Novel tumor antigens for melanoma and uses thereof

Abstract

While immune checkpoint blockade (ICB) therapy has significantly improved the outcome of metastatic melanoma, most patients do not derive long-term benefits. Previous studies suggest that treatment failure is partly due to insufficient immune recognition of tumor antigens (TAs). Cancer vaccines could potentially provide a complementary approach to boost antitumor immunity and act synergistically with ICIs. Novel tumor antigens shared by a large proportion of melanoma cells are described herein. Several of the tumor antigens described herein derives from aberrantly expressed unmutated genomic sequences, such as intronic and intergenic sequences, which are not expressed in normal tissues. Nucleic acids, compositions, cells and vaccines derived from these tumor antigens are described. The use of the tumor antigens, nucleic acids, compositions, cells and vaccines for the treatment of melanoma is also described.

Description

Abstract While immune checkpoint blockade (ICB) therapy has significantly improved the prognosis of metastatic melanoma, most patients do not experience long-term benefit. Previous studies have shown that treatment failure is partly due to insufficient immune recognition of tumor antigens (TAs). Cancer vaccines may potentially provide a complementary approach to enhance anti-tumor immunity and work synergistically with ICIs. This article describes novel tumor antigens common to most melanoma cells. Several tumor antigens described herein are derived from aberrantly expressed, unmutated genomic sequences, such as intragenic and intergenic sequences, which are not expressed in normal tissues. Nucleic acids, compositions, cells, and vaccines derived from these tumor antigens are described. The use of said tumor antigens, nucleic acids, compositions, cells, and vaccines for the treatment of melanoma is also described.

Claims

WHAT IS CLAIMED IS:

1. A tumor antigen peptide (TAP) comprising or consisting of one of the amino acid sequences set forth in SEQ ID NOs: 1-505.

2. The TAP of claim 1 , wherein the TAP binds to an HLA-A*01 :01 molecule and comprises or consists of the sequence of SEQ ID NO: 11 , 14, 20, 27, 29, 37, 86, 87, 121 , 150, 165, 173, 279, 288, 299, 308, 312, 316, 319, 331 , 340, 352, 362, 363, 384, 395, 398, 411 , 419, 429, 458, 474, 476, 487, 492, 500, or 501.

3. The TAP of claim 1 , wherein the TAP binds to an HLA-A*02:01 molecule and comprises or consists of the sequence of SEQ ID NO: 1 , 2, 4, 19, 22, 25, 40, 50, 52, 54, 60, 65, 67, 76, 81 , 89, 91 ,103, 107, 120, 124, 128, 135, 157, 175, 179, 186, 188, 201 , 208, 218, 219, 228, 232, 233, 240, 250,257, 261 , 263, 265, 266, 282, 286, 298, 311 , 315, 317, 325, 333, 337, 349, 367, 373, 387, 388, 393,399, 404, 412, 414, 415, 422, 434, 437, 455, 480, 489, or 494.

4. The TAP of claim 1 , wherein the TAP binds to an HLA-A*02:09 molecule and comprises or consists of the sequence of SEQ ID NO: 22, 40, 50, 62, 83, 89, 232, 265, 282, 311 , 315, 317, 337, 349, 367, 399, 407, 412, or 494.

5. The TAP of claim 1 , wherein the TAP binds to an HLA-A*03:01 molecule and comprises or consists of the sequence of SEQ ID NO: 209, 247, 272, 347, or 505.

6. The TAP of claim 1 , wherein the TAP binds to an HLA-A*23:01 molecule and comprises or consists of the sequence of SEQ ID NO: 48, 84, 129, 151 , 152, 171 , 174, 182, 223, 237, 245, 290, 358, 397, 426, 446, 481 , 482, or 486.

7. The TAP of claim 1 , wherein the TAP binds to an HLA-A*24:02 molecule and comprises or consists of the sequence of SEQ I D NO: 31 , 244 or 481.

8. The TAP of claim 1 , wherein the TAP binds to an HLA-A*25:01 molecule and comprises or consists of the sequence of SEQ ID NO: 11 , 31 , 249, 289, 403, 425, 464, or 490.

