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Williams EK, Shea C, Gonzalez-Perez P. Agenesis of Pectoralis Major Muscle in Late-Onset GFPT1-Related Congenital Myasthenic Syndrome: A Case Report. Neurol Genet 2023; 9:e200102. [PMID: 38235042 PMCID: PMC10523285 DOI: 10.1212/nxg.0000000000200102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/22/2023] [Indexed: 01/19/2024]
Abstract
Objectives The objective of this study was to expand the phenotypic spectrum of glutamine-fructose-6-phosphate transaminase 1 (GFPT1)-related congenital myasthenia syndrome (CMS). Methods A 61-year-old man with agenesis of the left pectoralis major muscle presented with progressive muscle weakness for a decade that transiently improved after exertion. Results His examination revealed proximal and distal muscle weakness in upper extremities and proximal muscle weakness in lower extremities. Muscle enzymes were elevated. An electromyogram revealed a myopathic pattern; however, a muscle biopsy of deltoid muscle and genetic testing for limb-girdle muscular dystrophies were nondiagnostic. A 3-Hz repetitive nerve stimulation of the spinal accessory nerve recording from trapezius muscle demonstrated a >20% drop in amplitude of the 5th compound motor action potential relative to 1st at both baseline and after 45-second exercise. Acetylcholine receptor binding, lipoprotein-related protein 4, muscle-specific kinase, and voltage-gated calcium channel P/Q antibodies were negative. Genetic testing targeting CMS revealed 2 likely pathogenic variants within GFPT1: novel c.7+2T>G (intron 1) that was predicted to result in a null allele and known c*22 C>A (exon 19) associated with reduced GFPT1 expression. His muscle strength dramatically improved after pyridostigmine initiation. Discussion In addition to other reported neurodevelopmental abnormalities, pectoralis major muscle agenesis (or Poland syndrome) may be a clinical manifestation of GFPT1-related CMS.
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Affiliation(s)
- Erika K Williams
- From the Department of Neurology (E.K.W., C.S., P.G.-P.), Massachusetts General Hospital; and Department of Neurology (E.K.W., C.S.), Brigham Women's Hospital, Harvard Medical School, Boston, MA
| | - Cristina Shea
- From the Department of Neurology (E.K.W., C.S., P.G.-P.), Massachusetts General Hospital; and Department of Neurology (E.K.W., C.S.), Brigham Women's Hospital, Harvard Medical School, Boston, MA
| | - Paloma Gonzalez-Perez
- From the Department of Neurology (E.K.W., C.S., P.G.-P.), Massachusetts General Hospital; and Department of Neurology (E.K.W., C.S.), Brigham Women's Hospital, Harvard Medical School, Boston, MA
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2
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Dofash LNH, Monahan GV, Servián-Morilla E, Rivas E, Faiz F, Sullivan P, Oates E, Clayton J, Taylor RL, Davis MR, Beilharz T, Laing NG, Cabrera-Serrano M, Ravenscroft G. A KLHL40 3' UTR splice-altering variant causes milder NEM8, an under-appreciated disease mechanism. Hum Mol Genet 2023; 32:1127-1136. [PMID: 36322148 DOI: 10.1093/hmg/ddac272] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 10/04/2022] [Accepted: 10/29/2022] [Indexed: 12/23/2022] Open
Abstract
Nemaline myopathy 8 (NEM8) is typically a severe autosomal recessive disorder associated with variants in the kelch-like family member 40 gene (KLHL40). Common features include fetal akinesia, fractures, contractures, dysphagia, respiratory failure and neonatal death. Here, we describe a 26-year-old man with relatively mild NEM8. He presented with hypotonia and bilateral femur fractures at birth, later developing bilateral Achilles' contractures, scoliosis, and elbow and knee contractures. He had walking difficulties throughout childhood and became wheelchair bound from age 13 after prolonged immobilization. Muscle magnetic resonance imaging at age 13 indicated prominent fat replacement in his pelvic girdle, posterior compartments of thighs and vastus intermedius. Muscle biopsy revealed nemaline bodies and intranuclear rods. RNA sequencing and western blotting of patient skeletal muscle indicated significant reduction in KLHL40 mRNA and protein, respectively. Using gene panel screening, exome sequencing and RNA sequencing, we identified compound heterozygous variants in KLHL40; a truncating 10.9 kb deletion in trans with a likely pathogenic variant (c.*152G > T) in the 3' untranslated region (UTR). Computational tools SpliceAI and Introme predicted the c.*152G > T variant created a cryptic donor splice site. RNA-seq and in vitro analyses indicated that the c.*152G > T variant induces multiple de novo splicing events that likely provoke nonsense mediated decay of KLHL40 mRNA explaining the loss of mRNA expression and protein abundance in the patient. Analysis of 3' UTR variants in ClinVar suggests variants that introduce aberrant 3' UTR splicing may be underrecognized in Mendelian disease. We encourage consideration of this mechanism during variant curation.
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Affiliation(s)
- Lein N H Dofash
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Gavin V Monahan
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Emilia Servián-Morilla
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla, Sevilla 41013, Spain
| | - Eloy Rivas
- Department of Pathology, Hospital Universitario Virgen del Rocío Sevilla, Sevilla 41013, Spain
| | - Fathimath Faiz
- Diagnostic Genomics, PathWest, Nedlands, WA 6009, Australia
| | - Patricia Sullivan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Emily Oates
- School of Biotechnology & Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2033, Australia
| | - Joshua Clayton
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Rhonda L Taylor
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Mark R Davis
- Diagnostic Genomics, PathWest, Nedlands, WA 6009, Australia
| | - Traude Beilharz
- Development and Stem Cells Program, Department of Biochemistry & Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton 3800 Victoria, Australia
| | - Nigel G Laing
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
| | - Macarena Cabrera-Serrano
- Department of Neurology, Neuromuscular Unit and Instituto de Biomedicina de Sevilla/CSIC, Hospital Universitario Virgen del Rocío, Sevilla 41013, Spain
| | - Gianina Ravenscroft
- Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, WA 6009, Australia
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3
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Coursimault J, Cassinari K, Lecoquierre F, Quenez O, Coutant S, Derambure C, Vezain M, Drouot N, Vera G, Schaefer E, Philippe A, Doray B, Lambert L, Ghoumid J, Smol T, Rama M, Legendre M, Lacombe D, Fergelot P, Olaso R, Boland A, Deleuze JF, Goldenberg A, Saugier-Veber P, Nicolas G. Deep intronic NIPBL de novo mutations and differential diagnoses revealed by whole genome and RNA sequencing in Cornelia de Lange syndrome patients. Hum Mutat 2022; 43:1882-1897. [PMID: 35842780 DOI: 10.1002/humu.24438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/23/2022] [Accepted: 07/09/2022] [Indexed: 01/25/2023]
Abstract
Cornelia de Lange syndrome (CdLS; MIM# 122470) is a rare developmental disorder. Pathogenic variants in 5 genes explain approximately 50% cases, leaving the other 50% unsolved. We performed whole genome sequencing (WGS) ± RNA sequencing (RNA-seq) in 5 unsolved trios fulfilling the following criteria: (i) clinical diagnosis of classic CdLS, (ii) negative gene panel sequencing from blood and saliva-isolated DNA, (iii) unaffected parents' DNA samples available and (iv) proband's blood-isolated RNA available. A pathogenic de novo mutation (DNM) was observed in a CdLS differential diagnosis gene in 3/5 patients, namely POU3F3, SPEN, and TAF1. In the other two, we identified two distinct deep intronic DNM in NIPBL predicted to create a novel splice site. RT-PCRs and RNA-Seq showed aberrant transcripts leading to the creation of a novel frameshift exon. Our findings suggest the relevance of WGS in unsolved suspected CdLS cases and that deep intronic variants may account for a proportion of them.
