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McDonald C, Alderson C, Birkbeck MG, Brown L, Del Din S, Gorman GG, Hollingsworth K, Massarella C, Rehman R, Rochester L, Sayer AA, Su H, Tuppen H, Warren C, Witham MD. A study protocol to investigate if acipimox improves muscle function and sarcopenia: an open-label, uncontrolled, before-and-after experimental medicine feasibility study in community-dwelling older adults. BMJ Open 2024; 14:e076518. [PMID: 38417968 PMCID: PMC10900389 DOI: 10.1136/bmjopen-2023-076518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024] Open
Abstract
INTRODUCTION Sarcopenia is the age-associated loss of muscle mass and strength. Nicotinamide adenine dinucleotide (NAD) plays a central role in both mitochondrial function and cellular ageing processes implicated in sarcopenia. NAD concentrations are low in older people with sarcopenia, and increasing skeletal muscle NAD concentrations may offer a novel therapy for this condition. Acipimox is a licensed lipid-lowering agent known to act as an NAD precursor. This open-label, uncontrolled, before-and-after proof-of-concept experimental medicine study will test whether daily supplementation with acipimox improves skeletal muscle NAD concentrations. METHODS AND ANALYSIS Sixteen participants aged 65 and over with probable sarcopenia will receive acipimox 250 mg and aspirin 75 mg orally daily for 4 weeks, with the frequency of acipimox administration being dependent on renal function. Muscle biopsy of the vastus lateralis and MRI scanning of the lower leg will be performed at baseline before starting acipimox and after 3 weeks of treatment. Adverse events will be recorded for the duration of the trial. The primary outcome, analysed in a per-protocol population, is the change in skeletal muscle NAD concentration between baseline and follow-up. Secondary outcomes include changes in phosphocreatine recovery rate by 31P magnetic resonance spectroscopy, changes in physical performance and daily activity (handgrip strength, 4 m walk and 7-day accelerometry), changes in skeletal muscle mitochondrial respiratory function, changes in skeletal muscle mitochondrial DNA copy number and changes in NAD concentrations in whole blood as a putative biomarker for future participant selection. ETHICS AND DISSEMINATION The trial is approved by the UK Medicines and Healthcare Products Regulatory Agency (EuDRACT 2021-000993-28) and UK Health Research Authority and Northeast - Tyne and Wear South Research Ethics Committee (IRAS 293565). Results will be made available to participants, their families, patients with sarcopenia, the public, regional and national clinical teams, and the international scientific community. PROTOCOL Acipimox feasibility study Clinical Trial Protocol V.2 2/11/21. TRIAL REGISTRATION NUMBER The ISRCTN trial database (ISRCTN87404878).
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Affiliation(s)
- Claire McDonald
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Gateshead Health NHS Foundation trust, Gateshead, UK
| | - Craig Alderson
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Matthew G Birkbeck
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Newcastle Magnetic Resonance Centre Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Laura Brown
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Silvia Del Din
- Brain and Movement Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Grainne G Gorman
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Kieren Hollingsworth
- Newcastle Magnetic Resonance Centre Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Clare Massarella
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Rana Rehman
- Brain and Movement Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Lynn Rochester
- NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
- Brain and Movement Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Avan Ap Sayer
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
| | - Huizhong Su
- Brain and Movement Research Group, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Helen Tuppen
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Charlotte Warren
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
| | - Miles D Witham
- AGE Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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2
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Mihaylov SR, Castelli LM, Lin YH, Gül A, Soni N, Hastings C, Flynn HR, Păun O, Dickman MJ, Snijders AP, Goldstone R, Bandmann O, Shelkovnikova TA, Mortiboys H, Ultanir SK, Hautbergue GM. The master energy homeostasis regulator PGC-1α exhibits an mRNA nuclear export function. Nat Commun 2023; 14:5496. [PMID: 37679383 PMCID: PMC10485026 DOI: 10.1038/s41467-023-41304-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
PGC-1α plays a central role in maintaining mitochondrial and energy metabolism homeostasis, linking external stimuli to transcriptional co-activation of genes involved in adaptive and age-related pathways. The carboxyl-terminus encodes a serine/arginine-rich (RS) region and an RNA recognition motif, however the RNA-processing function(s) were poorly investigated over the past 20 years. Here, we show that the RS domain of human PGC-1α directly interacts with RNA and the nuclear RNA export receptor NXF1. Inducible depletion of PGC-1α and expression of RNAi-resistant RS-deleted PGC-1α further demonstrate that its RNA/NXF1-binding activity is required for the nuclear export of some canonical mitochondrial-related mRNAs and mitochondrial homeostasis. Genome-wide investigations reveal that the nuclear export function is not strictly linked to promoter-binding, identifying in turn novel regulatory targets of PGC-1α in non-homologous end-joining and nucleocytoplasmic transport. These findings provide new directions to further elucidate the roles of PGC-1α in gene expression, metabolic disorders, aging and neurodegeneration.
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Affiliation(s)
- Simeon R Mihaylov
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Lydia M Castelli
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Ya-Hui Lin
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Aytac Gül
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Nikita Soni
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Christopher Hastings
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
| | - Helen R Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oana Păun
- Neural Stem Cell Biology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Sir Robert Hadfield Building, University of Sheffield, Mappin Street, Sheffield, S1 3JD, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Life Science Mass Spectrometry, Bruker Daltonics, Banner Lane, Coventry, CV4 9GH, UK
| | - Robert Goldstone
- Bioinformatics and Biostatistics Science and Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oliver Bandmann
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Tatyana A Shelkovnikova
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Heather Mortiboys
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Sila K Ultanir
- Kinases and Brain Development Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Guillaume M Hautbergue
- Sheffield Institute for Translational Neuroscience (SITraN), Department of Neuroscience, University of Sheffield, 385 Glossop Road, Sheffield, S10 2HQ, UK.
- Neuroscience Institute, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
- Healthy Lifespan Institute (HELSI), University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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Buchanan E, Mahony C, Bam S, Jaffer M, Macleod S, Mangali A, van der Watt M, de Wet S, Theart R, Jacobs C, Loos B, O'Ryan C. Propionic acid induces alterations in mitochondrial morphology and dynamics in SH-SY5Y cells. Sci Rep 2023; 13:13248. [PMID: 37582965 PMCID: PMC10427685 DOI: 10.1038/s41598-023-40130-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/04/2023] [Indexed: 08/17/2023] Open
Abstract
Propionic acid (PPA) is used to study the role of mitochondrial dysfunction in neurodevelopmental conditions like autism spectrum disorders. PPA is known to disrupt mitochondrial biogenesis, metabolism, and turnover. However, the effect of PPA on mitochondrial dynamics, fission, and fusion remains challenging to study due to the complex temporal nature of these mechanisms. Here, we use complementary quantitative visualization techniques to examine how PPA influences mitochondrial ultrastructure, morphology, and dynamics in neuronal-like SH-SY5Y cells. PPA (5 mM) induced a significant decrease in mitochondrial area (p < 0.01), Feret's diameter and perimeter (p < 0.05), and in area2 (p < 0.01). Mitochondrial event localiser analysis demonstrated a significant increase in fission and fusion events (p < 0.05) that preserved mitochondrial network integrity under stress. Moreover, mRNA expression of cMYC (p < 0.0001), NRF1 (p < 0.01), TFAM (p < 0.05), STOML2 (p < 0.0001), and OPA1 (p < 0.01) was significantly decreased. This illustrates a remodeling of mitochondrial morphology, biogenesis, and dynamics to preserve function under stress. Our data provide new insights into the influence of PPA on mitochondrial dynamics and highlight the utility of visualization techniques to study the complex regulatory mechanisms involved in the mitochondrial stress response.
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Affiliation(s)
- Erin Buchanan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, 7700, South Africa
| | - Caitlyn Mahony
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, 7700, South Africa
| | - Sophia Bam
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, 7700, South Africa
| | - Mohamed Jaffer
- Electron Microscope Unit, University of Cape Town, Cape Town, 7700, South Africa
| | - Sarah Macleod
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, 7700, South Africa
| | - Asandile Mangali
- Department of Physiological Sciences, Stellenbosch University, Matieland, Stellenbosch, 7602, South Africa
| | - Mignon van der Watt
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, 7700, South Africa
| | - Sholto de Wet
- Department of Physiological Sciences, Stellenbosch University, Matieland, Stellenbosch, 7602, South Africa
| | - Rensu Theart
- Department of Electrical and Electronic Engineering, Stellenbosch University, Matieland, Stellenbosch, 7602, South Africa
| | - Caron Jacobs
- Department of Pathology, Wellcome Centre for Infectious Diseases Research in Africa and IDM Microscopy Platform, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, 7700, South Africa
| | - Ben Loos
- Department of Physiological Sciences, Stellenbosch University, Matieland, Stellenbosch, 7602, South Africa
| | - Colleen O'Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, 7700, South Africa.
- Neuroscience Institute, University of Cape Town, Cape Town, 7700, South Africa.
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Pedersen ZO, Pedersen BS, Larsen S, Dysgaard T. A Scoping Review Investigating the "Gene-Dosage Theory" of Mitochondrial DNA in the Healthy Skeletal Muscle. Int J Mol Sci 2023; 24:ijms24098154. [PMID: 37175862 PMCID: PMC10179410 DOI: 10.3390/ijms24098154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/29/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023] Open
Abstract
This review provides an overview of the evidence regarding mtDNA and valid biomarkers for assessing mitochondrial adaptions. Mitochondria are small organelles that exist in almost all cells throughout the human body. As the only organelle, mitochondria contain their own DNA, mitochondrial DNA (mtDNA). mtDNA-encoded polypeptides are subunits of the enzyme complexes in the electron transport chain (ETC) that are responsible for production of ATP to the cells. mtDNA is frequently used as a biomarker for mitochondrial content, since changes in mitochondrial volume are thought to induce similar changes in mtDNA. However, some exercise studies have challenged this "gene-dosage theory", and have indicated that changes in mitochondrial content can adapt without changes in mtDNA. Thus, the aim of this scoping review was to summarize the studies that used mtDNA as a biomarker for mitochondrial adaptions and address the question as to whether changes in mitochondrial content, induce changes in mtDNA in response to aerobic exercise in the healthy skeletal muscle. The literature was searched in PubMed and Embase. Eligibility criteria included: interventional study design, aerobic exercise, mtDNA measurements reported pre- and postintervention for the healthy skeletal muscle and English language. Overall, 1585 studies were identified. Nine studies were included for analysis. Eight out of the nine studies showed proof of increased oxidative capacity, six found improvements in mitochondrial volume, content and/or improved mitochondrial enzyme activity and seven studies did not find evidence of change in mtDNA copy number. In conclusion, the findings imply that mitochondrial adaptions, as a response to aerobic exercise, can occur without a change in mtDNA copy number.
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Affiliation(s)
- Zandra Overgaard Pedersen
- Copenhagen Neuromuscular Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, 2730 Herlev, Denmark
| | - Britt Staevnsbo Pedersen
- Copenhagen Neuromuscular Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Steen Larsen
- Xlab, Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Clinical Research Centre, Medical University of Bialystok, 15-089 Bialystok, Poland
| | - Tina Dysgaard
- Copenhagen Neuromuscular Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark
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5
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Isolating Mitochondria, Mitoplasts, and mtDNA from Cultured Mammalian Cells. Methods Mol Biol 2023; 2615:17-30. [PMID: 36807781 DOI: 10.1007/978-1-0716-2922-2_2] [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: 02/23/2023]
Abstract
Mitochondria are double membrane-bound eukaryotic organelles with roles in a range of cellular activities including energy conversion, apoptosis, cell signalling, and the biosynthesis of enzyme cofactors. Mitochondria contain their own genome, called mtDNA, which encodes subunits of the oxidative phosphorylation machinery as well as the rRNA and tRNA molecules required for their translation within mitochondria. The ability to isolate highly purified mitochondria from cells has been instrumental in a number of studies of mitochondrial function. Differential centrifugation is a long-established method for the isolation of mitochondria. Cells are subjected to osmotic swelling and disruption, followed by centrifugation in isotonic sucrose solutions to separate mitochondria from other cellular components. We present a method using this principle for the isolation of mitochondria from cultured mammalian cell lines. Mitochondria purified by this method can be further fractionated to investigate protein localization, or act as a starting point to purify mtDNA.
