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Schoonover KE, Dienel SJ, Holly Bazmi H, Enwright JF, Lewis DA. Altered excitatory and inhibitory ionotropic receptor subunit expression in the cortical visuospatial working memory network in schizophrenia. Neuropsychopharmacology 2024; 49:1183-1192. [PMID: 38548877 PMCID: PMC11109337 DOI: 10.1038/s41386-024-01854-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: 11/01/2023] [Revised: 02/14/2024] [Accepted: 03/06/2024] [Indexed: 05/23/2024]
Abstract
Dysfunction of the cortical dorsal visual stream and visuospatial working memory (vsWM) network in individuals with schizophrenia (SZ) likely reflects alterations in both excitatory and inhibitory neurotransmission within nodes responsible for information transfer across the network, including primary visual (V1), visual association (V2), posterior parietal (PPC), and dorsolateral prefrontal (DLPFC) cortices. However, the expression patterns of ionotropic glutamatergic and GABAergic receptor subunits across these regions, and alterations of these patterns in SZ, have not been investigated. We quantified transcript levels of key subunits for excitatory N-methyl-D-aspartate receptors (NMDARs), excitatory alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptors (AMPARs), and inhibitory GABAA receptors (GABAARs) in postmortem total gray matter from V1, V2, PPC, and DLPFC of unaffected comparison (UC) and matched SZ subjects. In UC subjects, levels of most AMPAR and NMDAR mRNAs exhibited opposite rostral-to-caudal gradients, with AMPAR GRIA1 and GRIA2 mRNA levels highest in DLPFC and NMDAR GRIN1 and GRIN2A mRNA levels highest in V1. GABRA5 and GABRA1 mRNA levels were highest in DLPFC and V1, respectively. In SZ, most transcript levels were lower relative to UC subjects, with these differences largest in V1, intermediate in V2 and PPC, and smallest in DLPFC. In UC subjects, these distinct patterns of receptor transcript levels across the cortical vsWM network suggest that the balance between excitation and inhibition is achieved in a region-specific manner. In SZ subjects, the large deficits in excitatory and inhibitory receptor transcript levels in caudal sensory regions suggest that abnormalities early in the vsWM pathway might contribute to altered information processing in rostral higher-order regions.
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Affiliation(s)
- Kirsten E Schoonover
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Psychiatry and Behavioral Neurobiology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Samuel J Dienel
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Neuroscience, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA
- Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA, USA
| | - H Holly Bazmi
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John F Enwright
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A Lewis
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Neuroscience, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, USA.
- Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA, USA.
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Wang B, Otten LJ, Schulze K, Afrah H, Varney L, Cotic M, Saadullah Khani N, Linden JF, Kuchenbaecker K, McQuillin A, Hall MH, Bramon E. Is auditory processing measured by the N100 an endophenotype for psychosis? A family study and a meta-analysis. Psychol Med 2024; 54:1559-1572. [PMID: 37997703 DOI: 10.1017/s0033291723003409] [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: 11/25/2023]
Abstract
BACKGROUND The N100, an early auditory event-related potential, has been found to be altered in patients with psychosis. However, it is unclear if the N100 is a psychosis endophenotype that is also altered in the relatives of patients. METHODS We conducted a family study using the auditory oddball paradigm to compare the N100 amplitude and latency across 243 patients with psychosis, 86 unaffected relatives, and 194 controls. We then conducted a systematic review and a random-effects meta-analysis pooling our results and 14 previously published family studies. We compared data from a total of 999 patients, 1192 relatives, and 1253 controls in order to investigate the evidence and degree of N100 differences. RESULTS In our family study, patients showed reduced N100 amplitudes and prolonged N100 latencies compared to controls, but no significant differences were found between unaffected relatives and controls. The meta-analysis revealed a significant reduction of the N100 amplitude and delay of the N100 latency in both patients with psychosis (standardized mean difference [s.m.d.] = -0.48 for N100 amplitude and s.m.d. = 0.43 for N100 latency) and their relatives (s.m.d. = - 0.19 for N100 amplitude and s.m.d. = 0.33 for N100 latency). However, only the N100 latency changes in relatives remained significant when excluding studies with affected relatives. CONCLUSIONS N100 changes, especially prolonged N100 latencies, are present in both patients with psychosis and their relatives, making the N100 a promising endophenotype for psychosis. Such changes in the N100 may reflect changes in early auditory processing underlying the etiology of psychosis.
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Affiliation(s)
- Baihan Wang
- Division of Psychiatry, University College London, London, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Leun J Otten
- Institute of Cognitive Neuroscience, University College London, London, UK
| | - Katja Schulze
- South London and Maudsley NHS Foundation Trust, London, UK
| | - Hana Afrah
- Division of Psychiatry, University College London, London, UK
| | - Lauren Varney
- Division of Psychiatry, University College London, London, UK
| | - Marius Cotic
- Division of Psychiatry, University College London, London, UK
- Department of Genetics & Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | | | - Jennifer F Linden
- Ear Institute, University College London, London, UK
- Department of Neuroscience, Physiology & Pharmacology, University College London, London, UK
| | - Karoline Kuchenbaecker
- Division of Psychiatry, University College London, London, UK
- Division of Biosciences, UCL Genetics Institute, University College London, London, UK
| | | | - Mei-Hua Hall
- Psychosis Neurobiology Laboratory, Harvard Medical School, McLean Hospital, Belmont, MA, USA
| | - Elvira Bramon
- Division of Psychiatry, University College London, London, UK
- Institute of Cognitive Neuroscience, University College London, London, UK
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3
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Ruzicka WB, Mohammadi S, Fullard JF, Davila-Velderrain J, Subburaju S, Tso DR, Hourihan M, Jiang S, Lee HC, Bendl J, Voloudakis G, Haroutunian V, Hoffman GE, Roussos P, Kellis M. Single-cell multi-cohort dissection of the schizophrenia transcriptome. Science 2024; 384:eadg5136. [PMID: 38781388 DOI: 10.1126/science.adg5136] [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: 02/02/2023] [Accepted: 07/21/2023] [Indexed: 05/25/2024]
Abstract
The complexity and heterogeneity of schizophrenia have hindered mechanistic elucidation and the development of more effective therapies. Here, we performed single-cell dissection of schizophrenia-associated transcriptomic changes in the human prefrontal cortex across 140 individuals in two independent cohorts. Excitatory neurons were the most affected cell group, with transcriptional changes converging on neurodevelopment and synapse-related molecular pathways. Transcriptional alterations included known genetic risk factors, suggesting convergence of rare and common genomic variants on neuronal population-specific alterations in schizophrenia. Based on the magnitude of schizophrenia-associated transcriptional change, we identified two populations of individuals with schizophrenia marked by expression of specific excitatory and inhibitory neuronal cell states. This single-cell atlas links transcriptomic changes to etiological genetic risk factors, contextualizing established knowledge within the human cortical cytoarchitecture and facilitating mechanistic understanding of schizophrenia pathophysiology and heterogeneity.
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Affiliation(s)
- W Brad Ruzicka
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shahin Mohammadi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jose Davila-Velderrain
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Neurogenomics Research Center, Human Technopole, 20157 Milan, Italy
| | - Sivan Subburaju
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Reed Tso
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
| | - Makayla Hourihan
- Laboratory for Epigenomics in Human Psychopathology, McLean Hospital, Belmont, MA 02478, USA
| | - Shan Jiang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hao-Chih Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jaroslav Bendl
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georgios Voloudakis
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vahram Haroutunian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mental Illness Research, Education and Clinical Centers, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Gabriel E Hoffman
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Neurogenomics Research Center, Human Technopole, 20157 Milan, Italy
| | - Manolis Kellis
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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4
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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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5
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Novarino G, Bock C. Mapping the brain's gene-regulatory maze. Science 2024; 384:860-861. [PMID: 38781359 DOI: 10.1126/science.adp4663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
DNA sequences are connected to genes and functions in the developing and adult brain.
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Affiliation(s)
- Gaia Novarino
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Medical University of Vienna, Institute of Artificial Intelligence, Center for Medical Data Science, Vienna, Austria
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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] [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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Silva DB, Trinidad M, Ljungdahl A, Revalde JL, Berguig GY, Wallace W, Patrick CS, Bomba L, Arkin M, Dong S, Estrada K, Hutchinson K, LeBowitz JH, Schlessinger A, Johannesen KM, Møller RS, Giacomini KM, Froelich S, Sanders SJ, Wuster A. Haploinsufficiency underlies the neurodevelopmental consequences of SLC6A1 variants. Am J Hum Genet 2024:S0002-9297(24)00162-9. [PMID: 38781976 DOI: 10.1016/j.ajhg.2024.04.021] [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: 09/19/2023] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
Heterozygous variants in SLC6A1, encoding the GAT-1 GABA transporter, are associated with seizures, developmental delay, and autism. The majority of affected individuals carry missense variants, many of which are recurrent germline de novo mutations, raising the possibility of gain-of-function or dominant-negative effects. To understand the functional consequences, we performed an in vitro GABA uptake assay for 213 unique variants, including 24 control variants. De novo variants consistently resulted in a decrease in GABA uptake, in keeping with haploinsufficiency underlying all neurodevelopmental phenotypes. Where present, ClinVar pathogenicity reports correlated well with GABA uptake data; the functional data can inform future reports for the remaining 72% of unscored variants. Surface localization was assessed for 86 variants; two-thirds of loss-of-function missense variants prevented GAT-1 from being present on the membrane while GAT-1 was on the surface but with reduced activity for the remaining third. Surprisingly, recurrent de novo missense variants showed moderate loss-of-function effects that reduced GABA uptake with no evidence for dominant-negative or gain-of-function effects. Using linear regression across multiple missense severity scores to extrapolate the functional data to all potential SLC6A1 missense variants, we observe an abundance of GAT-1 residues that are sensitive to substitution. The extent of this missense vulnerability accounts for the clinically observed missense enrichment; overlap with hypermutable CpG sites accounts for the recurrent missense variants. Strategies to increase the expression of the wild-type SLC6A1 allele are likely to be beneficial across neurodevelopmental disorders, though the developmental stage and extent of required rescue remain unknown.
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Affiliation(s)
- Dina Buitrago Silva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Marena Trinidad
- BioMarin Pharmaceutical Inc., Novato, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alicia Ljungdahl
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford OX3 7TY, UK
| | - Jezrael L Revalde
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | | | | | - Cory S Patrick
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Michelle Arkin
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Katrine M Johannesen
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Rikke S Møller
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark; Department of Epilepsy Genetics and Personalized Medicine, Member of ERN Epicare, Danish Epilepsy Centre, Dianalund, Denmark
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | | | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA; Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford OX3 7TY, UK.
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9
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Cai W, Song W, Yu S, Zhao M, Lin GN. Human lineage mutations regulate RNA-protein binding of conserved genes NTRK2 and ITPR1 involved in human evolution. Gen Psychiatr 2024; 37:e101425. [PMID: 38770356 PMCID: PMC11103204 DOI: 10.1136/gpsych-2023-101425] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/14/2024] [Indexed: 05/22/2024] Open
Abstract
Background The role of human lineage mutations (HLMs) in human evolution through post-transcriptional modification is unclear. Aims To investigate the contribution of HLMs to human evolution through post-transcriptional modification. Methods We applied a deep learning model Seqweaver to predict how HLMs impact RNA-binding protein affinity. Results We found that only 0.27% of HLMs had significant impacts on RNA-binding proteins at the threshold of the top 1% of human common variations. These HLMs enriched in a set of conserved genes highly expressed in adult excitatory neurons and prenatal Purkinje neurons, and were involved in synapse organisation and the GTPase pathway. These genes also carried excess damaging coding mutations that caused neurodevelopmental disorders, ataxia and schizophrenia. Among these genes, NTRK2 and ITPR1 had the most aggregated evidence of functional importance, suggesting their essential roles in cognition and bipedalism. Conclusions Our findings suggest that a small subset of human-specific mutations have contributed to human speciation through impacts on post-transcriptional modification of critical brain-related genes.
