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Sung AY, Guerra RM, Steenberge LH, Alston CL, Murayama K, Okazaki Y, Shimura M, Prokisch H, Ghezzi D, Torraco A, Carrozzo R, Rötig A, Taylor RW, Keck JL, Pagliarini DJ. Systematic analysis of NDUFAF6 in complex I assembly and mitochondrial disease. Nat Metab 2024; 6:1128-1142. [PMID: 38720117 PMCID: PMC11395703 DOI: 10.1038/s42255-024-01039-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 03/28/2024] [Indexed: 06/27/2024]
Abstract
Isolated complex I (CI) deficiencies are a major cause of primary mitochondrial disease. A substantial proportion of CI deficiencies are believed to arise from defects in CI assembly factors (CIAFs) that are not part of the CI holoenzyme. The biochemistry of these CIAFs is poorly defined, making their role in CI assembly unclear, and confounding interpretation of potential disease-causing genetic variants. To address these challenges, we devised a deep mutational scanning approach to systematically assess the function of thousands of NDUFAF6 genetic variants. Guided by these data, biochemical analyses and cross-linking mass spectrometry, we discovered that the CIAF NDUFAF6 facilitates incorporation of NDUFS8 into CI and reveal that NDUFS8 overexpression rectifies NDUFAF6 deficiency. Our data further provide experimental support of pathogenicity for seven novel NDUFAF6 variants associated with human pathology and introduce functional evidence for over 5,000 additional variants. Overall, our work defines the molecular function of NDUFAF6 and provides a clinical resource for aiding diagnosis of NDUFAF6-related diseases.
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Affiliation(s)
- Andrew Y Sung
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Rachel M Guerra
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Laura H Steenberge
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Charlotte L Alston
- Mitochondrial Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutic of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Masaru Shimura
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Daniele Ghezzi
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Instituto Neurologico Carlo Besta, Milan, Italy
| | - Alessandra Torraco
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rosalba Carrozzo
- Unit of Cell Biology and Diagnosis of Mitochondrial Disorders, Laboratory of Medical Genetics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Agnès Rötig
- Université Paris Cité, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Robert W Taylor
- Mitochondrial Research Group, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
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Bhalla K, Rosier K, Monnens Y, Meulemans S, Vervoort E, Thorrez L, Agostinis P, Meier DT, Rochtus A, Resnick JL, Creemers JWM. Similar metabolic pathways are affected in both Congenital Myasthenic Syndrome-22 and Prader-Willi Syndrome. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167175. [PMID: 38626828 DOI: 10.1016/j.bbadis.2024.167175] [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: 12/18/2023] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 04/26/2024]
Abstract
Loss of prolyl endopeptidase-like (PREPL) encoding a serine hydrolase with (thio)esterase activity leads to the recessive metabolic disorder Congenital Myasthenic Syndrome-22 (CMS22). It is characterized by severe neonatal hypotonia, feeding problems, growth retardation, and hyperphagia leading to rapid weight gain later in childhood. The phenotypic similarities with Prader-Willi syndrome (PWS) are striking, suggesting that similar pathways are affected. The aim of this study was to identify changes in the hypothalamic-pituitary axis in mouse models for both disorders and to examine mitochondrial function in skin fibroblasts of patients and knockout cell lines. We have demonstrated that Prepl is downregulated in the brains of neonatal PWS-IC-p/+m mice. In addition, the hypothalamic-pituitary axis is similarly affected in both Prepl-/- and PWS-IC-p/+m mice resulting in defective orexigenic signaling and growth retardation. Furthermore, we demonstrated that mitochondrial function is altered in PREPL knockout HEK293T cells and can be rescued with the supplementation of coenzyme Q10. Finally, PREPL-deficient and PWS patient skin fibroblasts display defective mitochondrial bioenergetics. The mitochondrial dysfunction in PWS fibroblasts can be rescued by overexpression of PREPL. In conclusion, we provide the first molecular parallels between CMS22 and PWS, raising the possibility that PREPL substrates might become therapeutic targets for treating both disorders.
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Affiliation(s)
- Kritika Bhalla
- Laboratory for Biochemical Neuroendocrinology, Department of Human genetics, KU Leuven, 3000 Leuven, Belgium
| | - Karen Rosier
- Laboratory for Biochemical Neuroendocrinology, Department of Human genetics, KU Leuven, 3000 Leuven, Belgium
| | - Yenthe Monnens
- Laboratory for Biochemical Neuroendocrinology, Department of Human genetics, KU Leuven, 3000 Leuven, Belgium
| | - Sandra Meulemans
- Laboratory for Biochemical Neuroendocrinology, Department of Human genetics, KU Leuven, 3000 Leuven, Belgium
| | - Ellen Vervoort
- Laboratory for Cell Death Research & Therapy, VIB, Department of Cellular and Molecular Medicine, Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Lieven Thorrez
- Department of Development and Regeneration, KU Leuven Campus Kulak, 8500 Kortrijk, Belgium
| | - Patrizia Agostinis
- Laboratory for Cell Death Research & Therapy, VIB, Department of Cellular and Molecular Medicine, Center for Cancer Biology, KU Leuven, 3000 Leuven, Belgium
| | - Daniel T Meier
- Clinic of Endocrinology, Diabetes and Metabolism, University Hospital Basel, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Anne Rochtus
- Department of Development and Regeneration, UZ Leuven, 3000 Leuven, Belgium
| | - James L Resnick
- Department of Molecular genetics & Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - John W M Creemers
- Laboratory for Biochemical Neuroendocrinology, Department of Human genetics, KU Leuven, 3000 Leuven, Belgium.
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Leon Kropf V, Albany CJ, Zoccarato A, Green HLH, Yang Y, Brewer AC. TET3 is a positive regulator of mitochondrial respiration in Neuro2A cells. PLoS One 2024; 19:e0294187. [PMID: 38227585 PMCID: PMC10790995 DOI: 10.1371/journal.pone.0294187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/26/2023] [Indexed: 01/18/2024] Open
Abstract
Ten-Eleven-Translocase (TET) enzymes contribute to the regulation of the methylome via successive oxidation of 5-methyl cytosine (5mC) to derivatives which can be actively removed by base-excision-repair (BER) mechanisms in the absence of cell division. This is particularly important in post-mitotic neurons where changes in DNA methylation are known to associate with changes in neural function. TET3, specifically, is a critical regulator of both neuronal differentiation in development and mediates dynamic changes in the methylome of adult neurons associated with cognitive function. While DNA methylation is understood to regulate transcription, little is known of the specific targets of TET3-dependent catalytic activity in neurons. We report the results of an unbiased transcriptome analysis of the neuroblastoma-derived cell line; Neuro2A, in which Tet3 was silenced. Oxidative phosphorylation (OxPhos) was identified as the most significantly down-regulated functional canonical pathway, and these findings were confirmed by measurements of oxygen consumption rate in the Seahorse bioenergetics analyser. The mRNA levels of both nuclear- and mitochondrial-encoded OxPhos genes were reduced by Tet3-silencing, but we found no evidence for differential (hydroxy)methylation deposition at these gene loci. However, the mRNA expression of genes known to be involved in mitochondrial quality control were also shown to be significantly downregulated in the absence of TET3. One of these genes; EndoG, was identified as a direct target of TET3-catalytic activity at non-CpG methylated sites within its gene body. Accordingly, we propose that aberrant mitochondrial homeostasis may contribute to the decrease in OxPhos, observed upon Tet3-downregulation in Neuro2A cells.
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Affiliation(s)
- Valeria Leon Kropf
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Caraugh J. Albany
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Anna Zoccarato
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Hannah L. H. Green
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Youwen Yang
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
| | - Alison C. Brewer
- School of Cardiovascular and Metabolic Medicine & Sciences, King’s College London British Heart Foundation Centre of Excellence, London, United Kingdom
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McCormick EM, Keller K, Taylor JP, Coffey AJ, Shen L, Krotoski D, Harding B, Gai X, Falk MJ, Zolkipli-Cunningham Z, Rahman S. Expert Panel Curation of 113 Primary Mitochondrial Disease Genes for the Leigh Syndrome Spectrum. Ann Neurol 2023; 94:696-712. [PMID: 37255483 PMCID: PMC10763625 DOI: 10.1002/ana.26716] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
OBJECTIVE Primary mitochondrial diseases (PMDs) are heterogeneous disorders caused by inherited mitochondrial dysfunction. Classically defined neuropathologically as subacute necrotizing encephalomyelopathy, Leigh syndrome spectrum (LSS) is the most frequent manifestation of PMD in children, but may also present in adults. A major challenge for accurate diagnosis of LSS in the genomic medicine era is establishing gene-disease relationships (GDRs) for this syndrome with >100 monogenic causes across both nuclear and mitochondrial genomes. METHODS The Clinical Genome Resource (ClinGen) Mitochondrial Disease Gene Curation Expert Panel (GCEP), comprising 40 international PMD experts, met monthly for 4 years to review GDRs for LSS. The GCEP standardized gene curation for LSS by refining the phenotypic definition, modifying the ClinGen Gene-Disease Clinical Validity Curation Framework to improve interpretation for LSS, and establishing a scoring rubric for LSS. RESULTS The GDR with LSS across the nuclear and mitochondrial genomes was classified as definitive for 31 of 114 GDRs curated (27%), moderate for 38 (33%), limited for 43 (38%), and disputed for 2 (2%). Ninety genes were associated with autosomal recessive inheritance, 16 were maternally inherited, 5 were autosomal dominant, and 3 were X-linked. INTERPRETATION GDRs for LSS were established for genes across both nuclear and mitochondrial genomes. Establishing these GDRs will allow accurate variant interpretation, expedite genetic diagnosis of LSS, and facilitate precision medicine, multisystem organ surveillance, recurrence risk counseling, reproductive choice, natural history studies, and determination of eligibility for interventional clinical trials. ANN NEUROL 2023;94:696-712.
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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 (CHOP), Philadelphia, PA, USA
| | - Kierstin Keller
- Center for Mitochondrial and Epigenomic Medicine, Department of Pathology, CHOP, Philadelphia, PA, USA
| | - Julie P. Taylor
- Illumina Clinical Services Laboratory, Illumina Inc., San Diego, CA, USA
| | - Alison J. Coffey
- Illumina Clinical Services Laboratory, Illumina Inc., San Diego, CA, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Danuta Krotoski
- IDDB/NICHD, National Institutes of Health, Bethesda, MD, USA
| | - Brian Harding
- Departments of Pathology and Lab Medicine (Neuropathology), Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology & Laboratory Medicine, Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Marni J. Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Zarazuela Zolkipli-Cunningham
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shamima Rahman
- Mitochondrial Research Group, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, and Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
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Sun S, Zhong B, Zeng X, Li J, Chen Q. Transcription factor E4F1 as a regulator of cell life and disease progression. SCIENCE ADVANCES 2023; 9:eadh1991. [PMID: 37774036 PMCID: PMC10541018 DOI: 10.1126/sciadv.adh1991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/31/2023] [Indexed: 10/01/2023]
Abstract
E4F transcription factor 1 (E4F1), a member of the GLI-Kruppel family of zinc finger proteins, is now widely recognized as a transcription factor. It plays a critical role in regulating various cell processes, including cell growth, proliferation, differentiation, apoptosis and necrosis, DNA damage response, and cell metabolism. These processes involve intricate molecular regulatory networks, making E4F1 an important mediator in cell biology. Moreover, E4F1 has also been implicated in the pathogenesis of a range of human diseases. In this review, we provide an overview of the major advances in E4F1 research, from its first report to the present, including studies on its protein domains, molecular mechanisms of transcriptional regulation and biological functions, and implications for human diseases. We also address unresolved questions and potential research directions in this field. This review provides insights into the essential roles of E4F1 in human health and disease and may pave the way for facilitating E4F1 from basic research to clinical applications.
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Affiliation(s)
- Silu Sun
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Bing Zhong
- Upper Airways Research Laboratory, Department of Otolaryngology–Head and Neck Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xin Zeng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan 610041, China
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Invernizzi F, Izzo R, Colangelo I, Legati A, Zanetti N, Garavaglia B, Lamantea E, Peverelli L, Ardissone A, Moroni I, Maggi L, Bonanno S, Fiori L, Velardo D, Magri F, Comi GP, Ronchi D, Ghezzi D, Lamperti C. NGS-Based Genetic Analysis in a Cohort of Italian Patients with Suspected Inherited Myopathies and/or HyperCKemia. Genes (Basel) 2023; 14:1393. [PMID: 37510298 PMCID: PMC10379733 DOI: 10.3390/genes14071393] [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: 05/26/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Introduction/Aims HyperCKemia is considered a hallmark of neuromuscular diseases. It can be either isolated or associated with cramps, myalgia, weakness, myoglobinuria, or rhabdomyolysis, suggesting a metabolic myopathy. The aim of this work was to investigate possible genetic causes in order to help diagnose patients with recurrent hyperCKemia or clinical suspicion of inherited metabolic myopathy. Methods A cohort of 139 patients (90 adults and 49 children) was analyzed using a custom panel containing 54 genes associated with hyperCKemia. Results A definite genetic diagnosis was obtained in 15.1% of cases, while candidate variants or variants of uncertain significance were found in a further 39.5%. Similar percentages were obtained in patients with infantile or adult onset, with some different causative genes. RYR1 was the gene most frequently identified, either with single or compound heterozygous variants, while ETFDH variants were the most common cause for recessive cases. In one patient, mRNA analysis allowed identifying a large LPIN1 deletion missed by DNA sequencing, leading to a certain diagnosis. Conclusion These data confirm the high genetic heterogeneity of hyperCKemia and metabolic myopathies. The reduced diagnostic yield suggests the existence of additional genes associated with this condition but also allows speculation that a significant number of cases presenting with hyperCKemia or muscle symptoms are due to extrinsic, not genetic, factors.
