1
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Lu X, Ni P, Suarez-Meade P, Ma Y, Forrest EN, Wang G, Wang Y, Quiñones-Hinojosa A, Gerstein M, Jiang YH. Transcriptional determinism and stochasticity contribute to the complexity of autism-associated SHANK family genes. Cell Rep 2024; 43:114376. [PMID: 38900637 DOI: 10.1016/j.celrep.2024.114376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 05/08/2024] [Accepted: 05/31/2024] [Indexed: 06/22/2024] Open
Abstract
Precision of transcription is critical because transcriptional dysregulation is disease causing. Traditional methods of transcriptional profiling are inadequate to elucidate the full spectrum of the transcriptome, particularly for longer and less abundant mRNAs. SHANK3 is one of the most common autism causative genes. Twenty-four Shank3-mutant animal lines have been developed for autism modeling. However, their preclinical validity has been questioned due to incomplete Shank3 transcript structure. We apply an integrative approach combining cDNA-capture and long-read sequencing to profile the SHANK3 transcriptome in humans and mice. We unexpectedly discover an extremely complex SHANK3 transcriptome. Specific SHANK3 transcripts are altered in Shank3-mutant mice and postmortem brain tissues from individuals with autism spectrum disorder. The enhanced SHANK3 transcriptome significantly improves the detection rate for potential deleterious variants from genomics studies of neuropsychiatric disorders. Our findings suggest that both deterministic and stochastic transcription of the genome is associated with SHANK family genes.
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Affiliation(s)
- Xiaona Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Pengyu Ni
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | | | - Yu Ma
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | - Emily Niemitz Forrest
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Guilin Wang
- Keck Microarray Shared Resource, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yi Wang
- Department of Neurology, Children's Hospital of Fudan University, Shanghai 201102, China
| | | | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA; Department of Computer Science, Yale University, New Haven, CT 06520, USA; Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA; Department of Biomedical Informatics & Data Science, Yale University, New Haven, CT 06520, USA
| | - Yong-Hui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA; Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA; Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA.
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2
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Wang J, Jiang C, Guo Z, Chapman S, Kozhemiako N, Mylonas D, Su Y, Zhou L, Shen L, Qin S, Murphy M, Tan S, Manoach DS, Stickgold R, Huang H, Zhou Z, Purcell SM, Hall M, Hyman SE, Pan JQ. Study Protocol: Global Research Initiative on the Neurophysiology of Schizophrenia (GRINS) project. BMC Psychiatry 2024; 24:433. [PMID: 38858652 PMCID: PMC11165775 DOI: 10.1186/s12888-024-05882-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/31/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Objective and quantifiable markers are crucial for developing novel therapeutics for mental disorders by 1) stratifying clinically similar patients with different underlying neurobiological deficits and 2) objectively tracking disease trajectory and treatment response. Schizophrenia is often confounded with other psychiatric disorders, especially bipolar disorder, if based on cross-sectional symptoms. Awake and sleep EEG have shown promise in identifying neurophysiological differences as biomarkers for schizophrenia. However, most previous studies, while useful, were conducted in European and American populations, had small sample sizes, and utilized varying analytic methods, limiting comprehensive analyses or generalizability to diverse human populations. Furthermore, the extent to which wake and sleep neurophysiology metrics correlate with each other and with symptom severity or cognitive impairment remains unresolved. Moreover, how these neurophysiological markers compare across psychiatric conditions is not well characterized. The utility of biomarkers in clinical trials and practice would be significantly advanced by well-powered transdiagnostic studies. The Global Research Initiative on the Neurophysiology of Schizophrenia (GRINS) project aims to address these questions through a large, multi-center cohort study involving East Asian populations. To promote transparency and reproducibility, we describe the protocol for the GRINS project. METHODS The research procedure consists of an initial screening interview followed by three subsequent sessions: an introductory interview, an evaluation visit, and an overnight neurophysiological recording session. Data from multiple domains, including demographic and clinical characteristics, behavioral performance (cognitive tasks, motor sequence tasks), and neurophysiological metrics (both awake and sleep electroencephalography), are collected by research groups specialized in each domain. CONCLUSION Pilot results from the GRINS project demonstrate the feasibility of this study protocol and highlight the importance of such research, as well as its potential to study a broader range of patients with psychiatric conditions. Through GRINS, we are generating a valuable dataset across multiple domains to identify neurophysiological markers of schizophrenia individually and in combination. By applying this protocol to related mental disorders often confounded with each other, we can gather information that offers insight into the neurophysiological characteristics and underlying mechanisms of these severe conditions, informing objective diagnosis, stratification for clinical research, and ultimately, the development of better-targeted treatment matching in the clinic.
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Affiliation(s)
- Jun Wang
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, China
| | - Chenguang Jiang
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, China
| | - Zhenglin Guo
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Sinéad Chapman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Nataliia Kozhemiako
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Dimitrios Mylonas
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Yi Su
- Psychiatry Research Center, Beijing Huilongguan Hospital, Peking University Huilongguan Clinical Medical School, Beijing, China
| | - Lin Zhou
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Lu Shen
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Michael Murphy
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, United States
| | - Shuping Tan
- Psychiatry Research Center, Beijing Huilongguan Hospital, Peking University Huilongguan Clinical Medical School, Beijing, China
| | - Dara S Manoach
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Robert Stickgold
- Beth Israel Deaconess Medical Center, Boston, United States
- Department of Psychiatry, Harvard Medical School, Boston, United States
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, United States
| | - Zhenhe Zhou
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, China
| | - Shaun M Purcell
- Department of Psychiatry, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
- Department of Psychiatry, Harvard Medical School, Boston, United States
| | - Meihua Hall
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, United States
| | - Steven E Hyman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, United States.
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3
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Deng YT, Wu BS, Yang L, He XY, Kang JJ, Liu WS, Li ZY, Wu XR, Zhang YR, Chen SD, Ge YJ, Huang YY, Feng JF, Zhu Y, Dong Q, Mao Y, Cheng W, Yu JT. Large-scale whole-exome sequencing of neuropsychiatric diseases and traits in 350,770 adults. Nat Hum Behav 2024; 8:1194-1208. [PMID: 38589703 DOI: 10.1038/s41562-024-01861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
While numerous genomic loci have been identified for neuropsychiatric conditions, the contribution of protein-coding variants has yet to be determined. Here we conducted a large-scale whole-exome-sequencing study to interrogate the impact of protein-coding variants on 46 neuropsychiatric diseases and 23 traits in 350,770 adults from the UK Biobank. Twenty new genes were associated with neuropsychiatric diseases through coding variants, among which 16 genes had impacts on the longitudinal risks of diseases. Thirty new genes were associated with neuropsychiatric traits, with SYNGAP1 showing pleiotropic effects across cognitive function domains. Pairwise estimation of genetic correlations at the coding-variant level highlighted shared genetic associations among pairs of neurodegenerative diseases and mental disorders. Lastly, a comprehensive multi-omics analysis suggested that alterations in brain structures, blood proteins and inflammation potentially contribute to the gene-phenotype linkages. Overall, our findings characterized a compendium of protein-coding variants for future research on the biology and therapeutics of neuropsychiatric phenotypes.
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Affiliation(s)
- Yue-Ting Deng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Bang-Sheng Wu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liu Yang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao-Yu He
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ju-Jiao Kang
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Wei-Shi Liu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ze-Yu Li
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
| | - Xin-Rui Wu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ya-Ru Zhang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shi-Dong Chen
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yi-Jun Ge
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Yuan Huang
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian-Feng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China
- Department of Computer Science, University of Warwick, Coventry, UK
| | - Ying Zhu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Qiang Dong
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital Fudan University, Shanghai, China
| | - Wei Cheng
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Fudan University, Ministry of Education, Shanghai, China.
- Fudan ISTBI-ZJNU Algorithm Centre for Brain-inspired Intelligence, Zhejiang Normal University, Zhejiang, China.
| | - Jin-Tai Yu
- Department of Neurology and National Center for Neurological Disorders, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai, China.
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4
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Hara T, Kazuno AA, Toyota T, Ueda J, Shuno T, Mukai J, Sato TA, Matsumoto N, Yoshikawa T, Takata A. A case of bipolar I disorder with a loss-of-function variant of schizophrenia risk gene SETD1A: possible expansion of the relevant clinical spectrum supported by a meta-analysis. Psychiatry Clin Neurosci 2024; 78:374-375. [PMID: 38646907 DOI: 10.1111/pcn.13669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/21/2024] [Accepted: 03/10/2024] [Indexed: 04/23/2024]
Affiliation(s)
- Tomonori Hara
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan
- Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Sendai, Japan
- Hatsuishi Hospital, Kashiwa, Japan
| | - An-A Kazuno
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan
| | - Tomoko Toyota
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan
- Kokoro Medical Office, Akita, Japan
| | - Junko Ueda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan
| | | | - Jun Mukai
- Research and Development Center for Precision Medicine, University of Tsukuba, Tsukuba, Japan
| | - Taka-Aki Sato
- Research and Development Center for Precision Medicine, University of Tsukuba, Tsukuba, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Wako, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Bunkyo-Ku, Japan
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5
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Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ, de la Torre-Ubieta L. Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science 2024; 384:eadh7688. [PMID: 38781356 DOI: 10.1126/science.adh7688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/13/2024] [Indexed: 05/25/2024]
Abstract
RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders; yet, the role of cell type-specific splicing and transcript-isoform diversity during human brain development has not been systematically investigated. In this work, we leveraged single-molecule long-read sequencing to deeply profile the full-length transcriptome of the germinal zone and cortical plate regions of the developing human neocortex at tissue and single-cell resolution. We identified 214,516 distinct isoforms, of which 72.6% were novel (not previously annotated in Gencode version 33), and uncovered a substantial contribution of transcript-isoform diversity-regulated by RNA binding proteins-in defining cellular identity in the developing neocortex. We leveraged this comprehensive isoform-centric gene annotation to reprioritize thousands of rare de novo risk variants and elucidate genetic risk mechanisms for neuropsychiatric disorders.
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Affiliation(s)
- Ashok Patowary
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Pan Zhang
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Connor Jops
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Celine K Vuong
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Xinzhou Ge
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kangcheng Hou
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Minsoo Kim
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Naihua Gong
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael Margolis
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel Vo
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jingyi Jessica Li
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Statistics, University of California Los Angeles, Los Angeles, CA 90095, USA
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute at Penn Med and the Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Luis de la Torre-Ubieta
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
- Intellectual and Developmental Disabilities Research Center, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA 90095, USA
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6
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Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H, Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ. Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science 2024; 384:eadh0829. [PMID: 38781368 DOI: 10.1126/science.adh0829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/07/2024] [Indexed: 05/25/2024]
Abstract
Neuropsychiatric genome-wide association studies (GWASs), including those for autism spectrum disorder and schizophrenia, show strong enrichment for regulatory elements in the developing brain. However, prioritizing risk genes and mechanisms is challenging without a unified regulatory atlas. Across 672 diverse developing human brains, we identified 15,752 genes harboring gene, isoform, and/or splicing quantitative trait loci, mapping 3739 to cellular contexts. Gene expression heritability drops during development, likely reflecting both increasing cellular heterogeneity and the intrinsic properties of neuronal maturation. Isoform-level regulation, particularly in the second trimester, mediated the largest proportion of GWAS heritability. Through colocalization, we prioritized mechanisms for about 60% of GWAS loci across five disorders, exceeding adult brain findings. Finally, we contextualized results within gene and isoform coexpression networks, revealing the comprehensive landscape of transcriptome regulation in development and disease.
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Affiliation(s)
- Cindy Wen
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Margolis
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Rujia Dai
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Pan Zhang
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA
| | - Daniel D Vo
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Miao Tang
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Chuan Jiao
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, Team Krebs, 75014 Paris, France
| | - Minsoo Kim
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ellen Tsai
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Celine Hoh
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rebecca L Walker
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christos Chatzinakos
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
- McLean Hospital, Belmont, MA 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Declan Clarke
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Henry Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Mette A Peters
- CNS Data Coordination Group, Sage Bionetworks, Seattle, WA 98109, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
- Department of Computer Science, Yale University, New Haven, CT 06520, USA
- Department of Statistics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Nikolaos P Daskalakis
- Department of Psychiatry, Harvard Medical School, Boston, MA 02215, USA
- McLean Hospital, Belmont, MA 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Neumora Therapeutics, Watertown, MA 02472, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University School of Medicine, Cardiff CF24 4HQ, UK
| | - Nenad Sestan
- Department of Comparative Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Daniel H Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kathryn Roeder
- Department of Statistics & Data Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Alexander Gusev
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02215, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Bogdan Pasaniuc
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology, San Francisco, CA 94158, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008, China
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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7
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Aguzzoli Heberle B, Brandon JA, Page ML, Nations KA, Dikobe KI, White BJ, Gordon LA, Fox GA, Wadsworth ME, Doyle PH, Williams BA, Fox EJ, Shantaraman A, Ryten M, Goodwin S, Ghiban E, Wappel R, Mavruk-Eskipehlivan S, Miller JB, Seyfried NT, Nelson PT, Fryer JD, Ebbert MTW. Mapping medically relevant RNA isoform diversity in the aged human frontal cortex with deep long-read RNA-seq. Nat Biotechnol 2024:10.1038/s41587-024-02245-9. [PMID: 38778214 DOI: 10.1038/s41587-024-02245-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Determining whether the RNA isoforms from medically relevant genes have distinct functions could facilitate direct targeting of RNA isoforms for disease treatment. Here, as a step toward this goal for neurological diseases, we sequenced 12 postmortem, aged human frontal cortices (6 Alzheimer disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. We identified 1,917 medically relevant genes expressing multiple isoforms in the frontal cortex where 1,018 had multiple isoforms with different protein-coding sequences. Of these 1,018 genes, 57 are implicated in brain-related diseases including major depression, schizophrenia, Parkinson's disease and Alzheimer disease. Our study also uncovered 53 new RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. We also reported on five mitochondrially encoded, spliced RNA isoforms. We found 99 differentially expressed RNA isoforms between cases with Alzheimer disease and controls.
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Affiliation(s)
- Bernardo Aguzzoli Heberle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - J Anthony Brandon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Madeline L Page
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Kayla A Nations
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Ketsile I Dikobe
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Brendan J White
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Lacey A Gordon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Grant A Fox
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Mark E Wadsworth
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Patricia H Doyle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Brittney A Williams
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Edward J Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Mina Ryten
- UK Dementia Research Institute at The University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Elena Ghiban
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert Wappel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Justin B Miller
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY, USA
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Nicholas T Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Peter T Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - John D Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, AZ, USA
| | - Mark T W Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, USA.
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY, USA.
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8
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Zhou X, Lee YK, Li X, Kim H, Sanchez-Priego C, Han X, Tan H, Zhou S, Fu Y, Purtell K, Wang Q, Holstein GR, Tang B, Peng J, Yang N, Yue Z. Integrated proteomics reveals autophagy landscape and an autophagy receptor controlling PKA-RI complex homeostasis in neurons. Nat Commun 2024; 15:3113. [PMID: 38600097 PMCID: PMC11006854 DOI: 10.1038/s41467-024-47440-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
Autophagy is a conserved, catabolic process essential for maintaining cellular homeostasis. Malfunctional autophagy contributes to neurodevelopmental and neurodegenerative diseases. However, the exact role and targets of autophagy in human neurons remain elusive. Here we report a systematic investigation of neuronal autophagy targets through integrated proteomics. Deep proteomic profiling of multiple autophagy-deficient lines of human induced neurons, mouse brains, and brain LC3-interactome reveals roles of neuronal autophagy in targeting proteins of multiple cellular organelles/pathways, including endoplasmic reticulum (ER), mitochondria, endosome, Golgi apparatus, synaptic vesicle (SV) for degradation. By combining phosphoproteomics and functional analysis in human and mouse neurons, we uncovered a function of neuronal autophagy in controlling cAMP-PKA and c-FOS-mediated neuronal activity through selective degradation of the protein kinase A - cAMP-binding regulatory (R)-subunit I (PKA-RI) complex. Lack of AKAP11 causes accumulation of the PKA-RI complex in the soma and neurites, demonstrating a constant clearance of PKA-RI complex through AKAP11-mediated degradation in neurons. Our study thus reveals the landscape of autophagy degradation in human neurons and identifies a physiological function of autophagy in controlling homeostasis of PKA-RI complex and specific PKA activity in neurons.