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Affiliation(s)
- Wenxiang Cai
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Weichen Song
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Shunying Yu
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Min Zhao
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
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10
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Kraft J, Braun A, Awasthi S, Panagiotaropoulou G, Schipper M, Bell N, Posthuma D, Pardiñas AF, Ripke S, Heilbron K. Identifying drug targets for schizophrenia through gene prioritization. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307423. [PMID: 38798390 PMCID: PMC11118622 DOI: 10.1101/2024.05.15.24307423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Background Schizophrenia genome-wide association studies (GWASes) have identified >250 significant loci and prioritized >100 disease-related genes. However, gene prioritization efforts have mostly been restricted to locus-based methods that ignore information from the rest of the genome. Methods To more accurately characterize genes involved in schizophrenia etiology, we applied a combination of highly-predictive tools to a published GWAS of 67,390 schizophrenia cases and 94,015 controls. We combined both locus-based methods (fine-mapped coding variants, distance to GWAS signals) and genome-wide methods (PoPS, MAGMA, ultra-rare coding variant burden tests). To validate our findings, we compared them with previous prioritization efforts, known neurodevelopmental genes, and results from the PsyOPS tool. Results We prioritized 62 schizophrenia genes, 41 of which were also highlighted by our validation methods. In addition to DRD2 , the principal target of antipsychotics, we prioritized 9 genes that are targeted by approved or investigational drugs. These included drugs targeting glutamatergic receptors ( GRIN2A and GRM3 ), calcium channels ( CACNA1C and CACNB2 ), and GABA B receptor ( GABBR2 ). These also included genes in loci that are shared with an addiction GWAS ( e.g. PDE4B and VRK2 ). Conclusions We curated a high-quality list of 62 genes that likely play a role in the development of schizophrenia. Developing or repurposing drugs that target these genes may lead to a new generation of schizophrenia therapies. Rodent models of addiction more closely resemble the human disorder than rodent models of schizophrenia. As such, genes prioritized for both disorders could be explored in rodent addiction models, potentially facilitating drug development.
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11
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Sefik E, Duan K, Li Y, Sholar B, Evans L, Pincus J, Ammar Z, Murphy MM, Klaiman C, Saulnier CA, Pulver SL, Goldman-Yassen AE, Guo Y, Walker EF, Li L, Mulle JG, Shultz S. Structural deviations of the posterior fossa and the cerebellum and their cognitive links in a neurodevelopmental deletion syndrome. Mol Psychiatry 2024:10.1038/s41380-024-02584-8. [PMID: 38744992 DOI: 10.1038/s41380-024-02584-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
High-impact genetic variants associated with neurodevelopmental disorders provide biologically-defined entry points for mechanistic investigation. The 3q29 deletion (3q29Del) is one such variant, conferring a 40-100-fold increased risk for schizophrenia, as well as high risk for autism and intellectual disability. However, the mechanisms leading to neurodevelopmental disability remain largely unknown. Here, we report the first in vivo quantitative neuroimaging study in individuals with 3q29Del (N = 24) and neurotypical controls (N = 1608) using structural MRI. Given prior radiology reports of posterior fossa abnormalities in 3q29Del, we focused our investigation on the cerebellum and its tissue-types and lobules. Additionally, we compared the prevalence of cystic/cyst-like malformations of the posterior fossa between 3q29Del and controls and examined the association between neuroanatomical findings and quantitative traits to probe gene-brain-behavior relationships. 3q29Del participants had smaller cerebellar cortex volumes than controls, before and after correction for intracranial volume (ICV). An anterior-posterior gradient emerged in finer grained lobule-based and voxel-wise analyses. 3q29Del participants also had larger cerebellar white matter volumes than controls following ICV-correction and displayed elevated rates of posterior fossa arachnoid cysts and mega cisterna magna findings independent of cerebellar volume. Cerebellar white matter and subregional gray matter volumes were associated with visual-perception and visual-motor integration skills as well as IQ, while cystic/cyst-like malformations yielded no behavioral link. In summary, we find that abnormal development of cerebellar structures may represent neuroimaging-based biomarkers of cognitive and sensorimotor function in 3q29Del, adding to the growing evidence identifying cerebellar pathology as an intersection point between syndromic and idiopathic forms of neurodevelopmental disabilities.
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Affiliation(s)
- Esra Sefik
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Kuaikuai Duan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science, Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, USA
| | - Yiheng Li
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brittney Sholar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsey Evans
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Jordan Pincus
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Zeena Ammar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Melissa M Murphy
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Cheryl Klaiman
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Celine A Saulnier
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Neurodevelopmental Assessment & Consulting Services, Atlanta, GA, USA
| | - Stormi L Pulver
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Adam E Goldman-Yassen
- Department of Radiology, Children's Healthcare of Atlanta, Atlanta, GA, USA
- Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Ying Guo
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elaine F Walker
- Department of Psychology, Emory University, Atlanta, GA, USA
| | - Longchuan Li
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer G Mulle
- Department of Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA.
| | - Sarah Shultz
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Marcus Autism Center, Children's Healthcare of Atlanta and Emory University School of Medicine, Atlanta, GA, USA.
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12
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Burrack N, Yitzhaky A, Mizrahi L, Wang M, Stern S, Hertzberg L. Altered Expression of PDE4 Genes in Schizophrenia: Insights from a Brain and Blood Sample Meta-Analysis and iPSC-Derived Neurons. Genes (Basel) 2024; 15:609. [PMID: 38790238 PMCID: PMC11121586 DOI: 10.3390/genes15050609] [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: 06/04/2023] [Revised: 05/03/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Schizophrenia symptomatology includes negative symptoms and cognitive impairment. Several studies have linked schizophrenia with the PDE4 family of enzymes due to their genetic association and function in cognitive processes such as long-term potentiation. We conducted a systematic gene expression meta-analysis of four PDE4 genes (PDE4A-D) in 10 brain sample datasets (437 samples) and three blood sample datasets (300 samples). Subsequently, we measured mRNA levels in iPSC-derived hippocampal dentate gyrus neurons generated from fibroblasts of three groups: healthy controls, healthy monozygotic twins (MZ), and their MZ siblings with schizophrenia. We found downregulation of PDE4B in brain tissues, further validated by independent data of the CommonMind consortium (515 samples). Interestingly, the downregulation signal was present in a subgroup of the patients, while the others showed no differential expression or even upregulation. Notably, PDE4A, PDE4B, and PDE4D exhibited upregulation in iPSC-derived neurons compared to healthy controls, whereas in blood samples, PDE4B was found to be upregulated while PDE4A was downregulated. While the precise mechanism and direction of altered PDE4 expression necessitate further investigation, the observed multilevel differential expression across the brain, blood, and iPSC-derived neurons compellingly suggests the involvement of PDE4 genes in the pathophysiology of schizophrenia.
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Affiliation(s)
- Nitzan Burrack
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84101, Israel;
- Clinical Research Center, Soroka University Medical Center, Beer-Sheva 84101, Israel
| | - Assif Yitzhaky
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Liron Mizrahi
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3103301, Israel
| | - Meiyan Wang
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Shani Stern
- Sagol Department of Neurobiology, Faculty of Natural Sciences, University of Haifa, Haifa 3103301, Israel
| | - Libi Hertzberg
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
- Shalvata Mental Health Center, Affiliated with the Faculty of Medicine, Tel-Aviv University, 13 Aliat Hanoar St., Hod Hasharon 45100, Israel
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13
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Fatemi SH, Eschenlauer A, Aman J, Folsom TD, Chekouo T. Quantitative proteomics of dorsolateral prefrontal cortex reveals an early pattern of synaptic dysmaturation in children with idiopathic autism. Cereb Cortex 2024; 34:161-171. [PMID: 38696595 DOI: 10.1093/cercor/bhae044] [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: 12/26/2023] [Accepted: 01/23/2024] [Indexed: 05/04/2024] Open
Abstract
Autism spectrum disorder (ASD) is a developmental disorder with a rising prevalence and unknown etiology presenting with deficits in cognition and abnormal behavior. We hypothesized that the investigation of the synaptic component of prefrontal cortex may provide proteomic signatures that may identify the biological underpinnings of cognitive deficits in childhood ASD. Subcellular fractions of synaptosomes from prefrontal cortices of age-, brain area-, and postmortem-interval-matched samples from children and adults with idiopathic ASD vs. controls were subjected to HPLC-tandem mass spectrometry. Analysis of data revealed the enrichment of ASD risk genes that participate in slow maturation of the postsynaptic density (PSD) structure and function during early brain development. Proteomic analysis revealed down regulation of PSD-related proteins including AMPA and NMDA receptors, GRM3, DLG4, olfactomedins, Shank1-3, Homer1, CaMK2α, NRXN1, NLGN2, Drebrin1, ARHGAP32, and Dock9 in children with autism (FDR-adjusted P < 0.05). In contrast, PSD-related alterations were less severe or unchanged in adult individuals with ASD. Network analyses revealed glutamate receptor abnormalities. Overall, the proteomic data support the concept that idiopathic autism is a synaptopathy involving PSD-related ASD risk genes. Interruption in evolutionarily conserved slow maturation of the PSD complex in prefrontal cortex may lead to the development of ASD in a susceptible individual.
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Affiliation(s)
- S Hossein Fatemi
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Arthur Eschenlauer
- Minnesota Supercomputing Institute, 599 Walter Library, 117 Pleasant Street, Minneapolis, MN 55455, USA
| | - Justin Aman
- Department of Psychiatry and Behavioral Sciences, University of Minnesota Medical School, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Timothy D Folsom
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota Medical School, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Thierry Chekouo
- University of Minnesota School of Public Health, Minneapolis, MN 55455, USA
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14
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Besterman AD. A genetics-guided approach to the clinical management of schizophrenia. Schizophr Res 2024; 267:462-469. [PMID: 37813777 DOI: 10.1016/j.schres.2023.09.042] [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: 05/14/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/11/2023]
Abstract
Schizophrenia is a highly heritable, severe mental illness characterized by hallucinations, delusions, social withdrawal, and cognitive dysfunction present in ∼1% of populations across cultures. There have been recent major advancements in our understanding of the genetic architecture of schizophrenia. Both rare, highly penetrant genetic variants as well as common, low-penetrant genetic variants can predispose individuals to schizophrenia and can impact the way people metabolize psychoactive medications used to treat schizophrenia. However, the impact of these findings on the clinical management of schizophrenia remains limited. This review highlights the few places where genetics currently informs schizophrenia management strategies, discusses major limitations, and reviews promising areas of genetics research that are most likely to impact future schizophrenia care. Specifically, I focuss on psychiatric genetic counseling, genetic testing strategies, pharmacogenetics, polygenic risk, and genetics-guided treatment. Lastly, I emphasize important ethical considerations in the clinical use of genetics for schizophrenia management, including the exacerbation of healthcare inequalities and unintended consequences of new genetic technologies.
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Affiliation(s)
- Aaron D Besterman
- University of California San Diego, Department of Psychiatry, San Diego, CA, USA; Rady Children's Hospital San Diego, Division of Behavioral Health Services, San Diego, CA, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA, USA.
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15
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Marín O. Parvalbumin interneuron deficits in schizophrenia. Eur Neuropsychopharmacol 2024; 82:44-52. [PMID: 38490084 DOI: 10.1016/j.euroneuro.2024.02.010] [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: 12/21/2023] [Accepted: 02/16/2024] [Indexed: 03/17/2024]
Abstract
Parvalbumin-expressing (PV+) interneurons represent one of the most abundant subclasses of cortical interneurons. Owing to their specific electrophysiological and synaptic properties, PV+ interneurons are essential for gating and pacing the activity of excitatory neurons. In particular, PV+ interneurons are critically involved in generating and maintaining cortical rhythms in the gamma frequency, which are essential for complex cognitive functions. Deficits in PV+ interneurons have been frequently reported in postmortem studies of schizophrenia patients, and alterations in gamma oscillations are a prominent electrophysiological feature of the disease. Here, I summarise the main features of PV+ interneurons and review clinical and preclinical studies linking the developmental dysfunction of cortical PV+ interneurons with the pathophysiology of schizophrenia.
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Affiliation(s)
- Oscar Marín
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom; Medical Research Council Centre for Neurodevelopmental Disorders, King's College London, London SE1 1UL, United Kingdom.
