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Golomb BA, Han JH, Fung A, Berg BK, Miller BJ, Hamilton G. Bioenergetic impairment in Gulf War illness assessed via 31P-MRS. Sci Rep 2024; 14:7418. [PMID: 38548808 PMCID: PMC10979028 DOI: 10.1038/s41598-024-57725-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/21/2024] [Indexed: 04/01/2024] Open
Abstract
Time for post-exercise phosphocreatine-recovery (PCr-R), deemed a robust index of mitochondrial function in vivo, was previously reported to be elevated (signifying impaired ATP production) in veterans with Gulf War illness (GWI). Here we sought to replicate the finding and assess the impact of contravening previous eligibility requirements. The replication sample comprised white males. Cases reported ≥ moderate muscle-weakness to match the organ assessed to an organ affected; controls lacked recent headache or multiple symptoms. The expansion sample added cases without muscle-weakness, controls with recent headache, females, nonwhites. PCr-R, following pedal-depression-exercise, was compared in veterans with GWI versus controls (sample N = 38). In the replication sample, PCr-R results closely matched the prior report: PCr-R veterans with GWI mean(SD) = 47.7(16.5); control mean(SD) = 30.3(9.2), p = 0.017. (Prior-study PCr-R veterans with GWI mean(SD) = 46.1(17.9), control mean(SD) = 29.0(8.7), p = 0.023. Combined replication + prior samples: p = 0.001.) No case-control difference was observed in the expansion sample. In cases, PCr-R related to muscle-weakness: PCr-R = 29.9(7.1), 38.2(8.9), 47.8(15.2) for muscle-weakness rated none/low, intermediate, and high respectively (p for trend = 0.02), validating desirability of matching tissue assessed to tissue affected. In controls, headache/multiple symptoms, sex, and ethnicity each mattered (affecting PCr-R significantly). This study affirms mitochondrial/bioenergetic impairment in veterans with GWI. The importance of careful case/control selection is underscored.
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Affiliation(s)
- Beatrice Alexandra Golomb
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive # 0995, La Jolla, CA, 92093-0995, USA.
| | - Jun Hee Han
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive # 0995, La Jolla, CA, 92093-0995, USA
| | - Alexander Fung
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive # 0995, La Jolla, CA, 92093-0995, USA
- Clement Park Dental Care, Littleton, CO, 80123, USA
| | - Brinton Keith Berg
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive # 0995, La Jolla, CA, 92093-0995, USA
| | - Bruce J Miller
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive # 0995, La Jolla, CA, 92093-0995, USA
| | - Gavin Hamilton
- Department of Radiology, University of California, San Diego, La Jolla, CA, 92093, USA
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2
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Spinazzola A, Perez-Rodriguez D, Ježek J, Holt IJ. Mitochondrial DNA competition: starving out the mutant genome. Trends Pharmacol Sci 2024; 45:225-242. [PMID: 38402076 DOI: 10.1016/j.tips.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/26/2024]
Abstract
High levels of pathogenic mitochondrial DNA (mtDNA) variants lead to severe genetic diseases, and the accumulation of such mutants may also contribute to common disorders. Thus, selecting against these mutants is a major goal in mitochondrial medicine. Although mutant mtDNA can drift randomly, mounting evidence indicates that active forces play a role in the selection for and against mtDNA variants. The underlying mechanisms are beginning to be clarified, and recent studies suggest that metabolic cues, including fuel availability, contribute to shaping mtDNA heteroplasmy. In the context of pathological mtDNAs, remodeling of nutrient metabolism supports mitochondria with deleterious mtDNAs and enables them to outcompete functional variants owing to a replicative advantage. The elevated nutrient requirement represents a mutant Achilles' heel because small molecules that restrict nutrient consumption or interfere with nutrient sensing can purge cells of deleterious mtDNAs and restore mitochondrial respiration. These advances herald the dawn of a new era of small-molecule therapies to counteract pathological mtDNAs.
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Affiliation(s)
- Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK.
| | - Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Jan Ježek
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Ian J Holt
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK; Biodonostia Health Research Institute, 20014 San Sebastián, Spain; IKERBASQUE (Basque Foundation for Science), 48013 Bilbao, Spain; CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), 28031 Madrid, Spain; Universidad de País Vasco, Barrio Sarriena s/n, 48940 Leioa, Bilbao, Spain.
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3
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Volpe KE, Samuels DC, Elson JL, Steyn JS, Gebretsadik T, Ellis RJ, Heaton RK, Kallianpur AR, Letendre S, Hulgan T. Mitochondrial DNA mutation pathogenicity score and neurocognitive performance in persons with HIV. Mitochondrion 2024; 74:101820. [PMID: 37989461 PMCID: PMC10872545 DOI: 10.1016/j.mito.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 10/06/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) genetic variation is associated with neurocognitive (NC) impairment (NCI) in people with HIV (PWH). Other approaches use sequence conservation and protein structure to predict the impact of mtDNA variants on protein function. We examined predicted mtDNA variant pathogenicity in the CHARTER study using MutPred scores, hypothesizing that persons with higher scores (greater predicted pathogenicity) have more NCI. METHODS CHARTER included NC testing in PWH from 2003 to 2007. MutPred scores were assigned to CHARTER participants with mtDNA sequence; any score > 0.5 was considered potentially deleterious. Outcomes at cohort entry were NCI, defined by global and seven NC domain deficit scores, and by mean global and domain NC performance T-scores. Univariate and multivariable regression analyses assessed associations between having a deleterious variant and NCI. Additional models included estimated peripheral blood cell mtDNA copy number. RESULTS Data were available for 744 PWH (357 African ancestry; 317 European; 70 Hispanic). In the overall cohort, PWH having any potentially deleterious variant were less likely to have motor impairment (16 vs. 25 %, p = 0.001). In multivariable analysis, having a deleterious variant remained associated with lower likelihood of motor impairment (adjusted odds ratio 0.59 [95 % CI 0.41-0.88]; p = 0.009), and better motor performance by T-score (β 1.71 [0.31-3.10], p = 0.02). Associations persisted after adjustment for estimated mtDNA quantity. CONCLUSIONS In these PWH, having a potentially deleterious mtDNA variant was associated with less motor impairment. These unexpected findings suggest that potentially deleterious mtDNA variations may confer protection against impaired motor function by as yet unknown mechanisms.
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Affiliation(s)
- Karen E Volpe
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - David C Samuels
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joanna L Elson
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Jannetta S Steyn
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | | | | | | | | | | | - Todd Hulgan
- Vanderbilt University Medical Center, Nashville, TN, USA.
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4
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Broz AK, Sloan DB, Johnston IG. Stochastic organelle genome segregation through Arabidopsis development and reproduction. THE NEW PHYTOLOGIST 2024; 241:896-910. [PMID: 37925790 PMCID: PMC10841260 DOI: 10.1111/nph.19288] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 09/07/2023] [Indexed: 11/07/2023]
Abstract
Organelle DNA (oDNA) in mitochondria and plastids is vital for plant (and eukaryotic) life. Selection against damaged oDNA is mediated in part by segregation - sorting different oDNA types into different cells in the germline. Plants segregate oDNA very rapidly, with oDNA recombination protein MSH1 a key driver of this segregation, but we have limited knowledge of the dynamics of this segregation within plants and between generations. Here, we reveal how oDNA evolves through Arabidopsis thaliana development and reproduction. We combine stochastic modelling, Bayesian inference, and model selection with new and existing tissue-specific oDNA measurements from heteroplasmic Arabidopsis plant lines through development and between generations. Segregation proceeds gradually but continually during plant development, with a more rapid increase between inflorescence formation and the next generation. When MSH1 is compromised, the majority of observed segregation can be achieved through partitioning at cell divisions. When MSH1 is functional, mtDNA segregation is far more rapid; we show that increased oDNA gene conversion is a plausible mechanism quantitatively explaining this acceleration. These findings reveal the quantitative, time-dependent details of oDNA segregation in Arabidopsis. We also discuss the support for different models of the plant germline provided by these observations.
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Affiliation(s)
- Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, 5007, Norway
- Computational Biology Unit, University of Bergen, Bergen, 5007, Norway
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5
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Glynos A, Bozhilova LV, Frison M, Burr S, Stewart JB, Chinnery PF. High-throughput single-cell analysis reveals progressive mitochondrial DNA mosaicism throughout life. SCIENCE ADVANCES 2023; 9:eadi4038. [PMID: 37878704 PMCID: PMC10599618 DOI: 10.1126/sciadv.adi4038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/21/2023] [Indexed: 10/27/2023]
Abstract
Heteroplasmic mitochondrial DNA (mtDNA) mutations are a major cause of inherited disease and contribute to common late-onset human disorders. The late onset and clinical progression of mtDNA-associated disease is thought to be due to changing heteroplasmy levels, but it is not known how and when this occurs. Performing high-throughput single-cell genotyping in two mouse models of human mtDNA disease, we saw unanticipated cell-to-cell differences in mtDNA heteroplasmy levels that emerged prenatally and progressively increased throughout life. Proliferating spleen cells and nondividing brain cells had a similar single-cell heteroplasmy variance, implicating mtDNA or organelle turnover as the major force determining cell heteroplasmy levels. The two different mtDNA mutations segregated at different rates with no evidence of selection, consistent with different rates of random genetic drift in vivo, leading to the accumulation of cells with a very high mutation burden at different rates. This provides an explanation for differences in severity seen in human diseases caused by similar mtDNA mutations.
