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Rees E, Creeth HDJ, Hwu HG, Chen WJ, Tsuang M, Glatt SJ, Rey R, Kirov G, Walters JTR, Holmans P, Owen MJ, O'Donovan MC. Schizophrenia, autism spectrum disorders and developmental disorders share specific disruptive coding mutations. Nat Commun 2021; 12:5353. [PMID: 34504065 PMCID: PMC8429694 DOI: 10.1038/s41467-021-25532-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
People with schizophrenia are enriched for rare coding variants in genes associated with neurodevelopmental disorders, particularly autism spectrum disorders and intellectual disability. However, it is unclear if the same changes to gene function that increase risk to neurodevelopmental disorders also do so for schizophrenia. Using data from 3444 schizophrenia trios and 37,488 neurodevelopmental disorder trios, we show that within shared risk genes, de novo variants in schizophrenia and neurodevelopmental disorders are generally of the same functional category, and that specific de novo variants observed in neurodevelopmental disorders are enriched in schizophrenia (P = 5.0 × 10-6). The latter includes variants known to be pathogenic for syndromic disorders, suggesting that schizophrenia be included as a characteristic of those syndromes. Our findings imply that, in part, neurodevelopmental disorders and schizophrenia have shared molecular aetiology, and therefore likely overlapping pathophysiology, and support the hypothesis that at least some forms of schizophrenia lie on a continuum of neurodevelopmental disorders.
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Affiliation(s)
- Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Hugo D J Creeth
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Wei J Chen
- National Taiwan University, Taipei, Taiwan
| | - Ming Tsuang
- University of California, San Diego, La Jolla, CA, USA
| | | | - Romain Rey
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
- INSERM, U1028; CNRS, UMR5292; Lyon Neuroscience Research Center, Psychiatric Disorders: from Resistance to Response Team, Lyon, F-69000, France
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
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102
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Nguyen TH, He X, Brown RC, Webb BT, Kendler KS, Vladimirov VI, Riley BP, Bacanu SA. DECO: a framework for jointly analyzing de novo and rare case/control variants, and biological pathways. Brief Bioinform 2021; 22:bbab067. [PMID: 33791774 PMCID: PMC8425460 DOI: 10.1093/bib/bbab067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/25/2021] [Accepted: 02/09/2021] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Rare variant-based analyses are beginning to identify risk genes for neuropsychiatric disorders and other diseases. However, the identified genes only account for a fraction of predicted causal genes. Recent studies have shown that rare damaging variants are significantly enriched in specific gene-sets. Methods which are able to jointly model rare variants and gene-sets to identify enriched gene-sets and use these enriched gene-sets to prioritize additional risk genes could improve understanding of the genetic architecture of diseases. RESULTS We propose DECO (Integrated analysis of de novo mutations, rare case/control variants and omics information via gene-sets), an integrated method for rare-variant and gene-set analysis. The method can (i) test the enrichment of gene-sets directly within the statistical model, and (ii) use enriched gene-sets to rank existing genes and prioritize additional risk genes for tested disorders. In simulations, DECO performs better than a homologous method that uses only variant data. To demonstrate the application of the proposed protocol, we have applied this approach to rare-variant datasets of schizophrenia. Compared with a method which only uses variant information, DECO is able to prioritize additional risk genes. AVAILABILITY DECO can be used to analyze rare-variants and biological pathways or cell types for any disease. The package is available on Github https://github.com/hoangtn/DECO.
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Affiliation(s)
- Tan-Hoang Nguyen
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Xin He
- The Department of Human Genetics, University of Chicago, IL 60637, USA; Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, IL 60637, USA
| | - Ruth C Brown
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Bradley T Webb
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Kenneth S Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Vladimir I Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA; Department of Psychiatry & Behavioral Sciences, College of Medicine, Texas A&M University, College Station, TX, USA; and the Lieber Institute for Brain Development, Baltimore, MD, USA
| | - Brien P Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, USA
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103
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Jia X, Goes FS, Locke AE, Palmer D, Wang W, Cohen-Woods S, Genovese G, Jackson AU, Jiang C, Kvale M, Mullins N, Nguyen H, Pirooznia M, Rivera M, Ruderfer DM, Shen L, Thai K, Zawistowski M, Zhuang Y, Abecasis G, Akil H, Bergen S, Burmeister M, Chapman S, DelaBastide M, Juréus A, Kang HM, Kwok PY, Li JZ, Levy SE, Monson ET, Moran J, Sobell J, Watson S, Willour V, Zöllner S, Adolfsson R, Blackwood D, Boehnke M, Breen G, Corvin A, Craddock N, DiFlorio A, Hultman CM, Landen M, Lewis C, McCarroll SA, Richard McCombie W, McGuffin P, McIntosh A, McQuillin A, Morris D, Myers RM, O'Donovan M, Ophoff R, Boks M, Kahn R, Ouwehand W, Owen M, Pato C, Pato M, Posthuma D, Potash JB, Reif A, Sklar P, Smoller J, Sullivan PF, Vincent J, Walters J, Neale B, Purcell S, Risch N, Schaefer C, Stahl EA, Zandi PP, Scott LJ. Investigating rare pathogenic/likely pathogenic exonic variation in bipolar disorder. Mol Psychiatry 2021; 26:5239-5250. [PMID: 33483695 PMCID: PMC8295400 DOI: 10.1038/s41380-020-01006-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 01/30/2023]
Abstract
Bipolar disorder (BD) is a serious mental illness with substantial common variant heritability. However, the role of rare coding variation in BD is not well established. We examined the protein-coding (exonic) sequences of 3,987 unrelated individuals with BD and 5,322 controls of predominantly European ancestry across four cohorts from the Bipolar Sequencing Consortium (BSC). We assessed the burden of rare, protein-altering, single nucleotide variants classified as pathogenic or likely pathogenic (P-LP) both exome-wide and within several groups of genes with phenotypic or biologic plausibility in BD. While we observed an increased burden of rare coding P-LP variants within 165 genes identified as BD GWAS regions in 3,987 BD cases (meta-analysis OR = 1.9, 95% CI = 1.3-2.8, one-sided p = 6.0 × 10-4), this enrichment did not replicate in an additional 9,929 BD cases and 14,018 controls (OR = 0.9, one-side p = 0.70). Although BD shares common variant heritability with schizophrenia, in the BSC sample we did not observe a significant enrichment of P-LP variants in SCZ GWAS genes, in two classes of neuronal synaptic genes (RBFOX2 and FMRP) associated with SCZ or in loss-of-function intolerant genes. In this study, the largest analysis of exonic variation in BD, individuals with BD do not carry a replicable enrichment of rare P-LP variants across the exome or in any of several groups of genes with biologic plausibility. Moreover, despite a strong shared susceptibility between BD and SCZ through common genetic variation, we do not observe an association between BD risk and rare P-LP coding variants in genes known to modulate risk for SCZ.
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Affiliation(s)
- Xiaoming Jia
- Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Adam E Locke
- Division of Genomics & Bioinformatics, Department of Medicine and McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, 63108, USA
| | - Duncan Palmer
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Weiqing Wang
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sarah Cohen-Woods
- Discipline of Psychology and Flinders Centre for Innovation in Cancer, Flinders University, Adelaide, SA, Australia
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Anne U Jackson
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Chen Jiang
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94611, USA
| | - Mark Kvale
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Niamh Mullins
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hoang Nguyen
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mehdi Pirooznia
- Bioinformatics and Computational Core, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, USA
| | - Margarita Rivera
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Biochemistry and Molecular Biology II, Institute of Neurosciences, Center for Biomedical Research, University of Granada, Granada, Spain
| | - Douglas M Ruderfer
- Departments of Medicine, Psychiatry, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Ling Shen
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94611, USA
| | - Khanh Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94611, USA
| | - Matthew Zawistowski
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yongwen Zhuang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Gonçalo Abecasis
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Huda Akil
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sarah Bergen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Margit Burmeister
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Sinéad Chapman
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Melissa DelaBastide
- Division of Research, Cold Spring Harbor Laboratory, Cold Spring, Harbor, NY, 11797, USA
| | - Anders Juréus
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Pui-Yan Kwok
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Jun Z Li
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shawn E Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Eric T Monson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Jennifer Moran
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Janet Sobell
- Department of Psychiatry and Behavioral Sciences, University of Southern California, Los Angeles, CA, 90033, USA
| | - Stanley Watson
- Molecular & Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Virginia Willour
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
| | - Sebastian Zöllner
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Rolf Adolfsson
- Departments of Clinical Sciences and Psychiatry, Umea University, Umea, Sweden
| | | | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Gerome Breen
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- NIHR BRC for Mental Health, King's College London, London, UK
| | - Aiden Corvin
- Department of Psychiatry and Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
| | - Nick Craddock
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Arianna DiFlorio
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mikael Landen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Cathryn Lewis
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Department of Medical & Molecular Genetics, King's College London, London, UK
| | | | - W Richard McCombie
- Division of Research, Cold Spring Harbor Laboratory, Cold Spring, Harbor, NY, 11797, USA
| | - Peter McGuffin
- Medical Research Council Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Andrew McIntosh
- Division of Psychiatry, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | | | - Derek Morris
- Department of Psychiatry and Trinity Translational Medicine Institute, Trinity College Dublin, Dublin, Ireland
- Discipline of Biochemistry, Neuroimaging and Cognitive Genomics (NICOG) Centre, National University of Ireland Galway, Galway, Ireland
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Michael O'Donovan
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Roel Ophoff
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - Marco Boks
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, the Netherlands
| | - Rene Kahn
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Willem Ouwehand
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Michael Owen
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Carlos Pato
- Department of Psychiatry and Behavioral Sciences, University of Southern California, Los Angeles, CA, 90033, USA
- SUNY Downstate Medical Center, Brooklyn, NY, 11203, USA
| | - Michele Pato
- Department of Psychiatry and Behavioral Sciences, University of Southern California, Los Angeles, CA, 90033, USA
- Department of Psychiatry, SUNY Downstate Medical Center, Brooklyn, NY, 11203, USA
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Clinical Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam, the Netherlands
| | - James B Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Andreas Reif
- Department of Psychiatry, Psychosomatic Medicine and Psychotherapy, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Pamela Sklar
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jordan Smoller
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Patrick F Sullivan
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - John Vincent
- Molecular Neuropsychiatry and Development Laboratory, Campbell Family Mental Health Research Institute, Center for Addiction & Mental Health, Toronto, ON, Canada
- Department of Psychiatry and Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - James Walters
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, UK
| | - Benjamin Neale
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Analytical and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Shaun Purcell
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Neil Risch
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, 94611, USA
| | - Eli A Stahl
- Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA.
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
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104
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Zhan L, Li J, Jew B, Sul JH. Rare variants in the endocytic pathway are associated with Alzheimer's disease, its related phenotypes, and functional consequences. PLoS Genet 2021; 17:e1009772. [PMID: 34516545 PMCID: PMC8460036 DOI: 10.1371/journal.pgen.1009772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 09/23/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022] Open
Abstract
Late-onset Alzheimer's disease (LOAD) is the most common type of dementia causing irreversible brain damage to the elderly and presents a major public health challenge. Clinical research and genome-wide association studies have suggested a potential contribution of the endocytic pathway to AD, with an emphasis on common loci. However, the contribution of rare variants in this pathway to AD has not been thoroughly investigated. In this study, we focused on the effect of rare variants on AD by first applying a rare-variant gene-set burden analysis using genes in the endocytic pathway on over 3,000 individuals with European ancestry from three large whole-genome sequencing (WGS) studies. We identified significant associations of rare-variant burden within the endocytic pathway with AD, which were successfully replicated in independent datasets. We further demonstrated that this endocytic rare-variant enrichment is associated with neurofibrillary tangles (NFTs) and age-related phenotypes, increasing the risk of obtaining severer brain damage, earlier age-at-onset, and earlier age-of-death. Next, by aggregating rare variants within each gene, we sought to identify single endocytic genes associated with AD and NFTs. Careful examination using NFTs revealed one significantly associated gene, ANKRD13D. To identify functional associations, we integrated bulk RNA-Seq data from over 600 brain tissues and found two endocytic expression genes (eGenes), HLA-A and SLC26A7, that displayed significant influences on their gene expressions. Differential expressions between AD patients and controls of these three identified genes were further examined by incorporating scRNA-Seq data from 48 post-mortem brain samples and demonstrated distinct expression patterns across cell types. Taken together, our results demonstrated strong rare-variant effect in the endocytic pathway on AD risk and progression and functional effect of gene expression alteration in both bulk and single-cell resolution, which may bring more insight and serve as valuable resources for future AD genetic studies, clinical research, and therapeutic targeting.
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Affiliation(s)
- Lingyu Zhan
- Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Jiajin Li
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Brandon Jew
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Jae Hoon Sul
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, Los Angeles, California, United States of America
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105
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Li S, DeLisi LE, McDonough SI. Rare germline variants in individuals diagnosed with schizophrenia within multiplex families. Psychiatry Res 2021; 303:114038. [PMID: 34174581 DOI: 10.1016/j.psychres.2021.114038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/27/2021] [Indexed: 12/30/2022]
Abstract
An extensive catalog of common and rare genetic variants contributes to overall risk for schizophrenia and related disorders. As a complement to population genetics efforts, here we present whole genome sequences of multiple affected probands within individual families to search for possible high penetrance driver variants. From a total of 15 families diagnostically evaluated by a single research psychiatrist, we performed whole genome sequencing of a total of 61 affected individuals, called SNPs, indels, and copy number variants, and compared to reference genomes. In fourteen out of fifteen families, the schizophrenia polygenic risk score for each proband was within the control range defined by the Thousand Genomes cohort. In six families, each affected member carried a very rare or private, predicted-damaging, variant in at least one gene. Among these genes, variants in LRP1 and TENM2 suggest these are candidate disease-related genes when taken into context with existing population genetic studies and biological information. Results add to the number of pedigree sequences reported, suggest pathways for the investigation of biological mechanisms, and are consistent with the overall accumulating evidence that very rare damaging variants contribute to the heritability of schizophrenia.
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Affiliation(s)
| | - Lynn E DeLisi
- Cambridge Health Alliance, Cambridge, MA, United States; Harvard Medical School, Boston, MA, United States
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106
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Laighneach A, Desbonnet L, Kelly JP, Donohoe G, Morris DW. Meta-Analysis of Brain Gene Expression Data from Mouse Model Studies of Maternal Immune Activation Using Poly(I:C). Genes (Basel) 2021; 12:genes12091363. [PMID: 34573345 PMCID: PMC8471627 DOI: 10.3390/genes12091363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023] Open
Abstract
Maternal immune activation (MIA) is a known risk factor for schizophrenia (SCZ) and autism spectrum disorder (ASD) and is often modelled in animal studies in order to study the effect of prenatal infection on brain function including behaviour and gene expression. Although the effect of MIA on gene expression are highly heterogeneous, combining data from multiple gene expression studies in a robust method may shed light on the true underlying biological effects caused by MIA and this could inform studies of SCZ and ASD. This study combined four RNA-seq and microarray datasets in an overlap analysis and ranked meta-analysis in order to investigate genes, pathways and cell types dysregulated in the MIA mouse models. Genes linked to SCZ and ASD and crucial in neurodevelopmental processes including neural tube folding, regulation of cellular stress and neuronal/glial cell differentiation were among the most consistently dysregulated in these ranked analyses. Gene ontologies including K+ ion channel function, neuron and glial cell differentiation, synaptic structure, axonal outgrowth, cilia function and lipid metabolism were also strongly implicated. Single-cell analysis identified excitatory and inhibitory cell types in the cortex, hippocampus and striatum that may be affected by MIA and are also enriched for genes associated with SCZ, ASD and cognitive phenotypes. This points to the cellular location of molecular mechanisms that may be consistent between the MIA model and neurodevelopmental disease, improving our understanding of its utility to study prenatal infection as an environmental stressor.
