1
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Bianco SD, Parca L, Petrizzelli F, Biagini T, Giovannetti A, Liorni N, Napoli A, Carella M, Procaccio V, Lott MT, Zhang S, Vescovi AL, Wallace DC, Caputo V, Mazza T. APOGEE 2: multi-layer machine-learning model for the interpretable prediction of mitochondrial missense variants. Nat Commun 2023; 14:5058. [PMID: 37598215 PMCID: PMC10439926 DOI: 10.1038/s41467-023-40797-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 08/10/2023] [Indexed: 08/21/2023] Open
Abstract
Mitochondrial dysfunction has pleiotropic effects and is frequently caused by mitochondrial DNA mutations. However, factors such as significant variability in clinical manifestations make interpreting the pathogenicity of variants in the mitochondrial genome challenging. Here, we present APOGEE 2, a mitochondrially-centered ensemble method designed to improve the accuracy of pathogenicity predictions for interpreting missense mitochondrial variants. Built on the joint consensus recommendations by the American College of Medical Genetics and Genomics/Association for Molecular Pathology, APOGEE 2 features an improved machine learning method and a curated training set for enhanced performance metrics. It offers region-wise assessments of genome fragility and mechanistic analyses of specific amino acids that cause perceptible long-range effects on protein structure. With clinical and research use in mind, APOGEE 2 scores and pathogenicity probabilities are precompiled and available in MitImpact. APOGEE 2's ability to address challenges in interpreting mitochondrial missense variants makes it an essential tool in the field of mitochondrial genetics.
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Affiliation(s)
- Salvatore Daniele Bianco
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Luca Parca
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
- Italian Space Agency, Rome, Italy
| | - Francesco Petrizzelli
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
| | - Tommaso Biagini
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
| | - Agnese Giovannetti
- Clinical Genomics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
| | - Niccolò Liorni
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Alessandro Napoli
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
| | - Massimo Carella
- Medical Genetics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, (FG), Italy
| | - Vincent Procaccio
- University of Angers, Genetics Department CHU Angers, Mitolab UMR CNRS 6015-INSERM U1083, F-49000, Angers, France
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Angelo Luigi Vescovi
- ISBReMIT Institute for Stem Cell Biology, Regenerative Medicine and Innovative Therapies, Fondazione IRCSS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Division of Human Genetics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Viviana Caputo
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Tommaso Mazza
- Bioinformatics Laboratory, Fondazione IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo (FG), Italy.
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2
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Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Soto Albrecht Y, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Zhang S, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Bram Y, Kidane Y, Priebe W, Emmett MR, Meller R, Demharter S, Stentoft-Hansen V, Salvatore M, Galeano D, Enguita FJ, Grabham P, Trovao NS, Singh U, Haltom J, Heise MT, Moorman NJ, Baxter VK, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. Core mitochondrial genes are down-regulated during SARS-CoV-2 infection of rodent and human hosts. Sci Transl Med 2023; 15:eabq1533. [PMID: 37556555 DOI: 10.1126/scitranslmed.abq1533] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/20/2023] [Indexed: 08/11/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral proteins bind to host mitochondrial proteins, likely inhibiting oxidative phosphorylation (OXPHOS) and stimulating glycolysis. We analyzed mitochondrial gene expression in nasopharyngeal and autopsy tissues from patients with coronavirus disease 2019 (COVID-19). In nasopharyngeal samples with declining viral titers, the virus blocked the transcription of a subset of nuclear DNA (nDNA)-encoded mitochondrial OXPHOS genes, induced the expression of microRNA 2392, activated HIF-1α to induce glycolysis, and activated host immune defenses including the integrated stress response. In autopsy tissues from patients with COVID-19, SARS-CoV-2 was no longer present, and mitochondrial gene transcription had recovered in the lungs. However, nDNA mitochondrial gene expression remained suppressed in autopsy tissue from the heart and, to a lesser extent, kidney, and liver, whereas mitochondrial DNA transcription was induced and host-immune defense pathways were activated. During early SARS-CoV-2 infection of hamsters with peak lung viral load, mitochondrial gene expression in the lung was minimally perturbed but was down-regulated in the cerebellum and up-regulated in the striatum even though no SARS-CoV-2 was detected in the brain. During the mid-phase SARS-CoV-2 infection of mice, mitochondrial gene expression was starting to recover in mouse lungs. These data suggest that when the viral titer first peaks, there is a systemic host response followed by viral suppression of mitochondrial gene transcription and induction of glycolysis leading to the deployment of antiviral immune defenses. Even when the virus was cleared and lung mitochondrial function had recovered, mitochondrial function in the heart, kidney, liver, and lymph nodes remained impaired, potentially leading to severe COVID-19 pathology.
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Affiliation(s)
- Joseph W Guarnieri
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Joseph M Dybas
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Hossein Fazelinia
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Man S Kim
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | - Justin Frere
- Icahn School of Medicine at Mount Sinai, New York, NY 10023, USA
| | - Yuanchao Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Yentli Soto Albrecht
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Deborah G Murdock
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Scott L Weiss
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sonja M Best
- COVID-19 International Research Team, Medford, MA 02155, USA
- Rocky Mountain Laboratory, National Institute of Allergy and Infectious Disease, NIH, Hamilton, MT 59840, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Victoria Zaksas
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Chicago, Chicago, IL 60615, USA
- Clever Research Lab, Springfield, IL 62704, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team, Medford, MA 02155, USA
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | | | | | - Yaron Bram
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Yared Kidane
- COVID-19 International Research Team, Medford, MA 02155, USA
- Texas Scottish Rite Hospital for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark R Emmett
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team, Medford, MA 02155, USA
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | | | | | | | - Diego Galeano
- COVID-19 International Research Team, Medford, MA 02155, USA
- Facultad de Ingeniería, Universidad Nacional de Asunción, San Lorenzo, Central, Paraguay
| | - Francisco J Enguita
- COVID-19 International Research Team, Medford, MA 02155, USA
- Faculdade de Medicina, Universidade de Lisboa, Instituto de Medicina Molecular João Lobo Antunes, 1649-028 Lisboa, Portugal
| | - Peter Grabham
- College of Physicians and Surgeons, Columbia University, New York, NY 19103, USA
| | - Nidia S Trovao
- COVID-19 International Research Team, Medford, MA 02155, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Urminder Singh
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Jeffrey Haltom
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Mark T Heise
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Victoria K Baxter
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emily A Madden
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | | | - Wes A Sanders
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Stephen B Baylin
- COVID-19 International Research Team, Medford, MA 02155, USA
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team, Medford, MA 02155, USA
- Iowa State University, Ames, IA 50011, USA
| | - Pedro M Moraes-Vieira
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of Campinas, Campinas, SP, Brazil
| | - Deanne Taylor
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
| | - Christopher E Mason
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
- New York Genome Center, New York, NY 10013, USA
| | - Jonathan C Schisler
- COVID-19 International Research Team, Medford, MA 02155, USA
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Robert E Schwartz
- COVID-19 International Research Team, Medford, MA 02155, USA
- Weill Cornell Medicine, New York, NY 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team, Medford, MA 02155, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
- COVID-19 International Research Team, Medford, MA 02155, USA
- Division of Human Genetics, Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
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3
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Guarnieri JW, Dybas JM, Fazelinia H, Kim MS, Frere J, Zhang Y, Albrecht YS, Murdock DG, Angelin A, Singh LN, Weiss SL, Best SM, Lott MT, Cope H, Zaksas V, Saravia-Butler A, Meydan C, Foox J, Mozsary C, Kidane YH, Priebe W, Emmett MR, Meller R, Singh U, Bram Y, tenOever BR, Heise MT, Moorman NJ, Madden EA, Taft-Benz SA, Anderson EJ, Sanders WA, Dickmander RJ, Baxter VK, Baylin SB, Wurtele ES, Moraes-Vieira PM, Taylor D, Mason CE, Schisler JC, Schwartz RE, Beheshti A, Wallace DC. TARGETED DOWN REGULATION OF CORE MITOCHONDRIAL GENES DURING SARS-COV-2 INFECTION. bioRxiv 2022:2022.02.19.481089. [PMID: 35233572 PMCID: PMC8887073 DOI: 10.1101/2022.02.19.481089] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription profiles in nasopharyngeal and autopsy samples from patients and infected rodent models. While mitochondrial bioenergetics is repressed in the viral nasopharyngeal portal of entry, it is up regulated in autopsy lung tissues from deceased patients. In most disease stages and organs, discrete OXPHOS functions are blocked by the virus, and this is countered by the host broadly up regulating unblocked OXPHOS functions. No such rebound is seen in autopsy heart, results in severe repression of genes across all OXPHOS modules. Hence, targeted enhancement of mitochondrial gene expression may mitigate the pathogenesis of COVID-19.
