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Zhang X, Zhang G, Cao L, Zhou W, Tan C, Ma S, Yang J. Two novel SUCLA2 variants cause mitochondrial DNA depletion syndrome, type 5 in two siblings. Front Neurol 2024; 15:1394150. [PMID: 39070054 PMCID: PMC11273780 DOI: 10.3389/fneur.2024.1394150] [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: 03/01/2024] [Accepted: 07/03/2024] [Indexed: 07/30/2024] Open
Abstract
Mitochondrial DNA depletion syndrome (MDS), characterized by succinate-CoA ligase deficiency and loss of mitochondrial DNA (mtDNA), is caused by specific variants in nuclear genes responsible for mtDNA maintenance. SUCLA2-related mitochondrial DNA depletion syndrome, type 5 (MTDPS-5), presents as a rare, severe early progressive encephalomyopathy. This report investigates a new family exhibiting clinical manifestations of MTDPS-5 and elucidates the genetic basis of this disorder. In two affected siblings, a novel maternally inherited nonsense variant [c.1234C>T (p.Arg412*)] in the SUCLA2 gene and a unique paternally inherited indel variant (g.48569263-48571020del1758insATGA) were identified. Additionally, the siblings exhibited blood mtDNA content lower than 33% compared to age-matched controls. These findings underscore the importance of assessing SUCLA2 variants in patients with severe early progressive encephalomyopathy, even in the absence of methylmalonic aciduria or mtDNA loss, thereby broaden the mutational spectrum of this gene.
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Affiliation(s)
- Xiaohuan Zhang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center of Medical Genetics, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, China
| | - Guo Zhang
- Dean’s Office, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Li Cao
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center of Medical Genetics, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, China
| | - Wenjing Zhou
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center of Medical Genetics, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, China
| | - Chang Tan
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center of Medical Genetics, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, China
| | - Shi Ma
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center of Medical Genetics, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, China
| | - Jiyun Yang
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Center of Medical Genetics, Sichuan Provincial People’s Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Research Unit for Blindness Prevention of Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences, Chengdu, China
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Lancaster MS, Graham BH. Succinyl-CoA Synthetase Dysfunction as a Mechanism of Mitochondrial Encephalomyopathy: More than Just an Oxidative Energy Deficit. Int J Mol Sci 2023; 24:10725. [PMID: 37445899 PMCID: PMC10342173 DOI: 10.3390/ijms241310725] [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: 05/12/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023] Open
Abstract
Biallelic pathogenic variants in subunits of succinyl-CoA synthetase (SCS), a tricarboxylic acid (TCA) cycle enzyme, are associated with mitochondrial encephalomyopathy in humans. SCS catalyzes the interconversion of succinyl-CoA to succinate, coupled to substrate-level phosphorylation of either ADP or GDP, within the TCA cycle. SCS-deficient encephalomyopathy typically presents in infancy and early childhood, with many patients succumbing to the disease during childhood. Common symptoms include abnormal brain MRI, basal ganglia lesions and cerebral atrophy, severe hypotonia, dystonia, progressive psychomotor regression, and growth deficits. Although subunits of SCS were first identified as causal genes for progressive metabolic encephalomyopathy in the early 2000s, recent investigations are now beginning to unravel the pathomechanisms underlying this metabolic disorder. This article reviews the current understanding of SCS function within and outside the TCA cycle as it relates to the complex and multifactorial mechanisms underlying SCS-related mitochondrial encephalomyopathy.
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Affiliation(s)
| | - Brett H. Graham
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, 975 W. Walnut St., Room IB257, Indianapolis, IN 46202, USA;
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3
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Linn P, Kohno S, Sheng J, Kulathunga N, Yu H, Zhang Z, Voon D, Watanabe Y, Takahashi C. Targeting RB1 Loss in Cancers. Cancers (Basel) 2021; 13:cancers13153737. [PMID: 34359636 PMCID: PMC8345210 DOI: 10.3390/cancers13153737] [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: 05/18/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Irreversible defects in RB1 tumor suppressor functions often predict poor outcomes in cancer patients. However, the RB1-defecient status can be a benefit as well for them, as it generates a variety of vulnerabilities induced through the upregulation of RB1 targets, relief from functional restrictions due to RB1 binding, presence of genes whose inactivation cause synthetic lethality with RB1 loss, or collateral synthetic lethality owing to simultaneous loss of neighboring genes. Abstract Retinoblastoma protein 1 (RB1) is encoded by a tumor suppressor gene that was discovered more than 30 years ago. Almost all mitogenic signals promote cell cycle progression by braking on the function of RB1 protein through mono- and subsequent hyper-phosphorylation mediated by cyclin-CDK complexes. The loss of RB1 function drives tumorigenesis in limited types of malignancies including retinoblastoma and small cell lung cancer. In a majority of human cancers, RB1 function is suppressed during tumor progression through various mechanisms. The latter gives rise to the acquisition of various phenotypes that confer malignant progression. The RB1-targeted molecules involved in such phenotypic changes are good quarries for cancer therapy. Indeed, a variety of novel therapies have been proposed to target RB1 loss. In particular, the inhibition of a number of mitotic kinases appeared to be synthetic lethal with RB1 deficiency. A recent study focusing on a neighboring gene that is often collaterally deleted together with RB1 revealed a pharmacologically targetable vulnerability in RB1-deficient cancers. Here we summarize current understanding on possible therapeutic approaches targeting functional or genomic aberration of RB1 in cancers.
