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Fassio A, Esposito A, Kato M, Saitsu H, Mei D, Marini C, Conti V, Nakashima M, Okamoto N, Olmez Turker A, Albuz B, Semerci Gündüz CN, Yanagihara K, Belmonte E, Maragliano L, Ramsey K, Balak C, Siniard A, Narayanan V, Ohba C, Shiina M, Ogata K, Matsumoto N, Benfenati F, Guerrini R. De novo mutations of the ATP6V1A gene cause developmental encephalopathy with epilepsy. Brain 2019; 141:1703-1718. [PMID: 29668857 PMCID: PMC5972584 DOI: 10.1093/brain/awy092] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 02/10/2018] [Indexed: 12/30/2022] Open
Abstract
V-type proton (H+) ATPase (v-ATPase) is a multi-subunit proton pump that regulates pH homeostasis in all eukaryotic cells; in neurons, v-ATPase plays additional and unique roles in synapse function. Through whole exome sequencing, we identified de novo heterozygous mutations (p.Pro27Arg, p.Asp100Tyr, p.Asp349Asn, p.Asp371Gly) in ATP6V1A, encoding the A subunit of v-ATPase, in four patients with developmental encephalopathy with epilepsy. Early manifestations, observed in all patients, were developmental delay and febrile seizures, evolving to encephalopathy with profound delay, hypotonic/dyskinetic quadriparesis and intractable multiple seizure types in two patients (p.Pro27Arg, p.Asp100Tyr), and to moderate delay with milder epilepsy in the other two (p.Asp349Asn, p.Asp371Gly). Modelling performed on the available prokaryotic and eukaryotic structures of v-ATPase predicted p.Pro27Arg to perturb subunit interaction, p.Asp100Tyr to cause steric hindrance and destabilize protein folding, p.Asp349Asn to affect the catalytic function and p.Asp371Gly to impair the rotation process, necessary for proton transport. We addressed the impact of p.Asp349Asn and p.Asp100Tyr mutations on ATP6V1A expression and function by analysing ATP6V1A-overexpressing HEK293T cells and patients’ lymphoblasts. The p.Asp100Tyr mutant was characterized by reduced expression due to increased degradation. Conversely, no decrease in expression and clearance was observed for p.Asp349Asn. In HEK293T cells overexpressing either pathogenic or control variants, p.Asp349Asn significantly increased LysoTracker® fluorescence with no effects on EEA1 and LAMP1 expression. Conversely, p.Asp100Tyr decreased both LysoTracker® fluorescence and LAMP1 levels, leaving EEA1 expression unaffected. Both mutations decreased v-ATPase recruitment to autophagosomes, with no major impact on autophagy. Experiments performed on patients’ lymphoblasts using the LysoSensor™ probe revealed lower pH of endocytic organelles for p.Asp349Asn and a reduced expression of LAMP1 with no effect on the pH for p.Asp100Tyr. These data demonstrate gain of function for p.Asp349Asn characterized by an increased proton pumping in intracellular organelles, and loss of function for p.Asp100Tyr with decreased expression of ATP6V1A and reduced levels of lysosomal markers. We expressed p.Asp349Asn and p.Asp100Tyr in rat hippocampal neurons and confirmed significant and opposite effects in lysosomal labelling. However, both mutations caused a similar defect in neurite elongation accompanied by loss of excitatory inputs, revealing that altered lysosomal homeostasis markedly affects neurite development and synaptic connectivity. This study provides evidence that de novo heterozygous ATP6V1A mutations cause a developmental encephalopathy with a pathomechanism that involves perturbations of lysosomal homeostasis and neuronal connectivity, uncovering a novel role for v-ATPase in neuronal development.
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Affiliation(s)
- Anna Fassio
- Department of Experimental Medicine, University of Genoa, Genoa, Italy.,Center of Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Alessandro Esposito
- Department of Experimental Medicine, University of Genoa, Genoa, Italy.,Center of Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Mitsuhiro Kato
- Department of Paediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Davide Mei
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | - Carla Marini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | - Valerio Conti
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | | | - Burcu Albuz
- Department of Medical Genetics, Pamukkale University Hospital, Denizli, Turkey
| | | | - Keiko Yanagihara
- Department of Paediatric Neurology, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Elisa Belmonte
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Luca Maragliano
- Center of Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Keri Ramsey
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Chris Balak
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Ashley Siniard
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders and Neurogenomics Division Translational Genomics Research Institute, Phoenix, Arizona 85004, USA
| | | | - Chihiro Ohba
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masaaki Shiina
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Fabio Benfenati
- Department of Experimental Medicine, University of Genoa, Genoa, Italy.,Center of Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Florence, Italy.,IRCCS Fondazione Stella Maris, Pisa, Italy
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252
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Dyment DA, Terhal PA, Rustad CF, Tveten K, Griffith C, Jayakar P, Shinawi M, Ellingwood S, Smith R, van Gassen K, McWalter K, Innes AM, Lines MA. De novo substitutions of TRPM3 cause intellectual disability and epilepsy. Eur J Hum Genet 2019; 27:1611-1618. [PMID: 31278393 PMCID: PMC6777445 DOI: 10.1038/s41431-019-0462-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/26/2019] [Accepted: 06/25/2019] [Indexed: 02/04/2023] Open
Abstract
The developmental and epileptic encephalopathies (DEE) are a heterogeneous group of chronic encephalopathies frequently associated with rare de novo nonsynonymous coding variants in neuronally expressed genes. Here, we describe eight probands with a DEE phenotype comprising intellectual disability, epilepsy, and hypotonia. Exome trio analysis showed de novo variants in TRPM3, encoding a brain-expressed transient receptor potential channel, in each. Seven probands were identically heterozygous for a recurrent substitution, p.(Val837Met), in TRPM3's S4-S5 linker region, a conserved domain proposed to undergo conformational change during gated channel opening. The eighth individual was heterozygous for a proline substitution, p.(Pro937Gln), at the boundary between TRPM3's flexible pore-forming loop and an adjacent alpha-helix. General-population truncating variants and microdeletions occur throughout TRPM3, suggesting a pathomechanism other than simple haploinsufficiency. We conclude that de novo variants in TRPM3 are a cause of intellectual disability and epilepsy.
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Affiliation(s)
- David A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada.,Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada
| | - Paulien A Terhal
- Department of Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | | | | | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Sara Ellingwood
- Department of Pediatrics, Division of Genetics, Maine Medical Center, Portland, ME, USA
| | - Rosemarie Smith
- Department of Pediatrics, Division of Genetics, Maine Medical Center, Portland, ME, USA
| | - Koen van Gassen
- Department of Genetics, University Medical Centre Utrecht, Utrecht, the Netherlands
| | | | - A Micheil Innes
- Department of Medical Genetics and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Matthew A Lines
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, ON, Canada. .,Department of Pediatrics, University of Ottawa, Ottawa, ON, Canada.
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253
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Josephs KS, Berner A, George A, Scott RH, Firth HV, Tatton-Brown K. Genomics: the power, potential and pitfalls of the new technologies and how they are transforming healthcare. Clin Med (Lond) 2019; 19:269-272. [PMID: 31308101 PMCID: PMC6752247 DOI: 10.7861/clinmedicine.19-4-269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Powerful new genomic technologies are transforming healthcare. The faster, cheaper generation of genomic data is driving the integration of genomics into all healthcare specialties. Within the next decade, healthcare professionals will be using genomic data to diagnose and manage their patients.However, despite these exciting advances, few clinicians are aware of or prepared for this genomics-based future. Through five patient-focused scenarios with accompanying interviews, this article showcases new genomic technologies while highlighting the inherent challenges associated with complex genomic data.
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Affiliation(s)
- Katherine S Josephs
- South West Thames Regional Genetic Services, London, UK and St George's, University of London, London, UK
| | - Alison Berner
- Barts Cancer Institute, London, UK and clinical research fellow, Genomics England, London, UK
| | | | - Richard H Scott
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK and clinical lead for rare disease, 100,000 Genome Project, Genomics England, London, UK
| | - Helen V Firth
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK and Wellcome Sanger Institute, Cambridge, UK and Joint Committee on Genomics in Medicine, Royal College of Physicians, London, UK
| | - Katrina Tatton-Brown
- St George's University Hospitals NHS Foundation Trust, London, UK and professor in clinical genetics and genomic education, St George's, University of London, London, UK and Joint Committee on Genomics in Medicine, Royal College of Physicians, London, UK
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254
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Hernandez CC, XiangWei W, Hu N, Shen D, Shen W, Lagrange AH, Zhang Y, Dai L, Ding C, Sun Z, Hu J, Zhu H, Jiang Y, Macdonald RL. Altered inhibitory synapses in de novo GABRA5 and GABRA1 mutations associated with early onset epileptic encephalopathies. Brain 2019; 142:1938-1954. [PMID: 31056671 PMCID: PMC6598634 DOI: 10.1093/brain/awz123] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 02/20/2019] [Accepted: 03/07/2019] [Indexed: 12/22/2022] Open
Abstract
We performed next generation sequencing on 1696 patients with epilepsy and intellectual disability using a gene panel with 480 epilepsy-related genes including all GABAA receptor subunit genes (GABRs), and we identified six de novo GABR mutations, two novel GABRA5 mutations (c.880G>T, p.V294F and c.1238C>T, p.S413F), two novel GABRA1 mutations (c.778C>T, p.P260S and c.887T>C, p.L296S/c.944G>T, p.W315L) and two known GABRA1 mutations (c.335G>A, p.R112Q and c.343A>G, p.N115D) in six patients with intractable early onset epileptic encephalopathy. The α5(V294F and S413F) and α1(P260S and L296S/W315L) subunit residue substitutions were all in transmembrane domains, while the α1(R112Q and N115R) subunit residue substitutions were in the N-terminal GABA binding domain. Using multidisciplinary approaches, we compared effects of mutant GABAA receptor α5 and α1 subunits on the properties of recombinant α5β3γ2 and α1β3γ2 GABAA receptors in both neuronal and non-neuronal cells and characterized their effects on receptor clustering, biogenesis and channel function. GABAA receptors containing mutant α5 and α1 subunits all had reduced cell surface and total cell expression with altered endoplasmic reticulum processing, impaired synaptic clustering, reduced GABAA receptor function and decreased GABA binding potency. Our study identified GABRA5 as a causative gene for early onset epileptic encephalopathy and expands the mutant GABRA1 phenotypic spectrum, supporting growing evidence that defects in GABAergic neurotransmission contribute to early onset epileptic encephalopathy phenotypes.
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Affiliation(s)
- Ciria C Hernandez
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Wenshu XiangWei
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, China
- Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing, China
| | - Ningning Hu
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dingding Shen
- The Graduate Program of Neuroscience, Vanderbilt University, Nashville, TN, USA
- Department of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University, School of Medicine. Shanghai, China
| | - Wangzhen Shen
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andre H Lagrange
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Pharmacology and Molecular Physiology and Biophysics, Vanderbilt University, and the Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN, USA
| | - Yujia Zhang
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Lifang Dai
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Changhong Ding
- Department of Neurology, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Zhaohui Sun
- Epilepsy center of Yuquan Hospital, Tsinghua University, Beijing, China
| | - Jiasheng Hu
- Department of Neurology, Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongmin Zhu
- Department of Neurology, Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuwu Jiang
- Department of Pediatrics and Pediatric Epilepsy Center, Peking University First Hospital, Beijing, China
- Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing, China
| | - Robert L Macdonald
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
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255
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Lee Y, Han PL. Early-Life Stress in D2 Heterozygous Mice Promotes Autistic-like Behaviors through the Downregulation of the BDNF-TrkB Pathway in the Dorsal Striatum. Exp Neurobiol 2019; 28:337-351. [PMID: 31308794 PMCID: PMC6614072 DOI: 10.5607/en.2019.28.3.337] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/30/2019] [Accepted: 06/05/2019] [Indexed: 12/12/2022] Open
Abstract
A number of specific genetic variants including gene mutations and single nucleotide variations have been identified in genomewide association studies of autism spectrum disorder (ASD). ASD phenotypes in individuals carrying specific genetic variations are manifest mostly in a heterozygous state. Furthermore, individuals with most genetic variants show incomplete penetrance and phenotypic variability, suggesting that non-genetic factors are also involved in developing ASD. However, the mechanisms of how genetic and environmental factors interactively promote ASD are not clearly understood. In the present study, we investigated whether early-life stress (ELS) in D2 dopamine receptor heterozygous knockout (D2+/−) mice induces ASD-like symptoms. To address that, we exposed D2 heterozygous pups to maternal separation stress for 3 h daily for 13 days beginning on postnatal day 2. D2+/− adult mice that had experienced ELS exhibited impaired sociability in the three-chamber test and home-cage social interaction test and increased grooming behavior, whereas wildtype littermates exposed to ELS did not show those phenotypes. ELS-exposed D2+/− mice had decreased levels of BDNF, TrkB, phospho-ERK1/2 and phospho-CREB in the dorsal striatum. Administration of the TrkB agonist 7,8-dihydroxyflavone (7,8-DHF) to ELS-exposed D2+/− mice rescued the sociability deficits and repetitive behavior. In contrast, behavioral rescue by 7,8-DHF in ELS-exposed D2+/− mice was blocked when TrkB expression in the dorsal striatum was locally inhibited by the injection of TrkB-siRNA. Together, our results suggest that the interaction between ELS and defective D2 gene function promotes autistic-like behaviors by downregulating the BDNF-TrkB pathway in the dorsal striatum.
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Affiliation(s)
- Yunjin Lee
- Department of Brain and Cognitive Sciences, Ewha Womans University, Seoul 03760, Korea
| | - Pyung-Lim Han
- Department of Brain and Cognitive Sciences, Ewha Womans University, Seoul 03760, Korea.,Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
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256
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Xue L, Sun Q, Zhao H, Rovira X, Gai S, He Q, Pin JP, Liu J, Rondard P. Rearrangement of the transmembrane domain interfaces associated with the activation of a GPCR hetero-oligomer. Nat Commun 2019; 10:2765. [PMID: 31235691 PMCID: PMC6591306 DOI: 10.1038/s41467-019-10834-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 06/04/2019] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) can integrate extracellular signals via allosteric interactions within dimers and higher-order oligomers. However, the structural bases of these interactions remain unclear. Here, we use the GABAB receptor heterodimer as a model as it forms large complexes in the brain. It is subjected to genetic mutations mainly affecting transmembrane 6 (TM6) and involved in human diseases. By cross-linking, we identify the transmembrane interfaces involved in GABAB1-GABAB2, as well as GABAB1-GABAB1 interactions. Our data are consistent with an oligomer made of a row of GABAB1. We bring evidence that agonist activation induces a concerted rearrangement of the various interfaces. While the GB1-GB2 interface is proposed to involve TM5 in the inactive state, cross-linking of TM6s lead to constitutive activity. These data bring insight for our understanding of the allosteric interaction between GPCRs within oligomers. G protein-coupled receptors (GPCRs), such as GABAB, can integrate extracellular signals via allosteric interactions within dimers and oligomers. Here authors use crosslinking and identify two transmembrane interfaces in GABAB which undergo a concerted rearrangement upon agonist activation.
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Affiliation(s)
- Li Xue
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qian Sun
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Han Zhao
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Xavier Rovira
- Institut de Génomique Fonctionnelle (IGF), CNRS, INSERM, Université de Montpellier, Montpellier, 34094 Montpellier cedex 05, France.,Molecular Photopharmacology Research Group, The Tissue Repair and Regeneration Laboratory, University of Vic - Central University of Catalonia, C. de la Laura, 13, Vic, 08500, Spain
| | - Siyu Gai
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Qianwen He
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle (IGF), CNRS, INSERM, Université de Montpellier, Montpellier, 34094 Montpellier cedex 05, France.
| | - Jianfeng Liu
- Cellular Signaling laboratory, International Research Center for Sensory Biology and Technology of MOST, Key Laboratory of Molecular Biophysics of MOE, and College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, Hubei, China.
