Abstract
Recently proposed tumor fitness measures, based on profiling neoepitopes for reactive viral epitope similarity, have led to improved prediction models of response to immune checkpoint inhibitors in melanoma and small-cell lung cancer. Here we test if this checkpoint based fitness is associated with tumor T-cell infiltration, cytolytic activity (CYT), and abundance (TIL burden) in the treatment naive samples from the same tumor types using data from TCGA. We find no significant correlation between TIL burden or CYT and the proposed neoepitope based fitness measures. Similarly, no significant survival predictive power beyond that of overall patient tumor mutation burden in either cohort is observed. Further, we find suggestive evidence that tumor neoepitopes dominate viral epitopes in putative immunogenicity and drives immune response in liver cancer with hepatitis B virus infection (HBV) in the TCGA.
Significance In treatment naive patients, our results suggest TIL recruitment and cytolytic activity are essentially driven by tumor neoepitopes, regardless of the presence of viral epitopes. We also find that tumor fitness does not predict patient survival better than tumor mutation burden, unlike a simple measure of CYT.