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Carton RJ, Doyle MG, Kearney H, Steward CA, Lench NJ, Rogers A, Heinzen EL, McDonald S, Fay J, Lacey A, Beausang A, Cryan J, Brett F, El-Naggar H, Widdess-Walsh P, Costello D, Kilbride R, Doherty CP, Sweeney KJ, O'Brien DF, Henshall DC, Delanty N, Cavalleri GL, Benson KA. Somatic variants as a cause of drug-resistant epilepsy including mesial temporal lobe epilepsy with hippocampal sclerosis. Epilepsia 2024; 65:1451-1461. [PMID: 38491957 DOI: 10.1111/epi.17943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 02/14/2024] [Accepted: 02/26/2024] [Indexed: 03/18/2024]
Abstract
OBJECTIVE The contribution of somatic variants to epilepsy has recently been demonstrated, particularly in the etiology of malformations of cortical development. The aim of this study was to determine the diagnostic yield of somatic variants in genes that have been previously associated with a somatic or germline epilepsy model, ascertained from resected brain tissue from patients with multidrug-resistant focal epilepsy. METHODS Forty-two patients were recruited across three categories: (1) malformations of cortical development, (2) mesial temporal lobe epilepsy with hippocampal sclerosis, and (3) nonlesional focal epilepsy. Participants were subdivided based on histopathology of the resected brain. Paired blood- and brain-derived DNA samples were sequenced using high-coverage targeted next generation sequencing to high depth (585× and 1360×, respectively). Variants were identified using Genome Analysis ToolKit (GATK4) MuTect-2 and confirmed using high-coverage Amplicon-EZ sequencing. RESULTS Sequence data on 41 patients passed quality control. Four somatic variants were validated following amplicon sequencing: within CBL, ALG13, MTOR, and FLNA. The diagnostic yield across 41 patients was 10%, 9% in mesial temporal lobe epilepsy with hippocampal sclerosis and 20% in malformations of cortical development. SIGNIFICANCE This study provides novel insights into the etiology of mesial temporal lobe epilepsy with hippocampal sclerosis, highlighting a potential pathogenic role of somatic variants in CBL and ALG13. We also report candidate diagnostic somatic variants in FLNA in focal cortical dysplasia, while providing further insight into the importance of MTOR and related genes in focal cortical dysplasia. This work demonstrates the potential molecular diagnostic value of variants in both germline and somatic epilepsy genes.
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Affiliation(s)
- Robert J Carton
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Michael G Doyle
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
- Strategic Academic Recruitment Doctor of Medicine Programme, Royal College of Surgeons in Ireland in collaboration with Blackrock Clinic, Dublin, Ireland
| | - Hugh Kearney
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | | | | | - Anthony Rogers
- Congenica Limited, BioData Innovation Centre, Cambridge, UK
| | - Erin L Heinzen
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Seamus McDonald
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Joanna Fay
- Royal College of Surgeons in Ireland Biobanking Service, Dublin, Ireland
| | - Austin Lacey
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alan Beausang
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Jane Cryan
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Hany El-Naggar
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Peter Widdess-Walsh
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Daniel Costello
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Neurology, Cork University Hospital, Cork, Ireland
| | - Ronan Kilbride
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Colin P Doherty
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Neurology, St. James's Hospital, Dublin, Ireland
| | - Kieron J Sweeney
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Donncha F O'Brien
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - David C Henshall
