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Bury A, Pyle A, Vincent AE, Actis P, Hudson G. Nanobiopsy investigation of the subcellular mtDNA heteroplasmy in human tissues. Sci Rep 2024; 14:13789. [PMID: 38877095 PMCID: PMC11178779 DOI: 10.1038/s41598-024-64455-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Mitochondrial function is critical to continued cellular vitality and is an important contributor to a growing number of human diseases. Mitochondrial dysfunction is typically heterogeneous, mediated through the clonal expansion of mitochondrial DNA (mtDNA) variants in a subset of cells in a given tissue. To date, our understanding of the dynamics of clonal expansion of mtDNA variants has been technically limited to the single cell-level. Here, we report the use of nanobiopsy for subcellular sampling from human tissues, combined with next-generation sequencing to assess subcellular mtDNA mutation load in human tissue from mitochondrial disease patients. The ability to map mitochondrial mutation loads within individual cells of diseased tissue samples will further our understanding of mitochondrial genetic diseases.
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Affiliation(s)
- Alexander Bury
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK
- Bragg Centre for Materials Research, Leeds, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK.
- Bragg Centre for Materials Research, Leeds, UK.
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
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2
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Launay N, Lopez-Erauskin J, Bianchi P, Guha S, Parameswaran J, Coppa A, Torreni L, Schlüter A, Fourcade S, Paredes-Fuentes AJ, Artuch R, Casasnovas C, Ruiz M, Pujol A. Imbalanced mitochondrial dynamics contributes to the pathogenesis of X-linked adrenoleukodystrophy. Brain 2024; 147:2069-2084. [PMID: 38763511 DOI: 10.1093/brain/awae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/20/2023] [Accepted: 01/21/2024] [Indexed: 05/21/2024] Open
Abstract
The peroxisomal disease adrenoleukodystrophy (X-ALD) is caused by loss of the transporter of very-long-chain fatty acids (VLCFAs), ABCD1. An excess of VLCFAs disrupts essential homeostatic functions crucial for axonal maintenance, including redox metabolism, glycolysis and mitochondrial respiration. As mitochondrial function and morphology are intertwined, we set out to investigate the role of mitochondrial dynamics in X-ALD models. Using quantitative 3D transmission electron microscopy, we revealed mitochondrial fragmentation in corticospinal axons in Abcd1- mice. In patient fibroblasts, an excess of VLCFAs triggers mitochondrial fragmentation through the redox-dependent phosphorylation of DRP1 (DRP1S616). The blockade of DRP1-driven fission by the peptide P110 effectively preserved mitochondrial morphology. Furthermore, mRNA inhibition of DRP1 not only prevented mitochondrial fragmentation but also protected axonal health in a Caenorhabditis elegans model of X-ALD, underscoring DRP1 as a potential therapeutic target. Elevated levels of circulating cell-free mtDNA in patients' CSF align this leukodystrophy with primary mitochondrial disorders. Our findings underscore the intricate interplay between peroxisomal dysfunction, mitochondrial dynamics and axonal integrity in X-ALD, shedding light on potential avenues for therapeutic intervention.
