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Yazdani M. Cellular and Molecular Responses to Mitochondrial DNA Deletions in Kearns-Sayre Syndrome: Some Underlying Mechanisms. Mol Neurobiol 2024; 61:5665-5679. [PMID: 38224444 DOI: 10.1007/s12035-024-03938-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Kearns-Sayre syndrome (KSS) is a rare multisystem mitochondrial disorder. It is caused by mitochondrial DNA (mtDNA) rearrangements, mostly large-scale deletions of 1.1-10 kb. These deletions primarily affect energy supply through impaired oxidative phosphorylation and reduced ATP production. This impairment gives rise to dysfunction of several tissues, in particular those with high energy demand like brain and muscles. Over the past decades, changes in respiratory chain complexes and energy metabolism have been emphasized, whereas little attention has been paid to other reports on ROS overproduction, protein synthesis inhibition, myelin vacuolation, demyelination, autophagy, apoptosis, and involvement of lipid raft and oligodendrocytes in KSS. Therefore, this paper draws attention towards these relatively underemphasized findings that might further clarify the pathologic cascades following deletions in the mtDNA.
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Affiliation(s)
- Mazyar Yazdani
- Department of Medical Biochemistry, Oslo University Hospital, Rikshospitalet, Oslo, 0027, Norway.
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2
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Bernardino Gomes TM, Vincent AE, Menger KE, Stewart JB, Nicholls TJ. Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation. Biochem J 2024; 481:683-715. [PMID: 38804971 PMCID: PMC11346376 DOI: 10.1042/bcj20230262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies of mtDNA per cell, and their integrity, are maintained by nuclear-encoded mtDNA replication and repair machineries. Aberrant mtDNA replication and mtDNA breakage are believed to cause deletions within mtDNA. The genomic location and breakpoint sequences of these deletions show similar patterns across various inherited and acquired diseases, and are also observed during normal ageing, suggesting a common mechanism of deletion formation. However, an ongoing debate over the mechanism by which mtDNA replicates has made it difficult to develop clear and testable models for how mtDNA rearrangements arise and propagate at a molecular and cellular level. These deletions may impair energy metabolism if present in a high proportion of the mtDNA copies within the cell, and can be seen in primary mitochondrial diseases, either in sporadic cases or caused by autosomal variants in nuclear-encoded mtDNA maintenance genes. These mitochondrial diseases have diverse genetic causes and multiple modes of inheritance, and show notoriously broad clinical heterogeneity with complex tissue specificities, which further makes establishing genotype-phenotype relationships challenging. In this review, we aim to cover our current understanding of how the human mitochondrial genome is replicated, the mechanisms by which mtDNA replication and repair can lead to mtDNA instability in the form of large-scale rearrangements, how rearranged mtDNAs subsequently accumulate within cells, and the pathological consequences when this occurs.
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Affiliation(s)
- Tiago M. Bernardino Gomes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- NHS England Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, U.K
| | - Amy E. Vincent
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Katja E. Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - James B. Stewart
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Thomas J. Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
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3
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Cheng Q, Liu QQ, Lu CA. A state-of-the-science review of using mitochondrial DNA copy number as a biomarker for environmental exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123642. [PMID: 38402934 DOI: 10.1016/j.envpol.2024.123642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/06/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Mitochondria are bioenergetic, biosynthetic, and signaling organelles in eukaryotes, and contain their own genomes, mitochondrial DNA (mtDNA), to supply energy to cells by generating ATP via oxidative phosphorylation. Therefore, the threat to mitochondria' integrity and health resulting from environmental exposure could induce adverse health effects in organisms. In this review, we summarized the association between mtDNA copy number (mtDNAcn), and environmental exposures as reported in the literature. We conducted a literature search in the Web of Science using [Mitochondrial DNA copy number] and [Exposure] as two keywords and employed three selection criteria for the final inclusion of 97 papers for review. The consensus of data was that mtDNAcn could be used as a plausible biomarker for cumulative exposures to environmental chemical and physical agents. In order to furtherly expand the application of mtDNAcn in ecological and environmental health research, we suggested a series of algorithms aiming to standardize the calculation of mtDNAcn based on the PCR results in this review. We also discussed the pitfalls of using whole blood/plasma samples for mtDNAcn measurements and regard buccal cells a plausible and practical alternative. Finally, we recognized the importance of better understanding the mechanistic analysis and regulatory mechanism of mtDNAcn, in particular the signals release and regulation pathways. We believe that the development of using mtDNAcn as an exposure biomarker will revolutionize the evaluation of chronic sub-lethal toxicity of chemicals to organisms in ecological and environmental health research that has not yet been implemented.
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Affiliation(s)
- Qing Cheng
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Qing Qing Liu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Chensheng Alex Lu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China; School of Public Health, University of Washington, Seattle, WA, 98195, USA.
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4
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Vikramdeo KS, Sudan SK, Singh AP, Singh S, Dasgupta S. Mitochondrial respiratory complexes: Significance in human mitochondrial disorders and cancers. J Cell Physiol 2022; 237:4049-4078. [PMID: 36074903 DOI: 10.1002/jcp.30869] [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: 11/17/2021] [Revised: 07/18/2022] [Accepted: 08/23/2022] [Indexed: 11/07/2022]
Abstract
Mitochondria are pivotal organelles that govern cellular energy production through the oxidative phosphorylation system utilizing five respiratory complexes. In addition, mitochondria also contribute to various critical signaling pathways including apoptosis, damage-associated molecular patterns, calcium homeostasis, lipid, and amino acid biosynthesis. Among these diverse functions, the energy generation program oversee by mitochondria represents an immaculate orchestration and functional coordination between the mitochondria and nuclear encoded molecules. Perturbation in this program through respiratory complexes' alteration results in the manifestation of various mitochondrial disorders and malignancy, which is alarmingly becoming evident in the recent literature. Considering the clinical relevance and importance of this emerging medical problem, this review sheds light on the timing and nature of molecular alterations in various respiratory complexes and their functional consequences observed in various mitochondrial disorders and human cancers. Finally, we discussed how this wealth of information could be exploited and tailored to develop respiratory complex targeted personalized therapeutics and biomarkers for better management of various incurable human mitochondrial disorders and cancers.
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Affiliation(s)
- Kunwar Somesh Vikramdeo
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Sarabjeet Kour Sudan
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA
| | - Ajay P Singh
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Seema Singh
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
| | - Santanu Dasgupta
- Department of Pathology, Mitchell Cancer Institute, University of South Alabama, Mobile, Alabama, USA.,Department of Pathology, College of Medicine, University of South Alabama, Mobile, Alabama, USA.,Department of Biochemistry and Molecular Biology, University of South Alabama, Mobile, Alabama, USA
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5
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Abd Radzak SM, Mohd Khair SZN, Ahmad F, Patar A, Idris Z, Mohamed Yusoff AA. Insights regarding mitochondrial DNA copy number alterations in human cancer (Review). Int J Mol Med 2022; 50:104. [PMID: 35713211 PMCID: PMC9304817 DOI: 10.3892/ijmm.2022.5160] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/26/2022] [Indexed: 11/25/2022] Open
Abstract
Mitochondria are the critical organelles involved in various cellular functions. Mitochondrial biogenesis is activated by multiple cellular mechanisms which require a synchronous regulation between mitochondrial DNA (mtDNA) and nuclear DNA (nDNA). The mitochondrial DNA copy number (mtDNA-CN) is a proxy indicator for mitochondrial activity, and its alteration reflects mitochondrial biogenesis and function. Despite the precise mechanisms that modulate the amount and composition of mtDNA, which have not been fully elucidated, mtDNA-CN is known to influence numerous cellular pathways that are associated with cancer and as well as multiple other diseases. In addition, the utility of current technology in measuring mtDNA-CN contributes to its extensive assessment of diverse traits and tumorigenesis. The present review provides an overview of mtDNA-CN variations across human cancers and an extensive summary of the existing knowledge on the regulation and machinery of mtDNA-CN. The current information on the advanced methods used for mtDNA-CN assessment is also presented.
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Affiliation(s)
- Siti Muslihah Abd Radzak
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Siti Zulaikha Nashwa Mohd Khair
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Farizan Ahmad
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Azim Patar
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Zamzuri Idris
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
| | - Abdul Aziz Mohamed Yusoff
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan 16150, Malaysia
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6
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Longchamps RJ, Yang SY, Castellani CA, Shi W, Lane J, Grove ML, Bartz TM, Sarnowski C, Liu C, Burrows K, Guyatt AL, Gaunt TR, Kacprowski T, Yang J, De Jager PL, Yu L, Bergman A, Xia R, Fornage M, Feitosa MF, Wojczynski MK, Kraja AT, Province MA, Amin N, Rivadeneira F, Tiemeier H, Uitterlinden AG, Broer L, Van Meurs JBJ, Van Duijn CM, Raffield LM, Lange L, Rich SS, Lemaitre RN, Goodarzi MO, Sitlani CM, Mak ACY, Bennett DA, Rodriguez S, Murabito JM, Lunetta KL, Sotoodehnia N, Atzmon G, Ye K, Barzilai N, Brody JA, Psaty BM, Taylor KD, Rotter JI, Boerwinkle E, Pankratz N, Arking DE. Genome-wide analysis of mitochondrial DNA copy number reveals loci implicated in nucleotide metabolism, platelet activation, and megakaryocyte proliferation. Hum Genet 2022; 141:127-146. [PMID: 34859289 PMCID: PMC8758627 DOI: 10.1007/s00439-021-02394-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
Mitochondrial DNA copy number (mtDNA-CN) measured from blood specimens is a minimally invasive marker of mitochondrial function that exhibits both inter-individual and intercellular variation. To identify genes involved in regulating mitochondrial function, we performed a genome-wide association study (GWAS) in 465,809 White individuals from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and the UK Biobank (UKB). We identified 133 SNPs with statistically significant, independent effects associated with mtDNA-CN across 100 loci. A combination of fine-mapping, variant annotation, and co-localization analyses was used to prioritize genes within each of the 133 independent sites. Putative causal genes were enriched for known mitochondrial DNA depletion syndromes (p = 3.09 × 10-15) and the gene ontology (GO) terms for mtDNA metabolism (p = 1.43 × 10-8) and mtDNA replication (p = 1.2 × 10-7). A clustering approach leveraged pleiotropy between mtDNA-CN associated SNPs and 41 mtDNA-CN associated phenotypes to identify functional domains, revealing three distinct groups, including platelet activation, megakaryocyte proliferation, and mtDNA metabolism. Finally, using mitochondrial SNPs, we establish causal relationships between mitochondrial function and a variety of blood cell-related traits, kidney function, liver function and overall (p = 0.044) and non-cancer mortality (p = 6.56 × 10-4).