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Norman Delanty
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Epilepsy Programme, Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - Gianpiero L Cavalleri
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Katherine A Benson
- FutureNeuro Science Foundation Ireland Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
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Khoshkhoo S, Wang Y, Chahine Y, Erson-Omay EZ, Robert SM, Kiziltug E, Damisah EC, Nelson-Williams C, Zhu G, Kong W, Huang AY, Stronge E, Phillips HW, Chhouk BH, Bizzotto S, Chen MH, Adikari TN, Ye Z, Witkowski T, Lai D, Lee N, Lokan J, Scheffer IE, Berkovic SF, Haider S, Hildebrand MS, Yang E, Gunel M, Lifton RP, Richardson RM, Blümcke I, Alexandrescu S, Huttner A, Heinzen EL, Zhu J, Poduri A, DeLanerolle N, Spencer DD, Lee EA, Walsh CA, Kahle KT. Contribution of Somatic Ras/Raf/Mitogen-Activated Protein Kinase Variants in the Hippocampus in Drug-Resistant Mesial Temporal Lobe Epilepsy. JAMA Neurol 2023; 80:578-587. [PMID: 37126322 PMCID: PMC10152377 DOI: 10.1001/jamaneurol.2023.0473] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/31/2022] [Indexed: 05/02/2023]
Abstract
Importance Mesial temporal lobe epilepsy (MTLE) is the most common focal epilepsy subtype and is often refractory to antiseizure medications. While most patients with MTLE do not have pathogenic germline genetic variants, the contribution of postzygotic (ie, somatic) variants in the brain is unknown. Objective To test the association between pathogenic somatic variants in the hippocampus and MTLE. Design, Setting, and Participants This case-control genetic association study analyzed the DNA derived from hippocampal tissue of neurosurgically treated patients with MTLE and age-matched and sex-matched neurotypical controls. Participants treated at level 4 epilepsy centers were enrolled from 1988 through 2019, and clinical data were collected retrospectively. Whole-exome and gene-panel sequencing (each genomic region sequenced more than 500 times on average) were used to identify candidate pathogenic somatic variants. A subset of novel variants was functionally evaluated using cellular and molecular assays. Patients with nonlesional and lesional (mesial temporal sclerosis, focal cortical dysplasia, and low-grade epilepsy-associated tumors) drug-resistant MTLE who underwent anterior medial temporal lobectomy were eligible. All patients with available frozen tissue and appropriate consents were included. Control brain tissue was obtained from neurotypical donors at brain banks. Data were analyzed from June 2020 to August 2022. Exposures Drug-resistant MTLE. Main Outcomes and Measures Presence and abundance of pathogenic somatic variants in the hippocampus vs the unaffected temporal neocortex. Results Of 105 included patients with MTLE, 53 (50.5%) were female, and the median (IQR) age was 32 (26-44) years; of 30 neurotypical controls, 11 (36.7%) were female, and the median (IQR) age was 37 (18-53) years. Eleven pathogenic somatic variants enriched in the hippocampus relative to the unaffected temporal neocortex (median [IQR] variant allele frequency, 1.92 [1.5-2.7] vs 0.3 [0-0.9]; P = .01) were detected in patients with MTLE but not in controls. Ten of these variants were in PTPN11, SOS1, KRAS, BRAF, and NF1, all predicted to constitutively activate Ras/Raf/mitogen-activated protein kinase (MAPK) signaling. Immunohistochemical studies of variant-positive hippocampal tissue demonstrated increased Erk1/2 phosphorylation, indicative of Ras/Raf/MAPK activation, predominantly in glial cells. Molecular assays showed abnormal liquid-liquid phase separation for the PTPN11 variants as a possible dominant gain-of-function mechanism. Conclusions and Relevance Hippocampal somatic variants, particularly those activating Ras/Raf/MAPK signaling, may contribute to the pathogenesis of sporadic, drug-resistant MTLE. These findings may provide a novel genetic mechanism and highlight new therapeutic targets for this common indication for epilepsy surgery.
