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Kripps KA, Friederich MW, Chen T, Larson AA, Mirsky DM, Wang Y, Tanji K, Knight KM, Wong LJ, Van Hove JLK. A novel acceptor stem variant in mitochondrial tRNA Tyr impairs mitochondrial translation and is associated with a severe phenotype. Mol Genet Metab 2020; 131:398-404. [PMID: 33279411 PMCID: PMC7749820 DOI: 10.1016/j.ymgme.2020.11.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 11/25/2022]
Abstract
Genetic defects in mitochondrial DNA encoded tRNA genes impair mitochondrial translation with resultant defects in the mitochondrial respiratory chain and oxidative phosphorylation system. The phenotypic spectrum of disease seen in mitochondrial tRNA defects is variable and proving pathogenicity of new variants is challenging. Only three pathogenic variants have been described previously in the mitochondrial tRNATyr gene MT-TY, with the reported phenotypes consisting largely of adult onset myopathy and ptosis. We report a patient with a novel MT-TY acceptor stem variant m.5889A>G at high heteroplasmy in muscle, low in blood, and absent in the mother's blood. The phenotype consisted of a childhood-onset severe multi-system disorder characterized by a neurodegenerative course including ataxia and seizures, failure-to-thrive, combined myopathy and neuropathy, and hearing and vision loss. Brain imaging showed progressive atrophy and basal ganglia calcifications. Mitochondrial biomarkers lactate and GDF15 were increased. Functional studies showed a deficient activity of the respiratory chain enzyme complexes containing mtDNA-encoded subunits I, III and IV. There were decreased steady state levels of these mitochondrial complex proteins, and presence of incompletely assembled complex V forms in muscle. These changes are typical of a mitochondrial translational defect. These data support the pathogenicity of this novel variant. Careful review of variants in MT-TY additionally identified two other pathogenic variants, one likely pathogenic variant, nine variants of unknown significance, five likely benign and four benign variants.
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Affiliation(s)
- Kimberly A Kripps
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Marisa W Friederich
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA; Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, 13121 East 16th Avenue, Aurora, CO, USA
| | - Ting Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, China
| | - Austin A Larson
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - David M Mirsky
- Department of Radiology, University of Colorado, and Children's Hospital Colorado, Aurora, CO, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kurenai Tanji
- Division of Neuropathology, Columbia University Medical Center, New York, NY, USA
| | - Kaz M Knight
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Johan L K Van Hove
- Section of Clinical Genetics and Metabolism, Department of Pediatrics, University of Colorado, Aurora, CO, USA; Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, 13121 East 16th Avenue, Aurora, CO, USA.
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Lim AZ, McMacken G, Rastelli F, Oláhová M, Baty K, Hopton S, Falkous G, Töpf A, Lochmüller H, Marini-Bettolo C, McFarland R, Taylor RW. A novel, pathogenic dinucleotide deletion in the mitochondrial MT-TY gene causing myasthenia-like features. Neuromuscul Disord 2020; 30:661-668. [PMID: 32684384 PMCID: PMC7477489 DOI: 10.1016/j.nmd.2020.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA)-related diseases often pose a diagnostic challenge and require rigorous clinical and laboratory investigation. Pathogenic variants in the mitochondrial tRNA gene MT-TY, which encodes the tRNATyr, are a rare cause of mitochondrial disease. Here we describe a novel m.5860delTA anticodon variant in the MT-TY gene in a patient who initially presented with features akin to a childhood onset myasthenic syndrome. Using histochemical, immunohistochemical and protein studies we demonstrate that this mutation leads to severe biochemical defects of mitochondrial translation, which is reflected in the early onset and progressive phenotype. This case highlights the clinical overlap between mtDNA-related diseases and other neuromuscular disorders, and demonstrates the potential pitfalls in analysis of next generation sequencing results, given whole exome sequencing of a blood DNA sample failed to make a genetics diagnosis. Muscle biopsy remains an important requirement in the diagnosis of mitochondrial disease and in establishing the pathogenicity of novel mtDNA variants.
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Affiliation(s)
- Albert Z Lim
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Grace McMacken
- The John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK; Department of Neurosciences, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
| | - Francesca Rastelli
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Karen Baty
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne, UK
| | - Sila Hopton
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne, UK
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne, UK
| | - Ana Töpf
- The John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Hanns Lochmüller
- Department of Neuropediatrics and Muscle Disorders, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Research Institute, Children's Hospital of Eastern Ontario, Ottawa, Canada; Division of Neurology, Department of Medicine, Ottawa University, Ottawa, Canada
| | - Chiara Marini-Bettolo
- The John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne, UK; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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3
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Proximal Myopathy due to m.5835G>A Mutation in Mitochondrial MT-TY Gene. Case Rep Neurol Med 2019; 2018:8406712. [PMID: 30643656 PMCID: PMC6311237 DOI: 10.1155/2018/8406712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/31/2018] [Accepted: 12/02/2018] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial (mt) tRNA (MTT) gene mutations are an important cause of mitochondrial diseases and are associated with a wide range of clinical presentations. Most mutations fall into three mitochondrial tRNAs (tRNAIle, tRNALeu (UUR), and tRNALys) and are responsible for half of the mitochondrial diseasees associated with tRNA mutation, with MERRF, MELAS, mitochondrial myopathy, and Leigh syndrome being the most frequent phenotypes. More than 100 tRNA pathogenetic mutations are described, showing little correlation between the observed clinical phenotype and a specific mitochondrial tRNA mutation. Furthermore different mutation can manifest with similar clinical phenotypes, making the genotype-phenotype correlation difficult. Here we report the case of an Italian 53-year-old woman presenting with a proximal myopathy and the m.5835G>A mutation in MT-TY gene coding for the mitochondrial tRNA Tyrosine gene.