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Affiliation(s)
- R J Longchamps
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - S Y Yang
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - C A Castellani
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - W Shi
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - J Lane
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - M L Grove
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - T M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - C Sarnowski
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - C Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - K Burrows
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - A L Guyatt
- Department of Health Sciences, University of Leicester, University Road, Leicester, UK
| | - T R Gaunt
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - T Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
- Data Science in Biomedicine, Peter L. Reichertz Institute for Medical Informatics, TU Braunschweig and Hannover Medical School, Brunswick, Germany
| | - J Yang
- Rush Alzheimer's Disease Center and Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - P L De Jager
- Center for Translational and Systems Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - L Yu
- Rush Alzheimer's Disease Center and Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - A Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - R Xia
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - M Fornage
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, USA
| | - M F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, USA
| | - M K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, USA
| | - A T Kraja
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, USA
| | - M A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, USA
| | - N Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - F Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - H Tiemeier
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Social and Behavioral Science, Harvard T.H. School of Public Health, Boston, USA
| | - A G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - L Broer
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - J B J Van Meurs
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - C M Van Duijn
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - L M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - L Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - S S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R N Lemaitre
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - M O Goodarzi
- Division of Endocrinology, Diabetes and Metabolism, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - C M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - A C Y Mak
- Cardiovascular Research Institute and Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - D A Bennett
- Rush Alzheimer's Disease Center and Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - S Rodriguez
- MRC Integrative Epidemiology Unit at the University of Bristol, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, UK
| | - J M Murabito
- Boston University School of Medicine, Boston University, Boston, MA, USA
| | - K L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - N Sotoodehnia
- Cardiovascular Health Research Unit, Division of Cardiology, University of Washington, Seattle, WA, USA
| | - G Atzmon
- Department of Natural Science, University of Haifa, Haifa, Israel
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - K Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - N Barzilai
- Departments of Medicine and Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - J A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - B M Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, USA
| | - K D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - J I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - E Boerwinkle
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, Human Genetics Center, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, USA
| | - N Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - D E Arking
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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7
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BRAGARD LCA, SETE MRC, FREITAS-FERNANDES LB, SZTAJNBOK FR, FIGUEREDO CM, VALENTE AP, FIDALGO TKDS, SILVA FDB. Salivary metabolomic profile in adolescents with juvenile systemic lupus erythematosus. Braz Oral Res 2022; 36:e0128. [DOI: 10.1590/1807-3107bor-2022.vol36.0128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 06/02/2022] [Indexed: 11/13/2022] Open
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8
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Wu Z, Sainz AG, Shadel GS. Mitochondrial DNA: cellular genotoxic stress sentinel. Trends Biochem Sci 2021; 46:812-821. [PMID: 34088564 PMCID: PMC9809014 DOI: 10.1016/j.tibs.2021.05.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/24/2021] [Accepted: 05/08/2021] [Indexed: 02/08/2023]
Abstract
High copy number, damage prone, and lean on repair mechanisms are unique features of mitochondrial DNA (mtDNA) that are hard to reconcile with its essentiality for oxidative phosphorylation, the primary function ascribed to this maternally inherited component of our genome. We propose that mtDNA is also a genotoxic stress sentinel, as well as a direct second messenger of this type of cellular stress. Here, we discuss existing evidence for this sentinel/effector role through the ability of mtDNA to escape the confines of the mitochondrial matrix and activate nuclear DNA damage/repair responses via interferon-stimulated gene products and other downstream effectors. However, this arrangement may come at a cost, leading to cancer chemoresistance and contributing to inflammation, disease pathology, and aging.
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Affiliation(s)
- Zheng Wu
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA,Graduate Program in Genetics, Yale School of Medicine, New Haven, CT 06437, USA,These authors contributed equally to this work
| | - Alva G. Sainz
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA,Graduate Program in Experimental Pathology, Yale School of Medicine, New Haven, CT 06437, USA,These authors contributed equally to this work
| | - Gerald S. Shadel
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA,Correspondence: (G.S. Shadel)
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9
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Jang YH, Ahn SR, Shim JY, Lim KI. Engineering Genetic Systems for Treating Mitochondrial Diseases. Pharmaceutics 2021; 13:810. [PMID: 34071708 PMCID: PMC8227772 DOI: 10.3390/pharmaceutics13060810] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/23/2021] [Accepted: 05/24/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondria are intracellular energy generators involved in various cellular processes. Therefore, mitochondrial dysfunction often leads to multiple serious diseases, including neurodegenerative and cardiovascular diseases. A better understanding of the underlying mitochondrial dysfunctions of the molecular mechanism will provide important hints on how to mitigate the symptoms of mitochondrial diseases and eventually cure them. In this review, we first summarize the key parts of the genetic processes that control the physiology and functions of mitochondria and discuss how alterations of the processes cause mitochondrial diseases. We then list up the relevant core genetic components involved in these processes and explore the mutations of the components that link to the diseases. Lastly, we discuss recent attempts to apply multiple genetic methods to alleviate and further reverse the adverse effects of the core component mutations on the physiology and functions of mitochondria.
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Affiliation(s)
- Yoon-ha Jang
- Department of Chemical and Biological Engineering, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Korea; (Y.-h.J.); (J.-y.S.)
| | - Sae Ryun Ahn
- Industry Collaboration Center, Industry-Academic Cooperation Foundation, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Korea;
| | - Ji-yeon Shim
- Department of Chemical and Biological Engineering, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Korea; (Y.-h.J.); (J.-y.S.)
| | - Kwang-il Lim
- Department of Chemical and Biological Engineering, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Korea; (Y.-h.J.); (J.-y.S.)
- Industry Collaboration Center, Industry-Academic Cooperation Foundation, Sookmyung Women’s University, Yongsan-gu, Seoul 04310, Korea;
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10
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Kirby CS, Patel MR. Elevated mitochondrial DNA copy number found in ubiquinone-deficient clk-1 mutants is not rescued by ubiquinone precursor 2-4-dihydroxybenzoate. Mitochondrion 2021; 58:38-48. [PMID: 33581333 DOI: 10.1016/j.mito.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/13/2021] [Accepted: 02/01/2021] [Indexed: 01/28/2023]
Abstract
Inside mitochondria reside semi-autonomous genomes, called mtDNA. mtDNA is multi-copy per cell and mtDNA copy number can vary from hundreds to thousands of copies per cell. The variability of mtDNA copy number between tissues, combined with the lack of variability of copy number within a tissue, suggest a homeostatic copy number regulation mechanism. Mutations in the gene encoding the Caenorhabditis elegans hydroxylase, CLK-1, result in elevated mtDNA. CLK-1's canonical role in ubiquinone biosynthesis results in clk-1 mutants lacking ubiquinone. Importantly, clk-1 mutants also exhibit slowed biological timing phenotypes (pharyngeal pumping, defecation, development) and an activated stress response (UPRmt). These biological timing and stress phenotypes have been attributed to ubiquinone deficiency; however, it is unknown whether the mtDNA phenotype is also due to ubiquinone deficiency. To test this, in animals carrying the uncharacterized clk-1 (ok1247) mutant allele, we supplemented with an exogenous ubiquinone precursor 2-4-dihydroxybenzoate (DHB), which has previously been shown to restore ubiquinone biosynthesis. We measured phenotypes as a function of DHB across a log-scale range. Unlike the biological timing and stress phenotypes, the elevated mtDNA phenotype was not rescued. Since CLK-1's canonical role is in ubiquinone biosynthesis and DHB does not rescue mtDNA copy number, we infer CLK-1 has an additional function in homeostatic mtDNA copy number regulation.
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Affiliation(s)
- Cait S Kirby
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Diabetes Research and Training Center, Vanderbilt University, Nashville, TN 37232, USA.
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11
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Young CKJ, Wheeler JH, Rahman MM, Young MJ. The antiretroviral 2',3'-dideoxycytidine causes mitochondrial dysfunction in proliferating and differentiated HepaRG human cell cultures. J Biol Chem 2021; 296:100206. [PMID: 33334881 PMCID: PMC7948951 DOI: 10.1074/jbc.ra120.014885] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) were the first drugs used to treat human immunodeficiency virus infection, and their use can cause mitochondrial toxicity, including mitochondrial DNA (mtDNA) depletion in several cases. The first-generation NRTIs, including 2',3'-dideoxycytidine (ddC), were originally and are still pursued as anticancer agents. NRTI-sensitive DNA polymerases localizing to mitochondria allow for the opportunity to poison proliferating cancer cell mtDNA replication as certain cancers rely heavily on mitochondrial functions. However, mtDNA replication is independent of the cell cycle creating a significant concern that toxicants such as ddC impair mtDNA maintenance in both proliferating and nonproliferating cells. To examine this possibility, we tested the utility of the HepaRG cell line to study ddC-induced toxicity in isogenic proliferating (undifferentiated) and nonproliferating (differentiated) cells. Following ddC exposures, we measured cell viability, mtDNA copy number, and mitochondrial bioenergetics utilizing trypan blue, Southern blotting, and extracellular flux analysis, respectively. After 13 days of 1 μM ddC exposure, proliferating and differentiated HepaRG harbored mtDNA levels of 0.9% and 17.9% compared with control cells, respectively. Cells exposed to 12 μM ddC contained even less mtDNA. By day 13, differentiated cell viability was maintained but declined for proliferating cells. Proliferating HepaRG bioenergetic parameters were severely impaired by day 8, with 1 and 12 μM ddC, whereas differentiated cells displayed defects of spare and maximal respiratory capacities (day 8) and proton-leak linked respiration (day 14) with 12 μM ddC. These results indicate HepaRG is a useful model to study proliferating and differentiated cell mitochondrial toxicant exposures.
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Affiliation(s)
- Carolyn K J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA
| | - Joel H Wheeler
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA
| | - Md Mostafijur Rahman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA
| | - Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA.