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Affiliation(s)
- Federica Invernizzi
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Rossella Izzo
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Isabel Colangelo
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Andrea Legati
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Nadia Zanetti
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Barbara Garavaglia
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Eleonora Lamantea
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Lorenzo Peverelli
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - Anna Ardissone
- Child Neurology Unit-Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Isabella Moroni
- Child Neurology Unit-Department of Pediatric Neuroscience, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Lorenzo Maggi
- Department of Neuroimmunology and Neuromuscular Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Silvia Bonanno
- Department of Neuroimmunology and Neuromuscular Diseases, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Laura Fiori
- UOS di Malattie Metaboliche e Nutrizione, Ospedale dei Bambini Vittore Buzzi, 20154 Milan, Italy
| | - Daniele Velardo
- Neuromuscular and Rare Disease Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Francesca Magri
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Giacomo P Comi
- Neuromuscular and Rare Disease Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, 20122 Milan, Italy
| | - Dario Ronchi
- Neurology Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
- Department of Pathophysiology and Transplantation, Dino Ferrari Center, University of Milan, 20122 Milan, Italy
| | - Daniele Ghezzi
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
- Lab of Neurogenetics and Mitochondrial Disorders, Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy
| | - Costanza Lamperti
- Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
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Frascarelli C, Zanetti N, Nasca A, Izzo R, Lamperti C, Lamantea E, Legati A, Ghezzi D. Nanopore long-read next-generation sequencing for detection of mitochondrial DNA large-scale deletions. Front Genet 2023; 14:1089956. [PMID: 37456669 PMCID: PMC10344361 DOI: 10.3389/fgene.2023.1089956] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Primary mitochondrial diseases are progressive genetic disorders affecting multiple organs and characterized by mitochondrial dysfunction. These disorders can be caused by mutations in nuclear genes coding proteins with mitochondrial localization or by genetic defects in the mitochondrial genome (mtDNA). The latter include point pathogenic variants and large-scale deletions/rearrangements. MtDNA molecules with the wild type or a variant sequence can exist together in a single cell, a condition known as mtDNA heteroplasmy. MtDNA single point mutations are typically detected by means of Next-Generation Sequencing (NGS) based on short reads which, however, are limited for the identification of structural mtDNA alterations. Recently, new NGS technologies based on long reads have been released, allowing to obtain sequences of several kilobases in length; this approach is suitable for detection of structural alterations affecting the mitochondrial genome. In the present work we illustrate the optimization of two sequencing protocols based on long-read Oxford Nanopore Technology to detect mtDNA structural alterations. This approach presents strong advantages in the analysis of mtDNA compared to both short-read NGS and traditional techniques, potentially becoming the method of choice for genetic studies on mtDNA.
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Affiliation(s)
- Chiara Frascarelli
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Nadia Zanetti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Rossella Izzo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- Department of Pathophysiology and Transplantation (DEPT), University of Milan, Milan, Italy
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8
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Barretta F, Uomo F, Caldora F, Mocerino R, Adamo D, Testa F, Simonelli F, Scudiero O, Tinto N, Frisso G, Mazzaccara C. Combined MITOchondrial-NUCLEAR (MITO-NUCLEAR) Analysis for Mitochondrial Diseases Diagnosis: Validation and Implementation of a One-Step NGS Method. Genes (Basel) 2023; 14:genes14051087. [PMID: 37239447 DOI: 10.3390/genes14051087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) technology is revolutionizing diagnostic screening for mitochondrial diseases (MDs). Moreover, an investigation by NGS still requires analyzing the mitochondrial genome and nuclear genes separately, with limitations in terms of time and costs. We describe the validation and implementation of a custom blended MITOchondrial-NUCLEAR (MITO-NUCLEAR) assay for the simultaneous identification of genetic variants both in whole mtDNA and in nuclear genes included in a clinic exome panel. Furthermore, the MITO-NUCLEAR assay, implemented in our diagnostic process, has allowed us to arrive at a molecular diagnosis in a young patient. METHODS Massive sequencing strategy was applied for the validation experiments, performed using multiple tissues (blood, buccal swab, fresh tissue, tissue from slide, and formalin-fixed paraffin-embedded tissue section) and two different blend-in ratios of the mitochondrial probes: nuclear probes; 1:900 and 1:300. RESULTS Data suggested that 1:300 was the optimal probe dilution, where 100% of the mtDNA was covered at least 3000×, the median coverage was >5000×, and 93.84% of nuclear regions were covered at least 100×. CONCLUSIONS Our custom Agilent SureSelect MITO-NUCLEAR panel provides a potential "one-step" investigation that may be applied to both research and genetic diagnosis of MDs, allowing the simultaneous discovery of nuclear and mitochondrial mutations.
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Affiliation(s)
- Ferdinando Barretta
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
- CEINGE Advanced Biotechnologies Franco Salvatore, 80131 Naples, Italy
| | - Fabiana Uomo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Filomena Caldora
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Rossella Mocerino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Daniela Adamo
- Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples Federico II, 80131 Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania Luigi Vanvitelli, 80138 Naples, Italy
| | - Olga Scudiero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
- CEINGE Advanced Biotechnologies Franco Salvatore, 80131 Naples, Italy
| | - Nadia Tinto
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
- CEINGE Advanced Biotechnologies Franco Salvatore, 80131 Naples, Italy
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
- CEINGE Advanced Biotechnologies Franco Salvatore, 80131 Naples, Italy
| | - Cristina Mazzaccara
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
- CEINGE Advanced Biotechnologies Franco Salvatore, 80131 Naples, Italy
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9
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Paredes-Fuentes AJ, Oliva C, Urreizti R, Yubero D, Artuch R. Laboratory testing for mitochondrial diseases: biomarkers for diagnosis and follow-up. Crit Rev Clin Lab Sci 2023; 60:270-289. [PMID: 36694353 DOI: 10.1080/10408363.2023.2166013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The currently available biomarkers generally lack the specificity and sensitivity needed for the diagnosis and follow-up of patients with mitochondrial diseases (MDs). In this group of rare genetic disorders (mutations in approximately 350 genes associated with MDs), all clinical presentations, ages of disease onset and inheritance types are possible. Blood, urine, and cerebrospinal fluid surrogates are well-established biomarkers that are used in clinical practice to assess MD. One of the main challenges is validating specific and sensitive biomarkers for the diagnosis of disease and prediction of disease progression. Profiling of lactate, amino acids, organic acids, and acylcarnitine species is routinely conducted to assess MD patients. New biomarkers, including some proteins and circulating cell-free mitochondrial DNA, with increased diagnostic specificity have been identified in the last decade and have been proposed as potentially useful in the assessment of clinical outcomes. Despite these advances, even these new biomarkers are not sufficiently specific and sensitive to assess MD progression, and new biomarkers that indicate MD progression are urgently needed to monitor the success of novel therapeutic strategies. In this report, we review the mitochondrial biomarkers that are currently analyzed in clinical laboratories, new biomarkers, an overview of the most common laboratory diagnostic techniques, and future directions regarding targeted versus untargeted metabolomic and genomic approaches in the clinical laboratory setting. Brief descriptions of the current methodologies are also provided.
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Affiliation(s)
- Abraham J Paredes-Fuentes
- Division of Inborn Errors of Metabolism-IBC, Biochemistry and Molecular Genetics Department, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Clara Oliva
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Roser Urreizti
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Delia Yubero
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Genetic and Molecular Medicine-IPER, Institut de Recerca Sant Joan de Déu, Barcelona, Spain
| | - Rafael Artuch
- Clinical Biochemistry Department, Institut de Recerca Sant Joan de Déu, Hospital Sant Joan de Déu, Barcelona, Spain.,Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
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10
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Kaiyrzhanov R, Mohammed SEM, Maroofian R, Husain RA, Catania A, Torraco A, Alahmad A, Dutra-Clarke M, Grønborg S, Sudarsanam A, Vogt J, Arrigoni F, Baptista J, Haider S, Feichtinger RG, Bernardi P, Zulian A, Gusic M, Efthymiou S, Bai R, Bibi F, Horga A, Martinez-Agosto JA, Lam A, Manole A, Rodriguez DP, Durigon R, Pyle A, Albash B, Dionisi-Vici C, Murphy D, Martinelli D, Bugiardini E, Allis K, Lamperti C, Reipert S, Risom L, Laugwitz L, Di Nottia M, McFarland R, Vilarinho L, Hanna M, Prokisch H, Mayr JA, Bertini ES, Ghezzi D, Østergaard E, Wortmann SB, Carrozzo R, Haack TB, Taylor RW, Spinazzola A, Nowikovsky K, Houlden H. Bi-allelic LETM1 variants perturb mitochondrial ion homeostasis leading to a clinical spectrum with predominant nervous system involvement. Am J Hum Genet 2022; 109:1692-1712. [PMID: 36055214 PMCID: PMC9502063 DOI: 10.1016/j.ajhg.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 07/01/2022] [Indexed: 11/25/2022] Open
Abstract
Leucine zipper-EF-hand containing transmembrane protein 1 (LETM1) encodes an inner mitochondrial membrane protein with an osmoregulatory function controlling mitochondrial volume and ion homeostasis. The putative association of LETM1 with a human disease was initially suggested in Wolf-Hirschhorn syndrome, a disorder that results from de novo monoallelic deletion of chromosome 4p16.3, a region encompassing LETM1. Utilizing exome sequencing and international gene-matching efforts, we have identified 18 affected individuals from 11 unrelated families harboring ultra-rare bi-allelic missense and loss-of-function LETM1 variants and clinical presentations highly suggestive of mitochondrial disease. These manifested as a spectrum of predominantly infantile-onset (14/18, 78%) and variably progressive neurological, metabolic, and dysmorphic symptoms, plus multiple organ dysfunction associated with neurodegeneration. The common features included respiratory chain complex deficiencies (100%), global developmental delay (94%), optic atrophy (83%), sensorineural hearing loss (78%), and cerebellar ataxia (78%) followed by epilepsy (67%), spasticity (53%), and myopathy (50%). Other features included bilateral cataracts (42%), cardiomyopathy (36%), and diabetes (27%). To better understand the pathogenic mechanism of the identified LETM1 variants, we performed biochemical and morphological studies on mitochondrial K+/H+ exchange activity, proteins, and shape in proband-derived fibroblasts and muscles and in Saccharomyces cerevisiae, which is an important model organism for mitochondrial osmotic regulation. Our results demonstrate that bi-allelic LETM1 variants are associated with defective mitochondrial K+ efflux, swollen mitochondrial matrix structures, and loss of important mitochondrial oxidative phosphorylation protein components, thus highlighting the implication of perturbed mitochondrial osmoregulation caused by LETM1 variants in neurological and mitochondrial pathologies.
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Affiliation(s)
- Rauan Kaiyrzhanov
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Sami E M Mohammed
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Reza Maroofian
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Ralf A Husain
- Department of Neuropediatrics, Jena University Hospital, Jena 07747, Germany; Center for Rare Diseases, Jena University Hospital, Jena 07747, Germany
| | - Alessia Catania
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Alessandra Torraco
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Ahmad Alahmad
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; Kuwait Medical Genetics Centre, Al-Sabah Medical Area 80901, Kuwait
| | - Marina Dutra-Clarke
- Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, the University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Sabine Grønborg
- Center for Rare Diseases, Department of Pediatrics and Department of Genetics, Copenhagen University Hospital Rigshospitalet, Blegdamsvej 9, Copenhagen 2100, Denmark
| | - Annapurna Sudarsanam
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham B15 2TG, UK
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's and Children's Hospital, Birmingham B15 2TG, UK
| | - Filippo Arrigoni
- Paediatric Radiology and Neuroradiology Department, V. Buzzi Children's Hospital, Milan 20154, Italy
| | - Julia Baptista
- Peninsula Medical School, Faculty of Health, University of Plymouth, Plymouth PL4 8AA, UK
| | - Shahzad Haider
- Paediatrics Wah Medical College NUMS, Wah Cantonment, Punjab 44000, Pakistan
| | - René G Feichtinger
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg 5020, Austria
| | - Paolo Bernardi
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, Padova 35131, Italy
| | - Alessandra Zulian
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, Padova 35131, Italy
| | - Mirjana Gusic
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg 85764, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich 81675, Germany; Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | | | - Farah Bibi
- Institute of Biochemistry and Biotechnology, Pir Mehar Ali Shah Arid Agriculture University, Rawalpindi 44000, Pakistan
| | - Alejandro Horga
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK; Neuromuscular Diseases Unit, Department of Neurology, Hospital Clinico San Carlos and San Carlos Health Research Institute (IdISSC), Madrid 28040, Spain
| | - Julian A Martinez-Agosto
- Department of Human Genetics, Division of Medical Genetics, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amanda Lam
- Neurometabolic Unit, National Hospital for Neurology and Neurosurgery, London, UK; Department of Chemical Pathology, Great Ormond Street Hospital, WC1N 3BG London, UK
| | - Andreea Manole
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Diego-Perez Rodriguez
- Department of Clinical Movement Neurosciences, Royal Free Campus, University College of London, Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Romina Durigon
- Department of Clinical Movement Neurosciences, Royal Free Campus, University College of London, Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
| | - Buthaina Albash
- Kuwait Medical Genetics Centre, Al-Sabah Medical Area 80901, Kuwait
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Diego Martinelli
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | | | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy
| | - Siegfried Reipert
- Core Facility of Cell Imaging and Ultrastructure Research, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
| | - Lotte Risom
- Department of Genetics, Copenhagen University Hospital Rigshospitalet Blegdamsvej, Copenhagen 2100, Denmark
| | - Lucia Laugwitz
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, 72076 Tübingen, Germany; Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, Tübingen 72076, Germany
| | - Michela Di Nottia
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Laura Vilarinho
- Unit of Neonatal Screening, Metabolism and Genetics, Department of Human Genetics, National Institute of Health Dr Ricardo Jorge, Porto 4000-055, Portugal
| | - Michael Hanna
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg 85764, Germany; Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany
| | - Johannes A Mayr
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg 5020, Austria
| | - Enrico Silvio Bertini
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20126, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan 20122, Italy
| | - Elsebet Østergaard
- Department of Genetics, Copenhagen University Hospital Rigshospitalet Blegdamsvej, Copenhagen 2100, Denmark; Institute for Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Saskia B Wortmann
- University Children's Hospital, Salzburger Landeskliniken (SALK) and Paracelsus Medical University (PMU), Salzburg 5020, Austria; Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg 85764, Germany; Institute of Human Genetics, Technical University of Munich, Munich 81675, Germany; Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Amalia Children's Hospital, Radboudumc, Nijmegen 6525 EZ, the Netherlands
| | - Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome 00146, Italy
| | - Tobias B Haack
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Tübingen, Tübingen 72076, Germany; Centre for Rare Diseases, University of Tuebingen, Tübingen 72076, Germany
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 4LP, UK
| | - Antonella Spinazzola
- Department of Clinical Movement Neurosciences, Royal Free Campus, University College of London, Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Karin Nowikovsky
- Department of Biomedical Sciences, Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine Vienna, Vienna 1210, Austria; Department of Internal Medicine I, ASCTR and Comprehensive Cancer Center, Medical University of Vienna, Vienna 1090, Austria.
| | - Henry Houlden
- Department of Neuromuscular Diseases, University College London, Queen Square, Institute of Neurology, London WC1N 3BG, UK.