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Affiliation(s)
- Paing Linn
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
- Yangon General Hospital, Yangon, Myanmar
| | - Susumu Kohno
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
| | - Jindan Sheng
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
| | - Nilakshi Kulathunga
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
| | - Hai Yu
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
| | - Zhiheng Zhang
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
| | - Dominic Voon
- Institute of Frontier Sciences Initiative, Kanazawa University, Kanazawa 920-1192, Japan;
| | | | - Chiaki Takahashi
- Division of Oncology and Molecular Biology, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan; (P.L.); (S.K.); (J.S.); (N.K.); (H.Y.); (Z.Z.)
- Correspondence: ; Tel.: +81-76-264-6750; Fax: +81-76-234-4521
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Alkhater RA, Ahonen S, Minassian BA. SUCLA2 Arg407Trp mutation can cause a nonprogressive movement disorder - deafness syndrome. Ann Clin Transl Neurol 2020; 8:252-258. [PMID: 33231368 PMCID: PMC7818133 DOI: 10.1002/acn3.51247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/04/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022] Open
Abstract
SUCLA2 is a component of mitochondrial succinate‐CoA ligase and nucleotide diphosphokinase activities. Its absence results in Krebs cycle failure, mitochondrial DNA depletion, and a childhood‐fatal encephalomyopathy. We describe a purely neurologic allelic form of the disease consisting of deafness, putamenal hyperintensity on MRI and a myoclonic‐dystonic movement disorder unchanging from childhood into, so far, the late fourth decade. We show that succinate supplementation circumvents the Krebs cycle block, but does not correct the neurologic disease. Our patients’ Arg407Trp mutation has been reported in children with (yet) no MRI abnormalities. It remains possible that early succinate supplementation could impact the disease.
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Affiliation(s)
- Reem A. Alkhater
- Program in Genetics and Genome BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
- Institute of Medical SciencesUniversity of TorontoTorontoOntarioCanada
- Johns’ Hopkins Aramco HealthcareDhahranSaudi Arabia
| | - Saija Ahonen
- Program in Genetics and Genome BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
| | - Berge A. Minassian
- Program in Genetics and Genome BiologyThe Hospital for Sick ChildrenTorontoOntarioCanada
- Institute of Medical SciencesUniversity of TorontoTorontoOntarioCanada
- Division of NeurologyDepartment of PediatricsUniversity of Texas SouthwesternDallasTexasUSA
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SUCLA2 mutations cause global protein succinylation contributing to the pathomechanism of a hereditary mitochondrial disease. Nat Commun 2020; 11:5927. [PMID: 33230181 PMCID: PMC7684291 DOI: 10.1038/s41467-020-19743-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 10/26/2020] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial acyl-coenzyme A species are emerging as important sources of protein modification and damage. Succinyl-CoA ligase (SCL) deficiency causes a mitochondrial encephalomyopathy of unknown pathomechanism. Here, we show that succinyl-CoA accumulates in cells derived from patients with recessive mutations in the tricarboxylic acid cycle (TCA) gene succinyl-CoA ligase subunit-β (SUCLA2), causing global protein hyper-succinylation. Using mass spectrometry, we quantify nearly 1,000 protein succinylation sites on 366 proteins from patient-derived fibroblasts and myotubes. Interestingly, hyper-succinylated proteins are distributed across cellular compartments, and many are known targets of the (NAD+)-dependent desuccinylase SIRT5. To test the contribution of hyper-succinylation to disease progression, we develop a zebrafish model of the SCL deficiency and find that SIRT5 gain-of-function reduces global protein succinylation and improves survival. Thus, increased succinyl-CoA levels contribute to the pathology of SCL deficiency through post-translational modifications. The pathomechanism of succinyl-CoA ligase (SCL) deficiency, a hereditary mitochondrial disease, is not fully understood. Here, the authors show that increased succinyl-CoA levels contribute to SCL pathology by causing global protein hyper-succinylation.
