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Yuan Y, Yu L, Zhuang X, Wen D, He J, Hong J, Xie J, Ling S, Du X, Chen W, Wang X. Drosophila models used to simulate human ATP1A1 gene mutations that cause Charcot-Marie-Tooth type 2 disease and refractory seizures. Neural Regen Res 2025; 20:265-276. [PMID: 38767491 DOI: 10.4103/1673-5374.391302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/06/2023] [Indexed: 05/22/2024] Open
Abstract
JOURNAL/nrgr/04.03/01300535-202501000-00034/figure1/v/2024-05-14T021156Z/r/image-tiff Certain amino acids changes in the human Na+/K+-ATPase pump, ATPase Na+/K+ transporting subunit alpha 1 (ATP1A1), cause Charcot-Marie-Tooth disease type 2 (CMT2) disease and refractory seizures. To develop in vivo models to study the role of Na+/K+-ATPase in these diseases, we modified the Drosophila gene homolog, Atpα, to mimic the human ATP1A1 gene mutations that cause CMT2. Mutations located within the helical linker region of human ATP1A1 (I592T, A597T, P600T, and D601F) were simultaneously introduced into endogenous DrosophilaAtpα by CRISPR/Cas9-mediated genome editing, generating the AtpαTTTF model. In addition, the same strategy was used to generate the corresponding single point mutations in flies (AtpαI571T, AtpαA576T, AtpαP579T, and AtpαD580F). Moreover, a deletion mutation (Atpαmut) that causes premature termination of translation was generated as a positive control. Of these alleles, we found two that could be maintained as homozygotes (AtpαI571T and AtpαP579T). Three alleles (AtpαA576T, AtpαP579 and AtpαD580F) can form heterozygotes with the Atpαmut allele. We found that the Atpα allele carrying these CMT2-associated mutations showed differential phenotypes in Drosophila. Flies heterozygous for AtpαTTTF mutations have motor performance defects, a reduced lifespan, seizures, and an abnormal neuronal morphology. These Drosophila models will provide a new platform for studying the function and regulation of the sodium-potassium pump.
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Affiliation(s)
- Yao Yuan
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Lingqi Yu
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Xudong Zhuang
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian Province, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Dongjing Wen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Jin He
- Department of Neurology and Institute of Neurology of The First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jingmei Hong
- Department of Neurology and Institute of Neurology of The First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, Fujian Province, China
| | - Jiayu Xie
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Shengan Ling
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Xiaoyue Du
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Wenfeng Chen
- Institute of Life Sciences, College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian Province, China
| | - Xinrui Wang
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primate (Fujian Maternity and Child Health Hospital), Fuzhou, Fujian Province, China
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, Fujian Province, China
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2
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Costa B, Vale N. Virus-Induced Epilepsy vs. Epilepsy Patients Acquiring Viral Infection: Unravelling the Complex Relationship for Precision Treatment. Int J Mol Sci 2024; 25:3730. [PMID: 38612542 PMCID: PMC11011490 DOI: 10.3390/ijms25073730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/04/2024] [Accepted: 03/25/2024] [Indexed: 04/14/2024] Open
Abstract
The intricate relationship between viruses and epilepsy involves a bidirectional interaction. Certain viruses can induce epilepsy by infecting the brain, leading to inflammation, damage, or abnormal electrical activity. Conversely, epilepsy patients may be more susceptible to viral infections due to factors, such as compromised immune systems, anticonvulsant drugs, or surgical interventions. Neuroinflammation, a common factor in both scenarios, exhibits onset, duration, intensity, and consequence variations. It can modulate epileptogenesis, increase seizure susceptibility, and impact anticonvulsant drug pharmacokinetics, immune system function, and brain physiology. Viral infections significantly impact the clinical management of epilepsy patients, necessitating a multidisciplinary approach encompassing diagnosis, prevention, and treatment of both conditions. We delved into the dual dynamics of viruses inducing epilepsy and epilepsy patients acquiring viruses, examining the unique features of each case. For virus-induced epilepsy, we specify virus types, elucidate mechanisms of epilepsy induction, emphasize neuroinflammation's impact, and analyze its effects on anticonvulsant drug pharmacokinetics. Conversely, in epilepsy patients acquiring viruses, we detail the acquired virus, its interaction with existing epilepsy, neuroinflammation effects, and changes in anticonvulsant drug pharmacokinetics. Understanding this interplay advances precision therapies for epilepsy during viral infections, providing mechanistic insights, identifying biomarkers and therapeutic targets, and supporting optimized dosing regimens. However, further studies are crucial to validate tools, discover new biomarkers and therapeutic targets, and evaluate targeted therapy safety and efficacy in diverse epilepsy and viral infection scenarios.
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Affiliation(s)
- Bárbara Costa
- PerMed Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal
| | - Nuno Vale
- PerMed Research Group, Center for Health Technology and Services Research (CINTESIS), Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal;
- CINTESIS@RISE, Faculty of Medicine, University of Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal
- Department of Community Medicine, Information and Health Decision Sciences (MEDCIDS), Faculty of Medicine, University of Porto, Rua Doutor Plácido da Costa, s/n, 4200-450 Porto, Portugal
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3
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Weigel B, Tegethoff JF, Grieder SD, Lim B, Nagarajan B, Liu YC, Truberg J, Papageorgiou D, Adrian-Segarra JM, Schmidt LK, Kaspar J, Poisel E, Heinzelmann E, Saraswat M, Christ M, Arnold C, Ibarra IL, Campos J, Krijgsveld J, Monyer H, Zaugg JB, Acuna C, Mall M. MYT1L haploinsufficiency in human neurons and mice causes autism-associated phenotypes that can be reversed by genetic and pharmacologic intervention. Mol Psychiatry 2023; 28:2122-2135. [PMID: 36782060 PMCID: PMC10575775 DOI: 10.1038/s41380-023-01959-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 12/30/2022] [Accepted: 01/11/2023] [Indexed: 02/15/2023]
Abstract
MYT1L is an autism spectrum disorder (ASD)-associated transcription factor that is expressed in virtually all neurons throughout life. How MYT1L mutations cause neurological phenotypes and whether they can be targeted remains enigmatic. Here, we examine the effects of MYT1L deficiency in human neurons and mice. Mutant mice exhibit neurodevelopmental delays with thinner cortices, behavioural phenotypes, and gene expression changes that resemble those of ASD patients. MYT1L target genes, including WNT and NOTCH, are activated upon MYT1L depletion and their chemical inhibition can rescue delayed neurogenesis in vitro. MYT1L deficiency also causes upregulation of the main cardiac sodium channel, SCN5A, and neuronal hyperactivity, which could be restored by shRNA-mediated knockdown of SCN5A or MYT1L overexpression in postmitotic neurons. Acute application of the sodium channel blocker, lamotrigine, also rescued electrophysiological defects in vitro and behaviour phenotypes in vivo. Hence, MYT1L mutation causes both developmental and postmitotic neurological defects. However, acute intervention can normalise resulting electrophysiological and behavioural phenotypes in adulthood.
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Affiliation(s)
- Bettina Weigel
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Jana F Tegethoff
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Sarah D Grieder
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Bryce Lim
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Bhuvaneswari Nagarajan
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Yu-Chao Liu
- Department of Clinical Neurobiology, University Hospital Heidelberg and DKFZ, Heidelberg, Germany
| | - Jule Truberg
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Dimitris Papageorgiou
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120, Heidelberg, Germany
| | - Juan M Adrian-Segarra
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Laura K Schmidt
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Janina Kaspar
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Eric Poisel
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Elisa Heinzelmann
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Manu Saraswat
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Marleen Christ
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Christian Arnold
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69115, Heidelberg, Germany
| | - Ignacio L Ibarra
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69115, Heidelberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Joaquin Campos
- Chica and Heinz Schaller Research Group, Institute for Anatomy and Cell Biology, Heidelberg University, 69120, Heidelberg, Germany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Medical Faculty, Heidelberg University, 69120, Heidelberg, Germany
| | - Hannah Monyer
- Department of Clinical Neurobiology, University Hospital Heidelberg and DKFZ, Heidelberg, Germany
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69115, Heidelberg, Germany
| | - Claudio Acuna
- Chica and Heinz Schaller Research Group, Institute for Anatomy and Cell Biology, Heidelberg University, 69120, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany.
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany.
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany.
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4
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More RP, Warrier V, Brunel H, Buckingham C, Smith P, Allison C, Holt R, Bradshaw CR, Baron-Cohen S. Identifying rare genetic variants in 21 highly multiplex autism families: the role of diagnosis and autistic traits. Mol Psychiatry 2023; 28:2148-2157. [PMID: 36702863 PMCID: PMC10575770 DOI: 10.1038/s41380-022-01938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/27/2023]
Abstract
Autism is a highly heritable, heterogeneous, neurodevelopmental condition. Large-scale genetic studies, predominantly focussing on simplex families and clinical diagnoses of autism have identified hundreds of genes associated with autism. Yet, the contribution of these classes of genes to multiplex families and autistic traits still warrants investigation. Here, we conducted whole-genome sequencing of 21 highly multiplex autism families, with at least three autistic individuals in each family, to prioritise genes associated with autism. Using a combination of both autistic traits and clinical diagnosis of autism, we identify rare variants in genes associated with autism, and related neurodevelopmental conditions in multiple families. We identify a modest excess of these variants in autistic individuals compared to individuals without an autism diagnosis. Finally, we identify a convergence of the genes identified in molecular pathways related to development and neurogenesis. In sum, our analysis provides initial evidence to demonstrate the value of integrating autism diagnosis and autistic traits to prioritise genes.
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Affiliation(s)
- Ravi Prabhakar More
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom.
| | - Varun Warrier
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Helena Brunel
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Clara Buckingham
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Paula Smith
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Carrie Allison
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Rosemary Holt
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | | | - Simon Baron-Cohen
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom.
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Gracie L, Rostami‐Hochaghan D, Taweel B, Mirza N. The Seizure-Associated Genes Across Species (SAGAS) database offers insights into epilepsy genes, pathways and treatments. Epilepsia 2022; 63:2403-2412. [PMID: 35767389 PMCID: PMC9796383 DOI: 10.1111/epi.17352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/28/2022] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Decades of genetic studies on people with many different epilepsies, and on many nonhuman species, using many different technologies, have generated a huge body of literature about the genes associated with seizures/epilepsy. Collating these data can help uncover epilepsy genes, pathways, and treatments that would otherwise be overlooked. We aimed to collate and structure these data into a database, and use the database to identify novel epilepsy genes and pathways, and to prioritize promising treatments. METHODS We collated all the genes associated with all types of seizures/epilepsy in all species, and quantified the supporting evidence for each gene, by manually screening ~10 000 publications, and by extracting data from existing databases. RESULTS The largest published dataset of epilepsy genes includes only 977 genes, whereas our database (www.sagas.ac) includes 2876 genes, which demonstrates that the number of genes that can potentially contribute to seizures/epilepsy is much higher than previously envisaged. We use our database to identify 12 hitherto unreported polygenic epilepsy genes, 479 high-confidence monogenic epilepsy genes, and 394 more biological pathways than identified using the previously largest epilepsy gene dataset. We use a unique feature of Seizure-Associated Genes Across Species-the number of citations for each gene-to demonstrate that a drug is more likely to affect seizures if there is more evidence that the genes it affects are associated with seizures, and we use these data to identify promising candidate antiseizure drugs. SIGNIFICANCE This database offers insights into the causes of epilepsy and its treatments, and can accelerate future epilepsy research.