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Affiliation(s)
- Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics, Discipline of Biochemistry and School of Psychology, National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.L.); (G.D.)
| | - Lieve Desbonnet
- Discipline of Pharmacology and Therapeutics, National University of Ireland Galway, H91 TK33 Galway, Ireland; (L.D.); (J.P.K.)
| | - John P. Kelly
- Discipline of Pharmacology and Therapeutics, National University of Ireland Galway, H91 TK33 Galway, Ireland; (L.D.); (J.P.K.)
| | - Gary Donohoe
- Centre for Neuroimaging, Cognition and Genomics, Discipline of Biochemistry and School of Psychology, National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.L.); (G.D.)
| | - Derek W. Morris
- Centre for Neuroimaging, Cognition and Genomics, Discipline of Biochemistry and School of Psychology, National University of Ireland Galway, H91 TK33 Galway, Ireland; (A.L.); (G.D.)
- Correspondence:
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107
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Goes FS, Pirooznia M, Tehan M, Zandi PP, McGrath J, Wolyniec P, Nestadt G, Pulver AE. De novo variation in bipolar disorder. Mol Psychiatry 2021; 26:4127-4136. [PMID: 31776463 PMCID: PMC10754065 DOI: 10.1038/s41380-019-0611-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 11/10/2019] [Accepted: 11/14/2019] [Indexed: 11/09/2022]
Abstract
Bipolar disorder (BD) is a common, highly heritable disorder that affects 1-2% of the world's population. To date, most genetic studies of BD have focused on common gene variation, and while robustly associated loci have been identified, a substantial proportion of the heritability remains missing and could be partially attributable to rare variation. In this study, we apply a de novo paradigm in BD to identify newly arisen variants that have yet to undergo natural selection and may represent highly pathogenic variants. We performed whole genome sequencing of 97 trios of Ashkenazi Jewish descent, selecting "simplex" families with no family history of BD and an early age of onset. We found a total of 6882 de novo variants (an average of 70.9 ± 12.9 S.D. variants per trio), including 107 variants within protein-coding genes. We combined our exonic variations with the results of 79 previously published BD trios, identifying 20 loss-of-function (LoF) and 77 missense damaging de novo variants in BD. These variants showed significant enrichment for constrained genes and for genes located to the postsynaptic density (PSD) (all Bonferroni corrected p < 0.05). Pathway analyses showed enrichment in several pathways, including "Phosphoinositides (PI) and their downstream targets" (Bonferroni p = 4.2 × 10-6), a pathway prominently featured in lithium's hypothesized mechanism of action. In addition, while we found overall evidence for transmission of common variant polygenic risk of BD in our full sample (pTDT p = 2.21 × 10-4), specific trios with LoF variants showed no evidence of polygenic transmission. In sum, our findings support the de novo paradigm as a contributor to the genetic architecture of BD and provide evidence that constrained genes, as well as genes within the PSD and PI pathway harbor rare variation associated with BD.
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Affiliation(s)
- Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 550 N. Broadway, Suite 202, Baltimore, MD, 21287, USA.
| | - Mehdi Pirooznia
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 550 N. Broadway, Suite 202, Baltimore, MD, 21287, USA
| | - Martin Tehan
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 550 N. Broadway, Suite 202, Baltimore, MD, 21287, USA
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 550 N. Broadway, Suite 202, Baltimore, MD, 21287, USA
| | - John McGrath
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 550 N. Broadway, Suite 202, Baltimore, MD, 21287, USA
| | - Paula Wolyniec
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 550 N. Broadway, Suite 202, Baltimore, MD, 21287, USA
| | - Gerald Nestadt
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 550 N. Broadway, Suite 202, Baltimore, MD, 21287, USA
| | - Ann E Pulver
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, 550 N. Broadway, Suite 202, Baltimore, MD, 21287, USA
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Cleynen I, Engchuan W, Hestand MS, Heung T, Holleman AM, Johnston HR, Monfeuga T, McDonald-McGinn DM, Gur RE, Morrow BE, Swillen A, Vorstman JAS, Bearden CE, Chow EWC, van den Bree M, Emanuel BS, Vermeesch JR, Warren ST, Owen MJ, Chopra P, Cutler DJ, Duncan R, Kotlar AV, Mulle JG, Voss AJ, Zwick ME, Diacou A, Golden A, Guo T, Lin JR, Wang T, Zhang Z, Zhao Y, Marshall C, Merico D, Jin A, Lilley B, Salmons HI, Tran O, Holmans P, Pardinas A, Walters JTR, Demaerel W, Boot E, Butcher NJ, Costain GA, Lowther C, Evers R, van Amelsvoort TAMJ, van Duin E, Vingerhoets C, Breckpot J, Devriendt K, Vergaelen E, Vogels A, Crowley TB, McGinn DE, Moss EM, Sharkus RJ, Unolt M, Zackai EH, Calkins ME, Gallagher RS, Gur RC, Tang SX, Fritsch R, Ornstein C, Repetto GM, Breetvelt E, Duijff SN, Fiksinski A, Moss H, Niarchou M, Murphy KC, Prasad SE, Daly EM, Gudbrandsen M, Murphy CM, Murphy DG, Buzzanca A, Fabio FD, Digilio MC, Pontillo M, Marino B, Vicari S, Coleman K, Cubells JF, Ousley OY, Carmel M, Gothelf D, Mekori-Domachevsky E, Michaelovsky E, Weinberger R, Weizman A, Kushan L, Jalbrzikowski M, Armando M, Eliez S, Sandini C, Schneider M, Béna FS, Antshel KM, Fremont W, Kates WR, Belzeaux R, Busa T, Philip N, Campbell LE, McCabe KL, Hooper SR, Schoch K, Shashi V, Simon TJ, Tassone F, Arango C, Fraguas D, García-Miñaúr S, Morey-Canyelles J, Rosell J, Suñer DH, Raventos-Simic J, Epstein MP, Williams NM, Bassett AS. Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion. Mol Psychiatry 2021; 26:4496-4510. [PMID: 32015465 PMCID: PMC7396297 DOI: 10.1038/s41380-020-0654-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/01/2019] [Accepted: 01/16/2020] [Indexed: 12/17/2022]
Abstract
Schizophrenia occurs in about one in four individuals with 22q11.2 deletion syndrome (22q11.2DS). The aim of this International Brain and Behavior 22q11.2DS Consortium (IBBC) study was to identify genetic factors that contribute to schizophrenia, in addition to the ~20-fold increased risk conveyed by the 22q11.2 deletion. Using whole-genome sequencing data from 519 unrelated individuals with 22q11.2DS, we conducted genome-wide comparisons of common and rare variants between those with schizophrenia and those with no psychotic disorder at age ≥25 years. Available microarray data enabled direct comparison of polygenic risk for schizophrenia between 22q11.2DS and independent population samples with no 22q11.2 deletion, with and without schizophrenia (total n = 35,182). Polygenic risk for schizophrenia within 22q11.2DS was significantly greater for those with schizophrenia (padj = 6.73 × 10-6). Novel reciprocal case-control comparisons between the 22q11.2DS and population-based cohorts showed that polygenic risk score was significantly greater in individuals with psychotic illness, regardless of the presence of the 22q11.2 deletion. Within the 22q11.2DS cohort, results of gene-set analyses showed some support for rare variants affecting synaptic genes. No common or rare variants within the 22q11.2 deletion region were significantly associated with schizophrenia. These findings suggest that in addition to the deletion conferring a greatly increased risk to schizophrenia, the risk is higher when the 22q11.2 deletion and common polygenic risk factors that contribute to schizophrenia in the general population are both present.
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Affiliation(s)
| | - Worrawat Engchuan
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada
| | - Matthew S Hestand
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Tracy Heung
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | | | - H Richard Johnston
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Thomas Monfeuga
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Donna M McDonald-McGinn
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Raquel E Gur
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Bernice E Morrow
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ann Swillen
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Jacob A S Vorstman
- Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Carrie E Bearden
- Departments of Psychiatry and Biobehavioral Sciences and Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Eva W C Chow
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Marianne van den Bree
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Beverly S Emanuel
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Stephen T Warren
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Richard Duncan
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alex V Kotlar
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Jennifer G Mulle
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Anna J Voss
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Alexander Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Aaron Golden
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tingwei Guo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jhih-Rong Lin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tao Wang
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Zhengdong Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yingjie Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Christian Marshall
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Daniele Merico
- The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON, Canada
- Deep Genomics Inc., Toronto, ON, Canada
| | - Andrea Jin
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Brenna Lilley
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Harold I Salmons
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Oanh Tran
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Antonio Pardinas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Erik Boot
- Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, ON, Canada
| | - Nancy J Butcher
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Gregory A Costain
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Hospital for Sick Children, Toronto, ON, Canada
| | - Chelsea Lowther
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Rens Evers
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | | | - Esther van Duin
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Claudia Vingerhoets
- School for Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands
| | - Jeroen Breckpot
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Koen Devriendt
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Elfi Vergaelen
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Annick Vogels
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - T Blaine Crowley
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Daniel E McGinn
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Edward M Moss
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Robert J Sharkus
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marta Unolt
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Elaine H Zackai
- Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics and 22q and You Center, the Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Monica E Calkins
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert S Gallagher
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruben C Gur
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | - Sunny X Tang
- Department of Psychiatry and Lifespan Brain Institute, Penn Medicine-CHOP, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Elemi Breetvelt
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, Hospital for Sick Children, Toronto, ON, Canada
| | - Sasja N Duijff
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Ania Fiksinski
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hayley Moss
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Maria Niarchou
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | | | | | - Eileen M Daly
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Maria Gudbrandsen
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Clodagh M Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Declan G Murphy
- Department of Forensic and Neurodevelopmental Sciences, Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, London, UK
| | - Antonio Buzzanca
- Department of Human Neurosciences, University Sapienza of Rome, Rome, Italy
| | - Fabio Di Fabio
- Department of Human Neurosciences, University Sapienza of Rome, Rome, Italy
| | | | - Maria Pontillo
- Child and Adolescence Neuropsychiatry Unit, Department of Neuroscience, IRCSS Bambino Gesù Children's Hospital of Rome, Rome, Italy
| | | | - Stefano Vicari
- Child and Adolescence Neuropsychiatry Unit, Department of Neuroscience, IRCSS Bambino Gesù Children's Hospital of Rome, Rome, Italy
| | - Karlene Coleman
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Joseph F Cubells
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Opal Y Ousley
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, USA
| | - Miri Carmel
- Felsenstein Medical Research Center, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Doron Gothelf
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Ehud Mekori-Domachevsky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Elena Michaelovsky
- Felsenstein Medical Research Center, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ronnie Weinberger
- The Child Psychiatry Division, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
| | - Abraham Weizman
- Felsenstein Medical Research Center, Petach Tikva, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Geha Mental Health Center, Petach Tikva, Israel
| | - Leila Kushan
- Departments of Psychiatry and Biobehavioral Sciences and Psychology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Maria Jalbrzikowski
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marco Armando
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Stéphan Eliez
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Corrado Sandini
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Maude Schneider
- Developmental Imaging and Psychopathology, Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | | | - Kevin M Antshel
- Department of Psychology, Syracuse University, Syracuse, NY, USA
| | - Wanda Fremont
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Wendy R Kates
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY, USA
| | - Raoul Belzeaux
- Pôle de psychiatrie, Hopital Sainte Marguerite, Batiment Solaris, APHM, Marseille, France
| | - Tiffany Busa
- Departement de Genetique Medicale Hôpital d'Enfants de la Timone, APHM, Marseille, France
| | - Nicole Philip
- Departement de Genetique Medicale Aix Marseille Univ, INSERM, GMGF, APHM, Marseille, France
| | | | - Kathryn L McCabe
- University of Newcastle, Callaghan, Australia
- University of California Davis, Davis, CA, USA
| | - Stephen R Hooper
- Department of Allied Health Sciences, School of Medicine, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC, USA
| | - Tony J Simon
- MIND Institute and Department of Psychiatry and Behavioral Sciences, University of California Davis, Davis, CA, USA
| | - Flora Tassone
- Department of Microbiology and Molecular Medicine, University of California Davis, Davis, CA, USA
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - David Fraguas
- Department of Child and Adolescent Psychiatry, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, School of Medicine, Universidad Complutense, Madrid, Spain
| | - Sixto García-Miñaúr
- Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain
| | | | | | - Damià H Suñer
- Laboratorio Unidad de Diagnóstico Molecular y Genética Clínica, Hospital Universitari Son Espases, Palma de Mallorca, Spain
| | | | - Michael P Epstein
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA.
| | - Nigel M Williams
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - Anne S Bassett
- Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON, Canada.
- Dalglish Family 22q Clinic, Toronto General Hospital, University Health Network, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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109
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Kowalec K, Lu Y, Sariaslan A, Song J, Ploner A, Dalman C, Hultman CM, Larsson H, Lichtenstein P, Sullivan PF. Increased schizophrenia family history burden and reduced premorbid IQ in treatment-resistant schizophrenia: a Swedish National Register and Genomic Study. Mol Psychiatry 2021; 26:4487-4495. [PMID: 31712719 PMCID: PMC9731609 DOI: 10.1038/s41380-019-0575-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 09/23/2019] [Accepted: 10/23/2019] [Indexed: 01/29/2023]
Abstract
A high proportion of those with schizophrenia experience treatment non-response, placing them at higher risk for mortality and suicide attempts, compared to treatment responders. The clinical, social, and economic burden of treatment-resistant schizophrenia (TRS) are substantial. Previous genomic and epidemiological studies of TRS were often limited by sample size or lack of comprehensive genomic data. We aimed to systematically understand the clinical, demographic, and genomic correlates of TRS using epidemiological and genetic epidemiological modelling in a Swedish national population sample (n = 24,706) and then in a subgroup with common variant genetic risk scores, rare copy-number variant burden, and rare exonic burden (n = 4936). Population-based analyses identified increasing schizophrenia family history to be significantly associated with TRS (highest quartile of familial burden vs. lowest: adjusted odds ratio (aOR): 1.31, P = 4.8 × 10-8). In males, a decrease of premorbid IQ of one standard deviation was significantly associated with greater risk of TRS (minimal aOR: 0.94, P = 0.002). In a subset of cases with extensive genomic data, we found no significant association between the genetic risk scores of four psychiatric disorders and two cognitive traits with TRS (schizophrenia genetic risk score: aOR = 1.07, P = 0.067). The association between copy number variant and rare variant burden measures and TRS did not reach the pre-defined statistical significance threshold (all P ≥ 0.005). In conclusion, direct measures of genomic risk were not associated with TRS; however, premorbid IQ in males and schizophrenia family history were significantly correlated with TRS and points to new insights into the architecture of TRS.
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Affiliation(s)
- Kaarina Kowalec
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, College of Pharmacy, University of Manitoba, Winnipeg, MB, Canada
| | - Yi Lu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Amir Sariaslan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jie Song
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christina Dalman
- Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, Icahn School of Medicine, Department of Psychiatry, Mt. Sinai Hospital, New York, NY, USA
| | - Henrik Larsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, School of Medical Sciences, Örebo University, Örebo, Sweden
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrick F. Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, Departments of Genetics and Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Zuo Y, Wei D, Zhu C, Naveed O, Hong W, Yang X. Unveiling the Pathogenesis of Psychiatric Disorders Using Network Models. Genes (Basel) 2021; 12:1101. [PMID: 34356117 PMCID: PMC8304351 DOI: 10.3390/genes12071101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 01/13/2023] Open
Abstract
Psychiatric disorders are complex brain disorders with a high degree of genetic heterogeneity, affecting millions of people worldwide. Despite advances in psychiatric genetics, the underlying pathogenic mechanisms of psychiatric disorders are still largely elusive, which impedes the development of novel rational therapies. There has been accumulating evidence suggesting that the genetics of complex disorders can be viewed through an omnigenic lens, which involves contextualizing genes in highly interconnected networks. Thus, applying network-based multi-omics integration methods could cast new light on the pathophysiology of psychiatric disorders. In this review, we first provide an overview of the recent advances in psychiatric genetics and highlight gaps in translating molecular associations into mechanistic insights. We then present an overview of network methodologies and review previous applications of network methods in the study of psychiatric disorders. Lastly, we describe the potential of such methodologies within a multi-tissue, multi-omics approach, and summarize the future directions in adopting diverse network approaches.