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16
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Clifton NE, Lin JQ, Holt CE, O'Donovan MC, Mill J. Enrichment of the Local Synaptic Translatome for Genetic Risk Associated With Schizophrenia and Autism Spectrum Disorder. Biol Psychiatry 2024; 95:888-895. [PMID: 38103876 DOI: 10.1016/j.biopsych.2023.12.006] [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: 11/15/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Genes that encode synaptic proteins or messenger RNA targets of the RNA-binding protein FMRP (fragile X messenger ribonucleoprotein) have been linked to schizophrenia and autism spectrum disorder (ASD) through the enrichment of genetic variants that confer risk for these disorders. FMRP binds many transcripts with synaptic functions and is thought to regulate their local translation, a process that enables rapid and compartmentalized protein synthesis required for development and plasticity. METHODS We used summary statistics from large-scale genome-wide association studies of schizophrenia (74,776 cases, 101,023 controls) and ASD (18,381 cases, 27,969 controls) to test the hypothesis that the subset of synaptic genes that encode localized transcripts is more strongly associated with each disorder than nonlocalized transcripts. We also postulated that this subset of synaptic genes is responsible for associations attributed to FMRP targets. RESULTS Schizophrenia associations were enriched in genes encoding localized synaptic transcripts compared to the remaining synaptic genes or to the remaining localized transcripts; this also applied to ASD associations, although only for transcripts observed after stimulation by fear conditioning. The genetic associations with either disorder captured by these gene sets were independent of those derived from FMRP targets. Schizophrenia association was related to FMRP interactions with messenger RNAs in somata, but not in dendrites, while ASD association was related to FMRP binding in either compartment. CONCLUSIONS Our data suggest that synaptic transcripts capable of local translation are particularly relevant to the pathogenesis of schizophrenia and ASD, but they do not characterize the associations attributed to current sets of FMRP targets.
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Affiliation(s)
- Nicholas E Clifton
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom.
| | - Julie Qiaojin Lin
- UK Dementia Research Institute, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; UK Dementia Research Institute, King's College London, London, United Kingdom
| | - Christine E Holt
- Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Michael C O'Donovan
- Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, United Kingdom
| | - Jonathan Mill
- Department of Clinical & Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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17
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Kendall KM, Duffin D, Doherty J, Irving R, Procter A, Walters JTR. The translation of psychiatric genetic findings to the clinic. Schizophr Res 2024; 267:470-472. [PMID: 37919212 DOI: 10.1016/j.schres.2023.10.024] [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: 06/29/2023] [Revised: 10/06/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
Mental health and neurodevelopmental disorders are highly heritable and can affect morbidity and mortality. A large, growing body of evidence has implicated both common and rare variation in the risk of these disorders. Testing for rare variants, such as copy number variants, has been available in clinical practice for some time in the context of developmental disorders. However, until recently, individuals with mental health and neurodevelopmental disorders in the UK have not tended to access genetic counselling and testing. Here, we describe the development of the All Wales Psychiatric Genomics Service, a collaborative effort between psychiatric and clinical genetics services and the first of its kind in the UK. We provide an overview of the structure and function of the service, our referral criteria, a summary of the 40 referrals we have received to date and our future plans.
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Affiliation(s)
- Kimberley Marie Kendall
- Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, United Kingdom.
| | - Donna Duffin
- All Wales Medical Genomics Service, Heath Park, Cardiff CF14 4XW, United Kingdom.
| | - Joanne Doherty
- Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, United Kingdom.
| | - Rachel Irving
- All Wales Medical Genomics Service, Heath Park, Cardiff CF14 4XW, United Kingdom.
| | - Annie Procter
- All Wales Medical Genomics Service, Heath Park, Cardiff CF14 4XW, United Kingdom
| | - James Tynan Rhys Walters
- Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Hadyn Ellis Building, Maindy Road, Cardiff CF24 4HQ, United Kingdom.
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18
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Yu S, Qu Y, Du Z, Ou M, Lu R, Yuan J, Jiang Y, Zhu H. The expression of immune related genes and potential regulatory mechanisms in schizophrenia. Schizophr Res 2024; 267:507-518. [PMID: 37993327 DOI: 10.1016/j.schres.2023.11.007] [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: 07/03/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/24/2023]
Abstract
OBJECTIVE This study aimed to investigate the role of immune dysfunction in the pathogenesis of schizophrenia through single-cell transcriptome and bulk RNA data analyses. METHODS The single-cell RNA sequencing (scRNA-seq) was selected to assess the cellular composition and gene expression profiles of the brain tissue. Further, bulk RNA sequencing data was utilized to corroborate findings from the single-cell analyses and provide additional insights into the molecular changes associated with the disease. Gene-drug interaction data was also included to identify potential therapeutic drugs targeting these dysregulated immune-related genes in schizophrenia. RESULTS We discovered significant differences in cellular composition within schizophrenia tissue, including increased infiltration of fibroblasts, horizontal basal cells, monocytes, mesenchymal cells, and smooth muscle cells. The investigation of immune-related genes revealed significantly different expression of genes such as S100A2, CCL14, IGHA1, BPIFA1, GDF15, IL32, BPIFB2, HLA-DRA, S100A8, PTX3, TPM2, TNFRSF12A, GREM1 and others. These genes possibly contribute to the progression of schizophrenia through various pathways such as humoral immune response, IL-17 signaling pathway, adaptive immune response, antigen processing and presentation, and gut IgA production. Our findings also suggest possible transcriptional regulation in schizophrenia's immune dysfunction by transcription factors in monocytes, neutrophils, endothelial cells, and epithelial cells. Lastly, potential therapeutic drugs were identified through gene-drug interaction data, such as those targeting HLA-A and HLAB. CONCLUSION The cellular heterogeneity and immune-related gene dysregulation play important roles in schizophrenia, which provides a foundation for understanding the pathogenesis and developing new treatment methods.
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Affiliation(s)
- Shui Yu
- Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu 214151, China
| | - Yucai Qu
- Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu 214151, China
| | - Zhiqiang Du
- Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu 214151, China
| | - Mengmeng Ou
- Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu 214151, China
| | - Rongrong Lu
- Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu 214151, China
| | - Jianming Yuan
- Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu 214151, China
| | - Ying Jiang
- Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu 214151, China.
| | - Haohao Zhu
- Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu 214151, China.
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19
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Livingston NR, Kiemes A, Devenyi GA, Knight S, Lukow PB, Jelen LA, Reilly T, Dima A, Nettis MA, Casetta C, Agyekum T, Zelaya F, Spencer T, De Micheli A, Fusar-Poli P, Grace AA, Williams SCR, McGuire P, Egerton A, Chakravarty MM, Modinos G. Effects of diazepam on hippocampal blood flow in people at clinical high risk for psychosis. Neuropsychopharmacology 2024:10.1038/s41386-024-01864-9. [PMID: 38658738 DOI: 10.1038/s41386-024-01864-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/11/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Elevated hippocampal perfusion has been observed in people at clinical high risk for psychosis (CHR-P). Preclinical evidence suggests that hippocampal hyperactivity is central to the pathophysiology of psychosis, and that peripubertal treatment with diazepam can prevent the development of psychosis-relevant phenotypes. The present experimental medicine study examined whether diazepam can normalize hippocampal perfusion in CHR-P individuals. Using a randomized, double-blind, placebo-controlled, crossover design, 24 CHR-P individuals were assessed with magnetic resonance imaging (MRI) on two occasions, once following a single oral dose of diazepam (5 mg) and once following placebo. Regional cerebral blood flow (rCBF) was measured using 3D pseudo-continuous arterial spin labeling and sampled in native space using participant-specific hippocampus and subfield masks (CA1, subiculum, CA4/dentate gyrus). Twenty-two healthy controls (HC) were scanned using the same MRI acquisition sequence, but without administration of diazepam or placebo. Mixed-design ANCOVAs and linear mixed-effects models were used to examine the effects of group (CHR-P placebo/diazepam vs. HC) and condition (CHR-P diazepam vs. placebo) on rCBF in the hippocampus as a whole and by subfield. Under the placebo condition, CHR-P individuals (mean [±SD] age: 24.1 [±4.8] years, 15 F) showed significantly elevated rCBF compared to HC (mean [±SD] age: 26.5 [±5.1] years, 11 F) in the hippocampus (F(1,41) = 24.7, pFDR < 0.001) and across its subfields (all pFDR < 0.001). Following diazepam, rCBF in the hippocampus (and subfields, all pFDR < 0.001) was significantly reduced (t(69) = -5.1, pFDR < 0.001) and normalized to HC levels (F(1,41) = 0.4, pFDR = 0.204). In conclusion, diazepam normalized hippocampal hyperperfusion in CHR-P individuals, consistent with evidence implicating medial temporal GABAergic dysfunction in increased vulnerability for psychosis.
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Affiliation(s)
- Nicholas R Livingston
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK.
| | - Amanda Kiemes
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Gabriel A Devenyi
- Department of Psychiatry, McGill University, Montreal, QC, Canada
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal, QC, Canada
| | - Samuel Knight
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Paulina B Lukow
- Institute of Cognitive Neuroscience, University College London, London, UK
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Luke A Jelen
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Thomas Reilly
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Aikaterini Dima
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Maria Antonietta Nettis
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Cecilia Casetta
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Tyler Agyekum
- Department of Psychiatry, McGill University, Montreal, QC, Canada
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal, QC, Canada
| | - Fernando Zelaya
- Department of Neuroimaging, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Thomas Spencer
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- Outreach and Support in South-London (OASIS) service, South London and Maudsley (SLaM) NHS Foundation Trust, London, UK
| | - Andrea De Micheli
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- Outreach and Support in South-London (OASIS) service, South London and Maudsley (SLaM) NHS Foundation Trust, London, UK
| | - Paolo Fusar-Poli
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- Outreach and Support in South-London (OASIS) service, South London and Maudsley (SLaM) NHS Foundation Trust, London, UK
- Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Anthony A Grace
- Departments of Neuroscience, Psychiatry and Psychology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steve C R Williams
- Department of Neuroimaging, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - Philip McGuire
- Department of Psychiatry, University of Oxford, Oxford, UK
| | - Alice Egerton
- Department of Psychosis Studies, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
| | - M Mallar Chakravarty
- Department of Psychiatry, McGill University, Montreal, QC, Canada
- Cerebral Imaging Centre, Douglas Mental Health University Institute, Montreal, QC, Canada
| | - Gemma Modinos
- Department of Psychological Medicine, Institute of Psychiatry, Psychology, and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
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20
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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. [PMID: 38646907 DOI: 10.1111/pcn.13669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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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21
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Bhattacharyya U, John J, Lencz T, Lam M. Dissecting Schizophrenia Biology Using Pleiotropy with Cognitive Genomics. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.16.24305885. [PMID: 38699340 PMCID: PMC11065000 DOI: 10.1101/2024.04.16.24305885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Given the increasingly large number of loci discovered by psychiatric GWAS, specification of the key biological pathways underlying these loci has become a priority for the field. We have previously leveraged the pleiotropic genetic relationships between schizophrenia and two cognitive phenotypes (educational attainment and cognitive task performance) to differentiate two subsets of illness-relevant SNPs: (1) those with "concordant" alleles, which are associated with reduced cognitive ability/education and increased schizophrenia risk; and (2) those with "discordant" alleles linked to reduced educational and/or cognitive levels but lower schizophrenia susceptibility. In the present study, we extend our prior work, utilizing larger input GWAS datasets and a more powerful statistical approach to pleiotropic meta-analysis, the Pleiotropic Locus Exploration and Interpretation using Optimal test (PLEIO). Our pleiotropic meta-analysis of schizophrenia and the two cognitive phenotypes revealed 768 significant loci (159 novel). Among these, 347 loci harbored concordant SNPs, 270 encompassed discordant SNPs, and 151 "dual" loci contained concordant and discordant SNPs. Competitive gene-set analysis using MAGMA related concordant SNP loci with neurodevelopmental pathways (e.g., neurogenesis), whereas discordant loci were associated with mature neuronal synaptic functions. These distinctions were also observed in BrainSpan analysis of temporal enrichment patterns across developmental periods, with concordant loci containing more prenatally expressed genes than discordant loci. Dual loci were enriched for genes related to mRNA translation initiation, representing a novel finding in the schizophrenia literature.
