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Alqahtani T, Deore SL, Kide AA, Shende BA, Sharma R, Chakole RD, Nemade LS, Kale NK, Borah S, Deokar SS, Behera A, Dhawal Bhandari D, Gaikwad N, Azad AK, Ghosh A. Mitochondrial dysfunction and oxidative stress in Alzheimer's disease, and Parkinson's disease, Huntington's disease and Amyotrophic Lateral Sclerosis -An updated review. Mitochondrion 2023:S1567-7249(23)00051-X. [PMID: 37269968 DOI: 10.1016/j.mito.2023.05.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/18/2023] [Accepted: 05/27/2023] [Indexed: 06/05/2023]
Abstract
Misfolded proteins in the central nervous system can induce oxidative damage, which can contribute to neurodegenerative diseases in the mitochondria. Neurodegenerative patients face early mitochondrial dysfunction, impacting energy utilization. Amyloid-ß and tau problems both have an effect on mitochondria, which leads to mitochondrial malfunction and, ultimately, the onset of Alzheimer's disease. Cellular oxygen interaction yields reactive oxygen species within mitochondria, initiating oxidative damage to mitochondrial constituents. Parkinson's disease, linked to oxidative stress, α-synuclein aggregation, and inflammation, results from reduced brain mitochondria activity. Mitochondrial dynamics profoundly influence cellular apoptosis via distinct causative mechanisms. The condition known as Huntington's disease is characterized by an expansion of polyglutamine, primarily impactingthe cerebral cortex and striatum. Research has identified mitochondrial failure as an early pathogenic mechanism contributing to HD's selective neurodegeneration. The mitochondria are organelles that exhibit dynamism by undergoing fragmentation and fusion processes to attain optimal bioenergetic efficiency. They can also be transported along microtubules and regulateintracellular calcium homeostasis through their interaction with the endoplasmic reticulum. Additionally, the mitochondria produce free radicals. The functions of eukaryotic cells, particularly in neurons, have significantly deviated from the traditionally assigned role of cellular energy production. Most of them areimpaired in HD, which may lead to neuronal dysfunction before symptoms manifest. This article summarises the most important changes in mitochondrial dynamics that come from neurodegenerative diseases including Alzheimer's, Parkinson's, Huntington's and Amyotrophic Lateral Sclerosis. Finally, we discussed about novel techniques that can potentially treat mitochondrial malfunction and oxidative stress in four most dominating neuro disorders.
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Affiliation(s)
- Taha Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia.
| | | | | | | | - Ritika Sharma
- University institute of pharma sciences, Chandigarh University, Mohali, Punjab.
| | - Rita Dadarao Chakole
- Government College of Pharmacy Vidyanagar Karad Dist Satara Maharashtra Pin 415124.
| | - Lalita S Nemade
- Govindrao Nikam College of Pharmacy Sawarde Maharashtra 415606.
| | | | - Sudarshana Borah
- Department of Pharmacognosy, University of Science and Technology Meghalaya Technocity, Ri-Bhoi District Meghalaya.
| | | | - Ashok Behera
- Faculty of Pharmacy, DIT University, Dehradun,Uttarakhand.
| | - Divya Dhawal Bhandari
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014. India.
| | - Nikita Gaikwad
- Department of Pharmaceutics, P.E.S. Modern College of Pharmacy, Nigdi, Pune-411044.
| | - Abul Kalam Azad
- Faculty of Pharmacy MAHSA University Bandar Saujana putra, 42610, Selangor, Malaysia
| | - Arabinda Ghosh
- Department of Botany, Gauhati University, Guwahati, 781014, Assam, India
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Yang Z, Slone J, Huang T. Next-Generation Sequencing to Characterize Mitochondrial Genomic DNA Heteroplasmy. Curr Protoc 2022; 2:e412. [PMID: 35532282 DOI: 10.1002/cpz1.412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mitochondria play a very important role in many crucial cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondrial genomes. Mutant and wild-type mitochondrial DNA (mtDNA) may co-exist as heteroplasmy and cause human disease. The purpose of the protocols in this article is to simultaneously determine the mtDNA sequence and quantify the heteroplasmy level using parallel sequencing. The protocols include mitochondrial genomic DNA PCR amplification of two full-length products using two distinct sets of PCR primers. The PCR products are mixed at an equimolar ratio, and the samples are then barcoded and sequenced with high-throughput next-generation sequencing technology. This technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the degree/level of heteroplasmy. © 2022 Wiley Periodicals LLC. Basic Protocol 1: PCR amplification of mitochondrial DNA Basic Protocol 2: Analysis of next-generation sequencing of mitochondrial DNA Basic Protocol 3: Mutect2 pipeline for automated sample processing and large-scale data analysis.
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Affiliation(s)
- Zeyu Yang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Jesse Slone
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Taosheng Huang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
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Barcia G, Assouline Z, Magen M, Pennisi A, Rötig A, Munnich A, Bonnefont JP, Steffann J. Improving post-natal detection of mitochondrial DNA mutations. Expert Rev Mol Diagn 2020; 20:1003-1008. [PMID: 32902337 DOI: 10.1080/14737159.2020.1820326] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Currently, genetic testing of mitochondrial DNA mutations includes screening for single-nucleotide variants, several base pair insertions or deletions, large-scale deletions, or relative depletion of total mitochondrial DNA content. Within the last decade, next-generation sequencing (NGS) has resulted in remarkable advances in the field of mitochondrial diseases (MD) and has become a routine step of the diagnostic workup. AREAS COVERED We aimed to present an overview of current technologies employed in molecular diagnosis of mitochondrial DNA diseases. We report on the recent contributions of NGS testing to the diagnosis and understanding of MD. EXPERT OPINION The progress of NGS technologies allows the simultaneous detection of mutations and quantification of the heteroplasmy level, ensuring sensitivity and specificity requested for the detection of mitochondrial DNA point mutations. NGS protocols enabling the simultaneous analysis of mitochondrial and nuclear DNA are now efficient and cost-saving approaches, and have become the gold-standard technique in diagnostic laboratories.
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Affiliation(s)
- Giulia Barcia
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Zahra Assouline
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Maryse Magen
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France
| | - Alessandra Pennisi
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Agnès Rötig
- Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Arnold Munnich
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Jean-Paul Bonnefont
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
| | - Julie Steffann
- Université de Paris et Service de Génétique Moléculaire, Reference Center for Mitochondrial Diseases (CARAMMEL), Groupe Hospitalier Necker Enfants Malades, Assistance Publique-Hôpitaux de Paris , Paris, France.,Laboratory for Genetics of Mitochondrial Disorders, INSERM U1163, Université Paris Descartes-Sorbonne Paris Cité, Institut Imagine , Paris, France
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4
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Tabebi M, Safi W, Felhi R, Alila Fersi O, Keskes L, Abid M, Mnif M, Fakhfakh F. The first concurrent detection of mitochondrial DNA m.3243A>G mutation, deletion, and depletion in a family with mitochondrial diabetes. Mol Genet Genomic Med 2020; 8:e1292. [PMID: 32394641 PMCID: PMC7336730 DOI: 10.1002/mgg3.1292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mitochondrial diabetes (MD) is a rare monogenic form of diabetes and divided into type l and type 2. It is characterized by a strong familial clustering of diabetes with the presence of maternal transmission in conjunction with bilateral hearing impairment in most of the carriers. The most common form of MD is associated with the m.3243A>G mutation in the mitochondrial MT-TL1, but there are also association with a range of other point mutations, deletion, and depletion in mtDNA. METHODS The mitochondrial genome anomalies were investigated in a family with clinical features of MD, which includes a proband presenting severe MD conditions including cardiomyopathy, retinopathy, and psychomotor retardation. RESULTS By investigating the patient's blood leukocytes and skeletal muscle, we identified the m.3243A>G mutation in heteroplasmic state. This mutation was absent in the rest of the family members. In addition, our analysis revealed in the proband a large mtDNA heteroplasmic deletion (~1 kb) and a reduction in mtDNA copy number. CONCLUSION Our study points out, for the first time, a severe phenotypic expression of the m.3243A>G point mutation in association with mtDNA deletion and depletion in MD.
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Affiliation(s)
- Mouna Tabebi
- Molecular and Functional Genetics Laboratory, Faculty of Science of Sfax, University of Sfax, Sfax, Tunisia.,Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Wajdi Safi
- Department of Endocrinology Diabetology, CHU Hedi Chaker, Sfax, Tunisia
| | - Rahma Felhi
- Molecular and Functional Genetics Laboratory, Faculty of Science of Sfax, University of Sfax, Sfax, Tunisia
| | - Olfa Alila Fersi
- Molecular and Functional Genetics Laboratory, Faculty of Science of Sfax, University of Sfax, Sfax, Tunisia
| | - Leila Keskes
- Human Molecular Genetics Laboratory, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Mohamed Abid
- Department of Endocrinology Diabetology, CHU Hedi Chaker, Sfax, Tunisia
| | - Mouna Mnif
- Department of Endocrinology Diabetology, CHU Hedi Chaker, Sfax, Tunisia
| | - Faiza Fakhfakh
- Molecular and Functional Genetics Laboratory, Faculty of Science of Sfax, University of Sfax, Sfax, Tunisia
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Malik AN, Rosa HS, S. de Menezes E, Tamang P, Hamid Z, Naik A, Parsade CK, Sivaprasad S. The Detection and Partial Localisation of Heteroplasmic Mutations in the Mitochondrial Genome of Patients with Diabetic Retinopathy. Int J Mol Sci 2019; 20:ijms20246259. [PMID: 31835862 PMCID: PMC6940788 DOI: 10.3390/ijms20246259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/27/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022] Open
Abstract
Diabetic retinopathy (DR) is a common complication of diabetes and a major cause of acquired blindness in adults. Mitochondria are cellular organelles involved in energy production which contain mitochondrial DNA (mtDNA). We previously showed that levels of circulating mtDNA were dysregulated in DR patients, and there was some evidence of mtDNA damage. In the current project, our aim was to confirm the presence of, and determine the location and prevalence of, mtDNA mutation in DR. DNA isolated from peripheral blood from diabetes patients (n = 59) with and without DR was used to amplify specific mtDNA regions which were digested with surveyor nuclease S1 to determine the presence and location of heteroplasmic mtDNA mutations were present. An initial screen of the entire mtDNA genome of 6 DR patients detected a higher prevalence of mutations in amplicon P, covering nucleotides 14,443 to 1066 and spanning the control region. Further analysis of 42 subjects showed the presence of putative mutations in amplicon P in 36% (14/39) of DR subjects and in 10% (2/20) non-DR subjects. The prevalence of mutations in DR was not related to the severity of the disease. The detection of a high-prevalence of putative mtDNA mutations within a specific region of the mitochondrial genome supports the view that mtDNA damage contributes to DR. The exact location and functional impact of these mutations remains to be determined.
