Identification of WDFY3 neoantigens as prognostic markers in long-term survivors of extrahepatic cholangiocarcinoma.

BACKGROUND Neoantigens are newly formed antigens that have not been previously recognized by the immune system. They may arise from altered tumor proteins that form as a result of mutations. Although neoantigens have recently been linked to antitumor immunity in long-term survivors of cancers, such as melanoma and colorectal cancer, their prognostic and immune-modulatory role in many cancer types remains undefined. OBJECTIVE The purpose of this study is to identify prognostic markers for long-term extrahepatic cholangiocarcinoma (EHCC) survival. METHODS We investigated neoantigens in EHCC, a rare aggressive cancer with a 5-year overall survival rate lower than 10%, using a combination of whole exome sequencing (WES), RNA sequencing (RNA-seq), computational biophysics, and immunohistochemistry. RESULTS Our analysis revealed a decreased neutrophil infiltration-related trend of high-quality neoantigen load with IC50 <500 nM (r=0.445, P=0.043). Among 24 EHCC patients examined, we identified four long term survivors with WDFY3 neoantigens, and none with WDFY3 neoantigens in the short-term survivors. The WDFY3 neoantigens are associated with a lower infiltration of neutrophils (p=0.013), lower expression of CCL5 (p=0.025), CXCL9 (p=0.036) and TIGIT (p=0.016), and less favorable prognosis (p=0.030). In contrast, the prognosis was not significantly associated with tumor mutation burden, neoantigen load, or immune cell infiltration. CONCLUSION We suggest that the WDFY3 neoantigens may affect prognosis by regulating antitumor immunity and that the WDFY3 neoantigens may be harnessed as potential targets for immunotherapy of EHCC.