD, NGRF, DR4, DRS, KILLER, TRAIL-R2, TRICK2, DR6, Caspase ICE, Fos, c-jun, Sp-1, Ap-1, Ap- NIK, SAP K, SAP- TRAILrecDRC5, TRAIL-R3, TRAIL-R4, RANK, RANK LIGAND Ox40, Ox40 LIGAND NKG2D, MICA, MICB, NKG2A, NKG2B, NKG2C, NKG2E, NKG2F, TAPI, and TAP2.
[0256] Additional adjuvants include: MCP-1, MIP-la, MIP-lp, IL-8, RANTES, L-selectin, P-selectin,E-selectin, CD34, GlyCAM-1, MadCAM-1, LFA-1, VLA-1, Mac-1, pl50.95, PECAM, ICAM-1, ICAM-2, ICAM-3, CD2, LFA-3, M-CSF, G-CSF, IL-4, mutant forms of IL-18, CD40, CD40L, vascular growth factor, fibroblast growth factor, IL-7, IL-22, nerve growth factor, vascular endothelial growth factor, Fas, TNF receptor, Fit, Apo-1, p55, WSL-1, DR3, TRAMP, Apo-3, AIR, LARD, NGRF, DR4, DR5, KILLER, TRAIL-R2, TRICK2, DR6, Caspase ICE, Fos, c-jun, Sp-1, Ap-1, Ap-2, -1, JNK, interferon response RAIL, TRAILrec, TRAILrecDRC5, TRAIL-R3, TRAIL-R4, RANK, RANK LIGAND Ox40, Ox40 LIGAND NKG2D, MICA, MICB, NKG2A, NKG2B, NKG2C, NKG2E, NKG2F, TAP1, TAP2 and functional fragments thereof.WSGR Docket No. 50401-775.601
[0257] In some aspects, an adjuvant can be a modulator of a toll like recepto r. Examples ofmodulators of toll-like receptors include TLR9 agonists and are not limited to small molecule modulators of toll-like receptors such as Imiquimod. Sometimes, an adjuvant is selected from bacteria toxoids, polyoxypropylene-polyoxyethylene block polymers, aluminum salts, liposomes, CpG polymers, oil-in-water emulsions, or a combination thereof. Sometimes, an adjuvant is an oil-in-water emulsion. The oil-in-water emulsion can include at least one oil and at least one surfactant, with the oil(s) and surfactant(s) being biodegradable (metabolizable) and biocompatible. The oil droplets in the -micron diameter, with these small sizes being achieved with a microfluidiser to provide stable emulsions. Droplets with a size less than 220 nm can be subjected to filter sterilization.
[0258] In some instances, an immunogenic pharmaceutical composition can include carriers andexcipients (including but not limited to buffers, carbohydrates, mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, bacteriostats, chelating agents, suspending agents, thickening agents and / or preservatives), water, oils including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like, saline solutions, aqueous dextrose and glycerol solutions, flavoring agents, coloring agents, and other acceptable additives, adjuvants, or binders, other pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH buffering agents, tonicity adjusting agents, emulsifying agents, wetting agents and the like. Examples of excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. In anotherinstances, the pharmaceutical preparation is substantially free of preservatives. In o ther instances, thepharmaceutical preparation can contain at least one preservative. It will be recognized that, while any suitable carrier known to those of ordinary skill in the art can be employed to administer the pharmaceutical compositions described herein, the type of carrier will vary depending on the mode of administration.
[0259] An immunogenic pharmaceutical composition can include preservatives such as thiomersal or2-phenoxyethanol. In some instances, the immunogenic pharmaceutical composition is substantially --Tocopherol succinate may beused as an alternative to mercurial compounds.
[0260] For controlling the tonicity, a physiological salt such as sodium salt can be included in theimmunogenic pharmaceutical composition. Other salts can include potassium chloride, potassium dihydrogen phosphate, disodium phosphate, and / or magnesium chloride, or the like.WSGR Docket No. 50401-775.601
[0261] An immunogenic pharmaceutical composition can have an osmolality of between 200mOsm / kg and 400 mOsm / kg, between 240-360 mOsm / kg, or within the range of 290-310 mOsm / kg.
[0262] An immunogenic pharmaceutical composition can comprise one or more buffers, such as aTris buffer; a borate buffer; a succinate buffer; a histidine buffer (particularly with an aluminumhydroxide adjuvant); or a citrate buffer. Buffers, in some cases, are included in the 5 -20 or 10-50 mMrange.
[0263] The pH of the immunogenic pharmaceutical composition can be between about 5.0 and about8.5, between about 6.0 and about 8.0, between about 6.5 and about 7.5, or between about 7.0 and about 7.8.
[0264] An immunogenic pharmaceutical composition can be sterile. The immunogenicpharmaceutical composition can be non-pyrogenic e.g. containing <1 EU (endotoxin unit, a standardmeasure) per dose, and can be <0.1 EU per dose. The composition can be gluten free.
[0265] An immunogenic pharmaceutical composition can include detergent e.g. a polyoxyethylene-9 (Triton X-100) or t-octylphenoxypolyethoxyethanol). The detergent can be present only at trace amounts. The immunogenic pharmaceutical composition can include less than 1 mg / mL of each of octoxynol-10 andpolysorbate 80. Other residual components in trace amounts can be an tibiotics (e.g. neomycin,kanamycin, polymyxin B).
[0266] An immunogenic pharmaceutical composition can be formulated as a sterile solution orsuspension, in suitable vehicles, well known in the art. The pharmaceutical compositions can be sterilized by conventional, well-known sterilization techniques, or can be sterile filtered. The resulting aqueous solutions can be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration.
[0267] Pharmaceutical compositions comprising, for example, an active agent such as immune cellsdisclosed herein, in combination with one or more adjuvants can be formulated to comprise certainmolar ratios. For example, molar ratios of about 99:1 to about 1:99 of an active a gent such as animmune cell described herein, in combination with one or more adjuvants can be used. In some instances, the range of molar ratios of an active agent such as an immune cell described herein, in combination with one or more adjuvants can be selected from about 80:20 to about 20:80; about 75:25 to about 25:75, about 70:30 to about 30:70, about 66:33 to about 33:66, about 60:40 to about 40:60; about 50:50; and about 90:10 to about 10:90. The molar ratio of an active agent such as an immune cell described herein, in combination with one or more adjuvants can be about 1:9, and in some cases can be about 1:1. The active agent such as an immune cell described herein, in combination with oneWSGR Docket No. 50401-775.601 or more adjuvants can be formulated together, in the same dosage unit e.g., in one vial, suppository, tablet, capsule, an aerosol spray; or each agent, form, and / or compound can be formulated in separate units, e.g., two vials, suppositories, tablets, two capsules, a tablet and a vial, an aerosol spray, and the like.
[0268] In some instances, an immunogenic pharmaceutical composition can be administered with anadditional agent. The choice of the additional agent can depend, at least in part, on the condition being treated. The additional agent can include, for example, a checkpoint inhibitor agent such as an anti- PD1, anti-CTLA4, anti-PD-L1, anti CD40, or anti-TIM3 agent (e.g., an anti-PD1, anti-CTLA4, anti- PD-L1, anti CD40, or anti-TIM3 antibody); or any agents having a therapeutic effect for a pathogen infection (e.g. viral infection), including, e.g., drugs used to treat inflammatory conditions such as an NSAID, e.g., ibuprofen, naproxen, acetaminophen, ketoprofen, or aspirin. For example, the checkpoint inhibitor can be a PD-1 / PD- L1 antagonist selected from the group consisting of: nivolumab (ONO- 4538 / BMS-936558, MDX1106, OPDIVO), pembrolizumab (MK-3475, KEYTRUDA), pidilizumab (CT-011), and MPDL328OA (ROCHE). As another example, formulations can additionally contain one or more supplements, such as vitamin C, E or other anti-oxidants.
[0269] A pharmaceutical composition comprising an active agent such as an immune cell describedherein, in combination with one or more adjuvants can be formulated in conventional manner using one or more physiologically acceptable carriers, comprising excipients, diluents, and / or auxiliaries, e.g., which facilitate processing of the active agents into preparations that can be administered. Proper formulation can depend at least in part upon the route of administration chosen. The agent(s) described herein can be delivered to a patient using a number of routes or modes of administration, including oral, buccal, topical, rectal, transdermal, transmucosal, subcutaneous, intravenous, and intramuscular applications, as well as by inhalation.
[0270] The active agents can be formulated for parenteral administration (e.g., by injection, forexample bolus injection or continuous infusion) and can be presented in unit dose form in ampoules, pre-filled syringes, small volume infusion or in multi-dose containers with an added preservative. The compositions can take such forms as suspensions, solutions, or emulsions in oily or aqueous vehicles, for example solutions in aqueous polyethylene glycol.
[0271] For injectable formulations, the vehicle can be chosen from those known in art to be suitable,including aqueous solutions or oil suspensions, or emulsions, with sesame oil, corn oil, cottonseed oil, or peanut oil, as well as elixirs, mannitol, dextrose, or a sterile aqueous solution, and similar pharmaceutical vehicles. The formulation can also comprise polymer compositions which are biocompatible, biodegradable, such as poly(lactic-co-glycolic)acid. These materials can be made intoWSGR Docket No. 50401-775.601 micro or nanospheres, loaded with drug and further coated or derivatized to provide superior sustained release performance. Vehicles suitable for periocular or intraocular injection include, for example, suspensions of therapeutic agent in injection grade water, liposomes and vehicles suitable for lipophilic substances. Other vehicles for periocular or intraocular injection are well known in the art.
[0272] In some instances, pharmaceutical composition is formulated in accordance with routineprocedures as a pharmaceutical composition adapted for intravenous administration to human beings. Typically, compositions for intravenous administration are solutions in sterile isotonic aqueous buffer. Where necessary, the composition can also include a solubilizing agent and a local anesthetic such as lidocaine to ease pain at the site of the injection. Generally, the ingredients are supplied either separately or mixed together in unit dosage form, for example, as a dry lyophilized powder or water free concentrate in a hermetically sealed container such as an ampoule or sachette indicating the quantity of active agent. Where the composition is to be administered by infusion, it can be dispensed with an infusion bottle containing sterile pharmaceutical grade water or saline. Where the composition is administered by injection, an ampoule of sterile water for injection or saline can be provided so that the ingredients can be mixed prior to administration.
[0273] When administration is by injection, the active agent can be formulated in aqueous solutions,specifically in physiologically compatible buffers such as Hanks solution, R physiological saline buffer. The solution can contain formulatory agents such as suspending, stabilizing and / or dispersing agents. In another embodiment, the pharmaceutical composition does not comprise an adjuvant or any other substance added to enhance the immune response.
[0274] In addition to the formulations described previously, the active agents can also be formulatedas a depot preparation. Such long acting formulations can be administered by implantation or transcutaneous delivery (for example subcutaneously or intramuscularly), intramuscular injection or use of a transdermal patch. Thus, for example, the agents can be formulated with suitable polymeric or hydrophobic materials (for example as an emulsion in an acceptable oil) or ion exchange resins, oras sparingly soluble derivatives, for example, as a sparingly soluble salt.
[0275] In some cases, pharmaceutical compositions comprising one or more agents exert local andregional effects when administered topically or injected at or near particular sites of infection. Direct topical application, e.g., of a viscous liquid, solution, suspension, dimethylsulfoxide (DMSO)-based solutions, liposomal formulations, gel, jelly, cream, lotion, ointment, suppository, foam, or aerosol spray, can be used for local administration, to produce for example local and / or regional effects. Pharmaceutically appropriate vehicles for such formulation include, for example, lower aliphaticalcohols, polyglycols (e.g., glycerol or polyethylene glycol), esters of fatty acids, oils, fats, silicones,WSGR Docket No. 50401-775.601and the like. Such preparations can also include preservatives (e.g., p -hydroxybenzoic acid esters)and / or antioxidants (e.g., ascorbic acid and tocopherol). See also Dermatological Formulations: Percutaneous absorption, Barry (Ed.), Marcel Dekker Incl, 1983. In another embodiment, local / topical formulations comprising a transporter, carrier, or ion channel inhibitor are used to treat epidermal or mucosal viral infections.
[0276] Pharmaceutical compositions can contain adjuvants such as hydrophilic or lipophilic gellingagents, hydrophilic or lipophilic active agents, preserving agents, antioxidants, solvents, fragrances, fillers, sunscreens, odor-absorbers and dyestuffs. The amounts of these various adjuvants are those conventionally used in the fields considered and for example, are from about 0.01% to about 20% of the total weight of the composition. Depending on their nature, these adjuvants can be introduced into the fatty phase, into the aqueous phase and / or into the lipid vesicles. Cancer vaccines
[0277] The TCRs, recombinant nucleic acids encoding the TCRs, or cells comprising the TCRs orrecombinant nucleic acids encoding the TCRs described herein can be administered (concurrently, prior to, or subsequent to) with a cancer vaccine into a subject in need thereof. The cancer vaccine can comprise a GATA3 polypeptide or a nucleic acid encoding the GATA3 polypeptide. The GATA3 peptide can comprise a full-length GATA3 protein. The GATA3 polypeptide can comprise one or more epitopes described herein from GATA3 protein.
[0278] In some embodiments, the present invention is directed to a vaccine formulation comprisingthe GATA3 polypeptide, e.g., a pharmaceutical composition capable of raising a neoantigen-specific response (e.g., a humoral or cell-mediated immune response). In some embodiments, the vaccine formulation comprises a GATA3 polypeptide or recombinant nucleic acid encoding a GATA3 polypeptide. In some embodiments, the vaccine formulation comprises an immune cell comprising the recombinant nucleic acid encoding the GATA3 polypeptide.
