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Bury A, Pyle A, Vincent AE, Actis P, Hudson G. Nanobiopsy investigation of the subcellular mtDNA heteroplasmy in human tissues. Sci Rep 2024; 14:13789. [PMID: 38877095 PMCID: PMC11178779 DOI: 10.1038/s41598-024-64455-0] [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: 06/22/2023] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Mitochondrial function is critical to continued cellular vitality and is an important contributor to a growing number of human diseases. Mitochondrial dysfunction is typically heterogeneous, mediated through the clonal expansion of mitochondrial DNA (mtDNA) variants in a subset of cells in a given tissue. To date, our understanding of the dynamics of clonal expansion of mtDNA variants has been technically limited to the single cell-level. Here, we report the use of nanobiopsy for subcellular sampling from human tissues, combined with next-generation sequencing to assess subcellular mtDNA mutation load in human tissue from mitochondrial disease patients. The ability to map mitochondrial mutation loads within individual cells of diseased tissue samples will further our understanding of mitochondrial genetic diseases.
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Affiliation(s)
- Alexander Bury
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK
- Bragg Centre for Materials Research, Leeds, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK.
- Bragg Centre for Materials Research, Leeds, UK.
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
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2
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Kim M, Gorelick AN, Vàzquez-García I, Williams MJ, Salehi S, Shi H, Weiner AC, Ceglia N, Funnell T, Park T, Boscenco S, O'Flanagan CH, Jiang H, Grewal D, Tang C, Rusk N, Gammage PA, McPherson A, Aparicio S, Shah SP, Reznik E. Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes. Nat Genet 2024; 56:889-899. [PMID: 38741018 PMCID: PMC11096122 DOI: 10.1038/s41588-024-01724-8] [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: 06/21/2022] [Accepted: 03/20/2024] [Indexed: 05/16/2024]
Abstract
The extent of cell-to-cell variation in tumor mitochondrial DNA (mtDNA) copy number and genotype, and the phenotypic and evolutionary consequences of such variation, are poorly characterized. Here we use amplification-free single-cell whole-genome sequencing (Direct Library Prep (DLP+)) to simultaneously assay mtDNA copy number and nuclear DNA (nuDNA) in 72,275 single cells derived from immortalized cell lines, patient-derived xenografts and primary human tumors. Cells typically contained thousands of mtDNA copies, but variation in mtDNA copy number was extensive and strongly associated with cell size. Pervasive whole-genome doubling events in nuDNA associated with stoichiometrically balanced adaptations in mtDNA copy number, implying that mtDNA-to-nuDNA ratio, rather than mtDNA copy number itself, mediated downstream phenotypes. Finally, multimodal analysis of DLP+ and single-cell RNA sequencing identified both somatic loss-of-function and germline noncoding variants in mtDNA linked to heteroplasmy-dependent changes in mtDNA copy number and mitochondrial transcription, revealing phenotypic adaptations to disrupted nuclear/mitochondrial balance.
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Affiliation(s)
- Minsoo Kim
- Tri-Institutional PhD Program in Computational Biology & Medicine, Weill Cornell Medicine, New York City, NY, USA
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Alexander N Gorelick
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Ignacio Vàzquez-García
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Sohrab Salehi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Hongyu Shi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Adam C Weiner
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Nick Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Tyler Funnell
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Tricia Park
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Sonia Boscenco
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Ciara H O'Flanagan
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Hui Jiang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Diljot Grewal
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Cerise Tang
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Payam A Gammage
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- CRUK Beatson Institute, Glasgow, UK
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Sam Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
| | - Ed Reznik
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
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3
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Mertens J, Belva F, van Montfoort APA, Regin M, Zambelli F, Seneca S, Couvreu de Deckersberg E, Bonduelle M, Tournaye H, Stouffs K, Barbé K, Smeets HJM, Van de Velde H, Sermon K, Blockeel C, Spits C. Children born after assisted reproduction more commonly carry a mitochondrial genotype associating with low birthweight. Nat Commun 2024; 15:1232. [PMID: 38336715 PMCID: PMC10858059 DOI: 10.1038/s41467-024-45446-1] [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: 12/10/2022] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Children conceived through assisted reproductive technologies (ART) have an elevated risk of lower birthweight, yet the underlying cause remains unclear. Our study explores mitochondrial DNA (mtDNA) variants as contributors to birthweight differences by impacting mitochondrial function during prenatal development. We deep-sequenced the mtDNA of 451 ART and spontaneously conceived (SC) individuals, 157 mother-child pairs and 113 individual oocytes from either natural menstrual cycles or after ovarian stimulation (OS) and find that ART individuals carried a different mtDNA genotype than SC individuals, with more de novo non-synonymous variants. These variants, along with rRNA variants, correlate with lower birthweight percentiles, independent of conception mode. Their higher occurrence in ART individuals stems from de novo mutagenesis associated with maternal aging and OS-induced oocyte cohort size. Future research will establish the long-term health consequences of these changes and how these findings will impact the clinical practice and patient counselling in the future.
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Affiliation(s)
- Joke Mertens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Florence Belva
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Aafke P A van Montfoort
- Department of Obstetrics & Gynaecology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marius Regin
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Sara Seneca
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Herman Tournaye
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Research Group Biology of the Testis, Faculty of Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Katrien Stouffs
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Kurt Barbé
- Interfaculty Center Data Processing & Statistics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hubert J M Smeets
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
- MHeNs School Institute for Mental Health and Neuroscience, GROW Institute for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Hilde Van de Velde
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Research Group Reproduction and Immunology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Christophe Blockeel
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Department of Obstetrics and Gynaecology, School of Medicine, University of Zagreb, Šalata 3, Zagreb, 10000, Croatia
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium.
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Ali MA, Gioscia-Ryan R, Yang D, Sutton NR, Tyrrell DJ. Cardiovascular aging: spotlight on mitochondria. Am J Physiol Heart Circ Physiol 2024; 326:H317-H333. [PMID: 38038719 PMCID: PMC11219063 DOI: 10.1152/ajpheart.00632.2023] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/02/2023]
Abstract
Mitochondria are cellular organelles critical for ATP production and are particularly relevant to cardiovascular diseases including heart failure, atherosclerosis, ischemia-reperfusion injury, and cardiomyopathies. With advancing age, even in the absence of clinical disease, mitochondrial homeostasis becomes disrupted (e.g., redox balance, mitochondrial DNA damage, oxidative metabolism, and mitochondrial quality control). Mitochondrial dysregulation leads to the accumulation of damaged and dysfunctional mitochondria, producing excessive reactive oxygen species and perpetuating mitochondrial dysfunction. In addition, mitochondrial DNA, cardiolipin, and N-formyl peptides are potent activators of cell-intrinsic and -extrinsic inflammatory pathways. These age-related mitochondrial changes contribute to the development of cardiovascular diseases. This review covers the impact of aging on mitochondria and links these mechanisms to therapeutic implications for age-associated cardiovascular diseases.
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Affiliation(s)
- Md Akkas Ali
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Rachel Gioscia-Ryan
- Department of Anesthesiology, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, United States
| | - Dongli Yang
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
| | - Nadia R Sutton
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee, United States
| | - Daniel J Tyrrell
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States
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Meshrkey F, Scheulin KM, Littlejohn CM, Stabach J, Saikia B, Thorat V, Huang Y, LaFramboise T, Lesnefsky EJ, Rao RR, West FD, Iyer S. Induced pluripotent stem cells derived from patients carrying mitochondrial mutations exhibit altered bioenergetics and aberrant differentiation potential. Stem Cell Res Ther 2023; 14:320. [PMID: 37936209 PMCID: PMC10631039 DOI: 10.1186/s13287-023-03546-7] [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: 05/17/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Human mitochondrial DNA mutations are associated with common to rare mitochondrial disorders, which are multisystemic with complex clinical pathologies. The pathologies of these diseases are poorly understood and have no FDA-approved treatments leading to symptom management. Leigh syndrome (LS) is a pediatric mitochondrial disorder that affects the central nervous system during early development and causes death in infancy. Since there are no adequate models for understanding the rapid fatality associated with LS, human-induced pluripotent stem cell (hiPSC) technology has been recognized as a useful approach to generate patient-specific stem cells for disease modeling and understanding the origins of the phenotype. METHODS hiPSCs were generated from control BJ and four disease fibroblast lines using a cocktail of non-modified reprogramming and immune evasion mRNAs and microRNAs. Expression of hiPSC-associated intracellular and cell surface markers was identified by immunofluorescence and flow cytometry. Karyotyping of hiPSCs was performed with cytogenetic analysis. Sanger and next-generation sequencing were used to detect and quantify the mutation in all hiPSCs. The mitochondrial respiration ability and glycolytic function were measured by the Seahorse Bioscience XFe96 extracellular flux analyzer. RESULTS Reprogrammed hiPSCs expressed pluripotent stem cell markers including transcription factors POU5F1, NANOG and SOX2 and cell surface markers SSEA4, TRA-1-60 and TRA-1-81 at the protein level. Sanger sequencing analysis confirmed the presence of mutations in all reprogrammed hiPSCs. Next-generation sequencing demonstrated the variable presence of mutant mtDNA in reprogrammed hiPSCs. Cytogenetic analyses confirmed the presence of normal karyotype in all reprogrammed hiPSCs. Patient-derived hiPSCs demonstrated decreased maximal mitochondrial respiration, while mitochondrial ATP production was not significantly different between the control and disease hiPSCs. In line with low maximal respiration, the spare respiratory capacity was lower in all the disease hiPSCs. The hiPSCs also demonstrated neural and cardiac differentiation potential. CONCLUSION Overall, the hiPSCs exhibited variable mitochondrial dysfunction that may alter their differentiation potential and provide key insights into clinically relevant developmental perturbations.
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Affiliation(s)
- Fibi Meshrkey
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
- Department of Histology and Cell Biology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Kelly M Scheulin
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
- Neuroscience Program, Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, USA
| | - Christopher M Littlejohn
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Joshua Stabach
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA
| | - Bibhuti Saikia
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA
| | - Vedant Thorat
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yimin Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Edward J Lesnefsky
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, USA
- Cardiology Section Medical Service, McGuire Veterans Affairs Medical Center, Richmond, VA, USA
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, USA
- Division of Cardiology, Department of Internal Medicine, Pauley Heart Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Raj R Rao
- Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Franklin D West
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
- Neuroscience Program, Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, USA
| | - Shilpa Iyer
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA.
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA.
