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Wahl N, Espeso-Gil S, Chietera P, Nagel A, Laighneach A, Morris DW, Rajarajan P, Akbarian S, Dechant G, Apostolova G. SATB2 organizes the 3D genome architecture of cognition in cortical neurons. Mol Cell 2024; 84:621-639.e9. [PMID: 38244545 PMCID: PMC10923151 DOI: 10.1016/j.molcel.2023.12.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 10/02/2023] [Accepted: 12/15/2023] [Indexed: 01/22/2024]
Abstract
The DNA-binding protein SATB2 is genetically linked to human intelligence. We studied its influence on the three-dimensional (3D) epigenome by mapping chromatin interactions and accessibility in control versus SATB2-deficient cortical neurons. We find that SATB2 affects the chromatin looping between enhancers and promoters of neuronal-activity-regulated genes, thus influencing their expression. It also alters A/B compartments, topologically associating domains, and frequently interacting regions. Genes linked to SATB2-dependent 3D genome changes are implicated in highly specialized neuronal functions and contribute to cognitive ability and risk for neuropsychiatric and neurodevelopmental disorders. Non-coding DNA regions with a SATB2-dependent structure are enriched for common variants associated with educational attainment, intelligence, and schizophrenia. Our data establish SATB2 as a cell-type-specific 3D genome modulator, which operates both independently and in cooperation with CCCTC-binding factor (CTCF) to set up the chromatin landscape of pyramidal neurons for cognitive processes.
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Affiliation(s)
- Nico Wahl
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Sergio Espeso-Gil
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria; Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paola Chietera
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Amelie Nagel
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Aodán Laighneach
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Derek W Morris
- Centre for Neuroimaging, Cognition and Genomics (NICOG), School of Biological and Chemical Sciences, University of Galway, Galway, H91 TK33, Ireland
| | - Prashanth Rajarajan
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georg Dechant
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
| | - Galina Apostolova
- Institute for Neuroscience, Medical University of Innsbruck, Innsbruck 6020, Austria.
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Blaze J, Browne CJ, Futamura R, Javidfar B, Zachariou V, Nestler EJ, Akbarian S. tRNA epitranscriptomic alterations associated with opioid-induced reward-seeking and long-term opioid withdrawal in male mice. Neuropsychopharmacology 2024:10.1038/s41386-024-01813-6. [PMID: 38332016 DOI: 10.1038/s41386-024-01813-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/10/2024]
Abstract
DNA cytosine methylation has been documented as a potential epigenetic mechanism of transcriptional regulation underlying opioid use disorder. However, methylation of RNA cytosine residues, which would drive another level of biological influence as an epitranscriptomic mechanism of gene and protein regulation has not been studied in the context of addiction. Here, we probed whether chronic morphine exposure could alter tRNA cytosine methylation (m5C) and resulting expression levels in the medial prefrontal cortex (mPFC), a brain region crucial for reward processing and executive function that exhibits opioid-induced molecular restructuring. We identified dynamic changes in glycine tRNA (tRNAGlyGCC) cytosine methylation, corresponding to altered expression levels of this tRNA at multiple timepoints following 15 days of daily morphine. Additionally, a robust increase in methylation, coupled with decreased expression, was present after 30 days of withdrawal, suggesting that repeated opioid administration produces changes to the tRNA regulome long after discontinuation. Furthermore, forebrain-wide knockout of neuronal Nsun2, a tRNA methyltransferase, was associated with disruption of opioid conditioned place preference, and this effect was recapitulated by regional mPFC Nsun2 knockout. Taken together, these studies provide a foundational link between the regulation of tRNA cytosine methylation and opioid reward and highlight the tRNA machinery as a potential therapeutic target in addiction.
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Affiliation(s)
- Jennifer Blaze
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Caleb J Browne
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Brain Health Imaging Centre, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Rita Futamura
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Venetia Zachariou
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacology, Physiology, and Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Eric J Nestler
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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3
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Tandon R, Nasrallah H, Akbarian S, Carpenter WT, DeLisi LE, Gaebel W, Green MF, Gur RE, Heckers S, Kane JM, Malaspina D, Meyer-Lindenberg A, Murray R, Owen M, Smoller JW, Yassin W, Keshavan M. The schizophrenia syndrome, circa 2024: What we know and how that informs its nature. Schizophr Res 2024; 264:1-28. [PMID: 38086109 DOI: 10.1016/j.schres.2023.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 03/01/2024]
Abstract
With new data about different aspects of schizophrenia being continually generated, it becomes necessary to periodically revisit exactly what we know. Along with a need to review what we currently know about schizophrenia, there is an equal imperative to evaluate the construct itself. With these objectives, we undertook an iterative, multi-phase process involving fifty international experts in the field, with each step building on learnings from the prior one. This review assembles currently established findings about schizophrenia (construct, etiology, pathophysiology, clinical expression, treatment) and posits what they reveal about its nature. Schizophrenia is a heritable, complex, multi-dimensional syndrome with varying degrees of psychotic, negative, cognitive, mood, and motor manifestations. The illness exhibits a remitting and relapsing course, with varying degrees of recovery among affected individuals with most experiencing significant social and functional impairment. Genetic risk factors likely include thousands of common genetic variants that each have a small impact on an individual's risk and a plethora of rare gene variants that have a larger individual impact on risk. Their biological effects are concentrated in the brain and many of the same variants also increase the risk of other psychiatric disorders such as bipolar disorder, autism, and other neurodevelopmental conditions. Environmental risk factors include but are not limited to urban residence in childhood, migration, older paternal age at birth, cannabis use, childhood trauma, antenatal maternal infection, and perinatal hypoxia. Structural, functional, and neurochemical brain alterations implicate multiple regions and functional circuits. Dopamine D-2 receptor antagonists and partial agonists improve psychotic symptoms and reduce risk of relapse. Certain psychological and psychosocial interventions are beneficial. Early intervention can reduce treatment delay and improve outcomes. Schizophrenia is increasingly considered to be a heterogeneous syndrome and not a singular disease entity. There is no necessary or sufficient etiology, pathology, set of clinical features, or treatment that fully circumscribes this syndrome. A single, common pathophysiological pathway appears unlikely. The boundaries of schizophrenia remain fuzzy, suggesting the absence of a categorical fit and need to reconceptualize it as a broader, multi-dimensional and/or spectrum construct.
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Affiliation(s)
- Rajiv Tandon
- Department of Psychiatry, WMU Homer Stryker School of Medicine, Kalamazoo, MI 49008, United States of America.
| | - Henry Nasrallah
- Department of Psychiatry, University of Cincinnati College of Medicine Cincinnati, OH 45267, United States of America
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, United States of America
| | - William T Carpenter
- Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD 21201, United States of America
| | - Lynn E DeLisi
- Department of Psychiatry, Cambridge Health Alliance and Harvard Medical School, Cambridge, MA 02139, United States of America
| | - Wolfgang Gaebel
- Department of Psychiatry and Psychotherapy, LVR-Klinikum Dusseldorf, Heinrich-Heine University, Dusseldorf, Germany
| | - Michael F Green
- Department of Psychiatry and Biobehavioral Sciences, Jane and Terry Semel Institute of Neuroscience and Human Behavior, UCLA, Los Angeles, CA 90024, United States of America; Greater Los Angeles Veterans' Administration Healthcare System, United States of America
| | - Raquel E Gur
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, United States of America
| | - Stephan Heckers
- Department of Psychiatry, Vanderbilt University Medical Center, Nashville, TN 37232, United States of America
| | - John M Kane
- Department of Psychiatry, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Glen Oaks, NY 11004, United States of America
| | - Dolores Malaspina
- Department of Psychiatry, Neuroscience, Genetics, and Genomics, Icahn School of Medicine at Mt. Sinai, New York, NY 10029, United States of America
| | - Andreas Meyer-Lindenberg
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Mannhein/Heidelberg University, Mannheim, Germany
| | - Robin Murray
- Institute of Psychiatry, Psychology, and Neuroscience, Kings College, London, UK
| | - Michael Owen
- Centre for Neuropsychiatric Genetics and Genomics, and Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Jordan W Smoller
- Center for Precision Psychiatry, Department of Psychiatry, Psychiatric and Neurodevelopmental Unit, Center for Genomic Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, United States of America
| | - Walid Yassin
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, United States of America
| | - Matcheri Keshavan
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, United States of America
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Min AK, Javidfar B, Missall R, Doanman D, Durens M, Graziani M, Mordelt A, Marro SG, de Witte L, Chen BK, Swartz TH, Akbarian S. HIV-1 infection of genetically engineered iPSC-derived central nervous system-engrafted microglia in a humanized mouse model. J Virol 2023; 97:e0159523. [PMID: 38032195 PMCID: PMC10734545 DOI: 10.1128/jvi.01595-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/05/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Our mouse model is a powerful tool for investigating the genetic mechanisms governing central nervous system (CNS) human immunodeficiency virus type-1 (HIV-1) infection and latency in the CNS at a single-cell level. A major advantage of our model is that it uses induced pluripotent stem cell-derived microglia, which enables human genetics, including gene function and therapeutic gene manipulation, to be explored in vivo, which is more challenging to study with current hematopoietic stem cell-based models for neuroHIV. Our transgenic tracing of xenografted human cells will provide a quantitative medium to develop new molecular and epigenetic strategies for reducing the HIV-1 latent reservoir and to test the impact of therapeutic inflammation-targeting drug interventions on CNS HIV-1 latency.
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Affiliation(s)
- Alice K. Min
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Roy Missall
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Donald Doanman
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Madel Durens
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mara Graziani
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Annika Mordelt
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboud UMC, Nijmegen, the Netherlands
- Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, the Netherlands
| | - Samuele G. Marro
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lotje de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboud UMC, Nijmegen, the Netherlands
- Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, the Netherlands
| | - Benjamin K. Chen
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Talia H. Swartz
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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5
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Plaza-Jennings A, Akbarian S. Genomic Exploration of the Brain in People Infected with HIV-Recent Progress and the Road Ahead. Curr HIV/AIDS Rep 2023; 20:357-367. [PMID: 37947981 PMCID: PMC10719125 DOI: 10.1007/s11904-023-00675-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2023] [Indexed: 11/12/2023]
Abstract
PURPOSE OF REVIEW The adult human brain harbors billions of microglia and other myeloid and lymphoid cells highly susceptible to HIV infection and retroviral insertion into the nuclear DNA. HIV infection of the brain is important because the brain is a potentially large reservoir site that may be a barrier to HIV cure strategies and because infection can lead to the development of HIV-associated neurocognitive disorder. To better understand both the central nervous system (CNS) reservoir and how it can cause neurologic dysfunction, novel genomic, epigenomic, transcriptomic, and proteomic approaches need to be employed. Several characteristics of the reservoir are important to learn, including where the virus integrates, whether integrated proviruses are intact or defective, whether integrated proviruses can be reactivated from a latent state to seed ongoing infection, and how this all impacts brain function. RECENT FINDINGS Here, we discuss similarities and differences of viral integration sites between brain and blood and discuss evidence for and against the hypothesis that in the absence of susceptible T-lymphocytes in the periphery, the virus housing in the infected brain is not able to sustain a systemic infection. Moreover, microglia from HIV + brains across a wide range of disease severity appear to share one type of common alteration, which is defined by downregulated expression, and repressive chromosomal compartmentalization, for microglial genes regulating synaptic connectivity. Therefore, viral infection of the brain, including in immunocompetent cases with near-normal levels of CD4 blood lymphocytes, could be associated with an early disruption in microglia-dependent neuronal support functions, contributing to cognitive and neurological deficits in people living with HIV.
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Affiliation(s)
- Amara Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Department of Neuroscience, 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.
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6
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Garrison MA, Jang Y, Bae T, Cherskov A, Emery SB, Fasching L, Jones A, Moldovan JB, Molitor C, Pochareddy S, Peters MA, Shin JH, Wang Y, Yang X, Akbarian S, Chess A, Gage FH, Gleeson JG, Kidd JM, McConnell M, Mills RE, Moran JV, Park PJ, Sestan N, Urban AE, Vaccarino FM, Walsh CA, Weinberger DR, Wheelan SJ, Abyzov A. Genomic data resources of the Brain Somatic Mosaicism Network for neuropsychiatric diseases. Sci Data 2023; 10:813. [PMID: 37985666 PMCID: PMC10662356 DOI: 10.1038/s41597-023-02645-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 10/16/2023] [Indexed: 11/22/2023] Open
Abstract
Somatic mosaicism is defined as an occurrence of two or more populations of cells having genomic sequences differing at given loci in an individual who is derived from a single zygote. It is a characteristic of multicellular organisms that plays a crucial role in normal development and disease. To study the nature and extent of somatic mosaicism in autism spectrum disorder, bipolar disorder, focal cortical dysplasia, schizophrenia, and Tourette syndrome, a multi-institutional consortium called the Brain Somatic Mosaicism Network (BSMN) was formed through the National Institute of Mental Health (NIMH). In addition to genomic data of affected and neurotypical brains, the BSMN also developed and validated a best practices somatic single nucleotide variant calling workflow through the analysis of reference brain tissue. These resources, which include >400 terabytes of data from 1087 subjects, are now available to the research community via the NIMH Data Archive (NDA) and are described here.
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Affiliation(s)
- McKinzie A Garrison
- Program in Biochemistry, Molecular and Cellular Biology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Taejeong Bae
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Adriana Cherskov
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Attila Jones
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - John B Moldovan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Cindy Molitor
- Sage Bionetworks, 2901 Third Ave., Suite 330, Seattle, WA, 98121, USA
| | - Sirisha Pochareddy
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Mette A Peters
- Sage Bionetworks, 2901 Third Ave., Suite 330, Seattle, WA, 98121, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Xiaoxu Yang
- Rady Children's Institute for Genomic Medicine, 7910 Frost St., Suite #300, San Diego, CA, 92123, USA
- Department of Neurosciences, University of California San Diego, La Jolla, California, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrew Chess
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fred H Gage
- Laboratory of Genetics LOG-G, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Joseph G Gleeson
- Rady Children's Institute for Genomic Medicine, 7910 Frost St., Suite #300, San Diego, CA, 92123, USA
- Department of Neurosciences, University of California San Diego, La Jolla, California, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | | | - Ryan E Mills
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, 48109, USA
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, California, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Flora M Vaccarino
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT, 06520, USA
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Departments of Pediatrics and Neurology, Harvard Medical School, Boston, MA, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- McKusick Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Sarah J Wheelan
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- National Human Genome Research Institute, National Institutes of Health, 6700B Rockledge Dr, Bethesda, MD, 20892, USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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7
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Hou KC, Tsai MH, Akbarian S, Huang HS. Mir125b-1 is Not Imprinted in Human Brain and Shows Developmental Expression Changes in Mouse Brain. Neuroscience 2023; 529:99-106. [PMID: 37598835 DOI: 10.1016/j.neuroscience.2023.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/22/2023]
Abstract
Genomic imprinting is a predominantly brain and placenta-specific epigenetic process that contributes to parent-of-origin-specific gene expression. While microRNAs are highly expressed in the brain, their imprinting status in this tissue remains poorly studied. Previous research demonstrated that Mir125b-2 is imprinted in the human brain and regulates hippocampal circuits and functions in mice. However, the imprinting status of another isoform of miR125b, Mir125b-1, in the human brain, as well as its spatiotemporal expression patterns in mice, have not been elucidated. Here, we show MIR125B1 is not imprinted in the human brain. Moreover, miR-125b-1 was highly expressed in the brains of mice. Furthermore, miR-125b-1 was down-regulated during brain development in mice. Specifically, miR-125b-1 displayed preferential expression in the olfactory bulb, thalamus, and hypothalamus of the mouse brain. Notably, miR-125b-1 was enriched in GABAergic neurons, particularly somatostatin-expressing GABAergic neurons, compared with glutamatergic neurons. Taken together, our findings provide the imprinting status and comprehensive spatiotemporal expression profiling of Mir125b-1 in the brain.