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12
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Jaiswal KS, Khanna S, Ghosh A, Padhan P, Raghav SK, Gupta B. Differential mitochondrial genome in patients with Rheumatoid Arthritis. Autoimmunity 2020; 54:1-12. [PMID: 33191792 DOI: 10.1080/08916934.2020.1846182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Mitochondria play an important role in cell survival, function and lineage differentiation. Changes in mitochondrial DNA (mtDNA) may control mitochondrial functions and thus may impart an alternative cellular state thereby leading to a disease condition in the body. Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease wherein immune cells become self-reactive causing joint inflammation, swelling and pain in patients. The changes in mtDNA may alter cellular functions thereby directing the immune cells towards an inflammatory phenotype in RA. Therefore, it becomes pertinent to identify changes in mtDNA sequence in immune cells of RA patients to understand the pathogenesis and progression of RA. METHODS mtDNA from peripheral blood mono-nuclear cells (PBMCs) of 23 RA patients and 17 healthy controls (HCs) were sequenced using next-generation sequencing (NGS). Further, single nucleotide polymorphisms (SNPs) and other variable changes in mtDNA hypervariable and coding regions, amino acid changes with a putative impact on disease, levels of heteroplasmy, copy number variations and haplogroup analysis in RA patients and HCs were analysed and compared to identify any association of mtDNA changes and RA disease. RESULTS A total of 382 single nucleotide mtDNA variants were observed, 91 (23.82%) were present in hypervariable region and 291 (76.18%) in coding region of patients and HC. The variant 513 GCA > ACA, with G present in HVR-III, known to control the mitochondrial translation function, was significantly present in RA patients. The CYTB gene had larger number of SNPs in HC samples while RNR2 was more variable in RA patients. A non-synonymous heteroplasmy in ND1 gene was found at a single nucleotide position 3533 in an increased number of RA patients as compared to the controls. A significant increase in mtDNA duplication and a higher frequency of the haplogroup U was also characteristic of RA. Also, the presence of SNPs in mitochondrial tRNA genes at two positions 12308 A > G and 15924 A > G were found to be pathogenic. CONCLUSION We herein observed an altered mtDNA sequence in immune cells of RA patients and thus a possible role of mitochondrial genome in the development of RA. The observed nucleotide changes in mtDNA control region, RNR2 gene, increased heteroplasmy and mtDNA duplication in RA patients may alter sites for transcription factor binding thereby influencing mtDNA gene expression, as well as copy numbers thereby affecting the mitochondrial proteins and their functions. These changes in mtDNA could be one of the probable reasons among many leading to the progression of RA.
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Affiliation(s)
- Kumar Sagar Jaiswal
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Shweta Khanna
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Arup Ghosh
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Prasanta Padhan
- Department of Rheumatology, Kalinga Institute of Medical Sciences, Bhubaneswar, India
| | - Sunil Kumar Raghav
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Bhawna Gupta
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
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13
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Hoitzing H, Gammage PA, Haute LV, Minczuk M, Johnston IG, Jones NS. Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations. PLoS Comput Biol 2019; 15:e1007023. [PMID: 31242175 PMCID: PMC6615642 DOI: 10.1371/journal.pcbi.1007023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 07/09/2019] [Accepted: 04/11/2019] [Indexed: 12/28/2022] Open
Abstract
The dynamics of the cellular proportion of mutant mtDNA molecules is crucial for mitochondrial diseases. Cellular populations of mitochondria are under homeostatic control, but the details of the control mechanisms involved remain elusive. Here, we use stochastic modelling to derive general results for the impact of cellular control on mtDNA populations, the cost to the cell of different mtDNA states, and the optimisation of therapeutic control of mtDNA populations. This formalism yields a wealth of biological results, including that an increasing mtDNA variance can increase the energetic cost of maintaining a tissue, that intermediate levels of heteroplasmy can be more detrimental than homoplasmy even for a dysfunctional mutant, that heteroplasmy distribution (not mean alone) is crucial for the success of gene therapies, and that long-term rather than short intense gene therapies are more likely to beneficially impact mtDNA populations.
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Affiliation(s)
- Hanne Hoitzing
- Department of Mathematics, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Payam A. Gammage
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
- CRUK Beatson Institute for Cancer Research, Glasgow, United Kingdom
| | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Iain G. Johnston
- Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
- Alan Turing Institute, London, United Kingdom
| | - Nick S. Jones
- Department of Mathematics, Imperial College London, London, SW7 2AZ, United Kingdom
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14
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Wang Y, Zhao J, Liu X, Li W, Ouyang S, Zhu X. Identification of SNPs and copy number variations in mitochondrial genes related to the reproductive capacity of the cultured Asian yellow pond turtle (Mauremys mutica). Anim Reprod Sci 2019; 205:78-87. [DOI: 10.1016/j.anireprosci.2019.04.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/13/2019] [Accepted: 04/22/2019] [Indexed: 01/20/2023]
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15
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Karimova A, Hacioğlu Y, Bahtiyar N, Niyazoğlu M, Akbaş F, Yilmaz E, Ulutin T, Onaran I. Increased mitochondrial common deletion in platelets from patients with type 2 diabetes is not associated with abnormal platelet activity or mitochondrial function. Mol Med Rep 2018; 18:3529-3536. [PMID: 30066943 DOI: 10.3892/mmr.2018.9340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/07/2018] [Indexed: 11/05/2022] Open
Abstract
The present study examined the presence and frequency of the 4,977‑base pair mitochondrial (mt)DNA (mtDNA4977) deletion in blood platelets, and whether increased mtDNA4977 deletion was associated with abnormal mitochondrial and platelet function in type 2 diabetes mellitus. A total of 66 patients with type 2 diabetes mellitus and 23 healthy subjects were included in the present study. Patients were divided into three subgroups according to glycemic control, and the presence or absence of chronic diabetic complications: i) Good glycemic control [glycated hemoglobin (HbA1c) <7] without complications; ii) poor glycemic control (HbA1c ≥7) without complications; and iii) poor glycemic control (HbA1c ≥7) with complications. mtDNA4977 deletion, mtDNA copy number, adenine nucleotides, mitochondrial membrane potential and P‑selectin expression levels were analyzed in platelets. Although the frequency of mtDNA4977 deletion in platelets of the patient (96.9%) and control groups (95.6%) was extremely similar, the deletion level significantly increased in all the diabetic groups, compared with the healthy control group. However, the data from the present study revealed that an increased deletion frequency in platelets was not associated with disease severity, although there was clear interindividual variability. Furthermore, all other parameters were not significantly different among the groups, and there were no correlations between mtDNA4977 deletion frequency and all other studied parameters for any of the case groups. The results indicated that the mtDNA4977 deletion occurred in platelets, and increased deletion in patients with type 2 diabetes did not have a marked influence on mitochondrial and/or platelet dysfunction, when compared with the non‑diabetic subjects. Further research is required to elucidate the sources of inter‑individual variability observed in certain parameters.
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Affiliation(s)
- Ayla Karimova
- Department of Medical Biology and Genetics, Cerrahpasa Faculty of Medicine, Istanbul University, 34098 Istanbul, Turkey
| | - Yalçin Hacioğlu
- Department of Family Medicine, Istanbul Training and Research Hospital, 34098 Istanbul, Turkey
| | - Nurten Bahtiyar
- Department of Biophysics, Cerrahpasa Faculty of Medicine, Istanbul University, 34098 Istanbul, Turkey
| | - Mutlu Niyazoğlu
- Department of Endocrinology, Istanbul Training and Research Hospital, 34098 Istanbul, Turkey
| | - Fahri Akbaş
- Department of Medical Biology, Faculty of Medicine at Bezmialem Vakif University, 34093 Istanbul, Turkey
| | - Erkan Yilmaz
- Tissue Typing Laboratory, Cerrahpasa Faculty of Medicine, Istanbul University, 34098 Istanbul, Turkey
| | - Turgut Ulutin
- Department of Medical Biology and Genetics, Cerrahpasa Faculty of Medicine, Istanbul University, 34098 Istanbul, Turkey
| | - Ilhan Onaran
- Department of Medical Biology and Genetics, Cerrahpasa Faculty of Medicine, Istanbul University, 34098 Istanbul, Turkey
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16
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von Renesse A, Morales-Gonzalez S, Gill E, Salomons GS, Stenzel W, Schuelke M. Muscle Weakness, Cardiomyopathy, and L-2-Hydroxyglutaric Aciduria Associated with a Novel Recessive SLC25A4 Mutation. JIMD Rep 2018; 43:27-35. [PMID: 29654543 DOI: 10.1007/8904_2018_93] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/23/2018] [Accepted: 02/01/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Mutations in SLC25A4 (syn. ANT1, Adenine nucleotide translocase, type 1) are known to cause either autosomal dominant progressive external ophthalmoplegia (adPEO) or recessive mitochondrial myopathy, hypertrophic cardiomyopathy, and lactic acidosis. METHODS AND RESULTS Whole exome sequencing in a young man with myopathy, subsarcolemmal mitochondrial aggregations, cardiomyopathy, lactic acidosis, and L-2-hydroxyglutaric aciduria (L-2-HGA) revealed a new homozygous mutation in SLC25A4 [c.653A>C, NM_001151], leading to the replacement of a highly conserved glutamine by proline [p.(Q218P); NP_001142] that most likely affects the folding of the ANT1 protein. No pathogenic mutation was found in L2HGDH, which is associated with "classic" L-2-HGA. Furthermore, L-2-HGDH enzymatic activity in the patient fibroblasts was normal. Long-range PCR and Southern blot confirmed absence of mtDNA-deletions in blood and muscle. CONCLUSION The disturbed ADP/ATP transport across the inner mitochondrial membrane may lead to an accumulation of different TCA-cycle intermediates such as 2-ketoglutarate (2-KG) in our patient. As L-2-HG is generated from 2-KG we hypothesize that the L-2-HG increase is a secondary effect of 2-KG accumulation. Hence, our report expands the spectrum of laboratory findings in ANT1-related diseases and hints towards a connection with organic acidurias.
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Affiliation(s)
- Anja von Renesse
- NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.,Department of Neuropediatrics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Susanne Morales-Gonzalez
- NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Esther Gill
- NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Gajja S Salomons
- Metabolic Unit, Department of Clinical Chemistry, Amsterdam Neuroscience, VU University Medical Center, Amsterdam, The Netherlands
| | - Werner Stenzel
- Department of Neuropathology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Markus Schuelke
- NeuroCure Clinical Research Center, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany. .,Department of Neuropediatrics, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany.