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11
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Biallelic Variants in ENDOG Associated with Mitochondrial Myopathy and Multiple mtDNA Deletions. Cells 2022; 11:cells11060974. [PMID: 35326425 PMCID: PMC8946636 DOI: 10.3390/cells11060974] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 12/02/2022] Open
Abstract
Endonuclease G (ENDOG) is a nuclear-encoded mitochondrial-localized nuclease. Although its precise biological function remains unclear, its proximity to mitochondrial DNA (mtDNA) makes it an excellent candidate to participate in mtDNA replication, metabolism and maintenance. Indeed, several roles for ENDOG have been hypothesized, including maturation of RNA primers during mtDNA replication, splicing of polycistronic transcripts and mtDNA repair. To date, ENDOG has been deemed as a determinant of cardiac hypertrophy, but no pathogenic variants or genetically defined patients linked to this gene have been described. Here, we report biallelic ENDOG variants identified by NGS in a patient with progressive external ophthalmoplegia, mitochondrial myopathy and multiple mtDNA deletions in muscle. The absence of the ENDOG protein in the patient’s muscle and fibroblasts indicates that the identified variants are pathogenic. The presence of multiple mtDNA deletions supports the role of ENDOG in mtDNA maintenance; moreover, the patient’s clinical presentation is very similar to mitochondrial diseases caused by mutations in other genes involved in mtDNA homeostasis. Although the patient’s fibroblasts did not present multiple mtDNA deletions or delay in the replication process, interestingly, we detected an accumulation of low-level heteroplasmy mtDNA point mutations compared with age-matched controls. This may indicate a possible role of ENDOG in mtDNA replication or repair. Our report provides evidence of the association of ENDOG variants with mitochondrial myopathy.
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12
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Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders. Curr Issues Mol Biol 2022; 44:1127-1148. [PMID: 35723297 PMCID: PMC8947152 DOI: 10.3390/cimb44030074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 12/06/2022] Open
Abstract
Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs’s cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial as well as nuclear genes and homo- or heteroplasmic point mutations in mitochondrially encoded genes is a characteristic of heterogeneous, maternally inherited genetic disorders known as mitochondrial disorders that affect multisystemic tissues and organs with high energy requirements, resulting in various signs and symptoms. Several traditional diagnostic approaches, including magnetic resonance imaging of the brain, cardiac testing, biochemical screening, variable heteroplasmy genetic testing, identifying clinical features, and skeletal muscle biopsies, are associated with increased risks, high costs, a high degree of false-positive or false-negative results, or a lack of precision, which limits their diagnostic abilities for mitochondrial disorders. Variable heteroplasmy levels, mtDNA depletion, and the identification of pathogenic variants can be detected through genetic sequencing, including the gold standard Sanger sequencing. However, sequencing can be time consuming, and Sanger sequencing can result in the missed recognition of larger structural variations such as CNVs or copy-number variations. Although each sequencing method has its own limitations, genetic sequencing can be an alternative to traditional diagnostic methods. The ever-growing roster of possible mutations has led to the development of next-generation sequencing (NGS). The enhancement of NGS methods can offer a precise diagnosis of the mitochondrial disorder within a short period at a reasonable expense for both research and clinical applications.
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13
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Hwang J, Kim H, Han J, Lee J, Hong S, Kim S, Yoon SK, Choi K, Yang J, Park U, Kim K, Yim K, Kim Y, Choi Y. Identification of Survival-Specific Genes in Clear Cell Renal Cell Carcinoma Using a Customized Next-Generation Sequencing Gene Panel. J Pers Med 2022; 12:jpm12010113. [PMID: 35055428 PMCID: PMC8778284 DOI: 10.3390/jpm12010113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/31/2021] [Accepted: 01/10/2022] [Indexed: 12/03/2022] Open
Abstract
Purpose: Although mutations are associated with carcinogenesis, little is known about survival-specific genes in clear cell renal cell carcinoma (ccRCC). We developed a customized next-generation sequencing (NGS) gene panel with 156 genes. The purpose of this study was to investigate whether the survival-specific genes we found were present in Korean ccRCC patients, and their association with clinicopathological findings. Materials and Methods: DNA was extracted from the formalin-fixed, paraffin-embedded tissue of 22 ccRCC patients. NGS was performed using our survival-specific gene panel with an Illumina MiSeq. We analyzed NGS data and the correlations between mutations and clinicopathological findings and also compared them with data from the Cancer Genome Atlas-Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) and Renal Cell Cancer-European Union (RECA-EU). Results: We found a total of 100 mutations in 37 of the 156 genes (23.7%) in 22 ccRCC patients. Of the 37 mutated genes, 11 were identified as clinicopathologically significant. Six were novel survival-specific genes (ADAMTS10, CARD6, NLRP2, OBSCN, SECISBP2L, and USP40), and five were top-ranked mutated genes (AKAP9, ARID1A, BAP1, KDM5C, and SETD2). Only CARD6 was validated as an overall survival-specific gene in this Korean study (p = 0.04, r = −0.441), TCGA-KIRC cohort (p = 0.0003), RECA-EU (p = 0.0005). The 10 remaining gene mutations were associated with clinicopathological findings; disease-free survival, mortality, nuclear grade, sarcomatoid component, N-stage, sex, and tumor size. Conclusions: We discovered 11 survival-specific genes in ccRCC using data from TCGA-KIRC, RECA-EU, and Korean patients. We are the first to find a correlation between CARD6 and overall survival in ccRCC. The 11 genes, including CARD6, NLRP2, OBSCN, and USP40, could be useful diagnostic, prognostic, and therapeutic markers in ccRCC.
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Affiliation(s)
- Jia Hwang
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Heeeun Kim
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Jinseon Han
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Jieun Lee
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Sunghoo Hong
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (S.H.); (S.K.)
| | - Saewoong Kim
- Department of Urology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (S.H.); (S.K.)
| | - Sungjoo Kim Yoon
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (S.K.Y.); (K.C.)
| | - Keonwoo Choi
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (S.K.Y.); (K.C.)
| | - Jihoon Yang
- Department of Computer Science and Engineering, Sogang University, Seoul 04107, Korea; (J.Y.); (U.P.)
| | - Unsang Park
- Department of Computer Science and Engineering, Sogang University, Seoul 04107, Korea; (J.Y.); (U.P.)
| | | | - Kwangil Yim
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Yuil Kim
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
| | - Yeongjin Choi
- Department of Hospital Pathology, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea; (J.H.); (H.K.); (J.H.); (J.L.); (K.Y.); (Y.K.)
- Correspondence: ; Tel.: +82-(22)-2581616; Fax: +82-(22)-2581627
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14
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Lenzini L, Carecchio M, Iori E, Legati A, Lamantea E, Avogaro A, Vitturi N. A novel MRPS34 gene mutation with combined OXPHOS deficiency in an adult patient with Leigh syndrome. Mol Genet Metab Rep 2021; 30:100830. [PMID: 34938649 DOI: 10.1016/j.ymgmr.2021.100830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
We report a novel pathogenic variant (c.223G > C; p.Gly75Arg) in the gene encoding the small mitoribosomal subunit protein mS34 in a long-surviving patient with Leigh Syndrome who was genetically diagnosed at age 34 years. The patient presented with delayed motor milestones and a stepwise motor deterioration during life, along with brain MRI alterations involving the subcortical white matter, deep grey nuclei and in particular the internal globi pallidi, that appeared calcified on CT scan. The novel variant is associated with a reduction of mS34 protein levels and of the OXPHOS complex I and IV subunits in peripheral blood mononuclear cells of the case. This study expands the number of variants that, by affecting the stability of the mitoribosome, may cause an OXPHOS deficiency in Leigh Syndrome and reports, for the first time, an unusual long survival in a patient with a homozygous MRPS34 pathogenic variant.
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Affiliation(s)
- L Lenzini
- University of Padova, Department of Medicine-DIMED, University Hospital, Padova, Italy
| | - M Carecchio
- Movement Disorders Unit, Department of Neurosciences, University of Padova, Padova, Italy
| | - E Iori
- University of Padova, Department of Medicine-DIMED, Division of Metabolic Diseases, University Hospital, Padova, Italy
| | - A Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - E Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20126 Milan, Italy
| | - A Avogaro
- University of Padova, Department of Medicine-DIMED, Division of Metabolic Diseases, University Hospital, Padova, Italy
| | - N Vitturi
- University of Padova, Department of Medicine-DIMED, Division of Metabolic Diseases, University Hospital, Padova, Italy
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15
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Rosier K, McDevitt MT, Smet J, Floyd BJ, Verschoore M, Marcaida MJ, Bingman CA, Lemmens I, Dal Peraro M, Tavernier J, Cravatt BF, Gounko NV, Vints K, Monnens Y, Bhalla K, Aerts L, Rashan EH, Vanlander AV, Van Coster R, Régal L, Pagliarini DJ, Creemers JW. Prolyl endopeptidase-like is a (thio)esterase involved in mitochondrial respiratory chain function. iScience 2021; 24:103460. [PMID: 34888501 PMCID: PMC8634043 DOI: 10.1016/j.isci.2021.103460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/27/2021] [Accepted: 11/11/2021] [Indexed: 11/25/2022] Open
Abstract
Deficiency of the serine hydrolase prolyl endopeptidase-like (PREPL) causes a recessive metabolic disorder characterized by neonatal hypotonia, feeding difficulties, and growth hormone deficiency. The pathophysiology of PREPL deficiency and the physiological substrates of PREPL remain largely unknown. In this study, we connect PREPL with mitochondrial gene expression and oxidative phosphorylation by analyzing its protein interactors. We demonstrate that the long PREPLL isoform localizes to mitochondria, whereas PREPLS remains cytosolic. Prepl KO mice showed reduced mitochondrial complex activities and disrupted mitochondrial gene expression. Furthermore, mitochondrial ultrastructure was abnormal in a PREPL-deficient patient and Prepl KO mice. In addition, we reveal that PREPL has (thio)esterase activity and inhibition of PREPL by Palmostatin M suggests a depalmitoylating function. We subsequently determined the crystal structure of PREPL, thereby providing insight into the mechanism of action. Taken together, PREPL is a (thio)esterase rather than a peptidase and PREPLL is involved in mitochondrial homeostasis.
