1
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Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. A foundational atlas of autism protein interactions reveals molecular convergence. bioRxiv 2024:2023.12.03.569805. [PMID: 38076945 PMCID: PMC10705567 DOI: 10.1101/2023.12.03.569805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, transcriptional regulation, and chromatin modification. A PPI map of 54 patient-derived missense variants identified differential physical interactions, and we leveraged AlphaFold-Multimer predictions to prioritize direct PPIs and specific variants for interrogation in Xenopus tropicalis and human forebrain organoids. A mutation in the transcription factor FOXP1 led to reconfiguration of DNA binding sites and altered development of deep cortical layer neurons in forebrain organoids. This work offers new insights into molecular mechanisms underlying ASD and describes a powerful platform to develop and test therapeutic strategies for many genetically-defined conditions.
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2
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Sun N, Teyssier N, Wang B, Drake S, Seyler M, Zaltsman Y, Everitt A, Teerikorpi N, Willsey HR, Goodarzi H, Tian R, Kampmann M, Willsey AJ. Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis. bioRxiv 2024:2023.12.22.573108. [PMID: 38187634 PMCID: PMC10769323 DOI: 10.1101/2023.12.22.573108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Recent studies have identified over one hundred high-confidence (hc) autism spectrum disorder (ASD) genes. Systems biological and functional analyses on smaller subsets of these genes have consistently implicated excitatory neurogenesis. However, the extent to which the broader set of hcASD genes are involved in this process has not been explored systematically nor have the biological pathways underlying this convergence been identified. Here, we leveraged CROP-Seq to repress 87 hcASD genes in a human in vitro model of cortical neurogenesis. We identified 17 hcASD genes whose repression significantly alters developmental trajectory and results in a common cellular state characterized by disruptions in proliferation, differentiation, cell cycle, microtubule biology, and RNA-binding proteins (RBPs). We also characterized over 3,000 differentially expressed genes, 286 of which had expression profiles correlated with changes in developmental trajectory. Overall, we uncovered transcriptional disruptions downstream of hcASD gene perturbations, correlated these disruptions with distinct differentiation phenotypes, and reinforced neurogenesis, microtubule biology, and RBPs as convergent points of disruption in ASD.
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3
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Wang S, Wang B, Drury V, Drake S, Sun N, Alkhairo H, Arbelaez J, Duhn C, Bal VH, Langley K, Martin J, Hoekstra PJ, Dietrich A, Xing J, Heiman GA, Tischfield JA, Fernandez TV, Owen MJ, O'Donovan MC, Thapar A, State MW, Willsey AJ. Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD. Nat Commun 2023; 14:8077. [PMID: 38057346 PMCID: PMC10700338 DOI: 10.1038/s41467-023-43776-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/18/2023] [Indexed: 12/08/2023] Open
Abstract
Autism spectrum disorder (ASD), Tourette syndrome (TS), and attention-deficit/hyperactivity disorder (ADHD) display strong male sex bias, due to a combination of genetic and biological factors, as well as selective ascertainment. While the hemizygous nature of chromosome X (Chr X) in males has long been postulated as a key point of "male vulnerability", rare genetic variation on this chromosome has not been systematically characterized in large-scale whole exome sequencing studies of "idiopathic" ASD, TS, and ADHD. Here, we take advantage of informative recombinations in simplex ASD families to pinpoint risk-enriched regions on Chr X, within which rare maternally-inherited damaging variants carry substantial risk in males with ASD. We then apply a modified transmission disequilibrium test to 13,052 ASD probands and identify a novel high confidence ASD risk gene at exome-wide significance (MAGEC3). Finally, we observe that rare damaging variants within these risk regions carry similar effect sizes in males with TS or ADHD, further clarifying genetic mechanisms underlying male vulnerability in multiple neurodevelopmental disorders that can be exploited for systematic gene discovery.
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Affiliation(s)
- Sheng Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Vanessa Drury
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Sam Drake
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Hasan Alkhairo
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Juan Arbelaez
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Clif Duhn
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Vanessa H Bal
- Graduate School of Applied and Professional Psychology, Rutgers University, New Brunswick, NJ, USA
| | - Kate Langley
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
- School of Psychology, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Joanna Martin
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Pieter J Hoekstra
- University of Groningen, University Medical Center Groningen, Department of Child and Adolescent Psychiatry, Groningen, The Netherlands
- Accare Child Study Center, Groningen, The Netherlands
| | - Andrea Dietrich
- University of Groningen, University Medical Center Groningen, Department of Child and Adolescent Psychiatry, Groningen, The Netherlands
- Accare Child Study Center, Groningen, The Netherlands
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Gary A Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Thomas V Fernandez
- Yale Child Study Center and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Michael J Owen
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Michael C O'Donovan
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Anita Thapar
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA.
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94143, USA.
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4
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Lasser M, Sun N, Xu Y, Wang S, Drake S, Law K, Gonzalez S, Wang B, Drury V, Castillo O, Zaltsman Y, Dea J, Bader E, McCluskey KE, State MW, Willsey AJ, Willsey HR. Pleiotropy of autism-associated chromatin regulators. Development 2023; 150:dev201515. [PMID: 37366052 PMCID: PMC10399978 DOI: 10.1242/dev.201515] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 06/19/2023] [Indexed: 06/28/2023]
Abstract
Gene ontology analyses of high-confidence autism spectrum disorder (ASD) risk genes highlight chromatin regulation and synaptic function as major contributors to pathobiology. Our recent functional work in vivo has additionally implicated tubulin biology and cellular proliferation. As many chromatin regulators, including the ASD risk genes ADNP and CHD3, are known to directly regulate both tubulins and histones, we studied the five chromatin regulators most strongly associated with ASD (ADNP, CHD8, CHD2, POGZ and KMT5B) specifically with respect to tubulin biology. We observe that all five localize to microtubules of the mitotic spindle in vitro in human cells and in vivo in Xenopus. Investigation of CHD2 provides evidence that mutations present in individuals with ASD cause a range of microtubule-related phenotypes, including disrupted localization of the protein at mitotic spindles, cell cycle stalling, DNA damage and cell death. Lastly, we observe that ASD genetic risk is significantly enriched among tubulin-associated proteins, suggesting broader relevance. Together, these results provide additional evidence that the role of tubulin biology and cellular proliferation in ASD warrants further investigation and highlight the pitfalls of relying solely on annotated gene functions in the search for pathological mechanisms.
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Affiliation(s)
- Micaela Lasser
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sheng Wang
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sam Drake
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Karen Law
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Silvano Gonzalez
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vanessa Drury
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Octavio Castillo
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yefim Zaltsman
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ethel Bader
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kate E. McCluskey
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew W. State
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA 94143, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - A. Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158, USA
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5
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Tsetsos F, Topaloudi A, Jain P, Yang Z, Yu D, Kolovos P, Tumer Z, Rizzo R, Hartmann A, Depienne C, Worbe Y, Müller-Vahl KR, Cath DC, Boomsma DI, Wolanczyk T, Zekanowski C, Barta C, Nemoda Z, Tarnok Z, Padmanabhuni SS, Buxbaum JD, Grice D, Glennon J, Stefansson H, Hengerer B, Yannaki E, Stamatoyannopoulos JA, Benaroya-Milshtein N, Cardona F, Hedderly T, Heyman I, Huyser C, Mir P, Morer A, Mueller N, Munchau A, Plessen KJ, Porcelli C, Roessner V, Walitza S, Schrag A, Martino D, Tischfield JA, Heiman GA, Willsey AJ, Dietrich A, Davis LK, Crowley JJ, Mathews CA, Scharf JM, Georgitsi M, Hoekstra PJ, Paschou P. Genome-wide Association Study Points to Novel Locus for Gilles de la Tourette Syndrome. Biol Psychiatry 2023:S0006-3223(23)00051-3. [PMID: 36738982 PMCID: PMC10783199 DOI: 10.1016/j.biopsych.2023.01.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/23/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023]
Abstract
BACKGROUND Tourette syndrome (TS) is a childhood-onset neurodevelopmental disorder of complex genetic architecture and is characterized by multiple motor tics and at least one vocal tic persisting for more than 1 year. METHODS We performed a genome-wide meta-analysis integrating a novel TS cohort with previously published data, resulting in a sample size of 6133 individuals with TS and 13,565 ancestry-matched control participants. RESULTS We identified a genome-wide significant locus on chromosome 5q15. Integration of expression quantitative trait locus, Hi-C (high-throughput chromosome conformation capture), and genome-wide association study data implicated the NR2F1 gene and associated long noncoding RNAs within the 5q15 locus. Heritability partitioning identified statistically significant enrichment in brain tissue histone marks, while polygenic risk scoring of brain volume data identified statistically significant associations with right and left thalamus volumes and right putamen volume. CONCLUSIONS Our work presents novel insights into the neurobiology of TS, thereby opening up new directions for future studies.
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Affiliation(s)
- Fotis Tsetsos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Apostolia Topaloudi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Pritesh Jain
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Zhiyu Yang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Zeynep Tumer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen
| | - Renata Rizzo
- Child and Adolescent Neurology and Psychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Andreas Hartmann
- Department of Neurology, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Christel Depienne
- Institute for Human Genetics, University Hospital Essen, Essen, Germany
| | - Yulia Worbe
- Assistance Publique Hôpitaux de Paris, Hopital Saint Antoine, Paris France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Kirsten R. Müller-Vahl
- Department of Psychiatry, Social psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Danielle C. Cath
- Department of Clinical and health Psychology, Utrecht University, Utrecht, Netherlands
| | - Dorret I. Boomsma
- Institute for Anatomy and Cell Biology, Ulm University, Ulm, Germany
- EMGO+ Institute for Health and Care Research, VU University Medical Centre, Amsterdam, Netherlands
| | - Tomasz Wolanczyk
- Department of Child Psychiatry, Medical University of Warsaw, Warsaw, Poland
| | - Cezary Zekanowski
- Laboratory of Neurogenetics, Department of Neurodegenerative Disorders, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Csaba Barta
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zsofia Nemoda
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zsanett Tarnok
- Vadaskert Clinic for Child and Adolescent Psychiatry, Hungary
| | | | - Joseph D. Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, USA
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, USA
| | - Dorothy Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, USA
- Division of Tics, OCD, and Related Disorders, Icahn School of Medicine at Mount Sinai, USA
| | - Jeffrey Glennon
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Netherlands
| | | | - Bastian Hengerer
- Boehringer Ingelheim Pharma GmbH & Co. KG, CNS Research, Germany
| | - Evangelia Yannaki
- Hematology Department- Hematopoietic Cell Transplantation Unit, Gene and Cell Therapy Center, George Papanikolaou Hospital, Greece
- Department of Medicine, University of Washington, WA, USA
| | - John A. Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, WA, USA
- Department of Genome Sciences, University of Washington, WA, USA
- Department of Medicine, Division of Oncology, University of Washington, WA, USA
| | - Noa Benaroya-Milshtein
- Child and Adolescent Psychiatry Department, Schneider Children’s Medical Centre of Israel, Petah-Tikva. Affiliated to Sackler Faculty of Medicine, Tel Aviv University, Israel
| | - Francesco Cardona
- Department of Human Neurosciences, University La Sapienza of Rome, Rome, Italy
| | - Tammy Hedderly
- Evelina London Children’s Hospital GSTT, Kings Health Partners AHSC, London, UK
| | - Isobel Heyman
- Psychological Medicine, Great Ormond Street Hospital NHS Foundation Trust, Great Ormond Street, London, UK
| | - Chaim Huyser
- Levvel, Academic Center for Child and Adolescent Psychiatry, Amsterdam, The Netherlands
- Amsterdam UMC, Department of Child and Adolescent Psychiatry, Amsterdam, The Netherlands
| | - Pablo Mir
- Unidad de Trastornos del Movimiento. Instituto de Biomedicina de Sevilla (IBiS). Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla. Seville, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Astrid Morer
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic Universitari, Barcelona, Spain
- Institut d’Investigacions Biomediques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigacion en Red de Salud Mental (CIBERSAM), Instituto Carlos III, Spain
| | - Norbert Mueller
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
| | - Alexander Munchau
- Institute of Systems Motor Science, University of Lübeck, Lübeck, Germany
| | - Kerstin J Plessen
- Child and Adolescent Mental Health Centre, Mental Health Services, Capital Region of Denmark and University of Copenhagen, Copenhagen, Denmark
- Division of Child and Adolescent Psychiatry, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
| | - Cesare Porcelli
- ASL BA, Maternal and Childood Department; Adolescence and Childhood Neuropsychiatry Unit; Bari, Italy
| | - Veit Roessner
- Department of Child and Adolescent Psychiatry, Medical Faculty Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, University of Zurich, Zurich, Switzerland
| | - Anette Schrag
- Department of Clinical Neuroscience, UCL Institute of Neurology, University College London, London, UK
| | - Davide Martino
- Department of Clinical Neurosciences, Cumming School of Medicine & Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | | | | | | | | | | | | | - Jay A. Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Gary A. Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - A. Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Andrea Dietrich
- University of Groningen, University Medical Centre Groningen, Department of Child and Adolescent Psychiatry, Groningen, the Netherlands
| | - Lea K. Davis
- Division of Genetic Medicine, Department of Medicine Vanderbilt University Medical Center Nashville, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James J. Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Carol A. Mathews
- Department of Psychiatry and Genetics Institute, University of Florida College of Medicine, USA
| | - Jeremiah M. Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Marianthi Georgitsi
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
- 1st Laboratory of Medical Biology-Genetics, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Pieter J. Hoekstra
- University of Groningen, University Medical Centre Groningen, Department of Child and Adolescent Psychiatry, Groningen, the Netherlands
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
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6
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Willsey HR, Willsey AJ, Wang B, State MW. Genomics, convergent neuroscience and progress in understanding autism spectrum disorder. Nat Rev Neurosci 2022; 23:323-341. [PMID: 35440779 PMCID: PMC10693992 DOI: 10.1038/s41583-022-00576-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/31/2022]
Abstract
More than a hundred genes have been identified that, when disrupted, impart large risk for autism spectrum disorder (ASD). Current knowledge about the encoded proteins - although incomplete - points to a very wide range of developmentally dynamic and diverse biological processes. Moreover, the core symptoms of ASD involve distinctly human characteristics, presenting challenges to interpreting evolutionarily distant model systems. Indeed, despite a decade of striking progress in gene discovery, an actionable understanding of pathobiology remains elusive. Increasingly, convergent neuroscience approaches have been recognized as an important complement to traditional uses of genetics to illuminate the biology of human disorders. These methods seek to identify intersection among molecular-level, cellular-level and circuit-level functions across multiple risk genes and have highlighted developing excitatory neurons in the human mid-gestational prefrontal cortex as an important pathobiological nexus in ASD. In addition, neurogenesis, chromatin modification and synaptic function have emerged as key potential mediators of genetic vulnerability. The continued expansion of foundational 'omics' data sets, the application of higher-throughput model systems and incorporating developmental trajectories and sex differences into future analyses will refine and extend these results. Ultimately, a systems-level understanding of ASD genetic risk holds promise for clarifying pathobiology and advancing therapeutics.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA.