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Affiliation(s)
- Sattar Khoshkhoo
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Yilan Wang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Yasmine Chahine
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
| | - E. Zeynep Erson-Omay
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Stephanie M. Robert
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Emre Kiziltug
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Eyiyemisi C. Damisah
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | | | - Guangya Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Wenna Kong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - August Yue Huang
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Edward Stronge
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - H. Westley Phillips
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles
| | - Brian H. Chhouk
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Sara Bizzotto
- Sorbonne University, Paris Brain Institute (ICM), National Institute of Health and Medical Research (INSERM), National Center for Scientific Research (CNRS), Paris, France
| | - Ming Hui Chen
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Thiuni N. Adikari
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
| | - Zimeng Ye
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
| | - Tom Witkowski
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
| | - Dulcie Lai
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill
| | - Nadine Lee
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
| | - Julie Lokan
- Department of Anatomical Pathology, Austin Health, Heidelberg, Australia
| | - Ingrid E. Scheffer
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
- Murdoch Children’s Research Institute, Parkville, Australia
- Florey Institute of Neuroscience and Mental Health, Heidelberg, Australia
- Department of Pediatrics, University of Melbourne, Royal Children’s Hospital, Parkville, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Heidelberg, Australia
| | - Samuel F. Berkovic
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Heidelberg, Australia
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, United Kingdom
| | - Michael S. Hildebrand
- Department of Medicine (Austin Health), University of Melbourne, Heidelberg, Australia
- Murdoch Children’s Research Institute, Parkville, Australia
| | - Edward Yang
- Department of Radiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Murat Gunel
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Richard P. Lifton
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | | | - Ingmar Blümcke
- Department of Neuropathology, University Hospitals Erlangen, Erlangen, Germany
- Epilepsy Center, Cleveland Clinic, Cleveland, Ohio
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Anita Huttner
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Erin L. Heinzen
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill
- Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill
| | - Jidong Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Annapurna Poduri
- Epilepsy Genetics Program, Division of Epilepsy and Neurophysiology, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Nihal DeLanerolle
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Dennis D. Spencer
- Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut
| | - Eunjung Alice Lee
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Department of Neurology and Pediatrics, Harvard Medical School, Boston, Massachusetts
- Allen Discovery Center for Human Brain Evolution, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts
- Howard Hughes Medical Institute, Boston, Massachusetts
| | - Kristopher T. Kahle
- Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
- Department of Neurosurgery, Boston Children’s Hospital, Boston, Massachusetts
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Goldman AM. Oncogenic Pathways Provide Clue to the Etiology of Human Mesial Temporal Lobe Epilepsy. JAMA Neurol 2023:2804532. [PMID: 37126324 DOI: 10.1001/jamaneurol.2023.0465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Affiliation(s)
- Alica M Goldman
- Department of Neurology, Neurophysiology Section, Baylor College of Medicine, Houston, Texas
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Novel variants in GABA A receptor subunits: A possible association with benzodiazepine resistance in patients with drug-resistant epilepsy. Epilepsy Res 2023; 189:107056. [PMID: 36469977 DOI: 10.1016/j.eplepsyres.2022.107056] [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: 10/01/2021] [Revised: 10/12/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022]
Abstract
Benzodiazepines (BDZ) such as diazepam and lorazepam are popular as first-line treatment for acute seizures due to their rapid action and high efficacy. However, long-term usage of BDZ leads to benzodiazepine resistance, a phenomenon whose underlying mechanisms are still being investigated. One of the hypothesised mechanisms contributing to BDZ resistance is the presence of mutations in benzodiazepine-sensitive receptors. While a few genetic variants have been reported previously, knowledge of relevant pathogenic variants is still scarce. We used Sanger Sequencing to detect variants in the ligand-binding domain of BDZ-sensitive GABAA receptor subunits α1-3 and 5 expressed in resected brain tissues of drug-resistant epilepsy (DRE) patients with a history of BDZ resistance and found two previously unreported predicted pathogenic frameshifting variants - NM_000807.4(GABRA2):c.367_368insG and NM_000810.4(GABRA5):c.410del - significantly enriched in these patients. The findings were further explored in resected DRE brain tissues through cellular electrophysiological experiments.
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Perucca P, Stanley K, Harris N, McIntosh AM, Asadi-Pooya AA, Mikati MA, Andrade DM, Dugan P, Depondt C, Choi H, Heinzen EL, Cavalleri GL, Buono RJ, Devinsky O, Sperling MR, Berkovic SF, Delanty N, Goldstein DB, O'Brien TJ. Rare Genetic Variation and Outcome of Surgery for Mesial Temporal Lobe Epilepsy. Ann Neurol 2022; 93:752-761. [PMID: 36534060 DOI: 10.1002/ana.26581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/03/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVE Genetic factors have long been debated as a cause of failure of surgery for mesial temporal lobe epilepsy (MTLE). We investigated whether rare genetic variation influences seizure outcomes of MTLE surgery. METHODS We performed an international, multicenter, whole exome sequencing study of patients who underwent surgery for drug-resistant, unilateral MTLE with normal magnetic resonance imaging (MRI) or MRI evidence of hippocampal sclerosis and ≥2-year postsurgical follow-up. Patients with either sustained seizure freedom (favorable outcome) or ongoing uncontrolled seizures since surgery (unfavorable outcome) were included. Exomes of controls without epilepsy were also included. Gene set burden analyses were carried out to identify genes with significant enrichment of rare deleterious variants in patients compared to controls. RESULTS Nine centers from 3 continents contributed 206 patients operated for drug-resistant unilateral MTLE, of whom 196 (149 with favorable outcome and 47 with unfavorable outcome) were included after stringent quality control. Compared to 8,718 controls, MTLE cases carried a higher burden of ultrarare missense variants in constrained genes that are intolerant to loss-of-function (LoF) variants (odds ratio [OR] = 2.6, 95% confidence interval [CI] = 1.9-3.5, p = 1.3E-09) and in genes encoding voltage-gated cation channels (OR = 2.4, 95% CI = 1.4-3.8, p = 2.7E-04). Proportions of subjects with such variants were comparable between patients with favorable outcome and those with unfavorable outcome, with no significant between-group differences. INTERPRETATION Rare variation contributes to the genetic architecture of MTLE, but does not appear to have a major role in failure of MTLE surgery. These findings can be incorporated into presurgical decision-making and counseling. ANN NEUROL 2022.