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22
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Powers A, Angelos P, Bond A, Farina E, Fredericks C, Gandhi J, Greenwald M, Hernandez-Busot G, Hosein G, Kelley M, Mourgues C, Palmer W, Rodriguez-Sanchez J, Seabury R, Toribio S, Vin R, Weleff J, Benrimoh D. A computational account of the development and evolution of psychotic symptoms. ARXIV 2024:arXiv:2404.10954v1. [PMID: 38699166 PMCID: PMC11065053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
The mechanisms of psychotic symptoms like hallucinations and delusions are often investigated in fully-formed illness, well after symptoms emerge. These investigations have yielded key insights, but are not well-positioned to reveal the dynamic forces underlying symptom formation itself. Understanding symptom development over time would allow us to identify steps in the pathophysiological process leading to psychosis, shifting the focus of psychiatric intervention from symptom alleviation to prevention. We propose a model for understanding the emergence of psychotic symptoms within the context of an adaptive, developing neural system. We will make the case for a pathophysiological process that begins with cortical hyperexcitability and bottom-up noise transmission, which engenders inappropriate belief formation via aberrant prediction error signaling. We will argue that this bottom-up noise drives learning about the (im)precision of new incoming sensory information because of diminished signal-to-noise ratio, causing an adaptive relative over-reliance on prior beliefs. This over-reliance on priors predisposes to hallucinations and covaries with hallucination severity. An over-reliance on priors may also lead to increased conviction in the beliefs generated by bottom-up noise and drive movement toward conversion to psychosis. We will identify predictions of our model at each stage, examine evidence to support or refute those predictions, and propose experiments that could falsify or help select between alternative elements of the overall model. Nesting computational abnormalities within longitudinal development allows us to account for hidden dynamics among the mechanisms driving symptom formation and to view established symptomatology as a point of equilibrium among competing biological forces.
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Affiliation(s)
- Albert Powers
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Philip Angelos
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Alexandria Bond
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Emily Farina
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Carolyn Fredericks
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Jay Gandhi
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Maximillian Greenwald
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | | | - Gabriel Hosein
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Megan Kelley
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Catalina Mourgues
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - William Palmer
- Yale University Department of Psychology, New Haven, CT USA
| | | | - Rashina Seabury
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Silmilly Toribio
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Raina Vin
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - Jeremy Weleff
- Yale University School of Medicine and the Connecticut Mental Health Center, New Haven, CT, USA
| | - David Benrimoh
- Department of Psychiatry, McGill University, Montreal, Canada
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23
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Casey C, Fullard JF, Sleator RD. Unravelling the genetic basis of Schizophrenia. Gene 2024; 902:148198. [PMID: 38266791 DOI: 10.1016/j.gene.2024.148198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/07/2023] [Accepted: 01/19/2024] [Indexed: 01/26/2024]
Abstract
Neuronal development is a highly regulated mechanism that is central to organismal function in animals. In humans, disruptions to this process can lead to a range of neurodevelopmental phenotypes, including Schizophrenia (SCZ). SCZ has a significant genetic component, whereby an individual with an SCZ affected family member is eight times more likely to develop the disease than someone with no family history of SCZ. By examining a combination of genomic, transcriptomic and epigenomic datasets, large-scale 'omics' studies aim to delineate the relationship between genetic variation and abnormal cellular activity in the SCZ brain. Herein, we provide a brief overview of some of the key omics methods currently being used in SCZ research, including RNA-seq, the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and high-throughput chromosome conformation capture (3C) approaches (e.g., Hi-C), as well as single-cell/nuclei iterations of these methods. We also discuss how these techniques are being employed to further our understanding of the genetic basis of SCZ, and to identify associated molecular pathways, biomarkers, and candidate drug targets.
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Affiliation(s)
- Clara Casey
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland; Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - John F Fullard
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Roy D Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland.
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24
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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 2024:10.1038/s41562-024-01861-4. [PMID: 38589703 DOI: 10.1038/s41562-024-01861-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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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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Schijven D, Soheili-Nezhad S, Fisher SE, Francks C. Exome-wide analysis implicates rare protein-altering variants in human handedness. Nat Commun 2024; 15:2632. [PMID: 38565598 PMCID: PMC10987538 DOI: 10.1038/s41467-024-46277-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
Handedness is a manifestation of brain hemispheric specialization. Left-handedness occurs at increased rates in neurodevelopmental disorders. Genome-wide association studies have identified common genetic effects on handedness or brain asymmetry, which mostly involve variants outside protein-coding regions and may affect gene expression. Implicated genes include several that encode tubulins (microtubule components) or microtubule-associated proteins. Here we examine whether left-handedness is also influenced by rare coding variants (frequencies ≤ 1%), using exome data from 38,043 left-handed and 313,271 right-handed individuals from the UK Biobank. The beta-tubulin gene TUBB4B shows exome-wide significant association, with a rate of rare coding variants 2.7 times higher in left-handers than right-handers. The TUBB4B variants are mostly heterozygous missense changes, but include two frameshifts found only in left-handers. Other TUBB4B variants have been linked to sensorineural and/or ciliopathic disorders, but not the variants found here. Among genes previously implicated in autism or schizophrenia by exome screening, DSCAM and FOXP1 show evidence for rare coding variant association with left-handedness. The exome-wide heritability of left-handedness due to rare coding variants was 0.91%. This study reveals a role for rare, protein-altering variants in left-handedness, providing further evidence for the involvement of microtubules and disorder-relevant genes.
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Affiliation(s)
- Dick Schijven
- Language & Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Sourena Soheili-Nezhad
- Language & Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
| | - Simon E Fisher
- Language & Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Clyde Francks
- Language & Genetics Department, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.
- Department of Cognitive Neuroscience, Radboud University Medical Center, Nijmegen, The Netherlands.
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Akkouh IA, Ueland T, Szabo A, Hughes T, Smeland OB, Andreassen OA, Osete JR, Djurovic S. Longitudinal Transcriptomic Analysis of Human Cortical Spheroids Identifies Axonal Dysregulation in the Prenatal Brain as a Mediator of Genetic Risk for Schizophrenia. Biol Psychiatry 2024; 95:687-698. [PMID: 37661009 DOI: 10.1016/j.biopsych.2023.08.017] [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: 01/25/2023] [Revised: 07/28/2023] [Accepted: 08/22/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Schizophrenia (SCZ) has a known neurodevelopmental etiology, but limited access to human prenatal brain tissue hampers the investigation of basic disease mechanisms in early brain development. Here, we elucidate the molecular mechanisms contributing to SCZ risk in a disease-relevant model of the prenatal human brain. METHODS We generated induced pluripotent stem cell-derived organoids, termed human cortical spheroids (hCSs), from a large, genetically stratified sample of 14 SCZ cases and 14 age- and sex-matched controls. The hCSs were differentiated for 150 days, and comprehensive molecular characterization across 4 time points was carried out. RESULTS The transcriptional and cellular architecture of hCSs closely resembled that of fetal brain tissue at 10 to 24 postconception weeks, showing strongest spatial overlap with frontal regions of the cerebral cortex. A total of 3520 genes were differentially modulated between SCZ and control hCSs across organoid maturation, displaying a significant contribution of genetic loading, an overrepresentation of risk genes for autism spectrum disorder and SCZ, and the strongest enrichment for axonal processes in all hCS stages. The two axon guidance genes SEMA7A and SEMA5A, the first a promoter of synaptic functions and the second a repressor, were downregulated and upregulated, respectively, in SCZ hCSs. This expression pattern was confirmed at the protein level and replicated in a large postmortem sample. CONCLUSIONS Applying a disease-relevant model of the developing fetal brain, we identified consistent dysregulation of axonal genes as an early risk factor for SCZ, providing novel insights into the effects of genetic predisposition on the neurodevelopmental origins of the disorder.
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Affiliation(s)
- Ibrahim A Akkouh
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway.
| | - Thor Ueland
- Research Institute of Internal Medicine, Oslo University Hospital Rikshospitalet, Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway; K.G. Jebsen Thrombosis Research and Expertise Center, University of Tromsø, Tromsø, Norway
| | - Attila Szabo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Timothy Hughes
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Olav B Smeland
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Ole A Andreassen
- Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Jordi Requena Osete
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Division of Mental Health and Addiction, Oslo University Hospital, Oslo, Norway
| | - Srdjan Djurovic
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway; Norwegian Centre for Mental Disorders Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
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Qi X, Yu X, Wei L, Jiang H, Dong J, Li H, Wei Y, Zhao L, Deng W, Guo W, Hu X, Li T. Novel α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor (AMPAR) potentiator LT-102: A promising therapeutic agent for treating cognitive impairment associated with schizophrenia. CNS Neurosci Ther 2024; 30:e14713. [PMID: 38615362 PMCID: PMC11016348 DOI: 10.1111/cns.14713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 03/07/2024] [Accepted: 03/23/2024] [Indexed: 04/16/2024] Open
Abstract
AIMS We aimed to evaluate the potential of a novel selective α-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid receptor (AMPAR) potentiator, LT-102, in treating cognitive impairments associated with schizophrenia (CIAS) and elucidating its mechanism of action. METHODS The activity of LT-102 was examined by Ca2+ influx assays and patch-clamp in rat primary hippocampal neurons. The structure of the complex was determined by X-ray crystallography. The selectivity of LT-102 was evaluated by hERG tail current recording and kinase-inhibition assays. The electrophysiological characterization of LT-102 was characterized by patch-clamp recording in mouse hippocampal slices. The expression and phosphorylation levels of proteins were examined by Western blotting. Cognitive function was assessed using the Morris water maze and novel object recognition tests. RESULTS LT-102 is a novel and selective AMPAR potentiator with little agonistic effect, which binds to the allosteric site formed by the intradimer interface of AMPAR's GluA2 subunit. Treatment with LT-102 facilitated long-term potentiation in mouse hippocampal slices and reversed cognitive deficits in a phencyclidine-induced mouse model. Additionally, LT-102 treatment increased the protein level of brain-derived neurotrophic factor and the phosphorylation of GluA1 in primary neurons and hippocampal tissues. CONCLUSION We conclude that LT-102 ameliorates cognitive impairments in a phencyclidine-induced model of schizophrenia by enhancing synaptic function, which could make it a potential therapeutic candidate for CIAS.
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Affiliation(s)
- Xueyu Qi
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital and School of Brain Science and Brain MedicineZhejiang University School of MedicineHangzhouChina
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain‐Machine Integration, State Key Laboratory of Brain‐Machine IntelligenceZhejiang UniversityHangzhouChina
- NHC and CAMS Key Laboratory of Medical NeurobiologyZhejiang UniversityHangzhouChina
| | - Xueli Yu
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital and School of Brain Science and Brain MedicineZhejiang University School of MedicineHangzhouChina
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain‐Machine Integration, State Key Laboratory of Brain‐Machine IntelligenceZhejiang UniversityHangzhouChina
- NHC and CAMS Key Laboratory of Medical NeurobiologyZhejiang UniversityHangzhouChina
| | - Long Wei
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital and School of Brain Science and Brain MedicineZhejiang University School of MedicineHangzhouChina
| | - Han Jiang
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital and School of Brain Science and Brain MedicineZhejiang University School of MedicineHangzhouChina
| | - Jiangwen Dong
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital and School of Brain Science and Brain MedicineZhejiang University School of MedicineHangzhouChina
| | - Hongxing Li
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital and School of Brain Science and Brain MedicineZhejiang University School of MedicineHangzhouChina
| | - Yingying Wei
- The Psychiatric Laboratory, the State Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduSichuanChina
| | - Liansheng Zhao
- The Psychiatric Laboratory, the State Key Laboratory of BiotherapyWest China Hospital of Sichuan UniversityChengduSichuanChina
| | - Wei Deng
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital and School of Brain Science and Brain MedicineZhejiang University School of MedicineHangzhouChina
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain‐Machine Integration, State Key Laboratory of Brain‐Machine IntelligenceZhejiang UniversityHangzhouChina
- NHC and CAMS Key Laboratory of Medical NeurobiologyZhejiang UniversityHangzhouChina
| | - Wanjun Guo
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital and School of Brain Science and Brain MedicineZhejiang University School of MedicineHangzhouChina
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain‐Machine Integration, State Key Laboratory of Brain‐Machine IntelligenceZhejiang UniversityHangzhouChina
- NHC and CAMS Key Laboratory of Medical NeurobiologyZhejiang UniversityHangzhouChina
| | - Xun Hu
- The Clinical Research Center and Department of Pathology, The Second Affiliated HospitalZhejiang University School of MedicineZhejiangHangzhouChina
| | - Tao Li
- Affiliated Mental Health Center & Hangzhou Seventh People's Hospital and School of Brain Science and Brain MedicineZhejiang University School of MedicineHangzhouChina
- Liangzhu Laboratory, MOE Frontier Science Center for Brain Science and Brain‐Machine Integration, State Key Laboratory of Brain‐Machine IntelligenceZhejiang UniversityHangzhouChina
- NHC and CAMS Key Laboratory of Medical NeurobiologyZhejiang UniversityHangzhouChina
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Tendilla-Beltrán H, Garcés-Ramírez L, Martínez-Vásquez E, Nakakawa A, Gómez-Villalobos MDJ, Flores G. Differential Effects of Neonatal Ventral Hippocampus Lesion on Behavior and Corticolimbic Plasticity in Wistar-Kyoto and Spontaneously Hypertensive Rats. Neurochem Res 2024; 49:959-979. [PMID: 38157113 DOI: 10.1007/s11064-023-04074-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/24/2023] [Accepted: 11/21/2023] [Indexed: 01/03/2024]
Abstract
Dysfunction of the corticolimbic system, particularly at the dendritic spine level, is a recognized core mechanism in neurodevelopmental disorders such as schizophrenia. Neonatal ventral hippocampus lesion (NVHL) in Sprague-Dawley rats induces both a schizophrenia-related behavioral phenotype and dendritic spine pathology (reduced total number and mature spines) in corticolimbic areas, which is mitigated by antipsychotics. However, there is limited information on the impact of rat strain on NVHL outcomes and antipsychotic effects. We compared the behavioral performance in the open field, novel object recognition (NORT), and social interaction tests, as well as structural neuroplasticity with the Golgi-Cox stain in Wistar-Kyoto (WKY) and spontaneously hypertensive (SH) male rats with and without NVHL. Additionally, we explored the effect of the atypical antipsychotic risperidone (RISP). WKY rats with NVHL displayed motor hyperactivity without impairments in memory and social behavior, accompanied by dendritic spine pathology in the neurons of the prefrontal cortex (PFC) layer 3 and basolateral amygdala. RISP treatment reduced motor activity and had subtle and selective effects on the neuroplasticity alterations. In SH rats, NVHL increased the time spent in the border area during the open field test, impaired the short-term performance in NORT, and reduced social interaction time, deficits that were corrected after RISP administration. The NVHL caused dendritic spine pathology in the PFC layers 3 and 5 of SH rats, which RISP treatment ameliorated. Our results support the utility of the NVHL model for exploring neuroplasticity mechanisms in schizophrenia and understanding pharmacotherapy.
