1
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Kubant R, Cho CE, Pannia E, Hammoud R, Yang NV, Simonian R, Anderson GH. Methyl donor micronutrients, hypothalamic development and programming for metabolic disease. Neurosci Biobehav Rev 2024; 157:105512. [PMID: 38128771 DOI: 10.1016/j.neubiorev.2023.105512] [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: 05/18/2023] [Revised: 11/14/2023] [Accepted: 12/17/2023] [Indexed: 12/23/2023]
Abstract
Nutriture in utero is essential for fetal brain development through the regulation of neural stem cell proliferation, differentiation, and apoptosis, and has a long-lasting impact on risk of disease in offspring. This review examines the role of maternal methyl donor micronutrients in neuronal development and programming of physiological functions of the hypothalamus, with a focus on later-life metabolic outcomes. Although evidence is mainly derived from preclinical studies, recent research shows that methyl donor micronutrients (e.g., folic acid and choline) are critical for neuronal development of energy homeostatic pathways and the programming of characteristics of the metabolic syndrome in mothers and their children. Both folic acid and choline are active in one-carbon metabolism with their impact on epigenetic modification of gene expression. We conclude that an imbalance of folic acid and choline intake during gestation disrupts DNA methylation patterns affecting mechanisms of hypothalamic development, and thus elevates metabolic disease risk. Further investigation, including studies to determine translatability to humans, is required.
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Affiliation(s)
- Ruslan Kubant
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Clara E Cho
- Department of Human Health and Nutritional Sciences, University of Guelph, Guelph, ON, Canada
| | - Emanuela Pannia
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Rola Hammoud
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Neil Victor Yang
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Rebecca Simonian
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - G Harvey Anderson
- Department of Nutritional Sciences, University of Toronto, Toronto, ON, Canada; Department of Physiology, University of Toronto, Toronto, ON, Canada.
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2
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Baker MR, Lee AS, Rajadhyaksha AM. L-type calcium channels and neuropsychiatric diseases: Insights into genetic risk variant-associated genomic regulation and impact on brain development. Channels (Austin) 2023; 17:2176984. [PMID: 36803254 PMCID: PMC9980663 DOI: 10.1080/19336950.2023.2176984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 02/01/2023] [Indexed: 02/21/2023] Open
Abstract
Recent human genetic studies have linked a variety of genetic variants in the CACNA1C and CACNA1D genes to neuropsychiatric and neurodevelopmental disorders. This is not surprising given the work from multiple laboratories using cell and animal models that have established that Cav1.2 and Cav1.3 L-type calcium channels (LTCCs), encoded by CACNA1C and CACNA1D, respectively, play a key role in various neuronal processes that are essential for normal brain development, connectivity, and experience-dependent plasticity. Of the multiple genetic aberrations reported, genome-wide association studies (GWASs) have identified multiple single nucleotide polymorphisms (SNPs) in CACNA1C and CACNA1D that are present within introns, in accordance with the growing body of literature establishing that large numbers of SNPs associated with complex diseases, including neuropsychiatric disorders, are present within non-coding regions. How these intronic SNPs affect gene expression has remained a question. Here, we review recent studies that are beginning to shed light on how neuropsychiatric-linked non-coding genetic variants can impact gene expression via regulation at the genomic and chromatin levels. We additionally review recent studies that are uncovering how altered calcium signaling through LTCCs impact some of the neuronal developmental processes, such as neurogenesis, neuron migration, and neuron differentiation. Together, the described changes in genomic regulation and disruptions in neurodevelopment provide possible mechanisms by which genetic variants of LTCC genes contribute to neuropsychiatric and neurodevelopmental disorders.