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17
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Siegmund SE, Yang H, Sharma R, Javors M, Skinner O, Mootha V, Hirano M, Schon EA. Low-dose rapamycin extends lifespan in a mouse model of mtDNA depletion syndrome. Hum Mol Genet 2017; 26:4588-4605. [PMID: 28973153 PMCID: PMC5886265 DOI: 10.1093/hmg/ddx341] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/31/2017] [Accepted: 08/24/2017] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial disorders affecting oxidative phosphorylation (OxPhos) are caused by mutations in both the nuclear and mitochondrial genomes. One promising candidate for treatment is the drug rapamycin, which has been shown to extend lifespan in multiple animal models, and which was previously shown to ameliorate mitochondrial disease in a knock-out mouse model lacking a nuclear-encoded gene specifying an OxPhos structural subunit (Ndufs4). In that model, relatively high-dose intraperitoneal rapamycin extended lifespan and improved markers of neurological disease, via an unknown mechanism. Here, we administered low-dose oral rapamycin to a knock-in (KI) mouse model of authentic mtDNA disease, specifically, progressive mtDNA depletion syndrome, resulting from a mutation in the mitochondrial nucleotide salvage enzyme thymidine kinase 2 (TK2). Importantly, low-dose oral rapamycin was sufficient to extend Tk2KI/KI mouse lifespan significantly, and did so in the absence of detectable improvements in mitochondrial dysfunction. We found no evidence that rapamycin increased survival by acting through canonical pathways, including mitochondrial autophagy. However, transcriptomics and metabolomics analyses uncovered systemic metabolic changes pointing to a potential 'rapamycin metabolic signature.' These changes also implied that rapamycin may have enabled the Tk2KI/KI mice to utilize alternative energy reserves, and possibly triggered indirect signaling events that modified mortality through developmental reprogramming. From a therapeutic standpoint, our results support the possibility that low-dose rapamycin, while not targeting the underlying mtDNA defect, could represent a crucial therapy for the treatment of mtDNA-driven, and some nuclear DNA-driven, mitochondrial diseases.
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Affiliation(s)
| | | | - Rohit Sharma
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Martin Javors
- Department of Psychiatry, University of Texas, San Antonio, TX 78229, USA
| | - Owen Skinner
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Vamsi Mootha
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Eric A Schon
- Department of Neurology
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
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18
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Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR. Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans. Cell Metab 2016; 24:91-103. [PMID: 27411011 PMCID: PMC5287496 DOI: 10.1016/j.cmet.2016.06.008] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/27/2016] [Accepted: 06/13/2016] [Indexed: 02/08/2023]
Abstract
Mutant mitochondrial genomes (mtDNA) can be viewed as selfish genetic elements that persist in a state of heteroplasmy despite having potentially deleterious metabolic consequences. We sought to study regulation of selfish mtDNA dynamics. We establish that the large 3.1-kb deletion-bearing mtDNA variant uaDf5 is a selfish genome in Caenorhabditis elegans. Next, we show that uaDf5 mutant mtDNA replicates in addition to, not at the expense of, wild-type mtDNA. These data suggest the existence of a homeostatic copy-number control that is exploited by uaDf5 to "hitchhike" to high frequency. We also observe activation of the mitochondrial unfolded protein response (UPR(mt)) in uaDf5 animals. Loss of UPR(mt) causes a decrease in uaDf5 frequency, whereas its constitutive activation increases uaDf5 levels. UPR(mt) activation protects uaDf5 from mitophagy. Taken together, we propose that mtDNA copy-number control and UPR(mt) represent two homeostatic response mechanisms that play important roles in regulating selfish mitochondrial genome dynamics.
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Affiliation(s)
- Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Interdisciplinary Graduate Program, Vanderbilt University, Nashville, TN 37232, USA
| | - Cait S Kirby
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Biological Sciences Graduate Program, Vanderbilt University, Nashville, TN 37232, USA
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Rama D Gangula
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Simon A Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA 6150, Australia
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
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19
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Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions. Sci Rep 2016; 6:25186. [PMID: 27122135 PMCID: PMC4848546 DOI: 10.1038/srep25186] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 04/12/2016] [Indexed: 02/05/2023] Open
Abstract
Mitochondrial DNA (mtDNA) mutations are a common cause of primary mitochondrial disorders, and have also been implicated in a broad collection of conditions, including aging, neurodegeneration, and cancer. Prevalent among these pathogenic variants are mtDNA deletions, which show a strong bias for the loss of sequence in the major arc between, but not including, the heavy and light strand origins of replication. Because individual mtDNA deletions can accumulate focally, occur with multiple mixed breakpoints, and in the presence of normal mtDNA sequences, methods that detect broad-spectrum mutations with enhanced sensitivity and limited costs have both research and clinical applications. In this study, we evaluated semi-quantitative and digital PCR-based methods of mtDNA deletion detection using double-stranded reference templates or biological samples. Our aim was to describe key experimental assay parameters that will enable the analysis of low levels or small differences in mtDNA deletion load during disease progression, with limited false-positive detection. We determined that the digital PCR method significantly improved mtDNA deletion detection sensitivity through absolute quantitation, improved precision and reduced assay standard error.
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20
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Chattopadhyay E, De Sarkar N, Singh R, Ray A, Roy R, Paul RR, Pal M, Ghose S, Ghosh S, Kabiraj D, Banerjee R, Roy B. Genome-wide mitochondrial DNA sequence variations and lower expression of OXPHOS genes predict mitochondrial dysfunction in oral cancer tissue. Tumour Biol 2016; 37:11861-11871. [PMID: 27055661 DOI: 10.1007/s13277-016-5026-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/18/2016] [Indexed: 12/17/2022] Open
Abstract
Several studies reported that mtDNA mutations may play important roles in carcinogenesis although the mechanism is not clear yet. Most of the studies compared mtDNA sequences in a tumor with those in normal tissues from different individuals ignoring inter-individual variations. In this study, 271 SNPs, 7 novel SNPs (or SNVs), and 15 somatic mutations were detected in mtDNA of 8 oral cancer tissues with respect to reference (rCRS) and adjacent normal tissues, respectively, using Ion PGM next generation sequencing method. Most of the sequence variations (76 SNPs and 1 somatic) are present in D-loop region followed by CyB (36 SNPs), ATP6 (24 SNPs), ND5 (17 SNPs and 5 somatic), ND4 (18 coding and 2 somatic) and other non-coding and coding DNA sequences. A total of 53 and 8 non-synonymous SNPs and somatic mutations, respectively, were detected in tumor tissues and some of these variations may have deleterious effects on the protein function as predicted by bioinformatic analysis. Moreover, significantly low mtDNA contents and expression of several mitochondrial genes in tumor compared to adjacent normal tissues may have also affected mitochondrial functions. Taken together, this study suggests that mtDNA mutations as well as low expression of mtDNA coded genes may play important roles in tumor growth. Although the sample size is low, an important aspect of the study is the use of adjacent control tissues to find out somatic mutations and a change in the expression of mitochondrial genes, to rule out inter-individual and inter-tissue variations which are important issues in the study of mitochondrial genomics.
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Affiliation(s)
- Esita Chattopadhyay
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
| | - Navonil De Sarkar
- Fred Hutchinson Cancer Research center, University of Washington, Seattle, WA, USA
| | - Richa Singh
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
| | - Anindita Ray
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
| | - Roshni Roy
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India
| | - Ranjan Rashmi Paul
- Department of Oral Pathology, Guru Nanak Institute of Dental Science & Research, 157/F Nilganj Road, Kolkata, 700114, India
| | - Mousumi Pal
- Department of Oral Pathology, Guru Nanak Institute of Dental Science & Research, 157/F Nilganj Road, Kolkata, 700114, India
| | - Sandip Ghose
- Department of Oral Pathology, Dr. R Ahmed Dental College and Hospital, 114- AJC Bose Road, Kolkata, 700014, India
| | - Subhrendu Ghosh
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (formerly known as WBUT), BF-142, Sector 1, Salt Lake City, Kolkata, 700064, India
| | - Debajyoti Kabiraj
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (formerly known as WBUT), BF-142, Sector 1, Salt Lake City, Kolkata, 700064, India
| | - Raja Banerjee
- Department of Bioinformatics, Maulana Abul Kalam Azad University of Technology, West Bengal (formerly known as WBUT), BF-142, Sector 1, Salt Lake City, Kolkata, 700064, India
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology West Bengal (formerly known as WBUT), BF-142, Sector 1, Salt Lake City, Kolkata, 700064, India
| | - Bidyut Roy
- Human Genetics Unit, Indian Statistical Institute, 203 B T Road, Kolkata, 700108, India.
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21
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Zhang J, Ma J, Long K, Jin L, Liu Y, Zhou C, Tian S, Chen L, Luo Z, Tang Q, Jiang A, Wang X, Wang D, Jiang Z, Wang J, Li X, Li M. Dynamic gene expression profiles during postnatal development of porcine subcutaneous adipose. PeerJ 2016; 4:e1768. [PMID: 26989614 PMCID: PMC4793310 DOI: 10.7717/peerj.1768] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/16/2016] [Indexed: 02/04/2023] Open
Abstract
A better understanding of the control of lipogenesis is of critical importance for both human and animal physiology. This requires a better knowledge of the changes of gene expression during the process of adipose tissue development. Thus, the objective of the current study was to determine the effects of development on subcutaneous adipose tissue gene expression in growing and adult pigs. Here, we present a comprehensive investigation of mRNA transcriptomes in porcine subcutaneous adipose tissue across four developmental stages using digital gene expression profiling. We identified 3,274 differential expressed genes associated with oxidative stress, immune processes, apoptosis, energy metabolism, insulin stimulus, cell cycle, angiogenesis and translation. A set of universally abundant genes (ATP8, COX2, COX3, ND1, ND2, SCD and TUBA1B) was found across all four developmental stages. This set of genes may play important roles in lipogenesis and development. We also identified development-related gene expression patterns that are linked to the different adipose phenotypes. We showed that genes enriched in significantly up-regulated profiles were associated with phosphorylation and angiogenesis. In contrast, genes enriched in significantly down-regulated profiles were related to cell cycle and cytoskeleton organization, suggesting an important role for these biological processes in adipose growth and development. These results provide a resource for studying adipose development and promote the pig as a model organism for researching the development of human obesity, as well as being used in the pig industry.