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6
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Jennings MJ, Kagiava A, Vendredy L, Spaulding EL, Stavrou M, Hathazi D, Grüneboom A, De Winter V, Gess B, Schara U, Pogoryelova O, Lochmüller H, Borchers CH, Roos A, Burgess RW, Timmerman V, Kleopa KA, Horvath R. NCAM1 and GDF15 are biomarkers of Charcot-Marie-Tooth disease in patients and mice. Brain 2022; 145:3999-4015. [PMID: 35148379 PMCID: PMC9679171 DOI: 10.1093/brain/awac055] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/22/2021] [Accepted: 12/15/2021] [Indexed: 02/02/2023] Open
Abstract
Molecular markers scalable for clinical use are critical for the development of effective treatments and the design of clinical trials. Here, we identify proteins in sera of patients and mouse models with Charcot-Marie-Tooth disease (CMT) with characteristics that make them suitable as biomarkers in clinical practice and therapeutic trials. We collected serum from mouse models of CMT1A (C61 het), CMT2D (GarsC201R, GarsP278KY), CMT1X (Gjb1-null), CMT2L (Hspb8K141N) and from CMT patients with genotypes including CMT1A (PMP22d), CMT2D (GARS), CMT2N (AARS) and other rare genetic forms of CMT. The severity of neuropathy in the patients was assessed by the CMT Neuropathy Examination Score (CMTES). We performed multitargeted proteomics on both sample sets to identify proteins elevated across multiple mouse models and CMT patients. Selected proteins and additional potential biomarkers, such as growth differentiation factor 15 (GDF15) and cell free mitochondrial DNA, were validated by ELISA and quantitative PCR, respectively. We propose that neural cell adhesion molecule 1 (NCAM1) is a candidate biomarker for CMT, as it was elevated in Gjb1-null, Hspb8K141N, GarsC201R and GarsP278KY mice as well as in patients with both demyelinating (CMT1A) and axonal (CMT2D, CMT2N) forms of CMT. We show that NCAM1 may reflect disease severity, demonstrated by a progressive increase in mouse models with time and a significant positive correlation with CMTES neuropathy severity in patients. The increase in NCAM1 may reflect muscle regeneration triggered by denervation, which could potentially track disease progression or the effect of treatments. We found that member proteins of the complement system were elevated in Gjb1-null and Hspb8K141N mouse models as well as in patients with both demyelinating and axonal CMT, indicating possible complement activation at the impaired nerve terminals. However, complement proteins did not correlate with the severity of neuropathy measured on the CMTES scale. Although the complement system does not seem to be a prognostic biomarker, we do show complement elevation to be a common disease feature of CMT, which may be of interest as a therapeutic target. We also identify serum GDF15 as a highly sensitive diagnostic biomarker, which was elevated in all CMT genotypes as well as in Hspb8K141N, Gjb1-null, GarsC201R and GarsP278KY mouse models. Although we cannot fully explain its origin, it may reflect increased stress response or metabolic disturbances in CMT. Further large and longitudinal patient studies should be performed to establish the value of these proteins as diagnostic and prognostic molecular biomarkers for CMT.
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Affiliation(s)
- Matthew J Jennings
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Alexia Kagiava
- Department of Neuroscience and Neuromuscular Disorders Centre, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Leen Vendredy
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, Antwerp, Belgium
| | - Emily L Spaulding
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Marina Stavrou
- Department of Neuroscience and Neuromuscular Disorders Centre, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Denisa Hathazi
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Anika Grüneboom
- Leibniz-Institut für Analytische Wissenschaften—ISAS—e.V, Dortmund, Germany
| | - Vicky De Winter
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, Antwerp, Belgium
| | - Burkhard Gess
- Department of Neurology, University Hospital Aachen, Aachen, Germany
| | - Ulrike Schara
- Centre for Neuromuscular Disorders in Children, University of Duisburg-Essen, Essen, Germany
| | - Oksana Pogoryelova
- Directorate of Neurosciences, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals, NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Hanns Lochmüller
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Brain and Mind Research Institute and Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Department of Neuropediatrics and Muscle Disorders, Medical Center–University of Freiburg, Faculty of Medicine, Freiburg, Germany
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Andreas Roos
- Division of Neurology, Department of Medicine, The Ottawa Hospital, Brain and Mind Research Institute and Children’s Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
- Department of Neurology, Heimer Institute for Muscle Research, University Hospital Bergmannsheil, Ruhr University Bochum, Bochum, Germany
| | - Robert W Burgess
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469, USA
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, Institute Born Bunge, University of Antwerp, Antwerp, Belgium
| | - Kleopas A Kleopa
- Department of Neuroscience and Neuromuscular Disorders Centre, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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Menger KE, Chapman J, Díaz-Maldonado H, Khazeem M, Deen D, Erdinc D, Casement JW, Di Leo V, Pyle A, Rodríguez-Luis A, Cowell I, Falkenberg M, Austin C, Nicholls T. Two type I topoisomerases maintain DNA topology in human mitochondria. Nucleic Acids Res 2022; 50:11154-11174. [PMID: 36215039 PMCID: PMC9638942 DOI: 10.1093/nar/gkac857] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/03/2022] [Accepted: 09/26/2022] [Indexed: 11/12/2022] Open
Abstract
Genetic processes require the activity of multiple topoisomerases, essential enzymes that remove topological tension and intermolecular linkages in DNA. We have investigated the subcellular localisation and activity of the six human topoisomerases with a view to understanding the topological maintenance of human mitochondrial DNA. Our results indicate that mitochondria contain two topoisomerases, TOP1MT and TOP3A. Using molecular, genomic and biochemical methods we find that both proteins contribute to mtDNA replication, in addition to the decatenation role of TOP3A, and that TOP1MT is stimulated by mtSSB. Loss of TOP3A or TOP1MT also dysregulates mitochondrial gene expression, and both proteins promote transcription elongation in vitro. We find no evidence for TOP2 localisation to mitochondria, and TOP2B knockout does not affect mtDNA maintenance or expression. Our results suggest a division of labour between TOP3A and TOP1MT in mtDNA topology control that is required for the proper maintenance and expression of human mtDNA.
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Affiliation(s)
- Katja E Menger
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - James Chapman
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Héctor Díaz-Maldonado
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Mushtaq M Khazeem
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Dasha Deen
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Direnis Erdinc
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - John W Casement
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Valeria Di Leo
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Alejandro Rodríguez-Luis
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Ian G Cowell
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, 405 30 Gothenburg, Sweden
| | - Caroline A Austin
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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8
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Aboouf MA, Guscetti F, von Büren N, Armbruster J, Ademi H, Ruetten M, Meléndez-Rodríguez F, Rülicke T, Seymer A, Jacobs RA, Schneider Gasser EM, Aragones J, Neumann D, Gassmann M, Thiersch M. Erythropoietin receptor regulates tumor mitochondrial biogenesis through iNOS and pAKT. Front Oncol 2022; 12:976961. [PMID: 36052260 PMCID: PMC9425774 DOI: 10.3389/fonc.2022.976961] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Erythropoietin receptor (EPOR) is widely expressed in healthy and malignant tissues. In certain malignancies, EPOR stimulates tumor growth. In healthy tissues, EPOR controls processes other than erythropoiesis, including mitochondrial metabolism. We hypothesized that EPOR also controls the mitochondrial metabolism in cancer cells. To test this hypothesis, we generated EPOR-knockdown cancer cells to grow tumor xenografts in mice and analyzed tumor cellular respiration via high-resolution respirometry. Furthermore, we analyzed cellular respiratory control, mitochondrial content, and regulators of mitochondrial biogenesis in vivo and in vitro in different cancer cell lines. Our results show that EPOR controls tumor growth and mitochondrial biogenesis in tumors by controlling the levels of both, pAKT and inducible NO synthase (iNOS). Furthermore, we observed that the expression of EPOR is associated with the expression of the mitochondrial marker VDAC1 in tissue arrays of lung cancer patients, suggesting that EPOR indeed helps to regulate mitochondrial biogenesis in tumors of cancer patients. Thus, our data imply that EPOR not only stimulates tumor growth but also regulates tumor metabolism and is a target for direct intervention against progression.
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Affiliation(s)
- Mostafa A. Aboouf
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
- Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Franco Guscetti
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Nadine von Büren
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Julia Armbruster
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Hyrije Ademi
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Maja Ruetten
- PathoVet AG, Pathology Diagnostic Laboratory, Tagelswangen, Switzerland
| | | | - Thomas Rülicke
- Department of Biomedical Sciences, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Alexander Seymer
- Department for Sociology and Social Geography, Paris Lodron University of Salzburg (PLUS), Salzburg, Austria
| | - Robert A. Jacobs
- Department of Human Physiology & Nutrition, University of Colorado Colorado Springs (UCCS), Colorado Springs, CO, United States
| | - Edith M. Schneider Gasser
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Center of Neuroscience Zurich (ZNZ), University of Zurich, Zurich, Switzerland
| | - Julian Aragones
- Hospital Universitario Santa Cristina, Autonomous University of Madrid, Madrid, Spain
| | - Drorit Neumann
- Department of Cell and Developmental Biology, Sackler Faculty of Medicine, Tel Aviv University, Tel-Aviv, Israel
| | - Max Gassmann
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
| | - Markus Thiersch
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, Zurich, Switzerland
- Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
- *Correspondence: Markus Thiersch,
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Finelli R, Moreira BP, Alves MG, Agarwal A. Unraveling the Molecular Impact of Sperm DNA Damage on Human Reproduction. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1358:77-113. [DOI: 10.1007/978-3-030-89340-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Aboouf MA, Armbruster J, Thiersch M, Gassmann M, Gödecke A, Gnaiger E, Kristiansen G, Bicker A, Hankeln T, Zhu H, Gorr TA. Myoglobin, expressed in brown adipose tissue of mice, regulates the content and activity of mitochondria and lipid droplets. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:159026. [PMID: 34384891 DOI: 10.1016/j.bbalip.2021.159026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 08/02/2021] [Accepted: 08/04/2021] [Indexed: 12/19/2022]
Abstract
The identification of novel physiological regulators that stimulate energy expenditure through brown adipose tissue (BAT) activity in substrate catalysis is of utmost importance to understand and treat metabolic diseases. Myoglobin (MB), known to store or transport oxygen in heart and skeletal muscles, has recently been found to bind fatty acids with physiological constants in its oxygenated form (i.e., MBO2). Here, we investigated the in vivo effect of MB expression on BAT activity. In particular, we studied mitochondrial function and lipid metabolism as essential determinants of energy expenditure in this tissue. We show in a MB-null (MBko) mouse model that MB expression in BAT impacts on the activity of brown adipocytes in a twofold manner: i) by elevating mitochondrial density plus maximal respiration capacity, and through that, by stimulating BAT oxidative metabolism along with the organelles` uncoupled respiration; and ii) by influencing the free fatty acids pool towards a palmitate-enriched composition and shifting the lipid droplet (LD) equilibrium towards higher counts of smaller droplets. These metabolic changes were accompanied by the up-regulated expression of thermogenesis markers UCP1, CIDEA, CIDEC, PGC1-α and PPAR-α in the BAT of MB wildtype (MBwt) mice. Along with the emergence of the "browning" BAT morphology, MBwt mice exhibited a leaner phenotype when compared to MBko littermates at 20 weeks of age. Our data shed novel insights into MB's role in linking oxygen and lipid-based thermogenic metabolism. The findings suggest potential new strategies of targeting the MB pathway to treat metabolic disorders related to diminishing energy expenditure.
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Affiliation(s)
- Mostafa A Aboouf
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; Molecular and Translational Biomedicine PhD Program, Life Science Zurich Graduate School, 8057 Zurich, Switzerland; Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, 11566 Cairo, Egypt
| | - Julia Armbruster
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; Molecular and Translational Biomedicine PhD Program, Life Science Zurich Graduate School, 8057 Zurich, Switzerland
| | - Markus Thiersch
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Max Gassmann
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland; Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
| | - Axel Gödecke
- Institute of Cardiovascular Physiology (A.G.), Medical Faculty, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Erich Gnaiger
- Department of Visceral, Transplant and Thoracic Surgery, D. Swarovski Research Laboratory, Medical University Innsbruck, Innrain 66/6, A-6020 Innsbruck, Austria
| | - Glen Kristiansen
- Institute of Pathology, University Hospital Bonn, University of Bonn, D-53127 Bonn, Germany
| | - Anne Bicker
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Thomas Hankeln
- Institute of Organismic and Molecular Evolution, Molecular Genetics and Genome Analysis, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Hao Zhu
- Department of Clinical Laboratory Sciences, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA; Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
| | - Thomas A Gorr
- Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland.