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Affiliation(s)
- Madelyn R. Baker
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, USA
| | - Andrew S. Lee
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Developmental Biology Program, Sloan Kettering Institute, New York, USA
| | - Anjali M. Rajadhyaksha
- Neuroscience Program, Weill Cornell Graduate School of Medical Sciences, New York, USA
- Pediatric Neurology, Department of Pediatrics, Weill Cornell Medicine, New York, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, USA
- Weill Cornell Autism Research Program, Weill Cornell Medicine, New York, USA
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3
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Santiago JA, Quinn JP, Potashkin JA. Co-Expression Network Analysis Identifies Molecular Determinants of Loneliness Associated with Neuropsychiatric and Neurodegenerative Diseases. Int J Mol Sci 2023; 24:ijms24065909. [PMID: 36982982 PMCID: PMC10058494 DOI: 10.3390/ijms24065909] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/06/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Loneliness and social isolation are detrimental to mental health and may lead to cognitive impairment and neurodegeneration. Although several molecular signatures of loneliness have been identified, the molecular mechanisms by which loneliness impacts the brain remain elusive. Here, we performed a bioinformatics approach to untangle the molecular underpinnings associated with loneliness. Co-expression network analysis identified molecular 'switches' responsible for dramatic transcriptional changes in the nucleus accumbens of individuals with known loneliness. Loneliness-related switch genes were enriched in cell cycle, cancer, TGF-β, FOXO, and PI3K-AKT signaling pathways. Analysis stratified by sex identified switch genes in males with chronic loneliness. Male-specific switch genes were enriched in infection, innate immunity, and cancer-related pathways. Correlation analysis revealed that loneliness-related switch genes significantly overlapped with 82% and 68% of human studies on Alzheimer's (AD) and Parkinson's diseases (PD), respectively, in gene expression databases. Loneliness-related switch genes, BCAM, NECTIN2, NPAS3, RBM38, PELI1, DPP10, and ASGR2, have been identified as genetic risk factors for AD. Likewise, switch genes HLA-DRB5, ALDOA, and GPNMB are known genetic loci in PD. Similarly, loneliness-related switch genes overlapped in 70% and 64% of human studies on major depressive disorder and schizophrenia, respectively. Nine switch genes, HLA-DRB5, ARHGAP15, COL4A1, RBM38, DMD, LGALS3BP, WSCD2, CYTH4, and CNTRL, overlapped with known genetic variants in depression. Seven switch genes, NPAS3, ARHGAP15, LGALS3BP, DPP10, SMYD3, CPXCR1, and HLA-DRB5 were associated with known risk factors for schizophrenia. Collectively, we identified molecular determinants of loneliness and dysregulated pathways in the brain of non-demented adults. The association of switch genes with known risk factors for neuropsychiatric and neurodegenerative diseases provides a molecular explanation for the observed prevalence of these diseases among lonely individuals.
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Affiliation(s)
| | | | - Judith A Potashkin
- Center for Neurodegenerative Diseases and Therapeutics, Cellular and Molecular Pharmacology Department, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
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4
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Behrends M, Engmann O. Loop Interrupted: Dysfunctional Chromatin Relations in Neurological Diseases. Front Genet 2021; 12:732033. [PMID: 34422024 PMCID: PMC8376151 DOI: 10.3389/fgene.2021.732033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/20/2021] [Indexed: 12/19/2022] Open
Abstract
The majority of genetic variants for psychiatric disorders have been found within non-coding genomic regions. Physical interactions of gene promoters with distant regulatory elements carrying risk alleles may explain how the latter affect gene expression. Recently, whole genome maps of long-range chromosomal contacts from human postmortem brains have been integrated with gene sequence and chromatin accessibility data to decipher disease-specific alterations in chromatin architecture. Cell culture and rodent models provide a causal link between chromatin conformation, long-range chromosomal contacts, gene expression, and disease phenotype. Here, we give an overview of the techniques used to study chromatin contacts and their limitations in brain research. We present evidence for three-dimensional genome changes in physiological brain function and assess how its disturbance contributes to psychiatric disorders. Lastly, we discuss remaining questions and future research directions with a focus on clinical applications.
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Affiliation(s)
- Marthe Behrends
- Faculty of Medicine, Friedrich Schiller Universität, Jena, Thüringen, Germany
| | - Olivia Engmann
- Jena University Hospital, Institute for Human Genetics, Thüringen, Germany
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5
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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.
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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
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6
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Powell SK, O'Shea C, Brennand KJ, Akbarian S. Parsing the Functional Impact of Noncoding Genetic Variants in the Brain Epigenome. Biol Psychiatry 2021; 89:65-75. [PMID: 33131715 PMCID: PMC7718420 DOI: 10.1016/j.biopsych.2020.06.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 12/31/2022]
Abstract
The heritability of common psychiatric disorders has motivated global efforts to identify risk-associated genetic variants and elucidate molecular pathways connecting DNA sequence to disease-associated brain dysfunction. The overrepresentation of risk variants among gene regulatory loci instead of protein-coding loci, however, poses a unique challenge in discerning which among the many thousands of variants identified contribute functionally to disease etiology. Defined broadly, psychiatric epigenomics seeks to understand the effects of disease-associated genetic variation on functional readouts of chromatin in an effort to prioritize variants in terms of their impact on gene expression in the brain. Here, we provide an overview of epigenomic mapping in the human brain and highlight findings of particular relevance to psychiatric genetics. Computational methods, including convolutional neuronal networks, and other machine learning approaches hold great promise for elucidating the functional impact of both common and rare genetic variants, thereby refining the epigenomic architecture of psychiatric disorders and enabling integrative analyses of regulatory noncoding variants in the context of large population-level genome and phenome databases.
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Affiliation(s)
- Samuel K Powell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Callan O'Shea
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Kristen J Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York.