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Affiliation(s)
- Jie Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China.,Department of Animal Science, Southwest University at Rongchang, Chongqing, China
| | - Jideng Ma
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Keren Long
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Yihui Liu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Chaowei Zhou
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China.,Department of Aquaculture, Southwest University at Rongchang, Chongqing, China
| | - Shilin Tian
- Novogene Bioinformatics Institute, Beijing, China
| | - Lei Chen
- Chongqing Academy of Animal Science, Chongqing, China
| | - Zonggang Luo
- Department of Animal Science, Southwest University at Rongchang, Chongqing, China.,Chongqing Academy of Animal Science, Chongqing, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - An'an Jiang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Xun Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Dawei Wang
- Novogene Bioinformatics Institute, Beijing, China
| | - Zhi Jiang
- Novogene Bioinformatics Institute, Beijing, China
| | - Jinyong Wang
- Chongqing Academy of Animal Science, Chongqing, China
| | - Xuewei Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an, Sichuan, China
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Li X, Xu L, Zhou W, Zhao Q, Wang Y. Chronic exposure to microcystin-LR affected mitochondrial DNA maintenance and caused pathological changes of lung tissue in mice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 210:48-56. [PMID: 26706032 DOI: 10.1016/j.envpol.2015.12.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 11/11/2015] [Accepted: 12/01/2015] [Indexed: 06/05/2023]
Abstract
Microcystin-LR (MC-LR), an important variant of cyanotoxin family, was frequently encountered in the contaminated aquatic environment and taken as a potent hepatotoxin. However, a little was known on the association between the long-term MC-LR exposure and lung damage. In this study, we investigated the changes of the pulmonary histopathology, mitochondrial DNA (mtDNA) integrity and the expression of mtDNA encoded genes in the mice with chronic exposed to MC-LR at different concentrations (1, 5, 10, 20 and 40 μg/L) for 12 months. Our results showed that the long-term and persistent exposure to MC-LR disturbed the balance of redox system, influenced mtDNA stability, changed the expression of mitochondrial genes in the lung cells. Notably, MC-LR exposure influenced the level of inflammatory cytokines and resulted in thickening of the alveolar septa. In conclusion, chronic exposure to MC-LR affected mtDNA maintenance, and caused lung impairment in mice.
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Affiliation(s)
- Xinxiu Li
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
| | - Lizhi Xu
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
| | - Wei Zhou
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
| | - Qingya Zhao
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China
| | - Yaping Wang
- Department of Medical Genetics, Nanjing University School of Medicine, Nanjing, 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, 210093, China.
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23
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Cai N, Li Y, Chang S, Liang J, Lin C, Zhang X, Liang L, Hu J, Chan W, Kendler KS, Malinauskas T, Huang GJ, Li Q, Mott R, Flint J. Genetic Control over mtDNA and Its Relationship to Major Depressive Disorder. Curr Biol 2015; 25:3170-7. [PMID: 26687620 PMCID: PMC4691240 DOI: 10.1016/j.cub.2015.10.065] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/07/2015] [Accepted: 10/28/2015] [Indexed: 12/25/2022]
Abstract
Control over the number of mtDNA molecules per cell appears to be tightly regulated, but the mechanisms involved are largely unknown. Reversible alterations in the amount of mtDNA occur in response to stress suggesting that control over the amount of mtDNA is involved in stress-related diseases including major depressive disorder (MDD). Using low-coverage sequence data from 10,442 Chinese women to compute the normalized numbers of reads mapping to the mitochondrial genome as a proxy for the amount of mtDNA, we identified two loci that contribute to mtDNA levels: one within the TFAM gene on chromosome 10 (rs11006126, p value = 8.73 × 10(-28), variance explained = 1.90%) and one over the CDK6 gene on chromosome 7 (rs445, p value = 6.03 × 10(-16), variance explained = 0.50%). Both loci replicated in an independent cohort. CDK6 is thus a new molecule involved in the control of mtDNA. We identify increased rates of heteroplasmy in women with MDD, and show from an experimental paradigm using mice that the increase is likely due to stress. Furthermore, at least one heteroplasmic variant is significantly associated with changes in the amount of mtDNA (position 513, p value = 3.27 × 10(-9), variance explained = 0.48%) suggesting site-specific heteroplasmy as a possible link between stress and increase in amount of mtDNA. These findings indicate the involvement of mitochondrial genome copy number and sequence in an organism's response to stress.
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Affiliation(s)
- Na Cai
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Yihan Li
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Simon Chang
- Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan 33302, Taiwan
| | - Jieqin Liang
- BGI-Shenzhen, Floor 9 Complex Building, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Chongyun Lin
- BGI-Shenzhen, Floor 9 Complex Building, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Xiufei Zhang
- BGI-Shenzhen, Floor 9 Complex Building, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Lu Liang
- BGI-Shenzhen, Floor 9 Complex Building, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Jingchu Hu
- BGI-Shenzhen, Floor 9 Complex Building, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Wharton Chan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Tomas Malinauskas
- Cold Spring Harbor Laboratory, Beckman Building, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Guo-Jen Huang
- Department and Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan 33302, Taiwan
| | - Qibin Li
- BGI-Shenzhen, Floor 9 Complex Building, Beishan Industrial Zone, Yantian District, Shenzhen, Guangdong 518083, China
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK
| | - Jonathan Flint
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, UK.
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24
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van Osch FHM, Voets AM, Schouten LJ, Gottschalk RWH, Simons CCJM, van Engeland M, Lentjes MHFM, van den Brandt PA, Smeets HJM, Weijenberg MP. Mitochondrial DNA copy number in colorectal cancer: between tissue comparisons, clinicopathological characteristics and survival. Carcinogenesis 2015; 36:1502-10. [PMID: 26476438 DOI: 10.1093/carcin/bgv151] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/07/2015] [Indexed: 12/29/2022] Open
Abstract
Low mitochondrial DNA (mtDNA) copy number in tumors has been associated with worse prognosis in colorectal cancer (CRC). This study further deciphers the role of mtDNA copy number in CRC by comparing mtDNA copy number between healthy, adenoma and carcinoma tissue, by investigating its association according to several clinicopathological characteristics in CRC, and by relating it to CRC-specific survival in CRC patients. A hospital-based series of samples including cancer, adenoma and adjacent histologically normal tissue from primary CRC patients (n = 56) and recurrent CRC (n = 16) was studied as well as colon mucosa samples from healthy subjects (n = 76). Furthermore, mtDNA copy number was assessed in carcinomas of 693 CRC cases identified from the population-based Netherlands Cohort Study (NLCS). MtDNA copy number was significantly lower in carcinoma tissue (P = 0.011) and adjacent tissue (P < 0.001) compared to earlier resected adenoma tissue and in primary CRC tissue compared to recurrent CRC tissue (P = 0.011). Within both study populations, mtDNA copy number was significantly lower in mutated BRAF (P = 0.027 and P = 0.006) and in microsatellite unstable (MSI) tumors (P = 0.033 and P < 0.001) and higher in KRAS mutated tumors (P = 0.004). Furthermore, the association between mtDNA and survival seemed to follow an inverse U-shape with the highest HR observed in the second quintile of mtDNA copy number (HR = 1.70, 95% CI = 1.18, 2.44) compared to the first quintile. These results might reflect an association of mtDNA copy number with various malignant processes in cancer cells and warrants further research on tumor energy metabolism in CRC prognosis.
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Affiliation(s)
| | | | | | | | | | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht 6200MD, The Netherlands
| | - Marjolein H F M Lentjes
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht 6200MD, The Netherlands
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25
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Li X, Zhao Q, Zhou W, Xu L, Wang Y. Effects of chronic exposure to microcystin-LR on hepatocyte mitochondrial DNA replication in mice. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:4665-4672. [PMID: 25723732 DOI: 10.1021/es5059132] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Microcystins (MCs) are produced by cyanobacterial blooms, and microcystin-LR (MC-LR) is the most toxic among the 80 MC variants. Data have shown that the liver is one of the specific target organs for MC-LR, which can cause mitochondrial DNA (mtDNA) damage, resulting in mitochondrial dysfunction. However, the underlying mechanism is still unclear. In the present study, we evaluated the genetic toxicity of MC-LR in mice drinking water at different concentrations (1, 5, 10, 20, and 40 μg/L) for 12 months. Our results showed that long-term and persistent exposure to MC-LR increased the 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels of DNA in liver cells, damaged the integrity of mtDNA and nuclear DNA (nDNA), and altered the mtDNA content. Notably, MC-LR exposure can change the expression of mitochondrial genes and nuclear genes that are critical for regulating mtDNA replication and repairing oxidized DNA. They also further impaired the function of mitochondria and liver cells.
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Affiliation(s)
- Xinxiu Li
- †Department of Medical Genetics, and ‡Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China
| | - Qingya Zhao
- †Department of Medical Genetics, and ‡Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China
| | - Wei Zhou
- †Department of Medical Genetics, and ‡Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China
| | - Lizhi Xu
- †Department of Medical Genetics, and ‡Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China
| | - Yaping Wang
- †Department of Medical Genetics, and ‡Jiangsu Key Laboratory of Molecular Medicine, Nanjing University School of Medicine, Nanjing, Jiangsu 210093, People's Republic of China
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Abstract
Mitochondrial disease resulting in reduced bioenergetic output can be due to mutations in either nuclear DNA-encoded or mitochondrial DNA-encoded gene products. We summarize some of the underlying principles of mitochondrial genetics that impact the diagnosis and pathogenesis of mitochondrial disorders. In addition, we present a brief overview of a new frontier in the field, namely, mitochondrial "dynamics," which controls organellar fusion, fission, trafficking, and positioning, and exerts mitochondrial "quality control" by maintaining organellar integrity and viability. Analysis of mutations in gene products associated with this latter area has opened up new vistas in the study of disorders associated with compromised energy production.
