Methods of treating pancreatic cancer with a pd-1 axis binding antagonist and an RNA vaccine

Abstract

The present disclosure provides methods for treating an individual with pancreatic cancer with an individualized cancer vaccine and a PD-1 axis antagonist.

Description

CN Title: Method for Treating Pancreatic Cancer with PD-1 Axis Binding Antagonists and RNA Vaccines CN Abstract: This disclosure provides a method for treating individuals with pancreatic cancer using personalized cancer vaccines and PD-1 axis antagonists.

Claims

Attorney Docket No.14639-20649.40 CLAIMS What is claimed is:

1. A method for treating a pancreatic cancer tumor in a human patient in need thereof, comprising administering to the patient: (a) an individualized RNA vaccine comprising one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a pancreatic cancer tumor specimen obtained from the patient, (b) a PD-1 axis binding antagonist, and (c) a chemotherapeutic treatment; wherein the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment are administered to the patient during a priming phase, a chemotherapy phase after the priming phase, and a boost phase after the chemotherapy phase, wherein: (i) the priming phase comprises administering to the patient at least one dose of the RNA vaccine and at least one dose of the PD-1 axis binding antagonist, (ii) the chemotherapy phase comprises administering to the patient the chemotherapeutic treatment, and (iii) the boost phase comprises administering to the patient at least one dose of the RNA vaccine and at least one dose of the PD-1 axis binding antagonist.

2. The method of claim 1, wherein the pancreatic cancer tumor is a pancreatic ductal adenocarcinoma (PDAC) tumor.

3. The method of claim 1 or claim 2, wherein the pancreatic cancer tumor is resectable.

4. The method of claim 3, wherein the priming phase begins at least about 1 week, at least about 2 weeks, at least about 3 weeks, at least about 4 weeks, at least about 5 weeks, at least about 6 weeks, at least about 7 weeks, at least about 8 weeks, at least about 9 weeks, at least about 10 weeks, at least about 11 weeks, at least about 12 weeks, at least about 13 weeks, at least about 14 weeks, or at least about 15 weeks after resection of the pancreatic cancer tumor from the patient.

5. The method of claim 3, wherein the priming phase begins between about 6 weeks and about 12 weeks after resection of the pancreatic cancer tumor from the patient.

6. The method of any one of claims 1-5, wherein the priming phase comprises administering one dose of the PD-1 axis binding antagonist. -122-sf-5685228Attorney Docket No.14639-20649.40 7. The method of claim 6, wherein the priming phase comprises administering the PD-1 axis binding antagonist on day 1 of week 3 of the priming phase.

8. The method of any one of claims 1-5, wherein the priming phase comprises administering at least two doses of the PD-1 axis binding antagonist.

9. The method of any one of claims 1-5 and 8, wherein the priming phase comprises administering the PD-1 axis binding antagonist once every four weeks.

10. The method of claim 9, wherein the priming phase comprises administering the PD-1 axis binding antagonist on day 1 of week 1 of the priming phase and every four weeks thereafter.

11. The method of any one of claims 1-5 and 8-10, wherein the priming phase comprises administering two doses of the PD-1 axis binding antagonist.

12. The method of claim 11, wherein the priming phase comprises administering the PD-1 axis binding antagonist on day 1 of week 1 and on day 1 of week 5 of the priming phase.

13. The method of any one of claims 1-12, wherein the priming phase comprises administering any of 2, 3, 4, 5, 6, 7, or 8 doses of the RNA vaccine.

14. The method of claim 13, wherein the priming phase comprises administering 2 or 3 doses of the RNA vaccine.

15. The method of any one of claims 1-13, wherein the priming phase comprises administering between 6 and 8 doses of the RNA vaccine, or up to six doses of the RNA vaccine.

16. The method of claim 15, wherein the priming phase comprises administering 6 doses of the RNA vaccine.

17. The method of any one of claims 1-16, wherein the priming phase comprises administering the RNA vaccine once per week.

18. The method of claim 17, wherein the priming phase comprises administering the RNA vaccine on day 1 of week 1 of the priming phase and once per week thereafter.

19. The method of any one of claims 1-18, wherein the priming phase comprises administering six doses of the RNA vaccine.

20. The method of claim 19, wherein the priming phase comprises administering the RNA vaccine on day 1 of weeks 1, 2, 3, 4, 5, and 6 of the priming phase. -123-sf-5685228Attorney Docket No.14639-20649.40 21. The method of any one of claims 1-20, wherein each dose of the PD-1 axis binding antagonist administered to the patient during the priming phase is administered on the same day as administration of a dose of the RNA vaccine.

22. The method of any one of claims 1-21, wherein the priming phase comprises six weeks.

23. The method of claim 22, wherein the RNA vaccine is administered on day 1 of weeks 1, 2, 3, 4, 5, and 6 of the priming phase, and the PD-1 axis binding antagonist is administered on day 1 of week 3 of the priming phase.

24. The method of claim 22, wherein the RNA vaccine is administered on day 1 of weeks 1, 2, 3, 4, 5, and 6 of the priming phase, and the PD-1 axis binding antagonist is administered on day 1 of weeks 1 and 5 of the priming phase.

25. The method of any one of claims 1-24, wherein the chemotherapy phase comprises administering the chemotherapeutic treatment for at least about 8 weeks, at least about 9 weeks, at least about 10 weeks, at least about 11 weeks, at least about 12 weeks, at least about 13 weeks, at least about 14 weeks, at least about 15 weeks, at least about 16 weeks, at least about 17 weeks, at least about 18 weeks, at least about 19 weeks, at least about 20 weeks, at least about 21 weeks, at least about 22 weeks, at least about 23 weeks, at least about 24 weeks, at least about 25 weeks, at least about 26 weeks, at least about 27 weeks, at least about 28 weeks, at least about 29 weeks, at least about 30 weeks, or more.