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Arabshomali A, Bazzazzadehgan S, Mahdi F, Shariat-Madar Z. Potential Benefits of Antioxidant Phytochemicals in Type 2 Diabetes. Molecules 2023; 28:7209. [PMID: 37894687 PMCID: PMC10609456 DOI: 10.3390/molecules28207209] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
The clinical relationship between diabetes and inflammation is well established. Evidence clearly indicates that disrupting oxidant-antioxidant equilibrium and elevated lipid peroxidation could be a potential mechanism for chronic kidney disease associated with type 2 diabetes mellitus (T2DM). Under diabetic conditions, hyperglycemia, especially inflammation, and increased reactive oxygen species generation are bidirectionally associated. Inflammation, oxidative stress, and tissue damage are believed to play a role in the development of diabetes. Although the exact mechanism underlying oxidative stress and its impact on diabetes progression remains uncertain, the hyperglycemia-inflammation-oxidative stress interaction clearly plays a significant role in the onset and progression of vascular disease, kidney disease, hepatic injury, and pancreas damage and, therefore, holds promise as a therapeutic target. Evidence strongly indicates that the use of multiple antidiabetic medications fails to achieve the normal range for glycated hemoglobin targets, signifying treatment-resistant diabetes. Antioxidants with polyphenols are considered useful as adjuvant therapy for their potential anti-inflammatory effect and antioxidant activity. We aimed to analyze the current major points reported in preclinical, in vivo, and clinical studies of antioxidants in the prevention or treatment of inflammation in T2DM. Then, we will share our speculative vision for future diabetes clinical trials.
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Affiliation(s)
- Arman Arabshomali
- Department of Pharmacy Administration, School of Pharmacy, University of Mississippi, University, MS 38677, USA; (A.A.); (S.B.)
| | - Shadi Bazzazzadehgan
- Department of Pharmacy Administration, School of Pharmacy, University of Mississippi, University, MS 38677, USA; (A.A.); (S.B.)
| | - Fakhri Mahdi
- Department of BioMolecular Sciences, Division of Pharmacology, School of Pharmacy, University of Mississippi, University, MS 38677, USA;
| | - Zia Shariat-Madar
- Department of BioMolecular Sciences, Division of Pharmacology, School of Pharmacy, University of Mississippi, University, MS 38677, USA;
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7
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Wang Y, Zhang X, Wang Z. Cellular barcoding: From developmental tracing to anti-tumor drug discovery. Cancer Lett 2023:216281. [PMID: 37336285 DOI: 10.1016/j.canlet.2023.216281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/31/2023] [Accepted: 06/10/2023] [Indexed: 06/21/2023]
Abstract
Clonal evolution has gained immense attention in explaining cancer cell status, history, and fate during cancer progression. Current single-cell or spatial transcriptome technologies have broadened our understanding of various mechanisms underlying cancer initiation, relapse, and drug resistance. However, technical challenges still hinder a better understanding of the dynamics of distinctive phenotypic states and abnormal trajectories from normal physiological transition to malignant stages. Cellular barcoding enabled lineage tracing on parallelly massive cells at single-cell resolution through different mechanisms lately, enabling new insights into exploring developmental trajectories, cancer progression, and targeted therapies. This review summarizes the latest noteworthy and robust strategies for different types of cellular barcodes. To introduce the major characteristics, advantages and limitations of these different strategies, this review will further guide in choosing or improving cellular barcoding technologies and their applications in cancer research.
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Affiliation(s)
- Yuqing Wang
- Medical Center of Hematology, The Second Affiliated Hospital, Army Medical University, Chongqing, 40037, China; State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 40037, China
| | - Xi Zhang
- Medical Center of Hematology, The Second Affiliated Hospital, Army Medical University, Chongqing, 40037, China; State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 40037, China; Jinfeng Laboratory, Chongqing, 401329, China.
| | - Zheng Wang
- Medical Center of Hematology, The Second Affiliated Hospital, Army Medical University, Chongqing, 40037, China; State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, Chongqing, 40037, China; Bio-Med Informatics Research Center & Clinical Research Center, The Second Affiliated Hospital, Army Medical University, Chongqing, 400037, China; Jinfeng Laboratory, Chongqing, 401329, China.
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8
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Witte S, Boshnakovska A, Özdemir M, Chowdhury A, Rehling P, Aich A. Defective COX1 expression in aging mice liver. Biol Open 2023; 12:292575. [PMID: 36861685 PMCID: PMC10003073 DOI: 10.1242/bio.059844] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 03/03/2023] Open
Abstract
Mitochondrial defects are associated with aging processes and age-related diseases, including cardiovascular diseases, neurodegenerative diseases and cancer. In addition, some recent studies suggest mild mitochondrial dysfunctions appear to be associated with longer lifespans. In this context, liver tissue is considered to be largely resilient to aging and mitochondrial dysfunction. Yet, in recent years studies report dysregulation of mitochondrial function and nutrient sensing pathways in ageing livers. Therefore, we analyzed the effects of the aging process on mitochondrial gene expression in liver using wildtype C57BL/6N mice. In our analyses, we observed alteration in mitochondrial energy metabolism with age. To assess if defects in mitochondrial gene expression are linked to this decline, we applied a Nanopore sequencing based approach for mitochondrial transcriptomics. Our analyses show that a decrease of the Cox1 transcript correlates with reduced respiratory complex IV activity in older mice livers.
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Affiliation(s)
- Steffen Witte
- Department of Cellular Biochemistry, University Medical Center, Göttingen, 37073, Germany
| | - Angela Boshnakovska
- Department of Cellular Biochemistry, University Medical Center, Göttingen, 37073, Germany
| | - Metin Özdemir
- Department of Cellular Biochemistry, University Medical Center, Göttingen, 37073, Germany
| | - Arpita Chowdhury
- Department of Cellular Biochemistry, University Medical Center, Göttingen, 37073, Germany
| | - Peter Rehling
- Department of Cellular Biochemistry, University Medical Center, Göttingen, 37073, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, 37075, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy, Göttingen, 37075, Germany.,Max Planck Institute for Multidisciplinary Sciences, Göttingen, 37077, Germany
| | - Abhishek Aich
- Department of Cellular Biochemistry, University Medical Center, Göttingen, 37073, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, 37075, Germany
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9
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Metabolic landscape in cardiac aging: insights into molecular biology and therapeutic implications. Signal Transduct Target Ther 2023; 8:114. [PMID: 36918543 PMCID: PMC10015017 DOI: 10.1038/s41392-023-01378-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
Cardiac aging is evident by a reduction in function which subsequently contributes to heart failure. The metabolic microenvironment has been identified as a hallmark of malignancy, but recent studies have shed light on its role in cardiovascular diseases (CVDs). Various metabolic pathways in cardiomyocytes and noncardiomyocytes determine cellular senescence in the aging heart. Metabolic alteration is a common process throughout cardiac degeneration. Importantly, the involvement of cellular senescence in cardiac injuries, including heart failure and myocardial ischemia and infarction, has been reported. However, metabolic complexity among human aging hearts hinders the development of strategies that targets metabolic susceptibility. Advances over the past decade have linked cellular senescence and function with their metabolic reprogramming pathway in cardiac aging, including autophagy, oxidative stress, epigenetic modifications, chronic inflammation, and myocyte systolic phenotype regulation. In addition, metabolic status is involved in crucial aspects of myocardial biology, from fibrosis to hypertrophy and chronic inflammation. However, further elucidation of the metabolism involvement in cardiac degeneration is still needed. Thus, deciphering the mechanisms underlying how metabolic reprogramming impacts cardiac aging is thought to contribute to the novel interventions to protect or even restore cardiac function in aging hearts. Here, we summarize emerging concepts about metabolic landscapes of cardiac aging, with specific focuses on why metabolic profile alters during cardiac degeneration and how we could utilize the current knowledge to improve the management of cardiac aging.
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10
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Sanchez-Contreras M, Sweetwyne MT, Tsantilas KA, Whitson JA, Campbell MD, Kohrn BF, Kim HJ, Hipp MJ, Fredrickson J, Nguyen MM, Hurley JB, Marcinek DJ, Rabinovitch PS, Kennedy SR. The multi-tissue landscape of somatic mtDNA mutations indicates tissue-specific accumulation and removal in aging. eLife 2023; 12:e83395. [PMID: 36799304 PMCID: PMC10072880 DOI: 10.7554/elife.83395] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Accumulation of somatic mutations in the mitochondrial genome (mtDNA) has long been proposed as a possible mechanism of mitochondrial and tissue dysfunction that occurs during aging. A thorough characterization of age-associated mtDNA somatic mutations has been hampered by the limited ability to detect low-frequency mutations. Here, we used Duplex Sequencing on eight tissues of an aged mouse cohort to detect >89,000 independent somatic mtDNA mutations and show significant tissue-specific increases during aging across all tissues examined which did not correlate with mitochondrial content and tissue function. G→A/C→T substitutions, indicative of replication errors and/or cytidine deamination, were the predominant mutation type across all tissues and increased with age, whereas G→T/C→A substitutions, indicative of oxidative damage, were the second most common mutation type, but did not increase with age regardless of tissue. We also show that clonal expansions of mtDNA mutations with age is tissue- and mutation type-dependent. Unexpectedly, mutations associated with oxidative damage rarely formed clones in any tissue and were significantly reduced in the hearts and kidneys of aged mice treated at late age with elamipretide or nicotinamide mononucleotide. Thus, the lack of accumulation of oxidative damage-linked mutations with age suggests a life-long dynamic clearance of either the oxidative lesions or mtDNA genomes harboring oxidative damage.
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Affiliation(s)
| | - Mariya T Sweetwyne
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | | | - Jeremy A Whitson
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | | | - Brenden F Kohrn
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Hyeon Jeong Kim
- Department of Biology, University of WashingtonSeattleUnited States
| | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Jeanne Fredrickson
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Megan M Nguyen
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - James B Hurley
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - David J Marcinek
- Department of Radiology, University of WashingtonSeattleUnited States
| | - Peter S Rabinovitch
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
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11
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Whitehall JC, Smith ALM, Greaves LC. Mitochondrial DNA Mutations and Ageing. Subcell Biochem 2023; 102:77-98. [PMID: 36600130 DOI: 10.1007/978-3-031-21410-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mitochondria are subcellular organelles present in most eukaryotic cells which play a significant role in numerous aspects of cell biology. These include carbohydrate and fatty acid metabolism to generate cellular energy through oxidative phosphorylation, apoptosis, cell signalling, haem biosynthesis and reactive oxygen species production. Mitochondrial dysfunction is a feature of many human ageing tissues, and since the discovery that mitochondrial DNA mutations were a major underlying cause of changes in oxidative phosphorylation capacity, it has been proposed that they have a role in human ageing. However, there is still much debate on whether mitochondrial DNA mutations play a causal role in ageing or are simply a consequence of the ageing process. This chapter describes the structure of mammalian mitochondria, and the unique features of mitochondrial genetics, and reviews the current evidence surrounding the role of mitochondrial DNA mutations in the ageing process. It then focusses on more recent discoveries regarding the role of mitochondrial dysfunction in stem cell ageing and age-related inflammation.