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Affiliation(s)
- Karen Rosier
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Molly T. McDevitt
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joél Smet
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Brendan J. Floyd
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Maxime Verschoore
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Maria J. Marcaida
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Craig A. Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Irma Lemmens
- Center for Medical Biotechnology, VIB, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Matteo Dal Peraro
- Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Jan Tavernier
- Center for Medical Biotechnology, VIB, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Benjamin F. Cravatt
- The Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Natalia V. Gounko
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Katlijn Vints
- VIB-KU Leuven Center for Brain & Disease Research, Electron Microscopy Platform & VIB-Bioimaging Core, Leuven, Belgium
- Department of Neurosciences, Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Yenthe Monnens
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Kritika Bhalla
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Laetitia Aerts
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Edrees H. Rashan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Arnaud V. Vanlander
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Rudy Van Coster
- Department of Internal Medicine and Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Luc Régal
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Pediatrics, Pediatric Neurology and Metabolism, UZ Brussel, Brussels, Belgium
| | - David J. Pagliarini
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Departments of Cell Biology and Physiology, Biochemistry and Molecular Biophysics, and Genetics, Washington University School of Medicine, St Louis, MO 63110, USA
| | - John W.M. Creemers
- Laboratory for Biochemical Neuroendocrinology, Department of Human Genetics, KU Leuven, Leuven, Belgium
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16
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Yap ZY, Efthymiou S, Seiffert S, Vargas Parra K, Lee S, Nasca A, Maroofian R, Schrauwen I, Pendziwiat M, Jung S, Bhoj E, Striano P, Mankad K, Vona B, Cuddapah S, Wagner A, Alvi JR, Davoudi-Dehaghani E, Fallah MS, Gannavarapu S, Lamperti C, Legati A, Murtaza BN, Nadeem MS, Rehman MU, Saeidi K, Salpietro V, von Spiczak S, Sandoval A, Zeinali S, Zeviani M, Reich A, Jang C, Helbig I, Barakat TS, Ghezzi D, Leal SM, Weber Y, Houlden H, Yoon WH, Houlden H, Yoon WH. Bi-allelic variants in OGDHL cause a neurodevelopmental spectrum disease featuring epilepsy, hearing loss, visual impairment, and ataxia. Am J Hum Genet 2021; 108:2368-2384. [PMID: 34800363 DOI: 10.1016/j.ajhg.2021.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022] Open
Abstract
The 2-oxoglutarate dehydrogenase-like (OGDHL) protein is a rate-limiting enzyme in the Krebs cycle that plays a pivotal role in mitochondrial metabolism. OGDHL expression is restricted mainly to the brain in humans. Here, we report nine individuals from eight unrelated families carrying bi-allelic variants in OGDHL with a range of neurological and neurodevelopmental phenotypes including epilepsy, hearing loss, visual impairment, gait ataxia, microcephaly, and hypoplastic corpus callosum. The variants include three homozygous missense variants (p.Pro852Ala, p.Arg244Trp, and p.Arg299Gly), three compound heterozygous single-nucleotide variants (p.Arg673Gln/p.Val488Val, p.Phe734Ser/p.Ala327Val, and p.Trp220Cys/p.Asp491Val), one homozygous frameshift variant (p.Cys553Leufs∗16), and one homozygous stop-gain variant (p.Arg440Ter). To support the pathogenicity of the variants, we developed a novel CRISPR-Cas9-mediated tissue-specific knockout with cDNA rescue system for dOgdh, the Drosophila ortholog of human OGDHL. Pan-neuronal knockout of dOgdh led to developmental lethality as well as defects in Krebs cycle metabolism, which was fully rescued by expression of wild-type dOgdh. Studies using the Drosophila system indicate that p.Arg673Gln, p.Phe734Ser, and p.Arg299Gly are severe loss-of-function alleles, leading to developmental lethality, whereas p.Pro852Ala, p.Ala327Val, p.Trp220Cys, p.Asp491Val, and p.Arg244Trp are hypomorphic alleles, causing behavioral defects. Transcript analysis from fibroblasts obtained from the individual carrying the synonymous variant (c.1464T>C [p.Val488Val]) in family 2 showed that the synonymous variant affects splicing of exon 11 in OGDHL. Human neuronal cells with OGDHL knockout exhibited defects in mitochondrial respiration, indicating the essential role of OGDHL in mitochondrial metabolism in humans. Together, our data establish that the bi-allelic variants in OGDHL are pathogenic, leading to a Mendelian neurodevelopmental disease in humans.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Wan Hee Yoon
- Aging and Metabolism Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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17
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de Valles-Ibáñez G, Hildebrand MS, Bahlo M, King C, Coleman M, Green TE, Goldsmith J, Davis S, Gill D, Mandelstam S, Scheffer IE, Sadleir LG. Infantile-onset myoclonic developmental and epileptic encephalopathy: A new RARS2 phenotype. Epilepsia Open 2021; 7:170-180. [PMID: 34717047 PMCID: PMC8886097 DOI: 10.1002/epi4.12553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 09/29/2021] [Accepted: 10/25/2021] [Indexed: 11/11/2022] Open
Abstract
Recessive variants in RARS2, a nuclear gene encoding a mitochondrial protein, were initially reported in pontocerebellar hypoplasia. Subsequently, a recessive RARS2 early-infantile (<12 weeks) developmental and epileptic encephalopathy was described with hypoglycaemia and lactic acidosis. Here, we describe two unrelated patients with a novel RARS2 phenotype and reanalyse the published RARS2 epilepsy phenotypes and variants. Our novel cases had infantile-onset myoclonic developmental and epileptic encephalopathy, presenting with a progressive movement disorder from 9 months on a background of normal development. Development plateaued and regressed thereafter, with mild to profound impairment. Multiple drug-resistant generalized and focal seizures occurred with episodes of non-convulsive status epilepticus. Seizure types included absence, atonic, myoclonic, and focal seizures. Electroencephalograms showed diffuse slowing, multifocal, and generalised spike-wave activity, activated by sleep. Both patients had compound heterozygous RARS2 variants with likely impact on splicing and transcription. Remarkably, of the now 52 RARS2 variants reported in 54 patients, our reanalysis found that 44 (85%) have been shown to or are predicted to affect splicing or gene expression leading to protein truncation or nonsense-mediated decay. We expand the RARS2 phenotypic spectrum to include infantile encephalopathy and suggest this gene is enriched for pathogenic variants that disrupt splicing.
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Affiliation(s)
| | - Michael S Hildebrand
- Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Chontelle King
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
| | - Matthew Coleman
- Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Timothy E Green
- Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - John Goldsmith
- Waikids Paediatric Service, Waikato District Health Board, Hamilton, New Zealand
| | | | - Deepak Gill
- T.Y. Nelson Department of Neurology and Neurosurgery, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Simone Mandelstam
- Department of Medical Imaging, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine, Epilepsy Research Centre, University of Melbourne, Austin Health, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,The Florey Institute of Neuroscience and Mental Health, Melbourne, Victoria, Australia.,Departments of Paediatrics, University of Melbourne, Austin Health and Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago, Wellington, New Zealand
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18
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Zanfardino P, Doccini S, Santorelli FM, Petruzzella V. Tackling Dysfunction of Mitochondrial Bioenergetics in the Brain. Int J Mol Sci 2021; 22:8325. [PMID: 34361091 PMCID: PMC8348117 DOI: 10.3390/ijms22158325] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/15/2022] Open
Abstract
Oxidative phosphorylation (OxPhos) is the basic function of mitochondria, although the landscape of mitochondrial functions is continuously growing to include more aspects of cellular homeostasis. Thanks to the application of -omics technologies to the study of the OxPhos system, novel features emerge from the cataloging of novel proteins as mitochondrial thus adding details to the mitochondrial proteome and defining novel metabolic cellular interrelations, especially in the human brain. We focussed on the diversity of bioenergetics demand and different aspects of mitochondrial structure, functions, and dysfunction in the brain. Definition such as 'mitoexome', 'mitoproteome' and 'mitointeractome' have entered the field of 'mitochondrial medicine'. In this context, we reviewed several genetic defects that hamper the last step of aerobic metabolism, mostly involving the nervous tissue as one of the most prominent energy-dependent tissues and, as consequence, as a primary target of mitochondrial dysfunction. The dual genetic origin of the OxPhos complexes is one of the reasons for the complexity of the genotype-phenotype correlation when facing human diseases associated with mitochondrial defects. Such complexity clinically manifests with extremely heterogeneous symptoms, ranging from organ-specific to multisystemic dysfunction with different clinical courses. Finally, we briefly discuss the future directions of the multi-omics study of human brain disorders.
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Affiliation(s)
- Paola Zanfardino
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
| | - Stefano Doccini
- IRCCS Fondazione Stella Maris, Calambrone, 56128 Pisa, Italy;
| | | | - Vittoria Petruzzella
- Department of Medical Basic Sciences, Neurosciences and Sense Organs, University of Bari Aldo Moro, 70124 Bari, Italy;
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19
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Mazzaccara C, Mirra B, Barretta F, Caiazza M, Lombardo B, Scudiero O, Tinto N, Limongelli G, Frisso G. Molecular Epidemiology of Mitochondrial Cardiomyopathy: A Search Among Mitochondrial and Nuclear Genes. Int J Mol Sci 2021; 22:ijms22115742. [PMID: 34072184 PMCID: PMC8197938 DOI: 10.3390/ijms22115742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/18/2021] [Accepted: 05/22/2021] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial Cardiomyopathy (MCM) is a common manifestation of multi-organ Mitochondrial Diseases (MDs), occasionally present in non-syndromic cases. Diagnosis of MCM is complex because of wide clinical and genetic heterogeneity and requires medical, laboratory, and neuroimaging investigations. Currently, the molecular screening for MCM is fundamental part of MDs management and allows achieving the definitive diagnosis. In this article, we review the current genetic knowledge associated with MDs, focusing on diagnosis of MCM and MDs showing cardiac involvement. We searched for publications on mitochondrial and nuclear genes involved in MCM, mainly focusing on genetic screening based on targeted gene panels for the molecular diagnosis of the MCM, by using Next Generation Sequencing. Here we report twelve case reports, four case-control studies, eleven retrospective studies, and two prospective studies, for a total of twenty-nine papers concerning the evaluation of cardiac manifestations in mitochondrial diseases. From the analysis of published causal mutations, we identified 130 genes to be associated with mitochondrial heart diseases. A large proportion of these genes (34.3%) encode for key proteins involved in the oxidative phosphorylation system (OXPHOS), either as directly OXPHOS subunits (22.8%), and as OXPHOS assembly factors (11.5%). Mutations in several mitochondrial tRNA genes have been also reported in multi-organ or isolated MCM (15.3%). This review highlights the main disease-genes, identified by extensive genetic analysis, which could be included as target genes in next generation panels for the molecular diagnosis of patients with clinical suspect of mitochondrial cardiomyopathies.
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Affiliation(s)
- Cristina Mazzaccara
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
- Correspondence: ; Tel.: +39-0817-462-422
| | - Bruno Mirra
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Ferdinando Barretta
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Martina Caiazza
- Monaldi Hospital, AO Colli, 80131 Naples, Italy; (M.C.); (G.L.)
- Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy
| | - Barbara Lombardo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Olga Scudiero
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Nadia Tinto
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
| | - Giuseppe Limongelli
- Monaldi Hospital, AO Colli, 80131 Naples, Italy; (M.C.); (G.L.)
- Department of Translational Medical Sciences, University of Campania “Luigi Vanvitelli”, 80134 Naples, Italy
| | - Giulia Frisso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy; (B.M.); (F.B.); (B.L.); (O.S.); (N.T.); (G.F.)
- CEINGE Advanced Biotechnologies, 80145 Naples, Italy
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20
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Rius R, Compton AG, Baker NL, Welch AE, Coman D, Kava MP, Minoche AE, Cowley MJ, Thorburn DR, Christodoulou J. Application of Genome Sequencing from Blood to Diagnose Mitochondrial Diseases. Genes (Basel) 2021; 12:genes12040607. [PMID: 33924034 PMCID: PMC8072654 DOI: 10.3390/genes12040607] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/23/2022] Open
Abstract
Mitochondrial diseases can be caused by pathogenic variants in nuclear or mitochondrial DNA-encoded genes that often lead to multisystemic symptoms and can have any mode of inheritance. Using a single test, Genome Sequencing (GS) can effectively identify variants in both genomes, but it has not yet been universally used as a first-line approach to diagnosing mitochondrial diseases due to related costs and challenges in data analysis. In this article, we report three patients with mitochondrial disease molecularly diagnosed through GS performed on DNA extracted from blood to demonstrate different diagnostic advantages of this technology, including the detection of a low-level heteroplasmic pathogenic variant, an intragenic nuclear DNA deletion, and a large mtDNA deletion. Current technical improvements and cost reductions are likely to lead to an expanded routine diagnostic usage of GS and of the complementary “Omic” technologies in mitochondrial diseases.
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Affiliation(s)
- Rocio Rius
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Alison G. Compton
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
| | - Naomi L. Baker
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - AnneMarie E. Welch
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
| | - David Coman
- Department of Metabolic Medicine, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia;
- School of Clinical Medicine, University of Queensland, Brisbane, QLD 4072, Australia
- School of Medicine, Griffith University, Gold Coast, QLD 4222, Australia
| | - Maina P. Kava
- Department of Neurology, Perth Children’s Hospital, Perth, WA 6009, Australia;
- Department of Metabolic Medicine and Rheumatology, Perth Children’s Hospital, Perth, WA 6009, Australia
| | - Andre E. Minoche
- Kinghorn Centre for Clinical Genomics, Garvan Institute, University of New South Wales, Randwick, NSW 2010, Australia;
| | - Mark J. Cowley
- Precision Medicine Theme, Children’s Cancer Institute, Kensington, NSW 2750, Australia;
- School of Women’s and Children’s Health, University of New South Wales, Randwick, NSW 2031, Australia
| | - David R. Thorburn
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
| | - John Christodoulou
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia; (R.R.); (A.G.C.); (N.L.B.) (A.E.W.); (D.R.T.)
- Department of Paediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Victorian Clinical Genetic Services, Melbourne, VIC 3052, Australia
- Correspondence: ; Tel.: +61-39936-6353
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21
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Barp A, Mosca L, Sansone VA. Facilitations and Hurdles of Genetic Testing in Neuromuscular Disorders. Diagnostics (Basel) 2021; 11:diagnostics11040701. [PMID: 33919863 PMCID: PMC8070835 DOI: 10.3390/diagnostics11040701] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/11/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Neuromuscular disorders (NMDs) comprise a heterogeneous group of disorders that affect about one in every thousand individuals worldwide. The vast majority of NMDs has a genetic cause, with about 600 genes already identified. Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis to prevent the recurrence of the disease; furthermore, identification of specific genetic mutations still remains mandatory in some cases for clinical trial enrollment where new gene therapies are now approaching. Even though genetic analysis is catching on in the neuromuscular field, pitfalls and hurdles still remain and they should be taken into account by clinicians, as for example the use of next generation sequencing (NGS) where many single nucleotide variants of “unknown significance” can emerge, complicating the correct interpretation of genotype-phenotype relationship. Finally, when all efforts in terms of molecular analysis have been carried on, a portion of patients affected by NMDs still remain “not genetically defined”. In the present review we analyze the evolution of genetic techniques, from Sanger sequencing to NGS, and we discuss “facilitations and hurdles” of genetic testing which must always be balanced by clinicians, in order to ensure a correct diagnostic definition, but taking always into account the benefit that the patient could obtain especially in terms of “therapeutic offer”.
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Affiliation(s)
- Andrea Barp
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
- Correspondence:
| | - Lorena Mosca
- Medical Genetics Unit, ASST Grande Ospedale Metropolitano Niguarda, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
| | - Valeria Ada Sansone
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy;
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22
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Abstract
Neuromuscular disorders (NMDs) comprise a heterogeneous group of disorders that affect about one in every thousand individuals worldwide. The vast majority of NMDs has a genetic cause, with about 600 genes already identified. Application of genetic testing in NMDs can be useful for several reasons: correct diagnostic definition of a proband, extensive familial counselling to identify subjects at risk, and prenatal diagnosis to prevent the recurrence of the disease; furthermore, identification of specific genetic mutations still remains mandatory in some cases for clinical trial enrollment where new gene therapies are now approaching. Even though genetic analysis is catching on in the neuromuscular field, pitfalls and hurdles still remain and they should be taken into account by clinicians, as for example the use of next generation sequencing (NGS) where many single nucleotide variants of "unknown significance" can emerge, complicating the correct interpretation of genotype-phenotype relationship. Finally, when all efforts in terms of molecular analysis have been carried on, a portion of patients affected by NMDs still remain "not genetically defined". In the present review we analyze the evolution of genetic techniques, from Sanger sequencing to NGS, and we discuss "facilitations and hurdles" of genetic testing which must always be balanced by clinicians, in order to ensure a correct diagnostic definition, but taking always into account the benefit that the patient could obtain especially in terms of "therapeutic offer".
