1
|
Marques D, Vaziri N, Greenway SC, Bousman C. DNA methylation and histone modifications associated with antipsychotic treatment: a systematic review. Mol Psychiatry 2024:10.1038/s41380-024-02735-x. [PMID: 39227433 DOI: 10.1038/s41380-024-02735-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 08/21/2024] [Accepted: 08/28/2024] [Indexed: 09/05/2024]
Abstract
Antipsychotic medications are essential when treating schizophrenia spectrum and other psychotic disorders, but the efficacy and tolerability of these medications vary from person to person. This interindividual variation is likely mediated, at least in part, by epigenomic processes that have yet to be fully elucidated. Herein, we systematically identified and evaluated 65 studies that examine the influence of antipsychotic drugs on epigenomic changes, including global methylation (9 studies), genome-wide methylation (22 studies), candidate gene methylation (16 studies), and histone modification (18 studies). Our evaluation revealed that haloperidol was consistently associated with increased global hypermethylation, which corroborates with genome-wide analyses, mostly performed by methylation arrays. In contrast, clozapine seems to promote hypomethylation across the epigenome. Candidate-gene methylation studies reveal varying effects post-antipsychotic therapy. Some genes like Glra1 and Drd2 are frequently found to undergo hypermethylation, whereas other genes such as SLC6A4, DUSP6, and DTNBP1 are more likely to exhibit hypomethylation in promoter regions. In examining histone modifications, the literature suggests that clozapine changes histone methylation patterns in the prefrontal cortex, particularly elevating H3K4me3 at the Gad1 gene and affecting the transcription of genes like mGlu2 by modifying histone acetylation and interacting with HDAC2 enzymes. Risperidone and quetiapine, however, exhibit distinct impacts on histone marks across different brain regions and cell types, with risperidone reducing H3K27ac in the striatum and quetiapine modifying global H3K9me2 levels in the prefrontal cortex, suggesting antipsychotics demonstrate selective influence on histone modifications, which demonstrates a complex and targeted mode of action. While this review summarizes current knowledge, the intricate dynamics between antipsychotics and epigenetics clearly warrant more exhaustive exploration with the potential to redefine our understanding and treatment of psychiatric conditions. By deciphering the epigenetic changes associated with drug treatment and therapeutic outcomes, we can move closer to personalized medicine in psychiatry.
Collapse
Affiliation(s)
- Diogo Marques
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Nazanin Vaziri
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Steven C Greenway
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cardiac Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Chad Bousman
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| |
Collapse
|
2
|
Patel A, Dharap A. An Emerging Role for Enhancer RNAs in Brain Disorders. Neuromolecular Med 2024; 26:7. [PMID: 38546891 PMCID: PMC11263973 DOI: 10.1007/s12017-024-08776-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 04/02/2024]
Abstract
Noncoding DNA undergoes widespread context-dependent transcription to produce noncoding RNAs. In recent decades, tremendous advances in genomics and transcriptomics have revealed important regulatory roles for noncoding DNA elements and the RNAs that they produce. Enhancers are one such element that are well-established drivers of gene expression changes in response to a variety of factors such as external stimuli, cellular responses, developmental cues, and disease states. They are known to act at long distances, interact with multiple target gene loci simultaneously, synergize with other enhancers, and associate with dynamic chromatin architectures to form a complex regulatory network. Recent advances in enhancer biology have revealed that upon activation, enhancers transcribe long noncoding RNAs, known as enhancer RNAs (eRNAs), that have been shown to play important roles in enhancer-mediated gene regulation and chromatin-modifying activities. In the brain, enhancer dysregulation and eRNA transcription has been reported in numerous disorders from acute injuries to chronic neurodegeneration. Because this is an emerging area, a comprehensive understanding of eRNA function has not yet been achieved in brain disorders; however, the findings to date have illuminated a role for eRNAs in activity-driven gene expression and phenotypic outcomes. In this review, we highlight the breadth of the current literature on eRNA biology in brain health and disease and discuss the challenges as well as focus areas and strategies for future in-depth research on eRNAs in brain health and disease.
Collapse
Affiliation(s)
- Ankit Patel
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
- Byrd Alzheimer's Center & Research Institute, USF Health Neuroscience Institute, Tampa, FL, USA
| | - Ashutosh Dharap
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA.
- Byrd Alzheimer's Center & Research Institute, USF Health Neuroscience Institute, Tampa, FL, USA.
| |
Collapse
|
3
|
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] [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.
Collapse
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.
| |
Collapse
|
4
|
Gillespie B, Panthi S, Sundram S, Hill RA. The impact of maternal immune activation on GABAergic interneuron development: A systematic review of rodent studies and their translational implications. Neurosci Biobehav Rev 2024; 156:105488. [PMID: 38042358 DOI: 10.1016/j.neubiorev.2023.105488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
Mothers exposed to infections during pregnancy disproportionally birth children who develop autism and schizophrenia, disorders associated with altered GABAergic function. The maternal immune activation (MIA) model recapitulates this risk factor, with many studies also reporting disruptions to GABAergic interneuron expression, protein, cellular density and function. However, it is unclear if there are species, sex, age, region, or GABAergic subtype specific vulnerabilities to MIA. Furthermore, to fully comprehend the impact of MIA on the GABAergic system a synthesised account of molecular, cellular, electrophysiological and behavioural findings was required. To this end we conducted a systematic review of GABAergic interneuron changes in the MIA model, focusing on the prefrontal cortex and hippocampus. We reviewed 102 articles that revealed robust changes in a number of GABAergic markers that present as gestationally-specific, region-specific and sometimes sex-specific. Disruptions to GABAergic markers coincided with distinct behavioural phenotypes, including memory, sensorimotor gating, anxiety, and sociability. Findings suggest the MIA model is a valid tool for testing novel therapeutics designed to recover GABAergic function and associated behaviour.
Collapse
Affiliation(s)
- Brendan Gillespie
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Sandesh Panthi
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Suresh Sundram
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Rachel A Hill
- Department of Psychiatry, School of Clinical Sciences, Monash University, Clayton, VIC 3168, Australia.
| |
Collapse
|
5
|
Wu T, Cai W, Chen X. Epigenetic regulation of neurotransmitter signaling in neurological disorders. Neurobiol Dis 2023; 184:106232. [PMID: 37479091 DOI: 10.1016/j.nbd.2023.106232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/09/2023] [Accepted: 07/16/2023] [Indexed: 07/23/2023] Open
Abstract
Neurotransmission signaling is a highly conserved system attributed to various regulatory events. The excitatory and inhibitory neurotransmitter systems have been extensively studied, and their role in neuronal cell proliferation, synaptogenesis and dendrite formation in the adult brain is well established. Recent research has shown that epigenetic regulation plays a crucial role in mediating the expression of key genes associated with neurotransmitter pathways, including neurotransmitter receptor and transporter genes. The dysregulation of these genes has been linked to a range of neurological disorders such as attention-deficit/hyperactivity disorder, Parkinson's disease and schizophrenia. This article focuses on epigenetic regulatory mechanisms that control the expression of genes associated with four major chemical carriers in the brain: dopamine (DA), Gamma-aminobutyric acid (GABA), glutamate and serotonin. Additionally, we explore how aberrant epigenetic regulation of these genes can contribute to the pathogenesis of relevant neurological disorders. By targeting the epigenetic mechanisms that control neurotransmitter gene expression, there is a promising opportunity to advance the development of more effective treatments for neurological disorders with the potential to significantly improve the quality of life of individuals impacted by these conditions.
Collapse
Affiliation(s)
- Tingyan Wu
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China; Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China
| | - Weili Cai
- School of Medical Technology, Jiangsu College of Nursing, Huai'an 22305, China.
| | - Xi Chen
- Institute of Neurology, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 610072, China; Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, China.
| |
Collapse
|
6
|
Silveira PP, Meaney MJ. Examining the biological mechanisms of human mental disorders resulting from gene-environment interdependence using novel functional genomic approaches. Neurobiol Dis 2023; 178:106008. [PMID: 36690304 DOI: 10.1016/j.nbd.2023.106008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/30/2022] [Accepted: 01/18/2023] [Indexed: 01/21/2023] Open
Abstract
We explore how functional genomics approaches that integrate datasets from human and non-human model systems can improve our understanding of the effect of gene-environment interplay on the risk for mental disorders. We start by briefly defining the G-E paradigm and its challenges and then discuss the different levels of regulation of gene expression and the corresponding data existing in humans (genome wide genotyping, transcriptomics, DNA methylation, chromatin modifications, chromosome conformational changes, non-coding RNAs, proteomics and metabolomics), discussing novel approaches to the application of these data in the study of the origins of mental health. Finally, we discuss the multilevel integration of diverse types of data. Advance in the use of functional genomics in the context of a G-E perspective improves the detection of vulnerabilities, informing the development of preventive and therapeutic interventions.
Collapse
Affiliation(s)
- Patrícia Pelufo Silveira
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Ludmer Centre for Neuroinformatics and Mental Health, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada.
| | - Michael J Meaney
- Department of Psychiatry, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada; Translational Neuroscience Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (ASTAR), Singapore; Brain - Body Initiative, Agency for Science, Technology and Research (ASTAR), Singapore.
| |
Collapse
|
7
|
Girdhar K, Rahman S, Dong P, Fullard JF, Roussos P. The Neuroepigenome: Implications of Chemical and Physical Modifications of Genomic DNA in Schizophrenia. Biol Psychiatry 2022; 92:443-449. [PMID: 35750513 DOI: 10.1016/j.biopsych.2022.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/14/2022] [Accepted: 04/27/2022] [Indexed: 11/02/2022]
Abstract
Schizophrenia is a chronic mental illness with a substantial genetic component. To unfold the complex etiology of schizophrenia, it is important to understand the interplay between genetic and nongenetic factors. Genetic factors involve variation in the DNA sequences of protein-coding genes, which directly contribute to phenotypic traits, and variation in noncoding sequences, which comprise 98% of the genome and contain DNA elements known to play a role in regulating gene expression. The epigenome refers to the chemical modifications on both DNA and the structural proteins that package DNA into the nucleus, which together regulate gene expression in specific cell types, conditions, and developmental stages. The dynamic nature of the epigenome makes it an ideal tool to investigate the relationship between inherited genetic mutations associated with schizophrenia and altered gene regulation throughout the course of brain development. In this review, we focus on the current understanding of the role of epigenetic marks and their three-dimensional nuclear organization in the developmental trajectory of distinct brain cell types to decipher the complex gene regulatory mechanisms that are disrupted in schizophrenia.
