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Aaltio J, Euro L, Tynninen O, Vu HS, Ni M, DeBerardinis RJ, Suomalainen A, Isohanni P. Niacin supplementation in a child with novel MTTN variant m.5670A>G causing early onset mitochondrial myopathy and NAD + deficiency. Neuromuscul Disord 2024; 43:14-19. [PMID: 39173541 DOI: 10.1016/j.nmd.2024.07.005] [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: 03/14/2024] [Revised: 07/07/2024] [Accepted: 07/09/2024] [Indexed: 08/24/2024]
Abstract
Myopathy is a common manifestation in mitochondrial disorders, but the pathomechanisms are still insufficiently studied in children. Here, we report a severe, progressive mitochondrial myopathy in a four-year-old child, who died at eight years. He developed progressive loss of muscle strength with nocturnal hypoventilation and dilated cardiomyopathy. Skeletal muscle showed ragged red fibers and severe combined respiratory chain deficiency. Mitochondrial DNA sequencing revealed a novel m.5670A>G mutation in mitochondrial tRNAAsn (MTTN) with 88 % heteroplasmy in muscle. The proband also had systemic NAD+ deficiency but rescuing this with the NAD+ precursor niacin did not stop disease progression. Targeted metabolomics revealed an overall shift of metabolism towards controls after niacin supplementation, with normalized tryptophan metabolites and lipid-metabolic markers, but most amino acids did not respond to niacin therapy. To conclude, we report a new MTTN mutation, secondary NAD+ deficiency in childhood-onset mitochondrial myopathy with metabolic but meager clinical response to niacin supplementation.
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Affiliation(s)
- Juho Aaltio
- Research Programs Unit, Stem Cells and Metabolism Research, University of Helsinki, Helsinki, Finland.
| | - Liliya Euro
- Research Programs Unit, Stem Cells and Metabolism Research, University of Helsinki, Helsinki, Finland
| | - Olli Tynninen
- Department of Pathology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Hieu S Vu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Min Ni
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Anu Suomalainen
- Research Programs Unit, Stem Cells and Metabolism Research, University of Helsinki, Helsinki, Finland; HUS Diagnostic Centre, Helsinki University Hospital, Helsinki, Finland; HiLife, University of Helsinki, Helsinki, Finland
| | - Pirjo Isohanni
- Research Programs Unit, Stem Cells and Metabolism Research, University of Helsinki, Helsinki, Finland; Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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Nogueira C, Pereira C, Silva L, Laranjeira M, Lopes A, Neiva R, Rodrigues E, Campos T, Martins E, Bandeira A, Coelho M, Magalhães M, Damásio J, Gaspar A, Janeiro P, Gomes AL, Ferreira AC, Jacinto S, Vieira JP, Diogo L, Santos H, Mendonça C, Vilarinho L. The genetic landscape of mitochondrial diseases in the next-generation sequencing era: a Portuguese cohort study. Front Cell Dev Biol 2024; 12:1331351. [PMID: 38465286 PMCID: PMC10920333 DOI: 10.3389/fcell.2024.1331351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024] Open
Abstract
Introduction: Rare disorders that are genetically and clinically heterogeneous, such as mitochondrial diseases (MDs), have a challenging diagnosis. Nuclear genes codify most proteins involved in mitochondrial biogenesis, despite all mitochondria having their own DNA. The development of next-generation sequencing (NGS) technologies has revolutionized the understanding of many genes involved in the pathogenesis of MDs. In this new genetic era, using the NGS approach, we aimed to identify the genetic etiology for a suspected MD in a cohort of 450 Portuguese patients. Methods: We examined 450 patients using a combined NGS strategy, starting with the analysis of a targeted mitochondrial panel of 213 nuclear genes, and then proceeding to analyze the whole mitochondrial DNA. Results and Discussion: In this study, we identified disease-related variants in 134 (30%) analyzed patients, 88 with nuclear DNA (nDNA) and 46 with mitochondrial DNA (mtDNA) variants, most of them being pediatric patients (66%), of which 77% were identified in nDNA and 23% in mtDNA. The molecular analysis of this cohort revealed 72 already described pathogenic and 20 novel, probably pathogenic, variants, as well as 62 variants of unknown significance. For this cohort of patients with suspected MDs, the use of a customized gene panel provided a molecular diagnosis in a timely and cost-effective manner. Patients who cannot be diagnosed after this initial approach will be further selected for whole-exome sequencing. Conclusion: As a national laboratory for the study and research of MDs, we demonstrated the power of NGS to achieve a molecular etiology, expanding the mutational spectrum and proposing accurate genetic counseling in this group of heterogeneous diseases without therapeutic options.