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Affiliation(s)
- Afshan N. Malik
- Department of Diabetes, School of Life Course Sciences, Faculty of Life Science and Medicine, King’s College London, London SE1 1UL, UK
- Correspondence: ; Tel.: +44-207-848-6271
| | - Hannah S. Rosa
- Department of Diabetes, School of Life Course Sciences, Faculty of Life Science and Medicine, King’s College London, London SE1 1UL, UK
| | - Eliane S. de Menezes
- Department of Diabetes, School of Life Course Sciences, Faculty of Life Science and Medicine, King’s College London, London SE1 1UL, UK
| | - Priyanka Tamang
- Department of Diabetes, School of Life Course Sciences, Faculty of Life Science and Medicine, King’s College London, London SE1 1UL, UK
| | - Zaidi Hamid
- Department of Diabetes, School of Life Course Sciences, Faculty of Life Science and Medicine, King’s College London, London SE1 1UL, UK
| | - Anita Naik
- Department of Diabetes, School of Life Course Sciences, Faculty of Life Science and Medicine, King’s College London, London SE1 1UL, UK
| | - Chandani Kiran Parsade
- Department of Diabetes, School of Life Course Sciences, Faculty of Life Science and Medicine, King’s College London, London SE1 1UL, UK
| | - Sobha Sivaprasad
- NIHR Moorfields Biomedical Research Centre, Moorfields Eye Hospital, London EC1V 2PD, UK
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Filer JE, Channon RB, Henry CS, Geiss BJ. A Nuclease Protection ELISA Assay for Colorimetric and Electrochemical Detection of Nucleic Acids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2019; 11:1027-1034. [PMID: 31656535 PMCID: PMC6814143 DOI: 10.1039/c8ay02729c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Early and accurate diagnosis is crucial to monitor infection outcomes and provide timely interventions. However, gold standard polymerase chain reaction assays (PCR) are labor-intensive and require expensive reagents and instrumentation. Nuclease protection has been used for decades to detect and quantify nucleic acid but has not yet been investigated as a diagnostic tool for infectious disease. In this work, we describe a nuclease protection enzyme-linked immunosorbent assay (NP-ELISA) for accurate and sensitive detection of nucleic acid. Briefly, binding of a nucleic acid target to an oligo probe protects it from digestion of un-hybridized nucleic acid by S1 nuclease. Following the workflow of an ELISA, a horseradish peroxidase (HRP)-conjugated antibody binds the probe and oxidizes its substrate to generate signal. The assay was validated with three HRP substrates for absorbance, chemiluminescence, and electrochemical readouts, demonstrating great versatility. Electrochemical detection with 3,3',5,5'-Tetramethylbenzidine (TMB) gave the highest assay sensitivity with a limit of detection of 3.72×103 molecules mL-1. Furthermore, non-complementary targets did not generate a response, indicating a high degree of specificity. This proof of principle serves as a stepping stone towards developing miniaturized, multiplexed nuclease protection assays for point-of-care diagnosis.
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Affiliation(s)
- Jessica E. Filer
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO 80523, USA
| | - Robert B. Channon
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Charles S. Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
| | - Brian J. Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
- School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523, USA
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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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Abicht A, Scharf F, Kleinle S, Schön U, Holinski-Feder E, Horvath R, Benet-Pagès A, Diebold I. Mitochondrial and nuclear disease panel (Mito-aND-Panel): Combined sequencing of mitochondrial and nuclear DNA by a cost-effective and sensitive NGS-based method. Mol Genet Genomic Med 2018; 6:1188-1198. [PMID: 30406974 PMCID: PMC6305657 DOI: 10.1002/mgg3.500] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 01/21/2023] Open
Abstract
Background The diagnosis of mitochondrial disorders is challenging because of the clinical variability and genetic heterogeneity of these conditions. Next‐Generation Sequencing (NGS) technology offers a robust high‐throughput platform for nuclear and mitochondrial DNA (mtDNA) analyses. Method We developed a custom Agilent SureSelect Mitochondrial and Nuclear Disease Panel (Mito‐aND‐Panel) capture kit that allows parallel enrichment for subsequent NGS‐based sequence analysis of nuclear mitochondrial disease‐related genes and the complete mtDNA genome. Sequencing of enriched mtDNA simultaneously with nuclear genes was compared with the separated sequencing of the mitochondrial genome and whole exome sequencing (WES). Results The Mito‐aND‐Panel permits accurate detection of low‐level mtDNA heteroplasmy due to a very high sequencing depth compared to standard diagnostic procedures using Sanger sequencing/SNaPshot and WES which is crucial to identify maternally inherited mitochondrial disorders. Conclusion We established a NGS‐based method with combined sequencing of the complete mtDNA and nuclear genes which enables a more sensitive heteroplasmy detection of mtDNA mutations compared to traditional methods. Because the method promotes the analysis of mtDNA variants in large cohorts, it is cost‐effective and simple to setup, we anticipate this is a highly relevant method for sequence‐based genetic diagnosis in clinical diagnostic applications.
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Affiliation(s)
- Angela Abicht
- Medical Genetic Center Munich, Munich, Germany.,Department of Neurology, Friedrich-Baur-Institute, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
| | | | | | | | | | - Rita Horvath
- Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
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Koval T, Dohnálek J. Characteristics and application of S1–P1 nucleases in biotechnology and medicine. Biotechnol Adv 2018; 36:603-612. [DOI: 10.1016/j.biotechadv.2017.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 12/18/2022]
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10
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Albayrak L, Khanipov K, Pimenova M, Golovko G, Rojas M, Pavlidis I, Chumakov S, Aguilar G, Chávez A, Widger WR, Fofanov Y. The ability of human nuclear DNA to cause false positive low-abundance heteroplasmy calls varies across the mitochondrial genome. BMC Genomics 2016; 17:1017. [PMID: 27955616 PMCID: PMC5153897 DOI: 10.1186/s12864-016-3375-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 12/05/2016] [Indexed: 02/03/2023] Open
Abstract
Background Low-abundance mutations in mitochondrial populations (mutations with minor allele frequency ≤ 1%), are associated with cancer, aging, and neurodegenerative disorders. While recent progress in high-throughput sequencing technology has significantly improved the heteroplasmy identification process, the ability of this technology to detect low-abundance mutations can be affected by the presence of similar sequences originating from nuclear DNA (nDNA). To determine to what extent nDNA can cause false positive low-abundance heteroplasmy calls, we have identified mitochondrial locations of all subsequences that are common or similar (one mismatch allowed) between nDNA and mitochondrial DNA (mtDNA). Results Performed analysis revealed up to a 25-fold variation in the lengths of longest common and longest similar (one mismatch allowed) subsequences across the mitochondrial genome. The size of the longest subsequences shared between nDNA and mtDNA in several regions of the mitochondrial genome were found to be as low as 11 bases, which not only allows using these regions to design new, very specific PCR primers, but also supports the hypothesis of the non-random introduction of mtDNA into the human nuclear DNA. Conclusion Analysis of the mitochondrial locations of the subsequences shared between nDNA and mtDNA suggested that even very short (36 bases) single-end sequencing reads can be used to identify low-abundance variation in 20.4% of the mitochondrial genome. For longer (76 and 150 bases) reads, the proportion of the mitochondrial genome where nDNA presence will not interfere found to be 44.5 and 67.9%, when low-abundance mutations at 100% of locations can be identified using 417 bases long single reads. This observation suggests that the analysis of low-abundance variations in mitochondria population can be extended to a variety of large data collections such as NCBI Sequence Read Archive, European Nucleotide Archive, The Cancer Genome Atlas, and International Cancer Genome Consortium. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3375-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Levent Albayrak
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.,Department of Computer Science, University of Houston, Houston, TX, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.,Department of Computer Science, University of Houston, Houston, TX, USA
| | - Maria Pimenova
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - George Golovko
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Mark Rojas
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA.,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA
| | - Ioannis Pavlidis
- Department of Computer Science, University of Houston, Houston, TX, USA
| | - Sergei Chumakov
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Gerardo Aguilar
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Arturo Chávez
- Department of Physics, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - William R Widger
- Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, 77555-0144, USA. .,Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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Webber BR, Osborn MJ, McElroy AN, Twaroski K, Lonetree CL, DeFeo AP, Xia L, Eide C, Lees CJ, McElmurry RT, Riddle MJ, Kim CJ, Patel DD, Blazar BR, Tolar J. CRISPR/Cas9-based genetic correction for recessive dystrophic epidermolysis bullosa. NPJ Regen Med 2016; 1. [PMID: 28250968 PMCID: PMC5328670 DOI: 10.1038/npjregenmed.2016.14] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Recessive dystrophic epidermolysis bullosa (RDEB) is a severe disorder caused by mutations to the COL7A1 gene that deactivate production of a structural protein essential for skin integrity. Haematopoietic cell transplantation can ameliorate some of the symptoms; however, significant side effects from the allogeneic transplant procedure can occur and unresponsive areas of blistering persist. Therefore, we employed genome editing in patient-derived cells to create an autologous platform for multilineage engineering of therapeutic cell types. The clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 system facilitated correction of an RDEB-causing COL7A1 mutation in primary fibroblasts that were then used to derive induced pluripotent stem cells (iPSCs). The resulting iPSCs were subsequently re-differentiated into keratinocytes, mesenchymal stem cells (MSCs) and haematopoietic progenitor cells using defined differentiation strategies. Gene-corrected keratinocytes exhibited characteristic epithelial morphology and expressed keratinocyte-specific genes and transcription factors. iPSC-derived MSCs exhibited a spindle morphology and expression of CD73, CD90 and CD105 with the ability to undergo adipogenic, chondrogenic and osteogenic differentiation in vitro in a manner indistinguishable from bone marrow-derived MSCs. Finally, we used a vascular induction strategy to generate potent definitive haematopoietic progenitors capable of multilineage differentiation in methylcellulose-based assays. In totality, we have shown that CRISPR/Cas9 is an adaptable gene-editing strategy that can be coupled with iPSC technology to produce multiple gene-corrected autologous cell types with therapeutic potential for RDEB.
