Analysis and Characterization of Mitochondrial DNA Mutations in The Cancer Genome Atlas Hepatocellular Carcinoma Cohort

Hepatocellular carcinoma (HCC) is the most common primary hepatic malignancy and represents the second cause of cancer related death worldwide, characterized by high recurrence rates and poor survival, even when detected and treated at its early stages. Mitochondrial mutations have been known to play a role in carcinogenesis, but to date, few studies correctly prioritize and interpret the variants discovered. Thus, we aimed to identify and analyze the occurrence and clinical impact of mtDNA mutations in the HCC dataset from The Cancer Genome Atlas (TCGA) consortium - National Cancer Institute. Whole exome sequencing fastq files from 377 TCGA-HCC patients (paired tumor, non- tumor tissues) were processed to reconstruct the mtDNA genomes using the MToolBox automated pipeline. Pairwise comparison between blood/normal solid tissue and tumor was performed in order to identify the potentially germline and tumor-specific somatic mtDNA variants. Information regarding the variability and pathogenicity of the variants were obtained from HmtVar database. The assembly of the mitochondrial reads showed an adequate coverage and quality for 104 patients. Variants were classified as pathogenic based on the allele frequency and disease score using the HmtVar criteria. After discarding the germline variants used in haplogroup classification, fixing the heteroplasmic fraction (HF) at 0.4 and prioritizing the variants we found 13 pathogenic/likely-pathogenic missense mutations and three tRNA pathogenic mutations in tRNA genes. HCC tumors presented a total of 302 somatic variants. After applying the same criteria, we found 24 pathogenic mutations in 22 patients. The burden of pathogenic mtDNA mutations resulted associated with a poorer survival of these patients. We found 21% of HCC patients to harbor somatic pathogenic mtDNA mutations in their tumors. We found that these patients had a poorer survival than those harbouring non-pathogenic variants. mtDNA mutations could cause mitochondrial dysfunction and impact the prognosis and survival of HCC patients.