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Lu M, Feng R, Zhang C, Xiao Y, Yin C. Identifying Novel Drug Targets for Epilepsy Through a Brain Transcriptome-Wide Association Study and Protein-Wide Association Study with Chemical-Gene-Interaction Analysis. Mol Neurobiol 2023; 60:5055-5066. [PMID: 37246165 PMCID: PMC10415436 DOI: 10.1007/s12035-023-03382-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/04/2023] [Indexed: 05/30/2023]
Abstract
Epilepsy is a severe neurological condition affecting 50-65 million individuals worldwide that can lead to brain damage. Nevertheless, the etiology of epilepsy remains poorly understood. Meta-analyses of genome-wide association studies involving 15,212 epilepsy cases and 29,677 controls of the ILAE Consortium cohort were used to conduct transcriptome-wide association studies (TWAS) and protein-wide association studies (PWAS). Furthermore, a protein-protein interaction (PPI) network was generated using the STRING database, and significant epilepsy-susceptible genes were verified using chip data. Chemical-related gene set enrichment analysis (CGSEA) was performed to determine novel drug targets for epilepsy. TWAS analysis identified 21,170 genes, of which 58 were significant (TWASfdr < 0.05) in ten brain regions, and 16 differentially expressed genes were verified based on mRNA expression profiles. The PWAS identified 2249 genes, of which 2 were significant (PWASfdr < 0.05). Through chemical-gene set enrichment analysis, 287 environmental chemicals associated with epilepsy were identified. We identified five significant genes (WIPF1, IQSEC1, JAM2, ICAM3, and ZNF143) that had causal relationships with epilepsy. CGSEA identified 159 chemicals that were significantly correlated with epilepsy (Pcgsea < 0.05), such as pentobarbital, ketone bodies, and polychlorinated biphenyl. In summary, we performed TWAS, PWAS (for genetic factors), and CGSEA (for environmental factors) analyses and identified several epilepsy-associated genes and chemicals. The results of this study will contribute to our understanding of genetic and environmental factors for epilepsy and may predict novel drug targets.
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Affiliation(s)
- Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China
| | - Ruoyang Feng
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China
| | - Chenglin Zhang
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China
| | - Yanfeng Xiao
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China.
| | - Chunyan Yin
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China.
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Feria-Romero IA, Reyes-Cuayahuitl A, Sosa-Maldonado J, Montes-Aparicio AV, Rayo-Mares D, Pérez-Pérez D, Grijalva-Otero I, Orozco-Suarez S. Study of genetic variants and their clinical significance in Mexican pediatric patients with epilepsy. Gene 2023:147565. [PMID: 37315635 DOI: 10.1016/j.gene.2023.147565] [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: 02/14/2023] [Revised: 06/06/2023] [Accepted: 06/09/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND The use of novel and accurate techniques to identify genetic variants (with or without a record in the National Center for Biotechnology Information (NCBI) database) improves diagnosis, prognosis, and therapeutics for patients with epilepsy, especially in populations for whom such techniques exist. The aim of this study was to find a genetic profile in Mexican pediatric epilepsy patients by focusing on ten genes associated with drug-resistant epilepsy (DRE). METHODS This was a prospective, analytical, cross-sectional study of pediatric patients with epilepsy. Informed consent was granted by the patients' guardians or parents. Genomic DNA from the patients was sequenced using next-generation sequencing (NGS). For statistical analysis, Fisher's exact, Chi-square or Mann-Whitney U, and OR (95% CI) tests were performed, with significance values of p<0.05. RESULTS Fifty-five patients met the inclusion criteria (female 58.2%, ages 1-16 years); 32 patients had controlled epilepsy (CTR), and 23 had DRE. Four hundred twenty-two genetic variants were identified (71.3% with a known SNP registered in the NCBI database). A dominant genetic profile consisting of four haplotypes of the SCN1A, CYP2C9, and CYP2C19 genes was identified in most of the patients studied. When comparing the results between patients with DRE and CTR, the prevalence of polymorphisms in the SCN1A (rs10497275, rs10198801, and rs67636132), CYP2D6 (rs1065852), and CYP3A4 (rs2242480) genes showed statistical significance (p = 0.021). Finally, the number of missense genetic variants in patients in the nonstructural subgroup was significantly higher in DRE than in CTR (1 [0-2] vs. 3 [2-4]; p=0.014). CONCLUSIONS The Mexican pediatric epilepsy patients included in this cohort presented a characteristic genetic profile infrequent in the Mexican population. SNP rs1065852 (CYP2D6*10) is associated with DRE, especially with nonstructural damage. The presence of three genetic alterations affecting the CYP2B6, CYP2C9, and CYP2D6 cytochrome genes is associated with nonstructural DRE.
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Affiliation(s)
- Iris A Feria-Romero
- Unidad de Investigación Médica en Enfermedades Neurológicas, Hospital de Especialidades, "Dr. Bernardo Sepúlveda", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Aracely Reyes-Cuayahuitl
- Servicio de Neurología Pediátrica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | | | - Alexia V Montes-Aparicio
- Programa de Maestría, Escuela Superior de Medicina, Instituto Politécnico Nacional, Ciudad de México, México
| | - Darío Rayo-Mares
- Servicio de Neurología Pediátrica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Daniel Pérez-Pérez
- Institute of Pharmacology, Toxicology, and Pharmacy, Ludwig-Maximilian University, Munich, Germany
| | - Israel Grijalva-Otero
- Unidad de Investigación Médica en Enfermedades Neurológicas, Hospital de Especialidades, "Dr. Bernardo Sepúlveda", Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Sandra Orozco-Suarez
- Servicio de Neurología Pediátrica, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México.
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Identification of a Novel Idiopathic Epilepsy Risk Locus and a Variant in the CCDC85A Gene in the Dutch Partridge Dog. Animals (Basel) 2023; 13:ani13050810. [PMID: 36899667 PMCID: PMC10000155 DOI: 10.3390/ani13050810] [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: 01/18/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
(1) Idiopathic epilepsy (IE) is thought to have a genetic cause in several dog breeds. However, only two causal variants have been identified to date, and few risk loci are known. No genetic studies have been conducted on IE in the Dutch partridge dog (DPD), and little has been reported on the epileptic phenotype in this breed. (2) Owner-filled questionnaires and diagnostic investigations were used to characterize IE in the DPD. A genome-wide association study (GWAS) involving 16 cases and 43 controls was performed, followed by sequencing of the coding sequence and splice site regions of a candidate gene within the associated region. Subsequent whole-exome sequencing (WES) of one family (including one IE-affected dog, both parents, and an IE-free sibling) was performed. (3) IE in the DPD has a broad range in terms of age at onset, frequency, and duration of epileptic seizures. Most dogs showed focal epileptic seizures evolving into generalized seizures. A new risk locus on chromosome 12 (BICF2G630119560; praw = 4.4 × 10-7; padj = 0.043) was identified through GWAS. Sequencing of the GRIK2 candidate gene revealed no variants of interest. No WES variants were located within the associated GWAS region. However, a variant in CCDC85A (chromosome 10; XM_038680630.1: c.689C > T) was discovered, and dogs homozygous for the variant (T/T) had an increased risk of developing IE (OR: 6.0; 95% CI: 1.6-22.6). This variant was identified as likely pathogenic according to ACMG guidelines. (4) Further research is necessary before the risk locus or CCDC85A variant can be used for breeding decisions.
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Wang S, Cai X, Liu S, Zhou Q, Wang T, Du S, Wang D, Yang F, Wu Q, Han Y. A novel BCL11A polymorphism influences gene expression, therapeutic response and epilepsy risk: A multicenter study. Front Mol Neurosci 2022; 15:1010101. [PMID: 36568279 PMCID: PMC9780294 DOI: 10.3389/fnmol.2022.1010101] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/18/2022] [Indexed: 12/13/2022] Open
Abstract
Background Genetic factors have been found to be associated with the efficacy and adverse reactions of antiseizure medications. BCL11A is an important regulator of the development of neuronal networks. However, the role of BCL11A in epilepsy remains unclear. This study aimed to evaluate the genetic association of BCL11A with the susceptibility to develop epileptic seizures and therapeutic response of patients with epilepsy in Han Chinese. Methods We matched 450 epilepsy cases with 550 healthy controls and 131 drug-resistant epilepsy patients with 319 drug-responsive epilepsy patients from two different centers. Genetic association analysis, genetic interaction analysis, expression quantitative trait loci analysis and protein-protein interaction analysis were conducted. Results Our results showed that rs2556375 not only increases susceptibility to develop epileptic seizures (OR = 2.700, 95% = 1.366-5.338, p = 0.004 and OR = 2.984, 95% = 1.401-6.356, p = 0.005, respectively), but also increases the risk of drug resistance(OR = 21.336, 95%CI =2.489-183.402, p = 0.005). The interaction between rs2556375 and rs12477097 results in increased risk for pharma coresistant. In addition, rs2556375 regulated BCL11A expression in human brain tissues (p = 0.0096 and p = 0.033, respectively). Furthermore, the protein encoded by BCL11A interacted with targets of approved antiepileptic drugs. Conclusion BCL11A may be a potential therapeutic target for epilepsy. Rs2556375 may increase the risks of epilepsy and drug resistance by regulating BCL11A expression in human brain tissues. Moreover, the interaction between rs2556375 and rs12477097 results in increased risk for drug resistance.
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Affiliation(s)
- Shitao Wang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China,Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, China
| | - Xuemei Cai
- Department of Clinical Laboratory, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shiyong Liu
- Department of Neurosurgery, Xinqiao Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - Qixin Zhou
- Laboratory of Learning and Memory, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ting Wang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Sunbing Du
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Dan Wang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Fei Yang
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qian Wu
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yanbing Han
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China,*Correspondence: Yanbing Han,
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Genetic Variation in PADI6-PADI4 on 1p36.13 Is Associated with Common Forms of Human Generalized Epilepsy. Genes (Basel) 2021; 12:genes12091441. [PMID: 34573423 PMCID: PMC8472138 DOI: 10.3390/genes12091441] [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: 08/11/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
We performed a genome-wide association study (GWAS) to identify genetic variation associated with common forms of idiopathic generalized epilepsy (GE) and focal epilepsy (FE). Using a cohort of 2220 patients and 14,448 controls, we searched for single nucleotide polymorphisms (SNPs) associated with GE, FE and both forms combined. We did not find any SNPs that reached genome-wide statistical significance (p ≤ 5 × 10−8) when comparing all cases to all controls, and few SNPs of interest comparing FE cases to controls. However, we document multiple linked SNPs in the PADI6-PADI4 genes that reach genome-wide significance and are associated with disease when comparing GE cases alone to controls. PADI genes encode enzymes that deiminate arginine to citrulline in molecular pathways related to epigenetic regulation of histones and autoantibody formation. Although epilepsy genetics and treatment are focused strongly on ion channel and neurotransmitter mechanisms, these results suggest that epigenetic control of gene expression and the formation of autoantibodies may also play roles in epileptogenesis.