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11
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Habbane M, Montoya J, Rhouda T, Sbaoui Y, Radallah D, Emperador S. Human Mitochondrial DNA: Particularities and Diseases. Biomedicines 2021; 9:biomedicines9101364. [PMID: 34680481 PMCID: PMC8533111 DOI: 10.3390/biomedicines9101364] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/21/2021] [Accepted: 09/23/2021] [Indexed: 11/25/2022] Open
Abstract
Mitochondria are the cell’s power site, transforming energy into a form that the cell can employ for necessary metabolic reactions. These organelles present their own DNA. Although it codes for a small number of genes, mutations in mtDNA are common. Molecular genetics diagnosis allows the analysis of DNA in several areas such as infectiology, oncology, human genetics and personalized medicine. Knowing that the mitochondrial DNA is subject to several mutations which have a direct impact on the metabolism of the mitochondrion leading to many diseases, it is therefore necessary to detect these mutations in the patients involved. To date numerous mitochondrial mutations have been described in humans, permitting confirmation of clinical diagnosis, in addition to a better management of the patients. Therefore, different techniques are employed to study the presence or absence of mitochondrial mutations. However, new mutations are discovered, and to determine if they are the cause of disease, different functional mitochondrial studies are undertaken using transmitochondrial cybrid cells that are constructed by fusion of platelets of the patient that presents the mutation, with rho osteosarcoma cell line. Moreover, the contribution of next generation sequencing allows sequencing of the entire human genome within a single day and should be considered in the diagnosis of mitochondrial mutations.
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Affiliation(s)
- Mouna Habbane
- Laboratoire Biologie et Santé, Faculté des sciences Ben M’Sick, Hassan II University of Casablanca, Sidi Othman, Casablanca 20670, Morocco; (T.R.); (D.R.)
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/Miguel Servet, 177, 50013 Zaragoza, Spain; (J.M.); (S.E.)
- Correspondence: ; Tel.: +212-701-105-108
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/Miguel Servet, 177, 50013 Zaragoza, Spain; (J.M.); (S.E.)
- Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009 Zaragoza, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Taha Rhouda
- Laboratoire Biologie et Santé, Faculté des sciences Ben M’Sick, Hassan II University of Casablanca, Sidi Othman, Casablanca 20670, Morocco; (T.R.); (D.R.)
| | - Yousra Sbaoui
- Département de Biologie, Faculté des Sciences Ain Chock, Hassan II University of Casablanca, Casablanca 20000, Morocco;
| | - Driss Radallah
- Laboratoire Biologie et Santé, Faculté des sciences Ben M’Sick, Hassan II University of Casablanca, Sidi Othman, Casablanca 20670, Morocco; (T.R.); (D.R.)
| | - Sonia Emperador
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/Miguel Servet, 177, 50013 Zaragoza, Spain; (J.M.); (S.E.)
- Instituto de Investigación Sanitaria (IIS) de Aragón, Av. San Juan Bosco, 13, 50009 Zaragoza, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Av. Monforte de Lemos, 3-5, 28029 Madrid, Spain
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12
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Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications. Pharmacol Ther 2021; 232:107995. [PMID: 34592204 DOI: 10.1016/j.pharmthera.2021.107995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
The past thirty years have seen a surge in interest in pathophysiological roles of mitochondria, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. We conducted an in-depth survey of articles published between 1969 -- 2020 to create an overview of mCN values, to assess consensus values of tissue-specific mCN, and to evaluate consistency between methods of assessing mCN. We identify best practices for methods used to assess mCN, and we address the impact of using specific loci on the mitochondrial genome to determine mCN. Current data suggest that clinical measurement of mCN can provide diagnostic and prognostic value in a range of diseases and health conditions, with emphasis on cancer and cardiovascular disease, and the advent of means to measure absolute mCN should improve future clinical applications of mCN measurements.
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13
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Jacobs RA, Aboouf MA, Koester-Hegmann C, Muttathukunnel P, Laouafa S, Arias-Reyes C, Thiersch M, Soliz J, Gassmann M, Schneider Gasser EM. Erythropoietin promotes hippocampal mitochondrial function and enhances cognition in mice. Commun Biol 2021; 4:938. [PMID: 34354241 PMCID: PMC8342552 DOI: 10.1038/s42003-021-02465-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 07/19/2021] [Indexed: 11/22/2022] Open
Abstract
Erythropoietin (EPO) improves neuronal mitochondrial function and cognition in adults after brain injury and in those afflicted by psychiatric disorders. However, the influence of EPO on mitochondria and cognition during development remains unexplored. We previously observed that EPO stimulates hippocampal-specific neuronal maturation and synaptogenesis early in postnatal development in mice. Here we show that EPO promotes mitochondrial respiration in developing postnatal hippocampus by increasing mitochondrial content and enhancing cellular respiratory potential. Ultrastructurally, mitochondria profiles and total vesicle content were greater in presynaptic axon terminals, suggesting that EPO enhances oxidative metabolism and synaptic transmission capabilities. Behavioural tests of hippocampus-dependent memory at early adulthood, showed that EPO improves spatial and short-term memory. Collectively, we identify a role for EPO in the murine postnatal hippocampus by promoting mitochondrial function throughout early postnatal development, which corresponds to enhanced cognition by early adulthood. Robert Jacobs, Mostafa Aboouf, et al. examined the effect of erythropoietin (EPO) in hippocampal mitochondrial function and memory in two mouse models: one overexpressing EPO in the brain, and juvenile mice treated during three days with a high dose of intraperitoneal EPO. Their results suggest that erythropoietin in the neonatal brain may impact spatial memory by increasing mitochondrial content.
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Affiliation(s)
- Robert A Jacobs
- Institute of Veterinary Physiology, Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland.,Department of Human Physiology & Nutrition, University of Colorado, Colorado Springs, CO, USA
| | - Mostafa A Aboouf
- Institute of Veterinary Physiology, Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology (ZIPH), University of Zurich, Zurich, Switzerland.,Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Christina Koester-Hegmann
- Institute of Veterinary Physiology, Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland.,Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Paola Muttathukunnel
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland.,Center for Neuroscience Zurich (ZNZ), Zurich, Switzerland
| | - Sofien Laouafa
- Faculty of Medicine, Centre Hospitalier Universitaire de Québec (CHUQ), Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, QC, Canada
| | - Christian Arias-Reyes
- Faculty of Medicine, Centre Hospitalier Universitaire de Québec (CHUQ), Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, QC, Canada
| | - Markus Thiersch
- Institute of Veterinary Physiology, Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology (ZIPH), University of Zurich, Zurich, Switzerland
| | - Jorge Soliz
- Faculty of Medicine, Centre Hospitalier Universitaire de Québec (CHUQ), Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec, QC, Canada
| | - Max Gassmann
- Institute of Veterinary Physiology, Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology (ZIPH), University of Zurich, Zurich, Switzerland
| | - Edith M Schneider Gasser
- Institute of Veterinary Physiology, Vetsuisse-Faculty, University of Zurich, Zurich, Switzerland. .,Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland. .,Center for Neuroscience Zurich (ZNZ), Zurich, Switzerland.
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14
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Bam S, Buchanan E, Mahony C, O'Ryan C. DNA Methylation of PGC-1α Is Associated With Elevated mtDNA Copy Number and Altered Urinary Metabolites in Autism Spectrum Disorder. Front Cell Dev Biol 2021; 9:696428. [PMID: 34381777 PMCID: PMC8352569 DOI: 10.3389/fcell.2021.696428] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex disorder that is underpinned by numerous dysregulated biological pathways, including pathways that affect mitochondrial function. Epigenetic mechanisms contribute to this dysregulation and DNA methylation is an important factor in the etiology of ASD. We measured DNA methylation of peroxisome proliferator-activated receptor-gamma coactivator-1 alpha (PGC-1α), as well as five genes involved in regulating mitochondrial homeostasis to examine mitochondrial dysfunction in an ASD cohort of South African children. Using targeted Next Generation bisulfite sequencing, we found differential methylation (p < 0.05) at six key genes converging on mitochondrial biogenesis, fission and fusion in ASD, namely PGC-1α, STOML2, MFN2, FIS1, OPA1, and GABPA. PGC-1α, the transcriptional regulator of biogenesis, was significantly hypermethylated at eight CpG sites in the gene promoter, one of which contained a putative binding site for CAMP response binding element 1 (CREB1) (p = 1 × 10–6). Mitochondrial DNA (mtDNA) copy number, a marker of mitochondrial function, was elevated (p = 0.002) in ASD compared to controls and correlated significantly with DNA methylation at the PGC-1α promoter and there was a positive correlation between methylation at PGC-1α CpG#1 and mtDNA copy number (Spearman’s r = 0.2, n = 49, p = 0.04) in ASD. Furthermore, DNA methylation at PGC-1α CpG#1 and mtDNA copy number correlated significantly (p < 0.05) with levels of urinary organic acids associated with mitochondrial dysfunction, oxidative stress, and neuroendocrinology. Our data show differential methylation in ASD at six key genes converging on PGC-1α-dependent regulation of mitochondrial biogenesis and function. We demonstrate that methylation at the PGC-1α promoter is associated with elevated mtDNA copy number and metabolomic evidence of mitochondrial dysfunction in ASD. This highlights an unexplored role for DNA methylation in regulating specific pathways involved in mitochondrial biogenesis, fission and fusion contributing to mitochondrial dysfunction in ASD.
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Affiliation(s)
- Sophia Bam
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Erin Buchanan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Caitlyn Mahony
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Colleen O'Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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15
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Gu H, Zhou Y, Yang J, Li J, Peng Y, Zhang X, Miao Y, Jiang W, Bu G, Hou L, Li T, Zhang L, Xia X, Ma Z, Xiong Y, Zuo B. Targeted overexpression of PPARγ in skeletal muscle by random insertion and CRISPR/Cas9 transgenic pig cloning enhances oxidative fiber formation and intramuscular fat deposition. FASEB J 2021; 35:e21308. [PMID: 33481304 DOI: 10.1096/fj.202001812rr] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 11/11/2022]
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a master regulator of adipogenesis and lipogenesis. To understand its roles in fiber formation and fat deposition in skeletal muscle, we successfully generated muscle-specific overexpression of PPARγ in two pig models by random insertion and CRISPR/Cas9 transgenic cloning procedures. The content of intramuscular fat was significantly increased in PPARγ pigs while had no changes on lean meat ratio. PPARγ could promote adipocyte differentiation by activating adipocyte differentiating regulators such as FABP4 and CCAAT/enhancer-binding protein (C/EBP), along with enhanced expression of LPL, FABP4, and PLIN1 to proceed fat deposition. Proteomics analyses demonstrated that oxidative metabolism of fatty acids and respiratory chain were activated in PPARγ pigs, thus, gathered more Ca2+ in PPARγ pigs. Raising of Ca2+ could result in increased phosphorylation of CAMKII and p38 MAPK in PPARγ pigs, which can stimulate MEF2 and PGC1α to affect fiber type and oxidative capacity. These results support that skeletal muscle-specific overexpression of PPARγ can promote oxidative fiber formation and intramuscular fat deposition in pigs.
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Affiliation(s)
- Hao Gu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Ying Zhou
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Jianan Li
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Yaxin Peng
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Xia Zhang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Yiliang Miao
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Wei Jiang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Guowei Bu
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Liming Hou
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Ting Li
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Lin Zhang
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Xiaoliang Xia
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Zhiyuan Ma
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Yuanzhu Xiong
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, P.R. China
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16
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McGlynn ML, Schnitzler H, Shute R, Ruby B, Slivka D. The Acute Effects of Exercise and Temperature on Regional mtDNA. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:6382. [PMID: 34204828 PMCID: PMC8296217 DOI: 10.3390/ijerph18126382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/02/2021] [Accepted: 06/10/2021] [Indexed: 12/22/2022]
Abstract
A reduced mitochondrial DNA (mtDNA) copy number, the ratio of mitochondrial DNA to genomic DNA (mtDNA:gDNA), has been linked with dysfunctional mitochondria. Exercise can acutely induce mtDNA damage manifested as a reduced copy number. However, the influence of a paired (exercise and temperature) intervention on regional mtDNA (MINor Arc and MAJor Arc) are unknown. Thus, the purpose of this study was to determine the acute effects of exercise in cold (7 °C), room temperature (20 °C), and hot (33 °C) ambient temperatures, on regional mitochondrial copy number (MINcn and MAJcn). Thirty-four participants (24.4 ± 5.1 yrs, 87.1 ± 22.1 kg, 22.3 ± 8.5 %BF, and 3.20 ± 0.59 L·min-1 VO2peak) cycled for 1 h (261.1 ± 22.1 W) in either 7 °C, 20 °C, or 33 °C ambient conditions. Muscle biopsy samples were collected from the vastus lateralis to determine mtDNA regional copy numbers via RT-qPCR. mtDNA is sensitive to the stressors of exercise post-exercise (MIN fold change, -1.50 ± 0.11; MAJ fold change, -1.70 ± 0.12) and 4-h post-exercise (MIN fold change, -0.82 ± 0.13; MAJ fold change, -1.54 ± 0.11). The MAJ Arc seems to be more sensitive to heat, showing a temperature-trend (p = 0.056) for a reduced regional copy number ratio after exercise in the heat (fold change -2.81 ± 0.11; p = 0.019). These results expand upon our current knowledge of the influence of temperature and exercise on the acute remodeling of regional mtDNA.
