Somatic pathogenic mitochondrial DNA mutations independently predict worse prognosis in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the deadliest cancers worldwide, but its cancerization and progression mechanisms are still poorly understood. Mitochondrial DNA (mtDNA) mutations have been involved in tumor progression by influencing metabolic rewiring and plasticity. In this work, we aimed to investigate the contribution of mtDNA mutations to the pathogenesis and prognosis of HCC. Whole exome sequencing data from the TCGA-LIHC project were used to reconstruct the mitochondrial genomes. Discovered variants were classified using the HmtVar pathogenicity scoring system and the ACMG/AMP standard guidelines. The validation of results was performed on a separate in-house cohort of selected HCC cases from our hospital. Pathogenic mtDNA mutations were present in 33.6% of patients. GSEA revealed pathogenic mtDNA mutations mainly targeting the reactive oxygen species (ROS) pathway, suggesting an increased ROS production in these tumors which may contribute to the survival, proliferation and metastatization capacity. Survival analysis revealed a significant decrease in the overall survival of patients harboring pathogenic mtDNA variants (p = 0.01). A similar trend was observed in the validation cohort. Overall, we showed that somatic mtDNA mutations occur in a significant proportion of HCC cases, expectedly acting as modifiers on the ROS pathway, and that their occurrence confers a worse prognosis.