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Affiliation(s)
- Piero Perucca
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Melbourne, Victoria, Australia
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Kate Stanley
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Natasha Harris
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Anne M McIntosh
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Melbourne, Victoria, Australia
- Department of Neurology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ali A Asadi-Pooya
- Jefferson Comprehensive Epilepsy Center, Department of Neurology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohamad A Mikati
- Division of Pediatric Neurology and Developmental Medicine, Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | | | - Patricia Dugan
- Department of Neurology, New York University Langone Medical Center, New York, New York, USA
| | - Chantal Depondt
- Department of Neurology, Hôpital Universitaire de Bruxelles, Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Hyunmi Choi
- Department of Neurology, Columbia University, New York, New York, USA
| | - Erin L Heinzen
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Gianpiero L Cavalleri
- FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Russell J Buono
- Department of Biomedical Science, Cooper Medical School of Rowan University, Camden, New Jersey, USA
| | - Orrin Devinsky
- Department of Neurology, New York University Langone Medical Center, New York, New York, USA
| | - Michael R Sperling
- Jefferson Comprehensive Epilepsy Center, Department of Neurology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Samuel F Berkovic
- Epilepsy Research Centre, Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, Melbourne, Victoria, Australia
| | - Norman Delanty
- FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
- Department of Neurology, Beaumont Hospital, Dublin, Ireland
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Terence J O'Brien
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Neurology, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, Victoria, Australia
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Moloney PB, Dugan P, Widdess-Walsh P, Devinsky O, Delanty N. Genomics in the Presurgical Epilepsy Evaluation. Epilepsy Res 2022; 184:106951. [DOI: 10.1016/j.eplepsyres.2022.106951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/23/2022] [Accepted: 05/25/2022] [Indexed: 11/03/2022]
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7
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Turkdogan D, Turkyilmaz A, Sager G, Ozturk G, Unver O, Say M. Chromosomal microarray and exome sequencing in unexplained early infantile epileptic encephalopathies in a highly consanguineous population. Int J Neurosci 2021:1-18. [PMID: 34380004 DOI: 10.1080/00207454.2021.1967349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AIM To identify genetic causes for early infantile epileptic encephalopathies (EIEE) in Turkish children with mostly consanguineous parents. METHODS In a selected EIEE group (N = 59) based on results of nongenetic and initial genetic testing with unexplained etiology, 49 patients underwent array-based comparative genomic hybridization (aCGH) and 49 patients underwent whole exome sequencing (WES) including 39 with negative aCGH results and 10 with WES-only. RESULTS Diagnostic yield of aCGH and WES for pathogenic or likely pathogenic variants was 14.3% and 38.8%, respectively. Including de novo variants of uncertain significance linked to compatible phenotypes, increased the diagnostic yield of WES to 61.2%. Out of 38 positive variants, 18 (47.4%) were novel and 16 (42.1%) were de novo. Twenty-one (56.8%) patients had recessive variants inherited from mostly consanguineous healthy parents (85.7%). Fourteen (37.8%) of patients with diagnostic results had positive variants in established EIEE genes. Seizures started during neonatal period in 32.4% patients. Posture or movement disorders were comorbid with EIEE in 40.5% of diagnosed patients. We identified treatable metabolic disorders in 8.1% of patients and pathogenic variants in genes which support using targeted medicine in 19% of patients. CONCLUSIONS Detailed electro-clinical phenotyping led to expansion of some of the known phenotypes with non-neurological and neurological findings in addition to seizures, as well as suggestion of candidate genes (SEC24B, SLC16A2 and PRICKLE2) and a copy number variant (microduplication of Xp21.1p11.4). The high ratio of recessive inheritance could be important for family counseling.
