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Berasain L, Beati P, Trigila AP, Rubinstein M, Franchini LF. Accelerated evolution in the human lineage led to gain and loss of transcriptional enhancers in the RBFOX1 locus. SCIENCE ADVANCES 2024; 10:eadl1049. [PMID: 38924416 PMCID: PMC11204294 DOI: 10.1126/sciadv.adl1049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
A long-standing goal of evolutionary biology is to decode how changes in gene regulatory networks contribute to human-specific traits. Human accelerated regions (HARs) are prime candidates for driving gene regulatory modifications in human development. The RBFOX1 locus is densely populated with HARs, providing a set of potential regulatory elements that could have changed its expression in the human lineage. Here, we examined the role of RBFOX1-HARs using transgenic zebrafish reporter assays and identified 15 transcriptional enhancers that are active in the developing nervous system, 9 of which displayed differential activity between the human and chimpanzee sequences. The engineered loss of two selected RBFOX1-HARs in knockout mouse models modified Rbfox1 expression at specific developmental stages and tissues in the brain, influencing the expression and splicing of a high number of Rbfox1 target genes. Our results provided insight into the spatial and temporal changes in gene expression driven by RBFOX1-HARs.
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Affiliation(s)
- Lara Berasain
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Hector N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
| | - Paula Beati
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Hector N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
| | - Anabella P. Trigila
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Hector N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
| | - Marcelo Rubinstein
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Hector N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires 1428, Argentina
| | - Lucía F. Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI) “Dr. Hector N. Torres”, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1428, Argentina
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2
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Engal E, Zhang Z, Geminder O, Jaffe-Herman S, Kay G, Ben-Hur A, Salton M. The spectrum of pre-mRNA splicing in autism. WILEY INTERDISCIPLINARY REVIEWS. RNA 2024; 15:e1838. [PMID: 38509732 DOI: 10.1002/wrna.1838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/22/2024]
Abstract
Disruptions in spatiotemporal gene expression can result in atypical brain function. Specifically, autism spectrum disorder (ASD) is characterized by abnormalities in pre-mRNA splicing. Abnormal splicing patterns have been identified in the brains of individuals with ASD, and mutations in splicing factors have been found to contribute to neurodevelopmental delays associated with ASD. Here we review studies that shed light on the importance of splicing observed in ASD and that explored the intricate relationship between splicing factors and ASD, revealing how disruptions in pre-mRNA splicing may underlie ASD pathogenesis. We provide an overview of the research regarding all splicing factors associated with ASD and place a special emphasis on five specific splicing factors-HNRNPH2, NOVA2, WBP4, SRRM2, and RBFOX1-known to impact the splicing of ASD-related genes. In the discussion of the molecular mechanisms influenced by these splicing factors, we lay the groundwork for a deeper understanding of ASD's complex etiology. Finally, we discuss the potential benefit of unraveling the connection between splicing and ASD for the development of more precise diagnostic tools and targeted therapeutic interventions. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution RNA Evolution and Genomics > Computational Analyses of RNA RNA-Based Catalysis > RNA Catalysis in Splicing and Translation.
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Affiliation(s)
- Eden Engal
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Zhenwei Zhang
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Ophir Geminder
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shiri Jaffe-Herman
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asa Ben-Hur
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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3
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Smith J, Richerson G, Kouchi H, Duprat F, Mantegazza M, Bezin L, Rheims S. Are we there yet? A critical evaluation of sudden and unexpected death in epilepsy models. Epilepsia 2024; 65:9-25. [PMID: 37914406 DOI: 10.1111/epi.17812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/11/2023] [Accepted: 10/31/2023] [Indexed: 11/03/2023]
Abstract
Although animal models have helped to elaborate meaningful hypotheses about the pathophysiology of sudden and unexpected death in epilepsy (SUDEP), specific prevention strategies are still lacking, potentially reflecting the limitations of these models and the intrinsic difficulties of investigating SUDEP. The interpretation of preclinical data and their translation to diagnostic and therapeutic developments in patients thus require a high level of confidence in their relevance to model the human situation. Preclinical models of SUDEP are heterogeneous and include rodent and nonrodent species. A critical aspect is whether the animals have isolated seizures exclusively induced by a specific trigger, such as models where seizures are elicited by electrical stimulation, pharmacological intervention, or DBA mouse strains, or whether they suffer from epilepsy with spontaneous seizures, with or without spontaneous SUDEP, either of nongenetic epilepsy etiology or from genetically based developmental and epileptic encephalopathies. All these models have advantages and potential disadvantages, but it is important to be aware of these limitations to interpret data appropriately in a translational perspective. The majority of models with spontaneous seizures are of a genetic basis, whereas SUDEP cases with a genetic basis represent only a small proportion of the total number. In almost all models, cardiorespiratory arrest occurs during the course of the seizure, contrary to that in patients observed at the time of death, potentially raising the issue of whether we are studying models of SUDEP or models of periseizure death. However, some of these limitations are impossible to avoid and can in part be dependent on specific features of SUDEP, which may be difficult to model. Several preclinical tools are available to address certain gaps in SUDEP pathophysiology, which can be used to further validate current preclinical models.
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Affiliation(s)
- Jonathon Smith
- Lyon Neuroscience Research Center (CRNL, INSERM U1028/CNRS UMR 5292, Lyon 1 University), Lyon, France
| | - George Richerson
- Department of Neurology, University of Iowa, Iowa City, Iowa, USA
| | - Hayet Kouchi
- Lyon Neuroscience Research Center (CRNL, INSERM U1028/CNRS UMR 5292, Lyon 1 University), Lyon, France
| | - Fabrice Duprat
- University Cote d'Azur, Valbonne-Sophia Antipolis, France
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, Valbonne-Sophia Antipolis, France
- Inserm, Valbonne-Sophia Antipolis, France
| | - Massimo Mantegazza
- University Cote d'Azur, Valbonne-Sophia Antipolis, France
- CNRS UMR 7275, Institute of Molecular and Cellular Pharmacology, Valbonne-Sophia Antipolis, France
- Inserm, Valbonne-Sophia Antipolis, France
| | - Laurent Bezin
- Lyon Neuroscience Research Center (CRNL, INSERM U1028/CNRS UMR 5292, Lyon 1 University), Lyon, France
| | - Sylvain Rheims
- Lyon Neuroscience Research Center (CRNL, INSERM U1028/CNRS UMR 5292, Lyon 1 University), Lyon, France
- Department of Functional Neurology and Epileptology, Hospices Civils de Lyon and Lyon 1 University, Lyon, France
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4
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Dugger SA, Dhindsa RS, Sampaio GDA, Ressler AK, Rafikian EE, Petri S, Letts VA, Teoh J, Ye J, Colombo S, Peng Y, Yang M, Boland MJ, Frankel WN, Goldstein DB. Neurodevelopmental deficits and cell-type-specific transcriptomic perturbations in a mouse model of HNRNPU haploinsufficiency. PLoS Genet 2023; 19:e1010952. [PMID: 37782669 PMCID: PMC10569524 DOI: 10.1371/journal.pgen.1010952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 10/12/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023] Open
Abstract
Heterozygous de novo loss-of-function mutations in the gene expression regulator HNRNPU cause an early-onset developmental and epileptic encephalopathy. To gain insight into pathological mechanisms and lay the potential groundwork for developing targeted therapies, we characterized the neurophysiologic and cell-type-specific transcriptomic consequences of a mouse model of HNRNPU haploinsufficiency. Heterozygous mutants demonstrated global developmental delay, impaired ultrasonic vocalizations, cognitive dysfunction and increased seizure susceptibility, thus modeling aspects of the human disease. Single-cell RNA-sequencing of hippocampal and neocortical cells revealed widespread, yet modest, dysregulation of gene expression across mutant neuronal subtypes. We observed an increased burden of differentially-expressed genes in mutant excitatory neurons of the subiculum-a region of the hippocampus implicated in temporal lobe epilepsy. Evaluation of transcriptomic signature reversal as a therapeutic strategy highlights the potential importance of generating cell-type-specific signatures. Overall, this work provides insight into HNRNPU-mediated disease mechanisms and provides a framework for using single-cell RNA-sequencing to study transcriptional regulators implicated in disease.
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Affiliation(s)
- Sarah A. Dugger
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Ryan S. Dhindsa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute of Texas Children’s Hospital, Houston, Texas, United States of America
| | - Gabriela De Almeida Sampaio
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Andrew K. Ressler
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Elizabeth E. Rafikian
- Mouse Neurobehavioral Core Facility, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Sabrina Petri
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Verity A. Letts
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - JiaJie Teoh
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Junqiang Ye
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, New York, United States of America
- Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, New York, United States of America
| | - Sophie Colombo
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Yueqing Peng
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Mu Yang
- Mouse Neurobehavioral Core Facility, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Michael J. Boland
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Neurology, Columbia University Irving Medical Center, New York, New York, United States of America
| | - Wayne N. Frankel
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, New York, United States of America
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, New York, United States of America
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5
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Kamran M, Laighneach A, Bibi F, Donohoe G, Ahmed N, Rehman AU, Morris DW. Independent Associated SNPs at SORCS3 and Its Protein Interactors for Multiple Brain-Related Disorders and Traits. Genes (Basel) 2023; 14:482. [PMID: 36833409 PMCID: PMC9956385 DOI: 10.3390/genes14020482] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/26/2023] [Accepted: 02/06/2023] [Indexed: 02/16/2023] Open
Abstract
Sortilin-related vacuolar protein sorting 10 (VPS10) domain containing receptor 3 (SORCS3) is a neuron-specific transmembrane protein involved in the trafficking of proteins between intracellular vesicles and the plasma membrane. Genetic variation at SORCS3 is associated with multiple neuropsychiatric disorders and behavioural phenotypes. Here, we undertake a systematic search of published genome-wide association studies to identify and catalogue associations between SORCS3 and brain-related disorders and traits. We also generate a SORCS3 gene-set based on protein-protein interactions and investigate the contribution of this gene-set to the heritability of these phenotypes and its overlap with synaptic biology. Analysis of association signals at SORSC3 showed individual SNPs to be associated with multiple neuropsychiatric and neurodevelopmental brain-related disorders and traits that have an impact on the experience of feeling, emotion or mood or cognitive function, while multiple LD-independent SNPs were associated with the same phenotypes. Across these SNPs, alleles associated with the more favourable outcomes for each phenotype (e.g., decreased risk of neuropsychiatric illness) were associated with increased expression of the SORCS3 gene. The SORCS3 gene-set was enriched for heritability contributing to schizophrenia (SCZ), bipolar disorder (BPD), intelligence (IQ) and education attainment (EA). Eleven genes from the SORCS3 gene-set were associated with more than one of these phenotypes at the genome-wide level, with RBFOX1 associated with SCZ, IQ and EA. Functional annotation revealed that the SORCS3 gene-set is enriched for multiple ontologies related to the structure and function of synapses. Overall, we find many independent association signals at SORCS3 with brain-related disorders and traits, with the effect possibly mediated by reduced gene expression, resulting in a negative impact on synaptic function.
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Affiliation(s)
- Muhammad Kamran
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, H91 CF50 Galway, Ireland
| | - Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, H91 CF50 Galway, Ireland
| | - Farhana Bibi
- Department of Biosciences, Grand Asian University, Sialkot 51040, Pakistan
| | - Gary Donohoe
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, H91 CF50 Galway, Ireland
| | - Naveed Ahmed
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Asim Ur Rehman
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Derek W. Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences and School of Psychology, University of Galway, H91 CF50 Galway, Ireland
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6
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Belyaeva EO, Lebedev IN. Interloci CNV Interactions in Variability of the Phenotypes of Neurodevelopmental Disorders. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422100027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Szabo CA, Salinas FS. Neuroimaging in the Epileptic Baboon. Front Vet Sci 2022; 9:908801. [PMID: 35909685 PMCID: PMC9330034 DOI: 10.3389/fvets.2022.908801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/23/2022] [Indexed: 11/13/2022] Open
Abstract
Characterization of baboon model of genetic generalized epilepsy (GGE) is driven both electroclinically and by successful adoption of neuroimaging platforms, such as magnetic resonance imaging (MRI) and positron emission tomography (PET). Based upon its phylogenetic proximity and similar brain anatomy to humans, the epileptic baboon provides an excellent translational model. Its relatively large brain size compared to smaller nonhuman primates or rodents, a gyrencephalic structure compared to lissencephalic organization of rodent brains, and the availability of a large pedigreed colony allows exploration of neuroimaging markers of diseases. Similar to human idiopathic generalized epilepsy (IGE), structural imaging in the baboon is usually normal in individual subjects, but gray matter volume/concentration (GMV/GMC) changes are reported by statistical parametric mapping (SPM) analyses. Functional neuroimaging has been effective for mapping the photoepileptic responses, the epileptic network, altered functional connectivity of physiological networks, and the effects of anti-seizure therapies. This review will provide insights into our current understanding the baboon model of GGE through functional and structural imaging.
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Affiliation(s)
- C. Akos Szabo
- Department of Neurology, University of Texas Health San Antonio, San Antonio, TX, United States
- *Correspondence: C. Akos Szabo
| | - Felipe S. Salinas
- Research Imaging Institute, University of Texas Health San Antonio, San Antonio, TX, United States
- Department of Radiology, University of Texas Health San Antonio, San Antonio, TX, United States
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Malone TJ, Kaczmarek LK. The role of altered translation in intellectual disability and epilepsy. Prog Neurobiol 2022; 213:102267. [PMID: 35364140 PMCID: PMC10583652 DOI: 10.1016/j.pneurobio.2022.102267] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 02/18/2022] [Accepted: 03/24/2022] [Indexed: 11/29/2022]
Abstract
A very high proportion of cases of intellectual disability are genetic in origin and are associated with the occurrence of epileptic seizures during childhood. These two disorders together effect more than 5% of the world's population. One feature linking the two diseases is that learning and memory require the synthesis of new synaptic components and ion channels, while maintenance of overall excitability also requires synthesis of similar proteins in response to altered neuronal stimulation. Many of these disorders result from mutations in proteins that regulate mRNA processing, translation initiation, translation elongation, mRNA stability or upstream translation modulators. One theme that emerges on reviewing this field is that mutations in proteins that regulate changes in translation following neuronal stimulation are more likely to result in epilepsy with intellectual disability than general translation regulators with no known role in activity-dependent changes. This is consistent with the notion that activity-dependent translation in neurons differs from that in other cells types in that the changes in local cellular composition, morphology and connectivity that occur generally in response to stimuli are directly coupled to local synaptic activity and persist for months or years after the original stimulus.