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Affiliation(s)
- Nathalie Launay
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
| | - Jone Lopez-Erauskin
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA 92093, USA
| | - Patrizia Bianchi
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Physiology and Immunology, Facultat de Medicina, Institut de Neurociències and Department of Cell Biology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Sanjib Guha
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Nautilus Biotechnology, San Carlos, CA 94070, USA
| | - Janani Parameswaran
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Department of Cell Biology, Emory University, Atlanta, GA 30322, USA
| | - Andrea Coppa
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Lorenzo Torreni
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- Programa de Doctorat en Biomedicina, Universitat de Barcelona, 08193 Barcelona, Spain
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
| | - Stéphane Fourcade
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
| | - Abraham J Paredes-Fuentes
- Division of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, 08028 Barcelona, Spain
| | - Rafael Artuch
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, 08950 Barcelona, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
- Neuromuscular Unit, Neurology Department, Bellvitge University Hospital, Universitat de Barcelona, 08907 Lhospitalet de Llobregat, Barcelona, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Institute of Neuropathology, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, 28029 Madrid, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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3
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Tan DX. Mitochondrial dysfunction, a weakest link of network of aging, relation to innate intramitochondrial immunity of DNA recognition receptors. Mitochondrion 2024; 76:101886. [PMID: 38663836 DOI: 10.1016/j.mito.2024.101886] [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: 02/11/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 04/30/2024]
Abstract
Aging probably is the most complexed process in biology. It is manifested by a variety of hallmarks. These hallmarks weave a network of aging; however, each hallmark is not uniformly strong for the network. It is the weakest link determining the strengthening of the network of aging, or the maximum lifespan of an organism. Therefore, only improvement of the weakest link has the chance to increase the maximum lifespan but not others. We hypothesize that mitochondrial dysfunction is the weakest link of the network of aging. It may origin from the innate intramitochondrial immunity related to the activities of pathogen DNA recognition receptors. These receptors recognize mtDNA as the PAMP or DAMP to initiate the immune or inflammatory reactions. Evidence has shown that several of these receptors including TLR9, cGAS and IFI16 can be translocated into mitochondria. The potentially intramitochondrial presented pathogen DNA recognition receptors have the capacity to attack the exposed second structures of the mtDNA during its transcriptional or especially the replicational processes, leading to the mtDNA mutation, deletion, heteroplasmy colonization, mitochondrial dysfunction, and alterations of other hallmarks, as well as aging. Pre-consumption of the intramitochondrial presented pathogen DNA recognition receptors by medical interventions including development of mitochondrial targeted small molecule which can neutralize these receptors may retard or even reverse the aging to significantly improve the maximum lifespan of the organisms.
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Affiliation(s)
- Dun-Xian Tan
- Department of Cell Systems and Anatomy, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
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4
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Keraite I, Becker P, Canevazzi D, Frias-López C, Dabad M, Tonda-Hernandez R, Paramonov I, Ingham MJ, Brun-Heath I, Leno J, Abulí A, Garcia-Arumí E, Heath SC, Gut M, Gut IG. A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome. Nat Commun 2022; 13:5902. [PMID: 36202811 PMCID: PMC9537161 DOI: 10.1038/s41467-022-33530-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Here we describe a method to target, multiplex and sequence at high coverage full-length human mitochondrial genomes as native single-molecules, utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks, that define the mtDNA beginning and end of the sequencing reads, as barcodes, we achieve high demultiplexing specificity and delineation of the full-length of the mtDNA, regardless of the structural variant pattern. The long-read sequencing data is analysed with a pipeline where our custom-developed software, baldur, efficiently detects single nucleotide heteroplasmy to below 1%, physically determines phase and can accurately disentangle complex deletions. Our workflow is a tool for studying mtDNA variation and will accelerate mitochondrial research. Accurate analysis of mitochondrial DNA is important for mitochondrial disease clinical research and diagnostics. Here, authors present a method using Cas9 cleavage, nanopore sequencing and a custom pipeline to identify pathogenic variants, deletions and accurately quantify heteroplasmy to below 1%.
