NEOANTIGENS AND METHODS OF THEIR USE

1 - 294 . (canceled)

295 . A method of treating cancer in a human subject that has cancer comprising administering to the human subject a pharmaceutical composition comprising:

(i) a recombinant or synthetic HLA-matched neoantigenic peptide,

(ii) a polynucleotide encoding the recombinant neoantigenic peptide,

(iii) antigen presenting cells (APCs) comprising (i) or (ii),

(iv) T cells stimulated with APCs comprising (i) or (ii), or

(v) a T cell receptor (TCR) that binds to an MEW: peptide complex comprising a tumor-specific neoepitope of the recombinant or synthetic HLA-matched neoantigenic peptide; and

a pharmaceutically acceptable excipient;

wherein the neoantigenic peptide comprises a tumor-specific neoepitope comprising a mutant amino acid sequence encoded by a sequence downstream of a frameshift mutation in a GATA3 gene, wherein the tumor-specific neoepitope is (a) encoded by a GATA3 gene of cancer cells of the human subject, (b) expressed by the cancer cells of the human subject, (c) is not expressed by a gene of non-cancer cells of the human subject, and (d) is not encoded by a GATA3 gene of the non-cancer cells;

and wherein:

(a) the human subject expresses an MHC encoded by an HLA B08:01 allele and the tumor-specific neoepitope is LHFCRSSIM (SEQ ID NO: 556);

(b) the human subject expresses an MHC encoded by an HLA B08:01 allele or an HLA B07:02 allele and the tumor-specific neoepitope is EPHLALQPL (SEQ ID NO: 529);

(c) the human subject expresses an MHC encoded by an HLA A02:01 allele and the tumor-specific neoepitope is VLPEPHLAL (SEQ ID NO: 594); and/or

(d) the human subject expresses an MHC encoded by an HLA A03:01 allele and the tumor-specific neoepitope is VLWTTPPLQH (SEQ ID NO: 1430).

296 . The method of claim 295 , wherein the tumor-specific neoepitope binds to an MHC class I molecule with a binding affinity of 500 nM or less.

297 . The method of claim 295 , wherein the cancer is breast cancer.

298 . The method of claim 297 , wherein the breast cancer is selected from the group consisting of metastatic breast cancer, breast invasive carcinoma, luminal NS carcinoma of breast, HER-2-positive breast cancer and MSI+ breast cancer.

299 . The method of claim 295 , wherein the pharmaceutical composition further comprises an adjuvant.

300 . The method of claim 295 , wherein the method further comprises administering an immune checkpoint inhibitor.

301 . The method of claim 295 , wherein the polynucleotide encoding the recombinant neoantigenic peptide is DNA.

302 . The method of claim 295 , wherein the polynucleotide encoding the recombinant neoantigenic peptide is a messenger RNA (mRNA).

303 . The method of claim 295 , wherein the neoantigenic peptide is from 8 to 100 amino acids in length

304 . The method of claim 295 , wherein the neoantigenic peptide is from 8 to 50 amino acids in length.

305 . The method of claim 295 , wherein the human subject expresses an MHC encoded by an HLA B08:01 allele and the tumor-specific neoepitope is LHFCRSSIM (SEQ ID NO: 556).

306 . The method of claim 295 , wherein the human subject expresses an MHC encoded by an HLA B08:01 allele and the tumor-specific neoepitope is EPHLALQPL (SEQ ID NO: 529).

307 . The method of claim 295 , wherein the human subject expresses an MHC encoded by an HLA B07:02 allele and the tumor-specific neoepitope is EPHLALQPL (SEQ ID NO: 529).

308 . The method of claim 295 , wherein the human subject expresses an MHC encoded by an HLA A02:01 allele and the tumor-specific neoepitope is VLPEPHLAL (SEQ ID NO: 594).

309 . The method of claim 295 , wherein and the human subject expresses an WIC encoded by an HLA A03:01 allele and the tumor-specific neoepitope has a sequence of VLWTTPPLQH (SEQ ID NO: 1430).

310 . The method of claim 295 , wherein the neoantigenic peptide comprises at least two tumor-specific neoepitopes selected from the group consisting of LHFCRSSIM (SEQ ID NO: 556), EPHLALQPL (SEQ ID NO: 529), VLPEPHLAL (SEQ ID NO: 594) and VLWTTPPLQH (SEQ ID NO: 1430), and wherein the human subject expresses an WIC encoded by an HLA B08:01 allele, an HLA B07:02 allele, an HLA A02:01 allele, or an HLA A03:01 allele.

311 . The method of claim 295 , wherein the neoantigenic peptide comprises at least three tumor-specific neoepitopes selected from the group consisting of LHFCRSSIM (SEQ ID NO: 556), EPHLALQPL (SEQ ID NO: 529), VLPEPHLAL (SEQ ID NO: 594) and VLWTTPPLQH (SEQ ID NO: 1430), and wherein the human subject expresses an WIC encoded by an HLA B08:01 allele, an HLA B07:02 allele, an HLA A02:01 allele, or an HLA A03:01 allele.

