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Longchamps RJ, Yang SY, Castellani CA, Shi W, Lane J, Grove ML, Bartz TM, Sarnowski C, Liu C, Burrows K, Guyatt AL, Gaunt TR, Kacprowski T, Yang J, De Jager PL, Yu L, Bergman A, Xia R, Fornage M, Feitosa MF, Wojczynski MK, Kraja AT, Province MA, Amin N, Rivadeneira F, Tiemeier H, Uitterlinden AG, Broer L, Van Meurs JBJ, Van Duijn CM, Raffield LM, Lange L, Rich SS, Lemaitre RN, Goodarzi MO, Sitlani CM, Mak ACY, Bennett DA, Rodriguez S, Murabito JM, Lunetta KL, Sotoodehnia N, Atzmon G, Ye K, Barzilai N, Brody JA, Psaty BM, Taylor KD, Rotter JI, Boerwinkle E, Pankratz N, Arking DE. Genome-wide analysis of mitochondrial DNA copy number reveals loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation. Hum Genet 2022; 141:127-146. [PMID: 34859289 PMCID: PMC8758627 DOI: 10.1007/s00439-021-02394-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
Mitochondrial DNA copy number (mtDNA-CN) measured from blood specimens is a minimally invasive marker of mitochondrial function that exhibits both inter-individual and intercellular variation. To identify genes involved in regulating mitochondrial function, we performed a genome-wide association study (GWAS) in 465,809 White individuals from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the UK Biobank (UKB). We identified 133 SNPs with statistically significant, independent effects associated with mtDNA-CN across 100 loci. A combination of fine-mapping, variant annotation, and co-localization analyses was used to prioritize genes within each of the 133 independent sites. Putative causal genes were enriched for known mitochondrial DNA depletion syndromes (p = 3.09 × 10-15) and the gene ontology (GO) terms for mtDNA metabolism (p = 1.43 × 10-8) and mtDNA replication (p = 1.2 × 10-7). A clustering approach leveraged pleiotropy between mtDNA-CN associated SNPs and 41 mtDNA-CN associated phenotypes to identify functional domains, revealing three distinct groups, including platelet activation, megakaryocyte proliferation, and mtDNA metabolism. Finally, using mitochondrial SNPs, we establish causal relationships between mitochondrial function and a variety of blood cell-related traits, kidney function, liver function and overall (p = 0.044) and non-cancer mortality (p = 6.56 × 10-4).
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Affiliation(s)
- R J Longchamps
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Y Yang
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - C A Castellani
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - W Shi
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - J Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - M L Grove
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - T M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - C Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - C Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - K Burrows
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - A L Guyatt
- Department of Health Sciences, University of Leicester, University Road, Leicester, UK
| | - T R Gaunt
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - T Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
- Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, TU Braunschweig and Hannover Medical School, Brunswick, Germany
| | - J Yang
- Rush Alzheimer's Disease Center and Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - P L De Jager
- Center for Translational and Systems Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - L Yu
- Rush Alzheimer's Disease Center and Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - A Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - R Xia
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - M Fornage
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, USA
| | - M F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, USA
| | - M K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, USA
| | - A T Kraja
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, USA
| | - M A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, USA
| | - N Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - F Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - H Tiemeier
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Social and Behavioral Science, Harvard T.H. School of Public Health, Boston, USA
| | - A G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - L Broer
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - J B J Van Meurs
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - C M Van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - L M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - L Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - S S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R N Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - M O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - C M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - A C Y Mak
- Cardiovascular Research Institute and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - D A Bennett
- Rush Alzheimer's Disease Center and Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - S Rodriguez
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - J M Murabito
- Boston University School of Medicine, Boston University, Boston, MA, USA
| | - K L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - N Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, Seattle, WA, USA
| | - G Atzmon
- Department of Natural Science, University of Haifa, Haifa, Israel
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - K Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - N Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - J A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - B M Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, USA
| | - K D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - J I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - E Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, USA
| | - N Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - D E Arking
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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