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Affiliation(s)
- Ieva Keraite
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Philipp Becker
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Qiagen, Hilden, Germany
| | - Davide Canevazzi
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cristina Frias-López
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Raúl Tonda-Hernandez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ida Paramonov
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Matthew John Ingham
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Joint IRB-BSC Program in Computational Biology, Barcelona, Spain
| | - Jordi Leno
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Anna Abulí
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Elena Garcia-Arumí
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Research Group on Neuromuscular and Mitochondrial Disorders, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Simon Charles Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
| | - Ivo Glynne Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
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5
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Leukocyte cytokine responses in adult patients with mitochondrial DNA defects. J Mol Med (Berl) 2022; 100:963-971. [PMID: 35635577 PMCID: PMC9885136 DOI: 10.1007/s00109-022-02206-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/11/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023]
Abstract
Patients with oxidative phosphorylation (OxPhos) defects causing mitochondrial diseases appear particularly vulnerable to infections. Although OxPhos defects modulate cytokine production in vitro and in animal models, little is known about how circulating leukocytes of patients with inherited mitochondrial DNA (mtDNA) defects respond to acute immune challenges. In a small cohort of healthy controls (n = 21) and patients (n = 12) with either the m.3243A > G mutation or single, large-scale mtDNA deletions, we examined (i) cytokine responses (IL-6, TNF-α, IL-1β) in response to acute lipopolysaccharide (LPS) exposure and (ii) sensitivity to the immunosuppressive effects of glucocorticoid signaling (dexamethasone) on cytokine production. In dose-response experiments to determine the half-maximal effective LPS concentration (EC50), relative to controls, leukocytes from patients with mtDNA deletions showed 74-79% lower responses for IL-6 and IL-1β (pIL-6 = 0.031, pIL-1β = 0.009). Moreover, whole blood from patients with mtDNA deletions (pIL-6 = 0.006), but not patients with the m.3243A > G mutation, showed greater sensitivity to the immunosuppressive effects of dexamethasone. Together, these ex vivo data provide preliminary evidence that some systemic OxPhos defects may compromise immune cytokine responses and increase the sensitivity to immune cytokine suppression by glucocorticoids. Further work in larger cohorts is needed to define the nature of immune dysregulation in patients with mitochondrial disease, and their potential implications for disease phenotypes. KEY MESSAGES: Little is known about leukocyte cytokine responses in patients with mitochondrial diseases. Leukocytes of patients with mtDNA deletions show blunted LPS sensitivity and cytokine responses. Leukocytes of patients with mtDNA deletions are more sensitive to glucocorticoid-mediated IL-6 suppression. Work in larger cohorts is needed to delineate potential immune alterations in mitochondrial diseases.
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Olimpio C, Tiet MY, Horvath R. Primary mitochondrial myopathies in childhood. Neuromuscul Disord 2021; 31:978-987. [PMID: 34736635 DOI: 10.1016/j.nmd.2021.08.005] [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: 07/13/2021] [Revised: 07/29/2021] [Accepted: 08/05/2021] [Indexed: 12/30/2022]
Abstract
Primary mitochondrial myopathies are genetic metabolic disorders of mitochondrial dysfunction affecting mainly, but not exclusively, skeletal muscle. Although individually rare, they are the most common inherited metabolic disorders in childhood. They can be similar to other childhood muscle diseases such as congenital myopathies, dystrophies, myasthenic syndromes or metabolic myopathies and a muscle biopsy and genetic testing are important in the differential diagnosis. Mitochondrial myopathies can present at any age but typically childhood onset myopathies have more significant muscle involvement and are caused by genes encoded in the nuclear DNA. Mitochondrial myopathy in infants presents with hypotonia, muscle weakness and difficulty feeding. In toddlers and older children delayed motor development, exercise intolerance and premature fatigue are common. A number of nuclear DNA and mitochondrial DNA encoded genes are known to cause isolated myopathy in childhood and they are important in a range of mitochondrial functions such as oxidative phosphorylation, mitochondrial transcription/translation and mitochondrial fusion/fission. A rare cause of isolated myopathy in children, reversible infantile respiratory chain deficiency myopathy, is non-progressive and typically associated with spontaneous full recovery. Promising targeted treatments have been reported for a number or mitochondrial myopathies including riboflavin in ACAD9 and ETFDH-myopathies and deoxynucleoside for TK2-related disease.
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Affiliation(s)
- Catarina Olimpio
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - May Yung Tiet
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
| | - Rita Horvath
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom.