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Affiliation(s)
- Kuan-Chu Hou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Meng-Han Tsai
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NY 10029, USA
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei 10051, Taiwan.
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8
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Wei J, Lambert TY, Valada A, Patel N, Walker K, Lenders J, Schmidt CJ, Iskhakova M, Alazizi A, Mair-Meijers H, Mash DC, Luca F, Pique-Regi R, Bannon MJ, Akbarian S. Single nucleus transcriptomics of ventral midbrain identifies glial activation associated with chronic opioid use disorder. Nat Commun 2023; 14:5610. [PMID: 37699936 PMCID: PMC10497570 DOI: 10.1038/s41467-023-41455-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
Dynamic interactions of neurons and glia in the ventral midbrain mediate reward and addiction behavior. We studied gene expression in 212,713 ventral midbrain single nuclei from 95 individuals with history of opioid misuse, and individuals without drug exposure. Chronic exposure to opioids was not associated with change in proportions of glial and neuronal subtypes, however glial transcriptomes were broadly altered, involving 9.5 - 6.2% of expressed genes within microglia, oligodendrocytes, and astrocytes. Genes associated with activation of the immune response including interferon, NFkB signaling, and cell motility pathways were upregulated, contrasting with down-regulated expression of synaptic signaling and plasticity genes in ventral midbrain non-dopaminergic neurons. Ventral midbrain transcriptomic reprogramming in the context of chronic opioid exposure included 325 genes that previous genome-wide studies had linked to risk of substance use traits in the broader population, thereby pointing to heritable risk architectures in the genomic organization of the brain's reward circuitry.
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Affiliation(s)
- Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Tova Y Lambert
- Department of Psychiatry, Department of Neuroscience and Department of Genetics and Genomic Sciences, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aditi Valada
- Department of Psychiatry, Department of Neuroscience and Department of Genetics and Genomic Sciences, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Nikhil Patel
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Kellie Walker
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Jayna Lenders
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Carl J Schmidt
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Marina Iskhakova
- Department of Psychiatry, Department of Neuroscience and Department of Genetics and Genomic Sciences, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Henriette Mair-Meijers
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Deborah C Mash
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, 48201, USA
- Department of Biology, University of Tor Vergata, Rome, 00133, Italy
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, 48201, USA
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, 48201, USA
| | - Michael J Bannon
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Schahram Akbarian
- Department of Psychiatry, Department of Neuroscience and Department of Genetics and Genomic Sciences, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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9
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Akbarian S, Won H. Chromosomal contacts change with age. Science 2023; 381:1049-1050. [PMID: 37676934 DOI: 10.1126/science.adk0961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The three-dimensional organization of the genome is remodeled throughout life.
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Affiliation(s)
| | - Hyejung Won
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
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10
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Maury EA, Sherman MA, Genovese G, Gilgenast TG, Kamath T, Burris S, Rajarajan P, Flaherty E, Akbarian S, Chess A, McCarroll SA, Loh PR, Phillips-Cremins JE, Brennand KJ, Macosko EZ, Walters JT, O’Donovan M, Sullivan P, Sebat J, Lee EA, Walsh CA. Schizophrenia-associated somatic copy-number variants from 12,834 cases reveal recurrent NRXN1 and ABCB11 disruptions. Cell Genom 2023; 3:100356. [PMID: 37601975 PMCID: PMC10435376 DOI: 10.1016/j.xgen.2023.100356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/21/2022] [Accepted: 06/09/2023] [Indexed: 08/22/2023]
Abstract
While germline copy-number variants (CNVs) contribute to schizophrenia (SCZ) risk, the contribution of somatic CNVs (sCNVs)-present in some but not all cells-remains unknown. We identified sCNVs using blood-derived genotype arrays from 12,834 SCZ cases and 11,648 controls, filtering sCNVs at loci recurrently mutated in clonal blood disorders. Likely early-developmental sCNVs were more common in cases (0.91%) than controls (0.51%, p = 2.68e-4), with recurrent somatic deletions of exons 1-5 of the NRXN1 gene in five SCZ cases. Hi-C maps revealed ectopic, allele-specific loops forming between a potential cryptic promoter and non-coding cis-regulatory elements upon 5' deletions in NRXN1. We also observed recurrent intragenic deletions of ABCB11, encoding a transporter implicated in anti-psychotic response, in five treatment-resistant SCZ cases and showed that ABCB11 is specifically enriched in neurons forming mesocortical and mesolimbic dopaminergic projections. Our results indicate potential roles of sCNVs in SCZ risk.
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Affiliation(s)
- Eduardo A. Maury
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Bioinformatics & Integrative Genomics Program and Harvard/MIT MD-PHD Program, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Maxwell A. Sherman
- Brigham and Women’s Hospital, Division of Genetics & Center for Data Sciences, Boston, MA, USA
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Thomas G. Gilgenast
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Tushar Kamath
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biophysics, Harvard University, Cambridge, MA, USA
| | - S.J. Burris
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Prashanth Rajarajan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Department of Genetics & Genomics, Icahn Institute of Genomics and Multiscale Biology, Department of Psychiatry, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine of Mount Sinai, New York, NY, USA
| | - Erin Flaherty
- Nash Family Department of Neuroscience, Friedman Brain Institute, Department of Genetics & Genomics, Icahn Institute of Genomics and Multiscale Biology, Department of Psychiatry, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine of Mount Sinai, New York, NY, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Department of Genetics & Genomics, Icahn Institute of Genomics and Multiscale Biology, Department of Psychiatry, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine of Mount Sinai, New York, NY, USA
| | - Andrew Chess
- Nash Family Department of Neuroscience, Friedman Brain Institute, Department of Genetics & Genomics, Icahn Institute of Genomics and Multiscale Biology, Department of Psychiatry, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine of Mount Sinai, New York, NY, USA
| | - Steven A. McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Brigham and Women’s Hospital, Division of Genetics & Center for Data Sciences, Boston, MA, USA
| | | | - Kristen J. Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Department of Genetics & Genomics, Icahn Institute of Genomics and Multiscale Biology, Department of Psychiatry, Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine of Mount Sinai, New York, NY, USA
- Departments of Psychiatry and Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Evan Z. Macosko
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts General Hospital, Department of Psychiatry, Boston, MA, USA
| | - James T.R. Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, Wales
| | - Michael O’Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychiatry and Clinical Neurosciences, Cardiff University, Cardiff, Wales
| | - Patrick Sullivan
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan Sebat
- University of California San Diego, Department of Psychiatry, Department of Cellular & Molecular Medicine, Beyster Center of Psychiatric Genomics, San Diego, CA, USA
| | - Eunjung A. Lee
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christopher A. Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, Boston Children’s Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA, USA
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11
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Powell SK, Liao W, O’Shea C, Kammourh S, Ghorbani S, Rigat R, Elahi R, Deans PJM, Le DJ, Agarwal P, Seow WQ, Wang KC, Akbarian S, Brennand KJ. Schizophrenia Risk Mapping and Functional Engineering of the 3D Genome in Three Neuronal Subtypes. bioRxiv 2023:2023.07.17.549339. [PMID: 37502907 PMCID: PMC10370055 DOI: 10.1101/2023.07.17.549339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Common variants associated with schizophrenia are concentrated in non-coding regulatory sequences, but their precise target genes are context-dependent and impacted by cell-type-specific three-dimensional spatial chromatin organization. Here, we map long-range chromosomal conformations in isogenic human dopaminergic, GABAergic, and glutamatergic neurons to track developmentally programmed shifts in the regulatory activity of schizophrenia risk loci. Massive repressive compartmentalization, concomitant with the emergence of hundreds of neuron-specific multi-valent chromatin architectural stripes, occurs during neuronal differentiation, with genes interconnected to genetic risk loci through these long-range chromatin structures differing in their biological roles from genes more proximal to sequences conferring heritable risk. Chemically induced CRISPR-guided chromosomal loop-engineering for the proximal risk gene SNAP91 and distal risk gene BHLHE22 profoundly alters synaptic development and functional activity. Our findings highlight the large-scale cell-type-specific reorganization of chromosomal conformations at schizophrenia risk loci during neurodevelopment and establish a causal link between risk-associated gene-regulatory loop structures and neuronal function.
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Affiliation(s)
- Samuel K. Powell
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Will Liao
- New York Genome Center, New York, NY, 10029
| | - Callan O’Shea
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Sarah Kammourh
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Sadaf Ghorbani
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Raymond Rigat
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Rahat Elahi
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - PJ Michael Deans
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
| | - Derek J. Le
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Poonam Agarwal
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
| | - Wei Qiang Seow
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
| | - Kevin C. Wang
- Department of Dermatology, Program in Epithelial Biology, Stanford University School of Medicine, Stanford, 94305, California, USA
- Cancer Biology Program, Stanford University School of Medicine, Stanford, California, 94305, USA
- Veterans Affairs Palo Alto Healthcare System, Palo Alto, California, 94304, USA
| | - Schahram Akbarian
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kristen J. Brennand
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven CT, 06511
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12
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LaMarca EA, Saito A, Plaza-Jennings A, Espeso-Gil S, Hellmich A, Fernando MB, Javidfar B, Liao W, Estill M, Townsley K, Florio A, Ethridge JE, Do C, Tycko B, Shen L, Kamiya A, Tsankova NM, Brennand KJ, Akbarian S. R-loop landscapes in the developing human brain are linked to neural differentiation and cell-type specific transcription. bioRxiv 2023:2023.07.18.549494. [PMID: 37503149 PMCID: PMC10370098 DOI: 10.1101/2023.07.18.549494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Here, we construct genome-scale maps for R-loops, three-stranded nucleic acid structures comprised of a DNA/RNA hybrid and a displaced single strand of DNA, in the proliferative and differentiated zones of the human prenatal brain. We show that R-loops are abundant in the progenitor-rich germinal matrix, with preferential formation at promoters slated for upregulated expression at later stages of differentiation, including numerous neurodevelopmental risk genes. RNase H1-mediated contraction of the genomic R-loop space in neural progenitors shifted differentiation toward the neuronal lineage and was associated with transcriptomic alterations and defective functional and structural neuronal connectivity in vivo and in vitro. Therefore, R-loops are important for fine-tuning differentiation-sensitive gene expression programs of neural progenitor cells.
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Affiliation(s)
- Elizabeth A LaMarca
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Saito
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Amara Plaza-Jennings
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sergio Espeso-Gil
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Allyse Hellmich
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Fernando
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Will Liao
- New York Genome Center, New York, NY 10013, USA
| | - Molly Estill
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kayla Townsley
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Florio
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - James E Ethridge
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Catherine Do
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Benjamin Tycko
- Center for Discovery and Innovation, Hackensack Meridian Health, 111 Ideation Way, Nutley, NJ 07110, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Atsushi Kamiya
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21218, USA
| | - Nadejda M Tsankova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Current affiliation: Department of Psychiatry, Yale University, New Haven, CT 06511, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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13
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Powell SK, O'Shea C, Townsley K, Prytkova I, Dobrindt K, Elahi R, Iskhakova M, Lambert T, Valada A, Liao W, Ho SM, Slesinger PA, Huckins LM, Akbarian S, Brennand KJ. Induction of dopaminergic neurons for neuronal subtype-specific modeling of psychiatric disease risk. Mol Psychiatry 2023; 28:1970-1982. [PMID: 34493831 PMCID: PMC8898985 DOI: 10.1038/s41380-021-01273-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/22/2021] [Accepted: 08/19/2021] [Indexed: 11/08/2022]
Abstract
Dopaminergic neurons are critical to movement, mood, addiction, and stress. Current techniques for generating dopaminergic neurons from human induced pluripotent stem cells (hiPSCs) yield heterogenous cell populations with variable purity and inconsistent reproducibility between donors, hiPSC clones, and experiments. Here, we report the rapid (5 weeks) and efficient (~90%) induction of induced dopaminergic neurons (iDANs) through transient overexpression of lineage-promoting transcription factors combined with stringent selection across five donors. We observe maturation-dependent increase in dopamine synthesis and electrophysiological properties consistent with midbrain dopaminergic neuron identity, such as slow-rising after- hyperpolarization potentials, an action potential duration of ~3 ms, tonic sub-threshold oscillatory activity, and spontaneous burst firing at a frequency of ~1.0-1.75 Hz. Transcriptome analysis reveals robust expression of genes involved in fetal midbrain dopaminergic neuron identity. Specifically expressed genes in iDANs, as well as those from isogenic induced GABAergic and glutamatergic neurons, were enriched in loci conferring heritability for cannabis use disorder, schizophrenia, and bipolar disorder; however, each neuronal subtype demonstrated subtype-specific heritability enrichments in biologically relevant pathways, and iDANs alone were uniquely enriched in autism spectrum disorder risk loci. Therefore, iDANs provide a critical tool for modeling midbrain dopaminergic neuron development and dysfunction in psychiatric disease.
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Affiliation(s)
- Samuel K Powell
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Callan O'Shea
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Kayla Townsley
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Iya Prytkova
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristina Dobrindt
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Rahat Elahi
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marina Iskhakova
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tova Lambert
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aditi Valada
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Will Liao
- New York Genome Center, New York, NY, USA
| | - Seok-Man Ho
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Paul A Slesinger
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Schahram Akbarian
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Kristen J Brennand
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Division of Molecular Psychiatry, Department of Psychiatry, Yale University, New Haven, CT, USA.