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7
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Fazel Darbandi S, Robinson Schwartz SE, Pai ELL, Everitt A, Turner ML, Cheyette BNR, Willsey AJ, State MW, Sohal VS, Rubenstein JLR. Enhancing WNT Signaling Restores Cortical Neuronal Spine Maturation and Synaptogenesis in Tbr1 Mutants. Cell Rep 2021; 31:107495. [PMID: 32294447 PMCID: PMC7473600 DOI: 10.1016/j.celrep.2020.03.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 01/17/2020] [Accepted: 03/17/2020] [Indexed: 12/21/2022] Open
Abstract
Tbr1 is a high-confidence autism spectrum disorder (ASD)
gene encoding a transcription factor with distinct pre- and postnatal functions.
Postnatally, Tbr1 conditional knockout (CKO) mutants and
constitutive heterozygotes have immature dendritic spines and reduced synaptic
density. Tbr1 regulates expression of several genes that
underlie synaptic defects, including a kinesin (Kif1a) and a
WNT-signaling ligand (Wnt7b). Furthermore,
Tbr1 mutant corticothalamic neurons have reduced thalamic
axonal arborization. LiCl and a GSK3β inhibitor, two WNT-signaling
agonists, robustly rescue the dendritic spines and the synaptic and axonal
defects, suggesting that this could have relevance for therapeutic approaches in
some forms of ASD. Fazel Darbandi et al. demonstrate that TBR1 directly regulates
transcriptional circuits in cortical layers 5 and 6, which promote dendritic
spine and synaptic density. Enhancing WNT signaling rescues dendritic spine
maturation and synaptogenesis defects in Tbr1 mutants. These
results provide insights into mechanisms that underlie ASD pathophysiology.
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Affiliation(s)
- Siavash Fazel Darbandi
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sarah E Robinson Schwartz
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily Ling-Lin Pai
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amanda Everitt
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marc L Turner
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Benjamin N R Cheyette
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - A Jeremy Willsey
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew W State
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vikaas S Sohal
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience and Sloan-Swartz Center for Theoretical Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John L R Rubenstein
- Department of Psychiatry and UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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8
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Willsey HR, Exner CRT, Xu Y, Everitt A, Sun N, Wang B, Dea J, Schmunk G, Zaltsman Y, Teerikorpi N, Kim A, Anderson AS, Shin D, Seyler M, Nowakowski TJ, Harland RM, Willsey AJ, State MW. Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. Neuron 2021; 109:1409. [PMID: 33887193 DOI: 10.1016/j.neuron.2021.03.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Willsey HR, Exner CRT, Xu Y, Everitt A, Sun N, Wang B, Dea J, Schmunk G, Zaltsman Y, Teerikorpi N, Kim A, Anderson AS, Shin D, Seyler M, Nowakowski TJ, Harland RM, Willsey AJ, State MW. Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. Neuron 2021; 109:788-804.e8. [PMID: 33497602 DOI: 10.1016/j.neuron.2021.01.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 12/02/2020] [Accepted: 01/04/2021] [Indexed: 12/29/2022]
Abstract
Gene Ontology analyses of autism spectrum disorders (ASD) risk genes have repeatedly highlighted synaptic function and transcriptional regulation as key points of convergence. However, these analyses rely on incomplete knowledge of gene function across brain development. Here we leverage Xenopus tropicalis to study in vivo ten genes with the strongest statistical evidence for association with ASD. All genes are expressed in developing telencephalon at time points mapping to human mid-prenatal development, and mutations lead to an increase in the ratio of neural progenitor cells to maturing neurons, supporting previous in silico systems biological findings implicating cortical neurons in ASD vulnerability, but expanding the range of convergent functions to include neurogenesis. Systematic chemical screening identifies that estrogen, via Sonic hedgehog signaling, rescues this convergent phenotype in Xenopus and human models of brain development, suggesting a resilience factor that may mitigate a range of ASD genetic risks.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Amanda Everitt
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Galina Schmunk
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yefim Zaltsman
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nia Teerikorpi
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Albert Kim
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Aoife S Anderson
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David Shin
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Meghan Seyler
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Richard M Harland
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA 94143, USA.
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10
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Tsetsos F, Yu D, Sul JH, Huang AY, Illmann C, Osiecki L, Darrow SM, Hirschtritt ME, Greenberg E, Muller-Vahl KR, Stuhrmann M, Dion Y, Rouleau GA, Aschauer H, Stamenkovic M, Schlögelhofer M, Sandor P, Barr CL, Grados MA, Singer HS, Nöthen MM, Hebebrand J, Hinney A, King RA, Fernandez TV, Barta C, Tarnok Z, Nagy P, Depienne C, Worbe Y, Hartmann A, Budman CL, Rizzo R, Lyon GJ, McMahon WM, Batterson JR, Cath DC, Malaty IA, Okun MS, Berlin C, Woods DW, Lee PC, Jankovic J, Robertson MM, Gilbert DL, Brown LW, Coffey BJ, Dietrich A, Hoekstra PJ, Kuperman S, Zinner SH, Wagner M, Knowles JA, Jeremy Willsey A, Tischfield JA, Heiman GA, Cox NJ, Freimer NB, Neale BM, Davis LK, Coppola G, Mathews CA, Scharf JM, Paschou P, Barr CL, Batterson JR, Berlin C, Budman CL, Cath DC, Coppola G, Cox NJ, Darrow S, Davis LK, Dion Y, Freimer NB, Grados MA, Greenberg E, Hirschtritt ME, Huang AY, Illmann C, King RA, Kurlan R, Leckman JF, Lyon GJ, Malaty IA, Mathews CA, McMahon WM, Neale BM, Okun MS, Osiecki L, Robertson MM, Rouleau GA, Sandor P, Scharf JM, Singer HS, Smit JH, Sul JH, Yu D, Aschauer HAH, Barta C, Budman CL, Cath DC, Depienne C, Hartmann A, Hebebrand J, Konstantinidis A, Mathews CA, Müller-Vahl K, Nagy P, Nöthen MM, Paschou P, Rizzo R, Rouleau GA, Sandor P, Scharf JM, Schlögelhofer M, Stamenkovic M, Stuhrmann M, Tsetsos F, Tarnok Z, Wolanczyk T, Worbe Y, Brown L, Cheon KA, Coffey BJ, Dietrich A, Fernandez TV, Garcia-Delgar B, Gilbert D, Grice DE, Hagstrøm J, Hedderly T, Heiman GA, Heyman I, Hoekstra PJ, Huyser C, Kim YK, Kim YS, King RA, Koh YJ, Kook S, Kuperman S, Leventhal BL, Madruga-Garrido M, Mir P, Morer A, Münchau A, Plessen KJ, Roessner V, Shin EY, Song DH, Song J, Tischfield JA, Willsey AJ, Zinner S, Aschauer H, Barr CL, Barta C, Batterson JR, Berlin C, Brown L, Budman CL, Cath DC, Coffey BJ, Coppola G, Cox NJ, Darrow S, Davis LK, Depienne C, Dietrich A, Dion Y, Fernandez T, Freimer NB, Gilbert D, Grados MA, Greenberg E, Hartmann A, Hebebrand J, Heiman G, Hirschtritt ME, Hoekstra P, Huang AY, Illmann C, Jankovic J, King RA, Kuperman S, Lee PC, Lyon GJ, Malaty IA, Mathews CA, McMahon WM, Müller-Vahl K, Nagy P, Neale BM, Nöthen MM, Okun MS, Osiecki L, Paschou P, Rizzo R, Robertson MM, Rouleau GA, Sandor P, Scharf JM, Schlögelhofer M, Singer HS, Stamenkovic M, Stuhrmann M, Sul JH, Tarnok Z, Tischfield J, Tsetsos F, Willsey AJ, Woods D, Worbe Y, Yu D, Zinner S. Synaptic processes and immune-related pathways implicated in Tourette syndrome. Transl Psychiatry 2021; 11:56. [PMID: 33462189 PMCID: PMC7814139 DOI: 10.1038/s41398-020-01082-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 09/18/2020] [Accepted: 10/21/2020] [Indexed: 12/23/2022] Open
Abstract
Tourette syndrome (TS) is a neuropsychiatric disorder of complex genetic architecture involving multiple interacting genes. Here, we sought to elucidate the pathways that underlie the neurobiology of the disorder through genome-wide analysis. We analyzed genome-wide genotypic data of 3581 individuals with TS and 7682 ancestry-matched controls and investigated associations of TS with sets of genes that are expressed in particular cell types and operate in specific neuronal and glial functions. We employed a self-contained, set-based association method (SBA) as well as a competitive gene set method (MAGMA) using individual-level genotype data to perform a comprehensive investigation of the biological background of TS. Our SBA analysis identified three significant gene sets after Bonferroni correction, implicating ligand-gated ion channel signaling, lymphocytic, and cell adhesion and transsynaptic signaling processes. MAGMA analysis further supported the involvement of the cell adhesion and trans-synaptic signaling gene set. The lymphocytic gene set was driven by variants in FLT3, raising an intriguing hypothesis for the involvement of a neuroinflammatory element in TS pathogenesis. The indications of involvement of ligand-gated ion channel signaling reinforce the role of GABA in TS, while the association of cell adhesion and trans-synaptic signaling gene set provides additional support for the role of adhesion molecules in neuropsychiatric disorders. This study reinforces previous findings but also provides new insights into the neurobiology of TS.
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Grants
- R01 NS102371 NINDS NIH HHS
- R01 NS096207 NINDS NIH HHS
- R01 NS096008 NINDS NIH HHS
- R01 NS105746 NINDS NIH HHS
- R01 MH115958 NIMH NIH HHS
- K08 MH099424 NIMH NIH HHS
- K02 NS085048 NINDS NIH HHS
- R01 MH115963 NIMH NIH HHS
- U01 HG009086 NHGRI NIH HHS
- R56 MH120736 NIMH NIH HHS
- U54 MD010722 NIMHD NIH HHS
- UL1 TR001863 NCATS NIH HHS
- R01 DC016977 NIDCD NIH HHS
- DP2 HD098859 NICHD NIH HHS
- R01 MH115961 NIMH NIH HHS
- U24 MH068457 NIMH NIH HHS
- R25 NS108939 NINDS NIH HHS
- R01 MH114927 NIMH NIH HHS
- R01 NR014852 NINR NIH HHS
- R21 HG010652 NHGRI NIH HHS
- R01 MH113362 NIMH NIH HHS
- RM1 HG009034 NHGRI NIH HHS
- FT is co-financed by Greece and the European Union (European Social Fund- ESF) through the Operational Programme «Human Resources Development, Education and Lifelong Learning» in the context of the project “Reinforcement of Postdoctoral Researchers - 2nd Cycle” (MIS-5033021), implemented by the State Scholarships Foundation (IKY)
- KMV has received financial or material research support from the EU (FP7-HEALTH-2011 No. 278367, FP7-PEOPLE-2012-ITN No. 316978), the German Research Foundation (DFG: GZ MU 1527/3-1), the German Ministry of Education and Research (BMBF: 01KG1421), the National Institute of Mental Health (NIMH), the Tourette Gesellschaft Deutschland e.V., the Else-Kroner-Fresenius-Stiftung, and GW, Almirall, Abide Therapeutics, and Therapix Biosiences and has received consultant’s honoraria from Abide Therapeutics, Tilray, Resalo Vertrieb GmbH, and Wayland Group, speaker’s fees from Tilray and Cogitando GmbH, and royalties from Medizinisch Wissenschaftliche Verlagsgesellschaft Berlin, Elsevier, and Kohlhammer; and is a consultant for Nuvelution TS Pharma Inc., Zynerba Pharmaceuticals, Resalo Vertrieb GmbH, CannaXan GmbH, Therapix Biosiences, Syqe, Nomovo Pharma, and Columbia Care.
- MMN has received fees for memberships in Scientific Advisory Boards from the Lundbeck Foundation and the Robert-Bosch-Stiftung, and for membership in the Medical-Scientific Editorial Office of the Deutsches Ärzteblatt. MMN was reimbursed travel expenses for a conference participation by Shire Deutschland GmbH. MMN receives salary payments from Life & Brain GmbH and holds shares in Life & Brain GmbH. All this concerned activities outside the submitted work.
- IM has participated in research funded by the Parkinson Foundation, Tourette Association, Dystonia Coalition, AbbVie, Biogen, Boston Scientific, Eli Lilly, Impax, Neuroderm, Prilenia, Revance, Teva but has no owner interest in any pharmaceutical company. She has received travel compensation or honoraria from the Tourette Association of America, Parkinson Foundation, International Association of Parkinsonism and Related Disorders, Medscape, and Cleveland Clinic, and royalties for writing a book with Robert rose publishers.
- MSO serves as a consultant for the Parkinson’s Foundation, and has received research grants from NIH, Parkinson’s Foundation, the Michael J. Fox Foundation, the Parkinson Alliance, Smallwood Foundation, the Bachmann-Strauss Foundation, the Tourette Syndrome Association, and the UF Foundation. MSO’s DBS research is supported by: NIH R01 NR014852 and R01NS096008. MSO is PI of the NIH R25NS108939 Training Grant. MSO has received royalties for publications with Demos, Manson, Amazon, Smashwords, Books4Patients, Perseus, Robert Rose, Oxford and Cambridge (movement disorders books). MSO is an associate editor for New England Journal of Medicine Journal Watch Neurology. MSO has participated in CME and educational activities on movement disorders sponsored by the Academy for Healthcare Learning, PeerView, Prime, QuantiaMD, WebMD/Medscape, Medicus, MedNet, Einstein, MedNet, Henry Stewart, American Academy of Neurology, Movement Disorders Society and by Vanderbilt University. The institution and not MSO receives grants from Medtronic, Abbvie, Boston Scientific, Abbott and Allergan and the PI has no financial interest in these grants. MSO has participated as a site PI and/or co-I for several NIH, foundation, and industry sponsored trials over the years but has not received honoraria. Research projects at the University of Florida receive device and drug donations.