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7
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Rajarajan P, Akbarian S. Use of the epigenetic toolbox
to contextualize common variants associated with schizophrenia risk
. DIALOGUES IN CLINICAL NEUROSCIENCE 2020; 21:407-416. [PMID: 31949408 PMCID: PMC6952750 DOI: 10.31887/dcns.2019.21.4/sakbarian] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Schizophrenia is a debilitating psychiatric disorder with a complex genetic architecture and limited understanding of its neuropathology, reflected by the lack of diagnostic measures and effective pharmacological treatments. Geneticists have recently identified more than 145 risk loci comprising hundreds of common variants of small effect sizes, most of which lie in noncoding genomic regions. This review will discuss how the epigenetic toolbox can be applied to contextualize genetic findings in schizophrenia. Progress in next-generation sequencing, along with increasing methodological complexity, has led to the compilation of genome-wide maps of DNA methylation, histone modifications, RNA expression, and more. Integration of chromatin conformation datasets is one of the latest efforts in deciphering schizophrenia risk, allowing the identification of genes in contact with regulatory variants across 100s of kilobases. Large-scale multiomics studies will facilitate the prioritization of putative causal risk variants and gene networks that contribute to schizophrenia etiology, informing clinical diagnostics and treatment downstream.
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Affiliation(s)
- Prashanth Rajarajan
- Graduate School of Biomedical Sciences; Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai, New York, NY, US
| | - Schahram Akbarian
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai, New York, NY, US
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8
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Lu Y, Jiang J, Si J, Wu Q, Tian F, Jiao K, Mu Y, Dong P, Zhu Z. PDLIM5 improves depression-like behavior of prenatal stress offspring rats via methylation in male, but not female. Psychoneuroendocrinology 2020; 115:104629. [PMID: 32171900 DOI: 10.1016/j.psyneuen.2020.104629] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Prenatal stress (PS) contributes to depression-like behavior in the offspring. PDLIM5 is involved in the onset of mental disorders. This study is to investigate the role and mechanism of PDLIM5 in depression-like behavior of PS offspring rats. METHODS PS model was used to analyze the effects of different treatments to PS offspring rats with different sex, including PDLIM5, PDLIM5 shRNA and 5-aza-2' -deoxycytidine (5-azaD). The depression-like behavior was assessed by the sucrose preference test (SPT) and forced swimming test (FST). The mRNA and protein expression levels of PDLIM5 in the hippocampus of PS offspring rats were detected by qRT-PCR and western blot, respectively. The methylation of PDLIM5 promoter were analyzed by bisulfite sequencing. RESULTS Our data revealed that PS offspring rats showed a significant decrease in sucrose preference and a prolonged immobility time. Injection of PDLIM5 significantly improved the depression-like behavior in PS offspring rats, whereas administration of PDLIM5 shRNA aggravated it. In addition, PDLIM5 expression was decreased at the mRNA and protein levels, and the methylation level of PDLIM5 promoter was increased in hippocampus of PS male but not female offspring rats. Furthermore, microinjection of 5-azaD improved the PS induced depression-like behavior in offspring rats. Moreover, in male PS offspring rats, microinjection of 5-azaD reversed the effect of PS on PDLIM5 expression and promoter methylation. CONCLUSION PDLIM5 can significantly improve the depression-like behavior of both male and female PS offspring rats, while the PDLIM5 promoter methylation is only observed in male PS offspring rats. Our study may provide new mechanism for the pathogenesis of depression and experimental evidence for sex-based precise treatment.
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Affiliation(s)
- Yong Lu
- Central Laboratory, Heze Medical College, Heze, 274000, China
| | - Jiguo Jiang
- Central Laboratory, Heze Medical College, Heze, 274000, China
| | - Jingfang Si
- Central Laboratory, Heze Medical College, Heze, 274000, China
| | - Qi Wu
- Central Laboratory, Heze Medical College, Heze, 274000, China
| | - Fengjuan Tian
- Central Laboratory, Heze Medical College, Heze, 274000, China
| | - Keling Jiao
- Central Laboratory, Heze Medical College, Heze, 274000, China
| | - Yingjun Mu
- Central Laboratory, Heze Medical College, Heze, 274000, China
| | - Peng Dong
- Central Laboratory, Heze Medical College, Heze, 274000, China
| | - Zhongliang Zhu
- Maternal and Infant Health Research Institute and Medical College, Northwestern University, Xi'an, 710069, China.