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Affiliation(s)
- Hiram Tendilla-Beltrán
- Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla (BUAP), 14 Sur 6301, 72570, Puebla, Mexico
| | - Linda Garcés-Ramírez
- Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Edwin Martínez-Vásquez
- Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla (BUAP), 14 Sur 6301, 72570, Puebla, Mexico
| | - Andrea Nakakawa
- Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla (BUAP), 14 Sur 6301, 72570, Puebla, Mexico
| | | | - Gonzalo Flores
- Instituto de Fisiología, Benemérita Universidad Autónoma de Puebla (BUAP), 14 Sur 6301, 72570, Puebla, Mexico.
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Lu Y, Mu L, Elstrott J, Fu C, Sun C, Su T, Ma X, Yan J, Jiang H, Hanson JE, Geng Y, Chen Y. Differential depletion of GluN2A induces heterogeneous schizophrenia-related phenotypes in mice. EBioMedicine 2024; 102:105045. [PMID: 38471394 PMCID: PMC10943646 DOI: 10.1016/j.ebiom.2024.105045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 02/12/2024] [Accepted: 02/21/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Schizophrenia, a debilitating psychiatric disorder, displays considerable interindividual variation in clinical presentations. The ongoing debate revolves around whether this heterogeneity signifies a continuum of severity linked to a singular causative factor or a collection of distinct subtypes with unique origins. Within the realm of schizophrenia, the functional impairment of GluN2A, a subtype of the NMDA receptor, has been associated with an elevated risk. Despite GluN2A's expression across various neuronal types throughout the brain, its specific contributions to schizophrenia and its involvement in particular cell types or brain regions remain unexplored. METHODS We generated age-specific, cell type-specific or brain region-specific conditional knockout mice targeting GluN2A and conducted a comprehensive analysis using tests measuring phenotypes relevant to schizophrenia. FINDINGS Through the induction of germline ablation of GluN2A, we observed the emergence of numerous schizophrenia-associated abnormalities in adult mice. Intriguingly, GluN2A knockout performed at different ages, in specific cell types and within distinct brain regions, we observed overlapping yet distinct schizophrenia-related phenotypes in mice. INTERPRETATION Our interpretation suggests that the dysfunction of GluN2A is sufficient to evoke heterogeneous manifestations associated with schizophrenia, indicating that GluN2A stands as a prominent risk factor and a potential therapeutic target for schizophrenia. FUNDING This project received support from the Shanghai Municipal Science and Technology Major Project (Grant No. 2019SHZDZX02) awarded to Y.C. and the Natural Science Foundation of Shanghai (Grant No. 19ZR1468600 and 201409003800) awarded to G.Y.
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Affiliation(s)
- Yi Lu
- Interdisciplinary Research Centre on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd., Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longyu Mu
- Interdisciplinary Research Centre on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd., Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Justin Elstrott
- Department of Translational Imaging, Genentech Inc., South San Francisco, CA 94080, USA
| | - Chaoying Fu
- Interdisciplinary Research Centre on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd., Pudong New District, Shanghai 201210, China
| | - Cailu Sun
- Interdisciplinary Research Centre on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd., Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tonghui Su
- Interdisciplinary Research Centre on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd., Pudong New District, Shanghai 201210, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaofan Ma
- Department of Anaesthesiology, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai 200011, China
| | - Jia Yan
- Department of Anaesthesiology, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai 200011, China
| | - Hong Jiang
- Department of Anaesthesiology, Shanghai Jiao Tong University School of Medicine Affiliated Ninth People's Hospital, Shanghai 200011, China
| | - Jesse E Hanson
- Department of Neuroscience, Genentech Inc., South San Francisco, CA 94080, USA
| | - Yang Geng
- Interdisciplinary Research Centre on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd., Pudong New District, Shanghai 201210, China.
| | - Yelin Chen
- Interdisciplinary Research Centre on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, No.100 Haike Rd., Pudong New District, Shanghai 201210, China.
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31
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Nakamura T, Yoshihara T, Tanegashima C, Kadota M, Kobayashi Y, Honda K, Ishiwata M, Ueda J, Hara T, Nakanishi M, Takumi T, Itohara S, Kuraku S, Asano M, Kasahara T, Nakajima K, Tsuboi T, Takata A, Kato T. Transcriptomic dysregulation and autistic-like behaviors in Kmt2c haploinsufficient mice rescued by an LSD1 inhibitor. Mol Psychiatry 2024:10.1038/s41380-024-02479-8. [PMID: 38528071 DOI: 10.1038/s41380-024-02479-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 03/27/2024]
Abstract
Recent studies have consistently demonstrated that the regulation of chromatin and gene transcription plays a pivotal role in the pathogenesis of neurodevelopmental disorders. Among many genes involved in these pathways, KMT2C, encoding one of the six known histone H3 lysine 4 (H3K4) methyltransferases in humans and rodents, was identified as a gene whose heterozygous loss-of-function variants are causally associated with autism spectrum disorder (ASD) and the Kleefstra syndrome phenotypic spectrum. However, little is known about how KMT2C haploinsufficiency causes neurodevelopmental deficits and how these conditions can be treated. To address this, we developed and analyzed genetically engineered mice with a heterozygous frameshift mutation of Kmt2c (Kmt2c+/fs mice) as a disease model with high etiological validity. In a series of behavioral analyses, the mutant mice exhibit autistic-like behaviors such as impairments in sociality, flexibility, and working memory, demonstrating their face validity as an ASD model. To investigate the molecular basis of the observed abnormalities, we performed a transcriptomic analysis of their bulk adult brains and found that ASD risk genes were specifically enriched in the upregulated differentially expressed genes (DEGs), whereas KMT2C peaks detected by ChIP-seq were significantly co-localized with the downregulated genes, suggesting an important role of putative indirect effects of Kmt2c haploinsufficiency. We further performed single-cell RNA sequencing of newborn mouse brains to obtain cell type-resolved insights at an earlier stage. By integrating findings from ASD exome sequencing, genome-wide association, and postmortem brain studies to characterize DEGs in each cell cluster, we found strong ASD-associated transcriptomic changes in radial glia and immature neurons with no obvious bias toward upregulated or downregulated DEGs. On the other hand, there was no significant gross change in the cellular composition. Lastly, we explored potential therapeutic agents and demonstrate that vafidemstat, a lysine-specific histone demethylase 1 (LSD1) inhibitor that was effective in other models of neuropsychiatric/neurodevelopmental disorders, ameliorates impairments in sociality but not working memory in adult Kmt2c+/fs mice. Intriguingly, the administration of vafidemstat was shown to alter the vast majority of DEGs in the direction to normalize the transcriptomic abnormalities in the mutant mice (94.3 and 82.5% of the significant upregulated and downregulated DEGs, respectively, P < 2.2 × 10-16, binomial test), which could be the molecular mechanism underlying the behavioral rescuing. In summary, our study expands the repertoire of ASD models with high etiological and face validity, elucidates the cell-type resolved molecular alterations due to Kmt2c haploinsufficiency, and demonstrates the efficacy of an LSD1 inhibitor that might be generalizable to multiple categories of psychiatric disorders along with a better understanding of its presumed mechanisms of action.
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Affiliation(s)
- Takumi Nakamura
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Toru Yoshihara
- Institute of Laboratory Animals, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Chiharu Tanegashima
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
| | - Yuki Kobayashi
- Laboratory for Behavioral Genetics, RIKEN Center for Brain Science, Saitama, Japan
| | - Kurara Honda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Mizuho Ishiwata
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Junko Ueda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
| | - Tomonori Hara
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Organ Anatomy, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Moe Nakanishi
- Laboratory for Mental Biology, RIKEN Center for Brain Science, Saitama, Japan
- Laboratory for Molecular Mechanism of Brain Development, RIKEN Center for Brain Science, Saitama, Japan
| | - Toru Takumi
- Laboratory for Mental Biology, RIKEN Center for Brain Science, Saitama, Japan
- Department of Physiology and Cell Biology, Kobe University School of Medicine, Hyogo, Japan
| | - Shigeyoshi Itohara
- Laboratory for Behavioral Genetics, RIKEN Center for Brain Science, Saitama, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, Hyogo, Japan
- Molecular Life History Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takaoki Kasahara
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Kazuo Nakajima
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan
- Department of Physiology, Teikyo University School of Medicine, Tokyo, Japan
| | - Takashi Tsuboi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Saitama, Japan.
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan.
| | - Tadafumi Kato
- Department of Psychiatry and Behavioral Science, Juntendo University Graduate School of Medicine, Tokyo, Japan.
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, Saitama, Japan.
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González-Peñas J, Alloza C, Brouwer R, Díaz-Caneja CM, Costas J, González-Lois N, Gallego AG, de Hoyos L, Gurriarán X, Andreu-Bernabeu Á, Romero-García R, Fañanás L, Bobes J, González-Pinto A, Crespo-Facorro B, Martorell L, Arrojo M, Vilella E, Gutiérrez-Zotes A, Perez-Rando M, Moltó MD, Buimer E, van Haren N, Cahn W, O'Donovan M, Kahn RS, Arango C, Pol HH, Janssen J, Schnack H. Accelerated Cortical Thinning in Schizophrenia Is Associated With Rare and Common Predisposing Variation to Schizophrenia and Neurodevelopmental Disorders. Biol Psychiatry 2024:S0006-3223(24)01170-3. [PMID: 38521159 DOI: 10.1016/j.biopsych.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 02/22/2024] [Accepted: 03/05/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Schizophrenia is a highly heritable disorder characterized by increased cortical thinning throughout the life span. Studies have reported a shared genetic basis between schizophrenia and cortical thickness. However, no genes whose expression is related to abnormal cortical thinning in schizophrenia have been identified. METHODS We conducted linear mixed models to estimate the rates of accelerated cortical thinning across 68 regions from the Desikan-Killiany atlas in individuals with schizophrenia compared with healthy control participants from a large longitudinal sample (ncases = 169 and ncontrols = 298, ages 16-70 years). We studied the correlation between gene expression data from the Allen Human Brain Atlas and accelerated thinning estimates across cortical regions. Finally, we explored the functional and genetic underpinnings of the genes that contribute most to accelerated thinning. RESULTS We found a global pattern of accelerated cortical thinning in individuals with schizophrenia compared with healthy control participants. Genes underexpressed in cortical regions that exhibit this accelerated thinning were downregulated in several psychiatric disorders and were enriched for both common and rare disrupting variation for schizophrenia and neurodevelopmental disorders. In contrast, none of these enrichments were observed for baseline cross-sectional cortical thickness differences. CONCLUSIONS Our findings suggest that accelerated cortical thinning, rather than cortical thickness alone, serves as an informative phenotype for neurodevelopmental disruptions in schizophrenia. We highlight the genetic and transcriptomic correlates of this accelerated cortical thinning, emphasizing the need for future longitudinal studies to elucidate the role of genetic variation and the temporal-spatial dynamics of gene expression in brain development and aging in schizophrenia.