9. The TAP of claim 1 , wherein the TAP binds to an HLA-A*26:01 molecule and comprises or consists of the sequence of SEQ ID NO: 11 , 20, 27, 39, 41 , 42, 45, 114, 116, 122, 168, 181 , 268, 284, 329, 364, 398, 417, 430, 440, 447, 452, 457, 460, 462, 475, 490, or 497.

10. The TAP of claim 1 , wherein the TAP binds to an HLA-A*30:01 molecule and comprises or consists of the sequence of SEQ ID NO: 26, 304 or 376.

11. The TAP of claim 1 , wherein the TAP binds to an HI_A-A*30:02 molecule and comprises or consists of the sequence of SEQ I D NO: 117, 185, 190, 193, 197, 256, 294, 323, 471 , or 485.

12. The TAP of claim 1 , wherein the TAP binds to an HI_A-A*33:01 molecule and comprises or consists of the sequence of SEQ ID NO: 248.

13. The TAP of claim 1 , wherein the TAP binds to an HI_A-A*68:01 molecule and comprises or consists of the sequence of SEQ ID NO: 6-8, 12, 15, 23, 28, 41, 42, 47, 51, 53, 56, 59, 64, 66, 68, 70, 73-75, 77, 79, 80, 82, 85, 88, 92, 93, 96-99, 101, 102, 108-112, 118, 119, 123, 130, 131, 134, 137, 138, 141, 142, 144-147, 149, 153, 154, 156, 158, 160, 161 , 166, 169, 172, 176, 184, 198, 202,203, 212, 214, 216, 217, 220, 224, 226, 229, 234, 236, 239, 248, 254, 269, 270, 275, 280, 283, 287,293, 300, 301 , 303, 306, 310, 314, 320, 328, 332, 348, 354, 355, 359, 360, 366, 369, 370, 372, 381 ,382, 386, 389, 390, 392, 394, 402, 405, 406, 409, 413, 418, 424, 428, 436, 441-445, 449, 456, 459,465-468, 473, 479, 483, 488, 493, 499, or 502.

14. The TAP of claim 1 , wherein the TAP binds to an HLA-B*07:02 molecule and comprises or consists of the sequence of SEQ ID NO: 35, 36, 43, 104, 125, 127, 139, 140, 187, 191 , 196, 206, 231 , 243, 246, 251, 252, 260, 281 , 291 , 292, 321 , 330, 361, 408, 432, 435, 439, 451, 461 , 491 , or 503.

15. The TAP of claim 1 , wherein the TAP binds to an HLA-B*08:01 molecule and comprises or consists of the sequence of SEQ ID NO: 21 , 162, 189, 286, 307, 309, 317, 339, 343, 349, or 414.

16. The TAP of claim 1 , wherein the TAP binds to an HLA-B*13:02 molecule and comprises or consists of the sequence of SEQ ID NO: 207, 311, 393, 400, or 455.

17. The TAP of claim 1 , wherein the TAP binds to an HI_A-B*14:01 molecule and comprises or consists of the sequence of SEQ ID NO: 396.

18. The TAP of claim 1 , wherein the TAP binds to an HI_A-B*15:01 molecule and comprises or consists of the sequence of SEQ ID NO: 11, 26, 30, 63, 113, 132, 148, 192, 195, 200, 207, 210, 222, 235, 238, 258, 262, 267, 276, 295, 297, 305, 309, 318, 326, 336, 342, 374, 377, 383, 401 , 421, 427, 433, 438, 450, 463, 470, or 477.

19. The TAP of claim 1 , wherein the TAP binds to an HLA-B*18:01 molecule and comprises or consists of the sequence of SEQ ID NO: 3, 10, 33, 225 or 396.

20. The TAP of claim 1 , wherein the TAP binds to an HLA-B*37:01 molecule and comprises or consists of the sequence of SEQ ID NO: 302.

21. The TAP of claim 1 , wherein the TAP binds to an HI_A-B*38:01 molecule and comprises or consists of the sequence of SEQ ID NO: 26, 180, 338, 341 , 378, 380, 416, 448, 454, 496, or 498.

22. The TAP of claim 1 , wherein the TAP binds to an HI_A-B*40:01 molecule and comprises or consists of the sequence of SEQ ID NO: 215 or 322.

23. The TAP of claim 1 , wherein the TAP binds to an HI_A-B*40:02 molecule and comprises or consists of the sequence of SEQ ID NO: 213, 215, 339, or 351.