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9
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The Relationship between DNA Methylation and Antidepressant Medications: A Systematic Review. Int J Mol Sci 2020; 21:ijms21030826. [PMID: 32012861 PMCID: PMC7037192 DOI: 10.3390/ijms21030826] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/25/2020] [Accepted: 01/26/2020] [Indexed: 01/31/2023] Open
Abstract
Major depressive disorder (MDD) is the leading cause of disability worldwide and is associated with high rates of suicide and medical comorbidities. Current antidepressant medications are suboptimal, as most MDD patients fail to achieve complete remission from symptoms. At present, clinicians are unable to predict which antidepressant is most effective for a particular patient, exposing patients to multiple medication trials and side effects. Since MDD’s etiology includes interactions between genes and environment, the epigenome is of interest for predictive utility and treatment monitoring. Epigenetic mechanisms of antidepressant medications are incompletely understood. Differences in epigenetic profiles may impact treatment response. A systematic literature search yielded 24 studies reporting the interaction between antidepressants and eight genes (BDNF, MAOA, SLC6A2, SLC6A4, HTR1A, HTR1B, IL6, IL11) and whole genome methylation. Methylation of certain sites within BDNF, SLC6A4, HTR1A, HTR1B, IL11, and the whole genome was predictive of antidepressant response. Comparing DNA methylation in patients during depressive episodes, during treatment, in remission, and after antidepressant cessation would help clarify the influence of antidepressant medications on DNA methylation. Individuals’ unique methylation profiles may be used clinically for personalization of antidepressant choice in the future.
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10
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Chromatin profiling of cortical neurons identifies individual epigenetic signatures in schizophrenia. Transl Psychiatry 2019; 9:256. [PMID: 31624234 PMCID: PMC6797775 DOI: 10.1038/s41398-019-0596-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 09/09/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
Both heritability and environment contribute to risk for schizophrenia. However, the molecular mechanisms of interactions between genetic and non-genetic factors remain unclear. Epigenetic regulation of neuronal genome may be a presumable mechanism in pathogenesis of schizophrenia. Here, we performed analysis of open chromatin landscape of gene promoters in prefrontal cortical (PFC) neurons from schizophrenic patients. We cataloged cell-type-based epigenetic signals of transcriptional start sites (TSS) marked by histone H3-K4 trimethylation (H3K4me3) across the genome in PFC from multiple schizophrenia subjects and age-matched control individuals. One of the top-ranked chromatin alterations was found in the major histocompatibility (MHC) locus on chromosome 6 highlighting the overlap between genetic and epigenetic risk factors in schizophrenia. The chromosome conformation capture (3C) analysis in human brain cells revealed the architecture of multipoint chromatin interactions between the schizophrenia-associated genetic and epigenetic polymorphic sites and distantly located HLA-DRB5 and BTNL2 genes. In addition, schizophrenia-specific chromatin modifications in neurons were particularly prominent for non-coding RNA genes, including an uncharacterized LINC01115 gene and recently identified BNRNA_052780. Notably, protein-coding genes with altered epigenetic state in schizophrenia are enriched for oxidative stress and cell motility pathways. Our results imply the rare individual epigenetic alterations in brain neurons are involved in the pathogenesis of schizophrenia.
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11
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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.
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12
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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: 126] [Impact Index Per Article: 25.2] [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.
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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
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13
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Zhang X, Zhang Y, Zhu X, Purmann C, Haney MS, Ward T, Khechaduri A, Yao J, Weissman SM, Urban AE. Local and global chromatin interactions are altered by large genomic deletions associated with human brain development. Nat Commun 2018; 9:5356. [PMID: 30559385 PMCID: PMC6297223 DOI: 10.1038/s41467-018-07766-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/09/2018] [Indexed: 01/18/2023] Open
Abstract
Large copy number variants (CNVs) in the human genome are strongly associated with common neurodevelopmental, neuropsychiatric disorders such as schizophrenia and autism. Here we report on the epigenomic effects of the prominent large deletion CNVs on chromosome 22q11.2 and on chromosome 1q21.1. We use Hi-C analysis of long-range chromosome interactions, including haplotype-specific Hi-C analysis, ChIP-Seq analysis of regulatory histone marks, and RNA-Seq analysis of gene expression patterns. We observe changes on all the levels of analysis, within the deletion boundaries, in the deletion flanking regions, along chromosome 22q, and genome wide. We detect gene expression changes as well as pronounced and multilayered effects on chromatin states, chromosome folding and on the topological domains of the chromatin, that emanate from the large CNV locus. These findings suggest basic principles of how such large genomic deletions can alter nuclear organization and affect genomic molecular activity. Copy number variants in the human genome (CNVs) are associated with neurodevelopmental and psychiatric disorders such as schizophrenia and autism. Here the authors investigate how the large deletion CNV on chromosome 22q11.2 alters chromatin organization.
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Affiliation(s)
- Xianglong Zhang
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA
| | - Ying Zhang
- Department of Genetics, Yale University, New Haven, 06520, CT, USA.,Department of Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai & Sema4 NYC Laboratory, New York, 10029, NY, USA
| | - Xiaowei Zhu
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA
| | - Carolin Purmann
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA
| | - Michael S Haney
- Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA
| | - Thomas Ward
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA
| | - Arineh Khechaduri
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | - Jie Yao
- Department of Cell Biology, Yale University School of Medicine, New Haven, 06520, CT, USA.,Sun Yat-sen University, Guangzhou, 510080, Guangdong, China
| | | | - Alexander E Urban
- Department of Psychiatry and Behavioral Sciences, Stanford University School of Medicine, Stanford, 94304, CA, USA. .,Department of Genetics, Stanford University School of Medicine, Stanford, 94304, CA, USA.
