Mitochondrial DNA mutations are associated with ulcerative colitis preneoplasia but tend to be negatively selected in cancer.

The role of mitochondrial DNA (mtDNA) mutations in cancer remains controversial. Ulcerative Colitis (UC) is an inflammatory bowel disease that increases the risk of colorectal cancer and involves mitochondrial dysfunction, making it an ideal model to study the role of mtDNA in tumorigenesis. Our goal was to comprehensively characterize mtDNA mutations in UC tumorigenesis using Duplex Sequencing, an ultra-accurate next generation sequencing method. We analyzed 46 colon biopsies from non-UC and UC patients with and without cancer, including biopsies at all stages of dysplastic progression. mtDNA was sequenced at a mean depth of 1,417x. Mutations were classified by mutant allele frequency: clonal >0.95, subclonal 0.01-0.95, and very low frequency (VLF)<0.01. We identified 208 clonal and subclonal mutations and 56,764 VLF mutations. Mutations were randomly distributed across the mitochondrial genome. Clonal and subclonal mutations increased in number and pathogenicity in early dysplasia, but decreased in number and pathogenicity in cancer. Most clonal, subclonal, and VLF mutations were C>T transitions in the heavy strand of mtDNA, which likely arise from DNA replication errors. A subset of VLF mutations were C>A transversions, which are probably due to oxidative damage. VLF transitions and indels were less abundant in the non D-loop region and decreased with progression. Our results indicate that mtDNA mutations are frequent in UC preneoplasia but negatively selected in cancers. Implications: While mitochondrial DNA mutations might contribute to early UC tumorigenesis, they appear to be selected against in cancer, suggesting that functional mitochondria might be required for malignant transformation in UC.