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle (IGF), CNRS, INSERM, Université de Montpellier, Montpellier, 34094 Montpellier cedex 05, France
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257
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Helbig I, Lopez-Hernandez T, Shor O, Galer P, Ganesan S, Pendziwiat M, Rademacher A, Ellis CA, Hümpfer N, Schwarz N, Seiffert S, Peeden J, Shen J, Štěrbová K, Hammer TB, Møller RS, Shinde DN, Tang S, Smith L, Poduri A, Krause R, Benninger F, Helbig KL, Haucke V, Weber YG. A Recurrent Missense Variant in AP2M1 Impairs Clathrin-Mediated Endocytosis and Causes Developmental and Epileptic Encephalopathy. Am J Hum Genet 2019; 104:1060-1072. [PMID: 31104773 PMCID: PMC6556875 DOI: 10.1016/j.ajhg.2019.04.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 03/29/2019] [Indexed: 11/17/2022] Open
Abstract
The developmental and epileptic encephalopathies (DEEs) are heterogeneous disorders with a strong genetic contribution, but the underlying genetic etiology remains unknown in a significant proportion of individuals. To explore whether statistical support for genetic etiologies can be generated on the basis of phenotypic features, we analyzed whole-exome sequencing data and phenotypic similarities by using Human Phenotype Ontology (HPO) in 314 individuals with DEEs. We identified a de novo c.508C>T (p.Arg170Trp) variant in AP2M1 in two individuals with a phenotypic similarity that was higher than expected by chance (p = 0.003) and a phenotype related to epilepsy with myoclonic-atonic seizures. We subsequently found the same de novo variant in two individuals with neurodevelopmental disorders and generalized epilepsy in a cohort of 2,310 individuals who underwent diagnostic whole-exome sequencing. AP2M1 encodes the μ-subunit of the adaptor protein complex 2 (AP-2), which is involved in clathrin-mediated endocytosis (CME) and synaptic vesicle recycling. Modeling of protein dynamics indicated that the p.Arg170Trp variant impairs the conformational activation and thermodynamic entropy of the AP-2 complex. Functional complementation of both the μ-subunit carrying the p.Arg170Trp variant in human cells and astrocytes derived from AP-2μ conditional knockout mice revealed a significant impairment of CME of transferrin. In contrast, stability, expression levels, membrane recruitment, and localization were not impaired, suggesting a functional alteration of the AP-2 complex as the underlying disease mechanism. We establish a recurrent pathogenic variant in AP2M1 as a cause of DEEs with distinct phenotypic features, and we implicate dysfunction of the early steps of endocytosis as a disease mechanism in epilepsy.
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Affiliation(s)
- Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany; Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | | | - Oded Shor
- Department of Neurology, Rabin Medical Center, Petach Tikva 4941492, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Peter Galer
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shiva Ganesan
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Manuela Pendziwiat
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Annika Rademacher
- Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany
| | - Colin A Ellis
- Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Nadja Hümpfer
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195 Berlin, Germany
| | - Niklas Schwarz
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Simone Seiffert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Joseph Peeden
- East Tennessee Children's Hospital, University of Tennessee Department of Medicine, Knoxville, TN 37916, USA
| | - Joseph Shen
- Division of Genetics, Department of Pediatrics, University of California San Francisco, Fresno, CA 93701, USA
| | - Katalin Štěrbová
- Department of Child Neurology, Charles University 2nd Faculty of Medicine and University Hospital Motol, 150 06 Prague, Czech Republic
| | | | - Rikke S Møller
- Danish Epilepsy Centre Filadelfia, 4293 Dianalund, Denmark; Institute for Regional Health Services, University of Southern Denmark, 5230 Odense, Denmark
| | - Deepali N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Lacey Smith
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4365 Esch-sur-Alzette, Luxembourg
| | - Felix Benninger
- Department of Neurology, Rabin Medical Center, Petach Tikva 4941492, Israel; Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195 Berlin, Germany
| | - Yvonne G Weber
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany; Department of Neurosurgery, University of Tübingen, 72076 Tübingen, Germany
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258
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Shin W, Kweon H, Kang R, Kim D, Kim K, Kang M, Kim SY, Hwang SN, Kim JY, Yang E, Kim H, Kim E. Scn2a Haploinsufficiency in Mice Suppresses Hippocampal Neuronal Excitability, Excitatory Synaptic Drive, and Long-Term Potentiation, and Spatial Learning and Memory. Front Mol Neurosci 2019; 12:145. [PMID: 31249508 PMCID: PMC6582764 DOI: 10.3389/fnmol.2019.00145] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/17/2019] [Indexed: 01/13/2023] Open
Abstract
Nav1.2, a voltage-gated sodium channel subunit encoded by the Scn2a gene, has been implicated in various brain disorders, including epilepsy, autism spectrum disorder, intellectual disability, and schizophrenia. Nav1.2 is known to regulate the generation of action potentials in the axon initial segment and their propagation along axonal pathways. Nav1.2 also regulates synaptic integration and plasticity by promoting back-propagation of action potentials to dendrites, but whether Nav1.2 deletion in mice affects neuronal excitability, synaptic transmission, synaptic plasticity, and/or disease-related animal behaviors remains largely unclear. Here, we report that mice heterozygous for the Scn2a gene (Scn2a+/- mice) show decreased neuronal excitability and suppressed excitatory synaptic transmission in the presence of network activity in the hippocampus. In addition, Scn2a+/- mice show suppressed hippocampal long-term potentiation (LTP) in association with impaired spatial learning and memory, but show largely normal locomotor activity, anxiety-like behavior, social interaction, repetitive behavior, and whole-brain excitation. These results suggest that Nav1.2 regulates hippocampal neuronal excitability, excitatory synaptic drive, LTP, and spatial learning and memory in mice.
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Affiliation(s)
- Wangyong Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Hanseul Kweon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Ryeonghwa Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Doyoun Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, South Korea
| | - Kyungdeok Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Muwon Kang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Seo Yeong Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Sun Nam Hwang
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, South Korea
| | - Jin Yong Kim
- Department of Anatomy and Division of Brain Korea 21, Biomedical Science, College of Medicine, Korea University, Seoul, South Korea
| | - Esther Yang
- Department of Anatomy and Division of Brain Korea 21, Biomedical Science, College of Medicine, Korea University, Seoul, South Korea
| | - Hyun Kim
- Department of Anatomy and Division of Brain Korea 21, Biomedical Science, College of Medicine, Korea University, Seoul, South Korea
| | - Eunjoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.,Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, South Korea
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259
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Abstract
PURPOSE OF REVIEW The purpose of this review is to highlight the significant advances in the testing, interpretation, and diagnosis of genetic abnormalities in critically ill children and to emphasize that pediatric intensivists are uniquely positioned to search for genetic diagnoses in these patients. RECENT FINDINGS Ten years following the first clinical diagnosis made through whole exome sequencing, we remain in the dark about the function of roughly 75% of our genes. However, steady advancements in molecular techniques, particularly next-generation sequencing, have spurred a rapid expansion of our understanding of the genetic underpinnings of severe congenital diseases. This has resulted in not only improved clinical diagnostics but also a greater availability of research programs actively investigating rare, undiagnosed diseases. In this background, the scarcity of clinical geneticists compels nongeneticists to familiarize themselves with the types of patients that could benefit from genetic testing, interpretations of test results as well as the available resources for these patients. SUMMARY When caring for seriously ill children, critical care pediatricians should actively seek the possibility of an underlying genetic cause for their patients' conditions. This is true even in instances when a child has a descriptive diagnosis without a clear underlying molecular genetic mechanism. By promoting such diagnostics, in both clinical and research settings, pediatric intensivists can advance the care of their patients, improve the quality of information provided to families, and contribute to the knowledge of broad fields in medicine.
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260
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Bourgey M, Dali R, Eveleigh R, Chen KC, Letourneau L, Fillon J, Michaud M, Caron M, Sandoval J, Lefebvre F, Leveque G, Mercier E, Bujold D, Marquis P, Van PT, Anderson de Lima Morais D, Tremblay J, Shao X, Henrion E, Gonzalez E, Quirion PO, Caron B, Bourque G. GenPipes: an open-source framework for distributed and scalable genomic analyses. Gigascience 2019; 8:giz037. [PMID: 31185495 PMCID: PMC6559338 DOI: 10.1093/gigascience/giz037] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 09/28/2018] [Accepted: 03/10/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing. FINDINGS Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for high-performance computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA sequencing, chromatin immunoprecipitation sequencing, DNA sequencing, methylation sequencing, Hi-C, capture Hi-C, metagenomics, and Pacific Biosciences long-read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has already been configured on several servers, and a Docker image is also available to facilitate additional installations. CONCLUSIONS GenPipes offers genomics researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.
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Affiliation(s)
- Mathieu Bourgey
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Rola Dali
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Robert Eveleigh
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Kuang Chung Chen
- McGill HPC Centre, McGill University, Montréal, QC, Canada
- Calcul Québec, QC, Canada
| | - Louis Letourneau
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Joel Fillon
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Marc Michaud
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Maxime Caron
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Johanna Sandoval
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montréal, QC, Canada
| | - Francois Lefebvre
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Gary Leveque
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Eloi Mercier
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - David Bujold
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Pascale Marquis
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, Montréal, QC, Canada
| | - Xiaojian Shao
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Edouard Henrion
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Pierre-Olivier Quirion
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Bryan Caron
- McGill HPC Centre, McGill University, Montréal, QC, Canada
- Calcul Québec, QC, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
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261
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Ganapathy A, Mishra A, Soni MR, Kumar P, Sadagopan M, Kanthi AV, Patric IRP, George S, Sridharan A, Thyagarajan TC, Aswathy SL, Vidya HK, Chinnappa SM, Nayanala S, Prakash MB, Raghavendrachar VG, Parulekar M, Gowda VK, Nampoothiri S, Menon RN, Pachat D, Udani V, Naik N, Kamate M, Devi ARR, Mohammed Kunju PA, Nair M, Hegde AU, Kumar MP, Sundaram S, Tilak P, Puri RD, Shah K, Sheth J, Hasan Q, Sheth F, Agrawal P, Katragadda S, Veeramachaneni V, Chandru V, Hariharan R, Mannan AU. Multi-gene testing in neurological disorders showed an improved diagnostic yield: data from over 1000 Indian patients. J Neurol 2019; 266:1919-1926. [PMID: 31069529 DOI: 10.1007/s00415-019-09358-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/25/2019] [Accepted: 05/03/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Neurological disorders are clinically heterogeneous group of disorders and are major causes of disability and death. Several of these disorders are caused due to genetic aberration. A precise and confirmatory diagnosis in the patients in a timely manner is essential for appropriate therapeutic and management strategies. Due to the complexity of the clinical presentations across various neurological disorders, arriving at an accurate diagnosis remains a challenge. METHODS We sequenced 1012 unrelated patients from India with suspected neurological disorders, using TruSight One panel. Genetic variations were identified using the Strand NGS software and interpreted using the StrandOmics platform. RESULTS We were able to detect mutations in 197 genes in 405 (40%) cases and 178 mutations were novel. The highest diagnostic rate was observed among patients with muscular dystrophy (64%) followed by leukodystrophy and ataxia (43%, each). In our cohort, 26% of the patients who received definitive diagnosis were primarily referred with complex neurological phenotypes with no suggestive diagnosis. In terms of mutations types, 62.8% were truncating and in addition, 13.4% were structural variants, which are also likely to cause loss of function. CONCLUSION In our study, we observed an improved performance of multi-gene panel testing, with an overall diagnostic yield of 40%. Furthermore, we show that NGS (next-generation sequencing)-based testing is comprehensive and can detect all types of variants including structural variants. It can be considered as a single-platform genetic test for neurological disorders that can provide a swift and definitive diagnosis in a cost-effective manner.
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Affiliation(s)
- Aparna Ganapathy
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Avshesh Mishra
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Megha Rani Soni
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Priyanka Kumar
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Mukunth Sadagopan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Anil Vittal Kanthi
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Irene Rosetta Pia Patric
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Sobha George
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Aparajit Sridharan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - T C Thyagarajan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - S L Aswathy
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - H K Vidya
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Swathi M Chinnappa
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Swetha Nayanala
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Manasa B Prakash
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Vijayashree G Raghavendrachar
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Minothi Parulekar
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | | | | | - Ramshekhar N Menon
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | | | - Vrajesh Udani
- P. D. Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - Neeta Naik
- EN1 Neuro Services Pvt. Ltd., Mumbai, India
| | | | | | | | | | | | | | - Soumya Sundaram
- Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, India
| | - Preetha Tilak
- St. Johns Medical College Hospital, Bangalore, India
| | | | - Krati Shah
- ONE-Centre for Rheumatology and Genetics, Vadodara, India
| | - Jayesh Sheth
- FRIGE'S Institute of Human Genetics, Ahmedabad, India
| | | | - Frenny Sheth
- FRIGE'S Institute of Human Genetics, Ahmedabad, India
| | - Pooja Agrawal
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Shanmukh Katragadda
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Vamsi Veeramachaneni
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India
| | - Vijay Chandru
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India.,Indian Institute of Science, Bangalore, India
| | - Ramesh Hariharan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India.,Indian Institute of Science, Bangalore, India
| | - Ashraf U Mannan
- Strand Center for Genomics and Personalized Medicine, Strand Life Sciences, Bellary Road, Hebbal, Bangalore, 560024, India.
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262
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Belkady B, Elkhattabi L, Elkarhat Z, Zarouf L, Razoki L, Aboulfaraj J, Nassereddine S, Cadi R, Rouba H, Barakat A. Chromosomal Abnormalities in Patients with Intellectual Disability: A 21-Year Retrospective Study. Hum Hered 2019; 83:274-282. [PMID: 31064002 DOI: 10.1159/000499710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/19/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Intellectual disability (ID) has been defined as a considerably reduced ability to understand new or complex information and to learn new skills. It is associated with life-long intellectual and adaptive functioning impairments that have a profound impact on individuals, families, and society. It affects about 3% of the general population. ID often comes out with other mental conditions like attention deficit, hyperactivity, and autism spectrum disorders (ASD), and it can be part of a malformation syndrome that affects other organs. It may be syndromic (S-ID) or non-syndromic (NS-ID). OBJECTIVE The aims of this study were to identify the profile of intellectually disable patients being referred for cytogenetic analysis in Morocco, to determine the prevalence of chromosomal abnormalities in a Moroccan group, and to compare the results with those of analogous studies from other countries. PARTICIPANTS We included data from Moroccan patients with NS-ID and others with S-ID (mostly Down syndrome cases) who have been referred between 1996 and 2016. 1,626 patients were involved in this study, 1,200 were referred with a clinical diagnosis of Down syndrome, 37 were clinically diagnosed for ASD with ID, and 389 were suspected of NS-ID. RESULTS We identified 1,200 cases of Down syndrome. In 1,096 analyses (91.3%), a cytogenetic variant of trisomy 21 was identified: standard trisomy 21 in 1,037 cases (94.6%), a translocation in 34 cases (3.10%), and mosaicism in 25 cases (2.3%). The cytogenetic analysis among ASD with ID cases did not reveal any specific chromosomal abnormalities. The present study also shows that chromosomal abnormalities were present in 6.43% of the patients with NS-ID (25 abnormal karyotypes out of 389 NS-ID cases). Autosomal structural abnormalities were the largest proportion of chromosomal aberrations. CONCLUSION The high rate of chromosomal abnormalities found in the Moroccan patients studied demonstrates the capital importance of cytogenetic evaluation in patients who show ID or any clinical development abnormality.