[0279] In some embodiments, a vaccine formulation described herein is capable of raising a specificcytotoxic T cells response, specific helper T cell response, or a B cell response. In some embodiments, antigen polypeptides or polynucleotides can be provided as antigen presenting cells (e.g., dendritic cells) containing, for example, a GATA3 polypeptide or recombinant nucleic acid encoding a GATA3 polypeptide. In other embodiments, such antigen presenting cells are used to stimulate T cells for use in patients. In some embodiments, the antigen presenting cells are dendritic cells. In related embodiments, the dendritic cells are autologous dendritic cells that are pulsed with the neoantigenpeptide or nucleic acid. The neoantigen peptide can be any suitable peptide that gives rise to anappropriate T cell response. In some embodiments, the T cell is a CTL. In some embodiments, the TWSGR Docket No. 50401-775.601 cell is an HTL. Thus, one embodiment of the present disclosure is a vaccine formulation containing at least one antigen presenting cell (e.g., a dendritic cell) that is pulsed or loaded with one or more neoantigen polypeptides or polynucleotides described herein. In some embodiments, such APCs areautologous (e.g., autologous dendritic cells). Alternatively, peripheral blood mononuclear c ells(PBMCs) isolated from a patient can be loaded with neoantigen peptides or polynucleotides ex vivo. In related embodiments, such APCs or PBMCs are injected back into the patient. The polynucleotide can be any suitable polynucleotide that is capable of transducing the dendritic cell, thus resulting in the presentation of a neoantigen peptide and induction of immunity. In some embodiments, such antigen presenting cells (APCs) (e.g., dendritic cells) or peripheral blood mononuclear cells (PBMCs) are used to stimulate a T cell (e.g., an autologous T cell). In related embodiments, the T cell is a CTL.In other related embodiments, the T cell is an HTL. In some embodiments, the T cells are CD8 + Tcells. In some embodiments, the T cells are CD4+T cells. Such T cells are then injected into the patient. In some embodiments, CTL is injected into the patient. In some embodiments, HTL is injected into the patient. In some embodiments, both CTL and HTL are injected into the patient. Administration ofeither therapeutic can be performed simultaneously or sequentially and in any order.
[0280] In some embodiments, a GATA3 polypeptide or recombinant nucleic acids encoding aGATA3 polypeptide can be provided. One exemplary GATA3 polypeptide may comprise a sequence encoded by a neoORF, for example, PGRPLQTHVLPEPHLALQPLQPHADHAHADAPAIQPVLWTTPPLQHGHRHGLEPCSMLTGP PARVPAVPFDLHFCRSSIMKPKRDGYMFLKAESKIMFATLQRSSLWCLCSNH or a fragment thereof; or a polynucleic acid encoding the same. In some embodiments, an exemplary GATA3 polypeptide may comprise a sequence encoded by a neoORF, for example PRPRRCTRHPACPLDHTTPPAWSPPWVRALLDAHRAPSESPCSPFRLAFLQEQYHEA or a fragment thereof; or a polynucleic acid encoding the same. In some embodiments, an exemplary GATA3 polypeptide may comprise a sequence encoded by a neoORF, for example AQAKAVCSQESRDVLCELSDHHNHTLEEECQWGPCLQCLWALLQASQY or a fragment thereof; or a polynucleic acid encoding the same. In some embodiments, the GATA3 polypeptide or recombinant nucleic acid may comprise one or more neoepitopes selected from the GATA3polypeptide comprising a sequence encoded by a GATA3 neoORF. For example, the vaccine maycomprise one or more neoepitopes provided herein, but not limited to: HVLPEPHLAL (B07.02), RPLQTHVLPE (B07.02), VLWTTPPLQH (A03.01), APSESPCSPF (B07.02), CPLDHTTPPA (B07.02), FLQEQYHEA (A02.01, B08.01), RLAFLQEQYH (A03.01), SPCSPFRLAF (B07.02), SPPWVRALL (B07.02), YPACPLDHTT (B07.02), AIQPVLWTT (A02.01), ALQPLQPHAWSGR Docket No. 50401-775.601 (A02.01), DLHFCRSSIM (B08.01), EPHLALQPL (B07.02, B08.01), ESKIMFATL (B08.01), FATLQRSSL (B07.02, B08.01), FLKAESKIM (B08.01), FLKAESKIMF (B08.01), GPPARVPAV (B07.02), IMKPKRDGYM (B08.01), KIMFATLQR (A03.01), KPKRDGYMF (B07.02), KPKRDGYMFL (B07.02), LHFCRSSIM (B08.01), LQHGHRHGL (B08.01), MFATLQRSSL (B07.02, B08.01), MFLKAESKI (A24.02), MLTGPPARV (A02.01) (SEQ ID NO: 15), QPVLWTTPPL (B07.02), SMLTGPPARV (A02.01) (SEQ ID NO: 200), TLQRSSLWCL (A02.01), VLPEPHLAL (A02.01), VPAVPFDLHF (B07.02), YMFLKAESK (A03.01), YMFLKAESKI (A02.01, A03.01, A24.02, B08.01); shown in parenthesis are exemplary known MHC binding partners.
[0281] The concentration of antigen polypeptides can vary widely, i.e., from less than about 0.1%,usually at or at least about 2% to as much as 20% to 50% or more by weight, and will be selected by fluid volumes, viscosities, etc., according to the particular mode of administration selected.
[0282] In some embodiments, a vaccine formulation described herein for therapeutic treatment canbe formulated for parenteral, topical, nasal, oral or local administration. In some embodiments, the vaccine formulation described herein are administered parenterally, e.g., intravenously, subcutaneously, intradermally, or intramuscularly. In some embodiments, the vaccine formulation can be administered intratumorally. The vaccine formulation can be administered at the site of surgical excision to induce a local immune response to the tumor.
[0283] In some embodiments, described herein are compositions (e.g., vaccine formulations) forparenteral administration which comprise a solution of the neoantigen peptides and vaccine formulations are dissolved or suspended in an acceptable carrier, for example, an aqueous carrier. A variety of aqueous carriers can be used, e.g., water, buffered water, 0.9% saline, 0.3% glycine, hyaluronic acid and the like. These compositions can be sterilized by conventional, well known sterilization techniques, or can be sterile filtered. The resulting aqueous solutions can be packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration. The compositions can contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, etc.
[0284] The ability of an adjuvant to increase the immune response to an antigen is typicallymanifested by a significant increase in immune-mediated reaction, or reduction in disease symptoms. For example, an increase in humoral immunity can be manifested by a significant increase in the titer of antibodies raised to the antigen, and an increase in T cell activity can be manifested in increasedWSGR Docket No. 50401-775.601 cell proliferation, or cellular cytotoxicity, or cytokine secretion. An adjuvant can also alter an immune response, for example, by changing a primarily humoral or T helper 2 response into a primarily cellular, or T helper 1 response.
[0285] Suitable adjuvants are known in the art (see, WO 2015 / 095811) and include, but are notlimited to poly(I:C), poly-ICLC, STING agonist, 1018 ISS, aluminum salts, Amplivax, AS15, BCG, CP-870,893, CpG7909, CyaA, dSLIM, GM-CSF, IC30, IC31, Imiquimod, ImuFact IMP321, IS Patch, ISS, ISCOMATRIX, JuvImmune, LipoVac, MF59, monophosphoryl lipid A, Montanide IMS 1312, Montanide ISA 206, Montanide ISA 50V, Montanide ISA-51, OK-432, OM-174, OM-197-MP-EC, ONTAK, PepTel®vector system, PLG microparticles, resiquimod, SRL172, virosomes and othervirus-like particles, YF- -stimulon (Aquila Biotech, Worcester, Mass., USA) which is derived from saponin, mycobacterial extracts and synthetic bacterial cell wall mimics, and other proprietary adjuvants such as Ribi Quil or Superfos. Several immunological adjuvants (e.g., MF59) specific for dendritic cells and theirpreparation have been described (Dupuis M, et al., Cell Immunol.1998; 186(1):18 -27; Allison A C;Dev Biol Stand. 1998; 92:3-11) (Mosca et al. Frontiers in Bioscience, 2007; 12:4050-4060) (Gamvrellis et al. Immunol & Cell Biol. 2004; 82: 506-516). Also, cytokines can be used. Several cytokines have been directly linked to influencing dendritic cell migration to lymphoid tissues (e.g.,TNF- lerating the maturation of dendritic cells into efficient antigen-presenting cells for T-lymphocytes (e.g., GM-CSF, PGE1, PGE2, IL-1, IL- -4, IL-6 and CD40L) (U.S. Pat. No.5,849,589 incorporated herein by reference in its entirety) and acting as immunoadjuvants (e.g., IL- 12) (Gabrilovich D I, et al., J Immunother Emphasis Tumor Immunol.1996 (6):414-418).
[0286] CpG immunostimulatory oligonucleotides have also been reported to enhance the effects ofadjuvants in a therapeutic setting. Without being bound by theory, CpG oligonucleotides act by activating the innate (non-adaptive) immune system via Toll-like receptors (TLR), mainly TLR9. CpG triggered TLR9 activation enhances antigen-specific humoral and cellular responses to a wide variety of antigens, including peptide or protein antigens, live or killed viruses, dendritic cell vaccine formulations, autologous cellular vaccine formulations and polysaccharide conjugates in both prophylactic and therapeutic vaccine formulations. Importantly, it enhances dendritic cell maturation and differentiation, resulting in enhanced activation of TH1 cells and strong cytotoxic T-lymphocyte (CTL) generation, even in the absence of CD4+T cell help. The TH1 bias induced by TLR9 stimulation is maintained even in the presence o that normally promote a TH2 bias. CpG oligonucleotides show even greater adjuvant activity when formulated or co-administered with other adjuvants or in formulations such as microparticles,WSGR Docket No. 50401-775.601 nanoparticles, lipid emulsions or similar formulations, which are especially useful for inducing a strong response when the antigen is relatively weak. They can also accelerate the immune response and enabled the antigen doses to be reduced with comparable antibody responses to the full-dose vaccine formulation without CpG in some experiments (Arthur M. Krieg, Nature Reviews, Drug Discovery, 5, June 2006, 471-484). U.S. Pat. No.6,406,705 describes the combined use of CpG oligonucleotides, non-nucleic acid adjuvants and an antigen to induce an antigen-specific immune response. A commercially available CpG TLR9 antagonist is dSLIM (double Stem Loop Immunomodulator) by Mologen (Berlin, DE), which is a component of the pharmaceutical composition described herein. Other TLR binding molecules such as RNA binding TLR7, TLR8 and / or TLR9 can also be used.
[0287] Other examples of useful adjuvants include, but are not limited to, chemically modified CpGs(e.g. CpR, Idera), Poly(I and / or poly C)(e.g., polyI:CI2U), non-CpG bacterial DNA or RNA, ssRNA40 for TLR8, as well as immunoactive small molecules and antibodies such as cyclophosphamide, sunitinib, bevacizumab, celebrex, NCX-4016, sildenafil, tadalafil, vardenafil, sorafinib, XL-999, CP- 547632, pazopanib, ZD2171, AZD2171, ipilimumab, tremelimumab, and SC58175, which can act therapeutically and / or as an adjuvant. The amounts and concentrations of adjuvants and additives useful in the context of the present invention can readily be determined by the skilled artisan without undue experimentation. Additional adjuvants include colony-stimulating factors, such as Granulocyte Macrophage Colony Stimulating Factor (GM-CSF, sargramostim).
[0288] In some embodiments, a vaccine formulation according to the present disclosure can comprisemore than one different adjuvant. Furthermore, the invention encompasses a pharmaceutical composition comprising any adjuvant substance including any of the above or combinations thereof. In some embodiments, the vaccine formulation comprises a GATA3 polypeptide or recombinant nucleic acid encoding a GATA3 polypeptide. In some embodiments, the vaccine formulation comprises an immune cell comprising the recombinant nucleic acid encoding the GATA3 polypeptide. In some cases, the adjuvant can be administered separately in any appropriate sequence.
[0289] Lipidation can be classified into several different types, such as N-myristoylation,palmitoylation, GPI-anchor addition, prenylation, and several additional types of modifications. N- myristoylation is the covalent attachment of myristate, a C14 saturated acid, to a glycine residue. Palmitoylation is thioester linkage of long-chain fatty acids (C16) to cysteine residues. GPI-anchor addition is glycosyl-phosphatidylinositol (GPI) linkage via amide bond. Prenylation is the thioether linkage of an isoprenoid lipid (e.g., farnesyl (C-15), geranylgeranyl (C-20)) to cysteine residues. Additional types of modifications can include attachment of S-diacylglycerol by a sulfur atom ofWSGR Docket No. 50401-775.601 cysteines, O-octanoyl conjugation via serine or threonine residues, S-archaeol conjugation to cysteine residues, and cholesterol attachment.
[0290] Fatty acids for generating lipidated peptides can include C2 to C30 saturated,monounsaturated, or polyunsaturated fatty acyl groups. Exemplary fatty acids can includ e palmitoyl,myristoyl, stearoyl and decanoyl groups. In some instances, a lipid moiety that has adjuvant property is attached to a polypeptide of interest to elicit or enhance immunogenicity in the absence of an extrinsic adjuvant. A lipidated peptide or lipopeptide can be referred to as a self-adjuvant lipopeptide. Any of the fatty acids described above and elsewhere herein can elicit or enhance immunogenicity ofa polypeptide of interest. A fatty acid that can elicit or enhance immunogenicity can include palmitoyl,myristoyl, stearoyl, lauroyl, octanoyl, and decanoyl groups.