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Affiliation(s)
- Julia C Whitehall
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Anna L M Smith
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Laura C Greaves
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK.
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12
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Smith ALM, Whitehall JC, Greaves LC. Mitochondrial
DNA
mutations in aging and cancer. Mol Oncol 2022; 16:3276-3294. [PMID: 35842901 PMCID: PMC9490137 DOI: 10.1002/1878-0261.13291] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/18/2022] [Accepted: 07/15/2022] [Indexed: 11/09/2022] Open
Abstract
Advancing age is a major risk factor for malignant transformation and the development of cancer. As such, over 50% of neoplasms occur in individuals over the age of 70. The pathologies of both ageing and cancer have been characterized by respective groups of molecular hallmarks, and while some features are divergent between the two pathologies, several are shared. Perturbed mitochondrial function is one such common hallmark, and this observation therefore suggests that mitochondrial alterations may be of significance in age‐related cancer development. There is now considerable evidence documenting the accumulation of somatic mitochondrial DNA (mtDNA) mutations in ageing human postmitotic and replicative tissues. Similarly, mutations of the mitochondrial genome have been reported in human cancers for decades. The plethora of functions in which mitochondria partake, such as oxidative phosphorylation, redox balance, apoptosis and numerous biosynthetic pathways, manifests a variety of ways in which alterations in mtDNA may contribute to tumour growth. However, the specific mechanisms by which mtDNA mutations contribute to tumour progression remain elusive and often contradictory. This review aims to consolidate current knowledge and describe future direction within the field.
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Affiliation(s)
- Anna LM Smith
- Wellcome Centre for Mitochondrial Research, Biosciences Institute Newcastle University Newcastle Upon Tyne NE2 4HH UK
| | - Julia C Whitehall
- Wellcome Centre for Mitochondrial Research, Biosciences Institute Newcastle University Newcastle Upon Tyne NE2 4HH UK
| | - Laura C Greaves
- Wellcome Centre for Mitochondrial Research, Biosciences Institute Newcastle University Newcastle Upon Tyne NE2 4HH UK
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13
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Tong Y, Zhang Z, Wang S. Role of Mitochondria in Retinal Pigment Epithelial Aging and Degeneration. FRONTIERS IN AGING 2022; 3:926627. [PMID: 35912040 PMCID: PMC9337215 DOI: 10.3389/fragi.2022.926627] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/21/2022] [Indexed: 12/17/2022]
Abstract
Retinal pigment epithelial (RPE) cells form a monolayer between the neuroretina and choroid. It has multiple important functions, including acting as outer blood-retina barrier, maintaining the function of neuroretina and photoreceptors, participating in the visual cycle and regulating retinal immune response. Due to high oxidative stress environment, RPE cells are vulnerable to dysfunction, cellular senescence, and cell death, which underlies RPE aging and age-related diseases, including age-related macular degeneration (AMD). Mitochondria are the powerhouse of cells and a major source of cellular reactive oxygen species (ROS) that contribute to mitochondrial DNA damage, cell death, senescence, and age-related diseases. Mitochondria also undergo dynamic changes including fission/fusion, biogenesis and mitophagy for quality control in response to stresses. The role of mitochondria, especially mitochondrial dynamics, in RPE aging and age-related diseases, is still unclear. In this review, we summarize the current understanding of mitochondrial function, biogenesis and especially dynamics such as morphological changes and mitophagy in RPE aging and age-related RPE diseases, as well as in the biological processes of RPE cellular senescence and cell death. We also discuss the current preclinical and clinical research efforts to prevent or treat RPE degeneration by restoring mitochondrial function and dynamics.
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Affiliation(s)
- Yao Tong
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, United States
| | - Zunyi Zhang
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, United States
| | - Shusheng Wang
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, United States
- Department of Ophthalmology, Tulane University, New Orleans, LA, United States
- Tulane Personalized Health Institute, Tulane University, New Orleans, LA, United States
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14
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Long read mitochondrial genome sequencing using Cas9-guided adaptor ligation. Mitochondrion 2022; 65:176-183. [PMID: 35787470 DOI: 10.1016/j.mito.2022.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/11/2022] [Accepted: 06/19/2022] [Indexed: 11/21/2022]
Abstract
The mitochondrial genome (mtDNA) is an important source of disease-causing genetic variability, but existing sequencing methods limit understanding, precluding phased measurement of mutations and clear detection of large sporadic deletions. We adapted a method for amplification-free sequence enrichment using Cas9 cleavage to obtain full length nanopore reads of mtDNA. We then utilized the long reads to phase mutations in a patient with an mtDNA-linked syndrome and demonstrated that this method can map age-induced mtDNA deletions. We believe this method will offer deeper insight into our understanding of mtDNA variation.
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15
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Bakare AB, Dean J, Chen Q, Thorat V, Huang Y, LaFramboise T, Lesnefsky EJ, Iyer S. Evaluating the Bioenergetics Health Index Ratio in Leigh Syndrome Fibroblasts to Understand Disease Severity. Int J Mol Sci 2021; 22:ijms221910344. [PMID: 34638685 PMCID: PMC8508996 DOI: 10.3390/ijms221910344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 12/21/2022] Open
Abstract
Several pediatric mitochondrial disorders, including Leigh syndrome (LS), impact mitochondrial (mt) genetics, development, and metabolism, leading to complex pathologies and energy failure. The extent to which pathogenic mtDNA variants regulate disease severity in LS is currently not well understood. To better understand this relationship, we computed a glycolytic bioenergetics health index (BHI) for measuring mitochondrial dysfunction in LS patient fibroblast cells harboring varying percentages of pathogenic mutant mtDNA (T8993G, T9185C) exhibiting deficiency in complex V or complex I (T10158C, T12706C). A high percentage (>90%) of pathogenic mtDNA in cells affecting complex V and a low percentage (<39%) of pathogenic mtDNA in cells affecting complex I was quantified. Levels of defective enzyme activities of the electron transport chain correlated with the percentage of pathogenic mtDNA. Subsequent bioenergetics assays showed cell lines relied on both OXPHOS and glycolysis for meeting energy requirements. Results suggest that whereas the precise mechanism of LS has not been elucidated, a multi-pronged approach taking into consideration the specific pathogenic mtDNA variant, glycolytic BHI, and the composite BHI (average ratio of oxphos to glycolysis) can aid in better understanding the factors influencing disease severity in LS.
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Affiliation(s)
- Ajibola B. Bakare
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
| | - Joseph Dean
- Cardiology Section Medical Service, McGuire Veterans Affairs Medical Center, Richmond, VA 23284, USA; (J.D.); (E.J.L.)
| | - Qun Chen
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Vedant Thorat
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (V.T.); (Y.H.); (T.L.)
| | - Yimin Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (V.T.); (Y.H.); (T.L.)
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; (V.T.); (Y.H.); (T.L.)
| | - Edward J. Lesnefsky
- Cardiology Section Medical Service, McGuire Veterans Affairs Medical Center, Richmond, VA 23284, USA; (J.D.); (E.J.L.)
- Pauley Heart Center, Division of Cardiology, Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Shilpa Iyer
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR 72701, USA
- Correspondence: ; Tel.: +1-(479)-575-3400
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16
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Marshall AS, Jones NS. Discovering Cellular Mitochondrial Heteroplasmy Heterogeneity with Single Cell RNA and ATAC Sequencing. BIOLOGY 2021; 10:biology10060503. [PMID: 34198745 PMCID: PMC8230039 DOI: 10.3390/biology10060503] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 12/14/2022]
Abstract
Next-generation sequencing technologies have revolutionised the study of biological systems by enabling the examination of a broad range of tissues. Its application to single-cell genomics has generated a dynamic and evolving field with a vast amount of research highlighting heterogeneity in transcriptional, genetic and epigenomic state between cells. However, compared to these aspects of cellular heterogeneity, relatively little has been gleaned from single-cell datasets regarding cellular mitochondrial heterogeneity. Single-cell sequencing techniques can provide coverage of the mitochondrial genome which allows researchers to probe heteroplasmies at the level of the single cell, and observe interactions with cellular function. In this review, we give an overview of two popular single-cell modalities-single-cell RNA sequencing and single-cell ATAC sequencing-whose throughput and widespread usage offers researchers the chance to probe heteroplasmy combined with cell state in detailed resolution across thousands of cells. After summarising these technologies in the context of mitochondrial research, we give an overview of recent methods which have used these approaches for discovering mitochondrial heterogeneity. We conclude by highlighting current limitations of these approaches and open problems for future consideration.
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17
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Chen R, Aldred MA, Xu W, Zein J, Bazeley P, Comhair SAA, Meyers DA, Bleecker ER, Liu C, Erzurum SC, Hu B. Comparison of whole genome sequencing and targeted sequencing for mitochondrial DNA. Mitochondrion 2021; 58:303-310. [PMID: 33513442 PMCID: PMC8354572 DOI: 10.1016/j.mito.2021.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
Mitochondrial dysfunction has emerged to be associated with a broad spectrum of diseases, and there is an increasing demand for accurate detection of mitochondrial DNA (mtDNA) variants. Whole genome sequencing (WGS) has been the dominant sequencing approach to identify genetic variants in recent decades, but most studies focus on variants on the nuclear genome. Whole genome sequencing is also costly and time consuming. Sequencing specifically targeted for mtDNA is commonly used in the diagnostic settings and has lower costs. However, there is a lack of pairwise comparisons between these two sequencing approaches for calling mtDNA variants on a population basis. In this study, we compared WGS and mtDNA-targeted sequencing (targeted-seq) in analyzing mitochondrial DNA from 1499 participants recruited into the Severe Asthma Research Program (SARP). Our study reveals that targeted-sequencing and WGS have comparable capacity to determine genotypes and to call haplogroups and homoplasmies on mtDNA. However, there exists a large variability in calling heteroplasmies, especially for low-frequency heteroplasmies, which indicates that investigators should be cautious about heteroplasmies acquired from different sequencing methods. Further research is highly desired to improve variant detection methods for mitochondrial DNA.