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Affiliation(s)
- Joseph W. Guarnieri
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Joseph M. Dybas
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Hossein Fazelinia
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Man S. Kim
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- Kyung Hee University Hospital at Gangdong, Kyung Hee University, Seoul, South Korea
| | | | - Yuanchao Zhang
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Yentli Soto Albrecht
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | | | - Alessia Angelin
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Larry N. Singh
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Scott L. Weiss
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Sonja M. Best
- COVID-19 International Research Team
- Rocky Mountain Laboratories NIAID, Hamilton, MT 59840
| | - Marie T. Lott
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Henry Cope
- University of Nottingham, Nottingham, UK
| | - Viktorija Zaksas
- COVID-19 International Research Team
- University of Chicago, Chicago, IL, 60615, USA
| | - Amanda Saravia-Butler
- COVID-19 International Research Team
- Logyx, LLC, Mountain View, CA 94043, USA
- NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Cem Meydan
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | | | | | - Yared H. Kidane
- COVID-19 International Research Team
- Scottish Rite for Children, Dallas, TX 75219, USA
| | - Waldemar Priebe
- COVID-19 International Research Team
- University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mark R. Emmett
- COVID-19 International Research Team
- University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Robert Meller
- COVID-19 International Research Team
- Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Urminder Singh
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | | | - Mark T. Heise
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | - Emily A. Madden
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Wes A. Sanders
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | | | | | - Stephen B. Baylin
- COVID-19 International Research Team
- Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Eve Syrkin Wurtele
- COVID-19 International Research Team
- Iowa State University, Ames, IA 50011, USA
| | | | - Deanne Taylor
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
| | - Christopher E. Mason
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
- New York Genome Center, NY, USA
| | - Jonathan C. Schisler
- COVID-19 International Research Team
- University of North Carolina, Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Robert E. Schwartz
- COVID-19 International Research Team
- Weill Cornell Medicine, NY, 10065, USA
| | - Afshin Beheshti
- COVID-19 International Research Team
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- KBR, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Douglas C. Wallace
- The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
- COVID-19 International Research Team
- University of Pennsylvania, Philadelphia, PA 19104 USA
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4
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Abstract
Variation in the mitochondrial DNA (mtDNA) sequence is common in certain tumours. Two classes of cancer mtDNA variants can be identified: de novo mutations that act as 'inducers' of carcinogenesis and functional variants that act as 'adaptors', permitting cancer cells to thrive in different environments. These mtDNA variants have three origins: inherited variants, which run in families, somatic mutations arising within each cell or individual, and variants that are also associated with ancient mtDNA lineages (haplogroups) and are thought to permit adaptation to changing tissue or geographic environments. In addition to mtDNA sequence variation, mtDNA copy number and perhaps transfer of mtDNA sequences into the nucleus can contribute to certain cancers. Strong functional relevance of mtDNA variation has been demonstrated in oncocytoma and prostate cancer, while mtDNA variation has been reported in multiple other cancer types. Alterations in nuclear DNA-encoded mitochondrial genes have confirmed the importance of mitochondrial metabolism in cancer, affecting mitochondrial reactive oxygen species production, redox state and mitochondrial intermediates that act as substrates for chromatin-modifying enzymes. Hence, subtle changes in the mitochondrial genotype can have profound effects on the nucleus, as well as carcinogenesis and cancer progression.
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Affiliation(s)
- Piotr K Kopinski
- Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, USA
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Division of Human Genetics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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McCormick EM, Lott MT, Dulik MC, Shen L, Attimonelli M, Vitale O, Karaa A, Bai R, Pineda-Alvarez DE, Singh LN, Stanley CM, Wong S, Bhardwaj A, Merkurjev D, Mao R, Sondheimer N, Zhang S, Procaccio V, Wallace DC, Gai X, Falk MJ. Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation. Hum Mutat 2020; 41:2028-2057. [PMID: 32906214 DOI: 10.1002/humu.24107] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022]
Abstract
Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.
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Affiliation(s)
- Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew C Dulik
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Ornella Vitale
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Amel Karaa
- Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christine M Stanley
- Variantyx, Inc, Framingham, Massachusetts, USA.,QNA Diagnostics, Cambridge, Massachusetts, USA
| | | | - Anshu Bhardwaj
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Daria Merkurjev
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Rong Mao
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Neal Sondheimer
- Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, Angers, France
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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6
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Shen L, Attimonelli M, Bai R, Lott MT, Wallace DC, Falk MJ, Gai X. MSeqDR mvTool: A mitochondrial DNA Web and API resource for comprehensive variant annotation, universal nomenclature collation, and reference genome conversion. Hum Mutat 2018. [PMID: 29539190 DOI: 10.1002/humu.23422] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Accurate mitochondrial DNA (mtDNA) variant annotation is essential for the clinical diagnosis of diverse human diseases. Substantial challenges to this process include the inconsistency in mtDNA nomenclatures, the existence of multiple reference genomes, and a lack of reference population frequency data. Clinicians need a simple bioinformatics tool that is user-friendly, and bioinformaticians need a powerful informatics resource for programmatic usage. Here, we report the development and functionality of the MSeqDR mtDNA Variant Tool set (mvTool), a one-stop mtDNA variant annotation and analysis Web service. mvTool is built upon the MSeqDR infrastructure (https://mseqdr.org), with contributions of expert curated data from MITOMAP (https://www.mitomap.org) and HmtDB (https://www.hmtdb.uniba.it/hmdb). mvTool supports all mtDNA nomenclatures, converts variants to standard rCRS- and HGVS-based nomenclatures, and annotates novel mtDNA variants. Besides generic annotations from dbNSFP and Variant Effect Predictor (VEP), mvTool provides allele frequencies in more than 47,000 germline mitogenomes, and disease and pathogenicity classifications from MSeqDR, Mitomap, HmtDB and ClinVar (Landrum et al., 2013). mvTools also provides mtDNA somatic variants annotations. "mvTool API" is implemented for programmatic access using inputs in VCF, HGVS, or classical mtDNA variant nomenclatures. The results are reported as hyperlinked html tables, JSON, Excel, and VCF formats. MSeqDR mvTool is freely accessible at https://mseqdr.org/mvtool.php.
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Affiliation(s)
- Lishuang Shen
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | | | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Marni J Falk
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.,Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California.,Keck School of Medicine, University of Southern California, California
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7
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Sonney S, Leipzig J, Lott MT, Zhang S, Procaccio V, Wallace DC, Sondheimer N. Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP. PLoS Comput Biol 2017; 13:e1005867. [PMID: 29227991 PMCID: PMC5739504 DOI: 10.1371/journal.pcbi.1005867] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/21/2017] [Accepted: 11/02/2017] [Indexed: 11/18/2022] Open
Abstract
Novel or rare variants in mitochondrial tRNA sequences may be observed after mitochondrial DNA analysis. Determining whether these variants are pathogenic is critical, but confirmation of the effect of a variant on mitochondrial function can be challenging. We have used available databases of benign and pathogenic variants, alignment between diverse tRNAs, structural information and comparative genomics to predict the impact of all possible single-base variants and deletions. The Mitochondrial tRNA Informatics Predictor (MitoTIP) is available through MITOMAP at www.mitomap.org. The source code for MitoTIP is available at www.github.com/sonneysa/MitoTIP.
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Affiliation(s)
- Sanjay Sonney
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jeremy Leipzig
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Marie T. Lott
- The Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Shiping Zhang
- The Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Vincent Procaccio
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University Hospital, Angers, France
| | - Douglas C. Wallace
- The Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology, The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Neal Sondheimer
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, The University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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8
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Lott MT, Leipzig JN, Derbeneva O, Xie HM, Chalkia D, Sarmady M, Procaccio V, Wallace DC. mtDNA Variation and Analysis Using Mitomap and Mitomaster. ACTA ACUST UNITED AC 2016; 44:1.23.1-26. [PMID: 25489354 DOI: 10.1002/0471250953.bi0123s44] [Citation(s) in RCA: 304] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The Mitomap database of human mitochondrial DNA (mtDNA) information has been an important compilation of mtDNA variation for researchers, clinicians and genetic counselors for the past twenty-five years. The Mitomap protocol shows how users may look up human mitochondrial gene loci, search for public mitochondrial sequences, and browse or search for reported general population nucleotide variants as well as those reported in clinical disease. Within Mitomap is the powerful sequence analysis tool for human mitochondrial DNA, Mitomaster. The Mitomaster protocol gives step-by-step instructions showing how to submit sequences to identify nucleotide variants relative to the rCRS, to determine the haplogroup, and to view species conservation. User-supplied sequences, GenBank identifiers and single nucleotide variants may be analyzed.
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Affiliation(s)
- Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA
| | - Jeremy N Leipzig
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA; phone: 1-267-426-1375; fax: 1-215-590-5245
| | - Olga Derbeneva
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA; phone: 1-267-425-3064; fax: 1-267-426-0978; work cell: 1-215-866-8121
| | - H Michael Xie
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA; phone: 1-267-426-0675; fax: 1-215-590-5245
| | - Dimitra Chalkia
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA
| | - Mahdi Sarmady
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA; phone: 1-267-426-1373; fax: 1-215-590-5245
| | - Vincent Procaccio
- National Center for Neurodegenerative and Mitochondrial Diseases CHU Angers, Biochemistry and Genetics Department, Angers, France
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA; Department of Pathology and Laboratory Medicine; University of Pennsylvania, Philadelphia, PA; phone: 1-267-425-3078; fax: 1-267-426-0978
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9
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Shen L, Diroma MA, Gonzalez M, Navarro-Gomez D, Leipzig J, Lott MT, van Oven M, Wallace DC, Muraresku CC, Zolkipli-Cunningham Z, Chinnery PF, Attimonelli M, Zuchner S, Falk MJ, Gai X. MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease. Hum Mutat 2016; 37:540-548. [PMID: 26919060 DOI: 10.1002/humu.22974] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/03/2016] [Indexed: 11/11/2022]
Abstract
MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical diagnosis and research investigations of individual patient phenotypes, genomes, genes, and variants. A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers. MSeqDR also functions as a centralized application server for Web-based tools to analyze data across both mitochondrial and nuclear DNA, including investigator-driven whole exome or genome dataset analyses through MSeqDR-Genesis. MSeqDR-GBrowse genome browser supports interactive genomic data exploration and visualization with custom tracks relevant to mtDNA variation and mitochondrial disease. MSeqDR-LSDB is a locus-specific database that currently manages 178 mitochondrial diseases, 1,363 genes associated with mitochondrial biology or disease, and 3,711 pathogenic variants in those genes. MSeqDR Disease Portal allows hierarchical tree-style disease exploration to evaluate their unique descriptions, phenotypes, and causative variants. Automated genomic data submission tools are provided that capture ClinVar compliant variant annotations. PhenoTips will be used for phenotypic data submission on deidentified patients using human phenotype ontology terminology. The development of a dynamic informed patient consent process to guide data access is underway to realize the full potential of these resources.