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Affiliation(s)
- Angelos Glynos
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Lyuba V. Bozhilova
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Michele Frison
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Stephen Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - James B. Stewart
- Biosciences Institute, Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick F. Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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6
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Macken WL, Falabella M, Pizzamiglio C, Woodward CE, Scotchman E, Chitty LS, Polke JM, Bugiardini E, Hanna MG, Vandrovcova J, Chandler N, Labrum R, Pitceathly RDS. Enhanced mitochondrial genome analysis: bioinformatic and long-read sequencing advances and their diagnostic implications. Expert Rev Mol Diagn 2023; 23:797-814. [PMID: 37642407 DOI: 10.1080/14737159.2023.2241365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
INTRODUCTION Primary mitochondrial diseases (PMDs) comprise a large and heterogeneous group of genetic diseases that result from pathogenic variants in either nuclear DNA (nDNA) or mitochondrial DNA (mtDNA). Widespread adoption of next-generation sequencing (NGS) has improved the efficiency and accuracy of mtDNA diagnoses; however, several challenges remain. AREAS COVERED In this review, we briefly summarize the current state of the art in molecular diagnostics for mtDNA and consider the implications of improved whole genome sequencing (WGS), bioinformatic techniques, and the adoption of long-read sequencing, for PMD diagnostics. EXPERT OPINION We anticipate that the application of PCR-free WGS from blood DNA will increase in diagnostic laboratories, while for adults with myopathic presentations, WGS from muscle DNA may become more widespread. Improved bioinformatic strategies will enhance WGS data interrogation, with more accurate delineation of mtDNA and NUMTs (nuclear mitochondrial DNA segments) in WGS data, superior coverage uniformity, indirect measurement of mtDNA copy number, and more accurate interpretation of heteroplasmic large-scale rearrangements (LSRs). Separately, the adoption of diagnostic long-read sequencing could offer greater resolution of complex LSRs and the opportunity to phase heteroplasmic variants.
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Affiliation(s)
- William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Micol Falabella
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Chiara Pizzamiglio
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Cathy E Woodward
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lyn S Chitty
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - James M Polke
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Natalie Chandler
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Robyn Labrum
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
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7
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High-frequency and functional mitochondrial DNA mutations at the single-cell level. Proc Natl Acad Sci U S A 2023; 120:e2201518120. [PMID: 36577067 PMCID: PMC9910596 DOI: 10.1073/pnas.2201518120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Decline in mitochondrial function underlies aging and age-related diseases, but the role of mitochondrial DNA (mtDNA) mutations in these processes remains elusive. To investigate patterns of mtDNA mutations, it is particularly important to quantify mtDNA mutations and their associated pathogenic effects at the single-cell level. However, existing single-cell mtDNA sequencing approaches remain inefficient due to high cost and low mtDNA on-target rates. In this study, we developed a cost-effective mtDNA targeted-sequencing protocol called single-cell sequencing by targeted amplification of multiplex probes (scSTAMP) and experimentally validated its reliability. We then applied our method to assess single-cell mtDNA mutations in 768 B lymphocytes and 768 monocytes from a 76-y-old female. Across 632 B lymphocyte and 617 monocytes with medium mtDNA coverage over >100×, our results indicated that over 50% of cells carried at least one mtDNA mutation with variant allele frequencies (VAFs) over 20%, and that cells carried an average of 0.658 and 0.712 such mutation for B lymphocytes and monocytes, respectively. Surprisingly, more than 20% of the observed mutations had VAFs of over 90% in either cell population. In addition, over 60% of the mutations were in protein-coding genes, of which over 70% were nonsynonymous, and more than 50% of the nonsynonymous mutations were predicted to be highly pathogenic. Interestingly, about 80% of the observed mutations were singletons in the respective cell populations. Our results revealed mtDNA mutations with functional significance might be prevalent at advanced age, calling further investigation on age-related mtDNA mutation dynamics at the single-cell level.
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8
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Burgstaller JP, Chiaratti MR. Mitochondrial Inheritance Following Nuclear Transfer: From Cloned Animals to Patients with Mitochondrial Disease. Methods Mol Biol 2023; 2647:83-104. [PMID: 37041330 DOI: 10.1007/978-1-0716-3064-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Mitochondria are indispensable power plants of eukaryotic cells that also act as a major biochemical hub. As such, mitochondrial dysfunction, which can originate from mutations in the mitochondrial genome (mtDNA), may impair organism fitness and lead to severe diseases in humans. MtDNA is a multi-copy, highly polymorphic genome that is uniparentally transmitted through the maternal line. Several mechanisms act in the germline to counteract heteroplasmy (i.e., coexistence of two or more mtDNA variants) and prevent expansion of mtDNA mutations. However, reproductive biotechnologies such as cloning by nuclear transfer can disrupt mtDNA inheritance, resulting in new genetic combinations that may be unstable and have physiological consequences. Here, we review the current understanding of mitochondrial inheritance, with emphasis on its pattern in animals and human embryos generated by nuclear transfer.
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Affiliation(s)
- Jörg P Burgstaller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Marcos R Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.
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9
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Stochastic survival of the densest and mitochondrial DNA clonal expansion in aging. Proc Natl Acad Sci U S A 2022; 119:e2122073119. [PMID: 36442091 PMCID: PMC9894218 DOI: 10.1073/pnas.2122073119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The expansion of mitochondrial DNA molecules with deletions has been associated with aging, particularly in skeletal muscle fibers; its mechanism has remained unclear for three decades. Previous accounts have assigned a replicative advantage (RA) to mitochondrial DNA containing deletion mutations, but there is also evidence that cells can selectively remove defective mitochondrial DNA. Here we present a spatial model that, without an RA, but instead through a combination of enhanced density for mutants and noise, produces a wave of expanding mutations with speeds consistent with experimental data. A standard model based on RA yields waves that are too fast. We provide a formula that predicts that wave speed drops with copy number, consonant with experimental data. Crucially, our model yields traveling waves of mutants even if mutants are preferentially eliminated. Additionally, we predict that mutant loads observed in single-cell experiments can be produced by de novo mutation rates that are drastically lower than previously thought for neutral models. Given this exemplar of how spatial structure (multiple linked mtDNA populations), noise, and density affect muscle cell aging, we introduce the mechanism of stochastic survival of the densest (SSD), an alternative to RA, that may underpin other evolutionary phenomena.
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10
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Li D, Liang C, Zhang T, Marley JL, Zou W, Lian M, Ji D. Pathogenic mitochondrial DNA 3243A>G mutation: From genetics to phenotype. Front Genet 2022; 13:951185. [PMID: 36276941 PMCID: PMC9582660 DOI: 10.3389/fgene.2022.951185] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial DNA (mtDNA) m.3243A>G mutation is one of the most common pathogenic mtDNA variants, showing complex genetics, pathogenic molecular mechanisms, and phenotypes. In recent years, the prevention of mtDNA-related diseases has trended toward precision medicine strategies, such as preimplantation genetic diagnosis (PGD) and mitochondrial replacement therapy (MRT). These techniques are set to allow the birth of healthy children, but clinical implementation relies on thorough insights into mtDNA genetics. The genotype and phenotype of m.3243A>G vary greatly from mother to offspring, which compromises genetic counseling for the disease. This review is the first to systematically elaborate on the characteristics of the m.3243A>G mutation, from genetics to phenotype and the relationship between them, as well as the related influencing factors and potential strategies for preventing disease. These perceptions will provide clarity for clinicians providing genetic counseling to m.3243A>G patients.
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Affiliation(s)
- Danyang Li
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
| | - Chunmei Liang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
| | - Tao Zhang
- Department of Obstetrics and Gynecology, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Jordan Lee Marley
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Weiwei Zou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
| | - Muqing Lian
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Dongmei Ji
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
- *Correspondence: Dongmei Ji,
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Kowald A, Kemeth FP, Kirkwood TBL. An explanation of how mutant and wild-type mitochondria might stably co-exist in inherited mitochondrial diseases. PNAS NEXUS 2022; 1:pgac192. [PMID: 36714863 PMCID: PMC9802247 DOI: 10.1093/pnasnexus/pgac192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/13/2022] [Indexed: 02/01/2023]
Abstract
Mitochondria are cellular organelles of crucial relevance for the survival of metazoan organisms. Damage to the mitochondrial DNA can give rise to a variety of mitochondrial diseases and is thought also to be involved in the aging process. The fate of mtDNA mutants is controlled by their synthesis as well as degradation and mathematical models can help to better understand this complex interplay. We present here a model that combines a replicative advantage for mtDNA mutants with selective degradation enabled by mitochondrial fission and fusion processes. The model not only shows that the cell has efficient means to deal with (many) types of mutants but, surprisingly, also predicts that under certain conditions a stable co-existence of mutant and wild-type mtDNAs is possible. We discuss how this new finding might explain how mitochondria can be at the heart of processes with such different phenotypes as mitochondrial diseases and aging.
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Affiliation(s)
| | - Felix P Kemeth
- Physik-Department, Nonequilibrium Chemical Physics, Technische Universität München, James-Franck-Str. 1, D-85748 Garching, Germany
| | - Tom B L Kirkwood
- UK National Innovation Centre for Ageing, The Catalyst, 3 Science Square, Newcastle University, Newcastle upon Tyne NE4 5TG, UK,Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen N, Denmark
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12
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Higher buccal mitochondrial DNA and mitochondrial common deletion number are associated with markers of neurodegeneration and inflammation in cerebrospinal fluid. J Neurovirol 2022; 28:281-290. [PMID: 35157246 DOI: 10.1007/s13365-022-01052-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/03/2021] [Accepted: 01/11/2022] [Indexed: 11/27/2022]
Abstract
Human immunodeficiency virus (HIV) infection is potentially associated with premature aging, but demonstrating this is difficult due to a lack of reliable biomarkers. The mitochondrial (mt) DNA "common deletion" mutation (mtCDM) is a 4977-bp deletion associated with aging and neurodegenerative diseases. We examined how mtDNA and mtCDM correlate with markers of neurodegeneration and inflammation in people with and without HIV (PWH and PWOH). Data from 149 adults were combined from two projects involving PWH (n = 124) and PWOH (n = 25). We measured buccal mtDNA and mtCDM by digital droplet PCR and compared them to disease and demographic characteristics and soluble biomarkers in cerebrospinal fluid (CSF) and blood measured by immunoassay. Participants had a median age of 52 years, with 53% white and 81% men. Median mtDNA level was 1,332 copies/cell (IQR 1,201-1,493) and median mtCDM level was 0.36 copies × 102/cell (IQR 0.31-0.42); both were higher in PWH. In the best model adjusting for HIV status and demographics, higher mtDNA levels were associated with higher CSF amyloid-β 1-42 and 8-hydroxy-2'-deoxyguanosine and higher mtCDM levels were associated with higher plasma soluble tumor necrosis factor receptor II. The differences in mtDNA markers between PWH and PWOH support potential premature aging in PWH. Our findings suggest mtDNA changes in oral tissues may reflect CNS processes, allowing the use of inexpensive and easily accessible buccal biospecimens as a screening tool for CSF inflammation and neurodegeneration. Confirmatory and mechanistic studies on mt genome alterations by HIV and ART may identify interventions to prevent or treat neurodegenerative complications.
