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A P F Alves C, Goldstein A, Peterson J, Vossough A. Reply. AJNR Am J Neuroradiol 2024; 45:E32-E33. [PMID: 39122461 PMCID: PMC11383422 DOI: 10.3174/ajnr.a8415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2024]
Affiliation(s)
- Cesar A P F Alves
- Division of Neuroradiology, Radiology DepartmentBoston Children's HospitalHarvard Medical SchoolBoston, MassachusettsDepartment of RadiologyChildren's Hospital of PhiladelphiaPhiladelphia, Pennsylvania
| | - Amy Goldstein
- Mitochondrial Medicine Frontier ProgramDivision of Human GeneticsDepartment of PediatricsThe Children's Hospital of PhiladelphiaPhiladelphia, PennsylvaniaDepartment of PediatricsUniversity of Pennsylvania Perelman School of MedicinePhiladelphia, Pennsylvania
| | - James Peterson
- Mitochondrial Medicine Frontier ProgramDivision of Human GeneticsDepartment of PediatricsThe Children's Hospital of PhiladelphiaPhiladelphia, Pennsylvania
| | - Arastoo Vossough
- Department of RadiologyChildren's Hospital of PhiladelphiaPhiladelphia, Pennsylvania
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Yin X, Dong Q, Fan S, Yang L, Li H, Jin Y, Laurentinah MR, Chen X, Sysa A, Fang H, Lyu J, Yu Y, Wang Y. A novel pathogenic mitochondrial DNA variant m.4344T>C in tRNA Gln causes developmental delay. J Hum Genet 2024; 69:381-389. [PMID: 38730005 DOI: 10.1038/s10038-024-01254-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Mitochondrial diseases are a group of genetic diseases caused by mutations in mitochondrial DNA and nuclear DNA. However, the genetic spectrum of this disease is not yet complete. In this study, we identified a novel variant m.4344T>C in mitochondrial tRNAGln from a patient with developmental delay. The mutant loads of m.4344T>C were 95% and 89% in the patient's blood and oral epithelial cells, respectively. Multialignment analysis showed high evolutionary conservation of this nucleotide. TrRosettaRNA predicted that m.4344T>C variant would introduce an additional hydrogen bond and alter the conformation of the T-loop. The transmitochondrial cybrid-based study demonstrated that m.4344T>C variant impaired the steady-state level of mitochondrial tRNAGln and decreased the contents of mitochondrial OXPHOS complexes I, III, and IV, resulting in defective mitochondrial respiration, elevated mitochondrial ROS production, reduced mitochondrial membrane potential and decreased mitochondrial ATP levels. Altogether, this is the first report in patient carrying the m.4344T>C variant. Our data uncover the pathogenesis of the m.4344T>C variant and expand the genetic mutation spectrum of mitochondrial diseases, thus contributing to the clinical diagnosis of mitochondrial tRNAGln gene variants-associated mitochondrial diseases.
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Affiliation(s)
- Xiaojie Yin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Qiyu Dong
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Shuanglong Fan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Lina Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yijun Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Mahlatsi Refiloe Laurentinah
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xiandan Chen
- International Sakharov Environmental Institute of Belarusian State University, Minsk, 220070, Republic of Belarus
| | - Aliaksei Sysa
- International Sakharov Environmental Institute of Belarusian State University, Minsk, 220070, Republic of Belarus
| | - Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, 200092, China.
- Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, 200092, China.
| | - Ya Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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Sun L, Ren Y, Ma Y, Zhu Y, Wu Y, Wang S, Nie L, Xiao H, Jiang Y, Wang F. A de novo novel variant in the MT-TD gene is associated with prominent extra-neurologic manifestations. Clin Genet 2024. [PMID: 39056263 DOI: 10.1111/cge.14594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 07/07/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]
Abstract
Defects in the mitochondrial tRNA genes cause a group of highly clinically and genetically heterogeneous disorders, which poses a challenge for clinical identification and genetic diagnosis. Here, we present a pre-school boy with a novel MT-TD variant m.7560T>C at the heteroplasmy level of 76.53% in blood, 93.34% in urine sediments, and absent in the healthy mother's blood and urine. Besides convulsions, brain magnetic resonance imaging abnormalities and high plasma lactate, the boy presented with the prominent extra-neurologic phenotype including steroid-resistant nephrotic syndrome associated with focal segmental glomerulosclerosis characterized by abnormal mitochondria in podocytes, cortical blindness, and pancreatitis. To our knowledge, this is the unique case with MT-TD m.7560T>C-related multi-organ impairments, which expands the phenotypic and mutational spectrum of primary mitochondrial diseases.