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Affiliation(s)
- Lara Gracie
- Birmingham Medical SchoolUniversity of BirminghamBirminghamUK
| | | | - Basel Taweel
- Department of Pharmacology & Therapeutics, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Nasir Mirza
- Department of Pharmacology & Therapeutics, Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLiverpoolUK
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6
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Duan R, Li HM, Hu WB, Hong CG, Chen ML, Cao J, Wang ZX, Chen CY, Yin F, Hu ZH, Li JD, Xie H, Liu ZZ. Recurrent de novo single point variant on the gene encoding Na +/K + pump results in epilepsy. Prog Neurobiol 2022; 216:102310. [PMID: 35724808 DOI: 10.1016/j.pneurobio.2022.102310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 04/28/2022] [Accepted: 06/15/2022] [Indexed: 10/18/2022]
Abstract
The etiology of epilepsy remains undefined in two-thirds of patients. Here, we identified a de novo variant of ATP1A2 (c.2426 T > G, p.Leu809Arg), which encodes the α2 subunit of Na+/K+-ATPase, from a family with idiopathic epilepsy. This variant caused epilepsy with hemiplegic migraine in the study patients. We generated the point variant mouse model Atp1a2L809R, which recapitulated the epilepsy observed in the study patients. In Atp1a2L809R/WT mice, convulsions were observed and cognitive and memory function was impaired. This variant affected the potassium binding function of the protein, disabling its ion transport ability, thereby increasing the frequency of nerve impulses. Valproate (VPA) and Carbamazepine (CBZ) have limited therapeutic efficacy in ameliorating the epileptic syndromes of Atp1a2L809R/WT mice. Our work revealed that ATP1A2L809R variants cause a predisposition to epilepsy. Moreover, we provide a point variant mouse model for epilepsy research and drug screening.
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Affiliation(s)
- Ran Duan
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Hong-Ming Li
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Wen-Bao Hu
- Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Chun-Gu Hong
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Meng-Lu Chen
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jia Cao
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhen-Xing Wang
- Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Chun-Yuan Chen
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Fei Yin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Zhong-Hua Hu
- Institute of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jia-Da Li
- State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Hui Xie
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Hunan Key Laboratory of Organ Injury, Aging and Regenerative Medicine, Changsha, Hunan 410008, China; Hunan Key Laboratory of Bone Joint Degeneration and Injury, Changsha, Hunan 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan 410008, China.
| | - Zheng-Zhao Liu
- Department of Sports Medicine, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Movement System Injury and Repair Research Center, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China; Hunan Key Laboratory of Organ Injury, Aging and Regenerative Medicine, Changsha, Hunan 410008, China.
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CfDNA Measurement as a Diagnostic Tool for the Detection of Brain Somatic Mutations in Refractory Epilepsy. Int J Mol Sci 2022; 23:ijms23094879. [PMID: 35563270 PMCID: PMC9102996 DOI: 10.3390/ijms23094879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/21/2022] [Accepted: 04/26/2022] [Indexed: 02/04/2023] Open
Abstract
Epilepsy is a neurological disorder that affects more than 50 million people. Its etiology is unknown in approximately 60% of cases, although the existence of a genetic factor is estimated in about 75% of these individuals. Hundreds of genes involved in epilepsy are known, and their number is increasing progressively, especially with next-generation sequencing techniques. However, there are still many cases in which the results of these molecular studies do not fully explain the phenotype of the patients. Somatic mutations specific to brain tissue could contribute to the phenotypic spectrum of epilepsy. Undetectable in the genomic DNA of blood cells, these alterations can be identified in cell-free DNA (cfDNA). We aim to review the current literature regarding the detection of somatic variants in cfDNA to diagnose refractory epilepsy, highlighting novel research directions and suggesting further studies.
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Distinct Epileptogenic Mechanisms Associated with Seizures in Wolf-Hirschhorn Syndrome. Mol Neurobiol 2022; 59:3159-3169. [DOI: 10.1007/s12035-022-02792-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 03/04/2022] [Indexed: 11/25/2022]
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9
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Deficiency of autism risk factor ASH1L in prefrontal cortex induces epigenetic aberrations and seizures. Nat Commun 2021; 12:6589. [PMID: 34782621 PMCID: PMC8593046 DOI: 10.1038/s41467-021-26972-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/29/2021] [Indexed: 12/30/2022] Open
Abstract
ASH1L, a histone methyltransferase, is identified as a top-ranking risk factor for autism spectrum disorder (ASD), however, little is known about the biological mechanisms underlying the link of ASH1L haploinsufficiency to ASD. Here we show that ASH1L expression and H3K4me3 level are significantly decreased in the prefrontal cortex (PFC) of postmortem tissues from ASD patients. Knockdown of Ash1L in PFC of juvenile mice induces the downregulation of risk genes associated with ASD, intellectual disability (ID) and epilepsy. These downregulated genes are enriched in excitatory and inhibitory synaptic function and have decreased H3K4me3 occupancy at their promoters. Furthermore, Ash1L deficiency in PFC causes the diminished GABAergic inhibition, enhanced glutamatergic transmission, and elevated PFC pyramidal neuronal excitability, which is associated with severe seizures and early mortality. Chemogenetic inhibition of PFC pyramidal neuronal activity, combined with the administration of GABA enhancer diazepam, rescues PFC synaptic imbalance and seizures, but not autistic social deficits or anxiety-like behaviors. These results have revealed the critical role of ASH1L in regulating synaptic gene expression and seizures, which provides insights into treatment strategies for ASH1L-associated brain diseases.
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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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Toriumi K, Berto S, Koike S, Usui N, Dan T, Suzuki K, Miyashita M, Horiuchi Y, Yoshikawa A, Asakura M, Nagahama K, Lin HC, Sugaya Y, Watanabe T, Kano M, Ogasawara Y, Miyata T, Itokawa M, Konopka G, Arai M. Combined glyoxalase 1 dysfunction and vitamin B6 deficiency in a schizophrenia model system causes mitochondrial dysfunction in the prefrontal cortex. Redox Biol 2021; 45:102057. [PMID: 34198071 PMCID: PMC8253914 DOI: 10.1016/j.redox.2021.102057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Methylglyoxal (MG) is a reactive and cytotoxic α-dicarbonyl byproduct of glycolysis. Our bodies have several bio-defense systems to detoxify MG, including an enzymatic system by glyoxalase (GLO) 1 and GLO2. We identified a subtype of schizophrenia patients with novel mutations in the GLO1 gene that results in reductions of enzymatic activity. Moreover, we found that vitamin B6 (VB6) levels in peripheral blood of the schizophrenia patients with GLO1 dysfunction are significantly lower than that of healthy controls. However, the effects of GLO1 dysfunction and VB6 deficiency on the pathophysiology of schizophrenia remains poorly understood. Here, we generated a novel mouse model for this subgroup of schizophrenia patients by feeding Glo1 knockout mice VB6-deficent diets (KO/VB6(−)) and evaluated the combined effects of GLO1 dysfunction and VB6 deficiency on brain function. KO/VB6(−) mice accumulated homocysteine in plasma and MG in the prefrontal cortex (PFC), hippocampus, and striatum, and displayed behavioral deficits, such as impairments of social interaction and cognitive memory and a sensorimotor deficit in the prepulse inhibition test. Furthermore, we found aberrant gene expression related to mitochondria function in the PFC of the KO/VB6(−) mice by RNA-sequencing and weighted gene co-expression network analysis (WGCNA). Finally, we demonstrated abnormal mitochondrial respiratory function and subsequently enhanced oxidative stress in the PFC of KO/VB6(−) mice in the PFC. These findings suggest that the combination of GLO1 dysfunction and VB6 deficiency may cause the observed behavioral deficits via mitochondrial dysfunction and oxidative stress in the PFC. A combination of Glo1 KO and VB6 deficiency induces MG accumulation in the brain. Glo1 KO/VB6(−) mice exhibit schizophrenia-like behavioral deficits. Gene expression related to mitochondria is impaired in the PFC of the Glo1 KO/VB6(−). Mitochondria in the PFC of the Glo1 KO/VB6(−) mice show respiratory dysfunction. Oxidative stress is enhanced in the PFC of the Glo1 KO/VB6(−).
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Affiliation(s)
- Kazuya Toriumi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Stefano Berto
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA; Department of Neuroscience, Medical University of South Carolina, Charleston, SC 29403, USA
| | - Shin Koike
- Department of Analytical Biochemistry, Meiji Pharmaceutical University, Tokyo 204-8588, Japan
| | - Noriyoshi Usui
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA; Center for Medical Research and Education, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan; Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan; Global Center for Medical Engineering and Informatics, Osaka University, Osaka, 565-0871, Japan
| | - Takashi Dan
- Division of Molecular Medicine and Therapy, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Kazuhiro Suzuki
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan; Department of Psychiatry, Graduate School of Medicine, Shinshu University, Nagano, 390-8621, Japan
| | - Mitsuhiro Miyashita
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Yasue Horiuchi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Akane Yoshikawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan; Department of Psychiatry and Behavioral Science, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan
| | - Mai Asakura
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Kenichiro Nagahama
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hsiao-Chun Lin
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuki Sugaya
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takaki Watanabe
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuki Ogasawara
- Department of Analytical Biochemistry, Meiji Pharmaceutical University, Tokyo 204-8588, Japan
| | - Toshio Miyata
- Division of Molecular Medicine and Therapy, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Masanari Itokawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Makoto Arai
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan.
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12
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Lo AC, Rajan N, Gastaldo D, Telley L, Hilal ML, Buzzi A, Simonato M, Achsel T, Bagni C. Absence of RNA-binding protein FXR2P prevents prolonged phase of kainate-induced seizures. EMBO Rep 2021; 22:e51404. [PMID: 33779029 PMCID: PMC8024897 DOI: 10.15252/embr.202051404] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/26/2022] Open
Abstract
Status epilepticus (SE) is a condition in which seizures are not self-terminating and thereby pose a serious threat to the patient's life. The molecular mechanisms underlying SE are likely heterogeneous and not well understood. Here, we reveal a role for the RNA-binding protein Fragile X-Related Protein 2 (FXR2P) in SE. Fxr2 KO mice display reduced sensitivity specifically to kainic acid-induced SE. Immunoprecipitation of FXR2P coupled to next-generation sequencing of associated mRNAs shows that FXR2P targets are enriched in genes that encode glutamatergic post-synaptic components. Of note, the FXR2P target transcriptome has a significant overlap with epilepsy and SE risk genes. In addition, Fxr2 KO mice fail to show sustained ERK1/2 phosphorylation induced by KA and present reduced burst activity in the hippocampus. Taken together, our findings show that the absence of FXR2P decreases the expression of glutamatergic proteins, and this decrease might prevent self-sustained seizures.