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Multi-omics in mesial temporal lobe epilepsy with hippocampal sclerosis: Clues into the underlying mechanisms leading to disease. Seizure 2021; 90:34-50. [DOI: 10.1016/j.seizure.2021.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 02/07/2023] Open
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Suzuki T, Koike Y, Ashikawa K, Otomo N, Takahashi A, Aoi T, Kamatani N, Nakamura Y, Kubo M, Kamatani Y, Momozawa Y, Terao C, Yamakawa K. Genome-wide association study of epilepsy in a Japanese population identified an associated region at chromosome 12q24. Epilepsia 2021; 62:1391-1400. [PMID: 33913524 DOI: 10.1111/epi.16911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVE Although a number of genes responsible for epilepsy have been identified through Mendelian genetic approaches, and genome-wide association studies (GWASs) have implicated several susceptibility loci, the role of ethnic-specific markers remains to be fully explored. We aimed to identify novel genetic associations with epilepsy in a Japanese population. METHODS We conducted a GWAS on 1825 patients with a variety of epilepsies and 7975 control individuals. Expression quantitative trait locus (eQTL) analysis of epilepsy-associated single nucleotide polymorphisms (SNPs) was performed using Japanese eQTL data. RESULTS We identified a novel region, which is ~2 Mb (lead SNP rs149212747, p = 8.57 × 10-10 ), at chromosome 12q24 as a risk for epilepsy. Most of these loci were polymorphic in East Asian populations including Japanese, but monomorphic in the European population. This region harbors 24 transcripts including genes expressed in the brain such as CUX2, ATXN2, BRAP, ALDH2, ERP29, TRAFD1, HECTD4, RPL6, PTPN11, and RPH3A. The eQTL analysis revealed that the associated SNPs are also correlated to differential expression of genes at 12q24. SIGNIFICANCE These findings suggest that a gene or genes in the CUX2-RPH3A ~2-Mb region contribute to the pathology of epilepsy in the Japanese population.
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Affiliation(s)
- Toshimitsu Suzuki
- Department of Neurodevelopmental Disorder Genetics, Institute of Brain Science, Nagoya City University Graduate School of Medical Science, Aichi, Japan.,Laboratory for Neurogenetics, Institute of Physical and Chemical Research (RIKEN) Center for Brain Science, Saitama, Japan
| | - Yoshinao Koike
- Laboratory for Statistical and Translational Genetics, Institute of Physical and Chemical Research (RIKEN) Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Orthopedic Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Kyota Ashikawa
- Laboratory for Genotyping Development, Institute of Physical and Chemical Research (RIKEN) Center for Integrative Medical Sciences, Yokohama, Japan
| | - Nao Otomo
- Laboratory for Statistical and Translational Genetics, Institute of Physical and Chemical Research (RIKEN) Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, Institute of Physical and Chemical Research (RIKEN) Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Genomic Medicine, National Cerebral and Cardiovascular Center, Research Institute, Osaka, Japan
| | - Tomomi Aoi
- Laboratory for Genotyping Development, Institute of Physical and Chemical Research (RIKEN) Center for Integrative Medical Sciences, Yokohama, Japan
| | - Naoyuki Kamatani
- Center for Genomic Medicine, Institute of Physical and Chemical Research (RIKEN), Yokohama, Japan
| | - Yusuke Nakamura
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Cancer Precision Medicine Research Center, The Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Institute of Physical and Chemical Research (RIKEN) Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, Institute of Physical and Chemical Research (RIKEN) Center for Integrative Medical Sciences, Yokohama, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, Institute of Physical and Chemical Research (RIKEN) Center for Integrative Medical Sciences, Yokohama, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, Institute of Physical and Chemical Research (RIKEN) Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuhiro Yamakawa
- Department of Neurodevelopmental Disorder Genetics, Institute of Brain Science, Nagoya City University Graduate School of Medical Science, Aichi, Japan.,Laboratory for Neurogenetics, Institute of Physical and Chemical Research (RIKEN) Center for Brain Science, Saitama, Japan
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Sullo F, Pasquetti E, Patanè F, Lo Bianco M, Marino SD, Polizzi A, Falsaperla R, Ruggieri M, Zanghì A, Praticò AD. SCN1A and Its Related Epileptic Phenotypes. JOURNAL OF PEDIATRIC NEUROLOGY 2021. [DOI: 10.1055/s-0041-1727260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractEpilepsy is one of the most common neurological disorders, with a lifetime incidence of 1 in 26. Approximately two-thirds of epilepsy has a substantial genetic component in its etiology. As a result, simultaneous screening for mutations in multiple genes and performing whole exome sequencing (WES) are becoming very frequent in the clinical evaluation of children with epilepsy. In this setting, mutations in voltage-gated sodium channel (SCN) α-subunit genes are the most commonly identified cause of epilepsy, with sodium channel genes (i.e., SCN1A, SCN2A, SCN8A) being the most frequently identified causative genes. SCN1A mutations result in a wide spectrum of epilepsy phenotypes ranging from simple febrile seizures to Dravet syndrome, a severe epileptic encephalopathy. In case of mutation of SCN1A, it is also possible to observe behavioral alterations, such as impulsivity, inattentiveness, and distractibility, which can be framed in an attention deficit hyperactivity disorder (ADHD) like phenotype. Despite more than 1,200 SCN1A mutations being reported, it is not possible to assess a clear phenotype–genotype correlations. Treatment remains a challenge and seizure control is often partial and transitory.
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Affiliation(s)
- Federica Sullo
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Elisa Pasquetti
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Francesca Patanè
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Manuela Lo Bianco
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Simona D. Marino
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Agata Polizzi
- Chair of Pediatrics, Department of Educational Sciences, University of Catania, Catania, Italy
| | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
- Unit of Neonatal Intensive Care and Neonatology, University Hospital “Policlinico Rodolico-San Marco,” Catania, Italy
| | - Martino Ruggieri
- Pediatrics Postgraduate Residency Program, Section of Pediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Antonio Zanghì
- Department of Medical and Surgical Sciences and Advanced Technology “G.F. Ingrassia,” University of Catania, Catania, Italy
| | - Andrea D. Praticò
- Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, Section of Pediatrics and Child Neuropsychiatry, University of Catania, Catania, Italy
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Ding D, Zhou D, Sander JW, Wang W, Li S, Hong Z. Epilepsy in China: major progress in the past two decades. Lancet Neurol 2021; 20:316-326. [PMID: 33743240 DOI: 10.1016/s1474-4422(21)00023-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 12/15/2020] [Accepted: 01/07/2021] [Indexed: 02/08/2023]
Abstract
China has approximately 10 million people with epilepsy. There is a vast epilepsy treatment gap in China, mainly driven by deficiencies in health-care delivery and social discrimination resulting from cultural beliefs about epilepsy. WHO's Global Campaign Against Epilepsy project in China showed that it was possible to treat epilepsy in primary care settings, which was a notable milestone. The China Association Against Epilepsy has been a necessary force to stimulate interest in epilepsy care and research by the medical and scientific community. Nearly 20 different anti-seizure medications are now available in China. Non-pharmacological options are also available, but there are still unmet needs for epilepsy management. The Chinese epilepsy research portfolio is varied, but the areas in which there are the most concentrated focus and expertise are epidemiology and clinical research. The challenges for further improvement in delivering care for people with epilepsy in China are primarily related to public health and reducing inequalities within this vast country.
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Affiliation(s)
- Ding Ding
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China
| | - Dong Zhou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
| | - Josemir W Sander
- NIHR University College London Hospitals Biomedical Research Centre, UCL Queen Square Institute of Neurology, London, UK; Chalfont Centre for Epilepsy, Chalfont St Peter, Buckinghamshire, UK; Stichting Epilepsie Instellingen Nederland, Heemstede, Netherlands.
| | - Wenzhi Wang
- Department of Neuroepidemiology, Beijing Neurosurgical Institute, Beijing, China
| | - Shichuo Li
- China Association against Epilepsy, Beijing, China
| | - Zhen Hong
- Institute of Neurology, Huashan Hospital, Fudan University, Shanghai, China
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10
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Tiwari D, Schaefer TL, Schroeder-Carter LM, Krzeski JC, Bunk AT, Parkins EV, Snider A, Danzer R, Williams MT, Vorhees CV, Danzer SC, Gross C. The potassium channel Kv4.2 regulates dendritic spine morphology, electroencephalographic characteristics and seizure susceptibility in mice. Exp Neurol 2020; 334:113437. [PMID: 32822706 PMCID: PMC7642025 DOI: 10.1016/j.expneurol.2020.113437] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 01/21/2023]
Abstract
The voltage-gated potassium channel Kv4.2 is a critical regulator of dendritic excitability in the hippocampus and is crucial for dendritic signal integration. Kv4.2 mRNA and protein expression as well as function are reduced in several genetic and pharmacologically induced rodent models of epilepsy and autism. It is not known, however, whether reduced Kv4.2 is just an epiphenomenon or a disease-contributing cause of neuronal hyperexcitability and behavioral impairments in these neurological disorders. To address this question, we used male and female mice heterozygous for a Kv.2 deletion and adult-onset manipulation of hippocampal Kv4.2 expression in male mice to assess the role of Kv4.2 in regulating neuronal network excitability, morphology and anxiety-related behaviors. We observed a reduction in dendritic spine density and reduced proportions of thin and stubby spines but no changes in anxiety, overall activity, or retention of conditioned freezing memory in Kv4.2 heterozygous mice compared with wildtype littermates. Using EEG analyses, we showed elevated theta power and increased spike frequency in Kv4.2 heterozygous mice under basal conditions. In addition, the latency to onset of kainic acid-induced seizures was significantly shortened in Kv4.2 heterozygous mice compared with wildtype littermates, which was accompanied by a significant increase in theta power. By contrast, overexpressing Kv4.2 in wildtype mice through intrahippocampal injection of Kv4.2-expressing lentivirus delayed seizure onset and reduced EEG power. These results suggest that Kv4.2 is an important regulator of neuronal network excitability and dendritic spine morphology, but not anxiety-related behaviors. In the future, manipulation of Kv4.2 expression could be used to alter seizure susceptibility in epilepsy.
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Affiliation(s)
- Durgesh Tiwari
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Tori L Schaefer
- Division of Psychiatry, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | | | - Joseph C Krzeski
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Alexander T Bunk
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Emma V Parkins
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrew Snider
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Reese Danzer
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Michael T Williams
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Charles V Vorhees
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Steve C Danzer
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA; Department of Anesthesia, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Anesthesiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Christina Gross
- Division of Neurology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
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11
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Gramm M, Leu C, Pérez-Palma E, Ferguson L, Jehi L, Daly MJ, Najm IM, Busch RM, Lal D. Polygenic risk heterogeneity among focal epilepsies. Epilepsia 2020; 61:e179-e185. [PMID: 33090489 DOI: 10.1111/epi.16717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 11/30/2022]
Abstract
Focal epilepsy (FE) is clinically highly heterogeneous. It has been shown recently that not only rare but also a subset of common genetic variants confer risk for FE. The relatively modest power of genetic studies in FE suggests a high genetic heterogeneity of FE when grouped as one disorder. We hypothesize that the clinical heterogeneity of FE is correlated with genetic heterogeneity on a common risk variant level. To test the hypothesis, we used an FE polygenic risk score "FE-PRS" that combines small effect sizes of thousands of common variants from the largest FE-GWAS (genome-wide association study) into a single measure. We grouped 414 individuals with FE according to common clinical features into subgroups, either by one feature at a time or by all features combined in a cluster analysis. We examined their association with FE-PRS compared to 20 435 matched population controls and observed heterogeneous FE-PRS burden among the subgroups. The highest phenotypic variance explained by FE-PRS was identified in a cluster analysis-defined FE subgroup where all individuals had unknown etiologies and psychiatric comorbidities, and the majority had early onset seizures. Our results indicate that genetic factors associated with FE have differential burden among FE subtypes. Future studies using better-powered FE-PRS might have clinical utility.