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Affiliation(s)
- Xiaoting Zhou
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - You-Kyung Lee
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xianting Li
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Henry Kim
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Carlos Sanchez-Priego
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Institute for Regenerative Medicine, Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Xian Han
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Integrated Biomedical Sciences Program, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Haiyan Tan
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Yingxue Fu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kerry Purtell
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Qian Wang
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gay R Holstein
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Beisha Tang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
| | - Nan Yang
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Institute for Regenerative Medicine, Alper Center for Neural Development and Regeneration, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Zhenyu Yue
- Department of Neurology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Family Department of Neuroscience, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Center of Parkinson's Disease Neurobiology, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
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9
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Wang L, Kranzler HR, Gelernter J, Zhou H. Multi-ancestry Whole-exome Sequencing Study of Alcohol Use Disorder in Two Cohorts. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.05.24305412. [PMID: 38645055 PMCID: PMC11030482 DOI: 10.1101/2024.04.05.24305412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Alcohol use disorder (AUD) is a leading cause of death and disability worldwide. There has been substantial progress in identifying genetic variants underlying AUD. However, there are few whole-exome sequencing (WES) studies of AUD. We analyzed WES of 4,530 samples from the Yale-Penn cohort and 469,835 samples from the UK Biobank (UKB). After quality control, 1,420 AUD cases and 619 controls of European ancestry (EUR) and 1,142 cases and 608 controls of African ancestry (AFR) from Yale-Penn were retained for subsequent analyses. WES data from 415,617 EUR samples (12,861 cases), 6,142 AFR samples (130 cases) and 4,607 South Asian (SAS) samples (130 cases) from UKB were also analyzed. Single-variant association analysis identified the well-known functional variant rs1229984 in ADH1B ( P =4.88×10 -31 ) and several other common variants in ADH1C . Gene-based tests identified ADH1B ( P =1.00×10 -31 ), ADH1C ( P =5.23×10 -7 ), CNST ( P =1.19×10 -6 ), and IFIT5 (3.74×10 -6 ). This study extends our understanding of the genetic basis of AUD.
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10
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Phalnikar K, Srividya M, Mythri SV, Vasavi NS, Ganguly A, Kumar A, S P, Kalia K, Mishra SS, Dhanya SK, Paul P, Holla B, Ganesh S, Reddy PC, Sud R, Viswanath B, Muralidharan B. Altered neuroepithelial morphogenesis and migration defects in iPSC-derived cerebral organoids and 2D neural stem cells in familial bipolar disorder. OXFORD OPEN NEUROSCIENCE 2024; 3:kvae007. [PMID: 38638145 PMCID: PMC11024480 DOI: 10.1093/oons/kvae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 01/26/2024] [Accepted: 02/26/2024] [Indexed: 04/20/2024]
Abstract
Bipolar disorder (BD) is a severe mental illness that can result from neurodevelopmental aberrations, particularly in familial BD, which may include causative genetic variants. In the present study, we derived cortical organoids from BD patients and healthy (control) individuals from a clinically dense family in the Indian population. Our data reveal that the patient organoids show neurodevelopmental anomalies, including organisational, proliferation and migration defects. The BD organoids show a reduction in both the number of neuroepithelial buds/cortical rosettes and the ventricular zone size. Additionally, patient organoids show a lower number of SOX2-positive and EdU-positive cycling progenitors, suggesting a progenitor proliferation defect. Further, the patient neurons show abnormal positioning in the ventricular/intermediate zone of the neuroepithelial bud. Transcriptomic analysis of control and patient organoids supports our cellular topology data and reveals dysregulation of genes crucial for progenitor proliferation and neuronal migration. Lastly, time-lapse imaging of neural stem cells in 2D in vitro cultures reveals abnormal cellular migration in BD samples. Overall, our study pinpoints a cellular and molecular deficit in BD patient-derived organoids and neural stem cell cultures.
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Affiliation(s)
- Kruttika Phalnikar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - M Srividya
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - S V Mythri
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - N S Vasavi
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Archisha Ganguly
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Aparajita Kumar
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Padmaja S
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Kishan Kalia
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Srishti S Mishra
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Sreeja Kumari Dhanya
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
| | - Pradip Paul
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Bharath Holla
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Suhas Ganesh
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Puli Chandramouli Reddy
- Centre of Excellence in Epigenetics, Department of Life Sciences, Shiv Nadar Institution of Eminence, Delhi-NCR, India-201314
| | - Reeteka Sud
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Biju Viswanath
- National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road Bengaluru, Karnataka, India-560029
| | - Bhavana Muralidharan
- Institute for Stem Cell Science and Regenerative Medicine (inStem), GKVK - Post, Bellary Road, Bengaluru, Karnataka, India-560065
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11
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Holmgren A, Akkouh I, O'Connell KS, Osete JR, Bjørnstad PM, Djurovic S, Hughes T. Bipolar patients display stoichiometric imbalance of gene expression in post-mortem brain samples. Mol Psychiatry 2024; 29:1128-1138. [PMID: 38351171 PMCID: PMC11176081 DOI: 10.1038/s41380-023-02398-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 02/19/2024]
Abstract
Bipolar disorder is a severe neuro-psychiatric condition where genome-wide association and sequencing studies have pointed to dysregulated gene expression as likely to be causal. We observed strong correlation in expression between GWAS-associated genes and hypothesised that healthy function depends on balance in the relative expression levels of the associated genes and that patients display stoichiometric imbalance. We developed a method for quantifying stoichiometric imbalance and used this to predict each sample's diagnosis probability in four cortical brain RNAseq datasets. The percentage of phenotypic variance on the liability-scale explained by these probabilities ranged from 10.0 to 17.4% (AUC: 69.4-76.4%) which is a multiple of the classification performance achieved using absolute expression levels or GWAS-based polygenic risk scores. Most patients display stoichiometric imbalance in three to ten genes, suggesting that dysregulation of only a small fraction of associated genes can trigger the disorder, with the identity of these genes varying between individuals.
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Affiliation(s)
- Asbjørn Holmgren
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ibrahim Akkouh
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kevin Sean O'Connell
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Jordi Requena Osete
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- NORMENT, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Timothy Hughes
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
- Norwegian Centre for Mental Disorders Research, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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12
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Zhou P, Li L, Ming X, Cai W, Hao B, Hu Y, He Z, Chen X. Causal relationship between psychiatric disorders and sensorineural hearing loss: A bidirectional two-sample mendelian randomization analysis. J Psychosom Res 2024; 179:111641. [PMID: 38461621 DOI: 10.1016/j.jpsychores.2024.111641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 02/20/2024] [Accepted: 03/05/2024] [Indexed: 03/12/2024]
Abstract
OBJECTIVE This study employed bidirectional two-sample Mendelian randomization (MR) to investigate the causal links between psychiatric disorders and sensorineural hearing loss (SNHL). METHODS Instrumental variables were chosen from genome-wide association studies of schizophrenia (SCH, N = 127,906), bipolar disorder (BD, N = 51,710), major depressive disorder (MDD, N = 500,199), and SNHL (N = 212,544). In the univariable MR analysis, the inverse-variance weighted method (IVW) was conducted as the primary analysis, complemented by various sensitivity analyses to ensure result robustness. RESULTS SCH exhibited a decreased the risk of SNHL (OR = 0.949, P = 0.005), whereas BD showed an increased incidence of SNHL (OR = 1.145, P = 0.005). No causal association was found for MDD on SNHL (OR = 1.088, P = 0.246). Multivariable MR validated these results. In the reverse direction, genetically predicted SNHL was linked to a decreased risk of SCH with suggestive significance (OR = 0.912, P = 0.023). No reverse causal relationships were observed for SNHL influencing BD or MDD. These findings remained consistent across various MR methods and sensitivity analyses. CONCLUSION This study demonstrated that the causal relationships between diverse psychiatric disorders with SNHL were heterogeneous. Specifically, SCH was inversely associated with SNHL susceptibility, and similarly, a reduced risk of SNHL was observed in schizophrenia patients. In contrast, BD exhibited an increased incidence of SNHL, although SNHL did not influence the prevalence of BD. No causal association between MDD and SNHL was found.
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Affiliation(s)
- Peng Zhou
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China; Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ling Li
- Department of Nuclear Medicine, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China
| | - Xiaoping Ming
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China; Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Wanyue Cai
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China; Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Bin Hao
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China; Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yifan Hu
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China; Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - Zuhong He
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China.
| | - Xiong Chen
- Department of Otorhinolaryngology, Head and Neck Surgery, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, China; Sleep Medicine Centre, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China.
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13
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Lawrence JM, Breunig S, Foote IF, Tallis CB, Grotzinger AD. Genomic SEM applied to explore etiological divergences in bipolar subtypes. Psychol Med 2024; 54:1152-1159. [PMID: 37885278 DOI: 10.1017/s0033291723002957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
BACKGROUND Bipolar disorder (BD) is an overarching diagnostic class defined by the presence of at least one prior manic episode (BD I) or both a prior hypomanic episode and a prior depressive episode (BD II). Traditionally, BD II has been conceptualized as a less severe presentation of BD I, however, extant literature to investigate this claim has been mixed. METHODS We apply genomic structural equation modeling (Genomic SEM) to investigate divergent genetic pathways across BD's two major subtypes using the most recent GWAS summary statistics from the PGC. We begin by identifying divergences in genetic correlations across 98 external traits using a Bonferroni-corrected threshold. We also use a theoretically informed follow-up model to examine the extent to which the genetic variance in each subtype is explained by schizophrenia and major depression. Lastly, transcriptome-wide SEM (T-SEM) was used to identify neuronal gene expression patterns associated with BD subtypes. RESULTS BD II was characterized by significantly larger genetic overlap across non-psychiatric medical and internalizing traits (e.g. heart disease, neuroticism, insomnia), while stronger associations for BD I were absent. Consistent with these findings, follow-up modeling revealed a substantial major depression component for BD II. T-SEM results revealed 35 unique genes associated with shared risk across BD subtypes. CONCLUSIONS Divergent patterns of genetic relationships across external traits provide support for the distinction of the bipolar subtypes. However, our results also challenge the illness severity conceptualization of BD given stronger genetic overlap across BD II and a range of clinically relevant traits and disorders.
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Affiliation(s)
- Jeremy M Lawrence
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Sophie Breunig
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Isabelle F Foote
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Connor B Tallis
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Andrew D Grotzinger
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
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14
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Lu X, Ni P, Suarez-Meade P, Ma Y, Forrest EN, Wang G, Wang Y, Quiñones-Hinojosa A, Gerstein M, Jiang YH. Transcriptional Determinism and Stochasticity Contribute to the Complexity of Autism Associated SHANK Family Genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585480. [PMID: 38562714 PMCID: PMC10983920 DOI: 10.1101/2024.03.18.585480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Precision of transcription is critical because transcriptional dysregulation is disease causing. Traditional methods of transcriptional profiling are inadequate to elucidate the full spectrum of the transcriptome, particularly for longer and less abundant mRNAs. SHANK3 is one of the most common autism causative genes. Twenty-four Shank3 mutant animal lines have been developed for autism modeling. However, their preclinical validity has been questioned due to incomplete Shank3 transcript structure. We applied an integrative approach combining cDNA-capture and long-read sequencing to profile the SHANK3 transcriptome in human and mice. We unexpectedly discovered an extremely complex SHANK3 transcriptome. Specific SHANK3 transcripts were altered in Shank3 mutant mice and postmortem brains tissues from individuals with ASD. The enhanced SHANK3 transcriptome significantly improved the detection rate for potential deleterious variants from genomics studies of neuropsychiatric disorders. Our findings suggest the stochastic transcription of genome associated with SHANK family genes.
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Affiliation(s)
- Xiaona Lu
- Department of Genetics, Yale University School of Medicine New Haven, CT, 06520 USA
| | - Pengyu Ni
- Biomedical Informatics & Data Science, Yale University School of Medicine New Haven, CT, 06520 USA
| | | | - Yu Ma
- Department of Neurology, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | | | - Guilin Wang
- Yale Center for Genome Analysis, Yale University School of Medicine New Haven, CT, 06520 USA
| | - Yi Wang
- Department of Neurology, Children’s Hospital of Fudan University, Shanghai, 201102 China
| | | | - Mark Gerstein
- Biomedical Informatics & Data Science, Yale University School of Medicine New Haven, CT, 06520 USA
- Yale Center for Genome Analysis, Yale University School of Medicine New Haven, CT, 06520 USA
| | - Yong-hui Jiang
- Department of Genetics, Yale University School of Medicine New Haven, CT, 06520 USA
- Neuroscienc, Yale University School of Medicine New Haven, CT, 06520 USA
- Pediatrics, Yale University School of Medicine New Haven, CT, 06520 USA
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15
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Zhang H, Peyton L, McCarroll A, de León Guerrerro SD, Zhang S, Gowda P, Sirkin D, El Achwah M, Duhe A, Wood WG, Jamison B, Tracy G, Pollak R, Hart RP, Pato CN, Mulle JG, Sanders AR, Pang ZP, Duan J. Scaled and Efficient Derivation of Loss of Function Alleles in Risk Genes for Neurodevelopmental and Psychiatric Disorders in Human iPSC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585542. [PMID: 38562852 PMCID: PMC10983959 DOI: 10.1101/2024.03.18.585542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Translating genetic findings for neurodevelopmental and psychiatric disorders (NPD) into actionable disease biology would benefit from large-scale and unbiased functional studies of NPD genes. Leveraging the cytosine base editing (CBE) system, here we developed a pipeline for clonal loss-of-function (LoF) allele mutagenesis in human induced pluripotent stem cells (hiPSCs) by introducing premature stop-codons (iSTOP) that lead to mRNA nonsense-mediated-decay (NMD) or protein truncation. We tested the pipeline for 23 NPD genes on 3 hiPSC lines and achieved highly reproducible, efficient iSTOP editing in 22 NPD genes. Using RNAseq, we confirmed their pluripotency, absence of chromosomal abnormalities, and NMD. Interestingly, for three schizophrenia risk genes (SETD1A, TRIO, CUL1), despite the high efficiency of base editing, we only obtained heterozygous LoF alleles, suggesting their essential roles for cell growth. We replicated the reported neural phenotypes of SHANK3-haploinsufficiency and found CUL1-LoF reduced neurite branches and synaptic puncta density. This iSTOP pipeline enables a scaled and efficient LoF mutagenesis of NPD genes, yielding an invaluable shareable resource.
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Affiliation(s)
- Hanwen Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Lilia Peyton
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Ada McCarroll
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Sol Díaz de León Guerrerro
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Siwei Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL
| | - Prarthana Gowda
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - David Sirkin
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Mahmoud El Achwah
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Alexandra Duhe
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Whitney G Wood
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Brandon Jamison
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Gregory Tracy
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
| | - Rebecca Pollak
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ
| | - Ronald P Hart
- Department of Cell Biology and Neuroscience, Rutgers University
| | - Carlos N Pato
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ
| | - Jennifer G Mulle
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Center for Advanced Biotechnology and Medicine, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ
- Department of Psychiatry, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Alan R Sanders
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL
| | - Zhiping P Pang
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, IL
- Department of Psychiatry and Behavioral Neuroscience, The University of Chicago, Chicago, IL
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16
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Gobeil É, Bourgault J, Mitchell PL, Houessou U, Gagnon E, Girard A, Paulin A, Manikpurage HD, Côté V, Couture C, Marceau S, Bossé Y, Thériault S, Mathieu P, Vohl MC, Tchernof A, Arsenault BJ. Genetic inhibition of angiopoietin-like protein-3, lipids, and cardiometabolic risk. Eur Heart J 2024; 45:707-721. [PMID: 38243829 PMCID: PMC10906986 DOI: 10.1093/eurheartj/ehad845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 10/16/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND AND AIMS RNA-based, antibody-based, and genome editing-based therapies are currently under investigation to determine if the inhibition of angiopoietin-like protein-3 (ANGPTL3) could reduce lipoprotein-lipid levels and atherosclerotic cardiovascular disease (ASCVD) risk. Mendelian randomisation (MR) was used to determine whether genetic variations influencing ANGPTL3 liver gene expression, blood levels, and protein structure could causally influence triglyceride and apolipoprotein B (apoB) levels as well as coronary artery disease (CAD), ischaemic stroke (IS), and other cardiometabolic diseases. METHODS RNA sequencing of 246 explanted liver samples and genome-wide genotyping was performed to identify single-nucleotide polymorphisms (SNPs) associated with liver expression of ANGPTL3. Genome-wide summary statistics of plasma protein levels of ANGPTL3 from the deCODE study (n = 35 359) were used. A total of 647 carriers of ANGPTL3 protein-truncating variants (PTVs) associated with lower plasma triglyceride levels were identified in the UK Biobank. Two-sample MR using SNPs that influence ANGPTL3 liver expression or ANGPTL3 plasma protein levels as exposure and cardiometabolic diseases as outcomes was performed (CAD, IS, heart failure, non-alcoholic fatty liver disease, acute pancreatitis, and type 2 diabetes). The impact of rare PTVs influencing plasma triglyceride levels on apoB levels and CAD was also investigated in the UK Biobank. RESULTS In two-sample MR studies, common genetic variants influencing ANGPTL3 hepatic or blood expression levels of ANGPTL3 had a very strong effect on plasma triglyceride levels, a more modest effect on low-density lipoprotein cholesterol, a weaker effect on apoB levels, and no effect on CAD or other cardiometabolic diseases. In the UK Biobank, the carriers of rare ANGPTL3 PTVs providing lifelong reductions in median plasma triglyceride levels [-0.37 (interquartile range 0.41) mmol/L] had slightly lower apoB levels (-0.06 ± 0.32 g/L) and similar CAD event rates compared with non-carriers (10.2% vs. 10.9% in carriers vs. non-carriers, P = .60). CONCLUSIONS PTVs influencing ANGPTL3 protein structure as well as common genetic variants influencing ANGPTL3 hepatic expression and/or blood protein levels exhibit a strong effect on circulating plasma triglyceride levels, a weak effect on circulating apoB levels, and no effect on ASCVD. Near-complete inhibition of ANGPTL3 function in patients with very elevated apoB levels may be required to reduce ASCVD risk.
