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Martín Fernández-Mayoralas D, Muñoz Jareño N, Alba Menéndez A, Fernández-Jaén A. Periventricular heterotopia: broadening of the clinical spectrum of the clathrin 1 gene (CLTC) pathogenic variants. NEUROLOGÍA (ENGLISH EDITION) 2021. [DOI: 10.1016/j.nrleng.2020.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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152
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Combining exome/genome sequencing with data repository analysis reveals novel gene-disease associations for a wide range of genetic disorders. Genet Med 2021; 23:1551-1568. [PMID: 33875846 PMCID: PMC8354858 DOI: 10.1038/s41436-021-01159-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/10/2021] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Within this study, we aimed to discover novel gene-disease associations in patients with no genetic diagnosis after exome/genome sequencing (ES/GS). METHODS We followed two approaches: (1) a patient-centered approach, which after routine diagnostic analysis systematically interrogates variants in genes not yet associated to human diseases; and (2) a gene variant centered approach. For the latter, we focused on de novo variants in patients that presented with neurodevelopmental delay (NDD) and/or intellectual disability (ID), which are the most common reasons for genetic testing referrals. Gene-disease association was assessed using our data repository that combines ES/GS data and Human Phenotype Ontology terms from over 33,000 patients. RESULTS We propose six novel gene-disease associations based on 38 patients with variants in the BLOC1S1, IPO8, MMP15, PLK1, RAP1GDS1, and ZNF699 genes. Furthermore, our results support causality of 31 additional candidate genes that had little published evidence and no registered OMIM phenotype (56 patients). The phenotypes included syndromic/nonsyndromic NDD/ID, oral-facial-digital syndrome, cardiomyopathies, malformation syndrome, short stature, skeletal dysplasia, and ciliary dyskinesia. CONCLUSION Our results demonstrate the value of data repositories which combine clinical and genetic data for discovering and confirming gene-disease associations. Genetic laboratories should be encouraged to pursue such analyses for the benefit of undiagnosed patients and their families.
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153
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Genetic Neonatal-Onset Epilepsies and Developmental/Epileptic Encephalopathies with Movement Disorders: A Systematic Review. Int J Mol Sci 2021; 22:ijms22084202. [PMID: 33919646 PMCID: PMC8072943 DOI: 10.3390/ijms22084202] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023] Open
Abstract
Despite expanding next generation sequencing technologies and increasing clinical interest into complex neurologic phenotypes associating epilepsies and developmental/epileptic encephalopathies (DE/EE) with movement disorders (MD), these monogenic conditions have been less extensively investigated in the neonatal period compared to infancy. We reviewed the medical literature in the study period 2000–2020 to report on monogenic conditions characterized by neonatal onset epilepsy and/or DE/EE and development of an MD, and described their electroclinical, genetic and neuroimaging spectra. In accordance with a PRISMA statement, we created a data collection sheet and a protocol specifying inclusion and exclusion criteria. A total of 28 different genes (from 49 papers) leading to neonatal-onset DE/EE with multiple seizure types, mainly featuring tonic and myoclonic, but also focal motor seizures and a hyperkinetic MD in 89% of conditions, with neonatal onset in 22%, were identified. Neonatal seizure semiology, or MD age of onset, were not always available. The rate of hypokinetic MD was low, and was described from the neonatal period only, with WW domain containing oxidoreductase (WWOX) pathogenic variants. The outcome is characterized by high rates of associated neurodevelopmental disorders and microcephaly. Brain MRI findings are either normal or nonspecific in most conditions, but serial imaging can be necessary in order to detect progressive abnormalities. We found high genetic heterogeneity and low numbers of described patients. Neurological phenotypes are complex, reflecting the involvement of genes necessary for early brain development. Future studies should focus on accurate neonatal epileptic phenotyping, and detailed description of semiology and time-course, of the associated MD, especially for the rarest conditions.
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154
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Aoto K, Kato M, Akita T, Nakashima M, Mutoh H, Akasaka N, Tohyama J, Nomura Y, Hoshino K, Ago Y, Tanaka R, Epstein O, Ben-Haim R, Heyman E, Miyazaki T, Belal H, Takabayashi S, Ohba C, Takata A, Mizuguchi T, Miyatake S, Miyake N, Fukuda A, Matsumoto N, Saitsu H. ATP6V0A1 encoding the a1-subunit of the V0 domain of vacuolar H +-ATPases is essential for brain development in humans and mice. Nat Commun 2021; 12:2107. [PMID: 33833240 PMCID: PMC8032687 DOI: 10.1038/s41467-021-22389-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 03/05/2021] [Indexed: 02/01/2023] Open
Abstract
Vacuolar H+-ATPases (V-ATPases) transport protons across cellular membranes to acidify various organelles. ATP6V0A1 encodes the a1-subunit of the V0 domain of V-ATPases, which is strongly expressed in neurons. However, its role in brain development is unknown. Here we report four individuals with developmental and epileptic encephalopathy with ATP6V0A1 variants: two individuals with a de novo missense variant (R741Q) and the other two individuals with biallelic variants comprising one almost complete loss-of-function variant and one missense variant (A512P and N534D). Lysosomal acidification is significantly impaired in cell lines expressing three missense ATP6V0A1 mutants. Homozygous mutant mice harboring human R741Q (Atp6v0a1R741Q) and A512P (Atp6v0a1A512P) variants show embryonic lethality and early postnatal mortality, respectively, suggesting that R741Q affects V-ATPase function more severely. Lysosomal dysfunction resulting in cell death, accumulated autophagosomes and lysosomes, reduced mTORC1 signaling and synaptic connectivity, and lowered neurotransmitter contents of synaptic vesicles are observed in the brains of Atp6v0a1A512P/A512P mice. These findings demonstrate the essential roles of ATP6V0A1/Atp6v0a1 in neuronal development in terms of integrity and connectivity of neurons in both humans and mice. A member of the vacuolar H+-ATPase family, ATP6V0A1 is involved in lysosomal activity. Here, the authors report that ATP6V0A1 variants identified in individuals with developmental and epileptic encephalopathy are associated with impairment of lysosomal acidification, autophagy and mTORC1 signaling, suggesting an essential role of ATP6V0A1 in brain development.
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Affiliation(s)
- Kazushi Aoto
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Tenpei Akita
- Department of Neurophysiology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroki Mutoh
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Noriyuki Akasaka
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan.,Department of Pediatrics, Niigata Prefecture Hamagumi Medical Rehabilitation Center for Disabled Children, Niigata, Japan
| | - Jun Tohyama
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Yoshiko Nomura
- Segawa Neurological Clinic for Children, Tokyo, Japan.,Yoshiko Nomura Neurological Clinic for Children, Tokyo, Japan
| | - Kyoko Hoshino
- Segawa Neurological Clinic for Children, Tokyo, Japan.,Segawa Memorial Neurological Clinic for Children, Tokyo, Japan
| | - Yasuhiko Ago
- Department of Neonatology, Ibaraki Children's Hospital, Mito, Japan.,Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Japan
| | - Ryuta Tanaka
- Ibaraki Pediatric Education and Training Station, University of Tsukuba, Mito, Japan
| | - Orna Epstein
- Pediatric Neurology and Development Center, Shamir Medical Center, Tzrifin, Beer Yaakov, Israel
| | - Revital Ben-Haim
- Pediatric Neurology and Development Center, Shamir Medical Center, Tzrifin, Beer Yaakov, Israel
| | - Eli Heyman
- Pediatric Neurology and Development Center, Shamir Medical Center, Tzrifin, Beer Yaakov, Israel
| | - Takehiro Miyazaki
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hazrat Belal
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Shuji Takabayashi
- Laboratory Animal Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Chihiro Ohba
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsuo Fukuda
- Department of Neurophysiology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan.
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155
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John A, Ng-Cordell E, Hanna N, Brkic D, Baker K. The neurodevelopmental spectrum of synaptic vesicle cycling disorders. J Neurochem 2021; 157:208-228. [PMID: 32738165 DOI: 10.1111/jnc.15135] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/11/2022]
Abstract
In this review, we describe and discuss neurodevelopmental phenotypes arising from rare, high penetrance genomic variants which directly influence synaptic vesicle cycling (SVC disorders). Pathogenic variants in each SVC disorder gene lead to disturbance of at least one SVC subprocess, namely vesicle trafficking (e.g. KIF1A and GDI1), clustering (e.g. TRIO, NRXN1 and SYN1), docking and priming (e.g. STXBP1), fusion (e.g. SYT1 and PRRT2) or re-uptake (e.g. DNM1, AP1S2 and TBC1D24). We observe that SVC disorders share a common set of neurological symptoms (movement disorders, epilepsies), cognitive impairments (developmental delay, intellectual disabilities, cerebral visual impairment) and mental health difficulties (autism, ADHD, psychiatric symptoms). On the other hand, there is notable phenotypic variation between and within disorders, which may reflect selective disruption to SVC subprocesses, spatiotemporal and cell-specific gene expression profiles, mutation-specific effects, or modifying factors. Understanding the common cellular and systems mechanisms underlying neurodevelopmental phenotypes in SVC disorders, and the factors responsible for variation in clinical presentations and outcomes, may translate to personalized clinical management and improved quality of life for patients and families.
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Affiliation(s)
- Abinayah John
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Elise Ng-Cordell
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Nancy Hanna
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Diandra Brkic
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
| | - Kate Baker
- MRC Cognition and Brain Sciences Unit, University of Cambridge, Cambridge, UK
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156
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Courage C, Oliver KL, Park EJ, Cameron JM, Grabińska KA, Muona M, Canafoglia L, Gambardella A, Said E, Afawi Z, Baykan B, Brandt C, di Bonaventura C, Chew HB, Criscuolo C, Dibbens LM, Castellotti B, Riguzzi P, Labate A, Filla A, Giallonardo AT, Berecki G, Jackson CB, Joensuu T, Damiano JA, Kivity S, Korczyn A, Palotie A, Striano P, Uccellini D, Giuliano L, Andermann E, Scheffer IE, Michelucci R, Bahlo M, Franceschetti S, Sessa WC, Berkovic SF, Lehesjoki AE. Progressive myoclonus epilepsies-Residual unsolved cases have marked genetic heterogeneity including dolichol-dependent protein glycosylation pathway genes. Am J Hum Genet 2021; 108:722-738. [PMID: 33798445 DOI: 10.1016/j.ajhg.2021.03.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 03/05/2021] [Indexed: 02/04/2023] Open
Abstract
Progressive myoclonus epilepsies (PMEs) comprise a group of clinically and genetically heterogeneous rare diseases. Over 70% of PME cases can now be molecularly solved. Known PME genes encode a variety of proteins, many involved in lysosomal and endosomal function. We performed whole-exome sequencing (WES) in 84 (78 unrelated) unsolved PME-affected individuals, with or without additional family members, to discover novel causes. We identified likely disease-causing variants in 24 out of 78 (31%) unrelated individuals, despite previous genetic analyses. The diagnostic yield was significantly higher for individuals studied as trios or families (14/28) versus singletons (10/50) (OR = 3.9, p value = 0.01, Fisher's exact test). The 24 likely solved cases of PME involved 18 genes. First, we found and functionally validated five heterozygous variants in NUS1 and DHDDS and a homozygous variant in ALG10, with no previous disease associations. All three genes are involved in dolichol-dependent protein glycosylation, a pathway not previously implicated in PME. Second, we independently validate SEMA6B as a dominant PME gene in two unrelated individuals. Third, in five families, we identified variants in established PME genes; three with intronic or copy-number changes (CLN6, GBA, NEU1) and two very rare causes (ASAH1, CERS1). Fourth, we found a group of genes usually associated with developmental and epileptic encephalopathies, but here, remarkably, presenting as PME, with or without prior developmental delay. Our systematic analysis of these cases suggests that the small residuum of unsolved cases will most likely be a collection of very rare, genetically heterogeneous etiologies.
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Affiliation(s)
- Carolina Courage
- Folkhälsan Research Center, Helsinki 00290, Finland; Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki 00290, Finland
| | - Karen L Oliver
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg 3084, Victoria, Australia; Population Health and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, the University of Melbourne, Melbourne, VIC 3010, Australia
| | - Eon Joo Park
- Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, 10 Amistad Street, New Haven, CT 06520, USA
| | - Jillian M Cameron
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg 3084, Victoria, Australia
| | - Kariona A Grabińska
- Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, 10 Amistad Street, New Haven, CT 06520, USA
| | - Mikko Muona
- Folkhälsan Research Center, Helsinki 00290, Finland; Blueprint Genetics, Espoo 02150, Finland
| | - Laura Canafoglia
- Neurophysiopathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | | | - Edith Said
- Section of Medical Genetics, Mater dei Hospital, Msida MSD2090, Malta; Department of Anatomy and Cell Biology, University of Malta, Msida MSD2090, Malta
| | - Zaid Afawi
- Center for Neuroscience, Ben-Gurion University of the Negev, Be'er Sheva 8410402, Israel
| | - Betul Baykan
- Departments of Neurology and Clinical Neurophysiology, Istanbul Faculty of Medicine, Istanbul University, Istanbul 34452, Turkey
| | | | - Carlo di Bonaventura
- Department of Human Neurosciences, Sapienza University of Rome, Viale dell'Università, 30, 00185 Rome, Italy
| | - Hui Bein Chew
- Genetics Department, Kuala Lumpur Hospital, Ministry of Health Malaysia, Jalan Pahang, 50586 Kuala Lumpur, Malaysia
| | - Chiara Criscuolo
- Department of Neuroscience, Reproductive, and Odontostomatological Sciences, University of Naples Federico II, Naples 80138, Italy
| | - Leanne M Dibbens
- Epilepsy Research Group, Australian Centre for Precision Health, UniSA Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Barbara Castellotti
- Unit of Genetics of Neurodegenerative and Metabolic Diseases, IRCCS Istituto Neurologico Carlo Besta Milan 20133, Italy
| | - Patrizia Riguzzi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Unit of Neurology, Bellaria Hospital, Bologna 40139, Italy
| | - Angelo Labate
- Institute of Neurology, University Magna Græcia, Catanzaro 88100, Italy
| | - Alessandro Filla
- Department of Neuroscience, Reproductive, and Odontostomatological Sciences, University of Naples Federico II, Naples 80138, Italy
| | - Anna T Giallonardo
- Neurology Unit, Human Neurosciences Department, Sapienza University, Rome 00185, Italy
| | - Geza Berecki
- Ion Channels and Disease Group, Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3052, Australia
| | - Christopher B Jackson
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
| | | | - John A Damiano
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg 3084, Victoria, Australia
| | - Sara Kivity
- Epilepsy Unit, Schneider Children's Medical Center of Israel, Petah Tiqvah 4922297, Israel
| | - Amos Korczyn
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 60198, Israel
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki 00290, Finland; Analytic and Translational Genetics Unit, Department of Medicine, Department of Neurology and Department of Psychiatry Massachusetts General Hospital, Boston, MA 02114, USA; The Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, Boston, MA 02142, USA
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto "G. Gaslini," Genova 16147, Italy
| | - Davide Uccellini
- Neurology - Neurophysiology Unit, ASST dei Sette Laghi, Galmarini Tradate Hospital, Tradate 21049, Italy
| | - Loretta Giuliano
- Dipartimento "G.F. Ingrassia," Università degli Studi di Catania, Catania 95131, Italy
| | - Eva Andermann
- Neurogenetics Unit and Epilepsy Research Group, Montreal Neurological Hospital and Institute, Montreal, QC H3A 2B4, Canada; Departments of Neurology & Neurosurgery and Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg 3084, Victoria, Australia; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia; Department of Paediatrics, The University of Melbourne, Royal Children's Hospital, Parkville, VIC 3052, Australia; The Florey Institute, Parkville, VIC 3052, Australia
| | - Roberto Michelucci
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Unit of Neurology, Bellaria Hospital, Bologna 40139, Italy
| | - Melanie Bahlo
- Population Health and Immunity Division, the Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, the University of Melbourne, Melbourne, VIC 3010, Australia
| | - Silvana Franceschetti
- Neurophysiopathology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan 20133, Italy
| | - William C Sessa
- Department of Pharmacology and Vascular Biology and Therapeutics Program, Yale University School of Medicine, 10 Amistad Street, New Haven, CT 06520, USA
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg 3084, Victoria, Australia.
| | - Anna-Elina Lehesjoki
- Folkhälsan Research Center, Helsinki 00290, Finland; Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki 00290, Finland.