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Affiliation(s)
- Mark L. McGlynn
- School of Health and Kinesiology, University of Nebraska at Omaha, Omaha, NE 68182, USA; (M.L.M.); (H.S.); (R.S.)
| | - Halee Schnitzler
- School of Health and Kinesiology, University of Nebraska at Omaha, Omaha, NE 68182, USA; (M.L.M.); (H.S.); (R.S.)
| | - Robert Shute
- School of Health and Kinesiology, University of Nebraska at Omaha, Omaha, NE 68182, USA; (M.L.M.); (H.S.); (R.S.)
| | - Brent Ruby
- School of Integrative Physiology and Athletic Training, University of Montana, Missoula, MT 59812, USA;
| | - Dustin Slivka
- School of Health and Kinesiology, University of Nebraska at Omaha, Omaha, NE 68182, USA; (M.L.M.); (H.S.); (R.S.)
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17
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Bris C, Goudenège D, Desquiret-Dumas V, Gueguen N, Bannwarth S, Gaignard P, Rucheton B, Trimouille A, Allouche S, Rouzier C, Saadi S, Jardel C, Slama A, Barth M, Verny C, Spinazzi M, Cassereau J, Colin E, Armelle M, Pereon Y, Martin-Negrier ML, Paquis-Flucklinger V, Letournel F, Lenaers G, Bonneau D, Reynier P, Amati-Bonneau P, Procaccio V. Improved detection of mitochondrial DNA instability in mitochondrial genome maintenance disorders. Genet Med 2021; 23:1769-1778. [PMID: 34040194 DOI: 10.1038/s41436-021-01206-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Diseases caused by defects in mitochondrial DNA (mtDNA) maintenance machinery, leading to mtDNA deletions, form a specific group of disorders. However, mtDNA deletions also appear during aging, interfering with those resulting from mitochondrial disorders. METHODS Here, using next-generation sequencing (NGS) data processed by eKLIPse and data mining, we established criteria distinguishing age-related mtDNA rearrangements from those due to mtDNA maintenance defects. MtDNA deletion profiles from muscle and urine patient samples carrying pathogenic variants in nuclear genes involved in mtDNA maintenance (n = 40) were compared with age-matched controls (n = 90). Seventeen additional patient samples were used to validate the data mining model. RESULTS Overall, deletion number, heteroplasmy level, deletion locations, and the presence of repeats at deletion breakpoints were significantly different between patients and controls, especially in muscle samples. The deletion number was significantly relevant in adults, while breakpoint repeat lengths surrounding deletions were discriminant in young subjects. CONCLUSION Altogether, eKLIPse analysis is a powerful tool for measuring the accumulation of mtDNA deletions between patients of different ages, as well as in prioritizing novel variants in genes involved in mtDNA stability.
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Affiliation(s)
- Celine Bris
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - David Goudenège
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Valerie Desquiret-Dumas
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Naig Gueguen
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Sylvie Bannwarth
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | - Pauline Gaignard
- Service de Biochimie, CHU Bicêtre, APHP Université Paris Saclay, Le Kremlin-Bicêtre, France
| | - Benoit Rucheton
- Département de Biochimie et Génétique, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Aurelien Trimouille
- Service de Génétique médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Stephane Allouche
- Service de Biochimie, EA4650, Centre Hospitalier Universitaire, Caen, France
| | - Cecile Rouzier
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | - Samira Saadi
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | - Claude Jardel
- Département de Biochimie et Génétique, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Abdel Slama
- Service de Biochimie, CHU Bicêtre, APHP Université Paris Saclay, Le Kremlin-Bicêtre, France
| | - Magalie Barth
- Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Christophe Verny
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Marco Spinazzi
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Julien Cassereau
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Estelle Colin
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Magot Armelle
- Centre de Référence Maladies Neuromusculaires, CHU Nantes, Nantes, France
| | - Yann Pereon
- Centre de Référence Maladies Neuromusculaires, CHU Nantes, Nantes, France
| | | | | | - Franck Letournel
- UF de Neurobiologie-Neuropathologie, UMR INSERM 1066 - CNRS 6021, MINT, Angers, France
| | - Guy Lenaers
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Dominique Bonneau
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Pascal Reynier
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Patrizia Amati-Bonneau
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France. .,Département de Biochimie et Génétique, CHU d'Angers, Angers, France.
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18
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Rius R, Compton AG, Baker NL, Welch AE, Coman D, Kava MP, Minoche AE, Cowley MJ, Thorburn DR, Christodoulou J. Application of Genome Sequencing from Blood to Diagnose Mitochondrial Diseases. Genes (Basel) 2021; 12:genes12040607. [PMID: 33924034 PMCID: PMC8072654 DOI: 10.3390/genes12040607] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial diseases can be caused by pathogenic variants in nuclear or mitochondrial DNA-encoded genes that often lead to multisystemic symptoms and can have any mode of inheritance. Using a single test, Genome Sequencing (GS) can effectively identify variants in both genomes, but it has not yet been universally used as a first-line approach to diagnosing mitochondrial diseases due to related costs and challenges in data analysis. In this article, we report three patients with mitochondrial disease molecularly diagnosed through GS performed on DNA extracted from blood to demonstrate different diagnostic advantages of this technology, including the detection of a low-level heteroplasmic pathogenic variant, an intragenic nuclear DNA deletion, and a large mtDNA deletion. Current technical improvements and cost reductions are likely to lead to an expanded routine diagnostic usage of GS and of the complementary “Omic” technologies in mitochondrial diseases.
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Affiliation(s)
- Rocio Rius
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alison G. Compton
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Naomi L. Baker
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - AnneMarie E. Welch
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
| | - David Coman
- Department of Metabolic Medicine, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia;
- School of Clinical Medicine, University of Queensland, Brisbane, QLD 4072, Australia
- School of Medicine, Griffith University, Gold Coast, QLD 4222, Australia
| | - Maina P. Kava
- Department of Neurology, Perth Children’s Hospital, Perth, WA 6009, Australia;
- Department of Metabolic Medicine and Rheumatology, Perth Children’s Hospital, Perth, WA 6009, Australia
| | - Andre E. Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute, University of New South Wales, Randwick, NSW 2010, Australia;
| | - Mark J. Cowley
- Precision Medicine Theme, Children’s Cancer Institute, Kensington, NSW 2750, Australia;
- School of Women’s and Children’s Health, University of New South Wales, Randwick, NSW 2031, Australia
| | - David R. Thorburn
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - John Christodoulou
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
- Correspondence: ; Tel.: +61-39936-6353
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19
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Mehta AR, Gregory JM, Dando O, Carter RN, Burr K, Nanda J, Story D, McDade K, Smith C, Morton NM, Mahad DJ, Hardingham GE, Chandran S, Selvaraj BT. Mitochondrial bioenergetic deficits in C9orf72 amyotrophic lateral sclerosis motor neurons cause dysfunctional axonal homeostasis. Acta Neuropathol 2021; 141:257-279. [PMID: 33398403 PMCID: PMC7847443 DOI: 10.1007/s00401-020-02252-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/30/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022]
Abstract
Axonal dysfunction is a common phenotype in neurodegenerative disorders, including in amyotrophic lateral sclerosis (ALS), where the key pathological cell-type, the motor neuron (MN), has an axon extending up to a metre long. The maintenance of axonal function is a highly energy-demanding process, raising the question of whether MN cellular energetics is perturbed in ALS, and whether its recovery promotes axonal rescue. To address this, we undertook cellular and molecular interrogation of multiple patient-derived induced pluripotent stem cell lines and patient autopsy samples harbouring the most common ALS causing mutation, C9orf72. Using paired mutant and isogenic expansion-corrected controls, we show that C9orf72 MNs have shorter axons, impaired fast axonal transport of mitochondrial cargo, and altered mitochondrial bioenergetic function. RNAseq revealed reduced gene expression of mitochondrially encoded electron transport chain transcripts, with neuropathological analysis of C9orf72-ALS post-mortem tissue importantly confirming selective dysregulation of the mitochondrially encoded transcripts in ventral horn spinal MNs, but not in corresponding dorsal horn sensory neurons, with findings reflected at the protein level. Mitochondrial DNA copy number was unaltered, both in vitro and in human post-mortem tissue. Genetic manipulation of mitochondrial biogenesis in C9orf72 MNs corrected the bioenergetic deficit and also rescued the axonal length and transport phenotypes. Collectively, our data show that loss of mitochondrial function is a key mediator of axonal dysfunction in C9orf72-ALS, and that boosting MN bioenergetics is sufficient to restore axonal homeostasis, opening new potential therapeutic strategies for ALS that target mitochondrial function.
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Affiliation(s)
- Arpan R Mehta
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Jenna M Gregory
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
- MRC Edinburgh Brain Bank, Academic Department of Neuropathology, University of Edinburgh, Edinburgh, UK
- Edinburgh Pathology, University of Edinburgh, Edinburgh, UK
| | - Owen Dando
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Roderick N Carter
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Karen Burr
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Jyoti Nanda
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - David Story
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Karina McDade
- MRC Edinburgh Brain Bank, Academic Department of Neuropathology, University of Edinburgh, Edinburgh, UK
| | - Colin Smith
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
- MRC Edinburgh Brain Bank, Academic Department of Neuropathology, University of Edinburgh, Edinburgh, UK
- Edinburgh Pathology, University of Edinburgh, Edinburgh, UK
| | - Nicholas M Morton
- University/British Heart Foundation Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK
| | - Don J Mahad
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK
| | - Giles E Hardingham
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK.
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.
- Centre for Brain Development and Repair, inStem, Bangalore, India.
| | - Bhuvaneish T Selvaraj
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- Anne Rowling Regenerative Neurology Clinic, University of Edinburgh, Edinburgh, UK.
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK.
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20
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Lowes H, Kurzawa-Akanbi M, Pyle A, Hudson G. Post-mortem ventricular cerebrospinal fluid cell-free-mtDNA in neurodegenerative disease. Sci Rep 2020; 10:15253. [PMID: 32943697 PMCID: PMC7499424 DOI: 10.1038/s41598-020-72190-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
Cell-free mitochondrial DNA (cfmtDNA) is detectable in almost all human body fluids and has been associated with the onset and progression of several complex traits. In-life assessments indicate that reduced cfmtDNA is a feature of neurodegenerative diseases such as Parkinson's disease, Alzheimer's disease and multiple sclerosis. However, whether this feature is conserved across all neurodegenerative diseases and how it relates to the neurodegenerative processes remains unclear. In this study, we assessed the levels of ventricular cerebrospinal fluid-cfmtDNA (vCSF-cfmtDNA) in a diverse group of neurodegenerative diseases (NDDs) to determine if the in-life observations of reduced cfmtDNA seen in lumbar CSF translated to the post-mortem ventricular CSF. To investigate further, we compared vCSF-cfmtDNA levels to known protein markers of neurodegeneration, synaptic vesicles and mitochondrial integrity. Our data indicate that reduced vCSF-cfmtDNA is a feature specific to Parkinson's and appears consistent throughout the disease course. Interestingly, we observed increased vCSF-cfmtDNA in the more neuropathologically severe NDD cases, but no association to protein markers of neurodegeneration, suggesting that vCSF-cfmtDNA release is more complex than mere cellular debris produced following neuronal death. We conclude that vCSF-cfmtDNA is reduced in PD, but not other NDDs, and appears to correlate to pathology. Although its utility as a prognostic biomarker is limited, our data indicate that higher levels of vCSF-cfmtDNA is associated with more severe clinical presentations; suggesting that it is associated with the neurodegenerative process. However, as vCSF-cfmtDNA does not appear to correlate to established indicators of neurodegeneration or indeed indicators of mitochondrial mass, further work to elucidate its exact role is needed.