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Affiliation(s)
- Juliette Coursimault
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Kévin Cassinari
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - François Lecoquierre
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Olivier Quenez
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Céline Derambure
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Myriam Vezain
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Nathalie Drouot
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Gabriella Vera
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Elise Schaefer
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Anaïs Philippe
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Bérénice Doray
- Service de Génétique Médicale, Centre Hospitalier Universitaire Félix Guyon, Bellepierre Saint Denis, France
| | - Laëtitia Lambert
- Service de Génétique Clinique, CHRU NANCY, F-54000 France, UMR INSERM U 1256 N-GERE, F-54000, Nancy, France
| | - Jamal Ghoumid
- Université de Lille, ULR7364 RADEME, CHU Lille, Clinique de Génétique « Guy Fontaine », and FHU-G4 Génomique, F-59000, Lille, France
| | - Thomas Smol
- Université de Lille, ULR7364 RADEME, CHU Lille, Institut de Génétique Médicale, and FHU-G4 Génomique, F-59000, Lille, France
| | - Mélanie Rama
- Institut de Génétique Médicale, CHU de Lille, France
| | - Marine Legendre
- Service de Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Didier Lacombe
- INSERM U1211, Université de Bordeaux; Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Patricia Fergelot
- INSERM U1211, Université de Bordeaux; Génétique Médicale, CHU de Bordeaux, Bordeaux, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Alice Goldenberg
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245 and CHU Rouen, Department of Genetics and reference center for developmental disorders, FHU-G4 Génomique, F-76000, Rouen, France
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Papasavva PL, Patsali P, Loucari CC, Kurita R, Nakamura Y, Kleanthous M, Lederer CW. CRISPR Editing Enables Consequential Tag-Activated MicroRNA-Mediated Endogene Deactivation. Int J Mol Sci 2022; 23:1082. [PMID: 35163006 PMCID: PMC8834719 DOI: 10.3390/ijms23031082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/09/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Molecular therapies and functional studies greatly benefit from spatial and temporal precision of genetic intervention. We therefore conceived and explored tag-activated microRNA (miRNA)-mediated endogene deactivation (TAMED) as a research tool and potential lineage-specific therapy. For proof of principle, we aimed to deactivate γ-globin repressor BCL11A in erythroid cells by tagging the 3' untranslated region (UTR) of BCL11A with miRNA recognition sites (MRSs) for the abundant erythromiR miR-451a. To this end, we employed nucleofection of CRISPR/Cas9 ribonucleoprotein (RNP) particles alongside double- or single-stranded oligodeoxynucleotides for, respectively, non-homologous-end-joining (NHEJ)- or homology-directed-repair (HDR)-mediated MRS insertion. NHEJ-based tagging was imprecise and inefficient (≤6%) and uniformly produced knock-in- and indel-containing MRS tags, whereas HDR-based tagging was more efficient (≤18%), but toxic for longer donors encoding concatenated and thus potentially more efficient MRS tags. Isolation of clones for robust HEK293T cells tagged with a homozygous quadruple MRS resulted in 25% spontaneous reduction in BCL11A and up to 36% reduction after transfection with an miR-451a mimic. Isolation of clones for human umbilical cord blood-derived erythroid progenitor-2 (HUDEP-2) cells tagged with single or double MRS allowed detection of albeit weak γ-globin induction. Our study demonstrates suitability of TAMED for physiologically relevant modulation of gene expression and its unsuitability for therapeutic application in its current form.
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Affiliation(s)
- Panayiota L. Papasavva
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Constantinos C. Loucari
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Koto-ku, Tokyo 135-8521, Japan;
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba 305-0074, Japan;
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (P.L.P.); (P.P.); (C.C.L.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
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Abstract
MicroRNA target sites are often conserved during evolution and purifying selection to maintain such sites is expected. On the other hand, comparative analyses identified a paucity of microRNA target sites in coexpressed transcripts, and novel target sites can potentially be deleterious. We proposed that selection against novel target sites pervasive. The analysis of derived allele frequencies revealed that, when the derived allele is a target site, the proportion of nontarget sites is higher than expected, particularly for highly expressed microRNAs. Thus, new alleles generating novel microRNA target sites can be deleterious and selected against. When we analyzed ancestral target sites, the derived (nontarget) allele frequency does not show statistical support for microRNA target allele conservation. We investigated the joint effects of microRNA conservation and expression and found that selection against microRNA target sites depends mostly on the expression level of the microRNA. We identified microRNA target sites with relatively high levels of population differentiation. However, when we analyze separately target sites in which the target allele is ancestral to the population, the proportion of single-nucleotide polymorphisms with high Fst significantly increases. These findings support that population differentiation is more likely in target sites that are lost than in the gain of new target sites. Our results indicate that selection against novel microRNA target sites is prevalent and, although individual sites may have a weak selective pressure, the overall effect across untranslated regions is not negligible and should be accounted when studying the evolution of genomic sequences.
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Affiliation(s)
- Andrea Hatlen
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Antonio Marco
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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Jankowska KI, McGill J, Pezeshkpoor B, Oldenburg J, Sauna ZE, Atreya CD. Further Evidence That MicroRNAs Can Play a Role in Hemophilia A Disease Manifestation: F8 Gene Downregulation by miR-19b-3p and miR-186-5p. Front Cell Dev Biol 2020; 8:669. [PMID: 32850803 PMCID: PMC7406646 DOI: 10.3389/fcell.2020.00669] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/02/2020] [Indexed: 12/13/2022] Open
Abstract
Hemophilia A (HA) is a F8 gene mutational disorder resulting in deficiency or dysfunctional FVIII protein. However, surprisingly, in few cases, HA is manifested even without mutations in F8. To understand this anomaly, we recently sequenced microRNAs (miRNAs) of two patients with mild and moderate HA with no F8 gene mutations and selected two highly expressing miRNAs, miR-374b-5p and miR-30c-5p, from the pool to explain the FVIII deficiency that could be mediated by miRNA-based F8/FVIII suppression. In this report, an established orthogonal in vivo RNA-affinity purification approach was utilized to directly identify a group of F8-interacting miRNAs and we tested them for F8/FVIII suppression. From this pool, two miRNAs, miR-19b-3p and miR-186-5p, were found to be upregulated in a severe HA patient with a mutation in the F8 coding sequence and two HA patients without mutations in the F8 coding sequence were selected to demonstrate their role in F8 gene expression regulation in mammalian cells. Overall, these results provide further evidence for the hypothesis that by targeting the 3′UTR of F8, miRNAs can modulate FVIII protein levels. This mechanism could either be the primary cause of HA in patients who lack F8 mutations or control the severity of the disease in patients with F8 mutations.