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157
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Mary L, Nourisson E, Feger C, Laugel V, Chaigne D, Keren B, Afenjar A, Billette T, Trost D, Cieuta-Walti C, Gerard B, Piton A, Schaefer E. Pathogenic variants in KCNQ2 cause intellectual deficiency without epilepsy: Broadening the phenotypic spectrum of a potassium channelopathy. Am J Med Genet A 2021; 185:1803-1815. [PMID: 33754465 DOI: 10.1002/ajmg.a.62181] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 01/19/2021] [Accepted: 03/11/2021] [Indexed: 12/22/2022]
Abstract
High-throughput sequencing (HTS) improved the molecular diagnosis in individuals with intellectual deficiency (ID) and helped to broaden the phenotype of previously known disease-causing genes. We report herein four unrelated patients with isolated ID, carriers of a likely pathogenic variant in KCNQ2, a gene usually implicated in benign familial neonatal seizures (BFNS) or early onset epileptic encephalopathy (EOEE). Patients were diagnosed by targeted HTS or exome sequencing. Pathogenicity of the variants was assessed by multiple in silico tools. Patients' ID ranged from mild to severe with predominance of speech disturbance and autistic features. Three of the four variants disrupted the same amino acid. Compiling all the pathogenic variants previously reported, we observed a strong overlap between variants causing EOEE, isolated ID, and BFNS and an important intra-familial phenotypic variability, although missense variants in the voltage-sensing domain and the pore are significantly associated to EOEE (p < 0.01, Fisher test). Thus, pathogenic variants in KCNQ2 can be associated with isolated ID. We did not highlight strong related genotype-phenotype correlations in KCNQ2-related disorders. A second genetic hit, a burden of rare variants, or other extrinsic factors may explain such a phenotypic variability. However, it is of interest to study encephalopathy genes in non-epileptic ID patients.
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Affiliation(s)
- Laura Mary
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Elsa Nourisson
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Claire Feger
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Vincent Laugel
- Service de Neuropédiatrie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Denys Chaigne
- Service de Neuropédiatrie, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Boris Keren
- Département de Génétique, Centre de Référence des Déficiences Intellectuelles de Causes Rares, Groupe de Recherche Clinique "Déficiences Intellectuelles et Autisme," Université Pierre et Marie Curie, Hôpital de la Pitié-Salpêtrière, Paris, France.,Institut du Cerveau et de la Moelle Épinière, Sorbonne Universités, Université Pierre et Marie Curie (Université Paris 06), UMRS 1127, INSERM U 1127, CNRS UMR 7225, Paris, France
| | - Alexandra Afenjar
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Département de Génétique et Embryologie Médicale, Hôpital Trousseau, Sorbonne Universités, Paris, France
| | - Thierry Billette
- Assistance Publique-Hôpitaux de Paris, Service de Neuropédiatrie, Hôpital Armand Trousseau, Paris, France
| | | | | | - Bénédicte Gerard
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Amélie Piton
- Laboratoire de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.,Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR-7104, Inserm U964, Université de Strasbourg, Strasbourg, France
| | - Elise Schaefer
- Service de Génétique Médicale, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace, Strasbourg, France
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158
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Chen Z, Mino RE, Mettlen M, Michaely P, Bhave M, Reed DK, Schmid SL. Wbox2: A clathrin terminal domain-derived peptide inhibitor of clathrin-mediated endocytosis. J Cell Biol 2021; 219:151850. [PMID: 32520988 PMCID: PMC7480105 DOI: 10.1083/jcb.201908189] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/03/2019] [Accepted: 05/14/2020] [Indexed: 12/11/2022] Open
Abstract
Clathrin-mediated endocytosis (CME) occurs via the formation of clathrin-coated vesicles from clathrin-coated pits (CCPs). Clathrin is recruited to CCPs through interactions between the AP2 complex and its N-terminal domain, which in turn recruits endocytic accessory proteins. Inhibitors of CME that interfere with clathrin function have been described, but their specificity and mechanisms of action are unclear. Here we show that overexpression of the N-terminal domain with (TDD) or without (TD) the distal leg inhibits CME and CCP dynamics by perturbing clathrin interactions with AP2 and SNX9. TDD overexpression does not affect clathrin-independent endocytosis or, surprisingly, AP1-dependent lysosomal trafficking from the Golgi. We designed small membrane–permeant peptides that encode key functional residues within the four known binding sites on the TD. One peptide, Wbox2, encoding residues along the W-box motif binding surface, binds to SNX9 and AP2 and potently and acutely inhibits CME.
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Affiliation(s)
- Zhiming Chen
- Department of Cell Biology, University of Texas Southwestern Medical Center, TX
| | - Rosa E Mino
- Department of Cell Biology, University of Texas Southwestern Medical Center, TX
| | - Marcel Mettlen
- Department of Cell Biology, University of Texas Southwestern Medical Center, TX
| | - Peter Michaely
- Department of Cell Biology, University of Texas Southwestern Medical Center, TX
| | - Madhura Bhave
- Department of Cell Biology, University of Texas Southwestern Medical Center, TX
| | - Dana Kim Reed
- Department of Cell Biology, University of Texas Southwestern Medical Center, TX
| | - Sandra L Schmid
- Department of Cell Biology, University of Texas Southwestern Medical Center, TX
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159
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Refining Genotypes and Phenotypes in KCNA2-Related Neurological Disorders. Int J Mol Sci 2021; 22:ijms22062824. [PMID: 33802230 PMCID: PMC7999221 DOI: 10.3390/ijms22062824] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 02/06/2023] Open
Abstract
Pathogenic variants in KCNA2, encoding for the voltage-gated potassium channel Kv1.2, have been identified as the cause for an evolving spectrum of neurological disorders. Affected individuals show early-onset developmental and epileptic encephalopathy, intellectual disability, and movement disorders resulting from cerebellar dysfunction. In addition, individuals with a milder course of epilepsy, complicated hereditary spastic paraplegia, and episodic ataxia have been reported. By analyzing phenotypic, functional, and genetic data from published reports and novel cases, we refine and further delineate phenotypic as well as functional subgroups of KCNA2-associated disorders. Carriers of variants, leading to complex and mixed channel dysfunction that are associated with a gain- and loss-of-potassium conductance, more often show early developmental abnormalities and an earlier onset of epilepsy compared to individuals with variants resulting in loss- or gain-of-function. We describe seven additional individuals harboring three known and the novel KCNA2 variants p.(Pro407Ala) and p.(Tyr417Cys). The location of variants reported here highlights the importance of the proline(405)–valine(406)–proline(407) (PVP) motif in transmembrane domain S6 as a mutational hotspot. A novel case of self-limited infantile seizures suggests a continuous clinical spectrum of KCNA2-related disorders. Our study provides further insights into the clinical spectrum, genotype–phenotype correlation, variability, and predicted functional impact of KCNA2 variants.
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160
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Indelicato E, Boesch S. From Genotype to Phenotype: Expanding the Clinical Spectrum of CACNA1A Variants in the Era of Next Generation Sequencing. Front Neurol 2021; 12:639994. [PMID: 33737904 PMCID: PMC7960780 DOI: 10.3389/fneur.2021.639994] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
Ion channel dysfunction is a key pathological substrate of episodic neurological disorders. A classical gene associated to paroxysmal movement disorders is CACNA1A, which codes for the pore-forming subunit of the neuronal calcium channel P/Q. Non-polyglutamine CACNA1A variants underlie familial hemiplegic ataxia type 1 (FHM1) and episodic ataxia type 2 (EA2). Classical paroxysmal manifestations of FHM1 are migraine attacks preceded by motor aura consisting of hemiparesis, aphasia, and disturbances of consciousness until coma. Patients with EA2 suffer of recurrent episodes of vertigo, unbalance, diplopia, and vomiting. Beyond these typical presentations, several reports highlighted manifold clinical features associated with P/Q channelopathies, from chronic progressive cerebellar ataxia to epilepsy and psychiatric disturbances. These manifestations may often outlast the burden of classical episodic symptoms leading to pitfalls in the diagnostic work-up. Lately, the spreading of next generation sequencing techniques linked de novo CACNA1A variants to an even broader phenotypic spectrum including early developmental delay, autism spectrum disorders, epileptic encephalopathy, and early onset paroxysmal dystonia. The age-dependency represents a striking new aspect of these phenotypes und highlights a pivotal role for P/Q channels in the development of the central nervous system in a defined time window. While several reviews addressed the clinical presentation and treatment of FHM1 and EA2, an overview of the newly described age-dependent manifestations is lacking. In this Mini-Review we present a clinical update, delineate genotype-phenotype correlations as well as summarize evidence on the pathophysiological mechanisms underlying the expanded phenotype associated with CACNA1A variants.
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Affiliation(s)
| | - Sylvia Boesch
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
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Luo T, Li K, Ling Z, Zhao G, Li B, Wang Z, Wang X, Han Y, Xia L, Zhang Y, Zhou Q, Fang Z, Wang Y, Chen Q, Zhou X, Pan H, Zhao Y, Wang Y, Dong L, Huang Y, Hu Z, Pan Q, Xia K, Li J. De novo mutations in folate-related genes associated with common developmental disorders. Comput Struct Biotechnol J 2021; 19:1414-1422. [PMID: 33777337 PMCID: PMC7966843 DOI: 10.1016/j.csbj.2021.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 01/23/2023] Open
Abstract
Folate deficiency is an environmental risk factor for several developmental disorders. De novo mutations (DNMs) also play important etiological roles in various developmental disorders. However, it remains unclear whether DNMs in folate-related genes (FRGs) contribute to developmental disorders. We obtained a list of 1,821 FRGs from folate metabolism pathways and the Comparative Toxicogenomics Database, along with data concerning DNMs in 15,404 cases and 3,391 controls from the Gene4Denovo database. We used a TADA-Denovo model to prioritize candidate disease-associated FRGs, and characterized these genes in terms of genic intolerance, functional networks, and expression patterns. Compared with the controls, FRGs were significantly enriched in likely damaging DNMs (ldDNMs) in patients with developmental disorders (1.54 ≤ odds ratio ≤ 3.39, Padj ≤ 0.0075). Furthermore, FRGs with ldDNMs rather than with likely non-damaging DNMs (lndDNMs) overlapped significantly among the five developmental disorders included in the datasets. The TADA-Denovo model prioritized 96 candidate disease-associated FRGs, which were intolerant to genetic variants. Their functional networks mainly involved pathways associated with chromatin modification, organ development, and signal transduction pathways. DNMT3A, KMT2B, KMT2C, and YY1 emerged as hub FRGs from the protein–protein interaction network. These candidate disease-associated FRGs are preferentially expressed in the excitatory neurones during embryonic development, and in the cortex, cerebellum, striatum, and amygdala during foetal development. Overall, these findings show that DNMs in FRGs are associated with the risk of developmental disorders. Further research on these DNMs may facilitate the discovery of developmental disorder biomarkers and therapeutic targets, enabling detailed, personalized, and precise folate treatment plan.