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Affiliation(s)
- Ruoying Chen
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Micheala A Aldred
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN, USA
| | - Weiling Xu
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Joe Zein
- Respiratory Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Suzy A A Comhair
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | | | - Chunyu Liu
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Serpil C Erzurum
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Respiratory Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Bo Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
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18
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Bagge EK, Fujimori-Tonou N, Kubota-Sakashita M, Kasahara T, Kato T. Unbiased PCR-free spatio-temporal mapping of the mtDNA mutation spectrum reveals brain region-specific responses to replication instability. BMC Biol 2020; 18:150. [PMID: 33097039 PMCID: PMC7585204 DOI: 10.1186/s12915-020-00890-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/06/2020] [Indexed: 12/24/2022] Open
Abstract
Background The accumulation of mtDNA mutations in different tissues from various mouse models has been widely studied especially in the context of mtDNA mutation-driven ageing but has been confounded by the inherent limitations of the most widely used approaches. By implementing a method to sequence mtDNA without PCR amplification prior to library preparation, we map the full unbiased mtDNA mutation spectrum across six distinct brain regions from mice. Results We demonstrate that ageing-induced levels of mtDNA mutations (single nucleotide variants and deletions) reach stable levels at 50 weeks of age but can be further elevated specifically in the cortex, nucleus accumbens (NAc), and paraventricular thalamic nucleus (PVT) by expression of a proof-reading-deficient mitochondrial DNA polymerase, PolgD181A. The increase in single nucleotide variants increases the fraction of shared SNVs as well as their frequency, while characteristics of deletions remain largely unaffected. In addition, PolgD181A also induces an ageing-dependent accumulation of non-coding control-region multimers in NAc and PVT, a feature that appears almost non-existent in wild-type mice. Conclusions Our data provide a novel view of the spatio-temporal accumulation of mtDNA mutations using very limited tissue input. The differential response of brain regions to a state of replication instability provides insight into a possible heterogenic mitochondrial landscape across the brain that may be involved in the ageing phenotype and mitochondria-associated disorders.
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Affiliation(s)
- Emilie Kristine Bagge
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Noriko Fujimori-Tonou
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan.,Current address: Support Unit for Bio-Material Analysis, Research Resources Division, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Mie Kubota-Sakashita
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan.,Current address: Career Development Program, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Wako, Saitama, Japan. .,Department of Psychiatry and Behavioral Science, Juntendo University, Graduate School of Medicine, Hongo 2-1-1, Bunkyo, Tokyo 113-8421, Japan.
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19
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Abstract
Tracing cell lineages is fundamental for understanding the rules governing development in multicellular organisms and delineating complex biological processes involving the differentiation of multiple cell types with distinct lineage hierarchies. In humans, experimental lineage tracing is unethical, and one has to rely on natural-mutation markers that are created within cells as they proliferate and age. Recent studies have demonstrated that it is now possible to trace lineages in normal, noncancerous cells with a variety of data types using natural variations in the nuclear and mitochondrial DNA as well as variations in DNA methylation status. It is also apparent that the scientific community is on the verge of being able to make a comprehensive and detailed cell lineage map of human embryonic and fetal development. In this review, we discuss the advantages and disadvantages of different approaches and markers for lineage tracing. We also describe the general conceptual design for how to derive a lineage map for humans.
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Affiliation(s)
- Alexej Abyzov
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota 55905, USA;
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, Connecticut 06520, USA;
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20
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Martín-Jiménez R, Lurette O, Hebert-Chatelain E. Damage in Mitochondrial DNA Associated with Parkinson's Disease. DNA Cell Biol 2020; 39:1421-1430. [PMID: 32397749 DOI: 10.1089/dna.2020.5398] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are the only organelles that contain their own genetic material (mtDNA). Mitochondria are involved in several key physiological functions, including ATP production, Ca2+ homeostasis, and metabolism of neurotransmitters. Since these organelles perform crucial processes to maintain neuronal homeostasis, mitochondrial dysfunctions can lead to various neurodegenerative diseases. Several mitochondrial proteins involved in ATP production are encoded by mtDNA. Thus, any mtDNA alteration can ultimately lead to mitochondrial dysfunction and cell death. Accumulation of mutations, deletions, and rearrangements in mtDNA has been observed in animal models and patients suffering from Parkinson's disease (PD). Also, specific inherited variations associated with mtDNA genetic groups (known as mtDNA haplogroups) are associated with lower or higher risk of developing PD. Consequently, mtDNA alterations should now be considered important hallmarks of this neurodegenerative disease. This review provides an update about the role of mtDNA alterations in the physiopathology of PD.
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Affiliation(s)
- Rebeca Martín-Jiménez
- Department of Biology and Université de Moncton, Moncton, Canada
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Université de Moncton, Moncton, Canada
| | - Olivier Lurette
- Department of Biology and Université de Moncton, Moncton, Canada
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Université de Moncton, Moncton, Canada
| | - Etienne Hebert-Chatelain
- Department of Biology and Université de Moncton, Moncton, Canada
- Canada Research Chair in Mitochondrial Signaling and Physiopathology, Université de Moncton, Moncton, Canada
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21
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Lawless C, Greaves L, Reeve AK, Turnbull DM, Vincent AE. The rise and rise of mitochondrial DNA mutations. Open Biol 2020; 10:200061. [PMID: 32428418 PMCID: PMC7276526 DOI: 10.1098/rsob.200061] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/23/2020] [Indexed: 12/24/2022] Open
Abstract
How mitochondrial DNA mutations clonally expand in an individual cell is a question that has perplexed mitochondrial biologists for decades. A growing body of literature indicates that mitochondrial DNA mutations play a major role in ageing, metabolic diseases, neurodegenerative diseases, neuromuscular disorders and cancers. Importantly, this process of clonal expansion occurs for both inherited and somatic mitochondrial DNA mutations. To complicate matters further there are fundamental differences between mitochondrial DNA point mutations and deletions, and between mitotic and post-mitotic cells, that impact this pathogenic process. These differences, along with the challenges of investigating a longitudinal process occurring over decades in humans, have so far hindered progress towards understanding clonal expansion. Here we summarize our current understanding of the clonal expansion of mitochondrial DNA mutations in different tissues and highlight key unanswered questions. We then discuss the various existing biological models, along with their advantages and disadvantages. Finally, we explore what has been achieved with mathematical modelling so far and suggest future work to advance this important area of research.
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Affiliation(s)
| | | | | | - Doug M. Turnbull
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE2 4HH, UK
| | - Amy E. Vincent
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE2 4HH, UK
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22
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Whitehall JC, Greaves LC. Aberrant mitochondrial function in ageing and cancer. Biogerontology 2019; 21:445-459. [PMID: 31802313 PMCID: PMC7347693 DOI: 10.1007/s10522-019-09853-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 11/23/2019] [Indexed: 12/12/2022]
Abstract
Alterations in mitochondrial metabolism have been described as one of the major hallmarks of both ageing cells and cancer. Age is the biggest risk factor for the development of a significant number of cancer types and this therefore raises the question of whether there is a link between age-related mitochondrial dysfunction and the advantageous changes in mitochondrial metabolism prevalent in cancer cells. A common underlying feature of both ageing and cancer cells is the presence of somatic mutations of the mitochondrial genome (mtDNA) which we postulate may drive compensatory alterations in mitochondrial metabolism that are advantageous for tumour growth. In this review, we discuss basic mitochondrial functions, mechanisms of mtDNA mutagenesis and their metabolic consequences, and review the evidence for and against a role for mtDNA mutations in cancer development.
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Affiliation(s)
- Julia C Whitehall
- The Medical School, Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Laura C Greaves
- The Medical School, Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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23
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Knorre DA. Intracellular quality control of mitochondrial DNA: evidence and limitations. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190176. [PMID: 31787047 DOI: 10.1098/rstb.2019.0176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells can harbour mitochondria with markedly different transmembrane potentials. Intracellular mitochondrial quality-control mechanisms (e.g. mitophagy) rely on this intracellular variation to distinguish functional and damaged (depolarized) mitochondria. Given that intracellular mitochondrial DNA (mtDNA) genetic variation can induce mitochondrial heterogeneity, mitophagy could remove deleterious mtDNA variants in cells. However, the reliance of mitophagy on the mitochondrial transmembrane potential suggests that mtDNAs with deleterious mutations in ATP synthase can evade the control. This evasion is possible because inhibition of ATP synthase can increase the mitochondrial transmembrane potential. Moreover, the linkage of the mtDNA genotype to individual mitochondrial performance is expected to be weak owing to intracellular mitochondrial intercomplementation. Nonetheless, I reason that intracellular mtDNA quality control is possible and crucial at the zygote stage of the life cycle. Indeed, species with biparental mtDNA inheritance or frequent 'leakage' of paternal mtDNA can be vulnerable to invasion of selfish mtDNAs at the stage of gamete fusion. Here, I critically review recent findings on intracellular mtDNA quality control by mitophagy and discuss other mechanisms by which the nuclear genome can affect the competition of mtDNA variants in the cell. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Dmitry A Knorre
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Leninskiye Gory 1-40, Moscow 119991, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Trubetskaya Str. 8-2, Moscow 119991, Russia
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24
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Differential Expression of Cytochrome C Oxidase Subunit I Along the Colorectal Adenoma: Carcinoma Progression. Appl Immunohistochem Mol Morphol 2019; 26:689-696. [PMID: 28362707 DOI: 10.1097/pai.0000000000000509] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Loss in apoptosis competence often results in augmented genomic instability contributing to carcinogenesis. Cytochrome c oxidase subunit I (CcOI) can help assess apoptosis resistance in paraffin-embedded biopsies. In total, 50 colorectal cases including 10 control cases of colectomy for non-neoplastic condition, 15 cases of adenomatous colorectal polyps, and 25 cases of colorectal carcinoma were investigated in this retrospective study for immunohistochemical expression of CcOI. The staining pattern of CcOI was assessed and indices of aberrant expression were calculated as crypt-restricted loss and overall decreased immunostaining (ODI). ODI calculated in the adenocarcinoma tumor tissue was designated as Tr ODI. The crypt-restricted loss and ODI indices of the aberrant CcOI expression are significantly higher in the adenomatous polyps group (2.5% and 47.54%) and in the non-neoplastic mucosa among adenocarcinoma group (2.78% and 49.1%) when they are compared with the control group (0.55% and 7.32%) (P<0.001). A highly significant correlation was noted between Tr ODI and the tumor grade, the nodal status, and the stage among adenocarcinomas. In conclusion, colonic tumors arise in a field of crypts with aberrations in CcOI expression. This aberration is linked to biologically aggressive tumors. CcOI immunostaining may be applied on mucosal samples from patients with colonic adenomatous polyps and patients with previous cancer colon resection to determine individuals who are in need for frequent colonoscopies and/or chemopreventive strategies. Future follow-up studies are warranted to determine the level of expression predictive of recurrence or progression.