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Affiliation(s)
- Katarzyna I Jankowska
- OBRR/DBCD/LCH in the Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Joseph McGill
- OTAT/DPPT/HB in the Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Behnaz Pezeshkpoor
- Institute of Experimental Hematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - Johannes Oldenburg
- Institute of Experimental Hematology and Transfusion Medicine, University Clinic Bonn, Bonn, Germany.,Center for Rare Diseases Bonn (ZSEB), University Clinic Bonn, Bonn, Germany
| | - Zuben E Sauna
- OTAT/DPPT/HB in the Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Chintamani D Atreya
- OBRR/DBCD/LCH in the Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
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7
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Szelinger S, Krate J, Ramsey K, Strom SP, Shieh PB, Lee H, Belnap N, Balak C, Siniard AL, Russell M, Richholt R, Both MD, Claasen AM, Schrauwen I, Nelson SF, Huentelman MJ, Craig DW, Yang SP, Moore SA, Sivakumar K, Narayanan V, Rangasamy S. Congenital myasthenic syndrome caused by a frameshift insertion mutation in GFPT1. NEUROLOGY-GENETICS 2020; 6:e468. [PMID: 32754643 PMCID: PMC7357421 DOI: 10.1212/nxg.0000000000000468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 05/26/2020] [Indexed: 12/17/2022]
Abstract
Objective Description of a new variant of the glutamine-fructose-6-phosphate transaminase 1 (GFPT1) gene causing congenital myasthenic syndrome (CMS) in 3 children from 2 unrelated families. Methods Muscle biopsies, EMG, and whole-exome sequencing were performed. Results All 3 patients presented with congenital hypotonia, muscle weakness, respiratory insufficiency, head lag, areflexia, and gastrointestinal dysfunction. Genetic analysis identified a homozygous frameshift insertion in the GFPT1 gene (NM_001244710.1: c.686dupC; p.Arg230Ter) that was shared by all 3 patients. In one of the patients, inheritance of the variant was through uniparental disomy (UPD) with maternal origin. Repetitive nerve stimulation and single-fiber EMG was consistent with the clinical diagnosis of CMS with a postjunctional defect. Ultrastructural evaluation of the muscle biopsy from one of the patients showed extremely attenuated postsynaptic folds at neuromuscular junctions and extensive autophagic vacuolar pathology. Conclusions These results expand on the spectrum of known loss-of-function GFPT1 mutations in CMS12 and in one family demonstrate a novel mode of inheritance due to UPD.
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Affiliation(s)
- Szabolcs Szelinger
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Jonida Krate
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Keri Ramsey
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Samuel P Strom
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Perry B Shieh
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Hane Lee
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Newell Belnap
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Chris Balak
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Ashley L Siniard
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Megan Russell
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Ryan Richholt
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Matt De Both
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Ana M Claasen
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Isabelle Schrauwen
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Stanley F Nelson
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Matthew J Huentelman
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - David W Craig
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Samuel P Yang
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Steven A Moore
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Kumaraswamy Sivakumar
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Vinodh Narayanan
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
| | - Sampathkumar Rangasamy
- theNeurogenomics Division (S.S., J.K., K.R., N.B., C.B., A.L.S., M.R., R.R., M.D.B., A.M.C., M.J.H, V.N., S.R.), Translational Genomics Research Institute, Center for Rare Childhood Disorders, Phoenix, AZ; Fulgent Genetics (S.P.S.), Temple City, CA; Department of Neurology (P.B.S.), University of California Los Angeles; David Geffen School of Medicine (P.B.S.), Los Angeles; Department of Pathology and Laboratory Medicine (H.L., S.F.N.), University of California, Los Angeles; Department of Human Genetics (H.L., S.F.N.), David Geffen School of Medicine; Department of Neurology (I.S.), Columbia University, Center for Statistical Genetics, New York; Department of Translational Genomics (D.W.C.), University of Southern California, Los Angeles; Providence Sacred Heart Medical Center and Children's Hospital (S.P.Y.), Spokane, WA; Department of Pathology (S.A.M), University of Iowa, Carver College of Medicine; and Neuromuscular Clinic and Research Center (K.S.), Phoenix, AZ
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Gong J, Shao D, Xu K, Lu Z, Lu ZJ, Yang YT, Zhang QC. RISE: a database of RNA interactome from sequencing experiments. Nucleic Acids Res 2019; 46:D194-D201. [PMID: 29040625 PMCID: PMC5753368 DOI: 10.1093/nar/gkx864] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 09/29/2017] [Indexed: 12/12/2022] Open
Abstract
We present RISE (http://rise.zhanglab.net), a database of RNA Interactome from Sequencing Experiments. RNA-RNA interactions (RRIs) are essential for RNA regulation and function. RISE provides a comprehensive collection of RRIs that mainly come from recent transcriptome-wide sequencing-based experiments like PARIS, SPLASH, LIGR-seq, and MARIO, as well as targeted studies like RIA-seq, RAP-RNA and CLASH. It also includes interactions aggregated from other primary databases and publications. The RISE database currently contains 328,811 RNA-RNA interactions mainly in human, mouse and yeast. While most existing RNA databases mainly contain interactions of miRNA targeting, notably, more than half of the RRIs in RISE are among mRNA and long non-coding RNAs. We compared different RRI datasets in RISE and found limited overlaps in interactions resolved by different techniques and in different cell lines. It may suggest technology preference and also dynamic natures of RRIs. We also analyzed the basic features of the human and mouse RRI networks and found that they tend to be scale-free, small-world, hierarchical and modular. The analysis may nominate important RNAs or RRIs for further investigation. Finally, RISE provides a Circos plot and several table views for integrative visualization, with extensive molecular and functional annotations to facilitate exploration of biological functions for any RRI of interest.