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Affiliation(s)
- Javier González-Peñas
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain.
| | - Clara Alloza
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain
| | - Rachel Brouwer
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Covadonga M Díaz-Caneja
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain; School of Medicine, Universidad Complutense, Madrid, Spain
| | - Javier Costas
- Instituto de Investigación Sanitària de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde, Santiago de Compostela, Galicia, Spain
| | - Noemí González-Lois
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain
| | - Ana Guil Gallego
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain
| | - Lucía de Hoyos
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain
| | - Xaquín Gurriarán
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain
| | - Álvaro Andreu-Bernabeu
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain
| | - Rafael Romero-García
- Department of Medical Physiology and Biophysics, Instituto de Biomedicina de Sevilla, HUVR/CSIC/Universidad de Sevilla/CIBERSAM, Instituto de Salud Carlos III, Sevilla, Spain; Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Lourdes Fañanás
- CIBERSAM, Madrid, Spain; Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Julio Bobes
- CIBERSAM, Madrid, Spain; Faculty of Medicine and Health Sciences-Psychiatry, Universidad de Oviedo, Instituto de Investigación Sanitaria del Principado de Asturias, Instituto de Neurociencias del Principado de Asturias, Oviedo, Spain
| | - Ana González-Pinto
- CIBERSAM, Madrid, Spain; BIOARABA Health Research Institute, Organización Sanitaria Integrada Araba, University Hospital, University of the Basque Country, Vitoria, Spain
| | - Benedicto Crespo-Facorro
- CIBERSAM, Madrid, Spain; Hospital Universitario Virgen del Rocío, Department of Psychiatry, Universidad de Sevilla, Sevilla, Spain
| | - Lourdes Martorell
- CIBERSAM, Madrid, Spain; Hospital Universitari Institut Pere Mata, Institut d'Investigació Sanitària Pere Virgili-Centres de Recerca de Catalunya, Universitat Rovira i Virgili, Reus, Spain
| | - Manuel Arrojo
- Instituto de Investigación Sanitària de Santiago de Compostela, Complexo Hospitalario Universitario de Santiago de Compostela, Servizo Galego de Saúde, Santiago de Compostela, Galicia, Spain
| | - Elisabet Vilella
- CIBERSAM, Madrid, Spain; Hospital Universitari Institut Pere Mata, Institut d'Investigació Sanitària Pere Virgili-Centres de Recerca de Catalunya, Universitat Rovira i Virgili, Reus, Spain
| | - Alfonso Gutiérrez-Zotes
- CIBERSAM, Madrid, Spain; Hospital Universitari Institut Pere Mata, Institut d'Investigació Sanitària Pere Virgili-Centres de Recerca de Catalunya, Universitat Rovira i Virgili, Reus, Spain
| | - Marta Perez-Rando
- Fundación Investigación Hospital Clínico de València, Fundación Investigación Hospital Clínico de Valencia, València, Spain; Unidad de Neurobiología, Instituto de Biotecnología y Biomedicina, Universitat de València, València, Spain
| | - María Dolores Moltó
- CIBERSAM, Madrid, Spain; Unidad de Neurobiología, Instituto de Biotecnología y Biomedicina, Universitat de València, València, Spain; Department of Genetics, Universitat de València, Campus of Burjassot, València, Spain
| | - Elizabeth Buimer
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Neeltje van Haren
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Child and Adolescent Psychiatry/Psychology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Wiepke Cahn
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands; Altrecht Mental Health Institute, Altrecht Science, Utrecht, the Netherlands
| | - Michael O'Donovan
- Medical Research Council for Neuropsychiatric Genetics and Genomics and Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - René S Kahn
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain; School of Medicine, Universidad Complutense, Madrid, Spain
| | - Hilleke Hulshoff Pol
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Joost Janssen
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, Madrid, Spain; Instituto de Investigación Sanitària Gregorio Marañón, Madrid, Spain; CIBERSAM, Madrid, Spain; Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Hugo Schnack
- Department of Psychiatry, UMCU Brain Center, University Medical Center Utrecht, Utrecht, the Netherlands
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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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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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35
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Featherstone RE, Li H, Sengar A, Borgmann-Winter KE, Melnychenko O, Crown LM, Gifford RL, Amirfathi F, Banerjee A, Parekh K, Heller M, Zhang W, Marc AD, Salter MW, Siegel SJ, Hahn CG. Blocking Src-PSD-95 interaction rescues glutamatergic signaling dysregulation in schizophrenia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584132. [PMID: 38496466 PMCID: PMC10942437 DOI: 10.1101/2024.03.08.584132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The complex and heterogeneous genetic architecture of schizophrenia inspires us to look beyond individual risk genes for therapeutic strategies and target their interactive dynamics and convergence. Postsynaptic NMDA receptor (NMDAR) complexes are a site of such convergence. Src kinase is a molecular hub of NMDAR function, and its protein interaction subnetwork is enriched for risk-genes and altered protein associations in schizophrenia. Previously, Src activity was found to be decreased in post-mortem studies of schizophrenia, contributing to NMDAR hypofunction. PSD-95 suppresses Src via interacting with its SH2 domain. Here, we devised a strategy to suppress the inhibition of Src by PSD-95 via employing a cell penetrating and Src activating PSD-95 inhibitory peptide (TAT-SAPIP). TAT-SAPIP selectively increased post-synaptic Src activity in humans and mice, and enhanced synaptic NMDAR currents in mice. Chronic ICV injection of TAT-SAPIP rescued deficits in trace fear conditioning in Src hypomorphic mice. We propose blockade of the Src-PSD-95 interaction as a proof of concept for the use of interfering peptides as a therapeutic strategy to reverse NMDAR hypofunction in schizophrenia and other illnesses.
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Shin D, Kim CN, Ross J, Hennick KM, Wu SR, Paranjape N, Leonard R, Wang JC, Keefe MG, Pavlovic BJ, Donohue KC, Moreau C, Wigdor EM, Larson HH, Allen DE, Cadwell CR, Bhaduri A, Popova G, Bearden CE, Pollen AA, Jacquemont S, Sanders SJ, Haussler D, Wiita AP, Frost NA, Sohal VS, Nowakowski TJ. Thalamocortical organoids enable in vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders. Cell Stem Cell 2024; 31:421-432.e8. [PMID: 38382530 PMCID: PMC10939828 DOI: 10.1016/j.stem.2024.01.010] [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: 08/19/2022] [Revised: 12/14/2023] [Accepted: 01/25/2024] [Indexed: 02/23/2024]
Abstract
Thalamic dysfunction has been implicated in multiple psychiatric disorders. We sought to study the mechanisms by which abnormalities emerge in the context of the 22q11.2 microdeletion, which confers significant genetic risk for psychiatric disorders. We investigated early stages of human thalamus development using human pluripotent stem cell-derived organoids and show that the 22q11.2 microdeletion underlies widespread transcriptional dysregulation associated with psychiatric disorders in thalamic neurons and glia, including elevated expression of FOXP2. Using an organoid co-culture model, we demonstrate that the 22q11.2 microdeletion mediates an overgrowth of thalamic axons in a FOXP2-dependent manner. Finally, we identify ROBO2 as a candidate molecular mediator of the effects of FOXP2 overexpression on thalamic axon overgrowth. Together, our study suggests that early steps in thalamic development are dysregulated in a model of genetic risk for schizophrenia and contribute to neural phenotypes in 22q11.2 deletion syndrome.
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Affiliation(s)
- David Shin
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Chang N Kim
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jayden Ross
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kelsey M Hennick
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sih-Rong Wu
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Neha Paranjape
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA
| | - Rachel Leonard
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jerrick C Wang
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matthew G Keefe
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Bryan J Pavlovic
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kevin C Donohue
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Clara Moreau
- Sainte Justine Research Center, University of Montréal, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1C5, Canada; Imaging Genetics Center, Stevens Institute for Neuroimaging and Informatics, Keck School of Medicine, University of Southern California, Marina del Rey, CA, USA
| | - Emilie M Wigdor
- Institute of Developmental and Regenerative Medicine, University of Oxford, Headington, Oxford OX3 7TY, UK
| | - H Hanh Larson
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Denise E Allen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Cathryn R Cadwell
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Galina Popova
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Carrie E Bearden
- Integrative Center for Neurogenetics, Semel Institute for Neuroscience and Human Behavior, Departments of Psychiatry and Biobehavioral Sciences and Psychology, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, CA 90095, USA
| | - Alex A Pollen
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sebastien Jacquemont
- Sainte Justine Research Center, University of Montréal, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC H3T 1C5, Canada
| | - Stephan J Sanders
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Institute of Developmental and Regenerative Medicine, University of Oxford, Headington, Oxford OX3 7TY, UK
| | - David Haussler
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA 95060, USA; Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94107, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Nicholas A Frost
- Department of Neurology, University of Utah, Salt Lake City, UT 84108, USA
| | - Vikaas S Sohal
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tomasz J Nowakowski
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA; Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94158, USA.
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Zhang J, Qiu H, Zhao Q, Liao C, Guoli Y, Luo Q, Zhao G, Zhang N, Wang S, Zhang Z, Lei M, Liu F, Peng Y. Genetic overlap between schizophrenia and cognitive performance. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2024; 10:31. [PMID: 38443399 PMCID: PMC10914834 DOI: 10.1038/s41537-024-00453-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
Schizophrenia (SCZ), a highly heritable mental disorder, is characterized by cognitive impairment, yet the extent of the shared genetic basis between schizophrenia and cognitive performance (CP) remains poorly understood. Therefore, we aimed to explore the polygenic overlap between SCZ and CP. Specifically, the bivariate causal mixture model (MiXeR) was employed to estimate the extent of genetic overlap between SCZ (n = 130,644) and CP (n = 257,841), and conjunctional false discovery rate (conjFDR) approach was used to identify shared genetic loci. Subsequently, functional annotation and enrichment analysis were carried out on the identified genomic loci. The MiXeR analyses revealed that 9.6 K genetic variants are associated with SCZ and 10.9 K genetic variants for CP, of which 9.5 K variants are shared between these two traits (Dice coefficient = 92.8%). By employing conjFDR, 236 loci were identified jointly associated with SCZ and CP, of which 139 were novel for the two traits. Within these shared loci, 60 exhibited consistent effect directions, while 176 had opposite effect directions. Functional annotation analysis indicated that the shared genetic loci were mainly located in intronic and intergenic regions, and were found to be involved in relevant biological processes such as nervous system development, multicellular organism development, and generation of neurons. Together, our findings provide insights into the shared genetic architecture between SCZ and CP, suggesting common pathways and mechanisms contributing to both traits.
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Affiliation(s)
- Jianfei Zhang
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, Heilongjiang, China
| | - Hao Qiu
- College of Computer and Control Engineering, Qiqihar University, Qiqihar, Heilongjiang, China
| | - Qiyu Zhao
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Chongjian Liao
- School of Medical Imaging and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China
| | - Yuxuan Guoli
- The Second Hospital of Tianjin Medial University, Tianjin, China
| | - Qi Luo
- School of Medical Imaging and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China
| | - Guoshu Zhao
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Nannan Zhang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Shaoying Wang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhihui Zhang
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Minghuan Lei
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China
| | - Feng Liu
- Department of Radiology and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University General Hospital, Tianjin, China.
| | - Yanmin Peng
- School of Medical Imaging and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, Tianjin, China.
