Mitochondrial DNA Mutation Analysis in Breast Cancer: Shifting From Germline Heteroplasmy Toward Homoplasmy in Tumors

Abstract

Studies have suggested a potential role of somatic mitochondrial mutations in cancer development. To analyze the landscape of somatic mitochondrial mutation in breast cancer and to determine whether mitochondrial DNA (mtDNA) mutational burden is correlated with overall survival (OS), we sequenced whole mtDNA from 92 matched-paired primary breast tumors and peripheral blood. A total of 324 germline variants and 173 somatic mutations were found in the tumors. The most common germline allele was 663G (12S), showing lower heteroplasmy levels in peripheral blood lymphocytes than in their matched tumors, even reaching homoplasmic status in several cases. The heteroplasmy load was higher in tumors than in their paired normal tissues. Somatic mtDNA mutations were found in 73.9% of breast tumors; 59% of these mutations were located in the coding region (66.7% non-synonymous and 33.3% synonymous). Although the CO1 gene presented the highest number of mutations, tRNA genes (T,C, and W), rRNA 12S, and CO1 and ATP6 exhibited the highest mutation rates. No specific mtDNA mutational profile was associated with molecular subtypes of breast cancer, and we found no correlation between mtDNA mutational burden and OS. Future investigations will provide insight into the molecular mechanisms through which mtDNA mutations and heteroplasmy shifting contribute to breast cancer development.

Keywords: breast cancer; haplogroups; heteroplasmy; mitochondrial DNA; molecular subtypes; mutations.

FIGURE 1

Distribution of nucleotide substitutions in the mitochondrial genome: the number of the substitution according to the base change in (A) tumor variants and (B) somatic mutations.

FIGURE 2

Mutant allele frequency (MAF) of the mitochondrial germline variants in matched peripheral blood–tumor tissues. Higher MAF variability was observed in breast tumors than in blood samples. The boxes show the MAF values for each variant. Red circles represent patients. These germline variants were detected from 4.3 to 19.6% of the analyzed population.

FIGURE 3

Genomic distribution of mitochondrial somatic mutations in breast tumors. A total of 173 somatic mutations were identified in breast tumors. (A) Number of somatic mutations by gene (color bars) and the mutation rate by gene (black continuous line). (B) Genomic position of mitochondrial somatic mutations. Each point corresponds to one mutation. (C) Mitochondrial genome map. Colors represent coding genes for protein complexes or non-coding regions (yellow, complex I; green, complex III; purple, complex VI; red, complex V; blue, tRNA; gray, rRNA; brown, D-Loop region).