- DW receives royalties for books on Tourette Syndrome with Guilford Press, Oxford University Press, and Springer Press.
- BMN is a member of the scientific advisory board at Deep Genomics and consultant for Camp4 Therapeutics, Takeda Pharmaceutical and Biogen.
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Affiliation(s)
- Fotis Tsetsos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jae Hoon Sul
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Alden Y Huang
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Cornelia Illmann
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Sabrina M Darrow
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Matthew E Hirschtritt
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Erica Greenberg
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Kirsten R Muller-Vahl
- Clinic of Psychiatry, Social Psychiatry, and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Manfred Stuhrmann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Yves Dion
- McGill University Health Center, University of Montreal, McGill University Health Centre, Montreal, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Harald Aschauer
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
- Biopsychosocial Corporation, Vienna, Austria
| | - Mara Stamenkovic
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
| | | | - Paul Sandor
- University Health Network, Youthdale Treatment Centres, and University of Toronto, Toronto, Canada
| | - Cathy L Barr
- Krembil Research Institute, University Health Network, Hospital for Sick Children, and University of Toronto, Toronto, Canada
| | - Marco A Grados
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Harvey S Singer
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital Bonn, University of Bonn Medical School, Bonn, Germany
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anke Hinney
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Robert A King
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Thomas V Fernandez
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Csaba Barta
- Institute of Medical Chemistry, Molecular Biology, and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Zsanett Tarnok
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Peter Nagy
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
| | - Yulia Worbe
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique Hôpitaux de Paris, Hopital Saint Antoine, Paris, France
| | - Andreas Hartmann
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Cathy L Budman
- Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Renata Rizzo
- Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Gholson J Lyon
- Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, USA
| | - William M McMahon
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | | | - Danielle C Cath
- Department of Psychiatry, University Medical Center Groningen and Rijksuniversity Groningen, and Drenthe Mental Health Center, Groningen, the Netherlands
| | - Irene A Malaty
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Michael S Okun
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Cheston Berlin
- Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Douglas W Woods
- Marquette University and University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Paul C Lee
- Tripler Army Medical Center and University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Joseph Jankovic
- Parkinson's Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Mary M Robertson
- Division of Psychiatry, Department of Neuropsychiatry, University College London, London, UK
| | - Donald L Gilbert
- Division of Pediatric Neurology, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati, Cincinnati, USA
| | | | - Barbara J Coffey
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Pieter J Hoekstra
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Samuel Kuperman
- University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Samuel H Zinner
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Michael Wagner
- Department of Psychiatry and Psychotherapy, University Hospital Bonn, Bonn, Germany
| | | | - A Jeremy Willsey
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Gary A Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nelson B Freimer
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Benjamin M Neale
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Lea K Davis
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Giovanni Coppola
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
| | - Cathy L Barr
- Krembil Research Institute, University Health Network, Hospital for Sick Children, and University of Toronto, Toronto, Canada
| | | | - Cheston Berlin
- Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Cathy L Budman
- Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Danielle C Cath
- Department of Psychiatry, University Medical Center Groningen and Rijksuniversity Groningen, and Drenthe Mental Health Center, Groningen, the Netherlands
| | - Giovanni Coppola
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sabrina Darrow
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Lea K Davis
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yves Dion
- McGill University Health Center, University of Montreal, McGill University Health Centre, Montreal, Canada
| | - Nelson B Freimer
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Marco A Grados
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Erica Greenberg
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Matthew E Hirschtritt
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Alden Y Huang
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Cornelia Illmann
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Robert A King
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Roger Kurlan
- Atlantic Neuroscience Institute, Overlook Hospital, Summit, NJ, USA
| | - James F Leckman
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - Gholson J Lyon
- Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, USA
| | - Irene A Malaty
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - William M McMahon
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Benjamin M Neale
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Michael S Okun
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Mary M Robertson
- Division of Psychiatry, Department of Neuropsychiatry, University College London, London, UK
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Paul Sandor
- University Health Network, Youthdale Treatment Centres, and University of Toronto, Toronto, Canada
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Harvey S Singer
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Jan H Smit
- Department of Psychiatry, VU UniversityMedical Center, Amsterdam, The Netherlands
| | - Jae Hoon Sul
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Harald Aschauer Harald Aschauer
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
- Biopsychosocial Corporation, Vienna, Austria
| | - Csaba Barta
- Institute of Medical Chemistry, Molecular Biology, and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | - Cathy L Budman
- Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Danielle C Cath
- Department of Psychiatry, University Medical Center Groningen and Rijksuniversity Groningen, and Drenthe Mental Health Center, Groningen, the Netherlands
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
| | - Andreas Hartmann
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Anastasios Konstantinidis
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
- Center for Mental Health Muldenstrasse, BBRZMed, Linz, Austria
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Kirsten Müller-Vahl
- Clinic of Psychiatry, Social Psychiatry, and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Peter Nagy
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital Bonn, University of Bonn Medical School, Bonn, Germany
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Renata Rizzo
- Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Paul Sandor
- University Health Network, Youthdale Treatment Centres, and University of Toronto, Toronto, Canada
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Mara Stamenkovic
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
| | - Manfred Stuhrmann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Fotis Tsetsos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Zsanett Tarnok
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Tomasz Wolanczyk
- Department of Child Psychiatry, Medical University of Warsaw, 00-001, Warsaw, Poland
| | - Yulia Worbe
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique Hôpitaux de Paris, Hopital Saint Antoine, Paris, France
| | - Lawrence Brown
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Keun-Ah Cheon
- Yonsei University College of Medicine, Yonsei Yoo & Kim Mental Health Clinic, Seoul, South Korea
| | - Barbara J Coffey
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Thomas V Fernandez
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Blanca Garcia-Delgar
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clinic Universitari, Barcelona, Spain
| | - Donald Gilbert
- Division of Pediatric Neurology, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati, Cincinnati, USA
| | - Dorothy E Grice
- Department of Psychiatry, Friedman Brain Institute, Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Julie Hagstrøm
- Child and Adolescent Mental Health Center, Mental Health Services, Capital Region of Denmark and University of Copenhagen, Copenhagen, Denmark
| | - Tammy Hedderly
- Tic and Neurodevelopmental Movements Service (TANDeM), Evelina Children's Hospital, Guys and St Thomas' NHS Foundation Trust, London, UK
- Paediatric Neurosciences, Kings College London, London, UK
| | - Gary A Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Isobel Heyman
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK
- Psychological and Mental Health Services, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Pieter J Hoekstra
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Chaim Huyser
- De Bascule, Academic Centre for Child and Adolescent Psychiatry, Amsterdam, The Netherlands
| | | | - Young-Shin Kim
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Robert A King
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Yun-Joo Koh
- The Korea Institute for Children's Social Development, Rudolph Child Research Center, Seoul, South Korea
| | - Sodahm Kook
- Kangbuk Samsung Hospital, Seoul, South Korea
| | - Samuel Kuperman
- University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Bennett L Leventhal
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, USA
| | - Marcos Madruga-Garrido
- Sección de Neuropediatría, Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Seville, Spain
| | - Pablo Mir
- Hospital Universitario Virgen del Rocío, Sevilla, Spain
- Centro de Investigación en Red-Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Astrid Morer
- Department of Child and Adolescent Psychiatry and Psychology, Institute of Neurosciences, Hospital Clínic Universitari, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en red de Salud Mental (CIBERSAM), Barcelona, Spain
| | - Alexander Münchau
- Institute of Systems Motor Science, University of Lübeck, Lübeck, Germany
| | - Kerstin J Plessen
- Child and Adolescent Mental Health Centre, Mental Health Services, Capital Region of Denmark, Copenhagen, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Service of Child and Adolescent Psychiatry, Department of Psychiatry, University Medical Center, University of Lausanne, Lausanne, Switzerland
| | - Veit Roessner
- Department of Child and Adolescent Psychiatry, Faculty of Medicine, University Hospital Carl Gustav CarusTU Dresden, Dresden, Germany
| | - Eun-Young Shin
- Yonsei University College of Medicine, Yonsei Yoo & Kim Mental Health Clinic, Seoul, South Korea
| | - Dong-Ho Song
- Yonsei University College of Medicine, Yonsei Yoo & Kim Mental Health Clinic, Seoul, South Korea
| | - Jungeun Song
- National Health Insurance Service Ilsan Hospital, Goyang-Si, South Korea
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - A Jeremy Willsey
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Samuel Zinner
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Harald Aschauer
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
- Biopsychosocial Corporation, Vienna, Austria
| | - Cathy L Barr
- Krembil Research Institute, University Health Network, Hospital for Sick Children, and University of Toronto, Toronto, Canada
| | - Csaba Barta
- Institute of Medical Chemistry, Molecular Biology, and Pathobiochemistry, Semmelweis University, Budapest, Hungary
| | | | - Cheston Berlin
- Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Lawrence Brown
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Cathy L Budman
- Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Danielle C Cath
- Department of Psychiatry, University Medical Center Groningen and Rijksuniversity Groningen, and Drenthe Mental Health Center, Groningen, the Netherlands
| | - Barbara J Coffey
- Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Giovanni Coppola
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sabrina Darrow
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Lea K Davis
- Division of Genetic Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
| | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yves Dion
- McGill University Health Center, University of Montreal, McGill University Health Centre, Montreal, Canada
| | - Thomas Fernandez
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Nelson B Freimer
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Donald Gilbert
- Division of Pediatric Neurology, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati, Cincinnati, USA
| | - Marco A Grados
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Erica Greenberg
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Andreas Hartmann
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Johannes Hebebrand
- Department of Child and Adolescent Psychiatry, Psychosomatics, and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Gary Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Matthew E Hirschtritt
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Pieter Hoekstra
- Department of Child and Adolescent Psychiatry, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Alden Y Huang
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
| | - Cornelia Illmann
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph Jankovic
- Parkinson's Disease Center and Movement Disorders Clinic, Department of Neurology, Baylor College of Medicine, Houston, TX, USA
| | - Robert A King
- Yale Child Study Center and the Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Samuel Kuperman
- University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Paul C Lee
- Tripler Army Medical Center and University of Hawaii John A. Burns School of Medicine, Honolulu, HI, USA
| | - Gholson J Lyon
- Jervis Clinic, NYS Institute for Basic Research in Developmental Disabilities (IBR), Staten Island, NY, USA
| | - Irene A Malaty
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - William M McMahon
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Kirsten Müller-Vahl
- Clinic of Psychiatry, Social Psychiatry, and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Peter Nagy
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Benjamin M Neale
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Markus M Nöthen
- Institute of Human Genetics, University Hospital Bonn, University of Bonn Medical School, Bonn, Germany
| | - Michael S Okun
- Department of Neurology, Norman Fixel Institute for Neurological Diseases, University of Florida Health, Gainesville, FL, USA
| | - Lisa Osiecki
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Renata Rizzo
- Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Mary M Robertson
- Division of Psychiatry, Department of Neuropsychiatry, University College London, London, UK
| | - Guy A Rouleau
- Montreal Neurological Institute, Department of Neurology and Neurosurgery, McGill University, Montreal, Canada
| | - Paul Sandor
- University Health Network, Youthdale Treatment Centres, and University of Toronto, Toronto, Canada
| | - Jeremiah M Scharf
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Brigham and Women's Hospital, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Harvey S Singer
- Johns Hopkins University School of Medicine and the Kennedy Krieger Institute, Baltimore, MD, USA
| | - Mara Stamenkovic
- Department of Psychiatry and Psychotherapy, Medical University Vienna, Vienna, Austria
| | - Manfred Stuhrmann
- Institute of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Jae Hoon Sul
- Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA, USA
| | - Zsanett Tarnok
- Vadaskert Child and Adolescent Psychiatric Hospital, Budapest, Hungary
| | - Jay Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Fotis Tsetsos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - A Jeremy Willsey
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Douglas Woods
- Marquette University and University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Yulia Worbe
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, CNRS UMR 7225, ICM, Paris, France
- French Reference Centre for Gilles de la Tourette Syndrome, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique-Hôpitaux de Paris, Department of Neurology, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
- Assistance Publique Hôpitaux de Paris, Hopital Saint Antoine, Paris, France
| | - Dongmei Yu
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel Zinner
- Department of Pediatrics, University of Washington, Seattle, WA, USA
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11
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Willsey HR, Xu Y, Everitt A, Dea J, Exner CRT, Willsey AJ, State MW, Harland RM. Correction: The neurodevelopmental disorder risk gene DYRK1A is required for ciliogenesis and control of brain size in Xenopus embryos. Development 2020; 147:dev198317. [PMID: 33288503 PMCID: PMC10846505 DOI: 10.1242/dev.198317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Amanda Everitt
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard M Harland
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
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12
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Willsey HR, Xu Y, Everitt A, Dea J, Exner CRT, Willsey AJ, State MW, Harland RM. The neurodevelopmental disorder risk gene DYRK1A is required for ciliogenesis and control of brain size in Xenopus embryos. Development 2020; 147:dev189290. [PMID: 32467234 PMCID: PMC10755402 DOI: 10.1242/dev.189290] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/11/2020] [Indexed: 12/30/2023]
Abstract
DYRK1A [dual specificity tyrosine-(Y)-phosphorylation-regulated kinase 1 A] is a high-confidence autism risk gene that encodes a conserved kinase. In addition to autism, individuals with putative loss-of-function variants in DYRK1A exhibit microcephaly, intellectual disability, developmental delay and/or congenital anomalies of the kidney and urinary tract. DYRK1A is also located within the critical region for Down syndrome; therefore, understanding the role of DYRK1A in brain development is crucial for understanding the pathobiology of multiple developmental disorders. To characterize the function of this gene, we used the diploid frog Xenopus tropicalis We discover that Dyrk1a is expressed in ciliated tissues, localizes to ciliary axonemes and basal bodies, and is required for ciliogenesis. We also demonstrate that Dyrk1a localizes to mitotic spindles and that its inhibition leads to decreased forebrain size, abnormal cell cycle progression and cell death during brain development. These findings provide hypotheses about potential mechanisms of pathobiology and underscore the utility of X. tropicalis as a model system for understanding neurodevelopmental disorders.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Yuxiao Xu
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Amanda Everitt
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Jeanselle Dea
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
| | - Cameron R T Exner
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, Langley Porter Psychiatric Institute, Quantitative Biosciences Institute, and Weill Institute for Neurosciences University of California San Francisco, San Francisco, CA 94143, USA
| | - Richard M Harland
- Department of Psychiatry and Behavioral Sciences, Institute for Neurodegenerative Diseases, Quantitative Biosciences Institute, and Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94143, USA
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13
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Pașca AM, Park JY, Shin HW, Qi Q, Revah O, Krasnoff R, O'Hara R, Willsey AJ, Palmer TD, Pașca SP. Human 3D cellular model of hypoxic brain injury of prematurity. Nat Med 2019; 25:784-791. [PMID: 31061540 PMCID: PMC7020938 DOI: 10.1038/s41591-019-0436-0] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 03/25/2019] [Indexed: 12/20/2022]
Abstract
Owing to recent medical and technological advances in neonatal care, infants born extremely premature have increased survival rates1,2. After birth, these infants are at high risk of hypoxic episodes because of lung immaturity, hypotension and lack of cerebral-flow regulation, and can develop a severe condition called encephalopathy of prematurity3. Over 80% of infants born before post-conception week 25 have moderate-to-severe long-term neurodevelopmental impairments4. The susceptible cell types in the cerebral cortex and the molecular mechanisms underlying associated gray-matter defects in premature infants remain unknown. Here we used human three-dimensional brain-region-specific organoids to study the effect of oxygen deprivation on corticogenesis. We identified specific defects in intermediate progenitors, a cortical cell type associated with the expansion of the human cerebral cortex, and showed that these are related to the unfolded protein response and changes. Moreover, we verified these findings in human primary cortical tissue and demonstrated that a small-molecule modulator of the unfolded protein response pathway can prevent the reduction in intermediate progenitors following hypoxia. We anticipate that this human cellular platform will be valuable for studying the environmental and genetic factors underlying injury in the developing human brain.