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Key Words
- ADD, all five developmental disorders
- ASD, autism spectrum disorder
- CHD, congenital heart disease
- Candidate disease-associated genes
- DNMs, De novo mutations
- De novo mutation
- Developmental disorders
- Dmis, deleterious missense variants
- EE, epileptic encephalopathy
- Expression patterns
- FRGs, folate-related genes
- Folate-related gene
- ID, intellectual disability
- PPI, Protein–protein interaction
- PTV, protein-truncating variants
- RVIS, residual variation intolerance scores
- SNPs, single nucleotide polymorphisms
- TADA, Transmitted And De novo Association
- Tmis, tolerant missense variants
- UDD, undiagnosed developmental disorder
- ldDNMs, likely damaging DNMs
- lndDNMs, likely non-damaging DNMs
- pLI, probability of loss-of-function intolerance
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Affiliation(s)
- Tengfei Luo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kuokuo Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei 230022, Anhui, China
| | - Zhengbao Ling
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaomeng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Ying Han
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiao Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhenghuan Fang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yijing Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Chen
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xun Zhou
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongxu Pan
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuwen Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yige Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Lijie Dong
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yuanfeng Huang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhengmao Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qian Pan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
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162
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Jeffrey JS, Leathem J, King C, Mefford HC, Ross K, Sadleir LG. Developmental and epileptic encephalopathy: Personal utility of a genetic diagnosis for families. Epilepsia Open 2021; 6:149-159. [PMID: 33681658 PMCID: PMC7918330 DOI: 10.1002/epi4.12458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 11/11/2022] Open
Abstract
Objectives Identifying genetic pathogenic variants improves clinical outcomes for children with developmental and epileptic encephalopathy (DEE) by directing therapy and enabling accurate reproductive and prognostic information for families. We aimed to explore the additional personal utility of receiving a genetic diagnosis for families. Methods Semi-structured interviews were conducted with fifteen families of children with a DEE who had received a genetic diagnosis. The interviews stimulated discussion focusing on the impact of receiving a genetic diagnosis for the family. Interview transcripts were analyzed using the six-step systematic process of interpretative phenomenological analysis (IPA). Results Three key themes were identified: "Importance of the label," "Relief to end the diagnostic journey," and "Factors that influence personal utility." Families reported that receiving a genetic label improved their knowledge about the likely trajectory of the DEE, increased their hope for the future, and helped them communicate with others. The relief of finally having an answer for the cause of their child's DEE alleviated parental guilt and self-blame as well as helped families to process their grief and move forward. Delay in receipt of a genetic diagnosis diluted its psychological impact. Significance To date, the factors associated with the personal utility of a genetic diagnosis for DEEs have been under appreciated. This study demonstrates that identifying a genetic diagnosis for a child's DEE can be a psychological turning point for families. A genetic result has the potential to set these families on an adaptive path toward better quality of life through increased understanding, social connection, and support. Early access to genetic testing is important as it not only increases clinical utility, but also increases personal utility with early mitigation of family stress, trauma, and negative experiences.
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Affiliation(s)
| | - Janet Leathem
- School of PsychologyMassey UniversityWellingtonNew Zealand
| | - Chontelle King
- Department of Paediatrics and Child HealthUniversity of OtagoWellingtonNew Zealand
| | - Heather C. Mefford
- Department of PediatricsDivision of Genetic MedicineUniversity of WashingtonSeattleWAUSA
| | - Kirsty Ross
- School of PsychologyMassey UniversityWellingtonNew Zealand
| | - Lynette G. Sadleir
- Department of Paediatrics and Child HealthUniversity of OtagoWellingtonNew Zealand
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163
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Palmer EE, Sachdev R, Macintosh R, Melo US, Mundlos S, Righetti S, Kandula T, Minoche AE, Puttick C, Gayevskiy V, Hesson L, Idrisoglu S, Shoubridge C, Thai MHN, Davis RL, Drew AP, Sampaio H, Andrews PI, Lawson J, Cardamone M, Mowat D, Colley A, Kummerfeld S, Dinger ME, Cowley MJ, Roscioli T, Bye A, Kirk E. Diagnostic Yield of Whole Genome Sequencing After Nondiagnostic Exome Sequencing or Gene Panel in Developmental and Epileptic Encephalopathies. Neurology 2021; 96:e1770-e1782. [PMID: 33568551 DOI: 10.1212/wnl.0000000000011655] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/18/2020] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE To assess the benefits and limitations of whole genome sequencing (WGS) compared to exome sequencing (ES) or multigene panel (MGP) in the molecular diagnosis of developmental and epileptic encephalopathies (DEE). METHODS We performed WGS of 30 comprehensively phenotyped DEE patient trios that were undiagnosed after first-tier testing, including chromosomal microarray and either research ES (n = 15) or diagnostic MGP (n = 15). RESULTS Eight diagnoses were made in the 15 individuals who received prior ES (53%): 3 individuals had complex structural variants; 5 had ES-detectable variants, which now had additional evidence for pathogenicity. Eleven diagnoses were made in the 15 MGP-negative individuals (68%); the majority (n = 10) involved genes not included in the panel, particularly in individuals with postneonatal onset of seizures and those with more complex presentations including movement disorders, dysmorphic features, or multiorgan involvement. A total of 42% of diagnoses were autosomal recessive or X-chromosome linked. CONCLUSION WGS was able to improve diagnostic yield over ES primarily through the detection of complex structural variants (n = 3). The higher diagnostic yield was otherwise better attributed to the power of re-analysis rather than inherent advantages of the WGS platform. Additional research is required to assist in the assessment of pathogenicity of novel noncoding and complex structural variants and further improve diagnostic yield for patients with DEE and other neurogenetic disorders.
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Affiliation(s)
- Elizabeth Emma Palmer
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia.
| | - Rani Sachdev
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Rebecca Macintosh
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Uirá Souto Melo
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Stefan Mundlos
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Sarah Righetti
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Tejaswi Kandula
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Andre E Minoche
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Clare Puttick
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Velimir Gayevskiy
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Luke Hesson
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Senel Idrisoglu
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Cheryl Shoubridge
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Monica Hong Ngoc Thai
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Ryan L Davis
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Alexander P Drew
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Hugo Sampaio
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Peter Ian Andrews
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - John Lawson
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Michael Cardamone
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - David Mowat
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Alison Colley
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Sarah Kummerfeld
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Marcel E Dinger
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Mark J Cowley
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Tony Roscioli
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Ann Bye
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
| | - Edwin Kirk
- From the School of Women's and Children's Health (E.E.P., R.S., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., M.J.C., A.B., E.K.), The School of Biotechnology and Biomolecular Sciences (M.E.D.), Childrens Cancer Institute (M.J.C.), and NeuRA (T.R.), University of New South Wales; Sydney Childrens Hospital Randwick (E.E.P., R.S., R.M., S.R., T.K., H.S., P.I.A., J.L., M.C., D.M., A.B., E.K.), Sydney Childrens Hospital Network; GOLD Service (E.E.P.), Hunter Genetics; Kinghorn Centre for Clinical Genomics (E.E.P., A.E.M., C.P., V.G., L.H., S.I., R.L.D., A.P.D., S.K., M.J.C.), Garvan Institute of Medical Research, Sydney, Australia; RG Development & Disease (U.S.M., S.M.), Max Planck Institute for Molecular Genetics; Institute for Medical Genetics and Human Genetics (U.S.M., S.M.), Charité-Universitätsmedizin, Berlin, Germany; Faculty of Medicine, Prince of Wales Clinical School (L.H.), and Faculty of Medicine, St Vincents Clinical School (S.K.), UNSW Sydney, Randwick; Adelaide Medical School (C.S., M.H.N.T.), University of Adelaide; Kolling Institute (R.L.D.), University of Sydney; SWSLHD Liverpool Hospital (A.C.), Liverpool; and New South Wales Health Pathology Randwick Genomics Laboratory (T.R., E.K.), Australia
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Weißbach S, Sys S, Hewel C, Todorov H, Schweiger S, Winter J, Pfenninger M, Torkamani A, Evans D, Burger J, Everschor-Sitte K, May-Simera HL, Gerber S. Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines. BMC Genomics 2021; 22:62. [PMID: 33468057 PMCID: PMC7814447 DOI: 10.1186/s12864-020-07362-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022] Open
Abstract
Background Next Generation Sequencing (NGS) is the fundament of various studies, providing insights into questions from biology and medicine. Nevertheless, integrating data from different experimental backgrounds can introduce strong biases. In order to methodically investigate the magnitude of systematic errors in single nucleotide variant calls, we performed a cross-sectional observational study on a genomic cohort of 99 subjects each sequenced via (i) Illumina HiSeq X, (ii) Illumina HiSeq, and (iii) Complete Genomics and processed with the respective bioinformatic pipeline. We also repeated variant calling for the Illumina cohorts with GATK, which allowed us to investigate the effect of the bioinformatics analysis strategy separately from the sequencing platform’s impact. Results The number of detected variants/variant classes per individual was highly dependent on the experimental setup. We observed a statistically significant overrepresentation of variants uniquely called by a single setup, indicating potential systematic biases. Insertion/deletion polymorphisms (indels) were associated with decreased concordance compared to single nucleotide polymorphisms (SNPs). The discrepancies in indel absolute numbers were particularly prominent in introns, Alu elements, simple repeats, and regions with medium GC content. Notably, reprocessing sequencing data following the best practice recommendations of GATK considerably improved concordance between the respective setups. Conclusion We provide empirical evidence of systematic heterogeneity in variant calls between alternative experimental and data analysis setups. Furthermore, our results demonstrate the benefit of reprocessing genomic data with harmonized pipelines when integrating data from different studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07362-8.
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Affiliation(s)
- Stephan Weißbach
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,Institute of Developmental Biology and Neurobiology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Stanislav Sys
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Charlotte Hewel
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Hristo Todorov
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susann Schweiger
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,Leibniz Institute for Resilience Research, Mainz, Germany
| | - Jennifer Winter
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.,Leibniz Institute for Resilience Research, Mainz, Germany
| | - Markus Pfenninger
- Department of Molecular Ecology, Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Institute for Molecular and Organismic Evolution, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, 55128, Mainz, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity, and Climate Research Centre, Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Ali Torkamani
- Department of Integrative Structural and Computational Biology, Scripps Research Translational Institute, California Campus, San Diego, USA
| | - Doug Evans
- Department of Integrative Structural and Computational Biology, Scripps Research Translational Institute, California Campus, San Diego, USA
| | - Joachim Burger
- Institute of Anthropology, Johannes Gutenberg-University Mainz, Mainz, Germany
| | | | | | - Susanne Gerber
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany.
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165
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A patient with a 6q22.1 deletion and a phenotype of non-progressive early-onset generalized epilepsy with tremor. Epilepsy Behav Rep 2021; 15:100405. [PMID: 33437959 PMCID: PMC7786037 DOI: 10.1016/j.ebr.2020.100405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 11/21/2022] Open
Abstract
We report a patient with a 6q22.1 deletion, who presented with a rare syndrome of generalized epilepsy, myoclonic tremor, and intellectual disability. There was no clinical progression after follow-up for more than 10 years. Our report presents the genetic basis for a phenotype involving a non-progressive generalized epilepsy with tremor. The efficacy of valproic acid for seizure control and the partial efficacy of deep brain stimulation with propranolol for myoclonic tremor is detailed.
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166
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Fry AE, Marra C, Derrick AV, Pickrell WO, Higgins AT, Te Water Naude J, McClatchey MA, Davies SJ, Metcalfe KA, Tan HJ, Mohanraj R, Avula S, Williams D, Brady LI, Mesterman R, Tarnopolsky MA, Zhang Y, Yang Y, Wang X, Rees MI, Goldfarb M, Chung SK. Missense variants in the N-terminal domain of the A isoform of FHF2/FGF13 cause an X-linked developmental and epileptic encephalopathy. Am J Hum Genet 2021; 108:176-185. [PMID: 33245860 PMCID: PMC7820623 DOI: 10.1016/j.ajhg.2020.10.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/30/2020] [Indexed: 01/22/2023] Open
Abstract
Fibroblast growth factor homologous factors (FHFs) are intracellular proteins which regulate voltage-gated sodium (Nav) channels in the brain and other tissues. FHF dysfunction has been linked to neurological disorders including epilepsy. Here, we describe two sibling pairs and three unrelated males who presented in infancy with intractable focal seizures and severe developmental delay. Whole-exome sequencing identified hemi- and heterozygous variants in the N-terminal domain of the A isoform of FHF2 (FHF2A). The X-linked FHF2 gene (also known as FGF13) has alternative first exons which produce multiple protein isoforms that differ in their N-terminal sequence. The variants were located at highly conserved residues in the FHF2A inactivation particle that competes with the intrinsic fast inactivation mechanism of Nav channels. Functional characterization of mutant FHF2A co-expressed with wild-type Nav1.6 (SCN8A) revealed that mutant FHF2A proteins lost the ability to induce rapid-onset, long-term blockade of the channel while retaining pro-excitatory properties. These gain-of-function effects are likely to increase neuronal excitability consistent with the epileptic potential of FHF2 variants. Our findings demonstrate that FHF2 variants are a cause of infantile-onset developmental and epileptic encephalopathy and underline the critical role of the FHF2A isoform in regulating Nav channel function.