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Affiliation(s)
- Estela Area-Gomez
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Eric A Schon
- Department of Neurology, Columbia University Medical Center, New York, NY, USA Department of Genetics and Development, Columbia University Medical Center, New York, NY, USA
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27
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Cytoplasmic hybrid (cybrid) cell lines as a practical model for mitochondriopathies. Redox Biol 2014; 2:619-31. [PMID: 25460729 PMCID: PMC4297942 DOI: 10.1016/j.redox.2014.03.006] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 03/28/2014] [Indexed: 12/21/2022] Open
Abstract
Cytoplasmic hybrid (cybrid) cell lines can incorporate human subject mitochondria and perpetuate its mitochondrial DNA (mtDNA)-encoded components. Since the nuclear background of different cybrid lines can be kept constant, this technique allows investigators to study the influence of mtDNA on cell function. Prior use of cybrids has elucidated the contribution of mtDNA to a variety of biochemical parameters, including electron transport chain activities, bioenergetic fluxes, and free radical production. While the interpretation of data generated from cybrid cell lines has technical limitations, cybrids have contributed valuable insight into the relationship between mtDNA and phenotype alterations. This review discusses the creation of the cybrid technique and subsequent data obtained from cybrid applications. The cytoplasmic hybrid (cybrid) model can be used to determine mitochondrial DNA (mtDNA) contributions to phenotypic alterations. Cybrids are used to study mitochondriopathies such as Parkinson’s disease and Alzheimer’s disease. mtDNA heteroplasmy threshold and nuclear DNA-mtDNA compatibility can be determined using cybrid models.
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28
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Gilkerson R, Bravo L, Garcia I, Gaytan N, Herrera A, Maldonado A, Quintanilla B. The mitochondrial nucleoid: integrating mitochondrial DNA into cellular homeostasis. Cold Spring Harb Perspect Biol 2013; 5:a011080. [PMID: 23637282 DOI: 10.1101/cshperspect.a011080] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The packaging of mitochondrial DNA (mtDNA) into DNA-protein assemblies called nucleoids provides an efficient segregating unit of mtDNA, coordinating mtDNA's involvement in cellular metabolism. From the early discovery of mtDNA as "extranuclear" genetic material, its organization into nucleoids and integration into both the mitochondrial organellar network and the cell at large via a variety of signal transduction pathways, mtDNA is a crucial component of the cell's homeostatic network. The mitochondrial nucleoid is composed of a set of DNA-binding core proteins involved in mtDNA maintenance and transcription, and a range of peripheral factors, which are components of signaling pathways controlling mitochondrial biogenesis, metabolism, apoptosis, and retrograde mitochondria-to-nucleus signaling. The molecular interactions of nucleoid components with the organellar network and cellular signaling pathways provide exciting clues to the dynamic integration of mtDNA into cellular metabolic homeostasis.
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Affiliation(s)
- Robert Gilkerson
- Department of Biology, University of Texas-Pan American, Edinburg, TX 78539-2999, USA.
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29
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Michel S, Wanet A, De Pauw A, Rommelaere G, Arnould T, Renard P. Crosstalk between mitochondrial (dys)function and mitochondrial abundance. J Cell Physiol 2012; 227:2297-310. [PMID: 21928343 DOI: 10.1002/jcp.23021] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A controlled regulation of mitochondrial mass through either the production (biogenesis) or the degradation (mitochondrial quality control) of the organelle represents a crucial step for proper mitochondrial and cell function. Key steps of mitochondrial biogenesis and quality control are overviewed, with an emphasis on the role of mitochondrial chaperones and proteases that keep mitochondria fully functional, provided the mitochondrial activity impairment is not excessive. In this case, the whole organelle is degraded by mitochondrial autophagy or "mitophagy." Beside the maintenance of adequate mitochondrial abundance and functions for cell homeostasis, mitochondrial biogenesis might be enhanced, through discussed signaling pathways, in response to various physiological stimuli, like contractile activity, exposure to low temperatures, caloric restriction, and stem cells differentiation. In addition, mitochondrial dysfunction might also initiate a retrograde response, enabling cell adaptation through increased mitochondrial biogenesis.
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Affiliation(s)
- Sébastien Michel
- Laboratory of Biochemistry and Cell Biology (URBC), NARILIS (Namur Research Institute for Life Sciences), University of Namur (FUNDP), Namur, Belgium
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30
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Matsushima Y, Kaguni LS. Matrix proteases in mitochondrial DNA function. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:1080-7. [PMID: 22172992 DOI: 10.1016/j.bbagrm.2011.11.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 11/22/2011] [Accepted: 11/23/2011] [Indexed: 10/14/2022]
Abstract
Lon, ClpXP and m-AAA are the three major ATP-dependent proteases in the mitochondrial matrix. All three are involved in general quality control by degrading damaged or abnormal proteins. In addition to this role, they are proposed to serve roles in mitochondrial DNA functions including packaging and stability, replication, transcription and translation. In particular, Lon has been implicated in mtDNA metabolism in yeast, fly and humans. Here, we review the role of Lon protease in mitochondrial DNA functions, and discuss a putative physiological role for mitochondrial transcription factor A (TFAM) degradation by Lon protease. We also discuss the possible roles of m-AAA and ClpXP in mitochondrial DNA functions, and the putative candidate substrates for the three matrix proteases. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Yuichi Matsushima
- Department of Mental Retardation & Birth Defect Research, National Institute of Neuroscience, National Center of Neurology & Psychiatry, Tokyo 187-8502, Japan
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31
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Bogenhagen DF. Mitochondrial DNA nucleoid structure. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:914-20. [PMID: 22142616 DOI: 10.1016/j.bbagrm.2011.11.005] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 11/13/2011] [Accepted: 11/16/2011] [Indexed: 12/21/2022]
Abstract
Eukaryotic cells are characterized by their content of intracellular membrane-bound organelles, including mitochondria as well as nuclei. These two DNA-containing compartments employ two distinct strategies for storage and readout of genetic information. The diploid nuclei of human cells contain about 6 billion base pairs encoding about 25,000 protein-encoding genes, averaging 120 kB/gene, packaged in chromatin arranged as a regular nucleosomal array. In contrast, human cells contain hundreds to thousands of copies of a ca.16 kB mtDNA genome tightly packed with 13 protein-coding genes along with rRNA and tRNA genes required for their expression. The mtDNAs are dispersed throughout the mitochondrial network as histone-free nucleoids containing single copies or small clusters of genomes. This review will summarize recent advances in understanding the microscopic structure and molecular composition of mtDNA nucleoids in higher eukaryotes. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
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Affiliation(s)
- Daniel F Bogenhagen
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794-8651, USA.
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32
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Gianotti TF, Castaño G, Gemma C, Burgueño AL, Rosselli MS, Pirola CJ, Sookoian S. Mitochondrial DNA copy number is modulated by genetic variation in the signal transducer and activator of transcription 3 (STAT3). Metabolism 2011; 60:1142-9. [PMID: 21310444 DOI: 10.1016/j.metabol.2010.12.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 12/14/2010] [Accepted: 12/15/2010] [Indexed: 12/25/2022]
Abstract
The regulation of mitochondrial DNA (mtDNA) copy number not only is critical for the maintenance of the normal mitochondrial function but has a strong clinical significance. A recent report revealed that the signal transducer and activator of transcription 3 (STAT3) is involved in the regulation of the mitochondrial function and is required for the optimal function of the electron transport chain. In this study, we explored whether gene variants in the STAT3 influence the leukocyte mtDNA copy number. Clinical data and blood samples were collected from 179 subjects (aged 52.8 ± 0.9 years). Mitochondrial DNA quantification using nuclear DNA (nDNA) as a reference was carried out by a real-time quantitative polymerase chain reaction method; results are presented as the mtDNA/nDNA ratio. We selected 3 tag single nucleotide polymorphisms showing a minor allele frequency greater than 10% (rs2293152 C/G, rs6503695 C/T, and rs9891119 A/C), representing 24 polymorphic sites of the STAT3 (r(2) > 0.8). We observed a significant association between mtDNA/nDNA ratio and both rs6503695 and rs9891119, adjusted by age and homeostasis model assessment index. The proportion of the total variance of the mtDNA/nDNA ratio accounted for by the rs6503695 and rs9891119 genotypes was 4.7% and 6.53%, respectively. Common variation in the STAT3 may influence mtDNA copy number.
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Affiliation(s)
- Tomas Fernández Gianotti
- Department of Molecular Genetics and Biology of Complex Diseases, Institute of Medical Research A Lanari-IDIM, University of Buenos Aires-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
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33
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Zhang Y, Zhang L, Zhang L, Bai J, Ge H, Liu P. Expression changes in DNA repair enzymes and mitochondrial DNA damage in aging rat lens. Mol Vis 2010; 16:1754-63. [PMID: 20808729 PMCID: PMC2929939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Accepted: 08/24/2010] [Indexed: 12/04/2022] Open
Abstract
PURPOSE To determine if there is increased mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) damage with age in the lenses of rats. We also explored the immunolocalization of 8-oxoguanine DNA glycosylase 1 (OGG1) and AP endonuclease 1 (APE1) in the lens and studied three of the predominant base excision repair (BER) enzymes: OGG1, APE1, and DNA polymerase gamma (Polgamma). METHODS The methods used by this study include the selection of twenty-six male Wistar rats in each group (2 months old and 26 months old) and fourteen male Wistar rats in the 16 months old group. The total DNA of lenses were isolated and the DNA genome was amplified by a long extension-polymerase chain reaction (LX-PCR). We examined mtDNA and nDNA damage with a quantitative polymerase chain reaction (QPCR) assay that was combined with EvaGreen. We also studied the gene expression of mRNA and protein in these key BER enzymes with real time-polymerase chain reaction (RT-PCR) and western blot analysis. RESULTS There was an increase in oxidative DNA damage, which exists primarily in the mtDNA. The amount of 8-hydroxy-2'-deoxy-guanosine (8-OHdG) in DNA was significantly increased with age. Our experiments demonstrated that the gene expression of mRNA and protein in these key BER enzymes decreased with age. OGG1 and APE1 were localized by immunohistochemistry within lens epithelial cells (LECs) and superficial fiber cells. CONCLUSIONS The gene expression of mRNA and protein in these key BER enzymes decreased with age, which caused a decrease in the repairing capability of the mtDNA and the accumulation of mtDNA damage. The increased mtDNA damage and decreased expression of BER enzymes may cause a "vicious cycle" of oxidative stress that contributes to the accumulation of mtDNA mutations and age-related cataract pathogenesis.
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Affiliation(s)
- Yi Zhang
- Eye hospital, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Lu Zhang
- Eye hospital, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Lan Zhang
- Cardiovascular medicine, The Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Jie Bai
- Eye hospital, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - HongYan Ge
- Eye hospital, The First Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Ping Liu
- Eye hospital, The First Affiliated Hospital, Harbin Medical University, Harbin, China
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34
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Abstract
Until even only a few years ago, the idea that effective therapies for human mitochondrial disorders resulting from the dysfunction of the respiratory chain/oxidative phosphorylation system (OxPhos) could be developed was unimaginable. The obstacles to treating diseases caused by mutations in either mitochondrial DNA (mtDNA) or nuclear DNA (nDNA), and which had the potential to affect nearly every organ system, seemed overwhelming. However, although clinically applicable therapies remain largely in the future, the landscape has changed dramatically and we can now envision the possibility of treating some of these disorders. Among these are techniques to upregulate mitochondrial biogenesis, enhance organellar fusion and fission, "shift heteroplasmy" and eliminate the burden of mutant mtDNAs via cytoplasmic transfer.
