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NZ737891B2 - Shared neoantigens - Google Patents
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NZ737891B2 - Shared neoantigens - Google Patents

Shared neoantigens

Info

Publication number
NZ737891B2
NZ737891B2 NZ737891A NZ73789116A NZ737891B2 NZ 737891 B2 NZ737891 B2 NZ 737891B2 NZ 737891 A NZ737891 A NZ 737891A NZ 73789116 A NZ73789116 A NZ 73789116A NZ 737891 B2 NZ737891 B2 NZ 737891B2
Authority
NZ
New Zealand
Prior art keywords
seq
pharmaceutical composition
tumor
specific neoepitope
specific
Prior art date
Application number
NZ737891A
Other versions
NZ737891A (en
Inventor
Pavan Bachireddy
Edward F Fritsch
Nir Hacohen
Michael Steven Rooney
Sachet Ashok Shukla
Jing Sun
Catherine J Wu
Original Assignee
Dana Farber Cancer Institute Inc
The Broad Institute Inc
The General Hospital Corporation
Filing date
Publication date
Application filed by Dana Farber Cancer Institute Inc, The Broad Institute Inc, The General Hospital Corporation filed Critical Dana Farber Cancer Institute Inc
Priority to NZ776159A priority Critical patent/NZ776159B2/en
Priority claimed from PCT/US2016/033452 external-priority patent/WO2016187508A2/en
Publication of NZ737891A publication Critical patent/NZ737891A/en
Publication of NZ737891B2 publication Critical patent/NZ737891B2/en

Links

Classifications

    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/515—Animal cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/58—Medicinal preparations containing antigens or antibodies raising an immune response against a target which is not the antigen used for immunisation
    • A61K2039/585—Medicinal preparations containing antigens or antibodies raising an immune response against a target which is not the antigen used for immunisation wherein the target is cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/70—Multivalent vaccine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001102—Receptors, cell surface antigens or cell surface determinants
    • A61K39/001103—Receptors for growth factors
    • A61K39/001104—Epidermal growth factor receptors [EGFR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001102—Receptors, cell surface antigens or cell surface determinants
    • A61K39/001103—Receptors for growth factors
    • A61K39/001106—Her-2/neu/ErbB2, Her-3/ErbB3 or Her 4/ErbB4
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001148—Regulators of development
    • A61K39/00115—Apoptosis related proteins, e.g. survivin or livin
    • A61K39/001151—Apoptosis related proteins, e.g. survivin or livin p53
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001152—Transcription factors, e.g. SOX or c-MYC
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001154—Enzymes
    • A61K39/001162—Kinases, e.g. Raf or Src
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001154—Enzymes
    • A61K39/001164—GTPases, e.g. Ras or Rho
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001196—Fusion proteins originating from gene translocation in cancer cells
    • A61K39/001197—Breakpoint cluster region-abelson tyrosine kinase [BCR-ABL]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K47/00—Medicinal preparations characterised by the non-active ingredients used, e.g. carriers or inert additives; Targeting or modifying agents chemically bound to the active ingredient
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/46—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates
    • C07K14/47—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals
    • C07K14/4701—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans from vertebrates from mammals not used
    • C07K14/4748—Tumour specific antigens; Tumour rejection antigen precursors [TRAP], e.g. MAGE
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/30—Special therapeutic applications
    • C12N2320/31—Combination therapy
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/30—Special therapeutic applications
    • C12N2320/34—Allele or polymorphism specific uses
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/56—Staging of a disease; Further complications associated with the disease
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/60—Complex ways of combining multiple protein biomarkers for diagnosis
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/70—Mechanisms involved in disease identification
    • G01N2800/7023—(Hyper)proliferation
    • G01N2800/7028—Cancer
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Abstract

Disclosed herein in one aspect is a pharmaceutical composition comprising at least one neoantigenic peptide and a pharmaceutically acceptable carrier, the neoantigenic peptide comprising a tumor-specific neoepitope capable of binding to an HLA protein in a subject, the tumor-specific neoepitope comprising a tumor-specific mutation present in a tumor, wherein the tumor specific neoepitope arises from a tumor-specific GATA3 frameshift mutation.