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Zhang H, Esposito M, Pezet MG, Aryaman J, Wei W, Klimm F, Calabrese C, Burr SP, Macabelli CH, Viscomi C, Saitou M, Chiaratti MR, Stewart JB, Jones N, Chinnery PF. Mitochondrial DNA heteroplasmy is modulated during oocyte development propagating mutation transmission. SCIENCE ADVANCES 2021; 7:eabi5657. [PMID: 34878831 PMCID: PMC8654302 DOI: 10.1126/sciadv.abi5657] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/15/2021] [Indexed: 05/02/2023]
Abstract
Heteroplasmic mitochondrial DNA (mtDNA) mutations are a common cause of inherited disease, but a few recurrent mutations account for the vast majority of new families. The reasons for this are not known. We studied heteroplasmic mice transmitting m.5024C>T corresponding to a human pathogenic mutation. Analyzing 1167 mother-pup pairs, we show that m.5024C>T is preferentially transmitted from low to higher levels but does not reach homoplasmy. Single-cell analysis of the developing mouse oocytes showed the preferential increase in mutant over wild-type mtDNA in the absence of cell division. A similar inheritance pattern is seen in human pedigrees transmitting several pathogenic mtDNA mutations. In m.5024C>T mice, this can be explained by the preferential propagation of mtDNA during oocyte maturation, counterbalanced by purifying selection against high heteroplasmy levels. This could explain how a disadvantageous mutation in a carrier increases to levels that cause disease but fails to fixate, causing multigenerational heteroplasmic mtDNA disorders.
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Affiliation(s)
- Haixin Zhang
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Marco Esposito
- EPSRC Centre for the Mathematics of Precision Healthcare, Department of Mathematics, Imperial College, London, UK
- Leverhulme Centre for Cellular Bionics, Imperial College, London, UK
| | - Mikael G. Pezet
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Juvid Aryaman
- EPSRC Centre for the Mathematics of Precision Healthcare, Department of Mathematics, Imperial College, London, UK
| | - Wei Wei
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Florian Klimm
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- EPSRC Centre for the Mathematics of Precision Healthcare, Department of Mathematics, Imperial College, London, UK
| | - Claudia Calabrese
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Stephen P. Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Carolina H. Macabelli
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil
| | - Carlo Viscomi
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Marcos R. Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil
| | - James B. Stewart
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
- Biosciences Institute, Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Nick Jones
- EPSRC Centre for the Mathematics of Precision Healthcare, Department of Mathematics, Imperial College, London, UK
- Leverhulme Centre for Cellular Bionics, Imperial College, London, UK
| | - Patrick F. Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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14
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Gayathri N, Deepha S, Sharma S. Diagnosis of primary mitochondrial disorders -Emphasis on myopathological aspects. Mitochondrion 2021; 61:69-84. [PMID: 34592422 DOI: 10.1016/j.mito.2021.09.007] [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: 07/15/2021] [Revised: 09/03/2021] [Accepted: 09/22/2021] [Indexed: 12/29/2022]
Abstract
Mitochondrial disorders are one of the most common neurometabolic disorders affecting all age groups. The phenotype-genotype heterogeneity in these disorders can be attributed to the dual genetic control on mitochondrial functions, posing a challenge for diagnosis. Though the advancement in the high-throughput sequencing and other omics platforms resulted in a "genetics-first" approach, the muscle biopsy remains the benchmark in most of the mitochondrial disorders. This review focuses on the myopathological aspects of primary mitochondrial disorders. The utility of muscle biopsy is not limited to analyse the structural abnormalities; rather it also proves to be a potential tool to understand the deranged sub-cellular functions.
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Affiliation(s)
- Narayanappa Gayathri
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore 560 029, India.
| | - Sekar Deepha
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore 560 029, India
| | - Shivani Sharma
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore 560 029, India
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15
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Trapped topoisomerase-DNA covalent complexes in the mitochondria and their role in human diseases. Mitochondrion 2021; 60:234-244. [PMID: 34500116 DOI: 10.1016/j.mito.2021.08.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/24/2021] [Accepted: 08/27/2021] [Indexed: 11/22/2022]
Abstract
Topoisomerases regulate DNA topology, organization of the intracellular DNA, the transmission of genetic materials, and gene expressions. Other than the nuclear genome, mitochondria also harbor the small, circular DNA (mtDNA) that encodes a critical subset of proteins for the production of cellular ATP; however, mitochondria are solely dependent on the nucleus for all the mitochondrial proteins necessary for mtDNA replication, repair, and maintenance. Mitochondrial genome compiles topological stress from bidirectional transcription and replication, therefore imports four nuclear encoded topoisomerases (Top1mt, Top2α, Top2β, and Top3α) in the mitochondria to relax mtDNA supercoiling generated during these processes. Trapping of topoisomerase on DNA results in the formation of protein-linked DNA adducts (PDAs), which are widely exploited by topoisomerase-targeting anticancer drugs. Intriguingly mtDNA is potentially exposed to DNA damage that has been attributed to a variety of human diseases, including neurodegeneration, cancer, and premature aging. In this review, we focus on the role of different topoisomerases in the mitochondria and our current understanding of the mitochondrial DNA damage through trapped protein-DNA complexes, and the progress in the molecular mechanisms of the repair for trapped topoisomerase covalent complexes (Topcc). Finally, we have discussed how the pathological DNA lesions that cause mtDNA damage,trigger mitochondrial fission and mitophagy, which serve as quality control events for clearing damaged mtDNA.
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16
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Rossmann MP, Dubois SM, Agarwal S, Zon LI. Mitochondrial function in development and disease. Dis Model Mech 2021; 14:269120. [PMID: 34114603 PMCID: PMC8214736 DOI: 10.1242/dmm.048912] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are organelles with vital functions in almost all eukaryotic cells. Often described as the cellular ‘powerhouses’ due to their essential role in aerobic oxidative phosphorylation, mitochondria perform many other essential functions beyond energy production. As signaling organelles, mitochondria communicate with the nucleus and other organelles to help maintain cellular homeostasis, allow cellular adaptation to diverse stresses, and help steer cell fate decisions during development. Mitochondria have taken center stage in the research of normal and pathological processes, including normal tissue homeostasis and metabolism, neurodegeneration, immunity and infectious diseases. The central role that mitochondria assume within cells is evidenced by the broad impact of mitochondrial diseases, caused by defects in either mitochondrial or nuclear genes encoding for mitochondrial proteins, on different organ systems. In this Review, we will provide the reader with a foundation of the mitochondrial ‘hardware’, the mitochondrion itself, with its specific dynamics, quality control mechanisms and cross-organelle communication, including its roles as a driver of an innate immune response, all with a focus on development, disease and aging. We will further discuss how mitochondrial DNA is inherited, how its mutation affects cell and organismal fitness, and current therapeutic approaches for mitochondrial diseases in both model organisms and humans. Summary: Mitochondria have a plethora of functions beyond metabolism. This Review discusses the emerging and multifaceted roles of mitochondria in different model organisms and human disease biology.
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Affiliation(s)
- Marlies P Rossmann
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Sonia M Dubois
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Suneet Agarwal
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Leonard I Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA
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17
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van den Ameele J, Hong YT, Manavaki R, Kouli A, Biggs H, MacIntyre Z, Horvath R, Yu-Wai-Man P, Reid E, Williams-Gray CH, Bullmore ET, Aigbirhio FI, Fryer TD, Chinnery PF. [ 11C]PK11195-PET Brain Imaging of the Mitochondrial Translocator Protein in Mitochondrial Disease. Neurology 2021; 96:e2761-e2773. [PMID: 33883237 PMCID: PMC8205464 DOI: 10.1212/wnl.0000000000012033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/04/2021] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE To explore the possibilities of radioligands against the mitochondrial outer membrane translocator protein (TSPO) as biomarkers for mitochondrial disease, we performed brain PET-MRI with [11C]PK11195 in 14 patients with genetically confirmed mitochondrial disease and 33 matched controls. METHODS Case-control study of brain PET-MRI with the TSPO radioligand [11C]PK11195. RESULTS Forty-six percent of symptomatic patients had volumes of abnormal radiotracer binding greater than the 95th percentile in controls. [11C]PK11195 binding was generally greater in gray matter and significantly decreased in white matter. This was most striking in patients with nuclear TYMP or mitochondrial m.3243A>G MT-TL1 mutations, in keeping with differences in mitochondrial density seen postmortem. Some regional binding patterns corresponded to clinical presentation and underlying mutation, even in the absence of structural changes on MRI. This was most obvious for the cerebellum, where patients with ataxia had decreased binding in the cerebellar cortex, but not necessarily volume loss. Overall, there was a positive correlation between aberrant [11C]PK11195 binding and clinical severity. CONCLUSION These findings endorse the use of PET imaging with TSPO radioligands as a noninvasive in vivo biomarker of mitochondrial pathology. CLASSIFICATION OF EVIDENCE This study provides Class III evidence that brain PET-MRI with TSPO radioligands identifies mitochondrial pathology.