24. The TAP of claim 1 , wherein the TAP binds to an HI_A-B*44:02 molecule and comprises or consists of the sequence of SEQ ID NO: 346, 353, 356, or 453.

25. The TAP of claim 1 , wherein the TAP binds to an HI_A-B*49:01 molecule and comprises or consists of the sequence of SEQ ID NO: 9, 57, 78, 115, 136, 167, 255, 273, 274, 278, 313, 339, 480, 484, or 495.

26. The TAP of claim 1 , wherein the TAP binds to an HLA-B*51 :01 molecule and comprises or consists of the sequence of SEQ ID NO: 227 or 259.

27. The TAP of claim 1 , wherein the TAP binds to an HLA-C*03:03 molecule and comprises or consists of the sequence of SEQ ID NO: 24, 69, 204 or 388.

28. The TAP of claim 1 , wherein the TAP binds to an HLA-C*03:04 molecule and comprises or consists of the sequence of SEQ ID NO: 24, 49, 69, 159, 241 , 242 or 334.

29. The TAP of claim 1 , wherein the TAP binds to an HLA-C*06:02 molecule and comprises or consists of the sequence of SEQ ID NO: 13, 34 or 72.

30. The TAP of claim 1 , wherein the TAP binds to an HLA-C*07:01 molecule and comprises or consists of the sequence of SEQ ID NO: 13, 75, 133, 163, 183, 199, 205, 285, 334, 391 or 472.

31. The TAP of claim 1 , wherein the TAP binds to an HLA-C*07:02 molecule and comprises or consists of the sequence of SEQ ID NO: 13, 32, 36, 105, 177, 339, 371 or 478.

32. The TAP of claim 1 , wherein the TAP binds to an HLA-C*08:02 molecule and comprises or consists of the sequence of SEQ ID NO: 18, 54 or 379.

33. The TAP of claim 1 , wherein the TAP binds to an HLA-C*12:03 molecule and comprises or consists of the sequence of SEQ ID NO: 24, 49, 58, 71 , 94, 162, 178, 242, 289, 344, 345, 357, 367, 368, 375, 423 or 431.

34. The TAP of claim 1, wherein the TAP binds to an HLA-C*14:02 molecule and comprises or consists of the sequence of SEQ ID NO: 105, 271, 350, 365, 385, 410, 423, or 504.

35. The TAP of any one of claims 1-34, which is encoded by a sequence located a non-protein coding region of the genome or by a long non-coding RNA.

36. The TAP of claim 35, wherein said non-protein coding region of the genome is an intergenic region.

37. The TAP of claim 35, wherein said non-protein coding region of the genome is an intron.

38. The TAP of any one of claims 1 to 37, wherein said TAP is conjugated to a molecule that increases protease resistance, plasma protein binding, plasma half-life and / or intracellular penetration of the TAP.

39. A combination comprising at least two of the TAPs or nucleic acids defined in any one of claims 1-38.

40. A synthetic long peptide (SLP) comprising at least one of the amino acid sequences defined in claim 1.

41. A nucleic acid encoding one or more of the TAPs of claims 1 to 38, the combination of claim 39, or the SLP of claim 40.

42. The nucleic acid of claim 41, wherein the nucleic acid is an mRNA, and wherein the mRNA optionally comprises one or more 5’-end modifications, 3’-end modifications, and / or modified nucleosides to increase stability, improve translation and / or reduce immunogenicity of the mRNA.

43. The nucleic acid of claim 41 , wherein the nucleic acid is a DNA.

44. The nucleic acid of any one of claims 41-43, wherein the nucleic acid is a component of a viral vector.

45. A vesicle or particle comprising the TAP of any one of claims 1-38, the combination of claim39, the SLP of claim 40, or the nucleic acid of any one of claims 41-44.

46. The vesicle or particle of claim 45, wherein the vesicle is a lipid nanoparticle (LNP).

47. The vesicle or particle of claim 45 or 46, which comprises a cationic lipid.

48. A composition comprising the TAP of any one of claims 1-38, the combination of claim 39, theSLP of claim 40, the nucleic acid of any one of claims 41-44, or the vesicle or particle of any one of claims 45-47, and a pharmaceutically acceptable carrier.

