Mutation of mutator genes marks immunotherapy efficacy

Abstract Genomic instability is a hallmark of most cancers and presumably results from dysfunction of mutator genes. Yet methods to identify the complete catalogue of mutator genes in human and systematic investigations of their roles in cancer are lacking. Here we developed MutaGene to define genes associated with suppression of genomic instability and identified 1534 putative mutator genes based on the TCGA dataset. We observed that cancer patients with deficiency of mutator genes, in contrast to other genes in cancer pathways or DNA repair pathways, were coupled with strong immunogenicity, e.g., elevated neoantigen burden, immune infiltration, and expression of immune checkpoint inhibitors. The results suggest that patients with deficiency of mutator genes may be favorable candidates for immunotherapy due to their elevated mutation burden. We next integrated the mutator gene catalogue with data of cancer patients post immune checkpoint blockade treatment in the MSK-IMPACT cohort. We found that deficiency of mutator genes, particularly the ones suppressing insertion-deletion mutations, predicted strong anti-tumor effects of the immunotherapy and positive clinical outcomes. Taken together, the mutator genes identified in this study enabled fresh insights into genome instability and serve as robust biomarkers for cancer immunotherapy.