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Affiliation(s)
- Jelle van den Ameele
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Young T Hong
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Roido Manavaki
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Antonina Kouli
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Heather Biggs
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Zoe MacIntyre
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Rita Horvath
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Patrick Yu-Wai-Man
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Evan Reid
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Caroline H Williams-Gray
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Ed T Bullmore
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Franklin I Aigbirhio
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Tim D Fryer
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK
| | - Patrick F Chinnery
- From the Departments of Clinical Neurosciences (J.v.d.A., Y.T.H., A.K., H.B., Z.M., R.H., P.Y.-W.M., C.H.W.-G., F.I.A., T.D.F., P.F.C.), Radiology (R.M.), Medical Genetics (E.R.), and Psychiatry (E.T.B.), Cambridge Institute for Medical Research (E.R.), Cambridge Biomedical Campus, and MRC Mitochondrial Biology Unit (J.v.d.A., P.F.C.), University of Cambridge; Moorfields Eye Hospital NHS Foundation Trust (P.Y.-W.M.); and Institute of Ophthalmology (P.Y.-W.M.), University College London, UK.
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18
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Mitochondrial genome stability in human: understanding the role of DNA repair pathways. Biochem J 2021; 478:1179-1197. [DOI: 10.1042/bcj20200920] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 11/17/2022]
Abstract
Mitochondria are semiautonomous organelles in eukaryotic cells and possess their own genome that replicates independently. Mitochondria play a major role in oxidative phosphorylation due to which its genome is frequently exposed to oxidative stress. Factors including ionizing radiation, radiomimetic drugs and replication fork stalling can also result in different types of mutations in mitochondrial DNA (mtDNA) leading to genome fragility. Mitochondria from myopathies, dystonia, cancer patient samples show frequent mtDNA mutations such as point mutations, insertions and large-scale deletions that could account for mitochondria-associated disease pathogenesis. The mechanism by which such mutations arise following exposure to various DNA-damaging agents is not well understood. One of the well-studied repair pathways in mitochondria is base excision repair. Other repair pathways such as mismatch repair, homologous recombination and microhomology-mediated end joining have also been reported. Interestingly, nucleotide excision repair and classical nonhomologous DNA end joining are not detected in mitochondria. In this review, we summarize the potential causes of mitochondrial genome fragility, their implications as well as various DNA repair pathways that operate in mitochondria.
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19
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Stewart JB. Current progress with mammalian models of mitochondrial DNA disease. J Inherit Metab Dis 2021; 44:325-342. [PMID: 33099782 DOI: 10.1002/jimd.12324] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022]
Abstract
Mitochondrial disorders make up a large class of heritable diseases that cause a broad array of different human pathologies. They can affect many different organ systems, or display very specific tissue presentation, and can lead to illness either in childhood or later in life. While the over 1200 genes encoded in the nuclear DNA play an important role in human mitochondrial disease, it has been known for over 30 years that mutations of the mitochondria's own small, multicopy DNA chromosome (mtDNA) can lead to heritable human diseases. Unfortunately, animal mtDNA has resisted transgenic and directed genome editing technologies until quite recently. As such, animal models to aid in our understanding of these diseases, and to explore preclinical therapeutic research have been quite rare. This review will discuss the unusual properties of animal mitochondria that have hindered the generation of animal models. It will also discuss the existing mammalian models of human mtDNA disease, describe the methods employed in their generation, and will discuss recent advances in the targeting of DNA-manipulating enzymes to the mitochondria and how these may be employed to generate new models.
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Affiliation(s)
- James Bruce Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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20
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Müller‐Nedebock AC, Westhuizen FH, Kõks S, Bardien S. Nuclear Genes Associated with Mitochondrial
DNA
Processes as Contributors to Parkinson's Disease Risk. Mov Disord 2021; 36:815-831. [DOI: 10.1002/mds.28475] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022] Open
Affiliation(s)
- Amica C. Müller‐Nedebock
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | | | - Sulev Kõks
- Perron Institute for Neurological and Translational Science Nedlands Western Australia Australia
- Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Murdoch Western Australia Australia
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
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21
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Lechuga-Vieco AV, Justo-Méndez R, Enríquez JA. Not all mitochondrial DNAs are made equal and the nucleus knows it. IUBMB Life 2020; 73:511-529. [PMID: 33369015 PMCID: PMC7985871 DOI: 10.1002/iub.2434] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022]
Abstract
The oxidative phosphorylation (OXPHOS) system is the only structure in animal cells with components encoded by two genomes, maternally transmitted mitochondrial DNA (mtDNA), and biparentally transmitted nuclear DNA (nDNA). MtDNA‐encoded genes have to physically assemble with their counterparts encoded in the nucleus to build together the functional respiratory complexes. Therefore, structural and functional matching requirements between the protein subunits of these molecular complexes are rigorous. The crosstalk between nDNA and mtDNA needs to overcome some challenges, as the nuclear‐encoded factors have to be imported into the mitochondria in a correct quantity and match the high number of organelles and genomes per mitochondria that encode and synthesize their own components locally. The cell is able to sense the mito‐nuclear match through changes in the activity of the OXPHOS system, modulation of the mitochondrial biogenesis, or reactive oxygen species production. This implies that a complex signaling cascade should optimize OXPHOS performance to the cellular‐specific requirements, which will depend on cell type, environmental conditions, and life stage. Therefore, the mitochondria would function as a cellular metabolic information hub integrating critical information that would feedback the nucleus for it to respond accordingly. Here, we review the current understanding of the complex interaction between mtDNA and nDNA.
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Affiliation(s)
- Ana Victoria Lechuga-Vieco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Raquel Justo-Méndez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
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22
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Stewart JB, Chinnery PF. Extreme heterogeneity of human mitochondrial DNA from organelles to populations. Nat Rev Genet 2020; 22:106-118. [PMID: 32989265 DOI: 10.1038/s41576-020-00284-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
Contrary to the long-held view that most humans harbour only identical mitochondrial genomes, deep resequencing has uncovered unanticipated extreme genetic variation within mitochondrial DNA (mtDNA). Most, if not all, humans contain multiple mtDNA genotypes (heteroplasmy); specific patterns of variants accumulate in different tissues, including cancers, over time; and some variants are preferentially passed down or suppressed in the maternal germ line. These findings cast light on the origin and spread of mtDNA mutations at multiple scales, from the organelle to the human population, and challenge the conventional view that high percentages of a mutation are required before a new variant has functional consequences.
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Affiliation(s)
- James B Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. .,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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Røyrvik EC, Johnston IG. MtDNA sequence features associated with 'selfish genomes' predict tissue-specific segregation and reversion. Nucleic Acids Res 2020; 48:8290-8301. [PMID: 32716035 PMCID: PMC7470939 DOI: 10.1093/nar/gkaa622] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/25/2020] [Accepted: 07/15/2020] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial DNA (mtDNA) encodes cellular machinery vital for cell and organism survival. Mutations, genetic manipulation, and gene therapies may produce cells where different types of mtDNA coexist in admixed populations. In these admixtures, one mtDNA type is often observed to proliferate over another, with different types dominating in different tissues. This ‘segregation bias’ is a long-standing biological mystery that may pose challenges to modern mtDNA disease therapies, leading to substantial recent attention in biological and medical circles. Here, we show how an mtDNA sequence’s balance between replication and transcription, corresponding to molecular ‘selfishness’, in conjunction with cellular selection, can potentially modulate segregation bias. We combine a new replication-transcription-selection (RTS) model with a meta-analysis of existing data to show that this simple theory predicts complex tissue-specific patterns of segregation in mouse experiments, and reversion in human stem cells. We propose the stability of G-quadruplexes in the mtDNA control region, influencing the balance between transcription and replication primer formation, as a potential molecular mechanism governing this balance. Linking mtDNA sequence features, through this molecular mechanism, to cellular population dynamics, we use sequence data to obtain and verify the sequence-specific predictions from this hypothesis on segregation behaviour in mouse and human mtDNA.
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Affiliation(s)
- Ellen C Røyrvik
- Department of Clinical Science, University of Bergen, Norway.,K.G. Jebsen Center for Autoimmune Diseases, University of Bergen, Norway
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Norway.,Alan Turing Institute, London, UK
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24
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Carpagnano GE, Scioscia G, Lacedonia D, Soccio P, Quarato CMI, Cotugno G, Palumbo MG, Foschino Barbaro MP. Searching for Inflammatory and Oxidative Stress Markers Capable of Clustering Severe Asthma. Arch Bronconeumol 2020; 57:338-344. [PMID: 32593535 DOI: 10.1016/j.arbres.2020.04.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 12/26/2022]
Abstract
OBJECTIVE Asthma inflammation may feature an imbalance between oxidative stress and antioxidant defenses. Oxidative stress induces propagation of airways inflammation and corticosteroid insensitivity contributing to poor asthma control, and frequent severe acute exacerbations. This study assessed inflammation and oxidative stress in severe asthmatic subjects and evaluated the possible correlations between inflammatory and oxidative stress markers investigated and asthma severity. MATERIAL AND METHOD Fifty-three patients with severe asthma, 11 patients with mild-moderate asthma and 12 healthy subjects were enrolled and underwent fractional exhaled nitric oxide (FENO) analysis and blood and sputum count cell collection. The content of mitochondrial DNA (MtDNA) and nuclear DNA (nDNA) was measured in exhaled breath condensate (EBC) by Real Time PCR and the ratio between MtDNA/nDNA was calculated. We detected MtDNA/nDNA in the EBC of severe asthmatics. RESULTS We found higher exhaled MtDNA/nDNA in severe asthmatics respectively compared to mild-moderate ones and to healthy controls (10.4±2.2 vs 7.9±2.5, p<0.05 and 10.4±2.2 vs 6.51±0.21, p<0.05). The level of exhaled MtDNA/nDNA was significantly higher in Non-T2 endotype severe asthmatics than T2 (14.07±10. 8 vs 6.5±5.5, p<0.05). CONCLUSION Oxidative stress marker (MtDNA/nDNA) is increased significantly with asthma severity and may be useful for endotyping severe asthma.