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Affiliation(s)
- Eric A Schon
- Department of Neurology, Columbia University Medical Center, New York, NY, USA.
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35
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Zhuang X, Cheng CHC. ND6 gene "lost" and found: evolution of mitochondrial gene rearrangement in Antarctic notothenioids. Mol Biol Evol 2010; 27:1391-403. [PMID: 20106908 DOI: 10.1093/molbev/msq026] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Evolution of Antarctic notothenioids in the frigid and oxygen-rich Southern Ocean had led to remarkable genomic changes, most notably the gain of novel antifreeze glycoproteins and the loss of oxygen-binding hemoproteins in the icefish family. Recently, the mitochondrial (mt) NADH dehydrogenase subunit 6 (ND6) gene and the adjacent transfer RNA(Glu) (tRNA(Glu)) were also reportedly lost. ND6 protein is crucial for the assembly and function of Complex I of the mt electron transport chain that produces adenosine triphosphate (ATP) essential for life; thus, ND6 absence would be irreconcilable with Antarctic notothenioids being thriving species. Here we report our discovery that the ND6 gene and tRNA(Glu) were not lost but had been translocated to the control region (CR) from their canonical location between ND5 and cytochrome b genes. We characterized the CR and adjacent sequences of 22 notothenioid species representing all eight families of Notothenioidei to elucidate the mechanism and evolutionary history of this mtDNA rearrangement. Species of the three basal non-Antarctic families have the canonical vertebrate mt gene order, whereas species of all five Antarctic families have a rearranged CR bearing the embedded ND6 (ND6(CR)) and tRNA(Glu), with additional copies of tRNA(Thr), tRNA(Pro), and noncoding region in various lineages. We hypothesized that an initial duplication of the canonical mt region from ND6 through CR occurred in the common ancestor to the Antarctic clade, and we deduced the succession of loss or modification of the duplicated region leading to the extant patterns of mt DNA reorganization that is consistent with notothenioid evolutionary history. We verified that the ND6(CR) gene in Antarctic notothenioids is transcribed and therefore functional. However, ND6(CR)-encoded protein sequences differ substantially from basal non-Antarctic notothenioid ND6, and we detected lineage-specific positive selection on the branch leading to the Antarctic clade of ND6(CR) under the branch-site model. Collectively, the novel mt ND6(CR) genotype of the Antarctic radiation represents another major molecular change in Antarctic notothenioid evolution and may reflect an adaptive change conducive to the functioning of the protein (Complex I) machinery of mt respiration in the polar environment, driven by the advent of freezing, oxygen-rich conditions in the Southern Ocean.
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Affiliation(s)
- Xuan Zhuang
- Department of Animal Biology, University of Illinois at Urbana-Champaign, IL, USA
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Clay Montier LL, Deng JJ, Bai Y. Number matters: control of mammalian mitochondrial DNA copy number. J Genet Genomics 2009; 36:125-31. [PMID: 19302968 PMCID: PMC4706993 DOI: 10.1016/s1673-8527(08)60099-5] [Citation(s) in RCA: 378] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Revised: 01/13/2009] [Accepted: 01/19/2009] [Indexed: 12/15/2022]
Abstract
Regulation of mitochondrial biogenesis is essential for proper cellular functioning. Mitochondrial DNA (mtDNA) depletion and the resulting mitochondrial malfunction have been implicated in cancer, neurodegeneration, diabetes, aging, and many other human diseases. Although it is known that the dynamics of the mammalian mitochondrial genome are not linked with that of the nuclear genome, very little is known about the mechanism of mtDNA propagation. Nevertheless, our understanding of the mode of mtDNA replication has advanced in recent years, though not without some controversies. This review summarizes our current knowledge of mtDNA copy number control in mammalian cells, while focusing on both mtDNA replication and turnover. Although mtDNA copy number is seemingly in excess, we reason that mtDNA copy number control is an important aspect of mitochondrial genetics and biogenesis and is essential for normal cellular function.
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Affiliation(s)
- Laura L Clay Montier
- Department of Cellular and Structural Biology, The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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Gilkerson RW, Schon EA, Hernandez E, Davidson MM. Mitochondrial nucleoids maintain genetic autonomy but allow for functional complementation. ACTA ACUST UNITED AC 2008; 181:1117-28. [PMID: 18573913 PMCID: PMC2442202 DOI: 10.1083/jcb.200712101] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Mitochondrial DNA (mtDNA) is packaged into DNA-protein assemblies called nucleoids, but the mode of mtDNA propagation via the nucleoid remains controversial. Two mechanisms have been proposed: nucleoids may consistently maintain their mtDNA content faithfully, or nucleoids may exchange mtDNAs dynamically. To test these models directly, two cell lines were fused, each homoplasmic for a partially deleted mtDNA in which the deletions were nonoverlapping and each deficient in mitochondrial protein synthesis, thus allowing the first unequivocal visualization of two mtDNAs at the nucleoid level. The two mtDNAs transcomplemented to restore mitochondrial protein synthesis but were consistently maintained in discrete nucleoids that did not intermix stably. These results indicate that mitochondrial nucleoids tightly regulate their genetic content rather than freely exchanging mtDNAs. This genetic autonomy provides a molecular mechanism to explain patterns of mitochondrial genetic inheritance, in addition to facilitating therapeutic methods to eliminate deleterious mtDNA mutations.
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Affiliation(s)
- Robert W Gilkerson
- Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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38
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Bereiter-Hahn J, Vöth M, Mai S, Jendrach M. Structural implications of mitochondrial dynamics. Biotechnol J 2008; 3:765-80. [DOI: 10.1002/biot.200800024] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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39
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Swerdlow RH. Mitochondria in cybrids containing mtDNA from persons with mitochondriopathies. J Neurosci Res 2008; 85:3416-28. [PMID: 17243174 DOI: 10.1002/jnr.21167] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The cytoplasmic hybrid (cybrid) technique allows investigators to express selected mitochondrial DNA (mtDNA) sequences against fixed nuclear DNA (nDNA) backgrounds. Cybrids have been used to study the effects of known mtDNA mutations on mitochondrial biochemistry, mtDNA-nDNA inter-species compatibility, and mtDNA integrity in persons without mtDNA mutations defined previously. This review discusses events leading up to creation of the cybrid technique, as well as data obtained via application of the cybrid strategies listed above. Although interpreting cybrid data requires awareness of technique limitations, valuable insights into mtDNA genotype-functional phenotype relationships are suggested.
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Affiliation(s)
- Russell H Swerdlow
- Department of Neurology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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40
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Lund KC, Peterson LL, Wallace KB. Absence of a universal mechanism of mitochondrial toxicity by nucleoside analogs. Antimicrob Agents Chemother 2007; 51:2531-9. [PMID: 17470651 PMCID: PMC1913246 DOI: 10.1128/aac.00039-07] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 03/08/2007] [Accepted: 04/24/2007] [Indexed: 11/20/2022] Open
Abstract
Nucleoside analogs are associated with various mitochondrial toxicities, and it is becoming increasingly difficult to accommodate these differences solely in the context of DNA polymerase gamma inhibition. Therefore, we examined the toxicities of zidovudine (AZT) (10 and 50 microM; 2.7 and 13.4 microg/ml), didanosine (ddI) (10 and 50 microM; 2.4 and 11.8 microg/ml), and zalcitabine (ddC) (1 and 5 microM; 0.21 and 1.1 microg/ml) in HepG2 and H9c2 cells without the presumption of mitochondrial DNA (mtDNA) depletion. Ethidium bromide (EtBr) (0.5 microg/ml; 1.3 microM) was used as a positive control. AZT treatment resulted in metabolic disruption (increased lactate and superoxide) and increased cell mortality with decreased proliferation, while mtDNA remained unchanged or increased (HepG2 cells; 50 microM AZT). ddC caused pronounced mtDNA depletion in HepG2 cells but not in H9c2 cells and increased mortality in HepG2 cells, but no significant metabolic disruption in either cell type. ddI caused a moderate depletion of mtDNA in both cell types but showed no other effects. EtBr exposure resulted in metabolic disruption, increased cell mortality with decreased cell proliferation, and mtDNA depletion in both cell types. We conclude that nucleoside analogs display unique toxicities within and between culture models, and therefore, care should be taken when generalizing about the mechanisms of nucleoside reverse transcriptase inhibitor toxicity. Additionally, mtDNA abundance does not necessarily correlate with metabolic disruption, especially in cell culture; careful discernment is recommended in this regard.
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Affiliation(s)
- Kaleb C Lund
- Department of Biochemistry and Molecular Biology, Toxicology Graduate Program, University of Minnesota Medical School Duluth, 1035 University Drive, Duluth, MN 55812, USA.
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41
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Bacman SR, Williams SL, Hernandez D, Moraes CT. Modulating mtDNA heteroplasmy by mitochondria-targeted restriction endonucleases in a 'differential multiple cleavage-site' model. Gene Ther 2007; 14:1309-18. [PMID: 17597792 PMCID: PMC2771437 DOI: 10.1038/sj.gt.3302981] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ability to manipulate mitochondrial DNA (mtDNA) heteroplasmy would provide a powerful tool to treat mitochondrial diseases. Recent studies showed that mitochondria-targeted restriction endonucleases can modify mtDNA heteroplasmy in a predictable and efficient manner if it recognizes a single site in the mutant mtDNA. However, the applicability of such model is limited to mutations that create a novel cleavage site, not present in the wild-type mtDNA. We attempted to extend this approach to a 'differential multiple cleavage site' model, where an mtDNA mutation creates an extra restriction site to the ones normally present in the wild-type mtDNA. Taking advantage of a heteroplasmic mouse model harboring two haplotypes of mtDNA (NZB/BALB) and using adenovirus as a gene vector, we delivered a mitochondria-targeted Scal restriction endonuclease to different mouse tissues. Scal recognizes five sites in the NZB mtDNA but only three in BALB mtDNA. Our results showed that changes in mtDNA heteroplasmy were obtained by the expression of mitochondria-targeted ScaI in both liver, after intravenous injection, and in skeletal muscle, after intramuscular injection. Although mtDNA depletion was an undesirable side effect, our data suggest that under a regulated expression system, mtDNA depletion could be minimized and restriction endonucleases recognizing multiple sites could have a potential for therapeutic use.