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Affiliation(s)
- Marie Gramm
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Costin Leu
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Eduardo Pérez-Palma
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lisa Ferguson
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lara Jehi
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mark J Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.,Institute of Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Imad M Najm
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Robyn M Busch
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Neurology, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Dennis Lal
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.,Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Stanley Center for Psychiatric Research, Broad Institute of MIT & Harvard, Cambridge, MA, USA.,Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
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12
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Genetic Landscape of Common Epilepsies: Advancing towards Precision in Treatment. Int J Mol Sci 2020; 21:ijms21207784. [PMID: 33096746 PMCID: PMC7589654 DOI: 10.3390/ijms21207784] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/15/2022] Open
Abstract
Epilepsy, a neurological disease characterized by recurrent seizures, is highly heterogeneous in nature. Based on the prevalence, epilepsy is classified into two types: common and rare epilepsies. Common epilepsies affecting nearly 95% people with epilepsy, comprise generalized epilepsy which encompass idiopathic generalized epilepsy like childhood absence epilepsy, juvenile myoclonic epilepsy, juvenile absence epilepsy and epilepsy with generalized tonic-clonic seizure on awakening and focal epilepsy like temporal lobe epilepsy and cryptogenic focal epilepsy. In 70% of the epilepsy cases, genetic factors are responsible either as single genetic variant in rare epilepsies or multiple genetic variants acting along with different environmental factors as in common epilepsies. Genetic testing and precision treatment have been developed for a few rare epilepsies and is lacking for common epilepsies due to their complex nature of inheritance. Precision medicine for common epilepsies require a panoramic approach that incorporates polygenic background and other non-genetic factors like microbiome, diet, age at disease onset, optimal time for treatment and other lifestyle factors which influence seizure threshold. This review aims to comprehensively present a state-of-art review of all the genes and their genetic variants that are associated with all common epilepsy subtypes. It also encompasses the basis of these genes in the epileptogenesis. Here, we discussed the current status of the common epilepsy genetics and address the clinical application so far on evidence-based markers in prognosis, diagnosis, and treatment management. In addition, we assessed the diagnostic predictability of a few genetic markers used for disease risk prediction in individuals. A combination of deeper endo-phenotyping including pharmaco-response data, electro-clinical imaging, and other clinical measurements along with genetics may be used to diagnose common epilepsies and this marks a step ahead in precision medicine in common epilepsies management.
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13
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Mao BP, Ge R, Cheng CY. Role of microtubule +TIPs and -TIPs in spermatogenesis – Insights from studies of toxicant models. Reprod Toxicol 2020; 91:43-52. [DOI: 10.1016/j.reprotox.2019.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/10/2019] [Accepted: 11/18/2019] [Indexed: 12/19/2022]
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14
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HPO-Shuffle: an associated gene prioritization strategy and its application in drug repurposing for the treatment of canine epilepsy. Biosci Rep 2019; 39:BSR20191247. [PMID: 31427480 PMCID: PMC6732366 DOI: 10.1042/bsr20191247] [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: 04/28/2019] [Revised: 08/03/2019] [Accepted: 08/12/2019] [Indexed: 12/16/2022] Open
Abstract
Epilepsy is a common neurological disorder that affects mammalian species including human beings and dogs. In order to discover novel drugs for the treatment of canine epilepsy, multiomics data were analyzed to identify epilepsy associated genes. In this research, the original ranking of associated genes was obtained by two high-throughput bioinformatics experiments: Genome Wide Association Study (GWAS) and microarray analysis. The association ranking of genes was enhanced by a re-ranking system, HPO-Shuffle, which integrated information from GWAS, microarray analysis and Human Phenotype Ontology database for further downstream analysis. After applying HPO-Shuffle, the association ranking of epilepsy genes were improved. Afterward, a weighted gene coexpression network analysis (WGCNA) led to a set of gene modules, which hinted a clear relevance between the high ranked genes and the target disease. Finally, WGCNA and connectivity map (CMap) analysis were performed on the integrated dataset to discover a potential drug list, in which a well-known anticonvulsant phensuximide was included.
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15
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Nakagawa N, Plestant C, Yabuno-Nakagawa K, Li J, Lee J, Huang CW, Lee A, Krupa O, Adhikari A, Thompson S, Rhynes T, Arevalo V, Stein JL, Molnár Z, Badache A, Anton ES. Memo1-Mediated Tiling of Radial Glial Cells Facilitates Cerebral Cortical Development. Neuron 2019; 103:836-852.e5. [PMID: 31277925 DOI: 10.1016/j.neuron.2019.05.049] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 03/07/2019] [Accepted: 05/30/2019] [Indexed: 11/30/2022]
Abstract
Polarized, non-overlapping, regularly spaced, tiled organization of radial glial cells (RGCs) serves as a framework to generate and organize cortical neuronal columns, layers, and circuitry. Here, we show that mediator of cell motility 1 (Memo1) is a critical determinant of radial glial tiling during neocortical development. Memo1 deletion or knockdown leads to hyperbranching of RGC basal processes and disrupted RGC tiling, resulting in aberrant radial unit assembly and neuronal layering. Memo1 regulates microtubule (MT) stability necessary for RGC tiling. Memo1 deficiency leads to disrupted MT minus-end CAMSAP2 distribution, initiation of aberrant MT branching, and altered polarized trafficking of key basal domain proteins such as GPR56, and thus aberrant RGC tiling. These findings identify Memo1 as a mediator of RGC scaffold tiling, necessary to generate and organize neurons into functional ensembles in the developing cerebral cortex.
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Affiliation(s)
- Naoki Nakagawa
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Division of Neurogenetics, National Institute of Genetics, Mishima 411-8540, Japan; Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima 411-8540, Japan.
| | - Charlotte Plestant
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Keiko Yabuno-Nakagawa
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jingjun Li
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Janice Lee
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Chu-Wei Huang
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Amelia Lee
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Oleh Krupa
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Aditi Adhikari
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Suriya Thompson
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Tamille Rhynes
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Victoria Arevalo
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jason L Stein
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Zoltán Molnár
- Department of Physiology, Anatomy, and Genetics, University of Oxford, Oxford, UK
| | - Ali Badache
- Centre de Recherche en Cancérologie de Marseille, CRCM, Inserm, Institut Paoli-Calmettes, Aix-Marseille Université, CNRS, 13009 Marseille, France
| | - E S Anton
- UNC Neuroscience Center and the Department of Cell Biology and Physiology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA.
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16
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Xiong S, Wang Y, Li H, Zhang X. Interaction among GRIK2 gene on epilepsy susceptibility in Chinese children. Acta Neurol Scand 2019; 139:540-545. [PMID: 30908586 DOI: 10.1111/ane.13089] [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: 12/19/2018] [Revised: 03/12/2019] [Accepted: 03/16/2019] [Indexed: 11/29/2022]
Abstract
AIMS The association of single nucleotide polymorphisms (SNPs) of glutamate receptor 2 (GRIK2) gene, as well as gene-gene interaction with the risk of early-onset epilepsy susceptibility, was studied in Chinese children. METHODS Generalized multi-factor dimension reduction (GMDR) is used to identify the optimal linkage between interaction among four SNPs and early-onset epilepsy susceptibility. Logistic regression was performed to assess association between four SNPs within GRIK2 gene and the risk of epilepsy. RESULTS The results show that the risk of epilepsy in the rs4840200-T allele carriers was significantly higher than CC (CT/TT vs CC), adjusted OR (95% CI) = 1.74 (1.31-2.20), and the carrier of rs3213607-A allele was also higher than CC (CG/GG vs CC) with adjusted OR (95% CI) = 1.61 (1.23-2.10). We did not detect significant association between rs9390754 and rs2235076 within GRIK2 gene and epilepsy risk. In the GMDR analysis for the gene/gene interaction (2-4 locus models), we found a significant two-locus model (P = 0.001) involving rs4840200 and rs9390754. The cross-validation consistency was 10/10, and the prediction error was 0.632. Participants with rs4840200-CT/TT and rs9390754-GA/AA genotype within GRIK2 gene have the highest epilepsy risk, compared to participants with rs4840200-CC and rs9390754-GG genotype within GRIK2 gene, OR (95% CI) = 2.42 (1.78-3.11), after covariates adjustment for age and gender. CONCLUSIONS Both rs4840200-T and rs3213607-A, and the interactions between rs4840200 and rs9390754 are related to the increased risk of epilepsy risk.
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Affiliation(s)
- Shunjun Xiong
- Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanjun Wang
- Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Huijuan Li
- Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiaofang Zhang
- Department of Pediatrics, Zhongnan Hospital of Wuhan University, Wuhan, China
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17
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Chromosome 1q31.2q32.1 deletion in an adult male with intellectual disability, dysmorphic features and obesity. Clin Dysmorphol 2019; 28:131-136. [PMID: 31045593 DOI: 10.1097/mcd.0000000000000281] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Intermediate interstitial deletions of the long arm of chromosome 1 are typically associated with developmental delay and dysmorphic features. We describe the case of a 31-year-old male with intellectual disability, obesity and dysmorphic features, in whom array-comparative genomic hybridization identified a de novo 9.55 Mb deletion at 1q31.2q32.1. We discuss the genes encompassed within the deleted region; in particular, the implications of the deleted cancer-predisposing gene, CDC-73, and compare our clinical findings to other cases with similar deletions. The absence of microcephaly and growth retardation appears to differentiate more proximal interstitial 1q deletions from intermediate 1q deletions, and the presence of obesity is a newly reported phenotype within the 1q deletion spectrum. It is imperative that surveillance for CDC-73 related disorders, including parathyroid carcinoma, is considered in the management of interstitial intermediate 1q deletions.
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18
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Genome-wide mega-analysis identifies 16 loci and highlights diverse biological mechanisms in the common epilepsies. Nat Commun 2018; 9:5269. [PMID: 30531953 PMCID: PMC6288131 DOI: 10.1038/s41467-018-07524-z] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
The epilepsies affect around 65 million people worldwide and have a substantial missing heritability component. We report a genome-wide mega-analysis involving 15,212 individuals with epilepsy and 29,677 controls, which reveals 16 genome-wide significant loci, of which 11 are novel. Using various prioritization criteria, we pinpoint the 21 most likely epilepsy genes at these loci, with the majority in genetic generalized epilepsies. These genes have diverse biological functions, including coding for ion-channel subunits, transcription factors and a vitamin-B6 metabolism enzyme. Converging evidence shows that the common variants associated with epilepsy play a role in epigenetic regulation of gene expression in the brain. The results show an enrichment for monogenic epilepsy genes as well as known targets of antiepileptic drugs. Using SNP-based heritability analyses we disentangle both the unique and overlapping genetic basis to seven different epilepsy subtypes. Together, these findings provide leads for epilepsy therapies based on underlying pathophysiology. Epilepsies are common brain disorders and are classified based on clinical phenotyping, imaging and genetics. Here, the authors perform genome-wide association studies for 3 broad and 7 subtypes of epilepsy and identify 16 loci - 11 novel - that are further annotated by eQTL and partitioned heritability analyses.
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19
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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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20
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Cui ZJ, Liu YM, Zhu Q, Xia J, Zhang HY. Exploring the pathogenesis of canine epilepsy using a systems genetics method and implications for anti-epilepsy drug discovery. Oncotarget 2018; 9:13181-13192. [PMID: 29568349 PMCID: PMC5862570 DOI: 10.18632/oncotarget.23719] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 11/10/2017] [Indexed: 11/25/2022] Open
Abstract
Epilepsy is a common neurological disorder in domestic dogs. However, its complex mechanism involves multiple genetic and environmental factors that make it challenging to identify the real pathogenic factors contributing to epilepsy, particularly for idiopathic epilepsy. Conventional genome-wide association studies (GWASs) can detect various genes associated with epilepsy, although they primarily detect the effects of single-site mutations in epilepsy while ignoring their interactions. In this study, we used a systems genetics method combining both GWAS and gene interactions and obtained 26 significantly mutated subnetworks. Among these subnetworks, seven genes were reported to be involved in neurological disorders. Combined with gene ontology enrichment analysis, we focused on 4 subnetworks that included traditional GWAS-neglected genes. Moreover, we performed a drug enrichment analysis for each subnetwork and identified significantly enriched candidate anti-epilepsy drugs using a hypergeometric test. We discovered 22 potential drug combinations that induced possible synergistic effects for epilepsy treatment, and one of these drug combinations has been confirmed in the Drug Combination database (DCDB) to have beneficial anti-epileptic effects. The method proposed in this study provides deep insight into the pathogenesis of canine epilepsy and implications for anti-epilepsy drug discovery.