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Affiliation(s)
- Boutaina Belkady
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco.,Laboratory of Molecular Genetics and Biotechnology, Faculty of Science Ain Chock, Casablanca, Morocco
| | - Lamiae Elkhattabi
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Zouhair Elkarhat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Latifa Zarouf
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Lunda Razoki
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Jamila Aboulfaraj
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Sanaa Nassereddine
- Laboratory of Cytogenetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Rachida Cadi
- Laboratory of Molecular Genetics and Biotechnology, Faculty of Science Ain Chock, Casablanca, Morocco
| | - Hassan Rouba
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Abdelhamid Barakat
- Laboratory of Genomics and Human Genetics, Institut Pasteur du Maroc, Casablanca, Morocco,
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263
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Mehra C, Sil A, Hedderly T, Kyriakopoulos M, Lim M, Turnbull J, Happe F, Baird G, Absoud M. Childhood disintegrative disorder and autism spectrum disorder: a systematic review. Dev Med Child Neurol 2019; 61:523-534. [PMID: 30548847 DOI: 10.1111/dmcn.14126] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/25/2018] [Indexed: 12/01/2022]
Abstract
AIM In an attempt to clarify the debate surrounding the diagnostic validity of childhood disintegrative disorder (CDD), we systematically reviewed its characteristics and compared it with autism spectrum disorder (ASD). METHOD Four databases were searched (PubMed, PsycINFO, Embase, and Web of Science). Included articles had participants with CDD, as defined by symptoms present in the criteria of the Diagnostic and Statistical Manual of Mental Disorders, Fourth Edition, Text Revision and the International Classification of Diseases, 10th Revision. Comparison groups were those with ASD and ASD with regression. Case studies were excluded. RESULTS Twenty articles, comprising 96 participants with CDD (80 males, 16 females), were included. Most studies were cross-sectional. The prevalence of CDD was 1.1 to 9.2 per 100 000, with a mean age at regression of 3 years 2 months (SD 1y 1mo), with a range of 2 years to 7 years. In addition to core CDD symptoms, most had intellectual impairment, anxiety, challenging behaviours, and regressed in toileting skills. Participants with CDD and ASD shared core diagnostic and extra-diagnostic features. However, participants with CDD seemed to have more severe symptoms and a different symptom profile, including apparently typical development before regression, faster regression, more affective symptoms, and more global developmental deficit. Possible genetic and autoimmune neurobiological mechanisms were identified. INTERPRETATION There is limited high-quality evidence describing the aetiology and outcomes of CDD. However, given the qualitative and prognostic differences between ASD and CDD, we recommend that future diagnostic criteria should distinguish late-onset regression.
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Affiliation(s)
- Chirag Mehra
- Children's Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, King's Health Partners Academic Health Science Centre, London, UK
| | - Annesha Sil
- Institute of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Tammy Hedderly
- Children's Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, King's Health Partners Academic Health Science Centre, London, UK
| | - Marinos Kyriakopoulos
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- National and Specialist Acorn Lodge Inpatient Children's Unit, Child and Adolescent Mental Health Clinical Academic Group, South London and the Maudsley NHS Foundation Trust, London, UK
| | - Ming Lim
- Children's Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, King's Health Partners Academic Health Science Centre, London, UK
| | - Jessica Turnbull
- Evelina London Community Children's Services, Sunshine House Children and Young People's Development Centre, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Francesca Happe
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Gillian Baird
- Children's Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, King's Health Partners Academic Health Science Centre, London, UK
| | - Michael Absoud
- Children's Neurosciences, Evelina London Children's Hospital, St Thomas' Hospital, King's Health Partners Academic Health Science Centre, London, UK
- Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
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264
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Krenn M, Knaus A, Westphal DS, Wortmann SB, Polster T, Woermann FG, Karenfort M, Mayatepek E, Meitinger T, Wagner M, Distelmaier F. Biallelic mutations in PIGP cause developmental and epileptic encephalopathy. Ann Clin Transl Neurol 2019; 6:968-973. [PMID: 31139695 PMCID: PMC6530525 DOI: 10.1002/acn3.768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 12/29/2022] Open
Abstract
Developmental and epileptic encephalopathies are characterized by infantile seizures and psychomotor delay. Glycosylphosphatidylinositol biosynthesis defects, resulting in impaired tethering of various proteins to the cell surface, represent the underlying pathology in some patients. One of the genes involved, PIGP, has recently been associated with infantile seizures and developmental delay in two siblings. Here, we report the second family with a markedly overlapping phenotype due to a homozygous frameshift mutation (c.456delA;p.Glu153Asnfs*34) in PIGP. Flow cytometry of patient granulocytes confirmed reduced expression of glycosylphosphatidylinositol-anchored proteins as functional consequence. Our findings corroborate PIGP as a monogenic disease gene for developmental and epileptic encephalopathy.
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Affiliation(s)
- Martin Krenn
- Department of NeurologyMedical University of ViennaViennaAustria
- Institute of Human GeneticsTechnical University MunichMunichGermany
| | - Alexej Knaus
- Institute for Genomic Statistics and BioinformaticsRheinische Friedrich‐Wilhelms UniversitätBonnGermany
| | - Dominik S. Westphal
- Institute of Human GeneticsTechnical University MunichMunichGermany
- Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Saskia B. Wortmann
- Institute of Human GeneticsTechnical University MunichMunichGermany
- Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
- University Children's HospitalParacelsus Medical UniversitySalzburgAustria
| | | | | | - Michael Karenfort
- Department of General Pediatrics, Neonatology and Pediatric CardiologyUniversity Children's HospitalMedical FacultyHeinrich‐Heine‐University DüsseldorfDüsseldorfGermany
| | - Ertan Mayatepek
- Department of General Pediatrics, Neonatology and Pediatric CardiologyUniversity Children's HospitalMedical FacultyHeinrich‐Heine‐University DüsseldorfDüsseldorfGermany
| | - Thomas Meitinger
- Institute of Human GeneticsTechnical University MunichMunichGermany
- Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Matias Wagner
- Institute of Human GeneticsTechnical University MunichMunichGermany
- Institute of Human GeneticsHelmholtz Zentrum MünchenNeuherbergGermany
- Institute of NeurogenomicsHelmholtz Zentrum MünchenNeuherbergGermany
| | - Felix Distelmaier
- Department of General Pediatrics, Neonatology and Pediatric CardiologyUniversity Children's HospitalMedical FacultyHeinrich‐Heine‐University DüsseldorfDüsseldorfGermany
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265
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Lecoquierre F, Duffourd Y, Vitobello A, Bruel AL, Urteaga B, Coubes C, Garret P, Nambot S, Chevarin M, Jouan T, Moutton S, Tran-Mau-Them F, Philippe C, Sorlin A, Faivre L, Thauvin-Robinet C. Variant recurrence in neurodevelopmental disorders: the use of publicly available genomic data identifies clinically relevant pathogenic missense variants. Genet Med 2019; 21:2504-2511. [DOI: 10.1038/s41436-019-0518-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/12/2019] [Indexed: 12/19/2022] Open
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266
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Denis J, Villeneuve N, Cacciagli P, Mignon-Ravix C, Lacoste C, Lefranc J, Napuri S, Damaj L, Villega F, Pedespan JM, Moutton S, Mignot C, Doummar D, Lion-François L, Gataullina S, Dulac O, Martin M, Gueden S, Lesca G, Julia S, Cances C, Journel H, Altuzarra C, Ben Zeev B, Afenjar A, Barth M, Villard L, Milh M. Clinical study of 19 patients with SCN8A-related epilepsy: Two modes of onset regarding EEG and seizures. Epilepsia 2019; 60:845-856. [PMID: 31026061 DOI: 10.1111/epi.14727] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 01/29/2023]
Abstract
OBJECTIVE To describe the mode of onset of SCN8A-related severe epilepsy in order to facilitate early recognition, and eventually early treatment with sodium channel blockers. METHODS We reviewed the phenotype of patients carrying a mutation in the SCN8A gene, among a multicentric cohort of 638 patients prospectively followed by several pediatric neurologists. We focused on the way clinicians made the diagnosis of epileptic encephalopathy, the very first symptoms, electroencephalography (EEG) findings, and seizure types. We made genotypic/phenotypic correlation based on epilepsy-associated missense variant localization over the protein. RESULTS We found 19 patients carrying a de novo mutation of SCN8A, representing 3% of our cohort, with 9 mutations being novel. Age at onset of epilepsy was 1 day to 16 months. We found two modes of onset: 12 patients had slowly emerging onset with rare and/or subtle seizures and normal interictal EEG (group 1). The first event was either acute generalized tonic-clonic seizure (GTCS; Group 1a, n = 6) or episodes of myoclonic jerks that were often mistaken for sleep-related movements or other movement disorders (Group 1b, n = 6). Seven patients had a sudden onset of frequent tonic seizures or epileptic spasms with abnormal interictal EEG leading to rapid diagnosis of epileptic encephalopathy. Sodium channel blockers were effective or nonaggravating in most cases. SIGNIFICANCE SCN8A is the third most prevalent early onset epileptic encephalopathy gene and is associated with two modes of onset of epilepsy.
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Affiliation(s)
- Julien Denis
- Pediatric Neurology Department, Timone Children Hospital, Reference Center for Rare Epilepsies, APHM, Marseille, France
| | - Nathalie Villeneuve
- Pediatric Neurology Department, Timone Children Hospital, Reference Center for Rare Epilepsies, APHM, Marseille, France
| | - Pierre Cacciagli
- Medical Genetics Department, Timone Children Hospital, Marseille, France
| | | | - Caroline Lacoste
- Medical Genetics Department, Timone Children Hospital, Marseille, France
| | - Jeremie Lefranc
- Pediatrics and Medical Genetics Department, CHU Brest, Brest, France
| | - Sylvia Napuri
- Department of Pediatrics, Rennes University Hospital, Rennes, France
| | - Lena Damaj
- Department of Pediatrics, Rennes University Hospital, Rennes, France
| | - Frederic Villega
- Department of Pediatric Neurology, University Children's Hospital of Bordeaux, Bordeaux, France
| | - Jean-Michel Pedespan
- Department of Pediatric Neurology, University Children's Hospital of Bordeaux, Bordeaux, France
| | - Sebastien Moutton
- Medical Genetics Department, University Hospital of Bordeaux, Bordeaux, France
| | - Cyril Mignot
- Pediatric Neurology Department, Trousseau Hospital, AP-HP, Paris, France
| | - Diane Doummar
- Pediatric Neurology Department, Trousseau Hospital, AP-HP, Paris, France
| | | | - Svetlana Gataullina
- Paediatric Neurology Department, Paris-Sud University, Bicêtre Hospital, Kremlin-Bicêtre, France.,Inserm U1129, Necker Hospital, Paris, France
| | | | - Melanie Martin
- Department of Histology, Cytology, Cytogenetics and Cell Biology, University Hospital of Limoges, Limoges, France
| | - Sophie Gueden
- Pediatric Neurology Department, Angers Hospital and University, Angers, France
| | - Gaetan Lesca
- Department of Medical Genetics, Groupement Hospitalier Est, and ERN EpiCARE, University Hospitals of Lyon (HCL), Lyon, France.,Lyon Neuroscience Research Center, CNRS UMR5292, INSERM U1028, Lyon, France
| | - Sophie Julia
- Genetics Unit, Toulouse University Hospital, Toulouse, France
| | - Claude Cances
- Department of Pediatric Neurology, Toulouse Children Hospital, Toulouse University Hospital, Toulouse, France
| | - Hubert Journel
- Department of Genetics, Vannes Bretagne-Atlantique Hospital, Vannes, France
| | | | - Bruria Ben Zeev
- Chaim Sheba Medical Center, Edmond and Lily Safra Children's Hospital, Ramat Gan, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Alexandra Afenjar
- Medical Genetics Department, AP-HP, University hospital Armand Trousseau, Paris, France
| | - Magalie Barth
- Department of Genetics, Angers Hospital and University, Angers, France
| | - Laurent Villard
- Medical Genetics Department, Timone Children Hospital, Marseille, France.,Aix Marseille University, INSERM, UMR-S 1251, MMG, Marseille, France
| | - Mathieu Milh
- Pediatric Neurology Department, Timone Children Hospital, Reference Center for Rare Epilepsies, APHM, Marseille, France.,Aix Marseille University, INSERM, UMR-S 1251, MMG, Marseille, France
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267
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Park J, Colombo R, Schäferhoff K, Janiri L, Grimmel M, Sturm M, Grasshoff U, Dufke A, Haack TB, Kehrer M. Novel HIVEP2 Variants in Patients with Intellectual Disability. Mol Syndromol 2019; 10:195-201. [PMID: 31602191 DOI: 10.1159/000499060] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2019] [Indexed: 12/31/2022] Open
Abstract
Intellectual disability (ID) occurs in approximately 1% of the population. Over the last years, broad sequencing approaches such as whole exome sequencing (WES) substantially contributed to the definition of the molecular defects underlying nonsyndromic ID. Pathogenic variants in HIVEP2, which encodes the human immunodeficiency virus type I enhancer binding protein 2, have recently been reported as a cause of ID, developmental delay, behavioral disorders, and dysmorphic features. HIVEP2 serves as a transcriptional factor regulating NF-ĸB and diverse genes that are essential in neural development. To date, only 8 patients with pathogenic de novo nonsense or frameshift variants and 1 patient with a pathogenic missense variant in HIVEP2 have been reported. By WES, we identified 2 novel truncating HIVEP2 variants, c.6609_6616delTGAGGGTC (p.Glu2204*) and c.6667C>T (p.Arg2223*), in 2 young adults presenting with developmental delay and mild ID without any dysmorphic features, systemic malformations, or behavioral issues.
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Affiliation(s)
- Joohyun Park
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Roberto Colombo
- Institute of Clinical Biochemistry, Faculty of Medicine, Catholic University, Rome, Italy.,Institute of IRCCS Policlinico Gemelli, Rome, Italy
| | - Karin Schäferhoff
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Luigi Janiri
- Institute of Psychiatry and Psychology, Faculty of Medicine, Catholic University, Rome, Italy.,Institute of IRCCS Policlinico Gemelli, Rome, Italy
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Martin Kehrer
- Institute of Medical Genetics and Applied Genomics, Hertie Institute for Clinical Brain Research, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
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268
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Wang W, Corominas R, Lin GN. De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. Front Genet 2019; 10:258. [PMID: 31001316 PMCID: PMC6456656 DOI: 10.3389/fgene.2019.00258] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
Neurodevelopmental and psychiatric disorders are a highly disabling and heterogeneous group of developmental and mental disorders, resulting from complex interactions of genetic and environmental risk factors. The nature of multifactorial traits and the presence of comorbidity and polygenicity in these disorders present challenges in both disease risk identification and clinical diagnoses. The genetic component has been firmly established, but the identification of all the causative variants remains elusive. The development of next-generation sequencing, especially whole exome sequencing (WES), has greatly enriched our knowledge of the precise genetic alterations of human diseases, including brain-related disorders. In particular, the extensive usage of WES in research studies has uncovered the important contribution of de novo mutations (DNMs) to these disorders. Trio and quad familial WES are a particularly useful approach to discover DNMs. Here, we review the major WES studies in neurodevelopmental and psychiatric disorders and summarize how genes hit by discovered DNMs are shared among different disorders. Next, we discuss different integrative approaches utilized to interrogate DNMs and to identify biological pathways that may disrupt brain development and shed light on our understanding of the genetic architecture underlying these disorders. Lastly, we discuss the current state of the transition from WES research to its routine clinical application. This review will assist researchers and clinicians in the interpretation of variants obtained from WES studies, and highlights the need to develop consensus analytical protocols and validated lists of genes appropriate for clinical laboratory analysis, in order to reach the growing demands.