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Affiliation(s)
- Jing Gong
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Di Shao
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Kui Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
| | - Zhipeng Lu
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Zhi John Lu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yucheng T Yang
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095-1554, USA
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing 100084, China
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9
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Luo HY, Zhao L, Mao CY, Yang ZH, Yang J, Wang YL, Niu HX, Liu YT, Shi CH, Xu YM. Novel compound heterozygous GFPT1 mutations in a family with limb-girdle myasthenia with tubular aggregates. Neuromuscul Disord 2019; 29:549-553. [PMID: 31255525 DOI: 10.1016/j.nmd.2019.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/06/2019] [Accepted: 05/22/2019] [Indexed: 02/07/2023]
Abstract
Limb-girdle myasthenia with tubular aggregates, a subtype of congenital myasthenic syndrome, is an extremely rare autosomal recessive genetic disease characterized by prominent limb-girdle weakness and good response to acetylcholinesterase inhibitor therapy. Herein, we reported two novel mutations of GFPT1 gene in a Chinese pedigree. Two siblings presented with fatigue, weakness of limb-girdle and decrement of the muscle action potential with repetitive nerve stimulation. Thus, myasthenia gravis was initially suspected, but anti-AChR antibodies were negative. Two novel missense mutations (p.Lys154Asn and p.Asn363Ser) in GFPT1 were identified through genetic testing conducted on 167 well-established genes associated with muscular diseases by targeted high throughput sequencing. Both mutations have not been recorded in the dsSNP database, Exome Aggregation Consortium database and 1000 Genomes Project database. The mutation sites were co-segregated with the phenotype and conserved between the different species. The mutations were not found in the 200 unrelated normal controls. Muscle biopsies revealed tubular aggregates, in accordance with previous reports with GFPT1 mutations. Subsequently, dramatic improvement in strength occurred following anti-cholinesterase therapy. Our study will be helpful for the diagnosis and treatment for Limb-girdle myasthenia with tubular aggregates.
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Affiliation(s)
- Hai-Yang Luo
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jian-she East Road, Zhengzhou 450000, Henan, China; Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China
| | - Lu Zhao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jian-she East Road, Zhengzhou 450000, Henan, China
| | - Cheng-Yuan Mao
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jian-she East Road, Zhengzhou 450000, Henan, China
| | - Zhi-Hua Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jian-she East Road, Zhengzhou 450000, Henan, China
| | - Jing Yang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jian-she East Road, Zhengzhou 450000, Henan, China
| | - Yan-Lin Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jian-she East Road, Zhengzhou 450000, Henan, China
| | - Hui-Xia Niu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jian-she East Road, Zhengzhou 450000, Henan, China
| | - Yu-Tao Liu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jian-she East Road, Zhengzhou 450000, Henan, China
| | - Chang-He Shi
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jian-she East Road, Zhengzhou 450000, Henan, China.
| | - Yu-Ming Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, 1 Jian-she East Road, Zhengzhou 450000, Henan, China; Institute of Clinical Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan, China.
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Li Y, Zhang Y, Li X, Yi S, Xu J. Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology. Trends Biochem Sci 2019; 44:659-674. [PMID: 31047772 DOI: 10.1016/j.tibs.2019.03.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 02/08/2023]
Abstract
Advances in next-generation sequencing have identified thousands of genomic variants that perturb the normal functions of proteins, further contributing to diverse phenotypic consequences in cancer. Elucidating the functional pathways altered by loss-of-function (LOF) or gain-of-function (GOF) mutations will be crucial for prioritizing cancer-causing variants and their resultant therapeutic liabilities. In this review, we highlight the fundamental function of GOF mutations and discuss the potential mechanistic effects in the context of signaling networks. We also summarize advances in experimental and computational resources, which will dramatically help with studies on the functional and phenotypic consequences of mutations. Together, systematic investigations of the function of GOF mutations will provide an important missing piece for cancer biology and precision therapy.
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Affiliation(s)
- Yongsheng Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yunpeng Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; College of Bioinformatics, Hainan Medical University, Haikou 570100, China.
| | - Song Yi
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA; Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Juan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.
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Abstract
OBJECTIVES Congenital myasthenic syndromes (CMSs) are a genotypically and phenotypically heterogeneous group of neuromuscular disorders, which have in common an impaired neuromuscular transmission. Since the field of CMSs is steadily expanding, the present review aimed at summarizing and discussing current knowledge and recent advances concerning the etiology, clinical presentation, diagnosis, and treatment of CMSs. METHODS Systematic literature review. RESULTS Currently, mutations in 32 genes are made responsible for autosomal dominant or autosomal recessive CMSs. These mutations concern 8 presynaptic, 4 synaptic, 15 post-synaptic, and 5 glycosilation proteins. These proteins function as ion-channels, enzymes, or structural, signalling, sensor, or transporter proteins. The most common causative genes are CHAT, COLQ, RAPSN, CHRNE, DOK7, and GFPT1. Phenotypically, these mutations manifest as abnormal fatigability or permanent or fluctuating weakness of extra-ocular, facial, bulbar, axial, respiratory, or limb muscles, hypotonia, or developmental delay. Cognitive disability, dysmorphism, neuropathy, or epilepsy are rare. Low- or high-frequency repetitive nerve stimulation may show an abnormal increment or decrement, and SF-EMG an increased jitter or blockings. Most CMSs respond favourably to acetylcholine-esterase inhibitors, 3,4-diamino-pyridine, salbutamol, albuterol, ephedrine, fluoxetine, or atracurium. CONCLUSIONS CMSs are an increasingly recognised group of genetically transmitted defects, which usually respond favorably to drugs enhancing the neuromuscular transmission. CMSs need to be differentiated from neuromuscular disorders due to muscle or nerve dysfunction.
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Affiliation(s)
- Josef Finsterer
- Krankenanstalt Rudolfstiftung, Messerli Institute, Veterinary University of Vienna, Postfach 20, 1180, Vienna, Austria.
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12
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Helman G, Sharma S, Crawford J, Patra B, Jain P, Bent SJ, Urtizberea JA, Saran RK, Taft RJ, van der Knaap MS, Simons C. Leukoencephalopathy due to variants in GFPT1-associated congenital myasthenic syndrome. Neurology 2019; 92:e587-e593. [PMID: 30635494 DOI: 10.1212/wnl.0000000000006886] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/06/2018] [Indexed: 01/17/2023] Open
Abstract
OBJECTIVE To determine the molecular etiology of disease in 4 individuals from 2 unrelated families who presented with proximal muscle weakness and features suggestive of mitochondrial disease. METHODS Clinical information and neuroimaging were reviewed. Genome sequencing was performed on affected individuals and biological parents. RESULTS All affected individuals presented with muscle weakness and difficulty walking. In one family, both children had neonatal respiratory distress while the other family had 2 children with episodic deteriorations. In each family, muscle biopsy demonstrated ragged red fibers. MRI was suggestive of a mitochondrial leukoencephalopathy, with extensive deep cerebral white matter T2 hyperintense signal and selective involvement of the middle blade of the corpus callosum. Through genome sequencing, homozygous GFPT1 missense variants were identified in the affected individuals of each family. The variants detected (p.Arg14Leu and p.Thr151Lys) are absent from population databases and predicted to be damaging by in silico prediction tools. Following the genetic diagnosis, nerve conduction studies were performed and demonstrated a decremental response to repetitive nerve stimulation, confirming the diagnosis of myasthenia. Treatment with pyridostigmine was started in one family with favorable response. CONCLUSIONS GFPT1 encodes a widely expressed protein that controls the flux of glucose into the hexosamine-biosynthesis pathway that produces precursors for glycosylation of proteins. GFPT1 variants and defects in other enzymes of this pathway have previously been associated with congenital myasthenia. These findings identify leukoencephalopathy as a previously unrecognized phenotype in GFPT1-related disease and suggest that mitochondrial dysfunction could contribute to this disorder.
