Somatic mitochondrial DNA mutations are a source of heterogeneity among primary leukemic cells

Summary Somatic mitochondrial DNA (mtDNA) mutations are prevalent in tumors, yet defining their biological significance remains challenging due to the intricate interplay between selective pressure, heteroplasmy, and cell state. Utilizing bulk whole-genome sequencing data from matched tumor and normal samples from two cohorts of pediatric cancer patients, we uncover differences in the accumulation of synonymous and nonsynonymous mtDNA mutations in pediatric leukemias, indicating distinct selective pressures. By integrating single-cell sequencing (SCS) with mathematical modeling and network-based systems biology approaches, we identify a correlation between the extent of cell-state changes associated with tumor-enriched mtDNA mutations and the selective pressures shaping their distribution among individual leukemic cells. Our findings also reveal an association between specific heteroplasmic mtDNA mutations and cellular responses that may contribute to functional heterogeneity among leukemic cells and influence their fitness. This study highlights the potential of SCS strategies for distinguishing between pathogenic and passenger somatic mtDNA mutations in cancer. Highlights Nonsynonymous and synonymous mtDNA SNVs are subject to different selective pressures among pediatric leukemias The distribution of mtDNA SNV VAFs among individual leukemic cells can provide evidence for selective pressure The impact of mtDNA SNVs on gene expression is correlated with selective pressure Somatic mtDNA SNVs associated with cell state changes are a source of heterogeneity among leukemic cells Competing Interest Statement The authors have declared no competing interest. Funding Statement This study was funded by NIH R01GM132231, NIH R01GM134382, NIH R01CA36401, NIH P50GM115279, NIH U01 GM92666, and NIH CA21765 Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: St. Jude Institutional Review Board of St. Jude Children's Research Hospital gave ethical approval for the work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data Availability PCGP WGS and RNA-seq datasets are available through St. Jude Cloud (https://platform.stjude.cloud/data/cohorts), accession code SJC-DS-1001. Datasets from WGS of Chinese pediatric relapse tumors may be obtained from the corresponding author of Li et al., and WGS of relapsed PCGP genomes may be accessed from the European Genome-Phenome Archive (accession code EGAS00001003975). RNA-seq datasets used for PSP analysis can be found at the Gene Expression Omnibus (GEO) under accession codes GSE115525 and GSE124824. Otherwise, data in present work contained within manuscript. https://platform.stjude.cloud/data/cohorts