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14
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Min AK, Javidfar B, Missall R, Doanman D, Durens M, Vil SS, Masih Z, Graziani M, Mordelt A, Marro S, de Witte L, Chen BK, Swartz TH, Akbarian S. HIV-1 infection of genetically engineered iPSC-derived central nervous system-engrafted microglia in a humanized mouse model. bioRxiv 2023:2023.04.26.538461. [PMID: 37162838 PMCID: PMC10168358 DOI: 10.1101/2023.04.26.538461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The central nervous system (CNS) is a major human immunodeficiency virus type 1 reservoir. Microglia are the primary target cell of HIV-1 infection in the CNS. Current models have not allowed the precise molecular pathways of acute and chronic CNS microglial infection to be tested with in vivo genetic methods. Here, we describe a novel humanized mouse model utilizing human-induced pluripotent stem cell-derived microglia to xenograft into murine hosts. These mice are additionally engrafted with human peripheral blood mononuclear cells that served as a medium to establish a peripheral infection that then spread to the CNS microglia xenograft, modeling a trans-blood-brain barrier route of acute CNS HIV-1 infection with human target cells. The approach is compatible with iPSC genetic engineering, including inserting targeted transgenic reporter cassettes to track the xenografted human cells, enabling the testing of novel treatment and viral tracking strategies in a comparatively simple and cost-effective way vivo model for neuroHIV.
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Affiliation(s)
- Alice K. Min
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Behnam Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Roy Missall
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Donald Doanman
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Madel Durens
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Samantha St Vil
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Zahra Masih
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mara Graziani
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Annika Mordelt
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboud UMC, Nijmegen, Netherlands
- Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Netherlands
| | - Samuele Marro
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Lotje de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Human Genetics and Department of Cognitive Neuroscience, Radboud UMC, Nijmegen, Netherlands
- Centre for Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Nijmegen, Netherlands
| | - Benjamin K. Chen
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Talia H. Swartz
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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15
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Chou MY, Cao X, Hou KC, Tsai MH, Lee CY, Kuo MF, Wu VC, Huang HY, Akbarian S, Chang SK, Hu CY, Lin SW, Huang HS. Mir125b-2 imprinted in human but not mouse brain regulates hippocampal function and circuit in mice. Commun Biol 2023; 6:267. [PMID: 36918719 PMCID: PMC10014956 DOI: 10.1038/s42003-023-04655-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 03/03/2023] [Indexed: 03/16/2023] Open
Abstract
Genomic imprinting predominantly occurs in the placenta and brain. Few imprinted microRNAs have been identified in the brain, and their functional roles in the brain are not clear. Here we show paternal, but not maternal, expression of MIR125B2 in human but not mouse brain. Moreover, Mir125b-2m-/p- mice showed impaired learning and memory, and anxiety, whose functions were hippocampus-dependent. Hippocampal granule cells from Mir125b-2m-/p- mice displayed increased neuronal excitability, increased excitatory synaptic transmission, and decreased inhibitory synaptic transmission. Glutamate ionotropic receptor NMDA type subunit 2A (Grin2a), a key regulator of synaptic plasticity, was physically bound by miR-125b-2 and upregulated in the hippocampus of Mir125b-2m-/p- mice. Taken together, our findings demonstrate MIR125B2 imprinted in human but not mouse brain, mediated learning, memory, and anxiety, regulated excitability and synaptic transmission in hippocampal granule cells, and affected hippocampal expression of Grin2a. Our work provides functional mechanisms of a species-specific imprinted microRNA in the brain.
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Affiliation(s)
- Ming-Yi Chou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Xuhui Cao
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Kuan-Chu Hou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Meng-Han Tsai
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chih-Yu Lee
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Meng-Fai Kuo
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Vin-Cent Wu
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Hsin-Yi Huang
- Department of Pathology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sheng-Kai Chang
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chung-Yi Hu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Shu-Wha Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.
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16
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Wei J, Lambert TY, Valada A, Patel N, Walker K, Lenders J, Schmidt CJ, Iskhakova M, Alazizi A, Mair-Meijers H, Mash DC, Luca F, Pique-Regi R, Bannon MJ, Akbarian S. Single Nucleus Transcriptomics Reveals Pervasive Glial Activation in Opioid Overdose Cases. bioRxiv 2023:2023.03.07.531400. [PMID: 36945611 PMCID: PMC10028861 DOI: 10.1101/2023.03.07.531400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Dynamic interactions of neurons and glia in the ventral midbrain (VM) mediate reward and addiction behavior. We studied gene expression in 212,713 VM single nuclei from 95 human opioid overdose cases and drug-free controls. Chronic exposure to opioids left numerical proportions of VM glial and neuronal subtypes unaltered, while broadly affecting glial transcriptomes, involving 9.5 - 6.2% of expressed genes within microglia, oligodendrocytes, and astrocytes, with prominent activation of the immune response including interferon, NFkB signaling, and cell motility pathways, sharply contrasting with down-regulated expression of synaptic signaling and plasticity genes in VM non-dopaminergic neurons. VM transcriptomic reprogramming in the context of opioid exposure and overdose included 325 genes with genetic variation linked to substance use traits in the broader population, thereby pointing to heritable risk architectures in the genomic organization of the brain's reward circuitry.
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Affiliation(s)
- Julong Wei
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201
| | - Tova Y. Lambert
- Department of Psychiatry, Department of Neuroscience and Department of Genetics and Genomic Sciences, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Aditi Valada
- Department of Psychiatry, Department of Neuroscience and Department of Genetics and Genomic Sciences, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Nikhil Patel
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201
| | - Kellie Walker
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201
| | - Jayna Lenders
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201
| | - Carl J. Schmidt
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, MI 48109
| | - Marina Iskhakova
- Department of Psychiatry, Department of Neuroscience and Department of Genetics and Genomic Sciences, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201
| | - Henriette Mair-Meijers
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201
| | - Deborah C. Mash
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL 33136
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201
- Department of Biology, University of Tor Vergata, Rome, Italy, 00133
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI 48201
| | - Michael J Bannon
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201
| | - Schahram Akbarian
- Department of Psychiatry, Department of Neuroscience and Department of Genetics and Genomic Sciences, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, NY 10029
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17
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Kim YA, Siddiqui T, Blaze J, Cosacak MI, Winters T, Kumar A, Tein E, Sproul AA, Teich AF, Bartolini F, Akbarian S, Kizil C, Hargus G, Santa-Maria I. RNA methyltransferase NSun2 deficiency promotes neurodegeneration through epitranscriptomic regulation of tau phosphorylation. Acta Neuropathol 2023; 145:29-48. [PMID: 36357715 PMCID: PMC9807547 DOI: 10.1007/s00401-022-02511-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 11/12/2022]
Abstract
Epitranscriptomic regulation adds a layer of post-transcriptional control to brain function during development and adulthood. The identification of RNA-modifying enzymes has opened the possibility of investigating the role epitranscriptomic changes play in the disease process. NOP2/Sun RNA methyltransferase 2 (NSun2) is one of the few known brain-enriched methyltransferases able to methylate mammalian non-coding RNAs. NSun2 loss of function due to autosomal-recessive mutations has been associated with neurological abnormalities in humans. Here, we show NSun2 is expressed in adult human neurons in the hippocampal formation and prefrontal cortex. Strikingly, we unravel decreased NSun2 protein expression and an increased ratio of pTau/NSun2 in the brains of patients with Alzheimer's disease (AD) as demonstrated by Western blotting and immunostaining, respectively. In a well-established Drosophila melanogaster model of tau-induced toxicity, reduction of NSun2 exacerbated tau toxicity, while overexpression of NSun2 partially abrogated the toxic effects. Conditional ablation of NSun2 in the mouse brain promoted a decrease in the miR-125b m6A levels and tau hyperphosphorylation. Utilizing human induced pluripotent stem cell (iPSC)-derived neuronal cultures, we confirmed NSun2 deficiency results in tau hyperphosphorylation. We also found that neuronal NSun2 levels decrease in response to amyloid-beta oligomers (AβO). Notably, AβO-induced tau phosphorylation and cell toxicity in human neurons could be rescued by overexpression of NSun2. Altogether, these results indicate that neuronal NSun2 deficiency promotes dysregulation of miR-125b and tau phosphorylation in AD and highlights a novel avenue for therapeutic targeting.
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Affiliation(s)
- Yoon A Kim
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, USA
- Department of Pathology and Cell Biology, Columbia University, New York, USA
| | - Tohid Siddiqui
- German Center for Neurodegenerative Diseases (DZNE), Helmholtz Association, Dresden, Germany
| | - Jennifer Blaze
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Mehmet Ilyas Cosacak
- German Center for Neurodegenerative Diseases (DZNE), Helmholtz Association, Dresden, Germany
| | - Tristan Winters
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, USA
- Department of Pathology and Cell Biology, Columbia University, New York, USA
| | - Atul Kumar
- Department of Pathology and Cell Biology, Columbia University, New York, USA
| | - Ellen Tein
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, USA
| | - Andrew A Sproul
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, USA
- Department of Pathology and Cell Biology, Columbia University, New York, USA
| | - Andrew F Teich
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, USA
- Department of Pathology and Cell Biology, Columbia University, New York, USA
| | - Francesca Bartolini
- Department of Pathology and Cell Biology, Columbia University, New York, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Caghan Kizil
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, USA
- German Center for Neurodegenerative Diseases (DZNE), Helmholtz Association, Dresden, Germany
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, USA
| | - Gunnar Hargus
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, USA.
| | - Ismael Santa-Maria
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, USA.
- Facultad de Ciencias Experimentales, Universidad Francisco de Vitoria, Edificio E, Pozuelo de Alarcón, Madrid, 28223, Spain.
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18
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Plaza-Jennings AL, Valada A, O'Shea C, Iskhakova M, Hu B, Javidfar B, Ben Hutta G, Lambert TY, Murray J, Kassim B, Chandrasekaran S, Chen BK, Morgello S, Won H, Akbarian S. HIV integration in the human brain is linked to microglial activation and 3D genome remodeling. Mol Cell 2022; 82:4647-4663.e8. [PMID: 36525955 PMCID: PMC9831062 DOI: 10.1016/j.molcel.2022.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 09/12/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022]
Abstract
To explore genome organization and function in the HIV-infected brain, we applied single-nuclei transcriptomics, cell-type-specific chromosomal conformation mapping, and viral integration site sequencing (IS-seq) to frontal cortex from individuals with encephalitis (HIVE) and without (HIV+). Derepressive changes in 3D genomic compartment structures in HIVE microglia were linked to the transcriptional activation of interferon (IFN) signaling and cell migratory pathways, while transcriptional downregulation and repressive compartmentalization of neuronal health and signaling genes occurred in both HIVE and HIV+ microglia. IS-seq recovered 1,221 brain integration sites showing distinct genomic patterns compared with peripheral lymphocytes, with enrichment for sequences newly mobilized into a permissive chromatin environment after infection. Viral transcription occurred in a subset of highly activated microglia comprising 0.33% of all nuclei in HIVE brain. Our findings point to disrupted microglia-neuronal interactions in HIV and link retroviral integration to remodeling of the microglial 3D genome during infection.
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Affiliation(s)
- Amara L Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aditi Valada
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Callan O'Shea
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Iskhakova
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benxia Hu
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriella Ben Hutta
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tova Y Lambert
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jacinta Murray
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bibi Kassim
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sandhya Chandrasekaran
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Benjamin K Chen
- Division of Infectious Diseases, Department of Medicine, Immunology Institute, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Susan Morgello
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Hyejung Won
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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19
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Pai B, Tome‑Garcia J, Cheng WS, Nudelman G, Beaumont KG, Ghatan S, Panov F, Caballero E, Sarpong K, Marcuse L, Yoo J, Jiang Y, Schaefer A, Akbarian S, Sebra R, Pinto D, Zaslavsky E, Tsankova NM. Correction: High-resolution transcriptomics informs glial pathology in human temporal lobe epilepsy. Acta Neuropathol Commun 2022; 10:171. [DOI: 10.1186/s40478-022-01479-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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20
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Plaza-Jennings A, Valada A, Akbarian S. 3D Genome Plasticity in Normal and Diseased Neurodevelopment. Genes (Basel) 2022; 13:1999. [PMID: 36360237 PMCID: PMC9690570 DOI: 10.3390/genes13111999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 10/17/2023] Open
Abstract
Non-random spatial organization of the chromosomal material inside the nuclei of brain cells emerges as an important regulatory layer of genome organization and function in health and disease. Here, we discuss how integrative approaches assessing chromatin in context of the 3D genome is providing new insights into normal and diseased neurodevelopment. Studies in primate (incl. human) and rodent brain have confirmed that chromosomal organization in neurons and glia undergoes highly dynamic changes during pre- and early postnatal development, with potential for plasticity across a much wider age window. For example, neuronal 3D genomes from juvenile and adult cerebral cortex and hippocampus undergo chromosomal conformation changes at hundreds of loci in the context of learning and environmental enrichment, viral infection, and neuroinflammation. Furthermore, locus-specific structural DNA variations, such as micro-deletions, duplications, repeat expansions, and retroelement insertions carry the potential to disrupt the broader epigenomic and transcriptional landscape far beyond the boundaries of the site-specific variation, highlighting the critical importance of long-range intra- and inter-chromosomal contacts for neuronal and glial function.
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Affiliation(s)
- Amara Plaza-Jennings
- Graduate School of Biomedical Sciences, Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aditi Valada
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, 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
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21
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Pai B, Tome-Garcia J, Cheng WS, Nudelman G, Beaumont KG, Ghatan S, Panov F, Caballero E, Sarpong K, Marcuse L, Yoo J, Jiang Y, Schaefer A, Akbarian S, Sebra R, Pinto D, Zaslavsky E, Tsankova NM. High-resolution transcriptomics informs glial pathology in human temporal lobe epilepsy. Acta Neuropathol Commun 2022; 10:149. [PMID: 36274170 PMCID: PMC9590125 DOI: 10.1186/s40478-022-01453-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
The pathophysiology of epilepsy underlies a complex network dysfunction between neurons and glia, the molecular cell type-specific contributions of which remain poorly defined in the human disease. In this study, we validated a method that simultaneously isolates neuronal (NEUN +), astrocyte (PAX6 + NEUN–), and oligodendroglial progenitor (OPC) (OLIG2 + NEUN–) enriched nuclei populations from non-diseased, fresh-frozen human neocortex and then applied it to characterize the distinct transcriptomes of such populations isolated from electrode-mapped temporal lobe epilepsy (TLE) surgical samples. Nuclear RNA-seq confirmed cell type specificity and informed both common and distinct pathways associated with TLE in astrocytes, OPCs, and neurons. Compared to postmortem control, the transcriptome of epilepsy astrocytes showed downregulation of mature astrocyte functions and upregulation of development-related genes. To gain further insight into glial heterogeneity in TLE, we performed single cell transcriptomics (scRNA-seq) on four additional human TLE samples. Analysis of the integrated TLE dataset uncovered a prominent subpopulation of glia that express a hybrid signature of both reactive astrocyte and OPC markers, including many cells with a mixed GFAP + OLIG2 + phenotype. A further integrated analysis of this TLE scRNA-seq dataset and a previously published normal human temporal lobe scRNA-seq dataset confirmed the unique presence of hybrid glia only in TLE. Pseudotime analysis revealed cell transition trajectories stemming from this hybrid population towards both OPCs and reactive astrocytes. Immunofluorescence studies in human TLE samples confirmed the rare presence of GFAP + OLIG2 + glia, including some cells with proliferative activity, and functional analysis of cells isolated directly from these samples disclosed abnormal neurosphere formation in vitro. Overall, cell type-specific isolation of glia from surgical epilepsy samples combined with transcriptomic analyses uncovered abnormal glial subpopulations with de-differentiated phenotype, motivating further studies into the dysfunctional role of reactive glia in temporal lobe epilepsy.