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Affiliation(s)
- Taylor J Malone
- Departments of Pharmacology, and of Cellular & Molecular Physiology, Yale University, 333 Cedar Street B-309, New Haven, CT 06520, USA
| | - Leonard K Kaczmarek
- Departments of Pharmacology, and of Cellular & Molecular Physiology, Yale University, 333 Cedar Street B-309, New Haven, CT 06520, USA.
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9
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Servetti M, Pisciotta L, Tassano E, Cerminara M, Nobili L, Boeri S, Rosti G, Lerone M, Divizia MT, Ronchetto P, Puliti A. Neurodevelopmental Disorders in Patients With Complex Phenotypes and Potential Complex Genetic Basis Involving Non-Coding Genes, and Double CNVs. Front Genet 2021; 12:732002. [PMID: 34621295 PMCID: PMC8490884 DOI: 10.3389/fgene.2021.732002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/03/2021] [Indexed: 12/15/2022] Open
Abstract
Neurodevelopmental disorders (NDDs) are a heterogeneous class of brain diseases, with a complex genetic basis estimated to account for up to 50% of cases. Nevertheless, genetic diagnostic yield is about 20%. Array-comparative genomic hybridization (array-CGH) is an established first-level diagnostic test able to detect pathogenic copy number variants (CNVs), however, most identified variants remain of uncertain significance (VUS). Failure of interpretation of VUSs may depend on various factors, including complexity of clinical phenotypes and inconsistency of genotype-phenotype correlations. Indeed, although most NDD-associated CNVs are de novo, transmission from unaffected parents to affected children of CNVs with high risk for NDDs has been observed. Moreover, variability of genetic components overlapped by CNVs, such as long non-coding genes, genomic regions with long-range effects, and additive effects of multiple CNVs can make CNV interpretation challenging. We report on 12 patients with complex phenotypes possibly explained by complex genetic mechanisms, including involvement of antisense genes and boundaries of topologically associating domains. Eight among the 12 patients carried two CNVs, either de novo or inherited, respectively, by each of their healthy parents, that could additively contribute to the patients’ phenotype. CNVs overlapped either known NDD-associated or novel candidate genes (PTPRD, BUD13, GLRA3, MIR4465, ABHD4, and WSCD2). Bioinformatic enrichment analyses showed that genes overlapped by the co-occurring CNVs have synergistic roles in biological processes fundamental in neurodevelopment. Double CNVs could concur in producing deleterious effects, according to a two-hit model, thus explaining the patients’ phenotypes and the incomplete penetrance, and variable expressivity, associated with the single variants. Overall, our findings could contribute to the knowledge on clinical and genetic diagnosis of complex forms of NDD.
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Affiliation(s)
- Martina Servetti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy.,Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Livia Pisciotta
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy.,Child Neuropsychiatry Unit, ASST Fatebenefratelli Sacco, Milano, Italy
| | - Elisa Tassano
- Human Genetics Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maria Cerminara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
| | - Lino Nobili
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy.,Child Neuropsychiatry Unit, Istituto Giannina Gaslini, Genoa, Italy
| | - Silvia Boeri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy.,Child Neuropsychiatry Unit, Istituto Giannina Gaslini, Genoa, Italy
| | - Giulia Rosti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy
| | - Margherita Lerone
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | | | - Patrizia Ronchetto
- Human Genetics Laboratory, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Aldamaria Puliti
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health (DiNOGMI), University of Genoa, Genoa, Italy.,Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
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10
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Kos MZ, Carless MA, Blondell L, Leland MM, Knape KD, Göring HHH, Szabó CÁ. Whole Genome Sequence Data From Captive Baboons Implicate RBFOX1 in Epileptic Seizure Risk. Front Genet 2021; 12:714282. [PMID: 34490042 PMCID: PMC8417722 DOI: 10.3389/fgene.2021.714282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/27/2021] [Indexed: 01/18/2023] Open
Abstract
In this study, we investigate the genetic determinants that underlie epilepsy in a captive baboon pedigree and evaluate the potential suitability of this non-human primate model for understanding the genetic etiology of human epilepsy. Archived whole-genome sequence data were analyzed using both a candidate gene approach that targeted variants in baboon homologs of 19 genes (n = 20,881 SNPs) previously implicated in genetic generalized epilepsy (GGE) and a more agnostic approach that examined protein-altering mutations genome-wide as assessed by snpEff (n = 36,169). Measured genotype association tests for baboon cases of epileptic seizure were performed using SOLAR, as well as gene set enrichment analyses (GSEA) and protein–protein interaction (PPI) network construction of top association hits genome-wide (p < 0.01; n = 441 genes). The maximum likelihood estimate of heritability for epileptic seizure in the pedigreed baboon sample is 0.76 (SE = 0.77; p = 0.07). Among candidate genes for GGE, a significant association was detected for an intronic SNP in RBFOX1 (p = 5.92 × 10–6; adjusted p = 0.016). For protein-altering variants, no genome-wide significant results were observed for epilepsy status. However, GSEA revealed significant positive enrichment for genes involved in the extracellular matrix structure (ECM; FDR = 0.0072) and collagen formation (FDR = 0.017), which was reflected in a major PPI network cluster. This preliminary study highlights the potential role of RBFOX1 in the epileptic baboon, a protein involved in transcriptomic regulation of multiple epilepsy candidate genes in humans and itself previously implicated in human epilepsy, both focal and generalized. Moreover, protein-damaging variants from across the genome exhibit a pattern of association that links collagen-containing ECM to epilepsy risk. These findings suggest a shared genetic etiology between baboon and human forms of GGE and lay the foundation for follow-up research.
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Affiliation(s)
- Mark Z Kos
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg, TX, United States
| | - Melanie A Carless
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, United States.,Brain Health Consortium, The University of Texas at San Antonio, San Antonio, TX, United States
| | - Lucy Blondell
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg, TX, United States
| | - M Michelle Leland
- Laboratory Animal Research, UT Health San Antonio, San Antonio, TX, United States
| | - Koyle D Knape
- Department of Neurology, UT Health San Antonio, San Antonio, TX, United States
| | - Harald H H Göring
- Department of Human Genetics, South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Edinburg, TX, United States
| | - Charles Ákos Szabó
- Department of Neurology, UT Health San Antonio, San Antonio, TX, United States.,South Texas Comprehensive Epilepsy Center, San Antonio, TX, United States
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11
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Tascón-Arcila J, Rojas-Jiménez S, Cornejo-Sánchez D, Gómez-Builes P, Ucroz-Benavides A, Holguín BM, Restrepo-Arbeláez D, Gómez-Castillo C, Solarte-Mia R, Cornejo-Ochoa W, Pineda-Trujillo N. Differential Clinical Features in Colombian Patients With Rolandic Epilepsy and Suggestion of Unlikely Association With GRIN2A, RBFOX1, or RBFOX3 Gene Variants. J Child Neurol 2021; 36:875-882. [PMID: 34039076 DOI: 10.1177/08830738211015017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PURPOSE Our purpose was to describe the phenotypic features and test for association of genes GRIN2A, RBFOX1 and RBFOX3 with rolandic epilepsy in patients from Colombia. METHODS Thirty patients were enrolled. A structured interview was applied. In addition, saliva samples were collected from the patients and their parents. One polymorphism in each of GRIN2A, RBFOX1 and RBFOX3 genes was tested. RESULTS The average age at onset was 5.3 years. Almost half the sample presented prolonged seizures (>5 minutes); although the majority of the patients presented their seizures only while asleep, over a quarter presented them only while awake. The most frequent comorbidity was the presence of symptoms compatible with attention-deficit hyperactivity disorder (ADHD). Personal history of febrile seizures and parasomnias were equally frequent (20%). Family history of any type of epilepsy was reported in 80% of the patients, followed by migraine (73.3%) and poor academic performance (63.3%). About half the sample reported sleepwalking in parents or sibs. Most patients had received pharmacologic treatment. We found no association of rolandic epilepsy with the single nucleotide polymorphisms tested. CONCLUSIONS Our rolandic epilepsy cohort presents clinical features clearly different from other cohorts. For instance, age at onset is much earlier in our set of patients, and personal and family history of febrile seizures as well as parasomnias are highly prevalent in our sample. No association of rolandic epilepsy with variants at the 3 genes tested was found. This lack of association may reflect the high genetic heterogeneity of the epilepsies.
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Affiliation(s)
- José Tascón-Arcila
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Sara Rojas-Jiménez
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Diana Cornejo-Sánchez
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Paola Gómez-Builes
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Andrea Ucroz-Benavides
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Blear-Maria Holguín
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
| | | | - Christhian Gómez-Castillo
- Sección de Neuropediatria, IPS Universitaria, 27983Universidad de Antioquia UdeA, Medellín, Colombia
| | - Rodrigo Solarte-Mia
- Laboratorio de Correlación Electroclínica, CECLAB. IPS Universitaria, Universidad de Antioquia UdeA, Medellín, Colombia
| | - William Cornejo-Ochoa
- PEDIACIENCIAS, Departamento de Pediatría, Facultad de Medicina, 27983Universidad de Antioquia UdeA, Medellín, Colombia
| | - Nicolas Pineda-Trujillo
- Grupo Mapeo Genético, Departamento de Pediatría, Universidad de Antioquia UdeA, Medellín, Colombia
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Abstract
Autism is a common and complex neurologic disorder whose scientific underpinnings have begun to be established in the past decade. The essence of this breakthrough has been a focus on families, where genetic analyses are strongest, versus large-scale, case-control studies. Autism genetics has progressed in parallel with technology, from analyses of copy number variation to whole-exome sequencing (WES) and whole-genome sequencing (WGS). Gene mutations causing complete loss of function account for perhaps one-third of cases, largely detected through WES. This limitation has increased interest in understanding the regulatory variants of genes that contribute in more subtle ways to the disorder. Strategies combining biochemical analysis of gene regulation, WGS analysis of the noncoding genome, and machine learning have begun to succeed. The emerging picture is that careful control of the amounts of transcription, mRNA, and proteins made by key brain genes-stoichiometry-plays a critical role in defining the clinical features of autism.
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Affiliation(s)
- Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA;
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13
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The baboon in epilepsy research: Revelations and challenges. Epilepsy Behav 2021; 121:108012. [PMID: 34022622 PMCID: PMC8238811 DOI: 10.1016/j.yebeh.2021.108012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 04/17/2021] [Indexed: 11/23/2022]
Abstract
The baboon offers a natural model for genetic generalized epilepsy with photosensitivity. In this review, we will summarize some of the more important clinical, neuroimaging, and elctrophysiological findings form recent work performed at the Southwest National Primate Research Center (SNPRC, Texas Biomedical Research Institute, San Antonio, Texas), which houses the world's largest captive baboon pedigree. Due to the phylogenetic proximity of the baboon to humans, many of the findings are readily translatable, but there may be some important differences, such as the mutlifocality of the ictal and interictal epileptic discharges (IEDs) on intracranial electroencephalography (EEG) and greater parieto-occipital connectivity of baboon brain networks compared to juvenile myoclonic epilepsy in humans. Furthermore, there is still limited knowledge of the natural history of the epilepsy, which could be transformative for research into epileptogenesis in genetic generalized epilepsy (GGE) and sudden unexpected death in epilepsy (SUDEP).
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14
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Vasudevaraja V, Rodriguez JH, Pelorosso C, Zhu K, Buccoliero AM, Onozato M, Mohamed H, Serrano J, Tredwin L, Garonzi M, Forcato C, Zeck B, Ramaswami S, Stafford J, Faustin A, Friedman D, Hidalgo ET, Zagzag D, Skok J, Heguy A, Chiriboga L, Conti V, Guerrini R, Iafrate AJ, Devinsky O, Tsirigos A, Golfinos JG, Snuderl M. Somatic Focal Copy Number Gains of Noncoding Regions of Receptor Tyrosine Kinase Genes in Treatment-Resistant Epilepsy. J Neuropathol Exp Neurol 2021; 80:160-168. [PMID: 33274363 DOI: 10.1093/jnen/nlaa137] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Epilepsy is a heterogenous group of disorders defined by recurrent seizure activity due to abnormal synchronized activity of neurons. A growing number of epilepsy cases are believed to be caused by genetic factors and copy number variants (CNV) contribute to up to 5% of epilepsy cases. However, CNVs in epilepsy are usually large deletions or duplications involving multiple neurodevelopmental genes. In patients who underwent seizure focus resection for treatment-resistant epilepsy, whole genome DNA methylation profiling identified 3 main clusters of which one showed strong association with receptor tyrosine kinase (RTK) genes. We identified focal copy number gains involving epidermal growth factor receptor (EGFR) and PDGFRA loci. The dysplastic neurons of cases with amplifications showed marked overexpression of EGFR and PDGFRA, while glial and endothelial cells were negative. Targeted sequencing of regulatory regions and DNA methylation analysis revealed that only enhancer regions of EGFR and gene promoter of PDGFRA were amplified, while coding regions did not show copy number abnormalities or somatic mutations. Somatic focal copy number gains of noncoding regulatory represent a previously unrecognized genetic driver in epilepsy and a mechanism of abnormal activation of RTK genes. Upregulated RTKs provide a potential avenue for therapy in seizure disorders.
