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Xue B, Jian X, Peng L, Wu C, Fahira A, Syed AAS, Xia D, Wang B, Niu M, Jiang Y, Ding Y, Gao C, Zhao X, Zhang Q, Shi Y, Li Z. Dissecting the genetic and causal relationship between sleep-related traits and common brain disorders. Sleep Med 2024; 119:201-209. [PMID: 38703603 DOI: 10.1016/j.sleep.2024.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/14/2024] [Accepted: 04/24/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND There is a profound connection between abnormal sleep patterns and brain disorders, suggesting a shared influential association. However, the shared genetic basis and potential causal relationships between sleep-related traits and brain disorders are yet to be fully elucidated. METHODS Utilizing linkage disequilibrium score regression (LDSC) and bidirectional two-sample univariable Mendelian Randomization (UVMR) analyses with large-scale GWAS datasets, we investigated the genetic correlations and causal associations across six sleep traits and 24 prevalent brain disorders. Additionally, a multivariable Mendelian Randomization (MVMR) analysis evaluated the cumulative effects of various sleep traits on each brain disorder, complemented by genetic loci characterization to pinpoint pertinent genes and pathways. RESULTS LDSC analysis identified significant genetic correlations in 66 out of 144 (45.8 %) pairs between sleep-related traits and brain disorders, with the most pronounced correlations observed in psychiatric disorders (66 %, 48/72). UVMR analysis identified 29 causal relationships (FDR<0.05) between sleep traits and brain disorders, with 19 associations newly discovered according to our knowledge. Notably, major depression, attention-deficit/hyperactivity disorder, bipolar disorder, cannabis use disorder, and anorexia nervosa showed bidirectional causal relations with sleep traits, especially insomnia's marked influence on major depression (IVW beta 0.468, FDR = 5.24E-09). MVMR analysis revealed a nuanced interplay among various sleep traits and their impact on brain disorders. Genetic loci characterization underscored potential genes, such as HOXB2, while further enrichment analyses illuminated the importance of synaptic processes in these relationships. CONCLUSIONS This study provides compelling evidence for the causal relationships and shared genetic backgrounds between common sleep-related traits and brain disorders.
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Affiliation(s)
- Baiqiang Xue
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China; School of Public Health, Qingdao University, Qingdao, China
| | - Xuemin Jian
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Lixia Peng
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China; School of Pharmacy, Qingdao University, Qingdao, 266003, China
| | - Chuanhong Wu
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China; School of Basic Medicine, Qingdao University, Qingdao, 266003, China
| | - Aamir Fahira
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Ali Alamdar Shah Syed
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Disong Xia
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Baokun Wang
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China; School of Pharmacy, Qingdao University, Qingdao, 266003, China
| | - Mingming Niu
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China; School of Public Health, Qingdao University, Qingdao, China
| | - Yajie Jiang
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China; School of Public Health, Qingdao University, Qingdao, China
| | - Yonghe Ding
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China; School of Public Health, Qingdao University, Qingdao, China
| | - Chengwen Gao
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China
| | - Xiangzhong Zhao
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China
| | - Qian Zhang
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China
| | - Yongyong Shi
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China; School of Basic Medicine, Qingdao University, Qingdao, 266003, China; Shanghai Clinical Research Center for Mental Health, Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China; Shandong Provincial Key Laboratory of Metabolic Disease & the Metabolic Disease Institute of Qingdao University, Qingdao, 266003, China; Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, 200030, China; Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, 200030, China; Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, 200030, China; Department of Psychiatry, the First Teaching Hospital of Xinjiang Medical University, Urumqi, 830054, China; Changning Mental Health Center, Shanghai, 200042, China.
| | - Zhiqiang Li
- The Affiliated Hospital of Qingdao University, The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China; School of Public Health, Qingdao University, Qingdao, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), the Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, 200030, China; School of Pharmacy, Qingdao University, Qingdao, 266003, China; School of Basic Medicine, Qingdao University, Qingdao, 266003, China; Shanghai Clinical Research Center for Mental Health, Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, China; Shandong Provincial Key Laboratory of Metabolic Disease & the Metabolic Disease Institute of Qingdao University, Qingdao, 266003, China; Shanghai Key Laboratory of Sleep Disordered Breathing, Shanghai, 200030, China.
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Silva DB, Trinidad M, Ljungdahl A, Revalde JL, Berguig GY, Wallace W, Patrick CS, Bomba L, Arkin M, Dong S, Estrada K, Hutchinson K, LeBowitz JH, Schlessinger A, Johannesen KM, Møller RS, Giacomini KM, Froelich S, Sanders SJ, Wuster A. Haploinsufficiency underlies the neurodevelopmental consequences of SLC6A1 variants. Am J Hum Genet 2024; 111:1222-1238. [PMID: 38781976 PMCID: PMC11179425 DOI: 10.1016/j.ajhg.2024.04.021] [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: 09/19/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Heterozygous variants in SLC6A1, encoding the GAT-1 GABA transporter, are associated with seizures, developmental delay, and autism. The majority of affected individuals carry missense variants, many of which are recurrent germline de novo mutations, raising the possibility of gain-of-function or dominant-negative effects. To understand the functional consequences, we performed an in vitro GABA uptake assay for 213 unique variants, including 24 control variants. De novo variants consistently resulted in a decrease in GABA uptake, in keeping with haploinsufficiency underlying all neurodevelopmental phenotypes. Where present, ClinVar pathogenicity reports correlated well with GABA uptake data; the functional data can inform future reports for the remaining 72% of unscored variants. Surface localization was assessed for 86 variants; two-thirds of loss-of-function missense variants prevented GAT-1 from being present on the membrane while GAT-1 was on the surface but with reduced activity for the remaining third. Surprisingly, recurrent de novo missense variants showed moderate loss-of-function effects that reduced GABA uptake with no evidence for dominant-negative or gain-of-function effects. Using linear regression across multiple missense severity scores to extrapolate the functional data to all potential SLC6A1 missense variants, we observe an abundance of GAT-1 residues that are sensitive to substitution. The extent of this missense vulnerability accounts for the clinically observed missense enrichment; overlap with hypermutable CpG sites accounts for the recurrent missense variants. Strategies to increase the expression of the wild-type SLC6A1 allele are likely to be beneficial across neurodevelopmental disorders, though the developmental stage and extent of required rescue remain unknown.
