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Smith KK, Moreira JD, Wilson CR, Padera JO, Lamason AN, Xue L, Gopal DM, Flynn DB, Fetterman JL. A systematic review on the biochemical threshold of mitochondrial genetic variants. Genome Res 2024; 34:341-365. [PMID: 38627095 PMCID: PMC11067886 DOI: 10.1101/gr.278200.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 03/15/2024] [Indexed: 05/05/2024]
Abstract
Mitochondrial DNA (mtDNA) variants cause a range of diseases from severe pediatric syndromes to aging-related conditions. The percentage of mtDNA copies carrying a pathogenic variant, variant allele frequency (VAF), must reach a threshold before a biochemical defect occurs, termed the biochemical threshold. Whether the often-cited biochemical threshold of >60% VAF is similar across mtDNA variants and cell types is unclear. In our systematic review, we sought to identify the biochemical threshold of mtDNA variants in relation to VAF by human tissue/cell type. We used controlled vocabulary terms to identify articles measuring oxidative phosphorylation (OXPHOS) complex activities in relation to VAF. We identified 76 eligible publications, describing 69, 12, 16, and 49 cases for complexes I, III, IV, and V, respectively. Few studies evaluated OXPHOS activities in diverse tissue types, likely reflective of clinical access. A number of cases with similar VAFs for the same pathogenic variant had varying degrees of residual activity of the affected complex, alluding to the presence of modifying variants. Tissues and cells with VAFs <60% associated with low complex activities were described, suggesting the possibility of a biochemical threshold of <60%. Using Kendall rank correlation tests, the VAF of the m.8993T > G variant correlated with complex V activity in skeletal muscle (τ = -0.58, P = 0.01, n = 13); however, no correlation was observed in fibroblasts (P = 0.7, n = 9). Our systematic review highlights the need to investigate the biochemical threshold over a wider range of VAFs in disease-relevant cell types to better define the biochemical threshold for specific mtDNA variants.
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Affiliation(s)
- Karan K Smith
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - Jesse D Moreira
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
- Programs in Human Physiology, Department of Health Sciences, Boston University Sargent College, Boston, Massachusetts 02215, USA
| | - Callum R Wilson
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - June O Padera
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - Ashlee N Lamason
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - Liying Xue
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - Deepa M Gopal
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - David B Flynn
- Medical Sciences and Education, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA
| | - Jessica L Fetterman
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts 02118, USA;
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2
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Kim SJ, Miller B, Hartel NG, Ramirez R, Braniff RG, Leelaprachakul N, Huang A, Wang Y, Arpawong TE, Crimmins EM, Wang P, Sun X, Liu C, Levy D, Yen K, Petzinger GM, Graham NA, Jakowec MW, Cohen P. A naturally occurring variant of SHLP2 is a protective factor in Parkinson's disease. Mol Psychiatry 2024; 29:505-517. [PMID: 38167865 PMCID: PMC11116102 DOI: 10.1038/s41380-023-02344-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Mitochondrial DNA single nucleotide polymorphisms (mtSNPs) have been associated with a reduced risk of developing Parkinson's disease (PD), yet the underlying mechanisms remain elusive. In this study, we investigate the functional role of a PD-associated mtSNP that impacts the mitochondrial-derived peptide (MDP) Small Humanin-like Peptide 2 (SHLP2). We identify m.2158 T > C, a mtSNP associated with reduced PD risk, within the small open reading frame encoding SHLP2. This mtSNP results in an alternative form of SHLP2 (lysine 4 replaced with arginine; K4R). Using targeted mass spectrometry, we detect specific tryptic fragments of SHLP2 in neuronal cells and demonstrate its binding to mitochondrial complex 1. Notably, we observe that the K4R variant, associated with reduced PD risk, exhibits increased stability compared to WT SHLP2. Additionally, both WT and K4R SHLP2 show enhanced protection against mitochondrial dysfunction in in vitro experiments and confer protection against a PD-inducing toxin, a mitochondrial complex 1 inhibitor, in a mouse model. This study sheds light on the functional consequences of the m.2158 T > C mtSNP on SHLP2 and provides insights into the potential mechanisms by which this mtSNP may reduce the risk of PD.