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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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8
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Trifunov S, Paredes-Fuentes AJ, Badosa C, Codina A, Montoya J, Ruiz-Pesini E, Jou C, Garrabou G, Grau-Junyent JM, Yubero D, Montero R, Muchart J, Ortigoza-Escobar JD, O'Callaghan MM, Nascimento A, Català A, Garcia-Cazorla À, Jimenez-Mallebrera C, Artuch R. Circulating Cell-Free Mitochondrial DNA in Cerebrospinal Fluid as a Biomarker for Mitochondrial Diseases. Clin Chem 2021; 67:1113-1121. [PMID: 34352085 DOI: 10.1093/clinchem/hvab091] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 05/05/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Mitochondrial diseases (MD) are genetic metabolic disorders that impair normal mitochondrial structure or function. The aim of this study was to investigate the status of circulating cell-free mitochondrial DNA (ccfmtDNA) in cerebrospinal fluid (CSF), together with other biomarkers (growth differentiation factor-15 [GDF-15], alanine, and lactate), in a cohort of 25 patients with a molecular diagnosis of MD. METHODS Measurement of ccfmtDNA was performed by using droplet digital PCR. RESULTS The mean copy number of ccfmtDNA was approximately 6 times higher in the MD cohort compared to the control group; patients with mitochondrial deletion and depletion syndromes (MDD) had the higher levels. We also detected the presence of both wild-type mtDNA and mtDNA deletions in CSF samples of patients with single deletions. Patients with MDD with single deletions had significantly higher concentrations of GDF-15 in CSF than controls, whereas patients with point mutations in mitochondrial DNA presented no statistically significant differences. Additionally, we found a significant positive correlation between ccfmtDNA levels and GDF-15 concentrations (r = 0.59, P = 0.016). CONCLUSION CSF ccfmtDNA levels are significantly higher in patients with MD in comparison to controls and, thus, they can be used as a novel biomarker for MD research. Our results could also be valuable to support the clinical outcome assessment of MD patients.
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Affiliation(s)
- Selena Trifunov
- Neuromuscular Unit, Department of Neuropediatrics, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Abraham J Paredes-Fuentes
- Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Carmen Badosa
- Neuromuscular Unit, Department of Neuropediatrics, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Anna Codina
- Neuromuscular Unit, Department of Neuropediatrics, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Julio Montoya
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biology, Institute for Health Research of Aragón (IISAragón), University of Zaragoza, Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biology, Institute for Health Research of Aragón (IISAragón), University of Zaragoza, Zaragoza, Spain
| | - Cristina Jou
- Neuromuscular Unit, Department of Neuropediatrics, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Department of Pathology, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Glòria Garrabou
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Department of Internal Medicine, Laboratory of Muscle Research and Mitochondrial Function-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Science, University of Barcelona (UB), Hospital Clínic of Barcelona (HCB), Barcelona, Spain
| | - Josep M Grau-Junyent
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Department of Internal Medicine, Laboratory of Muscle Research and Mitochondrial Function-Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Science, University of Barcelona (UB), Hospital Clínic of Barcelona (HCB), Barcelona, Spain
| | - Dèlia Yubero
- Department of Genetics and Molecular Medicine, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Raquel Montero
- Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Jordi Muchart
- Department of Radiology, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | | | - Andrés Nascimento
- Neuromuscular Unit, Department of Neuropediatrics, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Albert Català
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Department of Hematology, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | | | - Cecilia Jimenez-Mallebrera
- Neuromuscular Unit, Department of Neuropediatrics, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Artuch
- Neuromuscular Unit, Department of Neuropediatrics, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
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9
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The Isolation and Deep Sequencing of Mitochondrial DNA. Methods Mol Biol 2021. [PMID: 34080167 DOI: 10.1007/978-1-0716-1270-5_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
In recent years, next-generation sequencing (NGS) has become a powerful tool for studying both inherited and somatic heteroplasmic mitochondrial DNA (mtDNA) variation. NGS has proved particularly powerful when combined with single-cell isolation techniques, allowing the investigation of low-level heteroplasmic variants both between cells and within tissues. Nevertheless, there remain significant challenges, especially around the selective enrichment of mtDNA from total cellular DNA and the avoidance of nuclear pseudogenes. This chapter summarizes the techniques needed to enrich, amplify, sequence, and analyse mtDNA using NGS .