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Affiliation(s)
| | | | - Cristiana Pelorosso
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | | | - Anna Maria Buccoliero
- Pathology Unit, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | - Maristela Onozato
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | | | | | | | | | | | | | | | - James Stafford
- Department of Neurological Sciences, University of Vermont, Larner College of Medicine, Burlington, Vermont
| | | | | | | | - David Zagzag
- Department of Neurosurgery, NYU Langone Health, New York, New York
| | | | | | | | - Valerio Conti
- Paediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Florence, Italy
| | - Renzo Guerrini
- Department of Neurosurgery, NYU Langone Health, New York, New York
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Orrin Devinsky
- Department of Neurology.,Comprehensive Epilepsy Center (DF, OD).,Department of Neurosurgery, NYU Langone Health, New York, New York
| | | | - John G Golfinos
- Department of Neurosurgery, NYU Langone Health, New York, New York
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15
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Genetic Landscape of Common Epilepsies: Advancing towards Precision in Treatment. Int J Mol Sci 2020; 21:ijms21207784. [PMID: 33096746 PMCID: PMC7589654 DOI: 10.3390/ijms21207784] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Epilepsy, a neurological disease characterized by recurrent seizures, is highly heterogeneous in nature. Based on the prevalence, epilepsy is classified into two types: common and rare epilepsies. Common epilepsies affecting nearly 95% people with epilepsy, comprise generalized epilepsy which encompass idiopathic generalized epilepsy like childhood absence epilepsy, juvenile myoclonic epilepsy, juvenile absence epilepsy and epilepsy with generalized tonic-clonic seizure on awakening and focal epilepsy like temporal lobe epilepsy and cryptogenic focal epilepsy. In 70% of the epilepsy cases, genetic factors are responsible either as single genetic variant in rare epilepsies or multiple genetic variants acting along with different environmental factors as in common epilepsies. Genetic testing and precision treatment have been developed for a few rare epilepsies and is lacking for common epilepsies due to their complex nature of inheritance. Precision medicine for common epilepsies require a panoramic approach that incorporates polygenic background and other non-genetic factors like microbiome, diet, age at disease onset, optimal time for treatment and other lifestyle factors which influence seizure threshold. This review aims to comprehensively present a state-of-art review of all the genes and their genetic variants that are associated with all common epilepsy subtypes. It also encompasses the basis of these genes in the epileptogenesis. Here, we discussed the current status of the common epilepsy genetics and address the clinical application so far on evidence-based markers in prognosis, diagnosis, and treatment management. In addition, we assessed the diagnostic predictability of a few genetic markers used for disease risk prediction in individuals. A combination of deeper endo-phenotyping including pharmaco-response data, electro-clinical imaging, and other clinical measurements along with genetics may be used to diagnose common epilepsies and this marks a step ahead in precision medicine in common epilepsies management.
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16
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Abstract
It is increasingly recognized that local protein synthesis (LPS) contributes to fundamental aspects of axon biology, in both developing and mature neurons. Mutations in RNA-binding proteins (RBPs), as central players in LPS, and other proteins affecting RNA localization and translation are associated with a range of neurological disorders, suggesting disruption of LPS may be of pathological significance. In this review, we substantiate this hypothesis by examining the link between LPS and key axonal processes, and the implicated pathophysiological consequences of dysregulated LPS. First, we describe how the length and autonomy of axons result in an exceptional reliance on LPS. We next discuss the roles of LPS in maintaining axonal structural and functional polarity and axonal trafficking. We then consider how LPS facilitates the establishment of neuronal connectivity through regulation of axonal branching and pruning, how it mediates axonal survival into adulthood and its involvement in neuronal stress responses.
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Affiliation(s)
- Julie Qiaojin Lin
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Island Research Building, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Christine E Holt
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
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17
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Shi XY, Wang G, Li T, Li Z, Leo P, Liu Z, Wu G, Zhu H, Zhang Y, Li D, Gao L, Yang L, Wang W, Liao J, Wang J, Zhou S, Wang H, Li X, Gao J, Zhang L, Shu X, Li D, Li Y, Chen C, Zhang X, Partida GC, Lundberg M, Reutens D, Bartlett P, Brown MA, Zou LP, Xu H. Identification of susceptibility variants to benign childhood epilepsy with centro-temporal spikes (BECTS) in Chinese Han population. EBioMedicine 2020; 57:102840. [PMID: 32580138 PMCID: PMC7317238 DOI: 10.1016/j.ebiom.2020.102840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/11/2020] [Accepted: 06/02/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Benign Childhood Epilepsy with Centro-temporal Spikes (BECTS) is the most common form of idiopathic epilepsy in children, accounting for up to 23% of pediatric epilepsy. The pathogenesis of BECTS is unknown, but it is thought that genetic factors play a role in susceptibility to the disease. METHODS To investigate the role of common genetic variants in BECTS pathogenesis, a 2-stage genome-wide association study (GWAS) was performed in 1,800 Chinese Han BECTS patients, and 7,090 healthy controls. Genetic findings were used in a Mendelian Randomization study in the UK Biobank dataset to investigate the potential role of smoking in BECTS. FINDINGS Definitive evidence of a role for common-variant heritability was demonstrated, with heritability of BECTS of >10% observed even with conservative disease prevalence assumptions. Although no individual locus achieved genome-wide significance, twelve loci achieved suggestive evidence of association (5 × 10-8<P<10-5). Using combined genetic and brain tissue gene expression data analyzed by Summary-data-based Mendelian Randomization (SMR), causative association of BECTS was demonstrated with SNP rs1948 and the CHRNA5 t3603436 transcript (Peqtl = 2·10 × 10-12, Psmr = 7·9 × 10-5). This finding indicates rs1948 is significantly associated with BECTS through effects on expression of CHRNA5 in brain tissue. The identification of novel loci suggests involvements of KALRN and the CHRNA5-A3-B4 cluster in BECTS. Using a generalized SMR approach we demonstrate that maternal smoking around birth is significantly associated with increased risk of BECTS (odds ratio = 3·90, P = 0·0099). INTERPRETATION This study shows that BECTS risk is at least partially heritable and due to common genetic variants. Additionally, we demonstrate that BECTS risk is substantially increased by maternal smoking around birth.
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Affiliation(s)
- Xiu-Yu Shi
- Department of Pediatrics, Chinese PLA General Hospital, 28 Fuxing Road, Haidian district, Beijing, China
| | - Geng Wang
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China; University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Ting Li
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhixiu Li
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, Australia
| | - Paul Leo
- Translational Genomics Group, Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Brisbane, Australia
| | - Zhisheng Liu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology Wuhan, Hubei, China
| | - Gefei Wu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology Wuhan, Hubei, China
| | - Hongmin Zhu
- Department of Neurology, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology Wuhan, Hubei, China
| | - Yuqin Zhang
- Department of Neurology, Tian Jin Children's hospital, 238 Longyan road, Beichen district, Tianjin, China
| | - Dong Li
- Department of Neurology, Tian Jin Children's hospital, 238 Longyan road, Beichen district, Tianjin, China
| | - Li Gao
- Department of Pediatrics, Henan Provincial People's Hospital, 7 Weiwu Road, Jinshui District, Zhengzhou, Henan Province, China
| | - Liu Yang
- Department of Pediatrics, Henan Provincial People's Hospital, 7 Weiwu Road, Jinshui District, Zhengzhou, Henan Province, China
| | - Wei Wang
- Department of Neurology, Harbin Children's Hospital, 57 YouYi Road, DaoLi District, Harbin, Heilongjiang Province, China
| | - Jianxiang Liao
- Department of Neurology, Shenzhen Children's Hospital, 7019 Yitian Road Futian, Shenzhen, Guangdong Province, China
| | - Jiwen Wang
- Department of Neurology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, 1678 Dongfang Road, New Pudong district, Shanghai, China
| | - Shuizhen Zhou
- Department of Neurology, Children's Hospital of Fudan University, 399 Wanyuan Road, Minhang District, Shanghai, China
| | - Hua Wang
- Department of Pediatric Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, Liaoning Province, China
| | - Xiaojing Li
- Department of Neurology, Guangzhou Women and Children's Medical Center, 9 Jinsui Road, Tianhe district, Guangzhou, Guangdong Province, China
| | - Jingyun Gao
- Department of Pediatric Neurology, Hebei Tangshan City maternal and child health care hospital,14 South Jianhe Road, Tangshan, Hebei Province, China
| | - Li Zhang
- Department of Pediatrics, Linyi People's Hospital, 130 Yizhou Road, Lanshan, Linyi, Shandong Province, China
| | - Xiaomei Shu
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical College, 149 Dalian Road, Zunyi, Guizhou Province, China
| | - Dan Li
- Department of Pediatrics, the Second affiliated Hospital of Xi'an Jiaotong University, 157 Xiwu Road, Xi'an, Shaanxi Province, China
| | - Yan Li
- Department of Neurology, Children's Hospital Affiliated to Soochow University, 92 Zhongnan Street, Suzhou, Jiangsu Province, China
| | - Chunhong Chen
- Department of Neurology, Beijing Children's Hospital, 56 South Lishi Road, Xicheng District, Beijing, China
| | - Xiuju Zhang
- Department of Pediatrics, Xingtai People's Hospital,16 Hongxing Street, Xingtai, Hebei Province, China
| | - Gabriel Cuellar Partida
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Mischa Lundberg
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - David Reutens
- Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Perry Bartlett
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Matthew A Brown
- Guy's & St Thomas' NHS Foundation Trust and King's College London, NIHR Biomedical Research Centre, London, England United Kingdom.
| | - Li-Ping Zou
- Department of Pediatrics, Chinese PLA General Hospital, 28 Fuxing Road, Haidian district, Beijing, China; Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing, China.
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China; Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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18
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Chaves TF, Baretto N, Oliveira LFD, Ocampos M, Barbato IT, Anselmi M, De Luca GR, Barbato Filho JH, Pinto LLDC, Bernardi P, Maris AF. Copy Number Variations in a Cohort of 420 Individuals with Neurodevelopmental Disorders From the South of Brazil. Sci Rep 2019; 9:17776. [PMID: 31780800 PMCID: PMC6882836 DOI: 10.1038/s41598-019-54347-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/13/2019] [Indexed: 01/04/2023] Open
Abstract
Chromosomal microarray (CMA) is now recommended as first tier for the evaluation in individuals with unexplained neurodevelopmental disorders (ND). However, in developing countries such as Brazil, classical cytogenetic tests are still the most used in clinical practice, as reflected by the scarcity of publications of microarray investigation in larger cohorts. This is a retrospective study which analyses the reading files of CMA and available clinical data from 420 patients from the south of Brazil, mostly children, with neurodevelopmental disorders requested by medical geneticists and neurologists for diagnostic purpose. Previous karyotyping was reported for 138 and includes 17 with abnormal results. The platforms used for CMA were CYTOSCAN 750K (75%) and CYTOSCAN HD (25%). The sex ratio of the patients was 1.625 males :1 female and the mean age was 9.5 years. A total of 96 pathogenic copy number variations (CNVs), 58 deletions and 38 duplications, were found in 18% of the patients and in all chromosomes, except chromosome 11. For 12% of the patients only variants of uncertain clinical significance were found. No clinically relevant CNV was found in 70%. The main referrals for chromosomal microarrays (CMA) were developmental delay (DD), intellectual disability (ID), facial dysmorphism and autism spectrum disorder (ASD). DD/ID were present in 80%, facial dysmorphism in 52% and ASD in 32%. Some phenotypes in this population could be predictive of a higher probability to carry a pathogenic CNV, as follows: dysmorphic facial features (p-value = < 0.0001, OR = 0.32), obesity (p-value = 0.006, OR = 0.20), short stature (p-value = 0.032, OR = 0.44), genitourinary anomalies (p-value = 0.032, OR = 0.63) and ASD (p-value = 0.039, OR = 1.94). The diagnostic rate for CMA in this study was 18%. We present the largest report of CMA data in a cohort with ND in Brazil. We characterize the rare CNVs found together with the main phenotypes presented by each patient, list phenotypes which could predict a higher diagnostic probability by CMA in patients with a neurodevelopmental disorder and show how CMA and classical karyotyping results are complementary.
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Affiliation(s)
| | - Nathacha Baretto
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | | | | | | | - Mayara Anselmi
- Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | | | | | | | - Pricila Bernardi
- University Hospital Professor Polydoro Ernani de São Thiago, Florianópolis, SC, Brazil
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19
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Fernández-Marmiesse A, Roca I, Díaz-Flores F, Cantarín V, Pérez-Poyato MS, Fontalba A, Laranjeira F, Quintans S, Moldovan O, Felgueroso B, Rodríguez-Pedreira M, Simón R, Camacho A, Quijada P, Ibanez-Mico S, Domingno MR, Benito C, Calvo R, Pérez-Cejas A, Carrasco ML, Ramos F, Couce ML, Ruiz-Falcó ML, Gutierrez-Solana L, Martínez-Atienza M. Rare Variants in 48 Genes Account for 42% of Cases of Epilepsy With or Without Neurodevelopmental Delay in 246 Pediatric Patients. Front Neurosci 2019; 13:1135. [PMID: 31780880 PMCID: PMC6856296 DOI: 10.3389/fnins.2019.01135] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 10/08/2019] [Indexed: 12/21/2022] Open
Abstract
In order to characterize the genetic architecture of epilepsy in a pediatric population from the Iberian Peninsula (including the Canary Islands), we conducted targeted exome sequencing of 246 patients with infantile-onset seizures with or without neurodevelopmental delay. We detected 107 variants in 48 different genes, which were implicated in neuronal excitability, neurodevelopment, synaptic transmission, and metabolic pathways. In 104 cases (42%) we detected variant(s) that we classified as pathogenic or likely pathogenic. Of the 48 mutated genes, 32 were dominant, 8 recessive and 8 X-linked. Of the patients for whom family studies could be performed and in whom pathogenic variants were identified in dominant or X-linked genes, 82% carried de novo mutations. The involvement of small copy number variations (CNVs) is 9%. The use of progressively updated custom panels with high mean vertical coverage enabled establishment of a definitive diagnosis in a large proportion of cases (42%) and detection of CNVs (even duplications) with high fidelity. In 10.5% of patients we detected associations that are pending confirmation via functional and/or familial studies. Our findings had important consequences for the clinical management of the probands, since a large proportion of the cohort had been clinically misdiagnosed, and their families were subsequently able to avail of genetic counseling. In some cases, a more appropriate treatment was selected for the patient in question, or an inappropriate treatment discontinued. Our findings suggest the existence of modifier genes that may explain the incomplete penetrance of some epilepsy-related genes. We discuss possible reasons for non-diagnosis and future research directions. Further studies will be required to uncover the roles of structural variants, epimutations, and oligogenic inheritance in epilepsy, thereby providing a more complete molecular picture of this disease. In summary, given the broad phenotypic spectrum of most epilepsy-related genes, efficient genomic tools like the targeted exome sequencing panel described here are essential for early diagnosis and treatment, and should be implemented as first-tier diagnostic tools for children with epilepsy without a clear etiologic basis.