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Affiliation(s)
- Lishuang Shen
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.,Massachusetts Eye and Ear Infirmary, Harvard Medical School, 243 Charles St, Boston, Massachusetts, USA
| | - Maria Angela Diroma
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,CEINGE-Biotecnologie Avanzate, Napoli, Italy
| | - Michael Gonzalez
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA.,The Genesis Project, Miami, Florida, USA
| | - Daniel Navarro-Gomez
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, 243 Charles St, Boston, Massachusetts, USA
| | - Jeremy Leipzig
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pathology, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Colleen Clarke Muraresku
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia USA
| | | | - Patrick F Chinnery
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, Florida, USA.,The Genesis Project, Miami, Florida, USA
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.,Massachusetts Eye and Ear Infirmary, Harvard Medical School, 243 Charles St, Boston, Massachusetts, USA
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10
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Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen AP, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X. MSeqDR: Making genomics accessible to the mitochondrial disease community. Mitochondrion 2015. [DOI: 10.1016/j.mito.2015.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Falk MJ, Shen L, Gonzalez M, Leipzig J, Lott MT, Stassen APM, Diroma MA, Navarro-Gomez D, Yeske P, Bai R, Boles RG, Brilhante V, Ralph D, DaRe JT, Shelton R, Terry SF, Zhang Z, Copeland WC, van Oven M, Prokisch H, Wallace DC, Attimonelli M, Krotoski D, Zuchner S, Gai X. Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities. Mol Genet Metab 2015; 114:388-96. [PMID: 25542617 PMCID: PMC4512182 DOI: 10.1016/j.ymgme.2014.11.016] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 11/26/2022]
Abstract
Success rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires the establishment of robust data resources to enable data sharing that informs accurate understanding of genes, variants, and phenotypes. The "Mitochondrial Disease Sequence Data Resource (MSeqDR) Consortium" is a grass-roots effort facilitated by the United Mitochondrial Disease Foundation to identify and prioritize specific genomic data analysis needs of the global mitochondrial disease clinical and research community. A central Web portal (https://mseqdr.org) facilitates the coherent compilation, organization, annotation, and analysis of sequence data from both nuclear and mitochondrial genomes of individuals and families with suspected mitochondrial disease. This Web portal provides users with a flexible and expandable suite of resources to enable variant-, gene-, and exome-level sequence analysis in a secure, Web-based, and user-friendly fashion. Users can also elect to share data with other MSeqDR Consortium members, or even the general public, either by custom annotation tracks or through the use of a convenient distributed annotation system (DAS) mechanism. A range of data visualization and analysis tools are provided to facilitate user interrogation and understanding of genomic, and ultimately phenotypic, data of relevance to mitochondrial biology and disease. Currently available tools for nuclear and mitochondrial gene analyses include an MSeqDR GBrowse instance that hosts optimized mitochondrial disease and mitochondrial DNA (mtDNA) specific annotation tracks, as well as an MSeqDR locus-specific database (LSDB) that curates variant data on more than 1300 genes that have been implicated in mitochondrial disease and/or encode mitochondria-localized proteins. MSeqDR is integrated with a diverse array of mtDNA data analysis tools that are both freestanding and incorporated into an online exome-level dataset curation and analysis resource (GEM.app) that is being optimized to support needs of the MSeqDR community. In addition, MSeqDR supports mitochondrial disease phenotyping and ontology tools, and provides variant pathogenicity assessment features that enable community review, feedback, and integration with the public ClinVar variant annotation resource. A centralized Web-based informed consent process is being developed, with implementation of a Global Unique Identifier (GUID) system to integrate data deposited on a given individual from different sources. Community-based data deposition into MSeqDR has already begun. Future efforts will enhance capabilities to incorporate phenotypic data that enhance genomic data analyses. MSeqDR will fill the existing void in bioinformatics tools and centralized knowledge that are necessary to enable efficient nuclear and mtDNA genomic data interpretation by a range of shareholders across both clinical diagnostic and research settings. Ultimately, MSeqDR is focused on empowering the global mitochondrial disease community to better define and explore mitochondrial diseases.
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Affiliation(s)
- Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, USA.
| | - Lishuang Shen
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA
| | - Michael Gonzalez
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, FL, USA
| | - Jeremy Leipzig
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Alphons P M Stassen
- Department of Clinical Genetics, Maastricht University Medical Centre, The Netherlands
| | - Maria Angela Diroma
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | | | - Philip Yeske
- United Mitochondrial Disease Foundation, Pittsburgh, PA, USA
| | | | | | - Virginia Brilhante
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, Finland
| | | | | | | | | | - Zhe Zhang
- Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - William C Copeland
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Mannis van Oven
- Department of Forensic Molecular Biology, Erasmus MC - University Medical Center Rotterdam, The Netherlands
| | - Holger Prokisch
- Institute of Human Genetics, Technical University Munich and Helmholtz Zentrum Munich, Munich, Germany
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pathology, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Danuta Krotoski
- National Institute of Child Health and Development, The National Institutes of Health, Bethesda, MD, USA
| | - Stephan Zuchner
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, FL, USA
| | - Xiaowu Gai
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA, USA.
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12
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Elson JL, Sweeney MG, Procaccio V, Yarham JW, Salas A, Kong QP, van der Westhuizen FH, Pitceathly RDS, Thorburn DR, Lott MT, Wallace DC, Taylor RW, McFarland R. Toward a mtDNA locus-specific mutation database using the LOVD platform. Hum Mutat 2012; 33:1352-8. [PMID: 22581690 DOI: 10.1002/humu.22118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 04/26/2012] [Indexed: 12/12/2022]
Abstract
The Human Variome Project (HVP) is a global effort to collect and curate all human genetic variation affecting health. Mutations of mitochondrial DNA (mtDNA) are an important cause of neurogenetic disease in humans; however, identification of the pathogenic mutations responsible can be problematic. In this article, we provide explanations as to why and suggest how such difficulties might be overcome. We put forward a case in support of a new Locus Specific Mutation Database (LSDB) implemented using the Leiden Open-source Variation Database (LOVD) system that will not only list primary mutations, but also present the evidence supporting their role in disease. Critically, we feel that this new database should have the capacity to store information on the observed phenotypes alongside the genetic variation, thereby facilitating our understanding of the complex and variable presentation of mtDNA disease. LOVD supports fast queries of both seen and hidden data and allows storage of sequence variants from high-throughput sequence analysis. The LOVD platform will allow construction of a secure mtDNA database; one that can fully utilize currently available data, as well as that being generated by high-throughput sequencing, to link genotype with phenotype enhancing our understanding of mitochondrial disease, with a view to providing better prognostic information.
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Affiliation(s)
- Joanna L Elson
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom.
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13
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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: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Ruiz-Pesini E, Lott MT, Procaccio V, Poole JC, Brandon MC, Mishmar D, Yi C, Kreuziger J, Baldi P, Wallace DC. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res 2006; 35:D823-8. [PMID: 17178747 PMCID: PMC1781213 DOI: 10.1093/nar/gkl927] [Citation(s) in RCA: 440] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The MITOMAP () data system for the human mitochondrial genome has been greatly enhanced by the addition of a navigable mutational mitochondrial DNA (mtDNA) phylogenetic tree of ∼3000 mtDNA coding region sequences plus expanded pathogenic mutation tables and a nuclear-mtDNA pseudogene (NUMT) data base. The phylogeny reconstructs the entire mutational history of the human mtDNA, thus defining the mtDNA haplogroups and differentiating ancient from recent mtDNA mutations. Pathogenic mutations are classified by both genotype and phenotype, and the NUMT sequences permits detection of spurious inclusion of pseudogene variants during mutation analysis. These additions position MITOMAP for the implementation of our automated mtDNA sequence analysis system, Mitomaster.