26. The method of any one of claims 1-25, wherein the chemotherapy phase comprises administering the chemotherapeutic treatment for 23 weeks.

27. The method of any one of claims 1-26, wherein the chemotherapeutic treatment is administered once every two weeks.

28. The method of claim 27, wherein the chemotherapy phase comprises administering the chemotherapeutic treatment on day 1 of week 1 of the chemotherapy phase and every two weeks thereafter.

29. The method of any one of claims 1-28, wherein the chemotherapy phase comprises administering at least 1, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 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, or at least 24, or more, administrations of the chemotherapeutic treatment. -124-sf-5685228Attorney Docket No.14639-20649.40 30. The method of claim 29, wherein the chemotherapy phase comprises administering 12 administrations of the chemotherapeutic treatment.

31. The method of any one of claims 1-30, wherein the chemotherapy phase comprises 24 weeks.

32. The method of any one of claims 1-31, wherein the chemotherapy phase comprises administering the chemotherapeutic treatment on day 1 of weeks 1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, and 23 of the chemotherapy phase.

33. The method of any one of claims 1-32, wherein the chemotherapy phase begins at least about 1 week, at least about 2 weeks, at least about 3 weeks, or at least about 4 weeks after the end of the priming phase and after the last administration of the RNA vaccine.

34. The method of any one of claims 1-32, wherein the chemotherapy phase begins no later than week 9, timing starting with week 1 of the priming phase.

35. The method of claim 34, wherein the priming phase comprises six weeks, and wherein the chemotherapy phase begins no later than week 9, timing starting with week 1 of the priming phase.

36. The method of any one of claims 1-35, wherein the priming phase comprises six weeks, and wherein the chemotherapy phase comprises administering the chemotherapeutic treatment starting on day 1 of week 7 and every two weeks thereafter, timing starting with week 1 of the priming phase.

37. The method of claim 36, wherein the chemotherapy phase comprises administering 12 administrations of the chemotherapeutic treatment.

38. The method of claim 37, wherein the chemotherapy phase comprises administering the chemotherapeutic treatment on day 1 of weeks 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, and 29, timing starting with week 1 of the priming phase.

39. The method of any one of claims 1-38, wherein the boost phase comprises administering 2, 3, 4, 5, 6, 7, or 8 doses of the RNA vaccine.

40. The method of any one of claims 1-39, wherein the boost phase comprises administering 2, 3, 4, 5, 6, 7, or 8 doses of the PD-1 axis binding antagonist.

41. The method of any one of claims 1-40, wherein the boost phase comprises administering 6 doses of the PD-1 axis binding antagonist and 6 doses of the RNA vaccine.

42. The method of any one of claims 1-41, wherein the boost phase comprises administering the PD-1 axis binding antagonist and the RNA vaccine once every four weeks. -125-sf-5685228Attorney Docket No.14639-20649.40 43. The method of any one of claims 1-42, wherein the boost phase comprises administering the PD-1 axis binding antagonist on day 1 of week 1 of the boost phase and every four weeks thereafter.

44. The method of any one of claims 1-43, wherein the boost phase comprises administering the RNA vaccine on day 1 of week 1 of the boost phase and every four weeks thereafter.

45. The method of any one of claims 1-44, wherein administrations of the RNA vaccine and the PD-1 axis binding antagonist during the boost phase occur on the same day.

46. The method of claim 45, wherein the boost phase comprises administering the PD-1 axis binding antagonist and the RNA vaccine on day 1 of week 1 of the boost phase and every four weeks thereafter.

47. The method of any one of claims 1-46, wherein the boost phase comprises 21 weeks.

48. The method of any one of claims 1-47, wherein the RNA vaccine and the PD-1 axis binding antagonist are administered on day 1 of weeks 1, 5, 9, 13, 17, and 21 of the boost phase.

49. The method of any one of claims 1-48, wherein the boost phase begins at least about 1 week, at least about 2 weeks, at least about 3 weeks, at least about 4 weeks, at least about 5 weeks, at least about 6 weeks, at least about 7 weeks, at least about 8 weeks, at least about 9 weeks, at least about 10 weeks, at least about 11 weeks, at least about 12 weeks, at least about 13 weeks, at least about 14 weeks, or at least about 15 weeks after the end of the chemotherapy phase.

50. The method of any one of claims 1-48, wherein the boost phase begins up to about 12 weeks after the end of the chemotherapy phase, optionally up to about 12 weeks after the last administration of the chemotherapeutic treatment.

51. The method of any one of claims 1-48, wherein the boost phase begins: between about 3 weeks to about 12 weeks after the end of the chemotherapy phase, optionally between about 3 weeks to about 12 weeks after the last administration of the chemotherapeutic treatment; or about three weeks or about four weeks after the end of the chemotherapy phase, optionally about three weeks or about four weeks after the last administration of the chemotherapeutic treatment.

52. The method of any one of claims 1-48, wherein the boost phase begins on week 27, timing starting with week 1 of the chemotherapy phase.

53. The method of any one of claims 1-48, wherein the boost phase begins on week 33, timing starting with week 1 of the priming phase. -126-sf-5685228Attorney Docket No.14639-20649.40 54. The method of claim 53, wherein the boost phase comprises administering the RNA vaccine and the PD-1 axis binding antagonist on day 1 of week 33 and every four weeks thereafter, timing starting with week 1 of the priming phase.

