T cell neo-epitope discovery in colorectal cancer by high throughput profiling of somatic mutations in expressed genes

Patient-specific (unique) tumor antigens, encoded by somatically mutated cancer genes, are implicated in the induction of tumor-controlling T cell responses. We report the identification of such antigens in colorectal cancers (CRC) by using high-throughput sequencing of cDNAs expressed by standard cancer cell cultures, and by parallel Cancer Stem/Initiating Cells (CSCs) cultures, coupled with a reverse immunology approach not requiring HLA allele-specific epitope predictions. Both CD8+ and CD4+ T cells, either patient's autologous or derived from HLA-matched healthy donors, are readily expanded by peptides spanning several cancer mutations and specifically recognize both differentiated cancer cells and CSC cultures. Unique antigen-specific CD8+ T cell frequency is also increased in a patient, compared to healthy donors. These results provide a proof-of-concept approach for the identification of unique epitopes that are immunogenic in CRC patients and can also target T cells against the most aggressive CSC component.