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25
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Chocron ES, Munkácsy E, Pickering AM. Cause or casualty: The role of mitochondrial DNA in aging and age-associated disease. Biochim Biophys Acta Mol Basis Dis 2019; 1865:285-297. [PMID: 30419337 PMCID: PMC6310633 DOI: 10.1016/j.bbadis.2018.09.035] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/20/2018] [Accepted: 09/04/2018] [Indexed: 12/19/2022]
Abstract
The mitochondrial genome (mtDNA) represents a tiny fraction of the whole genome, comprising just 16.6 kilobases encoding 37 genes involved in oxidative phosphorylation and the mitochondrial translation machinery. Despite its small size, much interest has developed in recent years regarding the role of mtDNA as a determinant of both aging and age-associated diseases. A number of studies have presented compelling evidence for key roles of mtDNA in age-related pathology, although many are correlative rather than demonstrating cause. In this review we will evaluate the evidence supporting and opposing a role for mtDNA in age-associated functional declines and diseases. We provide an overview of mtDNA biology, damage and repair as well as the influence of mitochondrial haplogroups, epigenetics and maternal inheritance in aging and longevity.
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Affiliation(s)
- E Sandra Chocron
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA
| | - Erin Munkácsy
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA
| | - Andrew M Pickering
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA; Department of Molecular Medicine, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78245-3207, USA.
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Kasahara T, Kato T. What Can Mitochondrial DNA Analysis Tell Us About Mood Disorders? Biol Psychiatry 2018; 83:731-738. [PMID: 29102411 DOI: 10.1016/j.biopsych.2017.09.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/11/2017] [Accepted: 09/12/2017] [Indexed: 12/11/2022]
Abstract
Variants in mitochondrial DNA (mtDNA) and nuclear genes encoding mitochondrial proteins in bipolar disorder, depression, or other psychiatric disorders have been studied for decades, since mitochondrial dysfunction was first suggested in the brains of patients with these diseases. Candidate gene association studies initially resulted in findings compatible with the mitochondrial dysfunction hypothesis. Many of those studies, however, were conducted with modest sample sizes (N < 1000), which could cause false positive findings. Furthermore, the DNA samples examined in these studies, including genome-wide association studies, were generally derived from peripheral tissues. One key unanswered question is whether there is an association between mood disorders and somatic mtDNA mutations (deletions and point mutations) in brain regions that accumulate a high amount of mtDNA mutations and/or are involved in the regulation of mood. Two lines of robust evidence supporting the importance of mtDNA mutations in brain tissues for mood disorders have come from clinical observation of mitochondrial disease patients who carry primary mtDNA mutations or accumulate secondary mtDNA mutations due to nuclear mutations and an animal model study. More than half of mitochondrial disease patients have comorbid mood disorders, and mice with neuron-specific accumulation of mtDNA mutations show spontaneous depression-like episodes. In this review, we first summarize the current knowledge of mtDNA and its genetics and discuss what mtDNA analysis tells us about neuropsychiatric disorders based on an example of Parkinson's disease. We also discuss challenges and future directions beyond mtDNA analysis toward an understanding of the pathophysiology of "idiopathic" mood disorders.
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Affiliation(s)
- Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako-shi, Saitama, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako-shi, Saitama, Japan.
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Zsurka G, Peeva V, Kotlyar A, Kunz WS. Is There Still Any Role for Oxidative Stress in Mitochondrial DNA-Dependent Aging? Genes (Basel) 2018; 9:genes9040175. [PMID: 29561808 PMCID: PMC5924517 DOI: 10.3390/genes9040175] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 03/09/2018] [Accepted: 03/16/2018] [Indexed: 11/21/2022] Open
Abstract
Recent deep sequencing data has provided compelling evidence that the spectrum of somatic point mutations in mitochondrial DNA (mtDNA) in aging tissues lacks G > T transversion mutations. This fact cannot, however, be used as an argument for the missing contribution of reactive oxygen species (ROS) to mitochondria-related aging because it is probably caused by the nucleotide selectivity of mitochondrial DNA polymerase γ (POLG). In contrast to point mutations, the age-dependent accumulation of mitochondrial DNA deletions is, in light of recent experimental data, still explainable by the segregation of mutant molecules generated by the direct mutagenic effects of ROS (in particular, of HO· radicals formed from H2O2 by a Fenton reaction). The source of ROS remains controversial, because the mitochondrial contribution to tissue ROS production is probably lower than previously thought. Importantly, in the discussion about the potential role of oxidative stress in mitochondria-dependent aging, ROS generated by inflammation-linked processes and the distribution of free iron also require careful consideration.
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Affiliation(s)
- Gábor Zsurka
- Institute of Experimental Epileptology and Neurocognition, University Bonn Medical Center, 53105 Bonn, Germany.
- Department of Epileptology, University Bonn Medical Center, 53105 Bonn, Germany.
| | - Viktoriya Peeva
- Institute of Experimental Epileptology and Neurocognition, University Bonn Medical Center, 53105 Bonn, Germany.
| | - Alexander Kotlyar
- Department of Biochemistry & Molecular Biology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Wolfram S Kunz
- Institute of Experimental Epileptology and Neurocognition, University Bonn Medical Center, 53105 Bonn, Germany.
- Department of Epileptology, University Bonn Medical Center, 53105 Bonn, Germany.
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28
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Recent Advances in Detecting Mitochondrial DNA Heteroplasmic Variations. Molecules 2018; 23:molecules23020323. [PMID: 29401641 PMCID: PMC6017848 DOI: 10.3390/molecules23020323] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 12/31/2022] Open
Abstract
The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed several methods of mtDNA heteroplasmy research, including the enrichment of mtDNA and the way of calling heteroplasmic variations. At the present, while calling the novel ultra-low level heteroplasmy, high-throughput sequencing method is dominant while the detection limit of recorded mutations is accurate to 0.01% using the other quantitative approaches. In the future, the studies of mtDNA heteroplasmy may pay more attention to the single-cell level and focus on the linkage of mutations.
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Ren Q, Zhang F, Xu H. Proliferation Cycle Causes Age Dependent Mitochondrial Deficiencies and Contributes to the Aging of Stem Cells. Genes (Basel) 2017; 8:genes8120397. [PMID: 29257059 PMCID: PMC5748715 DOI: 10.3390/genes8120397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/17/2017] [Accepted: 12/14/2017] [Indexed: 12/15/2022] Open
Abstract
In addition to chronological aging, stem cells are also subject to proliferative aging during the adult life span. However, the consequences of proliferative cycle and their contributions to stem cells aging have not been well investigated. Using Drosophila female germ line stem cells as a model, we found that the replication cycle leads to the age dependent decline of female fecundity, and is a major factor causing developmental abnormalities in the progeny of old females. The proliferative aging does not cause telomere shortening, but causes an accumulation of mitochondrial DNA (mtDNA) mutations or rearrangements at the control region. We propose that damaging mutations on mtDNA caused by accumulation of proliferation cycles in aged stem cells may disrupt mitochondrial respiration chain and impair mtDNA replication and represent a conserved mechanism underlying stem cell aging.
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Affiliation(s)
- Qiuting Ren
- Laboratory of Molecular Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Fan Zhang
- Laboratory of Molecular Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Hong Xu
- Laboratory of Molecular Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Williams ED, Rogers SC, Zhang X, Azhar G, Wei JY. p49/STRAP, a Serum Response Factor Binding Protein (SRFBP1), Is Involved in the Redistribution of Cytoskeletal F-Actin Proteins during Glucose Deprivation. J Nutr Health Aging 2017; 21:1142-1150. [PMID: 29188873 DOI: 10.1007/s12603-017-0925-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The functional decline that usually accompanies adult aging also encompasses cellular changes including cytoplasmic architecture. In addition to their role in cytoskeletal structure, actin microfilaments have important roles in various cellular processes, including cell-to-cell communication and intracellular signaling. Age-related diseases and late-stage cellular morphological appearances often correlate with altered f-actin structure, which has been observed most notably in cancer. What remains less clear are the molecular pathways that may be involved in normal and premature aging-induced f-actin changes. We report herein that p49/STRAP, a serum response factor binding protein (SRFBP1), is increased with normal aging and appears to be sensitive to low glucose-exposure. Our study results suggest that increased levels of p49/STRAP expression tend to correlate with f-actin redistribution genes, particularly cofilin, while siRNA-mediated knockdown of p49/STRAP resulted in a reduction of thymosin-β4. Furthermore, with the redistribution of f-actin, we observed an increase in the intermediate filament vimentin, compatible with the notion that vimentin may be increased due to its greater role in cytoskeletal dynamics during advancing population doubling levels (PDLs) and in response to a low-glucose exposure. Taken together, these data suggest that p49/STRAP may play a role in glucose-deprivation associated cytoskeletal changes.
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Affiliation(s)
- E D Williams
- Jeanne Y. Wei, M.D., Ph.D, Reynolds Institute on Aging, Department of Geriatrics, University of Arkansas for Medical Sciences, 4301 W. Markham St. #748, Little Rock, AR 72205, USA, Phone: (501) 526-6800, Fax: (501) 686-5300,
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31
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Mohanty K, Dada R, Dada T. Neurodegenerative Eye Disorders: Role of Mitochondrial Dynamics and Genomics. Asia Pac J Ophthalmol (Phila) 2016; 5:293-9. [PMID: 27101384 DOI: 10.1097/apo.0000000000000203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
As a major source of cellular energy, mitochondria are critical for optimal ocular function. They are also essential for cell differentiation and survival. Mitochondrial mutations and oxidative damage to the mitochondrial DNA are important factors underlying the pathology of many ocular disorders. With increasing age, mitochondrial DNA damage accumulates and results in several eye diseases. It is evident that the mitochondrial genome is more susceptible to stress and damage than the nuclear genome, as it lacks histone protection, a nucleotide excision repair system, and recombination repair, and it is the source and target of free radicals. Accumulation of mitochondrial mutations beyond a certain threshold explains the marked variations in phenotypes seen in mitochondrial diseases and the molecular mechanisms related to the pathogenesis of several chronic disorders in the eye. This review details the structure and function of mitochondria and the mitochondrial genome along with the mitochondrial involvement in various neurodegenerative ophthalmic disorders.
