1
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Pickup E, Moore SA, Suwannarat P, Grant C, Ah Mew N, Gropman A, Sen K. Expedited Exome Reanalysis Following Deep Phenotyping and Muscle Biopsy in Suspected Mitochondrial Disorder. Pediatr Neurol 2024; 156:178-181. [PMID: 38788280 DOI: 10.1016/j.pediatrneurol.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 05/26/2024]
Abstract
BACKGROUND Exome sequencing (ES) is a useful tool in diagnosing suspected mitochondrial disease but can miss pathogenic variants for several reasons. Additional testing, such as muscle biopsy or biochemical testing, can be helpful in exome-negative cases. METHODS We report a patient who presented with repeated episodes of lactic acidosis and failure to thrive. RESULTS ES and mitochondrial sequencing were initially negative but clinical suspicion for mitochondrial disease remained high. After muscle biopsy showed evidence of mitochondrial dysfunction, the ES was reanalyzed and revealed novel variants in AARS2. CONCLUSION This case demonstrates the importance of muscle biopsy and biochemical testing in evaluating patients with a high suspicion of mitochondrial disease, even in the genomics era. Closed-loop communication between molecular genetics laboratories and clinical geneticists is an important step to help establish diagnosis in unsolved cases.
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Affiliation(s)
- Elizabeth Pickup
- Division of Child Neurology, Children's National Hospital, Washington, District of Columbia.
| | - Steven A Moore
- Senator Paul D. Wellstone Muscular Dystrophy Specialized Research Center, Department of Pathology, Roy J. And Lucille A. Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Pim Suwannarat
- Division of Genetics, Mid-Atlantic Permanente Medical Group, Suitland, Maryland
| | - Christina Grant
- Rare Disease Institute, Children's National Hospital, Washington, District of Columbia
| | - Nicholas Ah Mew
- Rare Disease Institute, Children's National Hospital, Washington, District of Columbia
| | - Andrea Gropman
- Division of Neurogenetics and Neurodevelopmental Pediatrics, Children's National Hospital, Washington, District of Columbia
| | - Kuntal Sen
- Division of Neurogenetics and Neurodevelopmental Pediatrics, Children's National Hospital, Washington, District of Columbia
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2
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Gokalp S, Inci A, Kilic A, Ozsaydi E, Altun AN, Demir F, Ergin FB, Ozbek MN, Okur I, Ezgu F, Tumer L. A very rare presentation of mitochondrial elongation factor Tu deficiency- TUFM mutation and literature review. J Pediatr Endocrinol Metab 2024; 37:571-574. [PMID: 38630895 DOI: 10.1515/jpem-2023-0569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024]
Abstract
OBJECTIVES The mitochondrial elongation factor Tu (EF-Tu), encoded by the TUFM gene, is a GTPase, which is part of the mitochondrial protein translation mechanism. If it is activated, it delivers the aminoacyl-tRNAs to the mitochondrial ribosome. Here, a patient was described with a homozygous missense variant in the TUFM [c.1016G>A (p.Arg339Gln)] gene. To date, only six patients have been reported with bi-allelic pathogenic variants in TUFM, leading to combined oxidative phosphorylation deficiency 4 (COXPD4) characterized by severe early-onset lactic acidosis, encephalopathy, and cardiomyopathy. CASE PRESENTATION The patient presented here had the phenotypic features of TUFM-related disease, lactic acidosis, hypotonia, liver dysfunction, optic atrophy, and mild encephalopathy. CONCLUSIONS We aimed to expand the clinical spectrum of pathogenic variants of TUFM.
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Affiliation(s)
- Sabire Gokalp
- Department of Pediatric Metabolic Disorders, Gazi University Faculty of Medicine, Ankara, Türkiye
| | - Asli Inci
- Department of Pediatric Metabolic Disorders, Gazi University Faculty of Medicine, Ankara, Türkiye
| | - Ayse Kilic
- Department of Pediatric Metabolic Disorders, Gazi University Faculty of Medicine, Ankara, Türkiye
| | - Ekin Ozsaydi
- Department of Pediatric Metabolic Disorders, Gazi University Faculty of Medicine, Ankara, Türkiye
| | - Ayse Nur Altun
- Department of Pediatric Metabolic Disorders, Gazi University Faculty of Medicine, Ankara, Türkiye
| | - Fevzi Demir
- Department of Pediatric Metabolic Disorders, Gazi University Faculty of Medicine, Ankara, Türkiye
| | - Filiz Basak Ergin
- Department of Pediatric Metabolic Disorders, Gazi University Faculty of Medicine, Ankara, Türkiye
| | - Mehmet Nuri Ozbek
- Department of Pediatrics, Dicle University Faculty of Medicine, Diyarbakır, Türkiye
| | - Ilyas Okur
- Department of Pediatric Metabolic Disorders, Gazi University Faculty of Medicine, Ankara, Türkiye
| | - Fatih Ezgu
- Department of Pediatric Metabolic Disorders, Gazi University Faculty of Medicine, Ankara, Türkiye
| | - Leyla Tumer
- Department of Pediatric Metabolic Disorders, Gazi University Faculty of Medicine, Ankara, Türkiye
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3
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Yuan T, Kumar S, Skinner ME, Victor-Joseph R, Abuaita M, Keijer J, Zhang J, Kunkel TJ, Liu Y, Petrunak EM, Saunders TL, Lieberman AP, Stuckey JA, Neamati N, Al-Murshedi F, Alfadhel M, Spelbrink JN, Rodenburg R, de Boer VC, Lombard DB. Human SIRT5 variants with reduced stability and activity do not cause neuropathology in mice. iScience 2024; 27:109991. [PMID: 38846003 PMCID: PMC11154205 DOI: 10.1016/j.isci.2024.109991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 03/06/2024] [Accepted: 05/13/2024] [Indexed: 06/09/2024] Open
Abstract
SIRT5 is a sirtuin deacylase that removes negatively charged lysine modifications, in the mitochondrial matrix and elsewhere in the cell. In benign cells and mouse models, under basal conditions, the phenotypes of SIRT5 deficiency are quite subtle. Here, we identify two homozygous SIRT5 variants in patients suspected to have mitochondrial disease. Both variants, P114T and L128V, are associated with reduced SIRT5 protein stability and impaired biochemical activity, with no evidence of neomorphic or dominant negative properties. The crystal structure of the P114T enzyme was solved and shows only subtle deviations from wild-type. Via CRISPR-Cas9, we generated a mouse model that recapitulates the human P114T mutation; homozygotes show reduced SIRT5 levels and activity, but no obvious metabolic abnormalities, neuropathology, or other gross phenotypes. We conclude that these human SIRT5 variants most likely represent severe hypomorphs, but are likely not by themselves the primary pathogenic cause of the neuropathology observed in the patients.
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Affiliation(s)
- Taolin Yuan
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen, the Netherlands
| | - Surinder Kumar
- Department of Pathology & Laboratory Medicine, Miller School of Medicine, and Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mary E. Skinner
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan Victor-Joseph
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Majd Abuaita
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen, the Netherlands
| | - Jessica Zhang
- Department of Pathology & Laboratory Medicine, Miller School of Medicine, and Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | - Thaddeus J. Kunkel
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yanghan Liu
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elyse M. Petrunak
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas L. Saunders
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jeanne A. Stuckey
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fathiya Al-Murshedi
- Genetic and Developmental Medicine Clinic, Department of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Majid Alfadhel
- Medical Genomic Research Department, King Abdullah International Medical Research Center(KAIMRC), King Saud Bin Abdulaziz University for Health Sciences(KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- Genetics and Precision Medicine Department (GPM), King Abdullah Specialized Children’s Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Johannes N. Spelbrink
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Richard Rodenburg
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vincent C.J. de Boer
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen, the Netherlands
| | - David B. Lombard
- Department of Pathology & Laboratory Medicine, Miller School of Medicine, and Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
- Miami VA Healthcare System, Miami, FL 33125, USA
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4
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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 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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5
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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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6
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Heath O, Hammerl E, Spitzinger A, Wortmann SB. Ending an Odyssey? The Psychosocial Experiences of Parents after the Genetic Diagnosis of a Mitochondrial Disease in Children. J Pers Med 2024; 14:523. [PMID: 38793105 PMCID: PMC11122152 DOI: 10.3390/jpm14050523] [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: 04/10/2024] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Obtaining a genetic diagnosis of a primary mitochondrial disease (PMD) is often framed as a diagnostic odyssey. Yet, even after receiving a diagnosis, parents of affected children experience ongoing therapeutic and prognostic uncertainty and considerable psychosocial challenges. Semi-structured interviews (N = 24) were conducted with parents of 13 children (aged 2-19 years) with a genetically confirmed PMD. Paternal (N = 11) and maternal (N = 13) perspectives were obtained, and thematic analysis was performed on all interviews. A genetic diagnosis was valuable and empowering for parents, despite eliciting varied emotional responses. While the diagnosis helped focus management decisions, families often felt overwhelmed and unsupported in navigating the healthcare system. Most parents reported a serious impact on their romantic relationship. The sources of social support varied, with a preference for established friendship and family support networks over disease-specific community support groups. Most parents favored prenatal genetic testing in the event of a future pregnancy. This study provides insight into the lived experiences of parents after a genetic diagnosis of PMD in their children. The findings draw awareness to supportive care needs and highlight important gaps that should be addressed to ensure that parents feel supported within a holistic framework of management for PMDs.
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Affiliation(s)
- Oliver Heath
- University Children’s Hospital, Salzburger Landeskliniken (SALK), Paracelsus Medical University (PMU), Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (O.H.); (E.H.); (A.S.)
| | - Emma Hammerl
- University Children’s Hospital, Salzburger Landeskliniken (SALK), Paracelsus Medical University (PMU), Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (O.H.); (E.H.); (A.S.)
| | - Anna Spitzinger
- University Children’s Hospital, Salzburger Landeskliniken (SALK), Paracelsus Medical University (PMU), Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (O.H.); (E.H.); (A.S.)
- Institut für Klinische Psychologie der UK für Psychiatrie, Psychotherapie und Psychosomatik der PMU, 5020 Salzburg, Austria
| | - Saskia B. Wortmann
- University Children’s Hospital, Salzburger Landeskliniken (SALK), Paracelsus Medical University (PMU), Müllner Hauptstrasse 48, 5020 Salzburg, Austria; (O.H.); (E.H.); (A.S.)
- Nijmegen Centre for Mitochondrial Disorders (NCMD), Amalia Children’s Hospital, Radboudumc, 6525 Nijmegen, The Netherlands
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7
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Fadra N, Schultz-Rogers LE, Chanana P, Cousin MA, Macke EL, Ferrer A, Pinto E Vairo F, Olson RJ, Oliver GR, Mulvihill LA, Jenkinson G, Klee EW. Identification of skewed X chromosome inactivation using exome and transcriptome sequencing in patients with suspected rare genetic disease. BMC Genomics 2024; 25:371. [PMID: 38627676 PMCID: PMC11020449 DOI: 10.1186/s12864-024-10240-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND X-chromosome inactivation (XCI) is an epigenetic process that occurs during early development in mammalian females by randomly silencing one of two copies of the X chromosome in each cell. The preferential inactivation of either the maternal or paternal copy of the X chromosome in a majority of cells results in a skewed or non-random pattern of X inactivation and is observed in over 25% of adult females. Identifying skewed X inactivation is of clinical significance in patients with suspected rare genetic diseases due to the possibility of biased expression of disease-causing genes present on the active X chromosome. The current clinical test for the detection of skewed XCI relies on the methylation status of the methylation-sensitive restriction enzyme (Hpall) binding site present in proximity of short tandem polymorphic repeats on the androgen receptor (AR) gene. This approach using one locus results in uninformative or inconclusive data for 10-20% of tests. Further, recent studies have shown inconsistency between methylation of the AR locus and the state of inactivation of the X chromosome. Herein, we develop a method for estimating X inactivation status, using exome and transcriptome sequencing data derived from blood in 227 female samples. We built a reference model for evaluation of XCI in 135 females from the GTEx consortium. We tested and validated the model on 11 female individuals with different types of undiagnosed rare genetic disorders who were clinically tested for X-skew using the AR gene assay and compared results to our outlier-based analysis technique. RESULTS In comparison to the AR clinical test for identification of X inactivation, our method was concordant with the AR method in 9 samples, discordant in 1, and provided a measure of X inactivation in 1 sample with uninformative clinical results. We applied this method on an additional 81 females presenting to the clinic with phenotypes consistent with different hereditary disorders without a known genetic diagnosis. CONCLUSIONS This study presents the use of transcriptome and exome sequencing data to provide an accurate and complete estimation of X-inactivation and skew status in a cohort of female patients with different types of suspected rare genetic disease.