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10
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Lenaers G, Neutzner A, Le Dantec Y, Jüschke C, Xiao T, Decembrini S, Swirski S, Kieninger S, Agca C, Kim US, Reynier P, Yu-Wai-Man P, Neidhardt J, Wissinger B. Dominant optic atrophy: Culprit mitochondria in the optic nerve. Prog Retin Eye Res 2021; 83:100935. [PMID: 33340656 DOI: 10.1016/j.preteyeres.2020.100935] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Dominant optic atrophy (DOA) is an inherited mitochondrial disease leading to specific degeneration of retinal ganglion cells (RGCs), thus compromising transmission of visual information from the retina to the brain. Usually, DOA starts during childhood and evolves to poor vision or legal blindness, affecting the central vision, whilst sparing the peripheral visual field. In 20% of cases, DOA presents as syndromic disorder, with secondary symptoms affecting neuronal and muscular functions. Twenty years ago, we demonstrated that heterozygous mutations in OPA1 are the most frequent molecular cause of DOA. Since then, variants in additional genes, whose functions in many instances converge with those of OPA1, have been identified by next generation sequencing. OPA1 encodes a dynamin-related GTPase imported into mitochondria and located to the inner membrane and intermembrane space. The many OPA1 isoforms, resulting from alternative splicing of three exons, form complex homopolymers that structure mitochondrial cristae, and contribute to fusion of the outer membrane, thus shaping the whole mitochondrial network. Moreover, OPA1 is required for oxidative phosphorylation, maintenance of mitochondrial genome, calcium homeostasis and regulation of apoptosis, thus making OPA1 the Swiss army-knife of mitochondria. Understanding DOA pathophysiology requires the understanding of RGC peculiarities with respect to OPA1 functions. Besides the tremendous energy requirements of RGCs to relay visual information from the eye to the brain, these neurons present unique features related to their differential environments in the retina, and to the anatomical transition occurring at the lamina cribrosa, which parallel major adaptations of mitochondrial physiology and shape, in the pre- and post-laminar segments of the optic nerve. Three DOA mouse models, with different Opa1 mutations, have been generated to study intrinsic mechanisms responsible for RGC degeneration, and these have further revealed secondary symptoms related to mitochondrial dysfunctions, mirroring the more severe syndromic phenotypes seen in a subgroup of patients. Metabolomics analyses of cells, mouse organs and patient plasma mutated for OPA1 revealed new unexpected pathophysiological mechanisms related to mitochondrial dysfunction, and biomarkers correlated quantitatively to the severity of the disease. Here, we review and synthesize these data, and propose different approaches for embracing possible therapies to fulfil the unmet clinical needs of this disease, and provide hope to affected DOA patients.
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Affiliation(s)
- Guy Lenaers
- MitoLab Team, UMR CNRS 6015 - INSERM U1083, Institut MitoVasc, Angers University and Hospital, Angers, France.
| | - Albert Neutzner
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Department of Ophthalmology University Hospital Basel, University of Basel, Basel, Switzerland.
| | - Yannick Le Dantec
- MitoLab Team, UMR CNRS 6015 - INSERM U1083, Institut MitoVasc, Angers University and Hospital, Angers, France
| | - Christoph Jüschke
- Human Genetics, Faculty VI - School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Ting Xiao
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Sarah Decembrini
- Department of Biomedicine, University Hospital Basel, University of Basel, Basel, Switzerland; Department of Ophthalmology University Hospital Basel, University of Basel, Basel, Switzerland
| | - Sebastian Swirski
- Human Genetics, Faculty VI - School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany
| | - Sinja Kieninger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Cavit Agca
- Molecular Biology, Genetics and Bioengineering Program, Sabanci University, Istanbul, Turkey; Nanotechnology Research and Application Center (SUNUM), Sabanci University, Istanbul, Turkey
| | - Ungsoo S Kim
- Kim's Eye Hospital, Seoul, South Korea; Cambridge Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK; Moorfields Eye Hospital, London, UK
| | - Pascal Reynier
- MitoLab Team, UMR CNRS 6015 - INSERM U1083, Institut MitoVasc, Angers University and Hospital, Angers, France; Department of Biochemistry, University Hospital of Angers, Angers, France
| | - Patrick Yu-Wai-Man
- Cambridge Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK; Moorfields Eye Hospital, London, UK; UCL Institute of Ophthalmology, University College London, London, UK
| | - John Neidhardt
- Human Genetics, Faculty VI - School of Medicine and Health Sciences, University of Oldenburg, Oldenburg, Germany; Research Center Neurosensory Science, University Oldenburg, Oldenburg, Germany.