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Affiliation(s)
- Kuldeep Mohanty
- From the *Department of Ophthalmology, Dr. Rajendra Prasad Centre for Ophthalmic Sciences, AIIMS, New Delhi, India; and †Laboratory for Molecular Reproduction and Genetics, Department of Anatomy, AIIMS, New Delhi, India
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Zhang X, Williams ED, Azhar G, Rogers SC, Wei JY. Does p49/STRAP, a SRF-binding protein (SRFBP1), modulate cardiac mitochondrial function in aging? Exp Gerontol 2016; 82:150-9. [PMID: 27337995 DOI: 10.1016/j.exger.2016.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/31/2016] [Accepted: 06/19/2016] [Indexed: 02/06/2023]
Abstract
p49/STRAP (SRFBP1) is a transcriptional regulator that has been implicated in cardiac aging. p49/STRAP has a SRF binding domain and a BUD22 domain (which modulates cellular growth rate and cell size). We have observed that p49/STRAP alters the intracellular NAD/NADH ratio and induces protein deacetylation. Here we report that p49/STRAP overexpression caused the deacetylation of histone H4 on lysine 16 (H4K16) and suppressed the expression of PGC-1α as well as mitofusin-1 and mitofusin-2 at both the mRNA and protein levels. P49/STRAP also reduced mitochondrial size, mitochondrial membrane potential and the mitochondrial oxygen consumption rate. We noted that P49/STRAP expression was increased in the old versus young adult mouse hearts and also increased with advancing population doubling levels in cultured human umbilical vein endothelial cells (HUVECs). It is therefore very plausible that increased expression of p49/STRAP in late life may alter the status of histone acetylation and impact mitochondrial dynamics and thereby reduce mitochondrial function and cardiac performance during mammalian senescence.
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Affiliation(s)
- Xiaomin Zhang
- Donald W. Reynolds Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Emmanuel D Williams
- Donald W. Reynolds Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Gohar Azhar
- Donald W. Reynolds Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Steven C Rogers
- Donald W. Reynolds Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States
| | - Jeanne Y Wei
- Donald W. Reynolds Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, United States.
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Computational DNA hole spectroscopy: A new tool to predict mutation hotspots, critical base pairs, and disease 'driver' mutations. Sci Rep 2015; 5:13571. [PMID: 26310834 PMCID: PMC4550865 DOI: 10.1038/srep13571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/30/2015] [Indexed: 01/05/2023] Open
Abstract
We report on a new technique, computational DNA hole spectroscopy, which creates spectra of electron hole probabilities vs. nucleotide position. A hole is a site of positive charge created when an electron is removed. Peaks in the hole spectrum depict sites where holes tend to localize and potentially trigger a base pair mismatch during replication. Our studies of mitochondrial DNA reveal a correlation between L-strand hole spectrum peaks and spikes in the human mutation spectrum. Importantly, we also find that hole peak positions that do not coincide with large variant frequencies often coincide with disease-implicated mutations and/or (for coding DNA) encoded conserved amino acids. This enables combining hole spectra with variant data to identify critical base pairs and potential disease 'driver' mutations. Such integration of DNA hole and variance spectra could ultimately prove invaluable for pinpointing critical regions of the vast non-protein-coding genome. An observed asymmetry in correlations, between the spectrum of human mtDNA variations and the L- and H-strand hole spectra, is attributed to asymmetric DNA replication processes that occur for the leading and lagging strands.
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Abstract
In the past century, considerable efforts were made to understand the role of mitochondrial DNA (mtDNA) mutations and of oxidative stress in aging. The classic mitochondrial free radical theory of aging, in which mtDNA mutations cause genotoxic oxidative stress, which in turn creates more mutations, has been a central hypothesis in the field for decades. In the past few years, however, new elements have discredited this original theory. The major sources of mitochondrial DNA mutations seem to be replication errors and failure of the repair mechanisms, and the accumulation of these mutations as observed in aged organisms seems to occur by clonal expansion and not to be caused by a reactive oxygen species-dependent vicious cycle. New hypotheses of how age-associated mitochondrial dysfunction may lead to aging are based on the role of reactive oxygen species as signaling molecules and on their role in mediating stress responses to age-dependent damage. Here, we review the changes that mtDNA undergoes during aging and the past and most recent hypotheses linking these changes to the tissue failure observed in aging.
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Affiliation(s)
- Milena Pinto
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Carlos T Moraes
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Department of Cell Biology and Anatomy, Miller School of Medicine, University of Miami, Miami, FL 33136, USA.
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35
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Müller-Höcker J, Schäfer S, Krebs S, Blum H, Zsurka G, Kunz WS, Prokisch H, Seibel P, Jung A. Oxyphil cell metaplasia in the parathyroids is characterized by somatic mitochondrial DNA mutations in NADH dehydrogenase genes and cytochrome c oxidase activity-impairing genes. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 184:2922-35. [PMID: 25418474 DOI: 10.1016/j.ajpath.2014.07.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/14/2014] [Accepted: 07/17/2014] [Indexed: 02/01/2023]
Abstract
Oxyphil cell transformation of epithelial cells due to the accumulation of mitochondria occurs often during cellular aging. To understand the pathogenic mechanisms, we studied mitochondrial DNA (mtDNA) alterations in the three cell types of the parathyroids using multiplex real-time PCR and next-generation sequencing. mtDNA was analyzed from cytochrome c oxidase (COX)-positive and COX-negative areas of 19 parathyroids. Mitochondria-rich pre-oxyphil/oxyphil cells were more prone to develop COX defects than the mitochondria-poor clear chief cells (P < 0.001). mtDNA increased approximately 2.5-fold from clear chief to oxyphil cells. In COX deficiency, the increase was even more pronounced, and COX-negative oxyphil cells had approximately two times more mtDNA than COX-positive oxyphil cells (P < 0.001), illustrating the influence of COX deficiency on mtDNA biosynthesis, probably as a consequence of insufficient ATP synthesis. Next-generation sequencing revealed a broad spectrum of putative pathogenic mtDNA point mutations affecting NADH dehydrogenase and COX genes as well as regulatory elements of mtDNA. NADH dehydrogenase gene mutations preferentially accumulated in COX-positive pre-oxyphil/oxyphil cells and, therefore, could be essential for inducing oxyphil cell transformation by increasing mtDNA/mitochondrial biogenesis. In contrast, COX-negative cells predominantly harbored mutations in the MT-CO1 and MT-CO3 genes and in regulatory mtDNA elements, but only rarely NADH dehydrogenase mutations. Thus, multiple hits in NADH dehydrogenase and COX activity-impairing genes represent the molecular basis of oxyphil cell transformation in the parathyroids.
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Affiliation(s)
- Josef Müller-Höcker
- Institute for Pathology of the Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sabine Schäfer
- Institute for Pathology of the Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefan Krebs
- Gene Center of the Ludwig-Maximilians-Universität München, Campus Großhadern, Munich, Germany
| | - Helmut Blum
- Gene Center of the Ludwig-Maximilians-Universität München, Campus Großhadern, Munich, Germany
| | - Gábor Zsurka
- Division of Neurochemistry, Department of Epileptology and Life and Brain Center, University of Bonn, Bonn, Germany
| | - Wolfram S Kunz
- Division of Neurochemistry, Department of Epileptology and Life and Brain Center, University of Bonn, Bonn, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Helmholtz-Zentrum München, Neuherberg, Germany
| | - Peter Seibel
- Molekulare Zellbiologie, Biotechnological Biomedical Center, Universität Leipzig, Leipzig, Germany
| | - Andreas Jung
- Institute for Pathology of the Ludwig-Maximilians-Universität München, Munich, Germany; German Cancer Consortium and German Cancer Research Center, Heidelberg, Germany.
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36
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McKenzie M, Chiotis M, Hroudová J, Lopez Sanchez MIG, Lim SC, Cook MJ, McKelvie P, Cotton RGH, Murphy M, St John JC, Trounce IA. Capture of somatic mtDNA point mutations with severe effects on oxidative phosphorylation in synaptosome cybrid clones from human brain. Hum Mutat 2015; 35:1476-84. [PMID: 25219341 DOI: 10.1002/humu.22694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 09/03/2014] [Indexed: 01/13/2023]
Abstract
Mitochondrial DNA (mtDNA) is replicated throughout life in postmitotic cells, resulting in higher levels of somatic mutation than in nuclear genes. However, controversy remains as to the importance of low-level mtDNA somatic mutants in cancerous and normal human tissues. To capture somatic mtDNA mutations for functional analysis, we generated synaptosome cybrids from synaptic endings isolated from fresh hippocampus and cortex brain biopsies. We analyzed the whole mtDNA genome from 120 cybrid clones derived from four individual donors by chemical cleavage of mismatch and Sanger sequencing, scanning around two million base pairs. Seventeen different somatic point mutations were identified, including eight coding region mutations, four of which result in frameshifts. Examination of one cybrid clone with a novel m.2949_2953delCTATT mutation in MT-RNR2 (which encodes mitochondrial 16S rRNA) revealed a severe disruption of mtDNA-encoded protein translation. We also performed functional studies on a homoplasmic nonsense mutation in MT-ND1, previously reported in oncocytomas, and show that both ATP generation and the stability of oxidative phosphorylation complex I are disrupted. As the mtDNA remains locked against direct genetic manipulation, we demonstrate that the synaptosome cybrid approach can capture biologically relevant mtDNA mutants in vitro to study effects on mitochondrial respiratory chain function.
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Affiliation(s)
- Matthew McKenzie
- Centre for Genetic Diseases, MIMR-PHI Institute of Medical Research, Monash University, Clayton, Victoria, 3168, Australia; Monash University, Clayton, Victoria, 3168, Australia
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37
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Yao YG, Kajigaya S, Young NS. Mitochondrial DNA mutations in single human blood cells. Mutat Res 2015; 779:68-77. [PMID: 26149767 DOI: 10.1016/j.mrfmmm.2015.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 06/16/2015] [Accepted: 06/18/2015] [Indexed: 01/07/2023]
Abstract
Determination mitochondrial DNA (mtDNA) sequences from extremely small amounts of DNA extracted from tissue of limited amounts and/or degraded samples is frequently employed in medical, forensic, and anthropologic studies. Polymerase chain reaction (PCR) amplification followed by DNA cloning is a routine method, especially to examine heteroplasmy of mtDNA mutations. In this review, we compare the mtDNA mutation patterns detected by three different sequencing strategies. Cloning and sequencing methods that are based on PCR amplification of DNA extracted from either single cells or pooled cells yield a high frequency of mutations, partly due to the artifacts introduced by PCR and/or the DNA cloning process. Direct sequencing of PCR product which has been amplified from DNA in individual cells is able to detect the low levels of mtDNA mutations present within a cell. We further summarize the findings in our recent studies that utilized this single cell method to assay mtDNA mutation patterns in different human blood cells. Our data show that many somatic mutations observed in the end-stage differentiated cells are found in hematopoietic stem cells (HSCs) and progenitors within the CD34(+) cell compartment. Accumulation of mtDNA variations in the individual CD34+ cells is affected by both aging and family genetic background. Granulocytes harbor higher numbers of mutations compared with the other cells, such as CD34(+) cells and lymphocytes. Serial assessment of mtDNA mutations in a population of single CD34(+) cells obtained from the same donor over time suggests stability of some somatic mutations. CD34(+) cell clones from a donor marked by specific mtDNA somatic mutations can be found in the recipient after transplantation. The significance of these findings is discussed in terms of the lineage tracing of HSCs, aging effect on accumulation of mtDNA mutations and the usage of mtDNA sequence in forensic identification.