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Affiliation(s)
- Numrah Fadra
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Laura E Schultz-Rogers
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Pritha Chanana
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Margot A Cousin
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Erica L Macke
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Alejandro Ferrer
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Division of Hematology, Mayo Clinic, Rochester, MN, USA
| | - Filippo Pinto E Vairo
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Rory J Olson
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Gavin R Oliver
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Lindsay A Mulvihill
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Garrett Jenkinson
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Eric W Klee
- Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA.
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA.
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, USA.
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8
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Missen S, Wilson C, Potter H, Vincent AL, Murphy R, Roxburgh R, Rodrigues M, Poke G, Robertson SP, Thorburn DR, Glamuzina E. Mitochondrial disease in New Zealand: a nationwide prevalence study. Intern Med J 2024; 54:388-397. [PMID: 37732891 DOI: 10.1111/imj.16211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/01/2023] [Indexed: 09/22/2023]
Abstract
BACKGROUND The complexities of mitochondrial disease make epidemiological studies challenging, yet this information is important in understanding the healthcare burden and addressing service and educational needs. Existing studies are limited to quaternary centres or focus on a single genotype or phenotype and estimate disease prevalence at 12.5 per 100 000. New Zealand's (NZ) size and partially integrated national healthcare system make it amenable to a nationwide prevalence study. AIM To estimate the prevalence of molecularly confirmed and suspected mitochondrial disease on 31 December 2015 in NZ. METHODS Cases were identified from subspecialists and laboratory databases and through interrogation of the Ministry of Health National Minimum Dataset with a focus on presentations between 2000 and 2015. Patient records were reviewed, and those with a diagnosis of 'mitochondrial disease' who were alive and residing in NZ on the prevalence date were included. These were divided into molecularly confirmed and clinically suspected cases. Official NZ estimated resident population data were used to calculate prevalence. RESULTS Seven hundred twenty-three unique national health index numbers were identified. Five hundred five were excluded. The minimum combined prevalence for mitochondrial disease was 4.7 per 100 000 (95% confidence interval (CI): 4.1-5.4). The minimum prevalence for molecularly confirmed and suspected disease was 2.9 (95% CI 2.4-3.4) and 1.8 (95% CI 1.4-2.2) cases per 100 000 respectively. CONCLUSIONS Within the limitations of this study, comparison to similar prevalence studies performed by specialist referral centres suggests mitochondrial disease is underdiagnosed in NZ. This highlights a need for improved education and referral pathways for mitochondrial disease in NZ.
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Affiliation(s)
- Sarah Missen
- Child Health Service, Whangarei Hospital, Te Whatu Ora - Health New Zealand, Te Tai Tokerau, Whangarei, New Zealand
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Callum Wilson
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Adult and Paediatric National Metabolic Service, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
| | - Howard Potter
- Canterbury Health Labs, Te Whatu Ora - Health New Zealand, Waitaha Canterbury, Christchurch, New Zealand
| | - Andrea L Vincent
- Greenlane Eye Clinic, Greenlane Clinical Centre, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Rinki Murphy
- Auckland Diabetes Centre, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Te Mana Ki Tua, Specialist Weight Management Service, Middlemore Hospital, Te Whatu Ora - Health New Zealand, Counties Manukau, Auckland, New Zealand
| | - Richard Roxburgh
- Department of Neurology, Auckland City Hospital, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
- Centre for Brain Research, Neurogenetics Clinics, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Miriam Rodrigues
- Department of Neurology, Auckland City Hospital, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
- Centre for Brain Research, Neurogenetics Clinics, Faculty of Medicine and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Gemma Poke
- Central Hub, Genetic Health Service New Zealand, Te Whatu Ora - Health New Zealand, Wellington, New Zealand
| | | | - David R Thorburn
- Genomic Medicine Theme, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Emma Glamuzina
- Department of Paediatrics: Child and Youth Health, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
- Adult and Paediatric National Metabolic Service, Te Whatu Ora - Health New Zealand, Te Toka Tumai, Auckland, New Zealand
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9
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Baker ZN, Forny P, Pagliarini DJ. Mitochondrial proteome research: the road ahead. Nat Rev Mol Cell Biol 2024; 25:65-82. [PMID: 37773518 DOI: 10.1038/s41580-023-00650-7] [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] [Accepted: 08/08/2023] [Indexed: 10/01/2023]
Abstract
Mitochondria are multifaceted organelles with key roles in anabolic and catabolic metabolism, bioenergetics, cellular signalling and nutrient sensing, and programmed cell death processes. Their diverse functions are enabled by a sophisticated set of protein components encoded by the nuclear and mitochondrial genomes. The extent and complexity of the mitochondrial proteome remained unclear for decades. This began to change 20 years ago when, driven by the emergence of mass spectrometry-based proteomics, the first draft mitochondrial proteomes were established. In the ensuing decades, further technological and computational advances helped to refine these 'maps', with current estimates of the core mammalian mitochondrial proteome ranging from 1,000 to 1,500 proteins. The creation of these compendia provided a systemic view of an organelle previously studied primarily in a reductionist fashion and has accelerated both basic scientific discovery and the diagnosis and treatment of human disease. Yet numerous challenges remain in understanding mitochondrial biology and translating this knowledge into the medical context. In this Roadmap, we propose a path forward for refining the mitochondrial protein map to enhance its discovery and therapeutic potential. We discuss how emerging technologies can assist the detection of new mitochondrial proteins, reveal their patterns of expression across diverse tissues and cell types, and provide key information on proteoforms. We highlight the power of an enhanced map for systematically defining the functions of its members. Finally, we examine the utility of an expanded, functionally annotated mitochondrial proteome in a translational setting for aiding both diagnosis of mitochondrial disease and targeting of mitochondria for treatment.
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Affiliation(s)
- Zakery N Baker
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick Forny
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - David J Pagliarini
- Department of Cell Biology and Physiology, Washington University School of Medicine, 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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10
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Yuan T, Kumar S, Skinner M, Victor-Joseph R, Abuaita M, Keijer J, Zhang J, Kunkel TJ, Liu Y, Petrunak EM, Saunders TL, Lieberman AP, Stuckey JA, Neamati N, Al-Murshedi F, Alfadhel M, Spelbrink JN, Rodenburg R, de Boer VCJ, Lombard DB. SIRT5 variants from patients with mitochondrial disease are associated with reduced SIRT5 stability and activity, but not with neuropathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570371. [PMID: 38105987 PMCID: PMC10723467 DOI: 10.1101/2023.12.06.570371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
SIRT5 is a sirtuin deacylase that represents the major activity responsible for removal of negatively-charged lysine modifications, in the mitochondrial matrix and elsewhere in the cell. In benign cells and mouse models, under basal non-stressed conditions, the phenotypes of SIRT5 deficiency are generally quite subtle. Here, we identify two homozygous SIRT5 variants in human patients suffering from severe mitochondrial disease. Both variants, P114T and L128V, are associated with reduced SIRT5 protein stability and impaired biochemical activity, with no evidence of neomorphic or dominant negative properties. The crystal structure of the P114T enzyme was solved and shows only subtle deviations from wild-type. Via CRISPR-Cas9, we generate a mouse model that recapitulates the human P114T mutation; homozygotes show reduced SIRT5 levels and activity, but no obvious metabolic abnormalities, neuropathology or other gross evidence of severe disease. We conclude that these human SIRT5 variants most likely represent severe hypomorphs, and are likely not the primary pathogenic cause of the neuropathology observed in the patients.
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Affiliation(s)
- Taolin Yuan
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen, The Netherlands
| | - Surinder Kumar
- Department of Pathology & Laboratory Medicine, Miller School of Medicine, and Sylvester Comprehensive Cancer Center, University of Miami, Miami FL 33136
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Mary Skinner
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | | | - Majd Abuaita
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen, The Netherlands
| | - Jessica Zhang
- Department of Pathology & Laboratory Medicine, Miller School of Medicine, and Sylvester Comprehensive Cancer Center, University of Miami, Miami FL 33136
| | | | - Yanghan Liu
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109
| | - Elyse M. Petrunak
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Thomas L. Saunders
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | | | - Jeanne A. Stuckey
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy and Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan 48109
| | - Fathiya Al-Murshedi
- Genetic and Developmental Medicine Clinic, Department of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Oman
| | - Majid Alfadhel
- Medical Genomic Research Department, King Abdullah International Medical Research Center(KAIMRC), King Saud Bin Abdulaziz University for Health Sciences(KSAU-HS), Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
- Genetics and Precision Medicine department (GPM), King Abdullah Specialized Children’s Hospital (KASCH), King Abdulaziz Medical City, Ministry of National Guard Health Affairs (MNG-HA), Riyadh, Saudi Arabia
| | - Johannes N. Spelbrink
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richard Rodenburg
- Radboud Center for Mitochondrial Medicine, Department of Pediatrics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vincent C. J. de Boer
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen, The Netherlands
| | - David B. Lombard
- Department of Pathology & Laboratory Medicine, Miller School of Medicine, and Sylvester Comprehensive Cancer Center, University of Miami, Miami FL 33136
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109
- Miami VA Healthcare System, Miami FL 33125
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11
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Serag M, Plutino M, Charles P, Azulay JP, Chaussenot A, Paquis-Flucklinger V, Ait-El-Mkadem Saadi S, Rouzier C. A Case Report of SYNE1 Deficiency-Mimicking Mitochondrial Disease and the Value of Pangenomic Investigations. Genes (Basel) 2023; 14:2154. [PMID: 38136976 PMCID: PMC10743207 DOI: 10.3390/genes14122154] [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: 11/08/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Mitochondrial disorders are characterized by a huge clinical, biochemical, and genetic heterogeneity, which poses significant diagnostic challenges. Several studies report that more than 50% of patients with suspected mitochondrial disease could have a non-mitochondrial disorder. Thus, only the identification of the causative pathogenic variant can confirm the diagnosis. Herein, we describe the diagnostic journey of a family suspected of having a mitochondrial disorder who were referred to our Genetics Department. The proband presented with the association of cerebellar ataxia, COX-negative fibers on muscle histology, and mtDNA deletions. Whole exome sequencing (WES), supplemented by a high-resolution array, comparative genomic hybridization (array-CGH), allowed us to identify two pathogenic variants in the non-mitochondrial SYNE1 gene. The proband and her affected sister were found to be compound heterozygous for a known nonsense variant (c.13258C>T, p.(Arg4420Ter)), and a large intragenic deletion that was predicted to result in a loss of function. To our knowledge, this is the first report of a large intragenic deletion of SYNE1 in patients with cerebellar ataxia (ARCA1). This report highlights the interest in a pangenomic approach to identify the genetic basis in heterogeneous neuromuscular patients with the possible cause of mitochondrial disease. Moreover, even rare copy number variations should be considered in patients with a phenotype suggestive of SYNE1 deficiency.
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Affiliation(s)
- Mounir Serag
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| | - Morgane Plutino
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| | - Perrine Charles
- Service de Génétique, La Pitié-Salpêtrière, AP-HP, 75610 Paris, France;
| | | | - Annabelle Chaussenot
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| | - Véronique Paquis-Flucklinger
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| | - Samira Ait-El-Mkadem Saadi
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
| | - Cécile Rouzier
- Service de Génétique Médicale, Hôpital l’Archet 2, CHU de Nice, 151 Route Saint-Antoine de Ginestière, 06202 Nice, France; (M.S.); (M.P.); (A.C.); (V.P.-F.); (S.A.-E.-M.S.)
- CNRS UMR7284/ INSERM U1081, Faculté de Médecine, Université Côte d’Azur, 06107 Nice, France
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12
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Werren EA, Srinivasan VM, Gowda VK, Pandey A, Vaish S, Kabbur AR, Nandeesh BN, Srivastava A. A novel biallelic frameshift variant in C2orf69 causing developmental regression, seizures, microcephaly, autistic features, and hypertonia. Am J Med Genet A 2023; 191:2446-2450. [PMID: 37337918 DOI: 10.1002/ajmg.a.63310] [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: 01/11/2023] [Revised: 04/07/2023] [Accepted: 05/12/2023] [Indexed: 06/21/2023]
Abstract
Combined oxidative phosphorylation deficiency type 53 (COXPD53) is an autosomal recessive neurodevelopmental disorder (NDD) caused by homozygous variants in the gene C2orf69. Here, we report a novel frameshift variant c.187_191dupGCCGA, p.D64Efs*56 identified in an individual with clinical presentation of COXPD53 with developmental regression and autistic features. The variant c.187_191dupGCCGA, p.D64Efs*56 represents the most N-terminal part of C2orf69. Notable clinical features of COXPD53of the proband include developmental delay, developmental regression, seizures, microcephaly, and hypertonia. Structural brain defects of cerebral atrophy, cerebellar atrophy, hypomyelination, and thin corpus callosum were also observed. While we observe strong phenotypic overlap among affected individuals with C2orf69 variants, developmental regression and autistic features have not been previously described in individuals with COXPD53. Together, this case expands the genetic and clinical phenotypic spectrum of C2orf69-associated COXPD53.