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Affiliation(s)
- Dina Buitrago Silva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Marena Trinidad
- BioMarin Pharmaceutical Inc., Novato, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alicia Ljungdahl
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford OX3 7TY, UK
| | - Jezrael L Revalde
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Cory S Patrick
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Michelle Arkin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Katrine M Johannesen
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Rikke S Møller
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark; Department of Epilepsy Genetics and Personalized Medicine, Member of ERN Epicare, Danish Epilepsy Centre, Dianalund, Denmark
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford OX3 7TY, UK.
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3
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Karadag N, Hagen E, Shadrin AA, van der Meer D, O'Connell KS, Rahman Z, Kutrolli G, Parker N, Bahrami S, Fominykh V, Heuser K, Taubøll E, Steen NE, Djurovic S, Dale AM, Frei O, Andreassen OA, Smeland OB. Dissecting the Shared Genetic Architecture of Common Epilepsies With Cortical Brain Morphology. Neurol Genet 2024; 10:e200143. [PMID: 38817246 PMCID: PMC11139015 DOI: 10.1212/nxg.0000000000200143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/27/2024] [Indexed: 06/01/2024]
Abstract
Background and Objectives Epilepsies are associated with differences in cortical thickness (TH) and surface area (SA). However, the mechanisms underlying these relationships remain elusive. We investigated the extent to which these phenotypes share genetic influences. Methods We analyzed genome-wide association study data on common epilepsies (n = 69,995) and TH and SA (n = 32,877) using Gaussian mixture modeling MiXeR and conjunctional false discovery rate (conjFDR) analysis to quantify their shared genetic architecture and identify overlapping loci. We biologically interrogated the loci using a variety of resources and validated in independent samples. Results The epilepsies (2.4 k-2.9 k variants) were more polygenic than both SA (1.8 k variants) and TH (1.3 k variants). Despite absent genome-wide genetic correlations, there was a substantial genetic overlap between SA and genetic generalized epilepsy (GGE) (1.1 k), all epilepsies (1.1 k), and juvenile myoclonic epilepsy (JME) (0.7 k), as well as between TH and GGE (0.8 k), all epilepsies (0.7 k), and JME (0.8 k), estimated with MiXeR. Furthermore, conjFDR analysis identified 15 GGE loci jointly associated with SA and 15 with TH, 3 loci shared between SA and childhood absence epilepsy, and 6 loci overlapping between SA and JME. 23 loci were novel for epilepsies and 11 for cortical morphology. We observed a high degree of sign concordance in the independent samples. Discussion Our findings show extensive genetic overlap between generalized epilepsies and cortical morphology, indicating a complex genetic relationship with mixed-effect directions. The results suggest that shared genetic influences may contribute to cortical abnormalities in epilepsies.
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Affiliation(s)
- Naz Karadag
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Espen Hagen
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Alexey A Shadrin
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Dennis van der Meer
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Kevin S O'Connell
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Zillur Rahman
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Gleda Kutrolli
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Nadine Parker
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Shahram Bahrami
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Vera Fominykh
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Kjell Heuser
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Erik Taubøll
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Nils Eiel Steen
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Srdjan Djurovic
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Anders M Dale
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Oleksandr Frei
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Ole A Andreassen
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
| | - Olav B Smeland
- From the Institute of Clinical Medicine (N.K., E.H., A.A.S., D.M., K.S.O.C., Z.R., G.K., N.P., S.B., V.F., N.E.S., O.F., O.A.A., O.B.S.), NORMENT, University of Oslo; K.G. Jebsen Centre for Neurodevelopmental Disorders (A.A.S., O.A.A.), University of Oslo and Oslo University Hospital, Norway; Faculty of Health (D.M.), School of Mental Health and Neuroscience, Maastricht University, Netherlands; Department of Neurology (K.H., E.T.), Oslo University Hospital; Faculty of Medicine (E.T.), University of Oslo; Division of Mental Health and Addiction (N.E.S., O.A.A., O.B.S.), Oslo University Hospital; Department of Psychiatric Research (N.E.S.), Diakonhjemmet Hospital; Department of Medical Genetics (S.D.), Oslo University Hospital, Norway; Department of Clinical Science (S.D.), NORMENT, University of Bergen, Norway; Department of Cognitive Science (A.M.D.); Multimodal Imaging Laboratory (A.M.D.); Department of Psychiatry (A.M.D.); Department of Neurosciences (A.M.D.), University of California, San Diego; and Department of Informatics (O.F.), Center for Bioinformatics, University of Oslo, Norway
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4
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Sabnis G, Hession L, Mahoney JM, Mobley A, Santos M, Kumar V. Visual detection of seizures in mice using supervised machine learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.29.596520. [PMID: 38868170 PMCID: PMC11167691 DOI: 10.1101/2024.05.29.596520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Seizures are caused by abnormally synchronous brain activity that can result in changes in muscle tone, such as twitching, stiffness, limpness, or rhythmic jerking. These behavioral manifestations are clear on visual inspection and the most widely used seizure scoring systems in preclinical models, such as the Racine scale in rodents, use these behavioral patterns in semiquantitative seizure intensity scores. However, visual inspection is time-consuming, low-throughput, and partially subjective, and there is a need for rigorously quantitative approaches that are scalable. In this study, we used supervised machine learning approaches to develop automated classifiers to predict seizure severity directly from noninvasive video data. Using the PTZ-induced seizure model in mice, we trained video-only classifiers to predict ictal events, combined these events to predict an univariate seizure intensity for a recording session, as well as time-varying seizure intensity scores. Our results show, for the first time, that seizure events and overall intensity can be rigorously quantified directly from overhead video of mice in a standard open field using supervised approaches. These results enable high-throughput, noninvasive, and standardized seizure scoring for downstream applications such as neurogenetics and therapeutic discovery.