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Affiliation(s)
- Eduardo Ruiz-Pesini
- Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG) and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of CaliforniaIrvine, CA 92697-3900, USA
- Departamento de Bioquimica, Biologia Molecular y Celula, Universidad de ZaragozaZaragoza, Spain
| | - Marie T. Lott
- Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG) and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of CaliforniaIrvine, CA 92697-3900, USA
| | - Vincent Procaccio
- Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG) and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of CaliforniaIrvine, CA 92697-3900, USA
| | - Jason C. Poole
- Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG) and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of CaliforniaIrvine, CA 92697-3900, USA
| | - Marty C. Brandon
- Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG) and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of CaliforniaIrvine, CA 92697-3900, USA
- School of Information and Computer Science, University of CaliforniaIrvine, CA 92697-3425, USA
- Institute for Genomics and Bioinformatics, University of CaliforniaIrvine, CA 92697-2025, USA
| | - Dan Mishmar
- Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG) and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of CaliforniaIrvine, CA 92697-3900, USA
- Department of Life Sciences, Building 40Ben Gurion University, Beer Sheva, Israel
| | - Christina Yi
- Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG) and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of CaliforniaIrvine, CA 92697-3900, USA
| | - James Kreuziger
- Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG) and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of CaliforniaIrvine, CA 92697-3900, USA
| | - Pierre Baldi
- School of Information and Computer Science, University of CaliforniaIrvine, CA 92697-3425, USA
- Institute for Genomics and Bioinformatics, University of CaliforniaIrvine, CA 92697-2025, USA
| | - Douglas C. Wallace
- Center for Molecular and Mitochondrial Medicine and Genetics (MAMMAG) and Departments of Biological Chemistry, Ecology and Evolutionary Biology, and Pediatrics, University of CaliforniaIrvine, CA 92697-3900, USA
- School of Information and Computer Science, University of CaliforniaIrvine, CA 92697-3425, USA
- To whom correspondence should be addressed: Tel: +1 949 824 3490; Fax: +1 949 824 6388;
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15
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Starikovskaya EB, Sukernik RI, Derbeneva OA, Volodko NV, Ruiz-Pesini E, Torroni A, Brown MD, Lott MT, Hosseini SH, Huoponen K, Wallace DC. Mitochondrial DNA diversity in indigenous populations of the southern extent of Siberia, and the origins of Native American haplogroups. Ann Hum Genet 2005; 69:67-89. [PMID: 15638829 PMCID: PMC3905771 DOI: 10.1046/j.1529-8817.2003.00127.x] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In search of the ancestors of Native American mitochondrial DNA (mtDNA) haplogroups, we analyzed the mtDNA of 531 individuals from nine indigenous populations in Siberia. All mtDNAs were subjected to high-resolution RFLP analysis, sequencing of the control-region hypervariable segment I (HVS-I), and surveyed for additional polymorphic markers in the coding region. Furthermore, the mtDNAs selected according to haplogroup/subhaplogroup status were completely sequenced. Phylogenetic analyses of the resulting data, combined with those from previously published Siberian arctic and sub-arctic populations, revealed that remnants of the ancient Siberian gene pool are still evident in Siberian populations, suggesting that the founding haplotypes of the Native American A-D branches originated in different parts of Siberia. Thus, lineage A complete sequences revealed in the Mansi of the Lower Ob and the Ket of the Lower Yenisei belong to A1, suggesting that A1 mtDNAs occasionally found in the remnants of hunting-gathering populations of northwestern and northern Siberia belonged to a common gene pool of the Siberian progenitors of Paleoindians. Moreover, lineage B1, which is the most closely related to the American B2, occurred in the Tubalar and Tuvan inhabiting the territory between the upper reaches of the Ob River in the west, to the Upper Yenisei region in the east. Finally, the sequence variants of haplogroups C and D, which are most similar to Native American C1 and D1, were detected in the Ulchi of the Lower Amur. Overall, our data suggest that the immediate ancestors of the Siberian/Beringian migrants who gave rise to ancient (pre-Clovis) Paleoindians have a common origin with aboriginal people of the area now designated the Altai-Sayan Upland, as well as the Lower Amur/Sea of Okhotsk region.
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Affiliation(s)
- Elena B. Starikovskaya
- Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk
| | - Rem I. Sukernik
- Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk
| | - Olga A. Derbeneva
- Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk
- Center for Molecular Medicine, Emory University, Atlanta, GA
| | - Natalia V. Volodko
- Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk
| | | | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Universit di Pavia, Pavia, Italy
| | - Michael D. Brown
- Center for Molecular Medicine, Emory University, Atlanta, GA
- Correspondence should be addressed to: Dr. Rem I. Sukernik Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Russian Academy of Sciences Novosibirsk 630090, Russian Federation, Phone: 383-2-30-53-20, Fax: 383-2-33-12-78
| | - Marie T. Lott
- Center for Molecular Medicine, Emory University, Atlanta, GA
| | | | - Kirsi Huoponen
- Department of Medical Genetics, University in Turku, Finland
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16
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Abstract
MITOMAP (http://www.MITOMAP.org), a database for the human mitochondrial genome, has grown rapidly in data content over the past several years as interest in the role of mitochondrial DNA (mtDNA) variation in human origins, forensics, degenerative diseases, cancer and aging has increased dramatically. To accommodate this information explosion, MITOMAP has implemented a new relational database and an improved search engine, and all programs have been rewritten. System administrative changes have been made to improve security and efficiency, and to make MITOMAP compatible with a new automatic mtDNA sequence analyzer known as Mitomaster.
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Affiliation(s)
- Marty C Brandon
- Department of Information and Computer Science, University of California, Irvine, CA 92697, USA.
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17
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Derbeneva OA, Sukernik RI, Volodko NV, Hosseini SH, Lott MT, Wallace DC. Analysis of mitochondrial DNA diversity in the aleuts of the commander islands and its implications for the genetic history of beringia. Am J Hum Genet 2002; 71:415-21. [PMID: 12082644 PMCID: PMC379174 DOI: 10.1086/341720] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2002] [Accepted: 05/09/2002] [Indexed: 11/03/2022] Open
Abstract
The Aleuts are aboriginal inhabitants of the Aleutian archipelago, including Bering and Copper (Medny) Islands of the Commanders, and seem to be the survivors of the inhabitants of the southern belt of the Bering Land Bridge that connected Chukotka/Kamchatka and Alaska during the end of the Ice Age. Thirty mtDNA samples collected in the Commanders, as well as seven mtDNA samples from Sireniki Eskimos in Chukotka who belong to the Beringian-specific subhaplogroup D2, were studied through complete sequencing. This analysis has provided evidence that all 37 of these mtDNAs are closely related, since they share the founding haplotype for subhaplogroup D2. We also demonstrated that, unlike the Eskimos and Na-Dene, the Aleuts of the Commanders were founded by a single lineage of haplogroup D2, which had acquired the novel transversion mutation 8910A. The phylogeny of haplogroup D complete sequences showed that (1) the D2 root sequence type originated among the latest inhabitants of Beringia and (2) the Aleut 8910A sublineage of D2 is a part of larger radiation of rooted D2, which gave rise to D2a (Na-Dene), D2b (Aleut), and D2c (Eskimo) sublineages. The geographic specificity and remarkable intrinsic diversity of D2 lineages support the refugial hypothesis, which assumes that the founding population of Eskimo-Aleut originated in Beringan/southwestern Alaskan refugia during the early postglacial period, rather than having reached the shores of Alaska as the result of recent wave of migration from interior Siberia.
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Affiliation(s)
- Olga A. Derbeneva
- Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia; and Center for Molecular Medicine, Emory University, Atlanta
| | - Rem I. Sukernik
- Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia; and Center for Molecular Medicine, Emory University, Atlanta
| | - Natalia V. Volodko
- Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia; and Center for Molecular Medicine, Emory University, Atlanta
| | - Seyed H. Hosseini
- Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia; and Center for Molecular Medicine, Emory University, Atlanta
| | - Marie T. Lott
- Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia; and Center for Molecular Medicine, Emory University, Atlanta
| | - Douglas C. Wallace
- Laboratory of Human Molecular Genetics, Institute of Cytology and Genetics, Siberian Division, Russian Academy of Sciences, Novosibirsk, Russia; and Center for Molecular Medicine, Emory University, Atlanta
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18
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Abstract
Analysis of mitochondrial DNA (mtDNA) variation has permitted the reconstruction of the ancient migrations of women. This has provided evidence that our species arose in Africa about 150000 years before present (YBP), migrated out of Africa into Asia about 60000 to 70000 YBP and into Europe about 40000 to 50000 YBP, and migrated from Asia and possibly Europe to the Americas about 20000 to 30000 YBP. Although much of the mtDNA variation that exists in modern populations may be selectively neutral, studies of the mildly deleterious mtDNA mutations causing Leber's hereditary optic neuropathy (LHON) have demonstrated that some continent-specific mtDNA lineages are more prone to manifest the clinical symptoms of LHON than others. Hence, all mtDNA lineages are not equal, which may provide insights into the extreme environments that were encountered by our ancient ancestor, and which may be of great importance in understanding the pathophysiology of mitochondrial disease.
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Affiliation(s)
- D C Wallace
- Center for Molecular Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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19
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Abstract
We have continued to develop MITOMAP (http://www.gen.emory. edu/MITOMAP ), a comprehensive database for the human mitochondrial DNA (mtDNA). MITOMAP uses the mtDNA sequence as the unifying element for bringing together information on mitochondrial genome structure and function, pathogenic mutations and their clinical characteristics, population associated variation, and gene-gene interactions. Over the past year we have increased the degree of interlinking of MITOMAP information available on the web page, by using our generalized information management system, GENOME. As increasingly larger regions of the human genome are sequenced and characterized, the need for integrating such information is growing. Consequently, MITOMAP and GENOME provide a valuable reference for the mitochondrial biologist, in addition to being a model for the development of comprehensive, information storage and retrieval systems for other components of the human genome. This paper documents the changes to MITOMAP which have been implemented over the past year.
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Affiliation(s)
- A M Kogelnik
- Center for Molecular Medicine, Emory University School of Medicine, 1462 Clifton Road, Suite 420, Atlanta, GA 30322, USA
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20
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Abstract
We have continued to develop MITOMAP, a comprehensive database for the human mitochondrial DNA (mtDNA). MITOMAP uses the mtDNA sequence as the unifying element for bringing together information on mitochondrial genome structure and function, pathogenic mutations and their clinical characteristics, population associated variation and gene-gene interactions. As increasingly larger regions of the human genome are sequenced and characterized, the need for integrating such information will grow. Consequently, MITOMAP not only provides a valuable reference for the mitochondrial biologist, it will also provide a model for the development of comprehensive, multi-media information storage and retrieval systems for other components of the human genome. This paper is an update of the changes which have occurred to MITOMAP over the past year.