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Affiliation(s)
- Elizabeth A Werren
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Varunvenkat M Srinivasan
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Vykuntaraju K Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Akanksha Pandey
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Saurabh Vaish
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Anusha Raj Kabbur
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Bevinahalli N Nandeesh
- Department of Neuropathology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Anshika Srivastava
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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13
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Macken WL, Falabella M, Pizzamiglio C, Woodward CE, Scotchman E, Chitty LS, Polke JM, Bugiardini E, Hanna MG, Vandrovcova J, Chandler N, Labrum R, Pitceathly RDS. Enhanced mitochondrial genome analysis: bioinformatic and long-read sequencing advances and their diagnostic implications. Expert Rev Mol Diagn 2023; 23:797-814. [PMID: 37642407 DOI: 10.1080/14737159.2023.2241365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
INTRODUCTION Primary mitochondrial diseases (PMDs) comprise a large and heterogeneous group of genetic diseases that result from pathogenic variants in either nuclear DNA (nDNA) or mitochondrial DNA (mtDNA). Widespread adoption of next-generation sequencing (NGS) has improved the efficiency and accuracy of mtDNA diagnoses; however, several challenges remain. AREAS COVERED In this review, we briefly summarize the current state of the art in molecular diagnostics for mtDNA and consider the implications of improved whole genome sequencing (WGS), bioinformatic techniques, and the adoption of long-read sequencing, for PMD diagnostics. EXPERT OPINION We anticipate that the application of PCR-free WGS from blood DNA will increase in diagnostic laboratories, while for adults with myopathic presentations, WGS from muscle DNA may become more widespread. Improved bioinformatic strategies will enhance WGS data interrogation, with more accurate delineation of mtDNA and NUMTs (nuclear mitochondrial DNA segments) in WGS data, superior coverage uniformity, indirect measurement of mtDNA copy number, and more accurate interpretation of heteroplasmic large-scale rearrangements (LSRs). Separately, the adoption of diagnostic long-read sequencing could offer greater resolution of complex LSRs and the opportunity to phase heteroplasmic variants.
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Affiliation(s)
- William L Macken
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Micol Falabella
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Chiara Pizzamiglio
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Cathy E Woodward
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Elizabeth Scotchman
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lyn S Chitty
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - James M Polke
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Natalie Chandler
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Robyn Labrum
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
- Rare and Inherited Disease Laboratory, North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
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14
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Eliyan Y, Rezania K, Gomez CM, Seibert K. Pontine stroke in a patient with Chronic Progressive External Ophthalmoplegia (CPEO): a case report. BMC Neurol 2023; 23:231. [PMID: 37316776 DOI: 10.1186/s12883-023-03249-9] [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: 08/22/2022] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND Chronic progressive external ophthalmoplegia (CPEO) is a mitochondrial disease with slowly progressive bilateral ptosis and symmetric ophthalmoplegia due to a genetic mutation that results in defective oxidative phosphorylation. Common genes that are implicated in CPEO include POLG, RRM2B, ANT1 and PEO1/TWNK. Here, we report a case of a patient diagnosed with CPEO caused by a novel mutation in PEO/TWNK after suffering a right pontine stroke. CASE PRESENTATION A 70-year-old man with history of chronic progressive bilateral ptosis and ophthalmoplegia, as well as similar ocular symptoms in his father and grandfather, presented with acute onset of right hemifacial weakness and dysarthria. Brain MRI revealed an acute ischemic stroke in the right dorsal pons. The patient did not experience diplopia due to severe baseline ophthalmoplegia. Creatine kinase was elevated to 6,080 U/L upon admission and normalized over the course of one week; electromyography revealed a myopathic process. Genetic testing revealed a novel mutation c.1510G > A (p. Ala504Thr) in a pathogenic "hot spot" of the C10ORF2 gene (TWNK/PEO1), which is associated with CPEO. The mutation appears to be deleterious using several pathogenicity prediction tools. CONCLUSIONS This case report describes a patient with late-onset CPEO caused by a novel, likely pathogenic, mutation in the TWNK gene. Although the patient presented with a pontine stroke, it manifested with solely new onset facial palsy, as he had a severe underlying ophthalmoplegia secondary to his CPEO.
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Affiliation(s)
- Yazan Eliyan
- Pritzker School of Medicine, University of Chicago, Chicago, IL, USA
| | - Kourosh Rezania
- Department of Neurology, University of Chicago Medical Center, Chicago, IL, USA
| | - Christopher M Gomez
- Department of Neurology, University of Chicago Medical Center, Chicago, IL, USA
| | - Kaitlin Seibert
- Department of Neurology, University of Chicago Medical Center, Chicago, IL, USA.
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15
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Gedikbasi A, Toksoy G, Karaca M, Gulec C, Balci MC, Gunes D, Gunes S, Aslanger AD, Unverengil G, Karaman B, Basaran S, Demirkol M, Gokcay GF, Uyguner ZO. Clinical and bi-genomic DNA findings of patients suspected to have mitochondrial diseases. Front Genet 2023; 14:1191159. [PMID: 37377599 PMCID: PMC10292751 DOI: 10.3389/fgene.2023.1191159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/02/2023] [Indexed: 06/29/2023] Open
Abstract
Background: Mitochondrial diseases are the most common group of inherited metabolic disorders, causing difficulties in definite diagnosis due to clinical and genetic heterogeneity. Clinical components are predominantly associated with pathogenic variants shown in nuclear or mitochondrial genomes that affect vital respiratory chain function. The development of high-throughput sequencing technologies has accelerated the elucidation of the genetic etiology of many genetic diseases that previously remained undiagnosed. Methods: Thirty affected patients from 24 unrelated families with clinical, radiological, biochemical, and histopathological evaluations considered for mitochondrial diseases were investigated. DNA isolated from the peripheral blood samples of probands was sequenced for nuclear exome and mitochondrial DNA (mtDNA) analyses. MtDNA sequencing was also performed from the muscle biopsy material in one patient. For segregation, Sanger sequencing is performed for pathogenic alterations in five other affected family members and healthy parents. Results: Exome sequencing revealed 14 different pathogenic variants in nine genes encoding mitochondrial function peptides (AARS2, EARS2, ECHS1, FBXL4, MICOS13, NDUFAF6, OXCT1, POLG, and TK2) in 12 patients from nine families and four variants in genes encoding important for muscle structure (CAPN3, DYSF, and TCAP) in six patients from four families. Three probands carried pathogenic mtDNA variations in two genes (MT-ATP6 and MT-TL1). Nine variants in five genes are reported for the first time with disease association: (AARS2: c.277C>T/p.(R93*), c.845C>G/p.(S282C); EARS2: c.319C>T/p.(R107C), c.1283delC/p.(P428Lfs*); ECHS1: c.161G>A/p.(R54His); c.202G>A/p.(E68Lys); NDUFAF6: c.479delA/p.(N162Ifs*27); and OXCT1: c.1370C>T/p.(T457I), c.1173-139G>T/p.(?). Conclusion: Bi-genomic DNA sequencing clarified genetic etiology in 67% (16/24) of the families. Diagnostic utility by mtDNA sequencing in 13% (3/24) and exome sequencing in 54% (13/24) of the families prioritized searching for nuclear genome pathologies for the first-tier test. Weakness and muscle wasting observed in 17% (4/24) of the families underlined that limb-girdle muscular dystrophy, similar to mitochondrial myopathy, is an essential point for differential diagnosis. The correct diagnosis is crucial for comprehensive genetic counseling of families. Also, it contributes to making treatment-helpful referrals, such as ensuring early access to medication for patients with mutations in the TK2 gene.
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Affiliation(s)
- Asuman Gedikbasi
- Department of Pediatric Basic Sciences, Institute of Child Health Istanbul University, Istanbul, Türkiye
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Guven Toksoy
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Meryem Karaca
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Cagri Gulec
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Mehmet Cihan Balci
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Dilek Gunes
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Seda Gunes
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Ayca Dilruba Aslanger
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Gokcen Unverengil
- Department of Pathology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Birsen Karaman
- Department of Pediatric Basic Sciences, Institute of Child Health Istanbul University, Istanbul, Türkiye
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Seher Basaran
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Mubeccel Demirkol
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Gulden Fatma Gokcay
- Division of Pediatric Nutrition and Metabolism, Department of Pediatrics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
| | - Zehra Oya Uyguner
- Department of Medical Genetics, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Türkiye
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16
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Shabannejadian F, Masoomizadeh SZ, Andashti B. Molecular analysis of gene variants in an Iranian family with psychomotor retardation mitochondrial disorder patient. Clin Case Rep 2023; 11:e7308. [PMID: 37180333 PMCID: PMC10172453 DOI: 10.1002/ccr3.7308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/04/2023] [Accepted: 04/17/2023] [Indexed: 05/16/2023] Open
Abstract
In 1-year-old girl presenting with neurodegenerative mitochondrial disease (Leigh syndrome), mutation analysis was performed by whole exome sequencing. Pathogenic variants were then analyzed in parents and relatives by Sanger sequencing. We identified a point mutation c.G484A in NDUFS8 gene which was homozygous in patient and heterozygous in parents.
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Affiliation(s)
- Forough Shabannejadian
- Department of Biotechnology, Faculty of Basic ScienceAhvaz Branch, Islamic Azad UniversityAhvazIran
| | | | - Behnaz Andashti
- Department of Biology, Faculty of ScienceShahid Chamran UniversityAhvazIran
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17
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Wu TH, Peng J, Yang L, Chen YH, Lu XL, Huang JT, You JY, Ou-Yang WX, Sun YY, Xue YN, Mao X, Yan HM, Ren RN, Xie J, Chen ZH, Zhang VW, Lyu GZ, He F. Use of dual genomic sequencing to screen mitochondrial diseases in pediatrics: a retrospective analysis. Sci Rep 2023; 13:4193. [PMID: 36918699 PMCID: PMC10015028 DOI: 10.1038/s41598-023-31134-5] [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: 11/15/2022] [Accepted: 03/07/2023] [Indexed: 03/16/2023] Open
Abstract
Mitochondrial diseases (MDs) were a large group multisystem disorders, attributable in part to the dual genomic control. The advent of massively sequencing has improved diagnostic rates and speed, and was increasingly being used as a first-line diagnostic test. Paediatric patients (aged < 18 years) who underwent dual genomic sequencing were enrolled in this retrospective multicentre study. We evaluated the mitochondrial disease criteria (MDC) and molecular diagnostic yield of dual genomic sequencing. Causative variants were identified in 177 out of 503 (35.2%) patients using dual genomic sequencing. Forty-six patients (9.1%) had mitochondria-related variants, including 25 patients with nuclear DNA (nDNA) variants, 15 with mitochondrial DNA (mtDNA) variants, and six with dual genomic variants (MT-ND6 and POLG; MT-ND5 and RARS2; MT-TL1 and NARS2; MT-CO2 and NDUFS1; MT-CYB and SMARCA2; and CHRNA4 and MT-CO3). Based on the MDC, 15.2% of the patients with mitochondria-related variants were classified as "unlikely to have mitochondrial disorder". Moreover, 4.5% of the patients with non-mitochondria-related variants and 1.43% with negative genetic tests, were classified as "probably having mitochondrial disorder". Dual genomic sequencing in suspected MDs provided a more comprehensive and accurate diagnosis for pediatric patients, especially for patients with dual genomic variants.
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Affiliation(s)
- Teng-Hui Wu
- Department of Pediatrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Li Yang
- Department of Pediatrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Yan-Hui Chen
- Department of Pediatrics, Fujian Medical University Union Hospital, 29 Xinquan Road, Fuzhou, Fujian, China
| | - Xiu-Lan Lu
- Department of Pediatric Intensive Care Unit, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan, China
| | - Jiao-Tian Huang
- Department of Pediatric Intensive Care Unit, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan, China
| | - Jie-Yu You
- Department of Gastroenterology and Nutrition, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan, China
| | - Wen-Xian Ou-Yang
- Department of Hepatopathy, Hunan Children's Hospital, 86 Ziyuan Road, Changsha, Hunan, China
| | - Yue-Yu Sun
- Department of Pediatric Intensive Care Unit, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences (GAMS), 106 Zhongshan 2nd Road, Guangzhou, Guangdong, China
| | - Yi-Nan Xue
- Department of Pediatrics, Brain Hospital of Hunan Province, 427 Furong Road, Changsha, Hunan, China
| | - Xiao Mao
- Department of Medical Genetics, Maternal,, Child Health Hospital of Hunan Province, 53 Xiangchun Road, Changsha, Hunan, China
| | - Hui-Ming Yan
- Department of Medical Genetics, Maternal,, Child Health Hospital of Hunan Province, 53 Xiangchun Road, Changsha, Hunan, China
| | - Rong-Na Ren
- Department of Pediatrics, The 900Th Hospital of Joint Logistic Support Force, PLA, Fuzhou, Fujian, China
| | - Jing Xie
- Department of Pediatrics, The First Hospital of Hunan University of Chinese Medicine, 95 Shaoshan Road, Changsha, Hunan, China
| | - Zhi-Heng Chen
- Department of Pediatrics, The Third Xiangya Hospital, Central South University, 138 Tongzipo Road, Changsha, Hunan, China
| | - Victor-Wei Zhang
- Amcare Genomics Laboratory, Guangzhou, Guangdong, China.,Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Gui-Zhen Lyu
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Fang He
- Department of Pediatrics, Xiangya Hospital Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China.