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22
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Sey NYA, Hu B, Iskhakova M, Lee S, Sun H, Shokrian N, Ben Hutta G, Marks JA, Quach BC, Johnson EO, Hancock DB, Akbarian S, Won H. Correction: Chromatin architecture in addiction circuitry identifies risk genes and potential biological mechanisms underlying cigarette smoking and alcohol use traits. Mol Psychiatry 2022; 27:4368. [PMID: 35794187 DOI: 10.1038/s41380-022-01678-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nancy Y A Sey
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Benxia Hu
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Marina Iskhakova
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sool Lee
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Huaigu Sun
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Neda Shokrian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriella Ben Hutta
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jesse A Marks
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Bryan C Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
- Fellow Program, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Hyejung Won
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
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23
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Voloudakis G, Vicari JM, Venkatesh S, Hoffman GE, Dobrindt K, Zhang W, Beckmann ND, Higgins CA, Argyriou S, Jiang S, Hoagland D, Gao L, Corvelo A, Cho K, Lee KM, Bian J, Lee JS, Iyengar SK, Luoh SW, Akbarian S, Striker R, Assimes TL, Schadt EE, Lynch JA, Merad M, tenOever BR, Charney AW, Brennand KJ, Fullard JF, Roussos P. A translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility. NPJ Genom Med 2022; 7:52. [PMID: 36064543 PMCID: PMC9441828 DOI: 10.1038/s41525-022-00324-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 08/19/2022] [Indexed: 02/06/2023] Open
Abstract
Recent efforts have identified genetic loci that are associated with coronavirus disease 2019 (COVID-19) infection rates and disease outcome severity. Translating these genetic findings into druggable genes that reduce COVID-19 host susceptibility is a critical next step. Using a translational genomics approach that integrates COVID-19 genetic susceptibility variants, multi-tissue genetically regulated gene expression (GReX), and perturbagen signatures, we identified IL10RB as the top candidate gene target for COVID-19 host susceptibility. In a series of validation steps, we show that predicted GReX upregulation of IL10RB and higher IL10RB expression in COVID-19 patient blood is associated with worse COVID-19 outcomes and that in vitro IL10RB overexpression is associated with increased viral load and activation of disease-relevant molecular pathways.
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Affiliation(s)
- Georgios Voloudakis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
| | - James M Vicari
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sanan Venkatesh
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Gabriel E Hoffman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristina Dobrindt
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - Wen Zhang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Noam D Beckmann
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Christina A Higgins
- Department of Microbiology, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Medicine, Grossman School of Medicine, New York University, New York, NY, USA
- Vilcek Institute of Graduate Biomedical Sciences, New York University, New York, NY, USA
| | - Stathis Argyriou
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shan Jiang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daisy Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- VA Portland Health Care System, Portland, OR, USA
| | | | - Kelly Cho
- VA Boston Healthcare System, Boston, MA, USA
- Division of Aging, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Kyung Min Lee
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
| | - Jiantao Bian
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Jennifer S Lee
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Sudha K Iyengar
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Genetics and Genome Sciences, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- VA Northeast Ohio Healthcare System, Cleveland VA Medical Center, Cleveland, OH, USA
| | - Shiuh-Wen Luoh
- VA Portland Health Care System, Portland, OR, USA
- Department of Medicine, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert Striker
- Division of Infectious Diseases, Department of Medicine, University of Wisconsin, Madison, WI, USA
- William S. Middleton Memorial Veterans Hospital, Madison, WI, USA
| | - Themistocles L Assimes
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- VA Palo Alto Health Care System, Palo Alto, CA, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Sema4, Stamford, CT, USA
| | - Julie A Lynch
- VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, UT, USA
- Division of Epidemiology, University of Utah, Salt Lake City, UT, USA
| | - Miriam Merad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Benjamin R tenOever
- Department of Microbiology, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Medicine, Grossman School of Medicine, New York University, New York, NY, USA
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Virus Engineering Center for Therapeutics and Research, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander W Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Clinical Intelligence Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Yale University, New Haven, CT, USA
| | - John F Fullard
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Center for Disease Neurogenomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Mental Illness Research, Education, and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, NY, USA.
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24
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Blaze J, Akbarian S. The tRNA regulome in neurodevelopmental and neuropsychiatric disease. Mol Psychiatry 2022; 27:3204-3213. [PMID: 35505091 PMCID: PMC9630165 DOI: 10.1038/s41380-022-01585-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 12/14/2022]
Abstract
Transfer (t)RNAs are 70-90 nucleotide small RNAs highly regulated by 43 different types of epitranscriptomic modifications and requiring aminoacylation ('charging') for mRNA decoding and protein synthesis. Smaller cleavage products of mature tRNAs, or tRNA fragments, have been linked to a broad variety of noncanonical functions, including translational inhibition and modulation of the immune response. Traditionally, knowledge about tRNA regulation in brain is derived from phenotypic exploration of monogenic neurodevelopmental and neurodegenerative diseases associated with rare mutations in tRNA modification genes. More recent studies point to the previously unrecognized potential of the tRNA regulome to affect memory, synaptic plasticity, and affective states. For example, in mature cortical neurons, cytosine methylation sensitivity of the glycine tRNA family (tRNAGly) is coupled to glycine biosynthesis and codon-specific alterations in ribosomal translation together with robust changes in cognition and depression-related behaviors. In this Review, we will discuss the emerging knowledge of the neuronal tRNA landscape, with a focus on epitranscriptomic tRNA modifications and downstream molecular pathways affected by alterations in tRNA expression, charging levels, and cleavage while mechanistically linking these pathways to neuropsychiatric disease and provide insight into future areas of study for this field.
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Affiliation(s)
- Jennifer Blaze
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Schahram Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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25
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Rapanelli M, Williams JB, Ma K, Yang F, Zhong P, Patel R, Kumar M, Qin L, Rein B, Wang ZJ, Kassim B, Javidfar B, Couto L, Akbarian S, Yan Z. Targeting histone demethylase LSD1 for treatment of deficits in autism mouse models. Mol Psychiatry 2022; 27:3355-3366. [PMID: 35296809 PMCID: PMC9477974 DOI: 10.1038/s41380-022-01508-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 11/09/2022]
Abstract
Large-scale genetic studies have revealed that the most prominent genes disrupted in autism are chromatin regulators mediating histone methylation/demethylation, suggesting the central role of epigenetic dysfunction in this disorder. Here, we show that histone lysine 4 dimethylation (H3K4me2), a histone mark linked to gene activation, is significantly decreased in the prefrontal cortex (PFC) of autistic human patients and mutant mice with the deficiency of top-ranking autism risk factor Shank3 or Cul3. A brief treatment of the autism models with highly potent and selective inhibitors of the H3K4me2 demethylase LSD1 (KDM1A) leads to the robust rescue of core symptoms of autism, including social deficits and repetitive behaviors. Concomitantly, LSD1 inhibition restores NMDA receptor function in PFC and AMPA receptor-mediated currents in striatum of Shank3-deficient mice. Genome-wide RNAseq and ChIPseq reveal that treatment of Shank3-deficient mice with the LSD1 inhibitor restores the expression and H3K4me2 occupancy of downregulated genes enriched in synaptic signaling and developmental processes. The immediate early gene tightly linked to neuronal plasticity, Egr1, is on the top list of rescued genes. The diminished transcription of Egr1 is recapitulated in PFC of autistic human patients. Overexpression of Egr1 in PFC of Shank3-deficient mice ameliorates social preference deficits. These results have for the first time revealed an important role of H3K4me2 abnormality in ASD pathophysiology, and the therapeutic potential of targeting H3K4me2 demethylase LSD1 or the downstream molecule Egr1 for ASD.
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Affiliation(s)
- Maximiliano Rapanelli
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Jamal B Williams
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Kaijie Ma
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Fengwei Yang
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Ping Zhong
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Rajvi Patel
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Manasa Kumar
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Luye Qin
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Benjamin Rein
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Zi-Jun Wang
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Bibi Kassim
- Department of Psychiatry; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Behnam Javidfar
- Department of Psychiatry; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lizette Couto
- Department of Psychiatry; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Schahram Akbarian
- Department of Psychiatry; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhen Yan
- Department of Physiology and Biophysics, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA.
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26
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Sey NYA, Hu B, Iskhakova M, Lee S, Sun H, Shokrian N, Ben Hutta G, Marks JA, Quach BC, Johnson EO, Hancock DB, Akbarian S, Won H. Chromatin architecture in addiction circuitry identifies risk genes and potential biological mechanisms underlying cigarette smoking and alcohol use traits. Mol Psychiatry 2022; 27:3085-3094. [PMID: 35422469 PMCID: PMC9853312 DOI: 10.1038/s41380-022-01558-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 03/21/2022] [Accepted: 03/30/2022] [Indexed: 01/25/2023]
Abstract
Cigarette smoking and alcohol use are among the most prevalent substances used worldwide and account for a substantial proportion of preventable morbidity and mortality, underscoring the public health significance of understanding their etiology. Genome-wide association studies (GWAS) have successfully identified genetic variants associated with cigarette smoking and alcohol use traits. However, the vast majority of risk variants reside in non-coding regions of the genome, and their target genes and neurobiological mechanisms are unknown. Chromosomal conformation mappings can address this knowledge gap by charting the interaction profiles of risk-associated regulatory variants with target genes. To investigate the functional impact of common variants associated with cigarette smoking and alcohol use traits, we applied Hi-C coupled MAGMA (H-MAGMA) built upon cortical and newly generated midbrain dopaminergic neuronal Hi-C datasets to GWAS summary statistics of nicotine dependence, cigarettes per day, problematic alcohol use, and drinks per week. The identified risk genes mapped to key pathways associated with cigarette smoking and alcohol use traits, including drug metabolic processes and neuronal apoptosis. Risk genes were highly expressed in cortical glutamatergic, midbrain dopaminergic, GABAergic, and serotonergic neurons, suggesting them as relevant cell types in understanding the mechanisms by which genetic risk factors influence cigarette smoking and alcohol use. Lastly, we identified pleiotropic genes between cigarette smoking and alcohol use traits under the assumption that they may reveal substance-agnostic, shared neurobiological mechanisms of addiction. The number of pleiotropic genes was ~26-fold higher in dopaminergic neurons than in cortical neurons, emphasizing the critical role of ascending dopaminergic pathways in mediating general addiction phenotypes. Collectively, brain region- and neuronal subtype-specific 3D genome architecture helps refine neurobiological hypotheses for smoking, alcohol, and general addiction phenotypes by linking genetic risk factors to their target genes.
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Affiliation(s)
- Nancy Y A Sey
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Benxia Hu
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Marina Iskhakova
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sool Lee
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Huaigu Sun
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Neda Shokrian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Gabriella Ben Hutta
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jesse A Marks
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Bryan C Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
- Fellow Program, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, Chapel Hill, NC, 27709, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Hyejung Won
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, 27599, USA.
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA.
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27
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Chou MY, Hu MC, Chen PY, Hsu CL, Lin TY, Tan MJ, Lee CY, Kuo MF, Huang PH, Wu VC, Yang SH, Fan PC, Huang HY, Akbarian S, Loo TH, Stewart CL, Huang HP, Gau SSF, Huang HS. RTL1/PEG11 imprinted in human and mouse brain mediates anxiety-like and social behaviors and regulates neuronal excitability in the locus coeruleus. Hum Mol Genet 2022; 31:3161-3180. [PMID: 35567414 PMCID: PMC9476620 DOI: 10.1093/hmg/ddac110] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/01/2022] [Accepted: 05/09/2022] [Indexed: 11/24/2022] Open
Abstract
RTL1/PEG11, which has been associated with anxiety disorders, is a retrotransposon-derived imprinted gene in the placenta. However, imprinting patterns and functions of RTL1 in the brain have not been well-investigated. We found Rtl1 was paternally, but not maternally, expressed in brain stem, thalamus, and hypothalamus of mice, and imprinting status of RTL1 was maintained in human brain. Paternal Rtl1 knockout (Rtl1m+/p-) mice had higher neonatal death rates due to impaired suckling, and low body weights beginning on embryonic day 16.5. High paternal expression of Rtl1 was detected in the locus coeruleus (LC) and Rtl1m+/p- mice showed an increased delay in time of onset for action potentials and inward currents with decreased neuronal excitability of LC neurons. Importantly, Rtl1m+/p- mice exhibited behaviors associated with anxiety, depression, fear-related learning and memory, social dominance, and low locomotor activity. Taken together, our findings demonstrate RTL1 is imprinted in brain, mediates emotional and social behaviors, and regulates excitability in LC neurons.