[0291] Polypeptides such as naked peptides or lipidated peptides can be incorporated into a liposome.Sometimes, lipidated peptides can be incorporated into a liposome. For example, the lip id portion ofthe lipidated peptide can spontaneously integrate into the lipid bilayer of a liposome. Thus, a incorporation in the formulations include, and are not limited to, multilamellar vesicles (MLV), oligolamellar vesicles (OLV), unilamellar vesicles (UV), small unilamellar vesicles (SUV), medium- sized unilamellar vesicles (MUV), large unilamellar vesicles (LUV), giant unilamellar vesicles (GUV), multivesicular vesicles (MVV), single or oligolamellar vesicles made by reverse-phase evaporation method (REV), multilamellar vesicles made by the reverse-phase evaporation method (MLV-REV), stable plurilamellar vesicles (SPLV), frozen and thawed MLV (FATMLV), vesicles prepared by extrusion methods (VET), vesicles prepared by French press (FPV), vesicles prepared by fusion (FUV), dehydration-rehydration vesicles (DRV), and bubblesomes (BSV).
[0292] The GATA3 polypeptide and recombinant nucleic acids described herein can also beadministered via liposomes, which target the peptides to a particular cells tissue, such as lymphoidtissue. Liposomes are also useful in increasing the half -life of the peptides. Liposomes includeemulsions, foams, micelles, insoluble monolayers, liquid crystals, phospholipid dispersions, lamellar layers and the like. In these preparations the peptide to be delivered is incorporated as part of a liposome, alone or in conjunction with a molecule which binds to, e.g., a receptor prevalent amonglymphoid cells, such as monoclonal antibodies which bind to the DEC205 antigen, or with othertherapeutic or vaccine formulations. Thus, liposomes filled with a desired peptide or polynucleotide described herein can be directed to the site of lymphoid cells, where the liposomes then deliver the selected therapeutic / immunogenic polypeptide / polynucleotide compositions. Liposomes can be formed from standard vesicle-forming lipids, which generally include neutral and negatively chargedWSGR Docket No. 50401-775.601 phospholipids and a sterol, for example, cholesterol. The selection of lipids is generally guided by consideration of, e.g., liposome size, acid lability and stability of the liposomes in the blood stream. A variety of methods are available for preparing liposomes, as described in, e.g., Szoka et al., Ann. Rev. Biophys. Bioeng. 9; 467 (1980), U.S. Pat. Nos. 4,235,871, 4,501,728, 4,501,728, 4,837,028, and 5,019,369.
[0293] For targeting to the immune cells, a GATA3 polypeptide or recombinant nucleic acid to beincorporated into the liposome for cell surface determinants of the desired immune system cells. A liposome suspension containing a peptide can be administered intravenously, locally, topically, etc. ina dose which varies according to, inter alia, the manner of administration, the polypeptid e orrecombinant nucleic acid being delivered, and the stage of the disease being treated.
[0294] In some embodiments, the GATA3 polypeptide and recombinant nucleic acids are targeted todendritic cells. In some embodiments, the GATA3 polypeptide and recombinant nucleic acids are target to dendritic cells using the markers DEC205, XCR1, CD197, CD80, CD86, CD123, CD209, CD273, CD283, CD289, CD184, CD85h, CD85j, CD85k, CD85d, CD85g, CD85a, TSLP receptor, or CD1a.
[0295] For solid compositions, conventional or nanoparticle nontoxic solid carriers can be used whichinclude, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharin, talcum, cellulose, glucose, sucrose, magnesium carbonate, and the like. For oral administration, a pharmaceutically acceptable nontoxic composition is formed by incorporating any ofthe normally employed excipients, such as those carriers previously listed, and generally 10 -95% ofactive ingredient, that is, one or more GATA3 polypeptides and recombinant nucleic acids described herein at a concentration of 25%-75%.
[0296] For aerosol administration, the GATA3 polypeptide and recombinant nucleic acids can besupplied in finely divided form along with a surfactant and propellant. Representative of such agents are the esters or partial esters of fatty acids containing from 6 to 22 carbon atoms, such as caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic, olesteric and oleic acids with an aliphatic polyhydric alcohol or its cyclic anhydride. Mixed esters, such as mixed or natural glycerides can be employed. The surfactant can constitute 0.1%-20% by weight of the composition, or 0.25-5%. The balance of the composition can be propellant. A carrier can also be included as desired, as with, e.g., lecithin for intranasal delivery.
[0297] Additional methods for delivering the recombinant nucleic acids described herein are alsoapproach is described, for instance, in Wolff et al., Science 247: 1465-1468 (1990) as well as U.S. Pat.WSGR Docket No. 50401-775.601 Nos.5,580,859 and 5,589,466. The nucleic acids can also be administered using ballistic delivery as described, for instance, in U.S. Pat. No. 5,204,253. Particles comprised solely of DNA can beadministered. Alternatively, DNA can be adhered to particles, such as gold particles.
[0298] For therapeutic or immunization purposes, DNA or RNA encoding the GATA3 polypeptidecan also be administered to the subject. In some embodiments the recombinant nucleic acids encoding the GATA3 polypeptide may be part of a synthetic lipid nanoparticle formulation. In some embodiments, the recombinant nucleic acid is DNA. In some embodiments, the recombinant nucleic acid is mRNA.
[0299] The recombinant nucleic acids can also be delivered complexed to cationic compounds, suchas cationic lipids. In some embodiments, nucleic acids can be encapsulated in lipid nanoparticles (e.g., comprising cationic lipid, non-cationic lipids (e.g., phospholipids and / or sterol), and / or PEG-lipids). Lipid-mediated gene delivery methods are described, for instance, in WO 96 / 18372, WO 93 / 24640; Mannino & Gould-Fogerite, BioTechniques 6(7): 682-691 (1988); U.S. Pat. No. 5,279,833; WO 91 / 06309; and Feigner et al., Proc. Natl. Acad. Sci. USA 84: 7413-7414 (1987).
[0300] Depending on the method of preparation, liposomes can be unilamellar or multilamellar, andcan adsorb many types of cells and then release an incorporated agent (e.g., a peptide described herein). In some cases, the liposomes fuse with the target cell, whereby the contents of the liposome then empty into the target cell. A liposome can be endocytosed by cells that are phagocytic. Endocytosis can be followed by intralysosomal degradation of liposomal lipids and release of the encapsulated agents.
[0301] The liposomes provided herein can also comprise carrier lipids. In some embodiments thecarrier lipids are phospholipids. Carrier lipids capable of forming liposomes include, but are not limitedto dipalmitoylphosphatidylcholine (DPPC), phosphatidylcholine (PC; lecithin), phosphatidic acid (PA), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), phosphatidylserine (PS). Other suitable phospholipids further include distearoylphosphatidylcholine (DSPC), dimyristoylphosphatidylcholine (DMPC), dipalmitoylphosphatidyglycerol (DPPG), distearoylphosphatidyglycerol (DSPG), dimyristoylphosphatidylglycerol (DMPG), dipalmitoylphosphatidic acid (DPPA); dimyristoylphosphatidic acid (DMPA), distearoylphosphatidic acid (DSPA), dipalmitoylphosphatidylserine (DPPS), dimyristoylphosphatidylserine (DMPS), distearoylphosphatidylserine (DSPS), dipalmitoylphosphatidyethanolamine (DPPE), dimyristoylphosphatidylethanolamine (DMPE), distearoylphosphatidylethanolamine (DSPE) and the like, or combinations thereof. In some embodiments, the liposomes further comprise a sterol (e.g.,WSGR Docket No. 50401-775.601 cholesterol) which modulates liposome formation. The carrier lipids can be any known non-phosphate polar lipids.
[0302] Cell-based vaccine formulations can also be administered to a subject. For example, an antigenpresenting cell (APC) based vaccine formulation can be formulated using any of the well-known techniques, carriers, and excipients as suitable and as understood in the art. APCs include monocytes, monocyte-derived cells, macrophages, and dendritic cells. Sometimes, an APC based vaccine formulation can be a dendritic cell-based vaccine formulation.
[0303] A dendritic cell-based vaccine formulation can be prepared by any methods well known in theart. In some cases, dendritic cell-based vaccine formulations can be prepared through an ex vivo or in vivo method. The ex vivo method can comprise the use of autologous DCs pulsed ex vivo with the polypeptides described herein, to activate or load the DCs prior to administration into the patient. The in vivo method can comprise targeting specific DC receptors using antibodies coupled with the polypeptides described herein. The DC-based vaccine formulation can further comprise DC activators such as TLR3, TLR-7-8, and CD40 agonists. The DC-based vaccine formulation can further comprise adjuvants, and a pharmaceutically acceptable carrier.
[0304] An adjuvant can be used to enhance the immune response (humoral and / or cellular) elicitedin a patient receiving the vaccine formulation. Sometimes, adjuvants can elicit a Th1-type response. Other times, adjuvants can elicit a Th2-type response. A Th1-type response can be characterized bythe production of cytokines such as IFN- -type response which can becharacterized by the production of cytokines such as IL-4, IL-5 and IL-10.
[0305] In some aspects, lipid-based adjuvants, such as MPLA and MDP, can be used with the vaccineformulations disclosed herein. Monophosphoryl lipid A (MPLA), for example, is an adjuvant that causes increased presentation of liposomal antigen to specific T Lymphocytes. In addition, a muramyl dipeptide (MDP) can also be used as a suitable adjuvant in conjunction with the immunogenic pharmaceutical formulations described herein.
[0306] Adjuvant can also comprise stimulatory molecules such as cytokines. Non-limiting examples- - --CSF, epidermal growth factor (EGF), cutaneous T cell- attracting chemokine (CTACK), epithelial thymus-expressed chemokine (TECK), mucosae-associated epithelial chemokine (MEC), IL-12, IL-15, IL-28, MHC, CD80, CD86, IL-1, IL-2, IL-4, IL-5, IL-6, IL-10, IL-18, MCP-1, MIP-la, MIP-1-, IL-8, L- selectin, P-selectin, E-selectin, CD34, GlyCAM-1, MadCAM-1, LFA-1, VLA-1, Mac-1, pl50.95, PECAM, ICAM-1, ICAM-2, ICAM-3, CD2, LFA-3, M-CSF, G-CSF, mutant forms of IL-18, CD40, CD40L, vascular growth factor, fibroblast growthWSGR Docket No. 50401-775.601 factor, IL-7, nerve growth factor, vascular endothelial growth factor, Fas, TNF receptor, Fit, Apo-1, p55, WSL-1, DR3, TRAMP, Apo-3, AIR, LARD, NGRF, DR4, DRS, KILLER, TRAIL-R2, TRICK2,DR6, Caspase ICE, Fos, c-jun, Sp-1, Ap-1, Ap- ctiveNIK, SAP K, SAP- TRAILrecDRC5, TRAIL-R3, TRAIL-R4, RANK, RANK LIGAND, Ox40, Ox40 LIGAND, NKG2D, MICA, MICB, NKG2A, NKG2B, NKG2C, NKG2E, NKG2F, TAPI, and TAP2.
[0307] Additional adjuvants include: MCP-1, MIP-la, MIP-lp, IL-8, RANTES, L-selectin, P-selectin,E-selectin, CD34, GlyCAM-1, MadCAM-1, LFA-1, VLA-1, Mac-1, pl50.95, PECAM, ICAM-1, ICAM-2, ICAM-3, CD2, LFA-3, M-CSF, G-CSF, IL-4, mutant forms of IL-18, CD40, CD40L, vascular growth factor, fibroblast growth factor, IL-7, IL-22, nerve growth factor, vascular endothelial growth factor, Fas, TNF receptor, Fit, Apo-1, p55, WSL-1, DR3, TRAMP, Apo-3, AIR, LARD, NGRF, DR4, DR5, KILLER, TRAIL-R2, TRICK2, DR6, Caspase ICE, Fos, c-jun, Sp-1, Ap-1, Ap-2, -1, JNK, interferon response -R3, TRAIL-R4, RANK, RANK LIGAND, Ox40, Ox40 LIGAND, NKG2D, MICA, MICB, NKG2A, NKG2B, NKG2C, NKG2E, NKG2F, TAP1, TAP2 and functional fragments thereof.
[0308] In some aspects, an adjuvant can be a modulator of a toll like receptor. Examples ofmodulators of toll-like receptors include TLR9 agonists and are not limited to small molecule modulators of toll-like receptors such as Imiquimod. Sometimes, an adjuvant is selected from bacteria toxoids, polyoxypropylene-polyoxyethylene block polymers, aluminum salts, liposomes, CpG polymers, oil-in-water emulsions, or a combination thereof. Sometimes, an adjuvant is an oil-in-water emulsion. The oil-in-water emulsion can include at least one oil and at least one surfactant, with the oil(s) and surfactant(s) being biodegradable (metabolizable) and biocompatible. The oil droplets in the d can even have a sub-micron diameter, with these small sizes being achieved with a microfluidiser to provide stable emulsions. Droplets with a size less than 220 nm can be subjected to filter sterilization.