Collapse
Affiliation(s)
- Kiran Girdhar
- Center for Disease Neurogenomics, 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; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Samir Rahman
- Center for Disease Neurogenomics, 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; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Pengfei Dong
- Center for Disease Neurogenomics, 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; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - John F Fullard
- Center for Disease Neurogenomics, 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; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Panos Roussos
- Center for Disease Neurogenomics, 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; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, New York; Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, New York; Mental Illness Research Education and Clinical Center, James J. Peters VA Medical Center, Bronx, New York.
| |
Collapse
|
8
|
Chawla A, Nagy C, Turecki G. Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits. Int J Mol Sci 2021; 22:7612. [PMID: 34299232 PMCID: PMC8305586 DOI: 10.3390/ijms22147612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 01/04/2023] Open
Abstract
The genetic architecture of complex traits is multifactorial. Genome-wide association studies (GWASs) have identified risk loci for complex traits and diseases that are disproportionately located at the non-coding regions of the genome. On the other hand, we have just begun to understand the regulatory roles of the non-coding genome, making it challenging to precisely interpret the functions of non-coding variants associated with complex diseases. Additionally, the epigenome plays an active role in mediating cellular responses to fluctuations of sensory or environmental stimuli. However, it remains unclear how exactly non-coding elements associate with epigenetic modifications to regulate gene expression changes and mediate phenotypic outcomes. Therefore, finer interrogations of the human epigenomic landscape in associating with non-coding variants are warranted. Recently, chromatin-profiling techniques have vastly improved our understanding of the numerous functions mediated by the epigenome and DNA structure. Here, we review various chromatin-profiling techniques, such as assays of chromatin accessibility, nucleosome distribution, histone modifications, and chromatin topology, and discuss their applications in unraveling the brain epigenome and etiology of complex traits at tissue homogenate and single-cell resolution. These techniques have elucidated compositional and structural organizing principles of the chromatin environment. Taken together, we believe that high-resolution epigenomic and DNA structure profiling will be one of the best ways to elucidate how non-coding genetic variations impact complex diseases, ultimately allowing us to pinpoint cell-type targets with therapeutic potential.
Collapse
Affiliation(s)
- Anjali Chawla
- Integrated Program in Neuroscience, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada;
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
| | - Corina Nagy
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
- Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada
| | - Gustavo Turecki
- Integrated Program in Neuroscience, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada;
- McGill Group for Suicide Studies, Department of Psychiatry, Douglas Mental Health University Institute, McGill University, 6875 LaSalle Blvd, Verdun, QC H4H 1R3, Canada;
- Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, 845 Sherbrooke St W, Montreal, QC H3A 0G4, Canada
| |
Collapse
|
9
|
Zhang L, Li Z, Liu Q, Shao M, Sun F, Su X, Song M, Zhang Y, Ding M, Lu Y, Liu J, Yang Y, Li M, Li W, Lv L. Weak Association Between the Glutamate Decarboxylase 1 Gene (GAD1) and Schizophrenia in Han Chinese Population. Front Neurosci 2021; 15:677153. [PMID: 34234640 PMCID: PMC8255988 DOI: 10.3389/fnins.2021.677153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/26/2021] [Indexed: 11/15/2022] Open
Abstract
Objectives Schizophrenia (SZ) is a complex psychiatric disorder with high heritability, and genetic components are thought to be pivotal risk factors for this illness. The glutamate decarboxylase 1 gene (GAD1) was hypothesized to be a candidate risk locus for SZ given its crucial role in the GABAergic neurotransmission system, and previous studies have examined the associations of single nucleotide polymorphisms (SNPs) spanning the GAD1 gene with SZ. However, inconsistent results were obtained. We hence examined the associations between GAD1 SNPs and SZ in two independent case-control samples of Han Chinese ancestry. Materials and Methods Two Han Chinese SZ case-control samples, referred as the discovery sample and the replication sample, respectively, were recruited for the current study. The discovery sample comprised of 528 paranoid SZ cases (with age of first onset ≥ 18) and 528 healthy controls; the independent replication sample contained 1,256 early onset SZ cases (with age of first onset < 18) and 2,661 healthy controls. Logistic regression analysis was performed to examine the associations between GAD1 SNPs and SZ. Results Ten SNPs covering GAD1 gene were analyzed in the discovery sample, and two SNPs showed nominal associations with SZ (rs2241165, P = 0.0181, OR = 1.261; rs2241164, P = 0.0225, OR = 1.219). SNP rs2241164 was also nominally significant in the independent replication sample (P = 0.0462, OR = 1.110), and the significance became stronger in a subsequent meta-analysis combining both discovery and replication samples (P = 0.00398, OR = 1.138). Nevertheless, such association could not survive multiple corrections, although the effect size of rs2241164 was comparable with other SZ risk loci identified in genome-wide association studies (GWAS) in Han Chinese population. We also examined the associations between GAD1 SNPs and SZ in published datasets of SZ GWAS in East Asians and Europeans, and no significant associations were observed. Conclusion We observed weak associations between GAD1 SNPs and risk of SZ in Han Chinese populations. Further analyses in larger Han Chinese samples with more detailed phenotyping are necessary to elucidate the genetic correlation between GAD1 SNPs and SZ.
Collapse
Affiliation(s)
- Luwen Zhang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Zhen Li
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Qing Liu
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Minglong Shao
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Fuping Sun
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Xi Su
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Meng Song
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Yan Zhang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Minli Ding
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Yanli Lu
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yongfeng Yang
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Ming Li
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wenqiang Li
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China
| | - Luxian Lv
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, China.,Henan Key Lab of Biological Psychiatry, Xinxiang Medical University, Xinxiang, China.,International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang, China.,Henan Province People's Hospital, Zhengzhou, China
| |
Collapse
|
10
|
Richetto J, Meyer U. Epigenetic Modifications in Schizophrenia and Related Disorders: Molecular Scars of Environmental Exposures and Source of Phenotypic Variability. Biol Psychiatry 2021; 89:215-226. [PMID: 32381277 DOI: 10.1016/j.biopsych.2020.03.008] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/19/2020] [Accepted: 03/16/2020] [Indexed: 12/18/2022]
Abstract
Epigenetic modifications are increasingly recognized to play a role in the etiology and pathophysiology of schizophrenia and other psychiatric disorders with developmental origins. Here, we summarize clinical and preclinical findings of epigenetic alterations in schizophrenia and relevant disease models and discuss their putative origin. Recent findings suggest that certain schizophrenia risk loci can influence stochastic variation in gene expression through epigenetic processes, highlighting the intricate interaction between genetic and epigenetic control of neurodevelopmental trajectories. In addition, a substantial portion of epigenetic alterations in schizophrenia and related disorders may be acquired through environmental factors and may be manifested as molecular "scars." Some of these scars can influence brain functions throughout the entire lifespan and may even be transmitted across generations via epigenetic germline inheritance. Epigenetic modifications, whether caused by genetic or environmental factors, are plausible molecular sources of phenotypic heterogeneity and offer a target for therapeutic interventions. The further elucidation of epigenetic modifications thus may increase our knowledge regarding schizophrenia's heterogeneous etiology and pathophysiology and, in the long term, may advance personalized treatments through the use of biomarker-guided epigenetic interventions.
Collapse
Affiliation(s)
- Juliet Richetto
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, and Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.
| | - Urs Meyer
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, and Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
| |
Collapse
|
11
|
Powell SK, O'Shea CP, Shannon SR, Akbarian S, Brennand KJ. Investigation of Schizophrenia with Human Induced Pluripotent Stem Cells. ADVANCES IN NEUROBIOLOGY 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] [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.
Collapse
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.
| |
Collapse
|
12
|
Rajarajan P, Borrman T, Liao W, Espeso-Gil S, Chandrasekaran S, Jiang Y, Weng Z, Brennand KJ, Akbarian S. Spatial genome exploration in the context of cognitive and neurological disease. Curr Opin Neurobiol 2019; 59:112-119. [PMID: 31255842 PMCID: PMC6889018 DOI: 10.1016/j.conb.2019.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/24/2019] [Accepted: 05/28/2019] [Indexed: 01/01/2023]
Abstract
The 'non-linear' genome, or the spatial proximity of non-contiguous sequences, emerges as an important regulatory layer for genome organization and function, including transcriptional regulation. Here, we review recent genome-scale chromosome conformation mappings ('Hi-C') in developing and adult human and mouse brain. Neural differentiation is associated with widespread remodeling of the chromosomal contact map, reflecting dynamic changes in cell-type-specific gene expression programs, with a massive (estimated 20-50%) net loss of chromosomal contacts that is specific for the neuronal lineage. Hi-C datasets provided an unexpected link between locus-specific abnormal expansion of repeat sequences positioned at the boundaries of self-associating topological chromatin domains, and monogenic neurodevelopmental and neurodegenerative disease. Furthermore, integrative cell-type-specific Hi-C and transcriptomic analysis uncovered an expanded genomic risk space for sequences conferring liability for schizophrenia and other cognitive disease. We predict that spatial genome exploration will deliver radically new insights into the brain nucleome in health and disease.