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Affiliation(s)
| | | | | | | | | | - Vivek Kumar
- The Jackson Laboratory, Bar Harbor, ME USA
- School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, MA USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME USA
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5
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Moix S, Sadler MC, Kutalik Z, Auwerx C. Breaking down causes, consequences, and mediating effects of telomere length variation on human health. Genome Biol 2024; 25:125. [PMID: 38760657 PMCID: PMC11101352 DOI: 10.1186/s13059-024-03269-9] [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: 11/01/2023] [Accepted: 05/07/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Telomeres form repeated DNA sequences at the ends of chromosomes, which shorten with each cell division. Yet, factors modulating telomere attrition and the health consequences thereof are not fully understood. To address this, we leveraged data from 326,363 unrelated UK Biobank participants of European ancestry. RESULTS Using linear regression and bidirectional univariable and multivariable Mendelian randomization (MR), we elucidate the relationships between leukocyte telomere length (LTL) and 142 complex traits, including diseases, biomarkers, and lifestyle factors. We confirm that telomeres shorten with age and show a stronger decline in males than in females, with these factors contributing to the majority of the 5.4% of LTL variance explained by the phenome. MR reveals 23 traits modulating LTL. Smoking cessation and high educational attainment associate with longer LTL, while weekly alcohol intake, body mass index, urate levels, and female reproductive events, such as childbirth, associate with shorter LTL. We also identify 24 traits affected by LTL, with risk for cardiovascular, pulmonary, and some autoimmune diseases being increased by short LTL, while longer LTL increased risk for other autoimmune conditions and cancers. Through multivariable MR, we show that LTL may partially mediate the impact of educational attainment, body mass index, and female age at childbirth on proxied lifespan. CONCLUSIONS Our study sheds light on the modulators, consequences, and the mediatory role of telomeres, portraying an intricate relationship between LTL, diseases, lifestyle, and socio-economic factors.
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Affiliation(s)
- Samuel Moix
- Department of Computational Biology, UNIL, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.
| | - Marie C Sadler
- Department of Computational Biology, UNIL, Lausanne, 1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
- University Center for Primary Care and Public Health, Lausanne, 1015, Switzerland
| | - Zoltán Kutalik
- Department of Computational Biology, UNIL, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.
- University Center for Primary Care and Public Health, Lausanne, 1015, Switzerland.
| | - Chiara Auwerx
- Department of Computational Biology, UNIL, Lausanne, 1015, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland.
- University Center for Primary Care and Public Health, Lausanne, 1015, Switzerland.
- Center for Integrative Genetics, UNIL, Lausanne, 1015, Switzerland.
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Chowdhury SR, Whitney R, RamachandranNair R, Bijarnia Mahay S, Sharma S. Genetic Testing in Pediatric Epilepsy: Tools, Tips, and Navigating the Traps. Pediatr Neurol 2024; 157:42-49. [PMID: 38865949 DOI: 10.1016/j.pediatrneurol.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/17/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024]
Abstract
With the advent of high-throughput sequencing and computational methods, genetic testing has become an integral part of contemporary clinical practice, particularly in epilepsy. The toolbox for genetic testing has evolved from conventional chromosomal microarray and epilepsy gene panels to state-of-the-art sequencing techniques in the modern genomic era. Beyond its potential for therapeutic benefits through precision medicine, optimizing the choice of antiseizure medications, or exploring nonpharmacological therapeutic modalities, genetic testing carries substantial diagnostic, prognostic, and personal implications. Developmental and epileptic encephalopathies, the coexistence of neurodevelopmental comorbidities, early age of epilepsy onset, unexplained drug-refractory epilepsy, and positive family history have demonstrated the highest likelihood of yielding positive genetic test results. Given the diagnostic efficacy across different testing modalities, reducing costs of next-generation sequencing tests, and genetic diversity of epilepsies, exome sequencing or genome sequencing, where feasible and available, have been recommended as the first-tier test. Comprehensive clinical phenotyping at the outset, corroborative evidence from radiology and electrophysiology-based investigations, reverse phenotyping, and periodic reanalysis are some of the valuable strategies when faced with inconclusive test results. In this narrative review, the authors aim to simplify the approach to genetic testing in epilepsy by guiding on the selection of appropriate testing tools in the indicated clinical scenarios, addressing crucial aspects during pre- and post-test counseling sessions, adeptly navigating the traps posed by uncertain or negative genetic variants, and paving the way forward to the emerging testing modalities beyond DNA sequencing.
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Affiliation(s)
- Sayoni Roy Chowdhury
- Department of Paediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | - Robyn Whitney
- Comprehensive Paediatric Epilepsy Program, Division of Neurology, Department of Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Rajesh RamachandranNair
- Comprehensive Paediatric Epilepsy Program, Division of Neurology, Department of Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Sunita Bijarnia Mahay
- Sr. Consultant, Clinical & Metabolic Geneticist, Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Suvasini Sharma
- Department of Paediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India.
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Eyal AD, Eyal S. Increasing challenges to trial recruitment: Is it time to change the inclusion criteria for investigational compounds, not just for study participants? Epilepsia 2024. [PMID: 38713479 DOI: 10.1111/epi.17978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/28/2024] [Indexed: 05/08/2024]
Affiliation(s)
| | - Sara Eyal
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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Peña-Ceballos J, Moloney PB, Kilbride RD, Naggar HE, Widdess-Walsh P, Delanty N. Oligoepilepsy and lifelong seizure susceptibility in epilepsy with generalized tonic-clonic seizures alone: Experience at an adult tertiary center. Epilepsy Res 2024; 202:107362. [PMID: 38652996 DOI: 10.1016/j.eplepsyres.2024.107362] [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: 02/23/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 04/25/2024]
Abstract
OBJECTIVE Epilepsy with generalized tonic-clonic seizures alone (GTCA) is the least studied syndrome within the idiopathic generalized epilepsy (IGE) spectrum. We characterize a large cohort of adult patients with GTCA to understand natural history and drug responsiveness. METHODS In this retrospective single-center study using our epilepsy electronic record, we evaluated clinical characteristics, seizure outcomes, anti-seizure medication (ASM) response including seizure recurrence after ASM withdrawal, and sex differences in a cohort of GTCA patients aged ≥17 years. RESULTS Within a cohort of 434 IGE patients, 87 patients (20 %) with GTCA were included. The mean age was 34.9 years (range 17-73 years). Forty-six patients (52.8 %) were females. Seventy-two patients (82.8 %) were seizure-free and 15 (17.2 %) had active epilepsy over the previous 12 months. Thirty-four patients (39.1 %) had ≤5 lifetime seizures, aligning with a prior definition of 'oligoepilepsy'. Sixty-five patients (74.7 %) were treated with monotherapy, 19 (21.8 %) were treated with polytherapy, and three were not taking any ASM. Levetiracetam (37.9 %) was the most commonly prescribed ASM, followed by lamotrigine (32.1 %) and valproate (31 %). Seventeen patients (19.5 %) attempted to withdraw their ASM. The rate of seizure recurrence after ASM withdrawal was 88.2 % (15/17), including two patients who relapsed more than 20 years after ASM discontinuation. Females had more seizures in their lifetime and had trialed more ASM compared to males. SIGNIFICANCE GTCA has a relatively good prognosis, with most patients becoming seizure-free on monotherapy. The high rate of seizure recurrence after ASM withdrawal supports lifetime seizure susceptibility. We found potential sex differences in seizure outcomes and ASM response, although further research is needed to validate this finding.