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Affiliation(s)
- Andrea Barp
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
| | - Lorena Mosca
- Medical Genetics Unit, ASST Grande Ospedale Metropolitano Niguarda, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
| | - Valeria Ada Sansone
- The NEMO Clinical Center in Milan, Neurorehabilitation Unit, University of Milan, Piazza Ospedale Maggiore 3, 20162 Milano, Italy
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23
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Torraco A, Nasca A, Verrigni D, Pennisi A, Zaki MS, Olivieri G, Assouline Z, Martinelli D, Maroofian R, Rizza T, Di Nottia M, Invernizzi F, Lamantea E, Longo D, Houlden H, Prokisch H, Rötig A, Dionisi-Vici C, Bertini E, Ghezzi D, Carrozzo R, Diodato D. Novel NDUFA12 variants are associated with isolated complex I defect and variable clinical manifestation. Hum Mutat 2021; 42:699-710. [PMID: 33715266 DOI: 10.1002/humu.24195] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/27/2021] [Accepted: 03/06/2021] [Indexed: 12/18/2022]
Abstract
Isolated biochemical deficiency of mitochondrial complex I is the most frequent signature among mitochondrial diseases and is associated with a wide variety of clinical symptoms. Leigh syndrome represents the most frequent neuroradiological finding in patients with complex I defect and more than 80 monogenic causes have been involved in the disease. In this report, we describe seven patients from four unrelated families harboring novel NDUFA12 variants, with six of them presenting with Leigh syndrome. Molecular genetic characterization was performed using next-generation sequencing combined with the Sanger method. Biochemical and protein studies were achieved by enzymatic activities, blue native gel electrophoresis, and western blot analysis. All patients displayed novel homozygous mutations in the NDUFA12 gene, leading to the virtual absence of the corresponding protein. Surprisingly, despite the fact that in none of the analyzed patients, NDUFA12 protein was detected, they present a different onset and clinical course of the disease. Our report expands the array of genetic alterations in NDUFA12 and underlines phenotype variability associated with NDUFA12 defect.
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Affiliation(s)
- Alessandra Torraco
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessia Nasca
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Verrigni
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alessandra Pennisi
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Maha S Zaki
- Human Genetics and Genome Research Division, Clinical Genetics Department, National Research Centre, Cairo, Egypt
| | - Giorgia Olivieri
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Zahra Assouline
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Diego Martinelli
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Reza Maroofian
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Teresa Rizza
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Michela Di Nottia
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Invernizzi
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eleonora Lamantea
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniela Longo
- Department of Diagnostic Imaging, Unit of Neuroradiology, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, UK
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Agnès Rötig
- UNITE INSERM U1163 Imagine Institute, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Carlo Dionisi-Vici
- Department of Pediatric Subspecialties, Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Enrico Bertini
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniele Ghezzi
- Diagnostic and Technology Department, Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Rosalba Carrozzo
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daria Diodato
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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24
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Gusic M, Prokisch H. Genetic basis of mitochondrial diseases. FEBS Lett 2021; 595:1132-1158. [PMID: 33655490 DOI: 10.1002/1873-3468.14068] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 12/13/2022]
Abstract
Mitochondrial disorders are monogenic disorders characterized by a defect in oxidative phosphorylation and caused by pathogenic variants in one of over 340 different genes. The implementation of whole-exome sequencing has led to a revolution in their diagnosis, duplicated the number of associated disease genes, and significantly increased the diagnosed fraction. However, the genetic etiology of a substantial fraction of patients exhibiting mitochondrial disorders remains unknown, highlighting limitations in variant detection and interpretation, which calls for improved computational and DNA sequencing methods, as well as the addition of OMICS tools. More intriguingly, this also suggests that some pathogenic variants lie outside of the protein-coding genes and that the mechanisms beyond the Mendelian inheritance and the mtDNA are of relevance. This review covers the current status of the genetic basis of mitochondrial diseases, discusses current challenges and perspectives, and explores the contribution of factors beyond the protein-coding regions and monogenic inheritance in the expansion of the genetic spectrum of disease.
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Affiliation(s)
- Mirjana Gusic
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany.,DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Germany
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technical University of Munich, Germany
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25
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Lahalle A, Lacroix M, De Blasio C, Cissé MY, Linares LK, Le Cam L. The p53 Pathway and Metabolism: The Tree That Hides the Forest. Cancers (Basel) 2021; 13:cancers13010133. [PMID: 33406607 PMCID: PMC7796211 DOI: 10.3390/cancers13010133] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/28/2020] [Accepted: 12/28/2020] [Indexed: 12/18/2022] Open
Abstract
Simple Summary The p53 pathway is a major tumor suppressor pathway that prevents the propagation of abnormal cells by regulating DNA repair, cell cycle progression, cell death, or senescence. The multiple cellular processes regulated by p53 were more recently extended to the control of metabolism, and many studies support the notion that perturbations of p53-associated metabolic activities are linked to cancer development. Converging lines of evidence support the notion that, in addition to p53, other key components of this molecular cascade are also important regulators of metabolism. Here, we illustrate the underestimated complexity of the metabolic network controlled by the p53 pathway and show how its perturbation contributes to human diseases including cancer, aging, and metabolic diseases. Abstract The p53 pathway is functionally inactivated in most, if not all, human cancers. The p53 protein is a central effector of numerous stress-related molecular cascades. p53 controls a safeguard mechanism that prevents accumulation of abnormal cells and their transformation by regulating DNA repair, cell cycle progression, cell death, or senescence. The multiple cellular processes regulated by p53 were more recently extended to the control of metabolism and many studies support the notion that perturbations of p53-associated metabolic activities are linked to cancer development, as well as to other pathophysiological conditions including aging, type II diabetes, and liver disease. Although much less documented than p53 metabolic activities, converging lines of evidence indicate that other key components of this tumor suppressor pathway are also involved in cellular metabolism through p53-dependent as well as p53-independent mechanisms. Thus, at least from a metabolic standpoint, the p53 pathway must be considered as a non-linear pathway, but the complex metabolic network controlled by these p53 regulators and the mechanisms by which their activities are coordinated with p53 metabolic functions remain poorly understood. In this review, we highlight some of the metabolic pathways controlled by several central components of the p53 pathway and their role in tissue homeostasis, metabolic diseases, and cancer.
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Affiliation(s)
- Airelle Lahalle
- Université de Montpellier, F-34090 Montpellier, France; (A.L.); (M.L.); (C.D.B.); (L.K.L.)
- IRCM, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, F-34298 Montpellier, France
- INSERM, Institut National de la Santé et de la Recherche Médicale, U1194, F-24298 Montpellier, France
- Equipe Labellisée Ligue Contre le Cancer, F-75013 Paris, France
| | - Matthieu Lacroix
- Université de Montpellier, F-34090 Montpellier, France; (A.L.); (M.L.); (C.D.B.); (L.K.L.)
- IRCM, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, F-34298 Montpellier, France
- INSERM, Institut National de la Santé et de la Recherche Médicale, U1194, F-24298 Montpellier, France
- Equipe Labellisée Ligue Contre le Cancer, F-75013 Paris, France
| | - Carlo De Blasio
- Université de Montpellier, F-34090 Montpellier, France; (A.L.); (M.L.); (C.D.B.); (L.K.L.)
- IRCM, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, F-34298 Montpellier, France
- INSERM, Institut National de la Santé et de la Recherche Médicale, U1194, F-24298 Montpellier, France
- Equipe Labellisée Ligue Contre le Cancer, F-75013 Paris, France
| | - Madi Y. Cissé
- Department of Molecular Metabolism, Harvard, T.H Chan School of Public Health, Boston, MA 02115, USA;
| | - Laetitia K. Linares
- Université de Montpellier, F-34090 Montpellier, France; (A.L.); (M.L.); (C.D.B.); (L.K.L.)
- IRCM, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, F-34298 Montpellier, France
- INSERM, Institut National de la Santé et de la Recherche Médicale, U1194, F-24298 Montpellier, France
| | - Laurent Le Cam
- Université de Montpellier, F-34090 Montpellier, France; (A.L.); (M.L.); (C.D.B.); (L.K.L.)
- IRCM, Institut de Recherche en Cancérologie de Montpellier, F-34298 Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, F-34298 Montpellier, France
- INSERM, Institut National de la Santé et de la Recherche Médicale, U1194, F-24298 Montpellier, France
- Equipe Labellisée Ligue Contre le Cancer, F-75013 Paris, France
- Correspondence:
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26
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Martinez N, Rosales J, Medina N, Perez-Maturo J, Salinas V, Zavala L, Vega P, Rodríguez-Quiroga S, Morón DG, Kauffman MA. Molecular Diagnosis in an Argentinean Mitochondrial Disorders Cohort. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2021. [DOI: 10.1590/2326-4594-jiems-2020-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Nerina Martinez
- Centro Universitario de Neurología “José María Ramos Mejía”, Argentina; Universidad Austral, Argentina
| | - Julieta Rosales
- Centro Universitario de Neurología “José María Ramos Mejía”, Argentina
| | - Nancy Medina
- Centro Universitario de Neurología “José María Ramos Mejía”, Argentina
| | - Josefina Perez-Maturo
- Centro Universitario de Neurología “José María Ramos Mejía”, Argentina; Universidad Austral, Argentina
| | - Valeria Salinas
- Centro Universitario de Neurología “José María Ramos Mejía”, Argentina; Universidad Austral, Argentina
| | - Lucia Zavala
- Centro Universitario de Neurología “José María Ramos Mejía”, Argentina
| | - Patricia Vega
- Centro Universitario de Neurología “José María Ramos Mejía”, Argentina
| | - Sergio Rodríguez-Quiroga
- Centro Universitario de Neurología “José María Ramos Mejía”, Argentina; Centro Universitario de Neurologia “Jose Maria Ramos Mejia”, Argentina
| | | | - Marcelo A. Kauffman
- Centro Universitario de Neurología “José María Ramos Mejía”, Argentina; Universidad Austral, Argentina
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27
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Fernandez-Vizarra E, Zeviani M. Mitochondrial disorders of the OXPHOS system. FEBS Lett 2020; 595:1062-1106. [PMID: 33159691 DOI: 10.1002/1873-3468.13995] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/21/2020] [Accepted: 11/01/2020] [Indexed: 12/13/2022]
Abstract
Mitochondrial disorders are among the most frequent inborn errors of metabolism, their primary cause being the dysfunction of the oxidative phosphorylation system (OXPHOS). OXPHOS is composed of the electron transport chain (ETC), formed by four multimeric enzymes and two mobile electron carriers, plus an ATP synthase [also called complex V (cV)]. The ETC performs the redox reactions involved in cellular respiration while generating the proton motive force used by cV to synthesize ATP. OXPHOS biogenesis involves multiple steps, starting from the expression of genes encoded in physically separated genomes, namely the mitochondrial and nuclear DNA, to the coordinated assembly of components and cofactors building each individual complex and eventually the supercomplexes. The genetic cause underlying around half of the diagnosed mitochondrial disease cases is currently known. Many of these cases result from pathogenic variants in genes encoding structural subunits or additional factors directly involved in the assembly of the ETC complexes. Here, we review the historical and most recent findings concerning the clinical phenotypes and the molecular pathological mechanisms underlying this particular group of disorders.
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Affiliation(s)
- Erika Fernandez-Vizarra
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, UK
| | - Massimo Zeviani
- Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Neurosciences, University of Padova, Italy
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28
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Levy MA, Kerkhof J, Belmonte FR, Kaufman BA, Bhai P, Brady L, Bursztyn LLCD, Tarnopolsky M, Rupar T, Sadikovic B. Validation and clinical performance of a combined nuclear-mitochondrial next-generation sequencing and copy number variant analysis panel in a Canadian population. Am J Med Genet A 2020; 185:486-499. [PMID: 33300680 DOI: 10.1002/ajmg.a.61998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/17/2022]
Abstract
Diagnosing mitochondrial disorders is a challenge due to the heterogeneous clinical presentation and large number of associated genes. A custom next generation sequencing (NGS) panel was developed incorporating the full mitochondrial genome (mtDNA) plus 19 nuclear genes involved in structural mitochondrial defects and mtDNA maintenance. This assay is capable of simultaneously detecting small gene sequence variations and larger copy number variants (CNVs) in both the nuclear and mitochondrial components along with heteroplasmy detection down to 5%. We describe technical validations of this panel and its implementation for clinical testing in a Canadian reference laboratory, and report its clinical performance in the initial 950 patients tested. Using this assay, we demonstrate a diagnostic yield of 18.1% of patients with known pathogenic variants. In addition to the common 5 kb mtDNA deletion, we describe significant contribution of pathogenic CNVs in both the mitochondrial genome and nuclear genes in this patient population.
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Affiliation(s)
- Michael A Levy
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Frances R Belmonte
- Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brett A Kaufman
- Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Lauren Brady
- Division of Neuromuscular and Neurometabolic Disease, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | - Mark Tarnopolsky
- Division of Neuromuscular and Neurometabolic Disease, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Tony Rupar
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Departments of Biochemistry and Paediatrics, Schulich School of Medicine & Dentistry, Western University, and Biochemical Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
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29
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Alahmad A, Nasca A, Heidler J, Thompson K, Oláhová M, Legati A, Lamantea E, Meisterknecht J, Spagnolo M, He L, Alameer S, Hakami F, Almehdar A, Ardissone A, Alston CL, McFarland R, Wittig I, Ghezzi D, Taylor RW. Bi-allelic pathogenic variants in NDUFC2 cause early-onset Leigh syndrome and stalled biogenesis of complex I. EMBO Mol Med 2020; 12:e12619. [PMID: 32969598 PMCID: PMC7645371 DOI: 10.15252/emmm.202012619] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 08/14/2020] [Accepted: 08/26/2020] [Indexed: 01/13/2023] Open
Abstract
Leigh syndrome is a progressive neurodegenerative disorder, most commonly observed in paediatric mitochondrial disease, and is often associated with pathogenic variants in complex I structural subunits or assembly factors resulting in isolated respiratory chain complex I deficiency. Clinical heterogeneity has been reported, but key diagnostic findings are developmental regression, elevated lactate and characteristic neuroimaging abnormalities. Here, we describe three affected children from two unrelated families who presented with Leigh syndrome due to homozygous variants (c.346_*7del and c.173A>T p.His58Leu) in NDUFC2, encoding a complex I subunit. Biochemical and functional investigation of subjects’ fibroblasts confirmed a severe defect in complex I activity, subunit expression and assembly. Lentiviral transduction of subjects’ fibroblasts with wild‐type NDUFC2 cDNA increased complex I assembly supporting the association of the identified NDUFC2 variants with mitochondrial pathology. Complexome profiling confirmed a loss of NDUFC2 and defective complex I assembly, revealing aberrant assembly intermediates suggestive of stalled biogenesis of the complex I holoenzyme and indicating a crucial role for NDUFC2 in the assembly of the membrane arm of complex I, particularly the ND2 module.