Collapse
Affiliation(s)
- Prashanth Rajarajan
- Icahn School of Medicine MD/PhD Program, 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; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Will Liao
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; New York Genome Center, New York, NY 10013, USA
| | - Sergio Espeso-Gil
- 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
| | - Sandhya Chandrasekaran
- Icahn School of Medicine MD/PhD Program, 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; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yan Jiang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, 200032, China
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kristen J Brennand
- 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
| | - 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.
| |
Collapse
|
13
|
Genetic Variation in Long-Range Enhancers. Curr Top Behav Neurosci 2019; 42:35-50. [PMID: 31396896 DOI: 10.1007/7854_2019_110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Cis-regulatory elements (CREs), including insulators, promoters, and enhancers, play critical roles in the establishment and maintenance of normal cellular function. Within each cell, the 3D structure of chromatin is arranged in specific patterns to expose the CREs required for optimal spatiotemporal regulation of gene expression. CREs can act over large distances along the linear genome, facilitated by looping of the intervening chromatin to allow direct interaction between distal regulatory elements and their target genes. A number of pathologies are associated with dysregulation of CRE function, including developmental disorders, cancers, and neuropsychiatric disease. A majority of known neuropsychiatric disease risk loci are noncoding, and increasing evidence suggests that they contribute to disease through disruption of CREs. As such, rather than directly altering the amino acid content of proteins, these variants are instead thought to affect where, when, and to what extent a given gene is expressed. The distances over which CREs can operate often render their target genes difficult to identify. Furthermore, as many risk loci contain multiple variants in high linkage disequilibrium, identification of the causative single nucleotide polymorphism(s) therein is not straightforward. Thus, deciphering the genetic etiology of complex neuropsychiatric disorders presents a significant challenge.
Collapse
|
14
|
Chitaman JM, Fraser P, Feng J. Three-dimensional chromosome architecture and drug addiction. Curr Opin Neurobiol 2019; 59:137-145. [PMID: 31276935 DOI: 10.1016/j.conb.2019.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/04/2019] [Accepted: 05/28/2019] [Indexed: 10/26/2022]
Abstract
Aberrant gene expression underlies drug addiction. Therefore, studying the regulation of gene expression in drug addiction may provide mechanistic insights into this disease, for which there are still only limited treatments. Recently, the three-dimensional (3D) organization of linear DNA in the nucleus has been recognized as having a major influence on gene transcription. Here, we review its roles in both basic brain function and neuropsychiatric disorders, while also highlighting its emerging implications in drug addiction. Unraveling the 3D architecture of chromosomes in drug addiction is adding to our understanding of this disease and has the potential to trigger novel approaches for better diagnosis and therapy.
Collapse
Affiliation(s)
- Javed M Chitaman
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA; Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Jian Feng
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA; Program in Neuroscience, Florida State University, Tallahassee, FL 32306, USA.
| |
Collapse
|
15
|
Egervari G, Kozlenkov A, Dracheva S, Hurd YL. Molecular windows into the human brain for psychiatric disorders. Mol Psychiatry 2019; 24:653-673. [PMID: 29955163 PMCID: PMC6310674 DOI: 10.1038/s41380-018-0125-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 12/20/2022]
Abstract
Delineating the pathophysiology of psychiatric disorders has been extremely challenging but technological advances in recent decades have facilitated a deeper interrogation of molecular processes in the human brain. Initial candidate gene expression studies of the postmortem brain have evolved into genome wide profiling of the transcriptome and the epigenome, a critical regulator of gene expression. Here, we review the potential and challenges of direct molecular characterization of the postmortem human brain, and provide a brief overview of recent transcriptional and epigenetic studies with respect to neuropsychiatric disorders. Such information can now be leveraged and integrated with the growing number of genome-wide association databases to provide a functional context of trait-associated genetic variants linked to psychiatric illnesses and related phenotypes. While it is clear that the field is still developing and challenges remain to be surmounted, these recent advances nevertheless hold tremendous promise for delineating the neurobiological underpinnings of mental diseases and accelerating the development of novel medication strategies.
Collapse
Affiliation(s)
- Gabor Egervari
- 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
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Yasmin L Hurd
- 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.
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
16
|
Brookes E, Riccio A. Location, location, location: nuclear structure regulates gene expression in neurons. Curr Opin Neurobiol 2019; 59:16-25. [PMID: 31005709 DOI: 10.1016/j.conb.2019.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/27/2019] [Accepted: 03/18/2019] [Indexed: 12/27/2022]
Abstract
Genome architecture plays a critical role in regulating the expression of genes that are essential for nervous system development. During neuronal differentiation, spatially and temporally regulated transcription allows neuronal migration, the growth of dendrites and axons, and at later stages, synaptic formation and the establishment of neuronal circuitry. Genome topology and relocation of gene loci within the nucleus are now regarded as key factors that contribute to transcriptional regulation. Here, we review recent work supporting the hypothesis that the dynamic organization of chromatin within the nucleus impacts gene activation in response to extrinsic signalling and during neuronal differentiation. The consequences of disruption of the genome architecture on neuronal health will be also discussed.
Collapse
Affiliation(s)
- Emily Brookes
- MRC Laboratory of Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Antonella Riccio
- MRC Laboratory of Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK.
| |
Collapse
|
17
|
Rajarajan P, Borrman T, Liao W, Schrode N, Flaherty E, Casiño C, Powell S, Yashaswini C, LaMarca EA, Kassim B, Javidfar B, Espeso-Gil S, Li A, Won H, Geschwind DH, Ho SM, MacDonald M, Hoffman GE, Roussos P, Zhang B, Hahn CG, Weng Z, Brennand KJ, Akbarian S. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk. Science 2019; 362:362/6420/eaat4311. [PMID: 30545851 DOI: 10.1126/science.aat4311] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 11/07/2018] [Indexed: 12/11/2022]
Abstract
To explore the developmental reorganization of the three-dimensional genome of the brain in the context of neuropsychiatric disease, we monitored chromosomal conformations in differentiating neural progenitor cells. Neuronal and glial differentiation was associated with widespread developmental remodeling of the chromosomal contact map and included interactions anchored in common variant sequences that confer heritable risk for schizophrenia. We describe cell type-specific chromosomal connectomes composed of schizophrenia risk variants and their distal targets, which altogether show enrichment for genes that regulate neuronal connectivity and chromatin remodeling, and evidence for coordinated transcriptional regulation and proteomic interaction of the participating genes. Developmentally regulated chromosomal conformation changes at schizophrenia-relevant sequences disproportionally occurred in neurons, highlighting the existence of cell type-specific disease risk vulnerabilities in spatial genome organization.
Collapse
Affiliation(s)
- Prashanth Rajarajan
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Will Liao
- New York Genome Center, New York, NY 10013, USA
| | - Nadine Schrode
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Erin Flaherty
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Charlize Casiño
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Samuel Powell
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Chittampalli Yashaswini
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Elizabeth A LaMarca
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Bibi Kassim
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Sergio Espeso-Gil
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Aiqun Li
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Hyejung Won
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Daniel H Geschwind
- Neurogenetics Program, Department of Neurology, Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Seok-Man Ho
- Icahn School of Medicine M.D./Ph.D. Program, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Matthew MacDonald
- Neuropsychiatric Signaling Program, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriel E Hoffman
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Bin Zhang
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Chang-Gyu Hahn
- Neuropsychiatric Signaling Program, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA. .,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10027, USA
| |
Collapse
|
18
|
Andersson JD, Matuskey D, Finnema SJ. Positron emission tomography imaging of the γ-aminobutyric acid system. Neurosci Lett 2018; 691:35-43. [PMID: 30102960 DOI: 10.1016/j.neulet.2018.08.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 08/06/2018] [Accepted: 08/09/2018] [Indexed: 01/08/2023]
Abstract
In this review, we summarize the recent development of positron emission tomography (PET) radioligands for γ-aminobutyric acid A (GABAA) receptors and their potential to measure changes in endogenous GABA levels and highlight the clinical and translational applications of GABA-sensitive PET radioligands. We review the basic physiology of the GABA system with a focus on the importance of GABAA receptors in the brain and specifically the benzodiazepine binding site. Challenges for the development of central nervous system radioligands and particularly for radioligands with increased GABA sensitivity are outlined, as well as the status of established benzodiazepine site PET radioligands and agonist GABAA radioligands. We underline the challenge of using allosteric interactions to measure GABA concentrations and review the current state of PET imaging of changes in GABA levels. We conclude that PET tracers with increased GABA sensitivity are required to efficiently measure GABA release and that such a tool could be broadly applied to assess GABA transmission in vivo across several disorders.
Collapse
Affiliation(s)
- Jan D Andersson
- University of Alberta, Medical Isotope and Cyclotron Facility, Edmonton, Canada
| | - David Matuskey
- PET Center, Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA
| | - Sjoerd J Finnema
- PET Center, Department of Radiology and Biomedical Imaging, Yale University, New Haven, CT, USA; Center for Psychiatric Research, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
19
|
Punzi G, Bharadwaj R, Ursini G. Neuroepigenetics of Schizophrenia. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:195-226. [PMID: 30072054 DOI: 10.1016/bs.pmbts.2018.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Schizophrenia is a complex disorder of the brain, where genetic variants explain only a portion of risk. Neuroepigenetic mechanisms may explain the remaining share of risk, as well as the transition from susceptibility to the actual disease. Here, we discuss the most recent findings in the field of brain epigenetics applied to the study of schizophrenia. Methylome studies have found several candidates exhibiting methylation modifications in association with the disorder, but genes affected do not always overlap. Notably, these studies converge in that genes within the schizophrenia risk loci or genes differentially methylated in patients affected with the disorder are dynamically regulated during early life. They also imply that schizophrenia-associated genetic variation may affect DNA methylation in fetal and adult brains. Histone modifications may help mediating the effect of genetic risk variants associated with schizophrenia, and regulating chromatin higher-order structure. The 3D-organization of chromatin in the brain creates physical interactions within chromosomes, so that schizophrenia-associated genetic variants can be linked with genes distant from their loci; this suggests that chromatin conformation matters in the mechanism of risk for the disorder. Non-coding RNAs provide a novel and complex mechanism of gene regulation potentially significant for schizophrenia, as proposed by research on specific microRNAs and long non-coding RNAs (lncRNAs). Finally, a recent study in epitranscriptomics identifies RNA methylation as a further epigenetic mechanism active in human brain and specifically in a portion of the transcriptome associated with schizophrenia susceptibility. These findings indicate that, as expected from the complexity of the brain and its development, several epigenetic mechanisms may intervene in the etiopathogenesis of schizophrenia. An understanding of their roles calls for research approaches integrating the investigation of different epigenetic mechanisms and of environmental and genetic risk, in the context of development.