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Affiliation(s)
- Giovanna E Carpagnano
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Giulia Scioscia
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Policlinico "OO Riuniti", Foggia, Italy.
| | - Donato Lacedonia
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Policlinico "OO Riuniti", Foggia, Italy
| | - Piera Soccio
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Policlinico "OO Riuniti", Foggia, Italy
| | - Carla M I Quarato
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Policlinico "OO Riuniti", Foggia, Italy
| | - Grazia Cotugno
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Policlinico "OO Riuniti", Foggia, Italy
| | - Maria G Palumbo
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Policlinico "OO Riuniti", Foggia, Italy
| | - Maria P Foschino Barbaro
- Department of Medical and Surgical Sciences, Institute of Respiratory Diseases, University of Foggia, Policlinico "OO Riuniti", Foggia, Italy
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25
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Zekonyte U, Bacman SR, Moraes CT. DNA-editing enzymes as potential treatments for heteroplasmic mtDNA diseases. J Intern Med 2020; 287:685-697. [PMID: 32176378 PMCID: PMC7260085 DOI: 10.1111/joim.13055] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/04/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
Abstract
Mutations in the mitochondrial genome are the cause of many debilitating neuromuscular disorders. Currently, there is no cure or treatment for these diseases, and symptom management is the only relief doctors can provide. Although supplements and vitamins are commonly used in treatment, they provide little benefit to the patient and are only palliative. This is why gene therapy is a promising research topic to potentially treat and, in theory, even cure diseases caused by mutations in the mitochondrial DNA (mtDNA). Mammalian cells contain approximately a thousand copies of mtDNA, which can lead to a phenomenon called heteroplasmy, where both wild-type and mutant mtDNA molecules co-exist within the cell. Disease only manifests once the per cent of mutant mtDNA reaches a high threshold (usually >80%), which causes mitochondrial dysfunction and reduced ATP production. This is a useful feature to take advantage of for gene therapy applications, as not every mutant copy of mtDNA needs to be eliminated, but only enough to shift the heteroplasmic ratio below the disease threshold. Several DNA-editing enzymes have been used to shift heteroplasmy in cell culture and mice. This review provides an overview of these enzymes and discusses roadblocks of applying these to gene therapy in humans.
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Affiliation(s)
- U Zekonyte
- From the, Graduate Program in Human Genetics and Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | - S R Bacman
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - C T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
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26
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Jeppesen TD. Aerobic Exercise Training in Patients With mtDNA-Related Mitochondrial Myopathy. Front Physiol 2020; 11:349. [PMID: 32508662 PMCID: PMC7253634 DOI: 10.3389/fphys.2020.00349] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/26/2020] [Indexed: 01/15/2023] Open
Abstract
In patients with mitochondrial DNA (mtDNA) mutation, a pathogenic mtDNA mutation is heteroplasmically distributed among tissues. The ratio between wild-type and mutated mtDNA copies determines the mtDNA mutation load of the tissue, which correlates inversively with oxidative capacity of the tissue. In patients with mtDNA mutation, the mutation load is often very high in skeletal muscle compared to other tissues. Additionally, skeletal muscle can increase its oxygen demand up to 100-fold from rest to exercise, which is unmatched by any other tissue. Thus, exercise intolerance is the most common symptom in patients with mtDNA mutation. The impaired oxidative capacity in skeletal muscle in patients with mtDNA mutation results in limitation in physical capacity that interferes with daily activities and impairs quality of life. Additionally, patients with mitochondrial disease due to mtDNA mutation often live a sedentary lifestyle, which further impair oxidative capacity and exercise tolerance. Since aerobic exercise training increase mitochondrial function and volume density in healthy individuals, studies have investigated if aerobic training could be used to counteract the progressive exercise intolerance in patients with mtDNA mutation. Overall studies investigating the effect of aerobic training in patients with mtDNA mutation have shown that aerobic training is an efficient way to improve oxidative capacity in this condition, and aerobic training seems to be safe even for patients with high mtDNA mutation in skeletal muscle.
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Affiliation(s)
- Tina Dysgaard Jeppesen
- Copenhagen Neuromuscular Clinic, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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27
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Lawless C, Greaves L, Reeve AK, Turnbull DM, Vincent AE. The rise and rise of mitochondrial DNA mutations. Open Biol 2020; 10:200061. [PMID: 32428418 PMCID: PMC7276526 DOI: 10.1098/rsob.200061] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/23/2020] [Indexed: 12/24/2022] Open
Abstract
How mitochondrial DNA mutations clonally expand in an individual cell is a question that has perplexed mitochondrial biologists for decades. A growing body of literature indicates that mitochondrial DNA mutations play a major role in ageing, metabolic diseases, neurodegenerative diseases, neuromuscular disorders and cancers. Importantly, this process of clonal expansion occurs for both inherited and somatic mitochondrial DNA mutations. To complicate matters further there are fundamental differences between mitochondrial DNA point mutations and deletions, and between mitotic and post-mitotic cells, that impact this pathogenic process. These differences, along with the challenges of investigating a longitudinal process occurring over decades in humans, have so far hindered progress towards understanding clonal expansion. Here we summarize our current understanding of the clonal expansion of mitochondrial DNA mutations in different tissues and highlight key unanswered questions. We then discuss the various existing biological models, along with their advantages and disadvantages. Finally, we explore what has been achieved with mathematical modelling so far and suggest future work to advance this important area of research.
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Affiliation(s)
| | | | | | - Doug M. Turnbull
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE2 4HH, UK
| | - Amy E. Vincent
- Wellcome Centre for Mitochondrial Research, Clinical and Translational Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle NE2 4HH, UK
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28
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Klucnika A, Ma H. A battle for transmission: the cooperative and selfish animal mitochondrial genomes. Open Biol 2020; 9:180267. [PMID: 30890027 PMCID: PMC6451365 DOI: 10.1098/rsob.180267] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial genome is an evolutionarily persistent and cooperative component of metazoan cells that contributes to energy production and many other cellular processes. Despite sharing the same host as the nuclear genome, the multi-copy mitochondrial DNA (mtDNA) follows very different rules of replication and transmission, which translate into differences in the patterns of selection. On one hand, mtDNA is dependent on the host for its transmission, so selections would favour genomes that boost organismal fitness. On the other hand, genetic heterogeneity within an individual allows different mitochondrial genomes to compete for transmission. This intra-organismal competition could select for the best replicator, which does not necessarily give the fittest organisms, resulting in mito-nuclear conflict. In this review, we discuss the recent advances in our understanding of the mechanisms and opposing forces governing mtDNA transmission and selection in bilaterians, and what the implications of these are for mtDNA evolution and mitochondrial replacement therapy.
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Affiliation(s)
- Anna Klucnika
- 1 Wellcome Trust/Cancer Research UK Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN , UK.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
| | - Hansong Ma
- 1 Wellcome Trust/Cancer Research UK Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN , UK.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
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29
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Evolving mtDNA populations within cells. Biochem Soc Trans 2020; 47:1367-1382. [PMID: 31484687 PMCID: PMC6824680 DOI: 10.1042/bst20190238] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/14/2022]
Abstract
Mitochondrial DNA (mtDNA) encodes vital respiratory machinery. Populations of mtDNA molecules exist in most eukaryotic cells, subject to replication, degradation, mutation, and other population processes. These processes affect the genetic makeup of cellular mtDNA populations, changing cell-to-cell distributions, means, and variances of mutant mtDNA load over time. As mtDNA mutant load has nonlinear effects on cell functionality, and cell functionality has nonlinear effects on tissue performance, these statistics of cellular mtDNA populations play vital roles in health, disease, and inheritance. This mini review will describe some of the better-known ways in which these populations change over time in different organisms, highlighting the importance of quantitatively understanding both mutant load mean and variance. Due to length constraints, we cannot attempt to be comprehensive but hope to provide useful links to some of the many excellent studies on these topics.
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30
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van den Ameele J, Li AY, Ma H, Chinnery PF. Mitochondrial heteroplasmy beyond the oocyte bottleneck. Semin Cell Dev Biol 2020; 97:156-166. [DOI: 10.1016/j.semcdb.2019.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 09/17/2019] [Accepted: 10/01/2019] [Indexed: 12/31/2022]
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31
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Peripheral Blood Mitochondrial DNA Copy Number Obtained From Genome-Wide Genotype Data Is Associated With Neurocognitive Impairment in Persons With Chronic HIV Infection. J Acquir Immune Defic Syndr 2019; 80:e95-e102. [PMID: 30531306 DOI: 10.1097/qai.0000000000001930] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) copy number varies by cell type and energy demands. Blood mtDNA copy number has been associated with neurocognitive function in persons without HIV. Low mtDNA copy number may indicate disordered mtDNA replication; high copy number may reflect a response to mitochondrial dysfunction. We hypothesized that blood mtDNA copy number estimated from genome-wide genotyping data is related to neurocognitive impairment (NCI) in persons with HIV. METHODS In the CNS HIV Antiretroviral Therapy Effects Research (CHARTER) study, peripheral blood mtDNA copy number was obtained from genome-wide genotyping data as a ratio of mtDNA single-nucleotide polymorphism probe intensities relative to nuclear DNA single-nucleotide polymorphisms. In a multivariable regression model, associations between mtDNA copy number and demographics, blood cell counts, and HIV disease and treatment characteristics were tested. Associations of mtDNA copy number with the global deficit score (GDS), GDS-defined NCI (GDS ≥ 0.5), and HIV-associated neurocognitive disorder (HAND) diagnosis were tested by logistic regression, adjusting for potential confounders. RESULTS Among 1010 CHARTER participants, lower mtDNA copy number was associated with longer antiretroviral therapy duration (P < 0.001), but not with d-drug exposure (P = 0.85). mtDNA copy number was also associated with GDS (P = 0.007), GDS-defined NCI (P < 0.001), and HAND (P = 0.002). In all analyses, higher mtDNA copy number was associated with poorer cognitive performance. CONCLUSIONS Higher mtDNA copy number estimated from peripheral blood genotyping was associated with worse neurocognitive performance in adults with HIV. These results suggest a connection between peripheral blood mtDNA and NCI, and may represent increased mtDNA replication in response to mitochondrial dysfunction.