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Affiliation(s)
- Ze-Jia Cui
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Hubei, Wuhan, China
| | - Ye-Mao Liu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Hubei, Wuhan, China
| | - Qiang Zhu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Hubei, Wuhan, China
| | - Jingbo Xia
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Hubei, Wuhan, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Hubei, Wuhan, China
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21
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Gui H, Li M, Sham PC, Baum L, Kwan P, Cherny SS. Genetic overlap between epilepsy and schizophrenia: Evidence from cross phenotype analysis in Hong Kong Chinese population. Am J Med Genet B Neuropsychiatr Genet 2018; 177:86-92. [PMID: 29150900 DOI: 10.1002/ajmg.b.32607] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 10/06/2017] [Indexed: 01/05/2023]
Abstract
Epilepsy and schizophrenia are common and typical neurological or mental illness respectively, and sometimes they comorbid in the same patients, however the underlying genetic relationship between the two brain diseases is still not fully understood. To investigate the possible genetic contribution to their comorbidity, we performed polygenic risk score (PRS) analyses and genetic correlation estimation so as to identify the overall genetic overlap between the two diseases. The global schizophrenia PRS is strongly associated with schizophrenia phenotype in Hong Kong population (odds ratio = 1.7, p = 2.26E-16), and focal epilepsy PRS is moderately associated with epilepsy phenotype in Hong Kong population (odds ratio = 1.14, p = 0.013). However the disease-specific PRS can only predict its own well-matched phenotype but not the other ones (p > 0.05). This pattern is further supported by non-significant pairwise genetic correlation and insufficient statistical power for PRS association from the cross-phenotype analyses. Our study reveals there's limited shared genetic aetiology between schizophrenia and epilepsy, and thus supports a model of shared environmental factors to explain the comorbidity between the two phenotypes.
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Affiliation(s)
- Hongsheng Gui
- Center for Genomic Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Center for Health Policy and Health Research Service, Henry Ford Health System, Detroit, Michigan
| | - Miaoxin Li
- Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China
| | - Pak C Sham
- Center for Genomic Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China.,The State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Larry Baum
- Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Patrick Kwan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Hong Kong, SAR, China.,Department of Neurology, Royal Melbourne Hospital, Melbourne, Australia
| | - Stacey S Cherny
- Center for Genomic Sciences, The University of Hong Kong, Hong Kong, SAR, China.,Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China.,The State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, SAR, China
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22
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Genetic variation associated with the occurrence and progression of neurological disorders. Neurotoxicology 2017; 61:243-264. [DOI: 10.1016/j.neuro.2016.09.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 09/23/2016] [Indexed: 02/08/2023]
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23
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SNP-based HLA allele tagging, imputation and association with antiepileptic drug-induced cutaneous reactions in Hong Kong Han Chinese. THE PHARMACOGENOMICS JOURNAL 2017; 18:340-346. [PMID: 28398356 DOI: 10.1038/tpj.2017.11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/08/2017] [Accepted: 02/14/2017] [Indexed: 12/17/2022]
Abstract
Human leukocyte antigen (HLA) genes control the regulation of the human immune system and are involved in immune-related diseases. Population surveys on relationships between single nucleotide polymorphisms (SNP) and HLA alleles are essential to conduct genetic association between HLA variants and diseases. Samples were obtained from our in-house database for epilepsy genetics and pharmacogenetics research. Using 184 epilepsy patients with both genome-wide SNP array and HLA-A/B candidate gene sequencing data, we sought tagging SNPs that completely represent sixHLA risk alleles; in addition, a Hong Kong population-specific reference panel was constructed for SNP-based HLA imputation. The performance of our new panel was compared to a recent Han Chinese panel. Finally, genetic associations of HLA variants with mild skin rash were performed on the combined sample of 408 patients. Common SNPs rs2571375 and rs144295468 were found to successfully tag HLA risk alleles A*31:01 and B*13:01, respectively. HLA-B*15:02 can be predicted by rs144012689 with >95% sensitivity and specificity. The imputation reference panel for the Hong Kong population had comparable performance to the Han Chinese panel due to the large sample size for common HLA alleles, though it retained discordance for imputing rare alleles. No significant genetic associations were found between HLA genetic variants and mild skin rash induced by aromatic antiepileptic drugs. This study provides new information on the genetic structure of HLA regions in the Hong Kong population by identifying tagging SNPs and serving as a reference panel. Moreover, our comprehensive genetic analyses revealed no significant association between HLA alleles and mild skin rash in Hong Kong Han Chinese.
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Howard LM, Hoek KL, Goll JB, Samir P, Galassie A, Allos TM, Niu X, Gordy LE, Creech CB, Prasad N, Jensen TL, Hill H, Levy SE, Joyce S, Link AJ, Edwards KM. Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial. PLoS One 2017; 12:e0167488. [PMID: 28099485 PMCID: PMC5242433 DOI: 10.1371/journal.pone.0167488] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/15/2016] [Indexed: 12/28/2022] Open
Abstract
Background Vaccine development for influenza A/H5N1 is an important public health priority, but H5N1 vaccines are less immunogenic than seasonal influenza vaccines. Adjuvant System 03 (AS03) markedly enhances immune responses to H5N1 vaccine antigens, but the underlying molecular mechanisms are incompletely understood. Objective and Methods We compared the safety (primary endpoint), immunogenicity (secondary), gene expression (tertiary) and cytokine responses (exploratory) between AS03-adjuvanted and unadjuvanted inactivated split-virus H5N1 influenza vaccines. In a double-blinded clinical trial, we randomized twenty adults aged 18–49 to receive two doses of either AS03-adjuvanted (n = 10) or unadjuvanted (n = 10) H5N1 vaccine 28 days apart. We used a systems biology approach to characterize and correlate changes in serum cytokines, antibody titers, and gene expression levels in six immune cell types at 1, 3, 7, and 28 days after the first vaccination. Results Both vaccines were well-tolerated. Nine of 10 subjects in the adjuvanted group and 0/10 in the unadjuvanted group exhibited seroprotection (hemagglutination inhibition antibody titer > 1:40) at day 56. Within 24 hours of AS03-adjuvanted vaccination, increased serum levels of IL-6 and IP-10 were noted. Interferon signaling and antigen processing and presentation-related gene responses were induced in dendritic cells, monocytes, and neutrophils. Upregulation of MHC class II antigen presentation-related genes was seen in neutrophils. Three days after AS03-adjuvanted vaccine, upregulation of genes involved in cell cycle and division was detected in NK cells and correlated with serum levels of IP-10. Early upregulation of interferon signaling-related genes was also found to predict seroprotection 56 days after first vaccination. Conclusions Using this cell-based systems approach, novel mechanisms of action for AS03-adjuvanted pandemic influenza vaccination were observed. Trial Registration ClinicalTrials.gov NCT01573312
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Affiliation(s)
- Leigh M. Howard
- Vanderbilt Vaccine Research Program, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Kristen L. Hoek
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | | | - Parimal Samir
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Allison Galassie
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Tara M. Allos
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Xinnan Niu
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Laura E. Gordy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - C. Buddy Creech
- Vanderbilt Vaccine Research Program, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Nripesh Prasad
- HudsonAlpha Institute for Biotechnology; Huntsville, AL, United States of America
| | | | - Heather Hill
- The Emmes Corporation, Rockville, MD, United States of America
| | - Shawn E. Levy
- HudsonAlpha Institute for Biotechnology; Huntsville, AL, United States of America
| | - Sebastian Joyce
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
- Veterans Administration Tennessee Valley Healthcare System, Nashville, TN, United States of America
| | - Andrew J. Link
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN, United States of America
- * E-mail: (KME); (AJL)
| | - Kathryn M. Edwards
- Vanderbilt Vaccine Research Program, Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, United States of America
- * E-mail: (KME); (AJL)
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Chen T, Giri M, Xia Z, Subedi YN, Li Y. Genetic and epigenetic mechanisms of epilepsy: a review. Neuropsychiatr Dis Treat 2017; 13:1841-1859. [PMID: 28761347 PMCID: PMC5516882 DOI: 10.2147/ndt.s142032] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Epilepsy is a common episodic neurological disorder or condition characterized by recurrent epileptic seizures, and genetics seems to play a key role in its etiology. Early linkage studies have localized multiple loci that may harbor susceptibility genes to epilepsy, and mutational analyses have detected a number of mutations involved in both ion channel and nonion channel genes in patients with idiopathic epilepsy. Genome-wide studies of epilepsy have found copy number variants at 2q24.2-q24.3, 7q11.22, 15q11.2-q13.3, and 16p13.11-p13.2, some of which disrupt multiple genes, such as NRXN1, AUTS2, NLGN1, CNTNAP2, GRIN2A, PRRT2, NIPA2, and BMP5, implicated for neurodevelopmental disorders, including intellectual disability and autism. Unfortunately, only a few common genetic variants have been associated with epilepsy. Recent exome-sequencing studies have found some genetic mutations, most of which are located in nonion channel genes such as the LGI1, PRRT2, EFHC1, PRICKLE, RBFOX1, and DEPDC5 and in probands with rare forms of familial epilepsy, and some of these genes are involved with the neurodevelopment. Since epigenetics plays a role in neuronal function from embryogenesis and early brain development to tissue-specific gene expression, epigenetic regulation may contribute to the genetic mechanism of neurodevelopment through which a gene and the environment interacting with each other affect the development of epilepsy. This review focused on the analytic tools used to identify epilepsy and then provided a summary of recent linkage and association findings, indicating the existence of novel genes on several chromosomes for further understanding of the biology of epilepsy.
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Affiliation(s)
- Tian Chen
- Department of Health Management Center, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
| | - Mohan Giri
- National Center for Rheumatic Diseases, Ratopul, Gaushala, Kathmandu, Nepal
| | - Zhenyi Xia
- Department of Thoracic Surgery, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
| | - Yadu Nanda Subedi
- National Center for Rheumatic Diseases, Ratopul, Gaushala, Kathmandu, Nepal
| | - Yan Li
- Department of Health Management Center, Chongqing Three Gorges Central Hospital, Chongqing, People's Republic of China
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Progress from genome-wide association studies and copy number variant studies in epilepsy. Curr Opin Neurol 2016; 29:158-67. [PMID: 26886358 DOI: 10.1097/wco.0000000000000296] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
PURPOSE OF REVIEW The pace of gene discovery in epilepsy remains frenetic. Although most recent discoveries have come from next-generation sequencing studies, there has also been important progress using more established methodologies, such as genome-wide association studies (GWASs) and copy number variants (CNVs) identified through array-based techniques. Progress in these areas over the last year is reviewed. RECENT FINDINGS The first meta-analysis of GWASs was a landmark development for the epilepsy community, though more sizeable studies are sorely needed. Other GWASs point to potentially interesting discoveries, and are in need of replication and follow-up. Copy number variation is emerging as an important genetic contribution to causation across a wide range of epilepsies, with a number of discoveries in epilepsies from the common, such as genetic generalized epilepsies, to the individually comparatively rare, such as particular epileptic encephalopathies. The first studies of CNV analysis from next-generation sequencing data, and of the combination of sequencing and array-based data, have also emerged, allowing more comprehensive genetic evaluation of specific phenotypes. SUMMARY GWASs based on single nucleotide polymorphisms, and CNV analyses based on a variety of data sources, retain a place in the discovery of causation and susceptibility in the epilepsies, and will probably become more powerful in the near future through the use of large-scale next-generation sequencing studies. There are still discoveries to come through these routes.