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Affiliation(s)
- Adrian C Lo
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Nicholas Rajan
- Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium
| | - Denise Gastaldo
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Ludovic Telley
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Muna L Hilal
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Andrea Buzzi
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
| | - Michele Simonato
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy.,Division of Neuroscience, IRCCS San Raffaele Hospital, Milan, Italy
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,Department of Neurosciences and Leuven Brain Institute, KU Leuven, Leuven, Belgium.,Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
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13
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Luo FM, Deng MX, Yu R, Liu L, Fan LL. Case Report: Chorea-Acanthocytosis Presents as Epilepsy in a Consanguineous Family With a Nonsense Mutation of in VPS13A. Front Neurosci 2021; 15:604715. [PMID: 33679298 PMCID: PMC7928333 DOI: 10.3389/fnins.2021.604715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/21/2021] [Indexed: 12/20/2022] Open
Abstract
Chorea-Acanthocytosis (ChAc), a rare autosomal recessive inherited neurological disorder, originated from variants in Vacuolar Protein Sorting 13 homolog A (VPS13A) gene. The main symptoms of ChAc contain hyperkinetic movements, seizures, cognitive impairment, neuropsychiatric symptoms, elevated serum biochemical indicators, and acanthocytes detection in peripheral blood smear. Recently, researchers found that epilepsy may be a presenting and prominent symptom of ChAc. Here, we enrolled a consanguineous family with epilepsy and non-coordinated movement. Whole exome sequencing was employed to explore the genetic lesion of the family. After data filtering, co-separation analysis was performed by Sanger sequencing and bioinformatics analysis, the homozygous nonsense variant (NM_033305.2: c.8282C>G, p.S2761X) of VPS13A were identified which could be genetic factor of the patient. No other meaningful mutations were detected. This mutation (p.S2761X) led to a truncated protein in exon 60 of the VPS13A gene, was simultaneously absent in our 200 local control participants. The homozygous mutation (NM_033305.2: c.8282C>G, p.S2761X) of VPS13A may be the first time be identified in ChAc patient with epilepsy. Our study assisted to the diagnosis of ChAc in this patient and contributed to the genetic diagnosis and counseling of families with ChAc presented as epilepsy. Moreover, we further indicated that epilepsy was a crucial phenotype in ChAc patients caused by VPS13A mutations.
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Affiliation(s)
- Fang-Mei Luo
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second XiangYa Hospital of Central South University, Changsha, China.,Department of Cell Biology, The School of Life Sciences, Central South University, Changsha, China
| | - Ming-Xing Deng
- Department of Dermatology, Loudi Central Hospital, Loudi, China
| | - Rong Yu
- Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Lv Liu
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second XiangYa Hospital of Central South University, Changsha, China
| | - Liang-Liang Fan
- Department of Respiratory Medicine, Diagnosis and Treatment Center of Respiratory Disease, The Second XiangYa Hospital of Central South University, Changsha, China.,Department of Cell Biology, The School of Life Sciences, Central South University, Changsha, China.,Hunan Key Laboratory of Animal Models for Human Diseases, Changsha, China
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14
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Savitsky M, Solis GP, Kryuchkov M, Katanaev VL. Humanization of Drosophila Gαo to Model GNAO1 Paediatric Encephalopathies. Biomedicines 2020; 8:E395. [PMID: 33036271 PMCID: PMC7599900 DOI: 10.3390/biomedicines8100395] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 12/15/2022] Open
Abstract
Several hundred genes have been identified to contribute to epilepsy-the disease affecting 65 million people worldwide. One of these genes is GNAO1 encoding Gαo, the major neuronal α-subunit of heterotrimeric G proteins. An avalanche of dominant de novo mutations in GNAO1 have been recently described in paediatric epileptic patients, suffering, in addition to epilepsy, from motor dysfunction and developmental delay. Although occurring in amino acids conserved from humans to Drosophila, these mutations and their functional consequences have only been poorly analysed at the biochemical or neuronal levels. Adequate animal models to study the molecular aetiology of GNAO1 encephalopathies have also so far been lacking. As the first step towards modeling the disease in Drosophila, we here describe the humanization of the Gαo locus in the fruit fly. A two-step CRISPR/Cas9-mediated replacement was conducted, first substituting the coding exons 2-3 of Gαo with respective human GNAO1 sequences. At the next step, the remaining exons 4-7 were similarly replaced, keeping intact the gene Cyp49a1 embedded in between, as well as the non-coding exons, exon 1 and the surrounding regulatory sequences. The resulting flies, homozygous for the humanized GNAO1 loci, are viable and fertile without any visible phenotypes; their body weight, locomotion, and longevity are also normal. Human Gαo-specific antibodies confirm the endogenous-level expression of the humanized Gαo, which fully replaces the Drosophila functions. The genetic model we established will make it easy to incorporate encephalopathic GNAO1 mutations and will permit intensive investigations into the molecular aetiology of the human disease through the powerful toolkit of Drosophila genetics.
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Affiliation(s)
- Mikhail Savitsky
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; (M.S.); (G.P.S.); (M.K.)
| | - Gonzalo P. Solis
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; (M.S.); (G.P.S.); (M.K.)
| | - Mikhail Kryuchkov
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; (M.S.); (G.P.S.); (M.K.)
| | - Vladimir L. Katanaev
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; (M.S.); (G.P.S.); (M.K.)
- School of Biomedicine, Far Eastern Federal University, 690690 Vladivostok, Russia
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15
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Schieweck R, Ninkovic J, Kiebler MA. RNA-binding proteins balance brain function in health and disease. Physiol Rev 2020; 101:1309-1370. [PMID: 33000986 DOI: 10.1152/physrev.00047.2019] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Posttranscriptional gene expression including splicing, RNA transport, translation, and RNA decay provides an important regulatory layer in many if not all molecular pathways. Research in the last decades has positioned RNA-binding proteins (RBPs) right in the center of posttranscriptional gene regulation. Here, we propose interdependent networks of RBPs to regulate complex pathways within the central nervous system (CNS). These are involved in multiple aspects of neuronal development and functioning, including higher cognition. Therefore, it is not sufficient to unravel the individual contribution of a single RBP and its consequences but rather to study and understand the tight interplay between different RBPs. In this review, we summarize recent findings in the field of RBP biology and discuss the complex interplay between different RBPs. Second, we emphasize the underlying dynamics within an RBP network and how this might regulate key processes such as neurogenesis, synaptic transmission, and synaptic plasticity. Importantly, we envision that dysfunction of specific RBPs could lead to perturbation within the RBP network. This would have direct and indirect (compensatory) effects in mRNA binding and translational control leading to global changes in cellular expression programs in general and in synaptic plasticity in particular. Therefore, we focus on RBP dysfunction and how this might cause neuropsychiatric and neurodegenerative disorders. Based on recent findings, we propose that alterations in the entire regulatory RBP network might account for phenotypic dysfunctions observed in complex diseases including neurodegeneration, epilepsy, and autism spectrum disorders.
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Affiliation(s)
- Rico Schieweck
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Jovica Ninkovic
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Michael A Kiebler
- Biomedical Center (BMC), Department for Cell Biology and Anatomy, Medical Faculty, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
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16
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Suresh NT, E R V, U K. Multi-scale top-down approach for modelling epileptic protein-protein interaction network analysis to identify driver nodes and pathways. Comput Biol Chem 2020; 88:107323. [PMID: 32653778 DOI: 10.1016/j.compbiolchem.2020.107323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/04/2020] [Accepted: 06/23/2020] [Indexed: 12/23/2022]
Abstract
Protein - Protein Interaction Network (PPIN) analysis unveils molecular level mechanisms involved in disease condition. To explore the complex regulatory mechanisms behind epilepsy and to address the clinical and biological issues of epilepsy, in silico techniques are feasible in a cost- effective manner. In this work, a hierarchical procedure to identify influential genes and regulatory pathways in epilepsy prognosis is proposed. To obtain key genes and pathways causing epilepsy, integration of two benchmarked datasets which are exclusively devoted for complex disorders is done as an initial step. Using STRING database, PPIN is constructed for modelling protein-protein interactions. Further, key interactions are obtained from the established PPIN using network centrality measures followed by network propagation algorithm -Random Walk with Restart (RWR). The outcome of the method reveals some influential genes behind epilepsy prognosis, along with their associated pathways like PI3 kinase, VEGF signaling, Ras, Wnt signaling etc. In comparison with similar works, our results have shown improvement in identifying unique molecular functions, biological processes, gene co-occurrences etc. Also, CORUM provides an annotation for approximately 60% of similarity in human protein complexes with the obtained result. We believe that the formulated strategy can put-up the vast consideration of indigenous drugs towards meticulous identification of genes encoded by protein against several combinatorial disorders.
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Affiliation(s)
- Nikhila T Suresh
- Department of Computer Science and IT, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Kochi Campus, India
| | - Vimina E R
- Department of Computer Science and IT, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Kochi Campus, India.
| | - Krishnakumar U
- Department of Computer Science and IT, Amrita School of Arts and Sciences, Amrita Vishwa Vidyapeetham, Kochi Campus, India
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17
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Jaworski T. Control of neuronal excitability by GSK-3beta: Epilepsy and beyond. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118745. [PMID: 32450268 DOI: 10.1016/j.bbamcr.2020.118745] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/07/2020] [Accepted: 05/09/2020] [Indexed: 12/22/2022]
Abstract
Glycogen synthase kinase 3beta (GSK-3β) is an enzyme with a variety of cellular functions in addition to the regulation of glycogen metabolism. In the central nervous system, different intracellular signaling pathways converge on GSK-3β through a cascade of phosphorylation events that ultimately control a broad range of neuronal functions in the development and adulthood. In mice, genetically removing or increasing GSK-3β cause distinct functional and structural neuronal phenotypes and consequently affect cognition. Precise control of GSK-3β activity is important for such processes as neuronal migration, development of neuronal morphology, synaptic plasticity, excitability, and gene expression. Altered GSK-3β activity contributes to aberrant plasticity within neuronal circuits leading to neurological, psychiatric disorders, and neurodegenerative diseases. Therapeutically targeting GSK-3β can restore the aberrant plasticity of neuronal networks at least in animal models of these diseases. Although the complete repertoire of GSK-3β neuronal substrates has not been defined, emerging evidence shows that different ion channels and their accessory proteins controlling excitability, neurotransmitter release, and synaptic transmission are regulated by GSK-3β, thereby supporting mechanisms of synaptic plasticity in cognition. Dysregulation of ion channel function by defective GSK-3β activity sustains abnormal excitability in the development of epilepsy and other GSK-3β-linked human diseases.
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Affiliation(s)
- Tomasz Jaworski
- Laboratory of Animal Models, Nencki Institute of Experimental Biology, Warsaw, Poland.
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18
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Li X, Shi L, Wang Y, Zhong J, Zhao X, Teng H, Shi X, Yang H, Ruan S, Li M, Sun ZS, Zhan Q, Mao F. OncoBase: a platform for decoding regulatory somatic mutations in human cancers. Nucleic Acids Res 2020; 47:D1044-D1055. [PMID: 30445567 PMCID: PMC6323961 DOI: 10.1093/nar/gky1139] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/11/2018] [Indexed: 12/16/2022] Open
Abstract
Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers, and the vast majority of them are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput sequencing technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements were determined using three-dimensional (3D) chromatin looping. Herein, we present OncoBase (http://www.oncobase.biols.ac.cn/), an integrated database for annotating 81 385 242 somatic mutations in 68 cancer types from more than 120 cancer projects by exploring their roles in distal interactions between target genes and regulatory elements. OncoBase integrates local chromatin signatures, 3D chromatin interactions in different cell types and reconstruction of enhancer-target networks using state-of-the-art algorithms. It employs informative visualization tools to display the integrated local and 3D chromatin signatures and effects of somatic mutations on regulatory elements. Enhancer-promoter interactions estimated from chromatin interactions are integrated into a network diffusion system that quantitatively prioritizes somatic mutations and target genes from a large pool. Thus, OncoBase is a useful resource for the functional annotation of regulatory noncoding regions and systematically benchmarking the regulatory effects of embedded noncoding somatic mutations in human carcinogenesis.