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Affiliation(s)
- C. Nogueira
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - C. Pereira
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - L. Silva
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Mateus Laranjeira
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - A. Lopes
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - R. Neiva
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - E. Rodrigues
- Inherited Metabolic Diseases Reference Centre, São João Hospital University Centre, Porto, Portugal
| | - T. Campos
- Inherited Metabolic Diseases Reference Centre, São João Hospital University Centre, Porto, Portugal
| | - E. Martins
- Inherited Metabolic Diseases Reference Centre, Santo António Hospital University Centre, Porto, Portugal
| | - A. Bandeira
- Inherited Metabolic Diseases Reference Centre, Santo António Hospital University Centre, Porto, Portugal
| | - M. Coelho
- Inherited Metabolic Diseases Reference Centre, Santo António Hospital University Centre, Porto, Portugal
| | - M. Magalhães
- Neurology Department, Santo António Hospital University Centre, Porto, Portugal
| | - J. Damásio
- Neurology Department, Santo António Hospital University Centre, Porto, Portugal
| | - A. Gaspar
- Inherited Metabolic Diseases Reference Centre, Lisboa Norte Hospital University Centre, Lisboa, Portugal
| | - P Janeiro
- Inherited Metabolic Diseases Reference Centre, Lisboa Norte Hospital University Centre, Lisboa, Portugal
| | - A. Levy Gomes
- Neurology Department, Lisboa Norte Hospital University Centre, Lisboa, Portugal
| | - A. C. Ferreira
- Inherited Metabolic Diseases Reference Centre, Lisboa Central Hospital Centre, Lisboa, Portugal
| | - S. Jacinto
- Inherited Metabolic Diseases Reference Centre, Lisboa Central Hospital Centre, Lisboa, Portugal
| | - J. P. Vieira
- Inherited Metabolic Diseases Reference Centre, Lisboa Central Hospital Centre, Lisboa, Portugal
| | - L. Diogo
- Inherited Metabolic Diseases Reference Centre, Coimbra Hospital and University Centre, Coimbra, Portugal
| | - H. Santos
- Inherited Metabolic Diseases Reference Centre, Vila Nova de Gaia Hospital Centre, Vila Nova de Gaia, Portugal
| | - C. Mendonça
- Pediatric Department, Faro Hospital and University Centre, Faro, Portugal
| | - L. Vilarinho
- Research & Development Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
- Newborn Screening, Metabolism & Genetics Unit, Human Genetics Department, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
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Li L, Kolinjivadi AM, Ong KH, Young DM, Marini GPL, Chan SH, Chong ST, Chew EL, Lu H, Gole L, Yu W, Ngeow J. Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level. Bioinformatics 2022; 38:4395-4402. [PMID: 35881697 PMCID: PMC9477523 DOI: 10.1093/bioinformatics/btac533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/23/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION DNA fibre assay has a potential application in genomic medicine, cancer and stem cell research at the single-molecule level. A major challenge for the clinical and research implementation of DNA fibre assays is the slow speed in which manual analysis takes place as it limits the clinical actionability. While automatic detection of DNA fibres speeds up this process considerably, current publicly available software have limited features in terms of their user interface for manual correction of results, which in turn limit their accuracy and ability to account for atypical structures that may be important in diagnosis or investigative studies. We recognize that core improvements can be made to the GUI to allow for direct interaction with automatic results to preserve accuracy as well as enhance the versatility of automatic DNA fibre detection for use in variety of situations. RESULTS To address the unmet needs of diverse DNA fibre analysis investigations, we propose DNA Stranding, an open-source software that is able to perform accurate fibre length quantification (13.22% mean relative error) and fibre pattern recognition (R > 0.93) with up to six fibre patterns supported. With the graphical interface, we developed, user can conduct semi-automatic analyses which benefits from the advantages of both automatic and manual processes to improve workflow efficiency without compromising accuracy. AVAILABILITY AND IMPLEMENTATION The software package is available at https://github.com/lgole/DNAStranding. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Kok Haur Ong
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore,Bioinformatics Institute, A*STAR, Singapore 138671, Singapore
| | - David M Young
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore,Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA 94158, USA
| | | | - Sock Hoai Chan
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore 169610, Singapore,Oncology Academic Clinical Program, Duke-NUS Medical School Singapore, Singapore 169857, Singapore
| | - Siao Ting Chong
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Ee Ling Chew
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore 169610, Singapore
| | - Haoda Lu
- Bioinformatics Institute, A*STAR, Singapore 138671, Singapore
| | - Laurent Gole
- To whom correspondence should be addressed. or or
| | - Weimiao Yu
- To whom correspondence should be addressed. or or
| | - Joanne Ngeow
- To whom correspondence should be addressed. or or
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Mitochondrial Syndromes Revisited. J Clin Med 2021; 10:jcm10061249. [PMID: 33802970 PMCID: PMC8002645 DOI: 10.3390/jcm10061249] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/19/2022] Open
Abstract
In the last ten years, the knowledge of the genetic basis of mitochondrial diseases has significantly advanced. However, the vast phenotypic variability linked to mitochondrial disorders and the peculiar characteristics of their genetics make mitochondrial disorders a complex group of disorders. Although specific genetic alterations have been associated with some syndromic presentations, the genotype–phenotype relationship in mitochondrial disorders is complex (a single mutation can cause several clinical syndromes, while different genetic alterations can cause similar phenotypes). This review will revisit the most common syndromic pictures of mitochondrial disorders, from a clinical rather than a molecular perspective. We believe that the new phenotype definitions implemented by recent large multicenter studies, and revised here, may contribute to a more homogeneous patient categorization, which will be useful in future studies on natural history and clinical trials.
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