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Affiliation(s)
- Hannah Lowes
- Biosciences Institute, 4th Floor Cookson Building, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Marzena Kurzawa-Akanbi
- Biosciences Institute, 4th Floor Cookson Building, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Angela Pyle
- Clinical and Translational Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Gavin Hudson
- Biosciences Institute, 4th Floor Cookson Building, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.
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21
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Harvey NR, Voisin S, Lea RA, Yan X, Benton MC, Papadimitriou ID, Jacques M, Haupt LM, Ashton KJ, Eynon N, Griffiths LR. Investigating the influence of mtDNA and nuclear encoded mitochondrial variants on high intensity interval training outcomes. Sci Rep 2020; 10:11089. [PMID: 32632177 PMCID: PMC7338527 DOI: 10.1038/s41598-020-67870-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/26/2020] [Indexed: 02/08/2023] Open
Abstract
Mitochondria supply intracellular energy requirements during exercise. Specific mitochondrial haplogroups and mitochondrial genetic variants have been associated with athletic performance, and exercise responses. However, these associations were discovered using underpowered, candidate gene approaches, and consequently have not been replicated. Here, we used whole-mitochondrial genome sequencing, in conjunction with high-throughput genotyping arrays, to discover novel genetic variants associated with exercise responses in the Gene SMART (Skeletal Muscle Adaptive Response to Training) cohort (n = 62 completed). We performed a Principal Component Analysis of cohort aerobic fitness measures to build composite traits and test for variants associated with exercise outcomes. None of the mitochondrial genetic variants but eight nuclear encoded variants in seven separate genes were found to be associated with exercise responses (FDR < 0.05) (rs11061368: DIABLO, rs113400963: FAM185A, rs6062129 and rs6121949: MTG2, rs7231304: AFG3L2, rs2041840: NDUFAF7, rs7085433: TIMM23, rs1063271: SPTLC2). Additionally, we outline potential mechanisms by which these variants may be contributing to exercise phenotypes. Our data suggest novel nuclear-encoded SNPs and mitochondrial pathways associated with exercise response phenotypes. Future studies should focus on validating these variants across different cohorts and ethnicities.
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Affiliation(s)
- N R Harvey
- Health Sciences and Medicine Faculty, Bond University, Robina, QLD, 4226, Australia.,Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, 4059, Australia
| | - S Voisin
- Institute for Health and Sport (IHES), Victoria University, Footscray, VIC, 3011, Australia
| | - R A Lea
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, 4059, Australia
| | - X Yan
- Institute for Health and Sport (IHES), Victoria University, Footscray, VIC, 3011, Australia
| | - M C Benton
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, 4059, Australia
| | - I D Papadimitriou
- Institute for Health and Sport (IHES), Victoria University, Footscray, VIC, 3011, Australia
| | - M Jacques
- Institute for Health and Sport (IHES), Victoria University, Footscray, VIC, 3011, Australia
| | - L M Haupt
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, 4059, Australia
| | - K J Ashton
- Health Sciences and Medicine Faculty, Bond University, Robina, QLD, 4226, Australia
| | - N Eynon
- Institute for Health and Sport (IHES), Victoria University, Footscray, VIC, 3011, Australia
| | - L R Griffiths
- Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, 4059, Australia.
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22
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Cappa R, de Campos C, Maxwell AP, McKnight AJ. "Mitochondrial Toolbox" - A Review of Online Resources to Explore Mitochondrial Genomics. Front Genet 2020; 11:439. [PMID: 32457801 PMCID: PMC7225359 DOI: 10.3389/fgene.2020.00439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Mitochondria play a significant role in many biological systems. There is emerging evidence that differences in the mitochondrial genome may contribute to multiple common diseases, leading to an increasing number of studies exploring mitochondrial genomics. There is often a large amount of complex data generated (for example via next generation sequencing), which requires optimised bioinformatics tools to efficiently and effectively generate robust outcomes from these large datasets. Twenty-four online resources dedicated to mitochondrial genomics were reviewed. This 'mitochondrial toolbox' summary resource will enable researchers to rapidly identify the resource(s) most suitable for their needs. These resources fulfil a variety of functions, with some being highly specialised. No single tool will provide all users with the resources they require; therefore, the most suitable tool will vary between users depending on the nature of the work they aim to carry out. Genetics resources are well established for phylogeny and DNA sequence changes, but further epigenetic and gene expression resources need to be developed for mitochondrial genomics.
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Affiliation(s)
- Ruaidhri Cappa
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
| | - Cassio de Campos
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, United Kingdom
| | - Alexander P Maxwell
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
| | - Amy J McKnight
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
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23
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Heteroplasmy and Copy Number in the Common m.3243A>G Mutation-A Post-Mortem Genotype-Phenotype Analysis. Genes (Basel) 2020; 11:genes11020212. [PMID: 32085658 PMCID: PMC7073558 DOI: 10.3390/genes11020212] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/16/2022] Open
Abstract
Different mitochondrial DNA (mtDNA) mutations have been identified to cause mitochondrial encephalopathy, lactate acidosis and stroke-like episodes (MELAS). The underlying genetic cause leading to an enormous clinical heterogeneity associated with m.3243A>G-related mitochondrial diseases is still poorly understood. Genotype–phenotype correlation (heteroplasmy levels and clinical symptoms) was analysed in 16 patients (15 literature cases and one unreported case) harbouring the m.3243A>G mutation. mtDNA copy numbers were correlated to heteroplasmy levels in 30 different post-mortem tissue samples, including 14 brain samples of a 46-year-old female. In the central nervous system, higher levels of heteroplasmy correlated significantly with lower mtDNA copy numbers. Skeletal muscle levels of heteroplasmy correlated significantly with kidney and liver. There was no significant difference of heteroplasmy levels between clinically affected and unaffected patients. In the patient presented, we found >75% heteroplasmy levels in all central nervous system samples, without harbouring a MELAS phenotype. This underlines previous suggestions, that really high levels in tissues do not automatically lead to a specific phenotype. Missing significant differences of heteroplasmy levels between clinically affected and unaffected patients underline recent suggestions that there are additional factors such as mtDNA copy number and nuclear factors that may also influence disease severity.
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24
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Hjelm BE, Rollins B, Morgan L, Sequeira A, Mamdani F, Pereira F, Damas J, Webb MG, Weber MD, Schatzberg AF, Barchas JD, Lee FS, Akil H, Watson SJ, Myers RM, Chao EC, Kimonis V, Thompson PM, Bunney WE, Vawter MP. Splice-Break: exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders. Nucleic Acids Res 2019; 47:e59. [PMID: 30869147 PMCID: PMC6547454 DOI: 10.1093/nar/gkz164] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/28/2019] [Indexed: 12/20/2022] Open
Abstract
Deletions in the 16.6 kb mitochondrial genome have been implicated in numerous disorders that often display muscular and/or neurological symptoms due to the high-energy demands of these tissues. We describe a catalogue of 4489 putative mitochondrial DNA (mtDNA) deletions, including their frequency and relative read rate, using a combinatorial approach of mitochondria-targeted PCR, next-generation sequencing, bioinformatics, post-hoc filtering, annotation, and validation steps. Our bioinformatics pipeline uses MapSplice, an RNA-seq splice junction detection algorithm, to detect and quantify mtDNA deletion breakpoints rather than mRNA splices. Analyses of 93 samples from postmortem brain and blood found (i) the 4977 bp ‘common deletion’ was neither the most frequent deletion nor the most abundant; (ii) brain contained significantly more deletions than blood; (iii) many high frequency deletions were previously reported in MitoBreak, suggesting they are present at low levels in metabolically active tissues and are not exclusive to individuals with diagnosed mitochondrial pathologies; (iv) many individual deletions (and cumulative metrics) had significant and positive correlations with age and (v) the highest deletion burdens were observed in major depressive disorder brain, at levels greater than Kearns–Sayre Syndrome muscle. Collectively, these data suggest the Splice-Break pipeline can detect and quantify mtDNA deletions at a high level of resolution.
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Affiliation(s)
- Brooke E Hjelm
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA.,Department of Translational Genomics, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Brandi Rollins
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Ling Morgan
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Firoza Mamdani
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Filipe Pereira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4050-123, Portugal
| | - Joana Damas
- The Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Michelle G Webb
- Department of Translational Genomics, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Matthieu D Weber
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Alan F Schatzberg
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Jack D Barchas
- Department of Psychiatry, Weill Cornell Medical College at Cornell University, New York, NY 10065, USA
| | - Francis S Lee
- Department of Psychiatry, Weill Cornell Medical College at Cornell University, New York, NY 10065, USA
| | - Huda Akil
- The Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stanley J Watson
- The Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Elizabeth C Chao
- Division of Genetics and Genomic Medicine, Department of Pediatrics, UCI, Irvine, CA, USA
| | - Virginia Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, UCI, Irvine, CA, USA
| | - Peter M Thompson
- Southwest Brain Bank, Department of Psychiatry, Texas Tech University Health Sciences Center (TTUHSC), El Paso, TX 79905, USA
| | - William E Bunney
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
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25
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Lowes H, Pyle A, Duddy M, Hudson G. Cell-free mitochondrial DNA in progressive multiple sclerosis. Mitochondrion 2019; 46:307-312. [PMID: 30098422 PMCID: PMC6509276 DOI: 10.1016/j.mito.2018.07.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/24/2018] [Accepted: 07/31/2018] [Indexed: 01/03/2023]
Abstract
Recent studies have linked cell-free mitochondrial DNA (ccf-mtDNA) to neurodegeneration in both Alzheimer's and Parkinson's disease, raising the possibility that the same phenomenon could be seen in other diseases which manifest a neurodegenerative component. Here, we assessed the role of circulating cell-free mitochondrial DNA (ccf-mtDNA) in end-stage progressive multiple sclerosis (PMS), where neurodegeneration is evident, contrasting both ventricular cerebral spinal fluid ccf-mtDNA abundance and integrity between PMS cases and controls, and correlating ccf-mtDNA levels to known protein markers of neurodegeneration and PMS. Our data indicate that reduced ccf-mtDNA is a component of PMS, concluding that it may indeed be a hallmark of broader neurodegeneration.
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Affiliation(s)
- Hannah Lowes
- Institute of Genetic Medicine, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK; The Wellcome Centre for Mitochondrial Research, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Angela Pyle
- Institute of Genetic Medicine, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK; The Wellcome Centre for Mitochondrial Research, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Martin Duddy
- Royal Victoria Infirmary, Newcastle-upon-Tyne, UK
| | - Gavin Hudson
- Institute of Genetic Medicine, International Centre for Life, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK; The Wellcome Centre for Mitochondrial Research, Newcastle University, Medical School, Framlington Place, Newcastle upon Tyne NE2 4HH, UK.
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26
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Grady JP, Pickett SJ, Ng YS, Alston CL, Blakely EL, Hardy SA, Feeney CL, Bright AA, Schaefer AM, Gorman GS, McNally RJ, Taylor RW, Turnbull DM, McFarland R. mtDNA heteroplasmy level and copy number indicate disease burden in m.3243A>G mitochondrial disease. EMBO Mol Med 2019; 10:emmm.201708262. [PMID: 29735722 PMCID: PMC5991564 DOI: 10.15252/emmm.201708262] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial disease associated with the pathogenic m.3243A>G variant is a common, clinically heterogeneous, neurogenetic disorder. Using multiple linear regression and linear mixed modelling, we evaluated which commonly assayed tissue (blood N = 231, urine N = 235, skeletal muscle N = 77) represents the m.3243A>G mutation load and mitochondrial DNA (mtDNA) copy number most strongly associated with disease burden and progression. m.3243A>G levels are correlated in blood, muscle and urine (R2 = 0.61–0.73). Blood heteroplasmy declines by ~2.3%/year; we have extended previously published methodology to adjust for age. In urine, males have higher mtDNA copy number and ~20% higher m.3243A>G mutation load; we present formulas to adjust for this. Blood is the most highly correlated mutation measure for disease burden and progression in m.3243A>G‐harbouring individuals; increasing age and heteroplasmy contribute (R2 = 0.27, P < 0.001). In muscle, heteroplasmy, age and mtDNA copy number explain a higher proportion of variability in disease burden (R2 = 0.40, P < 0.001), although activity level and disease severity are likely to affect copy number. Whilst our data indicate that age‐corrected blood m.3243A>G heteroplasmy is the most convenient and reliable measure for routine clinical assessment, additional factors such as mtDNA copy number may also influence disease severity.
