Tumor-specific mutations as targets for cancer immunotherapy

Experimental and Applied Immunotherapy

Volumn , Issue , 2011, Pages 151-172

  Nelson, Brad H ^a   Webb, John R ^a  

^a BRITISH COLUMBIA CANCER AGENCY   (Canada)

Author keywords

Cancer genomics; High throughput sequencing; Somatic mutation; Tumor suppressor genes; Tumor specific mutation

Indexed keywords

EID: 84865852319     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-60761-980-2_7     Document Type: Chapter

References (99)

1. Bardelli A, Parsons DW et al (2003). Mutational analysis of the tyrosine kinome in colorectal cancers. Science 300:949.
2. Greenman C, Stephens P et al (2007). Patterns of somatic mutation in human cancer genomes. Nature 446:153-158.
3. Ding L, Getz G et al (2008). Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455:1069-1075.
4. Wood LD, Parsons DW et al (2007). The genomic landscapes of human breast and colorectal cancers. Science 318:1108-1113.
5. Shah SP, Morin RD et al (2009). Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature 461:809-813.
6. Jones S, Zhang X et al (2008). Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science 321:1801-1806.
7. Parsons DW, Jones S et al (2008). An integrated genomic analysis of human glioblastoma multiforme. Science 321:1807-1812.
8. Loeb LA, Bielas JH et al (2008). Cancers exhibit a mutator phenotype: clinical implications. Cancer Res 68:3551-3557; discussion 3557.
9. Lengauer C, Kinzler KW et al (1998). Genetic instabilities in human cancers. Nature 396:643-649.
10. Buckowitz A, Knaebel HP et al (2005). Microsatellite instability in colorectal cancer is associated with local lymphocyte infiltration and low frequency of distant metastases. Br J Cancer 92:1746-1753.
11. Lakhani SR (1999). The pathology of familial breast cancer: morphological aspects. Breast Cancer Res 1:31-35.
12. Kuroda H, Tamaru J et al (2005). Immunophenotype of lymphocytic infiltration in medullary carcinoma of the breast. Virchows Arch 446:10-14.
13. Clarke B, Tinker AV et al (2009). Intraepithelial T cells and prognosis in ovarian carcinoma: novel associations with stage, tumor type, and BRCA1 loss. Mod Pathol 22:393-402.
14. Forbes SA, Bhamra G et al (2008). The Catalogue of Somatic Mutations in Cancer (COSMIC). Curr Protoc Hum Genet Chapter 10: Unit 10 11.
15. Schinzel AC, and Hahn WC (2008). Oncogenic transformation and experimental models of human cancer. Front Biosci 13:71-84.
16. Beerenwinkel N, Antal T et al (2007). Genetic progression and the waiting time to cancer. PLoS Comput Biol 3:e225.
17. Stratton MR, Campbell PJ et al (2009). The cancer genome. Nature 458:719-724.
18. Vyas JM, Van der Veen AG et al (2008). The known unknowns of antigen processing and presentation. Nat Rev Immunol 8:607-618.
19. Rangel LB, Agarwal R et al (2004). Anomalous expression of the HLA-DR alpha and beta chains in ovarian and other cancers. Cancer Biol Ther 3:1021-1027.
20. Liu T, Liu W et al (2009). Computational prediction of the specificities of proteasome interaction with antigen protein. Cell Mol Immunol 6:135-142.
21. Horton R, Wilming L et al (2004). Gene map of the extended human MHC. Nat Rev Genet 5:889-899.
22. Bevan MJ (2006). Cross-priming. Nat Immunol 7:363-365.
23. Arstila TP, Casrouge A et al (1999). A direct estimate of the human alphabeta T cell receptor diversity. Science 286:958-961.
24. Echchakir H, Mami-Chouaib F et al (2001). A point mutation in the alpha-actinin-4 gene generates an antigenic peptide recognized by autologous cytolytic T lymphocytes on a human lung carcinoma. Cancer Res 61:4078-4083.
25. Sensi M, and Anichini A (2006). Unique tumor antigens: evidence for immune control of genome integrity and immunogenic targets for T cell-mediated patient-specific immunotherapy. Clin Cancer Res 12:5023-5032.
26. Jia J, Cui J et al (2009). Genome-scale search of tumor-specific antigens by collective analysis of mutations, expressions and T-cell recognition. Mol Immunol 46:1824-1829.
27. Wang HY, Zhou J et al (2002). Identification of a mutated fibronectin as a tumor antigen recognized by CD4+ T cells: its role in extracellular matrix formation and tumor metastasis. J Exp Med 195:1397-1406.