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Affiliation(s)
- Andrew E Fry
- Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4XW, UK; Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Christopher Marra
- Department of Biological Sciences, Hunter College of City University, 695 Park Avenue, New York, NY 10065, USA; Program in Biology, Graduate Center of City University, 365 Fifth Avenue, New York, NY 10016, USA
| | - Anna V Derrick
- Neurology and Molecular Neuroscience Research, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK
| | - William O Pickrell
- Neurology and Molecular Neuroscience Research, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK; Neurology department, Morriston Hospital, Swansea Bay University Hospital Health Board, Swansea SA6 6NL, UK
| | - Adam T Higgins
- Neurology and Molecular Neuroscience Research, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK
| | - Johann Te Water Naude
- Paediatric Neurology, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK
| | - Martin A McClatchey
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Sally J Davies
- Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - Kay A Metcalfe
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust and Institute of Human Development, University of Manchester, Manchester M13 9WL, UK
| | - Hui Jeen Tan
- Department of Paediatric Neurology, Royal Manchester Children's Hospital, Oxford Road, Manchester M13 9WL, UK
| | - Rajiv Mohanraj
- Department of Neurology, Salford Royal Hospital NHS Foundation Trust, Stott Lane, Salford M6 8HD, UK
| | - Shivaram Avula
- Department of Radiology, Alder Hey Children's NHS Foundation Trust, Eaton Road, Liverpool L12 2AP, UK
| | - Denise Williams
- West Midlands Regional Genetics Service, Clinical Genetics Unit, Birmingham Women's Hospital, Birmingham B15 2TG, UK
| | - Lauren I Brady
- Department of Paediatrics, McMaster University, 1200 Main St. W., Hamilton, ON L8N 3Z5, Canada
| | - Ronit Mesterman
- Department of Paediatrics, McMaster University, 1200 Main St. W., Hamilton, ON L8N 3Z5, Canada
| | - Mark A Tarnopolsky
- Department of Paediatrics, McMaster University, 1200 Main St. W., Hamilton, ON L8N 3Z5, Canada
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Xicheng District, Beijing 100034, China
| | - Ying Yang
- Department of Pediatrics, Peking University First Hospital, Xicheng District, Beijing 100034, China
| | | | - Mark I Rees
- Neurology and Molecular Neuroscience Research, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK; Faculty of Medicine and Health, Camperdown, University of Sydney, NSW 2006, Australia
| | - Mitchell Goldfarb
- Department of Biological Sciences, Hunter College of City University, 695 Park Avenue, New York, NY 10065, USA; Program in Biology, Graduate Center of City University, 365 Fifth Avenue, New York, NY 10016, USA
| | - Seo-Kyung Chung
- Neurology and Molecular Neuroscience Research, Institute of Life Science, Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK; Kids Neuroscience Centre, Kids Research, Children Hospital at Westmead, Sydney, NSW 2145, Australia; Brain and Mind Centre, Faculty of Medicine and Health, University of Sydney, NSW 2050, Australia
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167
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Gur-Hartman T, Berkowitz O, Yosovich K, Roubertie A, Zanni G, Macaya A, Heimer G, Dueñas BP, Sival DA, Pode-Shakked B, López-Laso E, Humbertclaude V, Riant F, Bosco L, Cayron LB, Nissenkorn A, Nicita F, Bertini E, Hassin S, Ben Zeev B, Zerem A, Libzon S, Lev D, Linder I, Lerman-Sagie T, Blumkin L. Clinical phenotypes of infantile onset CACNA1A-related disorder. Eur J Paediatr Neurol 2021; 30:144-154. [PMID: 33349592 DOI: 10.1016/j.ejpn.2020.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/11/2020] [Accepted: 10/14/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND CACNA1A-related disorders present with persistent progressive and non-progressive cerebellar ataxia and paroxysmal events: epileptic seizures and non-epileptic attacks. These phenotypes overlap and co-exist in the majority of patients. OBJECTIVE To describe phenotypes in infantile onset CACNA1A-related disorder and to explore intra-familial variations and genotype-phenotype correlations. MATERIAL AND METHODS This study was a multicenter international collaboration. A retrospective chart review of CACNA1A patients was performed. Clinical, radiological, and genetic data were collected and analyzed in 47 patients with infantile-onset disorder. RESULTS Paroxysmal non-epileptic events (PNEE) were observed in 68% of infants, with paroxysmal tonic upward gaze (PTU) noticed in 47% of infants. Congenital cerebellar ataxia (CCA) was diagnosed in 51% of patients including four patients with developmental delay and only one neurological sign. PNEEs were found in 63% of patients at follow-up, with episodic ataxia (EA) in 40% of the sample. Cerebellar ataxia was found in 58% of the patients at follow-up. Four patients had epilepsy in infancy and nine in childhood. Seven infants had febrile convulsions, three of which developed epilepsy later; all three patients had CCA. Cognitive difficulties were demonstrated in 70% of the children. Cerebellar atrophy was found in only one infant but was depicted in 64% of MRIs after age two. CONCLUSIONS Nearly all of the infants had CCA, PNEE or both. Cognitive difficulties were frequent and appeared to be associated with CCA. Epilepsy was more frequent after age two. Febrile convulsions in association with CCA may indicate risk of epilepsy in later childhood. Brain MRI was normal in infancy. There were no genotype-phenotype correlations found.
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Affiliation(s)
- Tamar Gur-Hartman
- Pediatric Neurology Unit, Wolfson Medical Center, Holon, Israel; Pediatric Movement Disorders Service, Wolfson Medical Center, Holon, Israel; School of Psychological Sciences, Tel-Aviv University, Israel
| | - Oren Berkowitz
- Department of Health Systems Management, Ariel University, Ariel, Israel
| | - Keren Yosovich
- Molecular Genetics Laboratory, Wolfson Medical Center, Holon, Israel
| | - Agathe Roubertie
- Departement de Neuropediatrie, CHU Gui de Chauliac, Institut des Neurosciences de Montpellier, Montpellier, France
| | - Ginevra Zanni
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, IRCCS Bambino Gesu' Children's Hospital, Rome, Italy
| | - Alfons Macaya
- Vall d'Hebron Research Institute, Pediatric Neurology Research Group, Autonomous University of Barcelona, Barcelona, Spain
| | - Gali Heimer
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Belén Pérez Dueñas
- Vall d'Hebron Research Institute, Pediatric Neurology Research Group, Autonomous University of Barcelona, Barcelona, Spain
| | - Deborah A Sival
- Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; The Institute for Rare Diseases, Edmond and Lily Safra Children's Hospital; Talpiot Medical Leadership Program, Sheba Medical Center, Ramat Gan, Israel
| | - Eduardo López-Laso
- University Hospital Reina Sofía, Pediatric Neurology Unit, IMIBIC and CIBERER, Córdoba, Spain
| | - Véronique Humbertclaude
- Service de Médecine Psychologique Enfants et Adolescents, CHU Saint Eloi, Montpellier, France
| | - Florence Riant
- AP-HP, GH Saint Louis-Lariboisière-Fernand Widal, Service de Génétique Moléculaire Neurovasculaire, Paris, France
| | - Luca Bosco
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, IRCCS Bambino Gesu' Children's Hospital, Rome, Italy
| | | | - Andreea Nissenkorn
- Pediatric Neurology Unit, Wolfson Medical Center, Holon, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, IRCCS Bambino Gesu' Children's Hospital, Rome, Italy
| | - Enrico Bertini
- Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, IRCCS Bambino Gesu' Children's Hospital, Rome, Italy
| | - Sharon Hassin
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Movement Disorders Institute and Department of Neurology, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Bruria Ben Zeev
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Ayelet Zerem
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Pediatric Neurology Unit TASMC, Tel-Aviv University, Israel
| | | | - Dorit Lev
- Molecular Genetics Laboratory, Wolfson Medical Center, Holon, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel; Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Ilan Linder
- Pediatric Epilepsy & Neurology Service, Barzilay Medical Center, Ashkelon, Israel
| | - Tally Lerman-Sagie
- Pediatric Neurology Unit, Wolfson Medical Center, Holon, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Lubov Blumkin
- Pediatric Neurology Unit, Wolfson Medical Center, Holon, Israel; Pediatric Movement Disorders Service, Wolfson Medical Center, Holon, Israel; Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
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168
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Zhang Y, Wang R, Liu Z, Jiang S, Du L, Qiu K, Li F, Wang Q, Jin J, Chen X, Li Z, Wu J, Zhang N. Distinct genetic patterns of shared and unique genes across four neurodevelopmental disorders. Am J Med Genet B Neuropsychiatr Genet 2021; 186:3-15. [PMID: 32929885 DOI: 10.1002/ajmg.b.32821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/04/2020] [Accepted: 08/15/2020] [Indexed: 01/09/2023]
Abstract
Neurodevelopmental disorders, including autism spectrum disorder (ASD), intellectual disability (ID), developmental disorders (DD) and epileptic encephalopathy (EE), have a strong clinical comorbidity, which indicates a common genetic etiology across various disorders. However, the underlying genetic mechanisms of comorbidity and specificity remain unknown across neurodevelopmental disorders. Based on de novo mutations, we compared systematically the functional characteristics between shared and unique genes under these disorders, as well as the spatiotemporal trajectory of development in brain and common molecular pathways of all shared genes. We observed that shared genes present more constrained against functional rare genetic variation, and harbor more pathogenic rare variants than do unique genes in each disorder. Furthermore, 71 shared genes formed two clusters related to synaptic transmission, transcription regulation and chromatin regulator. Particularly, we also found that two core genes STXBP1 and SCN2A, that were shared by the four neurodevelopmental disorders showed prominent pleiotropy. Our findings shed light on the shared and specific patterns across neurodevelopmental disorders and will enable us to further comprehend the etiology and provide valuable information for the diagnosis of neurodevelopmental disorders.
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Affiliation(s)
- Yijia Zhang
- Reproductive Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ruochen Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Lifeng Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kairui Qiu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Fengxia Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qiongdan Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jing Jin
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Na Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China.,Medicine & Technology School of Zunyi Medical University, Zunyi, China
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169
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Zhang P, Cui D, Liao P, Yuan X, Yang N, Zhen Y, Yang J, Huang Q. Case Report: Clinical Features of a Chinese Boy With Epileptic Seizures and Intellectual Disabilities Who Carries a Truncated NUS1 Variant. Front Pediatr 2021; 9:725231. [PMID: 34532305 PMCID: PMC8438189 DOI: 10.3389/fped.2021.725231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/02/2021] [Indexed: 11/29/2022] Open
Abstract
The mental retardation-55 with seizures (MRD55) is a rare genetic disease characterized by developmental delay, intellectual disability, language delay and multiple types of epileptic seizures. It is caused by pathogenic variants of the NUS1 gene, which encodes Nogo-B receptor (NgBR), a necessary subunit for the glycosylation reactions in mammals. To date, 25 disease-causing mutations of NUS1 have been reported, which are responsible for various diseases, including dystonia, Parkinson's disease, developmental and epileptic encephalopathy as well as congenital disorder of glycosylation. In addition, only 9 of these mutations were reported with detailed clinical features. There are no reports about Chinese cases with MRD55. In this study, a novel, de novo pathogenic variant of NUS1 (c.51_54delTCTG, p.L18Tfs*31) was identified in a Chinese patient with intellectual disability and epileptic seizures. This pathogenic variant resulted in truncated NgBR proteins, which might be the cause of the clinical features of the patient. Oxcarbazepine was an effective treatment for improving speech and movement of the patient, who consequently presented with no seizure. With this novel pathogenic variant found in NUS1, we expand the genotype spectrum of MRD55 and provide valuable insights into the potential genotype-phenotype correlation.
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Affiliation(s)
- Pingli Zhang
- Department of Pediatrics, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shangdong University, Qingdao, China
| | - Di Cui
- Running Gene Inc., Beijing, China
| | - Peiyuan Liao
- Department of Pediatrics, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shangdong University, Qingdao, China
| | - Xiang Yuan
- Department of Pediatrics, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shangdong University, Qingdao, China
| | - Nuan Yang
- Department of Pediatrics, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shangdong University, Qingdao, China
| | - Yuanyuan Zhen
- Department of Pediatrics, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shangdong University, Qingdao, China
| | - Jing Yang
- Department of Pediatrics, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shangdong University, Qingdao, China
| | - Qikun Huang
- Department of Pediatrics, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shangdong University, Qingdao, China
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170
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Sun D, Liu Y, Cai W, Ma J, Ni K, Chen M, Wang C, Liu Y, Zhu Y, Liu Z, Zhu F. Detection of Disease-Causing SNVs/Indels and CNVs in Single Test Based on Whole Exome Sequencing: A Retrospective Case Study in Epileptic Encephalopathies. Front Pediatr 2021; 9:635703. [PMID: 34055682 PMCID: PMC8155357 DOI: 10.3389/fped.2021.635703] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/24/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Epileptic encephalopathies (EEs) are a pediatric entity with highly phenotypic and genetic heterogeneity. Both single nucleotide variants (SNVs)/Indels and copy number variations (CNVs) could be the causes. Whole exome sequencing (WES) is widely applied to detect SNVs/Indels, but the bioinformatics approach for detecting CNVs is still limited and weak. In the current study, the possibility of profiling both disease-causing SNVs/Indels and CNVs in a single test based on WES in EEs was evaluated. Methods: The infants diagnosed with EEs were enrolled from a single pediatric epilepsy center between January 2018 and February 2020. Demographic and clinical data were collected. In WES data, the pathogenic SNVs were identified through an in-house pipeline, and pathogenic CNVs were identified by CNVkit. The diagnostic rate was evaluated, and the molecular findings were characterized. Results: A total of 73 infants were included; 36 (49.32%) of them were males. The median age was 7 months. Thirty-two (43.84%) infants had been diagnosed with epilepsy syndrome. The most common type of syndrome was West syndrome (22/73, 30.1%), followed by Dravet syndrome (20/77, 27.4%). Fifty-four (73.97%) had intellectual development delay. The genetic cause of EEs, pathogenic or likely pathogenic variants, were successfully discovered in 46.6% (34/73) of the infants, and 29 (39.7%) infants carried SNVs/Indels, while 5 (6.8%) carried CNVs. The majority of the disease-causing variants were inherited in de novo pattern (25, 71.4%). In addition to showing that the variants in the ion channel encoding genes accounted for the main etiology, we discovered and confirmed two new disease-causing genes, CACNA1E and WDR26. Five discovered CNVs were deletions of 2q24.3, 1p36, 15q11-q13, 16p11.2, and 17p13.3, and all were confirmed by array comparative genomic hybridization. Conclusion: The application of both SNVs/Indels and CNVs detection in a single test based on WES yielded a high diagnosis rate in EEs. WES may serve as a first-tier test with cost-effective benefit in EEs.
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Affiliation(s)
- Dan Sun
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Liu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Cai
- Department of Hematology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiehui Ma
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kun Ni
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ming Chen
- Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - Cheng Wang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yongchu Liu
- Aegicare Technology Co., Ltd. Shenzhen, China
| | | | - Zhisheng Liu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feng Zhu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Clinic Center of Human Gene Research, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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171
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El Achkar CM, Harrer M, Smith L, Kelly M, Iqbal S, Maljevic S, Niturad CE, Vissers LELM, Poduri A, Yang E, Lal D, Lerche H, Møller RS, Olson HE. Characterization of the GABRB2-Associated Neurodevelopmental Disorders. Ann Neurol 2020; 89:573-586. [PMID: 33325057 DOI: 10.1002/ana.25985] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 11/09/2022]
Abstract
OBJECTIVE We aimed to characterize the phenotypic spectrum and functional consequences associated with variants in the gene GABRB2, coding for the γ-aminobutyric acid type A (GABAA ) receptor subunit β2. METHODS We recruited and systematically evaluated 25 individuals with variants in GABRB2, 17 of whom are newly described and 8 previously reported with additional clinical data. Functional analysis was performed using a Xenopus laevis oocyte model system. RESULTS Our cohort of 25 individuals from 22 families with variants in GABRB2 demonstrated a range of epilepsy phenotypes from genetic generalized epilepsy to developmental and epileptic encephalopathy. Fifty-eight percent of individuals had pharmacoresistant epilepsy; response to medications targeting the GABAergic pathway was inconsistent. Developmental disability (present in 84%) ranged from mild intellectual disability to severe global disability; movement disorders (present in 44%) included choreoathetosis, dystonia, and ataxia. Disease-associated variants cluster in the extracellular N-terminus and transmembrane domains 1-3, with more severe phenotypes seen in association with variants in transmembrane domains 1 and 2 and the allosteric binding site between transmembrane domains 2 and 3. Functional analysis of 4 variants in transmembrane domains 1 or 2 (p.Ile246Thr, p.Pro252Leu, p.Ile288Ser, p.Val282Ala) revealed strongly reduced amplitudes of GABA-evoked anionic currents. INTERPRETATION GABRB2-related epilepsy ranges broadly in severity from genetic generalized epilepsy to developmental and epileptic encephalopathies. Developmental disability and movement disorder are key features. The phenotypic spectrum is comparable to other GABAA receptor-encoding genes. Phenotypic severity varies by protein domain. Experimental evidence supports loss of GABAergic inhibition as the mechanism underlying GABRB2-associated neurodevelopmental disorders. ANN NEUROL 2021;89:573-586.