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Affiliation(s)
- Xianfeng Li
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Leisheng Shi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jianing Zhong
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000,China
| | - Xiaolu Zhao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaohui Shi
- Sino-Danish college, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haonan Yang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shasha Ruan
- Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei 430072, China
| | - MingKun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Qimin Zhan
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
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19
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Dunn PJ, Maher BH, Albury CL, Stuart S, Sutherland HG, Maksemous N, Benton MC, Smith RA, Haupt LM, Griffiths LR. Tiered analysis of whole-exome sequencing for epilepsy diagnosis. Mol Genet Genomics 2020; 295:751-763. [DOI: 10.1007/s00438-020-01657-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 02/19/2020] [Indexed: 12/11/2022]
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20
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Chen YJ, Chen CY, Mai TL, Chuang CF, Chen YC, Gupta SK, Yen L, Wang YD, Chuang TJ. Genome-wide, integrative analysis of circular RNA dysregulation and the corresponding circular RNA-microRNA-mRNA regulatory axes in autism. Genome Res 2020; 30:375-391. [PMID: 32127416 PMCID: PMC7111521 DOI: 10.1101/gr.255463.119] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs), a class of long noncoding RNAs, are known to be enriched in mammalian neural tissues. Although a wide range of dysregulation of gene expression in autism spectrum disorder (ASD) have been reported, the role of circRNAs in ASD remains largely unknown. Here, we performed genome-wide circRNA expression profiling in postmortem brains from individuals with ASD and controls and identified 60 circRNAs and three coregulated modules that were perturbed in ASD. By integrating circRNA, microRNA, and mRNA dysregulation data derived from the same cortex samples, we identified 8170 ASD-associated circRNA-microRNA-mRNA interactions. Putative targets of the axes were enriched for ASD risk genes and genes encoding inhibitory postsynaptic density (PSD) proteins, but not for genes implicated in monogenetic forms of other brain disorders or genes encoding excitatory PSD proteins. This reflects the previous observation that ASD-derived organoids show overproduction of inhibitory neurons. We further confirmed that some ASD risk genes (NLGN1, STAG1, HSD11B1, VIP, and UBA6) were regulated by an up-regulated circRNA (circARID1A) via sponging a down-regulated microRNA (miR-204-3p) in human neuronal cells. Particularly, alteration of NLGN1 expression is known to affect the dynamic processes of memory consolidation and strengthening. To the best of our knowledge, this is the first systems-level view of circRNA regulatory networks in ASD cortex samples. We provided a rich set of ASD-associated circRNA candidates and the corresponding circRNA-microRNA-mRNA axes, particularly those involving ASD risk genes. Our findings thus support a role for circRNA dysregulation and the corresponding circRNA-microRNA-mRNA axes in ASD pathophysiology.
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Affiliation(s)
- Yen-Ju Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Te-Lun Mai
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chih-Fan Chuang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Chen Chen
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Sachin Kumar Gupta
- Department of Pathology and Immunology.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Laising Yen
- Department of Pathology and Immunology.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yi-Da Wang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Trees-Juen Chuang
- Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
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21
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Qi M, Fan S, Wang Z, Yang X, Xie Z, Chen K, Zhang L, Lin T, Liu W, Lin X, Yan Y, Yang Y, Zhao H. Identifying Common Genes, Cell Types and Brain Regions Between Diseases of the Nervous System. Front Genet 2019; 10:1202. [PMID: 31850066 PMCID: PMC6895906 DOI: 10.3389/fgene.2019.01202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 10/30/2019] [Indexed: 12/12/2022] Open
Abstract
Background: Diseases of the nervous system are widely considered to be caused by genetic mutations, and they have been shown to share pathogenic genes. Discovering the shared mechanisms of these diseases is useful for designing common treatments. Method: In this study, by reviewing 518 articles published after 2007 on 20 diseases of the nervous system, we compiled data on 1607 mutations occurring in 365 genes, totals that are 1.9 and 3.2 times larger than those collected in the Clinvar database, respectively. A combination with the Clinvar data gives 2434 pathogenic mutations and 424 genes. Using this information, we measured the genetic similarities between the diseases according to the number of genes causing two diseases simultaneously. Further detection was carried out on the similarity between diseases in terms of cell types. Disease-related cell types were defined as those with disease-related gene enrichment among the marker genes of cells, as ascertained by analyzing single-cell sequencing data. Enrichment profiles of the disease-related genes over 25 cell types were constructed. The disease similarity in terms of cell types was obtained by calculating the distances between the enrichment profiles of these genes. The same strategy was applied to measure the disease similarity in terms of brain regions by analyzing the gene expression data from 10 brain regions. Results: The disease similarity was first measured in terms of genes. The result indicated that the proportions of overlapped genes between diseases were significantly correlated to the DMN scores (phenotypic similarity), with a Pearson correlation coefficient of 0.40 and P-value = 6.0×10-3. The disease similarity analysis for cell types identified that the distances between enrichment profiles of the disease-related genes were negatively correlated to the DMN scores, with Spearman correlation coefficient = -0.26 (P-value = 1.5 × 10-2). However, the brain region enrichment profile distances of the disease-related genes were not significantly correlated with the DMN score. Besides the similarity of diseases, this study identified novel relationships between diseases and cell types. Conclusion: We manually constructed the most comprehensive dataset to date for genes with mutations related to 20 nervous system diseases. By using this dataset, the similarities between diseases in terms of genes and cell types were found to be significantly correlated to their phenotypic similarity. However, the disease similarities in terms of brain regions were not significantly correlated with the phenotypic similarities. Thus, the phenotypic similarity between the diseases is more likely to be caused by dysfunctions of the same genes or the same types of neurons rather than the same brain regions. The data are collected into the database NeurodisM, which is available at http://biomed-ai.org/neurodism.
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Affiliation(s)
- Mengling Qi
- Sun Yat-sen Memorial Hospital, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Shichao Fan
- Sun Yat-sen Memorial Hospital, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Zhi Wang
- Sun Yat-sen Memorial Hospital, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
| | - Xiaoxing Yang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Zicong Xie
- Software Institute, Nanjing University, Nanjing, China
| | - Ken Chen
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Lei Zhang
- Department of Hepatobiliary Surgery II, Zhujiang Hospital of Southern Medical University, Guangzhou, China
| | - Tao Lin
- Zhongshan Medical College, Sun Yat-sen University, Guangzhou, China
| | - Wei Liu
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xinlei Lin
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yan Yan
- School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China
| | - Huiying Zhao
- Sun Yat-sen Memorial Hospital, Guangzhou, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangzhou, China
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22
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Stephanou C, Tamana S, Minaidou A, Papasavva P, Kleanthous M, Kountouris P. Genetic Modifiers at the Crossroads of Personalised Medicine for Haemoglobinopathies. J Clin Med 2019; 8:jcm8111927. [PMID: 31717530 PMCID: PMC6912721 DOI: 10.3390/jcm8111927] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/25/2019] [Accepted: 11/05/2019] [Indexed: 12/20/2022] Open
Abstract
Haemoglobinopathies are common monogenic disorders with diverse clinical manifestations, partly attributed to the influence of modifier genes. Recent years have seen enormous growth in the amount of genetic data, instigating the need for ranking methods to identify candidate genes with strong modifying effects. Here, we present the first evidence-based gene ranking metric (IthaScore) for haemoglobinopathy-specific phenotypes by utilising curated data in the IthaGenes database. IthaScore successfully reflects current knowledge for well-established disease modifiers, while it can be dynamically updated with emerging evidence. Protein–protein interaction (PPI) network analysis and functional enrichment analysis were employed to identify new potential disease modifiers and to evaluate the biological profiles of selected phenotypes. The most relevant gene ontology (GO) and pathway gene annotations for (a) haemoglobin (Hb) F levels/Hb F response to hydroxyurea included urea cycle, arginine metabolism and vascular endothelial growth factor receptor (VEGFR) signalling, (b) response to iron chelators included xenobiotic metabolism and glucuronidation, and (c) stroke included cytokine signalling and inflammatory reactions. Our findings demonstrate the capacity of IthaGenes, together with dynamic gene ranking, to expand knowledge on the genetic and molecular basis of phenotypic variation in haemoglobinopathies and to identify additional candidate genes to potentially inform and improve diagnosis, prognosis and therapeutic management.
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Affiliation(s)
| | | | | | | | - Marina Kleanthous
- Correspondence: (M.K.); (P.K.); Tel.:+357-2239-2652 (M.K.); +357-2239-2623 (P.K.)
| | - Petros Kountouris
- Correspondence: (M.K.); (P.K.); Tel.:+357-2239-2652 (M.K.); +357-2239-2623 (P.K.)
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23
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A comparative study of the genetic components of three subcategories of autism spectrum disorder. Mol Psychiatry 2019; 24:1720-1731. [PMID: 29875476 DOI: 10.1038/s41380-018-0081-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 02/07/2018] [Accepted: 04/03/2018] [Indexed: 12/14/2022]
Abstract
The fifth edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) controversially combined previously distinct subcategories of autism spectrum disorder (ASD) into a single diagnostic category. However, genetic convergences and divergences between different ASD subcategories are unclear. By retrieving 1725 exonic de novo mutations (DNMs) from 1628 subjects with autistic disorder (AD), 1873 from 1564 subjects with pervasive developmental disorder not otherwise specified (PDD-NOS), 276 from 247 subjects with Asperger's syndrome (AS), and 2077 from 2299 controls, we found that rates of putative functional DNMs (loss-of-function, predicted deleterious missense, and frameshift) in all three subcategories were significantly higher than those in control. We then investigated the convergences and divergences of the three ASD subcategories based on four genetic aspects: whether any two ASD subcategories (1) shared significantly more genes with functional DNMs, (2) exhibited similar spatio-temporal expression patterns, (3) shared significantly more candidate genes, and (4) shared some ASD-associated functional pathways. It is revealed that AD and PDD-NOS were broadly convergent in terms of all four genetic aspects, suggesting these two ASD subcategories may be genetically combined. AS was divergent to AD and PDD-NOS for aspects of functional DNMs and expression patterns, whereas AS and AD/PDD-NOS were convergent for aspects of candidate genes and functional pathways. Our results indicated that the three ASD subcategories present more genetic convergences than divergences, favouring DSM-5's new classification. This study suggests that specifically defined genotypes and their corresponding phenotypes should be integrated analyzed for precise diagnosis of complex disorders, such as ASD.
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24
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Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders. Genome Med 2019; 11:65. [PMID: 31653223 PMCID: PMC6815046 DOI: 10.1186/s13073-019-0678-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 10/15/2019] [Indexed: 12/22/2022] Open
Abstract
Background Neurodevelopmental disorders (NDDs) such as autism spectrum disorder, intellectual disability, developmental disability, and epilepsy are characterized by abnormal brain development that may affect cognition, learning, behavior, and motor skills. High co-occurrence (comorbidity) of NDDs indicates a shared, underlying biological mechanism. The genetic heterogeneity and overlap observed in NDDs make it difficult to identify the genetic causes of specific clinical symptoms, such as seizures. Methods We present a computational method, MAGI-S, to discover modules or groups of highly connected genes that together potentially perform a similar biological function. MAGI-S integrates protein-protein interaction and co-expression networks to form modules centered around the selection of a single “seed” gene, yielding modules consisting of genes that are highly co-expressed with the seed gene. We aim to dissect the epilepsy phenotype from a general NDD phenotype by providing MAGI-S with high confidence NDD seed genes with varying degrees of association with epilepsy, and we assess the enrichment of de novo mutation, NDD-associated genes, and relevant biological function of constructed modules. Results The newly identified modules account for the increased rate of de novo non-synonymous mutations in autism, intellectual disability, developmental disability, and epilepsy, and enrichment of copy number variations (CNVs) in developmental disability. We also observed that modules seeded with genes strongly associated with epilepsy tend to have a higher association with epilepsy phenotypes than modules seeded at other neurodevelopmental disorder genes. Modules seeded with genes strongly associated with epilepsy (e.g., SCN1A, GABRA1, and KCNB1) are significantly associated with synaptic transmission, long-term potentiation, and calcium signaling pathways. On the other hand, modules found with seed genes that are not associated or weakly associated with epilepsy are mostly involved with RNA regulation and chromatin remodeling. Conclusions In summary, our method identifies modules enriched with de novo non-synonymous mutations and can capture specific networks that underlie the epilepsy phenotype and display distinct enrichment in relevant biological processes. MAGI-S is available at https://github.com/jchow32/magi-s.