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Robertson DS, Prevost AT, Bowden J. Accounting for selection and correlation in the analysis of two-stage genome-wide association studies. Biostatistics 2016; 17:634-49. [PMID: 26993061 PMCID: PMC5031943 DOI: 10.1093/biostatistics/kxw012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 11/11/2015] [Accepted: 01/15/2016] [Indexed: 11/15/2022] Open
Abstract
The problem of selection bias has long been recognized in the analysis of two-stage trials, where promising candidates are selected in stage 1 for confirmatory analysis in stage 2. To efficiently correct for bias, uniformly minimum variance conditionally unbiased estimators (UMVCUEs) have been proposed for a wide variety of trial settings, but where the population parameter estimates are assumed to be independent. We relax this assumption and derive the UMVCUE in the multivariate normal setting with an arbitrary known covariance structure. One area of application is the estimation of odds ratios (ORs) when combining a genome-wide scan with a replication study. Our framework explicitly accounts for correlated single nucleotide polymorphisms, as might occur due to linkage disequilibrium. We illustrate our approach on the measurement of the association between 11 genetic variants and the risk of Crohn's disease, as reported in Parkes and others (2007. Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility. Nat. Gen. 39: (7), 830-832.), and show that the estimated ORs can vary substantially if both selection and correlation are taken into account.
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Affiliation(s)
- David S Robertson
- MRC Biostatistics Unit, IPH Forvie Site, Robinson Way, Cambridge CB2 0SR, UK
| | - A Toby Prevost
- Imperial College London, 1st Floor, Stadium House, 68 Wood Lane, London W12 7RH, UK
| | - Jack Bowden
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol BS8 2BN, UK and MRC Biostatistics Unit, IPH Forvie Site, Robinson Way, Cambridge CB2 0SR, UK
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Alhusaini S, Whelan CD, Sisodiya SM, Thompson PM. Quantitative magnetic resonance imaging traits as endophenotypes for genetic mapping in epilepsy. NEUROIMAGE-CLINICAL 2016; 12:526-534. [PMID: 27672556 PMCID: PMC5030372 DOI: 10.1016/j.nicl.2016.09.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/21/2016] [Accepted: 09/05/2016] [Indexed: 12/18/2022]
Abstract
Over the last decade, the field of imaging genomics has combined high-throughput genotype data with quantitative magnetic resonance imaging (QMRI) measures to identify genes associated with brain structure, cognition, and several brain-related disorders. Despite its successful application in different psychiatric and neurological disorders, the field has yet to be advanced in epilepsy. In this article we examine the relevance of imaging genomics for future genetic studies in epilepsy from three perspectives. First, we discuss prior genome-wide genetic mapping efforts in epilepsy, considering the possibility that some studies may have been constrained by inherent theoretical and methodological limitations of the genome-wide association study (GWAS) method. Second, we offer a brief overview of the imaging genomics paradigm, from its original inception, to its role in the discovery of important risk genes in a number of brain-related disorders, and its successful application in large-scale multinational research networks. Third, we provide a comprehensive review of past studies that have explored the eligibility of brain QMRI traits as endophenotypes for epilepsy. While the breadth of studies exploring QMRI-derived endophenotypes in epilepsy remains narrow, robust syndrome-specific neuroanatomical QMRI traits have the potential to serve as accessible and relevant intermediate phenotypes for future genetic mapping efforts in epilepsy. QMRI traits have the potential to serve as robust intermediate phenotypes for brain-related disorders. Hippocampal volume is the most promising neuroimaging endophenotype for MTLE + HS. Imaging genomics holds great promise in advancing epilepsy genetic research. Studies are encouraged to explore the validity of QMRI traits as endophenotypes for epilepsy.
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Affiliation(s)
- Saud Alhusaini
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Christopher D Whelan
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, University College London Hospitals Biomedical Research Centre, UCL Institute of Neurology, London, UK
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
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29
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Tao H, Si L, Zhou X, Liu Z, Ma Z, Zhou H, Zhong W, Cui L, Zhang S, Li Y, Ma G, Zhao J, Huang W, Yao L, Xu Z, Zhao B, Li K. Role of glyoxalase I gene polymorphisms in late-onset epilepsy and drug-resistant epilepsy. J Neurol Sci 2016; 363:200-6. [PMID: 27000251 DOI: 10.1016/j.jns.2016.01.052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 01/16/2016] [Accepted: 01/25/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Recent studies indicate that increased expression of glyoxalase I (GLO1) could result in epileptic seizures; thus, this study further explored the association of GLO1 with epilepsy from the perspective of molecular genetics. MATERIAL AND METHODS GLO1 single nucleotide polymorphisms (SNPs; rs1130534, rs4746 and rs1049346) were investigated in cohort I (the initial samples: 249 cases and 289 controls). A replication study designed to confirm the positive findings in cohort I was performed in cohorts II (the additional samples: 130 cases and 191 controls) and I+II. RESULTS In cohorts I, II and I+II, the CC genotype at rs1049346 T>C exerts a protective effect against both late-onset epilepsy (odds ratio [OR]=2.437, p=0.013; OR=2.844, p=0.008; OR=2.645, p=0.000, q=0.003, respectively) and drug-resistant epilepsy (DRE) (OR=2.985, p=0.020; OR=2.943, p=0.014; OR=3.049, p=0.001, q=0.006, respectively). Further analyses in cohort I+II indicate that the presence of the TAC/AAT haplotypes (rs1130534-rs4746-rs1049346) may be used as a marker of predisposition to/protection against DRE (p=0.002, q=0.010; p=0.000, q=0.002, respectively). CONCLUSIONS This study is the first to demonstrate that the GLO1 SNPs are significantly associated with epilepsy. In particular, the rs1049346 T>C SNPs are potentially useful for risk assessment of late-onset epilepsy and DRE.
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Affiliation(s)
- Hua Tao
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Ligang Si
- Department of Pediatrics, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Xu Zhou
- Clinical Research Center, Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Zhou Liu
- Institute of Neurology, Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Zhonghua Ma
- Department of Neurology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China
| | - Haihong Zhou
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Wangtao Zhong
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Lili Cui
- Institute of Neurology, Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Shuyan Zhang
- Department of Neurology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - You Li
- Institute of Neurology, Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Guoda Ma
- Institute of Neurology, Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Jianghao Zhao
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Wenhui Huang
- Institute of Neurology, Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Lifen Yao
- Department of Pediatrics, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Zhien Xu
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China
| | - Bin Zhao
- Department of Neurology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524001, China; Institute of Neurology, Guangdong Medical University, Zhanjiang, Guangdong 524001, China.
| | - Keshen Li
- Institute of Neurology, Guangdong Medical University, Zhanjiang, Guangdong 524001, China.
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30
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Wight JE, Nguyen VH, Medina MT, Patterson C, Durón RM, Molina Y, Lin YC, Martínez-Juárez IE, Ochoa A, Jara-Prado A, Tanaka M, Bai D, Aftab S, Bailey JN, Delgado-Escueta AV. Chromosome loci vary by juvenile myoclonic epilepsy subsyndromes: linkage and haplotype analysis applied to epilepsy and EEG 3.5-6.0 Hz polyspike waves. Mol Genet Genomic Med 2016; 4:197-210. [PMID: 27066514 PMCID: PMC4799870 DOI: 10.1002/mgg3.195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 12/15/2022] Open
Abstract
Juvenile myoclonic epilepsy (JME), the most common genetic epilepsy, remains enigmatic because it is considered one disease instead of several diseases. We ascertained three large multigenerational/multiplex JME pedigrees from Honduras with differing JME subsyndromes, including Childhood Absence Epilepsy evolving to JME (CAE/JME; pedigree 1), JME with adolescent onset pyknoleptic absence (JME/pA; pedigree 2), and classic JME (cJME; pedigree 3). All phenotypes were validated, including symptomatic persons with various epilepsies, asymptomatic persons with EEG 3.5-6.0 Hz polyspike waves, and asymptomatic persons with normal EEGs. Two-point parametric linkage analyses were performed with 5185 single-nucleotide polymorphisms on individual pedigrees and pooled pedigrees using four diagnostic models based on epilepsy/EEG diagnoses. Haplotype analyses of the entire genome were also performed for each individual. In pedigree 1, haplotyping identified a 34 cM region in 2q21.2-q31.1 cosegregating with all affected members, an area close to 2q14.3 identified by linkage (Z max = 1.77; pedigree 1). In pedigree 2, linkage and haplotyping identified a 44 cM cosegregating region in 13q13.3-q31.2 (Z max = 3.50 at 13q31.1; pooled pedigrees). In pedigree 3, haplotyping identified a 6 cM cosegregating region in 17q12. Possible cosegregation was also identified in 13q14.2 and 1q32 in pedigree 3, although this could not be definitively confirmed due to the presence of uninformative markers in key individuals. Differing chromosome regions identified in specific JME subsyndromes may contain separate JME disease-causing genes, favoring the concept of JME as several distinct diseases. Whole-exome sequencing will likely identify a CAE/JME gene in 2q21.2-2q31.1, a JME/pA gene in 13q13.3-q31.2, and a cJME gene in 17q12.
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Affiliation(s)
- Jenny E Wight
- Epilepsy Genetics/Genomics LaboratoriesVA GLAHS - West Los AngelesLos AngelesCalifornia; GENESS International ConsortiumLos AngelesCalifornia
| | - Viet-Huong Nguyen
- Epilepsy Genetics/Genomics LaboratoriesVA GLAHS - West Los AngelesLos AngelesCalifornia; GENESS International ConsortiumLos AngelesCalifornia
| | - Marco T Medina
- GENESS International ConsortiumLos AngelesCalifornia; National Autonomous University of HondurasTegucigalpaHonduras
| | - Christopher Patterson
- Epilepsy Genetics/Genomics LaboratoriesVA GLAHS - West Los AngelesLos AngelesCalifornia; GENESS International ConsortiumLos AngelesCalifornia
| | - Reyna M Durón
- Epilepsy Genetics/Genomics LaboratoriesVA GLAHS - West Los AngelesLos AngelesCalifornia; GENESS International ConsortiumLos AngelesCalifornia; National Autonomous University of HondurasTegucigalpaHonduras; Universidad Tecnológica Centroamericana (UNITEC)TegucigalpaHonduras; Department of NeurologyDavid Geffen School of Medicine at UCLALos AngelesCalifornia
| | - Yolly Molina
- GENESS International ConsortiumLos AngelesCalifornia; National Autonomous University of HondurasTegucigalpaHonduras
| | - Yu-Chen Lin
- Epilepsy Genetics/Genomics LaboratoriesVA GLAHS - West Los AngelesLos AngelesCalifornia; GENESS International ConsortiumLos AngelesCalifornia
| | - Iris E Martínez-Juárez
- GENESS International ConsortiumLos AngelesCalifornia; National Institute of Neurology and NeurosurgeryMexico CityMexico
| | - Adriana Ochoa
- GENESS International ConsortiumLos AngelesCalifornia; National Institute of Neurology and NeurosurgeryMexico CityMexico
| | - Aurelio Jara-Prado
- GENESS International ConsortiumLos AngelesCalifornia; National Institute of Neurology and NeurosurgeryMexico CityMexico
| | - Miyabi Tanaka
- Epilepsy Genetics/Genomics LaboratoriesVA GLAHS - West Los AngelesLos AngelesCalifornia; GENESS International ConsortiumLos AngelesCalifornia; Department of NeurologyDavid Geffen School of Medicine at UCLALos AngelesCalifornia
| | - Dongsheng Bai
- Epilepsy Genetics/Genomics LaboratoriesVA GLAHS - West Los AngelesLos AngelesCalifornia; GENESS International ConsortiumLos AngelesCalifornia; Department of NeurologyDavid Geffen School of Medicine at UCLALos AngelesCalifornia
| | - Sumaya Aftab
- Epilepsy Genetics/Genomics LaboratoriesVA GLAHS - West Los AngelesLos AngelesCalifornia; GENESS International ConsortiumLos AngelesCalifornia; Department of NeurologyDavid Geffen School of Medicine at UCLALos AngelesCalifornia
| | - Julia N Bailey
- Epilepsy Genetics/Genomics LaboratoriesVA GLAHS - West Los AngelesLos AngelesCalifornia; GENESS International ConsortiumLos AngelesCalifornia; Department of EpidemiologyFielding School of Public Health at UCLALos AngelesCalifornia
| | - Antonio V Delgado-Escueta
- Epilepsy Genetics/Genomics LaboratoriesVA GLAHS - West Los AngelesLos AngelesCalifornia; GENESS International ConsortiumLos AngelesCalifornia; Department of NeurologyDavid Geffen School of Medicine at UCLALos AngelesCalifornia
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Abstract
Microtubules are cytoskeletal filaments that are intrinsically polarized, with two structurally and functionally distinct ends, the plus end and the minus end. Over the last decade, numerous studies have shown that microtubule plus-end dynamics play an important role in many vital cellular processes and are controlled by numerous factors, such as microtubule plus-end-tracking proteins (+TIPs). In contrast, the cellular machinery that controls the behavior and organization of microtubule minus ends remains one of the least well-understood facets of the microtubule cytoskeleton. The recent characterization of the CAMSAP/Patronin/Nezha family members as specific 'minus-end-targeting proteins' ('-TIPs') has provided important new insights into the mechanisms governing minus-end dynamics. Here, we review the current state of knowledge on how microtubule minus ends are controlled and how minus-end regulators contribute to non-centrosomal microtubule organization and function during cell division, migration and differentiation.