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18
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Thompson K, Stroud DA, Thorburn DR, Taylor RW. Investigation of oxidative phosphorylation activity and complex composition in mitochondrial disease. HANDBOOK OF CLINICAL NEUROLOGY 2023; 194:127-139. [PMID: 36813309 DOI: 10.1016/b978-0-12-821751-1.00008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
A multidisciplinary approach to the laboratory diagnosis of mitochondrial disease has long been applied, with crucial information provided by deep clinical phenotyping, blood investigations, and biomarker screening as well as histopathological and biochemical testing of biopsy material to support molecular genetic screening. In an era of second and third generation sequencing technologies, traditional diagnostic algorithms for mitochondrial disease have been replaced by gene agnostic, genomic strategies including whole-exome sequencing (WES) and whole-genome sequencing (WGS), increasingly supported by other 'omics technologies (Alston et al., 2021). Whether a primary testing strategy, or one used to validate and interpret candidate genetic variants, the availability of a range of tests aimed at determining mitochondrial function (i.e., the assessment of individual respiratory chain enzyme activities in a tissue biopsy or cellular respiration in a patient cell line) remains an important part of the diagnostic armory. In this chapter, we summarize several disciplines used in the laboratory investigation of suspected mitochondrial disease, including the histopathological and biochemical assessment of mitochondrial function, as well as protein-based techniques to assess the steady-state levels of oxidative phosphorylation (OXPHOS) subunits and assembly of OXPHOS complexes via traditional (immunoblotting) and cutting-edge (quantitative proteomic) approaches.
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Affiliation(s)
- Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - David A Stroud
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, VIC, Australia; Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - David R Thorburn
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Melbourne, VIC, Australia; Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia; Mitochondrial Laboratory, Victorian Clinical Genetic Services, Melbourne, VIC, Australia
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialised Services for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
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19
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Genetic testing for mitochondrial disease: the United Kingdom best practice guidelines. Eur J Hum Genet 2023; 31:148-163. [PMID: 36513735 PMCID: PMC9905091 DOI: 10.1038/s41431-022-01249-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 12/15/2022] Open
Abstract
Primary mitochondrial disease describes a diverse group of neuro-metabolic disorders characterised by impaired oxidative phosphorylation. Diagnosis is challenging; >350 genes, both nuclear and mitochondrial DNA (mtDNA) encoded, are known to cause mitochondrial disease, leading to all possible inheritance patterns and further complicated by heteroplasmy of the multicopy mitochondrial genome. Technological advances, particularly next-generation sequencing, have driven a shift in diagnostic practice from 'biopsy first' to genome-wide analyses of blood and/or urine DNA. This has led to the need for a reference framework for laboratories involved in mitochondrial genetic testing to facilitate a consistent high-quality service. In the United Kingdom, consensus guidelines have been prepared by a working group of Clinical Scientists from the NHS Highly Specialised Service followed by national laboratory consultation. These guidelines summarise current recommended technologies and methodologies for the analysis of mtDNA and nuclear-encoded genes in patients with suspected mitochondrial disease. Genetic testing strategies for diagnosis, family testing and reproductive options including prenatal diagnosis are outlined. Importantly, recommendations for the minimum levels of mtDNA testing for the most common referral reasons are included, as well as guidance on appropriate referrals and information on the minimal appropriate gene content of panels when analysing nuclear mitochondrial genes. Finally, variant interpretation and recommendations for reporting of results are discussed, focussing particularly on the challenges of interpreting and reporting mtDNA variants.
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20
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Schon KR, Chinnery PF. Whole-genome sequencing for mitochondrial disorders identifies unexpected mimics. Pract Neurol 2023; 23:2-3. [PMID: 36253087 DOI: 10.1136/pn-2022-003570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/18/2022] [Indexed: 02/02/2023]
Affiliation(s)
- Katherine R Schon
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, Cambridge, UK
- Academic Department of Medical Genetics, Cambridge Biomedical Campus, Cambridge, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
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21
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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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22
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Zheng F, Lin Z, Hu Y, Shi X, Zhao Q, Lin Z. Identification of a Novel Non-Canonical Splice-Site Variant in ABCD1. J Clin Med 2023; 12:jcm12020473. [PMID: 36675402 PMCID: PMC9863105 DOI: 10.3390/jcm12020473] [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: 11/29/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023] Open
Abstract
Cerebral adrenoleukodystrophy (CALD) is a fatal genetic disease characterized by rapid, devastating neurological decline, with a narrow curative treatment window in the early stage. Non-canonical splice-site (NCSS) variants can easily be missed during genomic DNA analyses, and only a few of them in ABCD1 have been explored. Here, we studied a Chinese patient with clinical features similar to those of early-stage CALD but with a negative molecular diagnosis and a sibling who had presumably died of CALD. Trio-based whole-exome sequencing (trio-WES) and RNA sequencing (RNA-Seq) revealed a novel hemizygote NCSS variant c.901-25_901-9 del in ABCD1 intron 1, resulting in a complex splicing pattern. The in vitro minigene assay revealed that the c.901-25_901-9 del construct contained two aberrant transcripts that caused skipping of exon 2 and a small 48-bp deletion on left of the same exon. We identified a novel NCSS variant, that extends the spectrum of the known ABCD1 variants, and demonstrated the pathogenicity of this gene variant. Our findings highlight the importance of combining RNA-Seq and WES techniques for prompt diagnosis of leukodystrophy with NCSS variants.
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Affiliation(s)
- Feixia Zheng
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Wenzhou Key Laboratory of Perinatal Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Zhongdong Lin
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Ying Hu
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Xulai Shi
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Qianlei Zhao
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Wenzhou Key Laboratory of Perinatal Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
| | - Zhenlang Lin
- Department of Pediatrics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Wenzhou Key Laboratory of Perinatal Medicine, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou 325027, China
- Correspondence: ; Tel.: +86-13-80-668-9800
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23
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Starosta RT, Shinawi M. Primary Mitochondrial Disorders in the Neonate. Neoreviews 2022; 23:e796-e812. [PMID: 36450643 DOI: 10.1542/neo.23-12-e796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Primary mitochondrial disorders (PMDs) are a heterogeneous group of disorders characterized by functional or structural abnormalities in the mitochondria that lead to a disturbance of cellular energy, reactive oxygen species, and free radical production, as well as impairment of other intracellular metabolic functions, causing single- or multiorgan dysfunction. PMDs are caused by pathogenic variants in nuclear and mitochondrial genes, resulting in distinct modes of inheritance. Onset of disease is variable and can occur in the neonatal period, with a high morbidity and mortality. In this article, we review the most common methods used for the diagnosis of PMDs, as well as their prenatal and neonatal presentations. We highlight the shift in the diagnostic approach for PMDs since the introduction of nontargeted molecular tests into clinical practice, which has significantly reduced the use of invasive studies. We discuss common PMDs that can present in the neonate, including general, nonsyndromic presentations as well as specific syndromic disorders. We also review current treatment advances, including the use of mitochondrial "cocktails" based on limited scientific evidence and theoretical reasoning, as well as the impending arrival of personalized mitochondrial-specific treatments.
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Affiliation(s)
| | - Marwan Shinawi
- Washington University School of Medicine, Saint Louis, MO
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24
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Dong X, Xiao T, Chen B, Lu Y, Zhou W. Precision medicine via the integration of phenotype-genotype information in neonatal genome project. FUNDAMENTAL RESEARCH 2022; 2:873-884. [PMID: 38933389 PMCID: PMC11197532 DOI: 10.1016/j.fmre.2022.07.003] [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: 04/26/2022] [Revised: 07/07/2022] [Accepted: 07/10/2022] [Indexed: 11/21/2022] Open
Abstract
The explosion of next-generation sequencing (NGS) has enabled the widespread use of genomic data in precision medicine. Currently, several neonatal genome projects have emerged to explore the advantages of NGS to diagnose or screen for rare genetic disorders. These projects have made remarkable achievements, but still the genome data could be further explored with the assistance of phenotype collection. In contrast, longitudinal birth cohorts are great examples to record and apply phenotypic information in clinical studies starting at the neonatal period, especially the trajectory analyses for health development or disease progression. It is obvious that efficient integration of genotype and phenotype benefits not only the clinical management of rare genetic disorders but also the risk assessment of complex diseases. Here, we first summarize the recent neonatal genome projects as well as some longitudinal birth cohorts. Then, we propose two simplified strategies by integrating genotypic and phenotypic information in precision medicine based on current studies. Finally, research collaborations, sociological issues, and future perspectives are discussed. How to maximize neonatal genomic information to benefit the pediatric population remains an area in need of more research and effort.
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Affiliation(s)
- Xinran Dong
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Tiantian Xiao
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
- Department of Neonatology, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu 610066, China
| | - Bin Chen
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Yulan Lu
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
- Division of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai 201102, China
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25
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De Pasquale L, Meo P, Fulia F, Anania A, Meli V, Mondello A, Raimondo MT, Tulino V, Coletta MS, Cacace C. A fatal case of neonatal onset multiple acyl-CoA dehydrogenase deficiency caused by novel mutation of ETFDH gene: case report. Ital J Pediatr 2022; 48:164. [PMID: 36064718 PMCID: PMC9446717 DOI: 10.1186/s13052-022-01356-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple acyl-CoA dehydrogenase deficiency (MADD) or glutaric aciduria type II is an extremely rare autosomal recessive inborn error of fatty acid beta oxidation and branched-chain amino acids, secondary to mutations in the genes encoding the electron transfer flavoproteins A and B (ETFs; ETFA or ETFB) or ETF dehydrogenase (ETFDH). The clinical manifestation of MADD are heterogeneous, from severe neonatal forms to mild late-onset forms. CASE PRESENTATION We report the case of a preterm newborn who died a few days after birth for a severe picture of untreatable metabolic acidosis. The diagnosis of neonatal onset MADD was suggested on the basis of clinical features displaying congenital abnormalities and confirmed by the results of expanded newborn screening, which arrived the day the newborn died. Molecular genetic test revealed a homozygous indel variant c.606 + 1 _606 + 2insT in the ETFDH gene, localized in a canonical splite site. This variant, segregated from the two heterozygous parents, is not present in the general population frequency database and has never been reported in the literature. DISCUSSION AND CONCLUSION Recently introduced Expanded Newborn Screening is very important for a timely diagnosis of Inherited Metabolic Disorders like MADD. In some cases which are the most severe, diagnosis may arrive after symptoms are already present or may be the neonate already died. This stress the importance of collecting all possible samples to give parents a proper diagnosis and a genetic counselling for future pregnacies.