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Affiliation(s)
- Émilie Gobeil
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Jérôme Bourgault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Patricia L Mitchell
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Ursula Houessou
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Eloi Gagnon
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Arnaud Girard
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Audrey Paulin
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Hasanga D Manikpurage
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Valérie Côté
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Christian Couture
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
| | - Simon Marceau
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- Department of Surgery, Faculty of Medicine, Université Laval, Québec, Canada
| | - Yohan Bossé
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Québec, Canada
| | - Sébastien Thériault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Université Laval, Québec, Canada
| | - Patrick Mathieu
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- Department of Surgery, Faculty of Medicine, Université Laval, Québec, Canada
| | - Marie-Claude Vohl
- School of Nutrition, Université Laval, Québec, Canada
- Centre Nutrition, santé et société, Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, Canada
| | - André Tchernof
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- School of Nutrition, Université Laval, Québec, Canada
| | - Benoit J Arsenault
- Centre de recherche de l’Institut universitaire de cardiologie et de pneumologie de Québec—Université Laval, 2725 chemin Ste-Foy, Québec, QC G1V 4G5, Canada
- Department of Medicine, Faculty of Medicine, Université Laval, 2325 Rue de l'Université, Québec, QC G1V 0A6, Canada
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17
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Tian R, Ge T, Kweon H, Rocha DB, Lam M, Liu JZ, Singh K, Levey DF, Gelernter J, Stein MB, Tsai EA, Huang H, Chabris CF, Lencz T, Runz H, Chen CY. Whole-exome sequencing in UK Biobank reveals rare genetic architecture for depression. Nat Commun 2024; 15:1755. [PMID: 38409228 PMCID: PMC10897433 DOI: 10.1038/s41467-024-45774-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/02/2024] [Indexed: 02/28/2024] Open
Abstract
Nearly two hundred common-variant depression risk loci have been identified by genome-wide association studies (GWAS). However, the impact of rare coding variants on depression remains poorly understood. Here, we present whole-exome sequencing analyses of depression with seven different definitions based on survey, questionnaire, and electronic health records in 320,356 UK Biobank participants. We showed that the burden of rare damaging coding variants in loss-of-function intolerant genes is significantly associated with risk of depression with various definitions. We compared the rare and common genetic architecture across depression definitions by genetic correlation and showed different genetic relationships between definitions across common and rare variants. In addition, we demonstrated that the effects of rare damaging coding variant burden and polygenic risk score on depression risk are additive. The gene set burden analyses revealed overlapping rare genetic variant components with developmental disorder, autism, and schizophrenia. Our study provides insights into the contribution of rare coding variants, separately and in conjunction with common variants, on depression with various definitions and their genetic relationships with neurodevelopmental disorders.
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Affiliation(s)
- Ruoyu Tian
- Biogen Inc, Cambridge, MA, USA
- Dewpoint Therapeutics, Boston, MA, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hyeokmoon Kweon
- Department of Economics, School of Business and Economics, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Autism & Developmental Medicine Institute, Geisinger Health System, Lewisburg, PA, USA
| | - Daniel B Rocha
- Phenomics Analytics and Clinical Data Core, Geisinger Health System, Danville, PA, USA
| | - Max Lam
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- North Region, Institute of Mental Health, Singapore, Singapore
| | - Jimmy Z Liu
- Biogen Inc, Cambridge, MA, USA
- GlaxoSmithKline, Upper Providence, Philadelphia, PA, USA
| | - Kritika Singh
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Daniel F Levey
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare Center, West Haven, CT, USA
| | - Joel Gelernter
- VA Connecticut Healthcare Center, West Haven, CT, USA
- Departments of Psychiatry, Genetics, and Neuroscience, Yale University School of Medicine, New Haven, CT, USA
| | - Murray B Stein
- VA San Diego Healthcare System, San Diego, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Hailiang Huang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Christopher F Chabris
- Autism & Developmental Medicine Institute, Geisinger Health System, Lewisburg, PA, USA
| | - Todd Lencz
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
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18
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Koromina M, Ravi A, Panagiotaropoulou G, Schilder BM, Humphrey J, Braun A, Bidgeli T, Chatzinakos C, Coombes B, Kim J, Liu X, Terao C, O.’Connell KS, Adams M, Adolfsson R, Alda M, Alfredsson L, Andlauer TFM, Andreassen OA, Antoniou A, Baune BT, Bengesser S, Biernacka J, Boehnke M, Bosch R, Cairns M, Carr VJ, Casas M, Catts S, Cichon S, Corvin A, Craddock N, Dafnas K, Dalkner N, Dannlowski U, Degenhardt F, Di Florio A, Dikeos D, Fellendorf FT, Ferentinos P, Forstner AJ, Forty L, Frye M, Fullerton JM, Gawlik M, Gizer IR, Gordon-Smith K, Green MJ, Grigoroiu-Serbanescu M, Guzman-Parra J, Hahn T, Henskens F, Hillert J, Jablensky AV, Jones L, Jones I, Jonsson L, Kelsoe JR, Kircher T, Kirov G, Kittel-Schneider S, Kogevinas M, Landén M, Leboyer M, Lenger M, Lissowska J, Lochner C, Loughland C, MacIntyre D, Martin NG, Maratou E, Mathews CA, Mayoral F, McElroy SL, McGregor NW, McIntosh A, McQuillin A, Michie P, Milanova V, Mitchell PB, Moutsatsou P, Mowry B, Müller-Myhsok B, Myers R, Nenadić I, Nöthen MM, O’Donovan C, O’Donovan M, Ophoff RA, Owen MJ, Pantelis C, Pato C, Pato MT, Patrinos GP, Pawlak JM, Perlis RH, Porichi E, Posthuma D, Ramos-Quiroga JA, Reif A, Reininghaus EZ, Ribasés M, Rietschel M, Schall U, Schulze TG, Scott L, Scott RJ, Serretti A, Weickert CS, Smoller JW, Artigas MS, Stein DJ, Streit F, Toma C, Tooney P, Vieta E, Vincent JB, Waldman ID, Weickert T, Witt SH, Hong KS, Ikeda M, Iwata N, Świątkowska B, Won HH, Edenberg HJ, Ripke S, Raj T, Coleman JRI, Mullins N. Fine-mapping genomic loci refines bipolar disorder risk genes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.12.24302716. [PMID: 38405768 PMCID: PMC10889003 DOI: 10.1101/2024.02.12.24302716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Bipolar disorder (BD) is a heritable mental illness with complex etiology. While the largest published genome-wide association study identified 64 BD risk loci, the causal SNPs and genes within these loci remain unknown. We applied a suite of statistical and functional fine-mapping methods to these loci, and prioritized 22 likely causal SNPs for BD. We mapped these SNPs to genes, and investigated their likely functional consequences by integrating variant annotations, brain cell-type epigenomic annotations, brain quantitative trait loci, and results from rare variant exome sequencing in BD. Convergent lines of evidence supported the roles of SCN2A, TRANK1, DCLK3, INSYN2B, SYNE1, THSD7A, CACNA1B, TUBBP5, PLCB3, PRDX5, KCNK4, AP001453.3, TRPT1, FKBP2, DNAJC4, RASGRP1, FURIN, FES, YWHAE, DPH1, GSDMB, MED24, THRA, EEF1A2, and KCNQ2 in BD. These represent promising candidates for functional experiments to understand biological mechanisms and therapeutic potential. Additionally, we demonstrated that fine-mapping effect sizes can improve performance and transferability of BD polygenic risk scores across ancestrally diverse populations, and present a high-throughput fine-mapping pipeline (https://github.com/mkoromina/SAFFARI).
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Affiliation(s)
- Maria Koromina
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ashvin Ravi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Brian M. Schilder
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alice Braun
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin, Berlin, Germany
| | | | | | - Brandon Coombes
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Jaeyoung Kim
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kevin S. O.’Connell
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- NORMENT, University of Oslo, Oslo, Norway
| | - Mark Adams
- Division of Psychiatry, Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Rolf Adolfsson
- Department of Clinical Sciences, Psychiatry, Umeå, University Medical Faculty, Umeå, Sweden
| | - Martin Alda
- Department 20 of Psychiatry, Dalhousie University, Halifax, NS, Canada
- National Institute of Mental Health, Klecany, Czech Republic
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Till F. M. Andlauer
- Department of Neurology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Ole A. Andreassen
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
- NORMENT, University of Oslo, Oslo, Norway
| | - Anastasia Antoniou
- National Kapodistrian University of Athens, 2nd Department of Psychiatry, Attikon General Hospital, Athens, Greece
| | - Bernhard T. Baune
- Department of Psychiatry, University of Münster, Münster, Germany
- Department of Psychiatry, Melbourne Medical School, The University of Melbourne, Melbourne, VIC, Australia
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Susanne Bengesser
- Medical University of Graz, Division of Psychiatry and Psychotherapeutic Medicine, Graz, Austria
| | - Joanna Biernacka
- Department of Quantitative Health Sciences Research, Mayo Clinic, Rochester, MN, USA
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Michael Boehnke
- Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | - Rosa Bosch
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Programa SJD MIND Escoles, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | | | - Vaughan J. Carr
- School of Clinical Medicine, Discipline of Psychiatry and Mental Health, University of New South Wales, Sydney, NSW, Australia
| | - Miquel Casas
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Programa SJD MIND Escoles, Hospital Sant Joan de Déu, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Spain
| | | | - Sven Cichon
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
| | - Aiden Corvin
- Neuropsychiatric Genetics Research Group, Dept of Psychiatry and Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Nicholas Craddock
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Konstantinos Dafnas
- National Kapodistrian University of Athens, 2nd Department of Psychiatry, Attikon General Hospital, Athens, Greece
| | - Nina Dalkner
- Medical University of Graz, Division of Psychiatry and Psychotherapeutic Medicine, Graz, Austria
| | - Udo Dannlowski
- Institute for Translatiol Psychiatry, University of Münster, Münster, Germany
| | - Franziska Degenhardt
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Duisburg, Germany
| | - Arianna Di Florio
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
- Department of Psychiatry, University of North Caroli at Chapel Hill, Chapel Hill, NC, USA
| | - Dimitris Dikeos
- National Kapodistrian University of Athens, 2nd Department of Psychiatry, Attikon General Hospital, Athens, Greece
| | | | - Panagiotis Ferentinos
- National Kapodistrian University of Athens, 2nd Department of Psychiatry, Attikon General Hospital, Athens, Greece
- Social, Genetic and Developmental Psychiatry Centre, King’s College London, London, UK
| | - Andreas J. Forstner
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich, Germany
- Centre for Human Genetics, University of Marburg, Marburg, Germany
| | - Liz Forty
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Mark Frye
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA
| | - Janice M. Fullerton
- Neuroscience Research Australia, Sydney, NSW, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Micha Gawlik
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital Würzburg, Würzburg, Germany
| | - Ian R. Gizer
- Department of Psychological Sciences, University of Missouri, Columbia, MO, USA
| | | | - Melissa J. Green
- Neuroscience Research Australia, Sydney, NSW, Australia
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Maria Grigoroiu-Serbanescu
- Biometric Psychiatric Genetics Research Unit, Alexandru Obregia Clinical Psychiatric Hospital, Bucharest, Romania
| | - José Guzman-Parra
- Mental Health Department, University Regional Hospital, Biomedicine Institute (IBIMA), Málaga, Spain
| | - Tim Hahn
- Institute for Translatiol Psychiatry, University of Münster, Münster, Germany
| | | | - Jan Hillert
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Lisa Jones
- Psychological Medicine, University of Worcester, Worcester, UK
| | - Ian Jones
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Lina Jonsson
- Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - John R. Kelsoe
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Tilo Kircher
- Department of Psychiatry and Psychotherapy, University of Marburg, Germany
| | - George Kirov
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Sarah Kittel-Schneider
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University Hospital Würzburg, Würzburg, Germany
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Frankfurt am Main, Germany
- Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | | | - Mikael Landén
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Marion Leboyer
- Université Paris Est Créteil, INSERM, IMRB, Translational Neuropsychiatry, Créteil, France
- Department of Psychiatry and Addiction Medicine, Assistance Publique - Hôpitaux de Paris, Paris, France
| | - Melanie Lenger
- Medical University of Graz, Division of Psychiatry and Psychotherapeutic Medicine, Graz, Austria
| | - Jolanta Lissowska
- Cancer Epidemiology and Prevention, M. Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Christine Lochner
- SA MRC Unit on Risk and Resilience in Mental Disorders, Dept of Psychiatry, Stellenbosch University, Stellenbosch, South Africa
| | | | - Donald MacIntyre
- Division of Psychiatry, Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Nicholas G. Martin
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Psychology, The University of Queensland, Brisbane, QLD, Australia
| | - Eirini Maratou
- National and Kapodistrian University of Athens, Medical School, Clinical Biochemistry Laboratory, Attikon General Hospital, Athens, Greece
| | - Carol A. Mathews
- Department of Psychiatry and Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Fermin Mayoral
- Mental Health Department, University Regional Hospital, Biomedicine Institute (IBIMA), Málaga, Spain
| | | | - Nathaniel W. McGregor
- Systems Genetics Working Group, Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Andrew McIntosh
- Division of Psychiatry, Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | | | | | - Vihra Milanova
- Psychiatric Clinic, Alexander University Hospital, Bulgaria
| | - Philip B. Mitchell
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
| | - Paraskevi Moutsatsou
- National Kapodistrian University of Athens, Medical School, Clinical Biochemistry Laboratory, Attikon General Hospital, Athens, Greece
| | - Bryan Mowry
- University of Queensland, Brisbane, QLD, Australia
| | - Bertram Müller-Myhsok
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Richard Myers
- Hudsolpha Institute for Biotechnology, Huntsville, AL, USA
| | - Igor Nenadić
- Department of Psychiatry and Psychotherapy, University of Marburg, Marburg, Germany
- Center for Mind, Brain and Behavior (CMBB), University of Marburg and Justus Liebig University Giessen, Giessen, Germany
| | - Markus M. Nöthen
- Institute of Human Genetics, University of Bonn, School of Medicine and University Hospital Bonn, Bonn, Germany
| | - Claire O’Donovan
- Department 20 of Psychiatry, Dalhousie University, Halifax, NS, Canada
| | - Michael O’Donovan
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Roel A. Ophoff
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Psychiatry and Biobehavioral Science, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael J Owen
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | | | - Carlos Pato
- Institute for Genomic Health, SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
| | - Michele T. Pato
- Institute for Genomic Health, SUNY Downstate Medical Center College of Medicine, Brooklyn, NY, USA
| | - George P. Patrinos
- University of Patras, School of Health Sciences, Department of Pharmacy, Laboratory of Pharmacogenomics and Individualized Therapy, Patras, Greece
- United Arab Emirates University, College of Medicine and Health Sciences, Department of Genetics and Genomics, Al-Ain, United Arab Emirates
- United Arab Emirates University, Zayed Center for Health Sciences, Al-Ain, United Arab Emirates
| | - Joanna M. Pawlak
- Department of Psychiatry, Departmet of Psychiatric Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Roy H. Perlis
- Psychiatry, Harvard Medical School, Boston, MA, USA
- Division of Clinical Research, Massachusetts General Hospital, Boston, MA, USA
| | - Evgenia Porichi
- National and Kapodistrian University of Athens, 2nd Department of Psychiatry, Attikon General Hospital, Athens, Greece
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | - Josep Antoni Ramos-Quiroga
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d´Hebron, Barcelo, Spain
- Department of Psychiatry and Forensic Medicine, Universitat Autònoma de Barcelo, Barcelo, Spain
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addictions, Vall d´Hebron Research Institut (VHIR), Universitat Autònoma de Barcelo, Barcelo, Spain
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Eva Z. Reininghaus
- Medical University of Graz, Division of Psychiatry and Psychotherapeutic Medicine, Graz, Austria
| | - Marta Ribasés
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d´Hebron, Barcelona, Spain
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addictions, Vall d´Hebron Research Institut (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain. Department of Genetics, Microbiology and Statistics, Faculty of Biology, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Thomas G. Schulze
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Laura Scott
- Center for Statistical Genetics and Department of Biostatistics, University of Michigan, Ann Arbor, MI, USA
| | | | - Alessandro Serretti
- Department of Biomedical and NeuroMotor Sciences, University of Bologna, Bologna, Italy
| | - Cynthia Shannon Weickert
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Department of Neuroscience, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Jordan W. Smoller
- Stanley Center for Psychiatric Research, Broad Institute, Cambridge, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit (PNGU), Massachusetts General Hospital, Boston, MA, USA
| | - Maria Soler Artigas
- Instituto de Salud Carlos III, Biomedical Network Research Centre on Mental Health (CIBERSAM), Madrid, Spain
- Department of Psychiatry, Hospital Universitari Vall d´Hebron, Barcelo, Spain
- Psychiatric Genetics Unit, Group of Psychiatry Mental Health and Addictions, Vall d´Hebron Research Institut (VHIR), Universitat Autònoma de Barcelo, Barcelo, Spain
- Department of Genetics, Microbiology, and Statistics, Faculty of Biology, Universitat de Barcelo, Barcelo, Spain
| | - Dan J. Stein
- SAMRC Unit on Risk and Resilience in Mental Disorders, Dept of Psychiatry and Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Claudio Toma
- Neuroscience Research Australia, Sydney, NSW, Australia
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid and CSIC, Madrid, Spain
| | - Paul Tooney
- University of Newcastle, Newcastle, NSW, Australia
| | - Eduard Vieta
- Clinical Institute of Neuroscience, Hospital Clinic, University of Barcelona, IDIBAPS, CIBERSAM, Barcelona, Spain
| | - John B. Vincent
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | | | - Thomas Weickert
- Discipline of Psychiatry and Mental Health, School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia
- Department of Neuroscience, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Stephanie H. Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kyung Sue Hong
- Department of Psychiatry, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, South Korea
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Beata Świątkowska
- Department of Environmental Epidemiology, Nofer Institute of Occupational Medicine, Lodz, Poland
| | - Hong-Hee Won
- Samsung Advanced Institute for Health Sciences and Technology (SAIHST), Sungkyunkwan University, Samsung Medical Center, Seoul, Republic of Korea
| | - Howard J. Edenberg
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, IN, USA
| | - Stephan Ripke
- Department of Psychiatry and Psychotherapy, Charité - Universitätsmedizin, Berlin, Germany
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Towfique Raj
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jonathan R. I. Coleman
- Social, Genetic and Developmental Psychiatry Centre, King’s College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Foundation Trust, London, UK
| | - Niamh Mullins
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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19
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Veeraraghavan P, Engmann AK, Hatch JJ, Itoh Y, Nguyen D, Addison T, Macklis JD. Dynamic subtype- and context-specific subcellular RNA regulation in growth cones of developing neurons of the cerebral cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.24.559186. [PMID: 38328182 PMCID: PMC10849483 DOI: 10.1101/2023.09.24.559186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Molecular mechanisms that cells employ to compartmentalize function via localization of function-specific RNA and translation are only partially elucidated. We investigate long-range projection neurons of the cerebral cortex as highly polarized exemplars to elucidate dynamic regulation of RNA localization, stability, and translation within growth cones (GCs), leading tips of growing axons. Comparison of GC-localized transcriptomes between two distinct subtypes of projection neurons- interhemispheric-callosal and corticothalamic- across developmental stages identifies both distinct and shared subcellular machinery, and intriguingly highlights enrichment of genes associated with neurodevelopmental and neuropsychiatric disorders. Developmental context-specific components of GC-localized transcriptomes identify known and novel potential regulators of distinct phases of circuit formation: long-distance growth, target area innervation, and synapse formation. Further, we investigate mechanisms by which transcripts are enriched and dynamically regulated in GCs, and identify GC-enriched motifs in 3' untranslated regions. As one example, we identify cytoplasmic adenylation element binding protein 4 (CPEB4), an RNA binding protein regulating localization and translation of mRNAs encoding molecular machinery important for axonal branching and complexity. We also identify RNA binding motif single stranded interacting protein 1 (RBMS1) as a dynamically expressed regulator of RNA stabilization that enables successful callosal circuit formation. Subtly aberrant associative and integrative cortical circuitry can profoundly affect cortical function, often causing neurodevelopmental and neuropsychiatric disorders. Elucidation of context-specific subcellular RNA regulation for GC- and soma-localized molecular controls over precise circuit development, maintenance, and function offers generalizable insights for other polarized cells, and might contribute substantially to understanding neurodevelopmental and behavioral-cognitive disorders and toward targeted therapeutics.