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Affiliation(s)
- Beau R Webber
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Mark J Osborn
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.,Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA.,Asan-Minnesota Institute for Innovating Transplantation, Seoul, Republic of Korea
| | - Amber N McElroy
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Kirk Twaroski
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Cara-Lin Lonetree
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Anthony P DeFeo
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Lily Xia
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Cindy Eide
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Christopher J Lees
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Ron T McElmurry
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Megan J Riddle
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Chong Jai Kim
- Asan-Minnesota Institute for Innovating Transplantation, Seoul, Republic of Korea
| | - Dharmeshkumar D Patel
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Bruce R Blazar
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Jakub Tolar
- Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN, USA.,Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA.,Asan-Minnesota Institute for Innovating Transplantation, Seoul, Republic of Korea
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12
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Comeron JM, Reed J, Christie M, Jacobs JS, Dierdorff J, Eberl DF, Manak JR. A Mismatch EndoNuclease Array-Based Methodology (MENA) for Identifying Known SNPs or Novel Point Mutations. MICROARRAYS (BASEL, SWITZERLAND) 2016; 5:E7. [PMID: 27600073 PMCID: PMC5003483 DOI: 10.3390/microarrays5020007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/21/2016] [Accepted: 03/30/2016] [Indexed: 11/30/2022]
Abstract
Accurate and rapid identification or confirmation of single nucleotide polymorphisms (SNPs), point mutations and other human genomic variation facilitates understanding the genetic basis of disease. We have developed a new methodology (called MENA (Mismatch EndoNuclease Array)) pairing DNA mismatch endonuclease enzymology with tiling microarray hybridization in order to genotype both known point mutations (such as SNPs) as well as identify previously undiscovered point mutations and small indels. We show that our assay can rapidly genotype known SNPs in a human genomic DNA sample with 99% accuracy, in addition to identifying novel point mutations and small indels with a false discovery rate as low as 10%. Our technology provides a platform for a variety of applications, including: (1) genotyping known SNPs as well as confirming newly discovered SNPs from whole genome sequencing analyses; (2) identifying novel point mutations and indels in any genomic region from any organism for which genome sequence information is available; and (3) screening panels of genes associated with particular diseases and disorders in patient samples to identify causative mutations. As a proof of principle for using MENA to discover novel mutations, we report identification of a novel allele of the beethoven (btv) gene in Drosophila, which encodes a ciliary cytoplasmic dynein motor protein important for auditory mechanosensation.
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Affiliation(s)
- Josep M Comeron
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
- Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.
| | - Jordan Reed
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Matthew Christie
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Julia S Jacobs
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Jason Dierdorff
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
| | - Daniel F Eberl
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
- Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.
| | - J Robert Manak
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA.
- Graduate Program in Genetics, University of Iowa, Iowa City, IA 52242, USA.
- Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA.
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Bannwarth S, Berg-Alonso L, Augé G, Fragaki K, Kolesar JE, Lespinasse F, Lacas-Gervais S, Burel-Vandenbos F, Villa E, Belmonte F, Michiels JF, Ricci JE, Gherardi R, Harrington L, Kaufman BA, Paquis-Flucklinger V. Inactivation of Pif1 helicase causes a mitochondrial myopathy in mice. Mitochondrion 2016; 30:126-37. [PMID: 26923168 DOI: 10.1016/j.mito.2016.02.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022]
Abstract
Mutations in genes coding for mitochondrial helicases such as TWINKLE and DNA2 are involved in mitochondrial myopathies with mtDNA instability in both human and mouse. We show that inactivation of Pif1, a third member of the mitochondrial helicase family, causes a similar phenotype in mouse. pif1-/- animals develop a mitochondrial myopathy with respiratory chain deficiency. Pif1 inactivation is responsible for a deficiency to repair oxidative stress-induced mtDNA damage in mouse embryonic fibroblasts that is improved by complementation with mitochondrial isoform mPif1(67). These results open new perspectives for the exploration of patients with mtDNA instability disorders.
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Affiliation(s)
- Sylvie Bannwarth
- IRCAN, CNRS UMR 7284/INSERM U1081/UNS, Faculté de Médecine, Nice, France; Service de Génétique Médicale, Hôpital Archet 2, CHU de Nice, Nice, France
| | | | - Gaëlle Augé
- IRCAN, CNRS UMR 7284/INSERM U1081/UNS, Faculté de Médecine, Nice, France; Service de Génétique Médicale, Hôpital Archet 2, CHU de Nice, Nice, France
| | - Konstantina Fragaki
- IRCAN, CNRS UMR 7284/INSERM U1081/UNS, Faculté de Médecine, Nice, France; Service de Génétique Médicale, Hôpital Archet 2, CHU de Nice, Nice, France
| | - Jill E Kolesar
- Department of Medicine, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, USA
| | | | - Sandra Lacas-Gervais
- Centre Commun de Microscopie Electronique Appliquée, Faculté des Sciences, Université de Nice Sophia Antipolis, Nice, France
| | | | - Elodie Villa
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), équipe "contrôle métabolique des morts cellulaires", Nice Sophia-Antipolis University, France
| | - Frances Belmonte
- Department of Medicine, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, USA
| | | | - Jean-Ehrland Ricci
- INSERM U1065, Centre Méditerranéen de Médecine Moléculaire (C3M), équipe "contrôle métabolique des morts cellulaires", Nice Sophia-Antipolis University, France
| | | | - Lea Harrington
- Université de Montréal, Institut de Recherche en Immunologie et en Cancérologie, 2950 chemin de Polytechnique, Montréal, Québec H3T 1J4, Canada
| | - Brett A Kaufman
- Department of Medicine, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Véronique Paquis-Flucklinger
- IRCAN, CNRS UMR 7284/INSERM U1081/UNS, Faculté de Médecine, Nice, France; Service de Génétique Médicale, Hôpital Archet 2, CHU de Nice, Nice, France.
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Efficient introgression of allelic variants by embryo-mediated editing of the bovine genome. Sci Rep 2015; 5:11735. [PMID: 26156133 PMCID: PMC4496724 DOI: 10.1038/srep11735] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 05/12/2015] [Indexed: 12/29/2022] Open
Abstract
The recent development of designer nucleases allows for the efficient and precise introduction of genetic change into livestock genomes. Most studies so far have focused on the introduction of random mutations in cultured cells and the use of nuclear transfer to generate animals with edited genotypes. To circumvent the intrinsic uncertainties of random mutations and the inefficiencies of nuclear transfer we directed our efforts to the introduction of specific genetic changes by homology-driven repair directly in in vitro produced embryos. Initially, we injected zinc finger nuclease (ZFN)-encoding mRNA or DNA into bovine zygotes to verify cleavage activity at their target site within the gene for beta-lactoglobulin (LGB) and detected ZFN-induced random mutations in 30% to 80% of embryos. Next, to precisely change the LGB sequence, we co-injected ZFNs or transcription activator-like effector nucleases (TALENs) with DNA oligonucleotides (ODNs). Analysis of co-injected embryos showed targeted changes in up to 33% (ZFNs) and 46% (TALENs) of blastocysts. Deep sequence analysis of selected embryos revealed contributions of the targeted LGB allele can reach 100% which implies that genome editing by zygote injections can facilitate the one-step generation of non-mosaic livestock animals with pre-designed biallelic modifications.
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15
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Deng H, Shen W, Gao Z. Colorimetric detection of single nucleotide polymorphisms in the presence of 10 3 - fold excess of a wild-type gene. Biosens Bioelectron 2015; 68:310-315. [DOI: 10.1016/j.bios.2015.01.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/05/2015] [Accepted: 01/07/2015] [Indexed: 12/18/2022]
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Quantitative assessment of heteroplasmy of mitochondrial genome: perspectives in diagnostics and methodological pitfalls. BIOMED RESEARCH INTERNATIONAL 2014; 2014:292017. [PMID: 24818137 PMCID: PMC4003915 DOI: 10.1155/2014/292017] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/14/2014] [Indexed: 11/17/2022]
Abstract
The role of alterations of mitochondrial DNA (mtDNA) in the development of human pathologies is not understood well. Most of mitochondrial mutations are characterized by the phenomenon of heteroplasmy which is defined as the presence of a mixture of more than one type of an organellar genome within a cell or tissue. The level of heteroplasmy varies in wide range, and the expression of disease is dependent on the percent of alleles bearing mutations, thus allowing consumption that an upper threshold level may exist beyond which the mitochondrial function collapses. Recent findings have demonstrated that some mtDNA heteroplasmic mutations are associated with widely spread chronic diseases, including atherosclerosis and cancer. Actually, each etiological mtDNA mutation has its own heteroplasmy threshold that needs to be measured. Therefore, quantitative evaluation of a mutant allele of mitochondrial genome is an obvious methodological challenge, since it may be a keystone for diagnostics of individual genetic predisposition to the disease. This review provides a comprehensive comparison of methods applicable to the measurement of heteroplasmy level of mitochondrial mutations associated with the development of pathology, in particular, in atherosclerosis and its clinical manifestations.
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Abstract
Alzheimer’s disease (AD) is a complex and heterogeneous neurodegenerative disorder, classified as either early onset (under 65 years of age), or late onset (over 65 years of age). Three main genes are involved in early onset AD: amyloid precursor protein (APP), presenilin 1 (PSEN1), and presenilin 2 (PSEN2). The apolipoprotein E (APOE) E4 allele has been found to be a main risk factor for late-onset Alzheimer’s disease. Additionally, genome-wide association studies (GWASs) have identified several genes that might be potential risk factors for AD, including clusterin (CLU), complement receptor 1 (CR1), phosphatidylinositol binding clathrin assembly protein (PICALM), and sortilin-related receptor (SORL1). Recent studies have discovered additional novel genes that might be involved in late-onset AD, such as triggering receptor expressed on myeloid cells 2 (TREM2) and cluster of differentiation 33 (CD33). Identification of new AD-related genes is important for better understanding of the pathomechanisms leading to neurodegeneration. Since the differential diagnoses of neurodegenerative disorders are difficult, especially in the early stages, genetic testing is essential for diagnostic processes. Next-generation sequencing studies have been successfully used for detecting mutations, monitoring the epigenetic changes, and analyzing transcriptomes. These studies may be a promising approach toward understanding the complete genetic mechanisms of diverse genetic disorders such as AD.