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Affiliation(s)
- Loredana De Pasquale
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy.
| | - Petronilla Meo
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Francesco Fulia
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Antonio Anania
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Valerio Meli
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Antonina Mondello
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Maria Tindara Raimondo
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Viviana Tulino
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Maria Sole Coletta
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
| | - Caterina Cacace
- Azienda Sanitaria Provinciale di Messina - Neonatal Intensive Care Unit, Barone Romeo Hospital, Patti, ME, Italy
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26
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Labory J, Le Bideau G, Pratella D, Yao JE, Ait-El-Mkadem Saadi S, Bannwarth S, El-Hami L, Paquis-Fluckinger V, Bottini S. ABEILLE: a novel method for ABerrant Expression Identification empLoying machine Learning from RNA-sequencing data. Bioinformatics 2022; 38:4754-4761. [PMID: 36063052 PMCID: PMC9563686 DOI: 10.1093/bioinformatics/btac603] [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: 07/12/2021] [Revised: 06/22/2022] [Accepted: 09/01/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Current advances in omics technologies are paving the diagnosis of rare diseases proposing as a complementary assay to identify the responsible gene. The use of transcriptomic data to identify aberrant gene expression (AGE) have demonstrated to yield potential pathogenic events. However popular approaches for AGE identification are limited by the use of statistical tests that imply the choice of arbitrary cut-off for significance assessment and the availability of several replicates not always possible in clinical contexts. RESULTS Hence we developed ABEILLE (ABerrant Expression Identification empLoying machine LEarning from sequencing data) a variational autoencoder (VAE) based method for the identification of AGEs from the analysis of RNA-seq data without the need of replicates or a control group. ABEILLE combines the use of a VAE, able to model any data without specific assumptions on their distribution, and a decision tree to classify genes as AGE or non-AGE. An anomaly score is associated to each gene in order to stratify AGE by severity of aberration. We tested ABEILLE on semi-synthetic and an experimental dataset demonstrating the importance of the flexibility of the VAE configuration to identify potential pathogenic candidates. AVAILABILITY ABEILLE source code is freely available at : https://github.com/UCA-MSI/ABEILLE. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Justine Labory
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France.,Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - Gwendal Le Bideau
- Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - David Pratella
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France
| | - Jean-Elisée Yao
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France
| | - Samira Ait-El-Mkadem Saadi
- Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - Sylvie Bannwarth
- Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - Loubna El-Hami
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France.,Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - Véronique Paquis-Fluckinger
- Université Côte d'Azur, Inserm U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre hospitalier universitaire (CHU) de Nice, Nice, France
| | - Silvia Bottini
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France
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27
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Davis RL, Kumar KR, Puttick C, Liang C, Ahmad KE, Edema-Hildebrand F, Park JS, Minoche AE, Gayevskiy V, Mallawaarachchi AC, Christodoulou J, Schofield D, Dinger ME, Cowley MJ, Sue CM. Use of Whole-Genome Sequencing for Mitochondrial Disease Diagnosis. Neurology 2022; 99:e730-e742. [PMID: 35641312 PMCID: PMC9484606 DOI: 10.1212/wnl.0000000000200745] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 04/04/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Mitochondrial diseases (MDs) are the commonest group of heritable metabolic disorders. Phenotypic diversity can make molecular diagnosis challenging, and causative genetic variants may reside in either mitochondrial or nuclear DNA. A single comprehensive genetic diagnostic test would be highly useful and transform the field. We applied whole-genome sequencing (WGS) to evaluate the variant detection rate and diagnostic capacity of this technology with a view to simplifying and improving the MD diagnostic pathway. METHODS Adult patients presenting to a specialist MD clinic in Sydney, Australia, were recruited to the study if they satisfied clinical MD (Nijmegen) criteria. WGS was performed on blood DNA, followed by clinical genetic analysis for known pathogenic MD-associated variants and MD mimics. RESULTS Of the 242 consecutive patients recruited, 62 participants had "definite," 108 had "probable," and 72 had "possible" MD classification by the Nijmegen criteria. Disease-causing variants were identified for 130 participants, regardless of the location of the causative genetic variants, giving an overall diagnostic rate of 53.7% (130 of 242). Identification of causative genetic variants informed precise treatment, restored reproductive confidence, and optimized clinical management of MD. DISCUSSION Comprehensive bigenomic sequencing accurately detects causative genetic variants in affected MD patients, simplifying diagnosis, enabling early treatment, and informing the risk of genetic transmission.
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28
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Lavorato M, Nakamaru-Ogiso E, Mathew ND, Herman E, Shah NK, Haroon S, Xiao R, Seiler C, Falk MJ. Dichloroacetate improves mitochondrial function, physiology, and morphology in FBXL4 disease models. JCI Insight 2022; 7:156346. [PMID: 35881484 PMCID: PMC9462489 DOI: 10.1172/jci.insight.156346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Pathogenic variants in the human F-box and leucine-rich repeat protein 4 (FBXL4) gene result in an autosomal recessive, multisystemic, mitochondrial disorder involving variable mitochondrial depletion and respiratory chain complex deficiencies with lactic acidemia. As no FDA-approved effective therapies for this disease exist, we sought to characterize translational C. elegans and zebrafish animal models, as well as human fibroblasts, to study FBXL4–/– disease mechanisms and identify preclinical therapeutic leads. Developmental delay, impaired fecundity and neurologic and/or muscular activity, mitochondrial dysfunction, and altered lactate metabolism were identified in fbxl-1(ok3741) C. elegans. Detailed studies of a PDHc activator, dichloroacetate (DCA), in fbxl-1(ok3741)C. elegans demonstrated its beneficial effects on fecundity, neuromotor activity, and mitochondrial function. Validation studies were performed in fbxl4sa12470 zebrafish larvae and in FBXL4–/– human fibroblasts; they showed DCA efficacy in preventing brain death, impairment of neurologic and/or muscular function, mitochondrial biochemical dysfunction, and stress-induced morphologic and ultrastructural mitochondrial defects. These data demonstrate that fbxl-1(ok3741) C. elegans and fbxl4sa12470 zebrafish provide robust translational models to study mechanisms and identify preclinical therapeutic candidates for FBXL4–/– disease. Furthermore, DCA is a lead therapeutic candidate with therapeutic benefit on diverse aspects of survival, neurologic and/or muscular function, and mitochondrial physiology that warrants rigorous clinical trial study in humans with FBXL4–/– disease.
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Affiliation(s)
- Manuela Lavorato
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, United States of America
| | - Eiko Nakamaru-Ogiso
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, United States of America
| | - Neal D Mathew
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, United States of America
| | - Elizabeth Herman
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, United States of America
| | - Nina K Shah
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, United States of America
| | - Suraiya Haroon
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, United States of America
| | - Rui Xiao
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, United States of America
| | - Christoph Seiler
- Aquatics Core Facility, Children's Hospital of Philadelphia, Philadelphia, United States of America
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, United States of America
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29
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Clinical Experience of Neurological Mitochondrial Diseases in Children and Adults: A Single-Center Study. Balkan J Med Genet 2022; 24:5-14. [PMID: 36249517 PMCID: PMC9524181 DOI: 10.2478/bjmg-2021-0019] [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] [Indexed: 11/20/2022] Open
Abstract
The goal of the study was to retrospectively evaluate a cohort of children and adults with mitochondrial diseases (MDs) in a single-center experience. Neurological clinical examination, brain magnetic resonance imaging (MRI) and spectroscopy, muscle biopsy, metabolic and molecular-genetic analysis were evaluated in 26 children and 36 adult patients with MD in Slovenia from 2004 to 2018. Nijmegen MD criteria (MDC) were applied to all patients and the need for a muscle biopsy was estimated. Exome-sequencing was used in half of the patients. Twenty children (77.0%) and 12 adults (35.0%) scored a total of ≥8 on MDC, a result that is compatible with the diagnosis of definite MD. Yield of exome-sequencing was 7/22 (31.0%), but the method was not applied systematically in all patients from the beginning of diagnostics. Brain MRI morphological changes, which can be an imaging clue for the diagnosis of MD, were found in 17/24 children (71.0%). In 7/26 (29.0%) children, and in 20/30 (67.0%) adults, abnormal mitochondria were found on electron microscopy (EM) and ragged-red fibers were found in 16/30 (53.0%) adults. Respiratory chain enzymes (RCEs) and/or pyruvate dehydrogenase complex (PDHc) activities were abnormal in all the children and six adult cases. First, our data revealed that MDC was useful in the clinical diagnosis of MD, and second, until the use of NGS methods, extensive, laborious and invasive diagnostic procedures were performed to reach a final diagnosis. In patients with suspected MD, there is a need to prioritize molecular diagnosis with the more modern next-generation sequencing (NGS) method.
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30
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Automatic Recognition of Ragged Red Fibers in Muscle Biopsy from Patients with Mitochondrial Disorders. Healthcare (Basel) 2022; 10:healthcare10030574. [PMID: 35327052 PMCID: PMC8949467 DOI: 10.3390/healthcare10030574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial dysfunction is considered to be a major cause of primary mitochondrial myopathy in children and adults, as reduced mitochondrial respiration and morphological changes such as ragged red fibers (RRFs) are observed in muscle biopsies. However, it is also possible to hypothesize the role of mitochondrial dysfunction in aging muscle or in secondary mitochondrial dysfunctions. The recognition of true histological patterns of mitochondrial myopathy can avoid unnecessary genetic investigations. The aim of our study was to develop and validate machine-learning methods for RRF detection in light microscopy images of skeletal muscle tissue. We used image sets of 489 color images captured from representative areas of Gomori’s trichrome-stained tissue retrieved from light microscopy images at a 20× magnification. We compared the performance of random forest, gradient boosting machine, and support vector machine classifiers. Our results suggested that the advent of scanning technologies, combined with the development of machine-learning models for image classification, make neuromuscular disorders’ automated diagnostic systems a concrete possibility.
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31
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2022 Overview of Metabolic Epilepsies. Genes (Basel) 2022; 13:genes13030508. [PMID: 35328062 PMCID: PMC8952328 DOI: 10.3390/genes13030508] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/04/2022] Open
Abstract
Understanding the genetic architecture of metabolic epilepsies is of paramount importance, both to current clinical practice and for the identification of further research directions. The main goals of our study were to identify the scope of metabolic epilepsies and to investigate their clinical presentation, diagnostic approaches and treatments. The International Classification of Inherited Metabolic Disorders and IEMbase were used as a basis for the identification and classification of metabolic epilepsies. Six hundred metabolic epilepsies have been identified, accounting for as much as 37% of all currently described inherited metabolic diseases (IMD). Epilepsy is a particularly common symptom in disorders of energy metabolism, congenital disorders of glycosylation, neurotransmitter disorders, disorders of the synaptic vesicle cycle and some other IMDs. Seizures in metabolic epilepsies may present variably, and most of these disorders are complex and multisystem. Abnormalities in routine laboratory tests and/or metabolic testing may be identified in 70% of all metabolic epilepsies, but in many cases they are non-specific. In total, 111 metabolic epilepsies (18% of all) have specific treatments that may significantly change health outcomes if diagnosed in time. Although metabolic epilepsies comprise an important and significant group of disorders, their real scope and frequency may have been underestimated.
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32
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Kashif M, Lu Z, Sang Y, Yan B, Shah SJ, Khan S, Azhar Hussain M, Tang H, Jiang C. Whole-Genome and Transcriptome Sequencing-Based Characterization of Bacillus Cereus NR1 From Subtropical Marine Mangrove and Its Potential Role in Sulfur Metabolism. Front Microbiol 2022; 13:856092. [PMID: 35356521 PMCID: PMC8959591 DOI: 10.3389/fmicb.2022.856092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Sulfur, organosulfur compounds, and sulfides are essential parts of life. Microbial sulfate assimilation is among the most active and ancient metabolic activities in the sulfur cycle that operates in various ecosystems. We analyzed the molecular basis of bacterial characterization. NR1 was isolated and purified from mangrove sediments. Whole-genome sequencing indicated that the NR1 isolate was closely related to Bacillus cereus. The genome contained 5,305 functional genes with a total length of 5,420,664 bp, a GC content of 35.62%, 42 rRNA, and 107 tRNA. DBT-grown cultures exhibited DBT utilization, fleeting emergence of DBT sulfone (DBTO2), and formation of 2-hydroxybiphenyl (2-HBP). Molecular analysis of the PCR products’ dsz operon revealed the presence of dszA, dszB, and dszC genes, which encoded for NR1’s 90% DBT desulfurization activity. Furthermore, 17 sulfur metabolism-related genes, including genes involved in assimilation sulfate reduction, APS and PAPS, and the cys, ssu, and TST gene families, were identified. In sulfate media, alkenesulfonate was converted to sulfite and inhibited ssu enzymes. Downregulated cysK variants were associated with nrnA expression and the regulation of L-cysteine synthesis. These findings established a scientific foundation for further research and application of bacteria to mangrove rehabilitation and ecological treatment by evaluating the bacterial characterization and sulfur degradation metabolic pathway. We used whole-genome and transcriptome sequencing to examine their genetic characteristics.