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Affiliation(s)
- Guy Helman
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Suvasini Sharma
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Joanna Crawford
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Bijoy Patra
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Puneet Jain
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Stephen J Bent
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - J Andoni Urtizberea
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Ravindra K Saran
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Ryan J Taft
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands
| | - Marjo S van der Knaap
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands.
| | - Cas Simons
- From the Murdoch Children's Research Institute (G.H., C.S.), Parkville, Melbourne; Institute for Molecular Bioscience (G.H., J.C., C.S.), the University of Queensland, Brisbane, Australia; Neurology Division (S.S., B.P., P.J.), Department of Pediatrics, Lady Hardinge Medical College, New Delhi, India; Division of Neurology (P.J.), Department of Pediatrics, the Hospital for Sick Children, Toronto, Canada; Data61 (S.J.B.), Commonwealth Scientific and Industrial Research Organisation, Brisbane, Australia; Hôpital Marin (J.A.U.), Centre Neuromusculaire, Filnemus, Hendaye, France; Department of Pathology (R.K.S.), G.B. Pant Hospital, New Delhi, India; Illumina, Inc. (R.J.T.), San Diego, CA; Department of Child Neurology (M.S.v.d.K.), Emma Children's Hospital, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam and Amsterdam Neuroscience; and Department of Functional Genomics (M.S.v.d.K.), Neuroscience Campus Amsterdam, the Netherlands.
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13
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Paolacci S, Li Y, Agolini E, Bellacchio E, Arboleda-Bustos CE, Carrero D, Bertola D, Al-Gazali L, Alders M, Altmüller J, Arboleda G, Beleggia F, Bruselles A, Ciolfi A, Gillessen-Kaesbach G, Krieg T, Mohammed S, Müller C, Novelli A, Ortega J, Sandoval A, Velasco G, Yigit G, Arboleda H, Lopez-Otin C, Wollnik B, Tartaglia M, Hennekam RC. Specific combinations of biallelic POLR3A variants cause Wiedemann-Rautenstrauch syndrome. J Med Genet 2018; 55:837-846. [PMID: 30323018 DOI: 10.1136/jmedgenet-2018-105528] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/28/2018] [Accepted: 09/09/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Wiedemann-Rautenstrauch syndrome (WRS) is a form of segmental progeria presenting neonatally, characterised by growth retardation, sparse scalp hair, generalised lipodystrophy with characteristic local fatty tissue accumulations and unusual face. We aimed to understand its molecular cause. METHODS We performed exome sequencing in two families, targeted sequencing in 10 other families and performed in silico modelling studies and transcript processing analyses to explore the structural and functional consequences of the identified variants. RESULTS Biallelic POLR3A variants were identified in eight affected individuals and monoallelic variants of the same gene in four other individuals. In the latter, lack of genetic material precluded further analyses. Multiple variants were found to affect POLR3A transcript processing and were mostly located in deep intronic regions, making clinical suspicion fundamental to detection. While biallelic POLR3A variants have been previously reported in 4H syndrome and adolescent-onset progressive spastic ataxia, recurrent haplotypes specifically occurring in individuals with WRS were detected. All WRS-associated POLR3A amino acid changes were predicted to perturb substantially POLR3A structure/function. CONCLUSION Biallelic mutations in POLR3A, which encodes for the largest subunit of the DNA-dependent RNA polymerase III, underlie WRS. No isolated functional sites in POLR3A explain the phenotype variability in POLR3A-related disorders. We suggest that specific combinations of compound heterozygous variants must be present to cause the WRS phenotype. Our findings expand the molecular mechanisms contributing to progeroid disorders.
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Affiliation(s)
- Stefano Paolacci
- Department of Experimental Medicine, Sapienza "University of Rome", Rome, Italy
| | - Yun Li
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Emanuele Agolini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Emanuele Bellacchio
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Carlos E Arboleda-Bustos
- Neuroscience and Cell Death Group, Faculty of Medicine and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Colombia
| | - Dido Carrero
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, and Centro de Investigación Biomédica en Red de Cáncer, Oviedo, Spain
| | - Debora Bertola
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, e Centro de Estudos sobre o Genoma Humano e Células-Tronco do Instituto de Biociências da Universidade de São Paulo, São Paulo, Brazil
| | - Lihadh Al-Gazali
- Department of Paediatric, College of Medicine and Health Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mariel Alders
- Department of Clinical Genetics, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Janine Altmüller
- Cologne Centre for Genomics and Centre for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Gonzalo Arboleda
- Neuroscience and Cell Death Group, Faculty of Medicine and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Colombia
| | - Filippo Beleggia
- Department of Internal Medicine I, University Hospital Cologne, Cologne, Germany
| | - Alessandro Bruselles
- Dipartimento di Oncologia e Medicina Molecolare, Istituto Superiore di Sanità, Rome, Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | | | - Thomas Krieg
- Department of Dermatology, University Hospital Cologne, Cologne, Germany
| | | | - Christian Müller
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Antonio Novelli
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Jenny Ortega
- Neuroscience and Cell Death Group, Faculty of Medicine and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Colombia
| | - Adrian Sandoval
- Neuroscience and Cell Death Group, Faculty of Medicine and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Colombia
| | - Gloria Velasco
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, and Centro de Investigación Biomédica en Red de Cáncer, Oviedo, Spain
| | - Gökhan Yigit
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Humberto Arboleda
- Neuroscience and Cell Death Group, Faculty of Medicine and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Colombia
| | - Carlos Lopez-Otin
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, and Centro de Investigación Biomédica en Red de Cáncer, Oviedo, Spain
| | - Bernd Wollnik
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Raoul C Hennekam
- Department of Paediatrics, Amsterdam UMC - location AMC, University of Amsterdam, Amsterdam, The Netherlands
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14
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Chen B, Chen J, Du Q, Zhou D, Wang L, Xie J, Li Y, Zhang D. Genetic variants in microRNA biogenesis genes as novel indicators for secondary growth in Populus. THE NEW PHYTOLOGIST 2018; 219:1263-1282. [PMID: 29916214 DOI: 10.1111/nph.15262] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/06/2018] [Indexed: 05/21/2023]
Abstract
MicroRNAs (miRNAs) function as key regulators of complex traits, but how genetic alterations in miRNA biogenesis genes (miRBGs) affect quantitative variation has not been elucidated. We conducted transcript analyses and association genetics to investigate how miRBGs, miRNA genes (MIRNAs) and their respective targets contribute to secondary growth in a natural population of 435 Populus tomentosa individuals. This analysis identified 29 843 common single-nucleotide polymorphisms (SNPs; frequency > 0.10) within 682 genes (80 miRBGs, 152 MIRNAs, and 457 miRNA targets). Single-SNP association analysis found SNPs in 234 candidate genes exhibited significant additive/dominant effects on phenotypes. Among these, specific candidates that associated with the same traits produced 791 miRBG-MIRNA-target combinations, suggesting possible genetic miRBG-MIRNA and MIRNA-target interactions, providing an important clue for the regulatory mechanisms of miRBGs. Multi-SNP association found 4672 epistatic pairs involving 578 genes that showed significant associations with traits and identified 106 miRBG-MIRNA-target combinations. Two multi-hierarchical networks were constructed based on correlations of miRBG-miRNA and miRNA-target expression to further probe the mechanisms of trait diversity underlying changes in miRBGs. Our study opens avenues for the investigation of miRNA function in perennial plants and underscored miRBGs as potentially modulating quantitative variation in traits.