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Affiliation(s)
- A M Kogelnik
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, 1462 Clifton Road, Suite 446, Atlanta, GA 30322, USA
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21
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Abstract
We have developed a comprehensive database (MITOMAP) for the human mitochondrial DNA (mtDNA), the first component of the human genome to be completely sequenced [Anderson et al. (1981) Nature 290, 457-465]. MITOMAP uses the mtDNA sequence as the unifying element for bringing together information on mitochondrial genome structure and function, pathogenic mutations and their clinical characteristics, population associated variation, and gene- gene interactions. As increasingly larger regions of the human genome are sequenced and characterized, the need for integrating such information will grow. Consequently, MITOMAP not only provides a valuable reference for the mitochondrial biologist, it may also provide a model for the development of information storage and retrieval systems for other components of the human genome.
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Affiliation(s)
- A M Kogelnik
- Department of Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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22
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Wallace DC, Shoffner JM, Trounce I, Brown MD, Ballinger SW, Corral-Debrinski M, Horton T, Jun AS, Lott MT. Mitochondrial DNA mutations in human degenerative diseases and aging. Biochim Biophys Acta 1995; 1271:141-51. [PMID: 7599200 DOI: 10.1016/0925-4439(95)00021-u] [Citation(s) in RCA: 171] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A wide variety of mitochondrial DNA (mtDNA) mutations have recently been identified in degenerative diseases of the brain, heart, skeletal muscle, kidney and endocrine system. Generally, individuals inheriting these mitochondrial diseases are relatively normal in early life, develop symptoms during childhood, mid-life, or old age depending on the severity of the maternally-inherited mtDNA mutation; and then undergo a progressive decline. These novel features of mtDNA disease are proposed to be the product of the high dependence of the target organs on mitochondrial bioenergetics, and the cumulative oxidative phosphorylation (OXPHOS) defect caused by the inherited mtDNA mutation together with the age-related accumulation mtDNA mutations in post-mitotic tissues.
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Affiliation(s)
- D C Wallace
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
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23
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Torroni A, Brown MD, Lott MT, Newman NJ, Wallace DC. African, Native American, and European mitochondrial DNAs in Cubans from Pinar del Rio Province and implications for the recent epidemic neuropathy in Cuba. Cuba Neuropathy Field Investigation Team. Hum Mutat 1995; 5:310-7. [PMID: 7627185 DOI: 10.1002/humu.1380050407] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Genetic predisposition, particularly specific mitochondrial DNA (mtDNA) backgrounds, has been proposed as a contributing factor in the expression of an epidemic of bilateral optic neuropathy that has affected residents of Cuba since 1991. To substantiate or refute the possibility that specific subsets of mtDNAs could participate in disease expression, we took advantage of the heterogeneous ethnic origin of the Cuban population and the recent identification of a number of mtDNA polymorphisms that appear to be specific for Africans, Native Americans, and Europeans. The screening of both carefully selected people with epidemic neuropathy and control subjects from the Pinar del Rio Province for these polymorphisms revealed that African, Native American, and European mtDNA haplotypes were equally represented among case and control subjects, and suggested that approximately 50% of Cuban mtDNAs originated from Europeans, 46% from Africans, and 4% from Native Americans. These findings demonstrate that mutations arising in specific mtDNAs are unlikely to play a role in the epidemic neuropathy and indicate that analysis of mtDNA haplotypes can be a valuable tool for assessing the relative maternal contribution of Africans, Native Americans, and Europeans in a mixed population.
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Affiliation(s)
- A Torroni
- Department of Genetics, Emory University School of Medicine, Atlanta, Georgia 30332, USA
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25
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Torroni A, Lott MT, Cabell MF, Chen YS, Lavergne L, Wallace DC. mtDNA and the origin of Caucasians: identification of ancient Caucasian-specific haplogroups, one of which is prone to a recurrent somatic duplication in the D-loop region. Am J Hum Genet 1994; 55:760-76. [PMID: 7942855 PMCID: PMC1918284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
mtDNA sequence variation was examined in 175 Caucasians from the United States and Canada by PCR amplification and high-resolution restriction-endonuclease analysis. The majority of the Caucasian mtDNAs were subsumed within four mtDNA lineages (haplogroups) defined by mutations that are rarely seen in Africans and Mongoloids. The sequence divergence of these haplogroups indicates that they arose early in Caucasian radiation and gave raise to modern European mtDNAs. Although ancient, none of these haplogroups is old enough to be compatible with a Neanderthal origin, suggesting that Homo sapiens sapiens displaced H. s. neanderthaliensis, rather than mixed with it. The mtDNAs of one of these haplogroups have a unique homoplasmic insertion between nucleotide pair (np) 573 and np 574, within the D-loop control region. This insertion makes these mtDNAs prone to a somatic mutation that duplicates a 270-bp portion of the D-loop region between np 309 and np 572. This finding suggests that certain nonpathogenic mtDNA mutations could predispose individuals to mtDNA rearrangements.
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Affiliation(s)
- A Torroni
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, GA 30322
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26
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Corral-Debrinski M, Horton T, Lott MT, Shoffner JM, McKee AC, Beal MF, Graham BH, Wallace DC. Marked changes in mitochondrial DNA deletion levels in Alzheimer brains. Genomics 1994; 23:471-6. [PMID: 7835898 DOI: 10.1006/geno.1994.1525] [Citation(s) in RCA: 210] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Levels of the common 4977 nucleotide pair (np) mitochondrial DNA (mtDNA) deletion (mtDNA4977) were quantitated in the cortex, putamen, and cerebellum of patients with Alzheimer disease (AD) and compared to age-matched controls. Although cerebellum deletion levels were comparably low in AD patients and controls of all ages, cortical deletion levels were clearly different. The levels of mtDNA deletions in control brains started low, but rose markedly after age 75, while those of AD patients started high and declined to low levels by age 80. Choosing age 75 to arbitrarily delineate between younger and older subjects, younger patients had 15 times more mtDNA deletions than younger controls, while older patients had one-fifth the deletion level of older controls. Younger AD patients also had fourfold more deletions than older AD patients. These results support the hypothesis that OXPHOS defects resulting from somatic mtDNA mutations may play a role in AD pathophysiology.
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Affiliation(s)
- M Corral-Debrinski
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, Georgia 30322
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27
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Newman NJ, Torroni A, Brown MD, Lott MT, Fernandez MM, Wallace DC. Epidemic neuropathy in Cuba not associated with mitochondrial DNA mutations found in Leber's hereditary optic neuropathy patients. Cuba Neuropathy Field Investigation Team. Am J Ophthalmol 1994; 118:158-68. [PMID: 8053461 DOI: 10.1016/s0002-9394(14)72895-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
An epidemic neuropathy in Cuba has caused bilateral optic neuropathies in more than 26,000 people during the past three years. Various pathogenetic factors have been proposed, including toxins, nutritional deficiencies, and an underlying genetic predisposition involving mitochondrial DNA. As part of a case-control collaborative investigation, 135 Cuban blood samples were analyzed for the most common mitochondrial DNA mutations associated with Leber's hereditary optic neuropathy. None of the participants tested were found to have the mitochondrial DNA mutations at nucleotide positions 11778, 3460, 14484, 7444, or 9804. Of 57 definite case subjects and 69 normal control subjects, three case and three control subjects had the mutation at nucleotide position 9438, three different case and three different control subjects had the mutation at position 13708, and one case and one control subject had the mutation at position 15257 in association with the mutation at position 13708. The most common mitochondrial DNA mutations associated with Leber's hereditary optic neuropathy do not appear to be contributing factors in the epidemic neuropathy in Cuba. We also identified a large Cuban family with maternally related members who experienced visual loss consistent with the diagnosis of Leber's hereditary optic neuropathy. Maternal family members harbored the highly pathogenetic mutation at nucleotide position 11778.
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Affiliation(s)
- N J Newman
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia 30322
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28
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Brown MD, Torroni A, Huoponen K, Chen YS, Lott MT, Wallace DC. Pathological significance of the mtDNA COX III mutation at nucleotide pair 9438 in Leber hereditary optic neuropathy. Am J Hum Genet 1994; 55:410-2. [PMID: 8037217 PMCID: PMC1918366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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29
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Torroni A, Chen YS, Semino O, Santachiara-Beneceretti AS, Scott CR, Lott MT, Winter M, Wallace DC. mtDNA and Y-chromosome polymorphisms in four Native American populations from southern Mexico. Am J Hum Genet 1994; 54:303-18. [PMID: 8304347 PMCID: PMC1918164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
mtDNA sequence variation was examined in 60 Native Americans (Mixtecs from the Alta, Mixtecs from the Baja, Valley Zapotecs, and Highland Mixe) from southern Mexico by PCR amplification and high-resolution restriction endonuclease analysis. Four groups of mtDNA haplotypes (haplogroups A, B, C, and D) characterize Amerind populations, but only three (haplogroups A, B, and C) were observed in these Mexican populations. The comparison of their mtDNA variation with that observed in other populations from Mexico and Central America permits a clear distinction among the different Middle American tribes and raises questions about some of their linguistic affiliations. The males of these population samples were also analyzed for Y-chromosome RFLPs with the probes 49a, 49f, and 12f2. This analysis suggests that certain Y-chromosome haplotypes were brought from Asia during the colonization of the Americas, and a differential gene flow was introduced into Native American populations from European males and females.