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25
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Goto A, Ishii A, Shibata M, Ihara Y, Cooper EC, Hirose S. Characteristics of
KCNQ
2
variants causing either benign neonatal epilepsy or developmental and epileptic encephalopathy. Epilepsia 2019; 60:1870-1880. [DOI: 10.1111/epi.16314] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/23/2019] [Accepted: 07/23/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Ayako Goto
- Department of Pediatrics School of Medicine Fukuoka University Fukuoka Japan
| | - Atsushi Ishii
- Department of Pediatrics School of Medicine Fukuoka University Fukuoka Japan
| | - Mami Shibata
- Central Research Institute for the Molecular Pathomechanisms of Epilepsy Fukuoka University Fukuoka Japan
| | - Yukiko Ihara
- Department of Pediatrics School of Medicine Fukuoka University Fukuoka Japan
| | - Edward C. Cooper
- Department of Neurology Baylor College of Medicine Houston Texas
| | - Shinichi Hirose
- Department of Pediatrics School of Medicine Fukuoka University Fukuoka Japan
- Central Research Institute for the Molecular Pathomechanisms of Epilepsy Fukuoka University Fukuoka Japan
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26
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Choudhary N, Singh V. Insights about multi-targeting and synergistic neuromodulators in Ayurvedic herbs against epilepsy: integrated computational studies on drug-target and protein-protein interaction networks. Sci Rep 2019; 9:10565. [PMID: 31332210 PMCID: PMC6646331 DOI: 10.1038/s41598-019-46715-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/03/2019] [Indexed: 12/24/2022] Open
Abstract
Epilepsy, that comprises a wide spectrum of neuronal disorders and accounts for about one percent of global disease burden affecting people of all age groups, is recognised as apasmara in the traditional medicinal system of Indian antiquity commonly known as Ayurveda. Towards exploring the molecular level complex regulatory mechanisms of 63 anti-epileptic Ayurvedic herbs and thoroughly examining the multi-targeting and synergistic potential of 349 drug-like phytochemicals (DPCs) found therein, in this study, we develop an integrated computational framework comprising of network pharmacology and molecular docking studies. Neuromodulatory prospects of anti-epileptic herbs are probed and, as a special case study, DPCs that can regulate metabotropic glutamate receptors (mGluRs) are inspected. A novel methodology to screen and systematically analyse the DPCs having similar neuromodulatory potential vis-à-vis DrugBank compounds (NeuMoDs) is developed and 11 NeuMoDs are reported. A repertoire of 74 DPCs having poly-pharmacological similarity with anti-epileptic DrugBank compounds and those under clinical trials is also reported. Further, high-confidence PPI-network specific to epileptic protein-targets is developed and the potential of DPCs to regulate its functional modules is investigated. We believe that the presented schema can open-up exhaustive explorations of indigenous herbs towards meticulous identification of clinically relevant DPCs against various diseases and disorders.
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Affiliation(s)
- Neha Choudhary
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala, 176206, India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, Dharamshala, 176206, India.
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27
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Wang Q, Liu Z, Lin Z, Zhang R, Lu Y, Su W, Li F, Xu X, Tu M, Lou Y, Zhao J, Zheng X. De Novo Germline Mutations in SEMA5A Associated With Infantile Spasms. Front Genet 2019; 10:605. [PMID: 31354784 PMCID: PMC6635550 DOI: 10.3389/fgene.2019.00605] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 06/07/2019] [Indexed: 11/13/2022] Open
Abstract
Infantile spasm (IS) is an early-onset epileptic encephalopathy that usually presents with hypsarrhythmia on an electroencephalogram with developmental impairment or regression. In this study, whole-exome sequencing was performed to detect potential pathogenic de novo mutations, and finally we identified a novel damaging de novo mutation in SEMA5A and a compound heterozygous mutation in CLTCL1 in three sporadic trios with IS. The expression profiling of SEMA5A in the human brain showed that it was mainly highly expressed in the cerebral cortex, during the early brain development stage (8 to 9 post-conception weeks and 0 to 5 months after birth). In addition, we identified a close protein-protein interaction network between SEMA5A and candidate genes associated with epilepsy, autism spectrum disorder (ASD) or intellectual disability. Gene enrichment and function analysis demonstrated that genes interacting with SEMA5A were significantly enriched in several brain regions across early fetal development, including the cortex, cerebellum, striatum and thalamus (q < 0.05), and were involved in axonal, neuronal and synapse-associated processes. Furthermore, SEMA5A and its interacting genes were associated with ASD, epilepsy syndrome and developmental disorders of mental health. Our results provide insightful information indicating that SEMA5A may contribute to the development of the brain and is associated with IS. However, further genetic studies are still needed to evaluate the role of SEMA5A in IS to definitively establish the role of SEMA5A in this disorder.
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Affiliation(s)
- Qiongdan Wang
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongdong Lin
- Department of Pediatric Neurology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Ru Zhang
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yutian Lu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Weijue Su
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Feng Li
- Department of Pediatric Neurology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xi Xu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Mengyun Tu
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yongliang Lou
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, Zhejiang, China
| | - Junzhao Zhao
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China
| | - Xiaoqun Zheng
- Department of Laboratory Medicine, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Key Laboratory of Laboratory Medicine, Ministry of Education, Wenzhou, Zhejiang, China
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28
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Functional Nutrients for Epilepsy. Nutrients 2019; 11:nu11061309. [PMID: 31185666 PMCID: PMC6628163 DOI: 10.3390/nu11061309] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 12/11/2022] Open
Abstract
Epilepsy is a common neurological disorder of which seizures are a core symptom. Approximately one third of epileptic patients are resistant to antiepileptic drugs and therefore require alternative therapeutic options. Dietary and nutritional supplements can in some cases replace drugs, but with the exception of ketogenic diets, there are no officially recommended dietary considerations for patients with epilepsy. In this review we summarize a selection of nutritional suggestions that have proved beneficial in treating different types of epilepsy. We describe the types of seizures and epilepsy and follow this with an introduction to basic molecular mechanisms. We then examine several functional nutrients for which there is clinical evidence of therapeutic efficacy in reducing seizures or epilepsy-associated sudden death. We also discuss experimental results that demonstrate possible molecular mechanisms elicited by the administration of various nutrients. The availability of multiple dietary and nutritional candidates that show favorable outcomes in animals implies that assessing the clinical potential of these substances will improve translational medicine, ultimately benefitting epilepsy patients.
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29
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Shao LR, Habela CW, Stafstrom CE. Pediatric Epilepsy Mechanisms: Expanding the Paradigm of Excitation/Inhibition Imbalance. CHILDREN-BASEL 2019; 6:children6020023. [PMID: 30764523 PMCID: PMC6406372 DOI: 10.3390/children6020023] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/31/2019] [Accepted: 01/31/2019] [Indexed: 02/07/2023]
Abstract
Mechanisms underlying seizures and epilepsy have traditionally been considered to involve abnormalities of ion channels or synaptic function. Those considerations gave rise to the excitation/inhibition (E/I) imbalance theory, whereby increased excitation, decreased inhibition, or both favor a hyperexcitable state and an increased propensity for seizure generation and epileptogenesis. Several recent findings warrant reconsideration and expansion of the E/I hypothesis: novel genetic mutations have been identified that do not overtly affect E/I balance; neurotransmitters may exert paradoxical effects, especially during development; anti-seizure medications do not necessarily work by decreasing excitation or increasing inhibition; and metabolic factors participate in the regulation of neuronal and network excitability. These novel conceptual and experimental advances mandate expansion of the E/I paradigm, with the expectation that new and exciting therapies will emerge from this broadened understanding of how seizures and epilepsy arise and progress.
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Affiliation(s)
- Li-Rong Shao
- Division of Pediatric Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Christa W Habela
- Division of Pediatric Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
| | - Carl E Stafstrom
- Division of Pediatric Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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30
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Ross KG, Molinaro AM, Romero C, Dockter B, Cable KL, Gonzalez K, Zhang S, Collins EMS, Pearson BJ, Zayas RM. SoxB1 Activity Regulates Sensory Neuron Regeneration, Maintenance, and Function in Planarians. Dev Cell 2019; 47:331-347.e5. [PMID: 30399335 DOI: 10.1016/j.devcel.2018.10.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/18/2018] [Accepted: 10/09/2018] [Indexed: 10/27/2022]
Abstract
SoxB1 genes play fundamental roles in neurodevelopmental processes and maintaining stem cell multipotency, but little is known about their function in regeneration. We addressed this question by analyzing the activity of the SoxB1 homolog soxB1-2 in the planarian Schmidtea mediterranea. Expression and functional analysis revealed that soxB1-2 marks ectodermal-lineage progenitors, and its activity is required for differentiation of subsets of ciliated epidermal and neuronal cells. Moreover, we show that inhibiting soxB1-2 or its candidate target genes leads to abnormal sensory neuron regeneration that causes planarians to display seizure-like movements or phenotypes associated with the loss of sensory modalities. Our analyses highlight soxB1-2-regulated genes that are expressed in sensory neurons and are homologous to factors implicated in epileptic disorders in humans and animal models of epilepsy, indicating that planarians can serve as a complementary model to investigate genetic causes of epilepsy.
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Affiliation(s)
- Kelly G Ross
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Alyssa M Molinaro
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Celeste Romero
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Brian Dockter
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Katrina L Cable
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Karla Gonzalez
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Siqi Zhang
- Department of Physics, University of California, San Diego, La Jolla, CA, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Eva-Maria S Collins
- Department of Physics, University of California, San Diego, La Jolla, CA, USA; Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Bret J Pearson
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ricardo M Zayas
- Department of Biology, San Diego State University, San Diego, CA, USA.
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31
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Jabbari K, Bobbili DR, Lal D, Reinthaler EM, Schubert J, Wolking S, Sinha V, Motameny S, Thiele H, Kawalia A, Altmüller J, Toliat MR, Kraaij R, van Rooij J, Uitterlinden AG, Ikram MA, Zara F, Lehesjoki AE, Krause R, Zimprich F, Sander T, Neubauer BA, May P, Lerche H, Nürnberg P. Rare gene deletions in genetic generalized and Rolandic epilepsies. PLoS One 2018; 13:e0202022. [PMID: 30148849 PMCID: PMC6110470 DOI: 10.1371/journal.pone.0202022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/26/2018] [Indexed: 12/30/2022] Open
Abstract
Genetic Generalized Epilepsy (GGE) and benign epilepsy with centro-temporal spikes or Rolandic Epilepsy (RE) are common forms of genetic epilepsies. Rare copy number variants have been recognized as important risk factors in brain disorders. We performed a systematic survey of rare deletions affecting protein-coding genes derived from exome data of patients with common forms of genetic epilepsies. We analysed exomes from 390 European patients (196 GGE and 194 RE) and 572 population controls to identify low-frequency genic deletions. We found that 75 (32 GGE and 43 RE) patients out of 390, i.e. ~19%, carried rare genic deletions. In particular, large deletions (>400 kb) represent a higher burden in both GGE and RE syndromes as compared to controls. The detected low-frequency deletions (1) share genes with brain-expressed exons that are under negative selection, (2) overlap with known autism and epilepsy-associated candidate genes, (3) are enriched for CNV intolerant genes recorded by the Exome Aggregation Consortium (ExAC) and (4) coincide with likely disruptive de novo mutations from the NPdenovo database. Employing several knowledge databases, we discuss the most prominent epilepsy candidate genes and their protein-protein networks for GGE and RE.