[0309] In some instances, a vaccine formulation can include carriers and excipients (including butnot limited to buffers, carbohydrates, mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, bacteriostats, chelating agents, suspending agents, thickening agents and / or preservatives), water, oils including those of petroleum, animal, vegetable or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil and the like, saline solutions, aqueous dextrose and glycerol solutions, flavoring agents, coloring agents, detackifiers and other acceptable additives, adjuvants, or binders, other pharmaceutically acceptable auxiliary substances as required toWSGR Docket No. 50401-775.601 approximate physiological conditions, such as pH buffering agents, tonicity adjusting agents, emulsifying agents, wetting agents and the like. Examples of excipients include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol and the like. In another instances, the pharmaceutical preparation is substantially free of preservatives. In other instances, the pharmaceutical preparation can contain at least one preservative. It will be recognized that, while any suitable carrier known to those of ordinary skill in the art can be employed to administer the pharmaceutical compositions described herein, the type of carrier will vary depending on the mode of administration.
[0310] A vaccine formulation can include preservatives such as thiomersal or 2-phenoxyethanol. Ine.g., thiomersal- -Tocopherol succinate may be used as an alternative to mercurial compounds.
[0311] For controlling the tonicity, a physiological salt such as sodium salt can be included in thevaccine formulation. Other salts can include potassium chloride, potassium dihydrogen phosphate,disodium phosphate, and / or magnesium chloride, or the like.
[0312] A vaccine formulation can have an osmolality of between 200 mOsm / kg and 400 mOsm / kg,between 240-360 mOsm / kg, or within the range of 290-310 mOsm / kg.
[0313] A vaccine formulation can comprise one or more buffers, such as a Tris buffer; a borate buffer;a succinate buffer; a histidine buffer (particularly with an aluminum hydroxide adjuvant); or a citrate buffer. Buffers, in some cases, are included in the 5-20 or 10-50 mM range.
[0314] The pH of the vaccine formulation can be between about 5.0 and about 8.5, between about 6.0and about 8.0, between about 6.5 and about 7.5, or between about 7.0 and about 7.8.
[0315] A vaccine formulation can be sterile. The vaccine formulation can be non-pyrogenic e.g.,containing <1 EU (endotoxin unit, a standard measure) per dose, and can be <0.1 EU per dose. The composition can be gluten free.
[0316] A vaccine formulation can include detergent e.g., a polyoxyethylene sorbitan ester surfactant-9 (Triton X-100) or t- octylphenoxypolyethoxyethanol). The detergent can be present only at trace amounts. The vaccine formulation can include less than 1 mg / mL of each of octoxynol-10 and polysorbate 80. Other residual components in trace amounts can be antibiotics (e.g., neomycin, kanamycin, polymyxin B).
[0317] A vaccine formulation can be formulated as a sterile solution or suspension, in suitablevehicles, well known in the art. The pharmaceutical compositions can be sterilized by conventional,well-known sterilization techniques, or can be sterile filtered. The resulting aqueous solutions can beWSGR Docket No. 50401-775.601 packaged for use as is, or lyophilized, the lyophilized preparation being combined with a sterile solution prior to administration.
[0318] In some instances, a vaccine formulation can be administered with an additional agent. Thechoice of the additional agent can depend, at least in part, on the condition being treated. The additional agent can include, for example, a checkpoint inhibitor agent such as an anti-PD1, anti-CTLA4, anti- PD-L1, anti CD40, or anti-TIM3 agent (e.g., an anti-PD1, anti-CTLA4, anti-PD-L1, anti CD40, or anti-TIM3 antibody); or any agents having a therapeutic effect for a pathogen infection (e.g. viral infection), including, e.g., drugs used to treat inflammatory conditions such as an NSAID, e.g., ibuprofen, naproxen, acetaminophen, ketoprofen, or aspirin. For example, the checkpoint inhibitor can be a PD-1 / PD- L1 antagonist selected from the group consisting of: nivolumab (ONO-4538 / BMS- 936558, MDX1106, OPDIVO), pembrolizumab (MK-3475, KEYTRUDA), pidilizumab (CT-011), and MPDL328OA (ROCHE). As another example, formulations can additionally contain one or more supplements, such as vitamin C, E or other anti-oxidants.
[0319] In some embodiments, the vaccine formulation comprises a nanoparticle. For example, thevaccine described herein (e.g., GATA3 vaccine) can be embedded or encapsulated within the nanoparticle. In some embodiments, the nanoparticle is a lipid nanoparticle or a liposome. In some nucleic acids such as RNA. Lipoplexes can be formed spontaneously when cationic liposomes, which lipid is comprised in a vesicle encapsulating the RNA. The vesicle may be a multilamellar vesicle, an unilamellar vesicle, or a mixture thereof. The vesicle may be a liposome.
[0320] In some embodiments, the nanoparticulate RNA formulations with defined particle size areprovided wherein the net charge of the particles is close to zero or negative. In some embodiments, the RNA nanoparticles are RNA lipoplexes. A strong immune response against a model antigen can be induced.
[0321] The lipoplexes can have a well-defined particle size distribution profile as measured bydynamic light scattering and with low fraction of subvisible particles, which may be needed forintravenous administration to patients. If formed by incubation of liposomes with RNA by self -assembly, the particle size of the original liposomes may not be affected, and no undesired moieties of large aggregates can be found. Different sizes can be obtained by selecting the size of the precursor liposomes and the mixing conditions. The particles can be frozen and thawed without formation of aggregates, while maintaining the original particle size profile, and maintaining the biological activity. The particles can be lyophilized and reconstituted with water without formation of aggregates, whileWSGR Docket No. 50401-775.601 maintaining the original particle size profile and maintaining the biological activity. The particles can be manufactured by different protocols which are scalable and which can be performed under controlled conditions. With such properties the lipoplex formulations of the present disclosure can fulfill important requirements for pharmaceutical formulations for application to patients, in terms of particle size distribution profile and stability. Furthermore, compared to positively charged lipopexes,the RNA nanoparticles described herein can be less toxic and to display less undesired seruminteractions. In particular, the formulations can be suitable for parenteral administration, including intravenous and subcutaneous administration.
[0322] In some embodiments, the nanoparticles are lipoplexes comprising DOTMA and DOPE in amolar ratio of 10:0 to 1:9, in some cases 8:2 to 3:7, and in some cases of 7:3 to 5:5 and wherein the charge ratio of positive charges in DOTMA to negative charges in the RNA is 1.8:2 to 0.8:2, in some cases 1.6:2 to 1:2, in some cases 1.4:2 to 1.1:2 and in some cases about 1.2:2. In some embodiments, the nanoparticles are lipoplexes comprising DOTMA and Cholesterol in a molar ratio of 10:0 to 1 :9, in some cases 8:2 to 3:7, and in some cases of 7:3 to 5:5 and wherein the charge ratio of positive charges in DOTMA to negative charges in the RNA is 1.8:2 to 0.8:2, in some cases 1.6:2 to 1:2, in some cases 1.4:2 to 1.1:2 and in some cases about 1.2:2. In some embodiments, the nanoparticles are lipoplexes comprising DOTAP and DOPE in a molar ratio of 10:0 to 1:9, in some cases 8:2 to 3:7, and in some cases of 7:3 to 5:5 and wherein the charge ratio of positive charges in DOTMA to negative charges in the RNA is 1.8:2 to 0.8:2, in some cases 1.6:2 to 1:2, in some cases 1.4:2 to 1.1:2 and in some cases about 1.2:2. In some embodiments, the nanoparticles are lipoplexes comprising DOTMA and DOPE in a molar ratio of 2:1 to 1:2, in some cases 2:1 to 1:1, and wherein the charge ratio of positive charges in DOTMA to negative charges in the RNA is 1.4:1 or less. In some embodiments, the nanoparticles are lipoplexes comprising DOTMA and cholesterol in a molar ratio of 2:1 to 1:2, in some cases 2:1 to 1:1, and wherein the charge ratio of positive charges in DOTMA to negative charges in the RNA is 1.4:1 or less. In some embodiments, the nanoparticles are lipoplexes comprising DOTAP and DOPE in a molar ratio of 2:1 to 1:2, in some cases 2: to 1:1, and wherein the charge ratio of positive charges in DOTAP to negative charges in the RNA is 1.4:1 or less. In some embodiments, the nanoparticles have an average diameter in the range of from about 50 nm to about 1000 nm, in some cases from about 50 nm to about 400 nm, in some cases about 100 nm to about 300 nm such as about 150 nm to about 200 nm. In some embodiments, the nanoparticles have a diameter in the range of about 200 to about 400 nm. In some embodiments, the polydispersity index of the nanoparticles described herein as measured by dynamic light scattering is 0.5 or less, in some cases 0.4 or less or in some cases 0.3 or less.WSGR Docket No. 50401-775.601
[0323] In some embodiments, the nanoparticles described herein are obtainable by one or more of thefollowing: (i) incubation of liposomes in an aqueous phase with the RNA in an aqueous phase, (ii)incubation of the lipid dissolved in an organic, water miscible solvent, such as ethanol, with the RNAin aqueous solution, (iii) reverse phase evaporation technique, (iv) freezing and thawing of the product, (v) dehydration and rehydration of the product, (vi) lyophilization and rehydration of the of the product, or (vii) spray drying and rehydration of the product.
[0324] In some embodiments, the lipid solutions, liposomes and RNA lipoplex particles describedherein include a cationic lipid. As used herein, a "cationic lipid" refers to a lipid having a net positive charge. Cationic lipids bind negatively charged RNA by electrostatic interaction to the lipid matrix. Generally, cationic lipids possess a lipophilic moiety, such as a sterol, an acyl or diacyl chain, and the head group of the lipid typically carries the positive charge. Examples of cationic lipids include, but are not limited to l,2-di-O-octadecenyl-3-trimethylammonium propane (DOTMA), dimethyldioctadecylammonium (DDAB); l,2-dioleoyl-3 -trimethylammonium propane (DOTAP); l,2- dioleoyl-3-dimethylammonium-propane (DODAP); l,2-diacyloxy-3- dimethylammonium propanes; l,2-dialkyloxy-3- dimethylammonium propanes; dioctadecyldimethyl ammonium chloride (DODAC),2,3-di(tetradecoxy)propyl-(2- hydroxyethyl)-dimethylazanium (DMRIE), 1 ,2-dimyristoyl-sn-glycero-3-ethylphosphocholine (DMEPC), l,2-dimyristoyl-3-trimethylammonium propane (DMTAP), l,2-dioleyloxypropyl-3- dimethyl-hydroxyethyl ammonium bromide (DORIE), and 2,3-dioleoyloxy- N-[2(spermine carboxamide)ethyl]-N,N-dimethyl-l-propanamium trifluoroacetate (DOSPA). Preferred are DOTMA, DOTAP, DODAC, and DOSPA. In specific embodiments, the at least one cationic lipid is DOTMA and / or DOTAP. In some embodiments, the at least one cationic lipid is DOTMA, in particular (R)-DOTMA.
[0325] An additional lipid may be incorporated to adjust the overall positive to negative charge ratioand physical stability of the RNA lipoplex particles. In certain embodiments, the additional lipid is a neutral lipid. As used herein, a "neutral lipid" refers to a lipid having a net charge of zero. Examples of neutral lipids include, but are not limited to, l,2-di-(9Z-octadecenoyl)-sn- glycero-3- phosphoethanolamine (DOPE), 1 ,2-dioleoyl-sn-glycero-3 -phosphocholine (DOPC), diacylphosphatidyl choline, diacylphosphatidyl ethanol amine, ceramide, sphingoemyelin, cephalin, cholesterol, and cerebroside. In specific embodiments, the second lipid is DOPE, cholesterol and / or DOPC.
[0326] In some embodiments, the RNA lipoplex particles include both a cationic lipid and anadditional lipid. In some embodiments, the cationic lipid is DOTMA and the additional lipid is DOPE. Without wishing to be bound by theory, the amount of the at least one cationic lipid compared to theWSGR Docket No. 50401-775.601 amount of the at least one additional lipid may affect important RNA lipoplex particle characteristics, such as charge, particle size, stability, tissue selectivity, and bioactivity of the RNA. Accordingly, in some embodiments, the molar ratio of the at least one cationic lipid to the at least one additional lipidis from about 10:0 to about 1 :9, about 4:1 to about 1 :2, o r about 3 : 1 to about 1 : 1. In someembodiments, the molar ratio may be about 3:1, about 2.75:1, about 2.5:1, about 2.25:1, about 2:1, about 1.75:1, about 1.5: 1, about 1.25:1, or about 1 : 1. In some embodiments, the molar ratio of the at least one cationic lipid to the at least one additional lipid is about 2:1. RNA Lipoplex Particles
[0327] Vaccine formulations may comprise RNA lipoplex particles described herein. According tothe present disclosure, the compositions described herein may comprise salts such as sodium chloride. Without wishing to be bound by theory, sodium chloride functions as an ionic osmolality agent for preconditioning RNA prior to mixing with the at least one cationic lipid. Certain embodiments contemplate alternative organic or inorganic salts to sodium chloride in the present disclosure. Alternative salts include, without limitation, potassium chloride, dipotassium phosphate, monopotassium phosphate, potassium acetate, potassium bicarbonate, potassium sulfate, potassium acetate, disodium phosphate, monosodium phosphate, sodium acetate, sodium bicarbonate, sodium sulfate, sodium acetate, lithium chloride, magnesium chloride, magnesium phosphate, calcium chloride, and sodium salts of ethyl enediaminetetraacetic acid (EDTA).