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Pharmacologically targetable vulnerability in prostate cancer carrying RB1-SUCLA2 deletion. Oncogene 2020; 39:5690-5707. [PMID: 32694611 DOI: 10.1038/s41388-020-1381-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/09/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
Abstract
RB1 gene is often homozygously deleted or mutated in prostate adenocarcinomas following acquirement of castration resistance and/or metastatic ability. We found that SUCLA2 gene is frequently involved in the deletion of the RB1 gene region in advanced prostate cancer. SUCLA2 constitutes the β-subunit of succinate CoA ligase heterodimer that reversibly converts succinyl CoA into succinate. We sought the possibility that deletion of SUCLA2 gives rise to a metabolic vulnerability that could be targeted therapeutically. We found a significant metabolic shift in SUCLA2-deleted prostate cancer cells, including lower mitochondrial respiratory activity. By screening a number of libraries for compounds that induce cell death selectively in SUCLA2-deficient prostate cancer cells, we identified thymoquinone (2-isopropyl-5-methylbenzo-1,4-quinone) and PMA (phorbol-12-myristate-13-acetate) from a natural compound library. These findings indicate that the metabolic vulnerability in SUCLA2-deficient prostate cancer cells is pharmacologically targetable.
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7
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Burgevin M, Lacroix A, Brown G, Mikaty M, Coutinho V, Netchine I, Odent S. Intellectual functioning in Silver-Russell syndrome: First study in adults. APPLIED NEUROPSYCHOLOGY-ADULT 2019; 28:391-402. [PMID: 31390893 DOI: 10.1080/23279095.2019.1644643] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Silver-Russell syndrome (SRS) is a rare genetic disorder (estimated incidence 1/30,000 to 100,000 live births). So far, only a few studies have focused on the cognitive profile of individuals with SRS, and these were conducted some time ago, concentrated on pediatric cohorts, and included patients who had been diagnosed using a variety of clinical diagnostic systems. There has yet to be any research on the intellectual functioning of adults with SRS. This study sought to establish the intelligence, strengths and weaknesses within intellectual profile of adults with SRS, compared with normative data. Ten individuals with 11p15 epimutation aged 18-39 years completed the Wechsler Adult Intelligence Scale-Fourth Edition. Measures of interest included participants' intelligence (Full Scale Intelligence Quotient [FSIQ]) and four domains of cognitive functioning: verbal comprehension, perceptual reasoning, working memory and processing speed. Discrepancy scores were calculated, and descriptive statistical and linear correlations were used to investigate factors associated with IQ outcome. Clinical and medical information such as rehabilitation, and perceived difficulties in daily life were collected by interviews and questionnaires. Results showed that the mean FSIQ score was in the average range (M = 95.40, SD = 18.55) and they performed best on verbal comprehension. Frequent daily difficulties were reported by patients and/or their families: learning disabilities and low self-esteem were perceived by 60% of adults. Early intervention and multidisciplinary care from childhood to adulthood are important in SRS for care potential medical, cognitive and psychosocial problems. This is the first study to document the intellectual functioning of adults with SRS.
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Affiliation(s)
- Mélissa Burgevin
- Univ Rennes, LP3C (Laboratoire de Psychologie: Cognition, Comportement, Communication), EA 1285, F-35000 Rennes, France
| | - Agnès Lacroix
- Univ Rennes, LP3C (Laboratoire de Psychologie: Cognition, Comportement, Communication), EA 1285, F-35000 Rennes, France
| | - Genavee Brown
- Univ Rennes, LP3C (Laboratoire de Psychologie: Cognition, Comportement, Communication), EA 1285, F-35000 Rennes, France
| | - Myriam Mikaty
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU de Rennes, Rennes, France
| | - Virginie Coutinho
- Service de Neuropédiatrie, Hôpital Armand Trousseau, Paris, France.,Centre de Recherche en Épidémiologie et Santé Des Populations, Inserm, Villejuif, France
| | - Irène Netchine
- Sorbonne Universités, Inserm, UMR S 938, Centre de Recherche Saint Antoine, Hôpital Armand Trousseau, Explorations Fonctionnelles Endocriniennes, Paris, France
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de Référence Maladies Rares CLAD-Ouest, CHU de Rennes, Rennes, France.,Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000 Rennes, France
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Abstract
OBJECTIVES Because the central nervous system (CNS) is the second most frequently affected organ in mitochondrial disorders (MIDs) and since paediatric MIDs are increasingly recognised, it is important to know about the morphological CNS abnormalities on imaging in these patients. This review aims at summarising and discussing current knowledge and recent advances concerning CNS imaging abnormalities in paediatric MIDs. METHODS A systematic literature review was conducted. RESULTS The most relevant CNS abnormalities in paediatric MIDs on imaging include white and grey matter lesions, stroke-like lesions as the morphological equivalent of stroke-like episodes, cerebral atrophy, calcifications, optic atrophy, and lactacidosis. Because these CNS lesions may be seen with or without clinical manifestations, it is important to screen all MID patients for cerebral involvement. Some of these lesions may remain unchanged for years whereas others may be dynamic, either in the sense of progression or regression. Typical dynamic lesions are stroke-like lesions and grey matter lesions. Clinically relevant imaging techniques for visualisation of CNS abnormalities in paediatric MIDs are computed tomography, magnetic resonance (MR) imaging, MR spectroscopy, single-photon emission computed tomography, positron-emission tomography, and angiography. CONCLUSIONS CNS imaging in paediatric MIDs is important for diagnosing and monitoring CNS involvement. It also contributes to the understanding of the underlying pathomechanisms that lead to CNS involvement in MIDs.