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14
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Kishi Y, Gotoh Y. Regulation of Chromatin Structure During Neural Development. Front Neurosci 2018; 12:874. [PMID: 30618540 PMCID: PMC6297780 DOI: 10.3389/fnins.2018.00874] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/09/2018] [Indexed: 11/13/2022] Open
Abstract
The regulation of genome architecture is a key determinant of gene transcription patterns and neural development. Advances in methodologies based on chromatin conformation capture (3C) have shed light on the genome-wide organization of chromatin in developmental processes. Here, we review recent discoveries regarding the regulation of three-dimensional (3D) chromatin conformation, including promoter-enhancer looping, and the dynamics of large chromatin domains such as topologically associated domains (TADs) and A/B compartments. We conclude with perspectives on how these conformational changes govern neural development and may go awry in disease states.
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Affiliation(s)
- Yusuke Kishi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
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15
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Chatterjee S, Cassel R, Schneider-Anthony A, Merienne K, Cosquer B, Tzeplaeff L, Halder Sinha S, Kumar M, Chaturbedy P, Eswaramoorthy M, Le Gras S, Keime C, Bousiges O, Dutar P, Petsophonsakul P, Rampon C, Cassel JC, Buée L, Blum D, Kundu TK, Boutillier AL. Reinstating plasticity and memory in a tauopathy mouse model with an acetyltransferase activator. EMBO Mol Med 2018; 10:e8587. [PMID: 30275019 PMCID: PMC6220301 DOI: 10.15252/emmm.201708587] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 12/17/2022] Open
Abstract
Chromatin acetylation, a critical regulator of synaptic plasticity and memory processes, is thought to be altered in neurodegenerative diseases. Here, we demonstrate that spatial memory and plasticity (LTD, dendritic spine formation) deficits can be restored in a mouse model of tauopathy following treatment with CSP-TTK21, a small-molecule activator of CBP/p300 histone acetyltransferases (HAT). At the transcriptional level, CSP-TTK21 re-established half of the hippocampal transcriptome in learning mice, likely through increased expression of neuronal activity genes and memory enhancers. At the epigenomic level, the hippocampus of tauopathic mice showed a significant decrease in H2B but not H3K27 acetylation levels, both marks co-localizing at TSS and CBP enhancers. Importantly, CSP-TTK21 treatment increased H2B acetylation levels at decreased peaks, CBP enhancers, and TSS, including genes associated with plasticity and neuronal functions, overall providing a 95% rescue of the H2B acetylome in tauopathic mice. This study is the first to provide in vivo proof-of-concept evidence that CBP/p300 HAT activation efficiently reverses epigenetic, transcriptional, synaptic plasticity, and behavioral deficits associated with Alzheimer's disease lesions in mice.
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Affiliation(s)
- Snehajyoti Chatterjee
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Raphaelle Cassel
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Anne Schneider-Anthony
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Karine Merienne
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Brigitte Cosquer
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Laura Tzeplaeff
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Sarmistha Halder Sinha
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Manoj Kumar
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Piyush Chaturbedy
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Muthusamy Eswaramoorthy
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Stéphanie Le Gras
- CNRS, Inserm, UMR 7104, Microarray and Sequencing Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
| | - Céline Keime
- CNRS, Inserm, UMR 7104, Microarray and Sequencing Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
| | - Olivier Bousiges
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- Laboratory of Biochemistry and Molecular Biology, Hôpital de Hautepierre, University Hospital of Strasbourg, Strasbourg, France
| | - Patrick Dutar
- Centre de Psychiatrie et Neurosciences, INSERM UMRS894, Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Petnoi Petsophonsakul
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Claire Rampon
- Centre de Recherches sur la Cognition Animale, Centre de Biologie Intégrative, CNRS, UPS, Université de Toulouse, Toulouse, France
| | - Jean-Christophe Cassel
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
| | - Luc Buée
- Inserm, CHU-Lille, UMR-S 1172, Alzheimer & Tauopathies, Université de Lille, Lille, France
| | - David Blum
- Inserm, CHU-Lille, UMR-S 1172, Alzheimer & Tauopathies, Université de Lille, Lille, France
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Anne-Laurence Boutillier
- Laboratoire de Neuroscience Cognitives et Adaptatives (LNCA), Université de Strasbourg, Strasbourg, France
- LNCA, CNRS UMR 7364, Strasbourg, France
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16