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38
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Leger BS, Meredith JJ, Ideker T, Sanchez-Roige S, Palmer AA. Rare and Common Variants Associated with Alcohol Consumption Identify a Conserved Molecular Network. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.26.582195. [PMID: 38464225 PMCID: PMC10925118 DOI: 10.1101/2024.02.26.582195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Genome-wide association studies (GWAS) have identified hundreds of common variants associated with alcohol consumption. In contrast, rare variants have only begun to be studied for their role in alcohol consumption. No studies have examined whether common and rare variants implicate the same genes and molecular networks. To address this knowledge gap, we used publicly available alcohol consumption GWAS summary statistics (GSCAN, N=666,978) and whole exome sequencing data (Genebass, N=393,099) to identify a set of common and rare variants for alcohol consumption. Gene-based analysis of each dataset have implicated 294 (common variants) and 35 (rare variants) genes, including ethanol metabolizing genes ADH1B and ADH1C, which were identified by both analyses, and ANKRD12, GIGYF1, KIF21B, and STK31, which were identified only by rare variant analysis, but have been associated with related psychiatric traits. We then used a network colocalization procedure to propagate the common and rare gene sets onto a shared molecular network, revealing significant overlap. The shared network identified gene families that function in alcohol metabolism, including ADH, ALDH, CYP, and UGT. 74 of the genes in the network were previously implicated in comorbid psychiatric or substance use disorders, but had not previously been identified for alcohol-related behaviors, including EXOC2, EPM2A, CACNB3, and CACNG4. Differential gene expression analysis showed enrichment in the liver and several brain regions supporting the role of network genes in alcohol consumption. Thus, genes implicated by common and rare variants identify shared functions relevant to alcohol consumption, which also underlie psychiatric traits and substance use disorders that are comorbid with alcohol use.
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Affiliation(s)
- Brittany S Leger
- Program in Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - John J Meredith
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Sandra Sanchez-Roige
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University, Nashville, TN, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA 92093, USA
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Mitchell KJ. Variability in Neural Circuit Formation. Cold Spring Harb Perspect Biol 2024; 16:a041504. [PMID: 38253418 PMCID: PMC10910361 DOI: 10.1101/cshperspect.a041504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The study of neural development is usually concerned with the question of how nervous systems get put together. Variation in these processes is usually of interest as a means of revealing these normative mechanisms. However, variation itself can be an object of study and is of interest from multiple angles. First, the nature of variation in both the processes and the outcomes of neural development is relevant to our understanding of how these processes and outcomes are encoded in the genome. Second, variation in the wiring of the brain in humans may underlie variation in all kinds of psychological and behavioral traits, as well as neurodevelopmental disorders. And third, genetic variation that affects circuit development provides the raw material for evolutionary change. Here, I examine these different aspects of variation in circuit development and consider what they may tell us about these larger questions.
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Affiliation(s)
- Kevin J Mitchell
- Smurfit Institute of Genetics and Institute of Neuroscience, Trinity College Dublin, Dublin D02 PN40, Ireland
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40
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Fei CJ, Li ZY, Ning J, Yang L, Wu BS, Kang JJ, Liu WS, He XY, You J, Chen SD, Yu H, Huang ZL, Feng JF, Yu JT, Cheng W. Exome sequencing identifies genes associated with sleep-related traits. Nat Hum Behav 2024; 8:576-589. [PMID: 38177695 DOI: 10.1038/s41562-023-01785-5] [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: 06/03/2023] [Accepted: 11/15/2023] [Indexed: 01/06/2024]
Abstract
Sleep is vital for human health and has a moderate heritability. Previous genome-wide association studies have limitations in capturing the role of rare genetic variants in sleep-related traits. Here we conducted a large-scale exome-wide association study of eight sleep-related traits (sleep duration, insomnia symptoms, chronotype, daytime sleepiness, daytime napping, ease of getting up in the morning, snoring and sleep apnoea) among 450,000 participants from UK Biobank. We identified 22 new genes associated with chronotype (ADGRL4, COL6A3, CLK4 and KRTAP3-3), daytime sleepiness (ST3GAL1 and ANKRD12), daytime napping (PLEKHM1, ANKRD12 and ZBTB21), snoring (WDR59) and sleep apnoea (13 genes). Notably, 20 of these genes were confirmed to be significantly associated with sleep disorders in the FinnGen cohort. Enrichment analysis revealed that these discovered genes were enriched in circadian rhythm and central nervous system neurons. Phenotypic association analysis showed that ANKRD12 was associated with cognition and inflammatory traits. Our results demonstrate the value of large-scale whole-exome analysis in understanding the genetic architecture of sleep-related traits and potential biological mechanisms.
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Affiliation(s)
- Chen-Jie Fei
- 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
| | - Jing Ning
- 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
| | - 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
| | - 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
| | - 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
| | - Jia You
- 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
| | - 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
| | - Huan 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
| | - Zhi-Li Huang
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science and Collaborative Innovation Center for Brain Science, 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
| | - 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.
| | - 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.
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41
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Ling E, Nemesh J, Goldman M, Kamitaki N, Reed N, Handsaker RE, Genovese G, Vogelgsang JS, Gerges S, Kashin S, Ghosh S, Esposito JM, Morris K, Meyer D, Lutservitz A, Mullally CD, Wysoker A, Spina L, Neumann A, Hogan M, Ichihara K, Berretta S, McCarroll SA. A concerted neuron-astrocyte program declines in ageing and schizophrenia. Nature 2024; 627:604-611. [PMID: 38448582 PMCID: PMC10954558 DOI: 10.1038/s41586-024-07109-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 01/23/2024] [Indexed: 03/08/2024]
Abstract
Human brains vary across people and over time; such variation is not yet understood in cellular terms. Here we describe a relationship between people's cortical neurons and cortical astrocytes. We used single-nucleus RNA sequencing to analyse the prefrontal cortex of 191 human donors aged 22-97 years, including healthy individuals and people with schizophrenia. Latent-factor analysis of these data revealed that, in people whose cortical neurons more strongly expressed genes encoding synaptic components, cortical astrocytes more strongly expressed distinct genes with synaptic functions and genes for synthesizing cholesterol, an astrocyte-supplied component of synaptic membranes. We call this relationship the synaptic neuron and astrocyte program (SNAP). In schizophrenia and ageing-two conditions that involve declines in cognitive flexibility and plasticity1,2-cells divested from SNAP: astrocytes, glutamatergic (excitatory) neurons and GABAergic (inhibitory) neurons all showed reduced SNAP expression to corresponding degrees. The distinct astrocytic and neuronal components of SNAP both involved genes in which genetic risk factors for schizophrenia were strongly concentrated. SNAP, which varies quantitatively even among healthy people of similar age, may underlie many aspects of normal human interindividual differences and may be an important point of convergence for multiple kinds of pathophysiology.
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Affiliation(s)
- Emi Ling
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - James Nemesh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Melissa Goldman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nolan Kamitaki
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nora Reed
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Robert E Handsaker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Jonathan S Vogelgsang
- McLean Hospital, Belmont, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Sherif Gerges
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Seva Kashin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | | | - Daniel Meyer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alyssa Lutservitz
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Christopher D Mullally
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Alec Wysoker
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Liv Spina
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Anna Neumann
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Marina Hogan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Kiku Ichihara
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Sabina Berretta
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- McLean Hospital, Belmont, MA, USA.
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA.
| | - Steven A McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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42
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Karunakaran KB, Jain S, Brahmachari SK, Balakrishnan N, Ganapathiraju MK. Parkinson's disease and schizophrenia interactomes contain temporally distinct gene clusters underlying comorbid mechanisms and unique disease processes. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2024; 10:26. [PMID: 38413605 PMCID: PMC10899210 DOI: 10.1038/s41537-024-00439-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Genome-wide association studies suggest significant overlaps in Parkinson's disease (PD) and schizophrenia (SZ) risks, but the underlying mechanisms remain elusive. The protein-protein interaction network ('interactome') plays a crucial role in PD and SZ and can incorporate their spatiotemporal specificities. Therefore, to study the linked biology of PD and SZ, we compiled PD- and SZ-associated genes from the DisGeNET database, and constructed their interactomes using BioGRID and HPRD. We examined the interactomes using clustering and enrichment analyses, in conjunction with the transcriptomic data of 26 brain regions spanning foetal stages to adulthood available in the BrainSpan Atlas. PD and SZ interactomes formed four gene clusters with distinct temporal identities (Disease Gene Networks or 'DGNs'1-4). DGN1 had unique SZ interactome genes highly expressed across developmental stages, corresponding to a neurodevelopmental SZ subtype. DGN2, containing unique SZ interactome genes expressed from early infancy to adulthood, correlated with an inflammation-driven SZ subtype and adult SZ risk. DGN3 contained unique PD interactome genes expressed in late infancy, early and late childhood, and adulthood, and involved in mitochondrial pathways. DGN4, containing prenatally-expressed genes common to both the interactomes, involved in stem cell pluripotency and overlapping with the interactome of 22q11 deletion syndrome (comorbid psychosis and Parkinsonism), potentially regulates neurodevelopmental mechanisms in PD-SZ comorbidity. Our findings suggest that disrupted neurodevelopment (regulated by DGN4) could expose risk windows in PD and SZ, later elevating disease risk through inflammation (DGN2). Alternatively, variant clustering in DGNs may produce disease subtypes, e.g., PD-SZ comorbidity with DGN4, and early/late-onset SZ with DGN1/DGN2.
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Affiliation(s)
- Kalyani B Karunakaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India.
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan.
| | - Sanjeev Jain
- National Institute of Mental Health and Neuro-Sciences (NIMHANS), Bangalore, India.
| | | | - N Balakrishnan
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India
| | - Madhavi K Ganapathiraju
- Department of Computer Science, Carnegie Mellon University Qatar, Doha, Qatar.
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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43
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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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44
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Yan Z, Ge F, Liu Y, Zhang Y, Li F, Song J, Yu DJ. TransEFVP: A Two-Stage Approach for the Prediction of Human Pathogenic Variants Based on Protein Sequence Embedding Fusion. J Chem Inf Model 2024; 64:1407-1418. [PMID: 38334115 DOI: 10.1021/acs.jcim.3c02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Studying the effect of single amino acid variations (SAVs) on protein structure and function is integral to advancing our understanding of molecular processes, evolutionary biology, and disease mechanisms. Screening for deleterious variants is one of the crucial issues in precision medicine. Here, we propose a novel computational approach, TransEFVP, based on large-scale protein language model embeddings and a transformer-based neural network to predict disease-associated SAVs. The model adopts a two-stage architecture: the first stage is designed to fuse different feature embeddings through a transformer encoder. In the second stage, a support vector machine model is employed to quantify the pathogenicity of SAVs after dimensionality reduction. The prediction performance of TransEFVP on blind test data achieves a Matthews correlation coefficient of 0.751, an F1-score of 0.846, and an area under the receiver operating characteristic curve of 0.871, higher than the existing state-of-the-art methods. The benchmark results demonstrate that TransEFVP can be explored as an accurate and effective SAV pathogenicity prediction method. The data and codes for TransEFVP are available at https://github.com/yzh9607/TransEFVP/tree/master for academic use.
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Affiliation(s)
- Zihao Yan
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Fang Ge
- State Key Laboratory of Organic Electronics and lnformation Displays & lnstitute of Advanced Materials (IAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing 210023, PR China
| | - Yan Liu
- Department of Computer Science, Yangzhou University, Yangzhou 225100, PR China
| | - Yumeng Zhang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, PR China
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Fuyi Li
- South Australian immunoGENomics Cancer Institute (SAiGENCI), Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria 3000, Australia
| | - Jiangning Song
- Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Dong-Jun Yu
- School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
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45
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Zhou T, Ho YY, Lee RX, Fath AB, He K, Scott J, Bajwa N, Hartley ND, Wilde J, Gao X, Li C, Hong E, Nassar MR, Wimmer RD, Singh T, Halassa MM, Feng G. Enhancement of mediodorsal thalamus rescues aberrant belief dynamics in a mouse model with schizophrenia-associated mutation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574745. [PMID: 38260581 PMCID: PMC10802391 DOI: 10.1101/2024.01.08.574745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Optimizing behavioral strategy requires belief updating based on new evidence, a process that engages higher cognition. In schizophrenia, aberrant belief dynamics may lead to psychosis, but the mechanisms underlying this process are unknown, in part, due to lack of appropriate animal models and behavior readouts. Here, we address this challenge by taking two synergistic approaches. First, we generate a mouse model bearing patient-derived point mutation in Grin2a (Grin2aY700X+/-), a gene that confers high-risk for schizophrenia and recently identified by large-scale exome sequencing. Second, we develop a computationally trackable foraging task, in which mice form and update belief-driven strategies in a dynamic environment. We found that Grin2aY700X+/- mice perform less optimally than their wild-type (WT) littermates, showing unstable behavioral states and a slower belief update rate. Using functional ultrasound imaging, we identified the mediodorsal (MD) thalamus as hypofunctional in Grin2aY700X+/- mice, and in vivo task recordings showed that MD neurons encoded dynamic values and behavioral states in WT mice. Optogenetic inhibition of MD neurons in WT mice phenocopied Grin2aY700X+/- mice, and enhancing MD activity rescued task deficits in Grin2aY700X+/- mice. Together, our study identifies the MD thalamus as a key node for schizophrenia-relevant cognitive dysfunction, and a potential target for future therapeutics.