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Affiliation(s)
| | - Patrick B Moloney
- Department of Neurology, Beaumont Hospital, Dublin, Ireland; School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland; FutureNeuro, the Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland
| | | | - Hany El Naggar
- Department of Neurology, Beaumont Hospital, Dublin, Ireland; School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland; FutureNeuro, the Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland
| | | | - Norman Delanty
- Department of Neurology, Beaumont Hospital, Dublin, Ireland; School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland; FutureNeuro, the Science Foundation Ireland Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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9
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Delanty N, Mohanraj R, Shankar R, Wehner T, Stephen LJ, D'Souza W, Cappucci S, McMurray R, Sainz-Fuertes R, Villanueva V. Perampanel for the treatment of epilepsy with genetic aetiology: Real-world evidence from the PERMIT Extension study. Epilepsy Res 2024; 202:107339. [PMID: 38492461 DOI: 10.1016/j.eplepsyres.2024.107339] [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: 12/08/2023] [Revised: 02/14/2024] [Accepted: 02/29/2024] [Indexed: 03/18/2024]
Abstract
Genetic factors contribute to the aetiology of epilepsy in >50% of cases, and information on the use of antiseizure medications in people with specific aetiologies will help guide treatment decisions. The PERMIT Extension study pooled data from two real-world studies (PERMIT and PROVE) to investigate the effectiveness and safety/tolerability of perampanel (PER) when used to treat people with focal and generalised epilepsy in everyday clinical practice. This post-hoc analysis of PERMIT Extension explored the use of PER when used to treat individuals presumed to have epilepsy with a genetic aetiology. Assessments included retention rate (evaluated at 3, 6 and 12 months), effectiveness (responder and seizure freedom rates; evaluated at 3, 6, 12 months and the last visit [last observation carried forward) and tolerability (adverse events [AEs]). Of the 6822 people with epilepsy included in PERMIT Extension, 1012 were presumed to have a genetic aetiology. The most common genetic aetiologies were idiopathic generalised epilepsy (IGE; 58.2%), tuberous sclerosis (1.1%), Dravet syndrome (0.8%) and genetic epilepsy with febrile seizures plus (GEFS+; 0.5%). Retention rates at 3, 6 and 12 months in the total genetic aetiology population were 89.3%, 79.7% and 65.9%, respectively. In the total genetic aetiology population, responder rates at 12 months and the last visit were 74.8% and 68.3%, respectively, and corresponding seizure freedom rates were 48.9% and 46.5%, respectively. For the specific aetiology subgroups, responder rates at 12 months and the last visit were, respectively: 90.4% and 84.4% (IGE), 100% and 57.1% (tuberous sclerosis), 100% and 71.4% (Dravet syndrome), and 33.3% and 20.0% (GEFS+). Corresponding seizure freedom rates were, respectively: 73.1% and 64.6% (IGE), 33.3% and 22.2% (tuberous sclerosis), 20.0% and 28.6% (Dravet syndrome), and 0% and 0% (GEFS+). The incidence of AEs was 46.5% for the total genetic aetiology population, 48.8% for IGE, 27.3% for tuberous sclerosis, 62.5% for Dravet syndrome, and 20% for GEFS+. Tolerability findings were consistent with PER's known safety profile. PER was effective and generally well tolerated when used in individuals with a presumed genetic epilepsy aetiology in clinical practice. PER was effective across a wide range of genetic aetiologies.
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Affiliation(s)
- Norman Delanty
- Department of Neurology, Beaumont Hospital, Dublin, Ireland.
| | - Rajiv Mohanraj
- Greater Manchester Neurosciences Centre, Salford Royal Hospital, UK
| | | | - Tim Wehner
- National Hospital for Neurology and Neurosurgery, UCLH Foundation Trust, and Department of Clinical and Experimental Epilepsy, UCL, London, UK
| | - Linda J Stephen
- Epilepsy Unit, West Glasgow Ambulatory Care Hospital, Glasgow, Scotland, UK
| | - Wendyl D'Souza
- Department of Medicine, St Vincent's Hospital Melbourne, The University of Melbourne, Victoria, Australia
| | | | | | | | - Vicente Villanueva
- Refractory Epilepsy Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
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10
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Nelson ED, Tippani M, Ramnauth AD, Divecha HR, Miller RA, Eagles NJ, Pattie EA, Kwon SH, Bach SV, Kaipa UM, Yao J, Kleinman JE, Collado-Torres L, Han S, Maynard KR, Hyde TM, Martinowich K, Page SC, Hicks SC. An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.26.590643. [PMID: 38712198 PMCID: PMC11071618 DOI: 10.1101/2024.04.26.590643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
The hippocampus contains many unique cell types, which serve the structure's specialized functions, including learning, memory and cognition. These cells have distinct spatial topography, morphology, physiology, and connectivity, highlighting the need for transcriptome-wide profiling strategies that retain cytoarchitectural organization. Here, we generated spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the anterior human hippocampus across ten adult neurotypical donors. We defined molecular profiles for hippocampal cell types and spatial domains. Using non-negative matrix factorization and transfer learning, we integrated these data to define gene expression patterns within the snRNA-seq data and infer the expression of these patterns in the SRT data. With this approach, we leveraged existing rodent datasets that feature information on circuit connectivity and neural activity induction to make predictions about axonal projection targets and likelihood of ensemble recruitment in spatially-defined cellular populations of the human hippocampus. Finally, we integrated genome-wide association studies with transcriptomic data to identify enrichment of genetic components for neurodevelopmental, neuropsychiatric, and neurodegenerative disorders across cell types, spatial domains, and gene expression patterns of the human hippocampus. To make this comprehensive molecular atlas accessible to the scientific community, both raw and processed data are freely available, including through interactive web applications.