55. The method of claim 54, wherein the RNA vaccine and the PD-1 axis binding antagonist are administered for six administrations during the boost phase.

56. The method of claim 55, wherein the boost phase comprises administering the RNA vaccine and the PD-1 axis binding antagonist on day 1 of weeks 33, 37, 41, 45, 49, and 53, timing starting with week 1 of the priming phase.

57. The method of any one of claims 1-7, 13-23 and 25-56, wherein: (a) the priming phase comprises administering the RNA vaccine on day 1 of weeks 1, 2, 3, 4, 5, and 6 of the priming phase, and the PD-1 axis binding antagonist on day 1 of week 3 of the priming phase; (b) the chemotherapy phase comprises administering the chemotherapeutic treatment on day 1 of weeks 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, and 29, timing starting with week 1 of the priming phase; and (c) the boost phase comprises administering the RNA vaccine and the PD-1 axis binding antagonist on day 1 of weeks 33, 37, 41, 45, 49, and 53, timing starting with week 1 of the priming phase.

58. The method of any one of claims 1-5, 8-22, and 24-56, wherein: (a) the priming phase comprises administering the RNA vaccine on day 1 of weeks 1, 2, 3, 4, 5, and 6 of the priming phase, and the PD-1 axis binding antagonist on day 1 of weeks 1 and 5 of the priming phase; (b) the chemotherapy phase comprises administering the chemotherapeutic treatment on day 1 of weeks 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, and 29, timing starting with week 1 of the priming phase; and (c) the boost phase comprises administering the RNA vaccine and the PD-1 axis binding antagonist on day 1 of weeks 33, 37, 41, 45, 49, and 53, timing starting with week 1 of the priming phase.

59. The method of claim 57 or claim 58, wherein the priming phase begins between about 6 weeks and about 12 weeks after resection of the pancreatic cancer tumor from the patient.

60. The method of any one of claims 1-59, wherein the PD-1 axis binding antagonist is a PD-1 binding antagonist. -127-sf-5685228Attorney Docket No.14639-20649.40 61. The method of claim 60, wherein the PD-1 binding antagonist is an anti-PD-1 antibody.

62. The method of claim 61, wherein the anti-PD-1 antibody is nivolumab or pembrolizumab.

63. The method of any one of claims 1-59, wherein the PD-1 axis binding antagonist is a PD-L1 binding antagonist.

64. The method of claim 63, wherein the PD-L1 binding antagonist is an anti-PD-L1 antibody.

65. The method of claim 64, wherein the anti-PD-L1 antibody is avelumab or durvalumab.

66. The method of claim 64, wherein the anti-PD-L1 antibody comprises: (a) a heavy chain variable region (VH) that comprises an HVR-H1 comprising an amino acid sequence GFTFSDSWIH (SEQ ID NO:1), an HVR-H2 comprising an amino acid sequence AWISPYGGSTYYADSVKG (SEQ ID NO:2), and HVR-H3 comprising an amino acid sequence RHWPGGFDY (SEQ ID NO:3), and (b) a light chain variable region (VL) that comprises an HVR-L1 comprising an amino acid sequence RASQDVSTAVA (SEQ ID NO:4), an HVR-L2 comprising an amino acid sequence SASFLYS (SEQ ID NO:5), and an HVR-L3 comprising an amino acid sequence QQYLYHPAT (SEQ ID NO:6).

67. The method of claim 64, wherein the anti-PD-L1 antibody comprises a heavy chain variable region (VH) comprising an amino acid sequence of SEQ ID NO:7 and a light chain variable region (VL) comprising an amino acid sequence of SEQ ID NO:

8.

68. The method of claim 64, wherein the anti-PD-L1 antibody is atezolizumab.

69. The method of any one of claims 1-68, wherein the PD-1 axis binding antagonist is administered intravenously to the patient.

70. The method of any one of claims 64-69, wherein the anti-PD-L1 antibody is administered to the patient at a dose of about 1200 mg or about 1680 mg.

71. The method of claim 70, wherein the anti-PD-L1 antibody is atezolizumab, and the atezolizumab is administered intravenously to the patient at a dose of about 1680 mg.

72. The method of any one of claims 1-71, wherein the chemotherapeutic treatment comprises one or more of gemcitabine, leucovorin, 5-fluorouracil, capecitabine, irinotecan, liposomal irinotecan, a platinum-based chemotherapeutic agent, a taxane, and any combination thereof. -128-sf-5685228Attorney Docket No.14639-20649.40 73. The method of claim 72, wherein the platinum-based chemotherapeutic agent is cisplatin, oxaliplatin, or both.

74. The method of claim 72 or claim 73, wherein the taxane is paclitaxel, docetaxel, albumin- bound paclitaxel, or any combination thereof.

75. The method of any one of claims 1-72, wherein the chemotherapeutic treatment comprises leucovorin, 5-fluorouracil, irinotecan, and oxaliplatin.

76. The method of any one of claims 1-72, wherein the chemotherapeutic treatment is a FOLFIRINOX treatment or an mFOLFIRINOX treatment.

77. The method of any one of claims 1-72, wherein the chemotherapeutic treatment comprises: oxaliplatin at a dose of about 85 mg / m2; leucovorin at a dose of about 400 mg / m2; irinotecan at a dose of about 150 mg / m2; and / or 5-fluorouracil at a dose of about 2400 mg / m2.

78. The method of any one of claims 1-77, wherein the chemotherapeutic treatment is administered intravenously to the patient.