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Affiliation(s)
- Anca M Pașca
- Department of Pediatrics, Division of Neonatology, Stanford University, Stanford, CA, USA
| | - Jin-Young Park
- Department of Psychiatry and Behavioral Sciences & Stanford Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA
| | - Hyun-Woo Shin
- Department of Psychiatry and Behavioral Sciences & Stanford Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA
- Department of Pharmacology and Biomedical Sciences, Seoul National University, Seoul, Republic of Korea
| | - Qihao Qi
- Institute for Neurodegenerative Diseases and Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Omer Revah
- Department of Psychiatry and Behavioral Sciences & Stanford Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA
| | - Rebecca Krasnoff
- Institute for Neurodegenerative Diseases and Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Ruth O'Hara
- Department of Psychiatry and Behavioral Sciences & Stanford Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA
| | - A Jeremy Willsey
- Institute for Neurodegenerative Diseases and Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Theo D Palmer
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Sergiu P Pașca
- Department of Psychiatry and Behavioral Sciences & Stanford Human Brain Organogenesis Program, Stanford University, Stanford, CA, USA.
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14
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Wang S, Mandell JD, Kumar Y, Sun N, Morris MT, Arbelaez J, Nasello C, Dong S, Duhn C, Zhao X, Yang Z, Padmanabhuni SS, Yu D, King RA, Dietrich A, Khalifa N, Dahl N, Huang AY, Neale BM, Coppola G, Mathews CA, Scharf JM, Fernandez TV, Buxbaum JD, De Rubeis S, Grice DE, Xing J, Heiman GA, Tischfield JA, Paschou P, Willsey AJ, State MW. De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis. Cell Rep 2018; 25:3544. [PMID: 30566877 DOI: 10.1016/j.celrep.2018.12.024] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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15
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An JY, Lin K, Zhu L, Werling DM, Dong S, Brand H, Wang HZ, Zhao X, Schwartz GB, Collins RL, Currall BB, Dastmalchi C, Dea J, Duhn C, Gilson MC, Klei L, Liang L, Markenscoff-Papadimitriou E, Pochareddy S, Ahituv N, Buxbaum JD, Coon H, Daly MJ, Kim YS, Marth GT, Neale BM, Quinlan AR, Rubenstein JL, Sestan N, State MW, Willsey AJ, Talkowski ME, Devlin B, Roeder K, Sanders SJ. Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. Science 2018; 362:eaat6576. [PMID: 30545852 PMCID: PMC6432922 DOI: 10.1126/science.aat6576] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 11/15/2018] [Indexed: 12/17/2022]
Abstract
Whole-genome sequencing (WGS) has facilitated the first genome-wide evaluations of the contribution of de novo noncoding mutations to complex disorders. Using WGS, we identified 255,106 de novo mutations among sample genomes from members of 1902 quartet families in which one child, but not a sibling or their parents, was affected by autism spectrum disorder (ASD). In contrast to coding mutations, no noncoding functional annotation category, analyzed in isolation, was significantly associated with ASD. Casting noncoding variation in the context of a de novo risk score across multiple annotation categories, however, did demonstrate association with mutations localized to promoter regions. We found that the strongest driver of this promoter signal emanates from evolutionarily conserved transcription factor binding sites distal to the transcription start site. These data suggest that de novo mutations in promoter regions, characterized by evolutionary and functional signatures, contribute to ASD.
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Affiliation(s)
- Joon-Yong An
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Kevin Lin
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Lingxue Zhu
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Donna M Werling
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Harrison Brand
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Harold Z Wang
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Xuefang Zhao
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Grace B Schwartz
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Ryan L Collins
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
| | - Claudia Dastmalchi
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Jeanselle Dea
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Clif Duhn
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Michael C Gilson
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Lindsay Liang
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | | | - Sirisha Pochareddy
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hilary Coon
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Mark J Daly
- Program in Medical and Population Genetics and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Young Shin Kim
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Gabor T Marth
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
- USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Analytical and Translational Genetics Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Aaron R Quinlan
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT, USA
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
- USTAR Center for Genetic Discovery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - John L Rubenstein
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, CA, USA
| | - Michael E Talkowski
- Center for Genomic Medicine and Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Department of Neurology, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics and the Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Departments of Pathology and Psychiatry, Massachusetts General Hospital, Boston, MA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, CA, USA
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16
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Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E, Iglesias GN, Shokat L, Tripathi S, Balasubramaniam V, Webb LG, Aguirre S, Willsey AJ, Garcia-Sastre A, Pollard KS, Cherry S, Gamarnik AV, Marazzi I, Taunton J, Fernandez-Sesma A, Bellen HJ, Andino R, Krogan NJ. Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell 2018; 175:1931-1945.e18. [PMID: 30550790 PMCID: PMC6474419 DOI: 10.1016/j.cell.2018.11.028] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 11/10/2018] [Accepted: 11/19/2018] [Indexed: 01/03/2023]
Abstract
Mosquito-borne flaviviruses, including dengue virus (DENV) and Zika virus (ZIKV), are a growing public health concern. Systems-level analysis of how flaviviruses hijack cellular processes through virus-host protein-protein interactions (PPIs) provides information about their replication and pathogenic mechanisms. We used affinity purification-mass spectrometry (AP-MS) to compare flavivirus-host interactions for two viruses (DENV and ZIKV) in two hosts (human and mosquito). Conserved virus-host PPIs revealed that the flavivirus NS5 protein suppresses interferon stimulated genes by inhibiting recruitment of the transcription complex PAF1C and that chemical modulation of SEC61 inhibits DENV and ZIKV replication in human and mosquito cells. Finally, we identified a ZIKV-specific interaction between NS4A and ANKLE2, a gene linked to hereditary microcephaly, and showed that ZIKV NS4A causes microcephaly in Drosophila in an ANKLE2-dependent manner. Thus, comparative flavivirus-host PPI mapping provides biological insights and, when coupled with in vivo models, can be used to unravel pathogenic mechanisms.
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Affiliation(s)
- Priya S Shah
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Nichole Link
- Department of Molecular and Human Genetics, and Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
| | - Gwendolyn M Jang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Phillip P Sharp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
| | - Tongtong Zhu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle L Swaney
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - John Von Dollen
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Holly R Ramage
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Satkamp
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Billy Newton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Marine J Petit
- Department of Chemical Engineering, Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA, USA
| | - Tierney Baum
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Amanda Everitt
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Orly Laufman
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Michel Tassetto
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Michael Shales
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Erica Stevenson
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | | | - Leila Shokat
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA
| | - Shashank Tripathi
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vinod Balasubramaniam
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor, Malaysia
| | - Laurence G Webb
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sebastian Aguirre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - A Jeremy Willsey
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katherine S Pollard
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California San Francisco, San Francisco, CA, USA; Chan-Zuckerberg Biohub, San Francisco, CA, USA
| | - Sara Cherry
- Department of Microbiology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Ivan Marazzi
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, and Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA; Jan and Dan Duncan Neurological Research Institute, Houston, TX, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA.
| | - Raul Andino
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
| | - Nevan J Krogan
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, CA, USA; The J. David Gladstone Institutes, San Francisco, CA, USA.
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17
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Fazel Darbandi S, Robinson Schwartz SE, Qi Q, Catta-Preta R, Pai ELL, Mandell JD, Everitt A, Rubin A, Krasnoff RA, Katzman S, Tastad D, Nord AS, Willsey AJ, Chen B, State MW, Sohal VS, Rubenstein JLR. Neonatal Tbr1 Dosage Controls Cortical Layer 6 Connectivity. Neuron 2018; 100:831-845.e7. [PMID: 30318412 DOI: 10.1016/j.neuron.2018.09.027] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 12/27/2022]
Abstract
An understanding of how heterozygous loss-of-function mutations in autism spectrum disorder (ASD) risk genes, such as TBR1, contribute to ASD remains elusive. Conditional Tbr1 deletion during late mouse gestation in cortical layer 6 neurons (Tbr1layer6 mutants) provides novel insights into its function, including dendritic patterning, synaptogenesis, and cell-intrinsic physiology. These phenotypes occur in heterozygotes, providing insights into mechanisms that may underlie ASD pathophysiology. Restoring expression of Wnt7b largely rescues the synaptic deficit in Tbr1layer6 mutant neurons. Furthermore, Tbr1layer6 heterozygotes have increased anxiety-like behavior, a phenotype seen ASD. Integrating TBR1 chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) data from layer 6 neurons and activity of TBR1-bound candidate enhancers provides evidence for how TBR1 regulates layer 6 properties. Moreover, several putative TBR1 targets are ASD risk genes, placing TBR1 in a central position both for ASD risk and for regulating transcriptional circuits that control multiple steps in layer 6 development essential for the assembly of neural circuits.
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Affiliation(s)
- Siavash Fazel Darbandi
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sarah E Robinson Schwartz
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Qihao Qi
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rinaldo Catta-Preta
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
| | - Emily Ling-Lin Pai
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeffrey D Mandell
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Amanda Everitt
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Anna Rubin
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rebecca A Krasnoff
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sol Katzman
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Tastad
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Alex S Nord
- Department of Neurobiology, Physiology, and Behavior and Department of Psychiatry and Behavioral Sciences, Center for Neuroscience, University of California, Davis, Davis, CA 95618, USA
| | - A Jeremy Willsey
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Matthew W State
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Vikaas S Sohal
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience and Sloan-Swartz Center for Theoretical Neurobiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA.
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18
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Wang S, Mandell JD, Kumar Y, Sun N, Morris MT, Arbelaez J, Nasello C, Dong S, Duhn C, Zhao X, Yang Z, Padmanabhuni SS, Yu D, King RA, Dietrich A, Khalifa N, Dahl N, Huang AY, Neale BM, Coppola G, Mathews CA, Scharf JM, Fernandez TV, Buxbaum JD, De Rubeis S, Grice DE, Xing J, Heiman GA, Tischfield JA, Paschou P, Willsey AJ, State MW. De Novo Sequence and Copy Number Variants Are Strongly Associated with Tourette Disorder and Implicate Cell Polarity in Pathogenesis. Cell Rep 2018; 24:3441-3454.e12. [PMID: 30257206 PMCID: PMC6475626 DOI: 10.1016/j.celrep.2018.08.082] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/13/2018] [Accepted: 08/27/2018] [Indexed: 12/30/2022] Open
Abstract
We previously established the contribution of de novo damaging sequence variants to Tourette disorder (TD) through whole-exome sequencing of 511 trios. Here, we sequence an additional 291 TD trios and analyze the combined set of 802 trios. We observe an overrepresentation of de novo damaging variants in simplex, but not multiplex, families; we identify a high-confidence TD risk gene, CELSR3 (cadherin EGF LAG seven-pass G-type receptor 3); we find that the genes mutated in TD patients are enriched for those related to cell polarity, suggesting a common pathway underlying pathobiology; and we confirm a statistically significant excess of de novo copy number variants in TD. Finally, we identify significant overlap of de novo sequence variants between TD and obsessive-compulsive disorder and de novo copy number variants between TD and autism spectrum disorder, consistent with shared genetic risk.
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Affiliation(s)
- Sheng Wang
- College of Biological Sciences, China Agricultural University, Beijing, China; National Institute of Biological Sciences, Beijing, China; Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Jeffrey D Mandell
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Yogesh Kumar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Nawei Sun
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Montana T Morris
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Juan Arbelaez
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Cara Nasello
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Clif Duhn
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Xin Zhao
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Department of Traditional Chinese Medicine, Xinhua Hospital Affiliated to Shanghai Jiatong University School of Medicine, Shanghai, China
| | - Zhiyu Yang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Dongmei Yu
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert A King
- Yale Child Study Center and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Andrea Dietrich
- Department of Child and Adolescent Psychiatry, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Najah Khalifa
- Department of Neuroscience, Child and Adolescent Psychiatry Uppsala University, Uppsala, Sweden; Centre for Research and Development, Region Gävleborg, Gävle, Sweden
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Alden Y Huang
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Benjamin M Neale
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Giovanni Coppola
- Department of Neurology, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, CA, USA
| | - Carol A Mathews
- Department of Psychiatry, Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Jeremiah M Scharf
- Center for Genomic Medicine, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Thomas V Fernandez
- Yale Child Study Center and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Silvia De Rubeis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dorothy E Grice
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Gary A Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
| | - A Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA.