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Affiliation(s)
- Beibei Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Jinhui Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Qingzhang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Daling Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Longxin Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Jianbo Xie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Ying Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, China
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Abstract
PURPOSE OF REVIEW Congenital myasthenic syndromes (CMS) are a group of heterogeneous inherited disorders caused by mutations in genes encoding proteins essential for the integrity of neuromuscular transmission. This review updates the reader on recent findings that have expanded the phenotypic spectrum and suggested improved treatment strategies. RECENT FINDINGS The use of next-generation sequencing is continuing to unearth new genes in which mutations can give rise to defective neuromuscular transmission. The defective transmission may be part of an overall more complex phenotype in which there may be muscle, central nervous system or other involvement. Notably, mutations in series of genes encoding presynaptic proteins are being identified. Further work on mutations found in the AGRN-MUSK acetylcholine receptor clustering pathway has helped characterize the role of LRP4 and broadened the phenotypic spectrum for AGRN mutations. Mutations in another extracellular matrix protein, collagen 13A1 and in GMPPB have also been found to cause a CMS. Finally, there are an increasing number of reports for the beneficial effects of treatment with β2-adrenergic receptor agonists. SUMMARY Recent studies of the CMS illustrate the increasing complexity of the genetics, pathophysiological mechanisms and the need to tailor therapy for the genetic disorders of the neuromuscular junction.
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Patel N, Khan AO, Al-Saif M, Moghrabi WN, AlMaarik BM, Ibrahim N, Abdulwahab F, Hashem M, Alshidi T, Alobeid E, Alomar RA, Al-Harbi S, Abouelhoda M, Khabar KSA, Alkuraya FS. A novel mechanism for variable phenotypic expressivity in Mendelian diseases uncovered by an AU-rich element (ARE)-creating mutation. Genome Biol 2017; 18:144. [PMID: 28754144 PMCID: PMC5534118 DOI: 10.1186/s13059-017-1274-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/06/2017] [Indexed: 01/09/2023] Open
Abstract
Background Variable expressivity is a well-known phenomenon in which patients with mutations in one gene display varying degrees of clinical severity, potentially displaying only subsets of the clinical manifestations associated with the multisystem disorder linked to the gene. This remains an incompletely understood phenomenon with proposed mechanisms ranging from allele-specific to stochastic. Results We report three consanguineous families in which an isolated ocular phenotype is linked to a novel 3′ UTR mutation in SLC4A4, a gene known to be mutated in a syndromic form of intellectual disability with renal and ocular involvement. Although SLC4A4 is normally devoid of AU-rich elements (AREs), a 3′ UTR motif that mediates post-transcriptional control of a subset of genes, the mutation we describe creates a functional ARE. We observe a marked reduction in the transcript level of SLC4A4 in patient cells. Experimental confirmation of the ARE-creating mutation is shown using a post-transcriptional reporter system that reveals consistent reduction in the mRNA-half life and reporter activity. Moreover, the neo-ARE binds and responds to the zinc finger protein ZFP36/TTP, an ARE-mRNA decay-promoting protein. Conclusions This novel mutational mechanism for a Mendelian disease expands the potential mechanisms that underlie variable phenotypic expressivity in humans to also include 3′ UTR mutations with tissue-specific pathology.
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Affiliation(s)
- Nisha Patel
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Arif O Khan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Eye Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, 112412, United Arab Emirates
| | - Maher Al-Saif
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Walid N Moghrabi
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Balsam M AlMaarik
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Niema Ibrahim
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Tarfa Alshidi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Eman Alobeid
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Rana A Alomar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Saad Al-Harbi
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Mohamed Abouelhoda
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Khalid S A Khabar
- Program in BioMolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
| | - Fowzan S Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia. .,Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
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17
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Mutations in GFPT1-related congenital myasthenic syndromes are associated with synaptic morphological defects and underlie a tubular aggregate myopathy with synaptopathy. J Neurol 2017; 264:1791-1803. [DOI: 10.1007/s00415-017-8569-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/03/2017] [Accepted: 07/11/2017] [Indexed: 12/22/2022]
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18
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MiR-19b and miR-16 cooperatively signaling target the regulator ADRA1A in Hypertensive heart disease. Biomed Pharmacother 2017; 91:1178-1183. [DOI: 10.1016/j.biopha.2017.04.041] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/29/2017] [Accepted: 04/10/2017] [Indexed: 12/21/2022] Open
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19
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Ahmed K, LaPierre MP, Gasser E, Denzler R, Yang Y, Rülicke T, Kero J, Latreille M, Stoffel M. Loss of microRNA-7a2 induces hypogonadotropic hypogonadism and infertility. J Clin Invest 2017; 127:1061-1074. [PMID: 28218624 DOI: 10.1172/jci90031] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/15/2016] [Indexed: 12/21/2022] Open
Abstract
MicroRNAs (miRNAs) are negative modulators of gene expression that fine-tune numerous biological processes. miRNA loss-of-function rarely results in highly penetrant phenotypes, but rather, influences cellular responses to physiologic and pathophysiologic stresses. Here, we have reported that a single member of the evolutionarily conserved miR-7 family, miR-7a2, is essential for normal pituitary development and hypothalamic-pituitary-gonadal (HPG) function in adulthood. Genetic deletion of mir-7a2 causes infertility, with low levels of gonadotropic and sex steroid hormones, small testes or ovaries, impaired spermatogenesis, and lack of ovulation in male and female mice, respectively. We found that miR-7a2 is highly expressed in the pituitary, where it suppresses golgi glycoprotein 1 (GLG1) expression and downstream bone morphogenetic protein 4 (BMP4) signaling and also reduces expression of the prostaglandin F2a receptor negative regulator (PTGFRN), an inhibitor of prostaglandin signaling and follicle-stimulating hormone (FSH) and luteinizing hormone (LH) secretion. Our results reveal that miR-7a2 critically regulates sexual maturation and reproductive function by interconnecting miR-7 genomic circuits that regulate FSH and LH synthesis and secretion through their effects on pituitary prostaglandin and BMP4 signaling.