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Luo D, Liu Y, Li J, Liu X, Zhang R, Liu X, Zhang N, Zhang W, Liu J, Zhang L, Wang T. Systematic Analysis of the Relationship Between Elevated Zinc and Epilepsy. J Mol Neurosci 2024; 74:39. [PMID: 38581598 DOI: 10.1007/s12031-024-02213-7] [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: 01/25/2024] [Accepted: 03/21/2024] [Indexed: 04/08/2024]
Abstract
Previous studies have indicated a potential relationship between zinc and epilepsy. The aim of this study is to investigate the causal relationship between zinc, zinc-dependent carbonic anhydrase, and gray matter volume in brain regions enriched with zinc and epilepsy, as well as explore the possible mechanisms by which zinc contributes to epilepsy. First, this study assessed the risk causality between zinc, carbonic anhydrase, and gray matter volume alterations in zinc-enriched brain regions and various subtypes of epilepsy based on Two-sample Mendelian randomization analysis. And then, this study conducted GO/KEGG analysis based on colocalization analysis, MAGMA analysis, lasso regression, random forest model, and XGBoost model. The results of Mendelian randomization analyses showed a causal relationship between zinc, carbonic anhydrase-4, and generalized epilepsy (p = 0.044 , p = 0.010). Additionally, carbonic anhydrase-1 and gray matter volume of the caudate nucleus were found to be associated with epilepsy and focal epilepsy (p = 0.014, p = 0.003 and p = 0.022, p = 0.009). A colocalization relationship was found between epilepsy and focal epilepsy (PP.H4.abf = 97.7e - 2). Meanwhile, the MAGMA analysis indicated that SNPs associated with epilepsy and focal epilepsy were functionally localized to zinc-finger-protein-related genes (p < 1.0e - 5). The genes associated with focal epilepsy were found to have a molecular function of zinc ion binding (FDR = 2.3e - 6). After the onset of epilepsy, the function of the gene whose expression changed in the rats with focal epilepsy was enriched in the biological process of vascular response (FDR = 4.0e - 5). These results revealed mechanism of the increased risk of epilepsy caused by elevated zinc may be related to the increase of zinc ion-dependent carbonic anhydrase or the increase of the volume of zinc-rich caudate gray matter.
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Affiliation(s)
- Dadong Luo
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China
| | - Yaqing Liu
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China
| | - Junqiang Li
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China
| | - Xuhui Liu
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China
| | - Ruirui Zhang
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China
| | - Xuejuan Liu
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China
| | - Ningning Zhang
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China
| | - Wenzhao Zhang
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China
| | - Jiayi Liu
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China
| | - Lan Zhang
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China
| | - Tiancheng Wang
- The Second Hospital & Clinical Medical School, Lanzhou University, Lanzhou, 730030, China.
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Karadag N, Hagen E, Shadrin AA, van der Meer D, O’Connell KS, Rahman Z, Kutrolli G, Parker N, Bahrami S, Fominykh V, Heuser K, Taubøll E, Ueland T, Steen NE, Djurovic S, Dale AM, Frei O, Andreassen OA, Smeland OB. Unraveling the shared genetics of common epilepsies and general cognitive ability. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.25.24304773. [PMID: 38585944 PMCID: PMC10996742 DOI: 10.1101/2024.03.25.24304773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Objective Cognitive impairment is prevalent among individuals with epilepsy, and it is possible that genetic factors can underlie this relationship. Here, we investigated the potential shared genetic basis of common epilepsies and general cognitive ability (COG). Methods We applied linkage disequilibrium score (LDSC) regression, MiXeR and conjunctional false discovery rate (conjFDR) to analyze different aspects of genetic overlap between COG and epilepsies. We used the largest available genome-wide association study data on COG (n = 269,867) and common epilepsies (n = 27,559 cases, 42,436 controls), including the broad phenotypes 'all epilepsy', focal epilepsies and genetic generalized epilepsies (GGE), and as well as specific subtypes. We functionally annotated the identified loci using a variety of biological resources and validated the results in independent samples. Results Using MiXeR, COG (11.2k variants) was estimated to be almost four times more polygenic than 'all epilepsy', GGE, juvenile myoclonic epilepsy (JME), and childhood absence epilepsy (CAE) (2.5k - 2.9k variants). The other epilepsy phenotypes were insufficiently powered for analysis. We show extensive genetic overlap between COG and epilepsies with significant negative genetic correlations (-0.23 to -0.04). COG was estimated to share 2.9k variants with both GGE and 'all epilepsy', and 2.3k variants with both JME and CAE. Using conjFDR, we identified 66 distinct loci shared between COG and epilepsies, including novel associations for GGE (27), 'all epilepsy' (5), JME (5) and CAE (5). The implicated genes were significantly expressed in multiple brain regions. The results were validated in independent samples (COG: p = 1.0 × 10-14; 'all epilepsy': p = 5.6 × 10-3). Significance Our study demonstrates a substantial genetic basis shared between epilepsies and COG and identifies novel overlapping genomic loci. Enhancing our understanding of the relationship between epilepsies and COG may lead to the development of novel comorbidity-targeted epilepsy treatments.