28. Gaudin C, Kremer F et al (1999). A hsp70-2 mutation recognized by CTL on a human renal cell carcinoma. J Immunol 162:1730-1738.
29. (+) T cells. J Exp Med 189:757-766.
30. Baurain JF, Colau D et al (2000). High frequency of autologous anti-melanoma CTL directed against an antigen generated by a point mutation in a new helicase gene. J Immunol 164:6057-6066.
31. Huang J, El-Gamil M et al (2004). T cells associated with tumor regression recognize frameshifted products of the CDKN2A tumor suppressor gene locus and a mutated HLA class I gene product. J Immunol 172:6057-6064.
32. Linard B, Bezieau S et al (2002). A RAS-mutated peptide targeted by CTL infiltrating a human melanoma lesion. J Immunol 168:4802-4808.
33. Robbins PF, El-Gamil M et al (1996). A mutated beta-catenin gene encodes a melanomaspecific antigen recognized by tumor infiltrating lymphocytes. J Exp Med 183:1185-1192.
34. Novellino L, Renkvist N et al (2003). Identification of a mutated receptor-like protein tyrosine phosphatase kappa as a novel, class II HLA-restricted melanoma antigen. J Immunol 170:6363-6370.
35. Kawakami Y, Wang X et al (2001). Isolation of a new melanoma antigen, MART-2, containing a mutated epitope recognized by autologous tumor-infiltrating T lymphocytes. J Immunol 166:2871-2877.
36. Karanikas V, Colau D et al (2001). High frequency of cytolytic T lymphocytes directed against a tumor-specific mutated antigen detectable with HLA tetramers in the blood of a lung carcinoma patient with long survival. Cancer Res 61:3718-3724.
37. Mami-Chouaib F, Echchakir H et al (2002). Antitumor cytotoxic T-lymphocyte response in human lung carcinoma: identification of a tumor-associated antigen. Immunol Rev 188:114-121.
38. Zorn E, and Hercend T (1999). A natural cytotoxic T cell response in a spontaneously regressing human melanoma targets a neoantigen resulting from a somatic point mutation. Eur J Immunol 29:592-601.
39. Wang HY, Peng G et al (2005). Recognition of a new ARTC1 peptide ligand uniquely expressed in tumor cells by antigen-specific CD4+ regulatory T cells. J Immunol 174:2661-2670.
40. Coulie PG, Lehmann F et al (1995). A mutated intron sequence codes for an antigenic peptide recognized by cytolytic T lymphocytes on a human melanoma. Proc Natl Acad Sci USA 92:7976-7980.
41. Topalian SL, Gonzales MI et al (2002). Revelation of a cryptic major histocompatibility complex class II-restricted tumor epitope in a novel RNA-processing enzyme. Cancer Res 62:5505-5509.
42. Maccalli C, Li YF et al (2003). Identification of a colorectal tumor-associated antigen (COA-1) recognized by CD4(+) T lymphocytes. Cancer Res 63:6735-6743.
43. Van Elsas A, Nijman HW et al (1995). Induction and characterization of cytotoxic T-lymphocytes recognizing a mutated p21RAS peptide presented by HLA-A∗0201. Int J Cancer 61:389-396.
44. + T-cell immunity to mutated RAS protein in pancreatic and colon cancer patients. Cancer Res 55:2984-2987.
45. Abrams SI, Hand PH et al (1996). Mutant RAS epitopes as targets for cancer vaccines. Semin Oncol 23:118-134.
46. (+) T-cell recognition of mutated B-RAF in melanoma patients harboring the V599E mutation. Cancer Res 64:1595-1599.
47. Schwitalle Y, Linnebacher M et al (2004). Immunogenic peptides generated by frameshift mutations in DNA mismatch repair-deficient cancer cells. Cancer Immun 4:14.
48. Ripberger E, Linnebacher M et al (2003). Identification of an HLA-A0201-restricted CTL epitope generated by a tumor-specific frameshift mutation in a coding microsatellite of the OGT gene. J Clin Immunol 23:415-423.
49. Linnebacher M, Gebert J et al (2001). Frameshift peptide-derived T-cell epitopes: a source of novel tumor-specific antigens. Int J Cancer 93:6-11.
50. Worley BS, van den Broeke LT et al (2001). Antigenicity of fusion proteins from sarcomaassociated chromosomal translocations. Cancer Res 61:6868-6875.
51. Yotnda P, Garcia F et al (1998). Cytotoxic T cell response against the chimeric ETV6-AML1 protein in childhood acute lymphoblastic leukemia. J Clin Invest 102:455-462.