79. The method of any one of claims 1-78, wherein the RNA vaccine comprises one or more polynucleotides encoding 5-20 or 10-20 neoepitopes resulting from cancer-specific somatic mutations present in the tumor specimen.

80. The method of any one of claims 1-79, wherein the one or more polynucleotides of the RNA vaccine are formulated with one or more lipids.

81. The method of claim 80, wherein the one or more polynucleotides of the RNA vaccine and the one or more lipids form a lipid nanoparticle.

82. The method of claim 80, wherein the one or more polynucleotides of the RNA vaccine and the one or more lipids form a lipoplex.

83. The method of claim 81 or claim 82, wherein the lipid nanoparticle or lipoplex comprises one or more lipids that form a multilamellar structure that encapsulates the one or more polynucleotides of the RNA vaccine.

84. The method of claim 83, wherein the one or more lipids comprise at least one cationic lipid and at least one helper lipid. -129-sf-5685228Attorney Docket No.14639-20649.40 85. The method of claim 83, wherein the one or more lipids comprise (R)-N,N,N−trimethyl−2,3−dioleyloxy−1−propanaminium chloride (DOTMA) and 1,2-dioleoyl-sn- glycero-3-phosphoethanolamine (DOPE).

86. The method of claim 85, wherein at physiological pH the overall charge ratio of positive charges to negative charges of the lipid nanoparticle or lipoplex is 1.3:2 (0.65).

87. The method of any one of claims 1-86, wherein the one or more polynucleotides of the RNA vaccine are RNA molecules, optionally messenger RNA molecules.

88. The method of any one of claims 1-87, wherein the RNA vaccine is administered to the patient at a dose of about 15 µg, about 21 µg, about 21.3 µg, about 25 µg, about 38 µg, or about 50 µg.

89. The method of claim 88, wherein the RNA vaccine is administered to the patient at a dose of about 25 µg.

90. The method of any one of claims 1-89, wherein the RNA vaccine is administered intravenously to the patient.

91. The method of any one of claims 1-90, wherein the RNA vaccine comprises an RNA molecule comprising, in the 5’ ^3’ direction: (1) a 5’ cap; (2) a 5’ untranslated region (UTR); (3) a polynucleotide sequence encoding a secretory signal peptide; (4) a polynucleotide sequence encoding the one or more neoepitopes resulting from cancer- specific somatic mutations present in the tumor specimen; (5) a polynucleotide sequence encoding at least a portion of a transmembrane and cytoplasmic domain of a major histocompatibility complex (MHC) molecule; (6) a 3’ UTR comprising: (a) a 3’ untranslated region of an Amino-Terminal Enhancer of Split (AES) mRNA or a fragment thereof; and (b) non-coding RNA of a mitochondrially encoded 12S RNA or a fragment thereof; and (7) a poly(A) sequence.

92. The method of claim 91, wherein the RNA molecule further comprises a polynucleotide sequence encoding an amino acid linker; wherein the polynucleotide sequences encoding the amino acid linker and a first of the one or more neoepitopes form a first linker-neoepitope module; and -130-sf-5685228Attorney Docket No.14639-20649.40 wherein the polynucleotide sequences forming the first linker-neoepitope module are between the polynucleotide sequence encoding the secretory signal peptide and the polynucleotide sequence encoding the at least portion of the transmembrane and cytoplasmic domain of the MHC molecule in the 5’ ^3’ direction.

93. The method of claim 92, wherein the amino acid linker comprises the sequence GGSGGGGSGG (SEQ ID NO:39).

94. The method of claim 92, wherein the polynucleotide sequence encoding the amino acid linker comprises the sequence GGCGGCUCUGGAGGAGGCGGCUCCGGAGGC (SEQ ID NO:37).

95. The method of any one of claims 92-94, wherein the RNA molecule further comprises, in the 5’ ^3’ direction: at least a second linker-neoepitope module, wherein the at least second linker- neoepitope module comprises a polynucleotide sequence encoding an amino acid linker and a polynucleotide sequence encoding a neoepitope; wherein the polynucleotide sequences forming the second linker-neoepitope module are between the polynucleotide sequence encoding the neoepitope of the first linker-neoepitope module and the polynucleotide sequence encoding the at least portion of the transmembrane and cytoplasmic domain of the MHC molecule in the 5’ ^3’ direction; and wherein the neoepitope of the first linker-neoepitope module is different from the neoepitope of the second linker-neoepitope module.

96. The method of claim 95, wherein the RNA molecule comprises 5 linker-neoepitope modules, and wherein the 5 linker-neoepitope modules each encode a different neoepitope.

97. The method of claim 95, wherein the RNA molecule comprises 10 linker-neoepitope modules, and wherein the 10 linker-neoepitope modules each encode a different neoepitope.

98. The method of claim 95, wherein the RNA molecule comprises 20 linker-neoepitope modules, and wherein the 20 linker-neoepitope modules each encode a different neoepitope.

99. The method of any one of claims 91-98, wherein the RNA molecule further comprises a second polynucleotide sequence encoding an amino acid linker, wherein the second polynucleotide sequence encoding the amino acid linker is between the polynucleotide sequence encoding the neoepitope that is most distal in the 3’ direction and the polynucleotide sequence encoding the at least portion of the transmembrane and cytoplasmic domain of the MHC molecule.

100. The method of any one of claims 91-99, wherein the 5’ cap comprises a D1 diastereoisomer of the structure: -131-sf-5685228Attorney Docket No.14639-20649.

40.