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Affiliation(s)
- Priya Veeraraghavan
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Anne K. Engmann
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - John J. Hatch
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Yasuhiro Itoh
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Duane Nguyen
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Thomas Addison
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Jeffrey D. Macklis
- Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA, USA
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20
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Peall KJ, Owen MJ, Hall J. Rare genetic brain disorders with overlapping neurological and psychiatric phenotypes. Nat Rev Neurol 2024; 20:7-21. [PMID: 38001363 DOI: 10.1038/s41582-023-00896-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2023] [Indexed: 11/26/2023]
Abstract
Understanding rare genetic brain disorders with overlapping neurological and psychiatric phenotypes is of increasing importance given the potential for developing disease models that could help to understand more common, polygenic disorders. However, the traditional clinical boundaries between neurology and psychiatry result in frequent segregation of these disorders into distinct silos, limiting cross-specialty understanding that could facilitate clinical and biological advances. In this Review, we highlight multiple genetic brain disorders in which neurological and psychiatric phenotypes are observed, but for which in-depth, cross-spectrum clinical phenotyping is rarely undertaken. We describe the combined phenotypes observed in association with genetic variants linked to epilepsy, dystonia, autism spectrum disorder and schizophrenia. We also consider common underlying mechanisms that centre on synaptic plasticity, including changes to synaptic and neuronal structure, calcium handling and the balance of excitatory and inhibitory neuronal activity. Further investigation is needed to better define and replicate these phenotypes in larger cohorts, which would help to gain greater understanding of the pathophysiological mechanisms and identify common therapeutic targets.
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Affiliation(s)
- Kathryn J Peall
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK.
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK.
| | - Michael J Owen
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
- Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Jeremy Hall
- Neuroscience and Mental Health Innovation Institute, Cardiff University, Cardiff, UK
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
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21
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Shapiro B, Fang Y, Sen S, Forger D. Unraveling the interplay of circadian rhythm and sleep deprivation on mood: A Real-World Study on first-year physicians. PLOS DIGITAL HEALTH 2024; 3:e0000439. [PMID: 38295082 PMCID: PMC10829990 DOI: 10.1371/journal.pdig.0000439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 12/25/2023] [Indexed: 02/02/2024]
Abstract
The interplay between circadian rhythms, time awake, and mood remains poorly understood in the real-world. Individuals in high-stress occupations with irregular schedules or nighttime shifts are particularly vulnerable to depression and other mood disorders. Advances in wearable technology have provided the opportunity to study these interactions outside of a controlled laboratory environment. Here, we examine the effects of circadian rhythms and time awake on mood in first-year physicians using wearables. Continuous heart rate, step count, sleep data, and daily mood scores were collected from 2,602 medical interns across 168,311 days of Fitbit data. Circadian time and time awake were extracted from minute-by-minute wearable heart rate and motion measurements. Linear mixed modeling determined the relationship between mood, circadian rhythm, and time awake. In this cohort, mood was modulated by circadian timekeeping (p<0.001). Furthermore, we show that increasing time awake both deteriorates mood (p<0.001) and amplifies mood's circadian rhythm nonlinearly. These findings demonstrate the contributions of both circadian rhythms and sleep deprivation to underlying mood and show how these factors can be studied in real-world settings using Fitbits. They underscore the promising opportunity to harness wearables in deploying chronotherapies for psychiatric illness.
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Affiliation(s)
- Benjamin Shapiro
- Department of Psychiatry, Dartmouth Health, Hanover, New Hampshire, United States of America
- Dartmouth College Geisel School of Medicine, Hanover, New Hampshire, United States of America
| | - Yu Fang
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Srijan Sen
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Daniel Forger
- Department of Mathematics, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
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22
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Panoyan MA, Wendt FR. The role of tandem repeat expansions in brain disorders. Emerg Top Life Sci 2023; 7:249-263. [PMID: 37401564 DOI: 10.1042/etls20230022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/05/2023] [Accepted: 06/19/2023] [Indexed: 07/05/2023]
Abstract
The human genome contains numerous genetic polymorphisms contributing to different health and disease outcomes. Tandem repeat (TR) loci are highly polymorphic yet under-investigated in large genomic studies, which has prompted research efforts to identify novel variations and gain a deeper understanding of their role in human biology and disease outcomes. We summarize the current understanding of TRs and their implications for human health and disease, including an overview of the challenges encountered when conducting TR analyses and potential solutions to overcome these challenges. By shedding light on these issues, this article aims to contribute to a better understanding of the impact of TRs on the development of new disease treatments.
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Affiliation(s)
- Mary Anne Panoyan
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
| | - Frank R Wendt
- Department of Anthropology, University of Toronto, Mississauga, ON, Canada
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
- Forensic Science Program, University of Toronto, Mississauga, ON, Canada
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23
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Heberle BA, Brandon JA, Page ML, Nations KA, Dikobe KI, White BJ, Gordon LA, Fox GA, Wadsworth ME, Doyle PH, Williams BA, Fox EJ, Shantaraman A, Ryten M, Goodwin S, Ghiban E, Wappel R, Mavruk-Eskipehlivan S, Miller JB, Seyfried NT, Nelson PT, Fryer JD, Ebbert MTW. Using deep long-read RNAseq in Alzheimer's disease brain to assess medical relevance of RNA isoform diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552162. [PMID: 37609156 PMCID: PMC10441303 DOI: 10.1101/2023.08.06.552162] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Due to alternative splicing, human protein-coding genes average over eight RNA isoforms, resulting in nearly four distinct protein coding sequences per gene. Long-read RNAseq (IsoSeq) enables more accurate quantification of isoforms, shedding light on their specific roles. To assess the medical relevance of measuring RNA isoform expression, we sequenced 12 aged human frontal cortices (6 Alzheimer's disease cases and 6 controls; 50% female) using one Oxford Nanopore PromethION flow cell per sample. Our study uncovered 53 new high-confidence RNA isoforms in medically relevant genes, including several where the new isoform was one of the most highly expressed for that gene. Specific examples include WDR4 (61%; microcephaly), MYL3 (44%; hypertrophic cardiomyopathy), and MTHFS (25%; major depression, schizophrenia, bipolar disorder). Other notable genes with new high-confidence isoforms include CPLX2 (10%; schizophrenia, epilepsy) and MAOB (9%; targeted for Parkinson's disease treatment). We identified 1,917 medically relevant genes expressing multiple isoforms in human frontal cortex, where 1,018 had multiple isoforms with different protein coding sequences, demonstrating the need to better understand how individual isoforms from a single gene body are involved in human health and disease, if at all. Exactly 98 of the 1,917 genes are implicated in brain-related diseases, including Alzheimer's disease genes such as APP (Aβ precursor protein; five), MAPT (tau protein; four), and BIN1 (eight). As proof of concept, we also found 99 differentially expressed RNA isoforms between Alzheimer's cases and controls, despite the genes themselves not exhibiting differential expression. Our findings highlight the significant knowledge gaps in RNA isoform diversity and their medical relevance. Deep long-read RNA sequencing will be necessary going forward to fully comprehend the medical relevance of individual isoforms for a "single" gene.
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Affiliation(s)
- Bernardo Aguzzoli Heberle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | | | - Madeline L. Page
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Kayla A. Nations
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Ketsile I. Dikobe
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Brendan J. White
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Lacey A. Gordon
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Grant A. Fox
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Mark E. Wadsworth
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - Patricia H. Doyle
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
| | - Brittney A. Williams
- Department of Pharmacology and Nutritional Sciences, College of Medicine, University of Kentucky, Lexington, KY
| | - Edward J. Fox
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | | | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Elena Ghiban
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Robert Wappel
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | | | - Justin B. Miller
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
- Department of Pathology and Laboratory Medicine, University of Kentucky, Lexington, KY, USA
- Microbiology, Immunology and Molecular Genetics, College of Medicine, University of Kentucky, Lexington, KY, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, USA
| | - Peter T. Nelson
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
| | - John D. Fryer
- Department of Neuroscience, Mayo Clinic, Scottsdale, Arizona
| | - Mark T. W. Ebbert
- Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY
- Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY
- Division of Biomedical Informatics, Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY
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24
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Scott MR, McClung CA. Bipolar Disorder. Curr Opin Neurobiol 2023; 83:102801. [PMID: 38223491 PMCID: PMC10786345 DOI: 10.1016/j.conb.2023.102801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
This review focuses on recent advances made towards understanding the neurobiology of bipolar disorder (BD), a chronic neuropsychiatric illness characterized by altered mood and energy states. The past few years have seen the completion of the largest genetic studies by far, which have emphasized the polygenic nature of BD as well as it's connection to other psychiatric illnesses. Furthermore, the use of inducible pluripotent stem cells has rapidly expanded. These studies support previous work that implicates dysregulation of neurodevelopment, mitochondria, and calcium homeostasis, while also allowing for investigation into the underlying mechanisms of individual responsivity to lithium. Sleep and circadian rhythms have also been heavily implicated in BD, from disruptions in activity patterns to molecular abnormalities.
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Affiliation(s)
- Madeline R Scott
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Colleen A McClung
- Translational Neuroscience Program, Department of Psychiatry, Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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25
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Zhu W, Yuan N, Wan C, Huang M, Fang S, Chen M, Chen J, Ma Q, Chen J. Mapping the scientific research on bipolar disorder: A scientometric study of hotspots, bursts, and trends. J Affect Disord 2023; 340:626-638. [PMID: 37595897 DOI: 10.1016/j.jad.2023.08.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
Bipolar disorder (BD) is a severe psychiatric illness with an increasing prevalence worldwide. Although the pathological mechanism of and pharmacological interventions for BD have been extensively investigated in preclinical and clinical studies, a scientometric analysis of the developmental trends, interdisciplinary frontiers, and research hotspots in this field has not yet been conducted. Therefore, we performed a comprehensive scientometric review of 55,358 published studies on BD over the past two decades (2002-2021) to identify the most frequently used keywords and explore research hotspots and trajectories. The present findings revealed the main distribution, knowledge structure, topic evolution, and emerging topics of BD research. Analysing the risk factors, pathogenesis, key brain regions, comorbid conditions, and treatment strategies for BD contributed to understanding of the aetiology, progression, and treatment of this disorder. These findings provided substantial support for continued research in this area.
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Affiliation(s)
- Wenjun Zhu
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China
| | - Naijun Yuan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China; Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, Shenzhen, Guangdong 518020, PR China; Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou 510632, PR China
| | - Chunmiao Wan
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China
| | - Minyi Huang
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China
| | - Shaoyi Fang
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China
| | - Man Chen
- College of Basic Medicine, Hubei University of Chinese Medicine, Wuhan, Hubei 430065, PR China
| | - Jianbei Chen
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, PR China
| | - Qingyu Ma
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China.
| | - Jiaxu Chen
- Guangzhou Key Laboratory of Formula-Pattern of Traditional Chinese Medicine, Formula-Pattern Research Center, School of Traditional Chinese Medicine, Jinan University, Guangzhou 510632, PR China; School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, PR China.
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26
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Kaiser J, Nay K, Horne CR, McAloon LM, Fuller OK, Muller AG, Whyte DG, Means AR, Walder K, Berk M, Hannan AJ, Murphy JM, Febbraio MA, Gundlach AL, Scott JW. CaMKK2 as an emerging treatment target for bipolar disorder. Mol Psychiatry 2023; 28:4500-4511. [PMID: 37730845 PMCID: PMC10914626 DOI: 10.1038/s41380-023-02260-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 09/22/2023]
Abstract
Current pharmacological treatments for bipolar disorder are inadequate and based on serendipitously discovered drugs often with limited efficacy, burdensome side-effects, and unclear mechanisms of action. Advances in drug development for the treatment of bipolar disorder remain incremental and have come largely from repurposing drugs used for other psychiatric conditions, a strategy that has failed to find truly revolutionary therapies, as it does not target the mood instability that characterises the condition. The lack of therapeutic innovation in the bipolar disorder field is largely due to a poor understanding of the underlying disease mechanisms and the consequent absence of validated drug targets. A compelling new treatment target is the Ca2+-calmodulin dependent protein kinase kinase-2 (CaMKK2) enzyme. CaMKK2 is highly enriched in brain neurons and regulates energy metabolism and neuronal processes that underpin higher order functions such as long-term memory, mood, and other affective functions. Loss-of-function polymorphisms and a rare missense mutation in human CAMKK2 are associated with bipolar disorder, and genetic deletion of Camkk2 in mice causes bipolar-like behaviours similar to those in patients. Furthermore, these behaviours are ameliorated by lithium, which increases CaMKK2 activity. In this review, we discuss multiple convergent lines of evidence that support targeting of CaMKK2 as a new treatment strategy for bipolar disorder.