Claims (82)

WHAT IS CLAIMED IS:
1. A pharmaceutical composition comprising: (i) a polypeptide that is from 8 to 50 amino acids in length, wherein the polypeptide comprises a tumor-specific neoepitope that binds to a protein encoded by an HLA allele, wherein the tumor-specific neoepitope arises from a tumor-specific GATA3 frameshift mutation, and wherein the tumor-specific neoepitope is the amino acid sequence KIMFATLQR (SEQ ID NO: 13441), MLTGPPARV (SEQ ID NO: 13437), SMLTGPPARV (SEQ ID NO: 13471), TLQRSSLWCL (SEQ ID NO: 13473), FATLQRSSL (SEQ ID NO: 13454), MFATLQRSSL (SEQ ID NO: 13487), FLKAESKIM (SEQ ID NO: 13438), FLKAESKIMF (SEQ ID NO: 13488), GPPARVPAV (SEQ ID NO: 13452), KPKRDGYMF (SEQ ID NO: 13453), KPKRDGYMFL (SEQ ID NOs: 13485), CSMLTGPPAR (SEQ ID NO: 13474), AVPFDLHFCR (SEQ ID NO: 13481), AESKIMFATL (SEQ ID NO: 13498), ESKIMFATL (SEQ ID NO: 13457), LQRSSLWCL (SEQ ID NO: 13467), LHFCRSSIM (SEQ ID NO: 13456), IMKPKRDGY (SEQ ID NO: 13447), IMKPKRDGYM (SEQ ID NOs: 13477), AESKIMFAT (SEQ ID NO: 13538), VPFDLHFCR (SEQ ID NO: 13449), ATLQRSSLW (SEQ ID NO: 13466), RSSIMKPKR (SEQ ID NO: 13446), VLPEPHLAL (SEQ ID NO: 13434), MFLKAESKI (SEQ ID NO: 13444), YMFLKAESK (SEQ ID NO: 13440), or YMFLKAESKI (SEQ ID NO: 13472), (ii) a nucleic acid encoding the polypeptide, (iii) antigen presenting cells (APCs) comprising (i) or (ii), or (iv) T cells stimulated with APCs comprising (i) or (ii), wherein the T cells specifically recognize the tumor specific neoepitope; and a pharmaceutically acceptable carrier.
2. The pharmaceutical composition according to claim 1, wherein the composition comprises at least two tumor specific neoepitopes.
3. The pharmaceutical composition according to claim 1 or claim 2, wherein the composition comprises at least three tumor specific neoepitopes.
4. The pharmaceutical composition according to any one of claims 1 to 3, wherein the pharmaceutical composition comprises at least twenty tumor specific neoepitopes.
5. The pharmaceutical composition according to any one of claims 1 to 4, wherein the tumor specific neoepitope binds to a protein encoded by a class II HLA allele with a binding affinity of less than 500 nM.
6. The pharmaceutical composition according to any one of claims 1 to 5, wherein the tumor specific neoepitope binds to a protein encoded by a class II HLA allele with a binding affinity of less than 1000 nM.
7. The pharmaceutical composition according to any one of claims 1 to 6, wherein the polypeptide further comprises an amino acid sequence selected from the group consisting of AIQPVLWTT,QPVLWTTPPL,VLPEPHLAL, HMSSLSHISA, TTPPLQHGHR, and SSLSHISAL
8. The pharmaceutical composition according to claim 1, wherein the tumor-specific neoepitope is ESKIMFATL (SEQ ID NO: 13457).
9. The pharmaceutical composition according to claim 1, wherein the tumor-specific neoepitope is FATLQRSSL (SEQ ID NO: 13454).
10. The pharmaceutical composition according to claim 1, wherein the tumor-specific neoepitope is FLKAESKIM (SEQ ID NO: 13438).
11. The pharmaceutical composition according to claim 1, wherein the tumor-specific neoepitope is FLKAESKIMF (SEQ ID NO: 13488).
12. The pharmaceutical composition according to claim 1, wherein the tumor-specific neoepitope is p GPPARVPAV (SEQ ID NO: 13452).
13. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is IMKPKRDGYM (SEQ ID NO: 13477).
14. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is KIMFATLQR (SEQ ID NO: 13441).
15. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is KPKRDGYMF (SEQ ID NO: 13453).
16. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is KPKRDGYMFL (SEQ ID NO: 13485).
17. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is LHFCRSSIM (SEQ ID NO: 13456).
18. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is MFATLQRSSL (SEQ ID NO: 13487).
19. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is MFLKAESKI (SEQ ID NO: 13444).
20. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is MLTGPPARV (SEQ ID NO: 13437).
21. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is QPVLWTTPPL (SEQ ID NO: 13484).
22. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is SMLTGPPARV (SEQ ID NO: 13471).
23. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is TLQRSSLWCL (SEQ ID NO: 13473).
24. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is VLPEPHLAL (SEQ ID NO: 13434).
25. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is YMFLKAESK (SEQ ID NO: 13440).
26. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is YMFLKAESKI (SEQ ID NO: 13472).
27. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is CSMLTGPPAR (SEQ ID NO: 13474).
28. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is AVPFDLHFCR (SEQ ID NO: 13481).
29. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is AESKIMFATL (SEQ ID NO: 13498).
30. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is LQRSSLWCL (SEQ ID NO: 13467).
31. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is IMKPKRDGY (SEQ ID NO: 13447).
32. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is HMSSLSHISA (SEQ ID NO: 13544).
33. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is AESKIMFAT (SEQ ID NO: 13538).
34. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is VPFDLHFCR (SEQ ID NO: 13449).
35. The pharmaceutical composition of claim 1, wherein the tumor-specific neoepitope is ATLQRSSLW (SEQ ID NO: 13466).
36. The pharmaceutical composition of claim 7, wherein the tumor-specific neoepitope is RSSIMKPKR (SEQ ID NO: 13446).
37. The pharmaceutical composition of claim 7, wherein the tumor-specific neoepitope is TTPPLQHGHR (SEQ ID NO: 13480).
38. The pharmaceutical composition of claim 7, wherein the tumor-specific neoepitope is SSLSHISAL (SEQ ID NO: 13515).
39. The pharmaceutical composition of claim 7, wherein the polypeptide comprises an amino acid sequence AIQPVLWTT.
40. The pharmaceutical composition of claim 1, wherein the pharmaceutical composition comprises (ii) the nucleic acid encoding the polypeptide of (i).
41. The pharmaceutical composition of claim 1, wherein the pharmaceutical composition comprises (iv) the T cells stimulated with APCs comprising (i) or (ii).
42. The pharmaceutical composition according to any one of claims 1 to 41, wherein the composition is an immunogenic or a vaccine composition.
43. The pharmaceutical composition according to claim 42, further comprising an immunomodulator or adjuvant.
44. Use of a pharmaceutical composition according to any one of claims 1 to 43, in the manufacture of a medicament for treating or preventing a cancer in a subject in need thereof.
45. The use according to claim 44, wherein the subject has a GATA3 frameshift mutation.
46. The use according to claim 45, wherein the GATA3 frameshift mutation is a GATA3:p.H434 frameshift mutation.
47. The use according to claim 44, wherein the cancer is breast cancer.
48. The use according to claim 47, wherein the breast cancer is non-metastatic breast cancer.
49. The use according to claim 47, wherein the breast cancer is metastatic breast cancer.
50. The use according to claim 47, wherein the breast cancer is HERpositive breast cancer.
51. The use according to claim 47, wherein the breast cancer is a stage I breast cancer, stage II breast cancer, stage IIA breast cancer or operable stage IIC breast cancer.
52. The use according to any one of claims 44 to 51 wherein the pharmaceutical composition is to be administered as a combination therapy with an additional cancer therapy.
53. The use of claim 52, wherein the additional cancer therapy is a checkpoint inhibitor.
54. The use of claim 52, wherein the additional cancer therapy is surgery, chemotherapy, or a targeted therapy.
55. Use of a pharmaceutical composition according to any one of claims 1 to 43 in the manufacture of a medicament for a prophylactic cancer treatment wherein: (a) a cancer drug is selected for a patient in need thereof, the drug selected from the group consisting of ibrutinib, erlotinib, imatinib, gefitinib, crizotinib, trastuzumab, vemurafenib, RAF/MEK inhibitors, and antiestrogen therapy; and (b) the pharmaceutical composition is to be prophylactically administered to the subject, wherein the at least one peptide in the composition is derived from drug resistant mutations associated with the selected cancer drug.
56. A pharmaceutical composition comprising (i) a polypeptide of 8-50 amino acids in length, wherein the polypeptide comprises a tumor-specific neoepitope that binds to a protein encoded by an HLA allele, wherein the tumor-specific neoepitope arises from a tumor- specific GATA3 frameshift mutation, and wherein the tumor-specific neoepitope is the amino acid sequence QWGPCLQCL (SEQ ID NO: 13810), TTTTTLWRL (SEQ ID NO: 13811), WALLQASQY (SEQ ID NO: 13812), EECQWGPCL (SEQ ID NO: 13813), QWGPCLQCLW (SEQ ID NO: 13814), LWALLQASQY (SEQ ID NO: 13815), QTTTTTLWRL (SEQ ID NO: 13816), and CQWGPCLQCL (SEQ ID NO: 13817), (ii) a nucleic acid encoding the polypeptide of (i), (iii) antigen presenting cells (APCs) comprising (i) or (ii), or (iv) T cells stimulated with APCs comprising (i) or (ii), wherein the T cells specifically recognize the tumor specific neoepitope; and a pharmaceutically acceptable carrier.