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Symmank J, Bayer C, Schmidt C, Hahn A, Pensold D, Zimmer-Bensch G. DNMT1 modulates interneuron morphology by regulating Pak6 expression through crosstalk with histone modifications. Epigenetics 2018; 13:536-556. [PMID: 29912614 DOI: 10.1080/15592294.2018.1475980] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epigenetic mechanisms of gene regulation, including DNA methylation and histone modifications, call increasing attention in the context of development and human health. Thereby, interactions between DNA methylating enzymes and histone modifications tremendously multiply the spectrum of potential regulatory functions. Epigenetic networks are critically involved in the establishment and functionality of neuronal circuits that are composed of gamma-aminobutyric acid (GABA)-positive inhibitory interneurons and excitatory principal neurons in the cerebral cortex. We recently reported a crucial role of the DNA methyltransferase 1 (DNMT1) during the migration of immature POA-derived cortical interneurons by promoting the migratory morphology through repression of Pak6. However, the DNMT1-dependent regulation of Pak6 expression appeared to occur independently of direct DNA methylation. Here, we show that in addition to its DNA methylating activity, DNMT1 can act on gene transcription by modulating permissive H3K4 and repressive H3K27 trimethylation in developing inhibitory interneurons, similar to what was found in other cell types. In particular, the transcriptional control of Pak6, interactions of DNMT1 with the Polycomb-repressor complex 2 (PCR2) core enzyme EZH2, mediating repressive H3K27 trimethylations at regulatory regions of the Pak6 gene locus. Similar to what was observed upon Dnmt1 depletion, inhibition of EZH2 caused elevated Pak6 expression levels accompanied by increased morphological complexity, which was rescued by siRNA-mediated downregulation of Pak6 expression. Together, our data emphasise the relevance of DNMT1-dependent crosstalk with histone tail methylation for transcriptional control of genes like Pak6 required for proper cortical interneuron migration.
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Affiliation(s)
- Judit Symmank
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Cathrin Bayer
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Christiane Schmidt
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Anne Hahn
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Daniel Pensold
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany
| | - Geraldine Zimmer-Bensch
- a Institute of Human Genetics , University Hospital Jena , Jena , Germany.,b Institute for Biology II , Division of Functional Epigenetics in the Animal Model, RWTH Aachen University , Aachen , Germany
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17
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Martin LJ, Chang Q. DNA Damage Response and Repair, DNA Methylation, and Cell Death in Human Neurons and Experimental Animal Neurons Are Different. J Neuropathol Exp Neurol 2018; 77:636-655. [PMID: 29788379 PMCID: PMC6005106 DOI: 10.1093/jnen/nly040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Neurological disorders affecting individuals in infancy to old age elude interventions for meaningful protection against neurodegeneration, and preclinical work has not translated to humans. We studied human neuron responses to injury and death stimuli compared to those of animal neurons in culture under similar settings of insult (excitotoxicity, oxidative stress, and DNA damage). Human neurons were differentiated from a cortical neuron cell line and the embryonic stem cell-derived H9 line. Mouse neurons were differentiated from forebrain neural stem cells and embryonic cerebral cortex; pig neurons were derived from forebrain neural stem cells. Mitochondrial morphology was different in human and mouse neurons. Human and mouse neurons challenged with DNA-damaging agent camptothecin showed different chromatin condensation, cell death, and DNA damage sensor activation. DNA damage accumulation and repair kinetics differed among human, mouse, and pig neurons. Promoter CpG island methylation microarrays showed significant differential DNA methylation in human and mouse neurons after injury. Therefore, DNA damage response, DNA repair, DNA methylation, and autonomous cell death mechanisms in human neurons and experimental animal neurons are different.
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Affiliation(s)
- Lee J Martin
- Department of Pathology, Division of Neuropathology
- Pathobiology Graduate Training Program
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Qing Chang
- Department of Pathology, Division of Neuropathology
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18
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Abstract
BACKGROUND Genetic studies have been consistent that bipolar disorder type I (BPI) runs in families and that this familial aggregation is strongly influenced by genes. In a preliminary study, we proved that anxiety trait meets endophenotype criteria for BPI. METHODS We assessed 619 individuals from the Central Valley of Costa Rica (CVCR) who have received evaluation for anxiety following the same methodological procedure used for the initial pilot study. Our goal was to conduct a multipoint quantitative trait linkage analysis to identify quantitative trait loci (QTLs) related to anxiety trait in subjects with BPI. We conducted the statistical analyses using Quantitative Trait Loci method (Variance-components models), implemented in Sequential Oligogenic Linkage Analysis Routines (SOLAR), using 5606 single nucleotide polymorphism (SNPs). RESULTS We identified a suggestive linkage signal with a LOD score of 2.01 at chromosome 2 (2q13-q14). LIMITATIONS Since confounding factors such as substance abuse, medical illness and medication history were not assessed in our study, these conclusions should be taken as preliminary. CONCLUSIONS We conclude that region 2q13-q14 may harbor a candidate gene(s) with an important role in the pathophysiology of BPI and anxiety.
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19
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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.