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Affiliation(s)
- Weidi Wang
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
| | - Roser Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras, Valencia, Spain
- Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Guan Ning Lin
- Shanghai Mental Health Center, School of Biomedical Engineering, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai, China
- Brain Science and Technology Research Center, Shanghai Jiao Tong University, Shanghai, China
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269
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Peng J, Guan J, Shang X. Predicting Parkinson's Disease Genes Based on Node2vec and Autoencoder. Front Genet 2019; 10:226. [PMID: 31001311 PMCID: PMC6454041 DOI: 10.3389/fgene.2019.00226] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/28/2019] [Indexed: 12/26/2022] Open
Abstract
Identifying genes associated with Parkinson's disease plays an extremely important role in the diagnosis and treatment of Parkinson's disease. In recent years, based on the guilt-by-association hypothesis, many methods have been proposed to predict disease-related genes, but few of these methods are designed or used for Parkinson's disease gene prediction. In this paper, we propose a novel prediction method for Parkinson's disease gene prediction, named N2A-SVM. N2A-SVM includes three parts: extracting features of genes based on network, reducing the dimension using deep neural network, and predicting Parkinson's disease genes using a machine learning method. The evaluation test shows that N2A-SVM performs better than existing methods. Furthermore, we evaluate the significance of each step in the N2A-SVM algorithm and the influence of the hyper-parameters on the result. In addition, we train N2A-SVM on the recent dataset and used it to predict Parkinson's disease genes. The predicted top-rank genes can be verified based on literature study.
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Affiliation(s)
| | | | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, China
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270
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Manti F, Nardecchia F, Barresi S, Venditti M, Pizzi S, Hamdan FF, Blau N, Burlina A, Tartaglia M, Leuzzi V. Neurotransmitter trafficking defect in a patient with clathrin (CLTC) variation presenting with intellectual disability and early-onset parkinsonism. Parkinsonism Relat Disord 2019; 61:207-210. [DOI: 10.1016/j.parkreldis.2018.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/20/2018] [Accepted: 10/10/2018] [Indexed: 01/02/2023]
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271
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Abstract
The solute carrier (SLC) group of membrane transport proteins includes about 400 members organized into more than 50 families. The SLC family that comprises nucleoside-sugar transporters is referred to as SLC35. One of the members of this family is SLC35F1. The function of SLC35F1 is still unknown; however, recent studies demonstrated that SLC35F1 mRNA is highly expressed in the brain and in the kidney. Therefore, we examine the distribution of Slc35f1 protein in the murine forebrain using immunohistochemistry. We could demonstrate that Slc35f1 is highly expressed in the adult mouse brain in a variety of different brain structures, including the cortex, hippocampus, amygdala, thalamus, basal ganglia, and hypothalamus. To examine the possible roles of Slc35f1 and its subcellular localization, we used an in vitro glioblastoma cell line expressing Slc35f1. Co-labeling experiments were performed to reveal the subcellular localization of Slc35f1. Our results indicate that Slc35f1 neither co-localizes with markers for the Golgi apparatus nor with markers for the endoplasmic reticulum. Time-lapse microscopy of living cells revealed that Slc35f1-positive structures are highly dynamic and resemble vesicles. Using super-resolution microscopy, these Slc35f1-positive spots clearly co-localize with the recycling endosome marker Rab11.
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272
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Hernandez CC, Macdonald RL. A structural look at GABA A receptor mutations linked to epilepsy syndromes. Brain Res 2019; 1714:234-247. [PMID: 30851244 DOI: 10.1016/j.brainres.2019.03.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/12/2022]
Abstract
Understanding the genetic variation in GABAA receptor subunit genes (GABRs), GABRA1-6, GABRB1-3, GABRG1-3 and GABRD, in individuals affected by epilepsy may improve the diagnosis and treatment of epilepsy syndromes through identification of disease-associated variants. However, the lack of functional analysis and validation of many novel and previously reported familial and de novo mutations have made it challenging to address meaningful gene associations with epilepsy syndromes. GABAA receptors belong to the Cys-loop receptor family. Even though GABAA receptor mutant residues are widespread among different GABRs, their frequent occurrence in important structural domains that share common functional features suggests associations between structure and function.
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Affiliation(s)
- Ciria C Hernandez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
| | - Robert L Macdonald
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
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273
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Dentici ML, Barresi S, Niceta M, Ciolfi A, Trivisano M, Bartuli A, Digilio MC, Specchio N, Dallapiccola B, Tartaglia M. Expanding the clinical spectrum associated withPACS2mutations. Clin Genet 2019; 95:525-531. [DOI: 10.1111/cge.13516] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 01/10/2019] [Accepted: 01/23/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Maria L. Dentici
- Medical Genetics, Academic Department of Pediatrics; Ospedale Pediatrico Bambino Gesù; Rome Italy
| | - Sabina Barresi
- Genetics and Rare Diseases Research Division; Ospedale Pediatrico Bambino Gesù; Rome Italy
| | - Marcello Niceta
- Genetics and Rare Diseases Research Division; Ospedale Pediatrico Bambino Gesù; Rome Italy
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division; Ospedale Pediatrico Bambino Gesù; Rome Italy
| | - Marina Trivisano
- Rare and Complex Epilepsy Unit, Department of Neuroscience and Neurorehabilitation; Ospedale Pediatrico Bambino Gesù; Rome Italy
| | - Andrea Bartuli
- Rare Disease and Medical Genetics, Academic Department of Pediatrics; Ospedale Pediatrico Bambino Gesù; Rome Italy
| | - Maria C. Digilio
- Medical Genetics, Academic Department of Pediatrics; Ospedale Pediatrico Bambino Gesù; Rome Italy
| | - Nicola Specchio
- Rare and Complex Epilepsy Unit, Department of Neuroscience and Neurorehabilitation; Ospedale Pediatrico Bambino Gesù; Rome Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division; Ospedale Pediatrico Bambino Gesù; Rome Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division; Ospedale Pediatrico Bambino Gesù; Rome Italy
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274
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Platzer K, Sticht H, Edwards SL, Allen W, Angione KM, Bonati MT, Brasington C, Cho MT, Demmer LA, Falik-Zaccai T, Gamble CN, Hellenbroich Y, Iascone M, Kok F, Mahida S, Mandel H, Marquardt T, McWalter K, Panis B, Pepler A, Pinz H, Ramos L, Shinde DN, Smith-Hicks C, Stegmann APA, Stöbe P, Stumpel CTRM, Wilson C, Lemke JR, Di Donato N, Miller KG, Jamra R. De Novo Variants in MAPK8IP3 Cause Intellectual Disability with Variable Brain Anomalies. Am J Hum Genet 2019; 104:203-212. [PMID: 30612693 DOI: 10.1016/j.ajhg.2018.12.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 12/11/2018] [Indexed: 01/28/2023] Open
Abstract
Using exome sequencing, we have identified de novo variants in MAPK8IP3 in 13 unrelated individuals presenting with an overlapping phenotype of mild to severe intellectual disability. The de novo variants comprise six missense variants, three of which are recurrent, and three truncating variants. Brain anomalies such as perisylvian polymicrogyria, cerebral or cerebellar atrophy, and hypoplasia of the corpus callosum were consistent among individuals harboring recurrent de novo missense variants. MAPK8IP3 has been shown to be involved in the retrograde axonal-transport machinery, but many of its specific functions are yet to be elucidated. Using the CRISPR-Cas9 system to target six conserved amino acid positions in Caenorhabditis elegans, we found that two of the six investigated human alterations led to a significantly elevated density of axonal lysosomes, and five variants were associated with adverse locomotion. Reverse-engineering normalized the observed adverse effects back to wild-type levels. Combining genetic, phenotypic, and functional findings, as well as the significant enrichment of de novo variants in MAPK8IP3 within our total cohort of 27,232 individuals who underwent exome sequencing, we implicate de novo variants in MAPK8IP3 as a cause of a neurodevelopmental disorder with intellectual disability and variable brain anomalies.
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Affiliation(s)
- Konrad Platzer
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig 04103, Germany.
| | - Heinrich Sticht
- Institute of Biochemistry, Emil-Fischer Center, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Stacey L Edwards
- Genetic Models of Disease Laboratory, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - William Allen
- Department of Genetics, Fullerton Genetics Center, Asheville, NC 28803, USA
| | - Kaitlin M Angione
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Maria T Bonati
- Clinic of Medical Genetics, IRCCS Istituto Auxologico Italiano, Milan 20149, Italy
| | - Campbell Brasington
- Department of Pediatrics, Clinical Genetics, Levine Children's Hospital at Carolina Healthcare System, Charlotte, NC 28203, USA
| | | | - Laurie A Demmer
- Department of Pediatrics, Clinical Genetics, Levine Children's Hospital at Carolina Healthcare System, Charlotte, NC 28203, USA
| | - Tzipora Falik-Zaccai
- Institute of Human Genetics, Galilee Medical Center, Nahariya 22100, Israel; The Azrieli School of Medicine, Bar-Ilan University, Safed 1311502, Israel
| | - Candace N Gamble
- Department of Pediatrics, University of Texas Health Medical School, Houston, TX 77030, USA
| | - Yorck Hellenbroich
- Institute of Human Genetics, University of Lübeck, Lübeck 23562, Germany
| | - Maria Iascone
- Laboratorio di Genetica Medica, Azienda Socio Sanitaria Territoriale Papa Giovanni XXIII, Bergamo 24127, Italy
| | - Fernando Kok
- Mendelics Genomic Analysis, São Paulo 04013-000, Brazil
| | - Sonal Mahida
- Department of Neurology, Kennedy Krieger Institute, the Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hanna Mandel
- Institute of Human Genetics, Galilee Medical Center, Nahariya 22100, Israel
| | - Thorsten Marquardt
- Department of Pediatrics, University Hospital Münster, Münster 48149, Germany
| | | | - Bianca Panis
- Department of Pediatrics, Zuyderland Medical Center, Heerlen and Sittard 6419, the Netherlands
| | - Alexander Pepler
- CeGaT GmbH and Praxis für Humangenetik Tübingen, Tübingen 72076, Germany
| | - Hailey Pinz
- Division of Medical Genetics, Department of Pediatrics, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Luiza Ramos
- Mendelics Genomic Analysis, São Paulo 04013-000, Brazil
| | - Deepali N Shinde
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Constance Smith-Hicks
- Department of Neurology, Kennedy Krieger Institute, the Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Alexander P A Stegmann
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht 6229, the Netherlands
| | - Petra Stöbe
- CeGaT GmbH and Praxis für Humangenetik Tübingen, Tübingen 72076, Germany
| | - Constance T R M Stumpel
- Department of Clinical Genetics and School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht 6229, the Netherlands
| | - Carolyn Wilson
- Department of Genetics, Fullerton Genetics Center, Asheville, NC 28803, USA
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig 04103, Germany
| | - Nataliya Di Donato
- Institute for Clinical Genetics, Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden 01307, Germany
| | - Kenneth G Miller
- Genetic Models of Disease Laboratory, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Rami Jamra
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig 04103, Germany
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275
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Møller RS, Hammer TB, Rubboli G, Lemke JR, Johannesen KM. From next-generation sequencing to targeted treatment of non-acquired epilepsies. Expert Rev Mol Diagn 2019; 19:217-228. [DOI: 10.1080/14737159.2019.1573144] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Rikke S. Møller
- Department of Epilepsy Genetics and Precision Medicine, The Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Trine B. Hammer
- Department of Epilepsy Genetics and Precision Medicine, The Danish Epilepsy Centre, Dianalund, Denmark
| | - Guido Rubboli
- Department of Epilepsy Genetics and Precision Medicine, The Danish Epilepsy Centre, Dianalund, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Johannes R. Lemke
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Katrine M. Johannesen
- Department of Epilepsy Genetics and Precision Medicine, The Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
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276
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Nicolas G, Veltman JA. The role of de novo mutations in adult-onset neurodegenerative disorders. Acta Neuropathol 2019; 137:183-207. [PMID: 30478624 PMCID: PMC6513904 DOI: 10.1007/s00401-018-1939-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022]
Abstract
The genetic underpinnings of the most common adult-onset neurodegenerative disorders (AOND) are complex in majority of the cases. In some families, however, the disease can be inherited in a Mendelian fashion as an autosomal-dominant trait. Next to that, patients carrying mutations in the same disease genes have been reported despite a negative family history. Although challenging to demonstrate due to the late onset of the disease in most cases, the occurrence of de novo mutations can explain this sporadic presentation, as demonstrated for severe neurodevelopmental disorders. Exome or genome sequencing of patient-parent trios allows a hypothesis-free study of the role of de novo mutations in AOND and the discovery of novel disease genes. Another hypothesis that may explain a proportion of sporadic AOND cases is the occurrence of a de novo mutation after the fertilization of the oocyte (post-zygotic mutation) or even as a late-somatic mutation, restricted to the brain. Such somatic mutation hypothesis, that can be tested with the use of novel sequencing technologies, is fully compatible with the seeding and spreading mechanisms of the pathological proteins identified in most of these disorders. We review here the current knowledge and future perspectives on de novo mutations in known and novel candidate genes identified in the most common AONDs such as Alzheimer's disease, Parkinson's disease, the frontotemporal lobar degeneration spectrum and Prion disorders. Also, we review the first lessons learned from recent genomic studies of control and diseased brains and the challenges which remain to be addressed.
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Affiliation(s)
- Gaël Nicolas
- Normandie Univ, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics and CNR-MAJ, Normandy Center for Genomic and Personalized Medicine, 22, Boulevard Gambetta, 76000, 76031, Rouen Cedex, France.
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Joris A Veltman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
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277
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Sánchez Fernández I, Loddenkemper T, Gaínza-Lein M, Sheidley BR, Poduri A. Diagnostic yield of genetic tests in epilepsy: A meta-analysis and cost-effectiveness study. Neurology 2019; 92:e418-e428. [PMID: 30610098 PMCID: PMC6369901 DOI: 10.1212/wnl.0000000000006850] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 08/30/2018] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE To compare the cost-effectiveness of genetic testing strategies in patients with epilepsy of unknown etiology. METHODS This meta-analysis and cost-effectiveness study compared strategies involving 3 genetic tests: chromosomal microarray (CMA), epilepsy panel (EP) with deletion/duplication testing, and whole-exome sequencing (WES) in a cost-effectiveness model, using "no genetic testing" as a point of comparison. RESULTS Twenty studies provided information on the diagnostic yield of CMA (8 studies), EP (9 studies), and WES (6 studies). The diagnostic yield was highest for WES: 0.45 (95% confidence interval [CI]: 0.33-0.57) (0.32 [95% CI: 0.22-0.44] adjusting for potential publication bias), followed by EP: 0.23 (95% CI: 0.18-0.29), and CMA: 0.08 (95% CI: 0.06-0.12). The most cost-effective test was WES with an incremental cost-effectiveness ratio (ICER) of $15,000/diagnosis. However, after adjusting for potential publication bias, the most cost-effective test was EP (ICER: $15,848/diagnosis) followed by WES (ICER: $34,500/diagnosis). Among combination strategies, the most cost-effective strategy was WES, then if nondiagnostic, EP, then if nondiagnostic, CMA (ICER: $15,336/diagnosis), although adjusting for potential publication bias, the most cost-effective strategy was EP ± CMA ± WES (ICER: $18,385/diagnosis). While the cost-effectiveness of individual tests and testing strategies overlapped, CMA was consistently less cost-effective than WES and EP. CONCLUSION WES and EP are the most cost-effective genetic tests for epilepsy. Our analyses support, for a broad population of patients with unexplained epilepsy, starting with these tests. Although less expensive, CMA has lower yield, and its use as the first-tier test is thus not supported from a cost-effectiveness perspective.