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Affiliation(s)
- Liuyu Sun
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| | - Yali Ren
- Department of Electron Microscopy, Peking University First Hospital, Beijing, People's Republic of China
| | - Yinan Ma
- Experimental Center, Peking University First Hospital, Beijing, People's Republic of China
| | - Ying Zhu
- Department of Medical Imaging, Peking University First Hospital, Beijing, People's Republic of China
| | - Ye Wu
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| | - Suxia Wang
- Department of Electron Microscopy, Peking University First Hospital, Beijing, People's Republic of China
| | - Lin Nie
- Department of Electron Microscopy, Peking University First Hospital, Beijing, People's Republic of China
| | - Huijie Xiao
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
| | - Fang Wang
- Department of Pediatrics, Peking University First Hospital, Beijing, People's Republic of China
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Rouzier C, Pion E, Chaussenot A, Bris C, Ait‐El‐Mkadem Saadi S, Desquiret‐Dumas V, Gueguen N, Fragaki K, Amati‐Bonneau P, Barcia G, Gaignard P, Steffann J, Pennisi A, Bonnefont J, Lebigot E, Bannwarth S, Francou B, Rucheton B, Sternberg D, Martin‐Negrier M, Trimouille A, Hardy G, Allouche S, Acquaviva‐Bourdain C, Pagan C, Lebre A, Reynier P, Cossee M, Attarian S, Paquis‐Flucklinger V, Procaccio V. Primary mitochondrial disorders and mimics: Insights from a large French cohort. Ann Clin Transl Neurol 2024; 11:1478-1491. [PMID: 38703036 PMCID: PMC11187946 DOI: 10.1002/acn3.52062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 03/23/2024] [Indexed: 05/06/2024] Open
Abstract
OBJECTIVE The objective of this study was to evaluate the implementation of NGS within the French mitochondrial network, MitoDiag, from targeted gene panels to whole exome sequencing (WES) or whole genome sequencing (WGS) focusing on mitochondrial nuclear-encoded genes. METHODS Over 2000 patients suspected of Primary Mitochondrial Diseases (PMD) were sequenced by either targeted gene panels, WES or WGS within MitoDiag. We described the clinical, biochemical, and molecular data of 397 genetically confirmed patients, comprising 294 children and 103 adults, carrying pathogenic or likely pathogenic variants in nuclear-encoded genes. RESULTS The cohort exhibited a large genetic heterogeneity, with the identification of 172 distinct genes and 253 novel variants. Among children, a notable prevalence of pathogenic variants in genes associated with oxidative phosphorylation (OXPHOS) functions and mitochondrial translation was observed. In adults, pathogenic variants were primarily identified in genes linked to mtDNA maintenance. Additionally, a substantial proportion of patients (54% (42/78) and 48% (13/27) in children and adults, respectively), undergoing WES or WGS testing displayed PMD mimics, representing pathologies that clinically resemble mitochondrial diseases. INTERPRETATION We reported the largest French cohort of patients suspected of PMD with pathogenic variants in nuclear genes. We have emphasized the clinical complexity of PMD and the challenges associated with recognizing and distinguishing them from other pathologies, particularly neuromuscular disorders. We confirmed that WES/WGS, instead of panel approach, was more valuable to identify the genetic basis in patients with "possible" PMD and we provided a genetic testing flowchart to guide physicians in their diagnostic strategy.
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Affiliation(s)
- Cécile Rouzier
- Service de génétique médicale, Centre de référence des maladies mitochondriales, CHU NiceUniversité Côte d'Azur, CNRS, INSERM, IRCANNiceFrance
| | - Emmanuelle Pion
- Filnemus, laboratoire de génétique moléculaire, CHUMontpellierFrance
| | - Annabelle Chaussenot
- Service de génétique médicale, Centre de référence des maladies mitochondriales, CHU NiceUniversité Côte d'Azur, CNRS, INSERM, IRCANNiceFrance
| | - Céline Bris
- Service de génétique, Institut de Biologie en santé, CHU AngersUniv Angers, INSERM, CNRS, MITOVASC, Equipe MitoLab, SFR ICATAngersFrance
| | - Samira Ait‐El‐Mkadem Saadi
- Service de génétique médicale, Centre de référence des maladies mitochondriales, CHU NiceUniversité Côte d'Azur, CNRS, INSERM, IRCANNiceFrance
| | - Valérie Desquiret‐Dumas
- Service de biochimie et biologie moléculaire, Institut de Biologie en santé, CHU AngersUniv Angers, INSERM, CNRS, MITOVASC, Equipe MitoLab, SFR ICATAngersFrance
| | - Naïg Gueguen
- Service de biochimie et biologie moléculaire, Institut de Biologie en santé, CHU AngersUniv Angers, INSERM, CNRS, MITOVASC, Equipe MitoLab, SFR ICATAngersFrance
| | - Konstantina Fragaki
- Service de génétique médicale, Centre de référence des maladies mitochondriales, CHU NiceUniversité Côte d'Azur, CNRS, INSERM, IRCANNiceFrance
| | - Patrizia Amati‐Bonneau
- Service de biochimie et biologie moléculaire, Institut de Biologie en santé, CHU AngersUniv Angers, INSERM, CNRS, MITOVASC, Equipe MitoLab, SFR ICATAngersFrance
| | - Giulia Barcia
- Service de médecine génomique des maladies rares, Hôpital Necker‐Enfants MaladesUniversité Paris Cité, Institut Imagine Unité UMR 1161ParisFrance
| | - Pauline Gaignard
- Service de Biochimie, GHU APHP Paris SaclayHôpital BicêtreLe Kremlin‐BicêtreFrance
| | - Julie Steffann
- Service de médecine génomique des maladies rares, Hôpital Necker‐Enfants MaladesUniversité Paris Cité, Institut Imagine Unité UMR 1161ParisFrance
| | - Alessandra Pennisi
- Service de médecine génomique des maladies rares, Hôpital Necker‐Enfants MaladesUniversité Paris Cité, Institut Imagine Unité UMR 1161ParisFrance
| | - Jean‐Paul Bonnefont
- Service de médecine génomique des maladies rares, Hôpital Necker‐Enfants MaladesUniversité Paris Cité, Institut Imagine Unité UMR 1161ParisFrance
| | - Elise Lebigot
- Service de Biochimie, GHU APHP Paris SaclayHôpital BicêtreLe Kremlin‐BicêtreFrance
| | - Sylvie Bannwarth
- Service de génétique médicale, Centre de référence des maladies mitochondriales, CHU NiceUniversité Côte d'Azur, CNRS, INSERM, IRCANNiceFrance
| | - Bruno Francou