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Affiliation(s)
- Eva Bagyinszky
- Department of BioNano Technology Gachon University, Gyeonggi-do, South Korea
| | - Young Chul Youn
- Department of Neurology, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Seong Soo A An
- Department of BioNano Technology Gachon University, Gyeonggi-do, South Korea
| | - SangYun Kim
- Department of Neurology, Seoul National University Budang Hospital, Gyeonggi-do, South Korea
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18
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Rio M, Lebre AS, Rötig A, Munnich A. Approccio diagnostico delle citopatie mitocondriali del bambino. Neurologia 2014. [DOI: 10.1016/s1634-7072(14)66665-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Bannwarth S, Procaccio V, Lebre AS, Jardel C, Chaussenot A, Hoarau C, Maoulida H, Charrier N, Gai X, Xie HM, Ferre M, Fragaki K, Hardy G, Mousson de Camaret B, Marlin S, Dhaenens CM, Slama A, Rocher C, Paul Bonnefont J, Rötig A, Aoutil N, Gilleron M, Desquiret-Dumas V, Reynier P, Ceresuela J, Jonard L, Devos A, Espil-Taris C, Martinez D, Gaignard P, Le Quan Sang KH, Amati-Bonneau P, Falk MJ, Florentz C, Chabrol B, Durand-Zaleski I, Paquis-Flucklinger V. Prevalence of rare mitochondrial DNA mutations in mitochondrial disorders. J Med Genet 2013; 50:704-14. [PMID: 23847141 PMCID: PMC3786640 DOI: 10.1136/jmedgenet-2013-101604] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background Mitochondrial DNA (mtDNA) diseases are rare disorders whose prevalence is estimated around 1 in 5000. Patients are usually tested only for deletions and for common mutations of mtDNA which account for 5–40% of cases, depending on the study. However, the prevalence of rare mtDNA mutations is not known. Methods We analysed the whole mtDNA in a cohort of 743 patients suspected of manifesting a mitochondrial disease, after excluding deletions and common mutations. Both heteroplasmic and homoplasmic variants were identified using two complementary strategies (Surveyor and MitoChip). Multiple correspondence analyses followed by hierarchical ascendant cluster process were used to explore relationships between clinical spectrum, age at onset and localisation of mutations. Results 7.4% of deleterious mutations and 22.4% of novel putative mutations were identified. Pathogenic heteroplasmic mutations were more frequent than homoplasmic mutations (4.6% vs 2.8%). Patients carrying deleterious mutations showed symptoms before 16 years of age in 67% of cases. Early onset disease (<1 year) was significantly associated with mutations in protein coding genes (mainly in complex I) while late onset disorders (>16 years) were associated with mutations in tRNA genes. MTND5 and MTND6 genes were identified as ‘hotspots’ of mutations, with Leigh syndrome accounting for the large majority of associated phenotypes. Conclusions Rare mitochondrial DNA mutations probably account for more than 7.4% of patients with respiratory chain deficiency. This study shows that a comprehensive analysis of mtDNA is essential, and should include young children, for an accurate diagnosis that is now accessible with the development of next generation sequencing technology.
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Affiliation(s)
- Sylvie Bannwarth
- IRCAN, CNRS UMR 7284/Inserm U1081/UNS, Faculté de Médecine, Nice, France
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The human MSH5 (MutS Homolog 5) protein localizes to mitochondria and protects the mitochondrial genome from oxidative damage. Mitochondrion 2012; 12:654-65. [DOI: 10.1016/j.mito.2012.07.111] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Revised: 07/14/2012] [Accepted: 07/20/2012] [Indexed: 01/07/2023]
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Fragaki K, Ait-El-Mkadem S, Chaussenot A, Gire C, Mengual R, Bonesso L, Bénéteau M, Ricci JE, Desquiret-Dumas V, Procaccio V, Rötig A, Paquis-Flucklinger V. Refractory epilepsy and mitochondrial dysfunction due to GM3 synthase deficiency. Eur J Hum Genet 2012; 21:528-34. [PMID: 22990144 DOI: 10.1038/ejhg.2012.202] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We report two children, born from consanguineous parents, who presented with early-onset refractory epilepsy associated with psychomotor delay, failure to thrive, blindness and deafness. Polarographic and spectrophotometric analyses in fibroblasts and liver revealed a respiratory chain (RC) dysfunction. Surprisingly, we identified a homozygous nonsense mutation in the GM3 synthase gene by using exome sequencing. GM3 synthase catalyzes the formation of GM3 ganglioside from lactosylceramide, which is the first step in the synthesis of complex ganglioside species. Mass spectrometry analysis revealed that the complete absence of GM3 ganglioside and its biosynthetic derivatives was associated with an upregulation of the alternative globoside pathway in fibroblasts. The accumulation of Gb3 and Gb4 globosides likely has a role in RC dysfunction and in the decrease of mitochondrial membrane potential leading to apoptosis, which we observed in fibroblasts. We show for the first time that GM3 synthase deficiency, responsible for early-onset epilepsy syndrome, leads to a secondary RC dysfunction. Our study highlights the role of secondary mitochondrial disorders that can interfere with the diagnosis and the evolution of other metabolic diseases.
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Affiliation(s)
- Konstantina Fragaki
- Department of Medical Genetics, National Center for Mitochondrial diseases, Nice Teaching Hospital, Nice, France
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Procaccio V, Neckelmann N, Paquis-Flucklinger V, Bannwarth S, Jimenez R, Davila A, Poole JC, Wallace DC. Detection of Low Levels of the Mitochondrial tRNALeu(UUR) 3243A>G Mutation in Blood Derived from Patients with Diabetes. Mol Diagn Ther 2012; 10:381-9. [PMID: 17154655 DOI: 10.1007/bf03256215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Mutations in the human mitochondrial genome have been suspected to play a significant role in the etiological development of mitochondrial diabetes. Detection of the 3243A>G mutation in the mitochondrial transfer RNALeu(UUR) gene (MTTL1), especially at low heteroplasmy levels, is highly desirable since it facilitates the diagnosis and subsequent management of the disease. The proportions of mutant mitochondrial DNA (mtDNA) can vary between tissues and are usually significantly higher in muscle than in blood, but muscle biopsies from patients with diabetes are rarely available. METHODS Here, we describe a technique that can not only determine the presence of MTTL1 3243A>G, but can also estimate the percentage of mutant DNA. The technique is based on the use of the WAVE system for the high-performance liquid chromatography (HPLC)-mediated analysis of mutation-specific restriction fragments derived from mutant PCR amplicons. PCR amplicon restriction fragment analysis by HPLC (PARFAH) can also be used for the detection of other mutations. RESULTS This PARFAH analytical approach led to the discovery of the 3243A>G mutation in blood samples from a series of patients who had initially been reported to lack the mutation, even though matrilineal relatives had been shown to harbor the mutation associated with maternally inherited diabetes and deafness (MIDD) or mitochondrial myopathy encephalopathy lactic acidosis stroke-like episodes (MELAS) phenotypes. We have established that the PARFAH method can reliably detect as little as 1% mutant DNA in a sample, which would normally be missed by commonly used gel electrophoresis or sequencing methods. CONCLUSIONS The PARFAH method not only provides a sensitive, high-throughput, and cost-effective strategy for the detection of low levels of mtDNA mutations in peripheral tissues, but also facilitates the estimation of the percentage of mutant DNA in the sample. The fact that samples can be readily obtained from peripheral tissues in many cases will avoid the need for invasive muscle biopsies. Our ability to detect low levels of mtDNA mutations in blood samples of carriers will allow us to reassess the prevalence of the MTTL1 3243A>G mutation in patients with diabetes.
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Affiliation(s)
- Vincent Procaccio
- Center for Molecular and Mitochondrial Medicine and Genetics, Department of Pediatrics, University of California, Irvine, California 92697, USA.
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Bannwarth S, Abbassi M, Valéro R, Fragaki K, Dubois N, Vialettes B, Paquis-Flucklinger V. A novel unstable mutation in mitochondrial DNA responsible for maternally inherited diabetes and deafness. Diabetes Care 2011; 34:2591-3. [PMID: 21994425 PMCID: PMC3220838 DOI: 10.2337/dc11-1012] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The m.3243A>G mutation in mitochondrial DNA (mtDNA) is responsible for maternally inherited diabetes and deafness (MIDD). Other mtDNA mutations are extremely rare. RESEARCH DESIGN AND METHODS We studied a patient presenting with diabetes and deafness who does not carry the m.3243A>G mutation. RESULTS We identified a deficiency of respiratory chain complex I in the patient's fibroblasts. mtDNA sequencing revealed a novel mutation that corresponds to an insertion of one or two cytosine residues in the coding region of the MT-ND6 gene (m.14535_14536insC or CC), leading to premature stop codons. This heteroplasmic mutation is unstable in the patient's somatic tissues. CONCLUSIONS We describe for the first time an unstable mutation in a mitochondrial gene coding for a complex I subunit, which is responsible for the MIDD phenotype. This mutation is likely favored by the m.14530T>C polymorphism, which is homoplasmic and leads to the formation of an 8-bp polyC tract responsible for genetic instability.
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Affiliation(s)
- Sylvie Bannwarth
- Department of Medical Genetics, Archet 2 Hospital, Centre Hospitalier Universitaire de Nice, Nice, France
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Huang T. Next generation sequencing to characterize mitochondrial genomic DNA heteroplasmy. CURRENT PROTOCOLS IN HUMAN GENETICS 2011; Chapter 19:19.8.1-19.8.12. [PMID: 21975941 PMCID: PMC4687495 DOI: 10.1002/0471142905.hg1908s71] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This protocol describes the methodology to characterize mitochondrial DNA (mtDNA) heteroplasmy by parallel sequencing. Mitochondria play an important role in essential cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondria genomes. Mutant and wild-type mtDNA may co-exist as heteroplasmy, and cause human disease. The purpose of this protocol is to simultaneously determine mtDNA sequence and quantify the heteroplasmic level. This protocol includes a two-fragment mitochondrial genome DNA PCR amplification. The PCR product is then mixed at an equimolar ratio. The samples are then barcoded and sequenced with high-throughput, next-generation sequencing technology. This technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the level of heteroplasmy.
