In this study we have identified a family affected with FAP from rural India in which 10 out of the 26 members carry a novel germline mutation in the APC gene. Of these, six have been diagnosed with polyps and four remain polyp free. From a novel therapeutic standpoint, we sought to determine if peptides derived from the novel APC gene mutation could induce a cytotoxic T cell response, thereby qualifying them as cancer vaccine candidates. Only one (of 5) mutant peptide derived from the novel APC gene mutation was found to be selectively immunogenic. Additionally, experimental testing of six previously reported APC gene mutation-derived peptides revealed one of the six to be immunogenic. We concluded that while not all APC mutant peptides are immunogenic, a library of empirically confirmed ones could qualify as vaccine candidates designed to target somatic mutations in the APC gene that drive the formation of colon polyps.

In this study, we identified a novel germline mutation in the APC (Adenomatous polyposis coli) gene in members of a FAP-affected (Familial adenomatous polyposis) family. This unique heterozygous variant (c.735_736insT; p.Ser246PhefsTer6) was identified in ten out of twenty six family members, ranging in age from 6 to 60 years. Polyps were detected in six of the ten individuals (35-60 years) carrying this mutation. The remaining four members (6-23 years) remain polyp free. A significant fraction of FAP affected individuals eventually develop colon cancer and therapeutic interventions to prevent cancer progression remain elusive. To address this issue, we sought to determine if peptides derived from the novel APC mutation could induce a cytotoxic T cell response, thereby qualifying them as vaccine candidates. Peptides harboring the variant amino acids were first interrogated in silico for their immunogenicity using a proprietary neoepitope prioritization pipeline, OncoPeptVAC. A single 9-mer peptide was predicted to be immunogenic. Remarkably, CD8+ T cells isolated from either an FAP+/ APCmut individual, or from a FAP-/ APCmut individual, failed to respond to the peptide, whereas those from either an unaffected family member (FAP-/ APCwt) or from healthy unrelated donors, showed a robust response, suggesting that CD8+ T cells from individuals carrying this germline APC mutation have been tolerized to the mutation. Furthermore, experimental testing of six additional reported APC gene mutation-derived peptides revealed one of the six to be immunogenic. While not all APC mutant peptides are inmmunogenic, a few qualify as vaccine candidates offering novel treatment opportunities to patients with somatic APC gene mutations to delay/treat colorectal cancer.