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Affiliation(s)
- Christelle M El Achkar
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA.,Department of Neurology, Harvard Medical School, Boston, MA
| | - Merle Harrer
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Lacey Smith
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA
| | - McKenna Kelly
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA.,Dartmouth Geisel School of Medicine, Hanover, NH
| | - Sumaiya Iqbal
- Center for Development of Therapeutics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Snezana Maljevic
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, Australia
| | - Cristina E Niturad
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition, and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Annapurna Poduri
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA.,Department of Neurology, Harvard Medical School, Boston, MA
| | - Edward Yang
- Department of Radiology, Boston Children's Hospital, Boston, MA
| | - Dennis Lal
- Cleveland Clinic Genomic Medicine Institute and Neurological Institute, Cleveland, OH
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Treatment, Danish Epilepsy Center Filadelfia, Dianalund, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Heather E Olson
- Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Department of Neurology, Boston Children's Hospital, Boston, MA.,Department of Neurology, Harvard Medical School, Boston, MA
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172
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Chatron N, Becker F, Morsy H, Schmidts M, Hardies K, Tuysuz B, Roselli S, Najafi M, Alkaya DU, Ashrafzadeh F, Nabil A, Omar T, Maroofian R, Karimiani EG, Hussien H, Kok F, Ramos L, Gunes N, Bilguvar K, Labalme A, Alix E, Sanlaville D, de Bellescize J, Poulat AL, Moslemi AR, Lerche H, May P, Lesca G, Weckhuysen S, Tajsharghi H. Bi-allelic GAD1 variants cause a neonatal onset syndromic developmental and epileptic encephalopathy. Brain 2020; 143:1447-1461. [PMID: 32282878 PMCID: PMC7241960 DOI: 10.1093/brain/awaa085] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 01/13/2020] [Accepted: 03/05/2020] [Indexed: 12/22/2022] Open
Abstract
Developmental and epileptic encephalopathies are a heterogeneous group of early-onset epilepsy syndromes dramatically impairing neurodevelopment. Modern genomic technologies have revealed a number of monogenic origins and opened the door to therapeutic hopes. Here we describe a new syndromic developmental and epileptic encephalopathy caused by bi-allelic loss-of-function variants in GAD1, as presented by 11 patients from six independent consanguineous families. Seizure onset occurred in the first 2 months of life in all patients. All 10 patients, from whom early disease history was available, presented with seizure onset in the first month of life, mainly consisting of epileptic spasms or myoclonic seizures. Early EEG showed suppression-burst or pattern of burst attenuation or hypsarrhythmia if only recorded in the post-neonatal period. Eight patients had joint contractures and/or pes equinovarus. Seven patients presented a cleft palate and two also had an omphalocele, reproducing the phenotype of the knockout Gad1-/- mouse model. Four patients died before 4 years of age. GAD1 encodes the glutamate decarboxylase enzyme GAD67, a critical actor of the γ-aminobutyric acid (GABA) metabolism as it catalyses the decarboxylation of glutamic acid to form GABA. Our findings evoke a novel syndrome related to GAD67 deficiency, characterized by the unique association of developmental and epileptic encephalopathies, cleft palate, joint contractures and/or omphalocele.
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Affiliation(s)
- Nicolas Chatron
- Genetics Department, Lyon University Hospital, Lyon, France.,Institut NeuroMyoGène CNRS UMR 5310 - INSERM U1217 Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Felicitas Becker
- Department of Neurology, University of Ulm, Ulm, Germany.,University of Tübingen, Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Heba Morsy
- Human Genetics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Miriam Schmidts
- Genome Research Division, Human Genetics Department, Radboud University Medical Center Nijmegen, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 10, 6525KL Nijmegen, The Netherlands.,Center for Pediatrics and Adolescent Medicine, University Hospital Freiburg, Freiburg University Faculty of Medicine, Freiburg, Germany
| | - Katia Hardies
- Neurogenetics Group, VIB-Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium
| | - Beyhan Tuysuz
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Medical Faculty, Istanbul, Turkey
| | - Sandra Roselli
- Department of Pathology, University of Gothenburg, Sahlgrenska University Hospital, Sweden
| | - Maryam Najafi
- Genome Research Division, Human Genetics Department, Radboud University Medical Center Nijmegen, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Geert Grooteplein Zuid 10, 6525KL Nijmegen, The Netherlands
| | - Dilek Uludag Alkaya
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Medical Faculty, Istanbul, Turkey
| | - Farah Ashrafzadeh
- Department of Paediatric Neurology, Ghaem Medical Centre, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amira Nabil
- Human Genetics Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Tarek Omar
- Pediatrics Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Reza Maroofian
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK
| | - Ehsan Ghayoor Karimiani
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St George's, University of London, Cranmer Terrace, London SW17 0RE, UK.,Innovative medical research center, Mashhad branch, Islamic Azad University, Mashhad, Iran
| | - Haytham Hussien
- Pediatrics Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Fernando Kok
- Universidade de Sao Paulo Faculdade de Medicina, Sao Paulo, SP, Brazil
| | - Luiza Ramos
- Universidade de Sao Paulo Faculdade de Medicina, Sao Paulo, SP, Brazil
| | - Nilay Gunes
- Department of Pediatric Genetics, Istanbul University-Cerrahpasa, Medical Faculty, Istanbul, Turkey
| | - Kaya Bilguvar
- Department of Genetics, Yale Center for Genome Analysis (YCGA), Yale University, School of Medicine, New Haven, Connecticut
| | - Audrey Labalme
- Genetics Department, Lyon University Hospital, Lyon, France
| | - Eudeline Alix
- Genetics Department, Lyon University Hospital, Lyon, France
| | - Damien Sanlaville
- Institut NeuroMyoGène CNRS UMR 5310 - INSERM U1217 Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Julitta de Bellescize
- Department of Pediatric Clinical Epileptology, Sleep Disorders and Functional Neurology, ERN EpiCARE, University Hospitals of Lyon, Lyon, France
| | - Anne-Lise Poulat
- Department of Pediatric Neurology, Lyon University Hospital, Lyon, France
| | | | - Ali-Reza Moslemi
- Department of Pathology, University of Gothenburg, Sahlgrenska University Hospital, Sweden
| | - Holger Lerche
- University of Tübingen, Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, Tübingen, Germany
| | - Patrick May
- Luxemburg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Gaetan Lesca
- Genetics Department, Lyon University Hospital, Lyon, France.,Institut NeuroMyoGène CNRS UMR 5310 - INSERM U1217 Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | - Sarah Weckhuysen
- Neurogenetics Group, VIB-Center for Molecular Neurology, University of Antwerp, Antwerp, Belgium.,Department of Neurology, University Hospital Antwerp, Antwerp, Belgium
| | - Homa Tajsharghi
- School of Health Sciences, Division Biomedicine, University of Skovde, Skovde, Sweden
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173
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Klöckner C, Sticht H, Zacher P, Popp B, Babcock HE, Bakker DP, Barwick K, Bonfert MV, Bönnemann CG, Brilstra EH, Chung WK, Clarke AJ, Devine P, Donkervoort S, Fraser JL, Friedman J, Gates A, Ghoumid J, Hobson E, Horvath G, Keller-Ramey J, Keren B, Kurian MA, Lee V, Leppig KA, Lundgren J, McDonald MT, McLaughlin HM, McTague A, Mefford HC, Mignot C, Mikati MA, Nava C, Raymond FL, Sampson JR, Sanchis-Juan A, Shashi V, Shieh JTC, Shinawi M, Slavotinek A, Stödberg T, Stong N, Sullivan JA, Taylor AC, Toler TL, van den Boogaard MJ, van der Crabben SN, van Gassen KLI, van Jaarsveld RH, Van Ziffle J, Wadley AF, Wagner M, Wigby K, Wortmann SB, Zarate YA, Møller RS, Lemke JR, Platzer K. De novo variants in SNAP25 cause an early-onset developmental and epileptic encephalopathy. Genet Med 2020; 23:653-660. [PMID: 33299146 DOI: 10.1038/s41436-020-01020-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE This study aims to provide a comprehensive description of the phenotypic and genotypic spectrum of SNAP25 developmental and epileptic encephalopathy (SNAP25-DEE) by reviewing newly identified and previously reported individuals. METHODS Individuals harboring heterozygous missense or loss-of-function variants in SNAP25 were assembled through collaboration with international colleagues, matchmaking platforms, and literature review. For each individual, detailed phenotyping, classification, and structural modeling of the identified variant were performed. RESULTS The cohort comprises 23 individuals with pathogenic or likely pathogenic de novo variants in SNAP25. Intellectual disability and early-onset epilepsy were identified as the core symptoms of SNAP25-DEE, with recurrent findings of movement disorders, cerebral visual impairment, and brain atrophy. Structural modeling for all variants predicted possible functional defects concerning SNAP25 or impaired interaction with other components of the SNARE complex. CONCLUSION We provide a comprehensive description of SNAP25-DEE with intellectual disability and early-onset epilepsy mostly occurring before the age of two years. These core symptoms and additional recurrent phenotypes show an overlap to genes encoding other components or associated proteins of the SNARE complex such as STX1B, STXBP1, or VAMP2. Thus, these findings advance the concept of a group of neurodevelopmental disorders that may be termed "SNAREopathies."
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Affiliation(s)
- Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Holly E Babcock
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA
| | - Dewi P Bakker
- Department of Child Neurology, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Katy Barwick
- Institute of Child Health, University Collge London, London, UK
| | - Michaela V Bonfert
- Department of Pediatric Neurology and Developmental Medicine and LMU Center for Children with Medical Complexity, Dr. von Hauner Children's Hospital, LMU - University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Eva H Brilstra
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Angus J Clarke
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Wales, UK
| | - Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Sandra Donkervoort
- Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Jamie L Fraser
- Rare Disease Institute, Division of Genetics and Metabolism, Children's National Hospital, Washington, DC, USA
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California San Diego and Division of Neurology, Rady Children's Hospital, San Diego, CA, USA.,Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Alyssa Gates
- Department of Genetic Services, Kaiser Permanente Washington, Seattle, WA, USA
| | - Jamal Ghoumid
- Service de Génétique Clinique, Hôpital Jeanne de Flandre, CHU Lille, Lille, France
| | - Emma Hobson
- Yorkshire Clinical Genetics Service, Chapel Allerton Hospital, Leeds, UK
| | - Gabriella Horvath
- Department of Pediatrics, Division of Biochemical Diseases, University of British Columbia, Vancouver, Canada
| | | | - Boris Keren
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Manju A Kurian
- Institute of Child Health, University Collge London, London, UK
| | - Virgina Lee
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen A Leppig
- Department of Genetic Services, Kaiser Permanente Washington, Seattle, WA, USA
| | - Johan Lundgren
- Institute of Clinical Sciences, Skane University Hospital, Lund, Sweden
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | | | - Amy McTague
- Institute of Child Health, University Collge London, London, UK
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Cyril Mignot
- Département de Génétique, Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié Salpêtrière et Hôpital Trousseau, APHP, Sorbonne Université, Paris, France
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Caroline Nava
- Sorbonne University, Paris Brain Institute, Inserm U1127, CNRS UMR 7225, AP-HP, Pitié Salpêtrière Hospital, Department of Genetics, Paris, France
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Julian R Sampson
- Division of Cancer & Genetics, School of Medicine, Cardiff University, Wales, UK
| | - Alba Sanchis-Juan
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Joseph T C Shieh
- Division of Medical Genetics, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Marwan Shinawi
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Anne Slavotinek
- Division of Medical Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Tommy Stödberg
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Jennifer A Sullivan
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Ashley C Taylor
- Section of Genetics, Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Tomi L Toler
- Department of Pediatrics, Division of Genetics and Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Saskia N van der Crabben
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Jessica Van Ziffle
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | | | - Matias Wagner
- Institute of Neurogenomics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Kristen Wigby
- Department of Pediatrics, Division of Genetics, University of California, San Diego and Rady Children's Hospital-San Diego, San Diego, CA, USA
| | - Saskia B Wortmann
- Amalia Children's Hospital, Radboud University Nijmegen, Nijmegen, The Netherlands.,University Childrens Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Yuri A Zarate
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Rikke S Møller
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark.,Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre Filadelfia, Dianalund, Denmark
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany.
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174
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秀芬 李, 上 遲, 啟仁 蔡. 全基因體定序對兒童神經疾病的診斷率和治療影響. Dev Med Child Neurol 2020; 63. [PMID: 33289097 DOI: 10.1111/dmcn.14729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
: (WGS) 。 : 2016 1 2019 12 , 。: 、、。。 : 214 ( 128 , 86 ) , (SD) 13.8 (27.6) , 1 15 5 , (SD) 71.7 (58.9) , 8 18 。 43.9% , 62.5%, 47.5%, 41.1% 15.4%。 94, 23.4% 。 : , , 。, (43.9%), , (23.4%) 。.