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Affiliation(s)
- Yanning Zuo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Don Wei
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Department of Psychiatry, Semel Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Carissa Zhu
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Ormina Naveed
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
| | - Weizhe Hong
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA; (Y.Z.); (D.W.); (W.H.)
- Department of Neurobiology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Brain Research Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095, USA; (C.Z.); (O.N.)
- Brain Research Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California at Los Angeles, Los Angeles, CA 90095, USA
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111
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Takahashi Y, Maynard KR, Tippani M, Jaffe AE, Martinowich K, Kleinman JE, Weinberger DR, Hyde TM. Single molecule in situ hybridization reveals distinct localizations of schizophrenia risk-related transcripts SNX19 and AS3MT in human brain. Mol Psychiatry 2021; 26:3536-3547. [PMID: 33649454 DOI: 10.1038/s41380-021-01046-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 01/20/2021] [Accepted: 02/02/2021] [Indexed: 11/09/2022]
Abstract
Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) associated with schizophrenia risk. Integration of RNA-sequencing data from postmortem human brains with these risk SNPs identified transcripts associated with increased schizophrenia susceptibility, including a class of exon 9-spliced isoforms of Sorting nexin-19 (SNX19d9) and an isoform of Arsenic methyltransferase (AS3MT) splicing out exons 2 and 3 (AS3MTd2d3). However, the biological function of these transcript variants is unclear. Defining the cell types where these risk transcripts are dominantly expressed is an important step to understand function, in prioritizing specific cell types and/or neural pathways in subsequent studies. To identify the cell type-specific localization of SNX19 and AS3MT in the human dorsolateral prefrontal cortex (DLPFC), we used single-molecule in situ hybridization techniques combined with automated quantification and machine learning approaches to analyze 10 postmortem brains of neurotypical individuals. These analyses revealed that both pan-SNX19 and pan-AS3MT were more highly expressed in neurons than non-neurons in layers II/III and VI of DLPFC. Furthermore, pan-SNX19 was preferentially expressed in glutamatergic neurons, while pan-AS3MT was preferentially expressed in GABAergic neurons. Finally, we utilized duplex BaseScope technology, to delineate the localization of SNX19d9 and AS3MTd2d3 splice variants, revealing consistent trends in spatial gene expression among pan-transcripts and schizophrenia risk-related transcript variants. These findings demonstrate that schizophrenia risk transcripts have distinct localization patterns in the healthy human brains, and suggest that SNX19 transcripts might disrupt the normal function of glutamatergic neurons, while AS3MT may lead to disturbances in the GABAergic system in the pathophysiology of schizophrenia.
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Affiliation(s)
- Yoichiro Takahashi
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Legal Medicine, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Keri Martinowich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
- Department of Psychiatry & Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA.
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112
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Clifton NE, Rees E, Holmans PA, Pardiñas AF, Harwood JC, Di Florio A, Kirov G, Walters JTR, O'Donovan MC, Owen MJ, Hall J, Pocklington AJ. Genetic association of FMRP targets with psychiatric disorders. Mol Psychiatry 2021; 26:2977-2990. [PMID: 33077856 PMCID: PMC8505260 DOI: 10.1038/s41380-020-00912-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 09/28/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022]
Abstract
Genes encoding the mRNA targets of fragile X mental retardation protein (FMRP) are enriched for genetic association with psychiatric disorders. However, many FMRP targets possess functions that are themselves genetically associated with psychiatric disorders, including synaptic transmission and plasticity, making it unclear whether the genetic risk is truly related to binding by FMRP or is alternatively mediated by the sampling of genes better characterised by another trait or functional annotation. Using published common variant, rare coding variant and copy number variant data, we examined the relationship between FMRP binding and genetic association with schizophrenia, major depressive disorder and bipolar disorder. High-confidence targets of FMRP, derived from studies of multiple tissue types, were enriched for common schizophrenia risk alleles, as well as rare loss-of-function and de novo nonsynonymous variants in schizophrenia cases. Similarly, through common variation, FMRP targets were associated with major depressive disorder, and we present novel evidence of association with bipolar disorder. These relationships could not be explained by other functional annotations known to be associated with psychiatric disorders, including those related to synaptic structure and function. This study reinforces the evidence that targeting by FMRP captures a subpopulation of genes enriched for genetic association with a range of psychiatric disorders.
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Affiliation(s)
- Nicholas E Clifton
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Peter A Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Janet C Harwood
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Arianna Di Florio
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Jeremy Hall
- Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, UK
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Andrew J Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK.
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113
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Tomov ML, O'Neil A, Abbasi HS, Cimini BA, Carpenter AE, Rubin LL, Bathe M. Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging. Commun Biol 2021; 4:786. [PMID: 34168275 PMCID: PMC8225800 DOI: 10.1038/s42003-021-02276-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/28/2021] [Indexed: 12/30/2022] Open
Abstract
Human induced pluripotent stem cell-derived (iPSC) neural cultures offer clinically relevant models of human diseases, including Amyotrophic Lateral Sclerosis, Alzheimer’s, and Autism Spectrum Disorder. In situ characterization of the spatial-temporal evolution of cell state in 3D culture and subsequent 2D dissociated culture models based on protein expression levels and localizations is essential to understanding neural cell differentiation, disease state phenotypes, and sample-to-sample variability. Here, we apply PRobe-based Imaging for Sequential Multiplexing (PRISM) to facilitate multiplexed imaging with facile, rapid exchange of imaging probes to analyze iPSC-derived cortical and motor neuron cultures that are relevant to psychiatric and neurodegenerative disease models, using over ten protein targets. Our approach permits analysis of cell differentiation, cell composition, and functional marker expression in complex stem-cell derived neural cultures. Furthermore, our approach is amenable to automation, offering in principle the ability to scale-up to dozens of protein targets and samples. Tomov et al. utilize DNA-PRISM to allow for multiplexed imaging of cultured cells using antibodies modified with oligonucleotide probes. The differentiation of iPSCs to cortical and motor neurons is characterized in model cultures, relevant for use in disease research and drug screening.
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Affiliation(s)
- Martin L Tomov
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Alison O'Neil
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Hamdah S Abbasi
- Imaging Platform at Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Beth A Cimini
- Imaging Platform at Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform at Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lee L Rubin
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Mark Bathe
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
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114
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Boussaad I, Obermaier CD, Hanss Z, Bobbili DR, Bolognin S, Glaab E, Wołyńska K, Weisschuh N, De Conti L, May C, Giesert F, Grossmann D, Lambert A, Kirchen S, Biryukov M, Burbulla LF, Massart F, Bohler J, Cruciani G, Schmid B, Kurz-Drexler A, May P, Duga S, Klein C, Schwamborn JC, Marcus K, Woitalla D, Vogt Weisenhorn DM, Wurst W, Baralle M, Krainc D, Gasser T, Wissinger B, Krüger R. A patient-based model of RNA mis-splicing uncovers treatment targets in Parkinson's disease. Sci Transl Med 2021; 12:12/560/eaau3960. [PMID: 32908004 DOI: 10.1126/scitranslmed.aau3960] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 01/24/2020] [Accepted: 06/22/2020] [Indexed: 12/18/2022]
Abstract
Parkinson's disease (PD) is a heterogeneous neurodegenerative disorder with monogenic forms representing prototypes of the underlying molecular pathology and reproducing to variable degrees the sporadic forms of the disease. Using a patient-based in vitro model of PARK7-linked PD, we identified a U1-dependent splicing defect causing a drastic reduction in DJ-1 protein and, consequently, mitochondrial dysfunction. Targeting defective exon skipping with genetically engineered U1-snRNA recovered DJ-1 protein expression in neuronal precursor cells and differentiated neurons. After prioritization of candidate drugs, we identified and validated a combinatorial treatment with the small-molecule compounds rectifier of aberrant splicing (RECTAS) and phenylbutyric acid, which restored DJ-1 protein and mitochondrial dysfunction in patient-derived fibroblasts as well as dopaminergic neuronal cell loss in mutant midbrain organoids. Our analysis of a large number of exomes revealed that U1 splice-site mutations were enriched in sporadic PD patients. Therefore, our study suggests an alternative strategy to restore cellular abnormalities in in vitro models of PD and provides a proof of concept for neuroprotection based on precision medicine strategies in PD.
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Affiliation(s)
- Ibrahim Boussaad
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Carolin D Obermaier
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg.,Department of Neurodegenerative Diseases and Hertie-Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | - Zoé Hanss
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Dheeraj R Bobbili
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Silvia Bolognin
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Enrico Glaab
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Katarzyna Wołyńska
- Department of Medical Genetics, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University Clinics Tübingen, 72076 Tübingen, Germany
| | - Laura De Conti
- ICGEB-International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Caroline May
- Medizinisches Proteom-Center, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Florian Giesert
- Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,German Center for Neurodegenerative Diseases (DZNE), Site Munich, Feodor-Lynen-Str. 17, 81377 Munich, Germany.,Technische Universität München-Weihenstephan, Developmental Genetics, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Dajana Grossmann
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Annika Lambert
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Susanne Kirchen
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Maria Biryukov
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Lena F Burbulla
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Francois Massart
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Jill Bohler
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Gérald Cruciani
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Benjamin Schmid
- Department of Neurodegenerative Diseases and Hertie-Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany
| | | | - Patrick May
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, 20089 Rozzano, Milan, Italy.,Humanitas Clinical and Research center, IRCCS, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Christine Klein
- Institute of Neurogenetics, University of Luebeck, 23562 Luebeck, Germany
| | - Jens C Schwamborn
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg
| | - Katrin Marcus
- Medizinisches Proteom-Center, Ruhr-University Bochum, 44801 Bochum, Germany
| | - Dirk Woitalla
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, 44791 Bochum, Germany
| | - Daniela M Vogt Weisenhorn
- Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,Technische Universität München-Weihenstephan, Developmental Genetics, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Wolfgang Wurst
- Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764 Neuherberg, Germany.,German Center for Neurodegenerative Diseases (DZNE), Site Munich, Feodor-Lynen-Str. 17, 81377 Munich, Germany.,Technische Universität München-Weihenstephan, Developmental Genetics, c/o Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany.,Munich Cluster for Systems Neurology (SyNergy), Feodor-Lynen-Str. 17, 81377 Munich, Germany
| | - Marco Baralle
- ICGEB-International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Thomas Gasser
- Department of Neurodegenerative Diseases and Hertie-Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), 72076 Tübingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University Clinics Tübingen, 72076 Tübingen, Germany
| | - Rejko Krüger
- LCSB, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 4362 Esch-Sur-Alzette, Luxembourg. .,Department of Neurodegenerative Diseases and Hertie-Institute for Clinical Brain Research, University of Tübingen, 72076 Tübingen, Germany.,Department of Neurology and Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), 1210 Luxembourg, Luxembourg.,Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1445 Strassen, Luxembourg
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115
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Systematic analysis of exonic germline and postzygotic de novo mutations in bipolar disorder. Nat Commun 2021; 12:3750. [PMID: 34145229 PMCID: PMC8213845 DOI: 10.1038/s41467-021-23453-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/29/2021] [Indexed: 12/30/2022] Open
Abstract
Bipolar disorder is a severe mental illness characterized by recurrent manic and depressive episodes. To better understand its genetic architecture, we analyze ultra-rare de novo mutations in 354 trios with bipolar disorder. For germline de novo mutations, we find significant enrichment of loss-of-function mutations in constrained genes (corrected-P = 0.0410) and deleterious mutations in presynaptic active zone genes (FDR = 0.0415). An analysis integrating single-cell RNA-sequencing data identifies a subset of excitatory neurons preferentially expressing the genes hit by deleterious mutations, which are also characterized by high expression of developmental disorder genes. In the analysis of postzygotic mutations, we observe significant enrichment of deleterious ones in developmental disorder genes (P = 0.00135), including the SRCAP gene mutated in two unrelated probands. These data collectively indicate the contributions of both germline and postzygotic mutations to the risk of bipolar disorder, supporting the hypothesis that postzygotic mutations of developmental disorder genes may contribute to bipolar disorder. The significance of rare and de novo variants in bipolar disorder is not well understood. Here, the authors have analyzed whole exome/genome data from trios to identify deleterious de novo variants associated with bipolar disorder.
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116
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Abstract
Severe neuropsychiatric disorders are so genetically heterogeneous that virtually every unrelated patient harbors different clinically significant alleles. By studying schizophrenia in the Ashkenazi Jewish founder population, Lencz and co-authors identified rare severe alleles each shared by a few patients. Experimental evaluation of an implicated protocadherin allele revealed failure to form homophilic cellular aggregates as a possible mechanism for defective development of neural circuits.
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Affiliation(s)
- Jon M McClellan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Mary-Claire King
- Department of Medicine and Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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117
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Kim M, Haney JR, Zhang P, Hernandez LM, Wang LK, Perez-Cano L, Olde Loohuis LM, de la Torre-Ubieta L, Gandal MJ. Brain gene co-expression networks link complement signaling with convergent synaptic pathology in schizophrenia. Nat Neurosci 2021; 24:799-809. [PMID: 33958802 PMCID: PMC8178202 DOI: 10.1038/s41593-021-00847-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/25/2021] [Indexed: 02/02/2023]
Abstract
The most significant common variant association for schizophrenia (SCZ) reflects increased expression of the complement component 4A (C4A). Yet, it remains unclear how C4A interacts with other SCZ risk genes or whether the complement system more broadly is implicated in SCZ pathogenesis. Here, we integrate several existing, large-scale genetic and transcriptomic datasets to interrogate the functional role of the complement system and C4A in the human brain. Unexpectedly, we find no significant genetic enrichment among known complement system genes for SCZ. Conversely, brain co-expression network analyses using C4A as a seed gene reveal that genes downregulated when C4A expression increases exhibit strong and specific genetic enrichment for SCZ risk. This convergent genomic signal reflects synaptic processes, is sexually dimorphic and most prominent in frontal cortical brain regions, and is accentuated by smoking. Overall, these results indicate that synaptic pathways-rather than the complement system-are the driving force conferring SCZ risk.
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Affiliation(s)
- Minsoo Kim
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jillian R. Haney
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Pan Zhang
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Leanna M. Hernandez
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Lee-kai Wang
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Laura Perez-Cano
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,STALICLA DDS, Barcelona, Spain
| | - Loes M. Olde Loohuis
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Luis de la Torre-Ubieta
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael J. Gandal
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.,Correspondence to:
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118
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Dysregulation of post-transcriptional modification by copy number variable microRNAs in schizophrenia with enhanced glycation stress. Transl Psychiatry 2021; 11:331. [PMID: 34050135 PMCID: PMC8163801 DOI: 10.1038/s41398-021-01460-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 04/30/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022] Open
Abstract
Previously, we identified a subpopulation of schizophrenia (SCZ) showing increased levels of plasma pentosidine, a marker of glycation and oxidative stress. However, its causative genetic factors remain largely unknown. Recently, it has been suggested that dysregulated posttranslational modification by copy number variable microRNAs (CNV-miRNAs) may contribute to the etiology of SCZ. Here, an integrative genome-wide CNV-miRNA analysis was performed to investigate the etiology of SCZ with accumulated plasma pentosidine (PEN-SCZ). The number of CNV-miRNAs and the gene ontology (GO) in the context of miRNAs within CNVs were compared between PEN-SCZ and non-PEN-SCZ groups. Gene set enrichment analysis of miRNA target genes was further performed to evaluate the pathways affected in PEN-SCZ. We show that miRNAs were significantly enriched within CNVs in the PEN-SCZ versus non-PEN-SCZ groups (p = 0.032). Of note, as per GO analysis, the dysregulated neurodevelopmental events in the two groups may have different origins. Additionally, gene set enrichment analysis of miRNA target genes revealed that miRNAs involved in glycation/oxidative stress and synaptic neurotransmission, especially glutamate/GABA receptor signaling, were possibly affected in PEN-SCZ. To the best of our knowledge, this is the first genome-wide CNV-miRNA study suggesting the role of CNV-miRNAs in the etiology of PEN-SCZ, through effects on genes related to glycation/oxidative stress and synaptic function. Our findings provide supportive evidence that glycation/oxidative stress possibly caused by genetic defects related to the posttranscriptional modification may lead to synaptic dysfunction. Therefore, targeting miRNAs may be one of the promising approaches for the treatment of PEN-SCZ.