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19
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Willsey AJ, Morris MT, Wang S, Willsey HR, Sun N, Teerikorpi N, Baum TB, Cagney G, Bender KJ, Desai TA, Srivastava D, Davis GW, Doudna J, Chang E, Sohal V, Lowenstein DH, Li H, Agard D, Keiser MJ, Shoichet B, von Zastrow M, Mucke L, Finkbeiner S, Gan L, Sestan N, Ward ME, Huttenhain R, Nowakowski TJ, Bellen HJ, Frank LM, Khokha MK, Lifton RP, Kampmann M, Ideker T, State MW, Krogan NJ. The Psychiatric Cell Map Initiative: A Convergent Systems Biological Approach to Illuminating Key Molecular Pathways in Neuropsychiatric Disorders. Cell 2018; 174:505-520. [PMID: 30053424 PMCID: PMC6247911 DOI: 10.1016/j.cell.2018.06.016] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/07/2018] [Accepted: 06/08/2018] [Indexed: 12/11/2022]
Abstract
Although gene discovery in neuropsychiatric disorders, including autism spectrum disorder, intellectual disability, epilepsy, schizophrenia, and Tourette disorder, has accelerated, resulting in a large number of molecular clues, it has proven difficult to generate specific hypotheses without the corresponding datasets at the protein complex and functional pathway level. Here, we describe one path forward-an initiative aimed at mapping the physical and genetic interaction networks of these conditions and then using these maps to connect the genomic data to neurobiology and, ultimately, the clinic. These efforts will include a team of geneticists, structural biologists, neurobiologists, systems biologists, and clinicians, leveraging a wide array of experimental approaches and creating a collaborative infrastructure necessary for long-term investigation. This initiative will ultimately intersect with parallel studies that focus on other diseases, as there is a significant overlap with genes implicated in cancer, infectious disease, and congenital heart defects.
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Affiliation(s)
- A Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Montana T Morris
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sheng Wang
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Helen R Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nawei Sun
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nia Teerikorpi
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tierney B Baum
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Kevin J Bender
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tejal A Desai
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Deepak Srivastava
- Gladstone Institutes, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Graeme W Davis
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward Chang
- Department of Neurological Surgery, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vikaas Sohal
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Daniel H Lowenstein
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hao Li
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David Agard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael J Keiser
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brian Shoichet
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mark von Zastrow
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lennart Mucke
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Steven Finkbeiner
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Li Gan
- Department of Neurology, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA
| | - Michael E Ward
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD 20892, USA
| | - Ruth Huttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tomasz J Nowakowski
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA; The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hugo J Bellen
- Departments of Molecular and Human Genetics and Neuroscience, Neurological Research Institute at TCH, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Loren M Frank
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Physiology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mustafa K Khokha
- Pediatric Genomics Discovery Program, Departments of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, NY 10065, USA
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94143, USA; Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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20
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Sanders SJ, Neale BM, Huang H, Werling DM, An JY, Dong S, Abecasis G, Arguello PA, Blangero J, Boehnke M, Daly MJ, Eggan K, Geschwind DH, Glahn DC, Goldstein DB, Gur RE, Handsaker RE, McCarroll SA, Ophoff RA, Palotie A, Pato CN, Sabatti C, State MW, Willsey AJ, Hyman SE, Addington AM, Lehner T, Freimer NB. Publisher Correction: Whole genome sequencing in psychiatric disorders: the WGSPD consortium. Nat Neurosci 2018; 21:1017. [PMID: 29549319 DOI: 10.1038/s41593-018-0102-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article initially published, the consortium authorship and corresponding authors were not presented correctly. In the PDF and print versions, the Whole Genome Sequencing for Psychiatric Disorders (WGSPD) consortium was missing from the author list at the beginning of the paper, where it should have appeared as the seventh author; it was present in the author list at the end of the paper, but the footnote directing readers to the Supplementary Note for a list of members was missing. In the HTML version, the consortium was listed as the last author instead of as the seventh, and the line directing readers to the Supplementary Note for a list of members appeared at the end of the paper under Author Information but not in association with the consortium name itself. Also, this line stated that both member names and affiliations could be found in the Supplementary Note; in fact, only names are given. In all versions of the paper, the corresponding author symbols were attached to A. Jeremy Willsey, Steven E. Hyman, Anjene M. Addington and Thomas Lehner; they should have been attached, respectively, to Steven E. Hyman, Anjene M. Addington, Thomas Lehner and Nelson B. Freimer. As a result of this shift, the respective contact links in the HTML version did not lead to the indicated individuals. The errors have been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Donna M Werling
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joon-Yong An
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, 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
| | - Goncalo Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, School of Medicine, Brownsville, TX, USA
| | - Michael Boehnke
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - David C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, New York, NY, USA
| | - Raquel E Gur
- Department of Psychiatry, Neuropsychiatry Section, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Roel A Ophoff
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California Los Angeles, Los Angeles, CA, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Carlos N Pato
- Department of Psychiatry, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chiara Sabatti
- Department of Health Research and Policy, Division of Biostatistics, Stanford University, Stanford, CA, USA
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Steven E Hyman
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | | | - Thomas Lehner
- National Institute of Mental Health, Bethesda, MD, USA.
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
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21
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Sanders SJ, Neale BM, Huang H, Werling DM, An JY, Dong S, Abecasis G, Arguello PA, Blangero J, Boehnke M, Daly MJ, Eggan K, Geschwind DH, Glahn DC, Goldstein DB, Gur RE, Handsaker RE, McCarroll SA, Ophoff RA, Palotie A, Pato CN, Sabatti C, State MW, Willsey AJ, Hyman SE, Addington AM, Lehner T, Freimer NB. Whole genome sequencing in psychiatric disorders: the WGSPD consortium. Nat Neurosci 2017; 20:1661-1668. [PMID: 29184211 PMCID: PMC7785336 DOI: 10.1038/s41593-017-0017-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As technology advances, whole genome sequencing (WGS) is likely to supersede other genotyping technologies. The rate of this change depends on its relative cost and utility. Variants identified uniquely through WGS may reveal novel biological pathways underlying complex disorders and provide high-resolution insight into when, where, and in which cell type these pathways are affected. Alternatively, cheaper and less computationally intensive approaches may yield equivalent insights. Understanding the role of rare variants in the noncoding gene-regulating genome, through pilot WGS projects, will be critical to determine which of these two extremes best represents reality. With large cohorts, well-defined risk loci, and a compelling need to understand the underlying biology, psychiatric disorders have a role to play in this preliminary WGS assessment. The WGSPD consortium will integrate data for 18,000 individuals with psychiatric disorders, beginning with autism spectrum disorder, schizophrenia, bipolar disorder, and major depressive disorder, along with over 150,000 controls.
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Affiliation(s)
- Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin M Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Donna M Werling
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Joon-Yong An
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, 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
| | - Goncalo Abecasis
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - John Blangero
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, School of Medicine, Brownsville, TX, USA
| | - Michael Boehnke
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - David C Glahn
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, Hammer Health Sciences, New York, NY, USA
| | - Raquel E Gur
- Department of Psychiatry, Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Roel A Ophoff
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Carlos N Pato
- Department of Psychiatry, Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chiara Sabatti
- Department of Health Research and Policy, Division of Biostatistics, Stanford University, Stanford, CA, USA
| | - Matthew W State
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Steven E Hyman
- Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
| | - Anjene M Addington
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
| | - Thomas Lehner
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
| | - Nelson B Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
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22
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Bishop SL, Farmer C, Bal V, Robinson E, Willsey AJ, Werling DM, Havdahl KA, Sanders SJ, Thurm A. Identification of Developmental and Behavioral Markers Associated With Genetic Abnormalities in Autism Spectrum Disorder. Am J Psychiatry 2017; 174:576-585. [PMID: 28253736 PMCID: PMC5578709 DOI: 10.1176/appi.ajp.2017.16101115] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Aside from features associated with risk of neurogenetic syndromes in general (e.g., cognitive impairment), limited progress has been made in identifying phenotype-genotype relationships in autism spectrum disorder (ASD). The objective of this study was to extend work in the Simons Simplex Collection by comparing the phenotypic profiles of ASD probands with or without identified de novo loss of function mutations or copy number variants in high-confidence ASD-associated genes or loci. METHOD Analyses preemptively accounted for documented differences in sex and IQ in affected individuals with de novo mutations by matching probands with and without these genetic events on sex, IQ, and age before comparing them on multiple behavioral domains. RESULTS Children with de novo mutations (N=112) had a greater likelihood of motor delay during early development (later age at walking), but they were less impaired on certain measures of ASD core symptoms (parent-rated social communication abnormalities and clinician-rated diagnostic certainty about ASD) in later childhood. These children also showed relative strengths in verbal and language abilities, including a smaller discrepancy between nonverbal and verbal IQ and a greater likelihood of having achieved fluent language (i.e., regular use of complex sentences). CONCLUSIONS Children with ASD with de novo mutations may exhibit a "muted" symptom profile with respect to social communication and language deficits relative to those with ASD with no identified genetic abnormalities. Such findings suggest that examining early milestone differences and standardized testing results may be helpful in etiologic efforts, and potentially in clinical differentiation of various subtypes of ASD, but only if developmental and demographic variables are properly accounted for first.
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Affiliation(s)
- Somer L. Bishop
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA
| | - Cristan Farmer
- Pediatrics & Developmental Neuroscience Branch, National Institute of Mental Health, Bethesda, MD
| | - Vanessa Bal
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA
| | - Elise Robinson
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA,Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA
| | - A. Jeremy Willsey
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA
| | - Donna M. Werling
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA
| | | | - Stephan J. Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA
| | - Audrey Thurm
- Pediatrics & Developmental Neuroscience Branch, National Institute of Mental Health, Bethesda, MD
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23
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Georgitsi M, Willsey AJ, Mathews CA, State M, Scharf JM, Paschou P. The Genetic Etiology of Tourette Syndrome: Large-Scale Collaborative Efforts on the Precipice of Discovery. Front Neurosci 2016; 10:351. [PMID: 27536211 PMCID: PMC4971013 DOI: 10.3389/fnins.2016.00351] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/12/2016] [Indexed: 12/17/2022] Open
Abstract
Gilles de la Tourette Syndrome (TS) is a childhood-onset neurodevelopmental disorder that is characterized by multiple motor and phonic tics. It has a complex etiology with multiple genes likely interacting with environmental factors to lead to the onset of symptoms. The genetic basis of the disorder remains elusive. However, multiple resources and large-scale projects are coming together, launching a new era in the field and bringing us on the verge of discovery. The large-scale efforts outlined in this report are complementary and represent a range of different approaches to the study of disorders with complex inheritance. The Tourette Syndrome Association International Consortium for Genetics (TSAICG) has focused on large families, parent-proband trios and cases for large case-control designs such as genomewide association studies (GWAS), copy number variation (CNV) scans, and exome/genome sequencing. TIC Genetics targets rare, large effect size mutations in simplex trios, and multigenerational families. The European Multicentre Tics in Children Study (EMTICS) seeks to elucidate gene-environment interactions including the involvement of infection and immune mechanisms in TS etiology. Finally, TS-EUROTRAIN, a Marie Curie Initial Training Network, aims to act as a platform to unify large-scale projects in the field and to educate the next generation of experts. Importantly, these complementary large-scale efforts are joining forces to uncover the full range of genetic variation and environmental risk factors for TS, holding great promise for identifying definitive TS susceptibility genes and shedding light into the complex pathophysiology of this disorder.