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175
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Jenkins ML, Harris NJ, Dalwadi U, Fleming KD, Ziemianowicz DS, Rafiei A, Martin EM, Schriemer DC, Yip CK, Burke JE. The substrate specificity of the human TRAPPII complex's Rab-guanine nucleotide exchange factor activity. Commun Biol 2020; 3:735. [PMID: 33277614 PMCID: PMC7719173 DOI: 10.1038/s42003-020-01459-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
The TRAnsport Protein Particle (TRAPP) complexes act as Guanine nucleotide exchange factors (GEFs) for Rab GTPases, which are master regulators of membrane trafficking in eukaryotic cells. In metazoans, there are two large multi-protein TRAPP complexes: TRAPPII and TRAPPIII, with the TRAPPII complex able to activate both Rab1 and Rab11. Here we present detailed biochemical characterisation of Rab-GEF specificity of the human TRAPPII complex, and molecular insight into Rab binding. GEF assays of the TRAPPII complex against a panel of 20 different Rab GTPases revealed GEF activity on Rab43 and Rab19. Electron microscopy and chemical cross-linking revealed the architecture of mammalian TRAPPII. Hydrogen deuterium exchange MS showed that Rab1, Rab11 and Rab43 share a conserved binding interface. Clinical mutations in Rab11, and phosphomimics of Rab43, showed decreased TRAPPII GEF mediated exchange. Finally, we designed a Rab11 mutation that maintained TRAPPII-mediated GEF activity while decreasing activity of the Rab11-GEF SH3BP5, providing a tool to dissect Rab11 signalling. Overall, our results provide insight into the GTPase specificity of TRAPPII, and how clinical mutations disrupt this regulation. Here the authors reveal unique structural organization of the mammalian TRAPPII complex, which is critical in regulating membrane trafficking. They find that TRAPPII serves as a guanine nucleotide exchange factor for unexpected Rab GTPases such as Rab43 and Rab19.
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Affiliation(s)
- Meredith L Jenkins
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Noah J Harris
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Udit Dalwadi
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Kaelin D Fleming
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Daniel S Ziemianowicz
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Emily M Martin
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, T2N 4N1, Canada.,Department of Chemistry, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada. .,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada.
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176
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Shankar R, Perera B, Thomas RH. Epilepsy, an orphan disorder within the neurodevelopmental family. J Neurol Neurosurg Psychiatry 2020; 91:1245-1247. [PMID: 32928935 DOI: 10.1136/jnnp-2020-324660] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/13/2020] [Accepted: 08/16/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Rohit Shankar
- Intellectual Disability Neuropsychiatry, Cornwall Partnership NHS Foundation Trust, Truro, UK .,Psychiatry and Neuroscience, University of Exeter Medical School, Truro, UK
| | - Bhathika Perera
- Learning Disability Services, Barnet Enfield and Haringey Mental Health NHS Trust, London, UK
| | - Rhys H Thomas
- Department of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
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177
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Schöneberg T, Liebscher I. Mutations in G Protein-Coupled Receptors: Mechanisms, Pathophysiology and Potential Therapeutic Approaches. Pharmacol Rev 2020; 73:89-119. [PMID: 33219147 DOI: 10.1124/pharmrev.120.000011] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
There are approximately 800 annotated G protein-coupled receptor (GPCR) genes, making these membrane receptors members of the most abundant gene family in the human genome. Besides being involved in manifold physiologic functions and serving as important pharmacotherapeutic targets, mutations in 55 GPCR genes cause about 66 inherited monogenic diseases in humans. Alterations of nine GPCR genes are causatively involved in inherited digenic diseases. In addition to classic gain- and loss-of-function variants, other aspects, such as biased signaling, trans-signaling, ectopic expression, allele variants of GPCRs, pseudogenes, gene fusion, and gene dosage, contribute to the repertoire of GPCR dysfunctions. However, the spectrum of alterations and GPCR involvement is probably much larger because an additional 91 GPCR genes contain homozygous or hemizygous loss-of-function mutations in human individuals with currently unidentified phenotypes. This review highlights the complexity of genomic alteration of GPCR genes as well as their functional consequences and discusses derived therapeutic approaches. SIGNIFICANCE STATEMENT: With the advent of new transgenic and sequencing technologies, the number of monogenic diseases related to G protein-coupled receptor (GPCR) mutants has significantly increased, and our understanding of the functional impact of certain kinds of mutations has substantially improved. Besides the classical gain- and loss-of-function alterations, additional aspects, such as biased signaling, trans-signaling, ectopic expression, allele variants of GPCRs, uniparental disomy, pseudogenes, gene fusion, and gene dosage, need to be elaborated in light of GPCR dysfunctions and possible therapeutic strategies.
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Affiliation(s)
- Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig, Germany
| | - Ines Liebscher
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig, Germany
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178
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Lu Q, Zhang MN, Shi XY, Zhang LQ, Wang YY, Liu LY, He W, Chen HM, He B, Zou LP. Association of HECW2 variants with developmental and epileptic encephalopathy and knockdown of zebrafish hecw2a. Am J Med Genet A 2020; 185:377-383. [PMID: 33205896 DOI: 10.1002/ajmg.a.61958] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/24/2020] [Accepted: 10/20/2020] [Indexed: 11/07/2022]
Abstract
Developmental and epileptic encephalopathy (DEE) is a severe encephalopathy in infants and early childhood. In this study we reported a recurrent de novo variant (c.3985C>T, p.R1330W) in HECW2 (HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2) (MIM# 617245) identified by screening 240 patients with DEE and summarized clinical features of published DEE patients with HECW2 variants. Functionally, transcriptional knockdown of zebrafish hecw2a led to early morphological abnormalities in the brain tissues. These results suggest a potential functional link between HECW2 dysfunction and brain development.
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Affiliation(s)
- Qian Lu
- Department of Pediatrics, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Meng-Na Zhang
- Department of Pediatrics, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiu-Yu Shi
- Department of Pediatrics, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Ling-Qiang Zhang
- State Key Laboratory of Proteomics, National Center of Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yang-Yang Wang
- Department of Pediatrics, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Li-Ying Liu
- Department of Pediatrics, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Wen He
- Department of Pediatrics, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hui-Min Chen
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
| | - Bing He
- Division of Matrix Biology, Department of Medical Biochemistry and Biophysics (MBB), Karolinksa Institute, Stockholm, Sweden
| | - Li-Ping Zou
- Department of Pediatrics, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- Beijing Institute of Brain Disorders, Laboratory of Brain Disorders, Ministry of Science and Technology, Collaborative Innovation Center for Brain Disorders, Capital Medical University, Beijing, China
- Southern Medical University, Guangzhou, China
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179
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Yuan L, Chen X, Song Z, Le W, Zheng W, Liu X, Deng H. Extended Study of NUS1 Gene Variants in Parkinson's Disease. Front Neurol 2020; 11:583182. [PMID: 33193043 PMCID: PMC7653662 DOI: 10.3389/fneur.2020.583182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 09/15/2020] [Indexed: 01/13/2023] Open
Abstract
Parkinson's disease (PD), is the second most common neurodegenerative disorder worldwide. Genetic, environmental factors, and aging are its primary development contributors. Recently the nuclear undecaprenyl pyrophosphate synthase 1 homolog (Saccharomyces cerevisiae) gene (NUS1) was reported as a candidate gene for PD, which raised our interest in the relationship between NUS1 and PD. This study was aimed to further explore the role of NUS1 variants in PD development. Genetic analysis for 308 Han-Chinese PD patients and 308 ethnically matched controls using whole exome sequencing was conducted. Additionally, a total of 60 articles involving in whole exome/whole genome sequencing or direct sequencing of the NUS1 gene from PubMed database between July 1, 2011 and August 26, 2020 were reviewed to evaluate PD-associated NUS1 variants. No potentially pathogenic NUS1 variant was found in 308 PD cases, and no frequency biases between 308 PD cases and 308 controls were observed for the only non-synonymous variant p.Asp179Glu (genotype: χ2 = 0.093, P = 0.761; allele: χ2 = 0.092, P = 0.762). No pathogenic or disease-associated NUS1 variant was reported in the 5,636 PD cases of the 60 articles. In summary, current findings indicate that NUS1 variant is not a common genetic factor contributing to PD.
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Affiliation(s)
- Lamei Yuan
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xiangyu Chen
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhi Song
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Weidong Le
- Center for Clinical Research on Neurological Diseases, The First Affiliated Hospital, Dalian Medical University, Dalian, China
| | - Wen Zheng
- Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Xin Liu
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
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180
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Abstract
Because of next-generation sequencing and the discovery of many new causative genes, genetic testing in epilepsy patients has become widespread. Pathologic variants resulting in epilepsy cause a variety of changes that can be broadly classified into syndromic disorders (i.e., chromosomal abnormalities), metabolic disorders, brain malformations, and abnormal cellular signaling. Here, we review the available genetic testing, reasons to pursue genetic testing, common genetic causes of epilepsy, the data behind what patients are found to have genetic epilepsies based on current testing, and discussing these results with patients. We propose an algorithm for testing patients with epilepsy to maximize yield and limit costs based on their phenotype (including electroencephalography and magnetic resonance imaging findings), age of seizure onset, and presence of other neurologic comorbidities. Being able to discern which type of genetic testing to order, using that information to give targeted and cost-effective patient care, and interpreting results accurately will be a crucial skill for the modern neurologist.
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Affiliation(s)
- David M Ritter
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Katherine Holland
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
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181
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Jaeken J. Congenital disorders of glycosylation: A multi-genetic disease family with multiple subcellular locations. JOURNAL OF MOTHER AND CHILD 2020; 24:14-20. [PMID: 33554500 PMCID: PMC8518092 DOI: 10.34763/jmotherandchild.20202402si.2005.000004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This review discusses a selection of congenital disorders of glycosylation that show peculiar features, such as an unusual presentation, different phenotypes, a novel biochemical/genetic mechanism, a relatively high frequency or a relatively efficient treatment.
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Affiliation(s)
- Jaak Jaeken
- Department of Development and Regeneration, Center for Metabolic Diseases, University Hospital Gasthuisberg, KU Leuven, Leuven, Belgium
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182
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Itai T, Hamanaka K, Sasaki K, Wagner M, Kotzaeridou U, Brösse I, Ries M, Kobayashi Y, Tohyama J, Kato M, Ong WP, Chew HB, Rethanavelu K, Ranza E, Blanc X, Uchiyama Y, Tsuchida N, Fujita A, Azuma Y, Koshimizu E, Mizuguchi T, Takata A, Miyake N, Takahashi H, Miyagi E, Tsurusaki Y, Doi H, Taguri M, Antonarakis SE, Nakashima M, Saitsu H, Miyatake S, Matsumoto N. De novo variants in CELF2 that disrupt the nuclear localization signal cause developmental and epileptic encephalopathy. Hum Mutat 2020; 42:66-76. [PMID: 33131106 DOI: 10.1002/humu.24130] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/16/2020] [Accepted: 10/17/2020] [Indexed: 12/20/2022]
Abstract
We report heterozygous CELF2 (NM_006561.3) variants in five unrelated individuals: Individuals 1-4 exhibited developmental and epileptic encephalopathy (DEE) and Individual 5 had intellectual disability and autistic features. CELF2 encodes a nucleocytoplasmic shuttling RNA-binding protein that has multiple roles in RNA processing and is involved in the embryonic development of the central nervous system and heart. Whole-exome sequencing identified the following CELF2 variants: two missense variants [c.1558C>T:p.(Pro520Ser) in unrelated Individuals 1 and 2, and c.1516C>G:p.(Arg506Gly) in Individual 3], one frameshift variant in Individual 4 that removed the last amino acid of CELF2 c.1562dup:p.(Tyr521Ter), possibly resulting in escape from nonsense-mediated mRNA decay (NMD), and one canonical splice site variant, c.272-1G>C in Individual 5, also probably leading to NMD. The identified variants in Individuals 1, 2, 4, and 5 were de novo, while the variant in Individual 3 was inherited from her mosaic mother. Notably, all identified variants, except for c.272-1G>C, were clustered within 20 amino acid residues of the C-terminus, which might be a nuclear localization signal. We demonstrated the extranuclear mislocalization of mutant CELF2 protein in cells transfected with mutant CELF2 complementary DNA plasmids. Our findings indicate that CELF2 variants that disrupt its nuclear localization are associated with DEE.
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Affiliation(s)
- Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Kazunori Sasaki
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technische Universität München, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Urania Kotzaeridou
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Ines Brösse
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Ries
- Department of Child Neurology and Metabolic Medicine, Center for Pediatric and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | - Yu Kobayashi
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Niigata, Japan
| | - Jun Tohyama
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Niigata, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Shinagawa-ku, Tokyo, Japan
| | - Winnie P Ong
- Department of Genetics, Kuala Lumpur Hospital, Jalan Pahang, Kuala Lumpur, Malaysia
| | - Hui B Chew
- Department of Genetics, Kuala Lumpur Hospital, Jalan Pahang, Kuala Lumpur, Malaysia
| | - Kavitha Rethanavelu
- Department of Genetics, Kuala Lumpur Hospital, Jalan Pahang, Kuala Lumpur, Malaysia
| | - Emmanuelle Ranza
- Swiss Institute of Genomic Medicine, Medigenome, Geneva, Switzerland
| | - Xavier Blanc
- Swiss Institute of Genomic Medicine, Medigenome, Geneva, Switzerland
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Rare Disease Genomics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Rare Disease Genomics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Etsuko Miyagi
- Department of Obstetrics and Gynecology, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Kanagawa, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
| | - Masataka Taguri
- Department of Data Science, Yokohama City University School of Data Science, Yokohama, Kanagawa, Japan
| | - Stylianos E Antonarakis
- Swiss Institute of Genomic Medicine, Medigenome, Geneva, Switzerland.,Department of Genetic Medicine, University of Geneva Medical School, Geneva, Switzerland
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Kanagawa, Japan
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183
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Alten B, Zhou Q, Shin OH, Esquivies L, Lin PY, White KI, Sun R, Chung WK, Monteggia LM, Brunger AT, Kavalali ET. Role of Aberrant Spontaneous Neurotransmission in SNAP25-Associated Encephalopathies. Neuron 2020; 109:59-72.e5. [PMID: 33147442 DOI: 10.1016/j.neuron.2020.10.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/09/2020] [Accepted: 10/07/2020] [Indexed: 01/19/2023]
Abstract
SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) complex, composed of synaptobrevin, syntaxin, and SNAP25, forms the essential fusion machinery for neurotransmitter release. Recent studies have reported several mutations in the gene encoding SNAP25 as a causative factor for developmental and epileptic encephalopathies of infancy and childhood with diverse clinical manifestations. However, it remains unclear how SNAP25 mutations give rise to these disorders. Here, we show that although structurally clustered mutations in SNAP25 give rise to related synaptic transmission phenotypes, specific alterations in spontaneous neurotransmitter release are a key factor to account for disease heterogeneity. Importantly, we identified a single mutation that augments spontaneous release without altering evoked release, suggesting that aberrant spontaneous release is sufficient to cause disease in humans.