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Affiliation(s)
- Dilsad Turkdogan
- Medical Faculty, Department of Pediatric Neurology, Marmara University, Pendik, Istanbul, Turkey
| | - Ayberk Turkyilmaz
- Medical Faculty, Department of Medical Genetics, Marmara University, Pendik, Istanbul, Turkey
| | - Gunes Sager
- Medical Faculty, Department of Pediatric Neurology, Marmara University, Pendik, Istanbul, Turkey
| | - Gulten Ozturk
- Medical Faculty, Department of Pediatric Neurology, Marmara University, Pendik, Istanbul, Turkey
| | - Olcay Unver
- Medical Faculty, Department of Pediatric Neurology, Marmara University, Pendik, Istanbul, Turkey
| | - Merve Say
- Bioinformatics, Private Practice, Kadıkoy, Istanbul, Turkey
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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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9
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Chaudhuri T, Chintalapati J, Hosur MV. Identification of 3'-UTR single nucleotide variants and prediction of select protein imbalance in mesial temporal lobe epilepsy patients. PLoS One 2021; 16:e0252475. [PMID: 34086756 PMCID: PMC8177469 DOI: 10.1371/journal.pone.0252475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/16/2021] [Indexed: 11/23/2022] Open
Abstract
The genetic influence in epilepsy, characterized by unprovoked and recurrent seizures, is through variants in genes critical to brain development and function. We have carried out variant calling in Mesial Temporal Lobe Epilepsy (MTLE) patients by mapping the RNA-Seq data available at SRA, NCBI, USA onto human genome assembly hg-19. We have identified 1,75,641 SNVs in patient samples. These SNVs are distributed over 14700 genes of which 655 are already known to be associated with epilepsy. Large number of variants occur in the 3'-UTR, which is one of the regions involved in the regulation of protein translation through binding of miRNAs and RNA-binding proteins (RBP). We have focused on studying the structure-function relationship of the 3'-UTR SNVs that are common to at-least 10 of the 35 patient samples. For the first time we find SNVs exclusively in the 3'-UTR of FGF12, FAR1, NAPB, SLC1A3, SLC12A6, GRIN2A, CACNB4 and FBXO28 genes. Structural modelling reveals that the variant 3'-UTR segments possess altered secondary and tertiary structures which could affect mRNA stability and binding of RBPs to form proper ribonucleoprotein (RNP) complexes. Secondly, these SNVs have either created or destroyed miRNA-binding sites, and molecular modeling reveals that, where binding sites are created, the additional miRNAs bind strongly to 3'-UTR of only variant mRNAs. These two factors affect protein production thereby creating an imbalance in the amounts of select proteins in the cell. We suggest that in the absence of missense and nonsense variants, protein-activity imbalances associated with MTLE patients can be caused through 3'-UTR variants in relevant genes by the mechanisms mentioned above. 3'-UTR SNV has already been identified as causative variant in the neurological disorder, Tourette syndrome. Inhibition of these miRNA-mRNA bindings could be a novel way of treating drug-resistant MTLE patients. We also suggest that joint occurrence of these SNVs could serve as markers for MTLE. We find, in the present study, SNV-mediated destruction of miRNA binding site in the 3'-UTR of the gene encoding glutamate receptor subunit, and, interestingly, overexpression of one of this receptor subunit is also associated with Febrile Seizures.
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Affiliation(s)
- Tanusree Chaudhuri
- Department of Natural Sciences and Engineering, National Institute of Advanced Studies, IISc campus, Bangalore, India
| | - Janaki Chintalapati
- CDAC-Centre for Development of Advanced Computing, Byappanahalli, Bangalore, India
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Abstract
Whether genetic factors contribute to acquired epilepsies has long been controversial. Supporters observe that, among individuals exposed to seemingly the same brain insult, only a minority develops unprovoked seizures. Yet, only in relatively recent years have studies started to build a case for genetic contributions. Here, we appraise this emerging evidence, by providing a critical review of studies published in the field.