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Affiliation(s)
- Ana Fernández-Marmiesse
- Unit for the Diagnosis and Treatment of Congenital Metabolic Diseases, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain.,Genomes & Disease Group, Molecular Medicine and Chronic Diseases Research Centre (CiMUS), Santiago de Compostela University-IDIS, Santiago de Compostela, Spain
| | - Iria Roca
- Unit for the Diagnosis and Treatment of Congenital Metabolic Diseases, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain.,Genomes & Disease Group, Molecular Medicine and Chronic Diseases Research Centre (CiMUS), Santiago de Compostela University-IDIS, Santiago de Compostela, Spain
| | - Felícitas Díaz-Flores
- Molecular Genetics Unit, Clinical University Hospital of Canarias, Santa Cruz de Tenerife, Spain
| | - Verónica Cantarín
- Neuropediatrics Unit, Niño Jesús Clinical University Hospital, Madrid, Spain
| | | | - Ana Fontalba
- Genetics Unit, Marqués de Valdecilla Clinical University Hospital, Santander, Spain
| | - Francisco Laranjeira
- Centro de Genética Médica Jacinto Magalhães, Centro Hospitalar Do Porto, Porto, Portugal
| | - Sofia Quintans
- Neuropediatrics Unit, Santa María Hospital, Lisbon, Portugal
| | - Oana Moldovan
- Genetics Unit, Santa María Hospital, Lisbon, Portugal
| | - Blanca Felgueroso
- Neuropediatrics Unit, Teresa Herrera Child's Hospital, A Coruña, Spain
| | | | - Rogelio Simón
- Neuropediatrics Unit, 12 de Octubre Clinical University Hospital, Madrid, Spain
| | - Ana Camacho
- Neuropediatrics Unit, 12 de Octubre Clinical University Hospital, Madrid, Spain.,Department of Medicine, Complutense University of Madrid, Madrid, Spain
| | - Pilar Quijada
- Metabolic Disorders Unit, 12 de Octubre Clinical University Hospital, Madrid, Spain
| | - Salvador Ibanez-Mico
- Neuropediatrics Unit, Virgen de la Arrixaca Clinical University Hospital, Murcia, Spain
| | - Mª Rosario Domingno
- Neuropediatrics Unit, Virgen de la Arrixaca Clinical University Hospital, Murcia, Spain
| | - Carmen Benito
- Genetics Unit, Clinical University Hospital of Málaga, Málaga, Spain
| | - Rocío Calvo
- Neuropediatrics Unit, Clinical University Hospital of Málaga, Málaga, Spain
| | - Antonia Pérez-Cejas
- Molecular Genetics Unit, Clinical University Hospital of Canarias, Santa Cruz de Tenerife, Spain
| | - Mª Llanos Carrasco
- Neuropediatrics Unit, Clinical University Hospital Severo Ochoa, Leganés, Madrid, Spain
| | - Feliciano Ramos
- Clinical Genetics Unit, Pediatrics, Clinical University Hospital of Zaragoza, Zaragoza, Spain
| | - Mª Luz Couce
- Unit for the Diagnosis and Treatment of Congenital Metabolic Diseases, Clinical University Hospital of Santiago de Compostela, Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mª Luz Ruiz-Falcó
- Neuropediatrics Unit, Niño Jesús Clinical University Hospital, Madrid, Spain
| | | | - Margarita Martínez-Atienza
- Genomes & Disease Group, Molecular Medicine and Chronic Diseases Research Centre (CiMUS), Santiago de Compostela University-IDIS, Santiago de Compostela, Spain.,Molecular Genetics Unit, Clinical University Hospital of Canarias, Santa Cruz de Tenerife, Spain.,Molecular Genetics Unit, Virgen de las Nieves Clinical University Hospital, Granada, Spain
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Rbfox1 Regulates Synaptic Transmission through the Inhibitory Neuron-Specific vSNARE Vamp1. Neuron 2019; 98:127-141.e7. [PMID: 29621484 DOI: 10.1016/j.neuron.2018.03.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 01/08/2018] [Accepted: 03/05/2018] [Indexed: 12/19/2022]
Abstract
Dysfunction of the neuronal RNA binding protein RBFOX1 has been linked to epilepsy and autism spectrum disorders. Rbfox1 loss in mice leads to neuronal hyper-excitability and seizures, but the physiological basis for this is unknown. We identify the vSNARE protein Vamp1 as a major Rbfox1 target. Vamp1 is strongly downregulated in Rbfox1 Nes-cKO mice due to loss of 3' UTR binding by RBFOX1. Cytoplasmic Rbfox1 stimulates Vamp1 expression in part by blocking microRNA-9. We find that Vamp1 is specifically expressed in inhibitory neurons, and that both Vamp1 knockdown and Rbfox1 loss lead to decreased inhibitory synaptic transmission and E/I imbalance. Re-expression of Vamp1 selectively within interneurons rescues the electrophysiological changes in the Rbfox1 cKO, indicating that Vamp1 loss is a major contributor to the Rbfox1 Nes-cKO phenotype. The regulation of interneuron-specific Vamp1 by Rbfox1 provides a paradigm for broadly expressed RNA-binding proteins performing specialized functions in defined neuronal subtypes.
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21
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Lipscombe D, Lopez Soto EJ. Alternative splicing of neuronal genes: new mechanisms and new therapies. Curr Opin Neurobiol 2019; 57:26-31. [PMID: 30703685 DOI: 10.1016/j.conb.2018.12.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 12/27/2018] [Indexed: 12/22/2022]
Abstract
Dynamic changes in alternative splicing during the life cycle of neurons support development and plasticity, and are implicated in disease pathology. Cell-specific alternative splicing programs coordinate exon selection across networks of functionally connected genes. In this opinion piece, we highlight recent publications that identify some of the molecular mechanisms-RNA and DNA binding proteins and epigenetic modifications-which direct cell-specific exon selection during pre-mRNA splicing. Aberrant splicing patterns are signature features of a growing number of diseases of the nervous system. Recent publications demonstrate the value of delineating basic mechanisms that dictate exon choice to inform the development of new therapeutic strategies that correct or compensate for damaging deficits in alternative splicing.
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Affiliation(s)
- Diane Lipscombe
- Robert J and Nancy D Carney Institute for Brain Science, Department of Neuroscience, Brown University, Providence, RI 02912, USA.
| | - Eduardo Javier Lopez Soto
- Robert J and Nancy D Carney Institute for Brain Science, Department of Neuroscience, Brown University, Providence, RI 02912, USA
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22
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Kong LL, Miao D, Tan L, Liu SL, Li JQ, Cao XP, Tan L. Genome-wide association study identifies RBFOX1 locus influencing brain glucose metabolism. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:436. [PMID: 30596066 PMCID: PMC6281526 DOI: 10.21037/atm.2018.07.05] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 06/21/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Fluorodeoxyglucose f18 positron emission tomography (18F-FDG PET) is regarded as the only functional neuroimaging biomarker for degeneration which can be used to increase the certainty of Alzheimer's disease (AD) pathophysiological process in research settings or as an optional clinical tool where available. Although a decline in FDG metabolism was confirmed in some regions known to be associated with AD, there was little known about the genetic association of FDG metabolism in AD cohorts. In this study, we present the first genome-wide association study (GWAS) analysis of brain FDG metabolism. METHODS A total of 222 individuals were included from the Alzheimer's Disease Neuroimaging Initiative 1 (ADNI-1) cohort. All subjects were restricted to non-Hispanic Caucasians and met all quality control (QC) criteria. Associations of 18F-FDG with the genetic variants were assessed using PLINK 1.07 under the additive genetic model. Genome-wide associations were visualized using a software program R 3.2.3. RESULTS One significant SNP rs12444565 in RNA-binding Fox1 (RBFOX1) was found to have a strong association with 18F-FDG (P=6.06×10-8). Rs235141, rs79037, rs12526331 and rs12529764 were identified as four suggestive loci associated with 18F-FDG. CONCLUSIONS Our study results suggest that a genome-wide significant SNP (rs12444565) in the RBFOX1, and four suggestive loci (rs235141, rs79037, rs12526331 and rs12529764) are associated with 18F-FDG.
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Affiliation(s)
- Ling-Li Kong
- Department of Geriatric Psychiatry, Qingdao Mental Health Center, Qingdao University, Qingdao 266071, China
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Dan Miao
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Lin Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Shu-Lei Liu
- Department of Neurology, Qingdao Center Hospital, Qingdao 266000, China
| | - Jie-Qiong Li
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Xi-Peng Cao
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Alzheimer’s Disease Neuroimaging Initiative*
- Department of Geriatric Psychiatry, Qingdao Mental Health Center, Qingdao University, Qingdao 266071, China
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
- Clinical Research Center, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
- Department of Neurology, Qingdao Center Hospital, Qingdao 266000, China
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23
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Lacey CJ, Doudney K, Bridgman PG, George PM, Mulder RT, Zarifeh JJ, Kimber B, Cadzow MJ, Black MA, Merriman TR, Lehnert K, Bickley VM, Pearson JF, Cameron VA, Kennedy MA. Copy number variants implicate cardiac function and development pathways in earthquake-induced stress cardiomyopathy. Sci Rep 2018; 8:7548. [PMID: 29765130 PMCID: PMC5954162 DOI: 10.1038/s41598-018-25827-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 04/25/2018] [Indexed: 02/07/2023] Open
Abstract
The pathophysiology of stress cardiomyopathy (SCM), also known as takotsubo syndrome, is poorly understood. SCM usually occurs sporadically, often in association with a stressful event, but clusters of cases are reported after major natural disasters. There is some evidence that this is a familial condition. We have examined three possible models for an underlying genetic predisposition to SCM. Our primary study cohort consists of 28 women who suffered SCM as a result of two devastating earthquakes that struck the city of Christchurch, New Zealand, in 2010 and 2011. To seek possible underlying genetic factors we carried out exome analysis, genotyping array analysis, and array comparative genomic hybridization on these subjects. The most striking finding was the observation of a markedly elevated rate of rare, heterogeneous copy number variants (CNV) of uncertain clinical significance (in 12/28 subjects). Several of these CNVs impacted on genes of cardiac relevance including RBFOX1, GPC5, KCNRG, CHODL, and GPBP1L1. There is no physical overlap between the CNVs, and the genes they impact do not appear to be functionally related. The recognition that SCM predisposition may be associated with a high rate of rare CNVs offers a novel perspective on this enigmatic condition.
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Affiliation(s)
- Cameron J Lacey
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand.
| | - Kit Doudney
- Molecular Pathology Laboratory, Canterbury Health Laboratories, Canterbury District Health Board, Christchurch, New Zealand
| | - Paul G Bridgman
- Department of Cardiology, Christchurch Hospital, Christchurch, New Zealand
| | - Peter M George
- Molecular Pathology Laboratory, Canterbury Health Laboratories, Canterbury District Health Board, Christchurch, New Zealand
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Roger T Mulder
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Julie J Zarifeh
- Psychiatric Consultation Service, Christchurch Hospital, Canterbury District Health Board, Christchurch, New Zealand
| | - Bridget Kimber
- Department of Psychological Medicine, University of Otago, Christchurch, New Zealand
| | - Murray J Cadzow
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Tony R Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Klaus Lehnert
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Vivienne M Bickley
- Molecular Pathology Laboratory, Canterbury Health Laboratories, Canterbury District Health Board, Christchurch, New Zealand
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Vicky A Cameron
- Christchurch Heart Institute, Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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24
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Koeleman BP. What do genetic studies tell us about the heritable basis of common epilepsy? Polygenic or complex epilepsy? Neurosci Lett 2018; 667:10-16. [DOI: 10.1016/j.neulet.2017.03.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 12/23/2022]
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25
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Pérez-Palma E, Helbig I, Klein KM, Anttila V, Horn H, Reinthaler EM, Gormley P, Ganna A, Byrnes A, Pernhorst K, Toliat MR, Saarentaus E, Howrigan DP, Hoffman P, Miquel JF, De Ferrari GV, Nürnberg P, Lerche H, Zimprich F, Neubauer BA, Becker AJ, Rosenow F, Perucca E, Zara F, Weber YG, Lal D. Heterogeneous contribution of microdeletions in the development of common generalised and focal epilepsies. J Med Genet 2017; 54:598-606. [PMID: 28756411 PMCID: PMC5574393 DOI: 10.1136/jmedgenet-2016-104495] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 06/21/2017] [Accepted: 06/26/2017] [Indexed: 11/27/2022]
Abstract
Background Microdeletions are known to confer risk to epilepsy, particularly at genomic rearrangement ‘hotspot’ loci. However, microdeletion burden not overlapping these regions or within different epilepsy subtypes has not been ascertained. Objective To decipher the role of microdeletions outside hotspots loci and risk assessment by epilepsy subtype. Methods We assessed the burden, frequency and genomic content of rare, large microdeletions found in a previously published cohort of 1366 patients with genetic generalised epilepsy (GGE) in addition to two sets of additional unpublished genome-wide microdeletions found in 281 patients with rolandic epilepsy (RE) and 807 patients with adult focal epilepsy (AFE), totalling 2454 cases. Microdeletions were assessed in a combined and subtype-specific approaches against 6746 controls. Results When hotspots are considered, we detected an enrichment of microdeletions in the combined epilepsy analysis (adjusted p=1.06×10−6,OR 1.89, 95% CI 1.51 to 2.35). Epilepsy subtype-specific analyses showed that hotspot microdeletions in the GGE subgroup contribute most of the overall signal (adjusted p=9.79×10−12, OR 7.45, 95% CI 4.20–13.5). Outside hotspots , microdeletions were enriched in the GGE cohort for neurodevelopmental genes (adjusted p=9.13×10−3,OR 2.85, 95% CI 1.62–4.94). No additional signal was observed for RE and AFE. Still, gene-content analysis identified known (NRXN1, RBFOX1 and PCDH7) and novel (LOC102723362) candidate genes across epilepsy subtypes that were not deleted in controls. Conclusions Our results show a heterogeneous effect of recurrent and non-recurrent microdeletions as part of the genetic architecture of GGE and a minor contribution in the aetiology of RE and AFE.