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Affiliation(s)
- Iván Sánchez Fernández
- From the Epilepsy Genetics Program (B.R.S., A.P.), Division of Epilepsy and Clinical Neurophysiology (I.S.F., T.L., M.G.-L., B.R.S., A.P.), Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Child Neurology (I.S.F.), Hospital Sant Joan de Déu, Universidad de Barcelona, Spain; and Facultad de Medicina (M.G.-L.), Universidad Austral de Chile, Valdivia
| | - Tobias Loddenkemper
- From the Epilepsy Genetics Program (B.R.S., A.P.), Division of Epilepsy and Clinical Neurophysiology (I.S.F., T.L., M.G.-L., B.R.S., A.P.), Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Child Neurology (I.S.F.), Hospital Sant Joan de Déu, Universidad de Barcelona, Spain; and Facultad de Medicina (M.G.-L.), Universidad Austral de Chile, Valdivia
| | - Marina Gaínza-Lein
- From the Epilepsy Genetics Program (B.R.S., A.P.), Division of Epilepsy and Clinical Neurophysiology (I.S.F., T.L., M.G.-L., B.R.S., A.P.), Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Child Neurology (I.S.F.), Hospital Sant Joan de Déu, Universidad de Barcelona, Spain; and Facultad de Medicina (M.G.-L.), Universidad Austral de Chile, Valdivia
| | - Beth Rosen Sheidley
- From the Epilepsy Genetics Program (B.R.S., A.P.), Division of Epilepsy and Clinical Neurophysiology (I.S.F., T.L., M.G.-L., B.R.S., A.P.), Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Child Neurology (I.S.F.), Hospital Sant Joan de Déu, Universidad de Barcelona, Spain; and Facultad de Medicina (M.G.-L.), Universidad Austral de Chile, Valdivia
| | - Annapurna Poduri
- From the Epilepsy Genetics Program (B.R.S., A.P.), Division of Epilepsy and Clinical Neurophysiology (I.S.F., T.L., M.G.-L., B.R.S., A.P.), Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA; Department of Child Neurology (I.S.F.), Hospital Sant Joan de Déu, Universidad de Barcelona, Spain; and Facultad de Medicina (M.G.-L.), Universidad Austral de Chile, Valdivia.
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278
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Mizuguchi T, Nakashima M, Moey LH, Ch’ng GS, Khoo TB, Mitsuhashi S, Miyatake S, Takata A, Miyake N, Saitsu H, Matsumoto N. A novel homozygous truncating variant of NECAP1 in early infantile epileptic encephalopathy: the second case report of EIEE21. J Hum Genet 2019; 64:347-350. [DOI: 10.1038/s10038-018-0556-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 11/09/2022]
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279
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Belousova ED, Sharkov AA. [Difficulties in the diagnosis, prognosis and treatment of genetic epileptic encephalopathies: the view of a neurologist]. Zh Nevrol Psikhiatr Im S S Korsakova 2019; 119:34-40. [PMID: 32207729 DOI: 10.17116/jnevro201911911234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic epileptic encephalopathies are a rather wide spectrum of childhood epilepsies with onset of epilepsy in the first 1.5-2 years of life, regression or delayed psychomotor and speech development and 'massive' epileptiform activity on electroencephalogram (EEG). The review discusses the difficulties of choosing the optimal method of genetic examination, problems with the interpretation of the results obtained, the formulation of the diagnosis, the determination of the prognosis of the course and targeted therapy. It is emphasized that the interpretation of the identified genetic variants is not an easy task, requiring close interaction between specialists in molecular genetics, bioinformatics, neurology and clinical genetics. The possibilities of targeted treatment of genetic epileptic encephalopathies are still limited, but knowledge of the genetic cause of epilepsy allows making a more informed choice of the treatment.
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Affiliation(s)
- E D Belousova
- Veltischev Research and Clinical Institute of Pediatrics, Pirogov Russian National Research Medical University, Moscow, Russia
| | - A A Sharkov
- Veltischev Research and Clinical Institute of Pediatrics, Pirogov Russian National Research Medical University, Moscow, Russia
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280
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Papuc SM, Abela L, Steindl K, Begemann A, Simmons TL, Schmitt B, Zweier M, Oneda B, Socher E, Crowther LM, Wohlrab G, Gogoll L, Poms M, Seiler M, Papik M, Baldinger R, Baumer A, Asadollahi R, Kroell-Seger J, Schmid R, Iff T, Schmitt-Mechelke T, Otten K, Hackenberg A, Addor MC, Klein A, Azzarello-Burri S, Sticht H, Joset P, Plecko B, Rauch A. The role of recessive inheritance in early-onset epileptic encephalopathies: a combined whole-exome sequencing and copy number study. Eur J Hum Genet 2018; 27:408-421. [PMID: 30552426 PMCID: PMC6460568 DOI: 10.1038/s41431-018-0299-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 10/05/2018] [Accepted: 10/25/2018] [Indexed: 11/16/2022] Open
Abstract
Early-onset epileptic encephalopathy (EE) and combined developmental and epileptic encephalopathies (DEE) are clinically and genetically heterogeneous severely devastating conditions. Recent studies emphasized de novo variants as major underlying cause suggesting a generally low-recurrence risk. In order to better understand the full genetic landscape of EE and DEE, we performed high-resolution chromosomal microarray analysis in combination with whole-exome sequencing in 63 deeply phenotyped independent patients. After bioinformatic filtering for rare variants, diagnostic yield was improved for recessive disorders by manual data curation as well as molecular modeling of missense variants and untargeted plasma-metabolomics in selected patients. In total, we yielded a diagnosis in ∼42% of cases with causative copy number variants in 6 patients (∼10%) and causative sequence variants in 16 established disease genes in 20 patients (∼32%), including compound heterozygosity for causative sequence and copy number variants in one patient. In total, 38% of diagnosed cases were caused by recessive genes, of which two cases escaped automatic calling due to one allele occurring de novo. Notably, we found the recessive gene SPATA5 causative in as much as 3% of our cohort, indicating that it may have been underdiagnosed in previous studies. We further support candidacy for neurodevelopmental disorders of four previously described genes (PIK3AP1, GTF3C3, UFC1, and WRAP53), three of which also followed a recessive inheritance pattern. Our results therefore confirm the importance of de novo causative gene variants in EE/DEE, but additionally illustrate the major role of mostly compound heterozygous or hemizygous recessive inheritance and consequently high-recurrence risk.
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Affiliation(s)
- Sorina M Papuc
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland.,Victor Babes National Institute of Pathology, Bucharest, 050096, Romania
| | - Lucia Abela
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland.,CRC Clinical Research Center University, Children's Hospital Zurich, Zurich, 8032, Switzerland.,radiz-Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases University of Zurich, Zurich, 8032, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Anaïs Begemann
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Thomas L Simmons
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Bernhard Schmitt
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland.,CRC Clinical Research Center University, Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Eileen Socher
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Lisa M Crowther
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Gabriele Wohlrab
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Laura Gogoll
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Martin Poms
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Michelle Seiler
- Pediatric Emergency Department, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Michael Papik
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Rosa Baldinger
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Reza Asadollahi
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Judith Kroell-Seger
- Children's department, Swiss Epilepsy Centre, Clinic Lengg, Zurich, 8000, Switzerland
| | - Regula Schmid
- Division of Child Neurology, Kantonsspital Winterthur, Winterthur, 8401, Switzerland
| | - Tobias Iff
- Municipal Hospital of Zurich Triemli, Zurich, 8063, Switzerland
| | | | - Karoline Otten
- Children's department, Swiss Epilepsy Centre, Clinic Lengg, Zurich, 8000, Switzerland
| | - Annette Hackenberg
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland
| | - Marie-Claude Addor
- Department of Woman-Mother-Child, University Medical Center CHUV, Lausanne, 1015, Switzerland
| | - Andrea Klein
- Division of Paediatric Neurology, University Childerns Hospital Basel, UKBB, 4031, Basel, Switzerland.,Division of Paediatric Neurology, Development and Rehabilitation, University Children's Hospital, 3010, Bern, Switzerland
| | - Silvia Azzarello-Burri
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, 91054, Germany
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland
| | - Barbara Plecko
- Division of Child Neurology, University Children's Hospital Zurich, Zurich, 8032, Switzerland.,CRC Clinical Research Center University, Children's Hospital Zurich, Zurich, 8032, Switzerland.,radiz-Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases University of Zurich, Zurich, 8032, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, 8057, Switzerland.,Division of General Pediatrics, Department of Pediatrics, Medical University of Graz, 8036, Graz, Austria
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren-Zurich, 8952, Switzerland. .,radiz-Rare Disease Initiative Zürich, Clinical Research Priority Program for Rare Diseases University of Zurich, Zurich, 8032, Switzerland. .,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, 8057, Switzerland. .,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, 8057, Switzerland.
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281
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Snoeijen-Schouwenaars FM, van Ool JS, Verhoeven JS, van Mierlo P, Braakman HMH, Smeets EE, Nicolai J, Schoots J, Teunissen MWA, Rouhl RPW, Tan IY, Yntema HG, Brunner HG, Pfundt R, Stegmann AP, Kamsteeg EJ, Schelhaas HJ, Willemsen MH. Diagnostic exome sequencing in 100 consecutive patients with both epilepsy and intellectual disability. Epilepsia 2018; 60:155-164. [DOI: 10.1111/epi.14618] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 11/13/2018] [Accepted: 11/13/2018] [Indexed: 12/11/2022]
Affiliation(s)
| | - Jans S. van Ool
- Department of Residential Care; Epilepsy Center Kempenhaeghe; Heeze The Netherlands
| | - Judith S. Verhoeven
- Academic Center for Epileptology Kempenhaeghe/Maastricht University Medical Center; Heeze The Netherlands
| | - Petra van Mierlo
- Academic Center for Epileptology Kempenhaeghe/Maastricht University Medical Center; Heeze The Netherlands
| | - Hilde M. H. Braakman
- Academic Center for Epileptology Kempenhaeghe/Maastricht University Medical Center; Heeze The Netherlands
| | - Eric E. Smeets
- Department of Human Genetics; Maastricht University Medical Center; Maastricht The Netherlands
| | - Joost Nicolai
- Academic Center for Epileptology Kempenhaeghe/Maastricht University Medical Center; Heeze The Netherlands
- Department of Neurology; Maastricht University Medical Center; Maastricht The Netherlands
| | - Jeroen Schoots
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Mariel W. A. Teunissen
- Academic Center for Epileptology Kempenhaeghe/Maastricht University Medical Center; Maastricht The Netherlands
| | - Rob P. W. Rouhl
- Department of Neurology; Maastricht University Medical Center; Maastricht The Netherlands
- Academic Center for Epileptology Kempenhaeghe/Maastricht University Medical Center; Maastricht The Netherlands
- School for Mental Health and Neurosciences; Maastricht University; Maastricht The Netherlands
| | - In Y. Tan
- Department of Residential Care; Epilepsy Center Kempenhaeghe; Heeze The Netherlands
| | - Helger G. Yntema
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Han G. Brunner
- Department of Human Genetics; Maastricht University Medical Center; Maastricht The Netherlands
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Alexander P. Stegmann
- Department of Human Genetics; Maastricht University Medical Center; Maastricht The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
| | - Helenius J. Schelhaas
- Academic Center for Epileptology Kempenhaeghe/Maastricht University Medical Center; Heeze The Netherlands
| | - Marjolein H. Willemsen
- Department of Human Genetics; Maastricht University Medical Center; Maastricht The Netherlands
- Department of Human Genetics; Radboud University Medical Center; Nijmegen The Netherlands
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282
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Fu YL, Han DY, Wang YJ, Di XJ, Yu HB, Mu TW. Remodeling the endoplasmic reticulum proteostasis network restores proteostasis of pathogenic GABAA receptors. PLoS One 2018; 13:e0207948. [PMID: 30481215 PMCID: PMC6258528 DOI: 10.1371/journal.pone.0207948] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/08/2018] [Indexed: 01/12/2023] Open
Abstract
Biogenesis of membrane proteins is controlled by the protein homeostasis (proteostasis) network. We have been focusing on protein quality control of γ-aminobutyric acid type A (GABAA) receptors, the major inhibitory neurotransmitter-gated ion channels in mammalian central nervous system. Proteostasis deficiency in GABAA receptors causes loss of their surface expression and thus function on the plasma membrane, leading to epilepsy and other neurological diseases. One well-characterized example is the A322D mutation in the α1 subunit that causes its extensive misfolding and expedited degradation in the endoplasmic reticulum (ER), resulting in autosomal dominant juvenile myoclonic epilepsy. We aimed to correct misfolding of the α1(A322D) subunits in the ER as an approach to restore their functional surface expression. Here, we showed that application of BIX, a specific, potent ER resident HSP70 family protein BiP activator, significantly increases the surface expression of the mutant receptors in human HEK293T cells and neuronal SH-SY5Y cells. BIX attenuates the degradation of α1(A322D) and enhances their forward trafficking and function. Furthermore, because BiP is one major target of the two unfolded protein response (UPR) pathways: ATF6 and IRE1, we continued to demonstrate that modest activations of the ATF6 pathway and IRE1 pathway genetically enhance the plasma membrane trafficking of the α1(A322D) protein in HEK293T cells. Our results underlie the potential of regulating the ER proteostasis network to correct loss-of-function protein conformational diseases.