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119
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Downregulation by CNNM2 of ATP5MD expression in the 10q24.32 schizophrenia-associated locus involved in impaired ATP production and neurodevelopment. NPJ SCHIZOPHRENIA 2021; 7:27. [PMID: 34021155 PMCID: PMC8139961 DOI: 10.1038/s41537-021-00159-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/21/2021] [Indexed: 12/11/2022]
Abstract
Genome-wide association studies (GWAS) have accelerated the discovery of numerous genetic variants associated with schizophrenia. However, most risk variants show a small effect size (odds ratio (OR) <1.2), suggesting that more functional risk variants remain to be identified. Here, we employed region-based multi-marker analysis of genomic annotation (MAGMA) to identify additional risk loci containing variants with large OR value from Psychiatry Genomics Consortium (PGC2) schizophrenia GWAS data and then employed summary-data-based mendelian randomization (SMR) to prioritize schizophrenia susceptibility genes. The top-ranked susceptibility gene ATP5MD, encoding an ATP synthase membrane subunit, is observed to be downregulated in schizophrenia by the risk allele of CNNM2-rs1926032 in the schizophrenia-associated 10q24.32 locus. The Atp5md knockout (KO) in mice was associated with abnormal startle reflex and gait, and ATP5MD knockdown (KD) in human induced pluripotent stem cell-derived neurons disrupted the neural development and mitochondrial respiration and ATP production. Moreover, CNNM2-rs1926032 KO could induce downregulation of ATP5MD expression and disruptions of mitochondrial respiration and ATP production. This study constitutes an important mechanistic component that links schizophrenia-associated CNNM2 regions to disruption in energy adenosine system modulation and neuronal function by long-distance chromatin domain downregulation of ATP5MD. This pathogenic mechanism provides therapeutic implications for schizophrenia.
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120
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More evidence on TRIO missense mutations in the spectrin repeat domain causing severe developmental delay and recognizable facial dysmorphism with macrocephaly. Neurogenetics 2021; 22:221-224. [PMID: 34013494 DOI: 10.1007/s10048-021-00648-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/12/2021] [Indexed: 01/18/2023]
Abstract
TRIO is a Dbl family guanine nucleotide exchange factor (GEF) and an important regulator of neuronal development. Most truncating and missense variants affecting the Dbl homology domain of TRIO are associated with a neurodevelopmental disorder with microcephaly (MIM617061). Recently, de novo missense variants affecting the spectrin repeat region of TRIO were associated with a novel phenotype comprising severe developmental delay and macrocephaly (MIM618825). Here, we provide more evidence on this new TRIO-associated phenotype by reporting two severely affected probands with de novo missense variants in TRIO affecting the spectrin repeat region upstream of the typically affected GEF1 domain of the protein.
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121
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Takata A, Hamanaka K, Matsumoto N. Refinement of the clinical variant interpretation framework by statistical evidence and machine learning. MED 2021; 2:611-632.e9. [PMID: 35590234 DOI: 10.1016/j.medj.2021.02.003] [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: 03/27/2020] [Revised: 09/28/2020] [Accepted: 02/16/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND Although the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines for variant interpretation are used widely in clinical genetics, there is room for improvement of these knowledge-based guidelines. METHODS Statistical assessment of average deleteriousness of start-lost, stop-lost, and in-frame insertion and deletion (indel) variants and extraction of deleterious subsets was performed, being informed by proportions of rare variants in the general population of the Genome Aggregation Database (gnomAD). A machine learning-based model scoring the pathogenicity of start-lost variants (the PoStaL model) was constructed by predicting possible translation initiation sites on transcripts by deep learning and training a random forest on known pathogenic and likely benign variants. FINDINGS The proportion of rare variants was highest in stop-lost variants, followed by in-frame indels and start-lost variants, suggesting that the criteria in the ACMG/AMP guidelines assigning PVS (pathogenic very strong) to start-lost variants and PM (pathogenic moderate) to stop-lost and in-frame indel variants would not be appropriate. Regarding deleterious subsets, stop-lost variants introducing extensions of more than 30 amino acids and in-frame indels computationally predicted to be damaging are enriched for rare and known pathogenic variants. For start-lost variants, we developed the PoStaL model, which outperforms existing tools. We also provide comprehensive lists of the PoStaL scores for start-lost variants and the length of extended amino acids by stop-lost variants. CONCLUSIONS Our study could contribute to refinement of the ACMG/AMP guidelines, provides resources for future investigation, and provides an example of how to improve knowledge-based frameworks by data-driven approaches. FUNDING The study was supported by grants from the Japan Agency for Medical Research and Development (AMED) and the Japan Society for the Promotion of Science (JSPS).
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Affiliation(s)
- Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan.
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122
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Bhattacharyya U, Deshpande SN, Bhatia T, Thelma BK. Revisiting Schizophrenia from an Evolutionary Perspective: An Association Study of Recent Evolutionary Markers and Schizophrenia. Schizophr Bull 2021; 47:827-836. [PMID: 33350444 PMCID: PMC8759809 DOI: 10.1093/schbul/sbaa179] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The persistence of schizophrenia in human populations at a high prevalence and with a large heritability estimate despite reduced fertility and increased mortality rate is a Darwinian paradox. This may be likely if the genomic components that predispose to schizophrenia are also advantageous for the acquisition of important human traits, such as language and cognition. Accordingly, an emerging group of genomic markers of recent evolution in humans, namely human accelerated regions (HARs), since our divergence from chimpanzees, are gaining importance for neurodevelopmental disorders, such as schizophrenia. We hypothesize that variants within HARs may affect the expression of genes under their control, thus contributing to disease etiology. A total of 49 HAR single nucleotide polymorphisms (SNPs) were prioritized from the complete repertoire of HARs (n = 2737) based on their functional relevance and prevalence in the South Asian population. Test of association using 2 independent schizophrenia case-control cohorts of north Indian ethnicity (discovery: n = 930; replication: n = 1104) revealed 3 SNPs (rs3800926, rs3801844, and rs764453) from chromosome 7 and rs77047799 from chromosome 3 to be significantly associated (combined analysis: Bonferroni corrected P < .002-.000004). Of note, these SNPs were found to alter the expression of neurodevelopmental genes such as SLC25A13, MAD1L1, and ULK4; a few from the HOX gene family; and a few genes that are implicated in mitochondrial function. These SNPs may most likely alter binding sites of transcription factors, including TFCP2, MAFK, SREBF2, E2F1, and/or methylation signatures around these genes. These findings reiterate a neurodevelopmental basis of schizophrenia and also open up a promising avenue to investigate HAR-mediated mitochondrial dysfunction in schizophrenia etiology.
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Affiliation(s)
| | | | | | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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123
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Pol-Fuster J, Cañellas F, Ruiz-Guerra L, Medina-Dols A, Bisbal-Carrió B, Asensio V, Ortega-Vila B, Marzese D, Vidal C, Santos C, Lladó J, Olmos G, Heine-Suñer D, Strauch K, Flaquer A, Vives-Bauzà C. Familial Psychosis Associated With a Missense Mutation at MACF1 Gene Combined With the Rare Duplications DUP3p26.3 and DUP16q23.3, Affecting the CNTN6 and CDH13 Genes. Front Genet 2021; 12:622886. [PMID: 33897758 PMCID: PMC8058362 DOI: 10.3389/fgene.2021.622886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/15/2021] [Indexed: 12/30/2022] Open
Abstract
Psychosis is a highly heritable and heterogeneous psychiatric condition. Its genetic architecture is thought to be the result of the joint effect of common and rare variants. Families with high prevalence are an interesting approach to shed light on the rare variant's contribution without the need of collecting large cohorts. To unravel the genomic architecture of a family enriched for psychosis, with four affected individuals, we applied a system genomic approach based on karyotyping, genotyping by whole-exome sequencing to search for rare single nucleotide variants (SNVs) and SNP array to search for copy-number variants (CNVs). We identified a rare non-synonymous variant, g.39914279 C > G, in the MACF1 gene, segregating with psychosis. Rare variants in the MACF1 gene have been previously detected in SCZ patients. Besides, two rare CNVs, DUP3p26.3 and DUP16q23.3, were also identified in the family affecting relevant genes (CNTN6 and CDH13, respectively). We hypothesize that the co-segregation of these duplications with the rare variant g.39914279 C > G of MACF1 gene precipitated with schizophrenia and schizoaffective disorder.
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Affiliation(s)
- Josep Pol-Fuster
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Department of Biology, University of Balearic Islands (UIB) and Institut Universitari d'Investigacions en Ciències de la Salut, IUNICS, Palma, Spain
| | - Francesca Cañellas
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Psychiatry Service, University Hospital Son Espases (HUSE), Palma, Spain
| | - Laura Ruiz-Guerra
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Research Unit, HUSE, Palma, Spain
| | - Aina Medina-Dols
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Research Unit, HUSE, Palma, Spain
| | - Bàrbara Bisbal-Carrió
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Department of Biology, University of Balearic Islands (UIB) and Institut Universitari d'Investigacions en Ciències de la Salut, IUNICS, Palma, Spain
| | - Víctor Asensio
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Genomic Service Balearic Islands (GEN-IB), HUSE, Palma, Spain
| | - Bernat Ortega-Vila
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Genomic Service Balearic Islands (GEN-IB), HUSE, Palma, Spain
| | - Diego Marzese
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Research Unit, HUSE, Palma, Spain
| | - Carme Vidal
- Genomic Service Balearic Islands (GEN-IB), HUSE, Palma, Spain
| | - Carmen Santos
- Genomic Service Balearic Islands (GEN-IB), HUSE, Palma, Spain
| | - Jerònia Lladó
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Department of Biology, University of Balearic Islands (UIB) and Institut Universitari d'Investigacions en Ciències de la Salut, IUNICS, Palma, Spain
| | - Gabriel Olmos
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Department of Biology, University of Balearic Islands (UIB) and Institut Universitari d'Investigacions en Ciències de la Salut, IUNICS, Palma, Spain
| | - Damià Heine-Suñer
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Genomic Service Balearic Islands (GEN-IB), HUSE, Palma, Spain
| | - Konstantin Strauch
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Antònia Flaquer
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany.,Institute of Genetic Epidemiology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg, Germany
| | - Cristòfol Vives-Bauzà
- Health Research Institute of Balearic Islands (IdISBa), Palma, Spain.,Department of Biology, University of Balearic Islands (UIB) and Institut Universitari d'Investigacions en Ciències de la Salut, IUNICS, Palma, Spain.,Research Unit, HUSE, Palma, Spain
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124
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Wang X, Ye F, Wen Z, Guo Z, Yu C, Huang WK, Rojas Ringeling F, Su Y, Zheng W, Zhou G, Christian KM, Song H, Zhang M, Ming GL. Structural interaction between DISC1 and ATF4 underlying transcriptional and synaptic dysregulation in an iPSC model of mental disorders. Mol Psychiatry 2021; 26:1346-1360. [PMID: 31444471 PMCID: PMC8444148 DOI: 10.1038/s41380-019-0485-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 04/01/2019] [Accepted: 05/17/2019] [Indexed: 01/01/2023]
Abstract
Psychiatric disorders are a collection of heterogeneous mental disorders arising from a contribution of genetic and environmental insults, many of which molecularly converge on transcriptional dysregulation, resulting in altered synaptic functions. The underlying mechanisms linking the genetic lesion and functional phenotypes remain largely unknown. Patient iPSC-derived neurons with a rare frameshift DISC1 (Disrupted-in-schizophrenia 1) mutation have previously been shown to exhibit aberrant gene expression and deficits in synaptic functions. How DISC1 regulates gene expression is largely unknown. Here we show that Activating Transcription Factor 4 (ATF4), a DISC1 binding partner, is more abundant in the nucleus of DISC1 mutant human neurons and exhibits enhanced binding to a collection of dysregulated genes. Functionally, overexpressing ATF4 in control neurons recapitulates deficits seen in DISC1 mutant neurons, whereas transcriptional and synaptic deficits are rescued in DISC1 mutant neurons with CRISPR-mediated heterozygous ATF4 knockout. By solving the high-resolution atomic structure of the DISC1-ATF4 complex, we show that mechanistically, the mutation of DISC1 disrupts normal DISC1-ATF4 interaction, and results in excessive ATF4 binding to DNA targets and deregulated gene expression. Together, our study identifies the molecular and structural basis of an DISC1-ATF4 interaction underlying transcriptional and synaptic dysregulation in an iPSC model of mental disorders.
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Affiliation(s)
- Xinyuan Wang
- School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Fei Ye
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
- Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Zhexing Wen
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, 30322, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Ziyuan Guo
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Chuan Yu
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Wei-Kai Huang
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Pathology Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Francisca Rojas Ringeling
- The Human Genetics Pre-doctoral Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yijing Su
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wei Zheng
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Guomin Zhou
- School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
| | - Kimberly M Christian
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- The Epigenetics Institute, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Mingjie Zhang
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
- Center of Systems Biology and Human Health, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
| | - Guo-Li Ming
- Department of Neuroscience and Mahoney Institute for Neurosciences, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Cell and Developmental Biology, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Regenerative Medicine, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Psychiatry, Perelman School for Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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125
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Morton SU, Shimamura A, Newburger PE, Opotowsky AR, Quiat D, Pereira AC, Jin SC, Gurvitz M, Brueckner M, Chung WK, Shen Y, Bernstein D, Gelb BD, Giardini A, Goldmuntz E, Kim RW, Lifton RP, Porter GA, Srivastava D, Tristani-Firouzi M, Newburger JW, Seidman JG, Seidman CE. Association of Damaging Variants in Genes With Increased Cancer Risk Among Patients With Congenital Heart Disease. JAMA Cardiol 2021; 6:457-462. [PMID: 33084842 PMCID: PMC7578917 DOI: 10.1001/jamacardio.2020.4947] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Importance Patients with congenital heart disease (CHD), the most common birth defect, have increased risks for cancer. Identification of the variables that contribute to cancer risk is essential for recognizing patients with CHD who warrant longitudinal surveillance and early interventions. Objective To compare the frequency of damaging variants in cancer risk genes among patients with CHD and control participants and identify associated clinical variables in patients with CHD who have cancer risk variants. Design, Setting, and Participants This multicenter case-control study included participants with CHD who had previously been recruited to the Pediatric Cardiac Genomics Consortium based on presence of structural cardiac anomaly without genetic diagnosis at the time of enrollment. Permission to use published sequencing data from unaffected adult participants was obtained from 2 parent studies. Data were collected for this study from December 2010 to April 2019. Exposures Presence of rare (allele frequency, <1 × 10-5) loss-of-function (LoF) variants in cancer risk genes. Main Outcomes and Measures Frequency of LoF variants in cancer risk genes (defined in the Catalogue of Somatic Mutations in Cancer-Cancer Gene Consensus database), were statistically assessed by binomial tests in patients with CHD and control participants. Results A total of 4443 individuals with CHD (mean [range] age, 13.0 [0-84] years; 2225 of 3771 with reported sex [59.0%] male) and 9808 control participants (mean [range] age, 52.1 [1-92] years; 4967 of 9808 [50.6%] male) were included. The frequency of LoF variants in regulatory cancer risk genes was significantly higher in patients with CHD than control participants (143 of 4443 [3.2%] vs 166 of 9808 [1.7%]; odds ratio [OR], 1.93 [95% CI, 1.54-2.42]; P = 1.38 × 10-12), and among CHD genes previously associated with cancer risk (58 of 4443 [1.3%] vs 18 of 9808 [0.18%]; OR, 7.2 [95% CI, 4.2-12.2]; P < 2.2 × 10-16). The LoF variants were also nominally increased in 14 constrained cancer risk genes with high expression in the developing heart. Seven of these genes (ARHGEF12, CTNNB1, LPP, MLLT4, PTEN, TCF12, and TFRC) harbored LoF variants in multiple patients with unexplained CHD. The highest rates for LoF variants in cancer risk genes occurred in patients with CHD and extracardiac anomalies (248 of 1482 individuals [16.7%]; control: 1099 of 9808 individuals [11.2%]; OR, 1.59 [95% CI, 1.37-1.85]; P = 1.3 × 10-10) and/or neurodevelopmental delay (209 of 1393 individuals [15.0%]; control: 1099 of 9808 individuals [11.2%]; OR, 1.40 [95% CI, 1.19-1.64]; P = 9.6 × 10-6). Conclusions and Relevance Genotypes of CHD may account for increased cancer risks. In this cohort, damaging variants were prominent in the 216 genes that predominantly encode regulatory proteins. Consistent with their fundamental developmental functions, patients with CHD and damaging variants in these genes often had extracardiac manifestations. These data may also implicate cancer risk genes that are repeatedly varied in patients with unexplained CHD as CHD genes.