101. The method of any one of claims 91-100, wherein the 5’ UTR comprises the sequence UUCUUCUGGUCCCCACAGACUCAGAGAGAACCCGCCACC (SEQ ID NO:23).

102. The method of any one of claims 91-100, wherein the 5’ UTR comprises the sequence GGCGAACUAGUAUUCUUCUGGUCCCCACAGACUCAGAGAGAACCCGCCACC (SEQ ID NO:21).

103. The method of any one of claims 91-102, wherein the secretory signal peptide comprises the amino acid sequence MRVMAPRTLILLLSGALALTETWAGS (SEQ ID NO:27).

104. The method of any one of claims 91-102, wherein the polynucleotide sequence encoding the secretory signal peptide comprises the sequence AUGAGAGUGAUGGCCCCCAGAACCCUGAUCCUGCUGCUGUCUGGCGCCCUGGCCCUGA CAGAGACAUGGGCCGGAAGC (SEQ ID NO:25).

105. The method of any one of claims 91-104, wherein the at least portion of the transmembrane and cytoplasmic domain of the MHC molecule comprises the amino acid sequence IVGIVAGLAVLAVVVIGAVVATVMCRRKSSGGKGGSYSQAASSDSAQGSDVSLTA (SEQ ID NO:30).

106. The method of any one of claims 91-104, wherein the polynucleotide sequence encoding the at least portion of the transmembrane and cytoplasmic domain of the MHC molecule comprises the sequence AUCGUGGGAAUUGUGGCAGGACUGGCAGUGCUGGCCGUGGUGGUGAUCGGAGCCGUG GUGGCUACCGUGAUGUGCAGACGGAAGUCCAGCGGAGGCAAGGGCGGCAGCUACAGC CAGGCCGCCAGCUCUGAUAGCGCCCAGGGCAGCGACGUGUCACUGACAGCC (SEQ ID NO:28).

107. The method of any one of claims 91-106, wherein the 3’ untranslated region of the AES mRNA comprises the sequence -132-sf-5685228Attorney Docket No.14639-20649.40 CUGGUACUGCAUGCACGCAAUGCUAGCUGCCCCUUUCCCGUCCUGGGUACCCCGAGUC UCCCCCGACCUCGGGUCCCAGGUAUGCUCCCACCUCCACCUGCCCCACUCACCACCUCU GCUAGUUCCAGACACCUCC (SEQ ID NO:33).

108. The method of any one of claims 91-107, wherein the non-coding RNA of the mitochondrially encoded 12S RNA comprises the sequence CAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACA GCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGG GUUGGUCAAUUUCGUGCCAGCCACACCG (SEQ ID NO:35).

109. The method of any one of claims 91-108, wherein the 3’ UTR comprises the sequence CUCGAGCUGGUACUGCAUGCACGCAAUGCUAGCUGCCCCUUUCCCGUCCUGGGUACCC CGAGUCUCCCCCGACCUCGGGUCCCAGGUAUGCUCCCACCUCCACCUGCCCCACUCACC ACCUCUGCUAGUUCCAGACACCUCCCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAG CCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUU UAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACACCGAGACCU GGUCCAGAGUCGCUAGCCGCGUCGCU (SEQ ID NO:31).

110. The method of any one of claims 91-109, wherein the poly(A) sequence comprises 120 adenine nucleotides.

111. The method of any one of claims 1-90, wherein the RNA vaccine comprises an RNA molecule comprising, in the 5’ ^3’ direction: the polynucleotide sequence GGCGAACUAGUAUUCUUCUGGUCCCCACAGACUCAGAGAGAACCCGCCACCAUGAGAG UGAUGGCCCCCAGAACCCUGAUCCUGCUGCUGUCUGGCGCCCUGGCCCUGACAGAGAC AUGGGCCGGAAGC (SEQ ID NO:19); a polynucleotide sequence encoding the one or more neoepitopes resulting from cancer- specific somatic mutations present in the tumor specimen; and the polynucleotide sequence AUCGUGGGAAUUGUGGCAGGACUGGCAGUGCUGGCCGUGGUGGUGAUCGGAGCCGUG GUGGCUACCGUGAUGUGCAGACGGAAGUCCAGCGGAGGCAAGGGCGGCAGCUACAGC CAGGCCGCCAGCUCUGAUAGCGCCCAGGGCAGCGACGUGUCACUGACAGCCUAGUAAC UCGAGCUGGUACUGCAUGCACGCAAUGCUAGCUGCCCCUUUCCCGUCCUGGGUACCCC GAGUCUCCCCCGACCUCGGGUCCCAGGUAUGCUCCCACCUCCACCUGCCCCACUCACCA CCUCUGCUAGUUCCAGACACCUCCCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGC CUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUU -133-sf-5685228Attorney Docket No.14639-20649.40 AACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACACCGAGACCUG GUCCAGAGUCGCUAGCCGCGUCGCU (SEQ ID NO:20).

112. The method of any one of claims 1-111, wherein the pancreatic cancer tumor is a resectable PDAC tumor, assessed by preoperative imaging in the patient with computed tomography (CT) scan with contrast or magnetic resonance imaging (MRI) prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

113. The method of any one of claims 1-112, wherein the pancreatic cancer tumor is a resectable PDAC tumor comprising one or more characteristics selected from the group consisting of: clear fat plane around the celiac and superior mesenteric arteries; patent superior mesenteric and portal veins; no encasement of the superior mesenteric vein or portal veins; no encasement of the superior mesenteric or hepatic arteries; absence of metastatic disease; and absence of extra-regional nodal disease.