52. Yotnda P, Firat H et al (1998). Cytotoxic T cell response against the chimeric p210 BCR-ABL protein in patients with chronic myelogenous leukemia. J Clin Invest 101:2290-2296.
53. Nieda M, Nicol A et al (1998). Dendritic cells stimulate the expansion of bcr-abl specific CD8+ T cells with cytotoxic activity against leukemic cells from patients with chronic myeloid leukemia. Blood 91:977-983.
54. + T cells elicited by primary in vitro immunization with a BCR-ABL breakpoint peptide. Blood 88:3522-3527.
55. Reddy EP, Reynolds RK et al (1982). A point mutation is responsible for the acquisition of transforming properties by the T24 human bladder carcinoma oncogene. Nature 300:149-152.
56. Tabin CJ, Bradley SM et al (1982). Mechanism of activation of a human oncogene. Nature 300:143-149.
57. Fossum B, Olsen AC et al (1995). CD8+ T cells from a patient with colon carcinoma, specific for a mutant p21-RAS-derived peptide (Gly13- > Asp), are cytotoxic towards a carcinoma cell line harbouring the same mutation. Cancer Immunol Immunother 40:165-172.
58. + T lymphocytes, generated by mutant p21-RAS (12Val) peptide vaccination of a patient, recognize 12Val-dependent nested epitopes present within the vaccine peptide and kill autologous tumour cells carrying this mutation. Int J Cancer 72:784-790.
59. Juretic A, Jurgens-Gobel J et al (1996). Cytotoxic T-lymphocyte responses against mutated p21 RAS peptides: an analysis of specific T-cell-receptor gene usage. Int J Cancer 68:471-478.
60. Gjertsen MK, Bakka A et al (1995). Vaccination with mutant RAS peptides and induction of T-cell responsiveness in pancreatic carcinoma patients carrying the corresponding RAS mutation. Lancet 346:1399-1400.
61. Gjertsen MK, Buanes T et al (2001). Intradermal RAS peptide vaccination with granulocytemacrophage colony-stimulating factor as adjuvant: clinical and immunological responses in patients with pancreatic adenocarcinoma. Int J Cancer 92:441-450.
62. Khleif SN, Abrams SI et al (1999). A phase I vaccine trial with peptides reflecting RAS oncogene mutations of solid tumors. J Immunother 22:155-165.
63. + T cell lines from patients immunized with RAS oncogene-derived peptides reflecting codon 12 mutations. Cell Immunol 182:137-151.
64. Toubaji A, Achtar M et al (2008). Pilot study of mutant RAS peptide-based vaccine as an adjuvant treatment in pancreatic and colorectal cancers. Cancer Immunol Immunother 57:1413-1420.
65. Meyer RG, Korn S et al (2007). An open-label, prospective phase I/II study evaluating the immunogenicity and safety of a RAS peptide vaccine plus GM-CSF in patients with nonsmall cell lung cancer. Lung Cancer 58:88-94.
66. Carbone DP, Ciernik IF et al (2005). Immunization with mutant p53- and K-RAS-derived peptides in cancer patients: immune response and clinical outcome. J Clin Oncol 23:5099-5107.
67. Hunger RE, Brand CU et al (2001). Successful induction of immune responses against mutant RAS in melanoma patients using intradermal injection of peptides and GM-CSF as adjuvant. Exp Dermatol 10:161-167.
68. Shtivelman E, Lifshitz B et al (1986). Alternative splicing of RNAs transcribed from the human ABL gene and from the BCR-ABL fused gene. Cell 47:277-284.
69. Bocchia M, Wentworth PA et al (1995). Specific binding of leukemia oncogene fusion protein peptides to HLA class I molecules. Blood 85:2680-2684.
70. Bocchia M, Korontsvit T et al (1996). Specific human cellular immunity to BCR-ABL oncogene-derived peptides. Blood 87:3587-3592.
71. Greco G, Fruci D et al (1996). Two BRC-ABL junction peptides bind HLA-A3 molecules and allow specific induction of human cytotoxic T lymphocytes. Leukemia 10:693-699.
72. Buzyn A, Ostankovitch M et al (1997). Peptides derived from the whole sequence of BCR- ABL bind to several class I molecules allowing specific induction of human cytotoxic T lymphocytes. Eur J Immunol 27:2066-2072.
73. Clark RE, Dodi IA et al (2001). Direct evidence that leukemic cells present HLA-associated immunogenic peptides derived from the BCR-ABL b3a2 fusion protein. Blood 98:2887-2893.
74. ten Bosch GJ, Toornvliet AC et al (1995). Recognition of peptides corresponding to the joining region of p210BCR-ABL protein by human T cells. Leukemia 9:1344-1348.