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Affiliation(s)
- Piero Perucca
- Department of Neuroscience, Central Clinical School, 161666Monash University, Melbourne, Victoria, Australia.,Departments of Medicine and Neurology, The Royal Melbourne Hospital, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Neurology, Alfred Health, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine, 2281Epilepsy Research Centre, Austin Health, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Paediatrics, Royal Children's Hospital, The University of Melbourne, Melbourne, Victoria, Australia.,The Florey Neuroscience and Murdoch Children's Research Institutes, Melbourne, Victoria, Australia
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Xiao W, Liu C, Zhong K, Ning S, Hou R, Deng N, Xu Y, Luo Z, Fu Y, Zeng Y, Xiao B, Long H, Long L. CpG methylation signature defines human temporal lobe epilepsy and predicts drug-resistant. CNS Neurosci Ther 2020; 26:1021-1030. [PMID: 32519815 PMCID: PMC7539843 DOI: 10.1111/cns.13394] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
Aims Temporal lobe epilepsy (TLE) is the most common focal epilepsy syndrome in adults and frequently develops drug resistance. Studies have investigated the value of peripheral DNA methylation signature as molecular biomarker for diagnosis or prognosis. We aimed to explore methylation biomarkers for TLE diagnosis and pharmacoresistance prediction. Methods We initially conducted genome‐wide DNA methylation profiling in TLE patients, and then selected candidate CpGs in training cohort and validated in another independent cohort by employing machine learning algorithms. Furthermore, nomogram comprising DNA methylation and clinicopathological data was generated to predict the drug response in the entire patient cohort. Lastly, bioinformatics analysis for CpG‐associated genes was performed using Ingenuity Pathway Analysis. Results After screening and validation, eight CpGs were identified for diagnostic biomarker with an area under the curve (AUC) of 0.81 and six CpGs for drug‐resistant prediction biomarker with an AUC of 0.79. The nomogram for drug‐resistant prediction comprised methylation risk score, disease course, seizure frequency, and hippocampal sclerosis, with AUC as high as 0.96. Bioinformatics analysis indicated drug response–related CpGs corresponding genes closely related to DNA methylation. Conclusions This study demonstrates the ability to use peripheral DNA methylation signature as molecular biomarker for epilepsy diagnosis and drug‐resistant prediction.
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Affiliation(s)
- Wenbiao Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Chaorong Liu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Kuo Zhong
- Tsinghua-Berkeley Shenzhen Institute, Tsinghua University, Shenzhen, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Rui Hou
- Shanghai Biotechnology Corporation, Shanghai, China
| | - Na Deng
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuchen Xu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaohui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yujiao Fu
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Zeng
- Department of Geriatrics, Second Xiangya Hospital, Central South University, Changsha, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyu Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Lili Long
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
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Dapas M, Sisk R, Legro RS, Urbanek M, Dunaif A, Hayes MG. Family-Based Quantitative Trait Meta-Analysis Implicates Rare Noncoding Variants in DENND1A in Polycystic Ovary Syndrome. J Clin Endocrinol Metab 2019; 104:3835-3850. [PMID: 31038695 PMCID: PMC6660913 DOI: 10.1210/jc.2018-02496] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 04/17/2019] [Indexed: 02/07/2023]
Abstract
CONTEXT Polycystic ovary syndrome (PCOS) is among the most common endocrine disorders of premenopausal women, affecting 5% to15% of this population depending on the diagnostic criteria applied. It is characterized by hyperandrogenism, ovulatory dysfunction, and polycystic ovarian morphology. PCOS is highly heritable, but only a small proportion of this heritability can be accounted for by the common genetic susceptibility variants identified to date. OBJECTIVE The objective of this study was to test whether rare genetic variants contribute to PCOS pathogenesis. DESIGN, PATIENTS, AND METHODS We performed whole-genome sequencing on DNA from 261 individuals from 62 families with one or more daughters with PCOS. We tested for associations of rare variants with PCOS and its concomitant hormonal traits using a quantitative trait meta-analysis. RESULTS We found rare variants in DENND1A (P = 5.31 × 10-5, adjusted P = 0.039) that were significantly associated with reproductive and metabolic traits in PCOS families. CONCLUSIONS Common variants in DENND1A have previously been associated with PCOS diagnosis in genome-wide association studies. Subsequent studies indicated that DENND1A is an important regulator of human ovarian androgen biosynthesis. Our findings provide additional evidence that DENND1A plays a central role in PCOS and suggest that rare noncoding variants contribute to disease pathogenesis.