114. The method of any one of claims 1-113, wherein the patient has a histologically confirmed diagnosis of PDAC prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

115. The method of any one of claims 1-114, wherein the patient has adenosquamous carcinoma of the pancreas prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

116. The method of any one of claims 1-115, wherein the pancreatic cancer tumor has tumor, lymph node, metastasis (TNM) pathological staging values of T1-T3, N0-N2, or M0 prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

117. The method of any one of claims 1-116, wherein the pancreatic cancer tumor is a resectable PDAC tumor, and wherein: the patient had no evidence of PDAC disease after resection of the PDAC tumor, and / or the patient had a macroscopically complete resection of the PDAC tumor, prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment, optionally wherein the patient had a R0 or R1 resection of the PDAC tumor. -134-sf-5685228Attorney Docket No.14639-20649.40 118. The method of claim 117, wherein the patient had unequivocal absence of PDAC after resection of the PDAC tumor, optionally wherein the absence of PDAC is assessed by CT or MRI scans, one or more biochemical assays and / or clinical findings.

119. The method of any one of claims 1-118, wherein the pancreatic cancer tumor is a resectable PDAC tumor, and wherein following resection of the tumor, the patient did not have unresolved ≥ Grade 3 postoperative complications prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment, optionally wherein the complications are assessed according to the Clavien-Dindo Classification of Surgical Complications.

120. The method of any one of claims 1-119, wherein the patient has a CA19-9 level of 180 U / mL or greater prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

121. The method of any one of claims 1-119, wherein the patient has a CA19-9 level of less than 180 U / mL prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

122. The method of any one of claims 1-121, wherein at least five neoepitopes resulting from cancer-specific somatic mutations are present in the tumor specimen obtained from the patient prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

123. The method of any one of claims 1-122, wherein the patient has an Eastern Cooperative Oncology Group (ECOG) Performance Status of 0 or 1 prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

124. The method of any one of claims 1-123, wherein the patient does not have intraductal papillary mucinous neoplasm-associated PDAC prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

125. The method of any one of claims 1-124, wherein the patient does not have a pancreatic endocrine tumor or acinar cell adenocarcinoma, pancreatic cystadenocarcinoma, or pancreatic malignant ampulloma prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

126. The method of any one of claims 1-125, wherein the patient has not received an adjuvant, neoadjuvant, or induction treatment for pancreatic cancer, or a systemic anti-cancer treatment for -135-sf-5685228Attorney Docket No.14639-20649.40 pancreatic cancer, prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment; optionally wherein the pancreatic cancer is PDAC.

127. The method of any one of claims 1-126, wherein the patient has not had a cytotoxic chemotherapy, immunotherapy, investigational therapy, or radiation therapy prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

128. The method of any one of claims 1-127, wherein the patient has a spleen prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

129. The method of any one of claims 1-128, wherein the patient has not had loss of spleen due to splenectomy, splenic injury / infarction, or functional asplenia prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

130. The method of any one of claims 1-129, wherein the patient has not had a distal pancreatectomy with splenectomy prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

131. The method of any one of claims 1-130, wherein the patient does not have preexisting neuropathy prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

132. The method of any one of claims 1-131, wherein the patient does not have an aUGT1A1 genotype associated with poor metabolizer phenotype prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

133. The method of any one of claims 1-132, wherein the patient does not have an autoimmune disease, immune deficiency, or primary immunodeficiency prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

134. The method of any one of claims 1-133, wherein the patient has not been treated with: monoamine oxidase inhibitors (MAOIs) within 3 weeks, a systemic immunostimulatory agent within 4 weeks or 5 drug-elimination half-lives, whichever is longer, or a systemic immunosuppressive medication within 2 weeks, prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment. -136-sf-5685228Attorney Docket No.14639-20649.40 135. The method of any one of claims 1-134, wherein the patient has not had an allogeneic stem cell or solid organ transplantation prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

136. The method of any one of claims 1-135, further comprising assessing disease-free survival (DFS) of the patient after treatment with the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

137. The method of claim 136, wherein administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment results in an improvement in DFS of the patient as compared to DFS of a corresponding patient not administered the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

138. The method of any one of claims 1-137, further comprising assessing overall survival (OS) of the patient after treatment with the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

139. The method of claim 138, wherein administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment results in an improvement in OS of the patient as compared to OS of a corresponding patient not administered the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

140. The method of any one of claims 1-139, further comprising performing one or more clinical assessments of the patient before, during and / or after treatment with the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment, wherein the one or more clinical assessments are selected from the group consisting of European Organisation for Research and Treatment of Cancer QLQ-C30 Questionnaire (EORTC QLQ C30), European Organisation for Research and Treatment of Cancer QLQ-PAN26 Questionnaire (EORTC QLQ PAN26), National Cancer Institute's Patient-Reported Outcomes Common Terminology Criteria for Adverse Events (PRO CTCAE), and European Organisation for Research and Treatment of Cancer Item Library 46 Questionnaire (EORTC IL46).

141. The method of claim 140, wherein administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment results in an improvement in the one or more clinical assessments as compared to the one or more clinical assessments in the patient prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment, and / or as compared to the one or more clinical assessments in a corresponding patient not administered the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment. -137-sf-5685228Attorney Docket No.14639-20649.40 142. The method of any one of claims 1-141, further comprising assessing antigen- and / or tumor- specific T-cell responses in the patient before, during and / or after treatment with the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

143. The method of claim 142, wherein administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment results in an improvement in antigen- and / or tumor- specific T-cell responses in the patient as compared to prior to administration of the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment, and / or as compared to a corresponding patient not administered the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic treatment.