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Zhou L, Wang H, Wei J, Wang Y, Wang Y. No association between mitochondrial tRNA(Val) T1658C mutation and chronic progressive external ophthalmoplegia (CPEO). ACTA ACUST UNITED AC 2013; 25:385-6. [PMID: 23815321 DOI: 10.3109/19401736.2013.803097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mutations in mitochondrial tRNA genes are one of the most important causes of mitochondrial diseases. Recently, a novel mt-tRNA(Val) T1658C mutation has been reported to be associated with chronic progressive external ophthalmoplegia (CPEO). To test this association, we performed a phylogenetic analysis of T1658C mutation, moreover, we used the bioinformatic tool to predict the thermodynamic change of tRNA(Val) with and without this mutation. Surprisingly, T1658C mutation was not evolutionary conserved and had little effect on tRNA(Val) folding. These data indicated that T1658C mutation should still be categorized as a polymorphism.
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Affiliation(s)
- Lijun Zhou
- First affiliated Hospital of Henan University of Science and Technology , Luoyang , People's Republic of China and
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Yarham JW, Al-Dosary M, Blakely EL, Alston CL, Taylor RW, Elson JL, McFarland R. A comparative analysis approach to determining the pathogenicity of mitochondrial tRNA mutations. Hum Mutat 2011; 32:1319-25. [PMID: 21882289 DOI: 10.1002/humu.21575] [Citation(s) in RCA: 140] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 07/07/2011] [Indexed: 01/24/2023]
Abstract
Distinguishing pathogenic from polymorphic changes poses significant problems for geneticists and despite 30 years of postgenomic experience this remains the case in mitochondrial genetics. Base substitutions in mitochondrial tRNA (mt-tRNA) genes are particularly difficult, but important, because they are common causes of pathology and associated with high rates of transmission. Providing accurate genetic advice to patients and their families is of paramount importance in disease prevention, and brings into sharp focus the factors used to distinguish pathogenic from polymorphic variants. We have reevaluated our pathogenicity scoring system for mt-tRNA mutations following a considerable increase in the number reported since the system was devised in 2004. This allowed us to address notable issues including the underestimation of "definitely pathogenic" mutations resulting from insufficient data collection. We illustrate the robustness of our revised scoring system using novel pathogenic and previously reported polymorphic changes and conclude that while clear evidence from single-fiber and/or trans-mitochondrial cybrid studies remains the gold standard for assigning pathogenicity, our scoring system is valuable for deciding which mt-tRNA mutations to investigate further using these labor-intensive techniques.
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Affiliation(s)
- John W Yarham
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, UK
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Yarham JW, Elson JL, Blakely EL, McFarland R, Taylor RW. Mitochondrial tRNA mutations and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:304-24. [DOI: 10.1002/wrna.27] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- John W. Yarham
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Joanna L. Elson
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Emma L. Blakely
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert McFarland
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Robert W. Taylor
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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20 years of human mtDNA pathologic point mutations: Carefully reading the pathogenicity criteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:476-83. [DOI: 10.1016/j.bbabio.2008.09.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Revised: 09/08/2008] [Accepted: 09/12/2008] [Indexed: 11/21/2022]
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Fendt L, Zimmermann B, Daniaux M, Parson W. Sequencing strategy for the whole mitochondrial genome resulting in high quality sequences. BMC Genomics 2009; 10:139. [PMID: 19331681 PMCID: PMC2669098 DOI: 10.1186/1471-2164-10-139] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 03/30/2009] [Indexed: 11/18/2022] Open
Abstract
Background It has been demonstrated that a reliable and fail-safe sequencing strategy is mandatory for high-quality analysis of mitochondrial (mt) DNA, as the sequencing and base-calling process is prone to error. Here, we present a high quality, reliable and easy handling manual procedure for the sequencing of full mt genomes that is also appropriate for laboratories where fully automated processes are not available. Results We amplified whole mitochondrial genomes as two overlapping PCR-fragments comprising each about 8500 bases in length. We developed a set of 96 primers that can be applied to a (manual) 96 well-based technology, which resulted in at least double strand sequence coverage of the entire coding region (codR). Conclusion This elaborated sequencing strategy is straightforward and allows for an unambiguous sequence analysis and interpretation including sometimes challenging phenomena such as point and length heteroplasmy that are relevant for the investigation of forensic and clinical samples.
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Affiliation(s)
- Liane Fendt
- Institute of Legal Medicine, Innsbruck Medical University, Müllerstrasse 44, Austria.
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