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Affiliation(s)
- Naz Karadag
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
| | - Espen Hagen
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
| | - Alexey A. Shadrin
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
- K.G. Jebsen Centre for Neurodevelopmental disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Dennis van der Meer
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
- School of Mental Health and Neuroscience, Faculty of Health, Maastricht University, Maastricht, Netherlands
| | - Kevin S. O’Connell
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
| | - Zillur Rahman
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
| | - Gleda Kutrolli
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
| | - Nadine Parker
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
| | - Shahram Bahrami
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
| | - Vera Fominykh
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
| | - Kjell Heuser
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Erik Taubøll
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Torill Ueland
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
| | - Nils Eiel Steen
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- Department of Psychiatric Research, Diakonhjemmet Hospital, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anders M. Dale
- Department of Cognitive Science, University of California, San Diego, United States
- Multimodal Imaging Laboratory, University of California, San Diego, United States
- Department of Psychiatry, University of California, San Diego, United States
- Department of Neurosciences, University of California, San Diego, United States
| | - Oleksandr Frei
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ole A. Andreassen
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
- K.G. Jebsen Centre for Neurodevelopmental disorders, University of Oslo and Oslo University Hospital, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Olav B. Smeland
- Centre for Precision Psychiatry, Division of Mental Health and Addiction, University of Oslo and Oslo University Hospital Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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13
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Ling E, Nemesh J, Goldman M, Kamitaki N, Reed N, Handsaker RE, Genovese G, Vogelgsang JS, Gerges S, Kashin S, Ghosh S, Esposito JM, Morris K, Meyer D, Lutservitz A, Mullally CD, Wysoker A, Spina L, Neumann A, Hogan M, Ichihara K, Berretta S, McCarroll SA. A concerted neuron-astrocyte program declines in ageing and schizophrenia. Nature 2024; 627:604-611. [PMID: 38448582 PMCID: PMC10954558 DOI: 10.1038/s41586-024-07109-5] [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: 12/04/2022] [Accepted: 01/23/2024] [Indexed: 03/08/2024]
Abstract
Human brains vary across people and over time; such variation is not yet understood in cellular terms. Here we describe a relationship between people's cortical neurons and cortical astrocytes. We used single-nucleus RNA sequencing to analyse the prefrontal cortex of 191 human donors aged 22-97 years, including healthy individuals and people with schizophrenia. Latent-factor analysis of these data revealed that, in people whose cortical neurons more strongly expressed genes encoding synaptic components, cortical astrocytes more strongly expressed distinct genes with synaptic functions and genes for synthesizing cholesterol, an astrocyte-supplied component of synaptic membranes. We call this relationship the synaptic neuron and astrocyte program (SNAP). In schizophrenia and ageing-two conditions that involve declines in cognitive flexibility and plasticity1,2-cells divested from SNAP: astrocytes, glutamatergic (excitatory) neurons and GABAergic (inhibitory) neurons all showed reduced SNAP expression to corresponding degrees. The distinct astrocytic and neuronal components of SNAP both involved genes in which genetic risk factors for schizophrenia were strongly concentrated. SNAP, which varies quantitatively even among healthy people of similar age, may underlie many aspects of normal human interindividual differences and may be an important point of convergence for multiple kinds of pathophysiology.
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Affiliation(s)
- Emi Ling
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Melissa Goldman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nolan Kamitaki
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nora Reed
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jonathan S Vogelgsang
- McLean Hospital, Belmont, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Sherif Gerges
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | | | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alyssa Lutservitz
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Christopher D Mullally
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alec Wysoker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Liv Spina
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Marina Hogan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Kiku Ichihara
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sabina Berretta
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McLean Hospital, Belmont, MA, USA.
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA.
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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14
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Chi W, Kiskinis E. Integrative analysis of epilepsy-associated genes reveals expression-phenotype correlations. Sci Rep 2024; 14:3587. [PMID: 38351047 PMCID: PMC10864290 DOI: 10.1038/s41598-024-53494-2] [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: 07/28/2023] [Accepted: 02/01/2024] [Indexed: 02/16/2024] Open
Abstract
Epilepsy is a highly prevalent neurological disorder characterized by recurrent seizures. Patients exhibit broad genetic, molecular, and clinical diversity involving mild to severe comorbidities. The factors that contribute to this phenotypic diversity remain unclear. Here we used publicly available datasets to systematically interrogate the expression pattern of 230 epilepsy-associated genes across human tissues, developmental stages, and central nervous system (CNS) cellular subtypes. We grouped genes based on their curated phenotypes into 3 broad classes: core epilepsy genes (CEG), where seizures are the dominant phenotype, developmental and epileptic encephalopathy genes (DEEG) that are associated with developmental and epileptic encephalopathy, and seizure-related genes (SRG), which are characterized by the presence of seizures and gross brain malformations. We find that compared to the other two groups of genes, DEEGs are highly expressed within the adult CNS, exhibit the highest and most dynamic expression in various brain regions across development, and are significantly enriched in GABAergic neurons. Our analysis provides an overview of the expression pattern of epilepsy-associated genes with spatiotemporal resolution and establishes a broad expression-phenotype correlation in epilepsy.
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Affiliation(s)
- Wanhao Chi
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA.
- Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA.
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15
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Gamirova R, Shagimardanova E, Sato T, Kannon T, Gamirova R, Tajima A. Identification of potential disease-associated variants in idiopathic generalized epilepsy using targeted sequencing. J Hum Genet 2024; 69:59-67. [PMID: 37993639 DOI: 10.1038/s10038-023-01208-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/28/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023]
Abstract
Many questions remain regarding the genetics of idiopathic generalized epilepsy (IGE), a subset of genetic generalized epilepsy (GGE). We aimed to identify the candidate coding variants of epilepsy panel genes in a cohort of affected individuals, using variant frequency information from a control cohort of the same region. We performed whole-exome sequencing analysis of 121 individuals and 10 affected relatives, focusing on variants of 950 candidate genes associated with epilepsy according to the Genes4Epilepsy curated panel. We identified 168 candidate variants (CVs) in 137 of 950 candidate genes in 88 of 121 affected individuals with IGE, of which 61 were novel variants. Notably, we identified five CVs in known GGE-associated genes (CHD2, GABRA1, RORB, SCN1A, and SCN1B) in five individuals and CVs shared by affected individuals in each of four family cases for other epilepsy candidate genes. The results of this study demonstrate that IGE is a disease with high heterogeneity and provide IGE-associated CVs whose pathogenicity should be proven by future studies, including advanced functional analysis. The low detection rate of CVs in the GGE-associated genes (4.1%) in this study suggests the current incompleteness of the Genes4Epilepsy panel for the diagnosis of IGE in clinical practice.
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Affiliation(s)
- Regina Gamirova
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | | | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Takayuki Kannon
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
- Department of Biomedical Data Science, Fujita Health University School of Medicine, Toyoake, Japan
| | - Rimma Gamirova
- Department of Neurology with Courses in Psychiatry, Clinical Psychology and Medical Genetics, Kazan Federal University, Kazan, Russia.
- Laboratory of Neurocognitive Investigations, Kazan Federal University, Kazan, Russia.
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan.