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, University of Tübingen, Tübingen, Germany.
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11
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mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences. Life (Basel) 2021; 11:life11070633. [PMID: 34209862 PMCID: PMC8307225 DOI: 10.3390/life11070633] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is predominately uniparentally transmitted. This results in organisms with a single type of mtDNA (homoplasmy), but two or more mtDNA haplotypes have been observed in low frequency in several species (heteroplasmy). In this review, we aim to highlight several aspects of heteroplasmy regarding its origin and its significance on mtDNA function and evolution, which has been progressively recognized in the last several years. Heteroplasmic organisms commonly occur through somatic mutations during an individual’s lifetime. They also occur due to leakage of paternal mtDNA, which rarely happens during fertilization. Alternatively, heteroplasmy can be potentially inherited maternally if an egg is already heteroplasmic. Recent advances in sequencing techniques have increased the ability to detect and quantify heteroplasmy and have revealed that mitochondrial DNA copies in the nucleus (NUMTs) can imitate true heteroplasmy. Heteroplasmy can have significant evolutionary consequences on the survival of mtDNA from the accumulation of deleterious mutations and for its coevolution with the nuclear genome. Particularly in humans, heteroplasmy plays an important role in the emergence of mitochondrial diseases and determines the success of the mitochondrial replacement therapy, a recent method that has been developed to cure mitochondrial diseases.
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12
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Pereira CV, Gitschlag BL, Patel MR. Cellular mechanisms of mtDNA heteroplasmy dynamics. Crit Rev Biochem Mol Biol 2021; 56:510-525. [PMID: 34120542 DOI: 10.1080/10409238.2021.1934812] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Heteroplasmy refers to the coexistence of more than one variant of the mitochondrial genome (mtDNA). Mutated or partially deleted mtDNAs can induce chronic metabolic impairment and cause mitochondrial diseases when their heteroplasmy levels exceed a critical threshold. These mutant mtDNAs can be maternally inherited or can arise de novo. Compelling evidence has emerged showing that mutant mtDNA levels can vary and change in a nonrandom fashion across generations and amongst tissues of an individual. However, our lack of understanding of the basic cellular and molecular mechanisms of mtDNA heteroplasmy dynamics has made it difficult to predict who will inherit or develop mtDNA-associated diseases. More recently, with the advances in technology and the establishment of tractable model systems, insights into the mechanisms underlying the selection forces that modulate heteroplasmy dynamics are beginning to emerge. In this review, we summarize evidence from different organisms, showing that mutant mtDNA can experience both positive and negative selection. We also review the recently identified mechanisms that modulate heteroplasmy dynamics. Taken together, this is an opportune time to survey the literature and to identify key cellular pathways that can be targeted to develop therapies for diseases caused by heteroplasmic mtDNA mutations.
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Affiliation(s)
- Claudia V Pereira
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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13
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Bury AG, Vincent AE, Turnbull DM, Actis P, Hudson G. Mitochondrial isolation: when size matters. Wellcome Open Res 2021; 5:226. [PMID: 33718619 PMCID: PMC7931255 DOI: 10.12688/wellcomeopenres.16300.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial vitality is critical to cellular function, with mitochondrial dysfunction linked to a growing number of human diseases. Tissue and cellular heterogeneity, in terms of genetics, dynamics and function means that increasingly mitochondrial research is conducted at the single cell level. Whilst there are several technologies that are currently available for single-cell analysis, each with their advantages, they cannot be easily adapted to study mitochondria with subcellular resolution. Here we review the current techniques and strategies for mitochondrial isolation, critically discussing each technology's limitations for future mitochondrial research. Finally, we highlight and discuss the recent breakthroughs in sub-cellular isolation techniques, with a particular focus on nanotechnologies that enable the isolation of mitochondria from subcellular compartments. This allows isolation of mitochondria with unprecedented spatial precision with minimal disruption to mitochondria and their immediate cellular environment.