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Affiliation(s)
- Kamel Jabbari
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Cologne Biocenter, Institute for Genetics, University of Cologne, Cologne, Germany
| | - Dheeraj R. Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Eva M. Reinthaler
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Julian Schubert
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Stefan Wolking
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Vishal Sinha
- Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Susanne Motameny
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Holger Thiele
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Amit Kawalia
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | | | - Robert Kraaij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | | | - M. Arfan Ikram
- Departments of Epidemiology, Neurology, and Radiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, Institute G. Gaslini, Genova, Italy
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Neuroscience Center and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Roland Krause
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Thomas Sander
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Bernd A. Neubauer
- Department of Neuropediatrics, Medical Faculty University Giessen, Giessen, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Holger Lerche
- Department of Neurology and Epileptology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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Chen C, Chen D, Xue H, Liu X, Zhang T, Tang S, Li W, Xu X. IDGenetics: a comprehensive database for genes and mutations of intellectual disability related disorders. Neurosci Lett 2018; 685:96-101. [PMID: 30144540 DOI: 10.1016/j.neulet.2018.08.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/22/2018] [Accepted: 08/21/2018] [Indexed: 11/19/2022]
Abstract
Intellectual disability (ID) is one of the most prevalent chronic developmental brain disorders or phenotype of syndromic ID, affecting nearly 1-2% of the general population worldwide. Over recent decades, tremendous effort and high-throughput platforms have been devised to explore the complex heterogeneity, numerous genes and variants have been associated with the ID, especially de novo mutations and copy number variants. An organized resource containing the increasing genetic data is imperative to assist ID research. In this study, the integrative and annotated intellectual disability database has been developed, named 'IDGenetics', which contains known information about ID, including 815 genes and 17102 variants associated with 918 clinical diseases (3001 clinical phenotype) collected from 3822 publications and ID-related databases. Furthermore, in-depth data mining was performed to obtain an understanding of each entry, including functional annotation, gene/disease/phenotype network establishment and overlap analysis focusing on comorbidity. 1478 candidate genes (483 high-confidence and 995 low-confidence) were collected and prioritized by adopting the annotations of 12 functional prediction tools and algorithm. In addition, IDGenetics database provides concise search methods, convenient browsing functions, intuitive graphical displays and constantly updated features. IDGenetics will be a valuable and integrative resource for deciphering the genetic and functional architecture of ID and the improvement of clinical diagnosis, intervention and treatment.
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Affiliation(s)
- Chong Chen
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, 325000, China
| | - Denghui Chen
- Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Huangqi Xue
- Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xinting Liu
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325035, China
| | - Tao Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325035, China
| | - Shaohua Tang
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, 325000, China; Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Wei Li
- Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Xueqin Xu
- Key Laboratory of Birth Defects, Department of Genetics, Wenzhou Central Hospital, Wenzhou, 325000, China.
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Abstract
Epilepsy is one of the most common neurological disorders with about 500 genes thought to be involved across the phenotypic spectrum (Busch et al. 2014; Ran et al. 2014), which includes monogenic, multigenic, epistatic and pleiotropic phenotype manifestations (Busch et al. 2014; Thomas et al. 2014), driving the need for a comprehensive diagnostic test. Next-generation sequencing (NGS) allows for the simultaneous investigation of a large number of genes, making it a very attractive option for a condition as diverse as epilepsy at a low cost compared to traditional Sanger sequencing (Lemke et al. 2012; Németh et al. 2013). Our 377 gene epilepsy NGS test was developed to include genes known to cause or have published association with epilepsy and seizure-related disorders. Given the scale of information that is generated, the efficacy of an NGS panel depends on a number of factors, including the genes present on the panel, prebioinformatic and postbioinformatic analysis protocols, as well as reporting criteria, prompting the current study, a retrospective analysis of 305 cases tested for the epilepsy panel.
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Hesse AN, Bevilacqua J, Shankar K, Reddi HV. Retrospective genotype-phenotype analysis in a 305 patient cohort referred for testing of a targeted epilepsy panel. Epilepsy Res 2018; 144:53-61. [PMID: 29778030 DOI: 10.1016/j.eplepsyres.2018.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/09/2018] [Accepted: 05/12/2018] [Indexed: 11/16/2022]
Abstract
PURPOSE Epilepsy is a diverse neurological condition with extreme genetic and phenotypic heterogeneity. The introduction of next-generation sequencing into the clinical laboratory has made it possible to investigate hundreds of associated genes simultaneously for a patient, even in the absence of a clearly defined syndrome. This has resulted in the detection of rare and novel mutations at a rate well beyond our ability to characterize their effects. This retrospective study reviews genotype data in the context of available phenotypic information on 305 patients spanning the epileptic spectrum to identify established and novel patterns of correlation. METHODS Our epilepsy panel comprising 377 genes was used to sequence 305 patients referred for genetic testing. Qualifying variants were annotated with phenotypic data obtained from either the test requisition form or supporting clinical documentation. Observed phenotypes were compared with established phenotypes in OMIM, published literature and the ILAEs 2010 report on genetic testing to assess congruity with known gene aberrations. RESULTS We identified a number of novel and recognized genetic variants consistent with established epileptic phenotypes. Forty-one pathogenic or predicted deleterious variants were detected in 39 patients with accompanying clinical documentation. Twenty-five of these variants across 15 genes were novel. Furthermore, evaluation of phenotype data for 194 patients with variants of unknown significance in genes with autosomal dominant and X-linked disease inheritance elucidated potentially disease-causing variants that were not currently characterized in the literature. CONCLUSIONS Assessment of key genotype-phenotype correlations from our cohort provide insight into variant classification, as well as the importance of including ILAE recommended genes as part of minimum panel content for comprehensive epilepsy tests. Many of the reported VUSs are likely genuine pathogenic variants driving the observed phenotypes, but not enough evidence is available for assertive classifications. Similar studies will provide more utility via mounting independent genotype-phenotype data from unrelated patients. The possible outcome would be a better molecular diagnostic product, with fewer indeterminate reports containing only VUSs.
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Affiliation(s)
- Andrew N Hesse
- Transgenomic Inc, 5 Science Park, New Haven, CT, 06511, USA
| | | | - Kritika Shankar
- Transgenomic Inc, 5 Science Park, New Haven, CT, 06511, USA.
| | - Honey V Reddi
- Transgenomic Inc, 5 Science Park, New Haven, CT, 06511, USA.
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Monlong J, Girard SL, Meloche C, Cadieux-Dion M, Andrade DM, Lafreniere RG, Gravel M, Spiegelman D, Dionne-Laporte A, Boelman C, Hamdan FF, Michaud JL, Rouleau G, Minassian BA, Bourque G, Cossette P. Global characterization of copy number variants in epilepsy patients from whole genome sequencing. PLoS Genet 2018; 14:e1007285. [PMID: 29649218 PMCID: PMC5978987 DOI: 10.1371/journal.pgen.1007285] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 04/24/2018] [Accepted: 03/04/2018] [Indexed: 12/17/2022] Open
Abstract
Epilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs. Using WGS and PopSV, we performed a comprehensive characterization of CNVs in 198 individuals affected with epilepsy and 301 controls. For both large and small variants, we found an enrichment of rare exonic events in epilepsy patients, especially in genes with predicted loss-of-function intolerance. Notably, this genome-wide survey also revealed an enrichment of rare non-coding CNVs near previously known epilepsy genes. This enrichment was strongest for non-coding CNVs located within 100 Kbp of an epilepsy gene and in regions associated with changes in the gene expression, such as expression QTLs or DNase I hypersensitive sites. Finally, we report on 21 potentially damaging events that could be associated with known or new candidate epilepsy genes. Our results suggest that comprehensive sequence-based profiling of CNVs could help explain a larger fraction of epilepsy cases.
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Affiliation(s)
- Jean Monlong
- Department of Human Genetics, McGill University, Montréal, Canada
- Canadian Center for Computational Genomics, Montréal, Canada
| | - Simon L. Girard
- Department of Human Genetics, McGill University, Montréal, Canada
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Caroline Meloche
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Maxime Cadieux-Dion
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
- Center for Pediatric Genomic Medicine, Children’s Mercy Hospital, Kansas City, Missouri, United States of America
| | - Danielle M. Andrade
- Epilepsy Genetics Program, Division of Neurology, Toronto Western Hospital, University of Toronto, Toronto, Canada
| | - Ron G. Lafreniere
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Micheline Gravel
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
| | - Dan Spiegelman
- Montreal Neurological Institute, McGill University, Montréal, Canada
| | | | - Cyrus Boelman
- Division of Neurology, BC Children’s Hospital, Vancouver, Canada
| | | | | | - Guy Rouleau
- Montreal Neurological Institute, McGill University, Montréal, Canada
| | | | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Canada
- Canadian Center for Computational Genomics, Montréal, Canada
- McGill University and Génome Québec Innovation Center, Montréal, Canada
- * E-mail: (GB); (PC)
| | - Patrick Cossette
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montréal, Canada
- * E-mail: (GB); (PC)
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Genome-wide profiling reveals functional diversification of ∆FosB gene targets in the hippocampus of an Alzheimer's disease mouse model. PLoS One 2018; 13:e0192508. [PMID: 29408867 PMCID: PMC5800686 DOI: 10.1371/journal.pone.0192508] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 01/24/2018] [Indexed: 01/20/2023] Open
Abstract
The activity-induced transcription factor ∆FosB has been implicated in Alzheimer’s disease (AD) as a critical regulator of hippocampal function and cognition downstream of seizures and network hyperexcitability. With its long half-life (> 1 week), ∆FosB is well-poised to modulate hippocampal gene expression over extended periods of time, enabling effects to persist even during seizure-free periods. However, the transcriptional mechanisms by which ∆FosB regulates hippocampal function are poorly understood due to lack of identified hippocampal gene targets. To identify putative ∆FosB gene targets, we employed high-throughput sequencing of genomic DNA bound to ∆FosB after chromatin immunoprecipitation (ChIP-sequencing). We compared ChIP-sequencing results from hippocampi of transgenic mice expressing mutant human amyloid precursor protein (APP) and nontransgenic (NTG) wild-type littermates. Surprisingly, only 52 ∆FosB gene targets were shared between NTG and APP mice; the vast majority of targets were unique to one genotype or the other. We also found a functional shift in the repertoire of ∆FosB gene targets between NTG and APP mice. A large number of targets in NTG mice are involved in neurodevelopment and/or cell morphogenesis, whereas in APP mice there is an enrichment of targets involved in regulation of membrane potential and neuronal excitability. RNA-sequencing and quantitative PCR experiments confirmed that expression of putative ∆FosB gene targets were altered in the hippocampus of APP mice. This study provides key insights into functional domains regulated by ∆FosB in the hippocampus, emphasizing remarkably different programs of gene regulation under physiological and pathological conditions.