Collapse
Affiliation(s)
- Giovanna Punzi
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Rahul Bharadwaj
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Gianluca Ursini
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
| |
Collapse
|
20
|
Chromosomal Conformations and Epigenomic Regulation in Schizophrenia. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:21-40. [PMID: 29933951 DOI: 10.1016/bs.pmbts.2017.11.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromosomal conformations, including promoter-enhancer loops, provide a critical regulatory layer for the transcriptional machinery. Therefore, schizophrenia, a common psychiatric disorder associated with broad changes in neuronal gene expression in prefrontal cortex and other brain regions implicated in psychosis, could be associated with alterations in higher-order chromatin. Here, we review early studies on spatial genome organization in the schizophrenia postmortem brain and discuss how integrative approaches using cell culture and animal model systems could gain deeper insight into the potential roles of higher-order chromatin for the neurobiology of and novel treatment avenues for common psychiatric disease.
Collapse
|
21
|
Mitchell AC, Javidfar B, Pothula V, Ibi D, Shen EY, Peter CJ, Bicks L, Fehr T, Jiang Y, Brennand KJ, Neve RL, Gonzalez-Maeso J, Akbarian S. MEF2C transcription factor is associated with the genetic and epigenetic risk architecture of schizophrenia and improves cognition in mice. Mol Psychiatry 2018; 23:123-132. [PMID: 28115742 PMCID: PMC5966823 DOI: 10.1038/mp.2016.254] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 10/30/2016] [Accepted: 12/06/2016] [Indexed: 12/20/2022]
Abstract
Large-scale consortia mapping the genomic risk architectures of schizophrenia provide vast amounts of molecular information, with largely unexplored therapeutic potential. We harnessed publically available information from the Psychiatric Genomics Consortium, and report myocyte enhancer factor 2C (MEF2C) motif enrichment in sequences surrounding the top scoring single-nucleotide polymorphisms within risk loci contributing by individual small effect to disease heritability. Chromatin profiling at base-pair resolution in neuronal nucleosomes extracted from prefrontal cortex of 34 subjects, including 17 cases diagnosed with schizophrenia, revealed MEF2C motif enrichment within cis-regulatory sequences, including neuron-specific promoters and superenhancers, affected by histone H3K4 hypermethylation in disease cases. Vector-induced short- and long-term Mef2c upregulation in mouse prefrontal projection neurons consistently resulted in enhanced cognitive performance in working memory and object recognition paradigms at baseline and after psychotogenic drug challenge, in conjunction with remodeling of local connectivity. Neuronal genome tagging in vivo by Mef2c-Dam adenine methyltransferase fusion protein confirmed the link between cognitive enhancement and MEF2C occupancy at promoters harboring canonical and variant MEF2C motifs. The multilayered integrative approaches presented here provide a roadmap to uncover the therapeutic potential of transcriptional regulators for schizophrenia and related disorders.
Collapse
Affiliation(s)
- Amanda C. Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Venu Pothula
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Daisuke Ibi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Erica Y. Shen
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Cyril J. Peter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Lucy Bicks
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Tristan Fehr
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Yan Jiang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kristen J. Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Rachael L. Neve
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge MA02139, USA
| | - Javier Gonzalez-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University Medical School, Richmond, Virginia 23298, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| |
Collapse
|
22
|
Javidfar B, Park R, Kassim BS, Bicks LK, Akbarian S. The epigenomics of schizophrenia, in the mouse. Am J Med Genet B Neuropsychiatr Genet 2017; 174:631-640. [PMID: 28699694 PMCID: PMC5573750 DOI: 10.1002/ajmg.b.32566] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/04/2017] [Accepted: 06/12/2017] [Indexed: 01/02/2023]
Abstract
Large-scale consortia including the Psychiatric Genomics Consortium, the Common Minds Consortium, BrainSeq and PsychENCODE, and many other studies taken together provide increasingly detailed insights into the genetic and epigenetic risk architectures of schizophrenia (SCZ) and offer vast amounts of molecular information, but with largely unexplored therapeutic potential. Here we discuss how epigenomic studies in human brain could guide animal work to test the impact of disease-associated alterations in chromatin structure and function on cognition and behavior. For example, transcription factors such as MYOCYTE-SPECIFIC ENHANCER FACTOR 2C (MEF2C), or multiple regulators of the open chromatin mark, methyl-histone H3-lysine 4, are associated with the genetic risk architectures of common psychiatric disease and alterations in chromatin structure and function in diseased brain tissue. Importantly, these molecules also affect cognition and behavior in genetically engineered mice, including virus-mediated expression changes in prefrontal cortex (PFC) and other key nodes in the circuitry underlying psychosis. Therefore, preclinical and small laboratory animal work could target genomic sequences affected by chromatin alterations in SCZ. To this end, in vivo editing of enhancer and other regulatory non-coding DNA by RNA-guided nucleases including CRISPR-Cas, and designer transcription factors, could be expected to deliver pipelines for novel therapeutic approaches aimed at improving cognitive dysfunction and other core symptoms of SCZ.
Collapse
Affiliation(s)
| | | | | | - Lucy K. Bicks
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai; New York New York
| | - Schahram Akbarian
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai; New York New York
| |
Collapse
|
23
|
Feng W, Chakraborty A. Fragility Extraordinaire: Unsolved Mysteries of Chromosome Fragile Sites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:489-526. [PMID: 29357071 DOI: 10.1007/978-981-10-6955-0_21] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chromosome fragile sites are a fascinating cytogenetic phenomenon now widely implicated in a slew of human diseases ranging from neurological disorders to cancer. Yet, the paths leading to these revelations were far from direct, and the number of fragile sites that have been molecularly cloned with known disease-associated genes remains modest. Moreover, as more fragile sites were being discovered, research interests in some of the earliest discovered fragile sites ebbed away, leaving a number of unsolved mysteries in chromosome biology. In this review we attempt to recount some of the early discoveries of fragile sites and highlight those phenomena that have eluded intense scrutiny but remain extremely relevant in our understanding of the mechanisms of chromosome fragility. We then survey the literature for disease association for a comprehensive list of fragile sites. We also review recent studies addressing the underlying cause of chromosome fragility while highlighting some ongoing debates. We report an observed enrichment for R-loop forming sequences in fragile site-associated genes than genomic average. Finally, we will leave the reader with some lingering questions to provoke discussion and inspire further scientific inquiries.
Collapse
Affiliation(s)
- Wenyi Feng
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
| | - Arijita Chakraborty
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
| |
Collapse
|
24
|
Ricq EL, Hooker JM, Haggarty SJ. Toward development of epigenetic drugs for central nervous system disorders: Modulating neuroplasticity via H3K4 methylation. Psychiatry Clin Neurosci 2016; 70:536-550. [PMID: 27485392 PMCID: PMC5764164 DOI: 10.1111/pcn.12426] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/29/2016] [Indexed: 12/19/2022]
Abstract
The mammalian brain dynamically activates or silences gene programs in response to environmental input and developmental cues. This neuroplasticity is controlled by signaling pathways that modify the activity, localization, and/or expression of transcriptional-regulatory enzymes in combination with alterations in chromatin structure in the nucleus. Consistent with this key neurobiological role, disruptions in the fine-tuning of epigenetic and transcriptional regulation have emerged as a recurrent theme in studies of the genetics of neurodevelopmental and neuropsychiatric disorders. Furthermore, environmental factors have been implicated in the increased risk of heterogeneous, multifactorial, neuropsychiatric disorders via epigenetic mechanisms. Aberrant epigenetic regulation of gene expression thus provides an attractive unifying model for understanding the complex risk architecture of mental illness. Here, we review emerging genetic evidence implicating dysregulation of histone lysine methylation in neuropsychiatric disease and outline advancements in small-molecule probes targeting this chromatin modification. The emerging field of neuroepigenetic research is poised to provide insight into the biochemical basis of genetic risk for diverse neuropsychiatric disorders and to develop the highly selective chemical tools and imaging agents necessary to dissect dynamic transcriptional-regulatory mechanisms in the nervous system. On the basis of these findings, continued advances may lead to the validation of novel, disease-modifying therapeutic targets for a range of disorders with aberrant chromatin-mediated neuroplasticity.
Collapse
Affiliation(s)
- Emily L. Ricq
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
- Chemical Neurobiology Laboratory, Center for Human Genetic Research, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jacob M. Hooker
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, United States
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory, Center for Human Genetic Research, Departments of Neurology & Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, United States
| |
Collapse
|
25
|
Fullard JF, Halene TB, Giambartolomei C, Haroutunian V, Akbarian S, Roussos P. Understanding the genetic liability to schizophrenia through the neuroepigenome. Schizophr Res 2016; 177:115-124. [PMID: 26827128 PMCID: PMC4963306 DOI: 10.1016/j.schres.2016.01.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 01/14/2016] [Accepted: 01/18/2016] [Indexed: 12/17/2022]
Abstract
The Psychiatric Genomics Consortium-Schizophrenia Workgroup (PGC-SCZ) recently identified 108 loci associated with increased risk for schizophrenia (SCZ). The vast majority of these variants reside within non-coding sequences of the genome and are predicted to exert their effects by affecting the mechanism of action of cis regulatory elements (CREs), such as promoters and enhancers. Although a number of large-scale collaborative efforts (e.g. ENCODE) have achieved a comprehensive mapping of CREs in human cell lines or tissue homogenates, it is becoming increasingly evident that many risk-associated variants are enriched for expression Quantitative Trait Loci (eQTLs) and CREs in specific tissues or cells. As such, data derived from previous research endeavors may not capture fully cell-type and/or region specific changes associated with brain diseases. Coupling recent technological advances in genomics with cell-type specific methodologies, we are presented with an unprecedented opportunity to better understand the genetics of normal brain development and function and, in turn, the molecular basis of neuropsychiatric disorders. In this review, we will outline ongoing efforts towards this goal and will discuss approaches with the potential to shed light on the mechanism(s) of action of cell-type specific cis regulatory elements and their putative roles in disease, with particular emphasis on understanding the manner in which the epigenome and CREs influence the etiology of SCZ.