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Affiliation(s)
- Eduardo Pérez-Palma
- Faculty of Biological Sciences and Medicine, Center for Biomedical Research, Universidad Andres Bello, Santiago, Chile.,Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Ingo Helbig
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel, Germany.,Division of Neurology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Karl Martin Klein
- Department of Neurology, Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital, Goethe-University Frankfurt, Frankfurt, Germany.,Department of Neurology, Epilepsy Center Hessen, University Hospitals Giessen & Marburg, and University of Marburg, Marburg, Germany
| | - Verneri Anttila
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Heiko Horn
- Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Padhraig Gormley
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea Ganna
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Andrea Byrnes
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Mohammad R Toliat
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Elmo Saarentaus
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel P Howrigan
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Per Hoffman
- Division of Medical Genetics Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Juan Francisco Miquel
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Giancarlo V De Ferrari
- Faculty of Biological Sciences and Medicine, Center for Biomedical Research, Universidad Andres Bello, Santiago, Chile
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research,University of Tübingen, Tübingen, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Bern A Neubauer
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
| | - Albert J Becker
- Department of Neuropathology, University of Bonn, Bonn, Germany
| | - Felix Rosenow
- Department of Neurology, Epilepsy Center Frankfurt Rhine-Main, Center of Neurology and Neurosurgery, University Hospital, Goethe-University Frankfurt, Frankfurt, Germany.,Department of Neurology, Epilepsy Center Hessen, University Hospitals Giessen & Marburg, and University of Marburg, Marburg, Germany
| | - Emilio Perucca
- C. Mondino National Neurological Institute, Pavia, Italy.,Department of Internal Medicine and Therapeutics, University of Pavia, Pavia, Italy
| | - Federico Zara
- Laboratory of Neurogenetics, Neuromuscular Disease Unit, Genova, Italy
| | - Yvonne G Weber
- Departamento de Gastroenterología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Dennis Lal
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany.,Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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26
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Rajman M, Metge F, Fiore R, Khudayberdiev S, Aksoy-Aksel A, Bicker S, Ruedell Reschke C, Raoof R, Brennan GP, Delanty N, Farrell MA, O'Brien DF, Bauer S, Norwood B, Veno MT, Krüger M, Braun T, Kjems J, Rosenow F, Henshall DC, Dieterich C, Schratt G. A microRNA-129-5p/Rbfox crosstalk coordinates homeostatic downscaling of excitatory synapses. EMBO J 2017; 36:1770-1787. [PMID: 28487411 DOI: 10.15252/embj.201695748] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 04/05/2017] [Accepted: 04/07/2017] [Indexed: 12/31/2022] Open
Abstract
Synaptic downscaling is a homeostatic mechanism that allows neurons to reduce firing rates during chronically elevated network activity. Although synaptic downscaling is important in neural circuit development and epilepsy, the underlying mechanisms are poorly described. We performed small RNA profiling in picrotoxin (PTX)-treated hippocampal neurons, a model of synaptic downscaling. Thereby, we identified eight microRNAs (miRNAs) that were increased in response to PTX, including miR-129-5p, whose inhibition blocked synaptic downscaling in vitro and reduced epileptic seizure severity in vivo Using transcriptome, proteome, and bioinformatic analysis, we identified the calcium pump Atp2b4 and doublecortin (Dcx) as miR-129-5p targets. Restoring Atp2b4 and Dcx expression was sufficient to prevent synaptic downscaling in PTX-treated neurons. Furthermore, we characterized a functional crosstalk between miR-129-5p and the RNA-binding protein (RBP) Rbfox1. In the absence of PTX, Rbfox1 promoted the expression of Atp2b4 and Dcx. Upon PTX treatment, Rbfox1 expression was downregulated by miR-129-5p, thereby allowing the repression of Atp2b4 and Dcx. We therefore identified a novel activity-dependent miRNA/RBP crosstalk during synaptic scaling, with potential implications for neural network homeostasis and epileptogenesis.
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Affiliation(s)
- Marek Rajman
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Franziska Metge
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Department of Internal Medicine III, German Center for Cardiovascular Research (DZHK), University Hospital Heidelberg, Heidelberg, Germany
| | - Roberto Fiore
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Sharof Khudayberdiev
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Ayla Aksoy-Aksel
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Silvia Bicker
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Rana Raoof
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Gary P Brennan
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | | | | | - Sebastian Bauer
- Epilepsiezentrum Frankfurt Rhein-Main, Neurozentrum, Goethe-Universität Frankfurt, Frankfurt, Germany.,Epilepsiezentrum Hessen - Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - Braxton Norwood
- Epilepsiezentrum Frankfurt Rhein-Main, Neurozentrum, Goethe-Universität Frankfurt, Frankfurt, Germany.,Epilepsiezentrum Hessen - Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - Morten T Veno
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Marcus Krüger
- Institute for Genetics, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Thomas Braun
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Felix Rosenow
- Epilepsiezentrum Frankfurt Rhein-Main, Neurozentrum, Goethe-Universität Frankfurt, Frankfurt, Germany.,Epilepsiezentrum Hessen - Marburg, Philipps-Universität Marburg, Marburg, Germany
| | - David C Henshall
- Physiology & Medical Physics Department, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Christoph Dieterich
- Section of Bioinformatics and Systems Cardiology, Klaus Tschira Institute for Integrative Computational Cardiology, Department of Internal Medicine III, German Center for Cardiovascular Research (DZHK), University Hospital Heidelberg, Heidelberg, Germany
| | - Gerhard Schratt
- Biochemisch-Pharmakologisches Centrum, Institut für Physiologische Chemie, Philipps-Universität Marburg, Marburg, Germany
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27
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Xiong W, Zhou D. Progress in unraveling the genetic etiology of rolandic epilepsy. Seizure 2017; 47:99-104. [PMID: 28351718 DOI: 10.1016/j.seizure.2017.02.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 02/05/2023] Open
Abstract
Rolandic epilepsy (RE), or benign epilepsy of childhood with centrotemporal spikes (BECT), is the most frequent idiopathic partial epilepsy syndrome of childhood, where the "idiopathic" implies a genetic predisposition. Although RE has long been presumed to have a genetic component, clinical and genetic studies have shown a complex inheritance pattern. Furthermore, the underlying major genetic influence in RE has been challenged by recent reports of twin studies. Meanwhile, many genes or loci have been shown to be associated the RE/atypical RE (ARE) spectrum, with a higher frequency of causative variants in ARE. However, a full understanding of the genetic basis in the more common forms of the RE spectrum remains elusive.
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Affiliation(s)
- Weixi Xiong
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China
| | - Dong Zhou
- Department of Neurology, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, People's Republic of China.
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28
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Chen T, Giri M, Xia Z, Subedi YN, Li Y. Genetic and epigenetic mechanisms of epilepsy: a review. Neuropsychiatr Dis Treat 2017; 13:1841-1859. [PMID: 28761347 PMCID: PMC5516882 DOI: 10.2147/ndt.s142032] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Epilepsy is a common episodic neurological disorder or condition characterized by recurrent epileptic seizures, and genetics seems to play a key role in its etiology. Early linkage studies have localized multiple loci that may harbor susceptibility genes to epilepsy, and mutational analyses have detected a number of mutations involved in both ion channel and nonion channel genes in patients with idiopathic epilepsy. Genome-wide studies of epilepsy have found copy number variants at 2q24.2-q24.3, 7q11.22, 15q11.2-q13.3, and 16p13.11-p13.2, some of which disrupt multiple genes, such as NRXN1, AUTS2, NLGN1, CNTNAP2, GRIN2A, PRRT2, NIPA2, and BMP5, implicated for neurodevelopmental disorders, including intellectual disability and autism. Unfortunately, only a few common genetic variants have been associated with epilepsy. Recent exome-sequencing studies have found some genetic mutations, most of which are located in nonion channel genes such as the LGI1, PRRT2, EFHC1, PRICKLE, RBFOX1, and DEPDC5 and in probands with rare forms of familial epilepsy, and some of these genes are involved with the neurodevelopment. Since epigenetics plays a role in neuronal function from embryogenesis and early brain development to tissue-specific gene expression, epigenetic regulation may contribute to the genetic mechanism of neurodevelopment through which a gene and the environment interacting with each other affect the development of epilepsy. This review focused on the analytic tools used to identify epilepsy and then provided a summary of recent linkage and association findings, indicating the existence of novel genes on several chromosomes for further understanding of the biology of epilepsy.
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Affiliation(s)
- Tian Chen
- Department of Health Management Center, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
| | - Mohan Giri
- National Center for Rheumatic Diseases, Ratopul, Gaushala, Kathmandu, Nepal
| | - Zhenyi Xia
- Department of Thoracic Surgery, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
| | - Yadu Nanda Subedi
- National Center for Rheumatic Diseases, Ratopul, Gaushala, Kathmandu, Nepal
| | - Yan Li
- Department of Health Management Center, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
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29
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Damianov A, Ying Y, Lin CH, Lee JA, Tran D, Vashisht AA, Bahrami-Samani E, Xing Y, Martin KC, Wohlschlegel JA, Black DL. Rbfox Proteins Regulate Splicing as Part of a Large Multiprotein Complex LASR. Cell 2016; 165:606-19. [PMID: 27104978 DOI: 10.1016/j.cell.2016.03.040] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 12/18/2015] [Accepted: 03/22/2016] [Indexed: 12/11/2022]
Abstract
Rbfox proteins control alternative splicing and posttranscriptional regulation in mammalian brain and are implicated in neurological disease. These proteins recognize the RNA sequence (U)GCAUG, but their structures and diverse roles imply a variety of protein-protein interactions. We find that nuclear Rbfox proteins are bound within a large assembly of splicing regulators (LASR), a multimeric complex containing the proteins hnRNP M, hnRNP H, hnRNP C, Matrin3, NF110/NFAR-2, NF45, and DDX5, all approximately equimolar to Rbfox. We show that splicing repression mediated by hnRNP M is stimulated by Rbfox. Virtually all the intron-bound Rbfox is associated with LASR, and hnRNP M motifs are enriched adjacent to Rbfox crosslinking sites in vivo. These findings demonstrate that Rbfox proteins bind RNA with a defined set of cofactors and affect a broader set of exons than previously recognized. The function of this multimeric LASR complex has implications for deciphering the regulatory codes controlling splicing networks.
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Affiliation(s)
- Andrey Damianov
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Ying
- Molecular Biology Interdepartmental Ph.D. Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ji-Ann Lee
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Diana Tran
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ajay A Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Emad Bahrami-Samani
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Xing
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kelsey C Martin
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Lara-Pezzi E, Desco M, Gatto A, Gómez-Gaviro MV. Neurogenesis: Regulation by Alternative Splicing and Related Posttranscriptional Processes. Neuroscientist 2016; 23:466-477. [PMID: 27837180 DOI: 10.1177/1073858416678604] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The complexity of the mammalian brain requires highly specialized protein function and diversity. As neurons differentiate and the neuronal circuitry is established, several mRNAs undergo alternative splicing and other posttranscriptional changes that expand the variety of protein isoforms produced. Recent advances are beginning to shed light on the molecular mechanisms that regulate isoform switching during neurogenesis and the role played by specific RNA binding proteins in this process. Neurogenesis and neuronal wiring were recently shown to also be regulated by RNA degradation through nonsense-mediated decay. An additional layer of regulatory complexity in these biological processes is the interplay between alternative splicing and long noncoding RNAs. Dysregulation of posttranscriptional regulation results in defective neuronal differentiation and/or synaptic connections that lead to neurodevelopmental and psychiatric disorders.
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Affiliation(s)
- Enrique Lara-Pezzi
- 1 Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,2 National Heart and Lung Institute, Imperial College London, London, UK
| | - Manuel Desco
- 3 Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III, Madrid, Spain.,4 Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Alberto Gatto
- 1 Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - María Victoria Gómez-Gaviro
- 3 Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III, Madrid, Spain.,4 Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
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Abstract
Tumor-associated alterations in RNA splicing result either from mutations in splicing-regulatory elements or changes in components of the splicing machinery. This review summarizes our current understanding of the role of splicing-factor alterations in human cancers. We describe splicing-factor alterations detected in human tumors and the resulting changes in splicing, highlighting cell-type-specific similarities and differences. We review the mechanisms of splicing-factor regulation in normal and cancer cells. Finally, we summarize recent efforts to develop novel cancer therapies, based on targeting either the oncogenic splicing events or their upstream splicing regulators.