144. The method of any one of claims 137, 139, 141, and 143, wherein the corresponding patient is a patient with a corresponding pancreatic cancer tumor, optionally wherein the pancreatic cancer tumor is a PDAC tumor and the corresponding patient has a PDAC tumor.

145. The method of any one of claims 137, 139, 141, and 143-144, wherein the corresponding patient was treated with a standard of care treatment for pancreatic cancer, PDAC, or resectable or resected PDAC.

146. The method of claim 145, wherein the standard of care treatment comprises a gemcitabine combination therapy or an mFOLFIRINOX chemotherapy.

147. The method of any one of claims 137, 139, 141, and 143-144, wherein the corresponding patient was treated with a control treatment comprising an mFOLFIRINOX chemotherapy.

148. The method of claim 146 or claim 147, wherein the mFOLFIRINOX chemotherapy comprises oxaliplatin at dose of about 85 mg / m2, leucovorin at dose of about 400 mg / m2, irinotecan at dose of about 150 mg / m2, and 5-fluorouracil at dose of about 2400 mg / m2, administered intravenously in 14-day cycles, on day 1 of each cycle for a total of up to 12 cycles.

149. The method of any one of claims 1-148, wherein the RNA vaccine dose is administered to the patient in two equal half-doses.

150. The method of claim 149, wherein the two equal half-doses are administered sequentially, optionally with an observation period between the administered equal half-doses.

151. The method of claim 89, wherein the dose of about 25 µg is split into two equal half-doses of about 12.5 µg, each administered over 1 minute, optionally with a 5-minute observation period between the administered equal half-doses. -138-sf-5685228Attorney Docket No.14639-20649.40 152. An individualized RNA vaccine for use in a method for treating a pancreatic cancer tumor in a human patient in need thereof, wherein the RNA vaccine is to be administered in combination with a PD-1 axis binding antagonist and a chemotherapeutic treatment according to the method of any one of claims 1-151, wherein the RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a pancreatic cancer tumor specimen obtained from the patient.

153. A PD-1 axis binding antagonist for use in a method for treating a pancreatic cancer tumor in a human patient in need thereof, wherein the PD-1 axis binding antagonist is to be administered in combination with an individualized RNA vaccine and a chemotherapeutic treatment according to the method of any one of claims 1-151, wherein the RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a pancreatic cancer tumor specimen obtained from the patient.

154. Use of an individualized RNA vaccine in the manufacture of a medicament for treating a pancreatic cancer tumor in a human patient in need thereof, wherein the RNA vaccine is to be administered in combination with a PD-1 axis binding antagonist and a chemotherapeutic treatment according to the method of any one of claims 1-151, and wherein the RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a pancreatic cancer tumor specimen obtained from the patient.

155. Use of a PD-1 axis binding antagonist in the manufacture of a medicament for treating a pancreatic cancer tumor in a human patient in need thereof, wherein the PD-1 axis binding antagonist is to be administered in combination with an individualized RNA vaccine and a chemotherapeutic treatment according to the method of any one of claims 1-151, and wherein the RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a pancreatic cancer tumor specimen obtained from the patient.

156. A kit comprising an individualized RNA vaccine, for use in a method for treating a pancreatic cancer tumor in a human patient in need thereof, wherein the RNA vaccine is to be administered in combination with a PD-1 axis binding antagonist and a chemotherapeutic treatment according to the method of any one of claims 1-151, -139-sf-5685228Attorney Docket No.14639-20649.40 wherein the RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a pancreatic cancer tumor specimen obtained from the patient.

157. A kit comprising a PD-1 axis binding antagonist for use in a method for treating a pancreatic cancer tumor in a human patient in need thereof, wherein the PD-1 axis binding antagonist is to be administered in combination with an individualized RNA vaccine and a chemotherapeutic treatment according to the method of any one of claims 1-151, wherein the RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a pancreatic cancer tumor specimen obtained from the patient.

158. A method of selecting a human patient having a cancer tumor as likely to respond to a therapy comprising an individualized RNA vaccine, the method comprising: a) measuring the number and / or frequency of de novo significantly expanded (SE) TCR clones in a sample from the patient by T cell receptor sequencing; b) comparing the number and / or frequency of de novo SE TCR clones measured in a) to a reference number and / or frequency; and c) selecting the patient as more likely to respond to the therapy comprising the individualized RNA vaccine when the number and / or frequency of de novo SE TCR clones in the sample from the patient is above the reference number and / or frequency; wherein the individualized RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a cancer tumor specimen obtained from the patient, and wherein a number and / or frequency of de novo SE TCR clones above the reference number and / or frequency indicates that the patient is more likely to respond to the therapy comprising the individualized RNA vaccine.

159. A method of selecting a human patient having a cancer tumor as likely to respond to a therapy comprising an individualized RNA vaccine, the method comprising: a) comparing the number and / or frequency of de novo significantly expanded (SE) TCR clones in a sample from the patient to a reference number and / or frequency; and b) selecting the patient as more likely to respond to the therapy comprising the individualized RNA vaccine when the number and / or frequency of de novo SE TCR clones in the sample from the patient is above the reference number and / or frequency; -140-sf-5685228Attorney Docket No.14639-20649.40 wherein the individualized RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a cancer tumor specimen obtained from the patient, wherein the number and / or frequency of de novo SE TCR clones is measured by T cell receptor sequencing, and wherein a number and / or frequency of de novo SE TCR clones above the reference number and / or frequency indicates that the patient is more likely to respond to the therapy comprising the individualized RNA vaccine.