- Service de génétique médicale, Centre de référence des maladies mitochondriales, CHU NiceUniversité Côte d'Azur, CNRS, INSERM, IRCANNiceFrance
| | | | - Damien Sternberg
- Unité Fonctionnelle de cardiogénétique et myogénétique moléculaire et cellulaire, Centre de génétique moléculaire et chromosomiqueAP‐HP Sorbonne Université, Hopital de la Pitié‐SalpêtrièreParisFrance
| | - Marie‐Laure Martin‐Negrier
- Unité fonctionnelle d'histologie moléculaire, Service de pathologieCHU Bordeaux‐GU PellegrinBordeauxFrance
| | - Aurélien Trimouille
- Unité fonctionnelle d'histologie moléculaire, Service de pathologieCHU Bordeaux‐GU PellegrinBordeauxFrance
| | - Gaëlle Hardy
- Laboratoire de Génétique Moléculaire: Maladies Héréditaires et OncologieInstitut de Biologie et de Pathologie, CHU Grenoble AlpesGrenobleFrance
| | - Stéphane Allouche
- Service de biochimieInstitut Territorial de Biologie en Santé, CHU Caen, Hôpital de la Côte de NacreCaenFrance
| | - Cécile Acquaviva‐Bourdain
- Service de biochimie et biologie moléculaire Grand Est, UM Maladies Héréditaires du Métabolisme, Centre de biologie et pathologie EstCHU Lyon HCL, GH EstLyonFrance
| | - Cécile Pagan
- Service de biochimie et biologie moléculaire Grand Est, UM Maladies Héréditaires du Métabolisme, Centre de biologie et pathologie EstCHU Lyon HCL, GH EstLyonFrance
| | - Anne‐Sophie Lebre
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266 [Krebs team]Université de Reims Champagne‐Ardenne (UFR médicale) ‐ CHU de Reims‐Université Paris CitéParisFrance
| | - Pascal Reynier
- Service de biochimie et biologie moléculaire, Institut de Biologie en santé, CHU AngersUniv Angers, INSERM, CNRS, MITOVASC, Equipe MitoLab, SFR ICATAngersFrance
| | - Mireille Cossee
- Laboratoire de Génétique Moléculaire, CHU Montpellier, PhyMedExpUniversité de Montpellier, INSERM, CNRSMontpellierFrance
| | - Shahram Attarian
- Service des Maladies Neuromusculaires et la SLA, FILNEMUS, Euro‐NMDAIX‐CHU La TimoneMarseille UniversitéMarseilleFrance
| | - Véronique Paquis‐Flucklinger
- Service de génétique médicale, Centre de référence des maladies mitochondriales, CHU NiceUniversité Côte d'Azur, CNRS, INSERM, IRCANNiceFrance
| | | | - Vincent Procaccio
- Service de génétique, Institut de Biologie en santé, CHU AngersUniv Angers, INSERM, CNRS, MITOVASC, Equipe MitoLab, SFR ICATAngersFrance
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Rudaks LI, Yeow D, Ng K, Deveson IW, Kennerson ML, Kumar KR. An Update on the Adult-Onset Hereditary Cerebellar Ataxias: Novel Genetic Causes and New Diagnostic Approaches. CEREBELLUM (LONDON, ENGLAND) 2024:10.1007/s12311-024-01703-z. [PMID: 38760634 DOI: 10.1007/s12311-024-01703-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
The hereditary cerebellar ataxias (HCAs) are rare, progressive neurologic disorders caused by variants in many different genes. Inheritance may follow autosomal dominant, autosomal recessive, X-linked or mitochondrial patterns. The list of genes associated with adult-onset cerebellar ataxia is continuously growing, with several new genes discovered in the last few years. This includes short-tandem repeat (STR) expansions in RFC1, causing cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS), FGF14-GAA causing spinocerebellar ataxia type 27B (SCA27B), and THAP11. In addition, the genetic basis for SCA4, has recently been identified as a STR expansion in ZFHX3. Given the large and growing number of genes, and different gene variant types, the approach to diagnostic testing for adult-onset HCA can be complex. Testing methods include targeted evaluation of STR expansions (e.g. SCAs, Friedreich ataxia, fragile X-associated tremor/ataxia syndrome, dentatorubral-pallidoluysian atrophy), next generation sequencing for conventional variants, which may include targeted gene panels, whole exome, or whole genome sequencing, followed by various potential additional tests. This review proposes a diagnostic approach for clinical testing, highlights the challenges with current testing technologies, and discusses future advances which may overcome these limitations. Implementing long-read sequencing has the potential to transform the diagnostic approach in HCA, with the overall aim to improve the diagnostic yield.
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Affiliation(s)
- Laura Ivete Rudaks
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Sydney, Australia.
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia.
- Genomics and Inherited Disease Program, The Garvan Institute of Medical Research, Sydney, Australia.
- Clinical Genetics Unit, Royal North Shore Hospital, Sydney, Australia.
| | - Dennis Yeow
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Sydney, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Genomics and Inherited Disease Program, The Garvan Institute of Medical Research, Sydney, Australia
- Neurodegenerative Service, Prince of Wales Hospital, Sydney, Australia
- Neuroscience Research Australia, Sydney, Australia
| | - Karl Ng
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Neurology Department, Royal North Shore Hospital, Sydney, Australia
| | - Ira W Deveson
- Genomics and Inherited Disease Program, The Garvan Institute of Medical Research, Sydney, Australia
- Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Marina L Kennerson
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Sydney, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- The Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney Local Health District, Sydney, Australia
| | - Kishore Raj Kumar
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Sydney, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Genomics and Inherited Disease Program, The Garvan Institute of Medical Research, Sydney, Australia
- Faculty of Medicine, University of New South Wales, Sydney, Australia
- Faculty of Medicine, St Vincent's Healthcare Campus, UNSW Sydney, Sydney, Australia
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Ferreira T, Rodriguez S. Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses. Genes (Basel) 2024; 15:617. [PMID: 38790246 PMCID: PMC11121663 DOI: 10.3390/genes15050617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease.