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Affiliation(s)
- Yan-Lin Fu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Dong-Yun Han
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Ya-Juan Wang
- Center for Proteomics and Bioinformatics and Department of Epidemiology and Biostatistics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Xiao-Jing Di
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Hai-Bo Yu
- School of Chemistry and Molecular Bioscience & Molecular Horizons, University of Wollongong, Wollongong, Australia
| | - Ting-Wei Mu
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
- * E-mail:
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283
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Shoubridge C, Harvey RJ, Dudding-Byth T. IQSEC2mutation update and review of the female-specific phenotype spectrum including intellectual disability and epilepsy. Hum Mutat 2018; 40:5-24. [DOI: 10.1002/humu.23670] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/11/2018] [Accepted: 10/15/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Cheryl Shoubridge
- Department of Paediatrics; University of Adelaide; Adelaide South Australia 5005 Australia
- Robinson Research Institute; University of Adelaide; Adelaide South Australia 5005 Australia
| | - Robert J. Harvey
- School of Health and Sport Sciences; University of the Sunshine Coast; Maroochydore DC Queensland 4558 Australia
- Sunshine Coast Health Institute; Birtinya Queensland 4575 Australia
| | - Tracy Dudding-Byth
- NSW Genetics of Learning Disability Service; Hunter New England Health Service; New South Wales 2298 Australia
- Grow-Up-Well Priority Research Centre; University of Newcastle; Newcastle New South Wales 2308 Australia
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284
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Eid L, Raju PK, Rossignol E. PHACTRing in actin: actin deregulation in genetic epilepsies. Brain 2018; 141:3084-3088. [PMID: 30364981 DOI: 10.1093/brain/awy272] [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)
- Lara Eid
- CHU Sainte-Justine Research Center, Montreal, Canada.,Department of Neurosciences, University of Montreal, Montreal, Canada
| | - Praveen K Raju
- CHU Sainte-Justine Research Center, Montreal, Canada.,Department of Neurosciences, University of Montreal, Montreal, Canada
| | - Elsa Rossignol
- CHU Sainte-Justine Research Center, Montreal, Canada.,Department of Neurosciences, University of Montreal, Montreal, Canada.,Department of Pediatrics, University of Montreal, Montreal, Canada
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285
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Miao P, Feng J, Guo Y, Wang J, Xu X, Wang Y, Li Y, Gao L, Zheng C, Cheng H. Genotype and phenotype analysis using an epilepsy‐associated gene panel in Chinese pediatric epilepsy patients. Clin Genet 2018; 94:512-520. [PMID: 30182498 DOI: 10.1111/cge.13441] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/23/2018] [Accepted: 08/29/2018] [Indexed: 02/02/2023]
Affiliation(s)
- Pu Miao
- Department of PediatricsSecond Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Jianhua Feng
- Department of PediatricsSecond Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Yufan Guo
- Department of PediatricsSecond Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Jianda Wang
- Department of PediatricsSecond Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Xiaoxiao Xu
- Department of PediatricsSecond Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Ye Wang
- Department of PediatricsSecond Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Yanfang Li
- Department of PediatricsSecond Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Liuyan Gao
- Department of PediatricsSecond Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Chaoguang Zheng
- Department of PediatricsSecond Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
| | - Haiying Cheng
- Department of PediatricsSecond Affiliated Hospital, Zhejiang University School of Medicine Hangzhou China
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286
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Arachchi H, Wojcik MH, Weisburd B, Jacobsen JOB, Valkanas E, Baxter S, Byrne AB, O'Donnell-Luria AH, Haendel M, Smedley D, MacArthur DG, Philippakis AA, Rehm HL. matchbox: An open-source tool for patient matching via the Matchmaker Exchange. Hum Mutat 2018; 39:1827-1834. [PMID: 30240502 DOI: 10.1002/humu.23655] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 08/29/2018] [Accepted: 09/18/2018] [Indexed: 12/11/2022]
Abstract
Rare disease investigators constantly face challenges in identifying additional cases to build evidence for gene-disease causality. The Matchmaker Exchange (MME) addresses this limitation by providing a mechanism for matching patients across genomic centers via a federated network. The MME has revolutionized searching for additional cases by making it possible to query across institutional boundaries, so that what was once a laborious and manual process of contacting researchers is now automated and computable. However, while the MME network is beginning to scale, the growth of additional nodes is limited by the lack of easy-to-use solutions that can be implemented by any rare disease database owner, even one without significant software engineering resources. Here, we describe matchbox, which is an open-source, platform-independent, portable bridge between any given rare disease genomic center and the MME network, which has already led to novel gene discoveries. We also describe how matchbox greatly reduces the barrier to participation by overcoming challenges for new databases to join the MME.
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Affiliation(s)
- Harindra Arachchi
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Monica H Wojcik
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Benjamin Weisburd
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Julius O B Jacobsen
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Elise Valkanas
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Samantha Baxter
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Alicia B Byrne
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, Australia.,School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, Australia
| | - Anne H O'Donnell-Luria
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Division of Genetics and Genomics, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Melissa Haendel
- Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, Oregon.,Linus Pauling Institute, Oregon State University, Corvallis, Oregon
| | - Damian Smedley
- William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Daniel G MacArthur
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Heidi L Rehm
- Center for Mendelian Genomics, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts
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287
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Mucha BE, Banka S, Ajeawung NF, Molidperee S, Chen GG, Koenig MK, Adejumo RB, Till M, Harbord M, Perrier R, Lemyre E, Boucher RM, Skotko BG, Waxler JL, Thomas MA, Hodge JC, Gecz J, Nicholl J, McGregor L, Linden T, Sisodiya SM, Sanlaville D, Cheung SW, Ernst C, Campeau PM. A new microdeletion syndrome involving TBC1D24, ATP6V0C, and PDPK1 causes epilepsy, microcephaly, and developmental delay. Genet Med 2018; 21:1058-1064. [DOI: 10.1038/s41436-018-0290-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/17/2018] [Indexed: 12/17/2022] Open
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288
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Structural determinants of Rab11 activation by the guanine nucleotide exchange factor SH3BP5. Nat Commun 2018; 9:3772. [PMID: 30217979 PMCID: PMC6138693 DOI: 10.1038/s41467-018-06196-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/14/2018] [Indexed: 12/18/2022] Open
Abstract
The GTPase Rab11 plays key roles in receptor recycling, oogenesis, autophagosome formation, and ciliogenesis. However, investigating Rab11 regulation has been hindered by limited molecular detail describing activation by cognate guanine nucleotide exchange factors (GEFs). Here, we present the structure of Rab11 bound to the GEF SH3BP5, along with detailed characterization of Rab-GEF specificity. The structure of SH3BP5 shows a coiled-coil architecture that mediates exchange through a unique Rab-GEF interaction. Furthermore, it reveals a rearrangement of the switch I region of Rab11 compared with solved Rab-GEF structures, with a constrained conformation when bound to SH3BP5. Mutation of switch I provides insights into the molecular determinants that allow for Rab11 selectivity over evolutionarily similar Rab GTPases present on Rab11-positive organelles. Moreover, we show that GEF-deficient mutants of SH3BP5 show greatly decreased Rab11 activation in cellular assays of active Rab11. Overall, our results give molecular insight into Rab11 regulation, and how Rab-GEF specificity is achieved.
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289
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Mignot C, McMahon AC, Bar C, Campeau PM, Davidson C, Buratti J, Nava C, Jacquemont ML, Tallot M, Milh M, Edery P, Marzin P, Barcia G, Barnerias C, Besmond C, Bienvenu T, Bruel AL, Brunga L, Ceulemans B, Coubes C, Cristancho AG, Cunningham F, Dehouck MB, Donner EJ, Duban-Bedu B, Dubourg C, Gardella E, Gauthier J, Geneviève D, Gobin-Limballe S, Goldberg EM, Hagebeuk E, Hamdan FF, Hančárová M, Hubert L, Ioos C, Ichikawa S, Janssens S, Journel H, Kaminska A, Keren B, Koopmans M, Lacoste C, Laššuthová P, Lederer D, Lehalle D, Marjanovic D, Métreau J, Michaud JL, Miller K, Minassian BA, Morales J, Moutard ML, Munnich A, Ortiz-Gonzalez XR, Pinard JM, Prchalová D, Putoux A, Quelin C, Rosen AR, Roume J, Rossignol E, Simon MEH, Smol T, Shur N, Shelihan I, Štěrbová K, Vyhnálková E, Vilain C, Soblet J, Smits G, Yang SP, van der Smagt JJ, van Hasselt PM, van Kempen M, Weckhuysen S, Helbig I, Villard L, Héron D, Koeleman B, Møller RS, Lesca G, Helbig KL, Nabbout R, Verbeek NE, Depienne C. IQSEC2-related encephalopathy in males and females: a comparative study including 37 novel patients. Genet Med 2018; 21:837-849. [PMID: 30206421 PMCID: PMC6752297 DOI: 10.1038/s41436-018-0268-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/31/2018] [Indexed: 12/19/2022] Open
Abstract
Purpose Variants in IQSEC2, escaping X inactivation, cause X-linked intellectual disability with frequent epilepsy in males and females. We aimed to investigate sex-specific differences. Methods We collected the data of 37 unpublished patients (18 males and 19 females) with IQSEC2 pathogenic variants and 5 individuals with variants of unknown significance and reviewed published variants. We compared variant types and phenotypes in males and females and performed an analysis of IQSEC2 isoforms. Results IQSEC2 pathogenic variants mainly led to premature truncation and were scattered throughout the longest brain-specific isoform, encoding the synaptic IQSEC2/BRAG1 protein. Variants occurred de novo in females but were either de novo (2/3) or inherited (1/3) in males, with missense variants being predominantly inherited. Developmental delay and intellectual disability were overall more severe in males than in females. Likewise, seizures were more frequently observed and intractable, and started earlier in males than in females. No correlation was observed between the age at seizure onset and severity of intellectual disability or resistance to antiepileptic treatments. Conclusion This study provides a comprehensive overview of IQSEC2-related encephalopathy in males and females, and suggests that an accurate dosage of IQSEC2 at the synapse is crucial during normal brain development.
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Affiliation(s)
- Cyril Mignot
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universites, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle epiniere, ICM, Paris, France. .,APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France.
| | - Aoife C McMahon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Claire Bar
- APHP, Reference Centre for Rare Epilepsies, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France.,INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Philippe M Campeau
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Claire Davidson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Julien Buratti
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Caroline Nava
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universites, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle epiniere, ICM, Paris, France.,APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | | | - Marilyn Tallot
- CHU La Reunion-Groupe Hospitalier Sud Reunion, La Reunion, France
| | - Mathieu Milh
- APHM, Hôpital d'Enfants de La Timone, Service de Neurologie Pediatrique, centre de reference deficiences intellectuelles de cause rare, Marseille, France.,Aix Marseille University, INSERM, MMG, UMR-S 1251, Faculte de medecine, Marseille, France
| | - Patrick Edery
- Service de Genetique, Centre de Reference Anomalies du Developpement, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Universite Claude Bernard Lyon 1, Bron, France.,Claude Bernard Lyon I University, Lyon, France
| | - Pauline Marzin
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Giulia Barcia
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France.,APHP, Service de genetique medicale, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | - Christine Barnerias
- APHP, Unite fonctionnelle de Neurologie, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | - Claude Besmond
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Thierry Bienvenu
- APHP, Laboratoire de Genetique et Biologie Moleculaires, Hôpital Cochin, HUPC, Paris, France.,Universite Paris Descartes Paris, Institut de Psychiatrie et de Neurosciences de Paris, Inserm U894, Paris, France
| | - Ange-Line Bruel
- FHU-TRANSLAD, Universite de Bourgogne/CHU Dijon, Dijon, France.,INSERM UMR 1231 GAD team, Genetics of Developmental disorders, Universite de Bourgogne-Franche Comte, Dijon, France
| | - Ledia Brunga
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Berten Ceulemans
- Department of Pediatric Neurology, University Hospital and University of Antwerp, Antwerp, Belgium
| | - Christine Coubes
- Departement de Genetique Medicale, Maladies rares et Medecine Personnalisee, CHU de Montpellier, Montpellier, France
| | - Ana G Cristancho
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Elizabeth J Donner
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Bénédicte Duban-Bedu
- Centre de Genetique Chromosomique, Hôpital St-Vincent-de-Paul, GHICL, Lille, France
| | - Christèle Dubourg
- CHU Rennes, Service de Genetique Moleculaire et Genomique, Rennes, France
| | - Elena Gardella
- Danish Epilepsy Centre Filadelfia, Dianalund, Denmark.,Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Julie Gauthier
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - David Geneviève
- Departement de Genetique Medicale, Maladies rares et Medecine Personnalisee, CHU de Montpellier, Montpellier, France.,INSERM U1183, Montpellier, France
| | - Stéphanie Gobin-Limballe
- APHP, Service de genetique medicale, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | - Ethan M Goldberg
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Eveline Hagebeuk
- Stichting Epilepsie Instellingen Nederland, SEIN, Zwolle, The Netherlands
| | - Fadi F Hamdan
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Miroslava Hančárová
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Laurence Hubert
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Christine Ioos
- APHP, University Hospital of Paris ïle-de-France ouest, Raymond Poincare Hospital, Garches, France
| | - Shoji Ichikawa
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Sandra Janssens
- Centre for Medical Genetics Ghent, Ghent University Hospital, C. Heymanslaan 10, Ghent, Belgium
| | - Hubert Journel
- Service de Genetique Medicale, Hôpital Chubert, Vannes, France
| | - Anna Kaminska
- APHP, Department of Clinical Neurophysiology, Necker-Enfants Malades Hospital, Paris, France
| | - Boris Keren
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Marije Koopmans
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline Lacoste
- Departement de Genetique Medicale, APHM, Hopital d'Enfants de La Timone, Marseille, France
| | - Petra Laššuthová
- Child Neurology Department, 2nd Faculty of Medicine, Charles University and Motol Hospital, Prague, Czech Republic
| | - Damien Lederer
- Centre de Genetique Humaine, Institut de Pathologie et de Genetique, Gosselies, Belgium
| | - Daphné Lehalle
- FHU-TRANSLAD, Universite de Bourgogne/CHU Dijon, Dijon, France.,Unite fonctionnelle de genetique clinique, Centre Hospitalier Intercommunal de Creteil, Creteil, France
| | | | - Julia Métreau
- APHP, Service de neurologie pediatrique, Hôpital Universitaire Bicetre, Le Kremlin-Bicetre, France
| | - Jacques L Michaud
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Kathryn Miller
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Berge A Minassian
- Division of Neurology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Marie-Laure Moutard
- APHP, Hôpital Trousseau, service de neuropediatrie, Paris, France.,Sorbonne Universite, GRC n°19, pathologies Congenitales du Cervelet-LeucoDystrophies, APHP, Hôpital Armand Trousseau, Paris, France
| | - Arnold Munnich
- INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France.,APHP, Service de genetique medicale, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France
| | | | - Jean-Marc Pinard
- Division of Neuropediatrics, CHU Raymond Poincare (APHP), Garches, France
| | - Darina Prchalová
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Audrey Putoux
- Service de Genetique, Centre de Reference Anomalies du Developpement, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Universite Claude Bernard Lyon 1, Bron, France.,Claude Bernard Lyon I University, Lyon, France
| | - Chloé Quelin
- Service de Genetique Medicale, CLAD Ouest CHU Hôpital Sud, Rennes, France
| | - Alyssa R Rosen
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joelle Roume
- Unite de Genetique Medicale, Centre de Reference des Maladies rares du Developpement (AnD DI Rares), CHI Poissy-St Germain en Laye, Poissy, France
| | - Elsa Rossignol
- Departments of Pediatrics and Neurosciences, CHU Sainte-Justine and University of Montreal, Montreal, Canada
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Thomas Smol
- Institut de Genetique Medicale, CHRU Lille, Universite de Lille, Lille, France
| | - Natasha Shur
- Department of Pediatrics, Albany Medical Center, Albany, NY, USA
| | - Ivan Shelihan
- Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and University of Montreal, Montreal, QC, Canada
| | - Katalin Štěrbová
- Child Neurology Department, 2nd Faculty of Medicine, Charles University and Motol Hospital, Prague, Czech Republic
| | - Emílie Vyhnálková
- Department of Biology and Medical Genetics, Charles University 2nd Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Catheline Vilain
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Universite Libre de Bruxelles, Brussels, Belgium
| | - Julie Soblet
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Universite Libre de Bruxelles, Brussels, Belgium
| | - Guillaume Smits
- Department of Genetics, Hôpital Universitaire des Enfants Reine Fabiola, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Department of Genetics, Hôpital Erasme, ULB Center of Human Genetics, Universite Libre de Bruxelles, Brussels, Belgium.,Interuniversity Institute of Bioinformatics in Brussels, Universite Libre de Bruxelles, Brussels, Belgium
| | - Samuel P Yang
- Clinical Genomics & Predictive Medicine, Providence Medical Group, Dayton, WA, USA
| | | | - Peter M van Hasselt
- Department of Metabolic Diseases, Wilhelmina Children's Hospital, University Medical Center, Utrecht, The Netherlands
| | - Marjan van Kempen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sarah Weckhuysen
- Neurogenetics Group, Center of Molecular Neurology, VIB, Antwerp, Belgium.,Neurology Department, University Hospital Antwerp, Antwerp, Belgium
| | - Ingo Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurent Villard
- Aix Marseille University, INSERM, MMG, UMR-S 1251, Faculte de medecine, Marseille, France.,Departement de Genetique Medicale, APHM, Hopital d'Enfants de La Timone, Marseille, France
| | - Delphine Héron
- APHP, Hôpital Pitie-Salpetriere, Departement de Genetique et de Cytogenetique; Centre de Reference Deficience Intellectuelle de Causes Rares; GRC UPMC «Deficience Intellectuelle et Autisme», Paris, France
| | - Bobby Koeleman
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rikke S Møller
- CHU Rennes, Service de Genetique Moleculaire et Genomique, Rennes, France.,Danish Epilepsy Centre Filadelfia, Dianalund, Denmark
| | - Gaetan Lesca
- Service de Genetique, Centre de Reference Anomalies du Developpement, Hospices Civils de Lyon, Bron, France.,INSERM U1028, CNRS UMR5292, Centre de Recherche en Neurosciences de Lyon, GENDEV Team, Universite Claude Bernard Lyon 1, Bron, France.,Claude Bernard Lyon I University, Lyon, France
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rima Nabbout
- APHP, Reference Centre for Rare Epilepsies, Necker-Enfants Malades Hospital, Imagine Institute, Paris Descartes University, Paris, France.,INSERM U1163, Imagine Institute, Paris, France.,Paris Descartes University, Paris, France
| | - Nienke E Verbeek
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Christel Depienne
- INSERM, U 1127, CNRS UMR 7225, Sorbonne Universites, UPMC Univ Paris 06 UMR S 1127, Institut du Cerveau et de la Moelle epiniere, ICM, Paris, France. .,IGBMC, CNRS UMR 7104/INSERM U964/Universite de Strasbourg, Illkirch, France. .,Institute of Human Genetics, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
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290
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Li T, Cheng M, Wang J, Hong S, Li M, Liao S, Xie L, Jiang L. De novo mutations of STXBP1 in Chinese children with early onset epileptic encephalopathy. GENES BRAIN AND BEHAVIOR 2018; 17:e12492. [PMID: 29896790 DOI: 10.1111/gbb.12492] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/04/2018] [Accepted: 06/11/2018] [Indexed: 11/30/2022]
Abstract
To detect syntaxin-binding protein 1 (STXBP1) mutations in Chinese patients with early onset epileptic encephalopathy (EOEE) of unknown etiology. Targeted next-generation sequencing was used to identify STXBP1 mutations in 143 Chinese patients with EOEE of unknown etiology. A filtering process was applied to prioritize rare variants of potential functional significance. Then Sanger sequencing was employed to validate the parental origin of the variants. Detailed clinical and genetic data were collected for 9 STXBP1-positive patients. Eight de novo heterozygous STXBP1 mutations were identified in 9 patients; 5 were novel mutations (c.1155delC, c.1030-1G>A, c.217G>C, c.268G>C, c.1480_1481 insT) and 3 were previously reported (c.1216C> T, c.1217G>A [2 cases], c.875G>A). Two patients had Ohtahara syndrome and 1 had West syndrome at onset, whereas the other 6 presented with EOEE that did not fit a specific recognized epilepsy syndrome. Six of these patients later evolved to West syndrome. All but 2 cases were prescribed more than 2 antiepileptic drugs (AEDs) plus other regimens. Four subjects showed good responses to levetiracetam (LEV) alone or in combination with other AEDs, and one case (1/3) achieved complete freedom from seizures with a ketogenic diet (KD). All patients exhibited severe to profound global developmental delay. Five novel heterozygous de novo STXBP1 mutations were discovered in patients with EOEE from China. STXBP1 mutational analysis should be performed in cases of EOEE of unknown etiology. LEV as monotherapy or adjunctive therapy with other regimens, as well as KD should be considered for management of this patient group.