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Affiliation(s)
- Ahmad Alahmad
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Kuwait Medical Genetics Centre, Al-Sabah Medical Area, Kuwait
| | - Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Juliana Heidler
- SFB815 Core Unit, Functional Proteomics, Medical School, Goethe-Universität, Frankfurt am Main, Germany
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Faculty of Medical Sciences, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Jana Meisterknecht
- SFB815 Core Unit, Functional Proteomics, Medical School, Goethe-Universität, Frankfurt am Main, Germany
| | - Manuela Spagnolo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Seham Alameer
- Pediatric Department, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia.,King Abdullah International Medical Research Center, Jeddah, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Fahad Hakami
- Section of Molecular Medicine, King Abdulaziz Medical City-WR, King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Abeer Almehdar
- Department of Medical Imaging, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City-WR, National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Anna Ardissone
- Child Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ilka Wittig
- SFB815 Core Unit, Functional Proteomics, Medical School, Goethe-Universität, Frankfurt am Main, Germany.,German Center for Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK.,Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Royal Victoria Infirmary, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
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30
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Novel NDUFA13 Mutations Associated with OXPHOS Deficiency and Leigh Syndrome: A Second Family Report. Genes (Basel) 2020; 11:genes11080855. [PMID: 32722639 PMCID: PMC7465247 DOI: 10.3390/genes11080855] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/10/2020] [Accepted: 07/24/2020] [Indexed: 01/23/2023] Open
Abstract
Leigh syndrome (LS) usually presents as an early onset mitochondrial encephalopathy characterized by bilateral symmetric lesions in the basal ganglia and cerebral stem. More than 75 genes have been associated with this condition, including genes involved in the biogenesis of mitochondrial complex I (CI). In this study, we used a next-generation sequencing (NGS) panel to identify two novel biallelic variants in the NADH:ubiquinone oxidoreductase subunit A13 (NDUFA13) gene in a patient with isolated CI deficiency in skeletal muscle. Our patient, who represents the second family report with mutations in the CI NDUFA13 subunit, presented with LS lesions in brain magnetic resonance imaging, mild hypertrophic cardiomyopathy, and progressive spastic tetraparesis. This phenotype manifestation is different from that previously described in the first NDUFA13 family, which was predominantly characterized by neurosensorial symptoms. Both in silico pathogenicity predictions and oxidative phosphorylation (OXPHOS) functional findings in patient’s skin fibroblasts (delayed cell growth, isolated CI enzyme defect, decreased basal and maximal oxygen consumption and as well as ATP production, together with markedly diminished levels of the NDUFA13 protein, CI, and respirasomes) suggest that these novel variants in the NDUFA13 gene are the underlying cause of the CI defect, expanding the genetic heterogeneity of LS.
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31
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Marchet S, Legati A, Nasca A, Di Meo I, Spagnolo M, Zanetti N, Lamantea E, Catania A, Lamperti C, Ghezzi D. Homozygous mutations in C1QBP as cause of progressive external ophthalmoplegia (PEO) and mitochondrial myopathy with multiple mtDNA deletions. Hum Mutat 2020; 41:1745-1750. [PMID: 32652806 DOI: 10.1002/humu.24081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/05/2020] [Accepted: 07/09/2020] [Indexed: 12/13/2022]
Abstract
Biallelic mutations in the C1QBP gene have been associated with mitochondrial cardiomyopathy and combined respiratory-chain deficiencies, with variable onset (including intrauterine or neonatal forms), phenotypes, and severity. We studied two unrelated adult patients from consanguineous families, presenting with progressive external ophthalmoplegia (PEO), mitochondrial myopathy, and without any heart involvement. Muscle biopsies from both patients showed typical mitochondrial alterations and the presence of multiple mitochondrial DNA deletions, whereas biochemical defects of the respiratory chain were present only in one subject. Using next-generation sequencing approaches, we identified homozygous mutations in C1QBP. Immunoblot analyses in patients' muscle samples revealed a strong reduction in the amount of the C1QBP protein and varied impairment of respiratory chain complexes, correlating with disease severity. Despite the original study indicated C1QBP mutations as causative for mitochondrial cardiomyopathy, our data indicate that mutations in C1QBP have to be considered in subjects with PEO phenotype or primary mitochondrial myopathy and without cardiomyopathy.
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Affiliation(s)
- Silvia Marchet
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Ivano Di Meo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Manuela Spagnolo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Nadia Zanetti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Alessia Catania
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milano, Italy.,Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, Università degli Studi di Milano, Milano, Italy
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32
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Rooney RJ. Multiple domains in the 50 kDa form of E4F1 regulate promoter-specific repression and E1A trans-activation. Gene 2020; 754:144882. [PMID: 32535047 DOI: 10.1016/j.gene.2020.144882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/25/2020] [Accepted: 06/06/2020] [Indexed: 11/28/2022]
Abstract
The 50 kDa N-terminal product of the cellular transcription factor E4F1 (p50E4F1) mediates E1A289R trans-activation of the adenovirus E4 gene, and suppresses E1A-mediated transformation by sensitizing cells to cell death. This report shows that while both E1A289R and E1A243R stimulate p50E4F1 DNA binding activity, E1A289R trans-activation, as measured using GAL-p50E4F1 fusion proteins, involves a p50E4F1 transcription regulatory (TR) region that must be promoter-bound and is dependent upon E1A CR3, CR1 and N-terminal domains. Trans-activation is promoter-specific, as GAL-p50E4F1 did not stimulate commonly used artificial promoters and was strongly repressive when competing against GAL-VP16. p50E4F1 and E1A289R stably associate in vivo using the p50E4F1 TR region and E1A CR3, although their association in vitro is indirect and paradoxically disrupted by MAP kinase phosphorylation of E1A289R, which stimulates E4 trans-activation in vivo. Multiple cellular proteins, including TBP, bind the p50E4F1 TR region in vitro. The mechanistic implications for p50E4F1 function are discussed.
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Affiliation(s)
- Robert J Rooney
- Department of Genetics, Duke University Medical Center, Durham, NC, USA.
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33
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Stenton SL, Prokisch H. Genetics of mitochondrial diseases: Identifying mutations to help diagnosis. EBioMedicine 2020; 56:102784. [PMID: 32454403 PMCID: PMC7248429 DOI: 10.1016/j.ebiom.2020.102784] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/21/2020] [Accepted: 04/22/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial diseases are amongst the most genetically and phenotypically diverse groups of inherited diseases. The vast phenotypic overlap with other disease entities together with the absence of reliable biomarkers act as driving forces for the integration of unbiased methodologies early in the diagnostic algorithm, such as whole exome sequencing (WES) and whole genome sequencing (WGS). Such approaches are used in variant discovery and in combination with high-throughput functional assays such as transcriptomics in simultaneous variant discovery and validation. By capturing all genes, they not only increase the diagnostic rate in heterogenous mitochondrial disease patients, but accelerate novel disease gene discovery, and are valuable in side-stepping the risk of overlooking unexpected or even treatable genetic disease diagnoses.
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Affiliation(s)
- Sarah L Stenton
- Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Trogerstraße 32, 81675 München, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany
| | - Holger Prokisch
- Institut für Humangenetik, Klinikum rechts der Isar, Technische Universität München, Trogerstraße 32, 81675 München, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Ingolstaedter Landstraße 1, D-85764 Neuherberg, Germany.
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Hu C, Li X, Zhao L, Shi Y, Zhou S, Wu B, Wang Y. Clinical and molecular characterization of pediatric mitochondrial disorders in south of China. Eur J Med Genet 2020; 63:103898. [PMID: 32348839 DOI: 10.1016/j.ejmg.2020.103898] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/15/2020] [Accepted: 02/19/2020] [Indexed: 12/30/2022]
Abstract
Mitochondrial disorders (MDs) are genetic ailments affecting all age groups. Epidemiological data and frequencies of gene mutations in pediatric patients in China are scarce. This retrospective study assessed 101 patients with suspected MDs treated at the Neurology Department of Children's Hospital, Fudan University, in 2011-2017. Mitochondrial (mtDNA) and nuclear (nDNA) samples were assessed by long-range polymerase chain reaction (PCR)-based whole mtDNA sequencing and whole exome sequencing (WES) for identifying pathogenic mutations. Muscle samples underwent various staining protocols and immunofluorescence for detecting selected proteins. Seventeen mutations in the MT-TL1, MT-COX2, MT-ND4, MT, tRNA TRNE, MT-TN, MT-TK, MT-ATP6, MT-ND6, MT-ND3 and MT-CO3 genes were identified in 39 patients, of which m.3243A > G, m.3303C > T, m.8993T > C/G, m.9176T > C, and m.10191T > C were most common. Mitochondrial myopathy and MELAS were most common for m.3243A > G mutation. Four novel mutations were detected, including m.9478insT, m.5666T > C, m.8265T > C, and m.8380-13600 deletion mutations related to Leigh syndrome, mitochondrial myopathy and KSS, respectively. Thirty-three mutations in the TK2, POLG, IBA57, HADHB, FBXL4, ALDH5A1, FOXRED1, TPK1, NDUFAF5, NDUFAF7, NDUFV1, CARS2, PDHA1, and HIBCH genes were identified in 19 patients, including 23 currently unknown. Higher rates of TK2, POLG, IBA57, and HADHB mutations were found in nDNA-mutated MD compared with the remaining individuals. Besides, IBA57 c.286T > C (p.Y96H), TK2 c.497A > T (p.D166V) founder mutations critically contributed to MDs. Comprehensive genomic analysis plays a critical role in pediatric MD diagnosis. These data summarize the relative frequencies of different gene mutations in a large Chinese population, and identified 23 novel MD-associated nDNA and 4 novel mtDNA mutations.
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Affiliation(s)
- Chaoping Hu
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China
| | - Xihua Li
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China.
| | - Lei Zhao
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China
| | - Yiyun Shi
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China
| | - Shuizhen Zhou
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Translational Research Center for Development and Disease, Children's Hospital of Fudan University, Shanghai, China
| | - Yi Wang
- Department of Neurology, Children's Hospital of Fudan University, Shanghai, China.
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35
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Bakula D, Scheibye-Knudsen M. MitophAging: Mitophagy in Aging and Disease. Front Cell Dev Biol 2020; 8:239. [PMID: 32373609 PMCID: PMC7179682 DOI: 10.3389/fcell.2020.00239] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/23/2020] [Indexed: 12/19/2022] Open
Abstract
Maintaining mitochondrial health is emerging as a keystone in aging and associated diseases. The selective degradation of mitochondria by mitophagy is of particular importance in keeping a pristine mitochondrial pool. Indeed, inherited monogenic diseases with defects in mitophagy display complex multisystem pathologies but particularly progressive neurodegeneration. Fortunately, therapies are being developed that target mitophagy allowing new hope for treatments for previously incurable diseases. Herein, we describe mitophagy and associated diseases, coin the term mitophaging and describe new small molecule interventions that target different steps in the mitophagic pathway. Consequently, several age-associated diseases may be treated by targeting mitophagy.
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Affiliation(s)
- Daniela Bakula
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Morten Scheibye-Knudsen
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
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36
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Yang Q, Hua R, Qian J, Yi S, Shen F, Zhang Q, Li M, Yi S, Luo J, Fan X. PREPL Deficiency: A Homozygous Splice Site PREPL Mutation in a Patient With Congenital Myasthenic Syndrome and Absence of Ovaries and Hypoplasia of Uterus. Front Genet 2020; 11:198. [PMID: 32218803 PMCID: PMC7078161 DOI: 10.3389/fgene.2020.00198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/20/2020] [Indexed: 11/13/2022] Open
Abstract
Prolyl endopeptidase-like (PREPL) deficiency (MIM 616224) is a very rare congenital disorder characterized by neonatal hypotonia and feeding difficulties, ptosis, neuromuscular symptoms, cognitive impairments, growth hormone deficiency, short stature, and hypergonadotropic hypogonadism. This syndrome is an autosomal recessive disease resulting from mutations in the PREPL gene. Previous reports have associated PREPL deficiency with only one nucleotide substitution, the deletion of four nucleotides, and eight small microdeletions in the PREPL gene In this study, we used whole exome sequencing (WES) to identify a novel homozygous splicing mutation (c.616 + 1G > T) in a 14-year-old Chinese girl with PREPL deficiency. Sequencing of the RT-PCR products from the patient’s blood sample revealed that the c.616 + 1G > T variant disrupted normal splicing in intron 4 leading to an aberrant inclusion of 43 nucleotides in intron, a frameshift, and premature termination codon. Our patient exhibited several of the common phenotypes, including severe neonatal hypotonia, growth impairment and cognitive problems. However, we also observed several unusual phenotypic characteristics: absence of the ovaries, hypoplasia of the uterus, microcephaly and a short neck in patient is alsoobserved. These results provide further evidence for the involvement of PREPL development of the ovaries and uterus. Our findings may provide further insight into the relationship between the genotype and phenotype in collagen-associated diseases and improve the clinical diagnosis of Prolyl endopeptidase-like deficiency.