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Affiliation(s)
- Sarah U Morton
- Division of Newborn Medicine, Department of Medicine, Boston Children's Hospital, Boston, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Akiko Shimamura
- Department of Pediatric Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts.,Dana Farber Cancer Institute, Boston, Massachusetts
| | - Peter E Newburger
- Department of Pediatrics University of Massachusetts Medical School, Worcester.,Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester
| | - Alexander R Opotowsky
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts.,Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Daniel Quiat
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | | | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut.,Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut
| | - Michelle Gurvitz
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Martina Brueckner
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut.,Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, New York.,Department of Medicine, Columbia University Medical Center, New York, New York
| | - Yufeng Shen
- Departments of Systems Biology, Columbia University Medical Center, New York, New York.,Departments of Biomedical Informatics, Columbia University Medical Center, New York, New York
| | - Daniel Bernstein
- Department of Pediatrics, Cardiology, Stanford University, Stanford, California
| | - Bruce D Gelb
- Mindich Child Health and Development Institute and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Elizabeth Goldmuntz
- Division of Cardiology, Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | - Richard W Kim
- Pediatric Cardiac Surgery, Children's Hospital of Los Angeles, Los Angeles, California
| | - Richard P Lifton
- Laboratory of Human Genetics and Genomics, The Rockefeller University, New York, New York
| | - George A Porter
- Department of Pediatrics, University of Rochester Medical Center, The School of Medicine and Dentistry, Rochester, New York
| | - Deepak Srivastava
- Gladstone Institute of Cardiovascular Disease, San Francisco, California
| | | | - Jane W Newburger
- Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - J G Seidman
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Christine E Seidman
- Cardiovascular Division, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
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126
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Kermath BA, Vanderplow AM, Cahill ME. Dysregulated Prefrontal Cortical RhoA Signal Transduction in Bipolar Disorder with Psychosis: New Implications for Disease Pathophysiology. Cereb Cortex 2021; 30:59-71. [PMID: 31220216 DOI: 10.1093/cercor/bhz070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
While research has identified alterations in dorsolateral prefrontal cortical function as a key factor to the etiology of bipolar disorder, few studies have uncovered robust changes in protein signal transduction pathways in this disorder. Given the direct relevance of protein-based expressional alterations to cellular functions and because many of the key regulatory mechanisms for the disease pathogenesis likely include alterations in protein activity rather than changes in expression alone, the identification of alterations in discrete signal transduction pathways in bipolar disorder would have broad implications for understanding the disease pathophysiology. As prior microarray data point to a previously unrecognized involvement of the RhoA network in bipolar disorder, here we investigate the protein expression and activity of key components of a RhoA signal transduction pathway in dorsolateral prefrontal cortical homogenates from subjects with bipolar disorder. The results of this investigation implicate overactivation of prefrontal cortical RhoA signaling in specific subtypes of bipolar disorder. The specificity of these findings is demonstrated by a lack of comparable changes in schizophrenia; however, our findings do identify convergence between both disorders at the level of activity-mediated actin cytoskeletal regulation. These findings have implications for understanding the altered cortical synaptic connectivity of bipolar disorder.
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Affiliation(s)
- Bailey A Kermath
- Department of Comparative Biosciences, University of Wisconsin at Madison, Madison, WI, USA
| | - Amanda M Vanderplow
- Department of Comparative Biosciences, University of Wisconsin at Madison, Madison, WI, USA
| | - Michael E Cahill
- Department of Comparative Biosciences, University of Wisconsin at Madison, Madison, WI, USA
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127
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Lencz T, Yu J, Khan RR, Flaherty E, Carmi S, Lam M, Ben-Avraham D, Barzilai N, Bressman S, Darvasi A, Cho JH, Clark LN, Gümüş ZH, Vijai J, Klein RJ, Lipkin S, Offit K, Ostrer H, Ozelius LJ, Peter I, Malhotra AK, Maniatis T, Atzmon G, Pe'er I. Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. Neuron 2021; 109:1465-1478.e4. [PMID: 33756103 DOI: 10.1016/j.neuron.2021.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/16/2020] [Accepted: 03/01/2021] [Indexed: 12/12/2022]
Abstract
The identification of rare variants associated with schizophrenia has proven challenging due to genetic heterogeneity, which is reduced in founder populations. In samples from the Ashkenazi Jewish population, we report that schizophrenia cases had a greater frequency of novel missense or loss of function (MisLoF) ultra-rare variants (URVs) compared to controls, and the MisLoF URV burden was inversely correlated with polygenic risk scores in cases. Characterizing 141 "case-only" genes (MisLoF URVs in ≥3 cases with none in controls), the cadherin gene set was associated with schizophrenia. We report a recurrent case mutation in PCDHA3 that results in the formation of cytoplasmic aggregates and failure to engage in homophilic interactions on the plasma membrane in cultured cells. Modeling purifying selection, we demonstrate that deleterious URVs are greatly overrepresented in the Ashkenazi population, yielding enhanced power for association studies. Identification of the cadherin/protocadherin family as risk genes helps specify the synaptic abnormalities central to schizophrenia.
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Affiliation(s)
- Todd Lencz
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA.
| | - Jin Yu
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Raiyan Rashid Khan
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Erin Flaherty
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, Faculty of Medicine, Hebrew University of Jerusalem, Ein Kerem, Jerusalem 9112102, Israel
| | - Max Lam
- Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Danny Ben-Avraham
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Nir Barzilai
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan Bressman
- Department of Neurology, Beth Israel Medical Center, New York, NY 10003, USA
| | - Ariel Darvasi
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Judy H Cho
- Institute for Personalized Medicine, 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
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Zeynep H Gümüş
- 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
| | - Joseph Vijai
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Taub Institute for Research of Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Steven Lipkin
- Departments of Medicine, Genetic Medicine and Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laurie J Ozelius
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Inga Peter
- 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
| | - Anil K Malhotra
- Departments of Psychiatry and Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY 11550, USA; Department of Psychiatry, Division of Research, The Zucker Hillside Hospital Division of Northwell Health, Glen Oaks, NY 11004, USA; Institute for Behavioral Science, The Feinstein Institutes for Medical Research, Manhasset, NY 11030, USA
| | - Tom Maniatis
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain and Behavior Institute, Columbia University, New York, NY 10027, USA; New York Genome Center, New York, NY 10013, USA
| | - Gil Atzmon
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Human Biology, Haifa University, Haifa, Israel
| | - Itsik Pe'er
- Department of Computer Science, Columbia University, New York, NY 10027, USA; Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.
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Kowalec K, Lu Y, Song J, Dalman C, Hultman CM, Larsson H, Lichtenstein P, Sullivan PF. The association between family history and genomic burden with schizophrenia mortality: a Swedish population-based register and genetic sample study. Transl Psychiatry 2021; 11:163. [PMID: 33723211 PMCID: PMC7960991 DOI: 10.1038/s41398-021-01282-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/08/2021] [Accepted: 01/15/2021] [Indexed: 11/09/2022] Open
Abstract
Individuals with schizophrenia (SCZ) have a 2-3-fold higher risk of mortality than the general population. Heritability of mortality in psychiatric disorders has been proposed; however, few have investigated SCZ family history and genetic variation, with all-cause and specific causes of death. We aimed to identify correlates of SCZ mortality using genetic epidemiological and genetic modelling in two samples: a Swedish national population sample and a genotyped subsample. In the Swedish national population sample followed from the first SCZ treatment contact until emigration, death or end of the follow-up, we investigated a standardised measure of SCZ family history. In a subgroup with comprehensive genetic data, we investigated the impact of common and rare genetic variation. Cox proportional hazards regression was used to estimate the association between various factors and mortality (all and specific causes). A total of 13727 SCZ cases fulfilled criteria for the population-based analyses (1268 deaths, 9.2%). The genomic subset contained 4991 cases (1353 deaths, 27.1%). Somatic mutations associated with clonal hematopoiesis with unknown drivers were associated with all-cause mortality (HR 1.77, 95% CI: 1.26-2.49). No other heritable measures were associated with all-cause mortality nor with any specific causes of death. Future studies in larger, comparable cohorts are warranted to further understand the association between hereditary measures and mortality in SCZ.
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Affiliation(s)
- Kaarina Kowalec
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. .,College of Pharmacy, University of Manitoba, Winnipeg, MN, Canada.
| | - Yi Lu
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jie Song
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Christina Dalman
- grid.4714.60000 0004 1937 0626Department of Global Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Christina M. Hultman
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden ,grid.416167.3Icahn School of Medicine, Department of Psychiatry, Mt Sinai Hospital, New York, NY USA
| | - Henrik Larsson
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden ,grid.15895.300000 0001 0738 8966School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Paul Lichtenstein
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patrick F. Sullivan
- grid.4714.60000 0004 1937 0626Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden ,grid.10698.360000000122483208Departments of Genetics and Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
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129
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Chen X, Zhou J, Zhang R, Wong AK, Park CY, Theesfeld CL, Troyanskaya OG. Tissue-specific enhancer functional networks for associating distal regulatory regions to disease. Cell Syst 2021; 12:353-362.e6. [PMID: 33689683 DOI: 10.1016/j.cels.2021.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/13/2020] [Accepted: 02/08/2021] [Indexed: 12/22/2022]
Abstract
Systematic study of tissue-specific function of enhancers and their disease associations is a major challenge. We present an integrative machine-learning framework, FENRIR, that integrates thousands of disparate epigenetic and functional genomics datasets to infer tissue-specific functional relationships between enhancers for 140 diverse human tissues and cell types, providing a regulatory-region-centric approach to systematically identify disease-associated enhancers. We demonstrated its power to accurately prioritize enhancers associated with 25 complex diseases. In a case study on autism, FENRIR-prioritized enhancers showed a significant proband-specific de novo mutation enrichment in a large, sibling-controlled cohort, indicating pathogenic signal. We experimentally validated transcriptional regulatory activities of eight enhancers, including enhancers not previously reported with autism, and demonstrated their differential regulatory potential between proband and sibling alleles. Thus, FENRIR is an accurate and effective framework for the study of tissue-specific enhancers and their role in disease. FENRIR can be accessed at fenrir.flatironinstitute.org/.
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Affiliation(s)
- Xi Chen
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Jian Zhou
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Ran Zhang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Aaron K Wong
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Christopher Y Park
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Chandra L Theesfeld
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Olga G Troyanskaya
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Computer Science, Princeton University, Princeton, NJ 08544, USA.
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130
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Ogata S, Hashizume K, Hayase Y, Kanno Y, Hori K, Balan S, Yoshikawa T, Takahashi H, Taya S, Hoshino M. Potential involvement of DSCAML1 mutations in neurodevelopmental disorders. Genes Cells 2021; 26:136-151. [PMID: 33501714 DOI: 10.1111/gtc.12831] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 12/24/2022]
Abstract
The molecular mechanisms underlying neurodevelopmental disorders (NDDs) remain unclear. We previously identified Down syndrome cell adhesion molecule like 1 (Dscaml1) as a responsible gene for Ihara epileptic rat (IER), a rat model for human NDDs with epilepsy. However, the relationship between NDDs and DSCAML1 in humans is still elusive. In this study, we screened databases of autism spectrum disorders (ASD), intellectual disability (ID)/developmental disorders (DD) and schizophrenia for genomic mutations in human DSCAML1. We then performed in silico analyses to estimate the potential damage to the mutated DSCAML1 proteins and chose three representative mutations (DSCAML1C729R , DSCAML1R1685* and DSCAML1K2108Nfs*37 ), which lacked a cysteine residue in the seventh Ig domain, the intracellular region and the C-terminal PDZ-binding motif, respectively. In overexpression experiments in a cell line, DSCAML1C729R lost its mature N-glycosylation, whereas DSCAML1K2108Nfs*37 was abnormally degraded via proteasome-dependent protein degradation. Furthermore, in primary hippocampal neurons, the ability of the wild-type DSCAML1 to regulate the number of synapses was lost with all mutant proteins. These results provide insight into understanding the roles of the domains in the DSCAML1 protein and further suggest that these mutations cause functional changes, albeit through different mechanisms, that likely affect the pathophysiology of NDDs.
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Affiliation(s)
- Shigehiro Ogata
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Koichi Hashizume
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Yoneko Hayase
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Yukie Kanno
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Kei Hori
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Shabeesh Balan
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Saitama, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Center for Brain Science, Saitama, Japan
| | - Hidehiko Takahashi
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Shinichiro Taya
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
| | - Mikio Hoshino
- Department of Biochemistry and Cellular Biology, National Institute of Neuroscience, NCNP, Tokyo, Japan
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131
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De Berardis D, De Filippis S, Masi G, Vicari S, Zuddas A. A Neurodevelopment Approach for a Transitional Model of Early Onset Schizophrenia. Brain Sci 2021; 11:brainsci11020275. [PMID: 33672396 PMCID: PMC7926620 DOI: 10.3390/brainsci11020275] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
In the last decades, the conceptualization of schizophrenia has dramatically changed, moving from a neurodegenerative process occurring in early adult life to a neurodevelopmental disorder starting be-fore birth, showing a variety of premorbid and prodromal symptoms and, in relatively few cases, evolving in the full-blown psychotic syndrome. High rates of co-occurring different neurodevelopmental disorders such as Autism spectrum disorder and ADHD, predating the onset of SCZ, and neurobio-logical underpinning with significant similarities, support the notion of a pan-developmental disturbance consisting of impairments in neuromotor, receptive language, social and cognitive development. Con-sidering that many SCZ risk factors may be similar to symptoms of other neurodevelopmental psychi-atric disorders, transition processes from child & adolescent to adult systems of care should include both high risk people as well as subject with other neurodevelopmental psychiatric disorders with different levels of severity. This descriptive mini-review discuss the need of innovative clinical approaches, re-considering specific diagnostic categories, stimulating a careful analysis of risk factors and promoting the appropriate use of new and safer medications.