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Affiliation(s)
- Matthew Dapas
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ryan Sisk
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Richard S Legro
- Department of Obstetrics and Gynecology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Margrit Urbanek
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Reproductive Science, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Andrea Dunaif
- Division of Endocrinology, Diabetes, and Bone Disease, Icahn School of Medicine at Mount Sinai, New York, New York
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Anthropology, Northwestern University, Evanston, Illinois
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Abstract
Protein coats are supramolecular complexes that assemble on the cytosolic face of membranes to promote cargo sorting and transport carrier formation in the endomembrane system of eukaryotic cells. Several types of protein coats have been described, including COPI, COPII, AP-1, AP-2, AP-3, AP-4, AP-5, and retromer, which operate at different stages of the endomembrane system. Defects in these coats impair specific transport pathways, compromising the function and viability of the cells. In humans, mutations in subunits of these coats cause various congenital diseases that are collectively referred to as coatopathies. In this article, we review the fundamental properties of protein coats and the diseases that result from mutation of their constituent subunits.
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Affiliation(s)
- Esteban C Dell'Angelica
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Juan S Bonifacino
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health, Bethesda, Maryland 20892, USA;
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Szaflarski JP. The Dilemma of the Chicken or the Egg-What Appears First in TLE-Seizures or Morphometric Changes in the Temporal Lobe? Epilepsy Curr 2019; 19:101-102. [PMID: 30955428 PMCID: PMC6610418 DOI: 10.1177/1535759719835675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Abnormal Temporal Lobe Morphology in Asymptomatic Relatives of Patients With Hippocampal Sclerosis: A Replication Study Yaakub SN, Barker GJ, Carr SJ, et al. Epilepsia. 2019;60(1):e1-e5. doi:10.1111/epi.14575. We investigated gray and white matter morphology in patients with mesial temporal lobe epilepsy with hippocampal sclerosis (mTLE + HS) and first-degree asymptomatic relatives of patients with mTLE+HS. Using T1-weighted magnetic resonance imaging (MRI), we sought to replicate previously reported findings of structural surface abnormalities of the anterior temporal lobe in asymptomatic relatives of patients with mTLE+HS in an independent cohort. We performed whole-brain MRI in 19 patients with mTLE+HS, 14 first-degree asymptomatic relatives of patients with mTLE+HS, and 32 healthy control participants. Structural alterations in patients and relatives compared to controls were assessed using automated hippocampal volumetry and cortical surface-based morphometry. We replicated previously reported cortical surface area contractions in the ipsilateral anterior temporal lobe in both patients and relatives compared to healthy controls, with asymptomatic relatives showing similar but less extensive changes than patients. These findings suggest morphologic abnormality in asymptomatic relatives of patients with mTLE+HS, suggesting an inherited brain structure endophenotype.
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2018: Year in Review and Message from the Editors to Our Reviewers. Neurol Genet 2019. [PMCID: PMC6384019 DOI: 10.1212/nxg.0000000000000309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Striano P, Nobile C. Whole-exome sequencing to disentangle the complex genetics of hippocampal sclerosis-temporal lobe epilepsy. Neurol Genet 2018; 4:e241. [PMID: 29904719 PMCID: PMC5999347 DOI: 10.1212/nxg.0000000000000241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit (P.S.), Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, "G. Gaslini" Institute, Genova; and CNR-Neuroscience Institute and Department of Biomedical Sciences (C.N.), University of Padua, Italy
| | - Carlo Nobile
- Pediatric Neurology and Muscular Diseases Unit (P.S.), Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, "G. Gaslini" Institute, Genova; and CNR-Neuroscience Institute and Department of Biomedical Sciences (C.N.), University of Padua, Italy
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