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Affiliation(s)
- Marianthi Georgitsi
- Department of Molecular Biology and Genetics, Democritus University of ThraceAlexandroupoli, Greece; Department of Medicine, Aristotle University of ThessalonikiThessaloniki, Greece
| | - A Jeremy Willsey
- Department of Psychiatry, University of California, San Francisco San Francisco, CA, USA
| | - Carol A Mathews
- Department of Psychiatry, University of Florida School of Medicine Gainesville, FL, USA
| | - Matthew State
- Department of Psychiatry, University of California, San Francisco San Francisco, CA, USA
| | - Jeremiah M Scharf
- Departments of Neurology and Psychiatry, Massachusetts General Hospital, Harvard Medical School Boston, MA, USA
| | - Peristera Paschou
- Department of Molecular Biology and Genetics, Democritus University of Thrace Alexandroupoli, Greece
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24
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Willsey HR, Zheng X, Carlos Pastor-Pareja J, Willsey AJ, Beachy PA, Xu T. Localized JNK signaling regulates organ size during development. eLife 2016; 5. [PMID: 26974344 PMCID: PMC4848088 DOI: 10.7554/elife.11491] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 03/12/2016] [Indexed: 11/17/2022] Open
Abstract
A fundamental question of biology is what determines organ size. Despite demonstrations that factors within organs determine their sizes, intrinsic size control mechanisms remain elusive. Here we show that Drosophila wing size is regulated by JNK signaling during development. JNK is active in a stripe along the center of developing wings, and modulating JNK signaling within this stripe changes organ size. This JNK stripe influences proliferation in a non-canonical, Jun-independent manner by inhibiting the Hippo pathway. Localized JNK activity is established by Hedgehog signaling, where Ci elevates dTRAF1 expression. As the dTRAF1 homolog, TRAF4, is amplified in numerous cancers, these findings provide a new mechanism for how the Hedgehog pathway could contribute to tumorigenesis, and, more importantly, provides a new strategy for cancer therapies. Finally, modulation of JNK signaling centers in developing antennae and legs changes their sizes, suggesting a more generalizable role for JNK signaling in developmental organ size control. DOI:http://dx.doi.org/10.7554/eLife.11491.001 A key challenge in biology is to understand what determines size. As an animal grows, signals are produced that control the size of its organs. Many of the signaling pathways that regulate size during normal animal development also contribute to the formation of tumors. Therefore, it is important to find out exactly how the signaling molecules that regulate size are linked to those that regulate tumor growth. A protein called JNK activates a signaling pathway that triggers tumor growth. JNK signaling also stimulates cells to multiply in tissues that need repair, but it is not known whether it also regulates the size of organs during animal development. Here, Willsey et al. investigate whether JNK is active in the developing wings of fruit flies, which are commonly used as models of animal development. The experiments show that JNK is active in a stripe across the developing wing and is required for the wing to grow to its proper size. A master signal protein called Hedgehog is responsible for establishing this stripe of JNK activity. Unexpectedly, rather than acting through its usual signaling pathway, JNK activates the Hippo pathway in the wing to control organ size during development. Willsey et al.’s findings highlight potential new targets for cancer therapies. A future challenge will be to find out whether small patches of JNK signaling are found in the developing organs of other animals, and whether they can help explain how size changes between species. DOI:http://dx.doi.org/10.7554/eLife.11491.002
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Affiliation(s)
- Helen Rankin Willsey
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
| | - Xiaoyan Zheng
- Departments of Biochemistry and Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States
| | - José Carlos Pastor-Pareja
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States
| | - A Jeremy Willsey
- Department of Psychiatry, University of California, San Francisco, San Francisco, United States
| | - Philip A Beachy
- Departments of Biochemistry and Developmental Biology, Institute for Stem Cell Biology and Regenerative Medicine, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States
| | - Tian Xu
- Department of Genetics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States.,State Key Laboratory of Genetic Engineering and National Center for International Research, Fudan-Yale Biomedical Research Center, Institute of Developmental Biology and Molecular Medicine, School of Life Sciences, Fudan University, Shanghai, China
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25
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Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, Weissman S, Sullivan PF, State MW, Weng Z, Peters MA, White KP, Gerstein MB, Amiri A, Armoskus C, Ashley-Koch AE, Bae T, Beckel-Mitchener A, Berman BP, Coetzee GA, Coppola G, Francoeur N, Fromer M, Gao R, Grennan K, Herstein J, Kavanagh DH, Ivanov NA, Jiang Y, Kitchen RR, Kozlenkov A, Kundakovic M, Li M, Li Z, Liu S, Mangravite LM, Mattei E, Markenscoff-Papadimitriou E, Navarro FCP, North N, Omberg L, Panchision D, Parikshak N, Poschmann J, Price AJ, Purcaro M, Reddy TE, Roussos P, Schreiner S, Scuderi S, Sebra R, Shibata M, Shieh AW, Skarica M, Sun W, Swarup V, Thomas A, Tsuji J, van Bakel H, Wang D, Wang Y, Wang K, Werling DM, Willsey AJ, Witt H, Won H, Wong CCY, Wray GA, Wu EY, Xu X, Yao L, Senthil G, Lehner T, Sklar P, Sestan N. The PsychENCODE project. Nat Neurosci 2016; 18:1707-12. [PMID: 26605881 DOI: 10.1038/nn.4156] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | - Chunyu Liu
- University of Illinois at Chicago, Chicago, Illinois, USA
| | - James A Knowles
- University of Southern California, Los Angeles, California, USA
| | | | - Peggy J Farnham
- University of Southern California, Los Angeles, California, USA
| | | | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Dalila Pinto
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stella Dracheva
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Jonathan Mill
- King's College London, London, and University of Exeter, Devon, UK
| | | | | | | | | | | | | | | | - Zhiping Weng
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | | | | | | | - Chris Armoskus
- University of Southern California, Los Angeles, California, USA
| | | | | | | | | | | | | | - Nancy Francoeur
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Menachem Fromer
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Robert Gao
- University of Southern California, Los Angeles, California, USA
| | - Kay Grennan
- University of Illinois at Chicago, Chicago, Illinois, USA
| | | | - David H Kavanagh
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nikolay A Ivanov
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Yan Jiang
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Alexey Kozlenkov
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Mingfeng Li
- Yale University, New Haven, Connecticut, USA
| | - Zhen Li
- Yale University, New Haven, Connecticut, USA
| | - Shuang Liu
- Yale University, New Haven, Connecticut, USA
| | | | - Eugenio Mattei
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | | | - Nicole North
- National Institute of Mental Health, Bethesda, Maryland, USA
| | | | | | | | | | - Amanda J Price
- Lieber Institute for Brain Development, Baltimore, Maryland, USA
| | - Michael Purcaro
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | | | - Panos Roussos
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Robert Sebra
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Annie W Shieh
- University of Illinois at Chicago, Chicago, Illinois, USA
| | | | - Wenjie Sun
- Genome Institute of Singapore, Singapore
| | - Vivek Swarup
- University of California, Los Angeles, California, USA
| | - Amber Thomas
- The University of Chicago, Chicago, Illinois, USA
| | - Junko Tsuji
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Harm van Bakel
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | - Yongjun Wang
- University of Illinois at Chicago, Chicago, Illinois, USA
| | - Kai Wang
- University of Southern California, Los Angeles, California, USA
| | | | | | - Heather Witt
- University of Southern California, Los Angeles, California, USA
| | - Hyejung Won
- University of California, Los Angeles, California, USA
| | - Chloe C Y Wong
- King's College London, London, and University of Exeter, Devon, UK
| | | | - Emily Y Wu
- University of California, Los Angeles, California, USA
| | - Xuming Xu
- Yale University, New Haven, Connecticut, USA
| | - Lijing Yao
- University of Southern California, Los Angeles, California, USA
| | - Geetha Senthil
- National Institute of Mental Health, Bethesda, Maryland, USA
| | - Thomas Lehner
- National Institute of Mental Health, Bethesda, Maryland, USA
| | - Pamela Sklar
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
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26
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Gockley J, Willsey AJ, Dong S, Dougherty JD, Constantino JN, Sanders SJ. The female protective effect in autism spectrum disorder is not mediated by a single genetic locus. Mol Autism 2015; 6:25. [PMID: 25973162 PMCID: PMC4429476 DOI: 10.1186/s13229-015-0014-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/25/2015] [Indexed: 02/04/2023] Open
Abstract
Background A 4:1 male to female sex bias has consistently been observed in autism spectrum disorder (ASD). Epidemiological and genetic studies suggest a female protective effect (FPE) may account for part of this bias; however, the mechanism of such protection is unknown. Quantitative assessment of ASD symptoms using the Social Responsiveness Scale (SRS) shows a bimodal distribution unique to females in multiplex families. This leads to the hypothesis that a single, common genetic locus on chromosome X might mediate the FPE and produce the ASD sex bias. Such a locus would represent a major therapeutic target and is likely to have been missed by conventional genome-wide association study (GWAS) analysis. Methods To explore this possibility, we performed an association study in affected versus unaffected females, considering three tiers of single nucleotide polymorphisms (SNPs) as follows: 1) regions of chromosome X that escape X-inactivation, 2) all of chromosome X, and 3) genome-wide. Results No evidence of a SNP meeting the criteria for a single FPE locus was observed, despite the analysis being well powered to detect this effect. Conclusions The results do not support the hypothesis that the FPE is mediated by a single genetic locus; however, this does not exclude the possibility of multiple genetic loci playing a role in the FPE. Electronic supplementary material The online version of this article (doi:10.1186/s13229-015-0014-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jake Gockley
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA
| | - A Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA ; Department of Psychiatry, University of California, San Francisco, 401 Parnassus Avenue, San Francisco, CA 94143 USA
| | - Shan Dong
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA ; Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, No.5 Yiheyuan Road, Haidian District, Beijing, 100871 People's Republic of China
| | - Joseph D Dougherty
- Department of Psychiatry, Washington University, 660 South Euclid Avenue, St Louis, MO 63110 USA ; Department of Genetics, Washington University, 4566 Scott Ave, St Louis, MO 63110 USA
| | - John N Constantino
- Department of Psychiatry, Washington University, 660 South Euclid Avenue, St Louis, MO 63110 USA
| | - Stephan J Sanders
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520 USA ; Department of Psychiatry, University of California, San Francisco, 401 Parnassus Avenue, San Francisco, CA 94143 USA
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27
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Chaste P, Klei L, Sanders SJ, Hus V, Murtha MT, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Mane SM, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, Martin CL, Beaudet AL, Lord C, State MW, Cook EH, Devlin B. A genome-wide association study of autism using the Simons Simplex Collection: Does reducing phenotypic heterogeneity in autism increase genetic homogeneity? Biol Psychiatry 2015; 77:775-84. [PMID: 25534755 PMCID: PMC4379124 DOI: 10.1016/j.biopsych.2014.09.017] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Phenotypic heterogeneity in autism has long been conjectured to be a major hindrance to the discovery of genetic risk factors, leading to numerous attempts to stratify children based on phenotype to increase power of discovery studies. This approach, however, is based on the hypothesis that phenotypic heterogeneity closely maps to genetic variation, which has not been tested. Our study examines the impact of subphenotyping of a well-characterized autism spectrum disorder (ASD) sample on genetic homogeneity and the ability to discover common genetic variants conferring liability to ASD. METHODS Genome-wide genotypic data of 2576 families from the Simons Simplex Collection were analyzed in the overall sample and phenotypic subgroups defined on the basis of diagnosis, IQ, and symptom profiles. We conducted a family-based association study, as well as estimating heritability and evaluating allele scores for each phenotypic subgroup. RESULTS Association analyses revealed no genome-wide significant association signal. Subphenotyping did not increase power substantially. Moreover, allele scores built from the most associated single nucleotide polymorphisms, based on the odds ratio in the full sample, predicted case status in subsets of the sample equally well and heritability estimates were very similar for all subgroups. CONCLUSIONS In genome-wide association analysis of the Simons Simplex Collection sample, reducing phenotypic heterogeneity had at most a modest impact on genetic homogeneity. Our results are based on a relatively small sample, one with greater homogeneity than the entire population; if they apply more broadly, they imply that analysis of subphenotypes is not a productive path forward for discovering genetic risk variants in ASD.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; FondaMental Foundation, Créteil; Centre Hospitalier Sainte Anne, Paris, France.
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of
Medicine, Pittsburgh, Pennsylvania, USA
| | - Stephan J. Sanders
- Department of Genetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, University of California at San Francisco,
California, USA
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI,
USA
| | - Michael T. Murtha
- Program on Neurogenetics, Yale University School of Medicine, New
Haven, Connecticut, USA
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism
Research and Treatment, Semel Institute, David Geffen School of Medicine, University
of California Los Angeles, Los Angeles, California, USA
| | - A. Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, University of California at San Francisco,
California, USA
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, Yale University School of Medicine, New
Haven, Connecticut, USA
| | - Timothy W. Yu
- Division of Genetics, Children's Hospital Boston, Harvard
Medical School, Boston, Massachusetts, USA
| | - Eric Fombonne
- Department of Psychiatry and Institute for Development and
disability, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for
Autism Research and Treatment, Semel Institute, David Geffen School of Medicine,
University of California Los Angeles, Los Angeles, California, USA
| | - Dorothy E. Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York,
New York, USA
| | - David H. Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health
System, Danville, Pennsylvania, USA
| | | | - Donna M. Martin
- Departments of Pediatrics and Human Genetics, University of
Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry,
Brown University, Providence, Rhode Island, USA,Department of Psychiatry and Human Behavior, Brown University,
Providence, Rhode Island, USA
| | - Christopher A. Walsh
- Howard Hughes Medical Institute and Division of Genetics,
Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical
School Center for Life Sciences, Boston, Massachusetts, USA
| | - James S. Sutcliffe
- Departments of Molecular Physiology & Biophysics and
Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN,
USA
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health
System, Danville, Pennsylvania, USA
| | - Arthur L. Beaudet
- Department of Human and Molecular Genetics, Baylor College of
Medicine, Houston, Texas, USA
| | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical
College, White Plains, New York, USA
| | - Matthew W. State
- Department of Genetics, Yale University School of Medicine, New
Haven, Connecticut, USA,Department of Psychiatry, University of California at San Francisco,
California, USA
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry,
University of Illinois at Chicago, Chicago, Illinois, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of
Medicine, Pittsburgh, Pennsylvania, USA
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28
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Cotney J, Muhle RA, Sanders SJ, Liu L, Willsey AJ, Niu W, Liu W, Klei L, Lei J, Yin J, Reilly SK, Tebbenkamp AT, Bichsel C, Pletikos M, Sestan N, Roeder K, State MW, Devlin B, Noonan JP. The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment. Nat Commun 2015; 6:6404. [PMID: 25752243 PMCID: PMC4355952 DOI: 10.1038/ncomms7404] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/22/2015] [Indexed: 01/09/2023] Open
Abstract
Recent studies implicate chromatin modifiers in autism spectrum disorder (ASD) through the identification of recurrent de novo loss of function mutations in affected individuals. ASD risk genes are co-expressed in human midfetal cortex, suggesting that ASD risk genes converge in specific regulatory networks during neurodevelopment. To elucidate such networks, we identify genes targeted by CHD8, a chromodomain helicase strongly associated with ASD, in human midfetal brain, human neural stem cells (hNSCs) and embryonic mouse cortex. CHD8 targets are strongly enriched for other ASD risk genes in both human and mouse neurodevelopment, and converge in ASD-associated co-expression networks in human midfetal cortex. CHD8 knockdown in hNSCs results in dysregulation of ASD risk genes directly targeted by CHD8. Integration of CHD8-binding data into ASD risk models improves detection of risk genes. These results suggest loss of CHD8 contributes to ASD by perturbing an ancient gene regulatory network during human brain development.
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Affiliation(s)
- Justin Cotney
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
| | - Rebecca A. Muhle
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Child Study Center, Yale School of Medicine, 230S. Frontage Road, New Haven, Connecticut 06519, USA
| | - Stephan J. Sanders
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Department of Psychiatry, University of California, 401 Parnassus Avenue, San Francisco, California 94143, USA
| | - Li Liu
- Department of Statistics, Carnegie Mellon University, Baker Hall 228B, Pittsburgh, Pennsylvania 15213, USA
| | - A. Jeremy Willsey
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Department of Psychiatry, University of California, 401 Parnassus Avenue, San Francisco, California 94143, USA
| | - Wei Niu
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Child Study Center, Yale School of Medicine, 230S. Frontage Road, New Haven, Connecticut 06519, USA
| | - Wenzhong Liu
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, Pennsylvania 15213, USA
| | - Jing Lei
- Department of Statistics, Carnegie Mellon University, Baker Hall 228B, Pittsburgh, Pennsylvania 15213, USA
| | - Jun Yin
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
| | - Steven K. Reilly
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
| | - Andrew T. Tebbenkamp
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Department of Neurobiology, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06510, USA
| | - Candace Bichsel
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Department of Neurobiology, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06510, USA
| | - Mihovil Pletikos
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Department of Neurobiology, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06510, USA
| | - Nenad Sestan
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
- Department of Neurobiology, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06510, USA
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Baker Hall 228B, Pittsburgh, Pennsylvania 15213, USA
- Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, 7401 Gates-Hillman Center, 5000 Forbes Avenue, Pittsburgh, Pennsylvania 15213, USA
| | - Matthew W. State
- Department of Psychiatry, University of California, 401 Parnassus Avenue, San Francisco, California 94143, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, 3811 O'Hara Street, Pittsburgh, Pennsylvania 15213, USA
| | - James P. Noonan
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, Connecticut 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, PO Box 208001, New Haven, Connecticut 06520, USA
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29
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Abstract
Advances in genome-wide technology, coupled with the availability of large cohorts, are finally yielding a steady stream of autism spectrum disorder (ASD) genes carrying mutations of large effect. These findings represent important molecular clues, but at the same time present notable challenges to traditional strategies for moving from genes to neurobiology. A remarkable degree of genetic heterogeneity, the biological pleiotropy of ASD genes, and the tremendous complexity of the human brain are prompting the development of new strategies for translating genetic discoveries into therapeutic targets. Recent developments in systems biology approaches that 'contextualize' these genetic findings along spatial, temporal, and cellular axes of human brain development are beginning to bridge the gap between high-throughput gene discovery and testable pathophysiological hypotheses.