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Affiliation(s)
- Su-Jeong Kim
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Brendan Miller
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Nicolas G Hartel
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA
| | - Ricardo Ramirez
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Regina Gonzalez Braniff
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Naphada Leelaprachakul
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Environmental Toxicology Program, Chulabhorn Graduate Institute, Bangkok, 10210, Thailand
| | - Amy Huang
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Yuzhu Wang
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Thalida Em Arpawong
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Eileen M Crimmins
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Penglong Wang
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xianbang Sun
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Chunyu Liu
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Daniel Levy
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Boston University's and National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Kelvin Yen
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Giselle M Petzinger
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Nicholas A Graham
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Michael W Jakowec
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
- Department of Biokinesiology and Physical Therapy, The George and MaryLou Boone Center for Parkinson's Disease Research, University of Southern California, Los Angeles, CA, USA
| | - Pinchas Cohen
- The Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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3
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Sun X, Bulekova K, Yang J, Lai M, Pitsillides AN, Liu X, Zhang Y, Guo X, Yong Q, Raffield LM, Rotter JI, Rich SS, Abecasis G, Carson AP, Vasan RS, Bis JC, Psaty BM, Boerwinkle E, Fitzpatrick AL, Satizabal CL, Arking DE, Ding J, Levy D, Liu C. Association analysis of mitochondrial DNA heteroplasmic variants: methods and application. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.12.24301233. [PMID: 38260412 PMCID: PMC10802757 DOI: 10.1101/2024.01.12.24301233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
We rigorously assessed a comprehensive association testing framework for heteroplasmy, employing both simulated and real-world data. This framework employed a variant allele fraction (VAF) threshold and harnessed multiple gene-based tests for robust identification and association testing of heteroplasmy. Our simulation studies demonstrated that gene-based tests maintained an appropriate type I error rate at α=0.001. Notably, when 5% or more heteroplasmic variants within a target region were linked to an outcome, burden-extension tests (including the adaptive burden test, variable threshold burden test, and z-score weighting burden test) outperformed the sequence kernel association test (SKAT) and the original burden test. Applying this framework, we conducted association analyses on whole-blood derived heteroplasmy in 17,507 individuals of African and European ancestries (31% of African Ancestry, mean age of 62, with 58% women) with whole genome sequencing data. We performed both cohort- and ancestry-specific association analyses, followed by meta-analysis on both pooled samples and within each ancestry group. Our results suggest that mtDNA-encoded genes/regions are likely to exhibit varying rates in somatic aging, with the notably strong associations observed between heteroplasmy in the RNR1 and RNR2 genes (p<0.001) and advance aging by the Original Burden test. In contrast, SKAT identified significant associations (p<0.001) between diabetes and the aggregated effects of heteroplasmy in several protein-coding genes. Further research is warranted to validate these findings. In summary, our proposed statistical framework represents a valuable tool for facilitating association testing of heteroplasmy with disease traits in large human populations.
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Affiliation(s)
- Xianbang Sun
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Katia Bulekova
- Research Computing Services, Boston University, Boston, MA 02215, USA
| | - Jian Yang
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Meng Lai
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | | | - Xue Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Yuankai Zhang
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Qian Yong
- Longitudinal Studies Section, Translational Gerontology Branch, NIA/NIH, Baltimore, MD 21224, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jerome 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 90502, USA
| | - Stephen S. Rich
- Department of Public Health Services, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Goncalo Abecasis
- TOPMed Informatics Research Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Ramachandran S. Vasan
- Sections of Preventive Medicine and Epidemiology, and Cardiovascular Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- Framingham Heart Study, NHLBI/NIH, Framingham, MA 01702, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Departments of Epidemiology, and Health Services, University of Washington, Seattle, WA 98101, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Annette L. Fitzpatrick
- Departments of Family Medicine, Epidemiology, and Global Health, University of Washington, Seattle, WA 98195, USA
| | - Claudia L. Satizabal
- Framingham Heart Study, NHLBI/NIH, Framingham, MA 01702, USA
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Dan E. Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, MD 21205, USA
| | - Jun Ding
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Daniel Levy
- Framingham Heart Study, NHLBI/NIH, Framingham, MA 01702, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA 02118, USA
- Framingham Heart Study, NHLBI/NIH, Framingham, MA 01702, USA
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4
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Hong YS, Battle SL, Shi W, Puiu D, Pillalamarri V, Xie J, Pankratz N, Lake NJ, Lek M, Rotter JI, Rich SS, Kooperberg C, Reiner AP, Auer PL, Heard-Costa N, Liu C, Lai M, Murabito JM, Levy D, Grove ML, Alonso A, Gibbs R, Dugan-Perez S, Gondek LP, Guallar E, Arking DE. Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality. Nat Commun 2023; 14:6113. [PMID: 37777527 PMCID: PMC10542802 DOI: 10.1038/s41467-023-41785-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 09/14/2023] [Indexed: 10/02/2023] Open
Abstract
Mitochondria carry their own circular genome and disruption of the mitochondrial genome is associated with various aging-related diseases. Unlike the nuclear genome, mitochondrial DNA (mtDNA) can be present at 1000 s to 10,000 s copies in somatic cells and variants may exist in a state of heteroplasmy, where only a fraction of the DNA molecules harbors a particular variant. We quantify mtDNA heteroplasmy in 194,871 participants in the UK Biobank and find that heteroplasmy is associated with a 1.5-fold increased risk of all-cause mortality. Additionally, we functionally characterize mtDNA single nucleotide variants (SNVs) using a constraint-based score, mitochondrial local constraint score sum (MSS) and find it associated with all-cause mortality, and with the prevalence and incidence of cancer and cancer-related mortality, particularly leukemia. These results indicate that mitochondria may have a functional role in certain cancers, and mitochondrial heteroplasmic SNVs may serve as a prognostic marker for cancer, especially for leukemia.