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Affiliation(s)
- John P Grady
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Sarah J Pickett
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Yi Shiau Ng
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Steven A Hardy
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Catherine L Feeney
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Alexandra A Bright
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew M Schaefer
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Gráinne S Gorman
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Richard Jq McNally
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
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27
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Fritzen AM, Thøgersen FB, Thybo K, Vissing CR, Krag TO, Ruiz-Ruiz C, Risom L, Wibrand F, Høeg LD, Kiens B, Duno M, Vissing J, Jeppesen TD. Adaptations in Mitochondrial Enzymatic Activity Occurs Independent of Genomic Dosage in Response to Aerobic Exercise Training and Deconditioning in Human Skeletal Muscle. Cells 2019; 8:cells8030237. [PMID: 30871120 PMCID: PMC6468422 DOI: 10.3390/cells8030237] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial DNA (mtDNA) replication is thought to be an integral part of exercise-training-induced mitochondrial adaptations. Thus, mtDNA level is often used as an index of mitochondrial adaptations in training studies. We investigated the hypothesis that endurance exercise training-induced mitochondrial enzymatic changes are independent of genomic dosage by studying mtDNA content in skeletal muscle in response to six weeks of knee-extensor exercise training followed by four weeks of deconditioning in one leg, comparing results to the contralateral untrained leg, in 10 healthy, untrained male volunteers. Findings were compared to citrate synthase activity, mitochondrial complex activities, and content of mitochondrial membrane markers (porin and cardiolipin). One-legged knee-extensor exercise increased endurance performance by 120%, which was accompanied by increases in power output and peak oxygen uptake of 49% and 33%, respectively (p < 0.01). Citrate synthase and mitochondrial respiratory chain complex I–IV activities were increased by 51% and 46–61%, respectively, in the trained leg (p < 0.001). Despite a substantial training-induced increase in mitochondrial activity of TCA and ETC enzymes, there was no change in mtDNA and mitochondrial inner and outer membrane markers (i.e., cardiolipin and porin). Conversely, deconditioning reduced endurance capacity by 41%, muscle citrate synthase activity by 32%, and mitochondrial complex I–IV activities by 29–36% (p < 0.05), without any change in mtDNA and porin and cardiolipin content in the previously trained leg. The findings demonstrate that the adaptations in mitochondrial enzymatic activity after aerobic endurance exercise training and the opposite effects of deconditioning are independent of changes in the number of mitochondrial genomes, and likely relate to changes in the rate of transcription of mtDNA.
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Affiliation(s)
- Andreas M Fritzen
- Copenhagen Neuromuscular Center, Section 3342, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Frank B Thøgersen
- Copenhagen Neuromuscular Center, Section 3342, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Kasper Thybo
- Copenhagen Neuromuscular Center, Section 3342, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Christoffer R Vissing
- Copenhagen Neuromuscular Center, Section 3342, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Thomas O Krag
- Copenhagen Neuromuscular Center, Section 3342, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
- Department of Neurology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Cristina Ruiz-Ruiz
- Copenhagen Neuromuscular Center, Section 3342, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Lotte Risom
- Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Flemming Wibrand
- Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Louise D Høeg
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Bente Kiens
- Section of Molecular Physiology, Department of Nutrition, Exercise and Sports, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Morten Duno
- Department of Clinical Genetics, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - John Vissing
- Copenhagen Neuromuscular Center, Section 3342, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
- Department of Neurology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Tina D Jeppesen
- Copenhagen Neuromuscular Center, Section 3342, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
- Department of Neurology, Rigshospitalet, University of Copenhagen, 2100 Copenhagen, Denmark.
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28
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Guyatt AL, Brennan RR, Burrows K, Guthrie PAI, Ascione R, Ring SM, Gaunt TR, Pyle A, Cordell HJ, Lawlor DA, Chinnery PF, Hudson G, Rodriguez S. A genome-wide association study of mitochondrial DNA copy number in two population-based cohorts. Hum Genomics 2019; 13:6. [PMID: 30704525 PMCID: PMC6357493 DOI: 10.1186/s40246-018-0190-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 12/27/2018] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Mitochondrial DNA copy number (mtDNA CN) exhibits interindividual and intercellular variation, but few genome-wide association studies (GWAS) of directly assayed mtDNA CN exist. We undertook a GWAS of qPCR-assayed mtDNA CN in the Avon Longitudinal Study of Parents and Children (ALSPAC) and the UK Blood Service (UKBS) cohort. After validating and harmonising data, 5461 ALSPAC mothers (16-43 years at mtDNA CN assay) and 1338 UKBS females (17-69 years) were included in a meta-analysis. Sensitivity analyses restricted to females with white cell-extracted DNA and adjusted for estimated or assayed cell proportions. Associations were also explored in ALSPAC children and UKBS males. RESULTS A neutrophil-associated locus approached genome-wide significance (rs709591 [MED24], β (change in SD units of mtDNA CN per allele) [SE] - 0.084 [0.016], p = 1.54e-07) in the main meta-analysis of adult females. This association was concordant in magnitude and direction in UKBS males and ALSPAC neonates. SNPs in and around ABHD8 were associated with mtDNA CN in ALSPAC neonates (rs10424198, β [SE] 0.262 [0.034], p = 1.40e-14), but not other study groups. In a meta-analysis of unrelated individuals (N = 11,253), we replicated a published association in TFAM (β [SE] 0.046 [0.017], p = 0.006), with an effect size much smaller than that observed in the replication analysis of a previous in silico GWAS. CONCLUSIONS In a hypothesis-generating GWAS, we confirm an association between TFAM and mtDNA CN and present putative loci requiring replication in much larger samples. We discuss the limitations of our work, in terms of measurement error and cellular heterogeneity, and highlight the need for larger studies to better understand nuclear genomic control of mtDNA copy number.
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Affiliation(s)
- Anna L. Guyatt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Rebecca R. Brennan
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Kimberley Burrows
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Philip A. I. Guthrie
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Raimondo Ascione
- Bristol Heart Institute, Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Susan M. Ring
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle, UK
| | | | - Debbie A. Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Patrick F. Chinnery
- Department of Clinical Neurosciences and MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle, UK
- Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Santiago Rodriguez
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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29
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Bolognin S, Fossépré M, Qing X, Jarazo J, Ščančar J, Moreno EL, Nickels SL, Wasner K, Ouzren N, Walter J, Grünewald A, Glaab E, Salamanca L, Fleming RMT, Antony PMA, Schwamborn JC. 3D Cultures of Parkinson's Disease-Specific Dopaminergic Neurons for High Content Phenotyping and Drug Testing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019; 6:1800927. [PMID: 30643711 PMCID: PMC6325628 DOI: 10.1002/advs.201800927] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/31/2018] [Indexed: 05/16/2023]
Abstract
Parkinson's disease (PD)-specific neurons, grown in standard 2D cultures, typically only display weak endophenotypes. The cultivation of PD patient-specific neurons, derived from induced pluripotent stem cells carrying the LRRK2-G2019S mutation, is optimized in 3D microfluidics. The automated image analysis algorithms are implemented to enable pharmacophenomics in disease-relevant conditions. In contrast to 2D cultures, this 3D approach reveals robust endophenotypes. High-content imaging data show decreased dopaminergic differentiation and branching complexity, altered mitochondrial morphology, and increased cell death in LRRK2-G2019S neurons compared to isogenic lines without using stressor agents. Treatment with the LRRK2 inhibitor 2 (Inh2) rescues LRRK2-G2019S-dependent dopaminergic phenotypes. Strikingly, a holistic analysis of all studied features shows that the genetic background of the PD patients, and not the LRRK2-G2019S mutation, constitutes the strongest contribution to the phenotypes. These data support the use of advanced in vitro models for future patient stratification and personalized drug development.
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Affiliation(s)
- Silvia Bolognin
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
- Braingineering Technologies SARL9 avenue des Hauts‐ForneauxEsch‐sur‐AlzetteL‐4362Luxembourg
| | - Marie Fossépré
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
- Braingineering Technologies SARL9 avenue des Hauts‐ForneauxEsch‐sur‐AlzetteL‐4362Luxembourg
| | - Xiaobing Qing
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Javier Jarazo
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Janez Ščančar
- Department of Environmental SciencesJožef Stefan InstituteJamova 391000LjubljanaSlovenia
| | - Edinson Lucumi Moreno
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Sarah L. Nickels
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Kobi Wasner
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Nassima Ouzren
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Jonas Walter
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
- Braingineering Technologies SARL9 avenue des Hauts‐ForneauxEsch‐sur‐AlzetteL‐4362Luxembourg
| | - Anne Grünewald
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
- Institute of NeurogeneticsUniversity of Lübeck23562LübeckGermany
| | - Enrico Glaab
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Luis Salamanca
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Ronan M. T. Fleming
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Paul M. A. Antony
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
| | - Jens C. Schwamborn
- Luxembourg Centre for Systems BiomedicineUniversity of Luxembourg6 avenue du SwingBelvauxL‐4367Luxembourg
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30
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Bris C, Goudenege D, Desquiret-Dumas V, Charif M, Colin E, Bonneau D, Amati-Bonneau P, Lenaers G, Reynier P, Procaccio V. Bioinformatics Tools and Databases to Assess the Pathogenicity of Mitochondrial DNA Variants in the Field of Next Generation Sequencing. Front Genet 2018; 9:632. [PMID: 30619459 PMCID: PMC6297213 DOI: 10.3389/fgene.2018.00632] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/27/2018] [Indexed: 11/13/2022] Open
Abstract
The development of next generation sequencing (NGS) has greatly enhanced the diagnosis of mitochondrial disorders, with a systematic analysis of the whole mitochondrial DNA (mtDNA) sequence and better detection sensitivity. However, the exponential growth of sequencing data renders complex the interpretation of the identified variants, thereby posing new challenges for the molecular diagnosis of mitochondrial diseases. Indeed, mtDNA sequencing by NGS requires specific bioinformatics tools and the adaptation of those developed for nuclear DNA, for the detection and quantification of mtDNA variants from sequence alignment to the calling steps, in order to manage the specific features of the mitochondrial genome including heteroplasmy, i.e., coexistence of mutant and wildtype mtDNA copies. The prioritization of mtDNA variants remains difficult, relying on a limited number of specific resources: population and clinical databases, and in silico tools providing a prediction of the variant pathogenicity. An evaluation of the most prominent bioinformatics tools showed that their ability to predict the pathogenicity was highly variable indicating that special efforts should be directed at developing new bioinformatics tools dedicated to the mitochondrial genome. In addition, massive parallel sequencing raised several issues related to the interpretation of very low mtDNA mutational loads, discovery of variants of unknown significance, and mutations unrelated to patient phenotype or the co-occurrence of mtDNA variants. This review provides an overview of the current strategies and bioinformatics tools for accurate annotation, prioritization and reporting of mtDNA variations from NGS data, in order to carry out accurate genetic counseling in individuals with primary mitochondrial diseases.
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Affiliation(s)
- Céline Bris
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - David Goudenege
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Valérie Desquiret-Dumas
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Majida Charif
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Estelle Colin
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Dominique Bonneau
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Patrizia Amati-Bonneau
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Guy Lenaers
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Pascal Reynier
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Vincent Procaccio
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
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31
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Goudenège D, Bris C, Hoffmann V, Desquiret-Dumas V, Jardel C, Rucheton B, Bannwarth S, Paquis-Flucklinger V, Lebre AS, Colin E, Amati-Bonneau P, Bonneau D, Reynier P, Lenaers G, Procaccio V. eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genet Med 2018; 21:1407-1416. [PMID: 30393377 DOI: 10.1038/s41436-018-0350-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/17/2018] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Accurate detection of mitochondrial DNA (mtDNA) alterations is essential for the diagnosis of mitochondrial diseases. The development of high-throughput sequencing technologies has enhanced the detection sensitivity of mtDNA pathogenic variants, but the detection of mtDNA rearrangements, especially multiple deletions, is still poorly processed. Here, we present eKLIPse, a sensitive and specific tool allowing the detection and quantification of large mtDNA rearrangements from single and paired-end sequencing data. METHODS The methodology was first validated using a set of simulated data to assess the detection sensitivity and specificity, and second with a series of sequencing data from mitochondrial disease patients carrying either single or multiple deletions, related to pathogenic variants in nuclear genes involved in mtDNA maintenance. RESULTS eKLIPse provides the precise breakpoint positions and the cumulated percentage of mtDNA rearrangements at a given gene location with a detection sensitivity lower than 0.5% mutant. eKLIPse software is available either as a script to be integrated in a bioinformatics pipeline, or as user-friendly graphical interface to visualize the results through a Circos representation ( https://github.com/dooguypapua/eKLIPse ). CONCLUSION Thus, eKLIPse represents a useful resource to study the causes and consequences of mtDNA rearrangements, for further genotype/phenotype correlations in mitochondrial disorders.