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Affiliation(s)
- Alexander G Bury
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Amy E Vincent
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Doug M Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Paolo Actis
- Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Gavin Hudson
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.,Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
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14
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Bury AG, Vincent AE, Turnbull DM, Actis P, Hudson G. Mitochondrial isolation: when size matters. Wellcome Open Res 2020; 5:226. [PMID: 33718619 PMCID: PMC7931255 DOI: 10.12688/wellcomeopenres.16300.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/23/2020] [Indexed: 01/31/2024] Open
Abstract
Mitochondrial vitality is critical to cellular function, with mitochondrial dysfunction linked to a growing number of human diseases. Tissue and cellular heterogeneity, in terms of genetics, dynamics and function means that increasingly mitochondrial research is conducted at the single cell level. Whilst there are several technologies that are currently available for single-cell analysis, each with their advantages, they cannot be easily adapted to study mitochondria with subcellular resolution. Here we review the current techniques and strategies for mitochondrial isolation, critically discussing each technology's limitations for future mitochondrial research. Finally, we highlight and discuss the recent breakthroughs in sub-cellular isolation techniques, with a particular focus on nanotechnologies that enable the isolation of mitochondria from subcellular compartments. This allows isolation of mitochondria with unprecedented spatial precision with minimal disruption to mitochondria and their immediate cellular environment.
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Affiliation(s)
- Alexander G. Bury
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Amy E. Vincent
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Doug M. Turnbull
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Paolo Actis
- Pollard Institute, School of Electronic and Electrical Engineering, University of Leeds, Leeds, LS2 9JT, UK
| | - Gavin Hudson
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
- Biosciences Institute, Medical School, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
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15
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Maeda R, Kami D, Maeda H, Shikuma A, Gojo S. High throughput single cell analysis of mitochondrial heteroplasmy in mitochondrial diseases. Sci Rep 2020; 10:10821. [PMID: 32616755 PMCID: PMC7331593 DOI: 10.1038/s41598-020-67686-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Accepted: 06/11/2020] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial heteroplasmy, which fundamentally means intracellular heterogeneity of mitochondrial DNA (mtDNA), has been measured in a group of cells, regardless of intercellular heterogeneity. Ordinal methods for mitochondrial heteroplasmy cannot discriminate between an intercellular homogenic population composed of cells with similar intracellular heterogeneity for mtDNA and an intercellular heterogenic population composed of cells with different rates of mutated mtDNA. A high-throughput method to determine mitochondrial heteroplasmy in a single cell was developed by using droplet digital PCR with TaqMan polymerase in this study. This technique revealed that there are three different cell populations of cultured fibroblasts derived from patients with mitochondrial disease carrying a mutation in the mtDNA; cells with homoplasmy of either mutated or healthy mtDNA; and cells mixed with mutated and healthy mtDNA. The presence of intercellular heterogeneity, even in uniformed cultured fibroblasts, suggests that heterogeneity should exist among different kinds of cells. The diagnosis of intercellular heterogeneity with respect to mitochondrial heteroplasmy by this methodology could provide novel insight into developing a treatment strategy for mitochondrial diseases.
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Affiliation(s)
- Ryotaro Maeda
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Daisuke Kami
- Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Hideki Maeda
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Akira Shikuma
- Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465, Kajii cho, Kamigyo ku, Kyoto, 802-8566, Japan.