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Affiliation(s)
- Yun Soo Hong
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Stephanie L Battle
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Natural Sciences, College of Arts and Sciences, Bowie State University, Bowie, MD, USA
| | - Wen Shi
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniela Puiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Vamsee Pillalamarri
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jiaqi Xie
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, VIC, Australia
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Jerome 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
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health & Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Nancy Heard-Costa
- Departments of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Chunyu Liu
- Framingham Heart Study, Framingham, MA, USA
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Meng Lai
- Department of Biostatistics, School of Public Health, Boston University, Boston, MA, USA
| | - Joanne M Murabito
- Section of General Internal Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Daniel Levy
- National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Megan L Grove
- Human Genetics Center; Department of Epidemiology, Human Genetics, and Environmental Sciences; School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Richard Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Shannon Dugan-Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Lukasz P Gondek
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Eliseo Guallar
- Department of Epidemiology and Medicine, and Welch Center for Prevention, Epidemiology, and Clinical Research, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Dan E Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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5
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Moreira JD, Gopal DM, Kotton DN, Fetterman JL. Gaining Insight into Mitochondrial Genetic Variation and Downstream Pathophysiology: What Can i(PSCs) Do? Genes (Basel) 2021; 12:1668. [PMID: 34828274 PMCID: PMC8624338 DOI: 10.3390/genes12111668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized organelles involved in energy production that have retained their own genome throughout evolutionary history. The mitochondrial genome (mtDNA) is maternally inherited and requires coordinated regulation with nuclear genes to produce functional enzyme complexes that drive energy production. Each mitochondrion contains 5-10 copies of mtDNA and consequently, each cell has several hundreds to thousands of mtDNAs. Due to the presence of multiple copies of mtDNA in a mitochondrion, mtDNAs with different variants may co-exist, a condition called heteroplasmy. Heteroplasmic variants can be clonally expanded, even in post-mitotic cells, as replication of mtDNA is not tied to the cell-division cycle. Heteroplasmic variants can also segregate during germ cell formation, underlying the inheritance of some mitochondrial mutations. Moreover, the uneven segregation of heteroplasmic variants is thought to underlie the heterogeneity of mitochondrial variation across adult tissues and resultant differences in the clinical presentation of mitochondrial disease. Until recently, however, the mechanisms mediating the relation between mitochondrial genetic variation and disease remained a mystery, largely due to difficulties in modeling human mitochondrial genetic variation and diseases. The advent of induced pluripotent stem cells (iPSCs) and targeted gene editing of the nuclear, and more recently mitochondrial, genomes now provides the ability to dissect how genetic variation in mitochondrial genes alter cellular function across a variety of human tissue types. This review will examine the origins of mitochondrial heteroplasmic variation and propagation, and the tools used to model mitochondrial genetic diseases. Additionally, we discuss how iPSC technologies represent an opportunity to advance our understanding of human mitochondrial genetics in disease.
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Affiliation(s)
- Jesse D. Moreira
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
| | - Deepa M. Gopal
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
- Cardiovascular Medicine Section, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Boston Medical Center, Center for Regenerative Medicine of Boston University, Boston, MA 02118, USA;
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jessica L. Fetterman
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
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