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Affiliation(s)
| | - Sinda Zarrouk-Mahjoub
- University of Tunis, El Manar and Genomics Platform, Pasteur Institute of Tunis, Tunisia
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Brasil S, Leal F, Vega A, Navarrete R, Ecay MJ, Desviat LR, Riera C, Padilla N, de la Cruz X, Couce ML, Martin-Hernández E, Morais A, Pedrón C, Peña-Quintana L, Rigoldi M, Specola N, de Almeida IT, Vives I, Yahyaoui R, Rodríguez-Pombo P, Ugarte M, Pérez-Cerda C, Merinero B, Pérez B. Improving the diagnosis of cobalamin and related defects by genomic analysis, plus functional and structural assessment of novel variants. Orphanet J Rare Dis 2018; 13:125. [PMID: 30041674 PMCID: PMC6057060 DOI: 10.1186/s13023-018-0862-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/29/2018] [Indexed: 12/04/2022] Open
Abstract
Background Cellular cobalamin defects are a locus and allelic heterogeneous disorder. The gold standard for coming to genetic diagnoses of cobalamin defects has for some time been gene-by-gene Sanger sequencing of individual DNA fragments. Enzymatic and cellular methods are employed before such sequencing to help in the selection of the gene defects to be sought, but this is time-consuming and laborious. Furthermore some cases remain undiagnosed because no biochemical methods have been available to test for cobalamin absorption and transport defects. Results This paper reports the use of massive parallel sequencing of DNA (exome analysis) for the accurate and rapid genetic diagnosis of cobalamin-related defects in a cohort of affected patients. The method was first validated in an initial cohort with different cobalamin defects. Mendelian segregation, the frequency of mutations, and the comprehensive structural and functional analysis of gene variants, identified disease-causing mutations in 12 genes involved in the absorption and synthesis of active cofactors of vitamin B12 (22 cases), and in the non-cobalamin metabolism-related genes ACSF3 (in four biochemically misdiagnosed patients) and SUCLA2 (in one patient with an unusual presentation). We have identified thirteen new variants all classified as pathogenic according to the ACGM recommendation but four were classified as variant likely pathogenic in MUT and SUCLA2. Functional and structural analysis provided evidences to classify them as pathogenic variants. Conclusions The present findings suggest that the technology used is sufficiently sensitive and specific, and the results it provides sufficiently reproducible, to recommend its use as a second-tier test after the biochemical detection of cobalamin disorder markers in the first days of life. However, for accurate diagnoses to be made, biochemical and functional tests that allow comprehensive clinical phenotyping are also needed. Electronic supplementary material The online version of this article (10.1186/s13023-018-0862-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandra Brasil
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Fátima Leal
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Ana Vega
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Rosa Navarrete
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - María Jesús Ecay
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Lourdes R Desviat
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Casandra Riera
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Natàlia Padilla
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier de la Cruz
- Grupo de Bioinformática Translacional Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,ICREA, Barcelona, Spain
| | - Mari Luz Couce
- Hospital Clínico Universitario de Santiago, Santiago de Compostela, CIBERER, Santiago de Compostela, Spain
| | | | - Ana Morais
- Hospital Universitario La Paz, Madrid, Spain
| | | | - Luis Peña-Quintana
- Hospital Universitario Materno Infantil, CIBEROBN, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Spain
| | - Miriam Rigoldi
- Center for Rare Disorders, ASST- Monza, Ospedale San Gerardo, Monza, Italy
| | - Norma Specola
- Unidad de Metabolismo Hospital de Niños de La Plata, La Plata, Argentina
| | | | | | - Raquel Yahyaoui
- Hospital Universitario Regional de Málaga, Instituto de Investigación Biomédica de Málaga (IBIMA), Málaga, Spain
| | - Pilar Rodríguez-Pombo
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Magdalena Ugarte
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Celia Pérez-Cerda
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Begoña Merinero
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain
| | - Belén Pérez
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular, Universidad Autónoma de Madrid, CIBERER, IdiPAZ, Madrid, Spain.