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Affiliation(s)
- A Torroni
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, Georgia 30322
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30
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Abstract
Recent discoveries in mitochondrial clinical genetics have revealed that a broad spectrum of clinical phenotypes are associated with mutations in mitochondrial DNA. Diseases caused by mutations in mitochondrial DNA are by nature quantitative. Myoclonic epilepsy and ragged-red fiber disease are caused by a mutation in the transfer RNA gene lysine. Although everyone in a maternal lineage will harbor the same mutation, the nature and severity of the symptoms vary markedly among individuals. This variability correlates with the inherited percentage of mutations in the individual's mitochondrial DNA and the individual's age. Age-related expression of mitochondrial disease has also been demonstrated for mitochondrial DNA deletions. Although deletions that retain both origins of replication result in late-onset disease because of the progressive enrichment of the deleted mitochondrial DNA, a 10.4-kb deletion that lacks the light-strand replication origin and maintains a stable mutant percentage in both tissues and cultured cells has been discovered. This deletion is associated with adult-onset diabetes and deafness, but not with ophthalmoplegia, ptosis, or mitochondrial myopathy. Biochemically, it causes a generalized defect in mitochondrial protein synthesis and oxidative phosphorylation. The age-related decline in oxidative phosphorylation could reflect the accumulation of somatic mitochondrial DNA mutations. Inhibition of oxidative phosphorylation stimulates this accumulation. The general paradigm for mitochondrial DNA diseases may be that inherited mutations inhibit the electron transport chain. This damages the mitochondrial DNA, further reducing oxidative phosphorylation. Ultimately, oxidative phosphorylation drops below the expression threshold of cells and tissues, and clinical symptoms appear.
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Affiliation(s)
- D C Wallace
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, Georgia 30322
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31
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Shoffner JM, Brown MD, Torroni A, Lott MT, Cabell MF, Mirra SS, Beal MF, Yang CC, Gearing M, Salvo R. Mitochondrial DNA variants observed in Alzheimer disease and Parkinson disease patients. Genomics 1993; 17:171-84. [PMID: 8104867 DOI: 10.1006/geno.1993.1299] [Citation(s) in RCA: 326] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Mitochondrial DNA (mtDNA) variants associated with Alzheimer disease (AD) and Parkinson disease (PD) were sought by restriction endonuclease analysis in a cohort of 71 late-onset Caucasian patients. A tRNA(Gln) gene variant at nucleotide pair (np) 4336 that altered a moderately conserved nucleotide was present in 9/173 (5.2%) of the patients surveyed but in only 0.7% of the general Caucasian controls. One of these patients harbored an additional novel 12S rRNA 5-nucleotide insertion at np 956-965, while a second had a missense variant at np 3397 that converted a highly conserved methionine to a valine. This latter mutation was also found in an independent AD + PD patient, as was a heteroplasmic 16S rRNA variant at np 3196. Additional studies will be required to determine the significance, if any, of these mutations.
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Affiliation(s)
- J M Shoffner
- Department of Genetics, Emory University School of Medicine, Atlanta, Georgia 30322
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32
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Abstract
OBJECTIVE Leber's hereditary optic neuropathy (LHON) is typically a familial disease of primarily young, male adults. Analysis of mitochondrial DNA has identified point mutations associated with LHON and allowed us to identify cases of LHON not consistent with traditional descriptions of the disease. DATA SOURCES The collective experience of three tertiary referral centers contributed to this report. STUDY SELECTION Patients with bilateral optic neuropathies who were positive for the 11778 LHON mutation were included in this study if they were female and there was no family history of visual loss. DATA EXTRACTION Six case histories are presented. DATA SYNTHESIS The diagnosis of LHON remained unknown in six female patients with bilateral optic neuropathies until molecular analysis revealed the 11778 mitochondrial DNA mutation. None of the patients had a family history of visual loss, and five were initially diagnosed as having factitious visual loss. Other individual features atypical for LHON included lack of the characteristic LHON funduscopic appearance, bitemporal hemianopia, optic disc cupping, and premonitory episodes of transient visual loss. In one patient the correct diagnosis was delayed 17 years. CONCLUSIONS The diagnosis of LHON should be considered in all cases of unexplained optic neuropathy, including those with negative family history, late or early age at onset, female gender, or normal funduscopic appearance.
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Affiliation(s)
- N C Weiner
- Department of Ophthalmology, Harvard Medical School, Boston, Mass
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33
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Corral-Debrinski M, Horton T, Lott MT, Shoffner JM, Beal MF, Wallace DC. Mitochondrial DNA deletions in human brain: regional variability and increase with advanced age. Nat Genet 1992; 2:324-9. [PMID: 1303288 DOI: 10.1038/ng1292-324] [Citation(s) in RCA: 627] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We have examined the role of somatic mitochondrial DNA (mtDNA) mutations in human ageing by quantitating the accumulation of the common 4977 nucleotide pair (np) deletion (mtDNA4977) in the cortex, putamen and cerebellum. A significant increase in the mtDNA4977 deletion was seen in elderly individuals. In the cortex, the deleted to total mtDNA ratio ranged from 0.00023 to 0.012 in 67-77 year old brains and up to 0.034 in subjects over 80. In the putamen, the deletion level ranged from 0.0016 to 0.010 in 67 to 77 years old up to 0.12 in individuals over the age of 80. The cerebellum remained relatively devoid of mtDNA deletions. Similar changes were observed with a different 7436 np deletion. These changes suggest that somatic mtDNA deletions might contribute to the neurological impairment often associated with ageing.
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Affiliation(s)
- M Corral-Debrinski
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, Georgia 30322
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34
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Abstract
The role of somatic mitochondrial DNA (mtDNA) damage in human aging and progressive diseases of oxidative phosphorylation (OXPHOS) was examined by quantitating the accumulation of mtDNA deletions in normal hearts and hearts with coronary atherosclerotic disease. In normal hearts, mtDNA deletions appeared after 40 and subsequently accumulated with age. The common 4977 nucleotide pair (np) deletion (mtDNA4977) reached a maximum of 0.007%, with the mtDNA7436 and mtDNA10,422 deletions appearing at the same time. In hearts deprived of mitochondrial substrates due to coronary artery disease, the level of the mtDNA4977 deletion was elevated 7-220-fold over age-matched controls, with the mtDNA7436 and mtDNA10,422 deletions increasing in parallel. This cumulative mtDNA damage was associated with a compensatory 3.5-fold induction of nuclear OXPHOS gene mRNA and regions of ischemic hearts subjected to the greatest work load (left ventricle) showed the greatest accumulation of mtDNA damage and OXPHOS gene induction. These observations support the hypothesis that mtDNA damage does accumulate with age and indicates that respiratory stress greatly elevates mitochondrial damage.
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Affiliation(s)
- M Corral-Debrinski
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, GA 30322
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35
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Brown MD, Yang CC, Trounce I, Torroni A, Lott MT, Wallace DC. A mitochondrial DNA variant, identified in Leber hereditary optic neuropathy patients, which extends the amino acid sequence of cytochrome c oxidase subunit I. Am J Hum Genet 1992; 51:378-85. [PMID: 1322638 PMCID: PMC1682694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A G-to-A transition at nucleotide pair (np) 7444 in the mtDNA was found to correlate with Leber hereditary optic neuropathy (LHON). The mutation eliminates the termination codon of the cytochrome c oxidase subunit I (COI) gene, extending the COI polypeptide by three amino acids. The mutation was discovered as an XbaI restriction-endonuclease-site loss present in 2 (9.1%) of 22 LHON patients who lacked the np 11778 LHON mutation and in 6 (1.1%) of 545 unaffected controls. The mutant polypeptide has an altered mobility on SDS-PAGE, suggesting a structural alteration, and the cytochrome c oxidase enzyme activity of patient lymphocytes is reduced approximately 40% relative to that in controls. These data suggest that the np 7444 mutation results in partial respiratory deficiency and thus contributes to the onset of LHON.
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Affiliation(s)
- M D Brown
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, GA 30322
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36
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Abstract
A number of human diseases have been attributed to defects in oxidative phosphorylation (OXPHOS) resulting from mutations in the mitochondrial DNA (mtDNA). One such disease is Leber's hereditary optic neuropathy (LHON), a neurodegenerative disease of young adults that results in blindness due to atrophy of the optic nerve. The etiology of LHON is genetically heterogeneous and in some cases multifactorial. Eleven mtDNA mutations have been associated with LHON, all of which are missense mutations in the subunit genes for the subunits of the electron transport chain complexes I, III, and IV. Molecular, biochemical, and population genetic studies have categorized these mutations as high risk (class I), low risk (class II), or intermediate risk (class I/II). Class I mutations appear to be primary genetic causes of LHON, while class II mutations are frequently found associated with class I genotypes and may serve as exacerbating genetic factors. Different LHON pedigrees can harbor different combinations of class I, II, or I/II mtDNA mutations, as shown by the complete sequence analysis of the mtDNAs of four LHON probands. The various mtDNA genotypes included an isolated class I mutation, combined class I+II mutations, and combined class I/II+II mutations. The occurrence of such genotypes supports the hypothesis that LHON may result from the additive effects of various genetic and environmental insults to OXPHOS, each of which increases the probability of blindness.