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Affiliation(s)
- Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan 650223, China.
| | - Sachiko Kajigaya
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Neal S Young
- Hematology Branch, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD 20892, USA
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Szklarczyk R, Nooteboom M, Osiewacz HD. Control of mitochondrial integrity in ageing and disease. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130439. [PMID: 24864310 DOI: 10.1098/rstb.2013.0439] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Various molecular and cellular pathways are active in eukaryotes to control the quality and integrity of mitochondria. These pathways are involved in keeping a 'healthy' population of this essential organelle during the lifetime of the organism. Quality control (QC) systems counteract processes that lead to organellar dysfunction manifesting as degenerative diseases and ageing. We discuss disease- and ageing-related pathways involved in mitochondrial QC: mtDNA repair and reorganization, regeneration of oxidized amino acids, refolding and degradation of severely damaged proteins, degradation of whole mitochondria by mitophagy and finally programmed cell death. The control of the integrity of mtDNA and regulation of its expression is essential to remodel single proteins as well as mitochondrial complexes that determine mitochondrial functions. The redundancy of components, such as proteases, and the hierarchies of the QC raise questions about crosstalk between systems and their precise regulation. The understanding of the underlying mechanisms on the genomic, proteomic, organellar and cellular levels holds the key for the development of interventions for mitochondrial dysfunctions, degenerative processes, ageing and age-related diseases resulting from impairments of mitochondria.
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Affiliation(s)
- Radek Szklarczyk
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands Department of Clinical Genetics, Unit Clinical Genomics, Maastricht University Medical Centre, 6200 MD Maastricht, The Netherlands
| | - Marco Nooteboom
- Department of Biochemistry (286), Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Heinz D Osiewacz
- Faculty for Biosciences and Cluster of Excellence 'Macromolecular Complexes', Goethe University, Molecular Developmental Biology, 60438 Frankfurt am Main, Germany
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Popadin K, Gunbin KV, Khrapko K. Mitochondrial DNA mutations and cancer: lessons from the parathyroid. THE AMERICAN JOURNAL OF PATHOLOGY 2014; 184:2852-4. [PMID: 25242389 DOI: 10.1016/j.ajpath.2014.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/08/2014] [Accepted: 09/11/2014] [Indexed: 10/24/2022]
Affiliation(s)
| | | | - Konstantin Khrapko
- Department of Biology, Northeastern University, Boston, Massachusetts; Department of Pharmaceutical Sciences, Northeastern University, Boston, Massachusetts.
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40
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Extensive pathogenicity of mitochondrial heteroplasmy in healthy human individuals. Proc Natl Acad Sci U S A 2014; 111:10654-9. [PMID: 25002485 DOI: 10.1073/pnas.1403521111] [Citation(s) in RCA: 172] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A majority of mitochondrial DNA (mtDNA) mutations reported to be implicated in diseases are heteroplasmic, a status with coexisting mtDNA variants in a single cell. Quantifying the prevalence of mitochondrial heteroplasmy and its pathogenic effect in healthy individuals could further our understanding of its possible roles in various diseases. A total of 1,085 human individuals from 14 global populations have been sequenced by the 1000 Genomes Project to a mean coverage of ∼2,000× on mtDNA. Using a combination of stringent thresholds and a maximum-likelihood method to define heteroplasmy, we demonstrated that ∼90% of the individuals carry at least one heteroplasmy. At least 20% of individuals harbor heteroplasmies reported to be implicated in disease. Mitochondrial heteroplasmy tend to show high pathogenicity, and is significantly overrepresented in disease-associated loci. Consistent with their deleterious effect, heteroplasmies with derived allele frequency larger than 60% within an individual show a significant reduction in pathogenicity, indicating the action of purifying selection. Purifying selection on heteroplasmies can also be inferred from nonsynonymous and synonymous heteroplasmy comparison and the unfolded site frequency spectra for different functional sites in mtDNA. Nevertheless, in comparison with population polymorphic mtDNA mutations, the purifying selection is much less efficient in removing heteroplasmic mutations. The prevalence of mitochondrial heteroplasmy with high pathogenic potential in healthy individuals, along with the possibility of these mutations drifting to high frequency inside a subpopulation of cells across lifespan, emphasizes the importance of managing mitochondrial heteroplasmy to prevent disease progression.
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Abstract
The free radical theory of aging was defined in the 1950s. On the base of this theory, the reactive oxygen species formed in the metabolic pathways can play pivotal role in ageing. The theory was modified by defining the mitochondrial respiration as the major cellular source of reactive oxygen species and got the new name mitochondrial theory of aging. Later on the existence of a "vicious cycle" was proposed, in which the reactive oxygen species formed in the mitochondrial respiration impair the mitochondrial DNA and its functions. The formation of reactive oxygen species are elevated due to mitochondrial dysfunction. The formation of mitochondrial DNA mutations can be accelerated by this "vicious cycle", which can lead to accelerated aging. The exonuclease activity of DNA polymerase γ, the polymerase responsible for the replication of mitochondrial DNA was impaired in mtDNA mutator mouse recently. The rate of somatic mutations in mitochondrial DNA was elevated and an aging phenotype could have been observed in these mice. Surprisingly, no oxidative impairment neither elevated reactive oxygen species formation could have been observed in the mtDNA mutator mice, which may question the existence of the "vicious cycle".
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Affiliation(s)
- András Szarka
- Semmelweis Egyetem, Általános Orvostudományi Kar Orvosi Vegytani Molekuláris Biológiai és Patobiokémiai Intézet Budapest Pf. 260 1444 Budapesti Műszaki és Gazdaságtudományi Egyetem, Vegyészmérnöki és Biomérnöki Kar Alkalmazott Biotechnológia és Élelmiszer-tudományi Tanszék, Biokémiai és Molekuláris Biológiai Laboratórium Budapest
| | - Gábor Bánhegyi
- Semmelweis Egyetem, Általános Orvostudományi Kar Orvosi Vegytani Molekuláris Biológiai és Patobiokémiai Intézet Budapest Pf. 260 1444
| | - Balázs Sümegi
- Pécsi Tudományegyetem, Általános Orvostudományi Kar Biokémiai és Orvosi Kémiai Intézet, Orvosi Biokémiai Tanszék Pécs MTA PTE Nukleáris-Mitokondriális Interakciós Kutatócsoport Pécs PTE Szentágothai János Kutatóközpont Pécs
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42
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Mechanism of homologous recombination and implications for aging-related deletions in mitochondrial DNA. Microbiol Mol Biol Rev 2014; 77:476-96. [PMID: 24006472 DOI: 10.1128/mmbr.00007-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Homologous recombination is a universal process, conserved from bacteriophage to human, which is important for the repair of double-strand DNA breaks. Recombination in mitochondrial DNA (mtDNA) was documented more than 4 decades ago, but the underlying molecular mechanism has remained elusive. Recent studies have revealed the presence of a Rad52-type recombination system of bacteriophage origin in mitochondria, which operates by a single-strand annealing mechanism independent of the canonical RecA/Rad51-type recombinases. Increasing evidence supports the notion that, like in bacteriophages, mtDNA inheritance is a coordinated interplay between recombination, repair, and replication. These findings could have profound implications for understanding the mechanism of mtDNA inheritance and the generation of mtDNA deletions in aging cells.
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Abstract
The global epidemic of cardiovascular disease remains the leading cause of death in the USA and across the world. Functional and structural integrity of mitochondria are essential for the physiological function of the cardiovascular system. The metabolic adaptation observed in normal heart is lost in the failing myocardium, which becomes progressively energy depleted leading to impaired myocardial contraction and relaxation. Uncoupling of electron transfer from ATP synthesis leads to excess generation of reactive species, leading to widespread cellular injury and cardiovascular disease. Accumulation of mitochondrial DNA mutation has been linked to ischaemic heart disease, cardiomyopathy and atherosclerotic vascular disease. Mitochondria are known to regulate apoptotic and autophagic pathways that have been shown to play an important role in the development of cardiomyopathy and atherosclerosis. A number of pharmacological and non-pharmacological treatment options have been explored in the management of mitochondrial diseases with variable success.
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Affiliation(s)
- Elizabeth A Dominic
- The George Washington School of Medicine, , Washington, District of Columbia, USA
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Khrapko K, Turnbull D. Mitochondrial DNA mutations in aging. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 127:29-62. [PMID: 25149213 DOI: 10.1016/b978-0-12-394625-6.00002-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The relationship of mitochondrial DNA mutations to aging is still debated. Most mtDNA mutations are recessive: there are multiple copies per cell and mutation needs to clonally expand to cause respiratory deficiency. Overall mtDNA mutant loads are low, so effects of mutations are limited to critical areas where mutations locally reach high fractions. This includes respiratory chain deficient zones in muscle fibers, respiratory-deficient crypts in colon, and massive expansions of deleted mtDNA in substantia nigra neurons. mtDNA "mutator" mouse with increased rate of mtDNA mutations is a useful model, although rates and distribution of mutations may significantly deviate from what is observed in human aging. Comparison of species with different longevity reveals intriguing longevity-related traits in mtDNA sequence, although their significance is yet to be evaluated. The impact of somatic mtDNA mutations rapidly increases with age, so their importance is expected to grow as human life expectancy increases.
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Affiliation(s)
- Konstantin Khrapko
- Harvard Medical School, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Doug Turnbull
- LLHW Centre for Ageing and Vitality, Newcastle University, Newcastle, United Kingdom
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45
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Otáhal J, Folbergrová J, Kovacs R, Kunz WS, Maggio N. Epileptic focus and alteration of metabolism. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 114:209-43. [PMID: 25078504 DOI: 10.1016/b978-0-12-418693-4.00009-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Epilepsy is one of the most common neurologic disorders affecting a substantial part of the population worldwide. Epileptic seizures represent the situation of increased neuronal activity associated with the enhanced demands for sufficient energy supply. For that purpose, very efficient regulatory mechanisms have to operate to ensure that cerebral blood flow, delivery of oxygen, and nutrients are continuously adapted to the local metabolic needs. The sophisticated regulation has to function in concert at several levels (systemic, tissue, cellular, and subcellular). Particularly, mitochondria play a key role not only in the energy production, but they are also central to many other processes including those leading to neuronal death. Impairment of any of the involved pathways can result in serious functional alterations, neurodegeneration, and potentially in epileptogenesis. The present review will address some of the important issues concerning vascular and metabolic changes in pathophysiology of epilepsy.