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Affiliation(s)
- Jacqueline Kaiser
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- School of Behavioural and Health Sciences, Australian Catholic University, Fitzroy, VIC, 3065, Australia
| | - Kevin Nay
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
| | - Christopher R Horne
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Luke M McAloon
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- School of Behavioural and Health Sciences, Australian Catholic University, Fitzroy, VIC, 3065, Australia
| | - Oliver K Fuller
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
| | - Abbey G Muller
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
| | - Douglas G Whyte
- School of Behavioural and Health Sciences, Australian Catholic University, Fitzroy, VIC, 3065, Australia
| | - Anthony R Means
- Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ken Walder
- The Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, 3220, Australia
| | - Michael Berk
- The Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, VIC, 3220, Australia
- Orygen, The National Centre of Excellence in Youth Mental Health, Parkville, VIC, 3052, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Anthony J Hannan
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - James M Murphy
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - Mark A Febbraio
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
| | - Andrew L Gundlach
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia
- Department of Anatomy and Physiology, The University of Melbourne, Parkville, VIC, 3052, Australia
| | - John W Scott
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, VIC, 3052, Australia.
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia.
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, 3052, Australia.
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27
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Farsi Z, Nicolella A, Simmons SK, Aryal S, Shepard N, Brenner K, Lin S, Herzog L, Moran SP, Stalnaker KJ, Shin W, Gazestani V, Song BJ, Bonanno K, Keshishian H, Carr SA, Pan JQ, Macosko EZ, Datta SR, Dejanovic B, Kim E, Levin JZ, Sheng M. Brain-region-specific changes in neurons and glia and dysregulation of dopamine signaling in Grin2a mutant mice. Neuron 2023; 111:3378-3396.e9. [PMID: 37657442 DOI: 10.1016/j.neuron.2023.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 05/19/2023] [Accepted: 08/04/2023] [Indexed: 09/03/2023]
Abstract
A genetically valid animal model could transform our understanding of schizophrenia (SCZ) disease mechanisms. Rare heterozygous loss-of-function (LoF) mutations in GRIN2A, encoding a subunit of the NMDA receptor, greatly increase the risk of SCZ. By transcriptomic, proteomic, and behavioral analyses, we report that heterozygous Grin2a mutant mice show (1) large-scale gene expression changes across multiple brain regions and in neuronal (excitatory and inhibitory) and non-neuronal cells (astrocytes and oligodendrocytes), (2) evidence of hypoactivity in the prefrontal cortex (PFC) and hyperactivity in the hippocampus and striatum, (3) an elevated dopamine signaling in the striatum and hypersensitivity to amphetamine-induced hyperlocomotion (AIH), (4) altered cholesterol biosynthesis in astrocytes, (5) a reduction in glutamatergic receptor signaling proteins in the synapse, and (6) an aberrant locomotor pattern opposite of that induced by antipsychotic drugs. These findings reveal potential pathophysiologic mechanisms, provide support for both the "hypo-glutamate" and "hyper-dopamine" hypotheses of SCZ, and underscore the utility of Grin2a-deficient mice as a genetic model of SCZ.
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Affiliation(s)
- Zohreh Farsi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Ally Nicolella
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean K Simmons
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sameer Aryal
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nate Shepard
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kira Brenner
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sherry Lin
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Linnea Herzog
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean P Moran
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine J Stalnaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wangyong Shin
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, South Korea
| | - Vahid Gazestani
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bryan J Song
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kevin Bonanno
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hasmik Keshishian
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Steven A Carr
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Evan Z Macosko
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts General Hospital, Department of Psychiatry, Boston, MA, USA
| | | | - Borislav Dejanovic
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eunjoon Kim
- Center for Synaptic Brain Dysfunctions, Institute for Basic Science, Daejeon, South Korea; Department of Biological Sciences, Korea Advanced Institute for Science and Technology, Daejeon, South Korea
| | - Joshua Z Levin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Morgan Sheng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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28
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Patowary A, Zhang P, Jops C, Vuong CK, Ge X, Hou K, Kim M, Gong N, Margolis M, Vo D, Wang X, Liu C, Pasaniuc B, Li JJ, Gandal MJ, de la Torre-Ubieta L. Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.25.534016. [PMID: 36993726 PMCID: PMC10055310 DOI: 10.1101/2023.03.25.534016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
RNA splicing is highly prevalent in the brain and has strong links to neuropsychiatric disorders, yet the role of cell-type-specific splicing or transcript-isoform diversity during human brain development has not been systematically investigated. Here, we leveraged single-molecule long-read sequencing to deeply profile the full-length transcriptome of the germinal zone (GZ) and cortical plate (CP) regions of the developing human neocortex at tissue and single-cell resolution. We identified 214,516 unique isoforms, of which 72.6% are novel (unannotated in Gencode-v33), and uncovered a substantial contribution of transcript-isoform diversity, regulated by RNA binding proteins, in defining cellular identity in the developing neocortex. We leveraged this comprehensive isoform-centric gene annotation to re-prioritize thousands of rare de novo risk variants and elucidate genetic risk mechanisms for neuropsychiatric disorders. One-Sentence Summary A cell-specific atlas of gene isoform expression helps shape our understanding of brain development and disease. Structured Abstract INTRODUCTION: The development of the human brain is regulated by precise molecular and genetic mechanisms driving spatio-temporal and cell-type-specific transcript expression programs. Alternative splicing, a major mechanism increasing transcript diversity, is highly prevalent in the human brain, influences many aspects of brain development, and has strong links to neuropsychiatric disorders. Despite this, the cell-type-specific transcript-isoform diversity of the developing human brain has not been systematically investigated.RATIONALE: Understanding splicing patterns and isoform diversity across the developing neocortex has translational relevance and can elucidate genetic risk mechanisms in neurodevelopmental disorders. However, short-read sequencing, the prevalent technology for transcriptome profiling, is not well suited to capturing alternative splicing and isoform diversity. To address this, we employed third-generation long-read sequencing, which enables capture and sequencing of complete individual RNA molecules, to deeply profile the full-length transcriptome of the germinal zone (GZ) and cortical plate (CP) regions of the developing human neocortex at tissue and single-cell resolution.RESULTS: We profiled microdissected GZ and CP regions of post-conception week (PCW) 15-17 human neocortex in bulk and at single-cell resolution across six subjects using high-fidelity long-read sequencing (PacBio IsoSeq). We identified 214,516 unique isoforms, of which 72.6% were novel (unannotated in Gencode), and >7,000 novel exons, expanding the proteome by 92,422 putative proteoforms. We uncovered thousands of isoform switches during cortical neurogenesis predicted to impact RNA regulatory domains or protein structure and implicating previously uncharacterized RNA-binding proteins in cellular identity and neuropsychiatric disease. At the single-cell level, early-stage excitatory neurons exhibited the greatest isoform diversity, and isoform-centric single-cell clustering led to the identification of previously uncharacterized cell states. We systematically assessed the contribution of transcriptomic features, and localized cell and spatio-temporal transcript expression signatures across neuropsychiatric disorders, revealing predominant enrichments in dynamic isoform expression and utilization patterns and that the number and complexity of isoforms per gene is strongly predictive of disease. Leveraging this resource, we re-prioritized thousands of rare de novo risk variants associated with autism spectrum disorders (ASD), intellectual disability (ID), and neurodevelopmental disorders (NDDs), more broadly, to potentially more severe consequences and revealed a larger proportion of cryptic splice variants with the expanded transcriptome annotation provided in this study.CONCLUSION: Our study offers a comprehensive landscape of isoform diversity in the human neocortex during development. This extensive cataloging of novel isoforms and splicing events sheds light on the underlying mechanisms of neurodevelopmental disorders and presents an opportunity to explore rare genetic variants linked to these conditions. The implications of our findings extend beyond fundamental neuroscience, as they provide crucial insights into the molecular basis of developmental brain disorders and pave the way for targeted therapeutic interventions. To facilitate exploration of this dataset we developed an online portal ( https://sciso.gandallab.org/ ).
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Kanwal A, Sheikh SA, Aslam F, Yaseen S, Beetham Z, Pankratz N, Clabots CR, Naz S, Pardo JV. Genome Sequencing of Consanguineous Family Implicates Ubiquitin-Specific Protease 53 ( USP53) Variant in Psychosis/Schizophrenia: Wild-Type Expression in Murine Hippocampal CA 1-3 and Granular Dentate with AMPA Synapse Interactions. Genes (Basel) 2023; 14:1921. [PMID: 37895270 PMCID: PMC10606770 DOI: 10.3390/genes14101921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Psychosis is a severe mental disorder characterized by abnormal thoughts and perceptions (e.g., hallucinations) occurring quintessentially in schizophrenia and in several other neuropsychiatric disorders. Schizophrenia is widely considered as a neurodevelopmental disorder that onsets during teenage/early adulthood. A multiplex consanguineous Pakistani family was afflicted with severe psychosis and apparent autosomal recessive transmission. The first-cousin parents and five children were healthy, whereas two teenage daughters were severely affected. Structured interviews confirmed the diagnosis of DSM-V schizophrenia. Probands and father underwent next-generation sequencing. All available relatives were subjected to confirmatory Sanger sequencing. Homozygosity mapping and directed a priori filtering identified only one rare variant [MAF < 5(10)-5] at a residue conserved across vertebrates. The variant was a non-catalytic deubiquitinase, USP53 (p.Cys228Arg), predicted in silico as damaging. Genome sequencing did not identify any other potentially pathogenic single nucleotide variant or structural variant. Since the literature on USP53 lacked relevance to mental illness or CNS expression, studies were conducted which revealed USP53 localization in regions of the hippocampus (CA 1-3) and granular dentate. The staining pattern was like that seen with GRIA2/GluA2 and GRIP2 antibodies. All three proteins coimmunoprecipitated. These findings support the glutamate hypothesis of schizophrenia as part of the AMPA-R interactome. If confirmed, USP53 appears to be one of the few Mendelian variants potentially causal to a common-appearing mental disorder that is a rare genetic form of schizophrenia.
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Affiliation(s)
- Ambreen Kanwal
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan; (A.K.); (F.A.); (S.Y.)
- Cognitive Neuroimaging Unit, Minneapolis Veterans Health Care System, Minneapolis, MN 55417, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN 55454, USA
| | - Sohail A. Sheikh
- Department of Psychiatry, Hawkes Bay Hospital, Hastings 4120, New Zealand;
| | - Faiza Aslam
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan; (A.K.); (F.A.); (S.Y.)
| | - Samina Yaseen
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan; (A.K.); (F.A.); (S.Y.)
| | - Zachary Beetham
- Division of Computational Pathology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; (Z.B.)
| | - Nathan Pankratz
- Division of Computational Pathology, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA; (Z.B.)
| | - Connie R. Clabots
- Medicine Patient Service Line, Minneapolis Veterans Health Care System, Minneapolis, MN 55417, USA;
| | - Sadaf Naz
- School of Biological Sciences, University of the Punjab, Lahore 54590, Pakistan; (A.K.); (F.A.); (S.Y.)
| | - José V. Pardo
- Cognitive Neuroimaging Unit, Minneapolis Veterans Health Care System, Minneapolis, MN 55417, USA
- Department of Psychiatry, University of Minnesota, Minneapolis, MN 55454, USA
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30
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Nishioka M, Takayama J, Sakai N, Kazuno AA, Ishiwata M, Ueda J, Hayama T, Fujii K, Someya T, Kuriyama S, Tamiya G, Takata A, Kato T. Deep exome sequencing identifies enrichment of deleterious mosaic variants in neurodevelopmental disorder genes and mitochondrial tRNA regions in bipolar disorder. Mol Psychiatry 2023; 28:4294-4306. [PMID: 37248276 PMCID: PMC10827672 DOI: 10.1038/s41380-023-02096-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/31/2023]
Abstract
Bipolar disorder (BD) is a global medical issue, afflicting around 1% of the population with manic and depressive episodes. Despite various genetic studies, the genetic architecture and pathogenesis of BD have not been fully resolved. Besides germline variants, postzygotic mosaic variants are proposed as new candidate mechanisms contributing to BD. Here, we performed extensive deep exome sequencing (DES, ~300×) and validation experiments to investigate the roles of mosaic variants in BD with 235 BD cases (194 probands of trios and 41 single cases) and 39 controls. We found an enrichment of developmental disorder (DD) genes in the genes hit by deleterious mosaic variants in BD (P = 0.000552), including a ClinVar-registered pathogenic variant in ARID2. An enrichment of deleterious mosaic variants was also observed for autism spectrum disorder (ASD) genes (P = 0.000428). The proteins coded by the DD/ASD genes with non-synonymous mosaic variants in BD form more protein-protein interaction than expected, suggesting molecular mechanisms shared with DD/ASD but restricted to a subset of cells in BD. We also found significant enrichment of mitochondrial heteroplasmic variants, another class of mosaic variants, in mitochondrial tRNA genes in BD (P = 0.0102). Among them, recurrent m.3243 A > G variants known as causal for mitochondrial diseases were found in two unrelated BD probands with allele fractions of 5-12%, lower than in mitochondrial diseases. Despite the limitation of using peripheral tissues, our DES investigation supports the possible contribution of deleterious mosaic variants in the nuclear genome responsible for severer phenotypes, such as DD/ASD, to the risk of BD and further demonstrates that the same paradigm can be applied to the mitochondrial genome. These results, as well as the enrichment of heteroplasmic mitochondrial tRNA variants in BD, add a new piece to the understanding of the genetic architecture of BD and provide general insights into the pathological roles of mosaic variants in human diseases.
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Affiliation(s)
- Masaki Nishioka
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
- Department of Molecular Pathology of Mood Disorders, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Jun Takayama
- Department of AI and Innovative Medicine, Tohoku University School of Medicine, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Naomi Sakai
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - An-A Kazuno
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Mizuho Ishiwata
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Ueda
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takashi Hayama
- Yokohama Mental Clinic Totsuka, 494-8 Kamikurata-cho, Totsuka-ku, Yokohama, 244-0816, Japan
| | - Kumiko Fujii
- Department of Psychiatry, Shiga University of Medical Science, Seta Tsukinowa-Cho, Otsu, Shiga, 520-2192, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, 757 Asahimachidori-ichibancho, Chuo-ku, Niigata, 951-8510, Japan
| | - Shinichi Kuriyama
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Department of Molecular Epidemiology, Tohoku University School of Medicine, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
| | - Gen Tamiya
- Department of AI and Innovative Medicine, Tohoku University School of Medicine, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8575, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-Ku, Sendai, Miyagi, 980-8573, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Atsushi Takata
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
- Department of Molecular Pathology of Mood Disorders, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan.
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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Park C, Hahn O, Gupta S, Moreno AJ, Marino F, Kedir B, Wang D, Villeda SA, Wyss-Coray T, Dubal DB. Platelet factors are induced by longevity factor klotho and enhance cognition in young and aging mice. NATURE AGING 2023; 3:1067-1078. [PMID: 37587231 PMCID: PMC10501899 DOI: 10.1038/s43587-023-00468-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/13/2023] [Indexed: 08/18/2023]
Abstract
Platelet factors regulate wound healing and can signal from the blood to the brain1,2. However, whether platelet factors modulate cognition, a highly valued and central manifestation of brain function, is unknown. Here we show that systemic platelet factor 4 (PF4) permeates the brain and enhances cognition. We found that, in mice, peripheral administration of klotho, a longevity and cognition-enhancing protein3-7, increased the levels of multiple platelet factors in plasma, including PF4. A pharmacologic intervention that inhibits platelet activation blocked klotho-mediated cognitive enhancement, indicating that klotho may require platelets to enhance cognition. To directly test the effects of platelet factors on the brain, we treated mice with vehicle or systemic PF4. In young mice, PF4 enhanced synaptic plasticity and cognition. In old mice, PF4 decreased cognitive deficits and restored aging-induced increases of select factors associated with cognitive performance in the hippocampus. The effects of klotho on cognition were still present in mice lacking PF4, suggesting this platelet factor is sufficient to enhance cognition but not necessary for the effects of klotho-and that other unidentified factors probably contribute. Augmenting platelet factors, possible messengers of klotho, may enhance cognition in the young brain and decrease cognitive deficits in the aging brain.
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Affiliation(s)
- Cana Park
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Shweta Gupta
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Arturo J Moreno
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Francesca Marino
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
- Neurosciences Graduate Program, University of California, San Francisco, CA, USA
| | - Blen Kedir
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Dan Wang
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Saul A Villeda
- Department of Anatomy, University of California, San Francisco, CA, USA
- Department of Physical Therapy and Rehabilitation Science, San Francisco, CA, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- The Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Dena B Dubal
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA.
- Neurosciences Graduate Program, University of California, San Francisco, CA, USA.