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32
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Johnston IG. Varied Mechanisms and Models for the Varying Mitochondrial Bottleneck. Front Cell Dev Biol 2019; 7:294. [PMID: 31824946 PMCID: PMC6879659 DOI: 10.3389/fcell.2019.00294] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial DNA (mtDNA) molecules exist in populations within cells, and may carry mutations. Different cells within an organism, and organisms within a family, may have different proportions of mutant mtDNA in these cellular populations. This diversity is often thought of as arising from a “genetic bottleneck.” This article surveys approaches to characterize and model the generation of this genetic diversity, aiming to provide an introduction to the range of concepts involved, and to highlight some recent advances in understanding. In particular, differences between the statistical “genetic bottleneck” (mutant proportion spread) and the physical mtDNA bottleneck and other cellular processes are highlighted. Particular attention is paid to the quantitative analysis of the “genetic bottleneck,” estimation of its magnitude from observed data, and inference of its underlying mechanisms. Evidence that the “genetic bottleneck” (mutant proportion spread) varies with age, between individuals and species, and across mtDNA sequences, is described. The interpretation issues that arise from sampling errors, selection, and different quantitative definitions are also discussed.
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Affiliation(s)
- Iain G Johnston
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
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33
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Müller-Nedebock AC, Brennan RR, Venter M, Pienaar IS, van der Westhuizen FH, Elson JL, Ross OA, Bardien S. The unresolved role of mitochondrial DNA in Parkinson's disease: An overview of published studies, their limitations, and future prospects. Neurochem Int 2019; 129:104495. [PMID: 31233840 PMCID: PMC6702091 DOI: 10.1016/j.neuint.2019.104495] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/27/2019] [Accepted: 06/21/2019] [Indexed: 12/21/2022]
Abstract
Parkinson's disease (PD), a progressive neurodegenerative disorder, has long been associated with mitochondrial dysfunction in both sporadic and familial forms of the disease. Mitochondria are crucial for maintaining cellular homeostasis, and their dysfunction is detrimental to dopaminergic neurons. These neurons are highly dependent on mitochondrial adenosine triphosphate (ATP) and degenerate in PD. Mitochondria contain their own genomes (mtDNA). The role of mtDNA has been investigated in PD on the premise that it encodes vital components of the ATP-generating oxidative phosphorylation (OXPHOS) complexes and accumulates somatic variation with age. However, the association between mtDNA variation and PD remains controversial. Herein, we provide an overview of previously published studies on the role of inherited as well as somatic (acquired) mtDNA changes in PD including point mutations, deletions and depletion. We outline limitations of previous investigations and the difficulties associated with studying mtDNA, which have left its role unresolved in the context of PD. Lastly, we highlight the potential for further research in this field and provide suggestions for future studies. Overall, the mitochondrial genome is indispensable for proper cellular function and its contribution to PD requires further, more extensive investigation.
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Affiliation(s)
- Amica C Müller-Nedebock
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | | | - Marianne Venter
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Ilse S Pienaar
- School of Life Sciences, University of Sussex, Falmer, BN1 9PH, United Kingdom; Centre for Neuroinflammation and Neurodegeneration, Imperial College London, London, United Kingdom
| | | | - Joanna L Elson
- Human Metabolomics, North-West University, Potchefstroom, South Africa; Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA; School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa.
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Aryaman J, Bowles C, Jones NS, Johnston IG. Mitochondrial Network State Scales mtDNA Genetic Dynamics. Genetics 2019; 212:1429-1443. [PMID: 31253641 PMCID: PMC6707450 DOI: 10.1534/genetics.119.302423] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/28/2019] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. mtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The role of the resulting mitochondrial networks in the time evolution of the cellular proportion of mutated mtDNA molecules (heteroplasmy), and cell-to-cell variability in heteroplasmy (heteroplasmy variance), remains incompletely understood. Heteroplasmy variance is particularly important since it modulates the number of pathological cells in a tissue. Here, we provide the first wide-reaching theoretical framework which bridges mitochondrial network and genetic states. We show that, under a range of conditions, the (genetic) rate of increase in heteroplasmy variance and de novo mutation are proportionally modulated by the (physical) fraction of unfused mitochondria, independently of the absolute fission-fusion rate. In the context of selective fusion, we show that intermediate fusion:fission ratios are optimal for the clearance of mtDNA mutants. Our findings imply that modulating network state, mitophagy rate, and copy number to slow down heteroplasmy dynamics when mean heteroplasmy is low could have therapeutic advantages for mitochondrial disease and healthy aging.
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Affiliation(s)
- Juvid Aryaman
- Department of Mathematics, Imperial College London, SW7 2AZ, United Kingdom
- Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ, United Kingdom
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, United Kingdom
| | - Charlotte Bowles
- School of Biosciences, University of Birmingham, B15 2TT, United Kingdom
| | - Nick S Jones
- Department of Mathematics, Imperial College London, SW7 2AZ, United Kingdom
- Engineering and Physical Sciences Research Council Centre for the Mathematics of Precision Healthcare, Imperial College London, SW7 2AZ, United Kingdom
| | - Iain G Johnston
- Faculty of Mathematics and Natural Sciences, University of Bergen, 5007, Norway
- Alan Turing Institute, London NW1 2DB, United Kingdom
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35
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Johnston IG. Tension and Resolution: Dynamic, Evolving Populations of Organelle Genomes within Plant Cells. MOLECULAR PLANT 2019; 12:764-783. [PMID: 30445187 DOI: 10.1016/j.molp.2018.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/25/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Mitochondria and plastids form dynamic, evolving populations physically embedded in the fluctuating environment of the plant cell. Their evolutionary heritage has shaped how the cell controls the genetic structure and the physical behavior of its organelle populations. While the specific genes involved in these processes are gradually being revealed, the governing principles underlying this controlled behavior remain poorly understood. As the genetic and physical dynamics of these organelles are central to bioenergetic performance and plant physiology, this challenges both fundamental biology and strategies to engineer better-performing plants. This article reviews current knowledge of the physical and genetic behavior of mitochondria and chloroplasts in plant cells. An overarching hypothesis is proposed whereby organelles face a tension between genetic robustness and individual control and responsiveness, and different species resolve this tension in different ways. As plants are immobile and thus subject to fluctuating environments, their organelles are proposed to favor individual responsiveness, sacrificing genetic robustness. Several notable features of plant organelles, including large genomes, mtDNA recombination, fragmented organelles, and plastid/mitochondrial differences may potentially be explained by this hypothesis. Finally, the ways that quantitative and systems biology can help shed light on the plethora of open questions in this field are highlighted.
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Affiliation(s)
- Iain G Johnston
- School of Biosciences, University of Birmingham, Birmingham, UK; Birmingham Institute for Forest Research, University of Birmingham, Birmingham, UK.
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36
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Abstract
Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.
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Affiliation(s)
- Justin C Havird
- Department of Integrative Biology, The University of Texas, Austin, TX 78712, USA.
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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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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Wei W, Tuna S, Keogh MJ, Smith KR, Aitman TJ, Beales PL, Bennett DL, Gale DP, Bitner-Glindzicz MAK, Black GC, Brennan P, Elliott P, Flinter FA, Floto RA, Houlden H, Irving M, Koziell A, Maher ER, Markus HS, Morrell NW, Newman WG, Roberts I, Sayer JA, Smith KGC, Taylor JC, Watkins H, Webster AR, Wilkie AOM, Williamson C, Ashford S, Penkett CJ, Stirrups KE, Rendon A, Ouwehand WH, Bradley JR, Raymond FL, Caulfield M, Turro E, Chinnery PF. Germline selection shapes human mitochondrial DNA diversity. Science 2019; 364:eaau6520. [PMID: 31123110 DOI: 10.1126/science.aau6520] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/22/2019] [Accepted: 04/03/2019] [Indexed: 02/02/2023]
Abstract
Approximately 2.4% of the human mitochondrial DNA (mtDNA) genome exhibits common homoplasmic genetic variation. We analyzed 12,975 whole-genome sequences to show that 45.1% of individuals from 1526 mother-offspring pairs harbor a mixed population of mtDNA (heteroplasmy), but the propensity for maternal transmission differs across the mitochondrial genome. Over one generation, we observed selection both for and against variants in specific genomic regions; known variants were more likely to be transmitted than previously unknown variants. However, new heteroplasmies were more likely to match the nuclear genetic ancestry as opposed to the ancestry of the mitochondrial genome on which the mutations occurred, validating our findings in 40,325 individuals. Thus, human mtDNA at the population level is shaped by selective forces within the female germ line under nuclear genetic control, which ensures consistency between the two independent genetic lineages.