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20
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Ohno K, Ohkawara B, Ito M. Recent advances in congenital myasthenic syndromes. ACTA ACUST UNITED AC 2016. [DOI: 10.1111/cen3.12316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Kinji Ohno
- Division of Neurogenetics; Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Bisei Ohkawara
- Division of Neurogenetics; Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
| | - Mikako Ito
- Division of Neurogenetics; Center for Neurological Diseases and Cancer; Nagoya University Graduate School of Medicine; Nagoya Japan
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21
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Target resequencing of neuromuscular disease-related genes using next-generation sequencing for patients with undiagnosed early-onset neuromuscular disorders. J Hum Genet 2016; 61:931-942. [PMID: 27357428 DOI: 10.1038/jhg.2016.79] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/23/2016] [Accepted: 05/16/2016] [Indexed: 01/24/2023]
Abstract
Neuromuscular disorders are clinically and genetically heterogeneous diseases with broadly overlapping clinical features. Progress in molecular genetics has led to the identification of numerous causative genes for neuromuscular disorders, but Sanger sequencing-based diagnosis remains labor-intensive and expensive because the genes are large, the genotypes and phenotypes of neuromuscular disorders overlap and multiple genes related to a single phenotype exist. Recently, the advent of next-generation sequencing (NGS) has enabled efficient, concurrent examination of several related genes. Thus, we used NGS for target resequencing of neuromuscular disease-related genes from 42 patients in whom undiagnosed early-onset neuromuscular disorders. Causative genes were identified in 19/42 (45.2%) patients (six, congenital muscular dystrophy; two, Becker muscular dystrophy (BMD); three, limb-girdle muscular dystrophy; one, concurrent BMD and Fukuyama congenital muscular dystrophy; three, nemaline myopathy; one, centronuclear myopathy; one, congenital fiber-type disproportion; one, myosin storage myopathy; and one, congenital myasthenic syndrome). We detected variants of uncertain significance in two patients. In 6/19 patients who received a definitive diagnosis, the diagnosis did not require muscle biopsy. Thus, for patients with suspected neuromuscular disorders not identified using conventional genetic testing alone, NGS-based target resequencing has the potential to serve as a powerful tool that allows definitive diagnosis.
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22
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Chen B, Du Q, Chen J, Yang X, Tian J, Li B, Zhang D. Dissection of allelic interactions among Pto-miR257 and its targets and their effects on growth and wood properties in Populus. Heredity (Edinb) 2016; 117:73-83. [PMID: 27118153 DOI: 10.1038/hdy.2016.26] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/02/2016] [Indexed: 11/09/2022] Open
Abstract
MicroRNAs (miRNAs) have important roles in the regulation of genes; however, for trees few studies have explored the potential impact of the interactions between miRNAs and their target genes. Here, we performed transcript profiling and association genetics (single-SNP, haplotype-based and multi-SNP associations) to study the genetic regulatory relationship of Pto-miR257 and its 12 target genes in 435 individuals of a natural population of Populus tomentosa. Expression profiling of Pto-miR257 and its targets showed a negative relationship between their expression levels. Of the 61 single-nucleotide polymorphisms (SNPs) detected in Pto-miR257, 6 in the pre-mature region strongly affected its secondary stability and 1 in the mature region could alter its target spectrum. Among the 1029 SNPs in the targets, 3 were located in target sites that could change the binding affinity of Pto-miR257. Single-SNP association analysis revealed that SNPs in Pto-miR257 and target genes associated with both growth and wood property traits, in agreement with haplotype-based identifications. Multi-SNP association found that 10 targets shared at least one common trait with Pto-miR257, with phenotypic variance from 0.5 to 8.5%, suggesting a possible internal genetic interaction between them. Epistasis analysis showed significant epistatic interactions among Pto-miR257 and its targets. Therefore, our study demonstrated Pto-miR257 and its 12 targets had roles in wood formation and revealed the genetic interaction network between the miRNA and its targets under additive, dominant and epistatic models. Thus, association genetics can be used to decipher the interactions between miRNAs and their target genes and to help understand the genetic architecture of complex traits.
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Affiliation(s)
- B Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - Q Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - J Chen
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - X Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - J Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
| | - B Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Department of Forestry, North Carolina State University, Raleigh, NC, USA
| | - D Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, People's Republic of China
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23
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Ji ML, Zhang XJ, Shi PL, Lu J, Wang SZ, Chang Q, Chen H, Wang C. Downregulation of microRNA-193a-3p is involved in invertebral disc degeneration by targeting MMP14. J Mol Med (Berl) 2016; 94:457-68. [PMID: 26620678 DOI: 10.1007/s00109-015-1371-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/08/2015] [Accepted: 11/17/2015] [Indexed: 01/06/2023]
Abstract
UNLABELLED Accumulating evidence suggests that microRNAs (miRNAs) play an important role in intervertebral disc degeneration (IDD), but the precise role of specific miRNAs involved in this disease remains elusive. The purpose of this study was to identify IDD-specific miRNAs, followed by functional validation of results. MiRNA expression profile was determined in nucleus pulposus (NP) tissues from patients with IDD and controls, employing Solexa sequencing and quantitative real-time PCR (qRT-PCR). Biological functions of differential expression miRNAs were further investigated in vitro and in vivo. Luciferase reporter assays and Western blotting were performed to determine miRNA targets. We identified 28 miRNAs that were differentially expressed in patients compared with controls. Following qRT-PCR confirmation, miR-193a-3p was significantly down-regulated in degenerative NP tissues. Moreover, its level was correlated with grade of disc degeneration. Through gain- and loss-of-function studies, miR-193a-3p was demonstrated to significantly promote type II collagen expression in NP cells. Knockdown of MMP14 induced effects on NP cells similar to those induced by miR-193a-3p. Bioinformatics target prediction identified MMP14 as a putative target of miR-193a-3p. Furthermore, luciferase reporter assays and Western blotting demonstrated that miR-193a-3p directly targets MMP14. MiR-193a-3p inhibited IDD in vitro and in vivo. The downregulation of miR-193a-3p induces the expression of MMP14, which promotes loss of type II collagen and thereby contributes to the development of human IDD. Our findings extend the role of miR-193a-3p in the pathogenesis of IDD and provide a potential novel therapeutic target for degenerative disc disease. KEY MESSAGES Intervertebral disc degeneration (ICC)-specific miRNA profile generated by next generation sequencing. Downregulation of miR-193a-3p promoted loss of type II collagen by directly targeting MMP14 in IDD. miR-193a-3p inhibited IDD in vitro and in vivo. miR-193a-3p may be a promising candidate for prevention of degenerative disc disease.
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Affiliation(s)
- Ming-Liang Ji
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Dingjiaqiao road 87, Nanjing, 210009, China
| | - Xue-Jun Zhang
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Dingjiaqiao road 87, Nanjing, 210009, China
| | - Pei-Liang Shi
- Key Laboratory of Model Animal for Disease Study of Ministry of Education, Model Animal Research Center, Collaborative Innovation Center of Genetics and Development, Nanjing University, Nanjing, China
| | - Jun Lu
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Dingjiaqiao road 87, Nanjing, 210009, China
| | - Shan-Zheng Wang
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Dingjiaqiao road 87, Nanjing, 210009, China
| | - Qing Chang
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Dingjiaqiao road 87, Nanjing, 210009, China
| | - Hui Chen
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Dingjiaqiao road 87, Nanjing, 210009, China
| | - Chen Wang
- Department of Orthopaedic Surgery, Zhongda Hospital, School of Medicine, Southeast University, Dingjiaqiao road 87, Nanjing, 210009, China.