75. Pawelec G, Max H et al (1996). BCR/ABL leukemia oncogene fusion peptides selectively bind to certain HLA-DR alleles and can be recognized by T cells found at low frequency in the repertoire of normal donors. Blood 88:2118-2124.
76. + T lymphocytes respond to dendritic cells pulsed with b3a2 peptide and antigen-presenting cells exposed to b3a2 containing cell lysates. Blood 90:290-297.
77. Pinilla-Ibarz J, Cathcart K et al (2000). Vaccination of patients with chronic myelogenous leukemia with BCR-ABL oncogene breakpoint fusion peptides generates specific immune responses. Blood 95:1781-1787.
78. Cathcart K, Pinilla-Ibarz J et al (2004). A multivalent BCR-ABL fusion peptide vaccination trial in patients with chronic myeloid leukemia. Blood 103:1037-1042.
79. Bocchia M, Gentili S et al (2005). Effect of a p210 multipeptide vaccine associated with imatinib or interferon in patients with chronic myeloid leukaemia and persistent residual disease: a multicentre observational trial. Lancet 365:657-662.
80. Rojas JM, Knight K et al (2007). Clinical evaluation of BCR-ABL peptide immunisation in chronic myeloid leukaemia: results of the EPIC study. Leukemia 21:2287-2295.
81. Maslak PG, Dao T et al (2008). A pilot vaccination trial of synthetic analog peptides derived from the BCR-ABL breakpoints in CML patients with minimal disease. Leukemia 22:1613-1616.
82. Jain N, Reuben JM et al (2009). Synthetic tumor-specific breakpoint peptide vaccine in patients with chronic myeloid leukemia and minimal residual disease: a phase 2 trial. Cancer 115:3924-3934.
83. Parker KC, Bednarek MA et al (1994). Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol 152:163-175.
84. Rammensee H, Bachmann J et al (1999). SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50:213-219.
85. Larsen MV, Lundegaard C et al (2007). Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics 8:424.
86. Larsen MV, Lundegaard C et al (2005). An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol 35:2295-2303.
87. Lundegaard C, Lamberth K et al (2008). NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res 36:W509-512.
88. Doytchinova IA, Guan P et al (2006). EpiJen: a server for multistep T cell epitope prediction. BMC Bioinformatics 7:131.
89. Hakenberg J, Nussbaum AK et al (2003). MAPPP: MHC class I antigenic peptide processing prediction. Appl Bioinformatics 2:155-158.
90. Zhang Q, Wang P et al (2008). Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res 36:W513-518.
91. Westrop SJ, Grageda N et al (2009). Novel approach to recognition of predicted HIV-1 Gag B3501-restricted CD8 T-cell epitopes by HLA-B3501(+) patients: confirmation by quantitative ELISpot analyses and characterisation using multimers. J Immunol Meth 341:76-85.
92. Wulf M, Hoehn P et al (2009). Identification of human MHC class I binding peptides using the iTOPIA- epitope discovery system. Meth Mol Biol 524:361-367.
93. Wilson CC, Olson WC et al (1999). HIV-1-specific CTL responses primed in vitro by blood- derived dendritic cells and Th1-biasing cytokines. J Immunol 162:3070-3078.
94. Tuting T, Wilson CC et al (1998). Autologous human monocyte-derived dendritic cells genetically modified to express melanoma antigens elicit primary cytotoxic T cell responses in vitro: enhancement by cotransfection of genes encoding the Th1-biasing cytokines IL-12 and IFNalpha. J Immunol 160:1139-1147.
95. Pascolo S (2005). HLA class I transgenic mice: development, utilisation and improvement. Expert Opin Biol Ther 5:919-938.
96. Hunter C, Smith R et al (2006). A hypermutation phenotype and somatic MSH6 mutations in recurrent human malignant gliomas after alkylator chemotherapy. Cancer Res 66:3987-3991.
97. The Cancer Genome Atlas (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455:1061-1068.
98. O'Hare T, Eide CA et al (2008). New BCR-ABL inhibitors in chronic myeloid leukemia: keeping resistance in check. Expert Opin Investig Drugs 17:865-878.
99. Yamamoto H, Toyooka S et al (2009). Impact of EGFR mutation analysis in non-small cell lung cancer. Lung Cancer 63:315-321.