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Affiliation(s)
- T Li
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
| | - M Cheng
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
| | - J Wang
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
| | - S Hong
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
| | - M Li
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
| | - S Liao
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
| | - L Xie
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
| | - L Jiang
- Department of Neurology, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing, China.,Key Laboratory of Pediatrics in Chongqing, Chongqing, China.,Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, China
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291
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Persistent Lin28 Expression Impairs Neurite Outgrowth and Cognitive Function in the Developing Mouse Neocortex. Mol Neurobiol 2018; 56:3780-3795. [PMID: 30203263 DOI: 10.1007/s12035-018-1297-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
Abstract
Many neurodevelopmental disorders feature learning and memory difficulties. Regulation of neurite outgrowth during development is critical for neural plasticity and memory function. Here, we show a novel regulator of neurite outgrowth during cortical neurogenesis, Lin28, which is an RNA-binding protein. Persistent Lin28 upregulation by in utero electroporation at E14.5 resulted in neurite underdevelopment during cortical neurogenesis. We also showed that Lin28-overexpressing cells had an attenuated response to excitatory inputs and altered membrane properties including higher input resistance, slower action potential repolarization, and smaller hyperpolarization-activated cation currents, supporting impaired neuronal functionality in Lin28-electroporated mice. When we ameliorated perturbed Lin28 expression by siRNA, Lin28-induced neurite underdevelopment was rescued with reduction of Lin28-downstream molecules, high mobility group AT-Hook 2, and insulin-like growth factor 1 receptor. Finally, Lin28-electroporated mice showed significant memory deficits as assessed by the Morris water maze test. Taken together, these findings demonstrate a new role and the essential requirement of Lin28 in developmental control of neurite outgrowth, which has an impact on synaptic plasticity and spatial memory. These findings suggest that targeting Lin28 may attenuate intellectual disabilities by correction of impaired dendritic complexity, providing a novel therapeutic candidate for treating neurodevelopmental disorders.
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292
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Tran Mau-Them F, Guibaud L, Duplomb L, Keren B, Lindstrom K, Marey I, Mochel F, van den Boogaard MJ, Oegema R, Nava C, Masurel A, Jouan T, Jansen FE, Au M, Chen AH, Cho M, Duffourd Y, Lozier E, Konovalov F, Sharkov A, Korostelev S, Urteaga B, Dickson P, Vera M, Martínez-Agosto JA, Begemann A, Zweier M, Schmitt-Mechelke T, Rauch A, Philippe C, van Gassen K, Nelson S, Graham JM, Friedman J, Faivre L, Lin HJ, Thauvin-Robinet C, Vitobello A. De novo truncating variants in the intronless IRF2BPL are responsible for developmental epileptic encephalopathy. Genet Med 2018; 21:1008-1014. [DOI: 10.1038/s41436-018-0143-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023] Open
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293
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Carneiro TN, Krepischi AC, Costa SS, Tojal da Silva I, Vianna-Morgante AM, Valieris R, Ezquina SA, Bertola DR, Otto PA, Rosenberg C. Utility of trio-based exome sequencing in the elucidation of the genetic basis of isolated syndromic intellectual disability: illustrative cases. APPLICATION OF CLINICAL GENETICS 2018; 11:93-98. [PMID: 30174453 PMCID: PMC6110279 DOI: 10.2147/tacg.s165799] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Introduction Exome sequencing is recognized as a powerful tool for identifying the genetic cause of intellectual disability (ID). It is uncertain, however, whether only the exome of the proband should be sequenced or if the sequencing of parental genomes is also required, and the resulting increase in diagnostic yield justifies the increase in costs. Patients and methods We sequenced the exomes of eight individuals with sporadic syndromic ID and their parents. Results and discussion Likely pathogenic variants were detected in eight candidate genes, namely homozygous or compound heterozygous variants in three autosomal genes (ADAMTSL2, NALCN, VPS13B), one in an X-linked gene (MID1), and de novo heterozygous variants in four autosomal genes (RYR2, GABBR2, CDK13, DDX3X). Two patients harbored rare variants in two or more candidate genes, while in three other patients no candidate was identified. In five probands (62%), the detected variants explained their clinical findings. The causative recessive variants would have led to diagnosis even without parental exome sequencing, but for the heterozygous dominant ones, the exome trio-based approach was fundamental in the identification of the de novo likely pathogenic variants.
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Affiliation(s)
- Thaise Nr Carneiro
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,
| | - Ana Cv Krepischi
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,
| | - Silvia S Costa
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,
| | - Israel Tojal da Silva
- Laboratory of Computational Biology and Bioinformatics, International Research Center, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Angela M Vianna-Morgante
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,
| | - Renan Valieris
- Laboratory of Computational Biology and Bioinformatics, International Research Center, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Suzana Am Ezquina
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,
| | - Debora R Bertola
- Genetics Unit, Instituto da Criança, Hospital das Clínicas, Medical School, University of São Paulo, São Paulo, Brazil
| | - Paulo A Otto
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,
| | - Carla Rosenberg
- Human Genome and Stem-Cell Research Center, Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,
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Myers KA, Johnstone DL, Dyment DA. Epilepsy genetics: Current knowledge, applications, and future directions. Clin Genet 2018; 95:95-111. [PMID: 29992546 DOI: 10.1111/cge.13414] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 12/12/2022]
Abstract
The rapid pace of disease gene discovery has resulted in tremendous advances in the field of epilepsy genetics. Clinical testing with comprehensive gene panels, exomes, and genomes are now available and have led to higher diagnostic rates and insights into the underlying disease processes. As such, the contribution to the care of patients by medical geneticists, neurogeneticists and genetic counselors are significant; the dysmorphic examination, the necessary pre- and post-test counseling, the selection of the appropriate next-generation sequencing-based test(s), and the interpretation of sequencing results require a care provider to have a comprehensive working knowledge of the strengths and limitations of the available testing technologies. As the underlying mechanisms of the encephalopathies and epilepsies are better understood, there may be opportunities for the development of novel therapies based on an individual's own specific genotype. Drug screening with in vitro and in vivo models of epilepsy can potentially facilitate new treatment strategies. The future of epilepsy genetics will also probably include other-omic approaches such as transcriptomes, metabolomes, and the expanded use of whole genome sequencing to further improve our understanding of epilepsy and provide better care for those with the disease.
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Affiliation(s)
- K A Myers
- Department of Pediatrics, University of McGill, Montreal, Canada.,Research Institute of the McGill University Health Centre, Montreal, Canada
| | - D L Johnstone
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada
| | - D A Dyment
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Canada
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295
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Butler KM, Moody OA, Schuler E, Coryell J, Alexander JJ, Jenkins A, Escayg A. De novo variants in GABRA2 and GABRA5 alter receptor function and contribute to early-onset epilepsy. Brain 2018; 141:2392-2405. [PMID: 29961870 PMCID: PMC6061692 DOI: 10.1093/brain/awy171] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 04/02/2018] [Accepted: 05/04/2018] [Indexed: 01/19/2023] Open
Abstract
GABAA receptors are ligand-gated anion channels that are important regulators of neuronal inhibition. Mutations in several genes encoding receptor subunits have been identified in patients with various types of epilepsy, ranging from mild febrile seizures to severe epileptic encephalopathy. Using whole-genome sequencing, we identified a novel de novo missense variant in GABRA5 (c.880G > C, p.V294L) in a patient with severe early-onset epilepsy and developmental delay. Targeted resequencing of 279 additional epilepsy patients identified 19 rare variants from nine GABAA receptor genes, including a novel de novo missense variant in GABRA2 (c.875C > A, p.T292K) and a recurrent missense variant in GABRB3 (c.902C > T, p.P301L). Patients with the GABRA2 and GABRB3 variants also presented with severe epilepsy and developmental delay. We evaluated the effects of the GABRA5, GABRA2 and GABRB3 missense variants on receptor function using whole-cell patch-clamp recordings from human embryonic kidney 293T cells expressing appropriate α, β and γ subunits. The GABRA5 p.V294L variant produced receptors that were 10-times more sensitive to GABA but had reduced maximal GABA-evoked current due to increased receptor desensitization. The GABRA2 p.T292K variant reduced channel expression and produced mutant channels that were tonically open, even in the absence of GABA. Receptors containing the GABRB3 p.P301L variant were less sensitive to GABA and produced less GABA-evoked current. These results provide the first functional evidence that de novo variants in the GABRA5 and GABRA2 genes contribute to early-onset epilepsy and developmental delay, and demonstrate that epilepsy can result from reduced neuronal inhibition via a wide range of alterations in GABAA receptor function.
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Affiliation(s)
- Kameryn M Butler
- Department of Human Genetics, Emory University, Atlanta, Georgia, 30322, USA
- Genetics and Molecular Biology Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, 30322, USA
| | - Olivia A Moody
- Departments of Anesthesiology and Pharmacology, Emory University, Atlanta, Georgia, 30322, USA
- Neuroscience Program, Graduate Division of Biological and Biomedical Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, 30322, USA
| | - Elisabeth Schuler
- Department for Pediatric Metabolic Medicine and Neurology, University Children’s Hospital, Heidelberg, 69120, Germany
| | - Jason Coryell
- Departments of Pediatrics and Neurology, School of Medicine, Oregon Health & Sciences University, Portland, Oregon, 97239, USA
| | - John J Alexander
- Department of Human Genetics, Emory University, Atlanta, Georgia, 30322, USA
- EGL Genetics, Tucker, Georgia, 30084, USA
| | - Andrew Jenkins
- Departments of Anesthesiology and Pharmacology, Emory University, Atlanta, Georgia, 30322, USA
| | - Andrew Escayg
- Department of Human Genetics, Emory University, Atlanta, Georgia, 30322, USA
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296
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Rare coding variants in genes encoding GABA A receptors in genetic generalised epilepsies: an exome-based case-control study. Lancet Neurol 2018; 17:699-708. [PMID: 30033060 DOI: 10.1016/s1474-4422(18)30215-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 05/17/2018] [Accepted: 05/29/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Genetic generalised epilepsy is the most common type of inherited epilepsy. Despite a high concordance rate of 80% in monozygotic twins, the genetic background is still poorly understood. We aimed to investigate the burden of rare genetic variants in genetic generalised epilepsy. METHODS For this exome-based case-control study, we used three different genetic generalised epilepsy case cohorts and three independent control cohorts, all of European descent. Cases included in the study were clinically evaluated for genetic generalised epilepsy. Whole-exome sequencing was done for the discovery case cohort, a validation case cohort, and two independent control cohorts. The replication case cohort underwent targeted next-generation sequencing of the 19 known genes encoding subunits of GABAA receptors and was compared to the respective GABAA receptor variants of a third independent control cohort. Functional investigations were done with automated two-microelectrode voltage clamping in Xenopus laevis oocytes. FINDINGS Statistical comparison of 152 familial index cases with genetic generalised epilepsy in the discovery cohort to 549 ethnically matched controls suggested an enrichment of rare missense (Nonsyn) variants in the ensemble of 19 genes encoding GABAA receptors in cases (odds ratio [OR] 2·40 [95% CI 1·41-4·10]; pNonsyn=0·0014, adjusted pNonsyn=0·019). Enrichment for these genes was validated in a whole-exome sequencing cohort of 357 sporadic and familial genetic generalised epilepsy cases and 1485 independent controls (OR 1·46 [95% CI 1·05-2·03]; pNonsyn=0·0081, adjusted pNonsyn=0·016). Comparison of genes encoding GABAA receptors in the independent replication cohort of 583 familial and sporadic genetic generalised epilepsy index cases, based on candidate-gene panel sequencing, with a third independent control cohort of 635 controls confirmed the overall enrichment of rare missense variants for 15 GABAA receptor genes in cases compared with controls (OR 1·46 [95% CI 1·02-2·08]; pNonsyn=0·013, adjusted pNonsyn=0·027). Functional studies for two selected genes (GABRB2 and GABRA5) showed significant loss-of-function effects with reduced current amplitudes in four of seven tested variants compared with wild-type receptors. INTERPRETATION Functionally relevant variants in genes encoding GABAA receptor subunits constitute a significant risk factor for genetic generalised epilepsy. Examination of the role of specific gene groups and pathways can disentangle the complex genetic architecture of genetic generalised epilepsy. FUNDING EuroEPINOMICS (European Science Foundation through national funding organisations), Epicure and EpiPGX (Sixth Framework Programme and Seventh Framework Programme of the European Commission), Research Unit FOR2715 (German Research Foundation and Luxembourg National Research Fund).