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Affiliation(s)
- Olga Anczuków
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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Turner SJ, Morgan AT, Perez ER, Scheffer IE. New genes for focal epilepsies with speech and language disorders. Curr Neurol Neurosci Rep 2016; 15:35. [PMID: 25921602 DOI: 10.1007/s11910-015-0554-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The last 2 years have seen exciting advances in the genetics of Landau-Kleffner syndrome and related disorders, encompassed within the epilepsy-aphasia spectrum (EAS). The striking finding of mutations in the N-methyl-D-aspartate (NMDA) receptor subunit gene GRIN2A as the first monogenic cause in up to 20% of patients with EAS suggests that excitatory glutamate receptors play a key role in these disorders. Patients with GRIN2A mutations have a recognizable speech and language phenotype that may assist with diagnosis. Other molecules involved in RNA binding and cell adhesion have been implicated in EAS; copy number variations are also found. The emerging picture highlights the overlap between the genetic determinants of EAS with speech and language disorders, intellectual disability, autism spectrum disorders and more complex developmental phenotypes.
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Affiliation(s)
- Samantha J Turner
- Department of Paediatrics, The University of Melbourne, The Royal Children's Hospital, Parkville, Australia,
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Tang BL. (WNK)ing at death: With-no-lysine (Wnk) kinases in neuropathies and neuronal survival. Brain Res Bull 2016; 125:92-8. [PMID: 27131446 DOI: 10.1016/j.brainresbull.2016.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/11/2016] [Accepted: 04/24/2016] [Indexed: 12/22/2022]
Abstract
Members of With-no-lysine (WNK) family of serine-threonine kinase are key regulators of chloride ion transport in diverse cell types, controlling the activity and the surface expression of cation-chloride (Na(+)/K(+)-Cl(-)) co-transporters. Mutations in WNK1 and WNK4 are linked to a hereditary form of hypertension, and WNKs have been extensively investigated pertaining to their roles in renal epithelial ion homeostasis. However, some members of the WNK family and their splice isoforms are also expressed in the mammalian brain, and have been implicated in aspects of hereditary neuropathy as well as neuronal and glial survival. WNK2, which is exclusively enriched in neurons, is well known as an anti-proliferative tumor suppressor. WNK3, on the other hand, appears to promote cell survival as its inhibition enhances neuronal apoptosis. However, loss of WNK3 has been recently shown to reduce ischemia-associated brain damage. In this review, I surveyed the potentially context-dependent roles of WNKs in neurological disorders and neuronal survival.
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Affiliation(s)
- Bor Luen Tang
- Department of Biochemistry, Yong Loo Lin School of Medicine, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore.
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34
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Affiliation(s)
- Chantal Depondt
- Department of Neurology, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
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Addis L, Rosch RE, Valentin A, Makoff A, Robinson R, Everett KV, Nashef L, Pal DK. Analysis of rare copy number variation in absence epilepsies. NEUROLOGY-GENETICS 2016; 2:e56. [PMID: 27123475 PMCID: PMC4830185 DOI: 10.1212/nxg.0000000000000056] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/04/2016] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To identify shared genes and pathways between common absence epilepsy (AE) subtypes (childhood absence epilepsy [CAE], juvenile absence epilepsy [JAE], and unclassified absence epilepsy [UAE]) that may indicate common mechanisms for absence seizure generation and potentially a diagnostic continuum. METHODS We used high-density single-nucleotide polymorphism arrays to analyze genome-wide rare copy number variation (CNV) in a cohort of 144 children with AEs (95 CAE, 26 UAE, and 23 JAE). RESULTS We identified CNVs that are known risk factors for AE in 4 patients, including 3x 15q11.2 deletion. We also expanded the phenotype at 4 regions more commonly identified in other neurodevelopmental disorders: 1p36.33 duplication, 1q21.1 deletion, 22q11.2 duplication, and Xp22.31 deletion and duplication. Fifteen patients (10.5%) were found to carry rare CNVs that disrupt genes associated with neuronal development and function (8 CAE, 2 JAE, and 5 UAE). Four categories of protein are each disrupted by several CNVs: (1) synaptic vesicle membrane or vesicle endocytosis, (2) synaptic cell adhesion, (3) synapse organization and motility via actin, and (4) gap junctions. CNVs within these categories are shared across the AE subtypes. CONCLUSIONS Our results have reinforced the complex and heterogeneous nature of the AEs and their potential for shared genetic mechanisms and have highlighted several pathways that may be important in epileptogenesis of absence seizures.
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Affiliation(s)
- Laura Addis
- Department of Basic and Clinical Neuroscience (L.A., R.E.R., A.V., A.M., D.K.P.), Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, United Kingdom; Neuroscience Discovery Research (L.A.), Eli Lilly and Company, Erl Wood, Surrey, United Kingdom; Wellcome Trust Centre for Neuroimaging (R.E.R.), Institute of Neurology, University College London, United Kingdom; Department of Clinical Neurophysiology (A.V.), Department of Neurology (L.N.), and Department of Child Health (D.K.P.), King's College Hospital, United Kingdom; Department of Paediatric Neurology (R.R.), Great Ormond Street Hospital, London, United Kingdom; and St George's University of London (K.V.E.), Cranmer Terrace, London, United Kingdom
| | - Richard E Rosch
- Department of Basic and Clinical Neuroscience (L.A., R.E.R., A.V., A.M., D.K.P.), Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, United Kingdom; Neuroscience Discovery Research (L.A.), Eli Lilly and Company, Erl Wood, Surrey, United Kingdom; Wellcome Trust Centre for Neuroimaging (R.E.R.), Institute of Neurology, University College London, United Kingdom; Department of Clinical Neurophysiology (A.V.), Department of Neurology (L.N.), and Department of Child Health (D.K.P.), King's College Hospital, United Kingdom; Department of Paediatric Neurology (R.R.), Great Ormond Street Hospital, London, United Kingdom; and St George's University of London (K.V.E.), Cranmer Terrace, London, United Kingdom
| | - Antonio Valentin
- Department of Basic and Clinical Neuroscience (L.A., R.E.R., A.V., A.M., D.K.P.), Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, United Kingdom; Neuroscience Discovery Research (L.A.), Eli Lilly and Company, Erl Wood, Surrey, United Kingdom; Wellcome Trust Centre for Neuroimaging (R.E.R.), Institute of Neurology, University College London, United Kingdom; Department of Clinical Neurophysiology (A.V.), Department of Neurology (L.N.), and Department of Child Health (D.K.P.), King's College Hospital, United Kingdom; Department of Paediatric Neurology (R.R.), Great Ormond Street Hospital, London, United Kingdom; and St George's University of London (K.V.E.), Cranmer Terrace, London, United Kingdom
| | - Andrew Makoff
- Department of Basic and Clinical Neuroscience (L.A., R.E.R., A.V., A.M., D.K.P.), Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, United Kingdom; Neuroscience Discovery Research (L.A.), Eli Lilly and Company, Erl Wood, Surrey, United Kingdom; Wellcome Trust Centre for Neuroimaging (R.E.R.), Institute of Neurology, University College London, United Kingdom; Department of Clinical Neurophysiology (A.V.), Department of Neurology (L.N.), and Department of Child Health (D.K.P.), King's College Hospital, United Kingdom; Department of Paediatric Neurology (R.R.), Great Ormond Street Hospital, London, United Kingdom; and St George's University of London (K.V.E.), Cranmer Terrace, London, United Kingdom
| | - Robert Robinson
- Department of Basic and Clinical Neuroscience (L.A., R.E.R., A.V., A.M., D.K.P.), Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, United Kingdom; Neuroscience Discovery Research (L.A.), Eli Lilly and Company, Erl Wood, Surrey, United Kingdom; Wellcome Trust Centre for Neuroimaging (R.E.R.), Institute of Neurology, University College London, United Kingdom; Department of Clinical Neurophysiology (A.V.), Department of Neurology (L.N.), and Department of Child Health (D.K.P.), King's College Hospital, United Kingdom; Department of Paediatric Neurology (R.R.), Great Ormond Street Hospital, London, United Kingdom; and St George's University of London (K.V.E.), Cranmer Terrace, London, United Kingdom
| | - Kate V Everett
- Department of Basic and Clinical Neuroscience (L.A., R.E.R., A.V., A.M., D.K.P.), Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, United Kingdom; Neuroscience Discovery Research (L.A.), Eli Lilly and Company, Erl Wood, Surrey, United Kingdom; Wellcome Trust Centre for Neuroimaging (R.E.R.), Institute of Neurology, University College London, United Kingdom; Department of Clinical Neurophysiology (A.V.), Department of Neurology (L.N.), and Department of Child Health (D.K.P.), King's College Hospital, United Kingdom; Department of Paediatric Neurology (R.R.), Great Ormond Street Hospital, London, United Kingdom; and St George's University of London (K.V.E.), Cranmer Terrace, London, United Kingdom
| | - Lina Nashef
- Department of Basic and Clinical Neuroscience (L.A., R.E.R., A.V., A.M., D.K.P.), Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, United Kingdom; Neuroscience Discovery Research (L.A.), Eli Lilly and Company, Erl Wood, Surrey, United Kingdom; Wellcome Trust Centre for Neuroimaging (R.E.R.), Institute of Neurology, University College London, United Kingdom; Department of Clinical Neurophysiology (A.V.), Department of Neurology (L.N.), and Department of Child Health (D.K.P.), King's College Hospital, United Kingdom; Department of Paediatric Neurology (R.R.), Great Ormond Street Hospital, London, United Kingdom; and St George's University of London (K.V.E.), Cranmer Terrace, London, United Kingdom
| | - Deb K Pal
- Department of Basic and Clinical Neuroscience (L.A., R.E.R., A.V., A.M., D.K.P.), Institute of Psychiatry, Psychology and Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, United Kingdom; Neuroscience Discovery Research (L.A.), Eli Lilly and Company, Erl Wood, Surrey, United Kingdom; Wellcome Trust Centre for Neuroimaging (R.E.R.), Institute of Neurology, University College London, United Kingdom; Department of Clinical Neurophysiology (A.V.), Department of Neurology (L.N.), and Department of Child Health (D.K.P.), King's College Hospital, United Kingdom; Department of Paediatric Neurology (R.R.), Great Ormond Street Hospital, London, United Kingdom; and St George's University of London (K.V.E.), Cranmer Terrace, London, United Kingdom
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Lee JA, Damianov A, Lin CH, Fontes M, Parikshak NN, Anderson ES, Geschwind DH, Black DL, Martin KC. Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes. Neuron 2015; 89:113-28. [PMID: 26687839 DOI: 10.1016/j.neuron.2015.11.025] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 09/03/2015] [Accepted: 11/06/2015] [Indexed: 12/31/2022]
Abstract
Human genetic studies have identified the neuronal RNA binding protein, Rbfox1, as a candidate gene for autism spectrum disorders. While Rbfox1 functions as a splicing regulator in the nucleus, it is also alternatively spliced to produce cytoplasmic isoforms. To investigate the function of cytoplasmic Rbfox1, we knocked down Rbfox proteins in mouse neurons and rescued with cytoplasmic or nuclear Rbfox1. Transcriptome profiling showed that nuclear Rbfox1 rescued splicing changes, whereas cytoplasmic Rbfox1 rescued changes in mRNA levels. iCLIP-seq of subcellular fractions revealed that Rbfox1 bound predominantly to introns in nascent RNA, while cytoplasmic Rbox1 bound to 3' UTRs. Cytoplasmic Rbfox1 binding increased target mRNA stability and translation, and Rbfox1 and miRNA binding sites overlapped significantly. Cytoplasmic Rbfox1 target mRNAs were enriched in genes involved in cortical development and autism. Our results uncover a new Rbfox1 regulatory network and highlight the importance of cytoplasmic RNA metabolism to cortical development and disease.
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Affiliation(s)
- Ji-Ann Lee
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Andrey Damianov
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chia-Ho Lin
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mariana Fontes
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Neelroop N Parikshak
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Erik S Anderson
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Douglas L Black
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kelsey C Martin
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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38
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Abstract
Epilepsy is a group of disorders characterized by recurrent seizures, and is one of the most common neurological conditions. The genetic basis of epilepsy is clear from epidemiological studies and from rare gene discoveries in large families. The three major classes of epilepsy disorders are genetic generalized, focal and encephalopathic epilepsies, with several specific disorders within each class. Advances in genomic technologies that facilitate genome-wide discovery of both common and rare variants have led to a rapid increase in our understanding of epilepsy genetics. Copy number variant and genome-wide association studies have contributed to our understanding of the complex genetic architecture of generalized epilepsy, while genetic insights into the focal epilepsies and epileptic encephalopathies have come primarily from exome sequencing. It is increasingly clear that epilepsy is genetically heterogeneous, and novel gene discoveries have moved the field beyond the known contribution of ion channels to implicate chromatin remodeling, transcriptional regulation and regulation of the mammalian target of rapamycin (mTOR) protein in the etiology of epilepsy. Such discoveries pave the way for new therapeutics, some of which are already being studied. In this review, we discuss the rapid pace of gene discovery in epilepsy, as facilitated by genomic technologies, and highlight several novel genes and potential therapies.
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Affiliation(s)
- Candace T Myers
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, 98195, USA.