[0328] Generally, compositions comprising RNA lipoplex particles described herein comprisesodium chloride at a concentration that preferably ranges from 0 mM to about 500 mM, from about 5mM to about 400 mM, or from about 10 mM to about 300 mM. In some embodiments, compositions comprising RNA lipoplex particles comprise an ionic strength corresponding to such sodium chloride concentrations.
[0329] Generally, compositions for and resulting from forming RNA lipoplex particles from RNAand liposomes such as those described herein comprise high sodium chloride concentrations, or comprises a high ionic strength. In some embodiments, the sodium chloride is at a concentration of at least 45 mM. In some embodiments, the sodium chloride is at a concentration of about 45 mM to about 300 mM, or from about 50 mM to about 150 mM. In some embodiments, the compositions comprise an ionic strength corresponding to such sodium chloride concentrations.
[0330] Generally, compositions for storing RNA lipoplex particles such as for freezing of RNAlipoplex particles such as those described herein comprise low sodium chloride concentrations, or comprises a low ionic strength. In some embodiments, the sodium chloride is at a concentration from 0 mM to about 50 mM, from 0 mM to about 40 mM, or from about 10 mM to about 50 mM. In specificWSGR Docket No. 50401-775.601 embodiments, the sodium chloride is at a concentration of about 1 mM, about 2 mM, about 3 mM, about 4 mM, about 5 mM, about 6 mM, about 7 mM, about 8 mM, about 9 mM, about 10 mM, about 11 mM, about 12 mM, about 13 mM, about 14 mM, about 15 mM, about 16 mM, about 17 mM, about 18 mM, about 19 mM, about 20 mM, about 21 mM, about 22 mM, about 23 mM, about 24 mM, about 25 mM, about 26 mM, about 27 mM, about 28 mM, about 29 mM, about 30 mM, about 31 mM, about 32 mM, about 33 mM, about 34 mM, about 35 mM, about 36 mM, about 37 mM, about 38 mM, about 39 mM, about 40 mM, about 41 mM, about 42 mM, about 43 mM, about 44 mM, about 45 mM, about 46 mM, about 47 mM, about 48 mM, about 49 mM, or about 50 mM. In some embodiments, the sodium chloride is at a concentration of about 20 mM, about 30 mM, or about 40 mM. In some embodiments, the sodium chloride is at a concentration of 20 mM. In some embodiments, the sodium chloride is at a concentration of 30 mM. In some embodiments, the compositions comprise an ionicstrength corresponding to such sodium chloride concentrations.
[0331] Generally, compositions resulting from thawing frozen RNA lipoplex particle compositionsand optionally adjusting the osmolality and ionic strength by adding an aqueous liquid comprise high sodium chloride concentrations, or comprises a high ionic strength. In some embodiments, the sodium chloride is at a concentration of about 50 mM to about 300 mM, or from about 80 mM to about 150 mM. In some embodiments, the compositions comprise an ionic strength corresponding to such sodium chloride concentrations.
[0332] Compositions described herein may comprise a stabilizer to avoid substantial loss of theproduct quality and, in particular, substantial loss of RNA activity during freezing, lyophilization or spray-drying and storage of the frozen, lyophilized or spray-dried composition. Such a composition is also referred to as stable herein. Typically the stabilizer is present prior to the freezing, lyophilization or spray-drying process and persists in the resulting frozen, lyophilized or freeze-dried preparation. It can be used to protect RNA lipoplex particles during freezing, lyophilization or spray-drying and storage of the frozen, lyophilized or freeze-dried preparation, for example to reduce or preventaggregation, particle collapse, RNA degradation and / or other types of damage.
[0333] In some embodiments, the stabilizer is a carbohydrate. The term "carbohydrate", as usedherein refers to and encompasses monosaccharides, disaccharides, trisaccharides, oligosaccharides and polysaccharides.
[0334] In some embodiments, the stabilizer is a monosaccharide. The term "monosaccharide", as usedherein refers to a single carbohydrate unit (e.g., a simple sugar) that cannot be hydrolyzed to simpler carbohydrate units. Exemplary monosaccharide stabilizers include glucose, fructose, galactose, xylose,ribose and the like.WSGR Docket No. 50401-775.601
[0335] In some embodiments, the stabilizer is a disaccharide. The term "disaccharide", as used hereinrefers to a compound or a chemical moiety formed by 2 monosaccharide units that are bonded together through a glycosidic linkage, for example through 1-4 linkages or 1-6 linkages. A disaccharide may be hydrolyzed into two monosaccharides. Exemplary disaccharide stabilizers include sucrose, trehalose, lactose, maltose and the like. The term "trisaccharide" means three sugars linked together toform one molecule. Examples of a trisaccharides include raffinose and melezitose.
[0336] In some embodiments, the stabilizer is an oligosaccharide. The term "oligosaccharide", asused herein refers to a compound or a chemical moiety formed by 3 to about 15, preferably 3 to about10 monosaccharide units that are bonded together through glycosidic linkages, for example through 1- 4 linkages or 1-6 linkages, to form a linear, branched or cyclic structure. Exemplary oligosaccharide stabilizers include cyclodextrins, raffinose, melezitose, maltotriose, stachyose, acarbose, and the like. An oligosaccharide can be oxidized or reduced. In some embodiments, the stabilizer is a cyclic oligosaccharide. The term "cyclic oligosaccharide", as used herein refers to a compound or a chemical moiety formed by 3 to about 15, preferably 6, 7, 8, 9, or 10 monosaccharide units that are bonded together through glycosidic linkages, for example through 1-4 linkages or 1-6 linkages, to form a cyclic structure. Exemplary cyclic oligosaccharide stabilizers include cyclic oligosaccharides that are discretecompounds, such as a cyclodextrin, b cyclodextrin, or g cyclodextrin.
[0337] Other exemplary cyclic oligosaccharide stabilizers include compounds which include acyclodextrin moiety in a larger molecular structure, such as a polymer that contains a cyclic oligosaccharide moiety. A cyclic oligosaccharide can be oxidized or reduced, for example, oxidized to dicarbonyl forms. The term "cyclodextrin moiety", as used herein refers to cyclodextrin (e.g., an a, b, or g cyclodextrin) radical that is incorporated into, or a part of, a larger molecular structure, such as a polymer. A cyclodextrin moiety can be bonded to one or more other moieties directly, or through an optional linker. A cyclodextrin moiety can be oxidized or reduced, for example, oxidized to dicarbonyl forms.
[0338] Carbohydrate stabilizers, e.g., cyclic oligosaccharide stabilizers, can be derivatizedcarbohydrates. For example, in some embodiments, the stabilizer is a derivatized cyclic oligosaccharide, e.g., a derivatized cyclodextrin, e.g., 2-hydroxypropyl^-cyclodextrin, e.g., partially etherified cyclodextrins (e.g., partially etherified b cyclodextrins).
[0339] An exemplary stabilizer is a polysaccharide. The term "polysaccharide", as used herein refersto a compound or a chemical moiety formed by at least 16 monosaccharide units that are bonded together through glycosidic linkages, for example through 1-4 linkages or 1-6 linkages, to form a linear, branched or cyclic structure, and includes polymers that comprise polysaccharides as part ofWSGR Docket No. 50401-775.601 their backbone structure. In backbones, the polysaccharide can be linear or cyclic. Exemplary polysaccharide stabilizers include glycogen, amylase, cellulose, dextran, maltodextrin and the like. In some embodiments, the stabilizer is a sugar alcohol. As used herein, the term "sugar alcohol" refers to reduction products of "sugars" and indicates that all oxygen atoms in a simple sugar alcohol moleculeare present in the form of hydroxyl groups. The sugar alcohols are "polyols". This term refers tochemical compounds containing three or more hydroxyl groups, and is synonymous with another customary term, polyhydric alcohol. Examples of sugar alcohols include, but are not limited to, sorbitol, mannitol, maltitol, lactitol, erythritol, glycerin, xylitol, or inositol.
[0340] According to the present disclosure, pharmaceutical compositions that include sucrose as astabilizer are provided. Without wishing to be bound by theory, sucrose functions to promote cryoprotection of the composition, thereby preventing RNA lipoplex particle aggregation and maintaining chemical and physical stability of the composition. Certain embodiments contemplate alternative stabilizers to sucrose in the present disclosure. Alternative stabilizers include, without limitation, trehalose, glucose, fructose, arginin, glycerin, mannitol, prolin, sorbitol, glycine betaine anddextran. In some embodiments, an alternative stabilizer to sucrose is trehalose.
[0341] In some embodiments, the stabilizer is at a concentration from about 5% (w / v) to about 35%(w / v), or from about 10% (w / v) to about 25% (w / v). In specific embodiments, the stabilizer is at a concentration of about 10% (w / v), about 11% (w / v), about 12% (w / v), about 13% (w / v), about 14% (w / v), about 15% (w / v), about 16% (w / v), about 17% (w / v), about 18% (w / v), about 19% (w / v), about 20% (w / v), about 21% (w / v), about 22% (w / v), about 23% (w / v), about 24% (w / v), or about 25% (w / v). In some embodiments, the stabilizer is at a concentration from about 15% (w / v) to about 25% (w / v). In some embodiments, the stabilizer is at a concentration from about 20% (w / v) to about 25% (w / v). In some embodiments, the stabilizer is at a concentration of about 25% (w / v). In some embodiments, the stabilizer is at a concentration of about 22% (w / v). In embodiments of the disclosure, the stabilizer is sucrose or trehalose. In an embodiment of the disclosure, the stabilizer is sucrose. In an embodiment of the disclosure, the stabilizer is trehalose.
[0342] According to the present disclosure, the RNA lipoplex particle compositions described hereinhave a stabilizer concentration suitable for the stability of the composition, in particular for the stability of the RNA lipoplex particles and for the stability of the RNA.
[0343] According to the present disclosure, the RNA lipoplex particle compositions described hereinhave a pH suitable for the stability of the RNA lipoplex particles and, in particular, for the stability of the RNA. In some embodiments, the RNA lipoplex particle compositions described herein have a pHWSGR Docket No. 50401-775.601 from about 5.7 to about 6.7. In specific embodiments, the compositions have a pH of about 5.7, about 5.8, about 5.9, about 6.0, about 6.1, about 6.2, about 6.3, about 6.4, about 6.5, about 6.6, or about 6.7.
[0344] According to the present disclosure, compositions that include buffer are provided. Withoutwishing to be bound by theory, the use of buffer maintains the pH of the composition during manufacturing, storage and use of the composition. In certain embodiments of the present disclosure, the buffer may be sodium bicarbonate, monosodium phosphate, disodium phosphate, monopotassium phosphate, dipotassium phosphate, [tris(hydroxymethyl)methylamino]propanesulfonic acid (TAPS), 2-(Bis(2- hydroxyethyl)amino)acetic acid (Bicine), 2-Amino-2-(hydroxymethyl)propane-l,3-diol (Tris), N-(2-Hydroxy-l,l-bis(hydroxymethyl)ethyl)glycine (Tricine), 3-[[l ,3-dihydroxy-2- (hydroxymethyl)propan-2-yl]amino]-2-hydroxypropane-l -sulfonic acid (TAPSO), 2-[4-(2- hydroxyethyl)piperazin-l-yl]ethanesulfonic acid (HEPES), 2-[[l,3-dihydroxy-2- (hydroxymethyl)propan-2-yl]amino]ethanesulfonic acid (TES), 1,4- piperazinediethanesulfonic acid (PIPES), dimethylarsinic acid, 2-morpholin-4- ylethanesulfonic acid (MES), 3-morpholino-2- hydroxypropanesulfonic acid (MOPSO), or phosphate buffered saline (PBS). Other suitable buffersmay be acetic acid in a salt, citric acid in a salt, boric acid in a salt and phosphoric acid in a salt.
[0345] In some embodiments, the buffer has a pH from about 5.7 to about 6.7. In specificembodiments, the buffer has a pH of about 5.7, about 5.8, about 5.9, about 6.0, about 6.1, about 6.2, about 6.3, about 6.4, about 6.5, about 6.6, or about 6.7. In some embodiments, the buffer is HEPES. In some embodiments, the HEPES has a pH from about 5.7 to about 6.7. In specific embodiments, the HEPES has a pH of about 5.7, about 5.8, about 5.9, about 6.0, about 6.1, about 6.2, about 6.3, about6.4, about 6.5, about 6.6, or about 6.7. In some embodiments, the HEPES has a pH of about 6.2.
[0346] In some embodiments, the buffer has a concentration from about 2.5 mM to about 10 mM. Inspecific embodiments where HEPES is the buffer, the concentration of HEPES is about 2.5 mM, about 2.75 mM, 3.0 mM, about 3.25 mM, about 3.5 mM, about 3.75 mM, about 4.0 mM, about 4.25 mM, about 4.5 mM, about 4.75 mM, about 5.0 mM, about 5.25 mM, about 5.5 mM, about 5.75 mM, about 6.0 mM, about 6.25 mM, about 6.5 mM, about 6.75 mM, about 7.0 mM, about 7.25 mM, about 7.5 mM, about 7.75 mM, about 8.0 mM, about 8.25 mM, about 8.5 mM, about 8.75 mM, about 9.0 mM, about 9.25 mM, about 9.5 mM, about 9.75 mM, or about 10.0 mM. In some embodiments, the HEPES is at a concentration of about 7.5 mM.