49. A vaccine comprising the TAP of any one of claims 1-38, the combination of claim 39, the SLP of claim 40, the nucleic acid of any one of claims 41-44, the vesicle or particle of any one of claims 45-47, or the composition of claim 48, and an adjuvant.

50. An isolated major histocompatibility complex (MHC) class I molecule comprising the TAP of any one of claims 1-38 in its peptide binding groove.

51. The isolated MHC class I molecule of claim 50, which is in the form of a multimer.

52. The isolated MHC class I molecule of claim 51 , wherein said multimer is a tetramer.

53. An isolated cell comprising (i) the TAP of any one of claims 1-38; (ii) the combination of claim 39; (iii) the SLP of claim 40; (iv) the nucleic acid of any one of claims 41-44; or (v) a vector comprising a nucleotide sequence encoding the TAP of any one of claims 1-38, the combination of claim 39 or the SLP of claim 40.

54. An isolated cell expressing at its surface major histocompatibility complex (MHC) class I molecules comprising the TAP or combination of any one of claims 1-38 in their peptide binding groove.

55. The cell of claim 53 or 54, which is an antigen-presenting cell (APC).

56. The cell of claim 55, wherein said APC is a dendritic cell.

57. A T-cell receptor (TCR) that specifically recognizes the isolated MHC class I molecule of any one of claims 50-52 and / or MHC class I molecules expressed at the surface of the cell of any one of claims 54-56, or a nucleic acid encoding said TCR.

58. The TCR of claim 57, which is a soluble TCR.

59. An antibody or an antigen-binding fragment thereof that specifically binds to the isolated MHC class I molecule of any one of claims 50-52 and / or MHC class I molecules expressed at the surface of the cell of any one of claims 54-56, or a nucleic acid encoding said antibody or antigen-binding fragment thereof.

60. The TCR of claim 57 or 58, or the antibody or antigen-binding fragment thereof according to claim 59, which is a bispecific TCR or a bispecific antibody or antigen-binding fragment thereof.

61. The TCR, antibody or antigen-binding fragment thereof according to claim 60, wherein the bispecific antibody or antigen-binding fragment thereof is a single-chain diabody (scDb).

62. The TCR, antibody or antigen-binding fragment thereof according to claim 60 or 61 , wherein the bispecific TCR, antibody or antigen-binding fragment thereof also specifically binds to a T cell signaling molecule.

63. The TCR, antibody or antigen-binding fragment thereof according to claim 62, wherein the T cell signaling molecule is a CD3 chain.

64. A chimeric antigen receptor (CAR) comprising the antibody or an antigen-binding fragment thereof of claim 59, or a nucleic acid encoding said CAR.

65. An isolated cell expressing at its cell surface the TCR of claim 57 or the CAR of claim 64.

66. The isolated cell of claim 65, which is a CD8+T lymphocyte.

67. A cell population comprising at least 0.5% of the isolated cell as defined in claim 65 or 66.

68. A method of treating cancer in a subject comprising administering to the subject an effective amount of:(a) a TAP comprising or consisting of any one of the sequences set forth in SEQ ID NOs: 1- 505 or any combination thereof, or a synthetic long peptide (SLP) comprising at least one of the sequences set forth in SEQ ID NOs: 1-505;(b) at least one nucleic acid encoding the TAP, combination thereof or SLP defined in (a);(c) a vesicle or particle comprising the TAP, combination thereof or SLP defined in (a) or the at least one nucleic acid defined in (b);(d) a composition comprising the TAP, combination thereof or SLP defined in (a), the at least one nucleic acid defined in (b), or the vesicle or particle defined in (c), and a pharmaceutically acceptable carrier;(e) a vaccine comprising the TAP, combination thereof or SLP defined in (a), the at least one nucleic acid defined in (b), the vesicle or particle defined in (c), or the composition defined in (d), and an adjuvant;(f) a cell expressing at its surface major histocompatibility complex (MHC) class I molecules comprising the TAP or combination thereof defined in (a) in their peptide binding groove;(g) a cell expressing at its cell surface a T-cell receptor (TCR) or a chimeric antigen receptor (CAR) that specifically recognizes MHC class I molecules expressed at the surface of the cell defined in (f); or(h) a soluble TCR, an antibody or an antigen-binding fragment thereof, or a CAR, that specifically binds to the MHC class I molecules expressed at the surface of the cell defined in(f), or a nucleic acid encoding said soluble TCR, antibody, antigen-binding fragment thereof, or CAR.