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Wolf P, Yacubian EMT, Avanzini G, Sander T, Schmitz B, Wandschneider B, Koepp M. Juvenile myoclonic epilepsy: A system disorder of the brain. Epilepsy Res 2015; 114:2-12. [DOI: 10.1016/j.eplepsyres.2015.04.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 04/14/2015] [Indexed: 12/28/2022]
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40
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Lal D, Pernhorst K, Klein KM, Reif P, Tozzi R, Toliat MR, Winterer G, Neubauer B, Nürnberg P, Rosenow F, Becker F, Lerche H, Kunz WS, Kurki MI, Hoffmann P, Becker AJ, Perucca E, Zara F, Sander T, Weber YG. Extending the phenotypic spectrum ofRBFOX1deletions: Sporadic focal epilepsy. Epilepsia 2015; 56:e129-33. [DOI: 10.1111/epi.13076] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Dennis Lal
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
- Department of Neuropediatrics; University Medical Center Giessen and Marburg; Giessen Germany
- Cologne Center for Genomics; University of Cologne; Cologne Germany
| | | | | | - Philipp Reif
- Department of Neurology; University of Marburg; Marburg Germany
| | - Rossana Tozzi
- C. Mondino National Neurological Institute; Pavia Italy
| | - Mohammad R. Toliat
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
| | - Georg Winterer
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
| | - Bernd Neubauer
- Department of Neuropediatrics; University Medical Center Giessen and Marburg; Giessen Germany
| | - Peter Nürnberg
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
| | - Felix Rosenow
- Department of Neurology; University of Marburg; Marburg Germany
| | - Felicitas Becker
- Department of Neurology and Epileptology; Hertie Institute for Clinical Brain Research; University of Tübingen; Tübingen Germany
| | - Holger Lerche
- Department of Neurology and Epileptology; Hertie Institute for Clinical Brain Research; University of Tübingen; Tübingen Germany
| | | | - Mitja I. Kurki
- Psychiatric and Neurodevelopmental Genetics Unit; Massachusetts General Hospital; Boston Massachusetts U.S.A
- Broad Institute of Harvard and MIT; Cambridge Massachusetts U.S.A
- Neurosurgery; NeuroCenter; Kuopio University Hospital; Kuopio Finland
| | - Per Hoffmann
- Institute of Human Genetics; University of Bonn; Bonn Germany
- Division of Medical Genetics; University Hospital; Basel Switzerland
- Department of Biomedicine; University of Basel; Basel Switzerland
| | | | - Emilio Perucca
- C. Mondino National Neurological Institute; Pavia Italy
- Department of Internal Medicine and Therapeutics; University of Pavia; Pavia Italy
| | - Federico Zara
- Laboratory of Neurogenetics; Neuromuscular Disease Unit; Istituto G. Gaslini; Genova Italy
| | - Thomas Sander
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
| | - Yvonne G. Weber
- Department of Neurology and Epileptology; Hertie Institute for Clinical Brain Research; University of Tübingen; Tübingen Germany
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41
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Lal D, Ruppert AK, Trucks H, Schulz H, de Kovel CG, Kasteleijn-Nolst Trenité D, Sonsma ACM, Koeleman BP, Lindhout D, Weber YG, Lerche H, Kapser C, Schankin CJ, Kunz WS, Surges R, Elger CE, Gaus V, Schmitz B, Helbig I, Muhle H, Stephani U, Klein KM, Rosenow F, Neubauer BA, Reinthaler EM, Zimprich F, Feucht M, Møller RS, Hjalgrim H, De Jonghe P, Suls A, Lieb W, Franke A, Strauch K, Gieger C, Schurmann C, Schminke U, Nürnberg P, Sander T. Burden analysis of rare microdeletions suggests a strong impact of neurodevelopmental genes in genetic generalised epilepsies. PLoS Genet 2015; 11:e1005226. [PMID: 25950944 PMCID: PMC4423931 DOI: 10.1371/journal.pgen.1005226] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/16/2015] [Indexed: 01/06/2023] Open
Abstract
Genetic generalised epilepsy (GGE) is the most common form of genetic epilepsy, accounting for 20% of all epilepsies. Genomic copy number variations (CNVs) constitute important genetic risk factors of common GGE syndromes. In our present genome-wide burden analysis, large (≥ 400 kb) and rare (< 1%) autosomal microdeletions with high calling confidence (≥ 200 markers) were assessed by the Affymetrix SNP 6.0 array in European case-control cohorts of 1,366 GGE patients and 5,234 ancestry-matched controls. We aimed to: 1) assess the microdeletion burden in common GGE syndromes, 2) estimate the relative contribution of recurrent microdeletions at genomic rearrangement hotspots and non-recurrent microdeletions, and 3) identify potential candidate genes for GGE. We found a significant excess of microdeletions in 7.3% of GGE patients compared to 4.0% in controls (P = 1.8 x 10-7; OR = 1.9). Recurrent microdeletions at seven known genomic hotspots accounted for 36.9% of all microdeletions identified in the GGE cohort and showed a 7.5-fold increased burden (P = 2.6 x 10-17) relative to controls. Microdeletions affecting either a gene previously implicated in neurodevelopmental disorders (P = 8.0 x 10-18, OR = 4.6) or an evolutionarily conserved brain-expressed gene related to autism spectrum disorder (P = 1.3 x 10-12, OR = 4.1) were significantly enriched in the GGE patients. Microdeletions found only in GGE patients harboured a high proportion of genes previously associated with epilepsy and neuropsychiatric disorders (NRXN1, RBFOX1, PCDH7, KCNA2, EPM2A, RORB, PLCB1). Our results demonstrate that the significantly increased burden of large and rare microdeletions in GGE patients is largely confined to recurrent hotspot microdeletions and microdeletions affecting neurodevelopmental genes, suggesting a strong impact of fundamental neurodevelopmental processes in the pathogenesis of common GGE syndromes.
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Affiliation(s)
- Dennis Lal
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
- EPICURE Consortium
| | - Ann-Kathrin Ruppert
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Holger Trucks
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Herbert Schulz
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
| | - Carolien G. de Kovel
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Anja C. M. Sonsma
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bobby P. Koeleman
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dick Lindhout
- EPICURE Consortium
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
- SEIN Epilepsy Institute in the Netherlands, Hoofddorp, The Netherlands
| | - Yvonne G. Weber
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Holger Lerche
- EPICURE Consortium
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Kapser
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Christoph J. Schankin
- EPICURE Consortium
- Department of Neurology, University of Munich Hospital—Großhadern, Munich, Germany
| | - Wolfram S. Kunz
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Rainer Surges
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Christian E. Elger
- EPICURE Consortium
- Department of Epileptology, University Clinics Bonn, Bonn, Germany
| | - Verena Gaus
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
| | - Bettina Schmitz
- EPICURE Consortium
- Department of Neurology, Charité University Medicine, Campus Virchow Clinic, Berlin, Germany
- Department of Neurology, Vivantes Humboldt-Klinikum, Berlin, Germany
| | - Ingo Helbig
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Hiltrud Muhle
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Ulrich Stephani
- EPICURE Consortium
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein (Kiel Campus), Kiel, Germany
| | - Karl M. Klein
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Felix Rosenow
- EPICURE Consortium
- Epilepsy-Center Hessen, Department of Neurology, Philipps-University Marburg, Marburg, Germany
- Epilepsy Center Frankfurt Rhein-Main, Department of Neurology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany
| | - Bernd A. Neubauer
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
| | - Eva M. Reinthaler
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Fritz Zimprich
- EPICURE Consortium
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Martha Feucht
- EPICURE Consortium
- Department of Pediatrics and Neonatology, Medical University of Vienna, Vienna, Austria
| | - Rikke S. Møller
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Helle Hjalgrim
- EPICURE Consortium
- Department of Neurology, Danish Epilepsy Centre, Dianalund, Denmark
- Institute for Regional Health Services, University of Southern Denmark, Odense, Denmark
| | - Peter De Jonghe
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Arvid Suls
- EPICURE Consortium
- Neurogenetics Group, VIB Department of Molecular Genetics, University of Antwerp, Antwerp, Belgium
- Laboratory of Neurogenetics, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Christian Albrechts University, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, and Chair of Genetic Epidemiology, Ludwig-Maximilians-University, Munich, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München—German Research Center for Environmental Health, Neuherberg, Germany
| | - Claudia Schurmann
- Interfaculty Institute for Genetics and Functional Genomics, Ernst Moritz Arndt University, Greifswald, Germany
| | - Ulf Schminke
- Department of Neurology, University Medicine Greifswald, Ernst Moritz Arndt University, Greifswald, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- EPICURE Consortium
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | | | - Thomas Sander
- Cologne Center for Genomics (CCG), University of Cologne, Cologne, Germany
- EPICURE Consortium
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42
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Reinthaler EM, Dejanovic B, Lal D, Semtner M, Merkler Y, Reinhold A, Pittrich DA, Hotzy C, Feucht M, Steinböck H, Gruber-Sedlmayr U, Ronen GM, Neophytou B, Geldner J, Haberlandt E, Muhle H, Ikram MA, van Duijn CM, Uitterlinden AG, Hofman A, Altmüller J, Kawalia A, Toliat MR, Nürnberg P, Lerche H, Nothnagel M, Thiele H, Sander T, Meier JC, Schwarz G, Neubauer BA, Zimprich F. Rare variants in γ-aminobutyric acid type A receptor genes in rolandic epilepsy and related syndromes. Ann Neurol 2015; 77:972-86. [PMID: 25726841 DOI: 10.1002/ana.24395] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/12/2015] [Accepted: 02/22/2015] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To test whether mutations in γ-aminobutyric acid type A receptor (GABAA -R) subunit genes contribute to the etiology of rolandic epilepsy (RE) or its atypical variants (ARE). METHODS We performed exome sequencing to compare the frequency of variants in 18 GABAA -R genes in 204 European patients with RE/ARE versus 728 platform-matched controls. Identified GABRG2 variants were functionally assessed for protein stability, trafficking, postsynaptic clustering, and receptor function. RESULTS Of 18 screened GABAA -R genes, we detected an enrichment of rare variants in the GABRG2 gene in RE/ARE patients (5 of 204, 2.45%) in comparison to controls (1 of 723, 0.14%; odds ratio = 18.07, 95% confidence interval = 2.01-855.07, p = 0.0024, pcorr = 0.043). We identified a GABRG2 splice variant (c.549-3T>G) in 2 unrelated patients as well as 3 nonsynonymous variations in this gene (p.G257R, p.R323Q, p.I389V). Functional assessment showed reduced surface expression of p.G257R and decreased GABA-evoked currents for p.R323Q. The p.G257R mutation displayed diminished levels of palmitoylation, a post-translational modification crucial for trafficking of proteins to the cell membrane. Enzymatically raised palmitoylation levels restored the surface expression of the p.G257R variant γ2 subunit. INTERPRETATION The statistical association and the functional evidence suggest that mutations of the GABRG2 gene may increase the risk of RE/ARE. Restoring the impaired membrane trafficking of some GABRG2 mutations by enhancing palmitoylation might be an interesting therapeutic approach to reverse the pathogenic effect of such mutants.
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Affiliation(s)
- Eva M Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Borislav Dejanovic
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Cologne, Germany
| | - Dennis Lal
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Marcus Semtner
- RNA Editing and Hyperexcitability Disorders Helmholtz Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Yvonne Merkler
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Cologne, Germany
| | - Annika Reinhold
- RNA Editing and Hyperexcitability Disorders Helmholtz Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Christoph Hotzy
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Martha Feucht
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | | | | | - Gabriel M Ronen
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Birgit Neophytou
- Department of Neuropediatrics, St Anna Children's Hospital, Vienna, Austria
| | - Julia Geldner
- Department of Pediatrics, SMZ Süd - Kaiser-Franz-Josef-Hospital, Vienna, Austria
| | - Edda Haberlandt
- Department of Pediatrics, Medical University of Innsbruck, Innsbruck, Austria
| | - Hiltrud Muhle
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian Albrechts University, Kiel, Germany
| | - M Arfan Ikram
- Departments of Epidemiology, Neurology, and Radiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Amit Kawalia
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Mohammad R Toliat
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | | | - Peter Nürnberg
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Jochen C Meier
- RNA Editing and Hyperexcitability Disorders Helmholtz Group, Max Delbrück Center for Molecular Medicine, Berlin, Germany.,Braunschweig University of Technology, Zoological Institute, Division of Cell Physiology, Braunschweig, Germany
| | - Günter Schwarz
- Institute of Biochemistry, Department of Chemistry, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Bernd A Neubauer
- Department of Neuropediatrics, University Medical Center Giessen and Marburg, Giessen, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
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43
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Wen M, Yan Y, Yan N, Chen XS, Liu SY, Feng ZH. Upregulation of RBFOX1 in the malformed cortex of patients with intractable epilepsy and in cultured rat neurons. Int J Mol Med 2015; 35:597-606. [PMID: 25571999 PMCID: PMC4314424 DOI: 10.3892/ijmm.2015.2061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Accepted: 12/22/2014] [Indexed: 02/07/2023] Open
Abstract
Mutations in RNA-binding Fox 1 (RBFOX1) are known to be associated with neurodevelopmental disorders including epilepsy, mental retardation and autism spectrum disorder. The deletion of the Rbfox1 gene in mice has been shown to result in heightened susceptibility to seizures. However, other studies have revealed mutations or the downregulation of RBFOX1 in specimens obtained from patients with epilepsy or malformations of cortical development (MCD). Generally, the expression of RBFOX1 varies according to tissue type. In this study, we demonstrated the upregulation of RBFOX1 protein in the cortex of patients with MCD and intractable epilepsy. Electrophysiological recordings of cultured rat cortical neurons with increased Rbfox1 expression also revealed a significantly increased amplitude of action potential (AP) and Na+ current density. Some of these neurons (26.32%) even displayed spontaneous, recurrent, epileptiform discharges (SREDs). Additionally, certain Rbfox1 target transcripts associated with epilepsy, including glutamate receptor, ionotropic, N-methyl D-aspartate 1 [Grin1, also known as N-methyl-D-aspartate receptor subunit NR1 (NMDAR1)], synaptosomal-associated protein, 25 kDa (SNAP-25 or Snap25) and sodium channel, voltage gated, type VIII, alpha subunit (Scn8a, also known as Nav1.6) were identified to be upregulated in these cultured cortical neurons with an upregulated Rbfox1 expression. These data suggest that the upregulation of RBFOX1 contributes to neuronal hyperexcitation and seizures. The upregulation of NMDAR1 (Grin1), SNAP-25 (Snap25) and Scn8a may thus be involved in Rbfox1-related neuronal hyperexcitation.