57. The pharmaceutical composition of claim 56, wherein the tumor specific neoepitope binds to a protein encoded by a class II HLA allele with a binding affinity of less than 1000 nM.
58. The pharmaceutical composition of claim 56, wherein the tumor-specific neoepitope is QWGPCLQCL (SEQ ID NO: 13810).
59. The pharmaceutical composition of claim 56, wherein the tumor-specific neoepitope is TTTTTLWRL (SEQ ID NO: 13811).
60. The pharmaceutical composition of claim 56, wherein the tumor-specific neoepitope is WALLQASQY (SEQ ID NOs: 13812).
61. The pharmaceutical composition of claim 56, wherein the tumor-specific neoepitope is EECQWGPCL (SEQ ID NO: 13813).
62. The pharmaceutical composition of claim 56, wherein the tumor-specific neoepitope is QWGPCLQCLW (SEQ ID NO: 13814).
63. The pharmaceutical composition of claim 56, wherein the tumor-specific neoepitope is LWALLQASQY (SEQ ID NOs: 13815).
64. The pharmaceutical composition of claim 56, wherein the tumor-specific neoepitope is QTTTTTLWRL (SEQ ID NO: 13816).
65. The pharmaceutical composition of claim 56, wherein the tumor-specific neoepitope is CQWGPCLQCL (SEQ ID NOs: 13817).
66. The pharmaceutical composition of claim 56, wherein the pharmaceutical composition comprises (iv).
67. The pharmaceutical composition of claim 56, wherein the pharmaceutical composition comprises (i) or (ii).
68. The pharmaceutical composition of claim 56, further comprising an adjuvant or an immunomodulator.
69. The pharmaceutical composition of claim 56, wherein the pharmaceutical composition is an immunogenic composition or a vaccine composition.
70. Use of a pharmaceutical composition for the manufacture of a medicament for treating or preventing a cancer, wherein the pharmaceutical composition is an immunogenic composition or a vaccine composition, comprising: (i) an isolated neoantigenic polypeptide from 8 to 50 amino acids in length comprising at least one amino acid sequence comprising a tumor-specific neoepitope, wherein the tumor-specific neoepitope arises from a tumor-specific GATA3 frameshift mutation, and wherein the tumor-specific neoepitope is an amino acid sequence selected from the group consisting of QWGPCLQCL (SEQ ID NO: 13810), TTTTTLWRL (SEQ ID NO: 13811), WALLQASQY (SEQ ID NO: 13812), EECQWGPCL (SEQ ID NO: 13813), QWGPCLQCLW (SEQ ID NO: 13814), LWALLQASQY (SEQ ID NO: 13815), QTTTTTLWRL (SEQ ID NO: 13816), and CQWGPCLQCL (SEQ ID NO: 13817), (ii) a nucleic acid encoding (i), (iii) antigen presenting cells (APCs) comprising (i) or (ii), or (iv) T cells stimulated with (iii), wherein the T cells specifically recognize the tumor specific neoepitope; and a pharmaceutically acceptable carrier.
71. Use of a pharmaceutical composition according to any one of claims 56 to 69, in the manufacture of a medicament for treating or preventing a cancer in a subject in need thereof.
72. The use according to claim 70 or 71, wherein the subject has a GATA3 frameshift mutation.
73. The use according to claim 72, wherein the GATA3 frameshift mutation is a GATA3:p.L328 frameshift mutation.
74. The use according to claim 70 or 71, wherein the cancer is breast cancer.
75. The use according to claim 74, wherein the breast cancer is non-metastatic breast cancer.
76. The use according to claim 74, wherein the breast cancer is metastatic breast cancer.
77. The use according to claim 74, wherein the breast cancer is HERpositive breast cancer.
78. The use according to claim 74, wherein the breast cancer is a stage I breast cancer, stage II breast cancer, stage IIA breast cancer or operable stage IIC breast cancer.
79. The use according to any one of claims 70 to 78 wherein the pharmaceutical composition is to be administered as a combination therapy with an additional cancer therapy.
80. The use of claim 79, wherein the additional cancer therapy is a check point inhibitor.
81. The use of claim 79, wherein the additional cancer therapy is surgery, chemotherapy, or a targeted therapy.
82. A pharmaceutical composition or use according to any one of claims 1-81, substantially as described herein and with reference to any example thereof.
NZ737891A 2016-05-20 Shared neoantigens NZ737891B2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
NZ776159A NZ776159B2 (en) 2016-05-20 Shared neoantigens

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201562179877P 2015-05-20 2015-05-20
US201662389377P 2016-02-23 2016-02-23
PCT/US2016/033452 WO2016187508A2 (en) 2015-05-20 2016-05-20 Shared neoantigens

Publications (2)

Publication Number Publication Date
NZ737891A NZ737891A (en) 2025-02-28
NZ737891B2 true NZ737891B2 (en) 2025-06-04

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