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Affiliation(s)
- Taosheng Huang
- Division of Human Genetics/Department of Pediatrics; Center for Molecular and Mitochondrial Medicine and Genetics; University of California, Irvine, CA, 92697
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25
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Poole JC, Procaccio V, Brandon MC, Merrick G, Wallace DC. Multiplex analysis of mitochondrial DNA pathogenic and polymorphic sequence variants. Biol Chem 2011; 391:1115-30. [PMID: 20707610 DOI: 10.1515/bc.2010.125] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The mitochondrial DNA (mtDNA) encompasses two classes of functionally important sequence variants: recent pathogenic mutations and ancient adaptive polymorphisms. To rapidly and cheaply evaluate both classes of single nucleotide variants (SNVs), we have developed an integrated system in which mtDNA SNVs are analyzed by multiplex primer extension using the SNaPshot system. A multiplex PCR amplification strategy was used to amplify the entire mtDNA, a computer program identifies optimal extension primers, and a complete global haplotyping system is also proposed. This system genotypes SNVs on multiplexed mtDNA PCR products or directly from enriched mtDNA samples and can quantify heteroplasmic variants down to 0.8% using a standard curve. With this system, we have developed assays for testing the common pathogenic mutations in four multiplex panels: two genotype the 13 most common pathogenic mtDNA mutations and two genotype the 10 most common Leber Hereditary Optic Neuropathy mutations along with haplogroups J and T. We use a hierarchal system of 140 SNVs to delineate the major global mtDNA haplogroups based on a global phylogenetic tree of coding region polymorphisms. This system should permit rapid and inexpensive genotyping of pathogenic and lineage-specific mtDNA SNVs by clinical and research laboratories.
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Affiliation(s)
- Jason C Poole
- Center for Molecular and Mitochondrial Medicine and Genetics, University of California, Irvine, CA 92697, USA
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Coenzyme Q is effective on anemia in a patient with sideroblastic anemia and mitochondrial myopathy. Blood 2010; 116:3681-2. [PMID: 21051567 DOI: 10.1182/blood-2010-07-299453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Pilch J, Asman M, Jamroz E, Kajor M, Kotrys-Puchalska E, Goss M, Krzak M, Witecka J, Gmiński J, Sieroń AL. Surveyor nuclease detection of mutations and polymorphisms of mtDNA in children. Pediatr Neurol 2010; 43:325-30. [PMID: 20933175 DOI: 10.1016/j.pediatrneurol.2010.05.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 01/27/2010] [Accepted: 05/26/2010] [Indexed: 10/19/2022]
Abstract
Mitochondrial encephalomyopathies are complex disorders with wide range of clinical manifestations. Particularly time-consuming is the identification of mutations in mitochondrial DNA. A group of 20 children with clinical manifestations of mitochondrial encephalomyopathies was selected for molecular studies. The aims were (a) to identify mutations in mtDNA isolated from muscle and (b) to verify detected mutations in DNA isolated from blood, in order to assess the utility of a Surveyor nuclease assay kit for patient screening. The most common changes found were polymorphisms, including a few missense mutations altering the amino acid sequence of mitochondrial proteins. In two boys with MELAS (i.e., mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episodes), a mutation A→G3243 was detected in the tRNALeu gene of mtDNA isolated from muscle and blood. In one boy, the carrier status of his mother was confirmed, based on molecular analysis of DNA isolated from blood. A method using Surveyor nuclease allows systematic screening for small mutations in mtDNA, using as its source blood of the patients and asymptomatic carriers. The method still requires confirmation studying a larger group. In some patients, the use of this method should precede and might limit indications for traumatic muscle and skin biopsy.
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Affiliation(s)
- Jacek Pilch
- Department of Child Neurology, Medical University of Silesia, ul. Medyków 16, Katowice, Poland.
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Li M, Schönberg A, Schaefer M, Schroeder R, Nasidze I, Stoneking M. Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes. Am J Hum Genet 2010; 87:237-49. [PMID: 20696290 PMCID: PMC2917713 DOI: 10.1016/j.ajhg.2010.07.014] [Citation(s) in RCA: 228] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Revised: 07/21/2010] [Accepted: 07/22/2010] [Indexed: 11/29/2022] Open
Abstract
Heteroplasmy, the existence of multiple mtDNA types within an individual, has been previously detected by using mostly indirect methods and focusing largely on just the hypervariable segments of the control region. Next-generation sequencing technologies should enable studies of heteroplasmy across the entire mtDNA genome at much higher resolution, because many independent reads are generated for each position. However, the higher error rate associated with these technologies must be taken into consideration to avoid false detection of heteroplasmy. We used simulations and phiX174 sequence data to design criteria for accurate detection of heteroplasmy with the Illumina Genome Analyzer platform, and we used artificial mixtures and replicate data to test and refine the criteria. We then applied these criteria to mtDNA sequence reads for 131 individuals from five Eurasian populations that had been generated via a parallel tagged approach. We identified 37 heteroplasmies at 10% frequency or higher at 34 sites in 32 individuals. The mutational spectrum does not differ between heteroplasmic mutations and polymorphisms in the same individuals, but the relative mutation rate at heteroplasmic mutations is significantly higher than that estimated for all mutable sites in the human mtDNA genome. Moreover, there is also a significant excess of nonsynonymous mutations observed among heteroplasmies, compared to polymorphism data from the same individuals. Both mutation-drift and negative selection influence the fate of heteroplasmies to determine the polymorphism spectrum in humans. With appropriate criteria for avoiding false positives due to sequencing errors, next-generation technologies can provide novel insights into genome-wide aspects of mtDNA heteroplasmy.
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Affiliation(s)
- Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Anna Schönberg
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Michael Schaefer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Roland Schroeder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Ivane Nasidze
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D04103 Leipzig, Germany
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Characterization of mitochondrial DNA heteroplasmy using a parallel sequencing system. Biotechniques 2010; 48:287-96. [DOI: 10.2144/000113389] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Characterization of human mitochondrial genome sequences is important for the molecular diagnosis of mitochondrial diseases, especially in samples with a low level of mitochondrial DNA (mtDNA) heteroplasmy (≥5%). Currently, no single methodology can simultaneously determine complete mtDNA sequences, identify mitochondrial genome–wide heteroplasmies, and quantify mtDNA heteroplasmy levels. The deep sampling inherent in “next-generation” sequencing approaches should enable the efficient detection of low-level DNA heteroplasmies and address this need. Herein, we used the Illumina Genome Analyzer to re-sequence human mtDNA samples from two subjects that were combined at five different ratios (1:99, 5:95, 10:90, 20:80, and 50:50). We assessed the sensitivity, specificity, and accuracy of this system, and our results show that mtDNA heteroplasmies ≥5% were detected 100% of the time with virtually no false positives and that the estimates of mtDNA heteroplasmy levels were remarkably close to the theoretical values (correlation coefficient = 0.96). Therefore, parallel sequencing provides a simple, high-throughput, and cost-effective platform for mitochondrial genome sequencing with sensitivity and specificity for mtDNA heteroplasmy detection.
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Krishnan KJ, Blackwood JK, Reeve AK, Turnbull DM, Taylor RW. Detection of mitochondrial DNA variation in human cells. Methods Mol Biol 2010; 628:227-257. [PMID: 20238085 DOI: 10.1007/978-1-60327-367-1_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The ability to detect mitochondrial DNA (mtDNA) variation within human cells is important not only to identify mutations causing mtDNA disease, but also as mtDNA mutations are being increasingly described in many ageing tissues and in complex diseases such as diabetes, neurodegeneration and cancer. In this review, we discuss the main molecular genetic techniques that can be applied to study the two main types of mtDNA mutation: point mutations and large-scale mtDNA rearrangements. We then describe in detail protocols routinely used within our laboratory to analyse mtDNA mutations in individual human cells such as single muscle fibres and individual neurons to study the relationship between mtDNA mutation load and respiratory chain dysfunction.
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Affiliation(s)
- Kim J Krishnan
- Mitochondrial Research Group, Newcastle University, Newcastle upon Tyne, Tyne and Wear, UK
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31
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[Strategy in diagnosis of mitochondrial diseases]. ACTA ACUST UNITED AC 2009; 58:353-6. [PMID: 19942370 DOI: 10.1016/j.patbio.2009.09.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 09/14/2009] [Indexed: 12/12/2022]
Abstract
Mitochondrial diseases (MD) are the most frequent metabolic disorders. They have in common a respiratory chain deficiency. Clinical presentation of MD is very heterogeneous and the major physiological functions may be affected. Diagnosis is complex due to the potential involvement of two genomes (nuclear or mitochondrial DNA), the large number of candidate genes to screen and the small number of patients reported for each type of MD. Clinical presentation, trait of inheritance, cerebral imaging (MRI and CT-Scan) and specialized biochemical investigations are good indicators, but identification of causing mutation(s) is the clue to confirm diagnosis. Task is huge and progress in diagnosis of MD should come from genotype-phenotype correlations studies and from major technical improvements in molecular diagnosis. Exhaustive study of mitochondrial DNA is the first necessary step that is now possible with methods like Surveyor and Affymetrix resequencing chip. Combination of data including clinical informations, cerebral imaging, respiratory chain deficiency and/or assembly profile of respiratory chain complexes (BN-PAGE profile) may contribute for orientation for nuclear DNA studies. Elucidation of the genetic bases of MD is important for patients: identification of causing mutation(s) allows offering genetic counselling and possibility of prenatal diagnosis.
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32
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Keeney PM, Quigley CK, Dunham LD, Papageorge CM, Iyer S, Thomas RR, Schwarz KM, Trimmer PA, Khan SM, Portell FR, Bergquist KE, Bennett JP. Mitochondrial gene therapy augments mitochondrial physiology in a Parkinson's disease cell model. Hum Gene Ther 2009; 20:897-907. [PMID: 19374590 DOI: 10.1089/hum.2009.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Neurodegeneration in Parkinson's disease (PD) affects mainly dopaminergic neurons in the substantia nigra, where age-related, increasing percentages of cells lose detectable respiratory activity associated with depletion of intact mitochondrial DNA (mtDNA). Replenishment of mtDNA might improve neuronal bioenergetic function and prevent further cell death. We developed a technology ("ProtoFection") that uses recombinant human mitochondrial transcription factor A (TFAM) engineered with an N-terminal protein transduction domain (PTD) followed by the SOD2 mitochondrial localization signal (MLS) to deliver mtDNA cargo to the mitochondria of living cells. MTD-TFAM (MTD = PTD + MLS = "mitochondrial transduction domain") binds mtDNA and rapidly transports it across plasma membranes to mitochondria. For therapeutic proof-of-principle we tested ProtoFection technology in Parkinson's disease cybrid cells, using mtDNA generated from commercially available human genomic DNA (gDNA; Roche). Nine to 11 weeks after single exposures to MTD-TFAM + mtDNA complex, PD cybrid cells with impaired respiration and reduced mtDNA genes increased their mtDNA gene copy numbers up to 24-fold, mtDNA-derived RNAs up to 35-fold, TFAM and ETC proteins, cell respiration, and mitochondrial movement velocities. Cybrid cells with no or minimal basal mitochondrial impairments showed reduced or no responses to treatment, suggesting the possibility of therapeutic selectivity. Exposure of PD but not control cybrid cells to MTD-TFAM protein alone or MTD-TFAM + mtDNA complex increased expression of PGC-1alpha, suggesting activation of mitochondrial biogenesis. ProtoFection technology for mitochondrial gene therapy holds promise for improving bioenergetic function in impaired PD neurons and needs additional development to define its pharmacodynamics and delineate its molecular mechanisms. It also is unclear whether single-donor gDNA for generating mtDNA would be a preferred therapeutic compared with the pooled gDNA used in this study.
