Mutational signatures driven by epigenetic determinants stratify patients for therapeutic interventions in gastric cancer

DNA mismatch repair deficiency (dMMR) leads to increased mutation load, which in turn may impact anti-tumor immune responses and treatment effectiveness. Currently, there are different mutational signatures described in primary cancers that are associated with dMMR. Whether the somatic and epigenetic changes in MMR genes precede one or more dMMR signatures, and if so by which mechanism remains unknown. To investigate the relationship between these changes and dMMR signatures, we performed a de novo extraction of mutational signatures in a large cohort of 787 gastric cancer patients. We detected three dMMR-related signatures, one of which clearly discriminates tumors with MLH1 gene silencing caused by hyper-methylation within its promoter (AUC = 98%). We then demonstrate that samples with the highest exposures to signature share features related to better prognosis, encompassing clinical and molecular aspects, as well as altered immune infiltrate composition, predictive of a better response to immune checkpoint inhibitors. Overall, our analysis explored the impact of modifications in MMR-related genes on shaping specific mutational signatures and we provide evidence that patient classification based on mutational signature exposure can identify a group of patients with a good prognosis and who are potentially good candidates for immunotherapy.