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Affiliation(s)
- Ming-Yi Chou
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Meng-Chuen Hu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Pin-Yu Chen
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chi-Lin Hsu
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Ting-Yu Lin
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Mao-Jia Tan
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chih-Yu Lee
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Meng-Fai Kuo
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Pei-Hsin Huang
- Department of Pathology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Vin-Cent Wu
- Department of Internal Medicine, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Shih-Hung Yang
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, 10051, Taiwan
| | - Pi-Chuan Fan
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Hsin-Yi Huang
- Department of Pathology, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, NY, 10029, USA
| | - Tsui-Han Loo
- A*STAR Skin Research Labs, Agency for Science, Technology and Research, 138632, Singapore
| | - Colin L Stewart
- A*STAR Skin Research Labs, Agency for Science, Technology and Research, 138632, Singapore
| | - Hsiang-Po Huang
- Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Susan Shur-Fen Gau
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan.,Department of Psychiatry, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Hsien-Sung Huang
- Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
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28
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Zajicek AS, Ruan H, Dai H, Skolfield MC, Phillips HL, Burnette WJ, Javidfar B, Sun SC, Akbarian S, Yao WD. Cylindromatosis drives synapse pruning and weakening by promoting macroautophagy through Akt-mTOR signaling. Mol Psychiatry 2022; 27:2414-2424. [PMID: 35449295 PMCID: PMC9278694 DOI: 10.1038/s41380-022-01571-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/04/2022] [Accepted: 04/07/2022] [Indexed: 11/09/2022]
Abstract
The lysine-63 deubiquitinase cylindromatosis (CYLD) is long recognized as a tumor suppressor in immunity and inflammation, and its loss-of-function mutations lead to familial cylindromatosis. However, recent studies reveal that CYLD is enriched in mammalian brain postsynaptic densities, and a gain-of-function mutation causes frontotemporal dementia (FTD), suggesting critical roles at excitatory synapses. Here we report that CYLD drives synapse elimination and weakening by acting on the Akt-mTOR-autophagy axis. Mice lacking CYLD display abnormal sociability, anxiety- and depression-like behaviors, and cognitive inflexibility. These behavioral impairments are accompanied by excessive synapse numbers, increased postsynaptic efficacy, augmented synaptic summation, and impaired NMDA receptor-dependent hippocampal long-term depression (LTD). Exogenous expression of CYLD results in removal of established dendritic spines from mature neurons in a deubiquitinase activity-dependent manner. In search of underlying molecular mechanisms, we find that CYLD knockout mice display marked overactivation of Akt and mTOR and reduced autophagic flux, and conversely, CYLD overexpression potently suppresses Akt and mTOR activity and promotes autophagy. Consequently, abrogating the Akt-mTOR-autophagy signaling pathway abolishes CYLD-induced spine loss, whereas enhancing autophagy in vivo by the mTOR inhibitor rapamycin rescues the synaptic pruning and LTD deficits in mutant mice. Our findings establish CYLD, via Akt-mTOR signaling, as a synaptic autophagy activator that exerts critical modulations on synapse maintenance, function, and plasticity.
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Affiliation(s)
- Alexis S Zajicek
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Neuroscience Graduate Program, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Hongyu Ruan
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Huihui Dai
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Mary C Skolfield
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Neuroscience Graduate Program, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Hannah L Phillips
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Neuroscience Graduate Program, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Wendi J Burnette
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Neuroscience Graduate Program, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Behnam Javidfar
- Friedman Brain Institute, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shao-Cong Sun
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Wei-Dong Yao
- Department of Psychiatry and Behavioral Sciences, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA.
- Neuroscience Graduate Program, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA.
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA.
- Harvard Medical School, New England Primate Research Center, Southborough, MA, USA.
- Department of Psychiatry, Beth Israel Deaconess Medical Center, Boston, MA, USA.
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29
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Wickramasinghe NM, Sachs D, Shewale B, Gonzalez DM, Dhanan-Krishnan P, Torre D, LaMarca E, Raimo S, Dariolli R, Serasinghe MN, Mayourian J, Sebra R, Beaumont K, Iyengar S, French DL, Hansen A, Eschenhagen T, Chipuk JE, Sobie EA, Jacobs A, Akbarian S, Ischiropoulos H, Ma'ayan A, Houten SM, Costa K, Dubois NC. PPARdelta activation induces metabolic and contractile maturation of human pluripotent stem cell-derived cardiomyocytes. Cell Stem Cell 2022; 29:559-576.e7. [PMID: 35325615 DOI: 10.1016/j.stem.2022.02.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 06/30/2021] [Accepted: 02/24/2022] [Indexed: 02/09/2023]
Abstract
Pluripotent stem-cell-derived cardiomyocytes (PSC-CMs) provide an unprecedented opportunity to study human heart development and disease, but they are functionally and structurally immature. Here, we induce efficient human PSC-CM (hPSC-CM) maturation through metabolic-pathway modulations. Specifically, we find that peroxisome-proliferator-associated receptor (PPAR) signaling regulates glycolysis and fatty acid oxidation (FAO) in an isoform-specific manner. While PPARalpha (PPARa) is the most active isoform in hPSC-CMs, PPARdelta (PPARd) activation efficiently upregulates the gene regulatory networks underlying FAO, increases mitochondrial and peroxisome content, enhances mitochondrial cristae formation, and augments FAO flux. PPARd activation further increases binucleation, enhances myofibril organization, and improves contractility. Transient lactate exposure, which is frequently used for hPSC-CM purification, induces an independent cardiac maturation program but, when combined with PPARd activation, still enhances oxidative metabolism. In summary, we investigate multiple metabolic modifications in hPSC-CMs and identify a role for PPARd signaling in inducing the metabolic switch from glycolysis to FAO in hPSC-CMs.
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Affiliation(s)
- Nadeera M Wickramasinghe
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David Sachs
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bhavana Shewale
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - David M Gonzalez
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Priyanka Dhanan-Krishnan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Denis Torre
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Elizabeth LaMarca
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Serena Raimo
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Rafael Dariolli
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Madhavika N Serasinghe
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua Mayourian
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristin Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Srinivas Iyengar
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mount Sinai Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Deborah L French
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Arne Hansen
- University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | | | - Jerry E Chipuk
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric A Sobie
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam Jacobs
- Department of Obstetrics and Gynecology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Harry Ischiropoulos
- Children's Hospital of Philadelphia Research Institute, Philadelphia, PA, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kevin Costa
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nicole C Dubois
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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30
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Affiliation(s)
- Abraham Reichenberg
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America.
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31
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Girdhar K, Hoffman GE, Bendl J, Rahman S, Dong P, Liao W, Hauberg ME, Sloofman L, Brown L, Devillers O, Kassim BS, Wiseman JR, Park R, Zharovsky E, Jacobov R, Flatow E, Kozlenkov A, Gilgenast T, Johnson JS, Couto L, Peters MA, Phillips-Cremins JE, Hahn CG, Gur RE, Tamminga CA, Lewis DA, Haroutunian V, Dracheva S, Lipska BK, Marenco S, Kundakovic M, Fullard JF, Jiang Y, Roussos P, Akbarian S. Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains. Nat Neurosci 2022; 25:474-483. [PMID: 35332326 PMCID: PMC8989650 DOI: 10.1038/s41593-022-01032-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/09/2022] [Indexed: 12/19/2022]
Abstract
Chromosomal organization, scaling from the 147 base pair nucleosome to
megabase-ranging domains encompassing multiple transcriptional units including
heritability loci for psychiatric traits, remains largely unexplored in the
human brain. Here, we construct promoter and enhancer enriched nucleosomal
histone modification landscapes for adult prefrontal cortex (PFC) from H3-lysine
27 acetylation and H3-lysine 4 trimethylation profiles, generated from (n=739)
388 controls and 351 subjects diagnosed with schizophrenia (SCZ) or bipolar
disorder (BD). We mapped thousands of cis-regulatory domains (CRDs), revealing
fine-grained, 104-106 bp chromosomal organization, firmly
integrated into Hi-C topologically associating domain (TAD) stratification by
open/repressive chromosomal environments and nuclear topography. Large clusters
of hyperacetylated CRDs were enriched for SCZ heritability, with prominent
representation of regulatory sequences governing fetal development and
glutamatergic neuron signaling. Therefore, SCZ and BD brains show coordinated
dysregulation of risk-associated regulatory sequences assembled into kilo- to
megabase-scaling chromosomal domains.
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Affiliation(s)
- Kiran Girdhar
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Gabriel E Hoffman
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jaroslav Bendl
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Samir Rahman
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pengfei Dong
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Will Liao
- New York Genome Center, New York, NY, USA
| | - Mads E Hauberg
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Laura Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Leanne Brown
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Olivia Devillers
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bibi S Kassim
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jennifer R Wiseman
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Royce Park
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elizabeth Zharovsky
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rivky Jacobov
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elie Flatow
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Gilgenast
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessica S Johnson
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lizette Couto
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jennifer E Phillips-Cremins
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Chang-Gyu Hahn
- Department of Psychiatry, Vickie and Jack Farber Institute for Neuroscience, Jefferson University, Philadelphia, PA, USA
| | - Raquel E Gur
- Department of Psychiatry, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Carol A Tamminga
- Department of Psychiatry, The University of Texas Southwestern Medical School, Dallas, TX, USA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Vahram Haroutunian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
| | | | - Stella Dracheva
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA
| | - Barbara K Lipska
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, MD, USA
| | - Stefano Marenco
- Human Brain Collection Core, National Institute of Mental Health-Intramural Research Program, Bethesda, MD, USA
| | - Marija Kundakovic
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Biological Sciences, Fordham University, Bronx, NY, USA
| | - John F Fullard
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Jiang
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Mental Illness Research Education and Clinical Center (MIRECC), James J. Peters VA Medical Center, Bronx, NY, USA. .,Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY, USA.
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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Blaze J, Navickas A, Phillips HL, Heissel S, Plaza-Jennings A, Miglani S, Asgharian H, Foo M, Katanski CD, Watkins CP, Pennington ZT, Javidfar B, Espeso-Gil S, Rostandy B, Alwaseem H, Hahn CG, Molina H, Cai DJ, Pan T, Yao WD, Goodarzi H, Haghighi F, Akbarian S. Author Correction: Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior. Nat Commun 2021; 12:7263. [PMID: 34880236 PMCID: PMC8654860 DOI: 10.1038/s41467-021-27501-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- J Blaze
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - A Navickas
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H L Phillips
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - S Heissel
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - A Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Miglani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H Asgharian
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - M Foo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C D Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C P Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Z T Pennington
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Javidfar
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Espeso-Gil
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Rostandy
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - H Alwaseem
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - C G Hahn
- Department of Neurosciences, Thomas Jefferson University, Philadelphia, PA, USA
| | - H Molina
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - D J Cai
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - T Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - W D Yao
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - H Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - F Haghighi
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.,Research and Development Service, James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - S Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA. .,Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA. .,Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
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33
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Blaze J, Navickas A, Phillips HL, Heissel S, Plaza-Jennings A, Miglani S, Asgharian H, Foo M, Katanski CD, Watkins CP, Pennington ZT, Javidfar B, Espeso-Gil S, Rostandy B, Alwaseem H, Hahn CG, Molina H, Cai DJ, Pan T, Yao WD, Goodarzi H, Haghighi F, Akbarian S. Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior. Nat Commun 2021; 12:4913. [PMID: 34389722 PMCID: PMC8363735 DOI: 10.1038/s41467-021-24969-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Epitranscriptomic mechanisms linking tRNA function and the brain proteome to cognition and complex behaviors are not well described. Here, we report bi-directional changes in depression-related behaviors after genetic disruption of neuronal tRNA cytosine methylation, including conditional ablation and transgene-derived overexpression of Nsun2 in the mouse prefrontal cortex (PFC). Neuronal Nsun2-deficiency was associated with a decrease in tRNA m5C levels, resulting in deficits in expression of 70% of tRNAGly isodecoders. Altogether, 1488/5820 proteins changed upon neuronal Nsun2-deficiency, in conjunction with glycine codon-specific defects in translational efficiencies. Loss of Gly-rich proteins critical for glutamatergic neurotransmission was associated with impaired synaptic signaling at PFC pyramidal neurons and defective contextual fear memory. Changes in the neuronal translatome were also associated with a 146% increase in glycine biosynthesis. These findings highlight the methylation sensitivity of glycinergic tRNAs in the adult PFC. Furthermore, they link synaptic plasticity and complex behaviors to epitranscriptomic modifications of cognate tRNAs and the proteomic homeostasis associated with specific amino acids.
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Affiliation(s)
- J Blaze
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - A Navickas
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H L Phillips
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - S Heissel
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - A Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Miglani
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - H Asgharian
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - M Foo
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C D Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - C P Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Z T Pennington
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Javidfar
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - S Espeso-Gil
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - B Rostandy
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - H Alwaseem
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - C G Hahn
- Department of Neurosciences, Thomas Jefferson University, Philadelphia, PA, USA
| | - H Molina
- The Rockefeller University Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - D J Cai
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
| | - T Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - W D Yao
- Departments of Psychiatry and Behavioral Sciences, Neuroscience and Physiology, Upstate Medical University, Syracuse, NY, USA
| | - H Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - F Haghighi
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Research and Development Service, James J. Peters Veterans Affairs Medical Center, Bronx, NY, USA
| | - S Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
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34
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Fullard JF, Lee HC, Voloudakis G, Suo S, Javidfar B, Shao Z, Peter C, Zhang W, Jiang S, Corvelo A, Wargnier H, Woodoff-Leith E, Purohit DP, Ahuja S, Tsankova NM, Jette N, Hoffman GE, Akbarian S, Fowkes M, Crary JF, Yuan GC, Roussos P. Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19. Genome Med 2021; 13:118. [PMID: 34281603 PMCID: PMC8287557 DOI: 10.1186/s13073-021-00933-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/06/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has been associated with neurological and neuropsychiatric illness in many individuals. We sought to further our understanding of the relationship between brain tropism, neuro-inflammation, and host immune response in acute COVID-19 cases. METHODS Three brain regions (dorsolateral prefrontal cortex, medulla oblongata, and choroid plexus) from 5 patients with severe COVID-19 and 4 controls were examined. The presence of the virus was assessed by western blot against viral spike protein, as well as viral transcriptome analysis covering > 99% of SARS-CoV-2 genome and all potential serotypes. Droplet-based single-nucleus RNA sequencing (snRNA-seq) was performed in the same samples to examine the impact of COVID-19 on transcription in individual cells of the brain. RESULTS Quantification of viral spike S1 protein and viral transcripts did not detect SARS-CoV-2 in the postmortem brain tissue. However, analysis of 68,557 single-nucleus transcriptomes from three distinct regions of the brain identified an increased proportion of stromal cells, monocytes, and macrophages in the choroid plexus of COVID-19 patients. Furthermore, differential gene expression, pseudo-temporal trajectory, and gene regulatory network analyses revealed transcriptional changes in the cortical microglia associated with a range of biological processes, including cellular activation, mobility, and phagocytosis. CONCLUSIONS Despite the absence of detectable SARS-CoV-2 in the brain at the time of death, the findings suggest significant and persistent neuroinflammation in patients with acute COVID-19.
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Affiliation(s)
- John F Fullard
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Hao-Chih Lee
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Georgios Voloudakis
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Shengbao Suo
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Behnam Javidfar
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Zhiping Shao
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Cyril Peter
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Wen Zhang
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Shan Jiang
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | | | - Heather Wargnier
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Neuropathology Brain Bank & Research Core, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Emma Woodoff-Leith
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Neuropathology Brain Bank & Research Core, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Dushyant P Purohit
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Sadhna Ahuja
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Nadejda M Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Nathalie Jette
- Department of Neurology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Gabriel E Hoffman
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Mary Fowkes
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - John F Crary
- Department of Pathology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Neuropathology Brain Bank & Research Core, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY, 10029, USA.