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Affiliation(s)
- Tomas Ferreira
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SL, UK
| | - Santiago Rodriguez
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1QU, UK
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Liang D, Zhu L, Zhu Y, Huang M, Lin Y, Li H, Hu P, Zhang J, Shen B, Xu Z. A PCR-independent approach for mtDNA enrichment and next-generation sequencing: comprehensive evaluation and clinical application. J Transl Med 2024; 22:386. [PMID: 38664838 PMCID: PMC11044483 DOI: 10.1186/s12967-024-05213-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/16/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Sequencing the mitochondrial genome has been increasingly important for the investigation of primary mitochondrial diseases (PMD) and mitochondrial genetics. To overcome the limitations originating from PCR-based mtDNA enrichment, we set out to develop and evaluate a PCR-independent approach in this study, named Pime-Seq (PCR-independent mtDNA enrichment and next generation Sequencing). RESULTS By using the optimized mtDNA enrichment procedure, the mtDNA reads ratio reached 88.0 ± 7.9% in the sequencing library when applied on human PBMC samples. We found the variants called by Pime-Seq were highly consistent among technical repeats. To evaluate the accuracy and reliability of this method, we compared Pime-Seq with lrPCR based NGS by performing both methods simultaneously on 45 samples, yielding 1677 concordant variants, as well as 146 discordant variants with low-level heteroplasmic fraction, in which Pime-Seq showed higher reliability. Furthermore, we applied Pime-Seq on 4 samples of PMD patients retrospectively, and successfully detected all the pathogenic mtDNA variants. In addition, we performed a prospective study on 192 apparently healthy pregnant women during prenatal screening, in which Pime-Seq identified pathogenic mtDNA variants in 4 samples, providing extra information for better health monitoring in these cases. CONCLUSIONS Pime-Seq can obtain highly enriched mtDNA in a PCR-independent manner for high quality and reliable mtDNA deep-sequencing, which provides us an effective and promising tool for detecting mtDNA variants for both clinical and research purposes.
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Affiliation(s)
- Dong Liang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, 210004, China
| | - Lin Zhu
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing Medical University, Nanjing, 211166, China
| | - Yuqing Zhu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, 210004, China
| | - Mingtao Huang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, 210004, China
| | - Ying Lin
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, 210004, China
| | - Hang Li
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, 210004, China
| | - Ping Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, 210004, China
| | - Jun Zhang
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing Medical University, Nanjing, 211166, China.
| | - Bin Shen
- State Key Laboratory of Reproductive Medicine and Offspring Health, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing Medical University, Nanjing, 211166, China.
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Women and Children's Healthcare Hospital, Nanjing, 210004, China.
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8
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Chitluri KK, Emerson IA. The importance of protein domain mutations in cancer therapy. Heliyon 2024; 10:e27655. [PMID: 38509890 PMCID: PMC10950675 DOI: 10.1016/j.heliyon.2024.e27655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Cancer is a complex disease that is caused by multiple genetic factors. Researchers have been studying protein domain mutations to understand how they affect the progression and treatment of cancer. These mutations can significantly impact the development and spread of cancer by changing the protein structure, function, and signalling pathways. As a result, there is a growing interest in how these mutations can be used as prognostic indicators for cancer prognosis. Recent studies have shown that protein domain mutations can provide valuable information about the severity of the disease and the patient's response to treatment. They may also be used to predict the response and resistance to targeted therapy in cancer treatment. The clinical implications of protein domain mutations in cancer are significant, and they are regarded as essential biomarkers in oncology. However, additional techniques and approaches are required to characterize changes in protein domains and predict their functional effects. Machine learning and other computational tools offer promising solutions to this challenge, enabling the prediction of the impact of mutations on protein structure and function. Such predictions can aid in the clinical interpretation of genetic information. Furthermore, the development of genome editing tools like CRISPR/Cas9 has made it possible to validate the functional significance of mutants more efficiently and accurately. In conclusion, protein domain mutations hold great promise as prognostic and predictive biomarkers in cancer. Overall, considerable research is still needed to better define genetic and molecular heterogeneity and to resolve the challenges that remain, so that their full potential can be realized.
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Affiliation(s)
- Kiran Kumar Chitluri
- Bioinformatics Programming Lab, Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Isaac Arnold Emerson
- Bioinformatics Programming Lab, Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
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9
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Cox SN, Lo Giudice C, Lavecchia A, Poeta ML, Chiara M, Picardi E, Pesole G. Mitochondrial and Nuclear DNA Variants in Amyotrophic Lateral Sclerosis: Enrichment in the Mitochondrial Control Region and Sirtuin Pathway Genes in Spinal Cord Tissue. Biomolecules 2024; 14:411. [PMID: 38672428 PMCID: PMC11048214 DOI: 10.3390/biom14040411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/19/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a progressive disease with prevalent mitochondrial dysfunctions affecting both upper and lower motor neurons in the motor cortex, brainstem, and spinal cord. Despite mitochondria having their own genome (mtDNA), in humans, most mitochondrial genes are encoded by the nuclear genome (nDNA). Our study aimed to simultaneously screen for nDNA and mtDNA genomes to assess for specific variant enrichment in ALS compared to control tissues. Here, we analysed whole exome (WES) and whole genome (WGS) sequencing data from spinal cord tissues, respectively, of 6 and 12 human donors. A total of 31,257 and 301,241 variants in nuclear-encoded mitochondrial genes were identified from WES and WGS, respectively, while mtDNA reads accounted for 73 and 332 variants. Despite technical differences, both datasets consistently revealed a specific enrichment of variants in the mitochondrial Control Region (CR) and in several of these genes directly associated with mitochondrial dynamics or with Sirtuin pathway genes within ALS tissues. Overall, our data support the hypothesis of a variant burden in specific genes, highlighting potential actionable targets for therapeutic interventions in ALS.