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Couser NL, Marchuk DS, Smith LD, Arreola A, Kaiser-Rogers KA, Muenzer J, Pandya A, Gucsavas-Calikoglu M, Powell CM. Co-occurring Down syndrome and SUCLA2-related mitochondrial depletion syndrome. Am J Med Genet A 2017; 173:2720-2724. [PMID: 28749033 DOI: 10.1002/ajmg.a.38351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/09/2017] [Accepted: 06/14/2017] [Indexed: 01/23/2023]
Abstract
Mitochondrial DNA depletion syndrome 5 (MIM 612073) is a rare autosomal recessive disorder caused by homozygous or compound heterozygous pathogenic variants in the beta subunit of the succinate-CoA ligase gene located within the 13q14 band. We describe two siblings of Hispanic descent with SUCLA2-related mitochondrial depletion syndrome (encephalomyopathic form with methylmalonic aciduria); the older sibling is additionally affected with trisomy 21. SUCLA2 sequencing identified homozygous p.Arg284Cys pathogenic variants in both patients. This mutation has previously been identified in four individuals of Italian and Caucasian descent. The older sibling with concomitant disease has a more severe phenotype than what is typically described in patients with either SUCLA2-related mitochondrial depletion syndrome or Down syndrome alone. The younger sibling, who has a normal female chromosome complement, is significantly less affected compared to her brother. While the clinical and molecular findings have been reported in about 50 patients affected with a deficiency of succinate-CoA ligase caused by pathogenic variants in SUCLA2, this report describes the first known individual affected with both a mitochondrial depletion syndrome and trisomy 21.
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Affiliation(s)
- Natario L Couser
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Ophthalmology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Daniel S Marchuk
- University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Laurie D Smith
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Alexandra Arreola
- Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Kathleen A Kaiser-Rogers
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Pathology & Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Joseph Muenzer
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Arti Pandya
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Muge Gucsavas-Calikoglu
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Cynthia M Powell
- Department of Pediatrics, Division of Genetics and Metabolism, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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11
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Huang X, Bedoyan JK, Demirbas D, Harris DJ, Miron A, Edelheit S, Grahame G, DeBrosse SD, Wong LJ, Hoppel CL, Kerr DS, Anselm I, Berry GT. Succinyl-CoA synthetase (SUCLA2) deficiency in two siblings with impaired activity of other mitochondrial oxidative enzymes in skeletal muscle without mitochondrial DNA depletion. Mol Genet Metab 2017; 120:213-222. [PMID: 27913098 PMCID: PMC5346465 DOI: 10.1016/j.ymgme.2016.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/09/2016] [Accepted: 11/10/2016] [Indexed: 12/18/2022]
Abstract
Mutations in SUCLA2 result in succinyl-CoA ligase (ATP-forming) or succinyl-CoA synthetase (ADP-forming) (A-SCS) deficiency, a mitochondrial tricarboxylic acid cycle disorder. The phenotype associated with this gene defect is largely encephalomyopathy. We describe two siblings compound heterozygous for SUCLA2 mutations, c.985A>G (p.M329V) and c.920C>T (p.A307V), with parents confirmed as carriers of each mutation. We developed a new LC-MS/MS based enzyme assay to demonstrate the decreased SCS activity in the siblings with this unique genotype. Both siblings shared bilateral progressive hearing loss, encephalopathy, global developmental delay, generalized myopathy, and dystonia with choreoathetosis. Prior to diagnosis and because of lactic acidosis and low activity of muscle pyruvate dehydrogenase complex (PDC), sibling 1 (S1) was placed on dichloroacetate, while sibling 2 (S2) was on a ketogenic diet. S1 developed severe cyclic vomiting refractory to therapy, while S2 developed Leigh syndrome, severe GI dysmotility, intermittent anemia, hypogammaglobulinemia and eventually succumbed to his disorder. The mitochondrial DNA contents in skeletal muscle (SM) were normal in both siblings. Pyruvate dehydrogenase complex, ketoglutarate dehydrogenase complex, and several mitochondrial electron transport chain (ETC) activities were low or at the low end of the reference range in frozen SM from S1 and/or S2. In contrast, activities of PDC, other mitochondrial enzymes of pyruvate metabolism, ETC and, integrated oxidative phosphorylation, in skin fibroblasts were not significantly impaired. Although we show that propionyl-CoA inhibits PDC, it does not appear to account for decreased PDC activity in SM. A better understanding of the mechanisms of phenotypic variability and the etiology for tissue-specific secondary deficiencies of mitochondrial enzymes of oxidative metabolism, and independently mitochondrial DNA depletion (common in other cases of A-SCS deficiency), is needed given the implications for control of lactic acidosis and possible clinical management.