312 . The method of claim 295 , wherein the neoantigenic peptide comprises at least four tumor-specific neoepitopes, wherein the at least four tumor-specific neoepitopes comprise LHFCRSSIM (SEQ ID NO: 556), EPHLALQPL (SEQ ID NO: 529), VLPEPHLAL (SEQ ID NO: 594) and VLWTTPPLQH (SEQ ID NO: 1430), and wherein the human subject expresses an MHC encoded by an HLA B08:01 allele, an HLA B07:02 allele, an HLA A02:01 allele, or an HLA A03:01 allele.

313 . The method of claim 295 , wherein the neoantigenic peptide comprises at least four tumor-specific neoepitopes, wherein the at least four tumor-specific neoepitopes comprise LHFCRSSIM (SEQ ID NO: 556), EPHLALQPL (SEQ ID NO: 529), VLPEPHLAL (SEQ ID NO: 594) and VLWTTPPLQH (SEQ ID NO: 1430), and wherein the human subject expresses at least two MHCs encoded by at least two HLA alleles selected from the group consisting of an HLA B08:01 allele, an HLA B07:02 allele, an HLA A02:01 allele, and an HLA A03:01 allele.

314 . The method of claim 295 , wherein the neoantigenic peptide comprises at least four tumor-specific neoepitopes, wherein the at least four tumor-specific neoepitopes comprise LHFCRSSIM (SEQ ID NO: 556), EPHLALQPL (SEQ ID NO: 529), VLPEPHLAL (SEQ ID NO: 594) and VLWTTPPLQH (SEQ ID NO: 1430), wherein the human subject expresses at least three MHCs encoded by at least three HLA alleles selected from the group consisting of an HLA B08:01 allele, an HLA B07:02 allele, an HLA A02:01 allele, and an HLA A03:01 allele.

315 . The method of claim 295 , wherein the neoantigenic peptide comprises at least four tumor-specific neoepitopes, wherein the at least four tumor-specific neoepitopes comprise LHFCRSSIM (SEQ ID NO: 556), EPHLALQPL (SEQ ID NO: 529), VLPEPHLAL (SEQ ID NO: 594) and VLWTTPPLQH (SEQ ID NO: 1430), wherein the human subject expresses an MEW encoded by an HLA B08:01 allele, an MEW encoded by an HLA B07:02 allele, an MHC encoded by an HLA A02:01 allele, and an MHC encoded by an HLA A03:01 allele.

316 . The method of claim 295 , wherein the neoantigenic peptide comprises the sequence PGRPLQTHVLPEPHLALQPLQPHADHAHADAPAIQPVLWTTPPLQHGHRHGLEP CSMLTGPPARVPAVPFDLHFCRSSIMKPKRDGYMFLKAESKIMFATLQRSSLWCL CSNH (SEQ ID NO: 60), and wherein the human subject expresses an MEW encoded by an HLA B08:01 allele, an HLA B07:02 allele, an HLA A02:01 allele, or an HLA A03:01 allele.

317 . A method of making a pharmaceutical composition comprising:

(i) a recombinant or synthetic HLA-matched neoantigenic peptide,

(ii) a polynucleotide encoding the recombinant neoantigenic peptide,

(iii) antigen presenting cells (APCs) comprising (i) or (ii),

(iv) T cells stimulated with APCs comprising (i) or (ii), or

(v) a T cell receptor (TCR) that binds to an MHC: peptide complex comprising a tumor-specific neoepitope of the recombinant or synthetic HLA-matched neoantigenic peptide; and

a pharmaceutically acceptable excipient;

the method comprising:

(A) selecting a neoantigenic peptide; wherein the neoantigenic peptide comprises a tumor-specific neoepitope comprising a mutant amino acid sequence encoded by a sequence downstream of a frameshift mutation in a GATA3 gene, wherein the tumor-specific neoepitope is (a) encoded by a GATA3 gene of cancer cells of the human subject, (b) expressed by the cancer cells of the human subject, (c) is not expressed by a gene of non-cancer cells of the human subject, and (d) is not encoded by a GATA3 gene of the non-cancer cells; and

(B) preparing a pharmaceutical formulation for each of the following,

wherein:

(a) the human subject expresses an MHC encoded by an HLA B08:01 allele and the tumor-specific neoepitope is LHFCRSSIM (SEQ ID NO: 556);

(b) the human subject expresses an MHC encoded by an HLA B08:01 allele or an HLA B07:02 allele and the tumor-specific neoepitope is EPHLALQPL (SEQ ID NO: 529);

(c) the human subject expresses an MHC encoded by an HLA A02:01 allele and the tumor-specific neoepitope is VLPEPHLAL (SEQ ID NO: 594); and/or

(d) the human subject expresses an MHC encoded by an HLA A03:01 allele and the tumor-specific neoepitope is VLWTTPPLQH (SEQ ID NO: 1430).