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Abstract
Cell-to-cell heterogeneity drives a range of (patho)physiologically important phenomena, such as cell fate and chemotherapeutic resistance. The role of metabolism, and particularly of mitochondria, is increasingly being recognized as an important explanatory factor in cell-to-cell heterogeneity. Most eukaryotic cells possess a population of mitochondria, in the sense that mitochondrial DNA (mtDNA) is held in multiple copies per cell, where the sequence of each molecule can vary. Hence, intra-cellular mitochondrial heterogeneity is possible, which can induce inter-cellular mitochondrial heterogeneity, and may drive aspects of cellular noise. In this review, we discuss sources of mitochondrial heterogeneity (variations between mitochondria in the same cell, and mitochondrial variations between supposedly identical cells) from both genetic and non-genetic perspectives, and mitochondrial genotype-phenotype links. We discuss the apparent homeostasis of mtDNA copy number, the observation of pervasive intra-cellular mtDNA mutation (which is termed "microheteroplasmy"), and developments in the understanding of inter-cellular mtDNA mutation ("macroheteroplasmy"). We point to the relationship between mitochondrial supercomplexes, cristal structure, pH, and cardiolipin as a potential amplifier of the mitochondrial genotype-phenotype link. We also discuss mitochondrial membrane potential and networks as sources of mitochondrial heterogeneity, and their influence upon the mitochondrial genome. Finally, we revisit the idea of mitochondrial complementation as a means of dampening mitochondrial genotype-phenotype links in light of recent experimental developments. The diverse sources of mitochondrial heterogeneity, as well as their increasingly recognized role in contributing to cellular heterogeneity, highlights the need for future single-cell mitochondrial measurements in the context of cellular noise studies.
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Affiliation(s)
- Juvid Aryaman
- Department of Mathematics, Imperial College London, London, United Kingdom
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Iain G. Johnston
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- EPSRC Centre for the Mathematics of Precision Healthcare, Imperial College London, London, United Kingdom
| | - Nick S. Jones
- Department of Mathematics, Imperial College London, London, United Kingdom
- EPSRC Centre for the Mathematics of Precision Healthcare, Imperial College London, London, United Kingdom
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Kallianpur AR, Gerschenson M, Hulgan T, Kaur H, Clifford DB, Haas DW, Murdock DG, McArthur JC, Samuels DC, Simpson DM. Hemochromatosis (HFE) Gene Variants Are Associated with Increased Mitochondrial DNA Levels During HIV-1 Infection and Antiretroviral Therapy. AIDS Res Hum Retroviruses 2018; 34:942-949. [PMID: 29968489 DOI: 10.1089/aid.2018.0025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Some HIV-associated complications involve mitochondrial dysfunction and may be less common in individuals with iron-loading HFE (hemochromatosis gene) variants. We evaluated HFE 845A and 187G alleles in relation to mitochondrial DNA (mtDNA) levels in peripheral blood mononuclear cells from 85 individuals with HIV infection on uninterrupted antiretroviral therapy (ART) for 15 or more consecutive weeks. Carriers of HFE gene variants (N = 24) had significantly higher mtDNA levels than noncarriers (N = 61), after adjusting for age, race, sex, and type of ART [adjusted β-coefficient 297, p-value < .001 for at least one HFE variant], but mtDNA declined among all individuals on study during 48 weeks on ART. Increased cellular mtDNA content may represent a compensatory response to mitochondrial stress that is influenced by iron-loading HFE variants.
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Affiliation(s)
- Asha R. Kallianpur
- Department of Genomic Medicine, Cleveland Clinic Foundation/Lerner Research Institute, Cleveland, Ohio
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, Ohio
| | - Mariana Gerschenson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu, Hawaii
| | - Todd Hulgan
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Harpreet Kaur
- Department of Genomic Medicine, Cleveland Clinic Foundation/Lerner Research Institute, Cleveland, Ohio
| | - David B. Clifford
- Department of Neurology, Washington University in Saint Louis, St. Louis, Missouri
| | - David W. Haas
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Deborah G. Murdock
- Children's Hospital of Philadelphia Research Institute & Center for Mitochondrial and Epigenomic Medicine, Philadelphia, Pennsylvania
| | - Justin C. McArthur
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David C. Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee
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Tranah GJ, Maglione JE, Yaffe K, Katzman SM, Manini TM, Kritchevsky S, Newman AB, Harris TB, Cummings SR. Mitochondrial DNA m.13514G>A heteroplasmy is associated with depressive symptoms in the elderly. Int J Geriatr Psychiatry 2018; 33:1319-1326. [PMID: 29984425 DOI: 10.1002/gps.4928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/14/2018] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Mitochondrial DNA (mtDNA) heteroplasmy is a mixture of normal and mutated mtDNA molecules in a cell. High levels of heteroplasmy at several mtDNA sites in complex I lead to inherited neurological neurologic diseases and brain magnetic resonance imaging (MRI) abnormalities. Here, we test the hypothesis that mtDNA heteroplasmy at these complex I sites is associated with depressive symptoms in the elderly. METHODS We examined platelet mtDNA heteroplasmy for associations with depressive symptoms among 137 participants over age 70 from the community-based Health, Aging and Body Composition Study. Depressive symptoms were assessed using the 10-point version of the Center for Epidemiologic Studies Depression Scale (CES-D 10). Complete mtDNA sequencing was performed and heteroplasmy derived for 5 mtDNA sites associated with neurologic mitochondrial diseases and tested for associations with depressive symptoms. RESULTS Of 5 candidate complex I mtDNA mutations examined for effects on depressive symptoms, increased heteroplasmy at m.13514A>G, ND5, was significantly associated with higher CES-D score (P = .01). A statistically significant interaction between m.13514A > G heteroplasmy and sex was detected (P = .04); in sex-stratified analyses, the impact of m.13514A>G heteroplasmy was stronger in male (P = .003) than in female (P = .98) participants. Men in highest tertile of mtDNA heteroplasmy exhibited significantly higher (P = .0001) mean ± SE CES-D 10 scores, 5.37 ± 0.58, when compared with those in the middle, 2.13 ± 0.52, and lowest tertiles, 2.47 ± 0.58. No associations between the 4 other candidate sites and depressive symptoms were observed. CONCLUSIONS Increased mtDNA heteroplasmy at m.13514A>G is associated with depressive symptoms in older men. Heteroplasmy may represent a novel biological risk factor for depression.
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Affiliation(s)
- Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, San Francisco, CA, USA
| | - Jeanne E Maglione
- University of California, San Diego, Department of Psychiatry, La Jolla, CA, USA
| | - Kristine Yaffe
- University of California, San Francisco, Departments of Psychiatry, Neurology, and Epidemiology, San Francisco, CA, USA.,San Francisco VA Medical Center, San Francisco, CA, USA
| | | | - Todd M Manini
- University of Florida, Department of Aging and Geriatric Research, Gainesville, FL, USA
| | - Stephen Kritchevsky
- Wake Forest School of Medicine, Sticht Center on Aging, Winston-Salem, NC, USA
| | - Anne B Newman
- University of Pittsburgh, Department of Epidemiology, Pittsburgh, PA, USA
| | - Tamara B Harris
- National Institute on Aging, Intramural Research Program, Laboratory of Epidemiology and Population Sciences, Bethesda, MD, USA
| | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, San Francisco, CA, USA
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42
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Tranah GJ, Katzman SM, Lauterjung K, Yaffe K, Manini TM, Kritchevsky S, Newman AB, Harris TB, Cummings SR. Mitochondrial DNA m.3243A > G heteroplasmy affects multiple aging phenotypes and risk of mortality. Sci Rep 2018; 8:11887. [PMID: 30089816 PMCID: PMC6082898 DOI: 10.1038/s41598-018-30255-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022] Open
Abstract
Mitochondria contain many copies of a circular DNA molecule (mtDNA), which has been observed as a mixture of normal and mutated states known as heteroplasmy. Elevated heteroplasmy at a single mtDNA site, m.3243A > G, leads to neurologic, sensory, movement, metabolic, and cardiopulmonary impairments. We measured leukocyte mtDNA m.3243A > G heteroplasmy in 789 elderly men and women from the bi-racial, population-based Health, Aging, and Body Composition Study to identify associations with age-related functioning and mortality. Mutation burden for the m.3243A > G ranged from 0–19% and elevated heteroplasmy was associated with reduced strength, cognitive, metabolic, and cardiovascular functioning. Risk of all-cause, dementia and stroke mortality was significantly elevated for participants in the highest tertiles of m.3243A > G heteroplasmy. These results indicate that the accumulation of a rare genetic disease mutation, m.3243A > G, manifests as several aging outcomes and that some diseases of aging may be attributed to the accumulation of mtDNA damage.
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Affiliation(s)
- Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA.
| | | | - Kevin Lauterjung
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Kristine Yaffe
- Departments of Psychiatry, Neurology, and Epidemiology, University of California, San Francisco and the San Francisco VA Medical Center, San Francisco, CA, 94121, USA
| | - Todd M Manini
- Department of Aging and Geriatric Research, University of Florida, Gainesville, FL, 32601, USA
| | - Stephen Kritchevsky
- Sticht Center on Aging, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Tamara B Harris
- Intramural Research Program, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD, 20892, USA
| | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
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43
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Genomic and transcriptomic characterization of the mitochondrial-rich oncocytic phenotype on a thyroid carcinoma background. Mitochondrion 2018; 46:123-133. [PMID: 29631022 DOI: 10.1016/j.mito.2018.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 12/22/2022]
Abstract
We conducted the first systematic omics study of the oncocytic phenotype in 488 papillary thyroid carcinomas (PTC) from The Cancer Genome Atlas. Oncocytic phenotype is secondary to PTC, being unrelated to several pathologic scores. The nuclear genome had low impact on this phenotype (except in specific copy number variation), which was mostly driven by the significant accumulation of mitochondrial DNA non-synonymous and frameshift mutations at high heteroplasmy levels. Energy and mitochondrial-related pathways were significantly enriched in oncocytic tumors that also displayed increased levels of expression for genes involved in autophagy and fusion of mitochondria. Our in vitro tests confirmed that autophagy is increased and functional while mitophagy is decreased in these tumors.