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Affiliation(s)
- M D Brown
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, Georgia 30322
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37
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Ortiz RG, Newman NJ, Manoukian SV, Diesenhouse MC, Lott MT, Wallace DC. Optic disk cupping and electrocardiographic abnormalities in an American pedigree with Leber's hereditary optic neuropathy. Am J Ophthalmol 1992; 113:561-6. [PMID: 1575231 DOI: 10.1016/s0002-9394(14)74730-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We examined the clinical characteristics of affected and unaffected members of an American black family with the 11778 mitochondrial DNA mutation associated with Leber's hereditary optic neuropathy. Thirty-six individuals from four generations were included. All maternally related subjects were shown to be essentially homoplasmic for the 11778 mitochondrial DNA mutation in blood. Paternally related subjects did not carry this mutation. Patients affected with optic neuropathy had optic nerve head cupping. Loss of unmyelinated axons from the prelaminar optic nerve may be responsible for cupping in these patients. Electrocardiographic analysis of subjects carrying the 11778 mitochondrial DNA mutation disclosed statistically significant (P = .02) prolongation of the corrected OT interval as compared to control subjects. While the clinical significance of this magnitude of corrected QT prolongation is unknown, it may represent a systemic manifestation of the 11778 mutation. No electrocardiographic evidence of preexcitation syndromes was seen.
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Affiliation(s)
- R G Ortiz
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia
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Stone EM, Newman NJ, Miller NR, Johns DR, Lott MT, Wallace DC. Visual recovery in patients with Leber's hereditary optic neuropathy and the 11778 mutation. J Clin Neuroophthalmol 1992; 12:10-4. [PMID: 1532593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Five patients with Leber's hereditary optic neuropathy (LHON) and the 11778 mitochondrial mutation spontaneously recovered 20/40 or better visual acuity in at least one eye after months to years of legal blindness. The patients ranged in age from 9 to 45 years, and the duration of visual loss before recovery ranged from several months to 5.9 years. These patients constitute only about 4% of the 136 affected LHON patients we have studied who also had the 11778 mutation in their mitochondrial DNA. Thus, even though the visual prognosis for most patients with LHON and the 11778 mutation is poor, a few individuals do recover near-normal vision in at least one eye even years after the initial visual loss.
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Affiliation(s)
- E M Stone
- Department of Ophthalmology, University of Iowa College of Medicine, Iowa City
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Abstract
A number of mitochondrial DNA (mtDNA) mutations have been identified which cause familial, late onset neuromuscular degenerative diseases. These include missense mutations in most of the mtDNA polypeptide genes as well as base substitutions in several tRNA genes. Missense mutations in the mitochondrial electron-transport genes cause Leber hereditary optic neuropathy. Ten mutations have been associated with this disease, but four at nps 11,178, 3460, 4160 and 15,257 appear sufficient in themselves to cause the disease. One missense mutation in the ATPase 6 gene at np 8993 causes a second phenotype, neurogenic muscle weakness, ataxia and retinitis pigmentosum. Transfer RNA mutations have been identified for myoclonic epilepsy and ragged-red fibre disease in the tRNA(Lys) gene at np 8344 and for the mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes syndrome and for maternal mitochondrial myopathy and cardiomyopathy syndrome in the tRNA(Leu)(UUR) gene at nps 3234 and 3260, respectively. Deficiencies in mitochondrial oxidative phosphorylation enzymes have been observed in several common neurodegenerative diseases such as Alzheimer and Parkinson diseases. Perhaps mtDNA mutations play a role in these as well.
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Affiliation(s)
- D C Wallace
- Department of Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, GA 30322
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Brown MD, Voljavec AS, Lott MT, Torroni A, Yang CC, Wallace DC. Mitochondrial DNA complex I and III mutations associated with Leber's hereditary optic neuropathy. Genetics 1992; 130:163-73. [PMID: 1732158 PMCID: PMC1204789 DOI: 10.1093/genetics/130.1.163] [Citation(s) in RCA: 195] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Four new missense mutations have been identified through restriction analysis and sequencing of the mitochondrial DNAs (mtDNA) from Leber's hereditary optic neuropathy (LHON) patients who lacked the previously identified 11778 mutation. Each altered a conserved amino acid and correlated with the LHON phenotype in population and phylogenetic analyses. The nucleotide pair (np) 13708 mutation (G to A, ND5 gene) changed an alanine to a threonine and was found in 6/25 (24%) of non-11778 LHON pedigrees and in 5.0% of controls, the np 15257 mutation (G to A, cytochrome b gene) changed an aspartate to an asparagine and was found in 4 of the 13708-positive pedigrees and 0.3% of controls, the np 15812 mutation (G to A, cytochrome b gene) changed a valine to a methionine and was detected in two of the 15257-positive pedigrees and 0.1% of controls and the np 5244 mutation (G to A, ND2 gene) changed a glycine to a serine and was found in one of the 15812-positive patients and none of 2103 controls. The 15257 mutation altered a highly conserved amino acid in an extramembrane domain of cytochrome b that is associated with the ligation of the low potential b566 heme and the 5244 mutation altered a strongly evolutionarily conserved region of the ND2 polypeptide. The 13708 and 15812 mutations changed moderately conserved amino acids. Haplotype and phylogenetic analysis of the four np 15257 mtDNAs revealed that all harbored the same rare Caucasian haplotype and that the np 13708, np 15257, np 15812 and np 5244 mutations were added sequentially along this mtDNA lineage. Since the percentage of sighted controls decreases as these mutations accumulate, it appears that they interact synergistically, each increasing the probability of blindness. The involvement of both mitochondrial complex I (np 5244, 11778, 13708) and complex III (np 15257, 15812) mutations in LHON indicates that the clinical manifestations of this disease are the product of an overall decrease in mitochondrial energy production rather than a defect in a specific mitochondrial enzyme.
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Affiliation(s)
- M D Brown
- Center for Genetics and Molecular Medicine, Emory University School of Medicine, Atlanta, Georgia 30322
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Corral-Debrinski M, Stepien G, Shoffner JM, Lott MT, Kanter K, Wallace DC. Hypoxemia is associated with mitochondrial DNA damage and gene induction. Implications for cardiac disease. JAMA 1991; 266:1812-6. [PMID: 1890710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVE --Oxidative phosphorylation (OXPHOS) deficiency due to hypoxemia or other causes was hypothesized to increase oxygen radical generation, damage mitochondrial DNA (mtDNA), and reduce adenosine triphosphate synthesis, resulting in compensatory OXPHOS gene induction. Therefore, we investigated the levels of mtDNA damage and OXPHOS transcripts in normal and ischemic hearts, and then in other forms of heart disease. DESIGN --DNA was extracted from the heart and the levels of the common 4977 base pair mtDNA deletion were quantitated as an index for mtDNA damage. Total RNA was extracted from hearts and analyzed for OXPHOS transcript levels. RESULTS --In control hearts, the 4977 base pair mtDNA deletion appeared at age 40 years and reached a maximum deletion of 0.0035%. Much higher levels were found in ischemic hearts (0.02% to 0.85%), as well as in three of 10 cases with other types of heart disease (0.017% to 0.16%). The OXPHOS transcripts were increased in all diseased hearts. CONCLUSION --Ischemic hearts have increased mtDNA damage and OXPHOS gene expression, suggesting that mtDNA damage is associated with OXPHOS deficiency. Oxidative phosphorylation defects may also play a role in some other forms of cardiac disease.
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Affiliation(s)
- M Corral-Debrinski
- Department of Genetics, Emory University School of Medicine, Atlanta, GA 30322
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Abstract
In a study of the phenotypic characteristics of pedigrees of Leber's hereditary optic neuropathy positive for the mitochondrial DNA mutation at position 11778, 28 of 49 pedigrees were represented by singleton cases. Seven families, including six singleton pedigrees, had maternal family members with a mixture of mutant and normal mitochondrial DNA (heteroplasmy). Seventy-two affected individuals from 43 families showed a male predominance of 81.9% (59/72) and ages of onset of visual loss ranging from 8 to 60 years. The time interval between affected eyes averaged 1.8 months; the duration of progression of visual loss in each eye averaged 3.7 months. Visual acuity was 20/200 or worse in 107 of 109 (98.2%) eyes. Telangiectatic microangiopathy, disk pseudoedema, or vascular tortuosity, ophthalmoscopic features believed to be classic of Leber's hereditary optic neuropathy, were noted in 30 of 52 patients. Visual-evoked responses were typically absent or abnormal. Electrocardiograms, fluorescein angiograms, cerebrospinal fluid analyses, brain computed tomography, and magnetic resonance imaging were usually normal. There were no consistent neurologic or systemic illnesses associated with these Leber's pedigrees. In many cases, the diagnosis would not have been suspected because of the absence of a compatible family history, typical clinical profile, or ophthalmoscopic appearance. Genetic analysis showed the mitochondrial DNA mutation at position 11778, which established the diagnosis of Leber's hereditary optic neuropathy and has allowed for a broader view of the clinical features of this disease.
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Affiliation(s)
- N J Newman
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, Georgia
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Wallace DC, Lott MT, Lezza AM, Seibel P, Voljavec AS, Shoffner JM. Mitochondrial DNA mutations associated with neuromuscular diseases: analysis and diagnosis using the polymerase chain reaction. Pediatr Res 1990; 28:525-8. [PMID: 2123980 DOI: 10.1203/00006450-199011000-00023] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A number of neuromuscular diseases are associated with molecular defects in the mitochondrial DNA (mtDNA). These include: 1) a missense mutation at nucleotide 11778 in the mtDNA of Leber's hereditary optic neuropathy patients; 2) a heterogeneous array of deletions in the mtDNA of ocular myopathy patients; and 3) small deletions and point mutations in the mtDNA of myoclonic epilepsy and ragged red fiber disease patients. We can now diagnose these diseases at the molecular level from small patient samples by amplifying the affected mtDNA regions using the polymerase chain reaction. Leber's hereditary optic neuropathy is diagnosed through loss of an SfaNI restriction site. Ocular myopathy deletions are identified by differential amplification across deletion breakpoints. Familial diseases such as myoclonic epilepsy and ragged red fiber disease might be diagnosed by identifying small deletions through amplification and electrophoretic analysis of the entire mtDNA genome or by identifying point mutations through differential oligonucleotide hybridization. As additional mtDNA molecular defects are identified, molecular analysis will likely become a primary tool for the diagnosis of these diseases.