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Ferraro TN. Barriers to the use of genetic information for the development of new epilepsy treatments. Expert Rev Neurother 2015; 16:5-8. [PMID: 26559170 DOI: 10.1586/14737175.2016.1115718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Genetic analysis is providing new information on the biological basis of epilepsy at a rapid pace; this article identifies factors acting as major barriers to use of these data for therapy development. Disease heterogeneity is a primary obstacle since so many genes can cause or predispose to epilepsy and the clinical presentation of epilepsy is so diverse, thus making it difficult to define the most therapeutically relevant targets. Further, many epilepsy genes affect brain development, an observation that represents a barrier unto itself given the challenge of reversing or preventing genetically mediated alterations of brain pathway formation. Finally, the lack of appropriate models for testing new therapies is also recognized as a fundamental limitation. Overcoming these barriers will be aided by full characterization of the genetic landscape of epilepsy, elucidation of key pathway points for therapeutic intervention and creation of unique experimental models to validate results.
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Affiliation(s)
- Thomas N Ferraro
- a Department of Biomedical Sciences , Cooper Medical School of Rowan University , Camden , NJ 08103 , USA
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33
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Contribution of GABRG2 Polymorphisms to Risk of Epilepsy and Febrile Seizure: a Multicenter Cohort Study and Meta-analysis. Mol Neurobiol 2015; 53:5457-67. [DOI: 10.1007/s12035-015-9457-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 09/25/2015] [Indexed: 10/23/2022]
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Association of BDNF Polymorphisms with the Risk of Epilepsy: a Multicenter Study. Mol Neurobiol 2015; 53:2869-2877. [PMID: 25876511 DOI: 10.1007/s12035-015-9150-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/19/2015] [Indexed: 12/23/2022]
Abstract
Epilepsy is a common neurological disease characterized by recurrent unprovoked seizures. Evidence suggested that abnormal activity of brain-derived neurotrophic factor (BDNF) contributes to the pathogenesis of epilepsy. Some previous studies identified association between genetic variants of BDNF and risk of epilepsy. In this study, this association has been examined in the Hong Kong and Malaysian epilepsy cohorts. Genomic DNA of 6047 subjects (1640 patients with epilepsy and 4407 healthy individuals) was genotyped for rs6265, rs11030104, rs7103411, and rs7127507 polymorphisms by using Sequenom MassArray and Illumina HumanHap 610-Quad or 550-Duo BeadChip arrays techniques. Results showed significant association between rs6265 T, rs7103411 C, and rs7127507 T and cryptgenic epilepsy risk (p = 0.00003, p = 0.0002, and p = 0.002, respectively) or between rs6265 and rs7103411 and symptomatic epilepsy risk in Malaysian Indians (TT vs. CC, p = 0.004 and T vs. C, p = 0.0002, respectively) as well as between rs6265 T and risk of cryptogenic epilepsy in Malaysian Chinese (p = 0.005). The Trs6265-Crs7103411-Trs7127507 was significantly associated with cryptogenic epilepsy in Malaysian Indians (p = 0.00005). In conclusion, our results suggest that BDNF polymorphisms might contribute to the risk of epilepsy in Malaysian Indians and Chinese.
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35
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Haerian BS, Sha'ari HM, Tan HJ, Fong CY, Wong SW, Ong LC, Raymond AA, Tan CT, Mohamed Z. RORA gene rs12912233 and rs880626 polymorphisms and their interaction with SCN1A rs3812718 in the risk of epilepsy: A case–control study in Malaysia. Genomics 2015; 105:229-36. [DOI: 10.1016/j.ygeno.2015.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/24/2015] [Accepted: 02/02/2015] [Indexed: 11/26/2022]
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Johnson MR, Behmoaras J, Bottolo L, Krishnan ML, Pernhorst K, Santoscoy PLM, Rossetti T, Speed D, Srivastava PK, Chadeau-Hyam M, Hajji N, Dabrowska A, Rotival M, Razzaghi B, Kovac S, Wanisch K, Grillo FW, Slaviero A, Langley SR, Shkura K, Roncon P, De T, Mattheisen M, Niehusmann P, O'Brien TJ, Petrovski S, von Lehe M, Hoffmann P, Eriksson J, Coffey AJ, Cichon S, Walker M, Simonato M, Danis B, Mazzuferi M, Foerch P, Schoch S, De Paola V, Kaminski RM, Cunliffe VT, Becker AJ, Petretto E. Systems genetics identifies Sestrin 3 as a regulator of a proconvulsant gene network in human epileptic hippocampus. Nat Commun 2015; 6:6031. [PMID: 25615886 DOI: 10.1038/ncomms7031] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 12/04/2014] [Indexed: 01/20/2023] Open
Abstract
Gene-regulatory network analysis is a powerful approach to elucidate the molecular processes and pathways underlying complex disease. Here we employ systems genetics approaches to characterize the genetic regulation of pathophysiological pathways in human temporal lobe epilepsy (TLE). Using surgically acquired hippocampi from 129 TLE patients, we identify a gene-regulatory network genetically associated with epilepsy that contains a specialized, highly expressed transcriptional module encoding proconvulsive cytokines and Toll-like receptor signalling genes. RNA sequencing analysis in a mouse model of TLE using 100 epileptic and 100 control hippocampi shows the proconvulsive module is preserved across-species, specific to the epileptic hippocampus and upregulated in chronic epilepsy. In the TLE patients, we map the trans-acting genetic control of this proconvulsive module to Sestrin 3 (SESN3), and demonstrate that SESN3 positively regulates the module in macrophages, microglia and neurons. Morpholino-mediated Sesn3 knockdown in zebrafish confirms the regulation of the transcriptional module, and attenuates chemically induced behavioural seizures in vivo.
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Affiliation(s)
- Michael R Johnson
- Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, London W12 0NN, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Leonardo Bottolo
- Department of Mathematics, Imperial College London, 180 Queen's Gate, London SW7 2AZ, UK
| | - Michelle L Krishnan
- Centre for the Developing Brain, Department of Perinatal Imaging and Health, St Thomas' Hospital, King's College London, London SE1 7EH, UK
| | - Katharina Pernhorst
- Section of Translational Epileptology, Department of Neuropathology, University of Bonn, Sigmund Freud Street 25, Bonn D-53127, Germany
| | - Paola L Meza Santoscoy
- Department of Biomedical Science, Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Tiziana Rossetti
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Doug Speed
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Prashant K Srivastava
- Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, London W12 0NN, UK.,Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, School of Public Health, MRC/PHE Centre for Environment and Health, Imperial College London, St Mary's Hospital, Norfolk Place, W21PG London, UK
| | - Nabil Hajji
- Department of Medicine, Centre for Pharmacology and Therapeutics, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Aleksandra Dabrowska
- Department of Medicine, Centre for Pharmacology and Therapeutics, Imperial College London, Du Cane Road, London W12 0NN, UK
| | - Maxime Rotival
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Banafsheh Razzaghi
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Stjepana Kovac
- Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Klaus Wanisch
- Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Federico W Grillo
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Anna Slaviero
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Sarah R Langley
- Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, London W12 0NN, UK.,Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Kirill Shkura
- Division of Brain Sciences, Imperial College London, Hammersmith Hospital Campus, Burlington Danes Building, London W12 0NN, UK.,Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Paolo Roncon
- Department of Medical Sciences, Section of Pharmacology and Neuroscience Center, University of Ferrara, 44121 Ferrara, Italy.,National Institute of Neuroscience, 44121 Ferrara, Italy
| | - Tisham De
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Manuel Mattheisen
- Department of Genomics, Life and Brain Center, University of Bonn, D-53127 Bonn, Germany.,Institute of Human Genetics, University of Bonn, D-53127 Bonn, Germany.,Institute for Genomic Mathematics, University of Bonn, D-53127 Bonn, Germany
| | - Pitt Niehusmann
- Section of Translational Epileptology, Department of Neuropathology, University of Bonn, Sigmund Freud Street 25, Bonn D-53127, Germany
| | - Terence J O'Brien
- Department of Medicine, RMH, University of Melbourne, Royal Melbourne Hospital, Royal Parade, Parkville, Victoria 3050, Australia
| | - Slave Petrovski
- Department of Neurology, Royal Melbourne Hospital, Melbourne, Parkville, Victoria 3050, Australia
| | - Marec von Lehe
- Department of Neurosurgery, University of Bonn Medical Center, Sigmund-Freud-Strasse 25, 53105 Bonn, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.,Department of Biomedicine, University of Basel, Hebelstrasse 20, 4056 Basel, Switzerland
| | - Johan Eriksson
- Folkhälsan Research Centre, Topeliusgatan 20, 00250 Helsinki, Finland.,Helsinki University Central Hospital, Unit of General Practice, Haartmaninkatu 4, Helsinki 00290, Finland.,Department of General Practice and Primary Health Care, University of Helsinki, 407, PO Box 20, Tukholmankatu 8 B, Helsinki 00014, Finland
| | - Alison J Coffey
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Sven Cichon
- Institute of Human Genetics, University of Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.,Department of Biomedicine, University of Basel, Hebelstrasse 20, 4056 Basel, Switzerland
| | - Matthew Walker
- Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Michele Simonato
- Department of Medical Sciences, Section of Pharmacology and Neuroscience Center, University of Ferrara, 44121 Ferrara, Italy.,National Institute of Neuroscience, 44121 Ferrara, Italy.,Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, 44121 Ferrara, Italy
| | - Bénédicte Danis
- Neuroscience TA, UCB Biopharma SPRL, Avenue de l'industrie, R9, B-1420 Braine l'Alleud, Belgium
| | - Manuela Mazzuferi
- Neuroscience TA, UCB Biopharma SPRL, Avenue de l'industrie, R9, B-1420 Braine l'Alleud, Belgium
| | - Patrik Foerch
- Neuroscience TA, UCB Biopharma SPRL, Avenue de l'industrie, R9, B-1420 Braine l'Alleud, Belgium
| | - Susanne Schoch
- Section of Translational Epileptology, Department of Neuropathology, University of Bonn, Sigmund Freud Street 25, Bonn D-53127, Germany.,Department of Epileptology, University of Bonn Medical Center, Sigmund-Freud-Strasse 25, Bonn D-53127, Germany
| | - Vincenzo De Paola
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | - Rafal M Kaminski
- Neuroscience TA, UCB Biopharma SPRL, Avenue de l'industrie, R9, B-1420 Braine l'Alleud, Belgium
| | - Vincent T Cunliffe
- Department of Biomedical Science, Bateson Centre, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - Albert J Becker
- Section of Translational Epileptology, Department of Neuropathology, University of Bonn, Sigmund Freud Street 25, Bonn D-53127, Germany
| | - Enrico Petretto
- Medical Research Council (MRC) Clinical Sciences Centre, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK.,Duke-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore
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Tan MS, Jiang T, Tan L, Yu JT. Genome-wide association studies in neurology. ANNALS OF TRANSLATIONAL MEDICINE 2015; 2:124. [PMID: 25568877 DOI: 10.3978/j.issn.2305-5839.2014.11.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 03/04/2013] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies (GWAS) are a powerful tool for understanding the genetic underpinnings of human disease. In this article, we briefly review the role and findings of GWAS in common neurological diseases, including Stroke, Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, migraine, amyotrophic lateral sclerosis, frontotemporal lobar degeneration, restless legs syndrome, intracranial aneurysm, human prion diseases and moyamoya disease. We then discuss the present and future implications of these findings with regards to disease prediction, uncovering basic biology, and the development of potential therapeutic agents.