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Affiliation(s)
- Muhammad Kashif
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Zhaomei Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- Key Laboratory of Bio-resources and Eco-environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yimeng Sang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | - Bing Yan
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Nanning, China
| | - Syed Jalil Shah
- MOE Key Laboratory of New Processing Technology for Non-ferrous Metals and Materials, Guangxi Key Laboratory of Processing for Non-ferrous Metals and Featured Materials, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, China
| | - Sohail Khan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
| | | | - Hongzhen Tang
- Key Laboratory and Cultivation Base of Prevention and Treatment of Traditional Chinese Medicine on Obesity, Guangxi University of Chinese Medicine, Nanning, China
- *Correspondence: Hongzhen Tang, Chengjian Jiang,
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzyme Engineering Technology, College of Life Science and Technology, Guangxi University, Nanning, China
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Guangxi Academy of Sciences, Nanning, China
- *Correspondence: Hongzhen Tang, Chengjian Jiang,
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33
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van Esveld SL, Rodenburg RJ, Al‐Murshedi F, Al‐Ajmi E, Al‐Zuhaibi S, Huynen MA, Spelbrink JN. Mitochondrial RNA processing defect caused by a SUPV3L1 mutation in two siblings with a novel neurodegenerative syndrome. J Inherit Metab Dis 2022; 45:292-307. [PMID: 35023579 PMCID: PMC9303385 DOI: 10.1002/jimd.12476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/08/2022] [Accepted: 01/11/2022] [Indexed: 11/06/2022]
Abstract
SUPV3L1 encodes a helicase that is mainly localized in the mitochondria. It has been shown in vitro to possess both double-stranded RNA and DNA unwinding activity that is ATP-dependent. Here we report the first two patients for this gene who presented with a homozygous preliminary stop codon resulting in a C-terminal truncation of the SUPV3L1 protein. They presented with a characteristic phenotype of neurodegenerative nature with progressive spastic paraparesis, growth restriction, hypopigmentation, and predisposition to autoimmune disease. Ophthalmological examination showed severe photophobia with corneal erosions, optic atrophy, and pigmentary retinopathy, while neuroimaging showed atrophy of the optic chiasm and the pons with calcification of putamina, with intermittent and mild elevation of lactate. We show that the amino acids that are eliminated by the preliminary stop codon are highly conserved and are predicted to form an amphipathic helix. To investigate if the mutation causes mitochondrial dysfunction, we examined fibroblasts of the proband. We observed very low expression of the truncated protein, a reduction in the mature ND6 mRNA species as well as the accumulation of double-stranded RNA. Lentiviral complementation with the full-length SUPV3L1 cDNA partly restored the observed RNA phenotypes, supporting that the SUPV3L1 mutation in these patients is pathogenic and the cause of the disease.
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Affiliation(s)
- Selma L. van Esveld
- Radboud Center for Mitochondrial Medicine & Center for Molecular and Biomolecular InformaticsRadboud Institute for Molecular Life SciencesNijmegenThe Netherlands
| | - Richard J. Rodenburg
- Radboud Center for Mitochondrial Medicine, Department of Paediatrics, RadboudumcNijmegenThe Netherlands
| | - Fathiya Al‐Murshedi
- Genetic and Developmental Medicine ClinicSultan Qaboos University HospitalMuscatOman
| | - Eiman Al‐Ajmi
- Department of Radiology and Molecular ImagingSultan Qaboos University HospitalMuscatOman
| | - Sana Al‐Zuhaibi
- Department of OphthalmologySultan Qaboos University HospitalMuscatOman
| | - Martijn A. Huynen
- Radboud Center for Mitochondrial Medicine & Center for Molecular and Biomolecular InformaticsRadboud Institute for Molecular Life SciencesNijmegenThe Netherlands
| | - Johannes N. Spelbrink
- Radboud Center for Mitochondrial Medicine, Department of Paediatrics, RadboudumcNijmegenThe Netherlands
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34
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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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35
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Montgomery SB, Bernstein JA, Wheeler MT. Toward transcriptomics as a primary tool for rare disease investigation. Cold Spring Harb Mol Case Stud 2022; 8:a006198. [PMID: 35217565 PMCID: PMC8958920 DOI: 10.1101/mcs.a006198] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
In the past 5 years transcriptome or RNA-sequencing (RNA-seq) has steadily emerged as a complementary assay for rare disease diagnosis and discovery. In this perspective, we summarize several recent developments and challenges in the use of RNA-seq for rare disease investigation. Using an accessible patient sample, such as blood, skin, or muscle, RNA-seq enables the assay of expressed RNA transcripts. Analysis of RNA-seq allows the identification of aberrant or outlier gene expression and alternative splicing as functional evidence to support rare disease study and diagnosis. Further, many types of variant effects can be profiled beyond coding variants, as the consequences of noncoding variants that impact gene expression and splicing can be directly observed. This is particularly apparent for structural variants that disproportionately underlie outlier gene expression and for splicing variants in which RNA-seq can both measure aberrant canonical splicing and detect deep intronic effects. However, a major potential limitation of RNA-seq in rare disease investigation is the developmental and cell type specificity of gene expression as a pathogenic variant's effect may be limited to a specific spatiotemporal context and access to a patient's tissue sample from the relevant tissue and timing of disease expression may not be possible. We speculate that as advances in computational methods and emerging experimental techniques overcome both developmental and cell type specificity, there will be broadening use of RNA sequencing and multiomics in rare disease diagnosis and delivery of precision health.
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Affiliation(s)
- Stephen B Montgomery
- Departments of Genetics and Pathology, Stanford University, California 94305, USA
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Matthew T Wheeler
- Division of Cardiovascular Medicine, Department of Medicine, Stanford University, California 94304, USA
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36
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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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37
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Wang Y, Zhao G, Fang Z, Pan H, Zhao Y, Wang Y, Zhou X, Wang X, Luo T, Zhang Y, Wang Z, Chen Q, Dong L, Huang Y, Zhou Q, Xia L, Li B, Guo J, Xia K, Tang B, Li J. Genetic landscape of human mitochondrial genome using whole genome sequencing. Hum Mol Genet 2021; 31:1747-1761. [PMID: 34897451 DOI: 10.1093/hmg/ddab358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/26/2021] [Accepted: 12/07/2021] [Indexed: 11/12/2022] Open
Abstract
Increasing evidences suggest that mitochondrial dysfunction is implicated in diseases and aging, and whole-genome sequencing (WGS) is the most unbiased method in analyzing the mitochondrial genome (mtDNA). However, the genetic landscape of mtDNA in the Chinese population has not been fully examined. Here, we described the genetic landscape of mtDNA using WGS data from Chinese individuals (n = 3241). We identified 3892 mtDNA variants, of which 3349 (86%) were rare variants. Interestingly, we observed a trend toward extreme heterogeneity of mtDNA variants. Our study observed a distinct purifying selection on mtDNA, which inhibits the accumulation of harmful heteroplasmies at the individual level: (1) mitochondrial dN/dS ratios were much less than 1; (2) the dN/dS ratio of heteroplasmies was higher than homoplasmies; (3) heteroplasmies had more indels and predicted deleterious variants than homoplasmies. Furthermore, we found that haplogroup M (20.27%) and D (20.15%) had the highest frequencies in the Chinese population, followed by B (18.51%) and F (16.45%). The number of variants per individual differed across haplogroup groups, with a higher number of homoplasmies for the M lineage. Meanwhile, mtDNA copy number was negatively correlated with age but positively correlated with the female sex. Finally, we developed an mtDNA variation database of Chinese populations called MTCards (http://genemed.tech/mtcards/) to facilitate the query of mtDNA variants in this study. In summary, these findings contribute to different aspects of understanding mtDNA, providing a better understanding of the genetic basis of mitochondrial-related diseases.
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Affiliation(s)
- Yijing Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zhenghuan Fang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Hongxu Pan
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yuwen Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yige Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xun Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xiaomeng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Tengfei Luo
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lijie Dong
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Yuanfeng Huang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jifeng Guo
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China
| | - Beisha Tang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China.,Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410008, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, China
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38
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Vidali S, Gerlini R, Thompson K, Urquhart JE, Meisterknecht J, Aguilar‐Pimentel JA, Amarie OV, Becker L, Breen C, Calzada‐Wack J, Chhabra NF, Cho Y, da Silva‐Buttkus P, Feichtinger RG, Gampe K, Garrett L, Hoefig KP, Hölter SM, Jameson E, Klein‐Rodewald T, Leuchtenberger S, Marschall S, Mayer‐Kuckuk P, Miller G, Oestereicher MA, Pfannes K, Rathkolb B, Rozman J, Sanders C, Spielmann N, Stoeger C, Szibor M, Treise I, Walter JH, Wurst W, Mayr JA, Fuchs H, Gärtner U, Wittig I, Taylor RW, Newman WG, Prokisch H, Gailus‐Durner V, Hrabě de Angelis M. Characterising a homozygous two-exon deletion in UQCRH: comparing human and mouse phenotypes. EMBO Mol Med 2021; 13:e14397. [PMID: 34750991 PMCID: PMC8649870 DOI: 10.15252/emmm.202114397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/06/2021] [Accepted: 10/07/2021] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial disorders are clinically and genetically diverse, with isolated complex III (CIII) deficiency being relatively rare. Here, we describe two affected cousins, presenting with recurrent episodes of severe lactic acidosis, hyperammonaemia, hypoglycaemia and encephalopathy. Genetic investigations in both cases identified a homozygous deletion of exons 2 and 3 of UQCRH, which encodes a structural complex III (CIII) subunit. We generated a mouse model with the equivalent homozygous Uqcrh deletion (Uqcrh-/- ), which also presented with lactic acidosis and hyperammonaemia, but had a more severe, non-episodic phenotype, resulting in failure to thrive and early death. The biochemical phenotypes observed in patient and Uqcrh-/- mouse tissues were remarkably similar, displaying impaired CIII activity, decreased molecular weight of fully assembled holoenzyme and an increase of an unexpected large supercomplex (SXL ), comprising mostly of one complex I (CI) dimer and one CIII dimer. This phenotypic similarity along with lentiviral rescue experiments in patient fibroblasts verifies the pathogenicity of the shared genetic defect, demonstrating that the Uqcrh-/- mouse is a valuable model for future studies of human CIII deficiency.
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Petersen USS, Doktor TK, Andresen BS. Pseudoexon activation in disease by non-splice site deep intronic sequence variation - wild type pseudoexons constitute high-risk sites in the human genome. Hum Mutat 2021; 43:103-127. [PMID: 34837434 DOI: 10.1002/humu.24306] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/02/2021] [Accepted: 11/06/2021] [Indexed: 12/27/2022]
Abstract
Accuracy of pre-messenger RNA (pre-mRNA) splicing is crucial for normal gene expression. Complex regulation supports the spliceosomal distinction between authentic exons and the many seemingly functional splice sites delimiting pseudoexons. Pseudoexons are nonfunctional intronic sequences that can be activated for aberrant inclusion in mRNA, which may cause disease. Pseudoexon activation is very challenging to predict, in particular when activation occurs by sequence variants that alter the splicing regulatory environment without directly affecting splice sites. As pseudoexon inclusion often evades detection due to activation of nonsense-mediated mRNA decay, and because conventional diagnostic procedures miss deep intronic sequence variation, pseudoexon activation is a heavily underreported disease mechanism. Pseudoexon characteristics have mainly been studied based on in silico predicted sequences. Moreover, because recognition of sequence variants that create or strengthen splice sites is possible by comparison with well-established consensus sequences, this type of pseudoexon activation is by far the most frequently reported. Here we review all known human disease-associated pseudoexons that carry functional splice sites and are activated by deep intronic sequence variants located outside splice site sequences. We delineate common characteristics that make this type of wild type pseudoexons distinct high-risk sites in the human genome.
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Affiliation(s)
- Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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40
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Velluva A, Radtke M, Horn S, Popp B, Platzer K, Gjermeni E, Lin CC, Lemke JR, Garten A, Schöneberg T, Blüher M, Abou Jamra R, Le Duc D. Phenotype-tissue expression and exploration (PTEE) resource facilitates the choice of tissue for RNA-seq-based clinical genetics studies. BMC Genomics 2021; 22:802. [PMID: 34743696 PMCID: PMC8573933 DOI: 10.1186/s12864-021-08125-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/26/2021] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND RNA-seq emerges as a valuable method for clinical genetics. The transcriptome is "dynamic" and tissue-specific, but typically the probed tissues to analyze (TA) are different from the tissue of interest (TI) based on pathophysiology. RESULTS We developed Phenotype-Tissue Expression and Exploration (PTEE), a tool to facilitate the decision about the most suitable TA for RNA-seq. We integrated phenotype-annotated genes, used 54 tissues from GTEx to perform correlation analyses and identify expressed genes and transcripts between TAs and TIs. We identified skeletal muscle as the most appropriate TA to inquire for cardiac arrhythmia genes and skin as a good proxy to study neurodevelopmental disorders. We also explored RNA-seq limitations and show that on-off switching of gene expression during ontogenesis or circadian rhythm can cause blind spots for RNA-seq-based analyses. CONCLUSIONS PTEE aids the identification of tissues suitable for RNA-seq for a given pathology to increase the success rate of diagnosis and gene discovery. PTEE is freely available at https://bioinf.eva.mpg.de/PTEE/.
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Affiliation(s)
- Akhil Velluva
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany.
| | - Maximillian Radtke
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany
| | - Susanne Horn
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany
| | - Bernt Popp
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany
| | - Erind Gjermeni
- Department of Electrophysiology, Heart Center Leipzig at University of Leipzig, 04289, Leipzig, Germany
- Department of Cardiology, Median Centre for Rehabilitation Schmannewitz, 04774, Dahlen, Germany
| | - Chen-Ching Lin
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Johannes R Lemke
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany
| | - Antje Garten
- Pediatric Research Center, University Hospital for Children and Adolescents, Leipzig University, 04103, Leipzig, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany
| | - Matthias Blüher
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany
| | - Rami Abou Jamra
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany
| | - Diana Le Duc
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
- Institute of Human Genetics, University Medical Center Leipzig, 04103, Leipzig, Germany.
