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Alibutud R, Hansali S, Cao X, Zhou A, Mahaganapathy V, Azaro M, Gwin C, Wilson S, Buyske S, Bartlett CW, Flax JF, Brzustowicz LM, Xing J. Structural Variations Contribute to the Genetic Etiology of Autism Spectrum Disorder and Language Impairments. Int J Mol Sci 2023; 24:13248. [PMID: 37686052 PMCID: PMC10487745 DOI: 10.3390/ijms241713248] [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: 06/17/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by restrictive interests and/or repetitive behaviors and deficits in social interaction and communication. ASD is a multifactorial disease with a complex polygenic genetic architecture. Its genetic contributing factors are not yet fully understood, especially large structural variations (SVs). In this study, we aimed to assess the contribution of SVs, including copy number variants (CNVs), insertions, deletions, duplications, and mobile element insertions, to ASD and related language impairments in the New Jersey Language and Autism Genetics Study (NJLAGS) cohort. Within the cohort, ~77% of the families contain SVs that followed expected segregation or de novo patterns and passed our filtering criteria. These SVs affected 344 brain-expressed genes and can potentially contribute to the genetic etiology of the disorders. Gene Ontology and protein-protein interaction network analysis suggested several clusters of genes in different functional categories, such as neuronal development and histone modification machinery. Genes and biological processes identified in this study contribute to the understanding of ASD and related neurodevelopment disorders.
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Affiliation(s)
- Rohan Alibutud
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Sammy Hansali
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Xiaolong Cao
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Anbo Zhou
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Vaidhyanathan Mahaganapathy
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Marco Azaro
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Christine Gwin
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Sherri Wilson
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Steven Buyske
- Department of Statistics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA;
| | - Christopher W. Bartlett
- The Steve Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA;
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43205, USA
| | - Judy F. Flax
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
| | - Linda M. Brzustowicz
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
- The Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; (R.A.); (S.H.); (X.C.); (A.Z.); (V.M.); (M.A.); (C.G.); (S.W.); (J.F.F.); (L.M.B.)
- The Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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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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