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Affiliation(s)
- Meng-Shan Tan
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Teng Jiang
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Lan Tan
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Jin-Tai Yu
- 1 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 2 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
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Abstract
Background The epilepsies are a clinically heterogeneous group of neurological disorders. Despite strong evidence for heritability, genome-wide association studies have had little success in identification of risk loci associated with epilepsy, probably because of relatively small sample sizes and insufficient power. We aimed to identify risk loci through meta-analyses of genome-wide association studies for all epilepsy and the two largest clinical subtypes (genetic generalised epilepsy and focal epilepsy). Methods We combined genome-wide association data from 12 cohorts of individuals with epilepsy and controls from population-based datasets. Controls were ethnically matched with cases. We phenotyped individuals with epilepsy into categories of genetic generalised epilepsy, focal epilepsy, or unclassified epilepsy. After standardised filtering for quality control and imputation to account for different genotyping platforms across sites, investigators at each site conducted a linear mixed-model association analysis for each dataset. Combining summary statistics, we conducted fixed-effects meta-analyses of all epilepsy, focal epilepsy, and genetic generalised epilepsy. We set the genome-wide significance threshold at p<1·66 × 10−8. Findings We included 8696 cases and 26 157 controls in our analysis. Meta-analysis of the all-epilepsy cohort identified loci at 2q24.3 (p=8·71 × 10−10), implicating SCN1A, and at 4p15.1 (p=5·44 × 10−9), harbouring PCDH7, which encodes a protocadherin molecule not previously implicated in epilepsy. For the cohort of genetic generalised epilepsy, we noted a single signal at 2p16.1 (p=9·99 × 10−9), implicating VRK2 or FANCL. No single nucleotide polymorphism achieved genome-wide significance for focal epilepsy. Interpretation This meta-analysis describes a new locus not previously implicated in epilepsy and provides further evidence about the genetic architecture of these disorders, with the ultimate aim of assisting in disease classification and prognosis. The data suggest that specific loci can act pleiotropically raising risk for epilepsy broadly, or can have effects limited to a specific epilepsy subtype. Future genetic analyses might benefit from both lumping (ie, grouping of epilepsy types together) or splitting (ie, analysis of specific clinical subtypes). Funding International League Against Epilepsy and multiple governmental and philanthropic agencies.
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Speed D, O'Brien TJ, Palotie A, Shkura K, Marson AG, Balding DJ, Johnson MR. Describing the genetic architecture of epilepsy through heritability analysis. ACTA ACUST UNITED AC 2014; 137:2680-9. [PMID: 25063994 PMCID: PMC4163034 DOI: 10.1093/brain/awu206] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Epilepsy is highly heritable, but its genetic architecture is poorly understood. Speed et al. estimate the number of susceptibility loci, show that common variants account for the majority of heritability, and demonstrate that epilepsy consists of genetically distinct subtypes. They conclude that gene-based prediction models may have clinical utility in first-seizure settings. Epilepsy is a disease with substantial missing heritability; despite its high genetic component, genetic association studies have had limited success detecting common variants which influence susceptibility. In this paper, we reassess the role of common variants on epilepsy using extensions of heritability analysis. Our data set consists of 1258 UK patients with epilepsy, of which 958 have focal epilepsy, and 5129 population control subjects, with genotypes recorded for over 4 million common single nucleotide polymorphisms. Firstly, we show that on the liability scale, common variants collectively explain at least 26% (standard deviation 5%) of phenotypic variation for all epilepsy and 27% (standard deviation 5%) for focal epilepsy. Secondly we provide a new method for estimating the number of causal variants for complex traits; when applied to epilepsy, our most optimistic estimate suggests that at least 400 variants influence disease susceptibility, with potentially many thousands. Thirdly, we use bivariate analysis to assess how similar the genetic architecture of focal epilepsy is to that of non-focal epilepsy; we demonstrate both significant differences (P = 0.004) and significant similarities (P = 0.01) between the two subtypes, indicating that although the clinical definition of focal epilepsy does identify a genetically distinct epilepsy subtype, there is also scope to improve the classification of epilepsy by incorporating genotypic information. Lastly, we investigate the potential value in using genetic data to diagnose epilepsy following a single epileptic seizure; we find that a prediction model explaining 10% of phenotypic variation could have clinical utility for deciding which single-seizure individuals are likely to benefit from immediate anti-epileptic drug therapy.
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Affiliation(s)
- Doug Speed
- 1 UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Terence J O'Brien
- 2 The Departments of Medicine and Neurology, The Royal Melbourne Hospital, The University of Melbourne, Australia
| | - Aarno Palotie
- 3 Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland 4 The Broad Institute of MIT and Harvard, Cambridge, USA 5 Department of Medical Genetics, University of Helsinki, Finland 6 University Central Hospital, Helsinki, Finland
| | - Kirill Shkura
- 7 Division of Brain Sciences, Imperial College London, London W6 8RF, UK 8 Medical Research Council (MRC) Clinical Sciences Centre, Faculty of Medicine, Imperial College London, UK
| | - Anthony G Marson
- 9 Department of Molecular and Clinical Pharmacology, University of Liverpool, UK
| | - David J Balding
- 1 UCL Genetics Institute, University College London, London WC1E 6BT, UK
| | - Michael R Johnson
- 7 Division of Brain Sciences, Imperial College London, London W6 8RF, UK
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40
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Haerian BS, Baum L, Kwan P, Tan HJ, Raymond AA, Mohamed Z. SCN1A, SCN2A and SCN3A gene polymorphisms and responsiveness to antiepileptic drugs: a multicenter cohort study and meta-analysis. Pharmacogenomics 2014; 14:1153-66. [PMID: 23859570 DOI: 10.2217/pgs.13.104] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Approximately a third of newly diagnosed epilepsy patients do not respond to antiepileptic drugs (AEDs). Evidence suggests that low penetrance variants in the genes of drug targets such as voltage-gated sodium channels may be involved in drug responsiveness. To examine this hypothesis, we compared data from two epilepsy cohorts from Malaysia and Hong Kong, as well as a meta-analysis from published data. MATERIALS & METHODS Genotype analysis of 39 polymorphisms located in the SCN1A, SCN2A and SCN3A genes was performed on 1504 epilepsy patients from Malaysia and Hong Kong who were receiving AEDs. Meta-analysis was performed for pooled data of SCN1A rs3812718 and rs2298771, and SCN2A rs17183814 polymorphisms. RESULTS Our data from the Hong Kong and Malaysia cohorts showed no significant allele, genotype and haplotype association of polymorphisms in the SCN1A, SCN2A, and SCN3A genes with drug responsiveness in epilepsy. This finding was supported by a meta-analysis for SCN1A rs3812718 and rs2298771, and for SCN2A rs17183814 polymorphisms. CONCLUSION Our comprehensive study suggests that common polymorphisms in SCN1A, SCN2A and SCN3A do not play major roles in influencing response to AEDs. Original submitted 11 March 2013; Revision submitted 31 May 2013.
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Affiliation(s)
- Batoul Sadat Haerian
- Pharmacogenomics Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
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41
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Marcette JD, Chen JJ, Nonet ML. The Caenorhabditis elegans microtubule minus-end binding homolog PTRN-1 stabilizes synapses and neurites. eLife 2014; 3:e01637. [PMID: 24569480 PMCID: PMC3930908 DOI: 10.7554/elife.01637] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 01/17/2014] [Indexed: 12/17/2022] Open
Abstract
Microtubule dynamics facilitate neurite growth and establish morphology, but the role of minus-end binding proteins in these processes is largely unexplored. CAMSAP homologs associate with microtubule minus-ends, and are important for the stability of epithelial cell adhesions. In this study, we report morphological defects in neurons and neuromuscular defects in mutants of the C. elegans CAMSAP, ptrn-1. Mechanosensory neurons initially extend wild-type neurites, and subsequently remodel by overextending neurites and retracting synaptic branches and presynaptic varicosities. This neuronal remodeling can be activated by mutations known to alter microtubules, and depends on a functioning DLK-1 MAP kinase pathway. We found that PTRN-1 localizes to both neurites and synapses, and our results suggest that alterations of microtubule structures caused by loss of PTRN-1 function activates a remodeling program leading to changes in neurite morphology. We propose a model whereby minus-end microtubule stabilization mediated by a functional PTRN-1 is necessary for morphological maintenance of neurons. DOI: http://dx.doi.org/10.7554/eLife.01637.001.
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Affiliation(s)
- Jana Dorfman Marcette
- Department of Anatomy and Neurobiology, Washington University School of Medicine, St. Louis, United States
| | - Jessica Jie Chen
- Department of Anatomy and Neurobiology, Washington University School of Medicine, St. Louis, United States
| | - Michael L Nonet
- Department of Anatomy and Neurobiology, Washington University School of Medicine, St. Louis, United States
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42
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Ferraro TN. The relationship between genes affecting the development of epilepsy and approaches to epilepsy therapy. Expert Rev Neurother 2014; 14:329-52. [DOI: 10.1586/14737175.2014.888651] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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King MDA, Phillips GW, Bignone PA, Hayes NVL, Pinder JC, Baines AJ. A conserved sequence in calmodulin regulated spectrin-associated protein 1 links its interaction with spectrin and calmodulin to neurite outgrowth. J Neurochem 2013; 128:391-402. [PMID: 24117850 PMCID: PMC4016758 DOI: 10.1111/jnc.12462] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 09/08/2013] [Accepted: 09/23/2013] [Indexed: 11/28/2022]
Abstract
Calmodulin regulated spectrin-associated protein 1 (CAMSAP1) is a vertebrate microtubule-binding protein, and a representative of a family of cytoskeletal proteins that arose with animals. We reported previously that the central region of the protein, which contains no recognized functional domain, inhibited neurite outgrowth when over-expressed in PC12 cells [Baines et al., Mol. Biol. Evol. 26 (2009), p. 2005]. The CKK domain (DUF1781) binds microtubules and defines the CAMSAP/ssp4 family of animal proteins (Baines et al. 2009). In the central region, three short well-conserved regions are characteristic of CAMSAP-family members. One of these, CAMSAP-conserved region 1 (CC1), bound to both βIIΣ1-spectrin and Ca2+/calmodulin in vitro. The binding of Ca2+/calmodulin inhibited spectrin binding. Transient expression of CC1 in PC12 cells inhibited neurite outgrowth. siRNA knockdown of CAMSAP1 inhibited neurite outgrowth in PC12 cells or primary cerebellar granule cells: this could be rescued in PC12 cells by wild-type CAMSAP1-enhanced green fluorescent protein, but not by a CC1 mutant. We conclude that CC1 represents a functional region of CAMSAP1, which links spectrin-binding to neurite outgrowth.