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24
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Garcia AI, Buisson M, Damiola F, Tessereau C, Barjhoux L, Verny-Pierre C, Sornin V, Dondon MG, Eon-Marchais S, Caron O, Gautier-Villars M, Coupier I, Buecher B, Vennin P, Belotti M, Lortholary A, Gesta P, Dugast C, Noguès C, Fricker JP, Faivre L, Stoppa-Lyonnet D, Andrieu N, Sinilnikova OM, Mazoyer S. Mutation screening of MIR146A/B and BRCA1/2 3'-UTRs in the GENESIS study. Eur J Hum Genet 2016; 24:1324-9. [PMID: 26785832 DOI: 10.1038/ejhg.2015.284] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/11/2015] [Accepted: 12/16/2015] [Indexed: 01/08/2023] Open
Abstract
Although a wide number of breast cancer susceptibility alleles associated with various levels of risk have been identified to date, about 50% of the heritability is still missing. Although the major BRCA1 and BRCA2 genes are being extensively screened for truncating and missense variants in breast and/or ovarian cancer families, potential regulatory variants affecting their expression remain largely unexplored. In an attempt to identify such variants, we focused our attention on gene regulation mediated by microRNAs (miRs). We screened two genes, MIR146A and MIR146B, producing miR-146a and miR-146b-5p, respectively, that regulate BRCA1, and the 3'- untranslated regions (3'-UTRs) of BRCA1 and BRCA2 in the GENESIS French national case/control study (BRCA1- and BRCA2-negative breast cancer cases with at least one sister with breast cancer and matched controls). We identified one rare variant in MIR146A, four in MIR146B, five in BRCA1 3'-UTR and one in BRCA2 3'-UTR in 716 index cases and 619 controls. Among these 11 rare variants, 7 were identified each in 1 index case. None of the three relevant MIR146A/MIR146B variants affected the pre-miR sequences. The potential causality of the four relevant BRCA1/BRCA2 3'-UTRs variants was evaluated with luciferase reporter assays and co-segregation studies, as well as with bioinformatics analyses to predict miRs-binding sites, RNA secondary structures and RNA accessibility. This is the first study to report the screening of miR genes and of BRCA2 3'-UTR in a large series of familial breast cancer cases. None of the variant identified in this study gave convincing evidence of potential pathogenicity.
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Affiliation(s)
- Amandine I Garcia
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Monique Buisson
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Francesca Damiola
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Chloé Tessereau
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Laure Barjhoux
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Carole Verny-Pierre
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Valérie Sornin
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
| | - Marie-Gabrielle Dondon
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France
| | - Séverine Eon-Marchais
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France
| | | | - Olivier Caron
- Département de Médecine Oncologique, Institut de Cancérologie Gustave Roussy, Villejuif, France
| | | | - Isabelle Coupier
- Hôpital Arnaud de Villeneuve, CHU Montpellier, Service de Génétique médicale et Oncogénétique, Montpellier, France.,ICM Val d'Aurel, Unité d'Oncogénétique, Montpellier, France
| | | | | | | | - Alain Lortholary
- Centre Catherine de Sienne, Service d'Oncologie Médicale, Nantes, France
| | - Paul Gesta
- CH Georges Renon, Service Oncogénétique pour la consultation oncogénétique régionale Poitou-Charentes, Niort, France
| | | | | | | | - Laurence Faivre
- Hôpital d'Enfants, Service de Génétique Médicale, Dijon, France.,Centre Georges François Leclerc, Oncogénétique, Dijon, France
| | - Dominique Stoppa-Lyonnet
- Institut Curie, Service de Génétique, Paris, France.,Inserm, U830, Université Paris-Descartes, Paris, France
| | - Nadine Andrieu
- INSERM, U900, Paris, France.,Institut Curie, Paris, France.,Mines ParisTech, Fontainebleau, France
| | - Olga M Sinilnikova
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France.,Unité Mixte de Génétique Constitutionnelle des Cancers Fréquents, Hospices Civils de Lyon/Centre Léon Bérard, Lyon, France
| | - Sylvie Mazoyer
- Cancer Research Centre of Lyon, CNRS UMR5286/Inserm U1052/Université Lyon 1, Centre Léon Bérard, Lyon, France
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25
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Willems AP, van Engelen BGM, Lefeber DJ. Genetic defects in the hexosamine and sialic acid biosynthesis pathway. Biochim Biophys Acta Gen Subj 2015; 1860:1640-54. [PMID: 26721333 DOI: 10.1016/j.bbagen.2015.12.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/18/2015] [Accepted: 12/19/2015] [Indexed: 01/10/2023]
Abstract
BACKGROUND Congenital disorders of glycosylation are caused by defects in the glycosylation of proteins and lipids. Classically, gene defects with multisystem disease have been identified in the ubiquitously expressed glycosyltransferases required for protein N-glycosylation. An increasing number of defects are being described in sugar supply pathways for protein glycosylation with tissue-restricted clinical symptoms. SCOPE OF REVIEW In this review, we address the hexosamine and sialic acid biosynthesis pathways in sugar metabolism. GFPT1, PGM3 and GNE are essential for synthesis of nucleotide sugars uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) and cytidine-5'-monophospho-N-acetylneuraminic acid (CMP-sialic acid) as precursors for various glycosylation pathways. Defects in these enzymes result in contrasting clinical phenotypes of congenital myasthenia, immunodeficiency or adult-onset myopathy, respectively. We therefore discuss the biochemical mechanisms of known genetic defects in the hexosamine and CMP-sialic acid synthesis pathway in relation to the clinical phenotypes. MAJOR CONCLUSIONS Both UDP-GlcNAc and CMP-sialic acid are important precursors for diverse protein glycosylation reactions and for conversion into other nucleotide-sugars. Defects in the synthesis of these nucleotide sugars might affect a wide range of protein glycosylation reactions. Involvement of multiple glycosylation pathways might contribute to disease phenotype, but the currently available biochemical information on sugar metabolism is insufficient to understand why defects in these pathways present with tissue-specific phenotypes. GENERAL SIGNIFICANCE Future research on the interplay between sugar metabolism and different glycosylation pathways in a tissue- and cell-specific manner will contribute to elucidation of disease mechanisms and will create new opportunities for therapeutic intervention. This article is part of a Special Issue entitled "Glycans in personalised medicine" Guest Editor: Professor Gordan Lauc.
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Affiliation(s)
- Anke P Willems
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Box 9101, 6500 HB Nijmegen, The Netherlands; Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboudumc Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Baziel G M van Engelen
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Box 9101, 6500 HB Nijmegen, The Netherlands
| | - Dirk J Lefeber
- Department of Neurology, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Centre, Box 9101, 6500 HB Nijmegen, The Netherlands; Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboudumc Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.
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26
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Allamand V. [Not Available]. Med Sci (Paris) 2015; 31 Spec No 3:28-9. [PMID: 26546928 DOI: 10.1051/medsci/201531s307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Valérie Allamand
- Centre de de Recherche en Myologie, Sorbonne Universités, UPMC - Inserm UMRS 974, CNRS FRE 3617, Institut de Myologie, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
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