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Affiliation(s)
- Sharon Natasha Cox
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Claudio Lo Giudice
- Institute of Biomedical Technologies, National Research Council, 70126 Bari, Italy;
| | - Anna Lavecchia
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Maria Luana Poeta
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
| | - Matteo Chiara
- Department of Biosciences, University of Milan, 20133 Milan, Italy;
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
| | - Ernesto Picardi
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnology and Environment, University of Bari “Aldo Moro”, 70126 Bari, Italy; (A.L.); (M.L.P.); (E.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnology, National Research Council, 70126 Bari, Italy
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10
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Ambrogetti R, Kavanagh E, ElTayeb K. Late-onset mitochondrial encephalopathy with lactic acidosis and stroke-like episodes and the role of serial imaging. BMJ Case Rep 2024; 17:e259102. [PMID: 38417938 PMCID: PMC10900402 DOI: 10.1136/bcr-2023-259102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024] Open
Abstract
Mitochondria are essential for human metabolic function. Over 350 genetic mutations are associated with mitochondrial diseases, which are inherited in a matrilineal fashion. In mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS), defective mitochondrial function and resultant impaired cellular energy production compromise vascular perfusion in affected tissues. Early diagnostic criteria suggested the diagnosis should be considered in those under 40. However, a broader range of phenotypes are now recognised, including those that present for the first time later in life. The primary presenting feature in MELAS is a stroke-like episode invariably resulting in patients undergoing neuroradiological imaging. We present a case of a woman with a first presentation of a stroke-like episode and seizures in her 40s who was eventually diagnosed with MELAS. We detail her clinical presentation, treatment and diagnosis, emphasising the role of serial imaging in her diagnosis.
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Affiliation(s)
- Robert Ambrogetti
- Internal Medicine, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Ethan Kavanagh
- University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Khalid ElTayeb
- Neurology, University Hospitals of Leicester NHS Trust, Leicester, UK
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11
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Cannon SJ, Hall T, Hawkes G, Colclough K, Boggan RM, Wright CF, Pickett SJ, Hattersley AT, Weedon MN, Patel KA. Penetrance and expressivity of mitochondrial variants in a large clinically unselected population. Hum Mol Genet 2024; 33:465-474. [PMID: 37988592 PMCID: PMC10877468 DOI: 10.1093/hmg/ddad194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023] Open
Abstract
Whole genome sequencing (WGS) from large clinically unselected cohorts provides a unique opportunity to assess the penetrance and expressivity of rare and/or known pathogenic mitochondrial variants in population. Using WGS from 179 862 clinically unselected individuals from the UK Biobank, we performed extensive single and rare variant aggregation association analyses of 15 881 mtDNA variants and 73 known pathogenic variants with 15 mitochondrial disease-relevant phenotypes. We identified 12 homoplasmic and one heteroplasmic variant (m.3243A>G) with genome-wide significant associations in our clinically unselected cohort. Heteroplasmic m.3243A>G (MAF = 0.0002, a known pathogenic variant) was associated with diabetes, deafness and heart failure and 12 homoplasmic variants increased aspartate aminotransferase levels including three low-frequency variants (MAF ~0.002 and beta~0.3 SD). Most pathogenic mitochondrial disease variants (n = 66/74) were rare in the population (<1:9000). Aggregated or single variant analysis of pathogenic variants showed low penetrance in unselected settings for the relevant phenotypes, except m.3243A>G. Multi-system disease risk and penetrance of diabetes, deafness and heart failure greatly increased with m.3243A>G level ≥ 10%. The odds ratio of these traits increased from 5.61, 12.3 and 10.1 to 25.1, 55.0 and 39.5, respectively. Diabetes risk with m.3243A>G was further influenced by type 2 diabetes genetic risk. Our study of mitochondrial variation in a large-unselected population identified novel associations and demonstrated that pathogenic mitochondrial variants have lower penetrance in clinically unselected settings. m.3243A>G was an exception at higher heteroplasmy showing a significant impact on health making it a good candidate for incidental reporting.