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, 04103, Leipzig, Germany.
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41
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Schon KR, Horvath R, Wei W, Calabrese C, Tucci A, Ibañez K, Ratnaike T, Pitceathly RDS, Bugiardini E, Quinlivan R, Hanna MG, Clement E, Ashton E, Sayer JA, Brennan P, Josifova D, Izatt L, Fratter C, Nesbitt V, Barrett T, McMullen DJ, Smith A, Deshpande C, Smithson SF, Festenstein R, Canham N, Caulfield M, Houlden H, Rahman S, Chinnery PF. Use of whole genome sequencing to determine genetic basis of suspected mitochondrial disorders: cohort study. BMJ 2021; 375:e066288. [PMID: 34732400 PMCID: PMC8565085 DOI: 10.1136/bmj-2021-066288] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To determine whether whole genome sequencing can be used to define the molecular basis of suspected mitochondrial disease. DESIGN Cohort study. SETTING National Health Service, England, including secondary and tertiary care. PARTICIPANTS 345 patients with suspected mitochondrial disorders recruited to the 100 000 Genomes Project in England between 2015 and 2018. INTERVENTION Short read whole genome sequencing was performed. Nuclear variants were prioritised on the basis of gene panels chosen according to phenotypes, ClinVar pathogenic/likely pathogenic variants, and the top 10 prioritised variants from Exomiser. Mitochondrial DNA variants were called using an in-house pipeline and compared with a list of pathogenic variants. Copy number variants and short tandem repeats for 13 neurological disorders were also analysed. American College of Medical Genetics guidelines were followed for classification of variants. MAIN OUTCOME MEASURE Definite or probable genetic diagnosis. RESULTS A definite or probable genetic diagnosis was identified in 98/319 (31%) families, with an additional 6 (2%) possible diagnoses. Fourteen of the diagnoses (4% of the 319 families) explained only part of the clinical features. A total of 95 different genes were implicated. Of 104 families given a diagnosis, 39 (38%) had a mitochondrial diagnosis and 65 (63%) had a non-mitochondrial diagnosis. CONCLUSION Whole genome sequencing is a useful diagnostic test in patients with suspected mitochondrial disorders, yielding a diagnosis in a further 31% after exclusion of common causes. Most diagnoses were non-mitochondrial disorders and included developmental disorders with intellectual disability, epileptic encephalopathies, other metabolic disorders, cardiomyopathies, and leukodystrophies. These would have been missed if a targeted approach was taken, and some have specific treatments.
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Affiliation(s)
- Katherine R Schon
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Wei Wei
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Claudia Calabrese
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Arianna Tucci
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Kristina Ibañez
- William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Thiloka Ratnaike
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Rosaline Quinlivan
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
| | - Emma Clement
- Department of Clinical Genetics and Genomic Medicine, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Emma Ashton
- NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Paul Brennan
- Northern Genetics Service, Newcastle Hospitals NHS Foundation Trust, International Centre for Life, Newcastle upon Tyne, UK
| | - Dragana Josifova
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Louise Izatt
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Carl Fratter
- NHS Highly Specialised Services for Rare Mitochondrial Disorders - Oxford Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Victoria Nesbitt
- NHS Highly Specialised Services for Rare Mitochondrial Disorders - Oxford Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Timothy Barrett
- Central and South Genome Medicine Service Alliance and Genomics Laboratory Hub, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Dominic J McMullen
- Central and South Genome Medicine Service Alliance and Genomics Laboratory Hub, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Audrey Smith
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Charulata Deshpande
- Department of Clinical Genetics, Guy's and St Thomas' NHS Foundation Trust, London, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester, UK
| | - Sarah F Smithson
- Department of Brain Sciences, London Institute of Medical Sciences, Mansfield Centre for Inovation, Imperial College, Hammersmith Hospital, London, UK
| | | | - Natalie Canham
- Liverpool Centre for Genomic Medicine, Liverpool Women's Hospital, Liverpool, UK
| | - Mark Caulfield
- Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, UK
- Neurology and Mitochondrial Disorders Genomics Clinical Interpretation Partnership, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Shamima Rahman
- Neurology and Mitochondrial Disorders Genomics Clinical Interpretation Partnership, William Harvey Research Institute, Queen Mary University of London, London, UK
- Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Mitochondrial Research Group, Department of Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
- Neurology and Mitochondrial Disorders Genomics Clinical Interpretation Partnership, William Harvey Research Institute, Queen Mary University of London, London, UK
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42
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García-Olivares V, Muñoz-Barrera A, Lorenzo-Salazar JM, Zaragoza-Trello C, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Iñigo-Campos A, González-Montelongo R, Flores C. A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data. Sci Rep 2021; 11:20510. [PMID: 34654896 PMCID: PMC8519921 DOI: 10.1038/s41598-021-99895-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships. Because of this and the advent of high-throughput sequencing (HTS) technology, there is a diversity of bioinformatic tools for haplogroup classification. We present a benchmarking of the 11 most salient tools for human mtDNA classification using empirical whole-genome (WGS) and whole-exome (WES) short-read sequencing data from 36 unrelated donors. We also assessed the best performing tool in third-generation long noisy read WGS data obtained with nanopore technology for a subset of the donors. We found that, for short-read WGS, most of the tools exhibit high accuracy for haplogroup classification irrespective of the input file used for the analysis. However, for short-read WES, Haplocheck and MixEmt were the most accurate tools. Based on the performance shown for WGS and WES, and the accompanying qualitative assessment, Haplocheck stands out as the most complete tool. For third-generation HTS data, we also showed that Haplocheck was able to accurately retrieve mtDNA haplogroups for all samples assessed, although only after following assembly-based approaches (either based on a referenced-based assembly or a hybrid de novo assembly). Taken together, our results provide guidance for researchers to select the most suitable tool to conduct the mtDNA analyses from HTS data.
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Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - José M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - Luis A Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
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43
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Sharma R, Reinstadler B, Engelstad K, Skinner OS, Stackowitz E, Haller RG, Clish CB, Pierce K, Walker MA, Fryer R, Oglesbee D, Mao X, Shungu DC, Khatri A, Hirano M, De Vivo DC, Mootha VK. Circulating markers of NADH-reductive stress correlate with mitochondrial disease severity. J Clin Invest 2021; 131:136055. [PMID: 33463549 DOI: 10.1172/jci136055] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 11/18/2020] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial disorders represent a large collection of rare syndromes that are difficult to manage both because we do not fully understand biochemical pathogenesis and because we currently lack facile markers of severity. The m.3243A>G variant is the most common heteroplasmic mitochondrial DNA mutation and underlies a spectrum of diseases, notably mitochondrial encephalomyopathy lactic acidosis and stroke-like episodes (MELAS). To identify robust circulating markers of m.3243A>G disease, we first performed discovery proteomics, targeted metabolomics, and untargeted metabolomics on plasma from a deeply phenotyped cohort (102 patients, 32 controls). In a validation phase, we measured concentrations of prioritized metabolites in an independent cohort using distinct methods. We validated 20 analytes (1 protein, 19 metabolites) that distinguish patients with MELAS from controls. The collection includes classic (lactate, alanine) and more recently identified (GDF-15, α-hydroxybutyrate) mitochondrial markers. By mining untargeted mass-spectra we uncovered 3 less well-studied metabolite families: N-lactoyl-amino acids, β-hydroxy acylcarnitines, and β-hydroxy fatty acids. Many of these 20 analytes correlate strongly with established measures of severity, including Karnofsky status, and mechanistically, nearly all markers are attributable to an elevated NADH/NAD+ ratio, or NADH-reductive stress. Our work defines a panel of organelle function tests related to NADH-reductive stress that should enable classification and monitoring of mitochondrial disease.
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Affiliation(s)
- Rohit Sharma
- Howard Hughes Medical Institute, Department of Molecular Biology, and.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
| | - Bryn Reinstadler
- Howard Hughes Medical Institute, Department of Molecular Biology, and.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
| | - Kristin Engelstad
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Owen S Skinner
- Howard Hughes Medical Institute, Department of Molecular Biology, and.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
| | - Erin Stackowitz
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Ronald G Haller
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Institute for Exercise and Environmental Medicine of Texas Health Presbyterian Hospital, Dallas, Texas, USA
| | | | | | - Melissa A Walker
- Howard Hughes Medical Institute, Department of Molecular Biology, and.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA.,Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Robert Fryer
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Devin Oglesbee
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Xiangling Mao
- Department of Radiology, Weill Cornell Medicine, New York, New York, USA
| | - Dikoma C Shungu
- Department of Radiology, Weill Cornell Medicine, New York, New York, USA
| | - Ashok Khatri
- Endocrine Division and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Michio Hirano
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Darryl C De Vivo
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute, Department of Molecular Biology, and.,Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA.,Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute, Cambridge, Massachusetts, USA
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44
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Ouyang X, Zhang Y, Zhang L, Luo J, Zhang T, Hu H, Liu L, Zhong L, Zeng S, Xu P, Bai Z, Wong LJ, Wang J, Wang C, Wang B, Zhang VW. Clinical Utility of Rapid Exome Sequencing Combined With Mitochondrial DNA Sequencing in Critically Ill Pediatric Patients With Suspected Genetic Disorders. Front Genet 2021; 12:725259. [PMID: 34490048 PMCID: PMC8416976 DOI: 10.3389/fgene.2021.725259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 02/04/2023] Open
Abstract
Genetic disorders are a frequent cause of hospitalization, morbidity and mortality in pediatric patients, especially in the neonatal or pediatric intensive care unit (NICU/PICU). In recent years, rapid genome-wide sequencing (exome or whole genome sequencing) has been applied in the NICU/PICU. However, mtDNA sequencing is not routinely available in rapid genetic diagnosis programs, which may fail to diagnose mtDNA mutation-associated diseases. Herein, we explored the clinical utility of rapid exome sequencing combined with mtDNA sequencing in critically ill pediatric patients with suspected genetic disorders. Rapid clinical exome sequencing (CES) was performed as a first-tier test in 40 critically ill pediatric patients (aged from 6 days to 15 years) with suspected genetic conditions. Blood samples were also collected from the parents for trio analysis. Twenty-six patients presented with neuromuscular abnormalities or other systemic abnormalities, suggestive of suspected mitochondrial diseases or the necessity for a differential diagnosis of other diseases, underwent rapid mtDNA sequencing concurrently. A diagnosis was made in 18 patients (45.0%, 18/40); three cases with de novo autosomal dominant variants, ten cases with homozygous or compound heterozygous variants, three cases with hemizygous variants inherited from mother, three cases with heterozygous variants inherited from either parent, and one case with a mtDNA mutation. The 18 patients were diagnosed with metabolic (n = 7), immunodeficiency (n = 4), cardiovascular (n = 2), neuromuscular (n = 2) disorders, and others. Genetic testing reports were generated with a median time of 5 days (range, 3–9 days). Thirteen patients that were diagnosed had an available medical treatment and resulted in a positive outcome. We propose that rapid exome sequencing combined with mitochondrial DNA sequencing should be available to patients with suspected mitochondrial diseases or undefined clinical features necessary for making a differential diagnosis of other diseases.
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Affiliation(s)
- Xuejun Ouyang
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yu Zhang
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Lijuan Zhang
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jixuan Luo
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Ting Zhang
- Department of Gastroenterology, Shanghai Children's Hospital, Shanghai, China
| | - Hui Hu
- Department of Gastroenterology, Shanghai Children's Hospital, Shanghai, China
| | - Lin Liu
- Department of Vasculocardiology, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Lieqiang Zhong
- Department of Vasculocardiology, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Shaoying Zeng
- Department of Vasculocardiology, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Pingyi Xu
- Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhenjiang Bai
- Department of Critical Care Medicine, Children's Hospital of Soochow University, Suzhou, China
| | - Lee-Jun Wong
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, United States
| | - Jing Wang
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, United States.,AmCare Genomics Lab, Guangzhou, China
| | | | - Bin Wang
- Department of Pediatrics, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Victor Wei Zhang
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, TX, United States.,AmCare Genomics Lab, Guangzhou, China
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Huddar A, Govindaraj P, Chiplunkar S, Deepha S, Jessiena Ponmalar JN, Philip M, Nagappa M, Narayanappa G, Mahadevan A, Sinha S, Taly AB, Parayil Sankaran B. Serum fibroblast growth factor 21 and growth differentiation factor 15: Two sensitive biomarkers in the diagnosis of mitochondrial disorders. Mitochondrion 2021; 60:170-177. [PMID: 34419687 DOI: 10.1016/j.mito.2021.08.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/25/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
Mitochondrial disorders are often difficult to diagnose because of diverse clinical phenotypes. FGF-21 and GDF-15 are metabolic hormones and promising biomarkers for the diagnosis of these disorders. This study has systematically evaluated serum FGF-21 and GDF-15 levels by ELISA in a well-defined cohort of patients with definite mitochondrial disorders (n = 30), neuromuscular disease controls (n = 36) and healthy controls (n = 36) and aimed to ascertain their utility in the diagnosis of mitochondrial disorders. Both serum FGF-21 and GDF-15 were significantly elevated in patients with mitochondrial disorders, especially in those with muscle involvement. The levels were higher in patients with mitochondrial deletions (both single and multiple) and translation disorders compared to respiratory chain subunit or assembly factor defects.