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Affiliation(s)
- Domenico De Berardis
- Department of Mental Health, Psychiatric Service of Diagnosis and Treatment, Hospital “G. Mazzini,” National Health Service (NHS), 64100 ASL 4 Teramo, Italy
- Department of Neurosciences and Imaging, University “G. D’Annunzio”, 66100 Chieti, Italy
- Correspondence:
| | - Sergio De Filippis
- Department of Neuropsychiatry, Villa von Siebenthal Neuropsychiatric Hospital and Clinic, Genzano di Roma, 100045 Rome, Italy;
| | - Gabriele Masi
- IRCCS Stella Maris, Scientific Institute of Child Neurology and Psychiatry, Calambrone, 56128 Pisa, Italy;
| | - Stefano Vicari
- Department of Life Sciences and Publich Health, Catholic University, 00135 Rome, Italy;
- Child & Adolescent Psychiatry, Bambino Gesù Children’s Hospital, 00168 Rome, Italy
| | - Alessandro Zuddas
- Child and Adolescent Neuropsychiatry Unit, Department of Biomedical Sciences, University of Cagliari and “A Cao” Paediatric Hospital, “G Brotzu” Hospital Trust, 109134 Cagliari, Italy;
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132
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A unique missense variant in the E1A-binding protein P400 gene is implicated in schizophrenia by whole-exome sequencing and mutant mouse models. Transl Psychiatry 2021; 11:132. [PMID: 33602898 PMCID: PMC7892873 DOI: 10.1038/s41398-021-01258-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/10/2021] [Accepted: 01/27/2021] [Indexed: 01/31/2023] Open
Abstract
Genetic and epidemiological evidence has suggested that genetic factors are important in schizophrenia, although its pathophysiology is poorly understood. This study used whole-exome sequencing to investigate potential novel schizophrenia-causing genes in a Japanese family containing several members affected by severe or treatment-resistant schizophrenia. A missense variant, chr12:132064747C>T (rs200626129, P2805L), in the E1A-binding protein P400 (EP400) gene completely segregated with schizophrenia in this family. Furthermore, numerous other EP400 mutations were identified in the targeted sequencing of a schizophrenia patient cohort. We also created two lines of Ep400 gene-edited mice, which had anxiety-like behaviours and reduced axon diameters. Our findings suggest that rs200626129 in EP400 is likely to cause schizophrenia in this Japanese family, and may lead to a better understanding and treatment of schizophrenia.
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133
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Feurle P, Abentung A, Cera I, Wahl N, Ablinger C, Bucher M, Stefan E, Sprenger S, Teis D, Fischer A, Laighneach A, Whitton L, Morris DW, Apostolova G, Dechant G. SATB2-LEMD2 interaction links nuclear shape plasticity to regulation of cognition-related genes. EMBO J 2021; 40:e103701. [PMID: 33319920 PMCID: PMC7849313 DOI: 10.15252/embj.2019103701] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/22/2020] [Accepted: 11/06/2020] [Indexed: 01/22/2023] Open
Abstract
SATB2 is a schizophrenia risk gene and is genetically associated with human intelligence. How it affects cognition at molecular level is currently unknown. Here, we show that interactions between SATB2, a chromosomal scaffolding protein, and the inner nuclear membrane protein LEMD2 orchestrate the response of pyramidal neurons to neuronal activation. Exposure to novel environment in vivo causes changes in nuclear shape of CA1 hippocampal neurons via a SATB2-dependent mechanism. The activity-driven plasticity of the nuclear envelope requires not only SATB2, but also its protein interactor LEMD2 and the ESCRT-III/VPS4 membrane-remodeling complex. Furthermore, LEMD2 depletion in cortical neurons, similar to SATB2 ablation, affects neuronal activity-dependent regulation of multiple rapid and delayed primary response genes. In human genetic data, LEMD2-regulated genes are enriched for de novo mutations reported in intellectual disability and schizophrenia and are, like SATB2-regulated genes, enriched for common variants associated with schizophrenia and cognitive function. Hence, interactions between SATB2 and the inner nuclear membrane protein LEMD2 influence gene expression programs in pyramidal neurons that are linked to cognitive ability and psychiatric disorder etiology.
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Affiliation(s)
- Patrick Feurle
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Andreas Abentung
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Isabella Cera
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Nico Wahl
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Cornelia Ablinger
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Michael Bucher
- Institute of Biochemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Eduard Stefan
- Institute of Biochemistry and Center for Molecular BiosciencesUniversity of InnsbruckInnsbruckAustria
| | - Simon Sprenger
- Institute for Cell BiologyMedical University of InnsbruckInnsbruckAustria
| | - David Teis
- Institute for Cell BiologyMedical University of InnsbruckInnsbruckAustria
| | - Andre Fischer
- Department of Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GoettingenGermany
- Department of Psychiatry and PsychotherapyUniversity Medical CenterGoettingenGermany
| | - Aodán Laighneach
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Laura Whitton
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Derek W Morris
- Neuroimaging, Cognition & Genomics (NICOG) CentreSchool of Psychology and Discipline of BiochemistryNational University of Ireland GalwayGalwayIreland
| | - Galina Apostolova
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
| | - Georg Dechant
- Institute for NeuroscienceMedical University of InnsbruckInnsbruckAustria
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134
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Abstract
Capture the full scope of variation to improve health care, equity and medical research globally.
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135
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Mojarad BA, Yin Y, Manshaei R, Backstrom I, Costain G, Heung T, Merico D, Marshall CR, Bassett AS, Yuen RKC. Genome sequencing broadens the range of contributing variants with clinical implications in schizophrenia. Transl Psychiatry 2021; 11:84. [PMID: 33526774 PMCID: PMC7851385 DOI: 10.1038/s41398-021-01211-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/28/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023] Open
Abstract
The range of genetic variation with potential clinical implications in schizophrenia, beyond rare copy number variants (CNVs), remains uncertain. We therefore analyzed genome sequencing data for 259 unrelated adults with schizophrenia from a well-characterized community-based cohort previously examined with chromosomal microarray for CNVs (none with 22q11.2 deletions). We analyzed these genomes for rare high-impact variants considered causal for neurodevelopmental disorders, including single-nucleotide variants (SNVs) and small insertions/deletions (indels), for potential clinical relevance based on findings for neurodevelopmental disorders. Also, we investigated a novel variant type, tandem repeat expansions (TREs), in 45 loci known to be associated with monogenic neurological diseases. We found several of these variants in this schizophrenia population suggesting that these variants have a wider clinical spectrum than previously thought. In addition to known pathogenic CNVs, we identified 11 (4.3%) individuals with clinically relevant SNVs/indels in genes converging on schizophrenia-relevant pathways. Clinical yield was significantly enriched in females and in those with broadly defined learning/intellectual disabilities. Genome analyses also identified variants with potential clinical implications, including TREs (one in DMPK; two in ATXN8OS) and ultra-rare loss-of-function SNVs in ZMYM2 (a novel candidate gene for schizophrenia). Of the 233 individuals with no pathogenic CNVs, we identified rare high-impact variants (i.e., clinically relevant or with potential clinical implications) for 14 individuals (6.0%); some had multiple rare high-impact variants. Mean schizophrenia polygenic risk score was similar between individuals with and without clinically relevant rare genetic variation; common variants were not sufficient for clinical application. These findings broaden the individual and global picture of clinically relevant genetic risk in schizophrenia, and suggest the potential translational value of genome sequencing as a single genetic technology for schizophrenia.
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Affiliation(s)
- Bahareh A. Mojarad
- grid.42327.300000 0004 0473 9646Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Yue Yin
- grid.42327.300000 0004 0473 9646Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Roozbeh Manshaei
- grid.42327.300000 0004 0473 9646Ted Rogers Centre for Heart Research, Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON Canada
| | - Ian Backstrom
- grid.42327.300000 0004 0473 9646Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada
| | - Gregory Costain
- grid.42327.300000 0004 0473 9646Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.42327.300000 0004 0473 9646Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON Canada
| | - Tracy Heung
- grid.155956.b0000 0000 8793 5925Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON Canada ,grid.231844.80000 0004 0474 0428The Dalglish Family 22q Clinic for Adults with 22q11.2 Deletion Syndrome, Toronto General Hospital, University Health Network, Toronto, ON Canada
| | - Daniele Merico
- grid.42327.300000 0004 0473 9646Deep Genomics Inc., Toronto, Ontario and The Centre for Applied Genomics (TCAG), The Hospital for Sick Children, Toronto, ON Canada
| | - Christian R. Marshall
- grid.17063.330000 0001 2157 2938Paediatric Laboratory Medicine, Genome Diagnostics, The Hospital for Sick Children, Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Anne S. Bassett
- grid.155956.b0000 0000 8793 5925Clinical Genetics Research Program, Centre for Addiction and Mental Health, Toronto, ON Canada ,grid.231844.80000 0004 0474 0428The Dalglish Family 22q Clinic for Adults with 22q11.2 Deletion Syndrome, Toronto General Hospital, University Health Network, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Psychiatry, University of Toronto, Toronto General Hospital Research Institute and Campbell Family Mental Health Research Institute, Toronto, ON Canada
| | - Ryan K. C. Yuen
- grid.42327.300000 0004 0473 9646Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON Canada ,grid.17063.330000 0001 2157 2938Department of Molecular Genetics, University of Toronto, Toronto, ON Canada
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136
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Special Article: Translational Science Update. Pharmacological Implications of Emerging Schizophrenia Genetics: Can the Bridge From 'Genomics' to 'Therapeutics' be Defined and Traversed? J Clin Psychopharmacol 2021; 40:323-329. [PMID: 32433256 DOI: 10.1097/jcp.0000000000001215] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Recent schizophrenia genome-wide association studies (GWAS) have identified genomic variants of common and rare frequency, significantly associated with schizophrenia. While numerous functional genomics efforts are ongoing to elucidate the biological effects of schizophrenia risk variants, a consideration of their therapeutic implications is timely and imperative, for patients as well as for an iterative effect on elucidating the underlying biology and pathophysiology of illness. The current article reviews efforts to translate emerging schizophrenia genomics into novel approaches to target discovery and therapeutic intervention. Though the path from 'genetic risk to therapy' is far from straightforward, there are provocative early possibilities that harbor the promise of treatment based on causation rather than phenomenology, as well as 'precision psychiatry,' a basis for stratifying patients to enable more precise and effective, personalized therapy.
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Su Y, Yang L, Li Z, Wang W, Xing M, Fang Y, Cheng Y, Lin GN, Cui D. The interaction of ASAH1 and NGF gene involving in neurotrophin signaling pathway contributes to schizophrenia susceptibility and psychopathology. Prog Neuropsychopharmacol Biol Psychiatry 2021; 104:110015. [PMID: 32569620 DOI: 10.1016/j.pnpbp.2020.110015] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 05/23/2020] [Accepted: 06/09/2020] [Indexed: 02/07/2023]
Abstract
The neurodevelopmental hypothesis of schizophrenia has been widely accepted. In light of our previous microarray data, two neurodevelopment-related genes were focused on inclduing the N-acylsphingosine amidohydrolase 1 gene (ASAH1) and the nerve growth factor gene (NGF). The evidence that ASAH1 and NGF are associated with schizophrenia is far from conclusive. Furthermore, their interactions in schizophrenia have not been investigated. Total 413 patients and 578 controls were included. Eleven single-nucleotide polymorphisms (SNPs) in ASAH1 and NGF were selected. A multifactor dimensionality reduction (MDR) was applied to investigate gene-gene interactions in schizophrenia, and the traditional odds ratio methods was applied to validate it. The effects of ASAH1, NGF and their interaction on the severity of the disease were analyzed by 3 × 3 covariance analysis of (ANCOVA). The biological interaction between ASAH1 and NGF was examined. KEGG was used to identify the related signaling pathways. After correction by Bonferroni, there were no differences in the genotypic, allelic, or haplotypic frequencies of 11 SNPs between patients and controls. However, the interaction of certain SNPs had effect on susceptibility to schizophrenia, including two high-risk and one low-risk genotypic combinations (OR = 1.49 [1.11-2.00]; OR = 1.45 [1.09-1.92], and OR = 0.64 [0.41-0.98]). ASAH1-rs7830490 and its interaction with NGF-rs4332358 were associated with the general psychopathological subscale score (F adjusted = 3.94, p adjusted = 0.01; F adjusted = 2.36, p adjusted = 0.03). We also found that ASAH1 and NGF interacted with CaMK2B involving in the neurotrophin signaling pathway. Our results suggest that the interaction of ASAH1 and NGF with CaMK2B involved in neurotrophin signaling pathway may contribute to schizophrenia susceptibility and psychopathology.
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Affiliation(s)
- Yousong Su
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu Yang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zezhi Li
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China; Department of Neurology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Weidi Wang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Mengjuan Xing
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China; Key Laboratory of Translational Psychiatry, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Fang
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China; Key Laboratory of Translational Psychiatry, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Cheng
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China; Key Laboratory of Translational Psychiatry, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Guan Ning Lin
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China
| | - Donghong Cui
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai, China; Key Laboratory of Translational Psychiatry, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.
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138
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Finucane BM, Ledbetter DH, Vorstman JA. Diagnostic genetic testing for neurodevelopmental psychiatric disorders: closing the gap between recommendation and clinical implementation. Curr Opin Genet Dev 2021; 68:1-8. [PMID: 33434711 DOI: 10.1016/j.gde.2020.12.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/09/2020] [Accepted: 12/22/2020] [Indexed: 12/19/2022]
Abstract
Advances in laboratory testing have significantly increased the detection of rare genetic etiologies of neurodevelopmental psychiatric disorders (NPD), particularly developmental delay/ intellectual disability, autism spectrum disorder, and schizophrenia. Establishing a genetic diagnosis has important medical and personal utility for individuals with these conditions. Diagnostic genetic tests for NPD are clinically available but underutilized outside of medical genetics settings. Without clear multidisciplinary consensus recommendations, active involvement of medical specialists working with NPD patients, and practical education and training, the implementation of genetic testing for NPD will continue to lag behind other areas of medicine. In the long-term, collaborative efforts to address educational, logistical, and workforce obstacles will improve patient care and pave the way for targeted, effective NPD treatments.
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Affiliation(s)
- Brenda M Finucane
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA USA.
| | - David H Ledbetter
- Autism & Developmental Medicine Institute, Geisinger, Lewisburg, PA USA
| | - Jacob As Vorstman
- Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada
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139
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Curtis D. Multiple Linear Regression Allows Weighted Burden Analysis of Rare Coding Variants in an Ethnically Heterogeneous Population. Hum Hered 2021; 85:1-10. [PMID: 33412546 DOI: 10.1159/000512576] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/20/2020] [Indexed: 11/19/2022] Open
Abstract
Weighted burden analysis has been used in exome-sequenced case-control studies to identify genes in which there is an excess of rare and/or functional variants associated with phenotype. Implementation in a ridge regression framework allows simultaneous analysis of all variants along with relevant covariates, such as population principal components. In order to apply the approach to a quantitative phenotype, a weighted burden score is derived for each subject and included in a linear regression analysis. The weighting scheme is adjusted in order to apply differential weights to rare and very rare variants and a score is derived based on both the frequency and predicted effect of each variant. When applied to an ethnically heterogeneous dataset consisting of 49,790 exome-sequenced UK Biobank subjects and using body mass index as the phenotype, the method produces a very inflated test statistic. However, this is almost completely corrected by including 20 population principal components as covariates. When this is done, the top 30 genes include a few which are quite plausibly associated with the phenotype, including LYPLAL1 and NSDHL. This approach offers a way to carry out gene-based analyses of rare variants identified by exome sequencing in heterogeneous datasets without requiring that data from ethnic minority subjects be discarded. This research has been conducted using the UK Biobank Resource.