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
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Farsi Z, Sheng M. Molecular mechanisms of schizophrenia: Insights from human genetics. Curr Opin Neurobiol 2023; 81:102731. [PMID: 37245257 DOI: 10.1016/j.conb.2023.102731] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/28/2023] [Accepted: 05/01/2023] [Indexed: 05/30/2023]
Abstract
Schizophrenia is a debilitating psychiatric disorder that affects millions of people worldwide; however, its etiology is poorly understood at the molecular and neurobiological levels. A particularly important advance in recent years is the discovery of rare genetic variants associated with a greatly increased risk of developing schizophrenia. These primarily loss-of-function variants are found in genes that overlap with those implicated by common variants and are involved in the regulation of glutamate signaling, synaptic function, DNA transcription, and chromatin remodeling. Animal models harboring mutations in these large-effect schizophrenia risk genes show promise in providing additional insights into the molecular mechanisms of the disease.
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Affiliation(s)
- Zohreh Farsi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Morgan Sheng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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Del Casale A, Simmaco M, Modesti MN, Zocchi C, Arena JF, Bilotta I, Alcibiade A, Sarli G, Cutillo L, Antonelli G, La Spina E, De Luca O, Preissner R, Borro M, Gentile G, Girardi P, Pompili M. DRD2, DRD3, and HTR2A Single-Nucleotide Polymorphisms Involvement in High Treatment Resistance to Atypical Antipsychotic Drugs. Biomedicines 2023; 11:2088. [PMID: 37509727 PMCID: PMC10377184 DOI: 10.3390/biomedicines11072088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The objective of this study was to investigate the DRD2 rs1800497, rs1799732, rs1801028, DRD3 rs6280, and HTR2A rs6314, rs7997012, and rs6311 single-nucleotide polymorphism (SNP) correlations with resistance to second-generation antipsychotics (SGAs) in a real-world sample of patients with treatment-resistant mental disorders. METHODS We divided 129 participants into a high treatment resistance (HTR) group (current treatment with two SGAs, or clozapine, or classic neuroleptics for a failure of previous SGAs trials) and a low treatment resistance (LTR) group (current treatment with one atypical antipsychotic). We used Next-Generation Sequencing on DNA isolated from peripheral blood samples to analyze the polymorphisms. We performed logistic regression to search for predictors of HTR membership. RESULTS A diagnosis of schizophrenia significantly predicted the HTR membership compared to other diagnoses. Other predictors were the DRD3 rs6280 C|T (OR = 22.195) and T|T (OR = 18.47) vs. C|C, HTR2A rs7997012 A|G vs. A|A (OR = 6.859) and vs. G|G (OR = 2.879), and DRD2 rs1799732 I|I vs. D|I (OR = 12.079) genotypes. CONCLUSIONS A diagnosis of schizophrenia and the DRD2 rs1799732, DRD3 rs6280, and HTR2A rs7997012 genotypes can predict high treatment resistance to SGAs.
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Affiliation(s)
- Antonio Del Casale
- Department of Dynamic and Clinical Psychology and Health Studies, Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
- Unit of Psychiatry, 'Sant'Andrea' University Hospital, 00189 Rome, Italy
| | - Maurizio Simmaco
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
- Unit of Laboratory and Advanced Molecular Diagnostics, 'Sant'Andrea' University Hospital, 00189 Rome, Italy
| | - Martina Nicole Modesti
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
| | - Clarissa Zocchi
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
| | - Jan Francesco Arena
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
| | - Irene Bilotta
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessandro Alcibiade
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
| | - Giuseppe Sarli
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
| | - Lorenzo Cutillo
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
| | - Giulia Antonelli
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
| | - Enrico La Spina
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
| | - Ottavia De Luca
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
- Unit of Laboratory and Advanced Molecular Diagnostics, 'Sant'Andrea' University Hospital, 00189 Rome, Italy
| | - Robert Preissner
- Structural Bioinformatics Group, Institute for Physiology, Charité-University Medicine Berlin, 10115 Berlin, Germany
| | - Marina Borro
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
- Unit of Laboratory and Advanced Molecular Diagnostics, 'Sant'Andrea' University Hospital, 00189 Rome, Italy
| | - Giovanna Gentile
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
- Unit of Laboratory and Advanced Molecular Diagnostics, 'Sant'Andrea' University Hospital, 00189 Rome, Italy
| | - Paolo Girardi
- Department of Dynamic and Clinical Psychology and Health Studies, Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
| | - Maurizio Pompili
- Unit of Psychiatry, 'Sant'Andrea' University Hospital, 00189 Rome, Italy
- Department of Neuroscience, Mental Health and Sensory Organs (NESMOS), Faculty of Medicine and Psychology, Sapienza University of Rome, 00185 Rome, Italy
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Zhao X, Song L, Yang A, Zhang Z, Zhang J, Yang YT, Zhao XM. Prioritizing genes associated with brain disorders by leveraging enhancer-promoter interactions in diverse neural cells and tissues. Genome Med 2023; 15:56. [PMID: 37488639 PMCID: PMC10364416 DOI: 10.1186/s13073-023-01210-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND Prioritizing genes that underlie complex brain disorders poses a considerable challenge. Despite previous studies have found that they shared symptoms and heterogeneity, it remained difficult to systematically identify the risk genes associated with them. METHODS By using the CAGE (Cap Analysis of Gene Expression) read alignment files for 439 human cell and tissue types (including primary cells, tissues and cell lines) from FANTOM5 project, we predicted enhancer-promoter interactions (EPIs) of 439 cell and tissue types in human, and examined their reliability. Then we evaluated the genetic heritability of 17 diverse brain disorders and behavioral-cognitive phenotypes in each neural cell type, brain region, and developmental stage. Furthermore, we prioritized genes associated with brain disorders and phenotypes by leveraging the EPIs in each neural cell and tissue type, and analyzed their pleiotropy and functionality for different categories of disorders and phenotypes. Finally, we characterized the spatiotemporal expression dynamics of these associated genes in cells and tissues. RESULTS We found that identified EPIs showed activity specificity and network aggregation in cell and tissue types, and enriched TF binding in neural cells played key roles in synaptic plasticity and nerve cell development, i.e., EGR1 and SOX family. We also discovered that most neurological disorders exhibit heritability enrichment in neural stem cells and astrocytes, while psychiatric disorders and behavioral-cognitive phenotypes exhibit enrichment in neurons. Furthermore, our identified genes recapitulated well-known risk genes, which exhibited widespread pleiotropy between psychiatric disorders and behavioral-cognitive phenotypes (i.e., FOXP2), and indicated expression specificity in neural cell types, brain regions, and developmental stages associated with disorders and phenotypes. Importantly, we showed the potential associations of brain disorders with brain regions and developmental stages that have not been well studied. CONCLUSIONS Overall, our study characterized the gene-enhancer regulatory networks and genetic mechanisms in the human neural cells and tissues, and illustrated the value of reanalysis of publicly available genomic datasets.
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Affiliation(s)
- Xingzhong Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Liting Song
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Anyi Yang
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Zichao Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Jinglong Zhang
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China
| | - Yucheng T Yang
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China.
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China.
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, and Department of Neurology of Zhongshan Hospital, Fudan University, 220 Handan Road, Shanghai, 200433, China.
- MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200433, China.
- State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Fudan University, Shanghai, 200032, China.
- Internatioal Human Phenome Institutes (Shanghai), Shanghai, 200433, China.
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Koido K, Malmgren CI, Pojskic L, Almos PZ, Bergen SE, Borg I, Božina N, Coviello DA, Degenhardt F, Ganoci L, Jensen UB, Durand-Lennad L, Laurent-Levinson C, McQuillin A, Navickas A, Pace NP, Paneque M, Rietschel M, Grigoroiu-Serbanescu M, Soller MJ, Suvisaari J, Utkus A, Van Assche E, Vissouze L, Zuckerman S, Chaumette B, Tammimies K. Lack of guidelines and translational knowledge is hindering the implementation of psychiatric genetic counseling and testing within Europe - A multi-professional survey study. Eur J Med Genet 2023; 66:104805. [PMID: 37406854 DOI: 10.1016/j.ejmg.2023.104805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/25/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023]
Abstract
Genetic research has identified a large number of genetic variants, both rare and common, underlying neurodevelopmental disorders (NDD) and major psychiatric disorders. Currently, these findings are being translated into clinical practice. However, there is a lack of knowledge and guidelines for psychiatric genetic testing (PsychGT) and genetic counseling (PsychGC). The European Union-funded COST action EnGagE (CA17130) network was started to investigate the current implementation status of PsychGT and PsychGC across 35 participating European countries. Here, we present the results of a pan-European online survey in which we gathered the opinions, knowledge, and practices of a self-selected sample of professionals involved/interested in the field. We received answers from 181 respondents. The three main occupational categories were genetic counselor (21.0%), clinical geneticist (24.9%), and researcher (25.4%). Of all 181 respondents, 106 provide GC for any psychiatric disorder or NDD, corresponding to 58.6% of the whole group ranging from 43.2% in Central Eastern Europe to 66.1% in Western Europe. Overall, 65.2% of the respondents reported that genetic testing is offered to individuals with NDD, and 26.5% indicated the same for individuals with major psychiatric disorders. Only 22.1% of the respondents indicated that they have guidelines for PsychGT. Pharmacogenetic testing actionable for psychiatric disorders was offered by 15%. Interestingly, when genetic tests are fully covered by national health insurance, more genetic testing is provided for individuals with NDD but not those with major psychiatric disorders. Our qualitative analyses of responses highlight the lack of guidelines and knowledge on utilizing and using genetic tests and education and training as the major obstacles to implementation. Indeed, the existence of psychiatric genetic training courses was confirmed by only 11.6% of respondents. The question on the relevance of up-to-date education and training in psychiatric genetics on everyday related practice was highly relevant. We provide evidence that PsychGC and PsychGT are already in use across European countries, but there is a lack of guidelines and education. Harmonization of practice and development of guidelines for genetic counseling, testing, and training professionals would improve equality and access to quality care for individuals with psychiatric disorders within Europe.
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Affiliation(s)
- Kati Koido
- Department of Physiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Charlotta Ingvoldstad Malmgren
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden; Center for Research and Bioethics, CRB, Uppsala University, Uppsala, Sweden
| | - Lejla Pojskic
- Laboratory for Human Genetics, University of Sarajevo - Institute for Genetic Engineering and Biotechnology, Sarajevo, Bosnia and Herzegovina
| | - Peter Z Almos
- Department of Psychiatry, University of Szeged, Szeged, Hungary
| | - Sarah E Bergen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Isabella Borg
- Pathology Department, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Nada Božina
- University of Zagreb School of Medicine, Department of Pharmacology, Zagreb, Croatia
| | | | - Franziska Degenhardt
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Lana Ganoci
- University Hospital Centre Zagreb, Department of Laboratory Diagnostics, Division for Pharmacogenomics and Therapy Individualization, Zagreb, Croatia
| | - Uffe B Jensen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Louise Durand-Lennad
- Université Paris Cité, INSERM U1266, Institute of Psychiatry and Neuroscience of Paris, Paris, France
| | - Claudine Laurent-Levinson
- Faculté de Médecine-Sorbonne Université, Groupe de Recherche Clinique N°15 - Troubles Psychiatriques et Développement (PSYDEV) & Centre de Référence des Maladies Rares à Expression Psychiatrique, DMU ORYGINE Femmes-Mères-Enfants, Service de Psychiatrie de l'Enfant et de l'Adolescent, Assistance Publique-Hôpitaux de Paris, Sorbonne Université, Paris, France
| | - Andrew McQuillin
- Molecular Psychiatry Laboratory, Division of Psychiatry, University College London, London, UK
| | - Alvydas Navickas
- Psychiatric Clinic, Institute of Clinical Medicine, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Nikolai P Pace
- Centre for Molecular Medicine and Biobanking, University of Malta, Malta
| | - Milena Paneque
- Center for Predictive and Preventive Genetics, Institute of Molecular and Cellular Biology, Institute for Research and Innovation in Health, University of Porto, Porto, Portugal
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Germany
| | - Maria Grigoroiu-Serbanescu
- Alexandru Obregia Clinical Psychiatric Hospital, Biometric Psychiatric Genetics Research Unit, Bucharest, Romania
| | - Maria Johansson Soller
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm and Karolinska Institutet, Stockholm, Sweden
| | - Jaana Suvisaari
- Finnish Institute for Health and Welfare, Department of Public Health and Welfare, Mental Health Team, Helsinki, Finland
| | - Algirdas Utkus
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | | | - Lily Vissouze
- Université Paris Cité, INSERM U1266, Institute of Psychiatry and Neuroscience of Paris, Paris, France
| | - Shachar Zuckerman
- Medical Genetic Institute, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Boris Chaumette
- Université Paris Cité, INSERM U1266, Institute of Psychiatry and Neuroscience of Paris, GHU-Paris Psychiatrie et Neurosciences, Paris, France; Department of Psychiatry, McGill University, Montreal, Canada
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Centre for Psychiatry Research, Department of Women's and Children's Health, Karolinska Institute, Region Stockholm, Stockholm, Sweden; Astrid Lindgren Children's Hospital, Karolinska University Hospital, Region Stockholm, Stockholm, Sweden.
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Hsu YHH, Pintacuda G, Liu R, Nacu E, Kim A, Tsafou K, Petrossian N, Crotty W, Suh JM, Riseman J, Martin JM, Biagini JC, Mena D, Ching JK, Malolepsza E, Li T, Singh T, Ge T, Egri SB, Tanenbaum B, Stanclift CR, Apffel AM, Carr SA, Schenone M, Jaffe J, Fornelos N, Huang H, Eggan KC, Lage K. Using brain cell-type-specific protein interactomes to interpret neurodevelopmental genetic signals in schizophrenia. iScience 2023; 26:106701. [PMID: 37207277 PMCID: PMC10189495 DOI: 10.1016/j.isci.2023.106701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 03/27/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Genetics have nominated many schizophrenia risk genes and identified convergent signals between schizophrenia and neurodevelopmental disorders. However, functional interpretation of the nominated genes in the relevant brain cell types is often lacking. We executed interaction proteomics for six schizophrenia risk genes that have also been implicated in neurodevelopment in human induced cortical neurons. The resulting protein network is enriched for common variant risk of schizophrenia in Europeans and East Asians, is down-regulated in layer 5/6 cortical neurons of individuals affected by schizophrenia, and can complement fine-mapping and eQTL data to prioritize additional genes in GWAS loci. A sub-network centered on HCN1 is enriched for common variant risk and contains proteins (HCN4 and AKAP11) enriched for rare protein-truncating mutations in individuals with schizophrenia and bipolar disorder. Our findings showcase brain cell-type-specific interactomes as an organizing framework to facilitate interpretation of genetic and transcriptomic data in schizophrenia and its related disorders.
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Affiliation(s)
- Yu-Han H. Hsu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Greta Pintacuda
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ruize Liu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eugeniu Nacu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - April Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kalliopi Tsafou
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Natalie Petrossian
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - William Crotty
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jung Min Suh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jackson Riseman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jacqueline M. Martin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Julia C. Biagini
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daya Mena
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joshua K.T. Ching
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Edyta Malolepsza
- Genomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Taibo Li
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Tian Ge
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shawn B. Egri
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Benjamin Tanenbaum
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Annie M. Apffel
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A. Carr
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Monica Schenone
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jake Jaffe
- Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nadine Fornelos
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Kevin C. Eggan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Harvard Stem Cell Institute and Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
- Institute of Biological Psychiatry, Mental Health Centre Sct. Hans, Mental Health Services Copenhagen, 4000 Roskilde, Denmark
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Aryal S, Bonanno K, Song B, Mani DR, Keshishian H, Carr SA, Sheng M, Dejanovic B. Deep proteomics identifies shared molecular pathway alterations in synapses of patients with schizophrenia and bipolar disorder and mouse model. Cell Rep 2023; 42:112497. [PMID: 37171958 DOI: 10.1016/j.celrep.2023.112497] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/10/2023] [Accepted: 04/26/2023] [Indexed: 05/14/2023] Open
Abstract
Synaptic dysfunction is implicated in the pathophysiology of schizophrenia (SCZ) and bipolar disorder (BP). We use quantitative mass spectrometry to carry out deep, unbiased proteomic profiling of synapses purified from the dorsolateral prefrontal cortex of 35 cases of SCZ, 35 cases of BP, and 35 controls. Compared with controls, SCZ and BP synapses show substantial and similar proteomic alterations. Network analyses reveal upregulation of proteins associated with autophagy and certain vesicle transport pathways and downregulation of proteins related to synaptic, mitochondrial, and ribosomal function in the synapses of individuals with SCZ or BP. Some of the same pathways are similarly dysregulated in the synaptic proteome of mutant mice deficient in Akap11, a recently discovered shared risk gene for SCZ and BP. Our work provides biological insights into molecular dysfunction at the synapse in SCZ and BP and serves as a resource for understanding the pathophysiology of these disorders.