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Affiliation(s)
- Akshata Huddar
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Periyasamy Govindaraj
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Neuromuscular Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, India
| | - Shwetha Chiplunkar
- Neuromuscular Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Clinical Neurosciences, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Sekar Deepha
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Neuromuscular Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - J N Jessiena Ponmalar
- Neuromuscular Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Mariyamma Philip
- Biostatistics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Madhu Nagappa
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Neuromuscular Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Gayathri Narayanappa
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Neuromuscular Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Anita Mahadevan
- Department of Neuropathology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Neuromuscular Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Sanjib Sinha
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Arun B Taly
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Neuromuscular Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Bindu Parayil Sankaran
- Department of Neurology, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; Neuromuscular Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India; The Children's Hospital at Westmead Clinical School, Sydney Medical School, The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
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46
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Kishita Y, Shimura M, Kohda M, Fushimi T, Nitta KR, Yatsuka Y, Hirose S, Ideguchi H, Ohtake A, Murayama K, Okazaki Y. Genome sequencing and RNA-seq analyses of mitochondrial complex I deficiency revealed Alu insertion-mediated deletion in NDUFV2. Hum Mutat 2021; 42:1422-1428. [PMID: 34405929 DOI: 10.1002/humu.24274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/25/2021] [Accepted: 07/15/2021] [Indexed: 11/08/2022]
Abstract
Isolated complex I deficiency is the most common cause of pediatric mitochondrial disease. Exome sequencing (ES) has revealed many complex I causative genes. However, there are limitations associated with identifying causative genes by ES analysis. In this study, we performed multiomics analysis to reveal the causal variants. We here report two cases with mitochondrial complex I deficiency. In both cases, ES identified a novel c.580G>A (p.Glu194Lys) variant in NDUFV2. One case additionally harbored c.427C>T (p.Arg143*), but no other variants were observed in the other case. RNA sequencing showed aberrant exon splicing of NDUFV2 in the unsolved case. Genome sequencing revealed a novel heterozygous deletion in NDUFV2, which included one exon and resulted in exon skipping. Detailed examination of the breakpoint revealed that an Alu insertion-mediated rearrangement caused the deletion. Our report reveals that combined use of transcriptome sequencing and GS was effective for diagnosing cases that were unresolved by ES.
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Affiliation(s)
- Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Life Science, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Masaru Shimura
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Masakazu Kohda
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Takuya Fushimi
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Kazuhiro R Nitta
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yukiko Yatsuka
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Shinichi Hirose
- General Medical Research Center, School of Medicine, Fukuoka University, Fukuoka, Japan
| | - Hiroshi Ideguchi
- Department of Pediatrics, Fukuoka Sanno Hospital, Fukuoka, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Saitama, Japan.,Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - Kei Murayama
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Department of Metabolism, Chiba Children's Hospital, Chiba, Japan.,Center for Medical Genetics, Chiba Children's Hospital, Chiba, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan.,Laboratory for Comprehensive Genomic Analysis, RIKEN Centre for Integrative Medical Sciences, Kanagawa, Japan
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47
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The Diagnostic Approach to Mitochondrial Disorders in Children in the Era of Next-Generation Sequencing: A 4-Year Cohort Study. J Clin Med 2021; 10:jcm10153222. [PMID: 34362006 PMCID: PMC8348083 DOI: 10.3390/jcm10153222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/08/2021] [Accepted: 07/20/2021] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial diseases (MDs) are a large group of genetically determined multisystem disorders, characterized by extreme phenotypic heterogeneity, attributable in part to the dual genomic control (nuclear and mitochondrial DNA) of the mitochondrial proteome. Advances in next-generation sequencing technologies over the past two decades have presented clinicians with a challenge: to select the candidate disease-causing variants among the huge number of data provided. Unfortunately, the clinical tools available to support genetic interpretations still lack specificity and sensitivity. For this reason, the diagnosis of MDs continues to be difficult, with the new “genotype first” approach still failing to diagnose a large group of patients. With the aim of investigating possible relationships between clinical and/or biochemical phenotypes and definitive molecular diagnoses, we performed a retrospective multicenter study of 111 pediatric patients with clinical suspicion of MD. In this cohort, the strongest predictor of a molecular (in particular an mtDNA-related) diagnosis of MD was neuroimaging evidence of basal ganglia (BG) involvement. Regression analysis confirmed that normal BG imaging predicted negative genetic studies for MD. Psychomotor regression was confirmed as an independent predictor of a definitive diagnosis of MD. The findings of this study corroborate previous data supporting a role for neuroimaging in the diagnostic approach to MDs and reinforce the idea that mtDNA sequencing should be considered for first-line testing, at least in specific groups of children.
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48
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Zweers H, van Wegberg AMJ, Janssen MCH, Wortmann SB. Ketogenic diet for mitochondrial disease: a systematic review on efficacy and safety. Orphanet J Rare Dis 2021; 16:295. [PMID: 34217336 PMCID: PMC8254320 DOI: 10.1186/s13023-021-01927-w] [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: 03/25/2021] [Accepted: 06/13/2021] [Indexed: 12/01/2022] Open
Abstract
Background No curative therapy for mitochondrial disease (MD) exists, prioritizing supportive treatment for symptom relief. In animal and cell models ketones decrease oxidative stress, increase antioxidants and scavenge free radicals, putting ketogenic diets (KDs) on the list of management options for MD. Furthermore, KDs are well-known, safe and effective treatments for epilepsy, a frequent symptom of MD. This systematic review evaluates efficacy and safety of KD for MD. Methods We searched Pubmed, Cochrane, Embase and Cinahl (November 2020) with search terms linked to MD and KD. From the identified records, we excluded studies on Pyruvate Dehydrogenase Complex deficiency. From these eligible reports, cases without a genetically confirmed diagnosis and cases without sufficient data on KD and clinical course were excluded. The remaining studies were included in the qualitative analysis. Results Only 20 cases (14 pediatric) from the 694 papers identified met the inclusion criteria (one controlled trial (n = 5), 15 case reports). KD led to seizure control in 7 out of 8 cases and improved muscular symptoms in 3 of 10 individuals. In 4 of 20 cases KD reversed the clinical phenotype (e.g. cardiomyopathy, movement disorder). In 5 adults with mitochondrial DNA deletion(s) related myopathy rhabdomyolysis led to cessation of KD. Three individuals with POLG mutations died while being on KD, however, their survival was not different compared to individuals with POLG mutations without KD. Conclusion Data on efficacy and safety of KD for MD is too scarce for general recommendations. KD should be considered in individuals with MD and therapy refractory epilepsy, while KD is contraindicated in mitochondrial DNA deletion(s) related myopathy. When considering KD for MD the high rate of adverse effects should be taken into account, but also spectacular improvements in individual cases. KD is a highly individual management option in this fragile patient group and requires an experienced team. To increase knowledge on this—individually—promising management option more (prospective) studies using adequate outcome measures are crucial. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01927-w.
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Affiliation(s)
- Heidi Zweers
- Department of Gastroenterology and Hepatology - Dietetics, Radboudumc, Postbus 9101, 6500 HB, Nijmegen, The Netherlands. .,Radboud Center for Mitochondrial Medicine (RCMM), Amalia Children's Hospital, Radboudumc, Nijmegen, The Netherlands.
| | - Annemiek M J van Wegberg
- Department of Gastroenterology and Hepatology - Dietetics, Radboudumc, Postbus 9101, 6500 HB, Nijmegen, The Netherlands.,Radboud Center for Mitochondrial Medicine (RCMM), Amalia Children's Hospital, Radboudumc, Nijmegen, The Netherlands
| | - Mirian C H Janssen
- Radboud Center for Mitochondrial Medicine (RCMM), Amalia Children's Hospital, Radboudumc, Nijmegen, The Netherlands.,Department of Internal Medicine, Radboudumc, Nijmegen, The Netherlands
| | - Saskia B Wortmann
- Radboud Center for Mitochondrial Medicine (RCMM), Amalia Children's Hospital, Radboudumc, Nijmegen, The Netherlands.,University Children's Hospital, Paracelsus Medical University, Salzburg, Austria
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49
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Kwong AK, Wong SS, Rodenburg RJT, Smeitink J, Chan GCF, Fung C. Human d-lactate dehydrogenase deficiency by LDHD mutation in a patient with neurological manifestations and mitochondrial complex IV deficiency. JIMD Rep 2021; 60:15-22. [PMID: 34258137 PMCID: PMC8260477 DOI: 10.1002/jmd2.12220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/18/2021] [Accepted: 04/06/2021] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND d-lactate, one of the isomers of lactate, exists in a low concentration in healthy individuals and it can be oxidized to pyruvate catalyzed by d-lactate dehydrogenase. Excessive amount of d-lactate causes d-lactate acidosis associated with neurological manifestations. METHODS AND RESULTS We report here a patient with developmental delay, cerebellar ataxia, and transient hepatomegaly. Enzyme analysis in the patient's skin fibroblast showed decreased mitochondrial complex IV activity. Using whole exome sequencing, we identified compound heterozygous variants in the LDHD gene, which encodes the d-lactate dehydrogenase, consisting of a splice site variant c.469+1dupG and a missense variant c.752C>T, p.(Thr251Met) which are pathogenic and likely pathogenic respectively according to the American College of Medical Genetics and Genomics (ACMG) classification. The serum d-lactate level was subsequently detected to be elevated (0.61 mmol/L, reference value: 0-0.25 mmol/L). CONCLUSION This is the third report on LDHD mutations associated with d-lactate elevation and was first reported to have decreased mitochondrial complex IV activity. The study provides more information on this rare metabolic condition but the association of LDHD deficiency with the clinical presentations requires further investigations.
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Affiliation(s)
- Anna Ka‐Yee Kwong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
| | - Sheila Suet‐Na Wong
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
- Department of Paediatrics and Adolescent MedicineHong Kong Children's HospitalHong Kong SARChina
| | - Richard J. T. Rodenburg
- Radboud Centre for Mitochondrial Medicine, Department of PaediatricsRadboud Institute for Molecular Life Sciences, Radboud University Nijmegen Medical CentreNijmegenThe Netherlands
| | - Jan Smeitink
- Radboud Centre for Mitochondrial Medicine, Department of PaediatricsRadboud Institute for Molecular Life Sciences, Radboud University Nijmegen Medical CentreNijmegenThe Netherlands
| | - Godfrey Chi Fung Chan
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
- Department of Paediatrics and Adolescent MedicineHong Kong Children's HospitalHong Kong SARChina
| | - Cheuk‐Wing Fung
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of MedicineThe University of Hong KongHong Kong SARChina
- Department of Paediatrics and Adolescent MedicineHong Kong Children's HospitalHong Kong SARChina
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50
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Shen L, McCormick EM, Muraresku CC, Falk MJ, Gai X. Clinical Bioinformatics in Precise Diagnosis of Mitochondrial Disease. Clin Lab Med 2021; 40:149-161. [PMID: 32439066 DOI: 10.1016/j.cll.2020.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Clinical bioinformatics system is well-established for diagnosing genetic disease based on next-generation sequencing, but requires special considerations when being adapted for the next-generation sequencing-based genetic diagnosis of mitochondrial diseases. Challenges are caused by the involvement of mitochondrial DNA genome in disease etiology. Heteroplasmy and haplogroup are key factors in interpreting mitochondrial DNA variant effects. Data resources and tools for analyzing variant and sequencing data are available at MSeqDR, MitoMap, and HmtDB. Revised specifications of the American College of Medical Genetics/Association of Molecular Pathology standards and guidelines for mitochondrial DNA variant interpretation are proposed by the MSeqDr Consortium and community experts.
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Affiliation(s)
- Lishuang Shen
- Keck School of Medicine of USC, Center for Personalized Medicine, Children's Hospital Los Angeles, Suite 300, 2100 West 3rd Street, Los Angeles, CA 90057, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Colleen Clarke Muraresku
- Mitochondrial Medicine Frontier Program, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Marni J Falk
- CHOP Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, The Children's Hospital of Philadelphia, ARC 1002c, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Xiaowu Gai
- Keck School of Medicine of USC, Center for Personalized Medicine, Children's Hospital Los Angeles, Suite 300, 2100 West 3rd Street, Los Angeles, CA 90057, USA.
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