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Affiliation(s)
- D C Wallace
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
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Shoffner JM, Lott MT, Lezza AM, Seibel P, Ballinger SW, Wallace DC. Myoclonic epilepsy and ragged-red fiber disease (MERRF) is associated with a mitochondrial DNA tRNA(Lys) mutation. Cell 1990; 61:931-7. [PMID: 2112427 DOI: 10.1016/0092-8674(90)90059-n] [Citation(s) in RCA: 1000] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
An A to G transition mutation at nucleotide pair 8344 in human mitochondrial DNA (mtDNA) has been identified as the cause of MERRF. The mutation alters the T psi C loop of the tRNA(Lys) gene and creates a CviJI restriction site, providing a simple molecular diagnostic test for the disease. This mutation was present in three independent MERRF pedigrees and absent in 75 controls, altered a conserved nucleotide, and was heteroplasmic. All MERRF patients and their less-affected maternal relatives had between 2% and 27% wild-type mtDNAs and showed an age-related association between genotype and phenotype. This suggests that a small percentage of normal mtDNAs has a large protective effect on phenotype. This mutation provides molecular confirmation that some forms of epilepsy are the result of deficiencies in mitochondrial energy production.
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Affiliation(s)
- J M Shoffner
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia 30322
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Abstract
Leber's hereditary optic neuropathy is caused by a single nucleotide change in the mitochondrial deoxyribonucleic acid (mtDNA). Each cell contains thousands of mitochondrial DNA molecules. We demonstrated that in certain isolated instances, the proband and close maternal lineage relatives can have mixtures of mutant and normal mitochondrial DNA molecules (heteroplasmy). The proportion of mutant mitochondrial DNA molecules was found to shift markedly across generations and within the tissues of an individual. One unaffected mother had 65% mutant mitochondrial DNA molecules whereas her affected son had essentially 100% mutant mitochondrial DNA molecules. Two affected individuals had predominantly mutant mitochondrial DNA in their blood, but significant normal mitochondrial DNA in their hair. The demonstration of heteroplasmy within maternal lineages and affected individuals means that the successful determination of the mitochondrial DNA genotype of a family or patient with Leber's hereditary optic neuropathy requires testing of more than one family member and more than one tissue from each individual.
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Affiliation(s)
- M T Lott
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30329
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Shoffner JM, Lott MT, Voljavec AS, Soueidan SA, Costigan DA, Wallace DC. Spontaneous Kearns-Sayre/chronic external ophthalmoplegia plus syndrome associated with a mitochondrial DNA deletion: a slip-replication model and metabolic therapy. Proc Natl Acad Sci U S A 1989; 86:7952-6. [PMID: 2554297 PMCID: PMC298190 DOI: 10.1073/pnas.86.20.7952] [Citation(s) in RCA: 316] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The muscle mitochondria of a patient with Kearns-Sayre/chronic external ophthalmoplegia plus syndrome were found to be completely deficient in respiratory complex I activity and partially deficient in complex IV and V activities. Treatment of the patient with coenzyme Q10 and succinate resulted in clinical improvement of respiratory function, consistent with the respiratory deficiencies. Restriction enzyme analysis of the muscle mtDNA revealed a 4.9-kilobase deletion in 50% of the mtDNA molecules. Polymerase chain reaction analysis demonstrated that the deletion was present in the patient's muscle but not in her lymphocytes or platelets. Furthermore, the deletion was not present in the muscle or platelets of two sisters. Hence, the mutation probably occurred in the patient's somatic cells. Direct sequencing of polymerase chain reaction-amplified DNA revealed a 4977-base-pair deletion removing four genes for subunits of complex I, one gene for complex IV, two genes for complex V, and five genes for tRNAs, which paralleled the respiratory enzymes affected in the disease. A 13-base-pair direct repeat was observed upstream from both breakpoints. Relative to the direction of heavy-strand replication, the first repeat was retained and the second repeat was deleted, suggesting a slip-replication mechanism. Sequence analysis of the human mtDNA revealed many direct repeats of 10 base pairs or greater, indicating that this mechanism could account for other reported deletions. We postulate that the prevalence of direct repeats in the mtDNA is a consequence of the guanine-cytosine bias of the heavy and light strands.
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Affiliation(s)
- J M Shoffner
- Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322
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Zheng X, Shoffner JM, Lott MT, Voljavec AS, Krawiecki NS, Winn K, Wallace DC. Evidence in a lethal infantile mitochondrial disease for a nuclear mutation affecting respiratory complexes I and IV. Neurology 1989; 39:1203-9. [PMID: 2549452 DOI: 10.1212/wnl.39.9.1203] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A child died at 4 months of age of a lethal infantile mitochondrial disease associated with cardiomyopathy. Detailed pathologic evaluation of this patient revealed abnormalities in the striated muscle, smooth muscle, heart, and liver, but not the central nervous system. Biochemical analysis revealed a combined complex I and IV deficiency in skeletal muscle, heart, and liver, but not in kidney and brain. Analysis of mitochondrial translation products and mitochondrial DNA failed to detect any abnormality. Parallel studies on both parents were uniformly normal. These data support the hypothesis that this disease was the result of a nuclear DNA mutation in a developmental stage-specific and tissue-specific oxidative phosphorylation-gene.
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Affiliation(s)
- X Zheng
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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48
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Abstract
Leber's hereditary optic neuropathy is a maternally inherited disease associated with the late onset of bilateral loss of central vision and cardiac dysrhythmias. The maternal inheritance is explained by the mitochondrial origin of the disease. Analysis of the sequence of a mitochondrial DNA has indicated that a single nucleotide change at position 11778 is associated with this disease. This mutation converts the 340th amino acid of NADH dehydrogenase subunit 4 from an arginine to a histidine and eliminates an SfaNI endonuclease restriction site. A survey of restriction-fragment-length polymorphisms in the mitochondrial DNA of three independent families with this disease (an American black and two white European families) and 10 controls confirmed that this SfaNI site is associated with the disease. A phylogenetic tree for mitochondrial DNA polymorphism and sequence variants from three probands with Leber's disease and four controls was constructed, and the mutation at position 11778 was found to be associated with two mitochondrial DNA backgrounds--an American black mitochondrial DNA and a European mitochondrial DNA. Thus, this mutation must have arisen twice independently. Since the mutation correlated with symptoms of Leber's disease in both cases, these findings indicate that the mutation is a cause of the disease. This genetic analysis has identified the specific point mutation in the mitochondrial DNA that results in Leber's hereditary optic neuropathy.
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Affiliation(s)
- G Singh
- Department of Biochemistry, Emory University, Atlanta, GA
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Wallace DC, Singh G, Lott MT, Hodge JA, Schurr TG, Lezza AM, Elsas LJ, Nikoskelainen EK. Mitochondrial DNA mutation associated with Leber's hereditary optic neuropathy. Science 1988; 242:1427-30. [PMID: 3201231 DOI: 10.1126/science.3201231] [Citation(s) in RCA: 1522] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Leber's hereditary optic neuropathy is a maternally inherited disease resulting in optic nerve degeneration and cardiac dysrhythmia. A mitochondrial DNA replacement mutation was identified that correlated with this disease in multiple families. This mutation converted a highly conserved arginine to a histidine at codon 340 in the NADH dehydrogenase subunit 4 gene and eliminated an Sfa NI site, thus providing a simple diagnostic test. This finding demonstrated that a nucleotide change in a mitochondrial DNA energy production gene can result in a neurological disease.
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Affiliation(s)
- D C Wallace
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
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Wallace DC, Zheng XX, Lott MT, Shoffner JM, Hodge JA, Kelley RI, Epstein CM, Hopkins LC. Familial mitochondrial encephalomyopathy (MERRF): genetic, pathophysiological, and biochemical characterization of a mitochondrial DNA disease. Cell 1988; 55:601-10. [PMID: 3180221 DOI: 10.1016/0092-8674(88)90218-8] [Citation(s) in RCA: 340] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A large MERRF pedigree permitted the direct testing of the predictions for a mitochondrial DNA (mtDNA) mutation. A mtDNA mutation was demonstrated by proving maternal inheritance and by identifying specific deficiencies in muscle energetics and mitochondrial respiratory complexes I and IV. mtDNA heteroplasmy (a mixture of mutant and wild-type mtDNAs) was demonstrated by showing variation in the mitochondrial energetic capacity between family members. The phenotypic consequences of differential tissue-specific reliance on mitochondrial ATP was shown by correlating individual respiratory deficiency with the nature and severity of patients' clinical manifestations. The observed spectrum of clinical manifestations resulting from this heteroplasmic mtDNA mutation implies that mtDNA disease may be much more prevalent than previously anticipated.
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Affiliation(s)
- D C Wallace
- Department of Biochemistry, W. M. B., Emory University School of Medicine, Atlanta, Georgia 30322
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