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Affiliation(s)
- Qi Yang
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Rong Hua
- The Guangxi Zhang Autonomous Region Reproductive Hospital, Nanning, China
| | - Jiale Qian
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Shang Yi
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Fei Shen
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Qiang Zhang
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Mengting Li
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Sheng Yi
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Jingsi Luo
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
| | - Xin Fan
- Genetic and Metabolic Central Laboratory, Guangxi Maternal and Child Health Hospital, Nanning, China
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37
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Thompson K, Collier JJ, Glasgow RIC, Robertson FM, Pyle A, Blakely EL, Alston CL, Oláhová M, McFarland R, Taylor RW. Recent advances in understanding the molecular genetic basis of mitochondrial disease. J Inherit Metab Dis 2020; 43:36-50. [PMID: 31021000 PMCID: PMC7041634 DOI: 10.1002/jimd.12104] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/03/2019] [Accepted: 04/24/2019] [Indexed: 12/22/2022]
Abstract
Mitochondrial disease is hugely diverse with respect to associated clinical presentations and underlying genetic causes, with pathogenic variants in over 300 disease genes currently described. Approximately half of these have been discovered in the last decade due to the increasingly widespread application of next generation sequencing technologies, in particular unbiased, whole exome-and latterly, whole genome sequencing. These technologies allow more genetic data to be collected from patients with mitochondrial disorders, continually improving the diagnostic success rate in a clinical setting. Despite these significant advances, some patients still remain without a definitive genetic diagnosis. Large datasets containing many variants of unknown significance have become a major challenge with next generation sequencing strategies and these require significant functional validation to confirm pathogenicity. This interface between diagnostics and research is critical in continuing to expand the list of known pathogenic variants and concomitantly enhance our knowledge of mitochondrial biology. The increasing use of whole exome sequencing, whole genome sequencing and other "omics" techniques such as transcriptomics and proteomics will generate even more data and allow further interrogation and validation of genetic causes, including those outside of coding regions. This will improve diagnostic yields still further and emphasizes the integral role that functional assessment of variant causality plays in this process-the overarching focus of this review.
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Affiliation(s)
- Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Jack J. Collier
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Ruth I. C. Glasgow
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Fiona M. Robertson
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
| | - Emma L. Blakely
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
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38
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Dharshini SAP, Taguchi YH, Gromiha MM. Investigating the energy crisis in Alzheimer disease using transcriptome study. Sci Rep 2019; 9:18509. [PMID: 31811163 PMCID: PMC6898285 DOI: 10.1038/s41598-019-54782-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 11/09/2019] [Indexed: 01/01/2023] Open
Abstract
Alzheimer disease (AD) is a devastating neurological disorder, which initiates from hippocampus and proliferates to cortical regions. The neurons of hippocampus require higher energy to preserve the firing pattern. In AD, aberrant energy metabolism is the critical factor for neurodegeneration. However, the reason for the energy crisis in hippocampus neurons is still unresolved. Transcriptome analysis enables us in understanding the underlying mechanism of energy crisis. In this study, we identified variants/differential gene/transcript expression profiles from hippocampus RNA-seq data. We predicted the effect of variants in transcription factor (TF) binding using in silico tools. Further, a hippocampus-specific co-expression and functional interaction network were designed to decipher the relationships between TF and differentially expressed genes (DG). Identified variants predominantly influence TF binding, which subsequently regulates the DG. From the results, we hypothesize that the loss of vascular integrity is the fundamental attribute for the energy crisis, which leads to neurodegeneration.
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Affiliation(s)
- S Akila Parvathy Dharshini
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India
| | - Y-H Taguchi
- Department of Physics, Chuo University, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, Tamilnadu, India.
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39
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Genes and Variants Underlying Human Congenital Lactic Acidosis-From Genetics to Personalized Treatment. J Clin Med 2019; 8:jcm8111811. [PMID: 31683770 PMCID: PMC6912785 DOI: 10.3390/jcm8111811] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/22/2019] [Accepted: 10/24/2019] [Indexed: 02/07/2023] Open
Abstract
Congenital lactic acidosis (CLA) is a rare condition in most instances due to a range of inborn errors of metabolism that result in defective mitochondrial function. Even though the implementation of next generation sequencing has been rapid, the diagnosis rate for this highly heterogeneous allelic condition remains low. The present work reports our group’s experience of using a clinical/biochemical analysis system in conjunction with genetic findings that facilitates the taking of timely clinical decisions with minimum need for invasive procedures. The system’s workflow combines different metabolomics datasets and phenotypic information with the results of clinical exome sequencing and/or RNA analysis. The system’s use detected genetic variants in 64% of a cohort of 39 CLA-patients; these variants, 14 of which were novel, were found in 19 different nuclear and two mitochondrial genes. For patients with variants of unknown significance, the genetic analysis was combined with functional genetic and/or bioenergetics analyses in an attempt to detect pathogenicity. Our results warranted subsequent testing of antisense therapy to rescue the abnormal splicing in cultures of fibroblasts from a patient with a defective GFM1 gene. The discussed system facilitates the diagnosis of CLA by avoiding the need to use invasive techniques and increase our knowledge of the causes of this condition.
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40
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41
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Bird MJ, Adant I, Windmolders P, Vander Elst I, Felgueira C, Altassan R, Gruenert SC, Ghesquière B, Witters P, Cassiman D, Vermeersch P. Oxygraphy Versus Enzymology for the Biochemical Diagnosis of Primary Mitochondrial Disease. Metabolites 2019; 9:metabo9100220. [PMID: 31658717 PMCID: PMC6835216 DOI: 10.3390/metabo9100220] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 09/27/2019] [Accepted: 10/09/2019] [Indexed: 12/12/2022] Open
Abstract
Primary mitochondrial disease (PMD) is a large group of genetic disorders directly affecting mitochondrial function. Although next generation sequencing technologies have revolutionized the diagnosis of these disorders, biochemical tests remain essential and functional confirmation of the critical genetic diagnosis. While enzymological testing of the mitochondrial oxidative phosphorylation (OXPHOS) complexes remains the gold standard, oxygraphy could offer several advantages. To this end, we compared the diagnostic performance of both techniques in a cohort of 34 genetically defined PMD patient fibroblast cell lines. We observed that oxygraphy slightly outperformed enzymology for sensitivity (79 ± 17% versus 68 ± 15%, mean and 95% CI), and had a better discriminatory power, identifying 58 ± 17% versus 35 ± 17% as “very likely” for oxygraphy and enzymology, respectively. The techniques did, however, offer synergistic diagnostic prediction, as the sensitivity rose to 88 ± 11% when considered together. Similarly, the techniques offered varying defect specific information, such as the ability of enzymology to identify isolated OXPHOS deficiencies, while oxygraphy pinpointed PDHC mutations and captured POLG mutations that were otherwise missed by enzymology. In summary, oxygraphy provides useful information for the diagnosis of PMD, and should be considered in conjunction with enzymology for the diagnosis of PMD.
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Affiliation(s)
- Matthew J Bird
- Laboratory of Hepatology, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
- Metabolomics Expertise Center, Center for Cancer Biology, CCB-VIB, 3000 Leuven, Belgium.
- Clinical Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium.
| | - Isabelle Adant
- Laboratory of Hepatology, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
- Department of Pediatrics, University Hospitals Leuven, 3000 Leuven, Belgium.
| | - Petra Windmolders
- Laboratory of Hepatology, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
| | - Ingrid Vander Elst
- Laboratory of Hepatology, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
| | - Catarina Felgueira
- Laboratory of Hepatology, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
| | - Ruqaiah Altassan
- Medical Genetics Department, King Faisal Specialist Hospital and Research Center, KSA MCD, Riyadh 43228, Saudi Arabia.
| | - Sarah C Gruenert
- Department of General Pediatrics, Adolescent Medicine and Neonatology, Medical Center-University of Freiburg, Faculty of Medicine, 79106 Freiburg, Germany.
| | - Bart Ghesquière
- Metabolomics Expertise Center, Center for Cancer Biology, CCB-VIB, 3000 Leuven, Belgium.
- Metabolomics Expertise Center, Department of Oncology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
| | - Peter Witters
- Metabolic Center, University Hospitals Leuven, 3000, Leuven, Belgium.
| | - David Cassiman
- Laboratory of Hepatology, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
- Metabolic Center, University Hospitals Leuven, 3000, Leuven, Belgium.
| | - Pieter Vermeersch
- Clinical Department of Laboratory Medicine, University Hospitals Leuven, 3000 Leuven, Belgium.
- Department of Cardiovascular Sciences, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
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42
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Saoura M, Powell CA, Kopajtich R, Alahmad A, AL‐Balool HH, Albash B, Alfadhel M, Alston CL, Bertini E, Bonnen PE, Bratkovic D, Carrozzo R, Donati MA, Di Nottia M, Ghezzi D, Goldstein A, Haan E, Horvath R, Hughes J, Invernizzi F, Lamantea E, Lucas B, Pinnock K, Pujantell M, Rahman S, Rebelo‐Guiomar P, Santra S, Verrigni D, McFarland R, Prokisch H, Taylor RW, Levinger L, Minczuk M. Mutations in ELAC2 associated with hypertrophic cardiomyopathy impair mitochondrial tRNA 3'-end processing. Hum Mutat 2019; 40:1731-1748. [PMID: 31045291 PMCID: PMC6764886 DOI: 10.1002/humu.23777] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/09/2019] [Accepted: 04/29/2019] [Indexed: 12/16/2022]
Abstract
Mutations in either the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA metabolism, including ELAC2. The ELAC2 gene codes for the mitochondrial RNase Z, responsible for endonucleolytic cleavage of the 3' ends of mitochondrial pre-tRNAs. Here, we report the identification of 16 novel ELAC2 variants in individuals presenting with mitochondrial respiratory chain deficiency, hypertrophic cardiomyopathy (HCM), and lactic acidosis. We provide evidence for the pathogenicity of the novel missense variants by studying the RNase Z activity in an in vitro system. We also modeled the residues affected by a missense mutation in solved RNase Z structures, providing insight into enzyme structure and function. Finally, we show that primary fibroblasts from the affected individuals have elevated levels of unprocessed mitochondrial RNA precursors. Our study thus broadly confirms the correlation of ELAC2 variants with severe infantile-onset forms of HCM and mitochondrial respiratory chain dysfunction. One rare missense variant associated with the occurrence of prostate cancer (p.Arg781His) impairs the mitochondrial RNase Z activity of ELAC2, suggesting a functional link between tumorigenesis and mitochondrial RNA metabolism.
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Affiliation(s)
| | | | - Robert Kopajtich
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsTechnische Universität MünchenMunichGermany
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Ahmad Alahmad
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- Kuwait Medical Genetics CenterKuwait CityKuwait
| | | | | | - Majid Alfadhel
- Genetics Division, Department of Pediatrics, King Abdullah International Medical Research CentreKing Saud bin Abdulaziz University for Health SciencesRiyadhSaudi Arabia
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Enrico Bertini
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Penelope E. Bonnen
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Drago Bratkovic
- Metabolic ClinicWomen's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Rosalba Carrozzo
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | | | - Michela Di Nottia
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Daniele Ghezzi
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
- Department of Pathophysiology and TransplantationUniversity of MilanMilanItaly
| | - Amy Goldstein
- Mitochondrial Medicine Frontier ProgramChildren's Hospital of PhiladelphiaPhiladelphiaUSA
| | - Eric Haan
- Metabolic ClinicWomen's and Children's HospitalNorth AdelaideSouth AustraliaAustralia
| | - Rita Horvath
- Wellcome Centre for Mitochondrial Research, Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
| | - Joanne Hughes
- National Centre for Inherited Metabolic DisordersTemple Street Children's University HospitalDublinIreland
| | - Federica Invernizzi
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Eleonora Lamantea
- Unit of Medical Genetics and NeurogeneticsFondazione IRCCS Istituto Neurologico Carlo BestaMilanItaly
| | - Benjamin Lucas
- York CollegeThe City University of New YorkJamaicaNew York
| | | | | | - Shamima Rahman
- Mitochondrial Research GroupUCL Great Ormond Street Institute of Child HealthLondonUK
| | - Pedro Rebelo‐Guiomar
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
- Graduate Program in Areas of Basic and Applied BiologyUniversity of PortoPortoPortugal
| | - Saikat Santra
- Department of Clinical Inherited Metabolic DisordersBirmingham Children's HospitalBirminghamUK
| | - Daniela Verrigni
- Department of Neurosciences, Unit of Muscular and Neurodegenerative Disorders, Laboratory of Molecular MedicineBambino Gesu' Children's Research Hospital, IRCCSRomeItaly
| | - Robert McFarland
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Holger Prokisch
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsTechnische Universität MünchenMunichGermany
- Genetics of Mitochondrial Disorders, Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Louis Levinger
- York CollegeThe City University of New YorkJamaicaNew York
| | - Michal Minczuk
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
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Brischigliaro M, Corrà S, Tregnago C, Fernandez-Vizarra E, Zeviani M, Costa R, De Pittà C. Knockdown of APOPT1/COA8 Causes Cytochrome c Oxidase Deficiency, Neuromuscular Impairment, and Reduced Resistance to Oxidative Stress in Drosophila melanogaster. Front Physiol 2019; 10:1143. [PMID: 31555154 PMCID: PMC6742693 DOI: 10.3389/fphys.2019.01143] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 08/22/2019] [Indexed: 12/31/2022] Open
Abstract
Cytochrome c oxidase (COX) deficiency is the biochemical hallmark of several mitochondrial disorders, including subjects affected by mutations in apoptogenic-1 (APOPT1), recently renamed as COA8 (HGNC:20492). Loss-of-function mutations are responsible for a specific infantile or childhood-onset mitochondrial leukoencephalopathy with a chronic clinical course. Patients deficient in COA8 show specific COX deficiency with distinctive neuroimaging features, i.e., cavitating leukodystrophy. In human cells, COA8 is rapidly degraded by the ubiquitin-proteasome system, but oxidative stress stabilizes the protein, which is then involved in COX assembly, possibly by protecting the complex from oxidative damage. However, its precise function remains unknown. The CG14806 gene (dCOA8) is the Drosophila melanogaster ortholog of human COA8 encoding a highly conserved COA8 protein. We report that dCOA8 knockdown (KD) flies show locomotor defects, and other signs of neurological impairment, reduced COX enzymatic activity, and reduced lifespan under oxidative stress conditions. Our data indicate that KD of dCOA8 in Drosophila phenocopies several features of the human disease, thus being a suitable model to characterize the molecular function/s of this protein in vivo and the pathogenic mechanisms associated with its defects.