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Affiliation(s)
- Paula M Keeney
- Morris K. Udall Parkinson's Disease Research Center of Excellence, University of Virginia, Charlottesville, VA 22908, USA
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Keeney PM, Dunham LD, Quigley CK, Morton SL, Bergquist KE, Bennett JP. Cybrid models of Parkinson's disease show variable mitochondrial biogenesis and genotype-respiration relationships. Exp Neurol 2009; 220:374-82. [PMID: 19815014 DOI: 10.1016/j.expneurol.2009.09.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 09/23/2009] [Accepted: 09/28/2009] [Indexed: 01/01/2023]
Abstract
Sporadic Parkinson's disease (sPD) is a nervous system-wide disease that presents with a bradykinetic movement disorder and frequently progresses to include depression and cognitive impairment. Cybrid models of sPD are based on expression of sPD platelet mitochondrial DNA (mtDNA) in neural cells and demonstrate some similarities to sPD brains. In sPD and CTL cybrids we characterized aspects of mitochondrial biogenesis, mtDNA genomics, composition of the respirasome and the relationships among isolated mitochondrial and intact cell respiration. Cybrid mtDNA levels varied and correlated with expression of PGC-1 alpha, a transcriptional co-activator regulator of mitochondrial biogenesis. Levels of mtDNA heteroplasmic mutations were asymmetrically distributed across the mitochondrial genome; numbers of heteroplasmies were more evenly distributed. Neither levels nor numbers of heteroplasmies distinguished sPD from CTL. sPD cybrid mitochondrial ETC subunit protein levels were not altered. Isolated mitochondrial complex I respiration rates showed limited correlation with whole cell complex I respiration rates in both sPD and CTL cybrids. Intact cell respiration during the normoxic-anoxic transition yielded K(m) values for oxygen that directly related to respiration rates in CTL but not in sPD cell lines. Both sPD and CTL cybrid cells are substantially heterogeneous in mitochondrial genomic and physiologic properties. Our results suggest that mtDNA depletion may occur in sPD neurons and could reflect impairment of mitochondrial biogenesis. Cybrids remain a valuable model for some aspects of sPD but their heterogeneity mitigates against a simple designation of sPD phenotype in this cell model.
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Affiliation(s)
- Paula M Keeney
- Morris K. Udall Parkinson's Research Center of Excellence, University of Virginia, PO Box 800394, Charlottesville, VA 22908, USA
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Arthur CR, Morton SL, Dunham LD, Keeney PM, Bennett JP. Parkinson's disease brain mitochondria have impaired respirasome assembly, age-related increases in distribution of oxidative damage to mtDNA and no differences in heteroplasmic mtDNA mutation abundance. Mol Neurodegener 2009; 4:37. [PMID: 19775436 PMCID: PMC2761382 DOI: 10.1186/1750-1326-4-37] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 09/23/2009] [Indexed: 12/21/2022] Open
Abstract
Background Sporadic Parkinson's disease (sPD) is a nervous system-wide disease that presents with a bradykinetic movement disorder and is frequently complicated by depression and cognitive impairment. sPD likely has multiple interacting causes that include increased oxidative stress damage to mitochondrial components and reduced mitochondrial bioenergetic capacity. We analyzed mitochondria from postmortem sPD and CTL brains for evidence of oxidative damage to mitochondrial DNA (mtDNA), heteroplasmic mtDNA point mutations and levels of electron transport chain proteins. We sought to determine if sPD brains possess any mtDNA genotype-respiratory phenotype relationships. Results Treatment of sPD brain mtDNA with the mitochondrial base-excision repair enzyme 8-oxyguanosine glycosylase-1 (hOGG1) inhibited, in an age-dependent manner, qPCR amplification of overlapping ~2 kbase products; amplification of CTL brain mtDNA showed moderate sensitivity to hOGG1 not dependent on donor age. hOGG1 mRNA expression was not different between sPD and CTL brains. Heteroplasmy analysis of brain mtDNA using Surveyor nuclease® showed asymmetric distributions and levels of heteroplasmic mutations across mtDNA but no patterns that statistically distinguished sPD from CTL. sPD brain mitochondria displayed reductions of nine respirasome proteins (respiratory complexes I-V). Reduced levels of sPD brain mitochondrial complex II, III and V, but not complex I or IV proteins, correlated closely with rates of NADH-driven electron flow. mtDNA levels and PGC-1α expression did not differ between sPD and CTL brains. Conclusion PD brain mitochondria have reduced mitochondrial respiratory protein levels in complexes I-V, implying a generalized defect in respirasome assembly. These deficiencies do not appear to arise from altered point mutational burden in mtDNA or reduction of nuclear signaling for mitochondrial biogenesis, implying downstream etiologies. The origin of age-related increases in distribution of oxidative mtDNA damage in sPD but not CTL brains is not clear, tracks with but does not determine the sPD phenotype, and may indicate a unique consequence of aging present in sPD that could contribute to mtDNA deletion generation in addition to mtDNA replication, transcription and sequencing errors. sPD frontal cortex experiences a generalized bioenergetic deficiency above and beyond aging that could contribute to mood disorders and cognitive impairments.
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Affiliation(s)
- Charles R Arthur
- Morris K Udall Parkinson's Disease Research Center of Excellence, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
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35
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Trimmer PA, Bennett JP. The cybrid model of sporadic Parkinson's disease. Exp Neurol 2009; 218:320-5. [PMID: 19328199 PMCID: PMC2735256 DOI: 10.1016/j.expneurol.2009.03.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 03/13/2009] [Accepted: 03/17/2009] [Indexed: 11/19/2022]
Abstract
Parkinson's disease (PD) is the eponym attached to the most prevalent neurodegenerative movement disorder of adults, derived from observations of an early nineteenth century physician and paleontologist, James Parkinson, and is now recognized to encompass much more than a movement disorder clinically or dopamine neuron death pathologically. Most PD ( approximately 90%) is sporadic (sPD), is associated with mitochondrial deficiencies and has been studied in cell and animal models arising from the use of mitochondrial toxins that unfortunately have not predicted clinical efficacy to slow disease progression in humans. We have extensively studied the cytoplasmic hybrid ("cybrid") model of sPD in which donor mtDNAs are introduced into and expressed in neural tumor cells with identical nuclear genetic and environmental backgrounds. sPD cybrids demonstrate many abnormalities in which increased oxidative stress drives downstream antioxidant response and cell death activating signaling pathways. sPD cybrids regulate mitochondrial ETC genes and gene ontology families like sPD brain. sPD cybrids spontaneously form Lewy bodies and Lewy neurites, linking mtDNA expression to neuropathology, and demonstrate impaired organelle transport in processes and reduced mitochondrial respiration. Our recent studies show that near-infrared laser light therapy normalizes mitochondrial movement and can stimulate respiration in sPD cybrid neurons, and mitochondrial gene therapy can restore respiration and stimulate mitochondrial ETC gene and protein expression. sPD cybrids have provided multiple lines of circumstantial evidence linking mtDNA to sPD pathogenesis and can serve as platforms for therapy development. sPD cybrid models can be improved by the use of non-tumor human stem cell-derived neural precursor cells and by an introduction of postmortem brain mtDNA to test its causality directly.
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Affiliation(s)
- Patricia A Trimmer
- Morris K. Udall Parkinson's Disease Research Center of Excellence, Department of Neurology, University of Virginia, Charlottesville, 22908, USA.
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36
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Voskarides K, Deltas C. Screening for mutations in kidney-related genes using SURVEYOR nuclease for cleavage at heteroduplex mismatches. J Mol Diagn 2009; 11:311-8. [PMID: 19525337 PMCID: PMC2710707 DOI: 10.2353/jmoldx.2009.080144] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2009] [Indexed: 11/20/2022] Open
Abstract
SURVEYOR is a new mismatch-specific plant DNA endonuclease that is very efficient for mutation scanning in heteroduplex DNA. It is much faster, cheaper, more sensitive, and easier to perform than other "traditional" mutation detection methods such as single-strand conformation polymorphism analysis, denaturing high-performance liquid chromatography, heteroduplex analysis, and phage resolvases. This is the first comprehensive report on the use of SURVEYOR for screening genes implicated in a spectrum of inherited renal diseases. Of the 48.2 kb screened, 44 variations were identified, accounting for one variation per 1.1 kb. The re-sequencing of multiple samples did not reveal any variation that had not been identified by SURVEYOR, attesting to its high fidelity. Additionally, we tested this enzyme against 15 known variants, 14 of which it identified, thus showing a sensitivity of 93%. We showed that the genetic heterogeneity of renal diseases can be easily overcome using this enzyme with a high degree of confidence and no bias for any specific variations. We also showed for the first time that SURVEYOR does not demonstrate any preference regarding mismatch cleavage at specific positions. Disadvantages of using SURVEYOR include enhanced exonucleolytic activity for some polymerase chain reaction products and less than 100% sensitivity. We report that SURVEYOR can be used as a mutation detection method with a high degree of confidence, offering an excellent alternative for low-budget laboratories and for the rapid manipulation of multiple genes.
