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Epitope Landscape in Breast and Colorectal Cancer

¹ Department of Medicine, ² Ludwig Center for Cancer Immunotherapy, and ³ Immunology Program, Memorial Sloan-Kettering Cancer Center, New York, New York; and ⁴ Ludwig Center for Cancer Genetics and Therapeutics at The Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland

Requests for reprints: James P. Allison, Ludwig Center of Cancer Immunotherapy, Memorial Sloan-Kettering Cancer Center, 415 East 68th Street, Z-1560, New York, NY 10065. E-mail: allisonj{at}mskcc.org.

Key Words: genomic instability • tumor antigens • HLA

The finding that individual cancers contain many mutant genes not present in normal tissues has prompted considerable interest in the cancer epitope landscape. To further understand such effects, we applied in silico–based epitope prediction algorithms and high throughput post hoc analysis to identify candidate tumor antigens. Analysis of 1,152 peptides containing missense mutations previously identified in breast and colorectal cancer revealed that individual cancers accumulate on average 10 and 7 novel and unique HLA-A*0201 epitopes, respectively, including genes implicated in the neoplastic process. These data suggest that, with appropriate manipulation of the immune system, tumor cell destruction in situ may provide a polyvalent tumor vaccine without a requirement for knowledge of the targeted antigens. [Cancer Res 2008;68(3):889–92]

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