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Affiliation(s)
- Stuart J Cannon
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Timothy Hall
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Gareth Hawkes
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Kevin Colclough
- Exeter Genomics Laboratory, RILD Building, Royal Devon University Healthcare NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, United Kingdom
| | - Roisin M Boggan
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Sarah J Pickett
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Andrew T Hattersley
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Michael N Weedon
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Kashyap A Patel
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
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McNeill A. 2023 in the European Journal of Human Genetics. Eur J Hum Genet 2024; 32:135-137. [PMID: 38332347 PMCID: PMC10853252 DOI: 10.1038/s41431-024-01540-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Affiliation(s)
- Alisdair McNeill
- Division of Neuroscience and Neuroscience Institute, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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13
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Saunders C, Longman C, Gorman G, James K, Oliwa A, Petty R, Snadden L, Farrugia ME. The West of Scotland Cohort of Mitochondrial Individuals with the m.3243A>G Variant: Variations in Phenotypes and Predictors of Disease Severity. J Neuromuscul Dis 2024; 11:179-189. [PMID: 38108361 PMCID: PMC10789362 DOI: 10.3233/jnd-230166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND The m.3243A>G variant is the commonest mitochondrial (mt) DNA pathogenic variant and a frequent cause of mitochondrial disease. Individuals present with a variety of clinical manifestations from diabetes to neurological events resembling strokes. Due to this, patients are commonly cared for by a multidisciplinary team. OBJECTIVES This project aimed to identify patients with confirmed mt.3243A>G-related mitochondrial disease attending the Muscle Clinic at Queen Elizabeth University Hospital in Glasgow. We explored potential correlates between clinical phenotypes and mtDNA heteroplasmy levels, HbA1c levels, body mass index, and specific clinical manifestations. We investigated if there were discrepancies between non-neurological speciality labelling in clinical records and individuals' phenotypes. METHODS Data were gathered from the West of Scotland electronic records. Phenotypes were ascertained by a clinician with expertise in mitochondrial disorders. Statistical analyses were applied to study relationships between tissue heteroplasmy, HbA1c and clinical phenotypes including body mass index (BMI). RESULTS Forty-six individuals were identified from 31 unrelated pedigrees. Maternally inherited diabetes and deafness was the prominent syndromic phenotype (48%). A significant association was found between overall number of symptoms and bowel dysmotility (p < 0.01). HbA1c was investigated as a predictor of severity with potential association seen. Although used widely as a prognosticator, neither corrected blood nor urine mtDNA heteroplasmy levels were associated with increased number of symptoms. In 74.1% of records, syndromic phenotypes were incorrectly used by non-neurological specialities. CONCLUSIONS This m.3243 A > G patient cohort present with marked clinical heterogeneity. Urine and blood heteroplasmy levels are not reliable predictors of disease severity. HbA1c may be a novel predictor of disease severity with further research required to investigate this association. We infer that prognosis may be worse in patients with low BMIs and in those with bowel dysmotility. These results underscore a multidisciplinary approach and highlight a problem with inaccurate use of the existing nomenclature.
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Affiliation(s)
- Charlie Saunders
- Neurology Department, Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Cheryl Longman
- Genetics Department, West Scotland Regional Genetics Service, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Grainne Gorman
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle-upon-Tyne, UK
| | - Kelly James
- Department of Geographical and Earth Sciences, University of Glasgow, Glasgow, G20 8QQ, UK
| | - Agata Oliwa
- Genetics Department, West Scotland Regional Genetics Service, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Richard Petty
- Neurology Department, Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Lesley Snadden
- Genetics Department, West Scotland Regional Genetics Service, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
| | - Maria Elena Farrugia
- Neurology Department, Institute of Neurological Sciences, Queen Elizabeth University Hospital, Glasgow G51 4TF, UK
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Conti F, Di Martino S, Drago F, Bucolo C, Micale V, Montano V, Siciliano G, Mancuso M, Lopriore P. Red Flags in Primary Mitochondrial Diseases: What Should We Recognize? Int J Mol Sci 2023; 24:16746. [PMID: 38069070 PMCID: PMC10706469 DOI: 10.3390/ijms242316746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Primary mitochondrial diseases (PMDs) are complex group of metabolic disorders caused by genetically determined impairment of the mitochondrial oxidative phosphorylation (OXPHOS). The unique features of mitochondrial genetics and the pivotal role of mitochondria in cell biology explain the phenotypical heterogeneity of primary mitochondrial diseases and the resulting diagnostic challenges that follow. Some peculiar features ("red flags") may indicate a primary mitochondrial disease, helping the physician to orient in this diagnostic maze. In this narrative review, we aimed to outline the features of the most common mitochondrial red flags offering a general overview on the topic that could help physicians to untangle mitochondrial medicine complexity.
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Affiliation(s)
- Federica Conti
- Department of Biomedical and Biotechnological Science, School of Medicine, University of Catania, 95123 Catania, Italy; (F.C.); (S.D.M.); (C.B.); (V.M.)
| | - Serena Di Martino
- Department of Biomedical and Biotechnological Science, School of Medicine, University of Catania, 95123 Catania, Italy; (F.C.); (S.D.M.); (C.B.); (V.M.)
| | - Filippo Drago
- Department of Biomedical and Biotechnological Science, School of Medicine, University of Catania, 95123 Catania, Italy; (F.C.); (S.D.M.); (C.B.); (V.M.)
| | - Claudio Bucolo
- Department of Biomedical and Biotechnological Science, School of Medicine, University of Catania, 95123 Catania, Italy; (F.C.); (S.D.M.); (C.B.); (V.M.)
- Center for Research in Ocular Pharmacology-CERFO, University of Catania, 95213 Catania, Italy
| | - Vincenzo Micale
- Department of Biomedical and Biotechnological Science, School of Medicine, University of Catania, 95123 Catania, Italy; (F.C.); (S.D.M.); (C.B.); (V.M.)
| | - Vincenzo Montano
- Neurological Institute, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy (P.L.)
| | - Gabriele Siciliano
- Neurological Institute, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy (P.L.)
| | - Michelangelo Mancuso
- Neurological Institute, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy (P.L.)
| | - Piervito Lopriore
- Neurological Institute, Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy (P.L.)