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20
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Chromosomal contacts connect loci associated with autism, BMI and head circumference phenotypes. Mol Psychiatry 2017; 22:836-849. [PMID: 27240531 PMCID: PMC5508252 DOI: 10.1038/mp.2016.84] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 03/18/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022]
Abstract
Copy number variants (CNVs) are major contributors to genomic imbalance disorders. Phenotyping of 137 unrelated deletion and reciprocal duplication carriers of the distal 16p11.2 220 kb BP2-BP3 interval showed that these rearrangements are associated with autism spectrum disorders and mirror phenotypes of obesity/underweight and macrocephaly/microcephaly. Such phenotypes were previously associated with rearrangements of the non-overlapping proximal 16p11.2 600 kb BP4-BP5 interval. These two CNV-prone regions at 16p11.2 are reciprocally engaged in complex chromatin looping, as successfully confirmed by 4C-seq, fluorescence in situ hybridization and Hi-C, as well as coordinated expression and regulation of encompassed genes. We observed that genes differentially expressed in 16p11.2 BP4-BP5 CNV carriers are concomitantly modified in their chromatin interactions, suggesting that disruption of chromatin interplays could participate in the observed phenotypes. We also identified cis- and trans-acting chromatin contacts to other genomic regions previously associated with analogous phenotypes. For example, we uncovered that individuals with reciprocal rearrangements of the trans-contacted 2p15 locus similarly display mirror phenotypes on head circumference and weight. Our results indicate that chromosomal contacts' maps could uncover functionally and clinically related genes.
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21
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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.
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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.
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22
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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.
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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
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23
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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.
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24
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Montalvo-Ortiz JL, Gelernter J, Hudziak J, Kaufman J. RDoC and translational perspectives on the genetics of trauma-related psychiatric disorders. Am J Med Genet B Neuropsychiatr Genet 2016; 171B:81-91. [PMID: 26592203 PMCID: PMC4754782 DOI: 10.1002/ajmg.b.32395] [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: 07/22/2015] [Accepted: 10/09/2015] [Indexed: 01/01/2023]
Abstract
Individuals with a history of child abuse are at high risk for depression, anxiety disorders, aggressive behavior, and substance use problems. The goal of this paper is to review studies of the genetics of these stress-related psychiatric disorders. An informative subset of studies that examined candidate gene by environment (GxE) predictors of these psychiatric problems in individuals maltreated as children is reviewed, together with extant genome wide association studies (GWAS). Emerging findings on epigenetic changes associated with adverse early experiences are also reviewed. Meta-analytic support and replicated findings are evident for several genetic risk factors; however, extant research suggests the effects are pleiotropic. Genetic factors are not associated with distinct psychiatric disorders, but rather diverse clinical phenotypes. Research also suggests adverse early life experiences are associated with changes in gene expression of multiple known candidate genes, genes involved in DNA transcription and translation, and genes necessary for brain circuitry development, with changes in gene expression reported in key brain structures implicated in the pathophysiology of psychiatric and substance use disorders. The finding of pleiotropy highlights the value of using the Research Domain Criteria (RDoC) framework in future studies of the genetics of stress-related psychiatric disorders, and not trying simply to link genes to multifaceted clinical syndromes, but to more limited phenotypes that map onto distinct neural circuits. Emerging work in the field of epigenetics also suggests that translational studies that integrate numerous unbiased genome-wide approaches will help to further unravel the genetics of stress-related psychiatric disorders.
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Affiliation(s)
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut,Veteran's Administration Connecticut Health Care Center, Newington, Connecticut
| | - James Hudziak
- Vermont Center for Children, Youth, and Families, University of Vermont, Burlington, Vermont
| | - Joan Kaufman
- Center for Child and Family Traumatic Stress, Kennedy Krieger Institute, Baltimore, Maryland,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland,Correspondence to: Joan Kaufman, Ph.D., Center for Child and Family Traumatic Stress, Kennedy Krieger Institute, 1750 East Fairmont Street, Baltimore, MD 21231.
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25
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Barr CL, Misener VL. Decoding the non-coding genome: elucidating genetic risk outside the coding genome. GENES, BRAIN, AND BEHAVIOR 2016; 15:187-204. [PMID: 26515765 PMCID: PMC4833497 DOI: 10.1111/gbb.12269] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/19/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
Current evidence emerging from genome-wide association studies indicates that the genetic underpinnings of complex traits are likely attributable to genetic variation that changes gene expression, rather than (or in combination with) variation that changes protein-coding sequences. This is particularly compelling with respect to psychiatric disorders, as genetic changes in regulatory regions may result in differential transcriptional responses to developmental cues and environmental/psychosocial stressors. Until recently, however, the link between transcriptional regulation and psychiatric genetic risk has been understudied. Multiple obstacles have contributed to the paucity of research in this area, including challenges in identifying the positions of remote (distal from the promoter) regulatory elements (e.g. enhancers) and their target genes and the underrepresentation of neural cell types and brain tissues in epigenome projects - the availability of high-quality brain tissues for epigenetic and transcriptome profiling, particularly for the adolescent and developing brain, has been limited. Further challenges have arisen in the prediction and testing of the functional impact of DNA variation with respect to multiple aspects of transcriptional control, including regulatory-element interaction (e.g. between enhancers and promoters), transcription factor binding and DNA methylation. Further, the brain has uncommon DNA-methylation marks with unique genomic distributions not found in other tissues - current evidence suggests the involvement of non-CG methylation and 5-hydroxymethylation in neurodevelopmental processes but much remains unknown. We review here knowledge gaps as well as both technological and resource obstacles that will need to be overcome in order to elucidate the involvement of brain-relevant gene-regulatory variants in genetic risk for psychiatric disorders.