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Affiliation(s)
- David Goudenège
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Celine Bris
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Virginie Hoffmann
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Valerie Desquiret-Dumas
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Claude Jardel
- Biochemistry Department and Genetics Center, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Benoit Rucheton
- Biochemistry Department and Genetics Center, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Sylvie Bannwarth
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | | | - Anne Sophie Lebre
- CHU Reims, Hôpital Maison Blanche, Pole de biologie, Service de génétique, Reims, France
| | - Estelle Colin
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Patrizia Amati-Bonneau
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Dominique Bonneau
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Pascal Reynier
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Guy Lenaers
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France. .,Biochemistry and Genetics Department, Angers Hospital, Angers, France.
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Brockhage R, Slone J, Ma Z, Hegde MR, Valencia CA, Huang T. Validation of the diagnostic potential of mtDNA copy number derived from whole genome sequencing. J Genet Genomics 2018; 45:S1673-8527(18)30098-5. [PMID: 29910094 DOI: 10.1016/j.jgg.2018.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/03/2018] [Accepted: 06/04/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Rachel Brockhage
- Division of Human Genetics, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jesse Slone
- Division of Human Genetics, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Zeqiang Ma
- PerkinElmer Genomics, Branford, CT 06405, USA
| | - Madhuri R Hegde
- PerkinElmer Genomics, Branford, CT 06405, USA; Department of Human Genetics, Emory University, Atlanta, GA 30322, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - C Alexander Valencia
- PerkinElmer Genomics, Branford, CT 06405, USA; West China Hospital, Sichuan University, Chengdu 610041, China
| | - Taosheng Huang
- Division of Human Genetics, Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Human Aging Research Institute, Nanchang University, Nanchang 330031, China.
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33
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Hefti E, Blanco JG. Mitochondrial DNA heteroplasmy in cardiac tissue from individuals with and without coronary artery disease. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:587-593. [PMID: 28521548 PMCID: PMC5694712 DOI: 10.1080/24701394.2017.1325480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/19/2017] [Accepted: 04/27/2017] [Indexed: 01/11/2023]
Abstract
The cellular environment associated with coronary artery disease (CAD) can lead to mitochondrial DNA (mtDNA) damage. Mitochondrial variants in some copies of mtDNA (heteroplasmy) and mtDNA content are potential genetic biomarkers for CAD-associated disease states. Massively parallel sequencing and qRT-PCR techniques were used to measure heteroplasmic variants and mtDNA content in heart samples from donors with (n = 8) and without (n = 7) documented CAD. Both groups showed increased numbers of heteroplasmic mtDNA variants in the control region (CR) (p < .0010, ANOVA). The donors with CAD displayed a 41.07% increase in heteroplasmic mtDNA variant number in the CR (p = .043), an 87.50% increase in the number of heteroplasmic mtDNA deletions (p = .12), and a 48.76% increase in the number of heteroplasmic mtDNA single nucleotide variants (p = .029). These data suggest potential trends towards higher cardiac mtDNA heteroplasmy levels in heart samples from donors with CAD.
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Affiliation(s)
- Erik Hefti
- Department of Pharmaceutical Sciences, The School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Javier G. Blanco
- Department of Pharmaceutical Sciences, The School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, New York, United States of America
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Accumulation of Mitochondrial DNA Common Deletion Since The Preataxic Stage of Machado-Joseph Disease. Mol Neurobiol 2018; 56:119-124. [PMID: 29679261 DOI: 10.1007/s12035-018-1069-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/09/2018] [Indexed: 12/27/2022]
Abstract
Molecular alterations reflecting pathophysiologic changes thought to occur many years before the clinical onset of Machado-Joseph disease (MJD)/spinocerebellar ataxia type 3 (SCA3), a late-onset polyglutamine disorder, remain unidentified. The absence of molecular biomarkers hampers clinical trials, which lack sensitive measures of disease progression, preventing the identification of events occurring prior to clinical onset. Our aim was to analyse the mtDNA content and the amount of the common deletion (m.8482_13460del4977) in a cohort of 16 preataxic MJD mutation carriers, 85 MJD patients and 101 apparently healthy age-matched controls. Relative expression levels of RPPH1, MT-ND1 and MT-ND4 genes were assessed by quantitative real-time PCR. The mtDNA content was calculated as the difference between the expression levels of a mitochondrial gene (MT-ND1) and a nuclear gene (RPPH1); the amount of mtDNA common deletion was calculated as the difference between expression levels of a deleted (MT-ND4) and an undeleted (MT-ND1) mitochondrial genes. mtDNA content in MJD carriers was similar to that of healthy age-matched controls, whereas the percentage of the common deletion was significantly increased in MJD subjects, and more pronounced in the preclinical stage (p < 0.05). The BCL2/BAX ratio was decreased in preataxic carriers compared to controls, suggesting that the mitochondrial-mediated apoptotic pathway is altered in MJD. Our findings demonstrate for the first time that accumulation of common deletion starts in the preclinical stage. Such early alterations provide support to the current understanding that any therapeutic intervention in MJD should start before the overt clinical phenotype.
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35
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Preferential amplification of a human mitochondrial DNA deletion in vitro and in vivo. Sci Rep 2018; 8:1799. [PMID: 29379065 PMCID: PMC5789095 DOI: 10.1038/s41598-018-20064-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 12/27/2017] [Indexed: 01/19/2023] Open
Abstract
We generated induced pluripotent stem cells (iPSCs) from patient fibroblasts to yield cell lines containing varying degrees of heteroplasmy for a m.13514 A > G mtDNA point mutation (2 lines) and for a ~6 kb single, large scale mtDNA deletion (3 lines). Long term culture of the iPSCs containing a single, large-scale mtDNA deletion showed consistent increase in mtDNA deletion levels with time. Higher levels of mtDNA heteroplasmy correlated with increased respiratory deficiency. To determine what changes occurred in deletion level during differentiation, teratomas comprising all three embryonic germ layers were generated from low (20%) and intermediate heteroplasmy (55%) mtDNA deletion clones. Regardless of whether iPSCs harbouring low or intermediate mtDNA heteroplasmy were used, the final levels of heteroplasmy in all teratoma germ layers increased to a similar high level (>60%). Thus, during human stem cell division, cells not only tolerate high mtDNA deletion loads but seem to preferentially replicate deleted mtDNA genomes. This has implications for the involvement of mtDNA deletions in both disease and ageing.
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36
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Kullar PJ, Gomez-Duran A, Gammage PA, Garone C, Minczuk M, Golder Z, Wilson J, Montoya J, Häkli S, Kärppä M, Horvath R, Majamaa K, Chinnery PF. Heterozygous SSBP1 start loss mutation co-segregates with hearing loss and the m.1555A>G mtDNA variant in a large multigenerational family. Brain 2018; 141:55-62. [PMID: 29182774 PMCID: PMC5837410 DOI: 10.1093/brain/awx295] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/10/2017] [Accepted: 09/25/2017] [Indexed: 11/30/2022] Open
Abstract
The m.1555A>G mtDNA variant causes maternally inherited deafness, but the reasons for the highly variable clinical penetrance are not known. Exome sequencing identified a heterozygous start loss mutation in SSBP1, encoding the single stranded binding protein 1 (SSBP1), segregating with hearing loss in a multi-generational family transmitting m.1555A>G, associated with mtDNA depletion and multiple deletions in skeletal muscle. The SSBP1 mutation reduced steady state SSBP1 levels leading to a perturbation of mtDNA metabolism, likely compounding the intra-mitochondrial translation defect due to m.1555A>G in a tissue-specific manner. This family demonstrates the importance of rare trans-acting genetic nuclear modifiers in the clinical expression of mtDNA disease.
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Affiliation(s)
- Peter J Kullar
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Aurora Gomez-Duran
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Payam A Gammage
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
| | - Caterina Garone
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
| | - Michal Minczuk
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
| | - Zoe Golder
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Janet Wilson
- Institute of Health and Society, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Julio Montoya
- Universidad de Zaragoza-CIBER de Enfermedades Raras (CIBERER)-Instituto de Investigación Sanitaria de Aragón, Spain
| | - Sanna Häkli
- Research Unit of Clinical Neuroscience, University of Oulu, Oulu, Finland and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Mikko Kärppä
- Research Unit of Clinical Neuroscience, University of Oulu, Oulu, Finland and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Rita Horvath
- Institute of Genetic Medicine, Newcastle University, UK
| | - Kari Majamaa
- Research Unit of Clinical Neuroscience, University of Oulu, Oulu, Finland and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Patrick F Chinnery
- MRC-Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0QQ, UK
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37
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Refinetti P, Warren D, Morgenthaler S, Ekstrøm PO. Quantifying mitochondrial DNA copy number using robust regression to interpret real time PCR results. BMC Res Notes 2017; 10:593. [PMID: 29132417 PMCID: PMC5683470 DOI: 10.1186/s13104-017-2913-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 11/02/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Real time PCR (rtPCR) is a quantitative assay to determine the relative DNA copy number in a sample versus a reference. The [Formula: see text] method is the standard for the analysis of the output data generated by an rtPCR experiment. We developed an alternative based on fitting a robust regression to the rtPCR signal. This new data analysis tool reduces potential biases and does not require all of the compared DNA fragments to have the same PCR efficiency. RESULTS Comparing the two methods when analysing 96 identical PCR preparations showed similar distributions of the estimated copy numbers. Estimating the efficiency with the [Formula: see text] method, however, required a dilution series, which is not necessary for the robust regression method. We used rtPCR to quantify mitochondrial DNA (mtDNA) copy numbers in three different tissues types: breast, colon and prostate. For each type, normal tissue and a tumor from the same three patients were analysed. This gives a total of six samples. The mitochondrial copy number is estimated to lie between 200 and 300 copies per cell. Similar results are obtained when using the robust regression or the [Formula: see text] method. Confidence ratios were slightly narrower for the robust regression. The new data analysis method has been implemented as an R package.
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Affiliation(s)
- Paulo Refinetti
- Ecole Polytechnique Féderale de Lausanne, 1015, Lausanne, Switzerland.
| | - David Warren
- Department of Medical Biochemistry, Radiumhospital, 0379, Oslo, Norway
| | | | - Per O Ekstrøm
- Department of Tumor Biology, Radiumhospital, 0379, Oslo, Norway
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38
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Herbst A, Widjaja K, Nguy B, Lushaj EB, Moore TM, Hevener AL, McKenzie D, Aiken JM, Wanagat J. Digital PCR Quantitation of Muscle Mitochondrial DNA: Age, Fiber Type, and Mutation-Induced Changes. J Gerontol A Biol Sci Med Sci 2017; 72:1327-1333. [PMID: 28460005 DOI: 10.1093/gerona/glx058] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/21/2017] [Indexed: 01/07/2023] Open
Abstract
Definitive quantitation of mitochondrial DNA (mtDNA) and mtDNA deletion mutation abundances would help clarify the role of mtDNA instability in aging. To more accurately quantify mtDNA, we applied the emerging technique of digital polymerase chain reaction to individual muscle fibers and muscle homogenates from aged rodents. Individual fiber mtDNA content correlated with fiber type and decreased with age. We adapted a digital polymerase chain reaction deletion assay that was accurate in mixing experiments to a mutation frequency of 0.03% and quantitated an age-induced increase in deletion frequency from rat muscle homogenates. Importantly, the deletion frequency measured in muscle homogenates strongly correlated with electron transport chain-deficient fiber abundance determined by histochemical analyses. These data clarify the temporal accumulation of mtDNA deletions that lead to electron chain-deficient fibers, a process culminating in muscle fiber loss.