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Affiliation(s)
- Baris Alten
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - Qiangjun Zhou
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - Ok-Ho Shin
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Pei-Yi Lin
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - K Ian White
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Rong Sun
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - Wendy K Chung
- Department of Pediatrics (in Medicine), Columbia University Medical Center, New York, NY 10032, USA
| | - Lisa M Monteggia
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ege T Kavalali
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA.
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184
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Fraiman P, Maia-de-Oliveira JP, Moreira-Neto M, Godeiro-Junior C. Psychosis in NUS1 de novo mutation: New phenotypical presentation. Clin Genet 2020; 99:475-476. [PMID: 33111323 DOI: 10.1111/cge.13867] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/13/2020] [Accepted: 10/16/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Pedro Fraiman
- Hospital Universitario Onofre Lopes, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - João Paulo Maia-de-Oliveira
- National Institute of Science and Technology in Translational Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Manuel Moreira-Neto
- Hospital Universitario Onofre Lopes, Universidade Federal do Rio Grande do Norte, Natal, Brazil
| | - Clecio Godeiro-Junior
- Hospital Universitario Onofre Lopes, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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185
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Akamine S, Okuzono S, Yamamoto H, Setoyama D, Sagata N, Ohgidani M, Kato TA, Ishitani T, Kato H, Masuda K, Matsushita Y, Ono H, Ishizaki Y, Sanefuji M, Saitsu H, Matsumoto N, Kang D, Kanba S, Nakabeppu Y, Sakai Y, Ohga S. GNAO1 organizes the cytoskeletal remodeling and firing of developing neurons. FASEB J 2020; 34:16601-16621. [PMID: 33107105 DOI: 10.1096/fj.202001113r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/03/2020] [Accepted: 10/13/2020] [Indexed: 01/03/2023]
Abstract
Developmental and epileptic encephalopathy (DEE) represents a group of neurodevelopmental disorders characterized by infantile-onset intractable seizures and unfavorable prognosis of psychomotor development. To date, hundreds of genes have been linked to the onset of DEE. GNAO1 is a DEE-associated gene encoding the alpha-O1 subunit of guanine nucleotide-binding protein (GαO ). Despite the increasing number of reported children with GNAO1 encephalopathy, the molecular mechanisms underlying their neurodevelopmental phenotypes remain elusive. We herein present that co-immunoprecipitation and mass spectrometry analyses identified another DEE-associated protein, SPTAN1, as an interacting partner of GαO . Silencing of endogenous Gnao1 attenuated the neurite outgrowth and calcium-dependent signaling. Inactivation of GNAO1 in human-induced pluripotent stem cells gave rise to anomalous brain organoids that only weakly expressed SPTAN1 and Ankyrin-G. Furthermore, GNAO1-deficient organoids failed to conduct synchronized firing to adjacent neurons. These data indicate that GαO and other DEE-associated proteins organize the cytoskeletal remodeling and functional polarity of neurons in the developing brain.
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Affiliation(s)
- Satoshi Akamine
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Sayaka Okuzono
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Yamamoto
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daiki Setoyama
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Noriaki Sagata
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahiro Ohgidani
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takahiro A Kato
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Tohru Ishitani
- Division of Integrated Signaling Systems, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan.,Department of Homeostatic Regulation, Division of Cellular and Molecular Biology. Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hiroki Kato
- Division of Oral Biological Sciences, Department of Molecular Cell Biology and Oral Anatomy, Graduate School of Dental Science, Kyushu University, Fukuoka, Japan
| | - Keiji Masuda
- Section of Oral Medicine for Children, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Yuki Matsushita
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ono
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshito Ishizaki
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masafumi Sanefuji
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigenobu Kanba
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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186
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Gamirova RG, Gamirova RR, Esin RG. [Genetics of epilepsy: successes, problems and development prospects]. Zh Nevrol Psikhiatr Im S S Korsakova 2020; 120:144-150. [PMID: 33081460 DOI: 10.17116/jnevro2020120091144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The authors present a detailed review of current advances in the field of genetics of epilepsy. Separately, new views on the etiology and pathogenesis of genetic epileptic encephalopathies, focal epilepsy and idiopathic generalized epilepsies are examined. The authors emphasize the importance of genetic discoveries for the clinical practice, including the prospects in the development of patients' personalized treatment. A comparative analysis of the value of various methods of genetic research in the diagnosis of epilepsy, methods of integrating molecular genetic analyses into everyday practical medicine is presented.
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Affiliation(s)
- R G Gamirova
- Kazan State Medical Academy - branch of Russian Medical Academy of Continuing Professional Education, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
| | - R R Gamirova
- Kazan (Volga Region) Federal University, Kazan, Russia
| | - R G Esin
- Kazan State Medical Academy - branch of Russian Medical Academy of Continuing Professional Education, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
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187
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Structural basis of heterotetrameric assembly and disease mutations in the human cis-prenyltransferase complex. Nat Commun 2020; 11:5273. [PMID: 33077723 PMCID: PMC7573591 DOI: 10.1038/s41467-020-18970-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/23/2020] [Indexed: 11/17/2022] Open
Abstract
The human cis-prenyltransferase (hcis-PT) is an enzymatic complex essential for protein N-glycosylation. Synthesizing the precursor of the glycosyl carrier dolichol-phosphate, mutations in hcis-PT cause severe human diseases. Here, we reveal that hcis-PT exhibits a heterotetrameric assembly in solution, consisting of two catalytic dehydrodolichyl diphosphate synthase (DHDDS) and inactive Nogo-B receptor (NgBR) heterodimers. Importantly, the 2.3 Å crystal structure reveals that the tetramer assembles via the DHDDS C-termini as a dimer-of-heterodimers. Moreover, the distal C-terminus of NgBR transverses across the interface with DHDDS, directly participating in active-site formation and the functional coupling between the subunits. Finally, we explored the functional consequences of disease mutations clustered around the active-site, and in combination with molecular dynamics simulations, we propose a mechanism for hcis-PT dysfunction in retinitis pigmentosa. Together, our structure of the hcis-PT complex unveils the dolichol synthesis mechanism and its perturbation in disease. The human cis-prenyltransferase (hcis-PT) complex synthesizes the precursor of the glycosyl carrier dolichol-phosphate and as such it is essential for protein N-glycosylation. The crystal structure of the complex reveals unusual tetrameric architecture and provides insights into dolichol synthesis mechanism and functional consequences of disease-associated hcis-PT mutations.
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188
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Melland H, Carr EM, Gordon SL. Disorders of synaptic vesicle fusion machinery. J Neurochem 2020; 157:130-164. [PMID: 32916768 DOI: 10.1111/jnc.15181] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/20/2020] [Accepted: 08/26/2020] [Indexed: 12/11/2022]
Abstract
The revolution in genetic technology has ushered in a new age for our understanding of the underlying causes of neurodevelopmental, neuromuscular and neurodegenerative disorders, revealing that the presynaptic machinery governing synaptic vesicle fusion is compromised in many of these neurological disorders. This builds upon decades of research showing that disturbance to neurotransmitter release via toxins can cause acute neurological dysfunction. In this review, we focus on disorders of synaptic vesicle fusion caused either by toxic insult to the presynapse or alterations to genes encoding the key proteins that control and regulate fusion: the SNARE proteins (synaptobrevin, syntaxin-1 and SNAP-25), Munc18, Munc13, synaptotagmin, complexin, CSPα, α-synuclein, PRRT2 and tomosyn. We discuss the roles of these proteins and the cellular and molecular mechanisms underpinning neurological deficits in these disorders.
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Affiliation(s)
- Holly Melland
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, Melbourne, Vic., Australia
| | - Elysa M Carr
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, Melbourne, Vic., Australia
| | - Sarah L Gordon
- The Florey Institute of Neuroscience and Mental Health, Melbourne Dementia Research Centre, The University of Melbourne, Melbourne, Vic., Australia
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Togashi N, Fujita A, Shibuya M, Uneoka S, Miyabayashi T, Sato R, Okubo Y, Endo W, Inui T, Jin K, Matsumoto N, Haginoya K. Fifteen-year follow-up of a patient with a DHDDS variant with non-progressive early onset myoclonic tremor and rare generalized epilepsy. Brain Dev 2020; 42:696-699. [PMID: 32654954 DOI: 10.1016/j.braindev.2020.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/16/2020] [Accepted: 06/21/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Generalized epilepsy and tremor phenotypes have been reported in some genetic disorders. Among them benign adult familial myoclonus epilepsy (BAFME) has been confirmed as a clearly defined clinical and genetic entity. On the other hand, non-progressive tremor and generalized epilepsy phenotypes have also been reported in patients with DHDDS variants. CASE PRESENTATION We report on a long term follow-up of patient with de novo missense variant of DHDDS, who revealed non progressive nature. This 18-year-old woman presented non-progressive tremor since her early infancy. She had rare seizures. Her tremor was considered as cortical myoclonic tremor with giant somatosensory evoked potentials. CONCLUSION In patients with early onset, non-progressive tremor and rare generalized epilepsy phenotypes, DHDDS variants may be considered in the genetic differential diagnosis.
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Affiliation(s)
- Noriko Togashi
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Moriei Shibuya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Saki Uneoka
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Takuya Miyabayashi
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Ryo Sato
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Yukimune Okubo
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Wakaba Endo
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Takehiko Inui
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan
| | - Kazutaka Jin
- Department of Epileptology, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, Sendai 989-3126, Japan.
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Yang Y, Xiangwei W, Zhang X, Xiao J, Chen J, Yang X, Jia T, Yang Z, Jiang Y, Zhang Y. Phenotypic spectrum of patients with GABRB2 variants: from mild febrile seizures to severe epileptic encephalopathy. Dev Med Child Neurol 2020; 62:1213-1220. [PMID: 32686847 DOI: 10.1111/dmcn.14614] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/26/2020] [Indexed: 12/19/2022]
Abstract
AIM To characterize the different phenotypes of GABRB2-related epilepsy and to establish a genotype-phenotype correlation. METHOD We used next-generation sequencing to identify GABRB2 variants in 15 patients. RESULTS Eleven GABRB2 variants were novel and 12 were de novo. The age at the onset of seizures ranged from 1 day to 26 months. Nine patients had multiple seizure types, including focal seizures, generalized tonic-clonic seizures, myoclonic seizures, epileptic spasms, and atonic seizures. Seizures were fever-sensitive in 13 out of the 15 patients. Eleven patients displayed developmental delay, while 11 had abnormal video electroencephalography. Abnormalities in the brain images included dysplasia of the frontal and temporal cortex, dysplasia of the corpus callosum, and delayed myelination in four patients. One patient was diagnosed with febrile seizures, three with febrile seizures plus, three with Dravet syndrome, three with West syndrome, one with Ohtahara syndrome, three with developmental delays and epilepsy, and one with non-specific early-onset epileptic encephalopathy. INTERPRETATION The most common phenotypes of patients with GABRB2 variants include early onset of seizure and fever sensitivity. Febrile seizures and febrile seizures plus are new phenotypes of GABRB2 variants. The phenotypic spectrum of GABRB2 variants ranges from mild febrile seizures to severe epileptic encephalopathy.
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Affiliation(s)
- Ying Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Wenshu Xiangwei
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoli Zhang
- Department of Pediatrics, The Third Affiliated Hospital of Zheng Zhou University, Zhengzhou, China
| | - Jiangxi Xiao
- Department of Radiology, Peking University First Hospital, Beijing, China
| | - Jiaoyang Chen
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Xiaoling Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Tianming Jia
- Department of Pediatrics, The Third Affiliated Hospital of Zheng Zhou University, Zhengzhou, China
| | - Zhixian Yang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuwu Jiang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
| | - Yuehua Zhang
- Department of Pediatrics, Peking University First Hospital, Beijing, China
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191
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Frye RE. Mitochondrial Dysfunction in Autism Spectrum Disorder: Unique Abnormalities and Targeted Treatments. Semin Pediatr Neurol 2020; 35:100829. [PMID: 32892956 DOI: 10.1016/j.spen.2020.100829] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Several lines of evidence implicate mitochondria in the pathophysiology of autism spectrum disorder (ASD). In this review, we outline some of the evidence supporting this notion, as well as discuss novel abnormalities in mitochondrial function that appear to be related to ASD, and treatments that both target mitochondria and have evidence of usefulness in the treatment of ASD in clinical trials. A suspicion of the mitochondrion's involvement in ASD can be traced back to 1985 when lactic acidosis was noted in a subset of children with ASD. A large population-based study in 2007 confirmed this notion and found that a subset of children with ASD (∼4%) could be diagnosed with a definite mitochondrial disease. Further studies suggested that children with ASD and mitochondrial disease may have certain characteristics such as fatigability, gastrointestinal disorders, unusual types of neurodevelopmental regression, seizures/epilepsy, and motor delay. Further research examining biomarkers of mitochondrial dysfunction and electron transport chain activity suggest that abnormalities of mitochondrial function could affect a much higher number of children with ASD, perhaps up to 80%. Recent research has identified a type of dysfunction of mitochondria in which the activity of the electron transport chain is significantly increased. This novel type of mitochondrial dysfunction may be associated with environmental exposures and neurodevelopmental regression. Several treatments that target mitochondria appear to have evidence for use in children with ASD, including cofactors such as L-Carnitine and the ketogenic diet. Although the understanding of the involvement of mitochondria in ASD is evolving, the mitochondrion is clearly a novel molecular target which can be helpful in understanding the etiology of ASD and treatments that may improve function of children with ASD.
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Affiliation(s)
- Richard E Frye
- Division of Neurology, Section on Neurodevelopmental Disorders, Barrow Neurological Institute at Phoenix Children's Hospital, Phoenix, AZ; Department of Child Health, University of Arizona College of Medicine - Phoenix, Phoenix, AZ.