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Affiliation(s)
- Sameer Aryal
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Bonanno
- The Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Bryan Song
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - D R Mani
- The Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hasmik Keshishian
- The Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Steven A Carr
- The Proteomics Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Morgan Sheng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
| | - Borislav Dejanovic
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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38
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Lawrence JM, Breunig S, Foote IF, Tallis CB, Grotzinger AD. Genomic SEM Applied to Explore Etiological Divergences in Bipolar Subtypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.04.29.23289281. [PMID: 37215038 PMCID: PMC10197718 DOI: 10.1101/2023.04.29.23289281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Background Bipolar Disorder (BD) is an overarching diagnostic class defined by the presence of at least one prior manic episode (BD I) or both a prior hypomanic episode and a prior depressive episode (BD II). Traditionally, BD II has been conceptualized as a less severe presentation of BD I, however, extant literature to investigate this claim has been mixed. Methods We apply Genomic Structural Equation Modeling (Genomic SEM) to investigate divergent genetic pathways across BD's two major subtypes using the most recent GWAS summary statistics from the PGC. We begin by identifying divergences in genetic correlations across 89 external traits using a Bonferroni corrected threshold. We also use a theoretically informed follow-up model to examine the extent to which the genetic variance in each subtype is explained by schizophrenia and major depression. Lastly, Transcriptome-wide SEM (T-SEM) was used to identify gene expression patterns associated with the BD subtypes. Results BD II was characterized by significantly larger genetic overlap with internalizing traits (e.g., neuroticism, insomnia, physical inactivity), while significantly stronger associations for BD I were limited. Consistent with these findings, the follow-up model revealed a much larger major depression component for BD II. T-SEM results revealed 41 unique genes associated with risk pathways across BD subtypes. Conclusions Divergent patterns of genetic relationships across external traits provide support for the distinction of the bipolar subtypes. However, our results also challenge the illness severity conceptualization of BD given stronger genetic overlap across BD II and a range of clinically relevant traits and disorders.
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Affiliation(s)
- Jeremy M Lawrence
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO
| | - Sophie Breunig
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO
| | - Isabelle F Foote
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO
| | - Connor B Tallis
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO
| | - Andrew D Grotzinger
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO
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Abstract
Bipolar disorders (BDs) are recurrent and sometimes chronic disorders of mood that affect around 2% of the world's population and encompass a spectrum between severe elevated and excitable mood states (mania) to the dysphoria, low energy, and despondency of depressive episodes. The illness commonly starts in young adults and is a leading cause of disability and premature mortality. The clinical manifestations of bipolar disorder can be markedly varied between and within individuals across their lifespan. Early diagnosis is challenging and misdiagnoses are frequent, potentially resulting in missed early intervention and increasing the risk of iatrogenic harm. Over 15 approved treatments exist for the various phases of bipolar disorder, but outcomes are often suboptimal owing to insufficient efficacy, side effects, or lack of availability. Lithium, the first approved treatment for bipolar disorder, continues to be the most effective drug overall, although full remission is only seen in a subset of patients. Newer atypical antipsychotics are increasingly being found to be effective in the treatment of bipolar depression; however, their long term tolerability and safety are uncertain. For many with bipolar disorder, combination therapy and adjunctive psychotherapy might be necessary to treat symptoms across different phases of illness. Several classes of medications exist for treating bipolar disorder but predicting which medication is likely to be most effective or tolerable is not yet possible. As pathophysiological insights into the causes of bipolar disorders are revealed, a new era of targeted treatments aimed at causal mechanisms, be they pharmacological or psychosocial, will hopefully be developed. For the time being, however, clinical judgment, shared decision making, and empirical follow-up remain essential elements of clinical care. This review provides an overview of the clinical features, diagnostic subtypes, and major treatment modalities available to treat people with bipolar disorder, highlighting recent advances and ongoing therapeutic challenges.
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Affiliation(s)
- Fernando S Goes
- Precision Medicine Center of Excellence in Mood Disorders, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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40
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Mallard TT, Grotzinger AD, Smoller JW. Examining the shared etiology of psychopathology with genome-wide association studies. Physiol Rev 2023; 103:1645-1665. [PMID: 36634217 PMCID: PMC9988537 DOI: 10.1152/physrev.00016.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/19/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
Genome-wide association studies (GWASs) have ushered in a new era of reproducible discovery in psychiatric genetics. The field has now identified hundreds of common genetic variants that are associated with mental disorders, and many of them influence more than one disorder. By advancing the understanding of causal biology underlying psychopathology, GWAS results are poised to inform the development of novel therapeutics, stratification of at-risk patients, and perhaps even the revision of top-down classification systems in psychiatry. Here, we provide a concise review of GWAS findings with an emphasis on findings that have elucidated the shared genetic etiology of psychopathology, summarizing insights at three levels of analysis: 1) genome-wide architecture; 2) networks, pathways, and gene sets; and 3) individual variants/genes. Three themes emerge from these efforts. First, all psychiatric phenotypes are heritable, highly polygenic, and influenced by many pleiotropic variants with incomplete penetrance. Second, GWAS results highlight the broad etiological roles of neuronal biology, system-wide effects over localized effects, and early neurodevelopment as a critical period. Third, many loci that are robustly associated with multiple forms of psychopathology harbor genes that are involved in synaptic structure and function. Finally, we conclude our review by discussing the implications that GWAS results hold for the field of psychiatry, as well as expected challenges and future directions in the next stage of psychiatric genetics.
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Affiliation(s)
- Travis T Mallard
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, United States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, Massachusetts, United States
| | - Andrew D Grotzinger
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, Colorado, United States
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado, United States
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, Massachusetts, United States
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, United States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Boston, Massachusetts, United States
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41
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Herzog LE, Wang L, Yu E, Choi S, Farsi Z, Song BJ, Pan JQ, Sheng M. Mouse mutants in schizophrenia risk genes GRIN2A and AKAP11 show EEG abnormalities in common with schizophrenia patients. Transl Psychiatry 2023; 13:92. [PMID: 36914641 PMCID: PMC10011509 DOI: 10.1038/s41398-023-02393-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 02/28/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
Schizophrenia is a heterogeneous psychiatric disorder with a strong genetic basis, whose etiology and pathophysiology remain poorly understood. Exome sequencing studies have uncovered rare, loss-of-function variants that greatly increase risk of schizophrenia [1], including loss-of-function mutations in GRIN2A (aka GluN2A or NR2A, encoding the NMDA receptor subunit 2A) and AKAP11 (A-Kinase Anchoring Protein 11). AKAP11 and GRIN2A mutations are also associated with bipolar disorder [2], and epilepsy and developmental delay/intellectual disability [1, 3, 4], respectively. Accessible in both humans and rodents, electroencephalogram (EEG) recordings offer a window into brain activity and display abnormal features in schizophrenia patients. Does loss of Grin2a or Akap11 in mice also result in EEG abnormalities? We monitored EEG in heterozygous and homozygous knockout Grin2a and Akap11 mutant mice compared with their wild-type littermates, at 3- and 6-months of age, across the sleep/wake cycle and during auditory stimulation protocols. Grin2a and Akap11 mutants exhibited increased resting gamma power, attenuated auditory steady-state responses (ASSR) at gamma frequencies, and reduced responses to unexpected auditory stimuli during mismatch negativity (MMN) tests. Sleep spindle density was reduced in a gene dose-dependent manner in Akap11 mutants, whereas Grin2a mutants showed increased sleep spindle density. The EEG phenotypes of Grin2a and Akap11 mutant mice show a variety of abnormal features that overlap considerably with human schizophrenia patients, reflecting systems-level changes caused by Grin2a and Akap11 deficiency. These neurophysiologic findings further substantiate Grin2a and Akap11 mutants as genetic models of schizophrenia and identify potential biomarkers for stratification of schizophrenia patients.
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Affiliation(s)
- Linnea E Herzog
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Lei Wang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eunah Yu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Soonwook Choi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Zohreh Farsi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bryan J Song
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jen Q Pan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Morgan Sheng
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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42
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Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H, Consortium P, Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ. Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.03.23286706. [PMID: 36945630 PMCID: PMC10029021 DOI: 10.1101/2023.03.03.23286706] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Genomic regulatory elements active in the developing human brain are notably enriched in genetic risk for neuropsychiatric disorders, including autism spectrum disorder (ASD), schizophrenia, and bipolar disorder. However, prioritizing the specific risk genes and candidate molecular mechanisms underlying these genetic enrichments has been hindered by the lack of a single unified large-scale gene regulatory atlas of human brain development. Here, we uniformly process and systematically characterize gene, isoform, and splicing quantitative trait loci (xQTLs) in 672 fetal brain samples from unique subjects across multiple ancestral populations. We identify 15,752 genes harboring a significant xQTL and map 3,739 eQTLs to a specific cellular context. We observe a striking drop in gene expression and splicing heritability as the human brain develops. Isoform-level regulation, particularly in the second trimester, mediates the greatest proportion of heritability across multiple psychiatric GWAS, compared with eQTLs. Via colocalization and TWAS, we prioritize biological mechanisms for ~60% of GWAS loci across five neuropsychiatric disorders, nearly two-fold that observed in the adult brain. Finally, we build a comprehensive set of developmentally regulated gene and isoform co-expression networks capturing unique genetic enrichments across disorders. Together, this work provides a comprehensive view of genetic regulation across human brain development as well as the stage-and cell type-informed mechanistic underpinnings of neuropsychiatric disorders.
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Affiliation(s)
- Cindy Wen
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Michael Margolis
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Rujia Dai
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse, NY, 13210, USA
| | - Pan Zhang
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Pawel F Przytycki
- Gladstone Institute of Data Science and Biotechnology; San Francisco, CA, 94158, USA
| | - Daniel D Vo
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia; Philadelphia, PA, 19104, USA
| | - Arjun Bhattacharya
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Nana Matoba
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
| | - Chuan Jiao
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse, NY, 13210, USA
| | - Minsoo Kim
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Ellen Tsai
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Celine Hoh
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Nil Aygün
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
| | - Rebecca L Walker
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Christos Chatzinakos
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02215, USA
- McLean Hospital; Belmont, MA, 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Declan Clarke
- Department of Molecular Biophysics and Biochemistry, Yale University; New Haven, CT, 06520, USA
| | - Henry Pratt
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School; Worcester, MA, 01605, USA
| | - PsychENCODE Consortium
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse, NY, 13210, USA
- Gladstone Institute of Data Science and Biotechnology; San Francisco, CA, 94158, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia; Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Institute for Quantitative and Computational Biosciences, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02215, USA
- McLean Hospital; Belmont, MA, 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
- Department of Molecular Biophysics and Biochemistry, Yale University; New Haven, CT, 06520, USA
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School; Worcester, MA, 01605, USA
- CNS Data Coordination Group, Sage Bionetworks; Seattle, WA, 98109, USA
- Program in Computational Biology and Bioinformatics, Yale University; New Haven, CT, 06520, USA
- Department of Computer Science, Yale University; New Haven, CT, 06520, USA
- Department of Statistics and Data Science, Yale University; New Haven, CT, 06520, USA
- Lieber Institute for Brain Development; Baltimore, MD, 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health; Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health; Baltimore, MD, 21205, USA
- Neumora Therapeutics; Watertown, MA, 02472, USA
- Department of Neurology, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University School of Medicine; Cardiff, CF24 4HQ, UK
- Department of Comparative Medicine, Yale University School of Medicine; New Haven, CT, 06520, USA
- Department of Neuroscience, Yale University School of Medicine; New Haven, CT, 06520, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Institute for Precision Health, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Statistics & Data Science, Carnegie Mellon University; Pittsburgh, PA, 15213, USA
- Computational Biology Department, Carnegie Mellon University; Pittsburgh, PA, 15213, USA
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute; Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
- Harvard Medical School; Boston, MA, 02215, USA
- Division of Genetics, Brigham and Women's Hospital; Boston, MA, 02215, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco; San Francisco, CA, 94158, USA
- Chan Zuckerberg Biohub; San Francisco, CA, 94158, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan, 410008, China
| | - Mette A Peters
- CNS Data Coordination Group, Sage Bionetworks; Seattle, WA, 98109, USA
| | - Mark Gerstein
- Department of Molecular Biophysics and Biochemistry, Yale University; New Haven, CT, 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University; New Haven, CT, 06520, USA
- Department of Computer Science, Yale University; New Haven, CT, 06520, USA
- Department of Statistics and Data Science, Yale University; New Haven, CT, 06520, USA
| | - Nikolaos P Daskalakis
- Department of Psychiatry, Harvard Medical School; Boston, MA, 02215, USA
- McLean Hospital; Belmont, MA, 02478, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School; Worcester, MA, 01605, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development; Baltimore, MD, 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health; Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health; Baltimore, MD, 21205, USA
- Neumora Therapeutics; Watertown, MA, 02472, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development; Baltimore, MD, 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development; Baltimore, MD, 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development; Baltimore, MD, 21205, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine; Baltimore, MD, 21205, USA
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University School of Medicine; Cardiff, CF24 4HQ, UK
| | - Nenad Sestan
- Department of Comparative Medicine, Yale University School of Medicine; New Haven, CT, 06520, USA
- Department of Neuroscience, Yale University School of Medicine; New Haven, CT, 06520, USA
| | - Daniel H Geschwind
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Institute for Precision Health, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Kathryn Roeder
- Department of Statistics & Data Science, Carnegie Mellon University; Pittsburgh, PA, 15213, USA
- Computational Biology Department, Carnegie Mellon University; Pittsburgh, PA, 15213, USA
| | - Alexander Gusev
- Department of Medical Oncology, Division of Population Sciences, Dana-Farber Cancer Institute; Boston, MA, 02215, USA
- Broad Institute of MIT and Harvard; Cambridge, MA, 02142, USA
- Harvard Medical School; Boston, MA, 02215, USA
- Division of Genetics, Brigham and Women's Hospital; Boston, MA, 02215, USA
| | - Bogdan Pasaniuc
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Institute for Precision Health, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Computational Medicine, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
| | - Michael I Love
- Department of Genetics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill; Chapel Hill, NC, 27599, USA
| | - Katherine S Pollard
- Gladstone Institute of Data Science and Biotechnology; San Francisco, CA, 94158, USA
- Department of Epidemiology & Biostatistics, University of California, San Francisco; San Francisco, CA, 94158, USA
- Chan Zuckerberg Biohub; San Francisco, CA, 94158, USA
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University; Syracuse, NY, 13210, USA
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University; Changsha, Hunan, 410008, China
| | - Michael J Gandal
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA, 19104, USA
- Lifespan Brain Institute, The Children's Hospital of Philadelphia; Philadelphia, PA, 19104, USA
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43
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Liu D, Meyer D, Fennessy B, Feng C, Cheng E, Johnson JS, Park YJ, Rieder MK, Ascolillo S, de Pins A, Dobbyn A, Lebovitch D, Moya E, Nguyen TH, Wilkins L, Hassan A, Burdick KE, Buxbaum JD, Domenici E, Frangou S, Hartmann AM, Laurent-Levinson C, Malhotra D, Pato CN, Pato MT, Ressler K, Roussos P, Rujescu D, Arango C, Bertolino A, Blasi G, Bocchio-Chiavetto L, Campion D, Carr V, Fullerton JM, Gennarelli M, González-Peñas J, Levinson DF, Mowry B, Nimgaokar VL, Pergola G, Rampino A, Cervilla JA, Rivera M, Schwab SG, Wildenauer DB, Daly M, Neale B, Singh T, O'Donovan MC, Owen MJ, Walters JT, Ayub M, Malhotra AK, Lencz T, Sullivan PF, Sklar P, Stahl EA, Huckins LM, Charney AW. Schizophrenia risk conferred by rare protein-truncating variants is conserved across diverse human populations. Nat Genet 2023; 55:369-376. [PMID: 36914870 PMCID: PMC10011128 DOI: 10.1038/s41588-023-01305-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/23/2023] [Indexed: 03/14/2023]
Abstract
Schizophrenia (SCZ) is a chronic mental illness and among the most debilitating conditions encountered in medical practice. A recent landmark SCZ study of the protein-coding regions of the genome identified a causal role for ten genes and a concentration of rare variant signals in evolutionarily constrained genes1. This recent study-and most other large-scale human genetics studies-was mainly composed of individuals of European (EUR) ancestry, and the generalizability of the findings in non-EUR populations remains unclear. To address this gap, we designed a custom sequencing panel of 161 genes selected based on the current knowledge of SCZ genetics and sequenced a new cohort of 11,580 SCZ cases and 10,555 controls of diverse ancestries. Replicating earlier work, we found that cases carried a significantly higher burden of rare protein-truncating variants (PTVs) among evolutionarily constrained genes (odds ratio = 1.48; P = 5.4 × 10-6). In meta-analyses with existing datasets totaling up to 35,828 cases and 107,877 controls, this excess burden was largely consistent across five ancestral populations. Two genes (SRRM2 and AKAP11) were newly implicated as SCZ risk genes, and one gene (PCLO) was identified as shared by individuals with SCZ and those with autism. Overall, our results lend robust support to the rare allelic spectrum of the genetic architecture of SCZ being conserved across diverse human populations.