- Mental Illness Research Education and Clinical Center (VISN 2 South), James J. Peters VA Medical Center, Bronx, 10468, NY, USA.
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35
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Hu B, Won H, Mah W, Park RB, Kassim B, Spiess K, Kozlenkov A, Crowley CA, Pochareddy S, Li Y, Dracheva S, Sestan N, Akbarian S, Geschwind DH. Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders. Nat Commun 2021; 12:3968. [PMID: 34172755 PMCID: PMC8233376 DOI: 10.1038/s41467-021-24243-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Cellular heterogeneity in the human brain obscures the identification of robust cellular regulatory networks, which is necessary to understand the function of non-coding elements and the impact of non-coding genetic variation. Here we integrate genome-wide chromosome conformation data from purified neurons and glia with transcriptomic and enhancer profiles, to characterize the gene regulatory landscape of two major cell classes in the human brain. We then leverage cell-type-specific regulatory landscapes to gain insight into the cellular etiology of several brain disorders. We find that Alzheimer's disease (AD)-associated epigenetic dysregulation is linked to neurons and oligodendrocytes, whereas genetic risk factors for AD highlighted microglia, suggesting that different cell types may contribute to disease risk, via different mechanisms. Moreover, integration of glutamatergic and GABAergic regulatory maps with genetic risk factors for schizophrenia (SCZ) and bipolar disorder (BD) identifies shared (parvalbumin-expressing interneurons) and distinct cellular etiologies (upper layer neurons for BD, and deeper layer projection neurons for SCZ). Collectively, these findings shed new light on cell-type-specific gene regulatory networks in brain disorders.
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Affiliation(s)
- Benxia Hu
- grid.410711.20000 0001 1034 1720UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA
| | - Hyejung Won
- grid.410711.20000 0001 1034 1720UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA
| | - Won Mah
- grid.410711.20000 0001 1034 1720UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA
| | - Royce B. Park
- grid.59734.3c0000 0001 0670 2351Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Bibi Kassim
- grid.59734.3c0000 0001 0670 2351Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Keeley Spiess
- grid.410711.20000 0001 1034 1720UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC USA
| | - Alexey Kozlenkov
- grid.59734.3c0000 0001 0670 2351Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.274295.f0000 0004 0420 1184James J. Peters VA Medical Center, Bronx, NY USA
| | - Cheynna A. Crowley
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA
| | - Sirisha Pochareddy
- grid.47100.320000000419368710Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT USA
| | | | - Yun Li
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Biostatistics, University of North Carolina, Chapel Hill, NC USA ,grid.410711.20000 0001 1034 1720Computer Science, University of North Carolina, Chapel Hill, NC USA
| | - Stella Dracheva
- grid.59734.3c0000 0001 0670 2351Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.274295.f0000 0004 0420 1184James J. Peters VA Medical Center, Bronx, NY USA
| | - Nenad Sestan
- grid.47100.320000000419368710Department of Psychiatry, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Department of Genetics, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Department of Comparative Medicine, Program in Integrative Cell Signaling and Neurobiology of Metabolism, Yale School of Medicine, New Haven, CT USA ,grid.47100.320000000419368710Program in Cellular Neuroscience, Neurodegeneration, and Repair and Yale Child Study Center, Yale School of Medicine, New Haven, CT USA
| | - Schahram Akbarian
- grid.59734.3c0000 0001 0670 2351Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA ,grid.59734.3c0000 0001 0670 2351Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Daniel H. Geschwind
- grid.19006.3e0000 0000 9632 6718Neurogenetics Program, Department of Neurology, David Geffen School of Medicine University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Department of Human Genetics, David Geffen School of Medicine University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine University of California, Los Angeles, CA USA
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Voloudakis G, Hoffman G, Venkatesh S, Lee KM, Dobrindt K, Vicari JM, Zhang W, Beckmann ND, Jiang S, Hoagland D, Bian J, Gao L, Corvelo A, Cho K, Lee JS, Iyengar SK, Luoh SW, Akbarian S, Striker R, Assimes TL, Schadt EE, Merad M, tenOever BR, Charney AW, Brennand KJ, Lynch JA, Fullard JF, Roussos P. IL10RB as a key regulator of COVID-19 host susceptibility and severity. medRxiv 2021:2021.05.31.21254851. [PMID: 34100031 PMCID: PMC8183086 DOI: 10.1101/2021.05.31.21254851] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND Recent efforts have identified genetic loci that are associated with coronavirus disease 2019 (COVID-19) infection rates and disease outcome severity. Translating these genetic findings into druggable genes and readily available compounds that reduce COVID-19 host susceptibility is a critical next step. METHODS We integrate COVID-19 genetic susceptibility variants, multi-tissue genetically regulated gene expression (GReX) and perturbargen signatures to identify candidate genes and compounds that reverse the predicted gene expression dysregulation associated with COVID-19 susceptibility. The top candidate gene is validated by testing both its GReX and observed blood transcriptome association with COVID-19 severity, as well as by in vitro perturbation to quantify effects on viral load and molecular pathway dysregulation. We validate the in silico drug repositioning analysis by examining whether the top candidate compounds decrease COVID-19 incidence based on epidemiological evidence. RESULTS We identify IL10RB as the top key regulator of COVID-19 host susceptibility. Predicted GReX up-regulation of IL10RB and higher IL10RB expression in COVID-19 patient blood is associated with worse COVID-19 outcomes. In vitro IL10RB overexpression is associated with increased viral load and activation of immune-related molecular pathways. Azathioprine and retinol are prioritized as candidate compounds to reduce the likelihood of testing positive for COVID-19. CONCLUSIONS We establish an integrative data-driven approach for gene target prioritization. We identify and validate IL10RB as a suitable molecular target for modulation of COVID-19 host susceptibility. Finally, we provide evidence for a few readily available medications that would warrant further investigation as drug repositioning candidates.
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Affiliation(s)
- Georgios Voloudakis
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Gabriel Hoffman
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Sanan Venkatesh
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Kyung Min Lee
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Kristina Dobrindt
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - James M Vicari
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Wen Zhang
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Noam D Beckmann
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Shan Jiang
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Daisy Hoagland
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Jiantao Bian
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Lina Gao
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - André Corvelo
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Kelly Cho
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Jennifer S Lee
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Sudha K Iyengar
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Shiuh-Wen Luoh
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Schahram Akbarian
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Robert Striker
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Themistocles L Assimes
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Eric E Schadt
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Miriam Merad
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Benjamin R tenOever
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Alexander W Charney
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Kristen J Brennand
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Julie A Lynch
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - John F Fullard
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
| | - Panos Roussos
- Department of Psychiatry (G.V., S.V., K.D., J.V., W.Z., S.J., S.A., A.W.C., K.J.B., P.R.), Pamela Sklar Division of Psychiatric Genomics (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., A.W.C., J. F.F., K.J.B., P.R.), Friedman Brain Institute (G.V., G.H., S.V., K.D., J.V., W.Z., S.J., S.A., J.F.F., K.J.B., P.R.), Department of Genetics and Genomic Science (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A., E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Icahn Institute for Data Science and Genomic Technology (G.V., G.H., S.V., K.D., J.V., W.Z., N.D.B., S.J., S.A, E.E.S., A.W.C., J.F.F., K.J.B., P.R.), Nash Family Department of Neuroscience (K.D., S.A, A.W.C., K.J.B.), Department of Microbiology (D.H., B.R.T.), Virus Engineering Center for Therapeutics and Research (D.H., B.R.T.), Global Health and Emerging Pathogens Institute (D.H., B.R.T.), Mount Sinai Clinical Intelligence Center (N.D.B., A.W.C.), Department of Oncological Sciences (M.M.), Precision Immunology Institute (M.M.) and Tisch Cancer Institute (M.M.) of the Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; the Mental Illness Research, Education, and Clinical Center (VISN 2 South) of the James J. Peters VA Medical Center (G.V., S.V., P.R.), Bronx, NY 10468, USA; VA Informatics and Computing Infrastructure (K.M.L., J.B., J.A.L.), VA Salt Lake City Health Care System, Salt Lake City, UT; Department of Psychiatry (K.D., K.J.B.) of the Yale University, New Haven, CT 06511, USA; Division of Epidemiology (J.B., J.A.L.), University of Utah, Salt Lake City, UT 84108, USA; New York Genome Center (A.C.), New York, NY 10013, USA; Biostatistics Shared Resources (L.G.) and Department of Medicine (S.-W.L.), Knight Cancer Institute, Oregon Health & Science University, Portland, OR 97229, USA; VA Boston Healthcare System (K.C.), Boston, MA, USA; Division of Aging (K.C.), Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Medicine (J.S.L., T.L.A.), Stanford University School of Medicine, Stanford, CA, 94304, USA; VA Palo Alto Health Care System (J.S.L., T.L.A.), Palo Alto, CA, 94304, USA; Department of Population and Quantitative Health Sciences (S.K.I), and Department of Genetics and Genome Sciences (S.K.I.), School of Medicine, Case Western Reserve University, Cleveland, OH 44106; VA Northeast Ohio Healthcare System (S.K.I.), Cleveland VA Medical Center, Cleveland, OH 44106; VA Portland Health Care System (S.-W.L.), Portland, OR 97239; Division of Infectious Diseases (R.S.), Department of Medicine, University of Wisconsin, Madison, WI; William S. Middleton Memorial Veterans Hospital (R.S.), Madison, WI 53705; and Sema4 (E.E.S.), Stamford, CT 06902, USA
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Espeso-Gil S, Holik AZ, Bonnin S, Jhanwar S, Chandrasekaran S, Pique-Regi R, Albaigès-Ràfols J, Maher M, Permanyer J, Irimia M, Friedländer MR, Pons-Espinal M, Akbarian S, Dierssen M, Maass PG, Hor CN, Ossowski S. Environmental Enrichment Induces Epigenomic and Genome Organization Changes Relevant for Cognition. Front Mol Neurosci 2021; 14:664912. [PMID: 34025350 PMCID: PMC8131874 DOI: 10.3389/fnmol.2021.664912] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 04/09/2021] [Indexed: 01/11/2023] Open
Abstract
In early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the epigenome and genome organization, we used the paradigm of environmental enrichment (EE) in young mice constantly receiving novel stimulation. We profiled epigenome and chromatin architecture in whole cortex and sorted neurons by deep-sequencing techniques. Specifically, we studied chromatin accessibility, gene and protein regulation, and 3D genome conformation, combined with predicted enhancer and chromatin interactions. We identified increased chromatin accessibility, transcription factor binding including CTCF-mediated insulation, differential occupancy of H3K36me3 and H3K79me2, and changes in transcriptional programs required for neuronal development. EE stimuli led to local genome re-organization by inducing increased contacts between chromosomes 7 and 17 (inter-chromosomal). Our findings support the notion that EE-induced learning and memory processes are directly associated with the epigenome and genome organization.
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Affiliation(s)
- Sergio Espeso-Gil
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada
| | - Aliaksei Z. Holik
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sarah Bonnin
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Shalu Jhanwar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sandhya Chandrasekaran
- MD/PhD Program in the Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Júlia Albaigès-Ràfols
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Michael Maher
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jon Permanyer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- ICREA, Pg. Lluis Companys 23, Barcelona, Spain
| | - Marc R. Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Meritxell Pons-Espinal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Schahram Akbarian
- Department of Psychiatry and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Mara Dierssen
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Philipp G. Maass
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Charlotte N. Hor
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
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Palmer RHC, Johnson EC, Won H, Polimanti R, Kapoor M, Chitre A, Bogue MA, Benca‐Bachman CE, Parker CC, Verma A, Reynolds T, Ernst J, Bray M, Kwon SB, Lai D, Quach BC, Gaddis NC, Saba L, Chen H, Hawrylycz M, Zhang S, Zhou Y, Mahaffey S, Fischer C, Sanchez‐Roige S, Bandrowski A, Lu Q, Shen L, Philip V, Gelernter J, Bierut LJ, Hancock DB, Edenberg HJ, Johnson EO, Nestler EJ, Barr PB, Prins P, Smith DJ, Akbarian S, Thorgeirsson T, Walton D, Baker E, Jacobson D, Palmer AA, Miles M, Chesler EJ, Emerson J, Agrawal A, Martone M, Williams RW. Integration of evidence across human and model organism studies: A meeting report. Genes Brain Behav 2021; 20:e12738. [PMID: 33893716 PMCID: PMC8365690 DOI: 10.1111/gbb.12738] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/11/2021] [Accepted: 04/21/2021] [Indexed: 12/13/2022]
Abstract
The National Institute on Drug Abuse and Joint Institute for Biological Sciences at the Oak Ridge National Laboratory hosted a meeting attended by a diverse group of scientists with expertise in substance use disorders (SUDs), computational biology, and FAIR (Findability, Accessibility, Interoperability, and Reusability) data sharing. The meeting's objective was to discuss and evaluate better strategies to integrate genetic, epigenetic, and 'omics data across human and model organisms to achieve deeper mechanistic insight into SUDs. Specific topics were to (a) evaluate the current state of substance use genetics and genomics research and fundamental gaps, (b) identify opportunities and challenges of integration and sharing across species and data types, (c) identify current tools and resources for integration of genetic, epigenetic, and phenotypic data, (d) discuss steps and impediment related to data integration, and (e) outline future steps to support more effective collaboration-particularly between animal model research communities and human genetics and clinical research teams. This review summarizes key facets of this catalytic discussion with a focus on new opportunities and gaps in resources and knowledge on SUDs.