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15
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Viering DH, Vermeltfoort L, Bindels RJ, Deinum J, de Baaij JH. Electrolyte Disorders in Mitochondrial Cytopathies: A Systematic Review. J Am Soc Nephrol 2023; 34:1875-1888. [PMID: 37678265 PMCID: PMC10631606 DOI: 10.1681/asn.0000000000000224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/25/2023] [Indexed: 09/09/2023] Open
Abstract
SIGNIFICANCE STATEMENT Several recent studies identified mitochondrial mutations in patients with Gitelman or Fanconi syndrome. Mitochondrial cytopathies are generally not considered in the diagnostic workup of patients with electrolyte disorders. In this systematic review, we investigated the presence of electrolyte disorders in patients with mitochondrial cytopathies to determine the relevance of mitochondrial mutation screening in this population. Our analysis demonstrates that electrolyte disorders are commonly reported in mitochondrial cytopathies, often as presenting symptoms. Consequently, more clinical attention should be raised for mitochondrial disease as cause for disturbances in electrolyte homeostasis. Further prospective cohort studies are required to determine the exact prevalence of electrolyte disorders in mitochondrial cytopathies. BACKGROUND Electrolyte reabsorption in the kidney has a high energy demand. Proximal and distal tubular epithelial cells have a high mitochondrial density for energy release. Recently, electrolyte disorders have been reported as the primary presentation of some mitochondrial cytopathies. However, the prevalence and the pathophysiology of electrolyte disturbances in mitochondrial disease are unknown. Therefore, we systematically investigated electrolyte disorders in patients with mitochondrial cytopathies. METHODS We searched PubMed, Embase, and Google Scholar for articles on genetically confirmed mitochondrial disease in patients for whom at least one electrolyte is reported. Patients with a known second genetic anomaly were excluded. We evaluated 214 case series and reports (362 patients) as well as nine observational studies. Joanna Briggs Institute criteria were used to evaluate the quality of included studies. RESULTS Of 362 reported patients, 289 had an electrolyte disorder, with it being the presenting or main symptom in 38 patients. The average number of different electrolyte abnormalities per patient ranged from 2.4 to 1.0, depending on genotype. Patients with mitochondrial DNA structural variants seemed most affected. Reported pathophysiologic mechanisms included renal tubulopathies and hormonal, gastrointestinal, and iatrogenic causes. CONCLUSIONS Mitochondrial diseases should be considered in the evaluation of unexplained electrolyte disorders. Furthermore, clinicians should be aware of electrolyte abnormalities in patients with mitochondrial disease.
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Affiliation(s)
- Daan H.H.M. Viering
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lars Vermeltfoort
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - René J.M. Bindels
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jaap Deinum
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jeroen H.F. de Baaij
- Department of Medical BioSciences, Radboud University Medical Center, Nijmegen, The Netherlands
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16
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Wu YT, Tay HY, Yang JT, Liao HH, Ma YS, Wei YH. Mitochondrial impairment and synaptic dysfunction are associated with neurological defects in iPSCs-derived cortical neurons of MERRF patients. J Biomed Sci 2023; 30:70. [PMID: 37605213 PMCID: PMC10441704 DOI: 10.1186/s12929-023-00966-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/08/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Myoclonic epilepsy with ragged-red fibers (MERRF) syndrome is a rare inherited mitochondrial disease mainly caused by the m.8344A > G mutation in mitochondrial tRNALys gene, and usually manifested as complex neurological disorders and muscle weakness. Currently, the pathogenic mechanism of this disease has not yet been resolved, and there is no effective therapy for MERRF syndrome. In this study, MERRF patients-derived iPSCs were used to model patient-specific neurons for investigation of the pathogenic mechanism of neurological disorders in mitochondrial disease. METHODS MERRF patient-derived iPSCs were differentiated into excitatory glutamatergic neurons to unravel the effects of the m.8344A > G mutation on mitochondrial bioenergetic function, neural-lineage differentiation and neuronal function. By the well-established differentiation protocol and electrophysiological activity assay platform, we examined the pathophysiological behaviors in cortical neurons of MERRF patients. RESULTS We have successfully established the iPSCs-derived neural progenitor cells and cortical-like neurons of patients with MERRF syndrome that retained the heteroplasmy of the m.8344A > G mutation from the patients' skin fibroblasts and exhibited the phenotype of the mitochondrial disease. MERRF neural cells harboring the m.8344A > G mutation exhibited impaired mitochondrial bioenergetic function, elevated ROS levels and imbalanced expression of antioxidant enzymes. Our findings indicate that neural immaturity and synaptic protein loss led to the impairment of neuronal activity and plasticity in MERRF neurons harboring the m.8344A > G mutation. By electrophysiological recordings, we monitored the in vivo neuronal behaviors of MERRF neurons and found that neurons harboring a high level of the m.8344A > G mutation exhibited impairment of the spontaneous and evoked potential-stimulated neuronal activities. CONCLUSIONS We demonstrated for the first time the link of mitochondrial impairment and synaptic dysfunction to neurological defects through impeding synaptic plasticity in excitatory neurons derived from iPSCs of MERRF patients harboring the m.8344A > G mutation. This study has provided new insight into the pathogenic mechanism of the tRNALys gene mutation of mtDNA, which is useful for the development of a patient-specific iPSCs platform for disease modeling and screening of new drugs to treat patients with MERRF syndrome.
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Affiliation(s)
- Yu-Ting Wu
- Center for Mitochondrial Medicine and Free Radical Research, Changhua Christian Hospital, Changhua City, Taiwan, 50046
| | - Hui-Yi Tay
- Center for Mitochondrial Medicine and Free Radical Research, Changhua Christian Hospital, Changhua City, Taiwan, 50046
| | - Jung-Tse Yang
- Center for Mitochondrial Medicine and Free Radical Research, Changhua Christian Hospital, Changhua City, Taiwan, 50046
| | - Hsiao-Hui Liao
- Center for Mitochondrial Medicine and Free Radical Research, Changhua Christian Hospital, Changhua City, Taiwan, 50046
| | - Yi-Shing Ma
- Center for Mitochondrial Medicine and Free Radical Research, Changhua Christian Hospital, Changhua City, Taiwan, 50046
| | - Yau-Huei Wei
- Center for Mitochondrial Medicine and Free Radical Research, Changhua Christian Hospital, Changhua City, Taiwan, 50046.