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Affiliation(s)
- Tingting Zhou
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Yi-Yun Ho
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Ray X Lee
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Amanda B Fath
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Kathleen He
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Jonathan Scott
- Department of Neuroscience, Tufts University School of Medicine
| | - Navdeep Bajwa
- Department of Neuroscience, Tufts University School of Medicine
| | - Nolan D Hartley
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard
| | - Jonathan Wilde
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Xian Gao
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Cui Li
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | - Evan Hong
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
| | | | - Ralf D Wimmer
- Department of Neuroscience, Tufts University School of Medicine
| | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard
| | | | - Guoping Feng
- Yang Tan Collection and McGovern Institute for Brain Research, Massachusetts Institute of Technology
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard
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46
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Kim TY, Roychaudhury A, Kim HT, Choi TI, Baek ST, Thyme SB, Kim CH. Impairments of cerebellar structure and function in a zebrafish KO of neuropsychiatric risk gene znf536. Transl Psychiatry 2024; 14:82. [PMID: 38331943 PMCID: PMC10853220 DOI: 10.1038/s41398-024-02806-1] [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: 04/26/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/10/2024] Open
Abstract
Genetic variants in ZNF536 contribute to the risk for neuropsychiatric disorders such as schizophrenia, autism, and others. The role of this putative transcriptional repressor in brain development and function is, however, largely unknown. We generated znf536 knockout (KO) zebrafish and studied their behavior, brain anatomy, and brain function. Larval KO zebrafish showed a reduced ability to compete for food, resulting in decreased total body length and size. This phenotype can be rescued by segregating the homozygous KO larvae from their wild-type and heterozygous siblings, enabling studies of adult homozygous KO animals. In adult KO zebrafish, we observed significant reductions in anxiety-like behavior and social interaction. These znf536 KO zebrafish have decreased cerebellar volume, corresponding to decreased populations of specific neuronal cells, especially in the valvular cerebelli (Va). Finally, using a Tg[mbp:mgfp] line, we identified a previously undetected myelin structure located bilaterally within the Va, which also displayed a reduction in volume and disorganization in KO zebrafish. These findings indicate an important role for ZNF536 in brain development and implicate the cerebellum in the pathophysiology of neuropsychiatric disorders.
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Affiliation(s)
- Tae-Yoon Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea
| | | | - Hyun-Taek Kim
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan, 31151, South Korea
| | - Tae-Ik Choi
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea
| | - Seung Tae Baek
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 37673, South Korea
| | - Summer B Thyme
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, Worcester, MA, USA.
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, 34134, South Korea.
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47
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Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. A foundational atlas of autism protein interactions reveals molecular convergence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.03.569805. [PMID: 38076945 PMCID: PMC10705567 DOI: 10.1101/2023.12.03.569805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
Abstract
Translating high-confidence (hc) autism spectrum disorder (ASD) genes into viable treatment targets remains elusive. We constructed a foundational protein-protein interaction (PPI) network in HEK293T cells involving 100 hcASD risk genes, revealing over 1,800 PPIs (87% novel). Interactors, expressed in the human brain and enriched for ASD but not schizophrenia genetic risk, converged on protein complexes involved in neurogenesis, tubulin biology, transcriptional regulation, and chromatin modification. A PPI map of 54 patient-derived missense variants identified differential physical interactions, and we leveraged AlphaFold-Multimer predictions to prioritize direct PPIs and specific variants for interrogation in Xenopus tropicalis and human forebrain organoids. A mutation in the transcription factor FOXP1 led to reconfiguration of DNA binding sites and altered development of deep cortical layer neurons in forebrain organoids. This work offers new insights into molecular mechanisms underlying ASD and describes a powerful platform to develop and test therapeutic strategies for many genetically-defined conditions.
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48
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Colijn MA, Carrion P, Poirier-Morency G, Rogic S, Torres I, Menon M, Lisonek M, Cook C, DeGraaf A, Thammaiah SP, Neelakant H, Willaeys V, Leonova O, White RF, Yip S, Mungall AJ, MacLeod PM, Gibson WT, Sullivan PF, Honer WG, Pavlidis P, Stowe RM. SETD1A variant-associated psychosis: A systematic review of the clinical literature and description of two new cases. Prog Neuropsychopharmacol Biol Psychiatry 2024; 129:110888. [PMID: 37918557 DOI: 10.1016/j.pnpbp.2023.110888] [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: 05/29/2023] [Revised: 09/18/2023] [Accepted: 10/29/2023] [Indexed: 11/04/2023]
Abstract
OBJECTIVE SETD1A encodes a histone methyltransferase involved in various cell cycle regulatory processes. Loss-of-function SETD1A variants have been associated with numerous neurodevelopmental phenotypes, including intellectual disability and schizophrenia. While the association between rare coding variants in SETD1A and schizophrenia has achieved genome-wide significance by rare variant burden testing, only a few studies have described the psychiatric phenomenology of such individuals in detail. This systematic review and case report aims to characterize the neurodevelopmental and psychiatric phenotypes of SETD1A variant-associated schizophrenia. METHODS A PubMed search was completed in July 2022 and updated in May 2023. Only studies that reported individuals with a SETD1A variant as well as a primary psychotic disorder were ultimately included. Additionally, another two previously unpublished cases of SETD1A variant-associated psychosis from our own sequencing cohort are described. RESULTS The search yielded 32 articles. While 15 articles met inclusion criteria, only five provided case descriptions. In total, phenotypic information was available for 11 individuals, in addition to our own two unpublished cases. Our findings suggest that although individuals with SETD1A variant-associated schizophrenia may share a number of common features, phenotypic variability nonetheless exists. Moreover, although such individuals may exhibit numerous other neurodevelopmental features suggestive of the syndrome, their psychiatric presentations appear to be similar to those of general schizophrenia populations. CONCLUSIONS Loss-of-function SETD1A variants may underlie the development of psychosis in a small percentage of individuals with schizophrenia. Identifying such individuals may become increasingly important, given the potential for advances in precision medicine treatment approaches.
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Affiliation(s)
- Mark A Colijn
- Department of Psychiatry, Hotchkiss Brain Institute, and Mathison Centre for Mental Health Research & Education, University of Calgary, Calgary, AB, Canada.
| | - Prescilla Carrion
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | | | - Sanja Rogic
- Department of Psychiatry and Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Ivan Torres
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada; BC Mental Health and Substance Use Services, Vancouver, BC, Canada
| | - Mahesh Menon
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | | | - Courtney Cook
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Ashley DeGraaf
- Heart Centre, St. Paul's Hospital and Providence Health, Vancouver, BC, Canada
| | | | - Harish Neelakant
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Veerle Willaeys
- BC Psychosis Program, British Columbia Mental Health & Substance Use Services, Vancouver, BC, Canada
| | - Olga Leonova
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Randall F White
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Patrick M MacLeod
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - William T Gibson
- Department of Medical Genetics, University of British Columbia and BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Patrick F Sullivan
- Psychiatry and Genetics, University of North Carolina at Chapel Hill, NC, USA; Karolinska Institut, Stockholm, Sweden
| | - William G Honer
- Department of Psychiatry, University of British Columbia, Vancouver, BC, Canada; BC Mental Health and Substance Use Services Research Institute, Vancouver, BC, Canada
| | - Paul Pavlidis
- Department of Psychiatry, Michael Smith Laboratories, and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Robert M Stowe
- Departments of Psychiatry and Neurology (Medicine), BC Neuropsychiatry Program, and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
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49
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Shepard N, Baez-Nieto D, Iqbal S, Kurganov E, Budnik N, Campbell AJ, Pan JQ, Sheng M, Farsi Z. Differential functional consequences of GRIN2A mutations associated with schizophrenia and neurodevelopmental disorders. Sci Rep 2024; 14:2798. [PMID: 38307912 PMCID: PMC10837427 DOI: 10.1038/s41598-024-53102-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 01/27/2024] [Indexed: 02/04/2024] Open
Abstract
Human genetic studies have revealed rare missense and protein-truncating variants in GRIN2A, encoding for the GluN2A subunit of the NMDA receptors, that confer significant risk for schizophrenia (SCZ). Mutations in GRIN2A are also associated with epilepsy and developmental delay/intellectual disability (DD/ID). However, it remains enigmatic how alterations to the same protein can result in diverse clinical phenotypes. Here, we performed functional characterization of human GluN1/GluN2A heteromeric NMDA receptors that contain SCZ-linked GluN2A variants, and compared them to NMDA receptors with GluN2A variants associated with epilepsy or DD/ID. Our findings demonstrate that SCZ-associated GRIN2A variants were predominantly loss-of-function (LoF), whereas epilepsy and DD/ID-associated variants resulted in both gain- and loss-of-function phenotypes. We additionally show that M653I and S809R, LoF GRIN2A variants associated with DD/ID, exert a dominant-negative effect when co-expressed with a wild-type GluN2A, whereas E58Ter and Y698C, SCZ-linked LoF variants, and A727T, an epilepsy-linked LoF variant, do not. These data offer a potential mechanism by which SCZ/epilepsy and DD/ID-linked variants can cause different effects on receptor function and therefore result in divergent pathological outcomes.
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Affiliation(s)
- Nate Shepard
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - David Baez-Nieto
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sumaiya Iqbal
- The Center for the Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Erkin Kurganov
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikita Budnik
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Arthur J Campbell
- 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.
| | - Zohreh Farsi
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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50
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Schoonover KE, Miller NE, Fish KN, Lewis DA. Scaling of smaller pyramidal neuron size and lower energy production in schizophrenia. Neurobiol Dis 2024; 191:106394. [PMID: 38176569 PMCID: PMC10898364 DOI: 10.1016/j.nbd.2023.106394] [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: 10/09/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Dorsolateral prefrontal cortex (DLPFC) dysfunction in schizophrenia appears to reflect alterations in layer 3 pyramidal neurons (L3PNs), including smaller cell bodies and lower expression of mitochondrial energy production genes. However, prior somal size studies used biased strategies for identifying L3PNs, and somal size and levels of energy production markers have not been assessed in individual L3PNs. STUDY DESIGN We combined fluorescent in situ hybridization (FISH) of vesicular glutamate transporter 1 (VGLUT1) mRNA and immunohistochemical-labeling of NeuN to determine if the cytoplasmic distribution of VGLUT1 mRNA permits the unbiased identification and somal size quantification of L3PNs. Dual-label FISH for VGLUT1 mRNA and cytochrome C oxidase subunit 4I1 (COX4I1) mRNA, a marker of energy production, was used to assess somal size and COX4I1 transcript levels in individual DLPFC L3PNs from schizophrenia (12 males; 2 females) and unaffected comparison (13 males; 1 female) subjects. STUDY RESULTS Measures of L3PN somal size with NeuN immunohistochemistry or VGLUT1 mRNA provided nearly identical results (ICC = 0.96, p < 0.0001). Mean somal size of VGLUT1-identified L3PNs was 8.7% smaller (p = 0.004) and mean COX4I1 mRNA levels per L3PN were 16.7% lower (p = 0.01) in schizophrenia. These measures were correlated across individual L3PNs in both subject groups (rrm = 0.81-0.86). CONCLUSIONS This preliminary study presents a novel method for combining unbiased neuronal identification with quantitative assessments of somal size and mRNA levels. We replicated findings of smaller somal size and lower COX4I1 mRNA levels in DLPFC L3PNs in schizophrenia. The normal scaling of COX4I1 mRNA levels with somal size in schizophrenia suggests that lower markers of energy production are secondary to L3PN morphological alterations in the illness.
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Affiliation(s)
- Kirsten E Schoonover
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Department of Psychiatry Biomedical Science Tower, W1653 3811 O'Hara Street Pittsburgh, PA 15213, United States of America
| | - Nora E Miller
- Department of Neuroscience, Dietrich School of Arts and Sciences, University of Pittsburgh, Department of Psychiatry, Biomedical Science Tower W1653 3811 O'Hara Street Pittsburgh, PA 15213, United States of America
| | - Kenneth N Fish
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Department of Psychiatry Biomedical Science Tower, W1653 3811 O'Hara Street Pittsburgh, PA 15213, United States of America
| | - David A Lewis
- Translational Neuroscience Program, Department of Psychiatry, School of Medicine, University of Pittsburgh, Department of Psychiatry Biomedical Science Tower, W1653 3811 O'Hara Street Pittsburgh, PA 15213, United States of America.
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