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Affiliation(s)
| | - Samantha Corrà
- Department of Biology, University of Padova, Padua, Italy
| | - Claudia Tregnago
- Department of Women and Children's Health, University of Padova, Padua, Italy
| | | | - Massimo Zeviani
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom.,Department of Neurosciences, University of Padova, Padua, Italy
| | - Rodolfo Costa
- Department of Biology, University of Padova, Padua, Italy
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44
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Matricardi S, Canafoglia L, Ardissone A, Moroni I, Ragona F, Ghezzi D, Lamantea E, Nardocci N, Franceschetti S, Granata T. Epileptic phenotypes in children with early-onset mitochondrial diseases. Acta Neurol Scand 2019; 140:184-193. [PMID: 31102535 DOI: 10.1111/ane.13130] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 05/02/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVES To determine the prevalence of epilepsy in children with early-onset mitochondrial diseases (MDs) and to evaluate the epileptic phenotypes and associated features. MATERIALS AND METHODS Children affected by MD with onset during the first year of life were enrolled. Patients were classified according to their mitochondrial phenotype, and all findings in patients with epilepsy versus patients without were compared. The epileptic features were analyzed. RESULTS The series includes 129 patients (70 females) with median age at disease onset of 3 months. The median time of follow-up was 5 years. Non-syndromic mitochondrial encephalopathy and pyruvate dehydrogenase complex deficiency were the main mitochondrial diseases associated with epilepsy (P < 0.05). Seizures occurred in 48%, and the presence of epilepsy was significantly associated with earlier age at disease onset, presence of perinatal manifestations, and early detection of developmental delay and regression (P < 0.001). Epileptic encephalopathy (EE) with spasms and EE with prominent focal seizures were the most detected epileptic syndromes (37% and 27.4%). Several seizure types were recorded in 53.2%, with the unusual association of generalized and focal epileptic pattern. Disabling epilepsy was detected in 63% and was associated with early seizure onset, presence of several seizure types, epileptic syndrome featuring EE, and the recurrence of episodes of status epilepticus and epilepsia partialis continua (P < 0.05). CONCLUSIONS Epilepsy in children with early-onset MD may be a presenting or a prominent symptom in a multisystemic clinical presentation. Epilepsy-related factors could determine a worst seizure outcome, leading to a more severe burned of the disease.
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Affiliation(s)
- Sara Matricardi
- Department of Pediatric Neuroscience Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
- Department of Neuropsychiatry Children's Hospital “G. Salesi”Ospedali Riuniti Ancona Ancona Italy
| | - Laura Canafoglia
- Department of Neurophysiology and Diagnostic Epileptology Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
| | - Anna Ardissone
- Department of Pediatric Neuroscience Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
| | - Isabella Moroni
- Department of Pediatric Neuroscience Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
| | - Francesca Ragona
- Department of Pediatric Neuroscience Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
| | - Daniele Ghezzi
- Medical Genetics and Neurogenetics Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
- Department of Pathophysiology and Transplantation University of Milan Milan Italy
| | - Eleonora Lamantea
- Medical Genetics and Neurogenetics Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
| | - Nardo Nardocci
- Department of Pediatric Neuroscience Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
| | - Silvana Franceschetti
- Department of Neurophysiology and Diagnostic Epileptology Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
| | - Tiziana Granata
- Department of Pediatric Neuroscience Fondazione IRCCS Istituto Neurologico Carlo Besta Milan Italy
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Targeted next generation sequencing identifies novel pathogenic variants and provides molecular diagnoses in a cohort of pediatric and adult patients with unexplained mitochondrial dysfunction. Mitochondrion 2019; 47:309-317. [DOI: 10.1016/j.mito.2019.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/14/2019] [Accepted: 02/26/2019] [Indexed: 12/28/2022]
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Catania A, Legati A, Peverelli L, Nanetti L, Marchet S, Zanetti N, Lamperti C, Ghezzi D. Homozygous variant in OTX2 and possible genetic modifiers identified in a patient with combined pituitary hormone deficiency, ocular involvement, myopathy, ataxia, and mitochondrial impairment. Am J Med Genet A 2019; 179:827-831. [PMID: 30773800 DOI: 10.1002/ajmg.a.61092] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/22/2022]
Abstract
Here we report on a singleton patient affected by a complicated congenital syndrome characterized by growth delay, retinal dystrophy, sensorineural deafness, myopathy, ataxia, combined pituitary hormone deficiency, associated with mitochondrial impairment. Targeted clinical exome sequencing led to the identification of a homozygous missense variant in OTX2. Since only dominant mutations within OTX2 have been associated with cases of syndromic microphthalmia, retinal dystrophy with or without pituitary dysfunctions, this represents the first report of an OTX2 recessive mutation. Part of the phenotype, including ataxia, myopathy and multiple mitochondrial respiratory chain defects, seemed not related to OTX2. Further analysis of next generation sequencing (NGS) data revealed additional candidate variants: a homozygous variant in LETM1, and heterozygous rare variants in AFG3L2 and POLG. All three genes encode mitochondrial proteins and the last two are known to be associated with ataxia, a neurological sign present also in the father of the proband. With our study, we aim to encourage the integration of NGS data with a detailed analysis of clinical description and family history in order to unravel composite genotypes sometimes associated with complicated phenotypes.
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Affiliation(s)
- Alessia Catania
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Lorenzo Peverelli
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Neuromuscular and Rare Diseases Unit, Department of Neuroscience, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Lorenzo Nanetti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Silvia Marchet
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Nadia Zanetti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Costanza Lamperti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
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47
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Muscle Involvement in a Large Cohort of Pediatric Patients with Genetic Diagnosis of Mitochondrial Disease. J Clin Med 2019; 8:jcm8010068. [PMID: 30634555 PMCID: PMC6352184 DOI: 10.3390/jcm8010068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 12/17/2018] [Accepted: 01/07/2019] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial diseases (MD) are a group of genetic and acquired disorders which present significant diagnostic challenges. Here we report the disease characteristics of a large cohort of pediatric MD patients (n = 95) with a definitive genetic diagnosis, giving special emphasis on clinical muscle involvement, biochemical and histopathological features. Of the whole cohort, 51 patients harbored mutations in nuclear DNA (nDNA) genes and 44 patients had mutations in mitochondrial DNA (mtDNA) genes. The nDNA patients were more likely to have a reduction in muscle fiber succinate dehydrogenase (SDH) stains and in SDH-positive blood vessels, while a higher frequency of mtDNA patients had ragged red (RRF) and blue fibers. The presence of positive histopathological features was associated with ophthalmoplegia, myopathic facies, weakness and exercise intolerance. In 17 patients younger than two years of age, RRF and blue fibers were observed only in one case, six cases presented cytochrome c oxidase (COX) reduction/COX-fibers, SDH reduction was observed in five and all except one presented SDH-positive blood vessels. In conclusion, muscle involvement was a frequent finding in our series of MD patients, especially in those harboring mutations in mtDNA genes.
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48
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Paiva Coelho M, Martins E, Vilarinho L. Diagnosis, management, and follow-up of mitochondrial disorders in childhood: a personalized medicine in the new era of genome sequence. Eur J Pediatr 2019; 178:21-32. [PMID: 30535772 DOI: 10.1007/s00431-018-3292-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/05/2018] [Accepted: 11/08/2018] [Indexed: 12/11/2022]
Abstract
Primary mitochondrial disorders are highly variable in clinical presentation, biochemistry, and molecular etiology. Mitochondrial disorders can be caused by genetic defects in the mitochondrial, in nuclear genome, or in the interplay between the two genomes. Biochemical screening tests may be inconclusive or misleading since patients, with confirmed mitochondrial disorders specially in pediatric age, may exhibit normal routine biochemistry, muscle histology, or enzymatic analysis of the mitochondrial respiratory chain. Diagnosis is often challenging even with combination of multiple criteria (clinical, biochemical, histological, and functional), as innumerous conditions cause secondary mitochondrial dysfunction. Nowadays, a definite diagnosis is only possible by genetic confirmation since no single score system is satisfactorily accurate, being sensitive but not specific.Conclusion: Awareness between physicians is of major importance considering that clinical suspicion may not be obvious regarding the heterogenicity in presentation and biochemical features of mitochondrial disorders. In this review, we provide information on diagnosis approach to patients suspected for mitochondrial disorders as well as management on chronic and acute settings. Follow-up should provide comprehensive information on patient's status, since intervention on these diseases is mostly supportive and prognosis is variable and sometimes unpredictable. What is Known: • Mitochondrial disorders are heterogenous and may present at any age, with any symptoms and any type of inheritance. • Mitochondrial disorders may be due to pathogenic variants in mitochondrial DNA (mtDNA) or nuclear genes (nDNA). What is New: • Since no single score system is satisfactorily accurate, a definite diagnosis is only possible with genetic studies with gene panels proving to be a cost-effective approach. • Clinical and biochemical features of patients without a confirmed diagnosis must be reviewed and other diagnosis must be considered. A wider genetic approach may be applied (WES or WGS).
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Affiliation(s)
- Margarida Paiva Coelho
- Pediatrics Department, Centro Materno Infantil do Norte, Centro Hospitalar do Porto, Largo da Maternidade, S/N, 4450, Porto, Portugal.
| | - Esmeralda Martins
- Reference Center for Inherited Metabolic Disorders, Centro Hospitalar do Porto, Porto, Portugal
| | - Laura Vilarinho
- Newborn Screening, Metabolism and Genetics Unit, Human Genetics Department, National Institute of Health Dr. Ricardo Jorge, Porto, Portugal
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Nasca A, Nardecchia F, Commone A, Semeraro M, Legati A, Garavaglia B, Ghezzi D, Leuzzi V. Clinical and Biochemical Features in a Patient With Mitochondrial Fission Factor Gene Alteration. Front Genet 2018; 9:625. [PMID: 30581454 PMCID: PMC6292958 DOI: 10.3389/fgene.2018.00625] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/23/2018] [Indexed: 01/27/2023] Open
Abstract
Mitochondrial Fission Factor (MFF) is part of a protein complex that promotes mitochondria and peroxisome fission. Hitherto, only 5 patients have been reported harboring mutations in MFF, all of them with the clinical features of a very early onset Leigh-like encephalopathy. We report on an 11-year-old boy with epileptic encephalopathy. He presented with neurological regression, epileptic myoclonic seizures, severe intellectual disability, microcephaly, tetraparesis, optic atrophy, and ophthalmoplegia. Brain MRI pattern was compatible with Leigh syndrome. NGS-based analysis of a gene panel for mitochondrial disorders revealed a homozygous c.892C>T (p. Arg298*) in the MFF gene. Fluorescence staining detected abnormal morphology of mitochondria and peroxisomes in fibroblasts from the patient; a strong reduction in MFF protein levels and the presence of truncated forms were observed. No biochemical alterations denoting peroxisomal disorders were found. As reported in other disorders affecting the dynamics of intracellular organelles, our patient showed clinical features suggesting both mitochondrial and peroxisomal impairment. High levels of lactate in our case suggested an involvement of the energetic metabolism but without clear respiratory chain deficiency, while biomarkers of peroxisomal dysfunction were normal. We confirm that MFF mutations are associated with epileptic encephalopathy with Leigh-like MRI pattern.
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Affiliation(s)
- Alessia Nasca
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Francesca Nardecchia
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Anna Commone
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Michela Semeraro
- Division of Metabolism and Research Unit of Metabolic Biochemistry, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Andrea Legati
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Barbara Garavaglia
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy.,Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Vincenzo Leuzzi
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
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50
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Abicht A, Scharf F, Kleinle S, Schön U, Holinski-Feder E, Horvath R, Benet-Pagès A, Diebold I. Mitochondrial and nuclear disease panel (Mito-aND-Panel): Combined sequencing of mitochondrial and nuclear DNA by a cost-effective and sensitive NGS-based method. Mol Genet Genomic Med 2018; 6:1188-1198. [PMID: 30406974 PMCID: PMC6305657 DOI: 10.1002/mgg3.500] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 09/27/2018] [Accepted: 10/10/2018] [Indexed: 01/21/2023] Open
Abstract
Background The diagnosis of mitochondrial disorders is challenging because of the clinical variability and genetic heterogeneity of these conditions. Next‐Generation Sequencing (NGS) technology offers a robust high‐throughput platform for nuclear and mitochondrial DNA (mtDNA) analyses. Method We developed a custom Agilent SureSelect Mitochondrial and Nuclear Disease Panel (Mito‐aND‐Panel) capture kit that allows parallel enrichment for subsequent NGS‐based sequence analysis of nuclear mitochondrial disease‐related genes and the complete mtDNA genome. Sequencing of enriched mtDNA simultaneously with nuclear genes was compared with the separated sequencing of the mitochondrial genome and whole exome sequencing (WES). Results The Mito‐aND‐Panel permits accurate detection of low‐level mtDNA heteroplasmy due to a very high sequencing depth compared to standard diagnostic procedures using Sanger sequencing/SNaPshot and WES which is crucial to identify maternally inherited mitochondrial disorders. Conclusion We established a NGS‐based method with combined sequencing of the complete mtDNA and nuclear genes which enables a more sensitive heteroplasmy detection of mtDNA mutations compared to traditional methods. Because the method promotes the analysis of mtDNA variants in large cohorts, it is cost‐effective and simple to setup, we anticipate this is a highly relevant method for sequence‐based genetic diagnosis in clinical diagnostic applications.
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Affiliation(s)
- Angela Abicht
- Medical Genetic Center Munich, Munich, Germany.,Department of Neurology, Friedrich-Baur-Institute, Klinikum der Ludwig-Maximilians-Universität München, Munich, Germany
| | | | | | | | | | - Rita Horvath
- Newcastle upon Tyne Hospitals NHS Trust, Newcastle upon Tyne, UK
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