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Affiliation(s)
- David Curtis
- UCL Genetics Institute, University College London, London, United Kingdom, .,Centre for Psychiatry, Queen Mary University of London, London, United Kingdom,
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140
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Shohat S, Amelan A, Shifman S. Convergence and Divergence in the Genetics of Psychiatric Disorders From Pathways to Developmental Stages. Biol Psychiatry 2021; 89:32-40. [PMID: 32682568 DOI: 10.1016/j.biopsych.2020.05.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
In the past decade, the identification of susceptibility genes for psychiatric disorders has become routine, but understanding the biology underlying these discoveries has proven extremely difficult. The large number of potential risk genes and the genetic overlap between disorders are major obstacles for studying the etiology of these conditions. Systems biology approaches relying on gene ontologies, gene coexpression, and protein-protein interactions are used to identify convergence of the genes in relation to biological processes, cell types, brain areas, and developmental stages. Across psychiatric disorders, there is a clear enrichment for genes expressed in the brain and especially in the cortex, but a higher resolution is vastly dependent on sample size and statistical power. There is indication that susceptibility genes tend to be expressed in the brain during periods preceding the typical onset of the disorders. Thus, the role of genes in prenatal brain development is more pronounced for childhood-onset disorders, such as autism spectrum disorder and attention-deficit/hyperactivity disorder, but is much less so for bipolar disorder and depression. One of the most consistent findings across multiple disorders and classes of genetic variants is the role of genes intolerant to mutations in psychiatric disorders, yet this association is more pronounced for disorders with a clear neurodevelopmental component. Notwithstanding, a detailed understanding of the neurobiology of psychiatric disorders is still lacking. It is possible that it will only be revealed by studying the risk genes at the level of the development and function of neuronal networks and circuits.
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Affiliation(s)
- Shahar Shohat
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alana Amelan
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sagiv Shifman
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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141
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Chen R, Chen J, Gao C, Wu C, Pan D, Zhang J, Zhou J, Wang K, Zhang Q, Yang Q, Jian X, Zhao Y, Wen Y, Wang Z, Shi Y, Li Z. Association analysis of potentially functional variants within 8p12 with schizophrenia in the Han Chinese population. World J Biol Psychiatry 2021; 22:27-33. [PMID: 32129128 DOI: 10.1080/15622975.2020.1738550] [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] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Chromosome 8p12 was first identified as a schizophrenia (SCZ) risk locus in Chinese populations and replicated in European populations. However, the underlying functional variants still need to be further explored. In this study, we sought to identify plausible causal variants within this locus. METHODS A total of 386 potentially functional variants from 29 genes within the 8p12 locus were analysed in 2403 SCZ cases and 2594 control subjects in the Han Chinese population using Affymetrix customised genotyping assays. SHEsisplus was used for association analysis. A multiple testing corrected p value (false discovery rate (FDR)) < .05 was considered significant, and an unadjusted p value < .05 was considered nominal evidence of an association. RESULTS We did not find significant associations between the tested variants and SCZ. However, nominal associations were found for rs201292574 (unadjusted p = .033, FDR p = .571; 95% confidence interval (CI): 0.265-0.945; TACC1, NP_006274.2:p.Ala211Thr) and rs45563241 (unadjusted p = .039, FDR p = .571; 95% CI: 1.023-1.866; a synonymous mutation in ADRB3). CONCLUSIONS Our results provide limited evidence for the associations between variants from protein coding regions in 8p12 and SCZ in the Chinese population. Analyses of both coding and regulatory variants in larger sample sizes are required to further clarify the causal variants for SCZ with this risk locus.
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Affiliation(s)
- Ruirui Chen
- School of Basic Medicine, Qingdao University, Qingdao, China.,Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Jianhua Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Chengwen Gao
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Chuanhong Wu
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Dun Pan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Jinmai Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Juan Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Zhang
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Qiangzhen Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Xuemin Jian
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yalin Zhao
- School of Basic Medicine, Qingdao University, Qingdao, China.,Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Yanqin Wen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Zhuo Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yongyong Shi
- School of Basic Medicine, Qingdao University, Qingdao, China.,Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China.,Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiqiang Li
- School of Basic Medicine, Qingdao University, Qingdao, China.,Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China.,Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China.,Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China.,Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China
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142
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Zhang Y, Wang R, Liu Z, Jiang S, Du L, Qiu K, Li F, Wang Q, Jin J, Chen X, Li Z, Wu J, Zhang N. Distinct genetic patterns of shared and unique genes across four neurodevelopmental disorders. Am J Med Genet B Neuropsychiatr Genet 2021; 186:3-15. [PMID: 32929885 DOI: 10.1002/ajmg.b.32821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 06/04/2020] [Accepted: 08/15/2020] [Indexed: 01/09/2023]
Abstract
Neurodevelopmental disorders, including autism spectrum disorder (ASD), intellectual disability (ID), developmental disorders (DD) and epileptic encephalopathy (EE), have a strong clinical comorbidity, which indicates a common genetic etiology across various disorders. However, the underlying genetic mechanisms of comorbidity and specificity remain unknown across neurodevelopmental disorders. Based on de novo mutations, we compared systematically the functional characteristics between shared and unique genes under these disorders, as well as the spatiotemporal trajectory of development in brain and common molecular pathways of all shared genes. We observed that shared genes present more constrained against functional rare genetic variation, and harbor more pathogenic rare variants than do unique genes in each disorder. Furthermore, 71 shared genes formed two clusters related to synaptic transmission, transcription regulation and chromatin regulator. Particularly, we also found that two core genes STXBP1 and SCN2A, that were shared by the four neurodevelopmental disorders showed prominent pleiotropy. Our findings shed light on the shared and specific patterns across neurodevelopmental disorders and will enable us to further comprehend the etiology and provide valuable information for the diagnosis of neurodevelopmental disorders.
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Affiliation(s)
- Yijia Zhang
- Reproductive Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ruochen Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Shan Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Lifeng Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Kairui Qiu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Fengxia Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Qiongdan Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jing Jin
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaomin Chen
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Na Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China.,Medicine & Technology School of Zunyi Medical University, Zunyi, China
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143
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Hernandez LM, Kim M, Hoftman GD, Haney JR, de la Torre-Ubieta L, Pasaniuc B, Gandal MJ. Transcriptomic Insight Into the Polygenic Mechanisms Underlying Psychiatric Disorders. Biol Psychiatry 2021; 89:54-64. [PMID: 32792264 PMCID: PMC7718368 DOI: 10.1016/j.biopsych.2020.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/20/2022]
Abstract
Over the past decade, large-scale genetic studies have successfully identified hundreds of genetic variants robustly associated with risk for psychiatric disorders. However, mechanistic insight and clinical translation continue to lag the pace of risk variant identification, hindered by the sheer number of targets and their predominant noncoding localization, as well as pervasive pleiotropy and incomplete penetrance. Successful next steps require identification of "causal" genetic variants and their proximal biological consequences; placing variants within biologically defined functional contexts, reflecting specific molecular pathways, cell types, circuits, and developmental windows; and characterizing the downstream, convergent neurobiological impact of polygenicity within an individual. Here, we discuss opportunities and challenges of high-throughput transcriptomic profiling in the human brain, and how transcriptomic approaches can help pinpoint mechanisms underlying genetic risk for psychiatric disorders at a scale necessary to tackle daunting levels of polygenicity. These include transcriptome-wide association studies for risk gene prioritization through integration of genome-wide association studies with expression quantitative trait loci. We outline transcriptomic results that inform our understanding of the brain-level molecular pathology of psychiatric disorders, including autism spectrum disorder, bipolar disorder, major depressive disorder, and schizophrenia. Finally, we discuss systems-level approaches for integration of distinct genetic, genomic, and phenotypic levels, including combining spatially resolved gene expression and human neuroimaging maps. Results highlight the importance of understanding gene expression (dys)regulation across human brain development as a major contributor to psychiatric disease pathogenesis, from common variants acting as expression quantitative trait loci to rare variants enriched for gene expression regulatory pathways.
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Affiliation(s)
- Leanna M Hernandez
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Minsoo Kim
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Gil D Hoftman
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Jillian R Haney
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Luis de la Torre-Ubieta
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Bogdan Pasaniuc
- Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California
| | - Michael J Gandal
- Department of Psychiatry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Program in Neurobehavioral Genetics, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California; Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California.
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144
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Hall LS, Medway CW, Pain O, Pardiñas AF, Rees EG, Escott-Price V, Pocklington A, Bray NJ, Holmans PA, Walters JTR, Owen MJ, O'Donovan MC. A transcriptome-wide association study implicates specific pre- and post-synaptic abnormalities in schizophrenia. Hum Mol Genet 2020; 29:159-167. [PMID: 31691811 PMCID: PMC7416679 DOI: 10.1093/hmg/ddz253] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 08/31/2019] [Accepted: 09/02/2019] [Indexed: 12/25/2022] Open
Abstract
Schizophrenia is a complex highly heritable disorder. Genome-wide association studies (GWAS) have identified multiple loci that influence the risk of developing schizophrenia, although the causal variants driving these associations and their impacts on specific genes are largely unknown. We identify a significant correlation between schizophrenia risk and expression at 89 genes in the dorsolateral prefrontal cortex (P ≤ 9.43 × 10-6), including 20 novel genes. Genes whose expression correlate with schizophrenia were enriched for those involved in abnormal CNS synaptic transmission (PFDR = 0.02) and antigen processing and presentation of peptide antigen via MHC class I (PFDR = 0.02). Within the CNS synaptic transmission set, we identify individual significant candidate genes to which we assign direction of expression changes in schizophrenia. The findings provide strong candidates for experimentally probing the molecular basis of synaptic pathology in schizophrenia.
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Affiliation(s)
- Lynsey S Hall
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Christopher W Medway
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Oliver Pain
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK.,Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AF, UK
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Elliott G Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Andrew Pocklington
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Nicholas J Bray
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Peter A Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff CF24 4HQ, UK
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145
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Gao R, van den Brink RL, Pfeffer T, Voytek B. Neuronal timescales are functionally dynamic and shaped by cortical microarchitecture. eLife 2020; 9:e61277. [PMID: 33226336 PMCID: PMC7755395 DOI: 10.7554/elife.61277] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 11/22/2020] [Indexed: 12/21/2022] Open
Abstract
Complex cognitive functions such as working memory and decision-making require information maintenance over seconds to years, from transient sensory stimuli to long-term contextual cues. While theoretical accounts predict the emergence of a corresponding hierarchy of neuronal timescales, direct electrophysiological evidence across the human cortex is lacking. Here, we infer neuronal timescales from invasive intracranial recordings. Timescales increase along the principal sensorimotor-to-association axis across the entire human cortex, and scale with single-unit timescales within macaques. Cortex-wide transcriptomic analysis shows direct alignment between timescales and expression of excitation- and inhibition-related genes, as well as genes specific to voltage-gated transmembrane ion transporters. Finally, neuronal timescales are functionally dynamic: prefrontal cortex timescales expand during working memory maintenance and predict individual performance, while cortex-wide timescales compress with aging. Thus, neuronal timescales follow cytoarchitectonic gradients across the human cortex and are relevant for cognition in both short and long terms, bridging microcircuit physiology with macroscale dynamics and behavior.
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Affiliation(s)
- Richard Gao
- Department of Cognitive Science, University of California, San DiegoLa JollaUnited States
| | - Ruud L van den Brink
- Section Computational Cognitive Neuroscience, Department of Neurophysiology and Pathophysiology, University Medical Center Hamburg-EppendorfHamburgGermany
| | - Thomas Pfeffer
- Center for Brain and Cognition, Computational Neuroscience Group, Universitat Pompeu FabraBarcelonaSpain
| | - Bradley Voytek
- Department of Cognitive Science, University of California, San DiegoLa JollaUnited States
- Halıcıoğlu Data Science Institute, University of California, San DiegoLa JollaUnited States
- Neurosciences Graduate Program, University of California, San DiegoLa JollaUnited States
- Kavli Institute for Brain and Mind, University of California, San DiegoLa JollaUnited States
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146
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Hoersting AK, Schmucker D. Axonal branch patterning and neuronal shape diversity: roles in developmental circuit assembly: Axonal branch patterning and neuronal shape diversity in developmental circuit assembly. Curr Opin Neurobiol 2020; 66:158-165. [PMID: 33232861 DOI: 10.1016/j.conb.2020.10.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
Recent progress in human genetics and single cell sequencing rapidly expands the list of molecular factors that offer important new contributions to our understanding of brain wiring. Yet many new molecular factors are being discovered that have never been studied in the context of neuronal circuit development. This is clearly asking for increased efforts to better understand the developmental mechanisms of circuit assembly [1]. Moreover, recent studies characterizing the developmental causes of some psychiatric diseases show impressive progress in reaching cellular resolution in their analysis. They provide concrete support emphasizing the importance of axonal branching and synapse formation as a hotspot for potential defects. Inspired by these new studies we will discuss progress but also challenges in understanding how neurite branching and neuronal shape diversity itself impacts on specificity of neuronal circuit assembly. We discuss the idea that neuronal shape acquisition itself is a key specificity factor in neuronal circuit assembly.
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Affiliation(s)
| | - Dietmar Schmucker
- Life and Medical Sciences Institute (LIMES), University Bonn, Bonn, Germany; Center for Brain and Disease Research, VIB Leuven, University Leuven, Belgium.
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147
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Nawa Y, Kimura H, Mori D, Kato H, Toyama M, Furuta S, Yu Y, Ishizuka K, Kushima I, Aleksic B, Arioka Y, Morikawa M, Okada T, Inada T, Kaibuchi K, Ikeda M, Iwata N, Suzuki M, Okahisa Y, Egawa J, Someya T, Nishimura F, Sasaki T, Ozaki N. Rare single-nucleotide DAB1 variants and their contribution to Schizophrenia and autism spectrum disorder susceptibility. Hum Genome Var 2020; 7:37. [PMID: 33298905 PMCID: PMC7655853 DOI: 10.1038/s41439-020-00125-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/24/2020] [Accepted: 09/27/2020] [Indexed: 01/09/2023] Open
Abstract
Disabled 1 (DAB1) is an intracellular adaptor protein in the Reelin signaling pathway and plays an essential role in correct neuronal migration and layer formation in the developing brain. DAB1 has been repeatedly reported to be associated with neurodevelopmental disorders including schizophrenia (SCZ) and autism spectrum disorders (ASD) in genetic, animal, and postmortem studies. Recently, increasing attention has been given to rare single-nucleotide variants (SNVs) found by deep sequencing of candidate genes. In this study, we performed exon-targeted resequencing of DAB1 in 370 SCZ and 192 ASD patients using next-generation sequencing technology to identify rare SNVs with a minor allele frequency <1%. We detected two rare missense mutations (G382C, V129I) and then performed a genetic association study in a sample comprising 1763 SCZ, 380 ASD, and 2190 healthy control subjects. Although no statistically significant association with the detected mutations was observed for either SCZ or ASD, G382C was found only in the case group, and in silico analyses and in vitro functional assays suggested that G382C alters the function of the DAB1 protein. The rare variants of DAB1 found in the present study should be studied further to elucidate their potential functional relevance to the pathophysiology of SCZ and ASD. A rare mutation could affect nerve development in the brain, potentially increasing susceptibility to schizophrenia and autism spectrum disorder. Hiroki Kimura of Nagoya University Graduate School of Medicine and colleagues in Japan screened the protein-coding parts of the gene DAB1 in people with schizophrenia or autism for rare nucleotide variations. DAB1 is important for neurodevelopment and synaptic function, and has been associated with neurodevelopmental disorders. Their investigations revealed a mutation that can change the structure and stability of the protein coded by DAB1, potentially increasing susceptibility to neurodevelopmental disorders. The mutation was found in people with schizophrenia and autism, but not in healthy controls. Further research with larger patient samples and investigations on mice engineered to include the mutation could clarify its impact on the pathophysiology of schizophrenia and autism.