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Affiliation(s)
- Jakub Otáhal
- Institute of Physiology, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic.
| | - Jaroslava Folbergrová
- Institute of Physiology, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Richard Kovacs
- Institute for Neurophysiology, Charité-Medical University Berlin, Berlin, Germany
| | - Wolfram S Kunz
- Department of Epileptology, University of Bonn, Bonn, Germany
| | - Nicola Maggio
- Department of Neurology, The Joseph Sagol Neuroscience Center, The Chaim Sheba Medical Center, Tel HaShomer, Israel; Talpiot Medical Leadership Program, The Chaim Sheba Medical Center, Tel HaShomer, Israel
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46
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Scialo F, Mallikarjun V, Stefanatos R, Sanz A. Regulation of lifespan by the mitochondrial electron transport chain: reactive oxygen species-dependent and reactive oxygen species-independent mechanisms. Antioxid Redox Signal 2013; 19:1953-69. [PMID: 22938137 DOI: 10.1089/ars.2012.4900] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
SIGNIFICANCE Aging is a consequence of the accumulation of cellular damage that impairs the capacity of an aging organism to adapt to stress. The Mitochondrial Free Radical Theory of Aging (MFRTA) has been one of the most influential ideas over the past 50 years. The MFRTA is supported by the accumulation of oxidative damage during aging along with comparative studies demonstrating that long-lived species or individuals produce fewer mitochondrial reactive oxygen species and have lower levels of oxidative damage. RECENT ADVANCES Recently, however, species that combine high oxidative damage with a longer lifespan (i.e., naked mole rats) have been described. Moreover, most of the interventions based on antioxidant supplementation do not increase longevity, as would be predicted by the MFRTA. Studies to date provide a clear understanding that mitochondrial function regulates the rate of aging, but the underlying mechanisms remain unclear. CRITICAL ISSUES Here, we review the reactive oxygen species (ROS)-dependent and ROS-independent mechanisms by which mitochondria can affect longevity. We discuss the role of different ROS (superoxide, hydrogen peroxide, and hydroxyl radical), both as oxidants as well as signaling molecules. We also describe how mitochondria can regulate longevity by ROS-independent mechanisms. We discuss alterations in mitochondrial DNA, accumulation of cellular waste as a consequence of glyco- and lipoxidative damage, and the regulation of DNA maintenance enzymes as mechanisms that can determine longevity without involving ROS. FUTURE DIRECTIONS We also show how the regulation of longevity is a complex process whereby ROS-dependent and ROS-independent mechanisms interact to determine the maximum lifespan of species and individuals.
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Affiliation(s)
- Filippo Scialo
- 1 Institute of Biomedical Technology and Tampere University Hospital , University of Tampere, Tampere, Finland
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47
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Zapico SC, Ubelaker DH. mtDNA Mutations and Their Role in Aging, Diseases and Forensic Sciences. Aging Dis 2013; 4:364-80. [PMID: 24307969 DOI: 10.14336/ad.2013.0400364] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/02/2013] [Accepted: 10/02/2013] [Indexed: 12/28/2022] Open
Abstract
Mitochondria are independent organelles with their own DNA. As a primary function, mitochondria produce the energy for the cell through Oxidative Phosphorylation (OXPHOS) in the Electron Transport Chain (ETC). One of the toxic products of this process is Reactive Oxygen Species (ROS), which can induce oxidative damage in macromolecules like lipids, proteins and DNA. Mitochondrial DNA (mtDNA) is less protected and has fewer reparation mechanisms than nuclear DNA (nDNA), and as such is more exposed to oxidative, mutation-inducing damage. This review analyzes the causes and consequences of mtDNA mutations and their relationship with the aging process. Neurodegenerative diseases, related with the aging, are consequences of mtDNA mutations resulting in a decrease in mitochondrial function. Also described are "mitochondrial diseases", pathologies produced by mtDNA mutations and whose symptoms are related with mitochondrial dysfunction. Finally, mtDNA haplogroups are defined in this review; these groups are important for determination of geographical origin of an individual. Additionally, different haplogroups exhibit variably longevity and risk of certain diseases. mtDNA mutations in aging and haplogroups are of special interest to forensic science research. Therefore this review will help to clarify the key role of mtDNA mutations in these processes and support further research in this area.
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Affiliation(s)
- Sara C Zapico
- Smithsonian Institution, National Museum of Natural History, Department of Anthropology, Washington, DC 20560, USA
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Kennedy SR, Salk JJ, Schmitt MW, Loeb LA. Ultra-sensitive sequencing reveals an age-related increase in somatic mitochondrial mutations that are inconsistent with oxidative damage. PLoS Genet 2013; 9:e1003794. [PMID: 24086148 PMCID: PMC3784509 DOI: 10.1371/journal.pgen.1003794] [Citation(s) in RCA: 254] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/29/2013] [Indexed: 01/12/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is believed to be highly vulnerable to age-associated damage and mutagenesis by reactive oxygen species (ROS). However, somatic mtDNA mutations have historically been difficult to study because of technical limitations in accurately quantifying rare mtDNA mutations. We have applied the highly sensitive Duplex Sequencing methodology, which can detect a single mutation among >107 wild type molecules, to sequence mtDNA purified from human brain tissue from both young and old individuals with unprecedented accuracy. We find that the frequency of point mutations increases ∼5-fold over the course of 80 years of life. Overall, the mutation spectra of both groups are comprised predominantly of transition mutations, consistent with misincorporation by DNA polymerase γ or deamination of cytidine and adenosine as the primary mutagenic events in mtDNA. Surprisingly, G→T mutations, considered the hallmark of oxidative damage to DNA, do not significantly increase with age. We observe a non-uniform, age-independent distribution of mutations in mtDNA, with the D-loop exhibiting a significantly higher mutation frequency than the rest of the genome. The coding regions, but not the D-loop, exhibit a pronounced asymmetric accumulation of mutations between the two strands, with G→A and T→C mutations occurring more often on the light strand than the heavy strand. The patterns and biases we observe in our data closely mirror the mutational spectrum which has been reported in studies of human populations and closely related species. Overall our results argue against oxidative damage being a major driver of aging and suggest that replication errors by DNA polymerase γ and/or spontaneous base hydrolysis are responsible for the bulk of accumulating point mutations in mtDNA. Owing to their evolutionary history, mitochondria harbor independently replicating genomes. Failure to faithfully transmit the genetic information of mtDNA during replication can lead to the production of dysfunctional electron transport proteins and a subsequent decline in energy production. Cellularly-derived reactive oxygen species (ROS) and environmental agents preferentially damage mtDNA compared to nuclear DNA. However, little is known about the consequences of mtDNA damage for mutagenesis. This lack of knowledge stems, in part, from an absence of methods capable of accurately detecting these mutations throughout the mitochondrial genome. Using a new, highly sensitive DNA sequencing strategy, we find that the frequency of point mutations is 10–100-fold lower than what has been previously reported using less precise means. Moreover, the frequency increases 5-fold over an 80 year lifespan. We also find that it is predominantly transition mutations, rather than mutations commonly associated with oxidative damage to mtDNA, that increase with age. This finding is inconsistent with free radical theories of aging. Finally, the mutagenic patterns and biases we observe in our data are similar to what is seen in population studies of mitochondrial polymorphisms and suggest a common mechanism by which somatic and germline mtDNA mutations arise.
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Affiliation(s)
- Scott R. Kennedy
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Jesse J. Salk
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Michael W. Schmitt
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Lawrence A. Loeb
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- Department of Biochemistry, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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49
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Kazachkova N, Ramos A, Santos C, Lima M. Mitochondrial DNA damage patterns and aging: revising the evidences for humans and mice. Aging Dis 2013; 4:337-50. [PMID: 24307967 DOI: 10.14336/ad.2013.0400337] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 01/07/2023] Open
Abstract
A significant body of work, accumulated over the years, strongly suggests that damage in mitochondrial DNA (mtDNA) contributes to aging in humans. Contradictory results, however, are reported in the literature, with some studies failing to provide support to this hypothesis. With the purpose of further understanding the aging process, several models, among which mouse models, have been frequently used. Although important affinities are recognized between humans and mice, differences on what concerns physiological properties, disease pathogenesis as well as life-history exist between the two; the extent to which such differences limit the translation, from mice to humans, of insights on the association between mtDNA damage and aging remains to be established. In this paper we revise the studies that analyze the association between patterns of mtDNA damage and aging, investigating putative alterations in mtDNA copy number as well as accumulation of deletions and of point mutations. Reports from the literature do not allow the establishment of a clear association between mtDNA copy number and age, either in humans or in mice. Further analysis, using a wide spectrum of tissues and a high number of individuals would be necessary to elucidate this pattern. Likewise humans, mice demonstrated a clear pattern of age-dependent and tissue-specific accumulation of mtDNA deletions. Deletions increase with age, and the highest amount of deletions has been observed in brain tissues both in humans and mice. On the other hand, mtDNA point mutations accumulation has been clearly associated with age in humans, but not in mice. Although further studies, using the same methodologies and targeting a larger number of samples would be mandatory to draw definitive conclusions, the revision of the available data raises concerns on the ability of mouse models to mimic the mtDNA damage patterns of humans, a fact with implications not only for the study of the aging process, but also for investigations of other processes in which mtDNA dysfunction is a hallmark, such as neurodegeneration.
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Affiliation(s)
- Nadiya Kazachkova
- Centre of Research in Natural Resources (CIRN), Department of Biology, University of the Azores, Ponta Delgada, Portugal ; Institute for Molecular and Cell Biology (IBMC), University of Porto, Porto, Portugal
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Kraytsberg Y, Nicholas A, Khrapko K. Are somatic mitochondrial DNA mutations relevant to our health? A challenge for mutation analysis techniques. ACTA ACUST UNITED AC 2013; 1:109-16. [PMID: 23489273 DOI: 10.1517/17530059.1.1.109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A role of somatic mitochondrial (mt)DNA mutations in ageing and degenerative diseases was postulated decades ago, but this hypothesis remains untested. A substantial number of genetically engineered 'mutator' mouse lines with increased mtDNA mutation rates were expected to test the hypothesis. However, the results of mutator experiments are inconclusive and their interpretations are often contradictory. The authors argue that the problem, to a great extent, is the absence of a universally accepted accurate methodology of mtDNA mutational analysis and hence the lack of consensus with respect to the actual fractions of mtDNA mutations. Estimates by different existing methods vary by more than two orders of magnitude and the reason for this enormous discrepancy has yet to be fully accounted for. Furthermore, studies usually lack the vitally important details, such as the analysis of individual cells and multiple cell types, which is indispensable for rigorous evaluation of the impact of mtDNA mutations. New methods capable of accurate and detailed mutational analysis of mtDNA are in great need. A cell-by-cell mutational analysis may offer a solution.
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