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Grinspan ZM, Tian N, Yozawitz EG, McGoldrick PE, Wolf SM, McDonough TL, Nelson A, Hafeez B, Johnson SB, Hesdorffer DC. Common terms for rare epilepsies: Synonyms, associated terms, and links to structured vocabularies. Epilepsia Open 2018; 3:91-97. [PMID: 29588993 PMCID: PMC5839304 DOI: 10.1002/epi4.12095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2017] [Indexed: 11/28/2022] Open
Abstract
Identifying individuals with rare epilepsy syndromes in electronic data sources is difficult, in part because of missing codes in the International Classification of Diseases (ICD) system. Our objectives were the following: (1) to describe the representation of rare epilepsies in other medical vocabularies, to identify gaps; and (2) to compile synonyms and associated terms for rare epilepsies, to facilitate text and natural language processing tools for cohort identification and population‐based surveillance. We describe the representation of 33 epilepsies in 3 vocabularies: Orphanet, SNOMED‐CT, and UMLS‐Metathesaurus. We compiled terms via 2 surveys, correspondence with parent advocates, and review of web resources and standard vocabularies. UMLS‐Metathesaurus had entries for all 33 epilepsies, Orphanet 32, and SNOMED‐CT 25. The vocabularies had redundancies and missing phenotypes. Emerging epilepsies (SCN2A‐, SCN8A‐, KCNQ2‐, SLC13A5‐, and SYNGAP‐related epilepsies) were underrepresented. Survey and correspondence respondents included 160 providers, 375 caregivers, and 11 advocacy group leaders. Each epilepsy syndrome had a median of 15 (range 6–28) synonyms. Nineteen had associated terms, with a median of 4 (range 1–41). We conclude that medical vocabularies should fill gaps in representation of rare epilepsies to improve their value for epilepsy research. We encourage epilepsy researchers to use this resource to develop tools to identify individuals with rare epilepsies in electronic data sources.
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Affiliation(s)
| | - Niu Tian
- Centers for Disease Control and Prevention Atlanta Georgia U.S.A
| | | | | | | | | | - Aaron Nelson
- New York University Langone Medical Center New York New York U.S.A
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Li J, Shi L, Zhang K, Zhang Y, Hu S, Zhao T, Teng H, Li X, Jiang Y, Ji L, Sun Z. VarCards: an integrated genetic and clinical database for coding variants in the human genome. Nucleic Acids Res 2018; 46:D1039-D1048. [PMID: 29112736 PMCID: PMC5753295 DOI: 10.1093/nar/gkx1039] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 10/16/2017] [Accepted: 10/18/2017] [Indexed: 12/24/2022] Open
Abstract
A growing number of genomic tools and databases were developed to facilitate the interpretation of genomic variants, particularly in coding regions. However, these tools are separately available in different online websites or databases, making it challenging for general clinicians, geneticists and biologists to obtain the first-hand information regarding some particular variants and genes of interest. Starting with coding regions and splice sties, we artificially generated all possible single nucleotide variants (n = 110 154 363) and cataloged all reported insertion and deletions (n = 1 223 370). We then annotated these variants with respect to functional consequences from more than 60 genomic data sources to develop a database, named VarCards (http://varcards.biols.ac.cn/), by which users can conveniently search, browse and annotate the variant- and gene-level implications of given variants, including the following information: (i) functional effects; (ii) functional consequences through different in silico algorithms; (iii) allele frequencies in different populations; (iv) disease- and phenotype-related knowledge; (v) general meaningful gene-level information; and (vi) drug-gene interactions. As a case study, we successfully employed VarCards in interpretation of de novo mutations in autism spectrum disorders. In conclusion, VarCards provides an intuitive interface of necessary information for researchers to prioritize candidate variations and genes.
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Affiliation(s)
- Jinchen Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410078, China
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Leisheng Shi
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Kun Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Yi Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Shanshan Hu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Tingting Zhao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Huajing Teng
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianfeng Li
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Jiang
- Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Liying Ji
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Zhongsheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
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Lin WH, Li XF, Lin MX, Zhou Y, Huang HP. Novel insights into the effect of paroxetine administration in pilocarpine‑induced chronic epileptic rats. Mol Med Rep 2017; 16:8245-8252. [PMID: 28983622 DOI: 10.3892/mmr.2017.7659] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 05/09/2017] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to investigate the role of paroxetine intervention in epilepsy, and its association with the expression of serotonin transporter (SERT) and hippocampal apoptosis. Thirty adult male Sprague Dawley rats were divided into control vehicle (n=6) and epileptic (n=24) groups. Status epilepticus (SE) was induced via systemic injection of pilocarpine, and seizure activity was monitored via video electroencephalogram. The epileptic group was then randomly divided into two groups; Four weeks following SE induction, paroxetine (5 mg/kg/day; SE + paroxetine group) or normal saline (SE group) was intraperitoneally injected for 4 weeks. Brain tissue was collected to evaluate apoptosis via terminal deoxynucleotidyl transferase dUTP nick‑end labeling. SERT, B‑cell lymphoma‑2 (Bcl‑2) and brain derived neurotropic factor (BDNF) expression levels were evaluated by western blotting, and miR‑16 expression was evaluated by reverse transcription‑quantitative polymerase chain reaction. Paroxetine did not affect the mortality of the pilocarpine‑induced chronic epileptic rats. Spontaneous recurrent seizures (SSRs) were observed 7‑28 days following SE induction. The frequency and stage of the SSRs were reduced by paroxetine administration. Apoptotic cells were observed in the epileptic hippocampus. Following paroxetine intervention, the staining intensity and number of apoptotic cells were significantly decreased. Expression levels of BDNF and Bcl‑2 were lower in the SE group compared with the vehicle group. The former was not altered by paroxetine injection; however, the latter was increased. In the SE group, SERT expression was not altered in the raphe nucleus but was decreased in the hippocampus. Following paroxetine administration, SERT expression was decreased in the raphe nucleus and increased in the hippocampus. In the SE group, miR‑16 expression was decreased in the raphe nucleus and increased in the hippocampus. Following paroxetine administration, miR‑16 expression was not altered in the raphe nucleus but was reduced in the hippocampus. In conclusion, the seizures and hippocampal apoptosis observed in chronic epileptic rats were alleviated by paroxetine treatment. This effect may be associated with the reduced Bcl‑2 and BDNF expression and the modulation of SERT expression. The alterations in miR‑16 expression may provide a potential explanation for the modulation of apoptosis; however, further research is required to determine the complete underlying molecular mechanism.
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Affiliation(s)
- Wan-Hui Lin
- Department of Neurology and Geriatrics, Union Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Xiao-Feng Li
- Department of Neurology, Union Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Ming-Xing Lin
- Department of Pediatrics, Union Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Ying Zhou
- Neuroscience Research Center of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Hua-Pin Huang
- Department of Neurology and Geriatrics, Union Hospital of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
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Lanser AJ, Rezende RM, Rubino S, Lorello PJ, Donnelly DJ, Xu H, Lau LA, Dulla CG, Caldarone BJ, Robson SC, Weiner HL. Disruption of the ATP/adenosine balance in CD39 -/- mice is associated with handling-induced seizures. Immunology 2017; 152:589-601. [PMID: 28742222 DOI: 10.1111/imm.12798] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 07/15/2017] [Accepted: 07/16/2017] [Indexed: 12/14/2022] Open
Abstract
Seizures are due to excessive, synchronous neuronal firing in the brain and are characteristic of epilepsy, the fourth most prevalent neurological disease. We report handling-induced and spontaneous seizures in mice deficient for CD39, a cell-surface ATPase highly expressed on microglial cells. CD39-/- mice with handling-induced seizures had normal input-output curves and paired-pulse ratio measured from hippocampal slices and lacked microgliosis, astrogliosis or overt cell loss in the hippocampus and cortex. As expected, however, the cerebrospinal fluid of CD39-/- mice contained increased levels of ATP and decreased levels of adenosine. To determine if immune activation was involved in seizure progression, we challenged mice with lipopolysaccharide (LPS) and measured the effect on microglia activation and seizure severity. Systemic LPS challenge resulted in increased cortical staining of Iba1/CD68 and gene array data from purified microglia predicted increased expression of interleukin-8, triggering receptor expressed on myeloid cells 1, p38, pattern recognition receptors, death receptor, nuclear factor-κB , complement, acute phase, and interleukin-6 signalling pathways in CD39-/- versus CD39+/+ mice. However, LPS treatment did not affect handling-induced seizures. In addition, microglia-specific CD39 deletion in adult mice was not sufficient to cause seizures, suggesting instead that altered expression of CD39 during development or on non-microglial cells such as vascular endothelial cells may promote the seizure phenotype. In summary, we show a correlation between altered extracellular ATP/adenosine ratio and a previously unreported seizure phenotype in CD39-/- mice. This work provides groundwork for further elucidation of the underlying mechanisms of epilepsy.
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Affiliation(s)
- Amanda J Lanser
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rafael M Rezende
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephen Rubino
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Paul J Lorello
- NeuroBehavior Laboratory, Harvard NeuroDiscovery Center, Department of Neurology, Brigham and Women's Hospital, Boston, MA, USA
| | - Dustin J Donnelly
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Huixin Xu
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lauren A Lau
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA
| | - Chris G Dulla
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA
| | - Barbara J Caldarone
- NeuroBehavior Laboratory, Harvard NeuroDiscovery Center; Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Simon C Robson
- Liver Center and The Transplant Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Howard L Weiner
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Liu Z, Li Z, Zhi X, Du Y, Lin Z, Wu J. Identification of De Novo DNMT3A Mutations That Cause West Syndrome by Using Whole-Exome Sequencing. Mol Neurobiol 2017; 55:2483-2493. [PMID: 28386848 DOI: 10.1007/s12035-017-0483-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/07/2017] [Indexed: 10/19/2022]
Abstract
Epileptic encephalopathies (EEs) are a group of severe neurodevelopmental disorders with extreme genetic heterogeneity. Recent trio-based whole-exome sequencing (WES) studies have demonstrated that de novo mutations (DNMs) play prominent roles in severe EE. In this study, we searched for potential causal DNMs by using high-coverage WES of four unrelated Chinese parent-offspring trios affected by West syndrome. Through extensive bioinformatic analysis, we identified three novel DNMs in DNMT3A, CDKL5, and MAMDC2 in three trios and two compound heterozygous mutations in KMT2A in one trio. The DNMs in CDKL5 and DNMT3A were considered to be deleterious on the basis of the consensus of several genetic damage prediction tools. In addition, spatiotemporal expression patterns revealed a high level of DNMT3A expression during the early embryonic stage in nearly all brain regions. We also observed that certain high-confidence genes for epilepsy were shared among the co-expression and genetic interaction networks of DNMT3A, CDKL5, and KMT2A. Furthermore, all the candidate epilepsy genes in the co-expression network of DNMT3A were significantly enriched in the early developmental stages of the brain according to a rank-based enrichment test. In particular, we found that the DNMs of DNMT3A were shared among EE, autism spectrum disorder (ASD), and intellectual disability (ID) and mainly occurred in the functional domain of DNMT3A. Together, our findings support an association between DNMT3A mutations and EE susceptibility and suggest a shared molecular pathophysiology among EE and other neuropsychiatric disorders.
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Affiliation(s)
- Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325027, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325027, China
| | - Xiao Zhi
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325027, China.,School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yaoqiang Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325027, China.,School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zhongdong Lin
- Department of Pediatric Neurology, The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, 325027, China.