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Affiliation(s)
- Ming Wen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, P.R. China
| | - Yong Yan
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, Chongqing 400016, P.R. China
| | - Ning Yan
- Department of Neurology, University‑Town Hospital of Chongqing Medical University, Chongqing 401331, P.R. China
| | - Xiao Shan Chen
- Department of Neurology, Xi'an Central Hospital, Xi'an 710003, P.R. China
| | - Shi Yong Liu
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, P.R. China
| | - Zhan Hui Feng
- Department of Neurology, Affiliated Hospital of Guiyang Medical University, Guiyang 550004, P.R. China
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44
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Leslie R, O'Donnell CJ, Johnson AD. GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database. Bioinformatics 2014; 30:i185-94. [PMID: 24931982 DOI: 10.1093/bioinformatics/btu273] [Citation(s) in RCA: 179] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
SUMMARY We created a deeply extracted and annotated database of genome-wide association studies (GWAS) results. GRASP v1.0 contains >6.2 million SNP-phenotype association from among 1390 GWAS studies. We re-annotated GWAS results with 16 annotation sources including some rarely compared to GWAS results (e.g. RNAediting sites, lincRNAs, PTMs). MOTIVATION To create a high-quality resource to facilitate further use and interpretation of human GWAS results in order to address important scientific questions. RESULTS GWAS have grown exponentially, with increases in sample sizes and markers tested, and continuing bias toward European ancestry samples. GRASP contains >100 000 phenotypes, roughly: eQTLs (71.5%), metabolite QTLs (21.2%), methylation QTLs (4.4%) and diseases, biomarkers and other traits (2.8%). cis-eQTLs, meQTLs, mQTLs and MHC region SNPs are highly enriched among significant results. After removing these categories, GRASP still contains a greater proportion of studies and results than comparable GWAS catalogs. Cardiovascular disease and related risk factors pre-dominate remaining GWAS results, followed by immunological, neurological and cancer traits. Significant results in GWAS display a highly gene-centric tendency. Sex chromosome X (OR = 0.18[0.16-0.20]) and Y (OR = 0.003[0.001-0.01]) genes are depleted for GWAS results. Gene length is correlated with GWAS results at nominal significance (P ≤ 0.05) levels. We show this gene-length correlation decays at increasingly more stringent P-value thresholds. Potential pleotropic genes and SNPs enriched for multi-phenotype association in GWAS are identified. However, we note possible population stratification at some of these loci. Finally, via re-annotation we identify compelling functional hypotheses at GWAS loci, in some cases unrealized in studies to date. CONCLUSION Pooling summary-level GWAS results and re-annotating with bioinformatics predictions and molecular features provides a good platform for new insights. AVAILABILITY The GRASP database is available at http://apps.nhlbi.nih.gov/grasp.
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Affiliation(s)
- Richard Leslie
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USACardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christopher J O'Donnell
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USACardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Andrew D Johnson
- Cardiovascular Epidemiology and Human Genomics Branch, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, University of Massachusetts Medical School, Worcester, MA 01655 and Division of Cardiology, Massachusetts General Hospital, Boston, MA 02114, USA
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45
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Fanciulli M, Pasini E, Malacrida S, Striano P, Striano S, Michelucci R, Ottman R, Nobile C. Copy number variations and susceptibility to lateral temporal epilepsy: A study of 21 pedigrees. Epilepsia 2014; 55:1651-8. [DOI: 10.1111/epi.12767] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2014] [Indexed: 11/28/2022]
Affiliation(s)
| | - Elena Pasini
- Unit of Neurology; Bellaria Hospital; IRCCS of Neurological Sciences; Bologna Italy
| | | | - Pasquale Striano
- Pediatric Neurology and Neuromuscular Disease Unit; Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health; “G. Gaslini” Institute; University of Genoa; Genova Italy
| | - Salvatore Striano
- Department of Neurological Sciences; Federico II University; Napoli Italy
| | - Roberto Michelucci
- Unit of Neurology; Bellaria Hospital; IRCCS of Neurological Sciences; Bologna Italy
| | - Ruth Ottman
- Departments of Epidemiology and Neurology and the G.H. Sergievsky Center; Columbia University; New York New York U.S.A
- Division of Epidemiology; New York State Psychiatric Institute; New York New York U.S.A
| | - Carlo Nobile
- CNR-Neuroscience Institute; Section of Padua; Padova Italy
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46
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Orchestration of neurodevelopmental programs by RBFOX1: implications for autism spectrum disorder. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2014; 113:251-67. [PMID: 24290388 DOI: 10.1016/b978-0-12-418700-9.00008-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Neurodevelopmental and neuropsychiatric disorders result from complex interactions between critical genetic factors and as-yet-unknown environmental components. To gain clinical insight, it is critical to develop a comprehensive understanding of these genetic components. RBFOX1, an RNA splicing factor, regulates expression of large genetic networks during early neuronal development, and haploinsufficiency causes severe neurodevelopmental phenotypes including autism spectrum disorder (ASD), intellectual disability, and epilepsy. Genomic testing in individuals and large patient cohorts has identified phenotypically similar cases possessing copy number variations in RBFOX1, implicating the gene as an important cause of neurodevelopmental disease. However, a significant proportion of the observed structural variation is inherited from phenotypically normal individuals, raising questions regarding overall pathogenicity of variation at the RBFOX1 locus. In this chapter, we discuss the molecular, cellular, and clinical evidence supporting the role of RBFOX1 in neurodevelopment and present a comprehensive model for the contribution of structural variation in RBFOX1 to ASD.
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47
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Dejanovic B, Lal D, Catarino CB, Arjune S, Belaidi AA, Trucks H, Vollmar C, Surges R, Kunz WS, Motameny S, Altmüller J, Köhler A, Neubauer BA, EPICURE Consortium, Nürnberg P, Noachtar S, Schwarz G, Sander T. Exonic microdeletions of the gephyrin gene impair GABAergic synaptic inhibition in patients with idiopathic generalized epilepsy. Neurobiol Dis 2014; 67:88-96. [DOI: 10.1016/j.nbd.2014.02.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 01/09/2014] [Accepted: 02/10/2014] [Indexed: 12/29/2022] Open
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48
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Reinthaler EM, Lal D, Lebon S, Hildebrand MS, Dahl HHM, Regan BM, Feucht M, Steinböck H, Neophytou B, Ronen GM, Roche L, Gruber-Sedlmayr U, Geldner J, Haberlandt E, Hoffmann P, Herms S, Gieger C, Waldenberger M, Franke A, Wittig M, Schoch S, Becker AJ, Hahn A, Männik K, Toliat MR, Winterer G, Lerche H, Nürnberg P, Mefford H, Scheffer IE, Berkovic SF, Beckmann JS, Sander T, Jacquemont S, Reymond A, Zimprich F, Neubauer BA. 16p11.2 600 kb Duplications confer risk for typical and atypical Rolandic epilepsy. Hum Mol Genet 2014; 23:6069-80. [PMID: 24939913 DOI: 10.1093/hmg/ddu306] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rolandic epilepsy (RE) is the most common idiopathic focal childhood epilepsy. Its molecular basis is largely unknown and a complex genetic etiology is assumed in the majority of affected individuals. The present study tested whether six large recurrent copy number variants at 1q21, 15q11.2, 15q13.3, 16p11.2, 16p13.11 and 22q11.2 previously associated with neurodevelopmental disorders also increase risk of RE. Our association analyses revealed a significant excess of the 600 kb genomic duplication at the 16p11.2 locus (chr16: 29.5-30.1 Mb) in 393 unrelated patients with typical (n = 339) and atypical (ARE; n = 54) RE compared with the prevalence in 65,046 European population controls (5/393 cases versus 32/65,046 controls; Fisher's exact test P = 2.83 × 10(-6), odds ratio = 26.2, 95% confidence interval: 7.9-68.2). In contrast, the 16p11.2 duplication was not detected in 1738 European epilepsy patients with either temporal lobe epilepsy (n = 330) and genetic generalized epilepsies (n = 1408), suggesting a selective enrichment of the 16p11.2 duplication in idiopathic focal childhood epilepsies (Fisher's exact test P = 2.1 × 10(-4)). In a subsequent screen among children carrying the 16p11.2 600 kb rearrangement we identified three patients with RE-spectrum epilepsies in 117 duplication carriers (2.6%) but none in 202 carriers of the reciprocal deletion. Our results suggest that the 16p11.2 duplication represents a significant genetic risk factor for typical and atypical RE.
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Affiliation(s)
| | - Dennis Lal
- Cologne Center for Genomics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany, Department of Neuropediatrics, University Medical Faculty Giessen and Marburg, Giessen, Germany
| | - Sebastien Lebon
- Unit of Pediatric Neurology and Neurorehabilitation, Department of Pediatrics
| | - Michael S Hildebrand
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Australia
| | - Hans-Henrik M Dahl
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Australia
| | - Brigid M Regan
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Australia
| | - Martha Feucht
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | | | - Birgit Neophytou
- Department of Neuropediatrics, St. Anna Children's Hospital, Vienna, Austria
| | - Gabriel M Ronen
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Laurian Roche
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | - Julia Geldner
- Department of Pediatrics, Hospital SMZ Süd Kaiser-Franz-Josef Spital, Vienna, Austria
| | - Edda Haberlandt
- Department of Pediatrics, Medical University of Innsbruck, Innsbruck, Austria
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany, Division of Medical Genetics, University Hospital and Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, Bonn, Germany, Division of Medical Genetics, University Hospital and Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Christian Gieger
- Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Institute of Genetic Epidemiology, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Susanne Schoch
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Albert J Becker
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Andreas Hahn
- Department of Neuropediatrics, University Medical Faculty Giessen and Marburg, Giessen, Germany
| | - Katrin Männik
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Georg Winterer
- Experimental and Clinical Research Center (ECRC) Charité, University Medicine Berlin, Berlin, Germany
| | | | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Heather Mefford
- Division of Genetic Medicine, University of Washington, Seattle, Washington, USA
| | - Ingrid E Scheffer
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Australia, Florey Institute and Department of Pediatrics, University of Melbourne, Royal Children's Hospital, Melbourne, Australia
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, Australia
| | - Jacques S Beckmann
- Service of Medical Genetics, Lausanne University Hospital, Lausanne, Switzerland, Swiss Institute of Bioinformatics, Lausanne, Switzerland and
| | | | | | | | - Sebastien Jacquemont
- Service of Medical Genetics, Lausanne University Hospital, Lausanne, Switzerland
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Bernd A Neubauer
- Department of Neuropediatrics, University Medical Faculty Giessen and Marburg, Giessen, Germany
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49
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Kamien B, Lionel AC, Bain N, Scherer SW, Hunter M. Outfoxed by RBFOX1-a caution about ascertainment bias. Am J Med Genet A 2014; 164A:1411-8. [PMID: 24664471 DOI: 10.1002/ajmg.a.36458] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 01/06/2014] [Indexed: 11/06/2022]
Abstract
We report on two patients with intragenic deletions of RBFOX1 and one patient with an intragenic duplication of RBFOX1. These patients, by report, all had autism spectrum disorder and/or developmental delay and had strong family histories of these conditions. We initially hypothesized that RBFOX1 was another susceptibility locus for autism spectrum disorder or developmental delay. However, epidemiological evidence examining large numbers of individuals did not support this hypothesis and the data presented here suggests that RBFOX1 intragenic copy number variants are not pathogenic. This contradicts previous reports that examined smaller numbers of patients and controls. © 2014 Wiley Periodicals, Inc.
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Affiliation(s)
- Benjamin Kamien
- Hunter Genetics, Newcastle, New South Wales, Australia; The University of Newcastle, School of Medicine and Public Health, Newcastle, New South Wales, Australia
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50
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Lal D, Reinthaler EM, Altmüller J, Toliat MR, Thiele H, Nürnberg P, Lerche H, Hahn A, Møller RS, Muhle H, Sander T, Zimprich F, Neubauer BA. RBFOX1 and RBFOX3 mutations in rolandic epilepsy. PLoS One 2013; 8:e73323. [PMID: 24039908 PMCID: PMC3765197 DOI: 10.1371/journal.pone.0073323] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 07/19/2013] [Indexed: 12/20/2022] Open
Abstract
Partial deletions of the gene encoding the neuronal splicing regulator RBFOX1 have been reported in a range of neurodevelopmental diseases, including idiopathic generalized epilepsy. The RBFOX1 protein and its homologues (RBFOX2 and RBFOX3) regulate alternative splicing of many neuronal transcripts involved in the homeostatic control of neuronal excitability. In this study, we explored if structural microdeletions and exonic sequence variations in RBFOX1, RBFOX2, RBFOX3 confer susceptibility to rolandic epilepsy (RE), a common idiopathic focal childhood epilepsy. By high-density SNP array screening of 289 unrelated RE patients, we identified two hemizygous deletions, a 365 kb deletion affecting two untranslated 5′-terminal exons of RBFOX1 and a 43 kb deletion spanning exon 3 of RBFOX3. Exome sequencing of 242 RE patients revealed two novel probably deleterious variants in RBFOX1, a frameshift mutation (p.A233Vfs*74) and a hexanucleotide deletion (p.A299_A300del), and a novel nonsense mutation in RBFOX3 (p.Y287*). Although the three variants were inherited from unaffected parents, they were present in all family members exhibiting the RE trait clinically or electroencephalographically with only one exception. In contrast, no deleterious mutations of RBFOX1 and RBFOX3 were found in the exomes of 6503 non-RE subjects deposited in the Exome Variant Server database. The observed RBFOX3 exon 3 deletion and nonsense mutation suggest that RBFOX3 represents a novel risk factor for RE, indicating that exon deletions and truncating mutations of RBFOX1 and RBFOX3 contribute to the genetic variance of partial and generalized idiopathic epilepsy syndromes.
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Affiliation(s)
- Dennis Lal
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department of Neuropediatrics, University Medical Clinic Giessen, Giessen, Germany
| | - Eva M. Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | | | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute of Clinical Brain Research, Eberhard-Karls University, Tuebingen, Germany
| | - Andreas Hahn
- Department of Neuropediatrics, University Medical Clinic Giessen, Giessen, Germany
| | | | - Hiltrud Muhle
- Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Christian-Albrechts University, Kiel, Germany
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Bernd A. Neubauer
- Department of Neuropediatrics, University Medical Clinic Giessen, Giessen, Germany
- * E-mail:
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