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Affiliation(s)
- Xiaoping Huang
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - Jirair K Bedoyan
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA; Center for Inherited Disorders of Energy Metabolism (CIDEM), University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Department of Pediatrics, Case Western Reserve University, Cleveland, OH, USA
| | - Didem Demirbas
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA
| | - David J Harris
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Alexander Miron
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Simone Edelheit
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - George Grahame
- Center for Inherited Disorders of Energy Metabolism (CIDEM), University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Suzanne D DeBrosse
- Center for Human Genetics, University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA; Department of Pediatrics, Case Western Reserve University, Cleveland, OH, USA
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Charles L Hoppel
- Center for Inherited Disorders of Energy Metabolism (CIDEM), University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Department of Pharmacology, Case Western Reserve University, Cleveland, OH, USA; Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Douglas S Kerr
- Center for Inherited Disorders of Energy Metabolism (CIDEM), University Hospitals Cleveland Medical Center, Cleveland, OH, USA; Department of Pediatrics, Case Western Reserve University, Cleveland, OH, USA
| | - Irina Anselm
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Gerard T Berry
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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12
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Winkler EC, Wiemann S. Findings made in gene panel to whole genome sequencing: data, knowledge, ethics – and consequences? Expert Rev Mol Diagn 2016; 16:1259-1270. [DOI: 10.1080/14737159.2016.1212662] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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13
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Two transgenic mouse models for β-subunit components of succinate-CoA ligase yielding pleiotropic metabolic alterations. Biochem J 2016; 473:3463-3485. [PMID: 27496549 PMCID: PMC5126846 DOI: 10.1042/bcj20160594] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/05/2016] [Indexed: 12/14/2022]
Abstract
Succinate-CoA ligase (SUCL) is a heterodimer enzyme composed of Suclg1 α-subunit and a substrate-specific Sucla2 or Suclg2 β-subunit yielding ATP or GTP, respectively. In humans, the deficiency of this enzyme leads to encephalomyopathy with or without methylmalonyl aciduria, in addition to resulting in mitochondrial DNA depletion. We generated mice lacking either one Sucla2 or Suclg2 allele. Sucla2 heterozygote mice exhibited tissue- and age-dependent decreases in Sucla2 expression associated with decreases in ATP-forming activity, but rebound increases in cardiac Suclg2 expression and GTP-forming activity. Bioenergetic parameters including substrate-level phosphorylation (SLP) were not different between wild-type and Sucla2 heterozygote mice unless a submaximal pharmacological inhibition of SUCL was concomitantly present. mtDNA contents were moderately decreased, but blood carnitine esters were significantly elevated. Suclg2 heterozygote mice exhibited decreases in Suclg2 expression but no rebound increases in Sucla2 expression or changes in bioenergetic parameters. Surprisingly, deletion of one Suclg2 allele in Sucla2 heterozygote mice still led to a rebound but protracted increase in Suclg2 expression, yielding double heterozygote mice with no alterations in GTP-forming activity or SLP, but more pronounced changes in mtDNA content and blood carnitine esters, and an increase in succinate dehydrogenase activity. We conclude that a partial reduction in Sucla2 elicits rebound increases in Suclg2 expression, which is sufficiently dominant to overcome even a concomitant deletion of one Suclg2 allele, pleiotropically affecting metabolic pathways associated with SUCL. These results as well as the availability of the transgenic mouse colonies will be of value in understanding SUCL deficiency.
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14
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Carrozzo R, Verrigni D, Rasmussen M, de Coo R, Amartino H, Bianchi M, Buhas D, Mesli S, Naess K, Born AP, Woldseth B, Prontera P, Batbayli M, Ravn K, Joensen F, Cordelli DM, Santorelli FM, Tulinius M, Darin N, Duno M, Jouvencel P, Burlina A, Stangoni G, Bertini E, Redonnet-Vernhet I, Wibrand F, Dionisi-Vici C, Uusimaa J, Vieira P, Osorio AN, McFarland R, Taylor RW, Holme E, Ostergaard E. Succinate-CoA ligase deficiency due to mutations in SUCLA2 and SUCLG1: phenotype and genotype correlations in 71 patients. J Inherit Metab Dis 2016; 39:243-52. [PMID: 26475597 DOI: 10.1007/s10545-015-9894-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/04/2015] [Accepted: 09/08/2015] [Indexed: 11/28/2022]
Abstract
