Mitochondrial heteroplasmy improves risk prediction for myeloid neoplasms

The most well-known pathogenic risk factor for myeloid neoplasms (MN) is clonal hematopoiesis of indeterminate potential (CHIP). However, MN can develop in CHIP negative individuals, indicating that additional markers of clonal expansion might also be informative. Heteroplasmy, defined as the presence of mitochondrial DNA (mtDNA) mutations in a subset of cellular mtDNA, has been associated with hematological malignancies and could represent a marker of clonal expansion. However, the relationship between heteroplamsy and CHIP, as well as its association with the incidence of MN in the general population is not known. In this study, we explored the association between somatic mtDNA and nuclear DNA (nDNA) mutations (mito-nuclear interaction), its impact on MN incidence, and whether its inclusion to the latest CHIP-based MN prediction algorithm could improve risk stratification in over 440,000 participants in the UK Biobank and Atherosclerosis Risk in Communities (ARIC) studies. We found that heteroplasmy count and heteroplasmic variants predicted to be more deleterious were enriched in individuals with CHIP, particularly in those with significantly expanded clones (VAF ≥20%), with more than one CHIP mutation, and with mutations in the spliceosome machinery. Individuals with both heteroplasmy and CHIP were more likely to develop MN than participants with either entity alone. Furthermore, we found a significant and independent association of predicted pathogenic effect of heteroplasmic variants with incident MN, suggesting a causal role of mtDNA variations in MN pathogenesis, even in the absence of CHIP. Finally, incorporating heteroplasmy into an existing risk score model for MN in individuals with CHIP significantly improved the sensitivity by 13.1% and identified 34.4% more cases in the high-risk group (10-year risk ≥10%). In sum, our findings suggest that heteroplasmy, in addition to being a marker of clonal expansion, may be a causal biomarker of MN development, with clinical utility in the general population. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was conducted using the UK Biobank Resource under Application Number 17731. This work was supported by National Heart, Lung and Blood Institute, National Institutes of Health (NIH) grants R01HL144569 (D.E.A) and NHLBI: R01HL156144 (L.P.G.). The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. ARIC Funding: The Atherosclerosis Risk in Communities study has been funded in whole or in part with Federal funds from the National Heart, Lung, and Blood Institute, National Institutes of Health, Department of Health and Human Services, under Contract nos. (75N92022D00001, 75N92022D00002, 75N92022D00003, 75N92022D00004, 75N92022D00005). Studies on cancer in ARIC are also supported by the National Cancer Institute (U01 CA164975, P01CA265748). Building on GWAS for NHLBI-diseases: the U.S. CHARGE consortium was provided by the NIH through the American Recovery and Reinvestment Act of 2009 (ARRA) (5RC2HL102419). Sequencing was carried out at the Baylor College of Medicine Human Genome Sequencing Center (U54 HG003273 and R01HL086694). The content of this work is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. ### 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: The current study was approved by the Johns Hopkins Medicine Institutional Review Boards. 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 UK Biobank data is available through application to the UK Biobank (Application Number 17731). ARIC WGS is available through dbGap accesstion number phs001211. Due to restrictions based on privacy regulations and informed consent of the participants, data cannot be made freely available in a public repository. Research data requests can be submitted to steering committee, which will be promptly reviewed for confidentiality or intellectual property restrictions and will not unreasonably be refused.