160. The method of claim 158 or claim 159, further comprising selecting the therapy comprising the individualized RNA vaccine or recommending the therapy comprising the individualized RNA vaccine.

161. A method of treating a human patient having a cancer tumor, the method comprising: a) measuring the number and / or frequency of de novo significantly expanded (SE) TCR clones in a sample from the patient by T cell receptor sequencing; b) comparing the number and / or frequency of de novo SE TCR clones measured in a) to a reference number and / or frequency; and c) selecting the patient as more likely to respond to the therapy comprising the individualized RNA vaccine when the number and / or frequency of de novo SE TCR clones in the sample from the patient is above the reference number and / or frequency, thereby treating the cancer tumor; wherein the individualized RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a cancer tumor specimen obtained from the patient, and wherein a number and / or frequency of de novo SE TCR clones above the reference number and / or frequency indicates that the patient is more likely to respond to the therapy comprising the individualized RNA vaccine.

162. A method of treating a human patient having a cancer tumor, the method comprising: a) comparing the number and / or frequency of de novo significantly expanded (SE) TCR clones in a sample from the patient to a reference number and / or frequency; and b) selecting the patient as more likely to respond to the therapy comprising the individualized RNA vaccine when the number and / or frequency of de novo SE TCR clones in the sample from the patient is above the reference number and / or frequency, thereby treating the cancer tumor; -141-sf-5685228Attorney Docket No.14639-20649.40 wherein the individualized RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a cancer tumor specimen obtained from the patient, wherein the number and / or frequency of de novo SE TCR clones is measured by T cell receptor sequencing, and wherein a number and / or frequency of de novo SE TCR clones above the reference number and / or frequency indicates that the patient is more likely to respond to the therapy comprising the individualized RNA vaccine.

163. The method of claim 161 or claim 162, further comprising administering the therapy comprising the individualized RNA vaccine to the patient when the number and / or frequency of de novo SE TCR clones in the sample from the patient is above the reference number and / or frequency, thereby treating the cancer tumor.

164. The method of claim 163, further comprising selecting the therapy comprising the individualized RNA vaccine when the number and / or frequency of de novo SE TCR clones in the sample from the patient is above the reference number and / or frequency, thereby treating the cancer tumor.

165. The method of any one of claims 158-164, wherein the number and / or frequency is measured after six doses of the individualized cancer vaccine.

166. The method of any one of claims 158-165, wherein the reference number is six de novo SE TCR clones.

167. The method of any one of claims 158-165, wherein the reference frequency is 10-4de novo SE TCR clones.

168. The method of any one of claims 158-167, wherein the cancer tumor is a pancreatic cancer tumor.

169. The method of any one of claims 158-168, wherein the cancer tumor is a pancreatic ductal adenocarcinoma (PDAC) tumor.

170. The method of any one of claims 158-169, wherein the therapy comprising the individualized RNA vaccine further comprises a PD-1 axis binding antagonist.

171. The method of claim 170, wherein the therapy further comprises a chemotherapeutic treatment and wherein the RNA vaccine, the PD-1 axis binding antagonist, and the chemotherapeutic -142-sf-5685228Attorney Docket No.14639-20649.40 treatment are administered to the patient during a priming phase, a chemotherapy phase after the priming phase, and a boost phase after the chemotherapy phase, wherein: (i) the priming phase comprises administering to the patient at least one dose of the RNA vaccine and at least one dose of the PD-1 axis binding antagonist, (ii) the chemotherapy phase comprises administering to the patient the chemotherapeutic treatment, and (iii) the boost phase comprises administering to the patient at least one dose of the RNA vaccine and at least one dose of the PD-1 axis binding antagonist.

172. The method of claim 170 or 171, wherein the PD-1 axis binding antagonist is atezolizumab.

173. The method of claim 171 or 172, wherein the chemotherapeutic treatment is a FOLFIRINOX treatment or an mFOLFIRINOX treatment.

174. The method of any one of claims 1-151, wherein, prior to the administering step, the patient is selected by a method comprising: a) measuring the number and / or frequency of de novo significantly expanded (SE) TCR clones in a sample from the patient by T cell receptor sequencing; b) comparing the number and / or frequency of de novo SE TCR clones measured in a) to a reference number and / or frequency; and c) selecting the patient as more likely to respond to the therapy comprising the individualized RNA vaccine when the number and / or frequency of de novo SE TCR clones in the sample from the patient is above the reference number and / or frequency; wherein the individualized RNA vaccine comprises one or more polynucleotides encoding one or more neoepitopes resulting from cancer-specific somatic mutations present in a cancer tumor specimen obtained from the patient, and wherein a number and / or frequency of de novo SE TCR clones above the reference number and / or frequency indicates that the patient is more likely to respond to the therapy comprising the individualized RNA vaccine.

175. In vitro use of number and / or frequency of de novo significantly expanded (SE) TCR clones for selecting a patient having a cancer tumor more likely to respond to a therapy comprising an individualized RNA vaccine, wherein a number and / or frequency of de novo SE TCR clones in the sample from the patient above a reference number and / or frequency selects that the patient is more likely to respond to the therapy comprising the individualized RNA vaccine. -143-sf-5685228Attorney Docket No.14639-20649.40 176. Use of a number and / or frequency of de novo significantly expanded (SE) TCR clones for the manufacture of a diagnostic for assessing the likelihood of a response of a patient having a cancer tumor to a therapy comprising an individualized RNA vaccine. -144-sf-5685228

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