Collapse
Affiliation(s)
- John F. Fullard
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tobias B. Halene
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA,Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA
| | | | - Vahram Haroutunian
- 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 (VISN 3), James J. Peters VA Medical Center, Bronx, 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
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Science and Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Mental Illness Research, Education, and Clinical Center (VISN 3), James J. Peters VA Medical Center, Bronx, NY, USA.
| |
Collapse
|
26
|
Rajarajan P, Gil SE, Brennand KJ, Akbarian S. Spatial genome organization and cognition. Nat Rev Neurosci 2016; 17:681-691. [PMID: 27708356 DOI: 10.1038/nrn.2016.124] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonrandom chromosomal conformations, including promoter-enhancer loopings that bypass kilobases or megabases of linear genome, provide a crucial layer of transcriptional regulation and move vast amounts of non-coding sequence into the physical proximity of genes that are important for neurodevelopment, cognition and behaviour. Activity-regulated changes in the neuronal '3D genome' could govern transcriptional mechanisms associated with learning and plasticity, and loop-bound intergenic and intronic non-coding sequences have been implicated in psychiatric and adult-onset neurodegenerative disease. Recent studies have begun to clarify the roles of spatial genome organization in normal and abnormal cognition.
Collapse
Affiliation(s)
- Prashanth Rajarajan
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 New York, USA
| | - Sergio Espeso Gil
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Plaça de la Mercè 10, Barcelona 08002, Spain
| | - Kristen J Brennand
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 New York, USA
| | - Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 New York, USA
| |
Collapse
|
27
|
Longitudinal assessment of neuronal 3D genomes in mouse prefrontal cortex. Nat Commun 2016; 7:12743. [PMID: 27597321 PMCID: PMC5025847 DOI: 10.1038/ncomms12743] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 07/28/2016] [Indexed: 12/15/2022] Open
Abstract
Neuronal epigenomes, including chromosomal loopings moving distal cis-regulatory elements into proximity of target genes, could serve as molecular proxy linking present-day-behaviour to past exposures. However, longitudinal assessment of chromatin state is challenging, because conventional chromosome conformation capture assays essentially provide single snapshots at a given time point, thus reflecting genome organization at the time of brain harvest and therefore are non-informative about the past. Here we introduce 'NeuroDam' to assess epigenome status retrospectively. Short-term expression of the bacterial DNA adenine methyltransferase Dam, tethered to the Gad1 gene promoter in mouse prefrontal cortex neurons, results in stable G(methyl)ATC tags at Gad1-bound chromosomal contacts. We show by NeuroDam that mice with defective cognition 4 months after pharmacological NMDA receptor blockade already were affected by disrupted chromosomal conformations shortly after drug exposure. Retrospective profiling of neuronal epigenomes is likely to illuminate epigenetic determinants of normal and diseased brain development in longitudinal context.
Collapse
|
28
|
Medrano-Fernández A, Barco A. Nuclear organization and 3D chromatin architecture in cognition and neuropsychiatric disorders. Mol Brain 2016; 9:83. [PMID: 27595843 PMCID: PMC5011999 DOI: 10.1186/s13041-016-0263-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/06/2016] [Indexed: 01/08/2023] Open
Abstract
The current view of neuroplasticity depicts the changes in the strength and number of synaptic connections as the main physical substrate for behavioral adaptation to new experiences in a changing environment. Although transcriptional regulation is known to play a role in these synaptic changes, the specific contribution of activity-induced changes to both the structure of the nucleus and the organization of the genome remains insufficiently characterized. Increasing evidence indicates that plasticity-related genes may work in coordination and share architectural and transcriptional machinery within discrete genomic foci. Here we review the molecular and cellular mechanisms through which neuronal nuclei structurally adapt to stimuli and discuss how the perturbation of these mechanisms can trigger behavioral malfunction.
Collapse
Affiliation(s)
- Alejandro Medrano-Fernández
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Angel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández-Consejo Superior de Investigaciones Científicas), Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
| |
Collapse
|
29
|
Kim D, Kang M, Biswas A, Liu C, Gao J. Integrative approach for inference of gene regulatory networks using lasso-based random featuring and application to psychiatric disorders. BMC Med Genomics 2016; 9 Suppl 2:50. [PMID: 27510319 PMCID: PMC4980788 DOI: 10.1186/s12920-016-0202-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Background Inferring gene regulatory networks is one of the most interesting research areas in the systems biology. Many inference methods have been developed by using a variety of computational models and approaches. However, there are two issues to solve. First, depending on the structural or computational model of inference method, the results tend to be inconsistent due to innately different advantages and limitations of the methods. Therefore the combination of dissimilar approaches is demanded as an alternative way in order to overcome the limitations of standalone methods through complementary integration. Second, sparse linear regression that is penalized by the regularization parameter (lasso) and bootstrapping-based sparse linear regression methods were suggested in state of the art methods for network inference but they are not effective for a small sample size data and also a true regulator could be missed if the target gene is strongly affected by an indirect regulator with high correlation or another true regulator. Results We present two novel network inference methods based on the integration of three different criteria, (i) z-score to measure the variation of gene expression from knockout data, (ii) mutual information for the dependency between two genes, and (iii) linear regression-based feature selection. Based on these criterion, we propose a lasso-based random feature selection algorithm (LARF) to achieve better performance overcoming the limitations of bootstrapping as mentioned above. Conclusions In this work, there are three main contributions. First, our z score-based method to measure gene expression variations from knockout data is more effective than similar criteria of related works. Second, we confirmed that the true regulator selection can be effectively improved by LARF. Lastly, we verified that an integrative approach can clearly outperform a single method when two different methods are effectively jointed. In the experiments, our methods were validated by outperforming the state of the art methods on DREAM challenge data, and then LARF was applied to inferences of gene regulatory network associated with psychiatric disorders.
Collapse
Affiliation(s)
- Dongchul Kim
- Department of Computer Science, University of Texas Rio Grande Valley, Edinburg, 78541, TX, US
| | - Mingon Kang
- Department of Computer Science, Kennesaw State University, Marietta, 30144, GA, US
| | - Ashis Biswas
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, 76019, TX, US
| | - Chunyu Liu
- Department of Psychiatry, University of Illinois at Chicago, Chicago, 60607, IL, US
| | - Jean Gao
- Department of Computer Science and Engineering, University of Texas at Arlington, Arlington, 76019, TX, US.
| |
Collapse
|
30
|
Markedly Lower Glutamic Acid Decarboxylase 67 Protein Levels in a Subset of Boutons in Schizophrenia. Biol Psychiatry 2016; 79:1006-15. [PMID: 26364548 PMCID: PMC4744808 DOI: 10.1016/j.biopsych.2015.07.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 07/14/2015] [Accepted: 07/22/2015] [Indexed: 11/24/2022]
Abstract
BACKGROUND Convergent findings indicate that cortical gamma-aminobutyric acid (GABA)ergic circuitry is altered in schizophrenia. Postmortem studies have consistently found lower levels of glutamic acid decarboxylase 67 (GAD67) messenger RNA (mRNA) in the prefrontal cortex (PFC) of subjects with schizophrenia. At the cellular level, the density of GABA neurons with detectable levels of GAD67 mRNA is ~30% lower across cortical layers. Knowing how this transcript deficit translates to GAD67 protein levels in axonal boutons is important for understanding the impact it might have on GABA synthesis. In addition, because reductions in GAD67 expression before, but not after, the maturation of GABAergic boutons results in a lower density of GABAergic boutons in mouse cortical cultures, knowing if GABAergic bouton density is altered in schizophrenia would provide insight into the timing of the GAD67 deficit. METHODS PFC tissue sections from 20 matched pairs of schizophrenia and comparison subjects were immunolabeled for the vesicular GABA transporter (vGAT) and GAD67. RESULTS vGAT+ bouton density did not differ between subject groups, consistent with findings that vGAT mRNA levels are unaltered in the illness and confirming that the number of cortical GABAergic boutons is not lower in schizophrenia. In contrast, in schizophrenia subjects, the proportion of vGAT+ boutons with detectable GAD67 levels (vGAT+/GAD67+ boutons) was 16% lower and mean GAD67 levels were 14% lower in the remaining vGAT+/GAD67+ boutons. CONCLUSIONS Our findings suggest that GABA production is markedly reduced in a subset of boutons in the PFC of schizophrenia subjects and that this reduction likely occurs after the maturation of GABAergic boutons.
Collapse
|
31
|
Cariaga-Martinez A, Saiz-Ruiz J, Alelú-Paz R. From Linkage Studies to Epigenetics: What We Know and What We Need to Know in the Neurobiology of Schizophrenia. Front Neurosci 2016; 10:202. [PMID: 27242407 PMCID: PMC4862989 DOI: 10.3389/fnins.2016.00202] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 04/25/2016] [Indexed: 01/15/2023] Open
Abstract
Schizophrenia is a complex psychiatric disorder characterized by the presence of positive, negative, and cognitive symptoms that lacks a unifying neuropathology. In the present paper, we will review the current understanding of molecular dysregulation in schizophrenia, including genetic and epigenetic studies. In relation to the latter, basic research suggests that normal cognition is regulated by epigenetic mechanisms and its dysfunction occurs upon epigenetic misregulation, providing new insights into missing heritability of complex psychiatric diseases, referring to the discrepancy between epidemiological heritability and the proportion of phenotypic variation explained by DNA sequence difference. In schizophrenia the absence of consistently replicated genetic effects together with evidence for lasting changes in gene expression after environmental exposures suggest a role of epigenetic mechanisms. In this review we will focus on epigenetic modifications as a key mechanism through which environmental factors interact with individual's genetic constitution to affect risk of psychotic conditions throughout life.