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Affiliation(s)
- A Jeremy Willsey
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, United States; Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143, United States
| | - Matthew W State
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, United States; Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143, United States.
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30
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Iossifov I, O'Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, Stessman HA, Witherspoon KT, Vives L, Patterson KE, Smith JD, Paeper B, Nickerson DA, Dea J, Dong S, Gonzalez LE, Mandell JD, Mane SM, Murtha MT, Sullivan CA, Walker MF, Waqar Z, Wei L, Willsey AJ, Yamrom B, Lee YH, Grabowska E, Dalkic E, Wang Z, Marks S, Andrews P, Leotta A, Kendall J, Hakker I, Rosenbaum J, Ma B, Rodgers L, Troge J, Narzisi G, Yoon S, Schatz MC, Ye K, McCombie WR, Shendure J, Eichler EE, State MW, Wigler M. The contribution of de novo coding mutations to autism spectrum disorder. Nature 2014; 515:216-21. [PMID: 25363768 PMCID: PMC4313871 DOI: 10.1038/nature13908] [Citation(s) in RCA: 1663] [Impact Index Per Article: 166.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/03/2014] [Indexed: 12/20/2022]
Abstract
Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females.
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Affiliation(s)
- Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Brian J O'Roak
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Molecular &Medical Genetics, Oregon Health &Science University, Portland, Oregon 97208, USA
| | - Stephan J Sanders
- 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Dan Levy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Holly A Stessman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Kali T Witherspoon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Laura Vives
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Karynne E Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Bryan Paeper
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Jeanselle Dea
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Shan Dong
- 1] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA [2] Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Luis E Gonzalez
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Jeffrey D Mandell
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Shrikant M Mane
- Yale Center for Genomic Analysis, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael T Murtha
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Catherine A Sullivan
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael F Walker
- Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA
| | - Zainulabedin Waqar
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Liping Wei
- 1] Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China [2] National Institute of Biological Sciences, Beijing 102206, China
| | - A Jeremy Willsey
- 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Boris Yamrom
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Yoon-ha Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Ewa Grabowska
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] New York Genome Center, New York, New York 10013, USA
| | - Ertugrul Dalkic
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] Department of Medical Biology, Bulent Ecevit University School of Medicine, 67600 Zonguldak, Turkey
| | - Zihua Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Steven Marks
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Peter Andrews
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Anthony Leotta
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jude Kendall
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Inessa Hakker
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Julie Rosenbaum
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Beicong Ma
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Linda Rodgers
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Jennifer Troge
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Giuseppe Narzisi
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA [2] New York Genome Center, New York, New York 10013, USA
| | - Seungtai Yoon
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Kenny Ye
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | | | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, Seattle, Washington 98195, USA
| | - Matthew W State
- 1] Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA [2] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA [3] Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA [4] Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Michael Wigler
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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31
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Dong S, Walker MF, Carriero NJ, DiCola M, Willsey AJ, Ye AY, Waqar Z, Gonzalez LE, Overton JD, Frahm S, Keaney JF, Teran NA, Dea J, Mandell JD, Hus Bal V, Sullivan CA, DiLullo NM, Khalil RO, Gockley J, Yuksel Z, Sertel SM, Ercan-Sencicek AG, Gupta AR, Mane SM, Sheldon M, Brooks AI, Roeder K, Devlin B, State MW, Wei L, Sanders SJ. De novo insertions and deletions of predominantly paternal origin are associated with autism spectrum disorder. Cell Rep 2014; 9:16-23. [PMID: 25284784 DOI: 10.1016/j.celrep.2014.08.068] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/04/2014] [Accepted: 08/27/2014] [Indexed: 11/27/2022] Open
Abstract
Whole-exome sequencing (WES) studies have demonstrated the contribution of de novo loss-of-function single-nucleotide variants (SNVs) to autism spectrum disorder (ASD). However, challenges in the reliable detection of de novo insertions and deletions (indels) have limited inclusion of these variants in prior analyses. By applying a robust indel detection method to WES data from 787 ASD families (2,963 individuals), we demonstrate that de novo frameshift indels contribute to ASD risk (OR = 1.6; 95% CI = 1.0-2.7; p = 0.03), are more common in female probands (p = 0.02), are enriched among genes encoding FMRP targets (p = 6 × 10(-9)), and arise predominantly on the paternal chromosome (p < 0.001). On the basis of mutation rates in probands versus unaffected siblings, we conclude that de novo frameshift indels contribute to risk in approximately 3% of individuals with ASD. Finally, by observing clustering of mutations in unrelated probands, we uncover two ASD-associated genes: KMT2E (MLL5), a chromatin regulator, and RIMS1, a regulator of synaptic vesicle release.
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Affiliation(s)
- Shan Dong
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China; Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael F Walker
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nicholas J Carriero
- Biomedical High Performance Computing Center, W.M. Keck Biotechnology Resource Laboratory, Department of Computer Science, Yale University, New Haven, CT 06520, USA
| | - Michael DiCola
- Bionomics Research and Technology, Environmental and Occupational Health Sciences Institute, Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - A Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Adam Y Ye
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China; National Institute of Biological Sciences, Beijing 102206, People's Republic of China
| | - Zainulabedin Waqar
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Luis E Gonzalez
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - John D Overton
- Yale Center for Genomic Analysis, Yale University School of Medicine, New Haven, CT 06520, USA; Regeneron Genetics Center, 777 Old Saw Mill River Road, Tarrytown, NY 10591, USA
| | - Stephanie Frahm
- Bionomics Research and Technology, Environmental and Occupational Health Sciences Institute, Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - John F Keaney
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA
| | - Nicole A Teran
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jeanselle Dea
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jeffrey D Mandell
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Vanessa Hus Bal
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Catherine A Sullivan
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nicholas M DiLullo
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rehab O Khalil
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Research on Children with Special Needs, National Research Center, Cairo 11787, Egypt
| | - Jake Gockley
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Zafer Yuksel
- Department of Medical Genetics, Gulhane Military Medical Academy, Ankara 06010, Turkey
| | - Sinem M Sertel
- Department of Molecular Biology and Genetics, Bilkent University, Ankara 06800, Turkey
| | - A Gulhan Ercan-Sencicek
- Department of Neurosurgery, Yale Neurogenetics Program, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Abha R Gupta
- Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shrikant M Mane
- Yale Center for Genomic Analysis, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael Sheldon
- Department of Genetics and the Human Genetics Institute, Rutgers University, 145 Bevier Road, Room 136, Piscataway, NJ 08854, USA
| | - Andrew I Brooks
- Bionomics Research and Technology, Environmental and Occupational Health Sciences Institute, Rutgers University, 170 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Kathryn Roeder
- Department of Statistics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Ray and Stephanie Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Matthew W State
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA; Child Study Center, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Psychiatry, Yale University School of Medicine, New Haven, CT 06520, USA.
| | - Liping Wei
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, People's Republic of China; National Institute of Biological Sciences, Beijing 102206, People's Republic of China.
| | - Stephan J Sanders
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94158, USA.
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32
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Glessner JT, Bick AG, Ito K, Homsy J, Rodriguez-Murillo L, Fromer M, Mazaika E, Vardarajan B, Italia M, Leipzig J, DePalma SR, Golhar R, Sanders SJ, Yamrom B, Ronemus M, Iossifov I, Willsey AJ, State MW, Kaltman JR, White PS, Shen Y, Warburton D, Brueckner M, Seidman C, Goldmuntz E, Gelb BD, Lifton R, Seidman J, Hakonarson H, Chung WK. Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circ Res 2014; 115:884-896. [PMID: 25205790 DOI: 10.1161/circresaha.115.304458] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
RATIONALE Congenital heart disease (CHD) is among the most common birth defects. Most cases are of unknown pathogenesis. OBJECTIVE To determine the contribution of de novo copy number variants (CNVs) in the pathogenesis of sporadic CHD. METHODS AND RESULTS We studied 538 CHD trios using genome-wide dense single nucleotide polymorphism arrays and whole exome sequencing. Results were experimentally validated using digital droplet polymerase chain reaction. We compared validated CNVs in CHD cases with CNVs in 1301 healthy control trios. The 2 complementary high-resolution technologies identified 63 validated de novo CNVs in 51 CHD cases. A significant increase in CNV burden was observed when comparing CHD trios with healthy trios, using either single nucleotide polymorphism array (P=7×10(-5); odds ratio, 4.6) or whole exome sequencing data (P=6×10(-4); odds ratio, 3.5) and remained after removing 16% of de novo CNV loci previously reported as pathogenic (P=0.02; odds ratio, 2.7). We observed recurrent de novo CNVs on 15q11.2 encompassing CYFIP1, NIPA1, and NIPA2 and single de novo CNVs encompassing DUSP1, JUN, JUP, MED15, MED9, PTPRE SREBF1, TOP2A, and ZEB2, genes that interact with established CHD proteins NKX2-5 and GATA4. Integrating de novo variants in whole exome sequencing and CNV data suggests that ETS1 is the pathogenic gene altered by 11q24.2-q25 deletions in Jacobsen syndrome and that CTBP2 is the pathogenic gene in 10q subtelomeric deletions. CONCLUSIONS We demonstrate a significantly increased frequency of rare de novo CNVs in CHD patients compared with healthy controls and suggest several novel genetic loci for CHD.
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Affiliation(s)
- Joseph T Glessner
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | | | - Kaoru Ito
- Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jason Homsy
- Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Laura Rodriguez-Murillo
- Mindich Child Health and Development Institute, Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Menachem Fromer
- Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Psychiatric Genomics in the Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erica Mazaika
- Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Badri Vardarajan
- Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Michael Italia
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jeremy Leipzig
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Ryan Golhar
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stephan J Sanders
- Genetics, Yale University, New Haven, CT 06520, USA.,Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Boris Yamrom
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Michael Ronemus
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - A Jeremy Willsey
- Genetics, Yale University, New Haven, CT 06520, USA.,Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Matthew W State
- Genetics, Yale University, New Haven, CT 06520, USA.,Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jonathan R Kaltman
- Cardiovascular Sciences, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, MD 20892, USA
| | - Peter S White
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yufeng Shen
- Systems Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Dorothy Warburton
- Genetics and Development (in Medicine), Columbia University Medical Center, New York, NY 10032, USA
| | | | | | - Elizabeth Goldmuntz
- Cardiology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard Lifton
- Genetics, Yale University, New Haven, CT 06520, USA.,Medicine, Yale University, New Haven, CT 06520, USA
| | | | - Hakon Hakonarson
- The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Wendy K Chung
- Pediatrics and Medicine, Columbia University Medical Center, New York, NY 10032, USA
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33
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Chaste P, Sanders SJ, Mohan KN, Klei L, Song Y, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, State MW, Martin CL, Devlin B, Beaudet AL, Cook EH, Kim SJ. Modest impact on risk for autism spectrum disorder of rare copy number variants at 15q11.2, specifically breakpoints 1 to 2. Autism Res 2014; 7:355-62. [PMID: 24821083 PMCID: PMC6003409 DOI: 10.1002/aur.1378] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 03/19/2014] [Indexed: 01/24/2023]
Abstract
The proximal region of chromosome 15 is one of the genomic hotspots for copy number variants (CNVs). Among the rearrangements observed in this region, CNVs from the interval between the common breakpoints 1 and 2 (BP1 and BP2) have been reported cosegregating with autism spectrum disorder (ASD). Although evidence supporting an association between BP1-BP2 CNVs and autism accumulates, the magnitude of the effect of BP1-BP2 CNVs remains elusive, posing a great challenge to recurrence-risk counseling. To gain further insight into their pathogenicity for ASD, we estimated the penetrance of the BP1-BP2 CNVs for ASD as well as their effects on ASD-related phenotypes in a well-characterized ASD sample (n = 2525 families). Transmission disequilibrium test revealed significant preferential transmission only for the duplicated chromosome in probands (20T:9NT). The penetrance of the BP1-BP2 CNVs for ASD was low, conferring additional risks of 0.3% (deletion) and 0.8% (duplication). Stepwise regression analyses suggest a greater effect of the CNVs on ASD-related phenotype in males and when maternally inherited. Taken together, the results are consistent with BP1-BP2 CNVs as risk factors for autism. However, their effect is modest, more akin to that seen for common variants. To be consistent with the current American College of Medical Genetics guidelines for interpretation of postnatal CNV, the BP1-BP2 deletion and duplication CNVs would probably best be classified as variants of uncertain significance (VOUS): they appear to have an impact on risk, but one so modest that these CNVs do not merit pathogenic status.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- FondaMental Foundation, Créteil, France
| | - Stephan J. Sanders
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Kommu N. Mohan
- Department of Biological Sciences, BITS Pilani-Hyderabad Campus, Hyderabad, India
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Youeun Song
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Michael T. Murtha
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - A. Jeremy Willsey
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Timothy W. Yu
- Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric Fombonne
- Department of Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Dorothy E. Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
| | - David H. Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical College, White Plains, New York, USA
| | | | - Donna M. Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
- Department of Psychiatry and Human Behavior, Brown University, Providence, Rhode Island, USA
| | - Christopher A. Walsh
- Howard Hughes Medical Institute and Division of Genetics, Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical School Center for Life Sciences, Boston, Massachusetts, USA
| | - James S. Sutcliffe
- Departments of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Matthew W. State
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Psychiatry, University of California at San Francisco, California, USA
| | - Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Arthur L. Beaudet
- Department of Human and Molecular Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Soo-Jeong Kim
- Center for Integrative Brain Research, Seattle Children's Research Institute & Department of Psychiatry and Behavioral Science, University of Washington, Seattle, WA, USA
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Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, Liu W, Liu L, Lu C, Xu X, Zhu Y, Mane SM, Lein ES, Wei L, Noonan JP, Roeder K, Devlin B, Sestan N, State MW. Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell 2014; 155:997-1007. [PMID: 24267886 DOI: 10.1016/j.cell.2013.10.020] [Citation(s) in RCA: 623] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 08/02/2013] [Accepted: 10/07/2013] [Indexed: 01/08/2023]
Abstract
Autism spectrum disorder (ASD) is a complex developmental syndrome of unknown etiology. Recent studies employing exome- and genome-wide sequencing have identified nine high-confidence ASD (hcASD) genes. Working from the hypothesis that ASD-associated mutations in these biologically pleiotropic genes will disrupt intersecting developmental processes to contribute to a common phenotype, we have attempted to identify time periods, brain regions, and cell types in which these genes converge. We have constructed coexpression networks based on the hcASD "seed" genes, leveraging a rich expression data set encompassing multiple human brain regions across human development and into adulthood. By assessing enrichment of an independent set of probable ASD (pASD) genes, derived from the same sequencing studies, we demonstrate a key point of convergence in midfetal layer 5/6 cortical projection neurons. This approach informs when, where, and in what cell types mutations in these specific genes may be productively studied to clarify ASD pathophysiology.