BACKGROUND The encephalomyopathic mtDNA depletion syndrome with methylmalonic aciduria is associated with deficiency of succinate-CoA ligase, caused by mutations in SUCLA2 or SUCLG1. We report here 25 new patients with succinate-CoA ligase deficiency, and review the clinical and molecular findings in these and 46 previously reported patients. PATIENTS AND RESULTS Of the 71 patients, 50 had SUCLA2 mutations and 21 had SUCLG1 mutations. In the newly-reported 20 SUCLA2 patients we found 16 different mutations, of which nine were novel: two large gene deletions, a 1 bp duplication, two 1 bp deletions, a 3 bp insertion, a nonsense mutation and two missense mutations. In the newly-reported SUCLG1 patients, five missense mutations were identified, of which two were novel. The median onset of symptoms was two months for patients with SUCLA2 mutations and at birth for SUCLG1 patients. Median survival was 20 years for SUCLA2 and 20 months for SUCLG1. Notable clinical differences between the two groups were hepatopathy, found in 38% of SUCLG1 cases but not in SUCLA2 cases, and hypertrophic cardiomyopathy which was not reported in SUCLA2 patients, but documented in 14% of cases with SUCLG1 mutations. Long survival, to age 20 years or older, was reported in 12% of SUCLA2 and in 10% of SUCLG1 patients. The most frequent abnormality on neuroimaging was basal ganglia involvement, found in 69% of SUCLA2 and 80% of SUCLG1 patients. Analysis of respiratory chain enzyme activities in muscle generally showed a combined deficiency of complexes I and IV, but normal histological and biochemical findings in muscle did not preclude a diagnosis of succinate-CoA ligase deficiency. In five patients, the urinary excretion of methylmalonic acid was only marginally elevated, whereas elevated plasma methylmalonic acid was consistently found. CONCLUSIONS To our knowledge, this is the largest study of patients with SUCLA2 and SUCLG1 deficiency. The most important findings were a significantly longer survival in patients with SUCLA2 mutations compared to SUCLG1 mutations and a trend towards longer survival in patients with missense mutations compared to loss-of-function mutations. Hypertrophic cardiomyopathy and liver involvement was exclusively found in patients with SUCLG1 mutations, whereas epilepsy was much more frequent in patients with SUCLA2 mutations compared to patients with SUCLG1 mutations. The mutation analysis revealed a number of novel mutations, including a homozygous deletion of the entire SUCLA2 gene, and we found evidence of two founder mutations in the Scandinavian population, in addition to the known SUCLA2 founder mutation in the Faroe Islands.
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Affiliation(s)
- Rosalba Carrozzo
- Unit of Muscular and Neurodegenerative Diseases, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniela Verrigni
- Unit of Muscular and Neurodegenerative Diseases, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Magnhild Rasmussen
- Department of Clinical Neurosciences for Children, Oslo University Hospital, Oslo, Norway
| | - Rene de Coo
- Department of Neurology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Hernan Amartino
- Servicio de Neurología Infantil, Hospital Universitario Austral, Buenos Aires, Argentina
| | - Marzia Bianchi
- Unit of Muscular and Neurodegenerative Diseases, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Daniela Buhas
- Department of Medical Genetics, Montreal Children's Hospital, Montréal, Quebéc, Canada
| | - Samir Mesli
- Biochemistry, CHU de Bordeaux, Bordeaux, France
| | - Karin Naess
- Department of Laboratory Medicine and Centre for Inherited Metabolic Diseases, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Alfred Peter Born
- Department of Pediatrics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Berit Woldseth
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Paolo Prontera
- Centro di Riferimento Regionale di Genetica Medica, Azienda Ospedaliera di Perugia, CREO, Perugia, Italy
| | - Mustafa Batbayli
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Kirstine Ravn
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Fróði Joensen
- Department of Pediatrics, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
| | - Duccio M Cordelli
- U.O. Neuropsichiatria Infantile - Franzoni, Policlinico S. Orsola Malpighi, Bologna, Italy
| | | | - Mar Tulinius
- Department of Pediatrics, University of Gothenburg, The Queen Silvia's Children Hospital, Gothenburg, Sweden
| | - Niklas Darin
- Department of Pediatrics, University of Gothenburg, The Queen Silvia's Children Hospital, Gothenburg, Sweden
| | - Morten Duno
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Philippe Jouvencel
- Neonatal and Pediatric Intensive Care Unit, Children's Hospital, Bordeaux, France
| | - Alberto Burlina
- Division of Inherited Metabolic Diseases, Department of Pediatrics, University Hospital of Padua, Padua, Italy
| | - Gabriela Stangoni
- Centro di Riferimento Regionale di Genetica Medica, Azienda Ospedaliera di Perugia, CREO, Perugia, Italy
| | - Enrico Bertini
- Unit of Muscular and Neurodegenerative Diseases, Laboratory of Molecular Medicine, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Flemming Wibrand
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Carlo Dionisi-Vici
- Division of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Johanna Uusimaa
- Institute of Clinical Medicine/Department of Paediatrics, Finland and Medical Research Center, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Paivi Vieira
- Institute of Clinical Medicine/Department of Paediatrics, Finland and Medical Research Center, University of Oulu, Oulu University Hospital, Oulu, Finland
| | - Andrés Nascimento Osorio
- Unidad de patología neuromuscular, Servicio de Neurología, Hospital Sant Joan de Déu. Hospital Sant Joan de Déu and CIBERER, ISCIII, Barcelona, Spain
| | - Robert McFarland
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Trust Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Elisabeth Holme
- Department of Clinical Chemistry, Institute of Biomedicine, The Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Elsebet Ostergaard
- Department of Clinical Genetics, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark.