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Affiliation(s)
- SR Bacman
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - SL Williams
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - D Hernandez
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - CT Moraes
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Cell Biology and Anatomy, Miller School of Medicine, University of Miami, Miami, FL, USA
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Yin S, Yu Z, Sockalingam R, Bance M, Sun G, Wang J. The role of mitochondrial DNA large deletion for the development of presbycusis in Fischer 344 rats. Neurobiol Dis 2007; 27:370-7. [PMID: 17618125 DOI: 10.1016/j.nbd.2007.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 05/14/2007] [Accepted: 06/04/2007] [Indexed: 10/23/2022] Open
Abstract
Age-related hearing loss, or presbycusis, has been associated with large-scale mitochondrial DNA (mtDNA) deletion in previous studies. However, the role of this mtDNA damage in presbycusis is still not clear because the deletion in inner ears has not been measured quantitatively and analyzed in parallel with the time course of presbycusis. In the present study, the deletion was quantified using quantitative real-time PCR (qRT-PCR) in male Fischer 344 rats of different ages. It was found that the deletion increased quickly during young adulthood and reached over 60% at 6 months of age. However, a significant hearing loss was not seen until after 12 months of age. The results suggest that the existence of the deletion per se does not necessarily imply cochlear damage, but rather a critical level of the accumulated deletion seems to precede the hearing loss. The long delay may indicate the involvement of mechanisms other than mtDNA deletion in the development of presbycusis.
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Affiliation(s)
- Shankai Yin
- Institute of Otolaryngology Research, JiaoTong University, Shanghai, 200233, China
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Affiliation(s)
- Ali Naini
- H. Houston Merritt Clinical Research Center for Muscular Dystrophy and Related disorders, Department of Neurology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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Kang D, Kim SH, Hamasaki N. Mitochondrial transcription factor A (TFAM): Roles in maintenance of mtDNA and cellular functions. Mitochondrion 2007; 7:39-44. [PMID: 17280879 DOI: 10.1016/j.mito.2006.11.017] [Citation(s) in RCA: 308] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2006] [Accepted: 09/21/2006] [Indexed: 10/23/2022]
Abstract
A growing body of evidence suggests that mammalian mitochondrial DNA takes on higher structure called nucleoid or mitochromosome corresponding to that of nuclear DNA. Mitochondrial transcription factor A (TFAM), which was cloned as a transcription factor for mitochondrial DNA, has known to be essential for the maintenance of mitochondrial DNA. Human TFAM has an ability to bind to DNA in a sequence-independent manner and is abundant enough to cover whole region of mitochondrial DNA, owing to which TFAM stabilizes mitochondrial DNA through formation of nucleoid and regulates (or titrates) the amount of mitochondrial DNA. Overexpression of human TFAM in mice increases the amount of mitochondrial DNA and dramatically ameliorates the cardiac dysfunctions caused by myocardial infarction. The maintenance of integrity of mitochondrial DNA is important for keeping proper cellular functions both under physiological and pathological conditions. TFAM may play a crucial role in maintaining mitochondrial DNA as a main component of the nucleoid.
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Affiliation(s)
- Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan.
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45
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Meany DL, Poe BG, Navratil M, Moraes CT, Arriaga EA. Superoxide released into the mitochondrial matrix. Free Radic Biol Med 2006; 41:950-9. [PMID: 16934678 DOI: 10.1016/j.freeradbiomed.2006.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 05/24/2006] [Accepted: 06/02/2006] [Indexed: 01/07/2023]
Abstract
Reactive oxygen species (ROS) that are produced by mitochondria are released toward the mitochondrial matrix or the intermembrane space. Each ROS pool is likely involved in different cellular mechanisms and damage. Unfortunately, it is difficult to distinguish the provenance and effects of ROS. Here we introduce a method to semiquantitate the steady-state levels of superoxide produced in the matrix of mitochondria. Superoxide produced during cellular respiration is capable of oxidizing hydroethidine, a probe that is membrane permeant. The poor membrane permeability of the hydroethidine oxidation products causes accumulation of these fluorescent products within the mitochondria. After isolation of mitochondria, a method based on the capillary electrophoretic separation of individual organelles and their detection by laser-induced fluorescence detection is used to determine their fluorescent contents. Use of this method for the analysis of organelle fractions obtained from cells treated with antimycin A or rotenone confirms that the detected fluorescence is associated with superoxide produced by mitochondria. Furthermore, using this method the superoxide levels in the mitochondrial matrix of a cytoplasmic hybrid (cybrid) cell line (DeltaH2-1) and one of its parent cell lines (143B) were compared.
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Affiliation(s)
- Danni L Meany
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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46
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Liu CS, Cheng WL, Lee CF, Ma YS, Lin CY, Huang CC, Wei YH. Alteration in the copy number of mitochondrial DNA in leukocytes of patients with mitochondrial encephalomyopathies. Acta Neurol Scand 2006; 113:334-41. [PMID: 16629770 DOI: 10.1111/j.1600-0404.2006.00586.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES We investigated whether mutation of mitochondrial DNA (mtDNA) affects the copy number of the mitochondrial genome in patients with mitochondrial myopathy encephalopathy with lactic acidosis and stroke-like episodes (MELAS) and those with myoclonic epilepsy with ragged-red fiber (MERRF) syndromes. MATERIALS AND METHODS Forty-eight Taiwanese patients with MELAS syndrome and 20 patients with MERRF syndrome were recruited in this study. RESULTS In relation to controls, the copy numbers of mtDNA in leukocytes of patients with MELAS or MERRF syndrome were significantly higher at a young age but lower at an advanced age. In addition, MELAS patients harboring higher proportions of mtDNA with A3243G transition had lower mtDNA copy numbers. The MELAS or MERRF patients with multi-system disorders had lower mtDNA copy numbers in leukocytes. Furthermore, higher proportions of mtDNA with 4977 bp deletion were found in leukocytes of MERRF patients with multi-system involvement. CONCLUSION In leukocytes, alteration in the copy number of mtDNA is related to the proportion of mtDNA with a point mutation or large-scale deletion, which may serve as a biomarker in the pathogenesis and disease progression of MELAS and MERRF syndromes.
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Affiliation(s)
- C-S Liu
- Vascular and Genomic Research Center, Changhua Christian Hospital, Changhua, Taiwan
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47
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Barr CM, Neiman M, Taylor DR. Inheritance and recombination of mitochondrial genomes in plants, fungi and animals. THE NEW PHYTOLOGIST 2005; 168:39-50. [PMID: 16159319 DOI: 10.1111/j.1469-8137.2005.01492.x] [Citation(s) in RCA: 226] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
It is generally assumed that mitochondrial genomes are uniparentally transmitted, homoplasmic and nonrecombining. However, these assumptions draw largely from early studies on animal mitochondrial DNA (mtDNA). In this review, we show that plants, animals and fungi are all characterized by episodes of biparental inheritance, recombination among genetically distinct partners, and selfish elements within the mitochondrial genome, but that the extent of these phenomena may vary substantially across taxa. We argue that occasional biparental mitochondrial transmission may allow organisms to achieve the best of both worlds by facilitating mutational clearance but continuing to restrict the spread of selfish genetic elements. We also show that methodological biases and disproportionately allocated study effort are likely to have influenced current estimates of the extent of biparental inheritance, heteroplasmy and recombination in mitochondrial genomes from different taxa. Despite these complications, there do seem to be discernible similarities and differences in transmission dynamics and likelihood of recombination of mtDNA in plant, animal and fungal taxa that should provide an excellent opportunity for comparative investigation of the evolution of mitochondrial genome dynamics.
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Affiliation(s)
- Camille M Barr
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.
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48
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Jacobs LJAM, de Wert G, Geraedts JPM, de Coo IFM, Smeets HJM. The transmission of OXPHOS disease and methods to prevent this. Hum Reprod Update 2005; 12:119-36. [PMID: 16199488 DOI: 10.1093/humupd/dmi042] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Diseases owing to defects of oxidative phosphorylation (OXPHOS) affect approximately 1 in 8,000 individuals. Clinical manifestations can be extremely variable and range from single-affected tissues to multisystemic syndromes. In general, tissues with a high energy demand, like brain, heart and muscle, are affected. The OXPHOS system is under dual genetic control, and mutations in both nuclear and mitochondrial genes can cause OXPHOS diseases. The expression and segregation of mitochondrial DNA (mtDNA) mutations is different from nuclear gene defects. The mtDNA mutations can be either homoplasmic or heteroplasmic and in the latter case disease becomes manifest when the mutation exceeds a tissue-specific threshold. This mutation load can vary between tissues and often an exact correlation between mutation load and phenotypic expression is lacking. The transmission of mtDNA mutations is exclusively maternal, but the mutation load between embryos can vary tremendously because of a segregational bottleneck. Diseases by nuclear gene mutations show a normal Mendelian inheritance pattern and often have a more constant clinical manifestation. Given the prevalence and severity of OXPHOS disorders and the lack of adequate therapy, existing and new methods for the prevention of transmission of OXPHOS disorders, like prenatal diagnosis (PND), preimplantation genetic diagnosis (PGD), cytoplasmic transfer (CT) and nuclear transfer (NT), are technically and ethically evaluated.
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Affiliation(s)
- L J A M Jacobs
- Department of Genetics and Cell Biology, University of Maastricht, 6200 MD Maastricht, The Netherlands
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49
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Mueller RL, Boore JL. Molecular Mechanisms of Extensive Mitochondrial Gene Rearrangement in Plethodontid Salamanders. Mol Biol Evol 2005; 22:2104-12. [PMID: 15987876 DOI: 10.1093/molbev/msi204] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light-strand replication and the nearby tRNA genes or the regions flanking the origin of heavy-strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and nontandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mitochondrial DNAs, up to 25% of the total length is composed of tandem duplications of noncoding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with the otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intramolecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.
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50
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Taanman JW, Llewelyn Williams S. The Human Mitochondrial Genome. OXIDATIVE STRESS AND DISEASE 2005. [DOI: 10.1201/9781420028843.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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