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Affiliation(s)
- Allen Herbst
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Canada
| | - Kevin Widjaja
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Beatrice Nguy
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Entela B Lushaj
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison
| | - Timothy M Moore
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Andrea L Hevener
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Debbie McKenzie
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Judd M Aiken
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Canada
| | - Jonathan Wanagat
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
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Blauwkamp MN, Fasching CL, Lin J, Guegler K, Hytopoulos E, Watson D, Harley CB. Analytical Validation of Relative Average Telomere Length Measurement in a Clinical Laboratory Environment. J Appl Lab Med 2017; 2:4-16. [PMID: 33636955 DOI: 10.1373/jalm.2016.022137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/15/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Average telomere length in whole blood has become a biomarker of aging, disease, and mortality risk across a broad range of clinical conditions. The most common method of telomere length measurement for large patient sample sets is based on quantitative PCR (qPCR). For laboratory-developed tests to be performed on clinical samples, they must undergo a rigorous analytical validation, currently regulated under CLIA. METHODS Whole blood samples from 40 donors were used in the analytical validation of methods for relative average telomere length (rATL) measurement. Three technical replicate DNA samples were extracted from each whole blood sample and placed in three independent wells on a sample plate. Each of these sample plates was assayed 12 times during the validation process. The study was conducted over a 20-day period, once in the morning and once in the evening, using 3 different operators. RESULTS Our process of rATL measurement beginning with DNA extraction followed by qPCR-based assay resulted in repeatability and reproducibility CV of <5% and amplification efficiencies near 100%. The validated assay was used to establish a reference interval derived from 2 cohorts of individuals: (a) San Francisco Bay area (n = 504) and (b) a US cross-sectional, demographic population (n = 357). CONCLUSIONS We present advances in the establishment of a highly reproducible analytically validated process for determining rATLs in a CLIA laboratory environment.
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Affiliation(s)
| | | | - Jue Lin
- Telomere Diagnostics, Inc., Menlo Park, CA
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40
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Sohn JH. Advanced Mitochondrial DNA Assay for Metabolic Syndrome. J Lifestyle Med 2016; 6:79-80. [PMID: 27924289 PMCID: PMC5115208 DOI: 10.15280/jlm.2016.6.2.79] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 11/22/2022] Open
Affiliation(s)
- Joon Hyung Sohn
- Institute of Lifestyle Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
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41
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Mitochondria in the Aging Muscles of Flies and Mice: New Perspectives for Old Characters. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2016; 2016:9057593. [PMID: 27630760 PMCID: PMC5007348 DOI: 10.1155/2016/9057593] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/30/2016] [Accepted: 05/16/2016] [Indexed: 12/22/2022]
Abstract
Sarcopenia is the loss of muscle mass accompanied by a decrease in muscle strength and resistance and is the main cause of disability among the elderly. Muscle loss begins long before there is any clear physical impact in the senior adult. Despite all this, the molecular mechanisms underlying muscle aging are far from being understood. Recent studies have identified that not only mitochondrial metabolic dysfunction but also mitochondrial dynamics and mitochondrial calcium uptake could be involved in the degeneration of skeletal muscle mass. Mitochondrial homeostasis influences muscle quality which, in turn, could play a triggering role in signaling of systemic aging. Thus, it has become apparent that mitochondrial status in muscle cells could be a driver of whole body physiology and organismal aging. In the present review, we discuss the existing evidence for the mitochondria related mechanisms underlying the appearance of muscle aging and sarcopenia in flies and mice.
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42
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Digital PCR methods improve detection sensitivity and measurement precision of low abundance mtDNA deletions. Sci Rep 2016; 6:25186. [PMID: 27122135 PMCID: PMC4848546 DOI: 10.1038/srep25186] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 04/12/2016] [Indexed: 02/05/2023] Open
Abstract
Mitochondrial DNA (mtDNA) mutations are a common cause of primary mitochondrial disorders, and have also been implicated in a broad collection of conditions, including aging, neurodegeneration, and cancer. Prevalent among these pathogenic variants are mtDNA deletions, which show a strong bias for the loss of sequence in the major arc between, but not including, the heavy and light strand origins of replication. Because individual mtDNA deletions can accumulate focally, occur with multiple mixed breakpoints, and in the presence of normal mtDNA sequences, methods that detect broad-spectrum mutations with enhanced sensitivity and limited costs have both research and clinical applications. In this study, we evaluated semi-quantitative and digital PCR-based methods of mtDNA deletion detection using double-stranded reference templates or biological samples. Our aim was to describe key experimental assay parameters that will enable the analysis of low levels or small differences in mtDNA deletion load during disease progression, with limited false-positive detection. We determined that the digital PCR method significantly improved mtDNA deletion detection sensitivity through absolute quantitation, improved precision and reduced assay standard error.
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43
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Mdaki KS, Larsen TD, Wachal AL, Schimelpfenig MD, Weaver LJ, Dooyema SDR, Louwagie EJ, Baack ML. Maternal high-fat diet impairs cardiac function in offspring of diabetic pregnancy through metabolic stress and mitochondrial dysfunction. Am J Physiol Heart Circ Physiol 2016; 310:H681-92. [PMID: 26801311 DOI: 10.1152/ajpheart.00795.2015] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/15/2016] [Indexed: 01/26/2023]
Abstract
Offspring of diabetic pregnancies are at risk of cardiovascular disease at birth and throughout life, purportedly through fuel-mediated influences on the developing heart. Preventative measures focus on glycemic control, but the contribution of additional offenders, including lipids, is not understood. Cellular bioenergetics can be influenced by both diabetes and hyperlipidemia and play a pivotal role in the pathophysiology of adult cardiovascular disease. This study investigated whether a maternal high-fat diet, independently or additively with diabetes, could impair fuel metabolism, mitochondrial function, and cardiac physiology in the developing offspring's heart. Sprague-Dawley rats fed a control or high-fat diet were administered placebo or streptozotocin to induce diabetes during pregnancy and then delivered offspring from four groups: control, diabetes exposed, diet exposed, and combination exposed. Cardiac function, cellular bioenergetics (mitochondrial stress test, glycolytic stress test, and palmitate oxidation assay), lipid peroxidation, mitochondrial histology, and copy number were determined. Diabetes-exposed offspring had impaired glycolytic and respiratory capacity and a reduced proton leak. High-fat diet-exposed offspring had increased mitochondrial copy number, increased lipid peroxidation, and evidence of mitochondrial dysfunction. Combination-exposed pups were most severely affected and demonstrated cardiac lipid droplet accumulation and diastolic/systolic cardiac dysfunction that mimics that of adult diabetic cardiomyopathy. This study is the first to demonstrate that a maternal high-fat diet impairs cardiac function in offspring of diabetic pregnancies through metabolic stress and serves as a critical step in understanding the role of cellular bioenergetics in developmentally programmed cardiac disease.
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Affiliation(s)
- Kennedy S Mdaki
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - Tricia D Larsen
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - Angela L Wachal
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | | | - Lucinda J Weaver
- Sanford School of Medicine-University of South Dakota, Sioux Falls, South Dakota
| | - Samuel D R Dooyema
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | | | - Michelle L Baack
- Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota; Sanford School of Medicine-University of South Dakota, Sioux Falls, South Dakota; Children's Health Specialty Clinic, Sanford Children's Hospital, Sioux Falls, South Dakota
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44
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Pyle A, Brennan R, Kurzawa-Akanbi M, Yarnall A, Thouin A, Mollenhauer B, Burn D, Chinnery PF, Hudson G. Reduced cerebrospinal fluid mitochondrial DNA is a biomarker for early-stage Parkinson's disease. Ann Neurol 2015; 78:1000-4. [PMID: 26343811 DOI: 10.1002/ana.24515] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/24/2015] [Accepted: 08/24/2015] [Indexed: 01/09/2023]
Abstract
The identification of cell-free circulating mitochondrial DNA (ccf-mtDNA) in early-stage Alzheimer's disease (AD) raised the possibility that the same neurodegenerative effect could be observed in Parkinson's disease (PD). Here, and for the first time, we investigated the role of ccf-mtDNA in PD, identifying a significant reduction of ccf-mtDNA in PD patient cerebrospinal fluid (CSF) when compared to controls. Our data demonstrates that CSF ccf-mtDNA is not only a powerful biomarker for PD, but, given that the effect is also observed in AD, is likely a biomarker for neurodegeneration.
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Affiliation(s)
- Angela Pyle
- Mitochondrial Research Group, University of Newcastle Upon Tyne, Newcastle Upon Tyne, United Kingdom
| | - Rebecca Brennan
- Mitochondrial Research Group, University of Newcastle Upon Tyne, Newcastle Upon Tyne, United Kingdom
| | - Marzena Kurzawa-Akanbi
- Mitochondrial Research Group, University of Newcastle Upon Tyne, Newcastle Upon Tyne, United Kingdom
| | - Alison Yarnall
- Insitutute of Neuroscience, University of Newcastle Upon Tyne, Newcastle Upon Tyne, United Kingdom
| | - Anais Thouin
- Insitutute of Neuroscience, University of Newcastle Upon Tyne, Newcastle Upon Tyne, United Kingdom
| | - Brit Mollenhauer
- Institute for Neuropathology, University of Goettingen, Goettingen, Germany
| | - David Burn
- Insitutute of Neuroscience, University of Newcastle Upon Tyne, Newcastle Upon Tyne, United Kingdom
| | - Patrick F Chinnery
- Mitochondrial Research Group, University of Newcastle Upon Tyne, Newcastle Upon Tyne, United Kingdom
| | - Gavin Hudson
- Mitochondrial Research Group, University of Newcastle Upon Tyne, Newcastle Upon Tyne, United Kingdom
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Pyle A, Anugrha H, Kurzawa-Akanbi M, Yarnall A, Burn D, Hudson G. Reduced mitochondrial DNA copy number is a biomarker of Parkinson's disease. Neurobiol Aging 2015; 38:216.e7-216.e10. [PMID: 26639155 PMCID: PMC4759605 DOI: 10.1016/j.neurobiolaging.2015.10.033] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 02/01/2023]
Abstract
Like any organ, the brain is susceptible to the march of time and a reduction in mitochondrial biogenesis is a hallmark of the aging process. In the largest investigation of mitochondrial copy number in Parkinson's disease (PD) to date and by using multiple tissues, we demonstrate that reduced Parkinson DNA (mitochondrial DNA mtDNA) copy number is a biomarker for the etiology of PD. We used established methods of mtDNA quantification to assess the copy number of mtDNA in n = 363 peripheral blood samples, n = 151 substantia nigra pars compacta tissue samples and n = 120 frontal cortex tissue samples from community-based PD cases fulfilling UK-PD Society brain bank criteria for the diagnosis of PD. Accepting technical limitations, our data show that PD patients suffer a significant reduction in mtDNA copy number in both peripheral blood and the vulnerable substantia nigra pars compacta when compared to matched controls. Our study indicates that reduced mtDNA copy number is restricted to the affected brain tissue, but is also reflected in the peripheral blood, suggesting that mtDNA copy number may be a viable diagnostic predictor of PD.
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Affiliation(s)
- Angela Pyle
- Mitochondrial Research Group, Institute of Genetic Medicine, University of Newcastle Upon Tyne, UK
| | - Haidyan Anugrha
- Mitochondrial Research Group, Institute of Genetic Medicine, University of Newcastle Upon Tyne, UK
| | - Marzena Kurzawa-Akanbi
- Mitochondrial Research Group, Institute of Genetic Medicine, University of Newcastle Upon Tyne, UK
| | - Alison Yarnall
- Insitutute of Neuroscience, University of Newcastle Upon Tyne, UK
| | - David Burn
- Insitutute of Neuroscience, University of Newcastle Upon Tyne, UK
| | - Gavin Hudson
- Mitochondrial Research Group, Institute of Genetic Medicine, University of Newcastle Upon Tyne, UK.
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Triplex real-time PCR--an improved method to detect a wide spectrum of mitochondrial DNA deletions in single cells. Sci Rep 2015; 5:9906. [PMID: 25989140 PMCID: PMC4437295 DOI: 10.1038/srep09906] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/11/2015] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial DNA (mtDNA) mutations are commonly found in the skeletal muscle of patients with mitochondrial disease, inflammatory myopathies and sarcopenia. The majority of these mutations are mtDNA deletions, which accumulate to high levels in individual muscle fibres causing a respiratory defect. Most mtDNA deletions are major arc deletions with breakpoints located between the origin of light strand (OL) and heavy strand (OH) replication within the major arc. However, under certain disease conditions, rarer, minor arc deletions are detected. Currently, there are few techniques which would allow the detection and quantification of both types of mtDNA deletions in single muscle fibres. We have designed a novel triplex real-time PCR assay which simultaneously amplifies the MT-ND4 gene in the major arc, the MT-ND1 gene in the minor arc, and the non-coding D-Loop region. We demonstrate that this assay is a highly sensitive and reliable tool for the detection and quantification of a broad range of major and minor arc mtDNA deletions with the potential to investigate the molecular pathogenesis in both research and diagnostic settings.
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