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297
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Ito Y, Carss KJ, Duarte ST, Hartley T, Keren B, Kurian MA, Marey I, Charles P, Mendonça C, Nava C, Pfundt R, Sanchis-Juan A, van Bokhoven H, van Essen A, van Ravenswaaij-Arts C, Boycott KM, Kernohan KD, Dyack S, Raymond FL, Aitman T, Bennett D, Caulfield M, Chinnery P, Gale D, Koziell A, Kuijpers TW, Laffan MA, Maher E, Markus HS, Morrell NW, Ouwehand WH, Perry DJ, Raymond FL, Roberts I, Smith KG, Thrasher A, Watkins H, Williamson C, Woods G, Ashford S, Bradley JR, Fletcher D, Hammerton T, James R, Kingston N, Penkett CJ, Stirrups K, Veltman M, Young T, Brown M, Clements-Brod N, Davis J, Dewhurst E, Dolling H, Erwood M, Frary A, Linger R, Martin JM, Papadia S, Rehnstrom K, Stark H, Allsup D, Austin S, Bakchoul T, Bariana TK, Bolton-Maggs P, Chalmers E, Collins J, Collins P, Erber WN, Everington T, Favier R, Freson K, Furie B, Gattens M, Gebhart J, Gomez K, Greene D, Greinacher A, Gresele P, Hart D, Heemskerk JW, Henskens Y, Kazmi R, Keeling D, Kelly AM, Lambert MP, Lentaigne C, Liesner R, Makris M, Mangles S, Mathias M, Millar CM, Mumford A, Nurden P, Payne J, Pasi J, Peerlinck K, Revel-Vilk S, Richards M, Rondina M, Roughley C, Schulman S, Schulze H, Scully M, Sivapalaratnam S, Stubbs M, Tait RC, Talks K, Thachil J, Toh CH, Turro E, Van Geet C, De Vries M, Warner TQ, Watson H, Westbury S, Furnell A, Mapeta R, Rayner-Matthews P, Simeoni I, Staines S, Stephens J, Watt C, Whitehorn D, Attwood A, Daugherty L, Deevi SV, Halmagyi C, Hu F, Matser V, Meacham S, Megy K, Shamardina O, Titterton C, Tuna S, Yu P, von Ziegenweldt J, Astle W, Bleda M, Carss KJ, Gräf S, Haimel M, Lango-Allen H, Richardson S, Calleja P, Rankin S, Turek W, Anderson J, Bryson C, Carmichael J, McJannet C, Stock S, Allen L, Ambegaonkar G, Armstrong R, Arno G, Bitner-Glindzicz M, Brady A, Canham N, Chitre M, Clement E, Clowes V, Deegan P, Deshpande C, Doffinger R, Firth H, Flinter F, French C, Gardham A, Ghali N, Gissen P, Grozeva D, Henderson R, Hensiek A, Holden S, Holder M, Holder S, Hurst J, Josifova D, Krishnakumar D, Kurian MA, Lees M, MacLaren R, Maw A, Mehta S, Michaelides M, Moore A, Murphy E, Park SM, Parker A, Patch C, Paterson J, Rankin J, Reid E, Rosser E, Sanchis-Juan A, Sandford R, Santra S, Scott R, Sohal A, Stein P, Thomas E, Thompson D, Tischkowitz M, Vogt J, Wakeling E, Wassmer E, Webster A, Ali S, Ali S, Boggard HJ, Church C, Coghlan G, Cookson V, Corris PA, Creaser-Myers A, DaCosta R, Dormand N, Eyries M, Gall H, Ghataorhe PK, Ghio S, Ghofrani A, Gibbs JSR, Girerd B, Greenhalgh A, Hadinnapola C, Houweling AC, Humbert M, in’t Veld AH, Kennedy F, Kiely DG, Kovacs G, Lawrie A, Ross RVM, Machado R, Masati L, Meehan S, Moledina S, Montani D, Othman S, Peacock AJ, Pepke-Zaba J, Pollock V, Polwarth G, Ranganathan L, Rhodes CJ, Rue-Albrecht K, Schotte G, Shipley D, Soubrier F, Southgate L, Scelsi L, Suntharalingam J, Tan Y, Toshner M, Treacy CM, Trembath R, Vonk Noordegraaf A, Walker S, Wanjiku I, Wharton J, Wilkins M, Wort SJ, Yates K, Alachkar H, Antrobus R, Arumugakani G, Bacchelli C, Baxendale H, Bethune C, Bibi S, Booth C, Browning M, Burns S, Chandra A, Cooper N, Davies S, Devlin L, Drewe E, Edgar D, Egner W, Ghurye R, Gilmour K, Goddard S, Gordins P, Grigoriadou S, Hackett S, Hague R, Harper L, Hayman G, Herwadkar A, Huissoon A, Jolles S, Kelleher P, Kumararatne D, Lear S, Longhurst H, Lorenzo L, Maimaris J, Manson A, McDermott E, Murng S, Nejentsev S, Noorani S, Oksenhendler E, Ponsford M, Qasim W, Quinti I, Richter A, Samarghitean C, Sargur R, Savic S, Seneviratne S, Sewell C, Staples E, Stauss H, Thaventhiran J, Thomas M, Welch S, Willcocks L, Yeatman N, Yong P, Ancliff P, Babbs C, Layton M, Louka E, McGowan S, Mead A, Roy N, Chambers J, Dixon P, Estiu C, Hague B, Marschall HU, Simpson M, Chong S, Emmerson I, Ginsberg L, Gosal D, Hadden R, Horvath R, Mahdi-Rogers M, Manzur A, Marshall A, Matthews E, McCarthy M, Reilly M, Renton T, Rice A, Themistocleous A, Vale T, Van Zuydam N, Walker S, Ormondroyd L, Hudson G, Wei W, Yu Wai Man P, Whitworth J, Afzal M, Colby E, Saleem M, Alavijeh OS, Cook HT, Johnson S, Levine AP, Wong EK, Tan R, Boycott KM, MacKenzie A, Majewski J, Brudno M, Bulman D, Dyment D. De Novo Truncating Mutations in WASF1 Cause Intellectual Disability with Seizures. Am J Hum Genet 2018; 103:144-153. [PMID: 29961568 PMCID: PMC6037130 DOI: 10.1016/j.ajhg.2018.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/04/2018] [Indexed: 10/28/2022] Open
Abstract
Next-generation sequencing has been invaluable in the elucidation of the genetic etiology of many subtypes of intellectual disability in recent years. Here, using exome sequencing and whole-genome sequencing, we identified three de novo truncating mutations in WAS protein family member 1 (WASF1) in five unrelated individuals with moderate to profound intellectual disability with autistic features and seizures. WASF1, also known as WAVE1, is part of the WAVE complex and acts as a mediator between Rac-GTPase and actin to induce actin polymerization. The three mutations connected by Matchmaker Exchange were c.1516C>T (p.Arg506Ter), which occurs in three unrelated individuals, c.1558C>T (p.Gln520Ter), and c.1482delinsGCCAGG (p.Ile494MetfsTer23). All three variants are predicted to partially or fully disrupt the C-terminal actin-binding WCA domain. Functional studies using fibroblast cells from two affected individuals with the c.1516C>T mutation showed a truncated WASF1 and a defect in actin remodeling. This study provides evidence that de novo heterozygous mutations in WASF1 cause a rare form of intellectual disability.
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298
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Nahorski MS, Maddirevula S, Ishimura R, Alsahli S, Brady AF, Begemann A, Mizushima T, Guzmán-Vega FJ, Obata M, Ichimura Y, Alsaif HS, Anazi S, Ibrahim N, Abdulwahab F, Hashem M, Monies D, Abouelhoda M, Meyer BF, Alfadhel M, Eyaid W, Zweier M, Steindl K, Rauch A, Arold ST, Woods CG, Komatsu M, Alkuraya FS. Biallelic UFM1 and UFC1 mutations expand the essential role of ufmylation in brain development. Brain 2018; 141:1934-1945. [PMID: 29868776 PMCID: PMC6022668 DOI: 10.1093/brain/awy135] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/03/2018] [Accepted: 03/23/2018] [Indexed: 12/31/2022] Open
Abstract
The post-translational modification of proteins through the addition of UFM1, also known as ufmylation, plays a critical developmental role as revealed by studies in animal models. The recent finding that biallelic mutations in UBA5 (the E1-like enzyme for ufmylation) cause severe early-onset encephalopathy with progressive microcephaly implicates ufmylation in human brain development. More recently, a homozygous UFM1 variant was proposed as a candidate aetiology of severe early-onset encephalopathy with progressive microcephaly. Here, we establish a locus for severe early-onset encephalopathy with progressive microcephaly based on two families, and map the phenotype to a novel homozygous UFM1 mutation. This mutation has a significantly diminished capacity to form thioester intermediates with UBA5 and with UFC1 (the E2-like enzyme for ufmylation), with resulting impaired ufmylation of cellular proteins. Remarkably, in four additional families where eight children have severe early-onset encephalopathy with progressive microcephaly, we identified two biallelic UFC1 mutations, which impair UFM1-UFC1 intermediate formation with resulting widespread reduction of cellular ufmylation, a pattern similar to that observed with UFM1 mutation. The striking resemblance between UFM1- and UFC1-related clinical phenotype and biochemical derangements strongly argues for an essential role for ufmylation in human brain development. The hypomorphic nature of UFM1 and UFC1 mutations and the conspicuous depletion of biallelic null mutations in the components of this pathway in human genome databases suggest that it is necessary for embryonic survival, which is consistent with the embryonic lethal nature of knockout models for the orthologous genes.
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Affiliation(s)
- Michael S Nahorski
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building Addenbrookes Hospital, Hills Rd, Cambridge, UK
| | - Sateesh Maddirevula
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Ryosuke Ishimura
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Saud Alsahli
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Angela F Brady
- North West Thames Genetics Service, Level 8V, St Mark’s Hospital, Northwick Park Hospital Watford Road, Harrow, UK
| | - Anaïs Begemann
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Tsunehiro Mizushima
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo, Japan
| | - Francisco J Guzmán-Vega
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal, Saudi Arabia
| | - Miki Obata
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Yoshinobu Ichimura
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Hessa S Alsaif
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Shams Anazi
- 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
| | - Dorota Monies
- 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
| | - 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
| | - Brian F Meyer
- 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
| | - Majid Alfadhel
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Wafa Eyaid
- King Abdullah International Medical Research Centre, King Saud bin Abdulaziz University for Health Sciences, Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs (NGHA), Riyadh, Saudi Arabia
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Stefan T Arold
- King Abdullah University of Science and Technology, Computational Bioscience Research Center, Division of Biological and Environmental Sciences and Engineering, Thuwal, Saudi Arabia
| | - C Geoffrey Woods
- Cambridge Institute for Medical Research, Wellcome Trust MRC Building Addenbrookes Hospital, Hills Rd, Cambridge, UK
| | - Masaaki Komatsu
- Department of Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, Japan
| | - Fowzan S Alkuraya
- 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
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
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299
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Vuillaume ML, Cogné B, Jeanne M, Boland A, Ung DC, Quinquis D, Besnard T, Deleuze JF, Redon R, Bézieau S, Laumonnier F, Toutain A. Whole genome sequencing identifies a de novo 2.1 Mb balanced paracentric inversion disrupting FOXP1 and leading to severe intellectual disability. Clin Chim Acta 2018; 485:218-223. [PMID: 29969624 DOI: 10.1016/j.cca.2018.06.048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/25/2018] [Accepted: 06/29/2018] [Indexed: 01/08/2023]
Abstract
The FOXP1 gene, located on chromosome 3p13, encodes the Forkhead-box protein P1, one of the four forkhead transcription factors which repress transcription by forming active homo- and heterodimers and regulate distinct patterns of gene expression crucial for embryogenesis and normal development. FOXP1 mutations, mostly truncating, have been described in patients with mild to moderate intellectual disability (ID), autism spectrum disorder (ASD), and speech and language impairment (MIM #613670). Here, we report a small de novo heterozygous balanced inversion of 2.1 Mb located at 3p14.1p13 identified by Whole Genomic Sequencing (WGS) and disrupting the genes FAM19A4 and FOXP1. This inversion was found in a patient with severe ID, ASD, seizures and very unusual vascular anomalies which were never described in the clinical spectrum of FOXP1 mutations. We show that the neurodevelopmental phenotype observed in the patient most likely results from FOXP1 haploinsufficiency as this heterozygous inversion leads to a 60 to 85% decrease of FOXP1 mRNA levels and to the complete absence of FOXP1 full-length protein. These findings, in addition to expanding the molecular spectrum of FOXP1 mutations, emphasize the emerging role of WGS in identifying small balanced chromosomal rearrangements responsible for neurodevelopmental disorders and not detected by conventional cytogenetics.
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Affiliation(s)
- M-L Vuillaume
- Service de Génétique, Centre Hospitalier Universitaire de Tours, France; UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - B Cogné
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Nantes, France; INSERM, CNRS, UNIV Nantes, l'Institut du Thorax, Nantes, France
| | - M Jeanne
- Service de Génétique, Centre Hospitalier Universitaire de Tours, France; UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - A Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Direction de La Recherche Fondamentale, CEA, Evry, France
| | - D-C Ung
- UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - D Quinquis
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Nantes, France
| | - T Besnard
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Nantes, France
| | - J-F Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, Direction de La Recherche Fondamentale, CEA, Evry, France
| | - R Redon
- INSERM, CNRS, UNIV Nantes, l'Institut du Thorax, Nantes, France
| | - S Bézieau
- Laboratoire de Génétique Moléculaire, Centre Hospitalier Universitaire de Nantes, France; INSERM, CNRS, UNIV Nantes, l'Institut du Thorax, Nantes, France
| | - F Laumonnier
- Service de Génétique, Centre Hospitalier Universitaire de Tours, France; UMR 1253, iBrain, Université de Tours, Inserm, Tours, France
| | - A Toutain
- Service de Génétique, Centre Hospitalier Universitaire de Tours, France; UMR 1253, iBrain, Université de Tours, Inserm, Tours, France.
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300
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Prioritization of Variants Detected by Next Generation Sequencing According to the Mutation Tolerance and Mutational Architecture of the Corresponding Genes. Int J Mol Sci 2018; 19:ijms19061584. [PMID: 29861492 PMCID: PMC6032105 DOI: 10.3390/ijms19061584] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/09/2018] [Accepted: 05/23/2018] [Indexed: 12/27/2022] Open
Abstract
The biggest challenge geneticists face when applying next-generation sequencing technology to the diagnosis of rare diseases is determining which rare variants, from the dozens or hundreds detected, are potentially implicated in the patient’s phenotype. Thus, variant prioritization is an essential step in the process of rare disease diagnosis. In addition to conducting the usual in-silico analyses to predict variant pathogenicity (based on nucleotide/amino-acid conservation and the differences between the physicochemical features of the amino-acid change), three important concepts should be borne in mind. The first is the “mutation tolerance” of the genes in which variants are located. This describes the susceptibility of a given gene to any functional mutation and depends on the strength of purifying selection acting against it. The second is the “mutational architecture” of each gene. This describes the type and location of mutations previously identified in the gene, and their association with different phenotypes or degrees of severity. The third is the mode of inheritance (inherited vs. de novo) of the variants detected. Here, we discuss the importance of each of these concepts for variant prioritization in the diagnosis of rare diseases. Using real data, we show how genes, rather than variants, can be prioritized by calculating a gene-specific mutation tolerance score. We also illustrate the influence of mutational architecture on variant prioritization using five paradigmatic examples. Finally, we discuss the importance of familial variant analysis as final step in variant prioritization.
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