69. The method of claim 68, wherein the cancer is melanoma.

70. The method of claim 68 or 69, further comprising administering at least one additional antitumor agent or therapy to the subject.

71. The method of claim 70, wherein said at least one additional antitumor agent or therapy is a chemotherapeutic agent, immunotherapy, an immune checkpoint inhibitor, radiotherapy or surgery.

72. Use of:(a) a TAP comprising or consisting of any one of the sequences set forth in SEQ ID NOs: 1- 505 or any combination thereof, or a synthetic long peptide (SLP) comprising at least one of the sequences set forth in SEQ ID NOs: 1-505;(b) at least one nucleic acid encoding the TAP, combination thereof or SLP defined in (a);(c) a vesicle or particle comprising the TAP, combination thereof or SLP defined in (a) or the at least one nucleic acid defined in (b);(d) a composition comprising the TAP, combination thereof or SLP defined in (a), the at least one nucleic acid defined in (b), or the vesicle or particle defined in (c), and a pharmaceutically acceptable carrier;(e) a vaccine comprising the TAP, combination thereof or SLP defined in (a), the at least one nucleic acid defined in (b), the vesicle or particle defined in (c), or the composition defined in (d), and an adjuvant;(f) a cell expressing at its surface major histocompatibility complex (MHC) class I molecules comprising the TAP or combination thereof defined in (a) in their peptide binding groove;(g) a cell expressing at its cell surface a T-cell receptor (TCR) or a chimeric antigen receptor (CAR) that specifically recognizes MHC class I molecules expressed at the surface of the cell defined in (f); or(h) a soluble TCR, an antibody or an antigen-binding fragment thereof, or a CAR, that specifically binds to the MHC class I molecules expressed at the surface of the cell defined in (f), or a nucleic acid encoding said soluble TCR, antibody, antigen-binding fragment thereof, or CAR; for treating cancer in a subject, or for the manufacture of a medicament for treating cancer in a subject.

73. The use of claim 72, wherein said cancer is melanoma.

74. The use of claim 72 or 73, further comprising the use at least one additional antitumor agent or therapy to the subject.

75. The use of claim 74, wherein said at least one additional antitumor agent or therapy is a chemotherapeutic agent, immunotherapy, an immune checkpoint inhibitor, radiotherapy or surgery.

76. An agent for use in treating cancer in a subject, wherein the agent is:(a) a TAP comprising or consisting of any one of the sequences set forth in SEQ ID NOs: 1- 505 or any combination thereof, or a synthetic long peptide (SLP) comprising at least one of the sequences set forth in SEQ ID NOs: 1-505;(b) at least one nucleic acid encoding the TAP, combination thereof or SLP defined in (a);(c) a vesicle or particle comprising the TAP, combination thereof or SLP defined in (a) or the at least one nucleic acid defined in (b);(d) a composition comprising the TAP, combination thereof or SLP defined in (a), the at least one nucleic acid defined in (b), or the vesicle or particle defined in (c), and a pharmaceutically acceptable carrier;(e) a vaccine comprising the TAP, combination thereof or SLP defined in (a), the at least one nucleic acid defined in (b), the vesicle or particle defined in (c), or the composition defined in (d), and an adjuvant;(f) a cell expressing at its surface major histocompatibility complex (MHC) class I molecules comprising the TAP or combination thereof defined in (a) in their peptide binding groove;(g) a cell expressing at its cell surface a T-cell receptor (TCR) or a chimeric antigen receptor (CAR) that specifically recognizes MHC class I molecules expressed at the surface of the cell defined in (f); or(h) a soluble TCR, an antibody or an antigen-binding fragment thereof, or a CAR, that specifically binds to the MHC class I molecules expressed at the surface of the cell defined in (f), or a nucleic acid encoding said soluble TCR, antibody, antigen-binding fragment thereof, or CAR.

77. The agent for use according to claim 76, wherein said cancer is melanoma.

78. The agent for use according to claim 76 or 77, further comprising the use at least one additional antitumor agent or therapy to the subject.

79. The agent for use according to claim 78, wherein said at least one additional antitumor agent or therapy is a chemotherapeutic agent, immunotherapy, an immune checkpoint inhibitor, radiotherapy or surgery.

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