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44
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Resolving the Enigma of the Clonal Expansion of mtDNA Deletions. Genes (Basel) 2018; 9:genes9030126. [PMID: 29495484 PMCID: PMC5867847 DOI: 10.3390/genes9030126] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/14/2018] [Accepted: 02/16/2018] [Indexed: 12/31/2022] Open
Abstract
Mitochondria are cell organelles that are special since they contain their own genetic material in the form of mitochondrial DNA (mtDNA). Damage and mutations of mtDNA are not only involved in several inherited human diseases but are also widely thought to play an important role during aging. In both cases, point mutations or large deletions accumulate inside cells, leading to functional impairment once a certain threshold has been surpassed. In most cases, it is a single type of mutant that clonally expands and out-competes the wild type mtDNA, with different mutant molecules being amplified in different cells. The challenge is to explain where the selection advantage for the accumulation comes from, why such a large range of different deletions seem to possess this advantage, and how this process can scale to species with different lifespans such as those of rats and man. From this perspective, we provide an overview of current ideas, present an update of our own proposal, and discuss the wider relevance of the phenomenon for aging.
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45
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Burr SP, Pezet M, Chinnery PF. Mitochondrial DNA Heteroplasmy and Purifying Selection in the Mammalian Female Germ Line. Dev Growth Differ 2018; 60:21-32. [PMID: 29363102 DOI: 10.1111/dgd.12420] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/08/2017] [Indexed: 01/19/2023]
Abstract
Inherited mutations in the mitochondrial (mt)DNA are a major cause of human disease, with approximately 1 in 5000 people affected by one of the hundreds of identified pathogenic mtDNA point mutations or deletions. Due to the severe, and often untreatable, symptoms of many mitochondrial diseases, identifying how these mutations are inherited from one generation to the next has been an area of intense research in recent years. Despite large advances in our understanding of this complex process, many questions remain unanswered, with one of the most hotly debated being whether or not purifying selection acts against pathogenic mutations during germline development.
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Affiliation(s)
- Stephen P Burr
- MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mikael Pezet
- MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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46
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Theurey P, Pizzo P. The Aging Mitochondria. Genes (Basel) 2018; 9:genes9010022. [PMID: 29315229 PMCID: PMC5793175 DOI: 10.3390/genes9010022] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 12/15/2017] [Accepted: 01/04/2018] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial dysfunction is a central event in many pathologies and contributes as well to age-related processes. However, distinguishing between primary mitochondrial dysfunction driving aging and a secondary mitochondrial impairment resulting from other cell alterations remains challenging. Indeed, even though mitochondria undeniably play a crucial role in aging pathways at the cellular and organismal level, the original hypothesis in which mitochondrial dysfunction and production of free radicals represent the main driving force of cell degeneration has been strongly challenged. In this review, we will first describe mitochondrial dysfunctions observed in aged tissue, and how these features have been linked to mitochondrial reactive oxygen species (ROS)–mediated cell damage and mitochondrial DNA (mtDNA) mutations. We will also discuss the clues that led to consider mitochondria as the starting point in the aging process, and how recent research has showed that the mitochondria aging axis represents instead a more complex and multifactorial signaling pathway. New working hypothesis will be also presented in which mitochondria are considered at the center of a complex web of cell dysfunctions that eventually leads to cell senescence and death.
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Affiliation(s)
- Pierre Theurey
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy.
| | - Paola Pizzo
- Department of Biomedical Sciences, University of Padova, Padova 35121, Italy.
- Neuroscience Institute, National Research Council (CNR), Padova 35121, Italy.
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47
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Paraskevaidi M, Martin-Hirsch PL, Kyrgiou M, Martin FL. Underlying role of mitochondrial mutagenesis in the pathogenesis of a disease and current approaches for translational research. Mutagenesis 2017; 32:335-342. [PMID: 27816931 DOI: 10.1093/mutage/gew058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 10/21/2016] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial diseases have been extensively investigated over the last three decades, but many questions regarding their underlying aetiologies remain unanswered. Mitochondrial dysfunction is not only responsible for a range of neurological and myopathy diseases but also considered pivotal in a broader spectrum of common diseases such as epilepsy, autism and bipolar disorder. These disorders are a challenge to diagnose and treat, as their aetiology might be multifactorial. In this review, the focus is placed on potential mechanisms capable of introducing defects in mitochondria resulting in disease. Special attention is given to the influence of xenobiotics on mitochondria; environmental factors inducing mutations or epigenetic changes in the mitochondrial genome can alter its expression and impair the whole cell's functionality. Specifically, we suggest that environmental agents can cause damage in mitochondrial DNA and consequently lead to mutagenesis. Moreover, we describe current approaches for handling mitochondrial diseases, as well as available prenatal diagnostic tests, towards eliminating these maternally inherited diseases. Undoubtedly, more research is required, as current therapeutic approaches mostly employ palliative therapies rather than targeting primary mechanisms or prophylactic approaches. Much effort is needed into further unravelling the relationship between xenobiotics and mitochondria, as the extent of influence in mitochondrial pathogenesis is increasingly recognised.
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Affiliation(s)
- Maria Paraskevaidi
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Pierre L Martin-Hirsch
- Department of Obstetrics and Gynaecology, Central Lancashire Teaching Hospitals NHS Foundation Trust, Preston PR5 6AW, UK and
| | - Maria Kyrgiou
- Faculty of Medicine, Institute of Reproductive and Developmental Biology, Imperial College, London W12 0NN, UK
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
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48
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Christie JR, Beekman M. Uniparental Inheritance Promotes Adaptive Evolution in Cytoplasmic Genomes. Mol Biol Evol 2017; 34:677-691. [PMID: 28025277 PMCID: PMC5896580 DOI: 10.1093/molbev/msw266] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Eukaryotes carry numerous asexual cytoplasmic genomes (mitochondria and plastids). Lacking recombination, asexual genomes should theoretically suffer from impaired adaptive evolution. Yet, empirical evidence indicates that cytoplasmic genomes experience higher levels of adaptive evolution than predicted by theory. In this study, we use a computational model to show that the unique biology of cytoplasmic genomes-specifically their organization into host cells and their uniparental (maternal) inheritance-enable them to undergo effective adaptive evolution. Uniparental inheritance of cytoplasmic genomes decreases competition between different beneficial substitutions (clonal interference), promoting the accumulation of beneficial substitutions. Uniparental inheritance also facilitates selection against deleterious cytoplasmic substitutions, slowing Muller's ratchet. In addition, uniparental inheritance generally reduces genetic hitchhiking of deleterious substitutions during selective sweeps. Overall, uniparental inheritance promotes adaptive evolution by increasing the level of beneficial substitutions relative to deleterious substitutions. When we assume that cytoplasmic genome inheritance is biparental, decreasing the number of genomes transmitted during gametogenesis (bottleneck) aids adaptive evolution. Nevertheless, adaptive evolution is always more efficient when inheritance is uniparental. Our findings explain empirical observations that cytoplasmic genomes-despite their asexual mode of reproduction-can readily undergo adaptive evolution.
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Affiliation(s)
- Joshua R Christie
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Madeleine Beekman
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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49
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Phadke R. Myopathology of Adult and Paediatric Mitochondrial Diseases. J Clin Med 2017; 6:jcm6070064. [PMID: 28677615 PMCID: PMC5532572 DOI: 10.3390/jcm6070064] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 06/21/2017] [Accepted: 06/28/2017] [Indexed: 01/09/2023] Open
Abstract
Mitochondria are dynamic organelles ubiquitously present in nucleated eukaryotic cells, subserving multiple metabolic functions, including cellular ATP generation by oxidative phosphorylation (OXPHOS). The OXPHOS machinery comprises five transmembrane respiratory chain enzyme complexes (RC). Defective OXPHOS gives rise to mitochondrial diseases (mtD). The incredible phenotypic and genetic diversity of mtD can be attributed at least in part to the RC dual genetic control (nuclear DNA (nDNA) and mitochondrial DNA (mtDNA)) and the complex interaction between the two genomes. Despite the increasing use of next-generation-sequencing (NGS) and various omics platforms in unravelling novel mtD genes and pathomechanisms, current clinical practice for investigating mtD essentially involves a multipronged approach including clinical assessment, metabolic screening, imaging, pathological, biochemical and functional testing to guide molecular genetic analysis. This review addresses the broad muscle pathology landscape including genotype–phenotype correlations in adult and paediatric mtD, the role of immunodiagnostics in understanding some of the pathomechanisms underpinning the canonical features of mtD, and recent diagnostic advances in the field.
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Affiliation(s)
- Rahul Phadke
- Division of Neuropathology, UCL Institute of Neurology, National Hospital for Neurology and Neurosurgery, UCLH NHS Foundation Trust, London WC1N 3BG, UK.
- Dubowitz Neuromuscular Centre, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK.
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50
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Evolution of Cell-to-Cell Variability in Stochastic, Controlled, Heteroplasmic mtDNA Populations. Am J Hum Genet 2016; 99:1150-1162. [PMID: 27843124 DOI: 10.1016/j.ajhg.2016.09.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/22/2016] [Indexed: 11/20/2022] Open
Abstract
Populations of physiologically vital mitochondrial DNA (mtDNA) molecules evolve in cells under control from the nucleus. The evolution of populations of mixed mtDNA types is complicated and poorly understood, and variability of these controlled admixtures plays a central role in the inheritance and onset of genetic disease. Here, we develop a mathematical theory describing the evolution of, and variability in, these stochastic populations for any type of cellular control, showing that cell-to-cell variability in mtDNA and mutant load inevitably increases with time, according to rates that we derive and which are notably independent of the mechanistic details of feedback signaling. We show with a set of experimental case studies that this theory explains disparate quantitative results from classical and modern experimental and computational research on heteroplasmy variance in different species. We demonstrate that our general model provides a host of specific insights, including a modification of the often-used but hard-to-interpret Wright formula to correspond directly to biological observables, the ability to quantify selective and mutational pressure in mtDNA populations, and characterization of the pronounced variability inevitably arising from the action of possible mtDNA quality-control mechanisms. Our general theoretical framework, supported by existing experimental results, thus helps us to understand and predict the evolution of stochastic mtDNA populations in cell biology.
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