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192
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Tang BL. SNAREs and developmental disorders. J Cell Physiol 2020; 236:2482-2504. [PMID: 32959907 DOI: 10.1002/jcp.30067] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/20/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Members of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) family mediate membrane fusion processes associated with vesicular trafficking and autophagy. SNAREs mediate core membrane fusion processes essential for all cells, but some SNAREs serve cell/tissue type-specific exocytic/endocytic functions, and are therefore critical for various aspects of embryonic development. Mutations or variants of their encoding genes could give rise to developmental disorders, such as those affecting the nervous system and immune system in humans. Mutations to components in the canonical synaptic vesicle fusion SNARE complex (VAMP2, STX1A/B, and SNAP25) and a key regulator of SNARE complex formation MUNC18-1, produce variant phenotypes of autism, intellectual disability, movement disorders, and epilepsy. STX11 and MUNC18-2 mutations underlie 2 subtypes of familial hemophagocytic lymphohistiocytosis. STX3 mutations contribute to variant microvillus inclusion disease. Chromosomal microdeletions involving STX16 play a role in pseudohypoparathyroidism type IB associated with abnormal imprinting of the GNAS complex locus. In this short review, I discuss these and other SNARE gene mutations and variants that are known to be associated with a variety developmental disorders, with a focus on their underlying cellular and molecular pathological basis deciphered through disease modeling. Possible pathogenic potentials of other SNAREs whose variants could be disease predisposing are also speculated upon.
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Affiliation(s)
- Bor L Tang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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193
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Pre- and Post-Zygotic TP53 De Novo Mutations in SHH-Medulloblastoma. Cancers (Basel) 2020; 12:cancers12092503. [PMID: 32899294 PMCID: PMC7564492 DOI: 10.3390/cancers12092503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/26/2020] [Accepted: 09/01/2020] [Indexed: 11/26/2022] Open
Abstract
Simple Summary Medulloblastoma is the most common malignant brain tumor in children. In a subset of cases, a causal factor is a constitutive mutation of the TP53 gene, which may be inherited or arise for the first time in a patient (de novo). Using an immunohistochemistry assay as a screening tool, we selected patients suspected of harboring a TP53 mutation and offered genetic counseling and germline testing. Our study, which was the first to investigate the parental origin of TP53 mutations in medulloblastoma, allowed the identification of two additional cases with de novo mutations. Moreover, we demonstrated that in one patient the mutation originated at a post-zygotic stage, resulting in somatic mosaicism. These findings have important implications for genetic counseling since they highlight the occurrence of both pre- and post-zygotic TP53 de novo mutations in medulloblastoma, pointing out that in a specific subgroup of patients genetic testing should be offered regardless of family history. Abstract Li-Fraumeni syndrome (LFS) is an autosomal dominant disorder caused by mutations in the TP53 gene, predisposing to a wide spectrum of early-onset cancers, including brain tumors. In medulloblastoma patients, the role of TP53 has been extensively investigated, though the prevalence of de novo mutations has not been addressed. We characterized TP53 mutations in a monocentric cohort of consecutive Sonic Hedgehog (SHH)-activated medulloblastoma patients. Germline testing was offered based on tumor p53 immunostaining positivity. Among 24 patients, three (12.5%) showed tumor p53 overexpression, of whom two consented to undergo germline testing and resulted as carriers of TP53 mutations. In the first case, family history was uneventful and the mutation was not found in either of the parents. The second patient, with a family history suggestive of LFS, unexpectedly resulted as a carrier of the mosaic mutation c.742=/C>T p.(Arg248=/Trp). The allele frequency was 26% in normal tissues and 42–77% in tumor specimens. Loss of heterozygosity (LOH) in the tumor was also confirmed. Notably, the mosaic case has been in complete remission for more than one year, while the first patient, as most TP53-mutated medulloblastoma cases from other cohorts, showed a severe and rapidly progressive disease. Our study reported the first TP53 mosaic mutation in medulloblastoma patients and confirmed the importance of germline testing in p53 overexpressed SHH-medulloblastoma, regardless of family history.
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194
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Edani BH, Grabińska KA, Zhang R, Park EJ, Siciliano B, Surmacz L, Ha Y, Sessa WC. Structural elucidation of the cis-prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation. Proc Natl Acad Sci U S A 2020; 117:20794-20802. [PMID: 32817466 PMCID: PMC7456142 DOI: 10.1073/pnas.2008381117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Cis-prenyltransferase (cis-PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis-PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme's active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis-PTase activity. Comparison of NgBR/DHDDS with homodimeric cis-PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme's active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis-PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.
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Affiliation(s)
- Ban H Edani
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Kariona A Grabińska
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Rong Zhang
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Eon Joo Park
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Benjamin Siciliano
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
| | - Liliana Surmacz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106, Warsaw, Poland
| | - Ya Ha
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520;
| | - William C Sessa
- Vascular Biology and Therapeutics Program, Yale University School of Medicine, New Haven, CT 06520;
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520
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195
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Abstract
BACKGROUND Retrospective observational study to determine diagnostic yield and utility of genetic testing in children with epilepsy attending the Epilepsy Clinic at Children's Hospital, London, Ontario, Canada. METHODS Children (birth-18 years) with epilepsy, who were seen in a 10-year period (January 1, 2008-March 31, 2018), were selected using defined inclusion criteria and by combining clinic datasets and laboratory records. RESULTS In total, 105 children (52.38% male and 47.61% female) with a variety of seizures were included in the analysis. Developmental delay was documented in the majority (83; 79.04%). Overall, a genetic diagnosis was established in 24 (22.85%) children. The diagnostic yield was highest for whole-exome sequencing (WES), at 35.71%. The yield from microarray was 8.33%. Yields of single-gene testing (18.60%) and targeted multigene panel testing (19.23%) were very similar. Several likely pathogenic and pathogenic variants not previously reported were identified and categorized using ACMG criteria. All diagnosed patients underwent a review of anti-seizure medication management and received counseling on natural history of their disease, possible complications, recurrence risks, and possibilities of preimplantation or prenatal genetic diagnosis. CONCLUSIONS Our study confirms the multiple benefits of detecting a genetic etiology in children with epilepsy. Similar yields in single versus multigene testing underscore the importance of accurate clinical phenotyping. Patients with epilepsy and their caregivers in Ontario would undoubtedly benefit from repatriation of multigene panels and WES to the province.
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196
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Richter F, Morton SU, Kim SW, Kitaygorodsky A, Wasson LK, Chen KM, Zhou J, Qi H, Patel N, DePalma SR, Parfenov M, Homsy J, Gorham JM, Manheimer KB, Velinder M, Farrell A, Marth G, Schadt EE, Kaltman JR, Newburger JW, Giardini A, Goldmuntz E, Brueckner M, Kim R, Porter GA, Bernstein D, Chung WK, Srivastava D, Tristani-Firouzi M, Troyanskaya OG, Dickel DE, Shen Y, Seidman JG, Seidman CE, Gelb BD. Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nat Genet 2020; 52:769-777. [PMID: 32601476 PMCID: PMC7415662 DOI: 10.1038/s41588-020-0652-z] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 05/22/2020] [Indexed: 02/07/2023]
Abstract
A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10-4). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10-5). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10-3). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10-5). Our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.
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Affiliation(s)
- Felix Richter
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah U Morton
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Newborn Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Seong Won Kim
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alexander Kitaygorodsky
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Lauren K Wasson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Hongjian Qi
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | - Nihir Patel
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Jason Homsy
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Center for External Innovation, Takeda Pharmaceuticals USA, Cambridge, MA, USA
| | - Joshua M Gorham
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Kathryn B Manheimer
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Matthew Velinder
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Andrew Farrell
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Gabor Marth
- Department of Human Genetics, Utah Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan R Kaltman
- Heart Development and Structural Diseases Branch, Division of Cardiovascular Sciences, NHLBI/NIH, Bethesda, MD, USA
| | | | | | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martina Brueckner
- Departments of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Richard Kim
- Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - George A Porter
- Department of Pediatrics, University of Rochester, Rochester, NY, USA
| | - Daniel Bernstein
- Department of Pediatrics, Stanford University, Palo Alto, CA, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease and University of California San Francisco, San Francisco, CA, USA
| | - Martin Tristani-Firouzi
- Division of Pediatric Cardiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Olga G Troyanskaya
- Flatiron Institute, Simons Foundation, New York, NY, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Lab, Berkeley, CA, USA
| | - Yufeng Shen
- Departments of Systems Biology and Biomedical Informatics, Columbia University, New York, NY, USA
| | | | - Christine E Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Cardiology, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce D Gelb
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Boonsimma P, Suwannachote S, Phokaew C, Ittiwut C, Suphapeetiporn K, Shotelersuk V. A case of GABRA5-related developmental and epileptic encephalopathy with response to a combination of antiepileptic drugs and a GABAering agent. Brain Dev 2020; 42:546-550. [PMID: 32249079 DOI: 10.1016/j.braindev.2020.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/01/2020] [Accepted: 03/18/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND GABAA receptors are ligand-gated chloride channels that regulate inhibitory neurotransmission in the central nervous system. Recently, monoallelic de novo mutations in GABRA5 resulting in altered inhibitory synapses were found in three patients with developmental and epileptic encephalopathy. Patient description: We report on a four-year and six-month-old girl with epilepsy and global developmental delay. Serial head growth measurement revealed postnatal onset microcephaly. RESULTS Magnetic resonance imaging (MRI) of the brain was normal at the age of eight months and subsequently showed a decrease in white matter volume and thin corpus callosum at the age of 3 years. Using whole-genome sequencing, we identified the fourth patient harboring a de novo missense mutation in GABRA5. Interestingly, the c.880G > C (p.V294F) affects the same position found in two of the three previously reported patients. CONCLUSION This study suggests that the nucleotide c.880G is a mutation hotspot. Our patient also demonstrated significant seizure reduction after benzodiazepine. To our knowledge, this is the first case describing the favorable outcome of a GABAergic agent in seizure control for GABRA5-related developmental and epileptic encephalopathy.
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Affiliation(s)
- Ponghatai Boonsimma
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Sirorat Suwannachote
- Division of Neurology, Department of Pediatrics, Faculty of Medicine, Queen Sirikit National Institute of Child Health, Bangkok 10400, Thailand
| | - Chureerat Phokaew
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Chupong Ittiwut
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand.
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand; Excellence Center for Genomics and Precision Medicine, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, 10330, Thailand
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198
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López-Rivera JA, Pérez-Palma E, Symonds J, Lindy AS, McKnight DA, Leu C, Zuberi S, Brunklaus A, Møller RS, Lal D. A catalogue of new incidence estimates of monogenic neurodevelopmental disorders caused by de novo variants. Brain 2020; 143:1099-1105. [PMID: 32168371 PMCID: PMC7174049 DOI: 10.1093/brain/awaa051] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/27/2019] [Accepted: 01/13/2020] [Indexed: 12/18/2022] Open
Abstract
A large fraction of rare and severe neurodevelopmental disorders are caused by sporadic de novo variants. Epidemiological disease estimates are not available for the vast majority of these de novo monogenic neurodevelopmental disorders because of phenotypic heterogeneity and the absence of large-scale genomic screens. Yet, knowledge of disease incidence is important for clinicians and researchers to guide health policy planning. Here, we adjusted a statistical method based on genetic data to predict, for the first time, the incidences of 101 known de novo variant-associated neurodevelopmental disorders as well as 3106 putative monogenic disorders. Two corroboration analyses supported the validity of the calculated estimates. First, greater predicted gene-disorder incidences positively correlated with larger numbers of pathogenic variants collected from patient variant databases (Kendall’s τ = 0.093, P-value = 6.9 × 10−6). Second, for six of seven (86%) de novo variant associated monogenic disorders for which epidemiological estimates were available (SCN1A, SLC2A1, SALL1, TBX5, KCNQ2, and CDKL5), the predicted incidence estimates matched the reported estimates. We conclude that in the absence of epidemiological data, our catalogue of 3207 incidence estimates for disorders caused by de novo variants can guide patient advocacy groups, clinicians, researchers, and policymakers in strategic decision-making.
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Affiliation(s)
- Javier A López-Rivera
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, USA
| | - Eduardo Pérez-Palma
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, USA.,Cologne Center for Genomics, University of Cologne, Cologne, NRW, Germany
| | - Joseph Symonds
- The Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,School of Medicine, University of Glasgow, Glasgow, UK
| | | | | | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, USA
| | - Sameer Zuberi
- The Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,School of Medicine, University of Glasgow, Glasgow, UK
| | - Andreas Brunklaus
- The Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK.,School of Medicine, University of Glasgow, Glasgow, UK
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund, Denmark.,Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Dennis Lal
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, USA.,Cologne Center for Genomics, University of Cologne, Cologne, NRW, Germany.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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199
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Bonnycastle K, Davenport EC, Cousin MA. Presynaptic dysfunction in neurodevelopmental disorders: Insights from the synaptic vesicle life cycle. J Neurochem 2020; 157:179-207. [PMID: 32378740 DOI: 10.1111/jnc.15035] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
The activity-dependent fusion, retrieval and recycling of synaptic vesicles is essential for the maintenance of neurotransmission. Until relatively recently it was believed that most mutations in genes that were essential for this process would be incompatible with life, because of this fundamental role. However, an ever-expanding number of mutations in this very cohort of genes are being identified in individuals with neurodevelopmental disorders, including autism, intellectual disability and epilepsy. This article will summarize the current state of knowledge linking mutations in presynaptic genes to neurodevelopmental disorders by sequentially covering the various stages of the synaptic vesicle life cycle. It will also discuss how perturbations of specific stages within this recycling process could translate into human disease. Finally, it will also provide perspectives on the potential for future therapy that are targeted to presynaptic function.
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Affiliation(s)
- Katherine Bonnycastle
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Elizabeth C Davenport
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
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200
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Stenson PD, Mort M, Ball EV, Chapman M, Evans K, Azevedo L, Hayden M, Heywood S, Millar DS, Phillips AD, Cooper DN. The Human Gene Mutation Database (HGMD ®): optimizing its use in a clinical diagnostic or research setting. Hum Genet 2020; 139:1197-1207. [PMID: 32596782 PMCID: PMC7497289 DOI: 10.1007/s00439-020-02199-3] [Citation(s) in RCA: 330] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/19/2020] [Indexed: 01/19/2023]
Abstract
The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that are thought to underlie, or are closely associated with human inherited disease. At the time of writing (June 2020), the database contains in excess of 289,000 different gene lesions identified in over 11,100 genes manually curated from 72,987 articles published in over 3100 peer-reviewed journals. There are primarily two main groups of users who utilise HGMD on a regular basis; research scientists and clinical diagnosticians. This review aims to highlight how to make the most out of HGMD data in each setting.
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Affiliation(s)
- Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Edward V Ball
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Molly Chapman
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Katy Evans
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Luisa Azevedo
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.,i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal
| | - Matthew Hayden
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Sally Heywood
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David S Millar
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Andrew D Phillips
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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