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Affiliation(s)
- Dongjing Liu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Dara Meyer
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Fennessy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Claudia Feng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Wellcome Sanger Institute, Hinxton, UK
| | - Esther Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica S Johnson
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - You Jeong Park
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marysia-Kolbe Rieder
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven Ascolillo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Agathe de Pins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Dobbyn
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dannielle Lebovitch
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emily Moya
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tan-Hoang Nguyen
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Lillian Wilkins
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Katherine E Burdick
- Department of Psychiatry, Brigham and Women's Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Enrico Domenici
- Centre for Computational and Systems Biology, Fondazione The Microsoft Research - University of Trento, Rovereto, Italy
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Sophia Frangou
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Annette M Hartmann
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Claudine Laurent-Levinson
- Faculté de Médecine Sorbonne Université, Groupe de Recherche Clinique n°15-Troubles Psychiatriques et Développement, Department of Child and Adolescent Psychiatry, Hôpital Universitaire de la Pitié-Salpêtrière, Paris, France
- Centre de Référence des Maladies Rares à Expression Psychiatrique, Department of Child and Adolescent Psychiatry, AP-HP Sorbonne Université, Hôpital Universitaire de la Pitié-Salpêtrière, Paris, France
| | - Dheeraj Malhotra
- Department of Neuroscience and Rare Diseases, Roche Pharma Research and Early Development, F. Hoffmann-La Roche, Basel, Switzerland
| | - Carlos N Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate College of Medicine, New York, NY, USA
| | - Michele T Pato
- Department of Psychiatry and Behavioral Sciences, SUNY Downstate College of Medicine, New York, NY, USA
| | - Kerry Ressler
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Division of Depression and Anxiety Disorders, McLean Hospital, Belmont, MA, USA
| | - Panos Roussos
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, New York, NY, USA
| | - Dan Rujescu
- Department of Psychiatry and Psychotherapy, Medical University of Vienna, Vienna, Austria
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Madrid, Spain
| | - Alessandro Bertolino
- Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Giuseppe Blasi
- Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Luisella Bocchio-Chiavetto
- Department of Theoretical and Applied Sciences, eCampus University, Novedrate, Italy
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Dominique Campion
- INSERM U1245, Rouen, France
- Centre Hospitalier du Rouvray, Rouen, France
| | - Vaughan Carr
- Neuroscience Research Australia, Sydney, New South Wales, Australia
- School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia
- Department of Psychiatry, School of Clinical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Janice M Fullerton
- Neuroscience Research Australia, Sydney, New South Wales, Australia
- School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Massimo Gennarelli
- Genetics Unit, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Javier González-Peñas
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Madrid, Spain
| | | | - Bryan Mowry
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- Queensland Centre for Mental Health Research, The University of Queensland, Brisbane, Queensland, Australia
| | - Vishwajit L Nimgaokar
- Department of Psychiatry, University of Pittsburgh School of Medicine, Western Psychiatric Hospital, Pittsburgh, PA, USA
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Giulio Pergola
- Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Antonio Rampino
- Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Jorge A Cervilla
- Institute of Neurosciences, Biomedical Research Centre, University of Granada, Granada, Spain
- Department of Psychiatry, San Cecilio University Hospital, University of Granada, Granada, Spain
| | - Margarita Rivera
- Institute of Neurosciences, Biomedical Research Centre, University of Granada, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Sibylle G Schwab
- Molecular Horizons, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales, Australia
| | | | - Mark Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Benjamin Neale
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Tarjinder Singh
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - James T Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Muhammad Ayub
- University College London, London, UK
- Department of Psychiatry, Queen's University, Kingston, Ontario, Canada
| | - Anil K Malhotra
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Institute for Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, New York, NY, USA
| | - Todd Lencz
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Institute for Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, New York, NY, USA
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Pamela Sklar
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Regeneron Pharmaceuticals, Tarrytown, NY, USA
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Alexander W Charney
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Dattani S, Sham PC, Jermy BS, Coleman JRI, Howard DM, Lewis CM. Common and rare variant associations with latent traits underlying depression, bipolar disorder, and schizophrenia. Transl Psychiatry 2023; 13:46. [PMID: 36746926 PMCID: PMC9902570 DOI: 10.1038/s41398-023-02324-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/07/2023] [Accepted: 01/18/2023] [Indexed: 02/08/2023] Open
Abstract
Genetic studies in psychiatry have primarily focused on the effects of common genetic variants, but few have investigated the role of rare genetic variants, particularly for major depression. In order to explore the role of rare variants in the gap between estimates of single nucleotide polymorphism (SNP) heritability and twin study heritability, we examined the contribution of common and rare genetic variants to latent traits underlying psychiatric disorders using high-quality imputed genotype data from the UK Biobank. Using a pre-registered analysis, we used items from the UK Biobank Mental Health Questionnaire relevant to three psychiatric disorders: major depression (N = 134,463), bipolar disorder (N = 117,376) and schizophrenia (N = 130,013) and identified a general hierarchical factor for each that described participants' responses. We calculated participants' scores on these latent traits and conducted single-variant genetic association testing (MAF > 0.05%), gene-based burden testing and pathway association testing associations with these latent traits. We tested for enrichment of rare variants (MAF 0.05-1%) in genes that had been previously identified by common variant genome-wide association studies, and genes previously associated with Mendelian disorders having relevant symptoms. We found moderate genetic correlations between the latent traits in our study and case-control phenotypes in previous genome-wide association studies, and identified one common genetic variant (rs72657988, minor allele frequency = 8.23%, p = 1.01 × 10-9) associated with the general factor of schizophrenia, but no other single variants, genes or pathways passed significance thresholds in this analysis, and we did not find enrichment in previously identified genes.
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Affiliation(s)
- Saloni Dattani
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
- Department of Psychiatry, Li Ka Shing (LKS) Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.
| | - Pak C Sham
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
- Department of Psychiatry, State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong SAR, China
- Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Bradley S Jermy
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
| | - Jonathan R I Coleman
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- NIHR Maudsley Biomedical Research Centre, South London and Maudsley NHS Trust, London, UK
| | - David M Howard
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Cathryn M Lewis
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, UK
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45
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Andreassen OA, Hindley GFL, Frei O, Smeland OB. New insights from the last decade of research in psychiatric genetics: discoveries, challenges and clinical implications. World Psychiatry 2023; 22:4-24. [PMID: 36640404 PMCID: PMC9840515 DOI: 10.1002/wps.21034] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 01/15/2023] Open
Abstract
Psychiatric genetics has made substantial progress in the last decade, providing new insights into the genetic etiology of psychiatric disorders, and paving the way for precision psychiatry, in which individual genetic profiles may be used to personalize risk assessment and inform clinical decision-making. Long recognized to be heritable, recent evidence shows that psychiatric disorders are influenced by thousands of genetic variants acting together. Most of these variants are commonly occurring, meaning that every individual has a genetic risk to each psychiatric disorder, from low to high. A series of large-scale genetic studies have discovered an increasing number of common and rare genetic variants robustly associated with major psychiatric disorders. The most convincing biological interpretation of the genetic findings implicates altered synaptic function in autism spectrum disorder and schizophrenia. However, the mechanistic understanding is still incomplete. In line with their extensive clinical and epidemiological overlap, psychiatric disorders appear to exist on genetic continua and share a large degree of genetic risk with one another. This provides further support to the notion that current psychiatric diagnoses do not represent distinct pathogenic entities, which may inform ongoing attempts to reconceptualize psychiatric nosology. Psychiatric disorders also share genetic influences with a range of behavioral and somatic traits and diseases, including brain structures, cognitive function, immunological phenotypes and cardiovascular disease, suggesting shared genetic etiology of potential clinical importance. Current polygenic risk score tools, which predict individual genetic susceptibility to illness, do not yet provide clinically actionable information. However, their precision is likely to improve in the coming years, and they may eventually become part of clinical practice, stressing the need to educate clinicians and patients about their potential use and misuse. This review discusses key recent insights from psychiatric genetics and their possible clinical applications, and suggests future directions.
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Affiliation(s)
- Ole A Andreassen
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Guy F L Hindley
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Oleksandr Frei
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Olav B Smeland
- NORMENT Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
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46
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Weiner DJ, Nadig A, Jagadeesh KA, Dey KK, Neale BM, Robinson EB, Karczewski KJ, O'Connor LJ. Polygenic architecture of rare coding variation across 394,783 exomes. Nature 2023; 614:492-499. [PMID: 36755099 PMCID: PMC10614218 DOI: 10.1038/s41586-022-05684-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/22/2022] [Indexed: 02/10/2023]
Abstract
Both common and rare genetic variants influence complex traits and common diseases. Genome-wide association studies have identified thousands of common-variant associations, and more recently, large-scale exome sequencing studies have identified rare-variant associations in hundreds of genes1-3. However, rare-variant genetic architecture is not well characterized, and the relationship between common-variant and rare-variant architecture is unclear4. Here we quantify the heritability explained by the gene-wise burden of rare coding variants across 22 common traits and diseases in 394,783 UK Biobank exomes5. Rare coding variants (allele frequency < 1 × 10-3) explain 1.3% (s.e. = 0.03%) of phenotypic variance on average-much less than common variants-and most burden heritability is explained by ultrarare loss-of-function variants (allele frequency < 1 × 10-5). Common and rare variants implicate the same cell types, with similar enrichments, and they have pleiotropic effects on the same pairs of traits, with similar genetic correlations. They partially colocalize at individual genes and loci, but not to the same extent: burden heritability is strongly concentrated in significant genes, while common-variant heritability is more polygenic, and burden heritability is also more strongly concentrated in constrained genes. Finally, we find that burden heritability for schizophrenia and bipolar disorder6,7 is approximately 2%. Our results indicate that rare coding variants will implicate a tractable number of large-effect genes, that common and rare associations are mechanistically convergent, and that rare coding variants will contribute only modestly to missing heritability and population risk stratification.
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Affiliation(s)
- Daniel J Weiner
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Ajay Nadig
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Karthik A Jagadeesh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Kushal K Dey
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Elise B Robinson
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luke J O'Connor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Pietiläinen O, Trehan A, Meyer D, Mitchell J, Tegtmeyer M, Valakh V, Gebre H, Chen T, Vartiainen E, Farhi SL, Eggan K, McCarroll SA, Nehme R. Astrocytic cell adhesion genes linked to schizophrenia correlate with synaptic programs in neurons. Cell Rep 2023; 42:111988. [PMID: 36640364 PMCID: PMC10721115 DOI: 10.1016/j.celrep.2022.111988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
The maturation of neurons and the development of synapses, although emblematic of neurons, also relies on interactions with astrocytes and other glia. Here, to study the role of glia-neuron interactions, we analyze the transcriptomes of human pluripotent stem cell (hPSC)-derived neurons, from 80 human donors, that were cultured with or without contact with glial cells. We find that the presence of astrocytes enhances synaptic gene-expression programs in neurons when in physical contact with astrocytes. These changes in neurons correlate with increased expression, in the cocultured glia, of genes that encode synaptic cell adhesion molecules. Both the neuronal and astrocyte gene-expression programs are enriched for genes associated with schizophrenia risk. Our results suggest that astrocyte-expressed genes with synaptic functions are associated with stronger expression of synaptic genetic programs in neurons, and they suggest a potential role for astrocyte-neuron interactions in schizophrenia.
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Affiliation(s)
- Olli Pietiläinen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA; Neuroscience Center, Helsinki Institute for Life Science, University of Helsinki, 00290 Helsinki, Finland.
| | - Aditi Trehan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jana Mitchell
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA
| | - Matthew Tegtmeyer
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA; Centre for Gene Therapy and Regenerative Medicine, King's College, London WC2R 2LS, UK
| | - Vera Valakh
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Hilena Gebre
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Theresa Chen
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Emilia Vartiainen
- Neuroscience Center, Helsinki Institute for Life Science, University of Helsinki, 00290 Helsinki, Finland
| | - Samouil L Farhi
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kevin Eggan
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ralda Nehme
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology and the Harvard Institute for Stem Cell Biology, Harvard University, Cambridge, MA 02138, USA.
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48
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Agarwal I, Fuller ZL, Myers SR, Przeworski M. Relating pathogenic loss-of-function mutations in humans to their evolutionary fitness costs. eLife 2023; 12:83172. [PMID: 36648429 PMCID: PMC9937649 DOI: 10.7554/elife.83172] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Causal loss-of-function (LOF) variants for Mendelian and severe complex diseases are enriched in 'mutation intolerant' genes. We show how such observations can be interpreted in light of a model of mutation-selection balance and use the model to relate the pathogenic consequences of LOF mutations at present to their evolutionary fitness effects. To this end, we first infer posterior distributions for the fitness costs of LOF mutations in 17,318 autosomal and 679 X-linked genes from exome sequences in 56,855 individuals. Estimated fitness costs for the loss of a gene copy are typically above 1%; they tend to be largest for X-linked genes, whether or not they have a Y homolog, followed by autosomal genes and genes in the pseudoautosomal region. We compare inferred fitness effects for all possible de novo LOF mutations to those of de novo mutations identified in individuals diagnosed with one of six severe, complex diseases or developmental disorders. Probands carry an excess of mutations with estimated fitness effects above 10%; as we show by simulation, when sampled in the population, such highly deleterious mutations are typically only a couple of generations old. Moreover, the proportion of highly deleterious mutations carried by probands reflects the typical age of onset of the disease. The study design also has a discernible influence: a greater proportion of highly deleterious mutations is detected in pedigree than case-control studies, and for autism, in simplex than multiplex families and in female versus male probands. Thus, anchoring observations in human genetics to a population genetic model allows us to learn about the fitness effects of mutations identified by different mapping strategies and for different traits.
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Affiliation(s)
- Ipsita Agarwal
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
- Department of Statistics, University of OxfordOxfordUnited Kingdom
| | - Zachary L Fuller
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Simon R Myers
- Department of Statistics, University of OxfordOxfordUnited Kingdom
- The Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Molly Przeworski
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
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Levchenko A, Plotnikova M. Genomic regulatory sequences in the pathogenesis of bipolar disorder. Front Psychiatry 2023; 14:1115924. [PMID: 36824672 PMCID: PMC9941178 DOI: 10.3389/fpsyt.2023.1115924] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/23/2023] [Indexed: 02/10/2023] Open
Abstract
The lifetime prevalence of bipolar disorder is estimated to be about 2%. Epigenetics defines regulatory mechanisms that determine relatively stable patterns of gene expression by controlling all key steps, from DNA to messenger RNA to protein. This Mini Review highlights recent discoveries of modified epigenetic control resulting from genetic variants associated with bipolar disorder in genome-wide association studies. The revealed epigenetic abnormalities implicate gene transcription and post-transcriptional regulation. In the light of these discoveries, the Mini Review focuses on the genes PACS1, MCHR1, DCLK3, HAPLN4, LMAN2L, TMEM258, GNL3, LRRC57, CACNA1C, CACNA1D, and NOVA2 and their potential biological role in the pathogenesis of bipolar disorder. Molecular mechanisms under control of these genes do not translate into a unified picture and substantially more research is needed to fill the gaps in knowledge and to solve current limitations in prognosis and treatment of bipolar disorder. In conclusion, the genetic and functional studies confirm the complex nature of bipolar disorder and indicate future research directions to explore possible targeted treatment options, eventually working toward a personalized approach.
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Affiliation(s)
- Anastasia Levchenko
- Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Maria Plotnikova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia
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50
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The autism risk factor CHD8 is a chromatin activator in human neurons and functionally dependent on the ERK-MAPK pathway effector ELK1. Sci Rep 2022; 12:22425. [PMID: 36575212 PMCID: PMC9794786 DOI: 10.1038/s41598-022-23614-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/02/2022] [Indexed: 12/28/2022] Open
Abstract
The chromodomain helicase DNA-binding protein CHD8 is the most frequently mutated gene in autism spectrum disorder. Despite its prominent disease involvement, little is known about its molecular function in the human brain. CHD8 is a chromatin regulator which binds to the promoters of actively transcribed genes through genomic targeting mechanisms which have yet to be fully defined. By generating a conditional loss-of-function and an endogenously tagged allele in human pluripotent stem cells, we investigated the molecular function and the interaction of CHD8 with chromatin in human neurons. Chromatin accessibility analysis and transcriptional profiling revealed that CHD8 functions as a transcriptional activator at its target genes in human neurons. Furthermore, we found that CHD8 chromatin targeting is cell context-dependent. In human neurons, CHD8 preferentially binds at ETS motif-enriched promoters. This enrichment is particularly prominent on the promoters of genes whose expression significantly changes upon the loss of CHD8. Indeed, among the ETS transcription factors, we identified ELK1 as being most highly correlated with CHD8 expression in primary human fetal and adult cortical neurons and most highly expressed in our stem cell-derived neurons. Remarkably, ELK1 was necessary to recruit CHD8 specifically to ETS motif-containing sites. These findings imply that ELK1 and CHD8 functionally cooperate to regulate gene expression and chromatin states at MAPK/ERK target genes in human neurons. Our results suggest that the MAPK/ERK/ELK1 axis potentially contributes to the pathogenesis caused by CHD8 mutations in human neurodevelopmental disorders.
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