Collapse
Affiliation(s)
- Ariel Cariaga-Martinez
- Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, Alcalá University Madrid, Spain
| | - Jerónimo Saiz-Ruiz
- Department of Psychiatry, Ramón y Cajal Hospital, IRYCISMadrid, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM)Madrid, Spain
| | - Raúl Alelú-Paz
- Laboratory for Neuroscience of Mental Disorders Elena Pessino, Department of Medicine and Medical Specialties, School of Medicine, Alcalá UniversityMadrid, Spain; Department of Psychiatry, Ramón y Cajal Hospital, IRYCISMadrid, Spain
| |
Collapse
|
32
|
Peedicayil J. Preclinical epigenetic models for screening epigenetic drugs for schizophrenia. J Pharmacol Toxicol Methods 2016; 77:1-5. [DOI: 10.1016/j.vascn.2015.09.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 08/18/2015] [Accepted: 09/05/2015] [Indexed: 01/09/2023]
|
33
|
Dong X, Tsuji J, Labadorf A, Roussos P, Chen JF, Myers RH, Akbarian S, Weng Z. The Role of H3K4me3 in Transcriptional Regulation Is Altered in Huntington's Disease. PLoS One 2015; 10:e0144398. [PMID: 26636336 PMCID: PMC4670094 DOI: 10.1371/journal.pone.0144398] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/17/2015] [Indexed: 01/22/2023] Open
Abstract
Huntington's disease (HD) is an autosomal-dominant neurodegenerative disorder resulting from expansion of CAG repeats in the Huntingtin (HTT) gene. Previous studies have shown mutant HTT can alter expression of genes associated with dysregulated epigenetic modifications. One of the most widely studied chromatin modifications is trimethylated lysine 4 of histone 3 (H3K4me3). Here, we conducted the first comprehensive study of H3K4me3 ChIP-sequencing in neuronal chromatin from the prefrontal cortex of six HD cases and six non-neurologic controls, and its association with gene expression measured by RNA-sequencing. We detected 2,830 differentially enriched H3K4me3 peaks between HD and controls, with 55% of them down-regulated in HD. Although H3K4me3 signals are expected to be associated with mRNA levels, we found an unexpected discordance between altered H3K4me3 peaks and mRNA levels. Gene ontology (GO) term enrichment analysis of the genes with differential H3K4me3 peaks, revealed statistically significantly enriched GO terms only in the genes with down-regulated signals in HD. The most frequently implicated biological process terms are organ morphogenesis and positive regulation of gene expression. More than 9,000 H3K4me3 peaks were located not near any recognized transcription start sites and approximately 36% of these "distal" peaks co-localized to known enhancer sites. Six transcription factors and chromatin remodelers are differentially enriched in HD H3K4me3 distal peaks, including EZH2 and SUZ12, two core subunits of the polycomb repressive complex 2 (PRC2). Moreover, PRC2 repressive state was significantly depleted in HD-enriched peaks, suggesting the epigenetic role of PRC2 inhibition associated with up-regulated H3K4me3 in Huntington's disease. In summary, our study provides new insights into transcriptional dysregulation of Huntington's disease by analyzing the differentiation of H3K4me3 enrichment.
Collapse
Affiliation(s)
- Xianjun Dong
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Junko Tsuji
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Adam Labadorf
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States of America
- Bioinformatics Program, Boston University, Boston, MA, United States of America
| | - Panos Roussos
- Friedman Brain Institute, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, United States of America
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, United States of America
| | - Jiang-Fan Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States of America
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA, United States of America
- Bioinformatics Program, Boston University, Boston, MA, United States of America
- Genome Science Institute, Boston University School of Medicine, Boston, MA, United States of America
| | - Schahram Akbarian
- Friedman Brain Institute, Department of Psychiatry, Mount Sinai School of Medicine, New York, NY, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, United States of America
| |
Collapse
|
34
|
Abstract
Schizophrenia is a chronic psychiatric disorder with a heterogeneous genetic and neurobiological background that influences early brain development, and is expressed as a combination of psychotic symptoms - such as hallucinations, delusions and disorganization - and motivational and cognitive dysfunctions. The mean lifetime prevalence of the disorder is just below 1%, but large regional differences in prevalence rates are evident owing to disparities in urbanicity and patterns of immigration. Although gross brain pathology is not a characteristic of schizophrenia, the disorder involves subtle pathological changes in specific neural cell populations and in cell-cell communication. Schizophrenia, as a cognitive and behavioural disorder, is ultimately about how the brain processes information. Indeed, neuroimaging studies have shown that information processing is functionally abnormal in patients with first-episode and chronic schizophrenia. Although pharmacological treatments for schizophrenia can relieve psychotic symptoms, such drugs generally do not lead to substantial improvements in social, cognitive and occupational functioning. Psychosocial interventions such as cognitive-behavioural therapy, cognitive remediation and supported education and employment have added treatment value, but are inconsistently applied. Given that schizophrenia starts many years before a diagnosis is typically made, the identification of individuals at risk and those in the early phases of the disorder, and the exploration of preventive approaches are crucial.
Collapse
|
35
|
Nestler EJ, Peña CJ, Kundakovic M, Mitchell A, Akbarian S. Epigenetic Basis of Mental Illness. Neuroscientist 2015; 22:447-63. [PMID: 26450593 DOI: 10.1177/1073858415608147] [Citation(s) in RCA: 199] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Psychiatric disorders are complex multifactorial illnesses involving chronic alterations in neural circuit structure and function as well as likely abnormalities in glial cells. While genetic factors are important in the etiology of most mental disorders, the relatively high rates of discordance among identical twins, particularly for depression and other stress-related syndromes, clearly indicate the importance of additional mechanisms. Environmental factors such as stress are known to play a role in the onset of these illnesses. Exposure to such environmental insults induces stable changes in gene expression, neural circuit function, and ultimately behavior, and these maladaptations appear distinct between developmental versus adult exposures. Increasing evidence indicates that these sustained abnormalities are maintained by epigenetic modifications in specific brain regions. Indeed, transcriptional dysregulation and the aberrant epigenetic regulation that underlies this dysregulation is a unifying theme in psychiatric disorders. Here, we provide a progress report of epigenetic studies of the three major psychiatric syndromes, depression, schizophrenia, and bipolar disorder. We review the literature derived from animal models of these disorders as well as from studies of postmortem brain tissue from human patients. While epigenetic studies of mental illness remain at early stages, understanding how environmental factors recruit the epigenetic machinery within specific brain regions to cause lasting changes in disease susceptibility and pathophysiology is revealing new insight into the etiology and treatment of these conditions.
Collapse
Affiliation(s)
- Eric J Nestler
- Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catherine J Peña
- Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marija Kundakovic
- Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Amanda Mitchell
- Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Schahram Akbarian
- Departments of Neuroscience and Psychiatry, The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| |
Collapse
|
36
|
Transcriptional regulation of GAD1 GABA synthesis gene in the prefrontal cortex of subjects with schizophrenia. Schizophr Res 2015; 167:28-34. [PMID: 25458568 PMCID: PMC4417100 DOI: 10.1016/j.schres.2014.10.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/08/2014] [Accepted: 10/13/2014] [Indexed: 12/20/2022]
Abstract
Expression of GAD1 GABA synthesis enzyme is highly regulated by neuronal activity and reaches mature levels in the prefrontal cortex not before adolescence. A significant portion of cases diagnosed with schizophrenia show deficits in GAD1 RNA and protein levels in multiple areas of adult cerebral cortex, possibly reflecting molecular or cellular defects in subtypes of GABAergic interneurons essential for network synchronization and cognition. Here, we review 20years of progress towards a better understanding of disease-related regulation of GAD1 gene expression. For example, deficits in cortical GAD1 RNA in some cases of schizophrenia are associated with changes in the epigenetic architecture of the promoter, affecting DNA methylation patterns and nucleosomal histone modifications. These localized chromatin defects at the 5' end of GAD1 are superimposed by disordered locus-specific chromosomal conformations, including weakening of long-range promoter-enhancer loopings and physical disconnection of GAD1 core promoter sequences from cis-regulatory elements positioned 50 kilobases further upstream. Studies on the 3-dimensional architecture of the GAD1 locus in neurons, including developmentally regulated higher order chromatin compromised by the disease process, together with exploration of locus-specific epigenetic interventions in animal models, could pave the way for future treatments of psychosis and schizophrenia.