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15
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Maas RR, Marina AD, de Brouwer APM, Wevers RA, Rodenburg RJ, Wortmann SB. SUCLA2 Deficiency: A Deafness-Dystonia Syndrome with Distinctive Metabolic Findings (Report of a New Patient and Review of the Literature). JIMD Rep 2015; 27:27-32. [PMID: 26409464 DOI: 10.1007/8904_2015_464] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/26/2015] [Accepted: 05/20/2015] [Indexed: 12/24/2022] Open
Abstract
SUCLA2 encodes for a subunit of succinyl-coenzyme A synthase, the enzyme that reversibly synthesises succinyl-coenzyme A and ATP from succinate, coenzyme A and ADP in the Krebs cycle. Disruption of SUCLA2 function can lead to mitochondrial DNA depletion. Patients with a SUCLA2 mutation present with a rare but distinctive deafness-dystonia syndrome. Additionally, they exhibit elevated levels of the characteristic biochemical markers: methylmalonate, C4-dicarboxylic carnitine and lactate are increased in both plasma and urine. Thus far, eight different disease-causing SUCLA2 mutations, of which six missense mutations and two splice site mutations, have been described in the literature. Here, we present the first patient with an intragenic deletion in SUCLA2 and review the patients described in literature.
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Affiliation(s)
- Roeltje R Maas
- Amalia Children's Hospital, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Adela Della Marina
- Department of Neuropediatrics, Developmental Neurology and Social Pediatrics, University of Essen, Essen, Germany
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Nijmegen, Nijmegen, The Netherlands.,Department of Cognitive Neurosciences, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Ron A Wevers
- Translational Metabolic Laboratory, Department of Laboratory Medicine, Radboud UMC, Nijmegen, The Netherlands
| | - Richard J Rodenburg
- Amalia Children's Hospital, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Saskia B Wortmann
- Amalia Children's Hospital, Radboud University Nijmegen, Nijmegen, The Netherlands.
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16
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Watson CM, Crinnion LA, Gurgel-Gianetti J, Harrison SM, Daly C, Antanavicuite A, Lascelles C, Markham AF, Pena SDJ, Bonthron DT, Carr IM. Rapid Detection of Rare Deleterious Variants by Next Generation Sequencing with Optional Microarray SNP Genotype Data. Hum Mutat 2015; 36:823-30. [PMID: 26037133 PMCID: PMC4744743 DOI: 10.1002/humu.22818] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/27/2015] [Indexed: 11/25/2022]
Abstract
Autozygosity mapping is a powerful technique for the identification of rare, autosomal recessive, disease‐causing genes. The ease with which this category of disease gene can be identified has greatly increased through the availability of genome‐wide SNP genotyping microarrays and subsequently of exome sequencing. Although these methods have simplified the generation of experimental data, its analysis, particularly when disparate data types must be integrated, remains time consuming. Moreover, the huge volume of sequence variant data generated from next generation sequencing experiments opens up the possibility of using these data instead of microarray genotype data to identify disease loci. To allow these two types of data to be used in an integrated fashion, we have developed AgileVCFMapper, a program that performs both the mapping of disease loci by SNP genotyping and the analysis of potentially deleterious variants using exome sequence variant data, in a single step. This method does not require microarray SNP genotype data, although analysis with a combination of microarray and exome genotype data enables more precise delineation of disease loci, due to superior marker density and distribution.
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Affiliation(s)
- Christopher M Watson
- School of Medicine, University of Leeds, Leeds, United Kingdom.,Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, United Kingdom
| | - Laura A Crinnion
- School of Medicine, University of Leeds, Leeds, United Kingdom.,Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, United Kingdom
| | - Juliana Gurgel-Gianetti
- Department of Pediatrics, Faculty of Medicine, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Catherine Daly
- School of Medicine, University of Leeds, Leeds, United Kingdom
| | | | | | | | - Sergio D J Pena
- Laboratory of Clinical Genomics, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,GENE-Nucleo de Genetica Medica de Minas Gerais, Belo Horizonte, Brazil
| | - David T Bonthron
- School of Medicine, University of Leeds, Leeds, United Kingdom.,Yorkshire Regional Genetics Service, St James's University Hospital, Leeds, United Kingdom
| | - Ian M Carr
- School of Medicine, University of Leeds, Leeds, United Kingdom
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