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Affiliation(s)
- A Jeremy Willsey
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA
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35
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Chaste P, Klei L, Sanders SJ, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin CL, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, State MW, Devlin B, Cook EH, Kim SJ. Adjusting head circumference for covariates in autism: clinical correlates of a highly heritable continuous trait. Biol Psychiatry 2013; 74:576-84. [PMID: 23746936 PMCID: PMC3772969 DOI: 10.1016/j.biopsych.2013.04.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 03/25/2013] [Accepted: 04/16/2013] [Indexed: 11/29/2022]
Abstract
BACKGROUND Brain development follows a different trajectory in children with autism spectrum disorders (ASD) than in typically developing children. A proxy for neurodevelopment could be head circumference (HC), but studies assessing HC and its clinical correlates in ASD have been inconsistent. This study investigates HC and clinical correlates in the Simons Simplex Collection cohort. METHODS We used a mixed linear model to estimate effects of covariates and the deviation from the expected HC given parental HC (genetic deviation). After excluding individuals with incomplete data, 7225 individuals in 1891 families remained for analysis. We examined the relationship between HC/genetic deviation of HC and clinical parameters. RESULTS Gender, age, height, weight, genetic ancestry, and ASD status were significant predictors of HC (estimate of the ASD effect = .2 cm). HC was approximately normally distributed in probands and unaffected relatives, with only a few outliers. Genetic deviation of HC was also normally distributed, consistent with a random sampling of parental genes. Whereas larger HC than expected was associated with ASD symptom severity and regression, IQ decreased with the absolute value of the genetic deviation of HC. CONCLUSIONS Measured against expected values derived from covariates of ASD subjects, statistical outliers for HC were uncommon. HC is a strongly heritable trait, and population norms for HC would be far more accurate if covariates including genetic ancestry, height, and age were taken into account. The association of diminishing IQ with absolute deviation from predicted HC values suggests HC could reflect subtle underlying brain development and warrants further investigation.
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Affiliation(s)
- Pauline Chaste
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA, FondaMental Foundation, Créteil, France
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Stephan J. Sanders
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michael T. Murtha
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Vanessa Hus
- Department of Psychology, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer K. Lowe
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - A. Jeremy Willsey
- Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Daniel Moreno-De-Luca
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Timothy W. Yu
- Division of Genetics, Children's Hospital Boston, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric Fombonne
- Department of Psychiatry, Oregon Health & Science University, Portland, Oregon, USA
| | - Daniel Geschwind
- Neurogenetics Program, Department of Neurology and Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Dorothy E. Grice
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
| | | | - Catherine Lord
- Center for Autism and the Developing Brain, Weill Cornell Medical College, White Plains, New York, USA
| | | | - Christa Lese Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Donna M. Martin
- Departments of Pediatrics and Human Genetics, University of Michigan Medical Center, Ann Arbor, Michigan, USA
| | - Eric M. Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry; and Institute for Brain Science, Brown University, Lab for Molecular Medicine, Providence, Rhode Island, USA, Developmental Disorders Genetics Research Program, Emma Pendleton Bradley Hospital and Department of Psychiatry and Human Behavior, Brown University Medical School, East Providence, Rhode Island, USA
| | - Christopher A. Walsh
- Howard Hughes Medical Institute and Division of Genetics, Children's Hospital Boston, and Neurology and Pediatrics, Harvard Medical School Center for Life Sciences, Boston, Massachusetts, USA
| | - James S. Sutcliffe
- Departments of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Matthew W. State
- Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, Child Study Center, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut, USA, Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Edwin H. Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Soo-Jeong Kim
- Center for Integrative Brain Research, Seattle Children's Research Institute & Department of Psychiatry and Behavioral Science, University of Washington, Seattle, WA, USA,Corresponding author Soo-Jeong Kim, M.D., Center for Integrative Brain Research, Seattle Children's Research Institute, 1900 9 Ave, Seattle, WA 98101, USA, , Tel: +12068841275, Fax:+12068841210
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36
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Moreno-De-Luca D, Sanders SJ, Willsey AJ, Mulle JG, Lowe JK, Geschwind DH, State MW, Martin CL, Ledbetter DH. Using large clinical data sets to infer pathogenicity for rare copy number variants in autism cohorts. Mol Psychiatry 2013; 18:1090-5. [PMID: 23044707 PMCID: PMC3720840 DOI: 10.1038/mp.2012.138] [Citation(s) in RCA: 124] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/24/2012] [Accepted: 08/20/2012] [Indexed: 11/16/2022]
Abstract
Copy number variants (CNVs) have a major role in the etiology of autism spectrum disorders (ASD), and several of these have reached statistical significance in case-control analyses. Nevertheless, current ASD cohorts are not large enough to detect very rare CNVs that may be causative or contributory (that is, risk alleles). Here, we use a tiered approach, in which clinically significant CNVs are first identified in large clinical cohorts of neurodevelopmental disorders (including but not specific to ASD), after which these CNVs are then systematically identified within well-characterized ASD cohorts. We focused our initial analysis on 48 recurrent CNVs (segmental duplication-mediated 'hotspots') from 24 loci in 31 516 published clinical cases with neurodevelopmental disorders and 13 696 published controls, which yielded a total of 19 deletion CNVs and 11 duplication CNVs that reached statistical significance. We then investigated the overlap of these 30 CNVs in a combined sample of 3955 well-characterized ASD cases from three published studies. We identified 73 deleterious recurrent CNVs, including 36 deletions from 11 loci and 37 duplications from seven loci, for a frequency of 1 in 54; had we considered the ASD cohorts alone, only 58 CNVs from eight loci (24 deletions from three loci and 34 duplications from five loci) would have reached statistical significance. In conclusion, until there are sufficiently large ASD research cohorts with enough power to detect very rare causative or contributory CNVs, data from larger clinical cohorts can be used to infer the likely clinical significance of CNVs in ASD.
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Affiliation(s)
- D Moreno-De-Luca
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA,Programs in Neurogenetics and Human Genetics and Genomics, Child Study Center and Departments of Psychiatry and Genetics, Yale University School of Medicine, New Haven, CT, USA,Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 315, Atlanta, GA 30322, USAE-mail:
| | - S J Sanders
- Programs in Neurogenetics and Human Genetics and Genomics, Child Study Center and Departments of Psychiatry and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - A J Willsey
- Programs in Neurogenetics and Human Genetics and Genomics, Child Study Center and Departments of Psychiatry and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - J G Mulle
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - J K Lowe
- Neurogenetics Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - D H Geschwind
- Neurogenetics Program, University of California, Los Angeles, Los Angeles, CA, USA
| | - M W State
- Programs in Neurogenetics and Human Genetics and Genomics, Child Study Center and Departments of Psychiatry and Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - C L Martin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - D H Ledbetter
- Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA,Genomic Medicine Institute, Geisinger Health System, Danville, PA, USA. E-mail:
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Watson C, Steinberg K, Huddleston J, Warren R, Malig M, Schein J, Willsey AJ, Joy J, Scott J, Graves TA, Wilson R, Holt R, Eichler E, Breden F. Complete haplotype sequence of the human immunoglobulin heavy-chain variable, diversity, and joining genes and characterization of allelic and copy-number variation. Am J Hum Genet 2013; 92:530-46. [PMID: 23541343 DOI: 10.1016/j.ajhg.2013.03.004] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 01/08/2013] [Accepted: 03/06/2013] [Indexed: 01/02/2023] Open
Abstract
The immunoglobulin heavy-chain locus (IGH) encodes variable (IGHV), diversity (IGHD), joining (IGHJ), and constant (IGHC) genes and is responsible for antibody heavy-chain biosynthesis, which is vital to the adaptive immune response. Programmed V-(D)-J somatic rearrangement and the complex duplicated nature of the locus have impeded attempts to reconcile its genomic organization based on traditional B-lymphocyte derived genetic material. As a result, sequence descriptions of germline variation within IGHV are lacking, haplotype inference using traditional linkage disequilibrium methods has been difficult, and the human genome reference assembly is missing several expressed IGHV genes. By using a hydatidiform mole BAC clone resource, we present the most complete haplotype of IGHV, IGHD, and IGHJ gene regions derived from a single chromosome, representing an alternate assembly of ∼1 Mbp of high-quality finished sequence. From this we add 101 kbp of previously uncharacterized sequence, including functional IGHV genes, and characterize four large germline copy-number variants (CNVs). In addition to this germline reference, we identify and characterize eight CNV-containing haplotypes from a panel of nine diploid genomes of diverse ethnic origin, discovering previously unmapped IGHV genes and an additional 121 kbp of insertion sequence. We genotype four of these CNVs by using PCR in 425 individuals from nine human populations. We find that all four are highly polymorphic and show considerable evidence of stratification (Fst = 0.3-0.5), with the greatest differences observed between African and Asian populations. These CNVs exhibit weak linkage disequilibrium with SNPs from two commercial arrays in most of the populations tested.
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Klei L, Sanders SJ, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Martin CL, Martin DM, Morrow EM, Walsh CA, Melhem NM, Chaste P, Sutcliffe JS, State MW, Cook EH, Roeder K, Devlin B. Common genetic variants, acting additively, are a major source of risk for autism. Mol Autism 2012; 3:9. [PMID: 23067556 PMCID: PMC3579743 DOI: 10.1186/2040-2392-3-9] [Citation(s) in RCA: 279] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 10/04/2012] [Indexed: 11/10/2022] Open
Abstract
Background Autism spectrum disorders (ASD) are early onset neurodevelopmental syndromes typified by impairments in reciprocal social interaction and communication, accompanied by restricted and repetitive behaviors. While rare and especially de novo genetic variation are known to affect liability, whether common genetic polymorphism plays a substantial role is an open question and the relative contribution of genes and environment is contentious. It is probable that the relative contributions of rare and common variation, as well as environment, differs between ASD families having only a single affected individual (simplex) versus multiplex families who have two or more affected individuals. Methods By using quantitative genetics techniques and the contrast of ASD subjects to controls, we estimate what portion of liability can be explained by additive genetic effects, known as narrow-sense heritability. We evaluate relatives of ASD subjects using the same methods to evaluate the assumptions of the additive model and partition families by simplex/multiplex status to determine how heritability changes with status. Results By analyzing common variation throughout the genome, we show that common genetic polymorphism exerts substantial additive genetic effects on ASD liability and that simplex/multiplex family status has an impact on the identified composition of that risk. As a fraction of the total variation in liability, the estimated narrow-sense heritability exceeds 60% for ASD individuals from multiplex families and is approximately 40% for simplex families. By analyzing parents, unaffected siblings and alleles not transmitted from parents to their affected children, we conclude that the data for simplex ASD families follow the expectation for additive models closely. The data from multiplex families deviate somewhat from an additive model, possibly due to parental assortative mating. Conclusions Our results, when viewed in the context of results from genome-wide association studies, demonstrate that a myriad of common variants of very small effect impacts ASD liability.
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Affiliation(s)
- Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, Willsey AJ, Ercan-Sencicek AG, DiLullo NM, Parikshak NN, Stein JL, Walker MF, Ober GT, Teran NA, Song Y, El-Fishawy P, Murtha RC, Choi M, Overton JD, Bjornson RD, Carriero NJ, Meyer KA, Bilguvar K, Mane SM, Sestan N, Lifton RP, Günel M, Roeder K, Geschwind DH, Devlin B, State MW. De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 2012; 485:237-41. [PMID: 22495306 DOI: 10.1038/nature10945] [Citation(s) in RCA: 1434] [Impact Index Per Article: 119.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 02/14/2012] [Indexed: 12/14/2022]
Abstract
Multiple studies have confirmed the contribution of rare de novo copy number variations to the risk for autism spectrum disorders. But whereas de novo single nucleotide variants have been identified in affected individuals, their contribution to risk has yet to be clarified. Specifically, the frequency and distribution of these mutations have not been well characterized in matched unaffected controls, and such data are vital to the interpretation of de novo coding mutations observed in probands. Here we show, using whole-exome sequencing of 928 individuals, including 200 phenotypically discordant sibling pairs, that highly disruptive (nonsense and splice-site) de novo mutations in brain-expressed genes are associated with autism spectrum disorders and carry large effects. On the basis of mutation rates in unaffected individuals, we demonstrate that multiple independent de novo single nucleotide variants in the same gene among unrelated probands reliably identifies risk alleles, providing a clear path forward for gene discovery. Among a total of 279 identified de novo coding mutations, there is a single instance in probands, and none in siblings, in which two independent nonsense variants disrupt the same gene, SCN2A (sodium channel, voltage-gated, type II, α subunit), a result that is highly unlikely by chance.
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Affiliation(s)
- Stephan J Sanders
- Program on Neurogenetics, Child Study Center, Department of Psychiatry, Yale University School of Medicine, 230 South Frontage Road, New Haven, Connecticut 06520, USA
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