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan, 112.
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Macken WL, Falabella M, Pizzamiglio C, Woodward CE, Scotchman E, Chitty LS, Polke JM, Bugiardini E, Hanna MG, Vandrovcova J, Chandler N, Labrum R, Pitceathly RDS. Enhanced mitochondrial genome analysis: bioinformatic and long-read sequencing advances and their diagnostic implications. Expert Rev Mol Diagn 2023; 23:797-814. [PMID: 37642407 DOI: 10.1080/14737159.2023.2241365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
INTRODUCTION Primary mitochondrial diseases (PMDs) comprise a large and heterogeneous group of genetic diseases that result from pathogenic variants in either nuclear DNA (nDNA) or mitochondrial DNA (mtDNA). Widespread adoption of next-generation sequencing (NGS) has improved the efficiency and accuracy of mtDNA diagnoses; however, several challenges remain. AREAS COVERED In this review, we briefly summarize the current state of the art in molecular diagnostics for mtDNA and consider the implications of improved whole genome sequencing (WGS), bioinformatic techniques, and the adoption of long-read sequencing, for PMD diagnostics. EXPERT OPINION We anticipate that the application of PCR-free WGS from blood DNA will increase in diagnostic laboratories, while for adults with myopathic presentations, WGS from muscle DNA may become more widespread. Improved bioinformatic strategies will enhance WGS data interrogation, with more accurate delineation of mtDNA and NUMTs (nuclear mitochondrial DNA segments) in WGS data, superior coverage uniformity, indirect measurement of mtDNA copy number, and more accurate interpretation of heteroplasmic large-scale rearrangements (LSRs). Separately, the adoption of diagnostic long-read sequencing could offer greater resolution of complex LSRs and the opportunity to phase heteroplasmic variants.
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Affiliation(s)
- William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Micol Falabella
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Chiara Pizzamiglio
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Cathy E Woodward
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lyn S Chitty
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - James M Polke
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Natalie Chandler
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Robyn Labrum
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
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18
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van de Peppel IP, Demirdas S, Özcan B. Commentary: The mutations and clinical variability in maternally inherited diabetes and deafness: an analysis of 161 patients. Front Endocrinol (Lausanne) 2023; 14:1205862. [PMID: 37351107 PMCID: PMC10284591 DOI: 10.3389/fendo.2023.1205862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/29/2023] [Indexed: 06/24/2023] Open
Affiliation(s)
- Ivo P. van de Peppel
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, Netherlands
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - Serwet Demirdas
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Behiye Özcan
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, Netherlands
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19
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Houshmand M, Zeinali V, Hosseini A, Seifi A, Danaei B, Kamfar S. Investigation of FGF21 mRNA levels and relative mitochondrial DNA copy number levels and their relation in nonalcoholic fatty liver disease: a case-control study. Front Mol Biosci 2023; 10:1203019. [PMID: 37347041 PMCID: PMC10279952 DOI: 10.3389/fmolb.2023.1203019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Background: Although the exact mechanisms of nonalcoholic fatty liver disease (NAFLD) are not fully understood, numerous pieces of evidence show that the variations in mitochondrial DNA (mtDNA) level and hepatic Fibroblast growth factor 21 (FGF21) expression may be related to NAFLD susceptibility. Objectives: The main objective of this study was to determine relative levels of mtDNA copy number and hepatic FGF21 expression in a cohort of Iranian NAFLD patients and evaluate the possible relationship. Methods: This study included 27 NAFLD patients (10 with nonalcoholic fatty liver (NAFL) and 17 with non-alcoholic steatohepatitis (NASH)) and ten healthy subjects. Total RNA and genomic DNA were extracted from liver tissue samples, and then mtDNA copy number and FGF21 expression levels were assessed by quantitative real-time PCR. Results: The relative level of hepatic mtDNA copy number was 3.9-fold higher in patients than in controls (p < 0.0001). NAFLD patients showed a 2.9-fold increase in hepatic FGF21 expression compared to controls (p < 0.013). Results showed that hepatic FGF21 expression was positively correlated with BMI, serum ALT, and AST levels (p < 0.05). The level of mitochondrial copy number and hepatic FGF21 expression was not significantly associated with stages of change in hepatic steatosis. Finally, there was a significant correlation between FGF21 expression and mitochondrial copy number in NAFLD patients (p = 0.027). Conclusion: Our findings suggest a considerable rise of hepatic FGF21 mRNA levels and mtDNA-CN and show a positive correlation between them in the liver tissue of NAFLD patients.
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Affiliation(s)
- Massoud Houshmand
- Department of Medical Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Vahide Zeinali
- Research Institute for Children’s Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amirhossein Hosseini
- Pediatric Gastroenterology, Hepatology, and Nutrition Research Center, Research Institute for Children’s Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atena Seifi
- Pediatric Nephrology Research Center, Research Institute for Children’s Health, Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Bardia Danaei
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sharareh Kamfar
- Pediatric Congenital Hematologic Disorders Research Center, Research Institute for Children’s Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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McNeill A. The value of exomes across the ages. Eur J Hum Genet 2023; 31:129-130. [PMID: 36750729 PMCID: PMC9905505 DOI: 10.1038/s41431-023-01281-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Affiliation(s)
- Alisdair McNeill
- Department of Neuroscience, The University of Sheffield, Sheffield, UK.
- Sheffield Clinical Genetics Department, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK.
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