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16
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Asadi-Pooya AA, Malekpour M, Taherifard E, Mallahzadeh A, Farjoud Kouhanjani M. Coexistence of temporal lobe epilepsy and idiopathic generalized epilepsy. Epilepsy Behav 2024; 151:109602. [PMID: 38160579 DOI: 10.1016/j.yebeh.2023.109602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/07/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVE We investigated the frequency of coexistence of temporal lobe epilepsy (TLE) and idiopathic generalized epilepsy (IGE) in a retrospective database study. We also explored the underlying pathomechanisms of the coexistence of TLE and IGE based on the available information, using bioinformatics tools. METHODS The first phase of the investigation was a retrospective study. All patients with an electro-clinical diagnosis of epilepsy were studied at the outpatient epilepsy clinic at Shiraz University of Medical Sciences, Shiraz, Iran, from 2008 until 2023. In the second phase, we searched the following databases for genetic variations (epilepsy-associated genetic polymorphisms) that are associated with TLE or syndromes of IGE: DisGeNET, genome-wide association study (GWAS) Catalog, epilepsy genetic association database (epiGAD), and UniProt. We also did a separate literature search using PubMed. RESULTS In total, 3760 patients with epilepsy were registered at our clinic; four patients with definitely mixed TLE and IGE were identified; 0.1% of all epilepsies. We could identify that rs1883415 of ALDH5A1, rs137852779 of EFHC1, rs211037 of GABRG2, rs1130183 of KCNJ10, and rs1045642 of ABCB1 genes are shared between TLE and syndromes of IGE. CONCLUSION While coexistence of TLE and IGE is a rare phenomenon, this could be explained by shared genetic variations.
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Affiliation(s)
- Ali A Asadi-Pooya
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran; Jefferson Comprehensive Epilepsy Center, Department of Neurology, Thomas Jefferson University, Philadelphia, PA, USA.
| | - Mahdi Malekpour
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ehsan Taherifard
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arashk Mallahzadeh
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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17
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Zhou J, Weinberger DR, Han S. Deep learning predicts DNA methylation regulatory variants in specific brain cell types and enhances fine mapping for brain disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576319. [PMID: 38293210 PMCID: PMC10827166 DOI: 10.1101/2024.01.18.576319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
DNA methylation (DNAm) is essential for brain development and function and potentially mediates the effects of genetic risk variants underlying brain disorders. We present INTERACT, a transformer-based deep learning model to predict regulatory variants impacting DNAm levels in specific brain cell types, leveraging existing single-nucleus DNAm data from the human brain. We show that INTERACT accurately predicts cell type-specific DNAm profiles, achieving an average area under the Receiver Operating Characteristic curve of 0.98 across cell types. Furthermore, INTERACT predicts cell type-specific DNAm regulatory variants, which reflect cellular context and enrich the heritability of brain-related traits in relevant cell types. Importantly, we demonstrate that incorporating predicted variant effects and DNAm levels of CpG sites enhances the fine mapping for three brain disorders-schizophrenia, depression, and Alzheimer's disease-and facilitates mapping causal genes to particular cell types. Our study highlights the power of deep learning in identifying cell type-specific regulatory variants, which will enhance our understanding of the genetics of complex traits.
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Affiliation(s)
- Jiyun Zhou
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21287, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21287, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shizhong Han
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21287, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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18
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Wang S, Xie Z, Jun T, Ma X, Zhang M, Rao F, Xu H, Lu J, Ding X, Li Z. Identification of potential crucial genes and therapeutic targets for epilepsy. Eur J Med Res 2024; 29:43. [PMID: 38212777 PMCID: PMC10782668 DOI: 10.1186/s40001-024-01643-8] [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: 03/14/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Epilepsy, a central neurological disorder, has a complex genetic architecture. There is some evidence suggesting that genetic factors play a role in both the occurrence of epilepsy and its treatment. However, the genetic determinants of epilepsy are largely unknown. This study aimed to identify potential therapeutic targets for epilepsy. METHODS Differentially expressed genes (DEGs) were extracted from the expression profiles of GSE44031 and GSE1834. Gene co-expression analysis was used to confirm the regulatory relationship between newly discovered epilepsy candidate genes and known epilepsy genes. Expression quantitative trait loci analysis was conducted to determine if epilepsy risk single-nucleotide polymorphisms regulate DEGs' expression in human brain tissue. Finally, protein-protein interaction analysis and drug-gene interaction analysis were performed to assess the role of DEGs in epilepsy treatment. RESULTS The study found that the protein tyrosine phosphatase receptor-type O gene (PTPRO) and the growth arrest and DNA damage inducible alpha gene (GADD45A) were significantly upregulated in epileptic rats compared to controls in both datasets. Gene co-expression analysis revealed that PTPRO was co-expressed with RBP4, NDN, PAK3, FOXG1, IDS, and IDS, and GADD45A was co-expressed with LRRK2 in human brain tissue. Expression quantitative trait loci analysis suggested that epilepsy risk single-nucleotide polymorphisms could be responsible for the altered PTPRO and GADD45A expression in human brain tissue. Moreover, the protein encoded by GADD45A had a direct interaction with approved antiepileptic drug targets, and GADD45A interacts with genistein and cisplatin. CONCLUSIONS The results of this study highlight PTPRO and GADD45A as potential genes for the diagnosis and treatment of epilepsy.
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Affiliation(s)
- Shitao Wang
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China.
| | - Zhenrong Xie
- The Medical Biobank, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, Yunnan, China
| | - Tian Jun
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Xuelu Ma
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Mengen Zhang
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Feng Rao
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Hui Xu
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Jinghong Lu
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
| | - Xiangqian Ding
- Department of Neurosurgery, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Zongyou Li
- Department of Neurology, Affiliated Fuyang People's Hospital of Anhui Medical University, Fuyang, 236000, Anhui, China
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19
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Ling E, Nemesh J, Goldman M, Kamitaki N, Reed N, Handsaker RE, Genovese G, Vogelgsang JS, Gerges S, Kashin S, Ghosh S, Esposito JM, French K, Meyer D, Lutservitz A, Mullally CD, Wysoker A, Spina L, Neumann A, Hogan M, Ichihara K, Berretta S, McCarroll SA. Concerted neuron-astrocyte gene expression declines in aging and schizophrenia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.574148. [PMID: 38260461 PMCID: PMC10802483 DOI: 10.1101/2024.01.07.574148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Human brains vary across people and over time; such variation is not yet understood in cellular terms. Here we describe a striking relationship between people's cortical neurons and cortical astrocytes. We used single-nucleus RNA-seq to analyze the prefrontal cortex of 191 human donors ages 22-97 years, including healthy individuals and persons with schizophrenia. Latent-factor analysis of these data revealed that in persons whose cortical neurons more strongly expressed genes for synaptic components, cortical astrocytes more strongly expressed distinct genes with synaptic functions and genes for synthesizing cholesterol, an astrocyte-supplied component of synaptic membranes. We call this relationship the Synaptic Neuron-and-Astrocyte Program (SNAP). In schizophrenia and aging - two conditions that involve declines in cognitive flexibility and plasticity 1,2 - cells had divested from SNAP: astrocytes, glutamatergic (excitatory) neurons, and GABAergic (inhibitory) neurons all reduced SNAP expression to corresponding degrees. The distinct astrocytic and neuronal components of SNAP both involved genes in which genetic risk factors for schizophrenia were strongly concentrated. SNAP, which varies quantitatively even among healthy persons of similar age, may underlie many aspects of normal human interindividual differences and be an important point of convergence for multiple kinds of pathophysiology.