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16
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Kaur P, Longley MJ, Pan H, Wang W, Countryman P, Wang H, Copeland WC. Single-molecule level structural dynamics of DNA unwinding by human mitochondrial Twinkle helicase. J Biol Chem 2020; 295:5564-5576. [PMID: 32213598 PMCID: PMC7186178 DOI: 10.1074/jbc.ra120.012795] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/24/2020] [Indexed: 11/06/2022] Open
Abstract
Knowledge of the molecular events in mitochondrial DNA (mtDNA) replication is crucial to understanding the origins of human disorders arising from mitochondrial dysfunction. Twinkle helicase is an essential component of mtDNA replication. Here, we employed atomic force microscopy imaging in air and liquids to visualize ring assembly, DNA binding, and unwinding activity of individual Twinkle hexamers at the single-molecule level. We observed that the Twinkle subunits self-assemble into hexamers and higher-order complexes that can switch between open and closed-ring configurations in the absence of DNA. Our analyses helped visualize Twinkle loading onto and unloading from DNA in an open-ringed configuration. They also revealed that closed-ring conformers bind and unwind several hundred base pairs of duplex DNA at an average rate of ∼240 bp/min. We found that the addition of mitochondrial single-stranded (ss) DNA-binding protein both influences the ways Twinkle loads onto defined DNA substrates and stabilizes the unwound ssDNA product, resulting in a ∼5-fold stimulation of the apparent DNA-unwinding rate. Mitochondrial ssDNA-binding protein also increased the estimated translocation processivity from 1750 to >9000 bp before helicase disassociation, suggesting that more than half of the mitochondrial genome could be unwound by Twinkle during a single DNA-binding event. The strategies used in this work provide a new platform to examine Twinkle disease variants and the core mtDNA replication machinery. They also offer an enhanced framework to investigate molecular mechanisms underlying deletion and depletion of the mitochondrial genome as observed in mitochondrial diseases.
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Affiliation(s)
- Parminder Kaur
- Physics Department, North Carolina State University, Raleigh, North Carolina 27695; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695.
| | - Matthew J Longley
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Hai Pan
- Physics Department, North Carolina State University, Raleigh, North Carolina 27695
| | - Wendy Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina 27695
| | - Preston Countryman
- Physics Department, North Carolina State University, Raleigh, North Carolina 27695
| | - Hong Wang
- Physics Department, North Carolina State University, Raleigh, North Carolina 27695; Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695; Toxicology Program, North Carolina State University, Raleigh, North Carolina 27695
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709.
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17
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Oliveira MT, Pontes CDB, Ciesielski GL. Roles of the mitochondrial replisome in mitochondrial DNA deletion formation. Genet Mol Biol 2020; 43:e20190069. [PMID: 32141473 PMCID: PMC7197994 DOI: 10.1590/1678-4685-gmb-2019-0069] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 08/12/2019] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletions are a common cause of human mitochondrial
diseases. Mutations in the genes encoding components of the mitochondrial
replisome, such as DNA polymerase gamma (Pol γ) and the mtDNA helicase Twinkle,
have been associated with the accumulation of such deletions and the development
of pathological conditions in humans. Recently, we demonstrated that changes in
the level of wild-type Twinkle promote mtDNA deletions, which implies that not
only mutations in, but also dysregulation of the stoichiometry between the
replisome components is potentially pathogenic. The mechanism(s) by which
alterations to the replisome function generate mtDNA deletions is(are) currently
under debate. It is commonly accepted that stalling of the replication fork at
sites likely to form secondary structures precedes the deletion formation. The
secondary structural elements can be bypassed by the replication-slippage
mechanism. Otherwise, stalling of the replication fork can generate single- and
double-strand breaks, which can be repaired through recombination leading to the
elimination of segments between the recombination sites. Here, we discuss
aberrances of the replisome in the context of the two debated outcomes, and
suggest new mechanistic explanations based on replication restart and template
switching that could account for all the deletion types reported for
patients.
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Affiliation(s)
- Marcos T Oliveira
- Universidade Estadual Paulista Júlio de Mesquita Filho, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
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18
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He J, Huang Y, Du G, Wang Z, Xiang Y, Wang Q. Lasting spatial learning and memory deficits following chronic cerebral hypoperfusion are associated with hippocampal mitochondrial aging in rats. Neuroscience 2019; 415:215-229. [DOI: 10.1016/j.neuroscience.2019.04.044] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/16/2022]
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