[0347] Certain embodiments of the present disclosure contemplate the use of a chelating agent.Chelating agents refer to chemical compounds that are capable of forming at least two coordinate covalent bonds with a metal ion, thereby generating a stable, water-soluble complex. Without wishing to be bound by theory, chelating agents reduce the concentration of free divalent ions, which mayWSGR Docket No. 50401-775.601 otherwise induce accelerated RNA degradation in the present disclosure. Examples of suitable chelating agents include, without limitation, ethylenediaminetetraacetic acid (EDTA), a salt of EDTA, desferrioxamine B, deferoxamine, dithiocarb sodium, penicillamine, pentetate calcium, a sodium salt of pentetic acid, succimer, trientine, nitrilotriacetic acid, trans-diaminocyclohexanetetraacetic acid (DCTA), diethylenetriaminepentaacetic acid (DTP A), bis(aminoethyl)glycolether-N,N,N',N'- tetraacetic acid, iminodiacetic acid, citric acid, tartaric acid, fumaric acid, or a salt thereof. In certain embodiments, the chelating agent is EDTA or a salt of EDTA. In some embodiments, the chelating agent is EDTA disodium dihydrate.
[0348] In some embodiments, the EDTA is at a concentration from about 0.25 mM to about 5 mM.In specific embodiments, the EDTA is at a concentration of about 0.25 mM, about 0.3 mM, about 0.4 mM, about 0.5 mM, about 0.6 mM, about 0.7 mM, about 0.8 mM, about 0.9 mM, about 1.0 mM, about 1.1 mM, about 1.2 mM, about 1.3 mM, about 1.4 mM, about 1.5 mM, about 1.6 mM, about 1.7 mM, about 1.8 mM, about 1.9 mM, about 2.0 mM, about 2.1 mM, about 2.2 mM, about 2.3 mM. about 2.4 mM, about 2.5 mM, about 2.6 mM, about 2.7 mM, about 2.8 mM, about 2.9 mM, about 3.0 mM, about 3.1 mM, about 3.2 mM, about 3.3 mM, about 3.4 mM, about 3.5 mM, about 3.6 mM, about 3.7 mM, about 3.8 mM, about 3.9 mM, about 4.0 mM, about 4.1 mM, about 4.2 mM, about 4.3 mM, about 4.4 mM, about 4.5 mM, about 4.6 mM, about 4.7 mM, about 4.8 mM, about 4.9 mM, or about 5.0 mM. In some embodiments, the EDTA is at a concentration of about 2.5 mM...
Claims
WSGR Docket No. 50401-775.601 CLAIMS What is claimed is:
1. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CATSDRGDSQETQYF (SEQ ID NO: 21).2 The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 1, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 19; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 20.3 The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 1 or claim 2, whereinthe TCR beta chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence set forth in SEQ ID NO: 27.4 The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of the precedingclaims, wherein, the TCR beta chain construct comprises a variable region having at least 90% sequence identity to an amino acid sequence set forth in SEQ ID NO: 27.5 The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of the precedingclaims, wherein, the TCR beta chain construct comprises a variable region having at least 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 27.6 The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of the precedingclaims, wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 27.7 The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of the precedingclaims, further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 16; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 17; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 18.8 The recombinant nucleic acid of any one of the preceding claims, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NOs: 25 or 26, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 21; andWSGR Docket No. 50401-775.601 (b) a sequence having at least 80% sequence identity with SEQ ID NO: 22 or 23, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 18.
9. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of the precedingclaims, wherein the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence set forth in SEQ ID NO: 24.
10. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of the precedingclaims, wherein, the TCR alpha chain construct comprises a variable region having at least 90% sequence identity to an amino acid sequence set forth in SEQ ID NO: 24.
11. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of the precedingclaims, wherein, the TCR alpha chain construct comprises a variable region having at least 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 24.
12. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of the precedingclaims, wherein, the TCR alpha chain construct comprises a variable region having an aminoacid sequence set forth in SEQ ID NO: 24.
13. The recombinant nucleic acid encoding a TCR of claim 1, wherein the TCR comprises: (a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 29, or SEQ ID NO: 126, or SEQ ID NO: 127, or SEQ ID NO: 128 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 29; or SEQ ID NO: 126, or SEQ ID NO: 127, or SEQ ID NO: 128; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 28, or SEQ ID NO: 125, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 28 or at least 80% identical to SEQ ID NO: 125.
14. The recombinant nucleic acid encoding a TCR of claim 1, wherein the TCR comprises: (a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 110, or an amino acidsequence that is at least 80% identical to SEQ ID NO: 110; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 109, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 109.
15. The recombinant nucleic acid encoding a TCR of any one of the preceding claims, wherein theTCR binds to a complex comprising (i) an epitope from human GATA3 comprising a sequenceset forth in SEQ ID NO: 30; and (ii) an MHC protein.
16. The recombinant nucleic acid of claim 15, wherein the MHC protein is encoded by an HLA-A*02:01 allele.WSGR Docket No. 50401-775.60117. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASQDREGGNQPQHF (SEQ ID NO: 66).
18. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 17, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 64; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 65.
19. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 17 or claim 18,wherein the TCR beta chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence set forth in SEQ ID NO: 72.
20. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 17-19,wherein the TCR beta chain construct comprises a variable region having at least 90% sequence identity to an amino acid sequence set forth in SEQ ID NO: 72.
21. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 17-20,wherein, the TCR beta chain construct comprises a variable region having at least 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 72.
22. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 17-21,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 72.
23. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 17-22,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 61; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 62; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 63.
24. The recombinant nucleic acid of any one of claims 17- 23, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NOs: 70 or 71, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 66; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 67 or 68, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 63.WSGR Docket No. 50401-775.60125. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 17-24,wherein the TCR alpha chain construct comprises a variable region having at least 80% sequence identity to an amino acid sequence set forth in SEQ ID NO: 69.
26. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 17-25,wherein, the TCR alpha chain construct comprises a variable region having at least 90% sequence identity to an amino acid sequence set forth in SEQ ID NO: 69.
27. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 17-26,wherein, the TCR alpha chain construct comprises a variable region having at least 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 69.
28. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 17-27,wherein, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 69.
29. The recombinant nucleic acid encoding a TCR of claim 17, wherein the TCR comprises: (a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 74, or SEQ ID NO: 138, or SEQ ID NO: 139, or SEQ ID NO: 140; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 74 or SEQ ID NO: 138, or SEQ ID NO: 139, or SEQ ID NO: 140; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 73, or SEQ ID NO: 137; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 73 or SEQ ID NO: 137.
30. The recombinant nucleic acid encoding a TCR of claim 17, wherein the TCR comprises: (a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 116, or an amino acidsequence that is at least 80% identical to SEQ ID NO: 116; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 115, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 115.
31. The recombinant nucleic acid encoding a TCR of any one of the claims 15-27, wherein theTCR binds to a complex comprising (i) an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 75; and (ii) an MHC protein.
32. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSSDIFYEQYF (SEQ ID NO: 6).
33. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 32, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequenceWSGR Docket No. 50401-775.601 set forth in SEQ ID NO: 4; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 5.
34. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 32 or 33, wherein theTCR beta chain construct comprises a variable region having at least 80%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 12.
35. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 32-34,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 12.
36. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 32-35,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 1; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 2; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 3.
37. The recombinant nucleic acid of any one of claims 32-36, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NOs: 10 or 11, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 6; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 7 or 8, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 3.
38. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 32-37,wherein the TCR alpha chain construct comprises a variable region having at least 80% , 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 9.
39. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 32-38,wherein, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 9.
40. The recombinant nucleic acid encoding a TCR of claim 32, wherein the TCR comprises:(a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 14, or SEQ ID NO: 122, or SEQ ID NO: 123 or SEQ ID NO: 124, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 14, SEQ ID NO: 122, SEQ ID NO: 123 or SEQ ID NO: 124; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 13, or SEQ ID NO: 121 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 13, or SEQ ID NO: 121.
41. The recombinant nucleic acid encoding a TCR of claim 32, wherein the TCR comprises:(a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 108, or an amino acidWSGR Docket No. 50401-775.601 sequence that is at least 80% identical to SEQ ID NO: 108; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 107, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 107.
42. The recombinant nucleic acid encoding a TCR of any one of any one of claims 32-40, whereinthe TCR binds to a complex comprising (i) an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 15; and (ii) an MHC protein.
43. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSLISLGAGEDTEAFF (SEQ ID NO: 96).
44. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 43, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 94; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 95.
45. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 43 or claim 44, whereinthe TCR beta chain construct comprises a variable region having at least 80%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 102.
46. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 43-45,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 102.
47. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 43-46,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 91; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 92; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 93.
48. The recombinant nucleic acid of any one of claims 43-47, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 100 or 101, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 96; and (b) a sequence having at least 80% sequence identity with SEQ ID NOs: 97 or 98, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 93.
49. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 43-48,wherein the TCR alpha chain construct comprises a variable region having at least 80% , 90%,WSGR Docket No. 50401-775.601 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 99.
50. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 43-49,wherein, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 99.
51. The recombinant nucleic acid encoding a TCR of claim 43, wherein the TCR comprises: (a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 104, or SEQ ID NO: 146, or SEQ ID NO: 147, or SEQ ID NO: 148; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 104, SEQ ID NO: 146, or SEQ ID NO: 147, or SEQ ID NO: 148; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 103, or SEQ ID NO: 145; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 103 or SEQ ID NO: 145.
52. The recombinant nucleic acid encoding a TCR of claim 43, wherein the TCR comprises: (a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 120, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 120; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 119, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 119.
53. The recombinant nucleic acid encoding a TCR of any one of any one of claims 43-51, whereinthe TCR binds to a complex comprising (i) an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 105; and (ii) an MHC protein.
54. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASQGPYSLDTQYF (SEQ ID NO: 36).
55. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 54, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 34; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 35.
56. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 54 or claim 55, whereinthe TCR beta chain construct comprises a variable region having at least 80%, 90%, 95%, 96%,97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 42.
57. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 54-56,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 42.WSGR Docket No. 50401-775.60158. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 54-57,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 31; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 32; andthe CDR3 has an amino acid sequence set forth in SEQ ID NO: 33.
59. The recombinant nucleic acid of any one of claims 54-58, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 40 or 41, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 36; and (b) a sequence having at least 80% sequence identity with SEQ ID NOs: 37 or 38, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 33.
60. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 54-59,wherein the TCR alpha chain construct comprises a variable region having at least 80% , 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 39.
61. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 54-60,wherein, the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 39.
62. The recombinant nucleic acid encoding a TCR of claim 54, wherein the TCR comprises:(a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 44, or SEQ ID NO: 130, or SEQ ID NO: 131, or SEQ ID NO: 132, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 44; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 43, or SEQ ID NO: 129, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 43 or SEQ ID NO: 129.
63. The recombinant nucleic acid encoding a TCR of claim 54, wherein the TCR comprises:(a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 112, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 112; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 111, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 111.
64. The recombinant nucleic acid encoding a TCR of any one of any one of claims 54-62, whereinthe TCR binds to a complex comprising (i) an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 45; and (ii) an MHC protein.WSGR Docket No. 50401-775.60165. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSLSETQYF (SEQ ID NO: 51).
66. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 65, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 49; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 50.
67. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 65 or claim 66, whereinthe TCR beta chain construct comprises a variable region having at least 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to an amino acid sequence set forth in SEQ ID NO: 57.
68. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 65-67,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 46; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 47; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 48.
69. The recombinant nucleic acid of any one of claims 65-68, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 55 or 56, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 51; and (b) a sequence having at least 80% sequence identity with SEQ ID NOs: 52 or 53, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 48.
70. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 65-69,wherein the TCR alpha chain construct comprises a variable region having at least 80% , 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to an amino acid sequence set forth in SEQ ID NO: 54.
71. The recombinant nucleic acid encoding a TCR of claim 65, wherein the TCR comprises: (a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 59, or SEQ ID NO: 134, or SEQ ID NO: 135, or SEQ ID NO: 136 or an amino acid sequence that is at least 80% identical to SEQ ID NO: 59, or SEQ ID NO: 134, or SEQ ID NO: 135, or SEQ ID NO: 136; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 58, or SEQ ID NO: 133, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 58 or SEQ ID NO: 133.WSGR Docket No. 50401-775.60172. The recombinant nucleic acid encoding a TCR of claim 65, wherein the TCR comprises: (a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 114, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 114; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 113, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 113.
73. The recombinant nucleic acid encoding a TCR of any one of any one of claims 65-71, whereinthe TCR binds to a complex comprising (i) an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 60; and (ii) an MHC protein.
74. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSTLTISTDTQYF (SEQ ID NO: 81).
75. The recombinant nucleic acid encoding the T cell receptor (TCR) of claim 74, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 79; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 80.
76. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 74 or claim 75, whereinthe TCR beta chain construct comprises a variable region having at least 80%, 90%, 95%, 96%, 97%, 98%, 99% or 100% sequence identity to an amino acid sequence set forth in SEQ ID NO: 87.
77. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 74-76,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 76; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 77; andthe CDR3 has an amino acid sequence set forth in SEQ ID NO: 78.
78. The recombinant nucleic acid of any one of claims 74-77, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 85 or 86, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 81; and (b) a sequence having at least 80% sequence identity with SEQ ID NOs: 82 or 83, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 78.
79. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 74-78,wherein the TCR alpha chain construct comprises a variable region having at least 80% , 90%,WSGR Docket No. 50401-775.601 95%, 96%, 97%, 98%, 99% or 100% sequence identity to an amino acid sequence set forth in SEQ ID NO: 84.