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Zhang S, Kwan P, Baum L. The potential role of CAMSAP1L1 in symptomatic epilepsy. Neurosci Lett 2013; 556:146-51. [PMID: 24148305 DOI: 10.1016/j.neulet.2013.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 10/02/2013] [Accepted: 10/10/2013] [Indexed: 11/18/2022]
Abstract
In a recent genome-wide association study (GWAS) of symptomatic epilepsy in the Chinese population, the most significant single nucleotide polymorphism (SNP) allele was rs2292096 [G] (P=1.0×10(-8), odds ratio [OR]=0.63), in the CAMSAP1L1 gene (also known as CAMSAP2). Here, we report that rs2292096 genotypes tended to associate with expression of CAMSAP1L1 RNA in the temporal lobe (p=0.054) and hippocampus (p=0.20) of epilepsy surgery patients, with expression tending to increase with the G allele. CAMSAP1L1 and β-tubulin double immunofluorescence exhibited partial overlap. CAMSAP1L1 siRNA transfection of human SH-SY5Y neuroblastoma cells treated with or without retinoic acid reduced the CAMSAP1L1 protein level nearly 60% and stimulated neurite outgrowth, as measured by total length, number of processes and number of branches. Therefore, the rs2292096 G allele of CAMSAP1L1, which was associated with reduced risk of symptomatic epilepsy, tended to associate with increased expression of CAMSAP1L1, which represses neurite outgrowth. Greater neurite growth in response to brain insults might increase formation of ectopic neural circuits and thus the risk of epileptogenesis.
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Affiliation(s)
- Shuai Zhang
- School of Pharmacy, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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45
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Handel AE, Disanto G, Ramagopalan SV. Next-generation sequencing in understanding complex neurological disease. Expert Rev Neurother 2013; 13:215-27. [PMID: 23368808 DOI: 10.1586/ern.12.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing techniques have made vast quantities of data on human genomes and transcriptomes available to researchers. Huge progress has been made towards understanding the basis of many Mendelian neurological conditions, but progress has been considerably slower in complex neurological diseases (multiple sclerosis, migraine, Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and so on). The authors review current next-generation sequencing methodologies and present selected studies illustrating how these have been used to cast light on the genetic etiology of complex neurological diseases with specific focus on multiple sclerosis. The authors highlight particular pitfalls in next-generation sequencing experiments and speculate on both clinical and research applications of these sequencing platforms for complex neurological disorders in the future.
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Affiliation(s)
- Adam E Handel
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
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46
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Speed D, Hoggart C, Petrovski S, Tachmazidou I, Coffey A, Jorgensen A, Eleftherohorinou H, De Iorio M, Todaro M, De T, Smith D, Smith PE, Jackson M, Cooper P, Kellett M, Howell S, Newton M, Yerra R, Tan M, French C, Reuber M, Sills GE, Chadwick D, Pirmohamed M, Bentley D, Scheffer I, Berkovic S, Balding D, Palotie A, Marson A, O'Brien TJ, Johnson MR. A genome-wide association study and biological pathway analysis of epilepsy prognosis in a prospective cohort of newly treated epilepsy. Hum Mol Genet 2013; 23:247-58. [PMID: 23962720 DOI: 10.1093/hmg/ddt403] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We present the analysis of a prospective multicentre study to investigate genetic effects on the prognosis of newly treated epilepsy. Patients with a new clinical diagnosis of epilepsy requiring medication were recruited and followed up prospectively. The clinical outcome was defined as freedom from seizures for a minimum of 12 months in accordance with the consensus statement from the International League Against Epilepsy (ILAE). Genetic effects on remission of seizures after starting treatment were analysed with and without adjustment for significant clinical prognostic factors, and the results from each cohort were combined using a fixed-effects meta-analysis. After quality control (QC), we analysed 889 newly treated epilepsy patients using 472 450 genotyped and 6.9 × 10(6) imputed single-nucleotide polymorphisms. Suggestive evidence for association (defined as Pmeta < 5.0 × 10(-7)) with remission of seizures after starting treatment was observed at three loci: 6p12.2 (rs492146, Pmeta = 2.1 × 10(-7), OR[G] = 0.57), 9p23 (rs72700966, Pmeta = 3.1 × 10(-7), OR[C] = 2.70) and 15q13.2 (rs143536437, Pmeta = 3.2 × 10(-7), OR[C] = 1.92). Genes of biological interest at these loci include PTPRD and ARHGAP11B (encoding functions implicated in neuronal development) and GSTA4 (a phase II biotransformation enzyme). Pathway analysis using two independent methods implicated a number of pathways in the prognosis of epilepsy, including KEGG categories 'calcium signaling pathway' and 'phosphatidylinositol signaling pathway'. Through a series of power curves, we conclude that it is unlikely any single common variant explains >4.4% of the variation in the outcome of newly treated epilepsy.
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Affiliation(s)
- Doug Speed
- UCL Genetics Institute, University College London WC1E 6BT, UK
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Buono RJ. Genome wide association studies (GWAS) and common forms of human epilepsy. Epilepsy Behav 2013; 28 Suppl 1:S63-5. [PMID: 23756483 PMCID: PMC3682226 DOI: 10.1016/j.yebeh.2012.07.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 07/11/2012] [Indexed: 11/25/2022]
Abstract
Several GWAS focused on common forms of epilepsy are underway. Currently, only one locus has been published that reached genome wide statistical significance. Two other loci that also reach genome wide statistical significance have been reported as preliminary data and are awaiting publication. Several additional loci identified in these studies fall just short of statistical significance, and it is hoped that future large scale meta-analyses will confirm these early findings and identify new loci that influence common forms of human epilepsy. Next generation DNA sequencing (NGS) studies are also underway and in the future will identify rare DNA variations of large effect that also contribute to the final epilepsy phenotypes under study. Finally, these studies have the potential to identify biomarkers of antiepileptic drug (AED) response as epilepsy patient GWAS and NGS data are stratified based on AED efficacy and tolerability.
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Bakir-Gungor B, Baykan B, Ugur İseri S, Tuncer FN, Sezerman OU. Identifying SNP targeted pathways in partial epilepsies with genome-wide association study data. Epilepsy Res 2013; 105:92-102. [PMID: 23498093 DOI: 10.1016/j.eplepsyres.2013.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 01/15/2013] [Accepted: 02/13/2013] [Indexed: 12/18/2022]
Abstract
PURPOSE In a recent genome-wide association study for partial epilepsies in the European population, a common genetic variation has been reported to affect partial epilepsy only modestly. However, in complex diseases such as partial epilepsy, multiple factors (e.g. single nucleotide polymorphisms, microRNAs, metabolic and epigenetic factors) may target different sets of genes in the same pathway, affecting its function and thus causing the disease development. In this regard, we hypothesize that the pathways are critical for elucidating the mechanisms underlying partial epilepsy. METHODS Previously we had developed a novel methodology with the aim of identifying the disease-related pathways. We had combined evidence of genetic association with current knowledge of (i) biochemical pathways, (ii) protein-protein interaction networks, and (iii) the functional information of selected single nucleotide polymorphisms. In our present study, we apply this methodology to a data set on partial epilepsy, including 3445 cases and 6935 controls of European ancestry. RESULTS We have identified 30 overrepresented pathways with corrected p-values smaller than 10(-12). These pathways include complement and coagulation cascades, cell cycle, focal adhesion, extra cellular matrix-receptor interaction, JAK-STAT signaling pathway, MAPK signaling pathway, proteasome, ribosome, calcium signaling and regulation of actin cytoskeleton pathways. Most of these pathways have growing scientific support in the literature as being associated with partial epilepsy. We also demonstrate that different factors affect distinct parts of the pathways, as shown here on complement and coagulation cascades pathway with a comparison of gene expression vs. genome-wide association study. CONCLUSIONS Traditional studies on genome-wide association have not revealed strong associations in epilepsies, since these single nucleotide polymorphisms are not shared by most of the patients. Our results suggest that it is more effective to incorporate the functional effect of a single nucleotide polymorphism on the gene product, protein-protein interaction networks and functional enrichment tools into genome-wide association studies. These can then be used to determine leading molecular pathways, which cannot be detected through traditional analyses. We hope that this type of analysis brings the research community one step closer to unraveling the complex genetic structure of epilepsies.
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Affiliation(s)
- B Bakir-Gungor
- Department of Genetics and Bioinformatics, Faculty of Arts and Sciences, Bahcesehir University, Ciragan Cad. Osmanpasa Mektebi Sok., No.: 4, 34353, Besiktas, Istanbul, Turkey.
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Unraveling the genetics of common epilepsies: approaches, platforms, and caveats. Epilepsy Behav 2013; 26:229-33. [PMID: 23103323 DOI: 10.1016/j.yebeh.2012.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 09/13/2012] [Indexed: 11/21/2022]
Abstract
With no known intervention to prevent or cure epilepsy, treatment is primarily symptomatic and requires long-term administration of medications to suppress seizure occurrence. Current antiepileptic drugs (AEDs) are ineffective in one-third of patients (Kwan and Brodie, 2000). Such therapeutic inadequacy is largely due to our insufficient understanding of the basic molecular pathophysiological processes that underlie epileptogenesis. Breakthroughs are needed in the identification of new molecular targets that will translate to novel intervention approaches. Discovering genetic variants that increase the susceptibility to disease is a promising avenue to identifying such targets. However, early candidate gene-based studies in epilepsy proved ineffective in identifying genetic risk factors for the non-Mendelian, complex epilepsies, which represent >95% of clinically encountered epilepsy. Furthermore, genome-wide association studies (GWAS) of epilepsy patients have been largely negative, with the exception of several putative susceptibility loci discovered in Han Chinese focal epilepsy and European Caucasian GGE patients (Kasperaviciute et al., 2010; Guo et al., 2012; Consortium et al., 2012). Results of these GWAS suggest that, similar to other common diseases, associations with common single nucleotide variants (SNV) appear likely to account for a small fraction of the heritability of epilepsy, thus fuelling the effort to also search for alternative genetic contributors, with a recent increased emphasis on rare variants with larger effects (Manolio et al., 2009). It is possible that both common and rare variants contribute to an increased susceptibility to common epilepsy syndromes (Mulley et al., 2005). We review the approaches that have been taken to identify genetic risk markers of the common epilepsy syndromes, the experimental platforms, and their caveats. We discuss current technologies and analytical frameworks that might expedite the discovery of these variants by leveraging advances in microarray-based, high-throughput, genotyping technology, and complementary interdisciplinary expertise of study teams including the need for meta-analyses under global collaborative frameworks. We briefly discuss the analytical options made available through rapid advances in sequencing and other genomic technologies.
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Abstract
Over the past year huge advances have been made in our ability to determine the genetic aetiology of many neurological diseases through the utilisation of next generation sequencing platforms. This technology is, on a daily basis, providing new breakthroughs in neurological disease. The aim of this article is to clearly describe the technological platforms, methods of data analysis, established breakthroughs, and potential future clinical and research applications of this innovative and exciting technique which has relevance to all those working within clinical neuroscience.
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Affiliation(s)
- M J Keogh
- Mitochondrial Research Group, Newcastle University, UK
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