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Whole-exome sequencing identifies a novel de novo mutation in DYNC1H1 in epileptic encephalopathies. Sci Rep 2017; 7:258. [PMID: 28325891 PMCID: PMC5428060 DOI: 10.1038/s41598-017-00208-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/14/2017] [Indexed: 11/23/2022] Open
Abstract
Epileptic encephalopathies (EE) are a group of severe childhood epilepsy disorders characterized by intractable seizures, cognitive impairment and neurological deficits. Recent whole-exome sequencing (WES) studies have implicated significant contribution of de novo mutations to EE. In this study, we utilized WES for identifying causal de novo mutations in 4 parent-offspring trios affected by West syndrome. As a result, we found two deleterious de novo mutations in DYNC1H1 and RTP1 in two trios. Expression profile analysis showed that DYNC1H1 and RTP1 are expressed in almost all brain regions and developmental stages. Interestingly, co-expression and genetic interaction network analyses suggested that DYNC1H1 and RTP1 are tightly associated with known epilepsy genes. Furthermore, we observed that the de novo mutations of DYNC1H1 were identified in several different neuropsychiatric disorders including EE, autism spectrum disorders and intellectual disabilities by previous studies, and these mutations primarily occurred in the functional domain of the protein. Taken together, these results demonstrate DYNC1H1 as a strong candidate and RTP1 as a potential candidate on the onset of EE. In addition, this work also proves WES as a powerful tool for the molecular genetic dissection of children affected by sporadic EE.
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John Lin CC, Yu K, Hatcher A, Huang TW, Lee HK, Carlson J, Weston MC, Chen F, Zhang Y, Zhu W, Mohila CA, Ahmed N, Patel AJ, Arenkiel BR, Noebels JL, Creighton CJ, Deneen B. Identification of diverse astrocyte populations and their malignant analogs. Nat Neurosci 2017; 20:396-405. [PMID: 28166219 PMCID: PMC5824716 DOI: 10.1038/nn.4493] [Citation(s) in RCA: 341] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/28/2016] [Indexed: 12/14/2022]
Abstract
Astrocytes are the most abundant cell type in the brain, where they perform a wide array of functions, yet the nature of their cellular heterogeneity and how it oversees these diverse roles remains shrouded in mystery. Using an intersectional fluorescence-activated cell sorting-based strategy, we identified five distinct astrocyte subpopulations present across three brain regions that show extensive molecular diversity. Application of this molecular insight toward function revealed that these populations differentially support synaptogenesis between neurons. We identified correlative populations in mouse and human glioma and found that the emergence of specific subpopulations during tumor progression corresponded with the onset of seizures and tumor invasion. In sum, we have identified subpopulations of astrocytes in the adult brain and their correlates in glioma that are endowed with diverse cellular, molecular and functional properties. These populations selectively contribute to synaptogenesis and tumor pathophysiology, providing a blueprint for understanding diverse astrocyte contributions to neurological disease.
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Affiliation(s)
- Chia-Ching John Lin
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA
| | - Kwanha Yu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA
| | - Asante Hatcher
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
| | - Teng-Wei Huang
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA
| | - Hyun Kyoung Lee
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Neurological Research Institute at Texas' Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
- Department of Pediatrics, Division of Neurology, Texas Children's Hospital, Houston, Texas, USA
| | - Jeffrey Carlson
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Matthew C Weston
- Department of Neurological Sciences, University of Vermont, Vermont, Vermont, USA
| | - Fengju Chen
- Dan L. Duncan Cancer Center, Division of Biostatistics, Baylor College of Medicine, Houston, Texas, USA
| | - Yiqun Zhang
- Dan L. Duncan Cancer Center, Division of Biostatistics, Baylor College of Medicine, Houston, Texas, USA
| | - Wenyi Zhu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA
| | - Carrie A Mohila
- Department of Pathology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
| | - Nabil Ahmed
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA
| | - Akash J Patel
- Neurological Research Institute at Texas' Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
| | - Benjamin R Arenkiel
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Neurological Research Institute at Texas' Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Jeffrey L Noebels
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
- Department of Neurology, Baylor College of Medicine, Houston, Texas, USA
| | - Chad J Creighton
- Dan L. Duncan Cancer Center, Division of Biostatistics, Baylor College of Medicine, Houston, Texas, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, USA
- Neurological Research Institute at Texas' Children's Hospital, Baylor College of Medicine, Houston, Texas, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
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Guo W, Shang DM, Cao JH, Feng K, He YC, Jiang Y, Wang S, Gao YF. Identifying and Analyzing Novel Epilepsy-Related Genes Using Random Walk with Restart Algorithm. BIOMED RESEARCH INTERNATIONAL 2017; 2017:6132436. [PMID: 28255556 PMCID: PMC5309434 DOI: 10.1155/2017/6132436] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Accepted: 01/15/2017] [Indexed: 02/07/2023]
Abstract
As a pathological condition, epilepsy is caused by abnormal neuronal discharge in brain which will temporarily disrupt the cerebral functions. Epilepsy is a chronic disease which occurs in all ages and would seriously affect patients' personal lives. Thus, it is highly required to develop effective medicines or instruments to treat the disease. Identifying epilepsy-related genes is essential in order to understand and treat the disease because the corresponding proteins encoded by the epilepsy-related genes are candidates of the potential drug targets. In this study, a pioneering computational workflow was proposed to predict novel epilepsy-related genes using the random walk with restart (RWR) algorithm. As reported in the literature RWR algorithm often produces a number of false positive genes, and in this study a permutation test and functional association tests were implemented to filter the genes identified by RWR algorithm, which greatly reduce the number of suspected genes and result in only thirty-three novel epilepsy genes. Finally, these novel genes were analyzed based upon some recently published literatures. Our findings implicate that all novel genes were closely related to epilepsy. It is believed that the proposed workflow can also be applied to identify genes related to other diseases and deepen our understanding of the mechanisms of these diseases.
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Affiliation(s)
- Wei Guo
- Department of Outpatient, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Dong-Mei Shang
- Department of Outpatient, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Jing-Hui Cao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic, Guangzhou 510507, China
| | - Yi-Chun He
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Yang Jiang
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - ShaoPeng Wang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yu-Fei Gao
- Department of Neurosurgery, China-Japan Union Hospital of Jilin University, Changchun 130033, China
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Genetic Variants Identified from Epilepsy of Unknown Etiology in Chinese Children by Targeted Exome Sequencing. Sci Rep 2017; 7:40319. [PMID: 28074849 PMCID: PMC5225856 DOI: 10.1038/srep40319] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 12/05/2016] [Indexed: 12/02/2022] Open
Abstract
Genetic factors play a major role in the etiology of epilepsy disorders. Recent genomics studies using next generation sequencing (NGS) technique have identified a large number of genetic variants including copy number (CNV) and single nucleotide variant (SNV) in a small set of genes from individuals with epilepsy. These discoveries have contributed significantly to evaluate the etiology of epilepsy in clinic and lay the foundation to develop molecular specific treatment. However, the molecular basis for a majority of epilepsy patients remains elusive, and furthermore, most of these studies have been conducted in Caucasian children. Here we conducted a targeted exome-sequencing of 63 trios of Chinese epilepsy families using a custom-designed NGS panel that covers 412 known and candidate genes for epilepsy. We identified pathogenic and likely pathogenic variants in 15 of 63 (23.8%) families in known epilepsy genes including SCN1A, CDKL5, STXBP1, CHD2, SCN3A, SCN9A, TSC2, MBD5, POLG and EFHC1. More importantly, we identified likely pathologic variants in several novel candidate genes such as GABRE, MYH1, and CLCN6. Our results provide the evidence supporting the application of custom-designed NGS panel in clinic and indicate a conserved genetic susceptibility for epilepsy between Chinese and Caucasian children.
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Wang J, Cao Y, Zhang H, Wang T, Tian Q, Lu X, Lu X, Kong X, Liu Z, Wang N, Zhang S, Ma H, Ning S, Wang L. NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases. Nucleic Acids Res 2016; 45:D902-D907. [PMID: 27899613 PMCID: PMC5210534 DOI: 10.1093/nar/gkw1038] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/17/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022] Open
Abstract
The Nervous System Disease NcRNAome Atlas (NSDNA) (http://www.bio-bigdata.net/nsdna/) is a manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDs represent a common group of disorders, some of which are characterized by high morbidity and disabilities. The pathogenesis of NSDs at the molecular level remains poorly understood. ncRNAs are a large family of functionally important RNA molecules. Increasing evidence shows that diverse ncRNAs play a critical role in various NSDs. Mining and summarizing NSD–ncRNA association data can help researchers discover useful information. Hence, we developed an NSDNA database that documents 24 713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD–ncRNA associations. It represents an extremely useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs.
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Affiliation(s)
- Jianjian Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Yuze Cao
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Huixue Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Tianfeng Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Qinghua Tian
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xiaoyu Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xiaoyan Lu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Xiaotong Kong
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Zhaojun Liu
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Ning Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Shuai Zhang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
| | - Heping Ma
- Department of Physiology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Lihua Wang
- Department of Neurology, The Second Affiliated Hospital of Harbin Medical University, Harbin 150081, China
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Jabbari K, Nürnberg P. A genomic view on epilepsy and autism candidate genes. Genomics 2016; 108:31-6. [PMID: 26772991 DOI: 10.1016/j.ygeno.2016.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 12/15/2015] [Accepted: 01/01/2016] [Indexed: 01/25/2023]
Abstract
Epilepsy is a common complex disorder most frequently associated with psychiatric and neurological diseases. Massive parallel sequencing of individual or cohort genomes and exomes led the identification of several disease associated genes. We review here the candidate genes in epilepsy genetics with focus on exome and gene panel data. Together with the examination of brain expressed genes and post synaptic proteome the results show that: (1) Non-metabolic epilepsies and autism candidate genes tend to be AT-rich and (2) large transcript size and local AT-richness are characteristic features of genes involved in developmental brain disorders and synaptic functions. These results point to the preferential location of core epilepsy and autism candidate genes in late replicating, GC-poor chromosomal regions (isochores). These results indicate that the genomic alterations leading to some brain disorders are confined to responsive chromatin areas harboring brain critical genes.
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Affiliation(s)
- Kamel Jabbari
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
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Joseph S, Barai RS, Bhujbalrao R, Idicula-Thomas S. PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome. Nucleic Acids Res 2015; 44:D1032-5. [PMID: 26578565 PMCID: PMC4702829 DOI: 10.1093/nar/gkv1146] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 10/19/2015] [Indexed: 12/22/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is one of the major causes of female subfertility worldwide and ≈7–10% of women in reproductive age are affected by it. The affected individuals exhibit varying types and levels of comorbid conditions, along with the classical PCOS symptoms. Extensive studies on PCOS across diverse ethnic populations have resulted in a plethora of information on dysregulated genes, gene polymorphisms and diseases linked to PCOS. However, efforts have not been taken to collate and link these data. Our group, for the first time, has compiled PCOS-related information available through scientific literature; cross-linked it with molecular, biochemical and clinical databases and presented it as a user-friendly, web-based online knowledgebase for the benefit of the scientific and clinical community. Manually curated information on associated genes, single nucleotide polymorphisms, diseases, gene ontology terms and pathways along with supporting reference literature has been collated and included in PCOSKB (http://pcoskb.bicnirrh.res.in).
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Affiliation(s)
- Shaini Joseph
- Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India
| | - Ram Shankar Barai
- Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India
| | | | - Susan Idicula-Thomas
- Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India
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Abstract
Decades of experimental work have established an imbalance of excitation and inhibition as the leading mechanism of the transition from normal brain function to seizure. In epilepsy, these transitions are rare and abrupt. Transition processes incorporating positive feedback, such as activity-dependent disinhibition, could provide these uncommon timing features. A rapidly expanding array of genetic etiologies will help delineate the molecular mechanism(s). This delineation will entail quite a bit of cell biology. The genes discovered so far are more remarkable for their diversity than their similarities.
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