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Affiliation(s)
- Yoshihiro Nawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.
| | - Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.,Brain and Mind Research Center, Nagoya University, Nagoya, Aichi, Japan
| | - Hidekazu Kato
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Miho Toyama
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Sho Furuta
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yanjie Yu
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kanako Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.,Institute for Advanced Research, Nagoya University, Nagoya, Aichi, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Yuko Arioka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan.,Institute for Advanced Research, Nagoya University, Nagoya, Aichi, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Aichi, Japan
| | - Mako Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Takashi Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Toshiya Inada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Kozo Kaibuchi
- Department of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Michio Suzuki
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - Yuko Okahisa
- Department of Neuropsychiatry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Jun Egawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Fumichika Nishimura
- Office for Mental Health Support, Center for Research on Counseling and Support Services, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Sasaki
- Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Aichi, Japan
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148
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Bigdeli TB, Genovese G, Georgakopoulos P, Meyers JL, Peterson RE, Iyegbe CO, Medeiros H, Valderrama J, Achtyes ED, Kotov R, Stahl EA, Abbott C, Azevedo MH, Belliveau RA, Bevilacqua E, Bromet EJ, Byerley W, Carvalho CB, Chapman SB, DeLisi LE, Dumont AL, O’Dushlaine C, Evgrafov OV, Fochtmann LJ, Gage D, Kennedy JL, Kinkead B, Macedo A, Moran JL, Morley CP, Dewan MJ, Nemesh J, Perkins DO, Purcell SM, Rakofsky JJ, Scolnick EM, Sklar BM, Sklar P, Smoller JW, Sullivan PF, Macciardi F, Marder SR, Gur RC, Gur RE, Braff DL, Nicolini H, Escamilla MA, Vawter MP, Sobell JL, Malaspina D, Lehrer DS, Buckley PF, Rapaport MH, Knowles JA, Fanous AH, Pato MT, McCarroll SA, Pato CN. Contributions of common genetic variants to risk of schizophrenia among individuals of African and Latino ancestry. Mol Psychiatry 2020; 25:2455-2467. [PMID: 31591465 PMCID: PMC7515843 DOI: 10.1038/s41380-019-0517-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/01/2019] [Accepted: 04/24/2019] [Indexed: 11/10/2022]
Abstract
Schizophrenia is a common, chronic and debilitating neuropsychiatric syndrome affecting tens of millions of individuals worldwide. While rare genetic variants play a role in the etiology of schizophrenia, most of the currently explained liability is within common variation, suggesting that variation predating the human diaspora out of Africa harbors a large fraction of the common variant attributable heritability. However, common variant association studies in schizophrenia have concentrated mainly on cohorts of European descent. We describe genome-wide association studies of 6152 cases and 3918 controls of admixed African ancestry, and of 1234 cases and 3090 controls of Latino ancestry, representing the largest such study in these populations to date. Combining results from the samples with African ancestry with summary statistics from the Psychiatric Genomics Consortium (PGC) study of schizophrenia yielded seven newly genome-wide significant loci, and we identified an additional eight loci by incorporating the results from samples with Latino ancestry. Leveraging population differences in patterns of linkage disequilibrium, we achieve improved fine-mapping resolution at 22 previously reported and 4 newly significant loci. Polygenic risk score profiling revealed improved prediction based on trans-ancestry meta-analysis results for admixed African (Nagelkerke's R2 = 0.032; liability R2 = 0.017; P < 10-52), Latino (Nagelkerke's R2 = 0.089; liability R2 = 0.021; P < 10-58), and European individuals (Nagelkerke's R2 = 0.089; liability R2 = 0.037; P < 10-113), further highlighting the advantages of incorporating data from diverse human populations.
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Affiliation(s)
- Tim B. Bigdeli
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA ,Department of Psychiatry, Veterans Affairs New York Harbor Healthcare System, Brooklyn, NY USA
| | - Giulio Genovese
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA USA
| | - Penelope Georgakopoulos
- grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Jacquelyn L. Meyers
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Roseann E. Peterson
- grid.224260.00000 0004 0458 8737Department of Psychiatry, Virginia Commonwealth University, Richmond, VA USA
| | - Conrad O. Iyegbe
- grid.13097.3c0000 0001 2322 6764Department of Psychosis Studies, King’s College London, London, UK
| | - Helena Medeiros
- grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Jorge Valderrama
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Eric D. Achtyes
- grid.17088.360000 0001 2150 1785Cherry Health and Michigan State University College of Human Medicine, Grand Rapids, MI USA
| | - Roman Kotov
- grid.36425.360000 0001 2216 9681Department of Psychiatry, Stony Brook University, Stony Brook, NY USA
| | - Eli A. Stahl
- grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Genetics & Genomics, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA
| | - Colony Abbott
- grid.42505.360000 0001 2156 6853Department of Psychiatry & Behavioral Sciences, University of Southern California, Los Angeles, CA USA
| | - Maria Helena Azevedo
- grid.8051.c0000 0000 9511 4342Institute of Medical Psychology, Faculty of Medicine, University of Coimbra, Coimbra, PT Portugal
| | - Richard A. Belliveau
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | | | - Evelyn J. Bromet
- grid.36425.360000 0001 2216 9681Department of Psychiatry, Stony Brook University, Stony Brook, NY USA
| | - William Byerley
- grid.266102.10000 0001 2297 6811Department of Psychiatry, University of California, San Francisco, CA USA
| | - Celia Barreto Carvalho
- grid.7338.f0000 0001 2096 9474Faculty of Social and Human Sciences, University of Azores, Ponta Delgada, Portugal
| | - Sinéad B. Chapman
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Lynn E. DeLisi
- grid.410370.10000 0004 4657 1992VA Boston Healthcare System, Brockton, MA USA ,grid.38142.3c000000041936754XDepartment of Psychiatry, Harvard Medical School, Boston, MA USA
| | - Ashley L. Dumont
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Colm O’Dushlaine
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Oleg V. Evgrafov
- grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Laura J. Fochtmann
- grid.36425.360000 0001 2216 9681Department of Psychiatry, Stony Brook University, Stony Brook, NY USA
| | - Diane Gage
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - James L. Kennedy
- grid.17063.330000 0001 2157 2938Neurogenetics Laboratory, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health; Department of Psychiatry, University of Toronto, Toronto, ON Canada
| | - Becky Kinkead
- grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA USA
| | - Antonio Macedo
- grid.8051.c0000 0000 9511 4342Institute of Medical Psychology, Faculty of Medicine, University of Coimbra, Coimbra, PT Portugal
| | - Jennifer L. Moran
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Christopher P. Morley
- grid.411023.50000 0000 9159 4457Department of Public Health and Preventive Medicine, State University of New York, Upstate Medical University, Syracuse, NY USA ,grid.411023.50000 0000 9159 4457Department of Family Medicine, State University of New York, Upstate Medical University, Syracuse, NY USA ,grid.411023.50000 0000 9159 4457Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY USA
| | - Mantosh J. Dewan
- grid.411023.50000 0000 9159 4457Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY USA
| | - James Nemesh
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Diana O. Perkins
- grid.410711.20000 0001 1034 1720Department of Psychiatry, University of North Carolina, Chapel Hill, NC USA
| | - Shaun M. Purcell
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.62560.370000 0004 0378 8294Department of Psychiatry, Brigham and Women’s Hospital, Boston, MA USA
| | - Jeffrey J. Rakofsky
- grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA USA
| | - Edward M. Scolnick
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Brooke M. Sklar
- grid.42505.360000 0001 2156 6853Department of Psychiatry & Behavioral Sciences, University of Southern California, Los Angeles, CA USA
| | - Pamela Sklar
- grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Genetics & Genomics, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA
| | - Jordan W. Smoller
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Psychiatry, Harvard Medical School, Boston, MA USA ,grid.32224.350000 0004 0386 9924Department of Psychiatry, Massachusetts General Hospital, Boston, MA USA ,grid.38142.3c000000041936754XDepartment of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA USA
| | - Patrick F. Sullivan
- grid.410711.20000 0001 1034 1720Department of Psychiatry, University of North Carolina, Chapel Hill, NC USA ,grid.465198.7Medical Epidemiology and Biostatistics, Karolinska Institutet, Solna, SE Sweden
| | - Fabio Macciardi
- grid.266093.80000 0001 0668 7243Department of Psychiatry and Human Behavior, University of California, Irvine, CA USA
| | - Stephen R. Marder
- grid.19006.3e0000 0000 9632 6718Department of Psychiatry and Biobehavioral Sciences, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Semel Institute for Neuroscience and Human Behavior, Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA
| | - Ruben C. Gur
- grid.25879.310000 0004 1936 8972Department of Psychiatry, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Child & Adolescent Psychiatry, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Lifespan Brain Institute, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Raquel E. Gur
- grid.25879.310000 0004 1936 8972Department of Psychiatry, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Child & Adolescent Psychiatry, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.25879.310000 0004 1936 8972Lifespan Brain Institute, University of Pennsylvania Perelman School of Medicine and Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - David L. Braff
- grid.266100.30000 0001 2107 4242Department of Psychiatry, University of California, La Jolla, San Diego, CA USA ,grid.410371.00000 0004 0419 2708VISN-22 Mental Illness, Research, Education and Clinical Center (MIRECC), VA San Diego Healthcare System, San Diego, CA USA
| | | | | | - Michael A. Escamilla
- grid.416992.10000 0001 2179 3554Department of Psychiatry, Texas Tech University Health Sciences Center, El Paso, TX USA
| | - Marquis P. Vawter
- grid.266093.80000 0001 0668 7243Department of Psychiatry and Human Behavior, University of California, Irvine, CA USA
| | - Janet L. Sobell
- grid.42505.360000 0001 2156 6853Department of Psychiatry & Behavioral Sciences, University of Southern California, Los Angeles, CA USA
| | - Dolores Malaspina
- grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Genetics & Genomics, Icahn School of Medicine at Mount Sinai, Mount Sinai, NY USA
| | - Douglas S. Lehrer
- grid.268333.f0000 0004 1936 7937Department of Psychiatry, Wright State University, Dayton, OH USA
| | - Peter F. Buckley
- grid.224260.00000 0004 0458 8737School of Medicine, Virginia Commonwealth University, Richmond, VA USA
| | - Mark H. Rapaport
- grid.189967.80000 0001 0941 6502Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA USA
| | - James A. Knowles
- grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY USA
| | | | - Ayman H. Fanous
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA ,Department of Psychiatry, Veterans Affairs New York Harbor Healthcare System, Brooklyn, NY USA
| | - Michele T. Pato
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA
| | - Steven A. McCarroll
- grid.66859.34Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA USA ,grid.38142.3c000000041936754XDepartment of Genetics, Harvard Medical School, Boston, MA USA
| | - Carlos N. Pato
- grid.262863.b0000 0001 0693 2202Department of Psychiatry and Behavioral Sciences, SUNY Downstate Medical Center, Brooklyn, NY USA ,grid.262863.b0000 0001 0693 2202Institute for Genomic Health, SUNY Downstate Medical Center, Brooklyn, NY USA
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149
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Clifton NE, Thomas KL, Wilkinson LS, Hall J, Trent S. FMRP and CYFIP1 at the Synapse and Their Role in Psychiatric Vulnerability. Complex Psychiatry 2020; 6:5-19. [PMID: 34883502 PMCID: PMC7673588 DOI: 10.1159/000506858] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/27/2020] [Indexed: 12/23/2022] Open
Abstract
There is increasing awareness of the role genetic risk variants have in mediating vulnerability to psychiatric disorders such as schizophrenia and autism. Many of these risk variants encode synaptic proteins, influencing biological pathways of the postsynaptic density and, ultimately, synaptic plasticity. Fragile-X mental retardation 1 (FMR1) and cytoplasmic fragile-X mental retardation protein (FMRP)-interacting protein 1 (CYFIP1) contain 2 such examples of highly penetrant risk variants and encode synaptic proteins with shared functional significance. In this review, we discuss the biological actions of FMRP and CYFIP1, including their regulation of (i) protein synthesis and specifically FMRP targets, (ii) dendritic and spine morphology, and (iii) forms of synaptic plasticity such as long-term depression. We draw upon a range of preclinical studies that have used genetic dosage models of FMR1 and CYFIP1 to determine their biological function. In parallel, we discuss how clinical studies of fragile X syndrome or 15q11.2 deletion patients have informed our understanding of FMRP and CYFIP1, and highlight the latest psychiatric genomic findings that continue to implicate FMRP and CYFIP1. Lastly, we assess the current limitations in our understanding of FMRP and CYFIP1 biology and how they must be addressed before mechanism-led therapeutic strategies can be developed for psychiatric disorders.
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Affiliation(s)
- Nicholas E. Clifton
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Kerrie L. Thomas
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Lawrence S. Wilkinson
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- School of Psychology, Cardiff University, Cardiff, United Kingdom
| | - Jeremy Hall
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, United Kingdom
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Simon Trent
- Neuroscience & Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom
- School of Life Sciences, Faculty of Natural Sciences, Keele University, Keele, United Kingdom
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150
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Cosgrove D, Whitton L, Fahey L, Ó Broin P, Donohoe G, Morris DW. Genes influenced by MEF2C contribute to neurodevelopmental disease via gene expression changes that affect multiple types of cortical excitatory neurons. Hum Mol Genet 2020; 30:961-970. [PMID: 32975584 DOI: 10.1093/hmg/ddaa213] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 12/19/2022] Open
Abstract
Myocyte enhancer factor 2 C (MEF2C) is an important transcription factor during neurodevelopment. Mutation or deletion of MEF2C causes intellectual disability (ID), and common variants within MEF2C are associated with cognitive function and schizophrenia risk. We investigated if genes influenced by MEF2C during neurodevelopment are enriched for genes associated with neurodevelopmental phenotypes and if this can be leveraged to identify biological mechanisms and individual brain cell types affected. We used a set of 1055 genes that were differentially expressed in the adult mouse brain following early embryonic deletion of Mef2c in excitatory cortical neurons. Using genome-wide association studies data, we found these differentially expressed genes (DEGs) to be enriched for genes associated with schizophrenia, intelligence and educational attainment but not autism spectrum disorder (ASD). For this gene set, genes that overlap with target genes of the Fragile X mental retardation protein (FMRP) are a major driver of these enrichments. Using trios data, we found these DEGs to be enriched for genes containing de novo mutations reported in ASD and ID, but not schizophrenia. Using single-cell RNA sequencing data, we identified that a number of different excitatory glutamatergic neurons in the cortex were enriched for these DEGs including deep layer pyramidal cells and cells in the retrosplenial cortex, entorhinal cortex and subiculum, and these cell types are also enriched for FMRP target genes. The involvement of MEF2C and FMRP in synapse elimination suggests that disruption of this process in these cell types during neurodevelopment contributes to cognitive function and risk of neurodevelopmental disorders.
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Affiliation(s)
- Donna Cosgrove
- Cognitive Genetics and Cognitive Therapy Group, Centre for Neuroimaging, Cognition and Genomics, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway H91CF50, Ireland
| | - Laura Whitton
- Cognitive Genetics and Cognitive Therapy Group, Centre for Neuroimaging, Cognition and Genomics, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway H91CF50, Ireland
| | - Laura Fahey
- Cognitive Genetics and Cognitive Therapy Group, Centre for Neuroimaging, Cognition and Genomics, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway H91CF50, Ireland.,School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway H91CF50, Ireland
| | - Pilib Ó Broin
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway H91CF50, Ireland
| | - Gary Donohoe
- Cognitive Genetics and Cognitive Therapy Group, Centre for Neuroimaging, Cognition and Genomics, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway H91CF50, Ireland
| | - Derek W Morris
- Cognitive Genetics and Cognitive Therapy Group, Centre for Neuroimaging, Cognition and Genomics, School of Psychology and Discipline of Biochemistry, National University of Ireland Galway, Galway H91CF50, Ireland
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