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Affiliation(s)
| | - Constantinos Deltas
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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37
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Tan YC, Blumenfeld JD, Anghel R, Donahue S, Belenkaya R, Balina M, Parker T, Levine D, Leonard DGB, Rennert H. Novel method for genomic analysis of PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease. Hum Mutat 2009; 30:264-73. [PMID: 18837007 DOI: 10.1002/humu.20842] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Genetic testing of PKD1 and PKD2 is useful for diagnosis and prognosis of autosomal dominant polycystic kidney disease (ADPKD), particularly in asymptomatic individuals or those without a family history. PKD1 testing is complicated by the large transcript size, complexity of the gene region, and the extent of gene variations. A molecular assay was developed using Transgenomic's SURVEYOR Nuclease and WAVE Nucleic Acid High Sensitivity Fragment Analysis System to screen for PKD1 and PKD2 variants, followed by sequencing of variant gene segments, thereby reducing the sequencing reactions by 80%. This method was compared to complete DNA sequencing performed by a reference laboratory for 25 ADPKD patients from 22 families. The pathogenic potential of gene variations of unknown significance was examined by evolutionary comparison, effects of amino acid substitutions on protein structure, and effects of splice-site alterations. A total of 90 variations were identified, including all 82 reported by the reference laboratory (100% sensitivity). A total of 76 variations (84.4%) were in PKD1 and 14 (15.6%) in PKD2. Definite pathogenic mutations (seven nonsense, four truncation, and three splicing defects) were detected in 64% (14/22) of families. The remaining 76 variants included 26 missense, 33 silent, and 17 intronic changes. Two heterozygous nonsense mutations were incorrectly determined by the reference laboratory as homozygous. "Probably pathogenic" mutations were identified in an additional five families (overall detection rate 86%). In conclusion, the SURVEYOR nuclease method was comparable to direct sequencing for detecting ADPKD mutations, achieving high sensitivity with lower cost, providing an important tool for genetic analysis of complex genes.
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Affiliation(s)
- Ying-Cai Tan
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, New York, USA
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38
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Pagniez-Mammeri H, Lombes A, Brivet M, Ogier-de Baulny H, Landrieu P, Legrand A, Slama A. Rapid screening for nuclear genes mutations in isolated respiratory chain complex I defects. Mol Genet Metab 2009; 96:196-200. [PMID: 19167255 DOI: 10.1016/j.ymgme.2008.12.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 12/05/2008] [Indexed: 11/30/2022]
Abstract
Complex I or reduced nicotinamide adenine dinucleotide (NADH): ubiquinone oxydoreductase deficiency is the most common cause of respiratory chain defects. Molecular bases of complex I deficiencies are rarely identified because of the dual genetic origin of this multi-enzymatic complex (nuclear DNA and mitochondrial DNA) and the lack of phenotype-genotype correlation. We used a rapid method to screen patients with isolated complex I deficiencies for nuclear genes mutations by Surveyor nuclease digestion of cDNAs. Eight complex I nuclear genes, among the most frequently mutated (NDUFS1, NDUFS2, NDUFS3, NDUFS4, NDUFS7, NDUFS8, NDUFV1 and NDUFV2), were studied in 22 cDNA fragments spanning their coding sequences in 8 patients with a biochemically proved complex I deficiency. Single nucleotide polymorphisms and missense mutations were detected in 18.7% of the cDNA fragments by Surveyor nuclease treatment. Molecular defects were detected in 3 patients. Surveyor nuclease screening is a reliable method for genotyping nuclear complex I deficiencies, easy to interpret, and limits the number of sequence reactions. Its use will enhance the possibility of prenatal diagnosis and help us for a better understanding of complex I molecular defects.
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Affiliation(s)
- Hélène Pagniez-Mammeri
- Laboratoire de Biochimie, APHP Hôpital de Bicêtre, 78, rue du Général Leclerc, 94275 Le Kremlin-Bicêtre Cedex, France
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39
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Brandon MC, Ruiz-Pesini E, Mishmar D, Procaccio V, Lott MT, Nguyen KC, Spolim S, Patil U, Baldi P, Wallace DC. MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences. Hum Mutat 2009; 30:1-6. [PMID: 18566966 DOI: 10.1002/humu.20801] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We have developed a computer system, MITOMASTER, to make analysis of human mitochondrial DNA (mtDNA) sequences efficient, accurate, and easily available. From imported sequences, the system identifies nucleotide variants, determines the haplogroup, rules out possible pseudogene contamination, identifies novel DNA sequence variants, and evaluates the potential biological significance of each variant. This system should be beneficial for mtDNA analyses of biomedical physicians and investigators, population biologists and forensic scientists. MITOMASTER can be accessed at http://mammag.web.uci.edu/twiki/bin/view/Mitomaster.
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Affiliation(s)
- Marty C Brandon
- Department of Information and Computer Science, University of California, Irvine, Irvine, California 92697-3940, USA
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40
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Rollins B, Martin MV, Sequeira PA, Moon EA, Morgan LZ, Watson SJ, Schatzberg A, Akil H, Myers RM, Jones EG, Wallace DC, Bunney WE, Vawter MP. Mitochondrial variants in schizophrenia, bipolar disorder, and major depressive disorder. PLoS One 2009; 4:e4913. [PMID: 19290059 PMCID: PMC2654519 DOI: 10.1371/journal.pone.0004913] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 02/15/2009] [Indexed: 02/06/2023] Open
Abstract
Background Mitochondria provide most of the energy for brain cells by the process of oxidative phosphorylation. Mitochondrial abnormalities and deficiencies in oxidative phosphorylation have been reported in individuals with schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD) in transcriptomic, proteomic, and metabolomic studies. Several mutations in mitochondrial DNA (mtDNA) sequence have been reported in SZ and BD patients. Methodology/Principal Findings Dorsolateral prefrontal cortex (DLPFC) from a cohort of 77 SZ, BD, and MDD subjects and age-matched controls (C) was studied for mtDNA sequence variations and heteroplasmy levels using Affymetrix mtDNA resequencing arrays. Heteroplasmy levels by microarray were compared to levels obtained with SNaPshot and allele specific real-time PCR. This study examined the association between brain pH and mtDNA alleles. The microarray resequencing of mtDNA was 100% concordant with conventional sequencing results for 103 mtDNA variants. The rate of synonymous base pair substitutions in the coding regions of the mtDNA genome was 22% higher (p = 0.0017) in DLPFC of individuals with SZ compared to controls. The association of brain pH and super haplogroup (U, K, UK) was significant (p = 0.004) and independent of postmortem interval time. Conclusions Focusing on haplogroup and individual susceptibility factors in psychiatric disorders by considering mtDNA variants may lead to innovative treatments to improve mitochondrial health and brain function.
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Affiliation(s)
- Brandi Rollins
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - Maureen V. Martin
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - P. Adolfo Sequeira
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - Emily A. Moon
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - Ling Z. Morgan
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - Stanley J. Watson
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alan Schatzberg
- Department of Psychiatry, Stanford University, Palo Alto, California, United States of America
| | - Huda Akil
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Richard M. Myers
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Edward G. Jones
- Neuroscience Center, University of California Davis, Davis, California, United States of America
| | - Douglas C. Wallace
- Molecular and Mitochondrial Medicine and Genetics, University of California Irvine, Irvine, California, United States of America
| | - William E. Bunney
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - Marquis P. Vawter
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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41
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Kraytsberg Y, Bodyak N, Myerow S, Nicholas A, Ebralidze K, Khrapko K. Quantitative analysis of somatic mitochondrial DNA mutations by single-cell single-molecule PCR. Methods Mol Biol 2009; 554:329-69. [PMID: 19513684 DOI: 10.1007/978-1-59745-521-3_21] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondrial genome integrity is an important issue in somatic mitochondrial genetics. Development of quantitative methods is indispensable to somatic mitochondrial genetics as quantitative studies are required to characterize heteroplasmy and mutation processes, as well as their effects on phenotypic developments. Quantitative studies include the identification and measurement of the load of pathogenic and non-pathogenic clonal mutations, screening mitochondrial genomes for mutations in order to determine the mutation spectra and characterize an ongoing mutation process. Single-molecule PCR (smPCR) has been shown to be an effective method that can be applied to all areas of quantitative studies. It has distinct advantages over conventional vector-based cloning techniques avoiding the well-known PCR-related artifacts such as the introduction of artificial mutations, preferential allelic amplifications, and "jumping" PCR. smPCR is a straightforward and robust method, which can be effectively used for molecule-by-molecule mutational analysis, even when mitochondrial whole genome (mtWG) analysis is involved. This chapter describes the key features of the smPCR method and provides three examples of its applications in single-cell analysis: di-plex smPCR for deletion quantification, smPCR cloning for clonal point mutation quantification, and smPCR cloning for whole genome sequencing (mtWGS).
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Affiliation(s)
- Yevgenya Kraytsberg
- Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
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Bannwarth S, Procaccio V, Paquis-Flucklinger V. Rapid identification of unknown heteroplasmic mitochondrial DNA mutations with mismatch-specific surveyor nuclease. Methods Mol Biol 2009; 554:301-313. [PMID: 19513682 DOI: 10.1007/978-1-59745-521-3_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Identification of mitochondrial DNA (mtDNA) mutations is essential for diagnosis and genetic counseling of mitochondrial diseases. In this chapter, we describe a strategy for the rapid identification of heteroplasmic mtDNA mutations that can be used routinely in molecular genetic laboratories. This protocol involves the following three steps: (i) PCR amplification of the entire human mitochondrial genome with 17 overlapping PCR products, (ii) localization of mtDNA mismatch(es) after digestion of the 17 amplicons by Surveyor Nuclease, a member of a family of plant DNA endonucleases that cleave double-strand DNA at any mismatch site, and (iii) identification of the mutation by sequencing the region containing the mismatch.
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Affiliation(s)
- Sylvie Bannwarth
- Department of Medical Genetics, Archet 2 Hospital, CHU Nice, France
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Azria D, Ozsahin M, Kramar A, Peters S, Atencio DP, Crompton NEA, Mornex F, Pèlegrin A, Dubois JB, Mirimanoff RO, Rosenstein BS. Single nucleotide polymorphisms, apoptosis, and the development of severe late adverse effects after radiotherapy. Clin Cancer Res 2008; 14:6284-8. [PMID: 18829510 DOI: 10.1158/1078-0432.ccr-08-0700] [Citation(s) in RCA: 127] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Evidence has accumulated in recent years suggestive of a genetic basis for a susceptibility to the development of radiation injury after cancer radiotherapy. The purpose of this study was to assess whether patients with severe radiation-induced sequelae (RIS; i.e., National Cancer Institute/CTCv3.0 grade, > or =3) display both a low capacity of radiation-induced CD8 lymphocyte apoptosis (RILA) in vitro and possess certain single nucleotide polymorphisms (SNP) located in candidate genes associated with the response of cells to radiation. EXPERIMENTAL DESIGN DNA was isolated from blood samples obtained from patients (n = 399) included in the Swiss prospective study evaluating the predictive effect of in vitro RILA and RIS. SNPs in the ATM, SOD2, XRCC1, XRCC3, TGFB1, and RAD21 genes were screened in patients who experienced severe RIS (group A, n = 16) and control subjects who did not manifest any evidence of RIS (group B, n = 18). RESULTS Overall, 13 and 21 patients were found to possess a total of <4 and > or =4 SNPs in the candidate genes. The median (range) RILA in group A was 9.4% (5.3-16.5) and 94% (95% confidence interval, 70-100) of the patients (15 of 16) had > or =4 SNPs. In group B, median (range) RILA was 25.7% (20.2-43.2) and 33% (95% confidence interval, 13-59) of patients (6 of 18) had > or =4 SNPs (P < 0.001). CONCLUSIONS The results of this study suggest that patients with severe RIS possess 4 or more SNPs in candidate genes and low radiation-induced CD8 lymphocyte apoptosis in vitro.