Collapse
|
37
|
Kimoto S, Zaki MM, Bazmi HH, Lewis DA. Altered Markers of Cortical γ-Aminobutyric Acid Neuronal Activity in Schizophrenia: Role of the NARP Gene. JAMA Psychiatry 2015; 72:747-56. [PMID: 26038830 PMCID: PMC4734385 DOI: 10.1001/jamapsychiatry.2015.0533] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE In schizophrenia, working memory deficits appear to reflect abnormalities in the generation of gamma oscillations in the dorsolateral prefrontal cortex. The generation of gamma oscillations requires the phasic excitation of inhibitory parvalbumin-containing interneurons. Thus, gamma oscillations depend, in part, on the number of synaptic glutamate receptors on parvalbumin interneurons. However, little is known about the molecular factors that regulate glutamate receptor-mediated excitation of parvalbumin interneurons in schizophrenia. OBJECTIVE To quantify in individuals with schizophrenia the expression of immediate early genes (NARP, ARC, and SGK1) regulating glutamate synaptic neurotransmission. DESIGN, SETTING, AND PARTICIPANTS Postmortem brain specimens (n = 206) were obtained from individuals with schizophrenia, bipolar disorder, or major depressive disorder and from well-matched healthy persons (controls). For a study of brain tissue, quantitative polymerase chain reaction, in situ hybridization, or microarray analyses were used to measure transcript levels in the dorsolateral prefrontal cortex at gray matter, laminar, and cellular levels of resolutions. This study was conducted between January 1, 2013, and November 30, 2014. MAIN OUTCOMES AND MEASURES Expression levels for NARP, ARC, and SGK1 messenger RNA (mRNA) were compared between specimens from individuals with schizophrenia and controls. Diagnostic specificity was assessed by quantifying NARP mRNA levels in specimens from individuals with mood disorders. RESULTS By quantitative polymerase chain reaction, levels of NARP mRNA were significantly lower by 25.6% in specimens from individuals with schizophrenia compared with the controls (mean [SD], 0.036 [0.018] vs 0.049 [0.015]; F1,114 = 21.0; P < .001). Levels of ARC (F1,112 = 0.93; P = .34) and SGK1 (F1,110 = 2.52; P = .12) were not significant. These findings were supported by in situ hybridization (NARP; individuals with schizophrenia vs controls: 40.1% lower [P = .003]) and microarray analyses (NARP; individuals with schizophrenia vs controls: 12.2% lower in layer 3 [P = .11] and 14.6% lower in layer 5 pyramidal cells [P = .001]). In schizophrenia specimens, NARP mRNA levels were positively correlated with GAD67 mRNA (r = 0.55; P < .001); the expression of GAD67 mRNA in parvalbumin interneurons is activity dependent. The NARP mRNA levels were also lower than healthy controls in bipolar disorder (-18.2%; F1,60 = 11.39; P = .001) and major depressive disorder (-21.7%; F1,30 = 5.36; P = .03) specimens, especially those from individuals with psychosis. In all 3 diagnostic groups, NARP mRNA levels were positively correlated (all r ≥ 0.53; all P ≤ .02) with somatostatin mRNA, the expression of which is activity dependent. CONCLUSIONS AND RELEVANCE Given the role of NARP in the formation of excitatory inputs to parvalbumin (and perhaps somatostatin) interneurons, our findings suggest that lower NARP mRNA expression contributes to lower excitatory drive onto parvalbumin interneurons in schizophrenia. This reduced excitatory drive may lead to lower synthesis of γ-aminobutyric acid in these interneurons, contributing to a reduced capacity to generate the gamma oscillations required for working memory.
Collapse
Affiliation(s)
- Sohei Kimoto
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania2Department of Psychiatry, Nara Medical University, Nara, Japan
| | - Mark M. Zaki
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania3Department of Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - H. Holly Bazmi
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - David A. Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania3Department of Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania
| |
Collapse
|
38
|
Abstract
Schizophrenia is a major psychiatric disorder that lacks a unifying neuropathology, while currently available pharmacological treatments provide only limited benefits to many patients. This review will discuss how the field of neuroepigenetics could contribute to advancements of the existing knowledge on the neurobiology and treatment of psychosis. Genome-scale mapping of DMA methylation, histone modifications and variants, and chromosomal loopings for promoter-enhancer interactions and other epigenetic determinants of genome organization and function are likely to provide important clues about mechanisms contributing to dysregulated expression of synaptic and metabolic genes in schizophrenia brain, including the potential links to the underlying genetic risk architecture and environmental exposures. In addition, studies in animal models are providing a rapidly increasing list of chromatin-regulatory mechanisms with significant effects on cognition and complex behaviors, thereby pointing to the therapeutic potential of epigenetic drug targets in the nervous system.
Collapse
Affiliation(s)
- Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, USA
| |
Collapse
|
39
|
Ruzicka WB, Subburaju S, Benes FM. Circuit- and Diagnosis-Specific DNA Methylation Changes at γ-Aminobutyric Acid-Related Genes in Postmortem Human Hippocampus in Schizophrenia and Bipolar Disorder. JAMA Psychiatry 2015; 72:541-51. [PMID: 25738424 PMCID: PMC5547581 DOI: 10.1001/jamapsychiatry.2015.49] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
IMPORTANCE Dysfunction related to γ-aminobutyric acid (GABA)-ergic neurotransmission in the pathophysiology of major psychosis has been well established by the work of multiple groups across several decades, including the widely replicated downregulation of GAD1. Prior gene expression and network analyses within the human hippocampus implicate a broader network of genes, termed the GAD1 regulatory network, in regulation of GAD1 expression. Several genes within this GAD1 regulatory network show diagnosis- and sector-specific expression changes within the circuitry of the hippocampus, influencing abnormal GAD1 expression in schizophrenia and bipolar disorder. OBJECTIVE To investigate the hypothesis that aberrant DNA methylation contributes to circuit- and diagnosis-specific abnormal expression of GAD1 regulatory network genes in psychotic illness. DESIGN, SETTING, AND PARTICIPANTS This epigenetic association study targeting GAD1 regulatory network genes was conducted between July 1, 2012, and June 30, 2014. Postmortem human hippocampus tissue samples were obtained from 8 patients with schizophrenia, 8 patients with bipolar disorder, and 8 healthy control participants matched for age, sex, postmortem interval, and other potential confounds from the Harvard Brain Tissue Resource Center, McLean Hospital, Belmont, Massachusetts. We extracted DNA from laser-microdissected stratum oriens tissue of cornu ammonis 2/3 (CA2/3) and CA1 postmortem human hippocampus, bisulfite modified it, and assessed it with the Infinium HumanMethylation450 BeadChip (Illumina, Inc). The subset of CpG loci associated with GAD1 regulatory network genes was analyzed in R version 3.1.0 software (R Foundation) using the minfi package. Findings were validated using bisulfite pyrosequencing. MAIN OUTCOMES AND MEASURES Methylation levels at 1308 GAD1 regulatory network-associated CpG loci were assessed both as individual sites to identify differentially methylated positions and by sharing information among colocalized probes to identify differentially methylated regions. RESULTS A total of 146 differentially methylated positions with a false detection rate lower than 0.05 were identified across all 6 groups (2 circuit locations in each of 3 diagnostic categories), and 54 differentially methylated regions with P < .01 were identified in single-group comparisons. Methylation changes were enriched in MSX1, CCND2, and DAXX at specific loci within the hippocampus of patients with schizophrenia and bipolar disorder. CONCLUSIONS AND RELEVANCE This work demonstrates diagnosis- and circuit-specific DNA methylation changes at a subset of GAD1 regulatory network genes in the human hippocampus in schizophrenia and bipolar disorder. These genes participate in chromatin regulation and cell cycle control, supporting the concept that the established GABAergic dysfunction in these disorders is related to disruption of GABAergic interneuron physiology at specific circuit locations within the human hippocampus.
Collapse
Affiliation(s)
- W. Brad Ruzicka
- Program in Structural and Molecular Neuroscience, McLean Hospital, Belmont, Massachusetts,Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Sivan Subburaju
- Program in Structural and Molecular Neuroscience, McLean Hospital, Belmont, Massachusetts,Department of Psychiatry, Harvard Medical School, Boston, Massachusetts
| | - Francine M. Benes
- Program in Structural and Molecular Neuroscience, McLean Hospital, Belmont, Massachusetts,Department of Psychiatry, Harvard Medical School, Boston, Massachusetts,Program in Neuroscience, Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
40
|
Abdolmaleky HM, Zhou JR, Thiagalingam S. An update on the epigenetics of psychotic diseases and autism. Epigenomics 2015; 7:427-49. [DOI: 10.2217/epi.14.85] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The examination of potential roles of epigenetic alterations in the pathogenesis of psychotic diseases have become an essential alternative in recent years as genetic studies alone are yet to uncover major gene(s) for psychosis. Here, we describe the current state of knowledge from the gene-specific and genome-wide studies of postmortem brain and blood cells indicating that aberrant DNA methylation, histone modifications and dysregulation of micro-RNAs are linked to the pathogenesis of mental diseases. There is also strong evidence supporting that all classes of psychiatric drugs modulate diverse features of the epigenome. While comprehensive environmental and genetic/epigenetic studies are uncovering the origins, and the key genes/pathways affected in psychotic diseases, characterizing the epigenetic effects of psychiatric drugs may help to design novel therapies in psychiatry.
Collapse
Affiliation(s)
- Hamid Mostafavi Abdolmaleky
- Departments of Medicine (Biomedical Genetics Section), Genetics & Genomics, Boston University School of Medicine, Boston, MA 02118, USA
- Nutrition/Metabolism Laboratory at Beth Israel Deaconess Medical Center, Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Jin-Rong Zhou
- Nutrition/Metabolism Laboratory at Beth Israel Deaconess Medical Center, Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Sam Thiagalingam
- Departments of Medicine (Biomedical Genetics Section), Genetics & Genomics, Boston University School of Medicine, Boston, MA 02118, USA
- Department of Pathology & Laboratory Medicine, Boston University School of Medicine, Boston, MA, USA
| |
Collapse
|
41
|
Morishita H, Kundakovic M, Bicks L, Mitchell A, Akbarian S. Interneuron epigenomes during the critical period of cortical plasticity: Implications for schizophrenia. Neurobiol Learn Mem 2015; 124:104-10. [PMID: 25849095 DOI: 10.1016/j.nlm.2015.03.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 10/23/2022]
Abstract
Schizophrenia, a major psychiatric disorder defined by delusions and hallucinations, among other symptoms, often with onset in early adulthood, is potentially associated with molecular and cellular alterations in parvalbumin-expressing fast spiking interneurons and other constituents of the cortical inhibitory GABAergic circuitry. The underlying mechanisms, including the role of disease-associated risk factors operating in adolescence such as drug abuse and social stressors, remain incompletely understood. Here, we summarize emerging findings from animal models, highlighting the ability of parvalbuminergic interneurons (PVI) to induce, during the juvenile period, long-term plastic changes in prefrontal and visual cortex, thereby altering perception, cognition and behavior in the adult. Of note, molecular alterations in PVI from subjects with schizophrenia, including downregulated expression of a subset of GABAergic genes, have also been found in juvenile stress models of the disorder. Some of the transcriptional alterations observed in schizophrenia postmortem brain could be linked to changes in the epigenetic architecture of GABAergic gene promoters, including dysregulated DNA methylation, histone modification patterns and disruption of promoter-enhancer interactions at site of chromosomal loop formations. Therefore, we predict that, in the not-to-distant future, PVI- and other cell-type specific epigenomic mappings in the animal model and human brain will provide novel insights into the pathophysiology of schizophrenia and related psychotic diseases, including the role of cortical GABAergic circuitry in shaping long-term plasticity and cognitive function of the cerebral cortex.