80. The recombinant nucleic acid encoding a TCR of claim 74, wherein the TCR comprises:(a) a beta chain having an amino acid sequence set forth in SEQ ID NO: 89, or SEQ ID NO: 142, or SEQ ID NO: 143, or SEQ ID NO: 144; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 89, or SEQ ID NO: 142, or SEQ ID NO: 143, or SEQ ID NO: 144; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 88, or SEQ ID NO: 141; or an amino acid sequence that is at least 80% identical to SEQ ID NO: 88 or SEQ ID NO: 141.
81. The recombinant nucleic acid encoding a TCR of claim 74, wherein the TCR comprises: (a) abeta chain having an amino acid sequence set forth in SEQ ID NO: 118, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 118; (b) an alpha chain having an amino acid sequence set forth in SEQ ID NO: 117, or an amino acid sequence that is at least 80% identical to SEQ ID NO: 117.
82. The recombinant nucleic acid encoding a TCR of any one of any one of claims 74-80, whereinthe TCR binds to a complex comprising (i) an epitope from human GATA3 comprising a sequence set forth in SEQ ID NO: 90; and (ii) an MHC protein.
83. A recombinant nucleic acid encoding soluble TCR, comprising at least a TCR variable domain,comprising a sequence selected from the group: CATSDRGDSQETQYF (SEQ ID NO: 21); CASQDREGGNQPQHF (SEQ ID NO: 66); CASSSDIFYEQYF (SEQ ID NO: 6); CASSLISLGAGEDTEAFF (SEQ ID NO: 96); CASQGPYSLDTQYF (SEQ ID NO: 36); CASSLSETQYF (SEQ ID NO: 51); CASSTLTISTDTQYF (SEQ ID NO: 81).
84. A vector comprising the recombinant nucleic acid of any one of the claims 1 -83.
85. A cell comprising the recombinant nucleic acid of any one of the claims 1-83 or the vector ofclaim 84.
86. A recombinant nucleic acid encoding a TCR construct comprising:(a) a TCR beta chain construct, and (b) a TCR alpha chain construct; wherein the TCR recognizes and binds to a complex comprising an epitope from human GATA3 comprising a frameshift mutation, the epitopeWSGR Docket No. 50401-775.601 being in a human MHC-protein complex, wherein the human MHC-protein is an HLA antigen encoded by HLA-A*02:01 allele.
87. The recombinant nucleic acid of claim 86, wherein the TCR beta chain construct comprises aCDR3 having an amino acid sequence selected from the group set forth in SEQ ID NOs: 6, 21, 36, 51, 66, 81, and 96.
88. The recombinant nucleic acid of any one of claims 1-87, wherein the epitope has a length offrom 8-50 amino acids.
89. The recombinant nucleic acid of any one of claims 1-88, wherein the epitope binds to thehuman MHC with a greater affinity than a wild-type GATA3 epitope.
90. The recombinant nucleic acid of any one of claims 1-89, wherein the epitope binds to a humanMHC protein within the complex comprising the epitope and the MHC protein with a KD or an IC50 less than 500 nM, 250 nM, 150 nM, 100 nM, 50 nM, 25 nM, 10 nM or less than 10 nM.
91. The recombinant nucleic acid of any one of claims 1-90, wherein the mutation is not present innon-cancer cells of a subject.
92. The recombinant nucleic acid of any one of claims 1-91, wherein the TCR binds to a complexcomprising (i) an epitope from human GATA3 and (ii) an MHC protein in an MHC-peptide complex with a KD or an IC50 of less than 500 nM, 250 nM, 150 nM, 100 nM, 50 nM, 25 nM, 10 nM or less than 10 nM.
93. The recombinant nucleic acid of any one of claims 1-92, wherein the TCR binds to a complexcomprising (i) an epitope from human GATA3 and (ii) an MHC protein, wherein the MHCprotein is encoded by HLA-A*02:01 allele.
94. The vector of claim 84, wherein the vector is a lentiviral vector.
95. The cell of claim 85, wherein the cell is a CD4+ T cell.
96. The cell of claim 85, wherein the cell is a CD8+ T cell.
97. The cell of any one of the claims 85, 95 and 96, wherein the cell is isolated from a subjecthaving a GATA3 mutation.
98. A pharmaceutical composition comprising: (a) the nucleic acid of any one of claims 1-82; or,the vector of any one of claims 0 and 94; or, the cell of any one of claims 85 and 95-97; and(b) a pharmaceutically acceptable excipient or diluent.
99. The pharmaceutical composition of claim 98, for use in treating an immune disease or cancer.
100. Use of the pharmaceutical composition of claim 98, for treating an immune disease or cancer.WSGR Docket No. 50401-775.601101. A method of treating a subject having a disease or condition, comprising administering to thesubject in need thereof the pharmaceutical composition of claims 98.
102. A method of identifying a subject with cancer as a candidate for a therapeutic, the methodcomprising determining the subject as a subject that expresses a protein encoded by an HLA- A*02:01 allele wherein therapeutic is the pharmaceutical composition of claim 98.
103. A soluble TCR, comprising at least a TCR variable domain, comprising a sequence selectedfrom the group: CATSDRGDSQETQYF (SEQ ID NO: 21); CASQDREGGNQPQHF (SEQ ID NO: 66); CASSSDIFYEQYF (SEQ ID NO: 6); CASSLISLGAGEDTEAFF (SEQ ID NO: 96); CASQGPYSLDTQYF (SEQ ID NO: 36); CASSLSETQYF (SEQ ID NO: 51); CASSTLTISTDTQYF (SEQ ID NO: 81).
104. A recombinant nucleic acid encoding a TCR comprising a TCR beta chain constructcomprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSQGVGESPEAFF (SEQ ID NO: 206).
105. The recombinant nucleic acid encoding a TCR of claim 104, wherein the TCR beta chainconstruct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 204; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 205.
106. The recombinant nucleic acid encoding a TCR of claim 104, or claim 105, wherein the TCRbeta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 210.
107. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 104-106,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 210.
108. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of the precedingclaims, further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 201; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 202; andWSGR Docket No. 50401-775.601 the CDR3 has an amino acid sequence set forth in SEQ ID NO: 203.
109. The recombinant nucleic acid of any one of the preceding claims, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 209, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 206; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 207, wh erein thesequence comprises a sequence encoding at least SEQ ID NO: 203.
110. The recombinant nucleic acid encoding a TCR of any one of the preceding claims, wherein theTCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 208.
111. The recombinant nucleic acid encoding a TCR of any one of the preceding claims, wherein,the TCR alpha chain construct comprises a variable region having an amino ac id sequence setforth in SEQ ID NO: 208.
112. A TCR having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 203; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 206, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200) and (ii) an MHC protein.
113. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSFPGTGYGNTEAFF (SEQ ID NO: 296).
114. The recombinant nucleic acid encoding a TCR of claim 113, wherein the TCR beta chainconstruct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 294; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 295.
115. The recombinant nucleic acid encoding a TCR of claim 113, or claim 114, wherein the TCRbeta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 300.
116. The recombinant nucleic acid encoding a TCR of any one of the preceding claims, wherein,the TCR beta chain construct comprises a variable region having an amino ac id sequence setforth in SEQ ID NO: 300.WSGR Docket No. 50401-775.601117. The recombinant nucleic acid encoding a TCR of any one of claims 113-116, furthercomprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 291; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 292; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 293.
118. The recombinant nucleic acid of any one of claims 113-117, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 299, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 296; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 297, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 293.
119. The recombinant nucleic acid encoding a TCR of any one of claims 113-118, wherein the TCRalpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 298.
120. The recombinant nucleic acid encoding a TCR of any one of claims 113-119, wherein, the TCRalpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 298.
121. A TCR having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 293; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 296, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200) and (ii) an MHC protein.
122. A recombinant nucleic acid encoding a TCR comprising a TCR beta chain constructcomprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSFTLGVSETQYF (SEQ ID NO: 326).
123. The recombinant nucleic acid encoding a TCR of claim 122, wherein the TCR beta chainconstruct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 324; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 325.
124. The recombinant nucleic acid encoding a TCR of claim 122 or claim 123, wherein the TCRbeta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 330.WSGR Docket No. 50401-775.601125. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 122-124,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 330.
126. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 122-125,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 321; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 322; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 323.
127. The recombinant nucleic acid of any one of claims 122-126, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 329, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 326; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 327, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 323.
128. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 122-127,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 328.
129. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 122-128,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 328.
130. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 323; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 326, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and(ii) an MHC protein.
131. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASRPEGGLYEQYF (SEQ ID NO: 336).
132. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 131, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequenceWSGR Docket No. 50401-775.601 set forth in SEQ ID NO: 334; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 335.
133. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 131 or claim 132,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 340.
134. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 131-133,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 340.
135. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of cla ims 131-134,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 331; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 332; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 333.
136. The recombinant nucleic acid of any one of claims 131-135, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 339, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 336; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 337, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 333.
137. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 131-136,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 338.
138. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 131-137,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 338.
139. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 333; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 336, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.WSGR Docket No. 50401-775.601140. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASRPEGGLYEQYF (SEQ ID NO: 346).
141. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 131, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 344; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 345.
142. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 131 or claim 132,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 350.
143. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 131-133,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 350.
144. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of c laims 131-134,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 341; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 342; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 343.
145. The recombinant nucleic acid of any one of claims 131-135, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 349, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 346; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 347, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 343.
146. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 131-136,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth inSEQ ID NO: 348.
147. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 131-137,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 348.WSGR Docket No. 50401-775.601148. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 343; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 346, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.
149. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSSVATGTIYEKLFF (SEQ ID NO: 366).
150. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 149, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 364; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 365.
151. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 149 or claim 150,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 370.
152. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 149-151,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 370.
153. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 149-152,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 361; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 362; andthe CDR3 has an amino acid sequence set forth in SEQ ID NO: 363.
154. The recombinant nucleic acid of any one of claims 149-153, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 369, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 366; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 367, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 363.
155. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 149-154,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%,WSGR Docket No. 50401-775.601 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 368.
156. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 149-155,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 368.
157. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 363; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 366, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.
158. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSPDSGQGWVNEQFF (SEQ ID NO: 386).
159. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 158, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 384; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 385.
160. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 158 or claim 159,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 390.
161. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 158-160,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 390.
162. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 158-161,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 381; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 382; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 383.
163. The recombinant nucleic acid of any one of claims 158-162, comprising:WSGR Docket No. 50401-775.601 (a) a sequence having at least 80% sequence identity with SEQ ID NO: 389, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 386; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 387, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 383.
164. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 158-163,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 388.
165. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 158-164,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 388.
166. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 383; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 386, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.
167. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSQDGIDLSGNTIYF (SEQ ID NO: 396).
168. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 167, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 394; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 395.
169. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 167 or claim 168,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 400.
170. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 167-169,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 400.WSGR Docket No. 50401-775.601171. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 167-170,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 391; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 392; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 393.
172. The recombinant nucleic acid of any one of claims 167-171, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 399, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 396; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 397, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 393.
173. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 167-172,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 398.
174. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 167-173,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 398.
75. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 393; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 396, and where in the TCR binds to a complex comprising (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.
76. A recombinant nucleic acid encoding a TCR comprising a TCR beta chain constructcomprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from CASSVDGRDADTQYF (SEQ ID NO: 216), CASSVDGRDADTQYF (SEQ ID NO: 226), CASSQGVGESPEAFF (SEQ ID NO: 236), CASRTNYGYTF (SEQ ID NO: 246), CASRTNYGYTF (SEQ ID NO: 256), CSARDWTGGYNGTEAFF (SEQ ID NO: 266), CASSFTLGVSETQYF (SEQ ID NO: 276), CASSFTLGVSETQYF (SEQ ID NO: 286), CASSFPGTGYGNTEAFF (SEQ ID NO: 306), CASSFTLGVSETQYF (SEQ ID NO: 316), CASSPPEGGNEQFF (SEQ ID NO: 356), CASSPDSGQGWVNEQFF (SEQ ID NO: 376), and CASSPPEGGNEQFF (SEQ ID NO: 406); wherein the TCR binds to a complex comprisingWSGR Docket No. 50401-775.601 (i) an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.
177. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 214, a CDR2 having a sequence of SEQ ID NO: 215, and a CDR3 having a sequence of SEQ ID NO: 216; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 211, a CDR2 having a sequence of SEQ ID NO: 212 and a CDR3 having a sequence of SEQ ID NO: 213.
178. The recombinant nucleic acid of claim 177, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 220; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 218.
179. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 224, a CDR2 having a sequence of SEQ ID NO: 225, and a CDR3 having a sequence of SEQ ID NO: 226; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 221, a CDR2 having a sequence of SEQ ID NO: 222 and a CDR3 having a sequence of SEQ ID NO: 223.
180. The recombinant nucleic acid of claim 179, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 230; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 228.
181. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 234, a CDR2 having a sequence of SEQ ID NO: 235, and a CDR3 having a sequence of SEQ ID NO: 236; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 231, a CDR2 having a sequence of SEQ ID NO: 232 and a CDR3 having a sequence of SEQ ID NO: 233.
182. The recombinant nucleic acid of claim 181, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 240; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 238.
183. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 244, a CDR2 having a sequence of SEQ ID NO: 245, and a CDR3 having a sequence of SEQ ID NO: 246; and (b) an alpha chain,WSGR Docket No. 50401-775.601 comprising a CDR1 having a sequence of SEQ ID NO: 241, a CDR2 having a sequence of SEQ ID NO: 242 and a CDR3 having a sequence of SEQ ID NO: 243.
184. The recombinant nucleic acid of claim 183, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 250; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 248.
185. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 254, a CDR2 having a sequence of SEQ ID NO: 255, and a CDR3 having a sequence of SEQ ID NO: 256; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 251, a CDR2 having a sequence ofSEQ ID NO: 252 and a CDR3 having a sequence of SEQ ID NO: 253.
186. The recombinant nucleic acid of claim 185, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 260; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 258.
187. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 264, a CDR2 having a sequence of SEQ ID NO: 265, and a CDR3 having a sequence of SEQ ID NO: 266; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 261, a CDR2 having a sequence of SEQ ID NO: 262 and a CDR3 having a sequence of SEQ ID NO: 263.
188. The recombinant nucleic acid of claim 187, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 270; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 268.
189. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 274, a CDR2 having a sequence of SEQ ID NO: 275, and a CDR3 having a sequence of SEQ ID NO: 276; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 271, a CDR2 having a sequence of SEQ ID NO: 272 and a CDR3 having a sequence of SEQ ID NO: 273.
190. The recombinant nucleic acid of claim 189, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 280; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 278.WSGR Docket No. 50401-775.601191. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 284, a CDR2 having a sequence of SEQ ID NO: 285, and a CDR3 having a sequence of SEQ ID NO: 286; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 281, a CDR2 having a sequence of SEQ ID NO: 282 and a CDR3 having a sequence of SEQ ID NO: 283.
192. The recombinant nucleic acid of claim 187, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 290; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 288.
193. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 304, a CDR2 having a sequence of SEQ ID NO: 305, and a CDR3 having a sequence of SEQ ID NO: 306; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 301, a CDR2 having a sequence of SEQ ID NO: 302 and a CDR3 having a sequence of SEQ ID NO: 303.
194. The recombinant nucleic acid of claim 193, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 310; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 308.
195. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 314, a CDR2 having a sequence of SEQ ID NO: 315, and a CDR3 having a sequence of SEQ ID NO: 316; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 311, a CDR2 having a sequence of SEQ ID NO: 312 and a CDR3 having a sequence of SEQ ID NO: 313.
196. The recombinant nucleic acid of claim 195, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 320; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 318.
197. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 354, a CDR2 having a sequence ofSEQ ID NO: 355, and a CDR3 having a sequence of SEQ ID NO: 356; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 351, a CDR2 having a sequence of SEQ ID NO: 352 and a CDR3 having a sequence of SEQ ID NO: 353.WSGR Docket No. 50401-775.601198. The recombinant nucleic acid of claim 197, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 360; and(b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 358.
199. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 374, a CDR2 having a sequence of SEQ ID NO: 375, and a CDR3 having a sequence of SEQ ID NO: 376; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 371, a CDR2 having a sequence of SEQ ID NO: 372 and a CDR3 having a sequence of SEQ ID NO: 373.
200. The recombinant nucleic acid of claim 199, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 380; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 378.
201. The recombinant nucleic acid of claim 176, wherein, the TCR comprises: (a) a beta chain,comprising a CDR1 having a sequence of SEQ ID NO: 404, a CDR2 having a sequence of SEQ ID NO: 405, and a CDR3 having a sequence of SEQ ID NO: 406; and (b) an alpha chain, comprising a CDR1 having a sequence of SEQ ID NO: 401, a CDR2 having a sequence of SEQ ID NO: 402 and a CDR3 having a sequence of SEQ ID NO: 403.
202. The recombinant nucleic acid of claim 201, wherein, the TCR comprises: (a) a beta chaincomprising a variable region having at least 80% sequence identity to SEQ ID NO: 410; and (b) an alpha chain, comprising a variable region having at least 80% sequence identity to SEQ ID NO: 408.
203. The recombinant nucleic acid of any one of claims 101 to 202, wherein the TCR binds to acomplex comprising (i) a peptide MHC complex comprising an epitope MLTGPPARV (SEQ ID NO: 15), or an epitope SMLTGPPARV (SEQ ID NO: 200), and (ii) an MHC protein.
204. The recombinant nucleic acid of 203, wherein the MHC protein is encoded by HLA-A*A02:01.
205. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASNVGQGYTDTQYF (SEQ ID NO: 426).
206. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 205, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequenceWSGR Docket No. 50401-775.601 set forth in SEQ ID NO: 424; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 425.
207. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 205 or claim 206,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 430.
208. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 205-207,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 430.
209. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 205-208,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 421; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 422; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 423.
210. The recombinant nucleic acid of any one of claims 205-209, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 429, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 426; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 427, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 423.
211. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 205-210,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth inSEQ ID NO: 428.
212. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 205-211,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 428.
213. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 423; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 426, and where in the TCR binds to a complex comprising (i) an epitope KPKRDGYMF, or an epitope KPKRDGYMFL, and (ii) an MHC protein.
214. The TCR of claim 213, wherein the MHC is encoded by HLA-B*07:02 allele.WSGR Docket No. 50401-775.601215. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSPTSGISYEQYF (SEQ ID NO: 516).
216. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 215, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 514; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 515.
217. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 215 or claim 216,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 520.
218. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 215-217,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 520.
219. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 215-218,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 511; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 512; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 513.
220. The recombinant nucleic acid of any one of claims 215-219, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 519, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 516; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 517, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 513.
221. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 215-220,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 518.
222. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 215-221,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 518.WSGR Docket No. 50401-775.601223. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 513; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 516, and where in the TCR binds to a complex comprising (i) an epitope KPKRDGYMF, or an epitope KPKRDGYMFL, and (ii) an MHC protein.
224. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSSQGWGTEAFF (SEQ ID NO: 526).
225. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 224, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 524; and the CDR2 has an amino acid sequence set forth in SEQ IDNO: 525.
226. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 224 or claim 225,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 530.
227. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 224-226,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 530.
228. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 224-227,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 521; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 522; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 523.
229. The recombinant nucleic acid of any one of claims 224-228, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 529, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 526; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 527, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 523.
230. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 224-229,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%,WSGR Docket No. 50401-775.601 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 528.
231. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 215-230,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 528.
232. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 523; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 526, and where in the TCR binds to a complex comprising (i) an epitope KPKRDGYMF, or an epitope KPKRDGYMFL, and (ii) an MHC protein.
233. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSVGVSLTNEKLFF (SEQ ID NO: 596).
234. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 233, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 594; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 595.
235. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 233 or claim 234,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 600.
236. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 234-235,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 600.
237. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 234-236,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 591; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 592; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 593.
238. The recombinant nucleic acid of any one of claims 234-237, comprising:WSGR Docket No. 50401-775.601 (a) a sequence having at least 80% sequence identity with SEQ ID NO: 599, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 596; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 597, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 593.
239. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 234-238,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 598.
240. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 234-239,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 598.
241. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 593; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 596, and where in the TCR binds to a complex comprising (i) an epitope KPKRDGYMF, or an epitope KPKRDGYMFL, and (ii) an MHC protein.
242. A recombinant nucleic acid encoding a TCR comprising a TCR beta chain constructcomprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from CASSSEIVGPSQYF (SEQ ID NO: 416), CASSPGAGPGQPQHF (SEQ ID NO: 436), CASTTGGRGYTF (SEQ ID NO: 456), CASTTGGRGYTF (SEQ ID NO: 466), CASTQYKDEQFF (SEQ ID NO: 476), CASSLDRTSGSYNEQFF (SEQ ID NO: 486), CASSLDRTSGSYNEQFF (SEQ ID NO: 496), CASSPTSGISYEQYF (SEQ ID NO: 506), CASTPAGGNTGELFF (SEQ ID NO: 536), CSARDGQGSSYEQYF (SEQ ID NO: 546), CASWGEGAYEQYF (SEQ ID NO: 556), CASSPRLAQFSRNEQFF (SEQ ID NO: 566), CASMTGGLDEQFF (SEQ ID NO: 576), CASWGEGAYEQYF (SEQ ID NO: 586), CASMTGGLDEQFF (SEQ ID NO: 606), CASSPGQGWDSPLHF (SEQ ID NO: 616) and CASSLHHPTVYGYTF (SEQ ID NO: 626); wherein the TCR binds to a complex comprising (i) an epitope KPKRDGYMF, or an epitope KPKRDGYMFL.
243. The recombinant nucleic acid of any one of claims 205-242, wherein the encoded TCR bindsto a complex comprising (i) a peptide-MHC complex comprising an epitope KPKRDGYMF, or an epitope KPKRDGYMFL, and (ii) an MHC protein.
244. The recombinant nucleic acid of claim 243, wherein the MHC protein is encoded by HLA-B*07:02 allele.WSGR Docket No. 50401-775.601245. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASGSTGTAYEQYF (SEQ ID NO: 676).
246. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 245, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 674; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 675.
247. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 245 or claim 246,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 680.
248. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 245-247,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 680.
249. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of cla ims 245-248,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 671; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 672; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 673.
250. The recombinant nucleic acid of any one of claims 245-249, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 679, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 676; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 677, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 673.
251. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 245-250,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 678.
252. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 245-251,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 678.WSGR Docket No. 50401-775.601253. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 673; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 676, and where in the TCR binds to a complex comprising (i) an epitope ESKIMFATL, and (ii) an MHC protein.
254. A recombinant nucleic acid encoding a T cell receptor (TCR) comprising a TCR beta chainconstruct comprising a complementarity determining region 3 (CDR3) having an amino acid sequence CASSPDPGSYGYTF (SEQ ID NO: 686).
255. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 254, wherein the TCRbeta chain construct further comprises a complementarity determining region 1 (CDR1) and a complementarity determining region 2 (CDR2), wherein the CDR1 has an amino acid sequence set forth in SEQ ID NO: 684; and the CDR2 has an amino acid sequence set forth in SEQ ID NO: 685.
256. The recombinant nucleic acid encoding a T cell receptor (TCR) of claim 254 or claim 255,wherein the TCR beta chain construct comprises a variable region having about 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 690.
257. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 254-256,wherein, the TCR beta chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 690.
258. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of c laims 254-257,further comprising a TCR alpha chain construct having a CDR1, a CDR2, and a CDR3, wherein, the CDR1 has an amino acid sequence set forth in SEQ ID NO: 681; the CDR2 has an amino acid sequence set forth in SEQ ID NO: 682; and the CDR3 has an amino acid sequence set forth in SEQ ID NO: 683.
259. The recombinant nucleic acid of any one of claims 254-258, comprising:(a) a sequence having at least 80% sequence identity with SEQ ID NO: 689, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 686; and (b) a sequence having at least 80% sequence identity with SEQ ID NO: 687, wherein the sequence comprises a sequence encoding at least SEQ ID NO: 683.
260. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 254-259,wherein the TCR alpha chain construct comprises a variable region having about 80%, 85%,WSGR Docket No. 50401-775.601 90%, 95%, 96%, 97%, 98% or 99% sequence identity to an amino acid sequence set forth in SEQ ID NO: 688.
261. The recombinant nucleic acid encoding a T cell receptor (TCR) of any one of claims 254-260,wherein the TCR alpha chain construct comprises a variable region having an amino acid sequence set forth in SEQ ID NO: 688.
262. A TCR, having a TCR alpha chain and a TCR beta chain, wherein the TCR alpha chaincomprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 683; and the TCR beta chain comprises a CDR3 has an amino acid sequence set forth in SEQ ID NO: 686, and where in the TCR binds to a complex comprising (i) an epitope ESKIMFATL and (ii) an MHC protein.
263. A recombinant nucleic acid encoding a TCR comprising a TCR beta chain constructcomprising a complementarity determining region 3 (CDR3) having an amino acid sequence selected from CASSPSGVFNEQYF (SEQ ID NO: 636), CASSQEGQGVVKLFF (SEQ ID NO: 646), CASSLSLGRIAYEQYF (SEQ ID NO: 656), and CASGSTGTAYEQYF (SEQ ID NO: 666), wherein the TCR binds to an epitope ESKIMFATL in complex with an MHC protein.
264. A recombinant nucleic acid of any one of claims 245-263, wherein the TCR binds to a complexcomprising (i) an epitope ESKIMFATL and (ii) an MHC protein.
265. The recombinant nucleic acid of claim 264, wherein the MHC protein is encoded by HLA-B*08:01 allele.
266. An engineered cell, comprising any one of the recombinant nucleic acids of any one of claims1-83, 86-93, 104-111, 113-121, 122-129, 131-138, 140-147, 149-156, 158-165, 167-174, 176- 213, 215-222, 224-231, 232-240, 242-261, or the TCR of any one of claims 112, 121, 130, 139, 148, 157, 166, 175, 214, 223, 232, 241, and 262.
267. The engineered cell of claim 266, wherein the cell is a T cell.
268. A method of treating a disease in a subject in need thereof, comprising administerin g to thesubject a composition comprising an engineered cell of claim 266 or 267.
269. A method of treating a disease in subject in need thereof, comprising administering to thesubject a composition comprising a recombinant nucleic acid of any one of claims 1 -263 in aformulation suitable for expressing in a cell in vivo.
270. The method of treating of claim 268 or 269, wherein the disease is cancer.
271. The method of treating of any one of claims 268-270, wherein the cancer is a breast cancer.WSGR Docket No. 50401-775.601272. The method of treating any one of claims 268-271, wherein the cancer is estrogen receptorpositive breast cancer.
273. The method of treating any one of claims 268-271, wherein the cancer is hormone receptornegative breast cancer.
274. A pharmaceutical composition comprising the recombinant nucleic acid of any one of claims1-271; or the TCR of any one of claims 112, 121, 130, 139, 148, 157, 166, 175, 214, 223, 232, 241, and 262; or the engineered cell of claim 266 or 267.