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Affiliation(s)
- David Azria
- INSERM U896, Institut de Recherche en Cancérologie de Montpellier, Department of Radiation Oncology, CRLC Val d'Aurelle-Paul Lamarque, Montpellier, France
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Rossner P, Gammon MD, Zhang YJ, Terry MB, Hibshoosh H, Memeo L, Mansukhani M, Long CM, Garbowski G, Agrawal M, Kalra TS, Gaudet MM, Teitelbaum SL, Neugut AI, Santella RM. Mutations in p53, p53 protein overexpression and breast cancer survival. J Cell Mol Med 2008; 13:3847-57. [PMID: 19602056 PMCID: PMC2832100 DOI: 10.1111/j.1582-4934.2008.00553.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
p53 is an important tumour suppressor gene that encodes p53 protein, a molecule involved in cell cycle regulation and has been inconsistently linked to breast cancer survival. Using archived tumour tissue from a population-based sample of 859 women diagnosed with breast cancer between 1996 and 1997, we determined p53 mutations in exons 5–8 and p53 protein overexpression. We examined the association of p53 mutations with overexpression and selected tumour clinical parameters. We assessed whether either p53 marker was associated with survival through 2002, adjusting for other tumour markers and prognostic factors. The prevalence of protein overexpression in the tumour was 36% (307/859) and of any p53 mutation was 15% (128/859). p53 overexpression was positively associated with the presence of any p53 mutation (odds ratio [OR]= 2.2, 95% confidence interval [CI]= 1.5–3.2), particularly missense mutations (ER = 7.0, 95% CI = 3.6–13.7). Negative oestrogen and progesterone receptor (ER/PR) status was positively associated with both p53 protein overexpression (= 2.6, 95% CI = 1.7–4.0) and p53 mutation (OR = 3.9, 95% CI = 2.4–6.5). Any p53 mutation and missense mutations, but not p53 protein overexpression, were associated with breast cancer-specific mortality (hazard ratio [HR]= 1.7, 95% CI = 1.0–2.8; HR = 2.0, 95% CI = 1.1–3.6, respectively) and all-cause mortality (HR = 1.5, 95% CI = 1.0–2.4; HR = 2.0, 95% CI = 1.2–3.4, respectively); nonsense mutations were associated only with breast cancer-specific mortality (HR = 3.0, 95% CI = 1.1–8.1). These associations however did not remain after adjusting for ER/PR status. Thus, in this population-based cohort of women with breast cancer, although p53 protein overexpression and p53 mutations were associated with each other, neither independently impacted breast cancer-specific or all-causing mortality, after considering ER/PR status.
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Affiliation(s)
- Pavel Rossner
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
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Cross MJ, Waters DLE, Lee LS, Henry RJ. Endonucleolytic mutation analysis by internal labeling (EMAIL). Electrophoresis 2008; 29:1291-301. [PMID: 18288672 DOI: 10.1002/elps.200700452] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mismatch-specific endonucleases are efficient tools for the targeted scanning of populations for subtle DNA variations. Conventional protocols involve 5'-labeled amplicon substrates and the detection of digestion products by LIF electrophoresis. A shortcoming of such protocols, however, is the limited 5'-signal strength. Normally the sensitivity of fluorescent DNA analyzers is superior to that of intercalating dye/agarose systems, however, pooling capacities of the former and latter approaches to mismatch scanning are somewhat similar. Detection is further limited by significant background. We investigated the activity of CEL nucleases using amplicon substrates labeled both internally and at each 5'-terminus. The amplicons were generated from exon 8 of the rice starch synthase IIa encoding gene. Signal of both 5'-labels was significantly reduced by enzyme activity, while that of the internal label was largely unaffected. In addition, background resulting from internal labeling was a significant improvement on that associated with 5'-labeling. Sizing of the multilabeled substrates suggests that 5'-modification enhances exonucleolytic activity, resulting in the removal of the dye-labeled terminal nucleotides. We have developed an alternative approach to mismatch detection, in which amplicon labeling is achieved via the incorporation of fluorescently labeled deoxynucleotides, which we have named Endonucleolytic Mutation Analysis by Internal Labeling (EMAIL). The strength of the EMAIL assay was demonstrated by the reclassification of a rice line as being heterozygous for the starch gene. This cultivar was assigned as being homozygous by a previous resequencing study. EMAIL shows potential for the clear identification of multiple mutations amongst allelic pools.
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Affiliation(s)
- Michael J Cross
- Grain Foods CRC, Centre for Plant Conservation Genetics, Southern Cross University, Lismore, NSW, Australia.
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Álvarez-Iglesias V, Barros F, Carracedo Á, Salas A. Minisequencing mitochondrial DNA pathogenic mutations. BMC MEDICAL GENETICS 2008; 9:26. [PMID: 18402672 PMCID: PMC2377236 DOI: 10.1186/1471-2350-9-26] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 04/10/2008] [Indexed: 12/18/2022]
Abstract
BACKGROUND There are a number of well-known mutations responsible of common mitochondrial DNA (mtDNA) diseases. In order to overcome technical problems related to the analysis of complete mtDNA genomes, a variety of different techniques have been proposed that allow the screening of coding region pathogenic mutations. METHODS We here propose a minisequencing assay for the analysis of mtDNA mutations. In a single reaction, we interrogate a total of 25 pathogenic mutations distributed all around the whole mtDNA genome in a sample of patients suspected for mtDNA disease. RESULTS We have detected 11 causal homoplasmic mutations in patients suspected for Leber disease, which were further confirmed by standard automatic sequencing. Mutations m.11778G>A and m.14484T>C occur at higher frequency than expected by change in the Galician (northwest Spain) patients carrying haplogroup J lineages (Fisher's Exact test, P-value < 0.01). The assay performs well in mixture experiments of wild:mutant DNAs that emulate heteroplasmic conditions in mtDNA diseases. CONCLUSION We here developed a minisequencing genotyping method for the screening of the most common pathogenic mtDNA mutations which is simple, fast, and low-cost. The technique is robust and reproducible and can easily be implemented in standard clinical laboratories.
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Affiliation(s)
- Vanesa Álvarez-Iglesias
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Hospital Clínico Universitario, Universidad de Santiago de Compostela, Galicia, Spain
| | - Francisco Barros
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Hospital Clínico Universitario, Universidad de Santiago de Compostela, Galicia, Spain
| | - Ángel Carracedo
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain
- Fundación Pública Galega de Medicina Xenómica (FPGMX), Hospital Clínico Universitario, Universidad de Santiago de Compostela, Galicia, Spain
| | - Antonio Salas
- Unidade de Xenética, Instituto de Medicina Legal, Facultad de Medicina, Universidad de Santiago de Compostela, Galicia, Spain
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Bannwarth S, Procaccio V, Rouzier C, Fragaki K, Poole J, Chabrol B, Desnuelle C, Pouget J, Azulay JP, Attarian S, Pellissier JF, Gargus JJ, Abdenur JE, Mozaffar T, Calvas P, Labauge P, Pages M, Wallace DC, Lambert JC, Paquis-Flucklinger V. Rapid identification of mitochondrial DNA (mtDNA) mutations in neuromuscular disorders by using surveyor strategy. Mitochondrion 2007; 8:136-45. [PMID: 18078792 DOI: 10.1016/j.mito.2007.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Revised: 10/22/2007] [Accepted: 10/26/2007] [Indexed: 11/18/2022]
Abstract
Mutations of mitochondrial genome are responsible for respiratory chain defects in numerous patients. We have used a strategy, based on the use of a mismatch-specific DNA endonuclease named " Surveyor Nuclease", for screening the entire mtDNA in a group of 50 patients with neuromuscular features, suggesting a respiratory chain dysfunction. We identified mtDNA mutations in 20% of patients (10/50). Among the identified mutations, four are not found in any mitochondrial database and have not been reported previously. We also confirm that mtDNA polymorphisms are frequently found in a heteroplasmic state (15 different polymorphisms were identified among which five were novel).
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Affiliation(s)
- S Bannwarth
- Department of Medical Genetics, Archet 2 Hospital, CHU Nice, France
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Bannwarth S, Procaccio V, Paquis-Flucklinger V. Rapid identification of unknown heteroplasmic mutations across the entire human mitochondrial genome with mismatch-specific Surveyor Nuclease. Nat Protoc 2007; 1:2037-47. [PMID: 17487193 DOI: 10.1038/nprot.2006.318] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations are responsible for mitochondrial diseases in numerous patients. But, until now, no rapid method was available for the identification of unknown deleterious point mutations. Here, we describe a new strategy for the rapid identification of heteroplasmic mtDNA mutations using mismatch-specific Surveyor Nuclease. This protocol involves the following three steps: (i) PCR amplification of the entire human mitochondrial genome in 17 overlapping fragments; (ii) localization of mtDNA mismatch(es) after digestion of the 17 amplicons by Surveyor Nuclease; and (iii) identification of the mutation by sequencing the region containing the mismatch. This Surveyor Nuclease-based strategy allows a systematic screening of the entire mtDNA to identify a mutation within 2 days. It represents an important diagnostic approach for mitochondrial diseases that can be routinely used in molecular diagnostic laboratories.
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Affiliation(s)
- Sylvie Bannwarth
- Department of Medical Genetics, Archet 2 Hospital, CHU Nice, France
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Vogiatzakis N, Kekou K, Sophocleous C, Kitsiou S, Mavrou A, Bakoula C, Kanavakis E. Screening Human Genes for Small Alterations Performing an Enzymatic Cleavage Mismatched Analysis (ECMA) Protocol. Mol Biotechnol 2007; 55:1-9. [DOI: 10.1007/s12033-007-0062-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 06/26/2007] [Indexed: 12/12/2022]
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50
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Screening Human Genes for Small Alterations Performing an Enzymatic Cleavage Mismatched Analysis (ECMA) Protocol. Mol Biotechnol 2007; 37:212-9. [DOI: 10.1007/s12033-007-0065-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 06/26/2007] [Indexed: 02/06/2023]
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