Collapse
Affiliation(s)
- Hirofumi Morishita
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, United States; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, United States; Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, United States; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, United States.
| | - Marija Kundakovic
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, United States; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, United States
| | - Lucy Bicks
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, United States; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, United States
| | - Amanda Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, United States; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, United States
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, United States; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, United States.
| |
Collapse
|
42
|
Lower glutamic acid decarboxylase 65-kDa isoform messenger RNA and protein levels in the prefrontal cortex in schizoaffective disorder but not schizophrenia. Biol Psychiatry 2015; 77:167-76. [PMID: 24993056 PMCID: PMC4247819 DOI: 10.1016/j.biopsych.2014.05.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/13/2014] [Accepted: 05/21/2014] [Indexed: 01/27/2023]
Abstract
BACKGROUND Altered gamma-aminobutyric acid (GABA) signaling in the prefrontal cortex (PFC) has been associated with cognitive dysfunction in patients with schizophrenia and schizoaffective disorder. Levels of the GABA-synthesizing enzyme glutamic acid decarboxylase 67-kDa isoform (GAD67) in the PFC have been consistently reported to be lower in patients with these disorders, but the status of the second GABA-synthesizing enzyme, glutamic acid decarboxylase 65-kDa isoform (GAD65), remains unclear. METHODS GAD65 messenger RNA (mRNA) levels were quantified in PFC area 9 by quantitative polymerase chain reaction from 62 subjects with schizophrenia or schizoaffective disorder and 62 matched healthy comparison subjects. In a subset of subject pairs, GAD65 relative protein levels were quantified by confocal immunofluorescence microscopy. RESULTS Mean GAD65 mRNA levels were 13.6% lower in subjects with schizoaffective disorder but did not differ in subjects with schizophrenia relative to their matched healthy comparison subjects. In the subjects with schizoaffective disorder, mean GAD65 protein levels were 19.4% lower and were correlated with GAD65 mRNA levels. Lower GAD65 mRNA and protein levels within subjects with schizoaffective disorder were not attributable to factors commonly comorbid with the diagnosis. CONCLUSIONS In concert with previous studies, these findings suggest that schizoaffective disorder is associated with lower levels of both GAD65 and GAD67 mRNA and protein in the PFC, whereas subjects with schizophrenia have lower mean levels of only GAD67 mRNA and protein. Because cognitive function is generally better preserved in patients with schizoaffective disorder relative to patients with schizophrenia, these findings may support an interpretation that GAD65 downregulation provides a homeostatic response complementary to GAD67 downregulation that serves to reduce inhibition in the face of lower PFC network activity.
Collapse
|
43
|
Bharadwaj R, Peter CJ, Jiang Y, Roussos P, Vogel-Ciernia A, Shen EY, Mitchell AC, Mao W, Whittle C, Dincer A, Jakovcevski M, Pothula V, Rasmussen TP, Giakoumaki SG, Bitsios P, Sherif A, Gardner PD, Ernst P, Ghose S, Sklar P, Haroutunian V, Tamminga C, Myers RH, Futai K, Wood MA, Akbarian S. Conserved higher-order chromatin regulates NMDA receptor gene expression and cognition. Neuron 2014; 84:997-1008. [PMID: 25467983 PMCID: PMC4258154 DOI: 10.1016/j.neuron.2014.10.032] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2014] [Indexed: 12/17/2022]
Abstract
Three-dimensional chromosomal conformations regulate transcription by moving enhancers and regulatory elements into spatial proximity with target genes. Here we describe activity-regulated long-range loopings bypassing up to 0.5 Mb of linear genome to modulate NMDA glutamate receptor GRIN2B expression in human and mouse prefrontal cortex. Distal intronic and 3' intergenic loop formations competed with repressor elements to access promoter-proximal sequences, and facilitated expression via a "cargo" of AP-1 and NRF-1 transcription factors and TALE-based transcriptional activators. Neuronal deletion or overexpression of Kmt2a/Mll1 H3K4- and Kmt1e/Setdb1 H3K9-methyltransferase was associated with higher-order chromatin changes at distal regulatory Grin2b sequences and impairments in working memory. Genetic polymorphisms and isogenic deletions of loop-bound sequences conferred liability for cognitive performance and decreased GRIN2B expression. Dynamic regulation of chromosomal conformations emerges as a novel layer for transcriptional mechanisms impacting neuronal signaling and cognition.
Collapse
Affiliation(s)
- Rahul Bharadwaj
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cyril J Peter
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yan Jiang
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Panos Roussos
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; James J. Peters Veterans Affairs Medical Center, Bronx, New York, NY 10468, USA
| | - Annie Vogel-Ciernia
- Department of Neurobiology and Behavior, University of California at Irvine, Irvine, CA 92697, USA
| | - Erica Y Shen
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amanda C Mitchell
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wenjie Mao
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Catheryne Whittle
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Aslihan Dincer
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Venu Pothula
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Theodore P Rasmussen
- Department of Pharmaceutical Sciences and U.Conn Stem Cell Institute, University of Connecticut, Storrs, CT 06269, USA
| | - Stella G Giakoumaki
- Department of Psychiatry, University of Crete, 71003 Iraklion, Greece; Department of Psychology, University of Crete, 71003 Iraklion, Greece
| | - Panos Bitsios
- Computational Medicine Laboratory, Institute of Computer Science, Foundation for Research and Technology Hellas, 71003 Iraklion, Greece; Department of Psychiatry, University of Crete, 71003 Iraklion, Greece
| | - Ajfar Sherif
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Paul D Gardner
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Patricia Ernst
- Department of Genetics and Department of Microbiology and Immunology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Subroto Ghose
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pamela Sklar
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Vahram Haroutunian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; James J. Peters Veterans Affairs Medical Center, Bronx, New York, NY 10468, USA
| | - Carol Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Richard H Myers
- Department of Neurology, Boston University, Boston, MA 02118, USA
| | - Kensuke Futai
- Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, University of California at Irvine, Irvine, CA 92697, USA
| | - Schahram Akbarian
- Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| |
Collapse
|
44
|
Loss of neuronal 3D chromatin organization causes transcriptional and behavioural deficits related to serotonergic dysfunction. Nat Commun 2014; 5:4450. [PMID: 25034090 DOI: 10.1038/ncomms5450] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/18/2014] [Indexed: 12/20/2022] Open
Abstract
The interior of the neuronal cell nucleus is a highly organized three-dimensional (3D) structure where regions of the genome that are linearly millions of bases apart establish sub-structures with specialized functions. To investigate neuronal chromatin organization and dynamics in vivo, we generated bitransgenic mice expressing GFP-tagged histone H2B in principal neurons of the forebrain. Surprisingly, the expression of this chimeric histone in mature neurons caused chromocenter declustering and disrupted the association of heterochromatin with the nuclear lamina. The loss of these structures did not affect neuronal viability but was associated with specific transcriptional and behavioural deficits related to serotonergic dysfunction. Overall, our results demonstrate that the 3D organization of chromatin within neuronal cells provides an additional level of epigenetic regulation of gene expression that critically impacts neuronal function. This in turn suggests that some loci associated with neuropsychiatric disorders may be particularly sensitive to changes in chromatin architecture.
Collapse
|
45
|
Lewis DA. Inhibitory neurons in human cortical circuits: substrate for cognitive dysfunction in schizophrenia. Curr Opin Neurobiol 2014; 26:22-6. [PMID: 24650500 PMCID: PMC4024332 DOI: 10.1016/j.conb.2013.11.003] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 10/23/2013] [Accepted: 11/06/2013] [Indexed: 12/22/2022]
Abstract
Schizophrenia is a disorder of cognitive neurodevelopment. At least some of the core cognitive deficits of the illness appear to be the product of impaired gamma frequency oscillations which depend, in part, on the inhibitory actions of a subpopulation of cortical GABA neurons that express the calcium binding protein parvalbumin (PV). Recent studies have revealed new facets of the development of PV neurons in primate neocortex and of the nature of their molecular alterations in individuals with schizophrenia. Other recent studies in model systems provide insight into how these alterations may arise in the course of cortical circuitry development.
Collapse
Affiliation(s)
- David A Lewis
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, United States.
| |
Collapse
|
46
|
|
47
|
Mitchell A, Roussos P, Peter C, Tsankova N, Akbarian S. The future of neuroepigenetics in the human brain. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 128:199-228. [PMID: 25410546 DOI: 10.1016/b978-0-12-800977-2.00008-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Complex mechanisms shape the genome of brain cells into transcriptional units, clusters of condensed chromatin, and many other features that distinguish between various cell types and developmental stages sharing the same genetic material. Only a few years ago, the field's focus was almost entirely on a single mark, CpG methylation; the emerging complexity of neuronal and glial epigenomes now includes multiple types of DNA cytosine methylation, more than 100 residue-specific posttranslational histone modifications and histone variants, all of which superimposed by a dynamic and highly regulated three-dimensional organization of the chromosomal material inside the cell nucleus. Here, we provide an update on the most innovative approaches in neuroepigenetics and their potential contributions to approach cognitive functions and disorders unique to human. We propose that comprehensive, cell type-specific mappings of DNA and histone modifications, chromatin-associated RNAs, and chromosomal "loopings" and other determinants of three-dimensional genome organization will critically advance insight into the pathophysiology of the disease. For example, superimposing the epigenetic landscapes of neuronal and glial genomes onto genetic maps for complex disorders, ranging from Alzheimer's disease to schizophrenia, could provide important clues about neurological function for some of the risk-associated noncoding sequences in the human genome.
Collapse
Affiliation(s)
- Amanda Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Cyril Peter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Nadejda Tsankova
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| |
Collapse
|