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Affiliation(s)
- Rohan H. C. Palmer
- Behavioral Genetics of Addiction Laboratory, Department of PsychologyEmory UniversityAtlantaGeorgiaUSA
| | - Emma C. Johnson
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Hyejung Won
- Department of Genetics and Neuroscience CenterUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
| | - Renato Polimanti
- Department of PsychiatryYale University School of MedicineWest HavenConnecticutUSA
| | - Manav Kapoor
- Nash Family Department of Neuroscience and Friedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Apurva Chitre
- Department of PsychiatryUniversity of California, San DiegoLa JollaCaliforniaUSA
| | | | - Chelsie E. Benca‐Bachman
- Behavioral Genetics of Addiction Laboratory, Department of PsychologyEmory UniversityAtlantaGeorgiaUSA
| | - Clarissa C. Parker
- Department of Psychology and Program in NeuroscienceMiddlebury CollegeMiddleburyVermontUSA
| | - Anurag Verma
- Biomedical and Translational Informatics LaboratoryUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | | | - Jason Ernst
- Department of Biological ChemistryUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Michael Bray
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Soo Bin Kwon
- Department of Biological ChemistryUniversity of California Los AngelesLos AngelesCaliforniaUSA
| | - Dongbing Lai
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Bryan C. Quach
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology DivisionRTI InternationalResearch Triangle ParkNorth CarolinaUSA
| | - Nathan C. Gaddis
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology DivisionRTI InternationalResearch Triangle ParkNorth CarolinaUSA
| | - Laura Saba
- Department of Pharmaceutical SciencesUniversity of Colorado, Anschutz Medical CampusAuroraColoradoUSA
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and ToxicologyUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | | | - Shan Zhang
- Department of Statistics and ProbabilityMichigan State UniversityEast LansingMichiganUSA
| | - Yuan Zhou
- Department of Department of BiostatisticsUniversity of FloridaGainesvilleFloridaUSA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, School of PharmacyUniversity of Colorado DenverAuroraColoradoUSA
| | - Christian Fischer
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Sandra Sanchez‐Roige
- Department of PsychiatryUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Anita Bandrowski
- Department of NeuroscienceUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Qing Lu
- Department of Department of BiostatisticsUniversity of FloridaGainesvilleFloridaUSA
| | - Li Shen
- Nash Family Department of Neuroscience and Friedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | | | - Joel Gelernter
- Department of PsychiatryYale University School of MedicineWest HavenConnecticutUSA
| | - Laura J. Bierut
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Dana B. Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology DivisionRTI InternationalResearch Triangle ParkNorth CarolinaUSA
| | - Howard J. Edenberg
- Department of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
- Department of Biochemistry and Molecular BiologyIndiana University School of MedicineIndianapolisIndianaUSA
| | - Eric O. Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology DivisionRTI InternationalResearch Triangle ParkNorth CarolinaUSA
| | - Eric J. Nestler
- Nash Family Department of Neuroscience and Friedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Peter B. Barr
- Department of PsychologyVirginia Commonwealth UniversityRichmondVirginiaUSA
| | - Pjotr Prins
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
| | - Desmond J. Smith
- Department of Molecular and Medical PharmacologyDavid Geffen School of Medicine, UCLALos AngelesCaliforniaUSA
| | - Schahram Akbarian
- Friedman Brain Institute and Departments of Psychiatry and NeuroscienceIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | | | | | - Erich Baker
- Department of Computer ScienceBaylor UniversityWacoTexasUSA
| | - Daniel Jacobson
- Computational and Predictive Biology, BiosciencesOak Ridge National LaboratoryOak RidgeTennesseeUSA
- Department of PsychologyUniversity of Tennessee KnoxvilleKnoxvilleTennesseeUSA
| | - Abraham A. Palmer
- Department of PsychiatryUniversity of California, San DiegoLa JollaCaliforniaUSA
- Institute for Genomic Medicine, University of California San DiegoLa JollaCaliforniaUSA
| | - Michael Miles
- Department of Pharmacology and ToxicologyVirginia Commonwealth UniversityRichmondVirginiaUSA
| | | | | | - Arpana Agrawal
- Department of PsychiatryWashington University School of MedicineSt. LouisMissouriUSA
| | - Maryann Martone
- Department of NeuroscienceUniversity of California, San DiegoLa JollaCaliforniaUSA
| | - Robert W. Williams
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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Mussa Z, Tome-Garcia J, Jiang Y, Akbarian S, Tsankova NM. Isolation of Adult Human Astrocyte Populations from Fresh-frozen Cortex using Fluorescence-Activated Nuclei Sorting. J Vis Exp 2021. [PMID: 33938880 DOI: 10.3791/62405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The complexity of human astrocytes remains poorly defined in primary human tissue, requiring better tools for their isolation and molecular characterization. Fluorescence-activated nuclei sorting (FANS) can be used to successfully isolate and study human neuronal nuclei (NeuN+) populations from frozen archival tissue, thereby avoiding problems associated with handling fresh tissue. However, efforts to similarly isolate astroglia from the non-neuronal (NeuN-) element are lacking. A recently developed and validated immunotagging strategy uses three transcription factor antibodies to simultaneously isolate enriched neuronal (NeuN+), astrocyte (paired box protein 6 (PAX6)+NeuN-), and oligodendrocyte progenitor (OLIG2+NeuN-) nuclei populations from non-diseased, fresh (unfixed) snap-frozen postmortem human temporal neocortex tissue. This technique was shown to be useful for the characterization of cell type-specific transcriptome alterations in primary pathological epilepsy neocortex. Transcriptomic analyses confirmed that PAX6+NeuN- sorted populations are robustly enriched for pan-astrocyte markers and capture astrocytes in both resting and reactive conditions. This paper describes the FANS methodology for the isolation of astrocyte-enriched nuclei populations from fresh-frozen human cortex, including tissue dissociation into single-nucleus (sn) suspension; immunotagging of nuclei with anti-NeuN and anti-PAX6 fluorescently conjugated antibodies; FANS gating strategies and quality control metrics for optimizing sensitivity and specificity during sorting and for confirming astrocyte enrichment; and recommended procurement for downstream transcriptome and chromatin accessibility sequencing at bulk or sn resolution. This protocol is applicable for non-necrotic, fresh-frozen, human cortical specimens with various pathologies and recommended postmortem tissue collection within 24 h.
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Affiliation(s)
- Zarmeen Mussa
- Department of Pathology, Icahn School of Medicine at Mount Sinai; Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai
| | - Jessica Tome-Garcia
- Department of Pathology, Icahn School of Medicine at Mount Sinai; Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai
| | - Yan Jiang
- Institutes of Brian Science, Fudan University
| | - Schahram Akbarian
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai; Department of Psychiatry, Icahn School of Medicine at Mount Sinai
| | - Nadejda M Tsankova
- Department of Pathology, Icahn School of Medicine at Mount Sinai; Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai;
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40
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Wang Y, Bae T, Thorpe J, Sherman MA, Jones AG, Cho S, Daily K, Dou Y, Ganz J, Galor A, Lobon I, Pattni R, Rosenbluh C, Tomasi S, Tomasini L, Yang X, Zhou B, Akbarian S, Ball LL, Bizzotto S, Emery SB, Doan R, Fasching L, Jang Y, Juan D, Lizano E, Luquette LJ, Moldovan JB, Narurkar R, Oetjens MT, Rodin RE, Sekar S, Shin JH, Soriano E, Straub RE, Zhou W, Chess A, Gleeson JG, Marquès-Bonet T, Park PJ, Peters MA, Pevsner J, Walsh CA, Weinberger DR, Vaccarino FM, Moran JV, Urban AE, Kidd JM, Mills RE, Abyzov A. Comprehensive identification of somatic nucleotide variants in human brain tissue. Genome Biol 2021; 22:92. [PMID: 33781308 PMCID: PMC8006362 DOI: 10.1186/s13059-021-02285-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/01/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Post-zygotic mutations incurred during DNA replication, DNA repair, and other cellular processes lead to somatic mosaicism. Somatic mosaicism is an established cause of various diseases, including cancers. However, detecting mosaic variants in DNA from non-cancerous somatic tissues poses significant challenges, particularly if the variants only are present in a small fraction of cells. RESULTS Here, the Brain Somatic Mosaicism Network conducts a coordinated, multi-institutional study to examine the ability of existing methods to detect simulated somatic single-nucleotide variants (SNVs) in DNA mixing experiments, generate multiple replicates of whole-genome sequencing data from the dorsolateral prefrontal cortex, other brain regions, dura mater, and dural fibroblasts of a single neurotypical individual, devise strategies to discover somatic SNVs, and apply various approaches to validate somatic SNVs. These efforts lead to the identification of 43 bona fide somatic SNVs that range in variant allele fractions from ~ 0.005 to ~ 0.28. Guided by these results, we devise best practices for calling mosaic SNVs from 250× whole-genome sequencing data in the accessible portion of the human genome that achieve 90% specificity and sensitivity. Finally, we demonstrate that analysis of multiple bulk DNA samples from a single individual allows the reconstruction of early developmental cell lineage trees. CONCLUSIONS This study provides a unified set of best practices to detect somatic SNVs in non-cancerous tissues. The data and methods are freely available to the scientific community and should serve as a guide to assess the contributions of somatic SNVs to neuropsychiatric diseases.
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Affiliation(s)
- Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Taejeong Bae
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jeremy Thorpe
- Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Maxwell A Sherman
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- MIT Department of Electrical Engineering and Computer Science, Cambridge, MA, USA
| | - Attila G Jones
- Department of Cell, Developmental and Regenerative Biology, 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
| | - Sean Cho
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Present Address: Arcus Biosciences, Hayward, CA, 94545, USA
| | | | - Yanmei Dou
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Javier Ganz
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Alon Galor
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Irene Lobon
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
| | - Reenal Pattni
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Chaggai Rosenbluh
- Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Simone Tomasi
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Livia Tomasini
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Xiaoxu Yang
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Bo Zhou
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurel L Ball
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Sara Bizzotto
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ryan Doan
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Liana Fasching
- Child Study Center, Yale University, New Haven, CT, 06520, USA
| | - Yeongjun Jang
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - David Juan
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
| | - Esther Lizano
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
| | - Lovelace J Luquette
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - John B Moldovan
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Rujuta Narurkar
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
| | - Matthew T Oetjens
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Rachel E Rodin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shobana Sekar
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eduardo Soriano
- Department of Cell Biology, Physiology and Immunology, and Institute of Neurosciences, University of Barcelona, 08028, Barcelona, Spain
- Vall d'Hebron Institut de Recerca, 08035, Barcelona, Spain
- Centro de Investigación en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28031, Madrid, Spain
- ICREA Academia, 08010 Barcelona, Spain
| | - Richard E Straub
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Andrew Chess
- Department of Cell, Developmental and Regenerative Biology, 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
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Data Science and Genomic Technologies, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | - Tomas Marquès-Bonet
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), PRBB, 08003, Barcelona, Catalonia, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), 08036, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Barcelona, Spain
| | - Peter J Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA
- Departments of Neurology and Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel R Weinberger
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Lieber Institute for Brain Development, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Flora M Vaccarino
- Child Study Center, Yale University, New Haven, CT, 06520, USA
- Department of Neuroscience, Yale University, New Haven, 06520, CT, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Tashia and John Morgridge Faculty Scholar, Stanford Child Health Research Institute, Stanford, CA, 94305, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Alexej Abyzov
- Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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41
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Dobrindt K, Hoagland DA, Seah C, Kassim B, O'Shea CP, Murphy A, Iskhakova M, Fernando MB, Powell SK, Deans PJM, Javidfar B, Peter C, Møller R, Uhl SA, Garcia MF, Kimura M, Iwasawa K, Crary JF, Kotton DN, Takebe T, Huckins LM, tenOever BR, Akbarian S, Brennand KJ. Common Genetic Variation in Humans Impacts In Vitro Susceptibility to SARS-CoV-2 Infection. Stem Cell Reports 2021; 16:505-518. [PMID: 33636110 PMCID: PMC7881728 DOI: 10.1016/j.stemcr.2021.02.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 01/05/2023] Open
Abstract
The host response to SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, demonstrates significant interindividual variability. In addition to showing more disease in males, the elderly, and individuals with underlying comorbidities, SARS-CoV-2 can seemingly afflict healthy individuals with profound clinical complications. We hypothesize that, in addition to viral load and host antibody repertoire, host genetic variants influence vulnerability to infection. Here we apply human induced pluripotent stem cell (hiPSC)-based models and CRISPR engineering to explore the host genetics of SARS-CoV-2. We demonstrate that a single-nucleotide polymorphism (rs4702), common in the population and located in the 3' UTR of the protease FURIN, influences alveolar and neuron infection by SARS-CoV-2 in vitro. Thus, we provide a proof-of-principle finding that common genetic variation can have an impact on viral infection and thus contribute to clinical heterogeneity in COVID-19. Ongoing genetic studies will help to identify high-risk individuals, predict clinical complications, and facilitate the discovery of drugs.
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Affiliation(s)
- Kristina Dobrindt
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daisy A Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carina Seah
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bibi Kassim
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Callan P O'Shea
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aleta Murphy
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Iskhakova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael B Fernando
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Samuel K Powell
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - P J Michael Deans
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ben Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cyril Peter
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rasmus Møller
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Skyler A Uhl
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA; Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Meilin Fernandez Garcia
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Masaki Kimura
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Center for Stem Cell and Organoid Medicine (CuSTOM), Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Kentaro Iwasawa
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Center for Stem Cell and Organoid Medicine (CuSTOM), Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - John F Crary
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology and Nutrition, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Center for Stem Cell and Organoid Medicine (CuSTOM), Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mental Illness Research, Education and Clinical Centers, James J. Peters Department of Veterans Affairs Medical Center, Bronx, NY 10468, USA
| | - Benjamin R tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Kristen J Brennand
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Dobrindt K, Zhang H, Das D, Abdollahi S, Prorok T, Ghosh S, Weintraub S, Genovese G, Powell SK, Lund A, Akbarian S, Eggan K, McCarroll S, Duan J, Avramopoulos D, Brennand KJ. Publicly Available hiPSC Lines with Extreme Polygenic Risk Scores for Modeling Schizophrenia. Complex Psychiatry 2021; 6:68-82. [PMID: 34883504 PMCID: PMC7923934 DOI: 10.1159/000512716] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/27/2020] [Indexed: 07/23/2023] Open
Abstract
Schizophrenia (SZ) is a common and debilitating psychiatric disorder with limited effective treatment options. Although highly heritable, risk for this polygenic disorder depends on the complex interplay of hundreds of common and rare variants. Translating the growing list of genetic loci significantly associated with disease into medically actionable information remains an important challenge. Thus, establishing platforms with which to validate the impact of risk variants in cell-type-specific and donor-dependent contexts is critical. Towards this, we selected and characterized a collection of 12 human induced pluripotent stem cell (hiPSC) lines derived from control donors with extremely low and high SZ polygenic risk scores (PRS). These hiPSC lines are publicly available at the California Institute for Regenerative Medicine (CIRM). The suitability of these extreme PRS hiPSCs for CRISPR-based isogenic comparisons of neurons and glia was evaluated across 3 independent laboratories, identifying 9 out of 12 meeting our criteria. We report a standardized resource of publicly available hiPSCs on which we hope to perform genome engineering and generate diverse kinds of functional data, with comparisons across studies facilitated by the use of a common set of genetic backgrounds.