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Affiliation(s)
- Emi Ling
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Melissa Goldman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nolan Kamitaki
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Nora Reed
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Robert E. Handsaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan S. Vogelgsang
- McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
| | - Sherif Gerges
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | | | | | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alyssa Lutservitz
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher D. Mullally
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Alec Wysoker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Liv Spina
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Marina Hogan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Kiku Ichihara
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sabina Berretta
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
- Program in Neuroscience, Harvard Medical School, Boston, MA 02215, USA
| | - Steven A. McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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20
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Auwerx C, Jõeloo M, Sadler MC, Tesio N, Ojavee S, Clark CJ, Mägi R, Reymond A, Kutalik Z. Rare copy-number variants as modulators of common disease susceptibility. Genome Med 2024; 16:5. [PMID: 38185688 PMCID: PMC10773105 DOI: 10.1186/s13073-023-01265-5] [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: 07/17/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described. METHODS Assessing four modes of CNV action, we performed genome-wide association scans (GWASs) between the copy-number of CNV-proxy probes and 60 curated ICD-10 based clinical diagnoses in 331,522 unrelated white British UK Biobank (UKBB) participants with replication in the Estonian Biobank. RESULTS We identified 73 signals involving 40 diseases, all of which indicating that CNVs increased disease risk and caused earlier onset. We estimated that 16% of these associations are indirect, acting by increasing body mass index (BMI). Signals mapped to 45 unique, non-overlapping regions, nine of which being linked to known GDs. Number and identity of genes affected by CNVs modulated their pathogenicity, with many associations being supported by colocalization with both common and rare single-nucleotide variant association signals. Dissection of association signals provided insights into the epidemiology of known gene-disease pairs (e.g., deletions in BRCA1 and LDLR increased risk for ovarian cancer and ischemic heart disease, respectively), clarified dosage mechanisms of action (e.g., both increased and decreased dosage of 17q12 impacted renal health), and identified putative causal genes (e.g., ABCC6 for kidney stones). Characterization of the pleiotropic pathological consequences of recurrent CNVs at 15q13, 16p13.11, 16p12.2, and 22q11.2 in adulthood indicated variable expressivity of these regions and the involvement of multiple genes. Finally, we show that while the total burden of rare CNVs-and especially deletions-strongly associated with disease risk, it only accounted for ~ 0.02% of the UKBB disease burden. These associations are mainly driven by CNVs at known GD CNV regions, whose pleiotropic effect on common diseases was broader than anticipated by our CNV-GWAS. CONCLUSIONS Our results shed light on the prominent role of rare CNVs in determining common disease susceptibility within the general population and provide actionable insights for anticipating later-onset comorbidities in carriers of recurrent CNVs.
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Affiliation(s)
- Chiara Auwerx
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
| | - Maarja Jõeloo
- Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Marie C Sadler
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland
| | - Nicolò Tesio
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Sven Ojavee
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Charlie J Clark
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
| | - Zoltán Kutalik
- Department of Computational Biology, University of Lausanne, Genopode building, 1015, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
- University Center for Primary Care and Public Health, 1005, Lausanne, Switzerland.
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21
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Hullett PW, Lowenstein DH. Major advances in epilepsy research in 2023. Lancet Neurol 2024; 23:19-20. [PMID: 38101887 DOI: 10.1016/s1474-4422(23)00457-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/17/2023]
Affiliation(s)
- Patrick W Hullett
- Department of Neurology, University of California, San Francisco, CA 94143, USA.
| | - Daniel H Lowenstein
- Department of Neurology, University of California, San Francisco, CA 94143, USA
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22
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Zeibich R, Kwan P, J. O’Brien T, Perucca P, Ge Z, Anderson A. Applications for Deep Learning in Epilepsy Genetic Research. Int J Mol Sci 2023; 24:14645. [PMID: 37834093 PMCID: PMC10572791 DOI: 10.3390/ijms241914645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/11/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Epilepsy is a group of brain disorders characterised by an enduring predisposition to generate unprovoked seizures. Fuelled by advances in sequencing technologies and computational approaches, more than 900 genes have now been implicated in epilepsy. The development and optimisation of tools and methods for analysing the vast quantity of genomic data is a rapidly evolving area of research. Deep learning (DL) is a subset of machine learning (ML) that brings opportunity for novel investigative strategies that can be harnessed to gain new insights into the genomic risk of people with epilepsy. DL is being harnessed to address limitations in accuracy of long-read sequencing technologies, which improve on short-read methods. Tools that predict the functional consequence of genetic variation can represent breaking ground in addressing critical knowledge gaps, while methods that integrate independent but complimentary data enhance the predictive power of genetic data. We provide an overview of these DL tools and discuss how they may be applied to the analysis of genetic data for epilepsy research.
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Affiliation(s)
- Robert Zeibich
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Neurology, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Neurology, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Terence J. O’Brien
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Neurology, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Neurology, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Piero Perucca
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Neurology, Alfred Health, Melbourne, VIC 3004, Australia
- Department of Neurology, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
- Epilepsy Research Centre, Department of Medicine, Austin Health, The University of Melbourne, Melbourne, VIC 3084, Australia
- Bladin-Berkovic Comprehensive Epilepsy Program, Department of Neurology, Austin Health, The University of Melbourne, Melbourne, VIC 3084, Australia
| | - Zongyuan Ge
- Faculty of Engineering, Monash University, Melbourne, VIC 3800, Australia;
- Monash-Airdoc Research, Monash University, Melbourne, VIC 3800, Australia
| | - Alison Anderson
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia; (R.Z.); (P.K.); (T.J.O.); (P.P.)
- Department of Medicine, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3052, Australia
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