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Affiliation(s)
- Kristina Dobrindt
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Hanwen Zhang
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Debamitra Das
- Department of Genetic Medicine and Psychiatry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Sara Abdollahi
- Department of Genetic Medicine and Psychiatry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Tim Prorok
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Sulagna Ghosh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Sarah Weintraub
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Samuel K. Powell
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Anina Lund
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kevin Eggan
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Steven McCarroll
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jubao Duan
- Center for Psychiatric Genetics, NorthShore University HealthSystem, Evanston, Illinois, USA
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, Illinois, USA
| | - Dimitrios Avramopoulos
- Department of Genetic Medicine and Psychiatry, Johns Hopkins University, Baltimore, Maryland, USA
| | - Kristen J. Brennand
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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43
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Powell SK, O'Shea C, Brennand KJ, Akbarian S. Parsing the Functional Impact of Noncoding Genetic Variants in the Brain Epigenome. Biol Psychiatry 2021; 89:65-75. [PMID: 33131715 PMCID: PMC7718420 DOI: 10.1016/j.biopsych.2020.06.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022]
Abstract
The heritability of common psychiatric disorders has motivated global efforts to identify risk-associated genetic variants and elucidate molecular pathways connecting DNA sequence to disease-associated brain dysfunction. The overrepresentation of risk variants among gene regulatory loci instead of protein-coding loci, however, poses a unique challenge in discerning which among the many thousands of variants identified contribute functionally to disease etiology. Defined broadly, psychiatric epigenomics seeks to understand the effects of disease-associated genetic variation on functional readouts of chromatin in an effort to prioritize variants in terms of their impact on gene expression in the brain. Here, we provide an overview of epigenomic mapping in the human brain and highlight findings of particular relevance to psychiatric genetics. Computational methods, including convolutional neuronal networks, and other machine learning approaches hold great promise for elucidating the functional impact of both common and rare genetic variants, thereby refining the epigenomic architecture of psychiatric disorders and enabling integrative analyses of regulatory noncoding variants in the context of large population-level genome and phenome databases.
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Affiliation(s)
- Samuel K Powell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Callan O'Shea
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
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44
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Bicks LK, Peng M, Taub A, Akbarian S, Morishita H. An Adolescent Sensitive Period for Social Dominance Hierarchy Plasticity Is Regulated by Cortical Plasticity Modulators in Mice. Front Neural Circuits 2021; 15:676308. [PMID: 34054438 PMCID: PMC8149998 DOI: 10.3389/fncir.2021.676308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 04/19/2021] [Indexed: 01/08/2023] Open
Abstract
Social dominance hierarchies are a common adaptation to group living and exist across a broad range of the animal kingdom. Social dominance is known to rely on the prefrontal cortex (PFC), a brain region that shows a protracted developmental trajectory in mice. However, it is unknown to what extent the social dominance hierarchy is plastic across postnatal development and how it is regulated. Here we identified a sensitive period for experience-dependent social dominance plasticity in adolescent male mice, which is regulated by mechanisms that affect cortical plasticity. We show that social dominance hierarchies in male mice are already formed at weaning and are highly stable into adulthood. However, one experience of forced losing significantly reduces social dominance during the adolescent period but not in adulthood, suggesting adolescence as a sensitive period for experience-dependent social dominance plasticity. Notably, robust adolescent plasticity can be prolonged into adulthood by genetic deletion of Lynx1, a molecular brake that normally limits cortical plasticity through modulation of cortical nicotinic signaling. This plasticity is associated with increased activation of established nodes of the social dominance network including dorsal medial PFC and medial dorsal thalamus evidenced by increased c-Fos. Pharmacologically mediated elevation of cortical plasticity by valproic acid rapidly destabilizes the hierarchy of adult wildtype animals. These findings provide insight into mechanisms through which increased behavioral plasticity may be achieved to improve therapeutic recovery from psychiatric disorders that are associated with social deficits.
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Affiliation(s)
- Lucy K Bicks
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Michelle Peng
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Alana Taub
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Hirofumi Morishita
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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45
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Dobrindt K, Hoagland DA, Seah C, Kassim B, O’Shea CP, Iskhakova M, Fernando MB, Deans PM, Powell SK, Javidfar B, Murphy A, Peter C, Møeller R, Garcia MF, Kimura M, Iwasawa K, Crary J, Kotton DN, Takebe T, Huckins LM, tenOever BR, Akbarian S, Brennand KJ. Common genetic variation in humans impacts in vitro susceptibility to SARS-CoV-2 infection. bioRxiv 2020:2020.09.20.300574. [PMID: 32995783 PMCID: PMC7523109 DOI: 10.1101/2020.09.20.300574] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The host response to SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, demonstrates significant inter-individual variability. In addition to showing more disease in males, the elderly, and individuals with underlying comorbidities, SARS-CoV-2 can seemingly render healthy individuals with profound clinical complications. We hypothesize that, in addition to viral load and host antibody repertoire, host genetic variants also impact vulnerability to infection. Here we apply human induced pluripotent stem cell (hiPSC)-based models and CRISPR-engineering to explore the host genetics of SARS-CoV-2. We demonstrate that a single nucleotide polymorphism (rs4702), common in the population at large, and located in the 3'UTR of the protease FURIN, impacts alveolar and neuron infection by SARS-CoV-2 in vitro. Thus, we provide a proof-of-principle finding that common genetic variation can impact viral infection, and thus contribute to clinical heterogeneity in SARS-CoV-2. Ongoing genetic studies will help to better identify high-risk individuals, predict clinical complications, and facilitate the discovery of drugs that might treat disease.
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Affiliation(s)
- Kristina Dobrindt
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Daisy A. Hoagland
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Carina Seah
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Bibi Kassim
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Callan P. O’Shea
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Marina Iskhakova
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Michael B. Fernando
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - P.J. Michael Deans
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Samuel K. Powell
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ben Javidfar
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Aleta Murphy
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Cyril Peter
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Rasmus Møeller
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Meilin Fernandez Garcia
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Masaki Kimura
- Division of Gastroenterology, Hepatology and Nutrition; Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center; Center for Stem Cell and Organoid Medicine (CuSTOM); Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Kentaro Iwasawa
- Division of Gastroenterology, Hepatology and Nutrition; Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center; Center for Stem Cell and Organoid Medicine (CuSTOM); Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - John Crary
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA
| | - Takanori Takebe
- Division of Gastroenterology, Hepatology and Nutrition; Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center; Center for Stem Cell and Organoid Medicine (CuSTOM); Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States; Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Laura M. Huckins
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Mental Illness Research, Education and Clinical Centers, James J. Peters Department of Veterans Affairs Medical Center, Bronx, NY 10468, USA
| | - Benjamin R. tenOever
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
| | - Schahram Akbarian
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kristen J. Brennand
- Pamela Sklar Division of Psychiatric Genomics, Department of Genetics and Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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Akbarian S. Epigenetic Clocks in Schizophrenia: Promising Biomarkers, Foggy Clockwork. Biol Psychiatry 2020; 88:210-211. [PMID: 32674842 DOI: 10.1016/j.biopsych.2020.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Schahram Akbarian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York.
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47
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Rabin R, Radmanesh A, Glass IA, Dobyns WB, Aldinger KA, Shieh JT, Romoser S, Bombei H, Dowsett L, Trapane P, Bernat JA, Baker J, Mendelsohn NJ, Popp B, Siekmeyer M, Sorge I, Sansbury FH, Watts P, Foulds NC, Burton J, Hoganson G, Hurst JA, Menzies L, Osio D, Kerecuk L, Cobben JM, Jizi K, Jacquemont S, Bélanger SA, Löhner K, Veenstra-Knol HE, Lemmink HH, Keller-Ramey J, Wentzensen IM, Punj S, McWalter K, Lenberg J, Ellsworth KA, Radtke K, Akbarian S, Pappas J. Genotype-phenotype correlation at codon 1740 of SETD2. Am J Med Genet A 2020; 182:2037-2048. [PMID: 32710489 DOI: 10.1002/ajmg.a.61724] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/10/2020] [Accepted: 05/08/2020] [Indexed: 11/06/2022]
Abstract
The SET domain containing 2, histone lysine methyltransferase encoded by SETD2 is a dual-function methyltransferase for histones and microtubules and plays an important role for transcriptional regulation, genomic stability, and cytoskeletal functions. Specifically, SETD2 is associated with trimethylation of histone H3 at lysine 36 (H3K36me3) and methylation of α-tubulin at lysine 40. Heterozygous loss of function and missense variants have previously been described with Luscan-Lumish syndrome (LLS), which is characterized by overgrowth, neurodevelopmental features, and absence of overt congenital anomalies. We have identified 15 individuals with de novo variants in codon 1740 of SETD2 whose features differ from those with LLS. Group 1 consists of 12 individuals with heterozygous variant c.5218C>T p.(Arg1740Trp) and Group 2 consists of 3 individuals with heterozygous variant c.5219G>A p.(Arg1740Gln). The phenotype of Group 1 includes microcephaly, profound intellectual disability, congenital anomalies affecting several organ systems, and similar facial features. Individuals in Group 2 had moderate to severe intellectual disability, low normal head circumference, and absence of additional major congenital anomalies. While LLS is likely due to loss of function of SETD2, the clinical features seen in individuals with variants affecting codon 1740 are more severe suggesting an alternative mechanism, such as gain of function, effects on epigenetic regulation, or posttranslational modification of the cytoskeleton. Our report is a prime example of different mutations in the same gene causing diverging phenotypes and the features observed in Group 1 suggest a new clinically recognizable syndrome uniquely associated with the heterozygous variant c.5218C>T p.(Arg1740Trp) in SETD2.
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Affiliation(s)
- Rachel Rabin
- Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, New York, USA
| | - Alireza Radmanesh
- Division of Pediatric Neuroradiology, Department of Radiology, NYU School of Medicine, New York, New York, USA
| | - Ian A Glass
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA.,Department of Pediatrics, Division of Medical Genetics, University of Washington, Seattle, Washington, USA.,Department of Neurology, University of Washington, Seattle, Washington, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Joseph T Shieh
- Institute for Human Genetics, Division of Medical Genetics, Department of Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, California, USA
| | - Shelby Romoser
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Hannah Bombei
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Leah Dowsett
- Kapi'olani Medical Specialists and Department of Pediatrics, University of Hawai'i John A. Burns School of Medicine, Honolulu, Hawaii, USA
| | - Pamela Trapane
- Division of Pediatric Genetics, Department of Pediatrics, University of Florida College of Medicine-Jacksonville, Jacksonville, Florida, USA
| | - John A Bernat
- Division of Medical Genetics and Genomics, Stead Family Department of Pediatrics, University of Iowa Hospitals, Iowa City, Iowa, USA
| | - Janice Baker
- Genomic Medicine, Children's Minnesota, Minneapolis, Minnesota, USA
| | | | - Bernt Popp
- Institute of Human Genetics, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Manuela Siekmeyer
- Department of Pediatrics Hospital for Children and Adolescents, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Ina Sorge
- Department of Pediatric Radiology, University of Leipzig Hospitals and Clinics, Leipzig, Germany
| | - Francis Hugh Sansbury
- All Wales Medical Genomics Service, Institute of Medical Genetics, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Patrick Watts
- Department of Ophthalmology, Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - Nicola C Foulds
- Wessex Clinical Genetics Services, Southampton University Hospital NHS Foundation Trust, Southampton, UK
| | - Jennifer Burton
- University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - George Hoganson
- University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - Jane A Hurst
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Lara Menzies
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Deborah Osio
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Larissa Kerecuk
- Renal Department, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Jan M Cobben
- North West Thames Regional Genetic Services, Northwick Park Hospitals NHS Foundation Trust, London, UK.,Emma Children Hospital, Amsterdam, The Netherlands
| | - Khadijé Jizi
- CHU Sainte-Justine Hospital, Montreal, Quebec, Canada
| | - Sebastien Jacquemont
- CHU Sainte-Justine Research Centre, Montreal, Quebec, Canada.,Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
| | - Stacey A Bélanger
- Development Clinic, CHU Sainte-Justine Hospital, Montreal, Quebec, Canada.,Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Katharina Löhner
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Hermine E Veenstra-Knol
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Henny H Lemmink
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | | | | | | | - Jerica Lenberg
- Rady Children's Hospital Institute for Genomic Medicine, San Diego, California, USA
| | | | - Kelly Radtke
- Department of Clinical Diagnostics, Ambry Genetics, Aliso Viejo, California, USA
| | - Schahram Akbarian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - John Pappas
- Clinical Genetic Services, Department of Pediatrics, NYU School of Medicine, New York, New York, USA.,Clinical Genetics, NYU Orthopedic Hospital, New York, New York, USA
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48
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Powell SK, O'Shea CP, Shannon SR, Akbarian S, Brennand KJ. Investigation of Schizophrenia with Human Induced Pluripotent Stem Cells. Adv Neurobiol 2020; 25:155-206. [PMID: 32578147 DOI: 10.1007/978-3-030-45493-7_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Schizophrenia is a chronic and severe neuropsychiatric condition manifested by cognitive, emotional, affective, perceptual, and behavioral abnormalities. Despite decades of research, the biological substrates driving the signs and symptoms of the disorder remain elusive, thus hampering progress in the development of treatments aimed at disease etiologies. The recent emergence of human induced pluripotent stem cell (hiPSC)-based models has provided the field with a highly innovative approach to generate, study, and manipulate living neural tissue derived from patients, making possible the exploration of fundamental roles of genes and early-life stressors in disease-relevant cell types. Here, we begin with a brief overview of the clinical, epidemiological, and genetic aspects of the condition, with a focus on schizophrenia as a neurodevelopmental disorder. We then highlight relevant technical advancements in hiPSC models and assess novel findings attained using hiPSC-based approaches and their implications for disease biology and treatment innovation. We close with a critical appraisal of the developments necessary for both further expanding knowledge of schizophrenia and the translation of new insights into therapeutic innovations.
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Affiliation(s)
- Samuel K Powell
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Callan P O'Shea
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sara Rose Shannon
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Schahram Akbarian
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen J Brennand
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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49
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Abstract
Schizophrenia is a debilitating psychiatric disorder with a complex genetic architecture and limited understanding of its neuropathology, reflected by the lack of diagnostic measures and effective pharmacological treatments. Geneticists have recently identified more than 145 risk loci comprising hundreds of common variants of small effect sizes, most of which lie in noncoding genomic regions. This review will discuss how the epigenetic toolbox can be applied to contextualize genetic findings in schizophrenia. Progress in next-generation sequencing, along with increasing methodological complexity, has led to the compilation of genome-wide maps of DNA methylation, histone modifications, RNA expression, and more. Integration of chromatin conformation datasets is one of the latest efforts in deciphering schizophrenia risk, allowing the identification of genes in contact with regulatory variants across 100s of kilobases. Large-scale multiomics studies will facilitate the prioritization of putative causal risk variants and gene networks that contribute to schizophrenia etiology, informing clinical diagnostics and treatment downstream.
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Affiliation(s)
- Prashanth Rajarajan
- Graduate School of Biomedical Sciences; Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai, New York, NY, US
| | - Schahram Akbarian
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai, New York, NY, US
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50
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Serafini RA, Sakloth F, Pryce K, Bertherat F, Akbarian S, Zachariou V. MEF2C Mediates Chronic Pain in Rodent Neuropathy Models. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.02107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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