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Affiliation(s)
- C. L. Barr
- Toronto Western Research Institute, University Health Network, Toronto, ON, Canada
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
| | - V. L. Misener
- Toronto Western Research Institute, University Health Network, Toronto, ON, Canada
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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: 189] [Impact Index Per Article: 21.0] [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.
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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
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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.
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Berretta S, Heckers S, Benes FM. Searching human brain for mechanisms of psychiatric disorders. Implications for studies on schizophrenia. Schizophr Res 2015; 167:91-7. [PMID: 25458567 PMCID: PMC4427537 DOI: 10.1016/j.schres.2014.10.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 10/10/2014] [Accepted: 10/13/2014] [Indexed: 12/14/2022]
Abstract
In the past 25years, research on the human brain has been providing a clear path toward understanding the pathophysiology of psychiatric illnesses. The successes that have been accrued are matched by significant difficulties identifying and controlling a large number of potential confounding variables. By systematically and effectively accounting for unwanted variance in data from imaging and postmortem human brain studies, meaningful and reliable information regarding the pathophysiology of human brain disorders can be obtained. This perspective paper focuses on postmortem investigations to discuss some of the most challenging sources of variance, including diagnosis, comorbidity, substance abuse and pharmacological treatment, which confound investigations of the human brain.
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Affiliation(s)
- Sabina Berretta
- Translational Neuroscience Laboratory, McLean Hospital, 115 Mill St., Belmont, MA 02478, USA; Department of Psychiatry, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA; Program in Neuroscience, Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA.
| | - Stephan Heckers
- Department of Psychiatry, Vanderbilt University. 161 21st Ave S. #T1217 Nashville, TN, USA
| | - Francine M. Benes
- Dept. of Psychiatry, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA,Program in Neuroscience, Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA,Program in Structural and Molecular Neuroscience, 115 Mill St. Belmont MA, 02478, USA
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Kaufman J, Gelernter J, Hudziak J, Tyrka AR, Coplan JD. The Research Domain Criteria (RDoC) Project and Studies of Risk and Resilience in Maltreated Children. J Am Acad Child Adolesc Psychiatry 2015; 54. [PMID: 26210330 PMCID: PMC4515569 DOI: 10.1016/j.jaac.2015.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE The Research Domain Criteria (RDoC) project was initiated to develop, for research purposes, new ways of classifying mental disorders based on dimensions of observable behavior and neurobiological measures. This article reviews the rationale behind the RDoC program, its goals, and central tenets; discusses application of an RDoC framework to research with maltreated children; and highlights some clinical implications of this work. METHOD Published RDoC papers were reviewed, together with relevant preclinical and clinical studies that guide our work on risk and resilience in maltreated children. RESULTS The ultimate long-term goal of the RDoC initiative is precision medicine in psychiatry. In the interim, the RDoC initiative provides a framework to organize research to help develop the database required to derive a new psychiatric nomenclature that can appropriately match treatments to patients. The primary focus of RDoC is on neural circuitry, with levels of analyses that span from molecules to behavior. There has been some concern that the RDoC framework is reductionist, with an overemphasis on neural circuits and genetics; however, the briefly reviewed, burgeoning literature on neuroplasticity and epigenetics highlights that this concern is unwarranted, as one cannot study neural circuits and genetics without considering experience. CONCLUSION The study of maltreated children has a number of advantages for the RDoC project, including the following: study of a subset of patients who are often not responsive to standard interventions; examination of a relatively homogenous sample with onset of psychopathology proposed to be associated with stress-related mechanisms; and well-established, relevant animal models to facilitate translational research.
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Affiliation(s)
- Joan Kaufman
- Yale University School of Medicine and Veteran's Administration Connecticut Health Care Center, New Haven, CT; Kennedy Krieger Institute and Johns Hopkins School of Medicine, Baltimore.
| | | | - James Hudziak
- Vermont Center for Children, Youth, and Families, University of Vermont, Burlington
| | - Audrey R. Tyrka
- Butler Hospital Mood Disorders Research Program, Laboratory for Clinical and Translational Neuroscience, and the Alpert Medical School of Brown University, Providence, RI
| | - Jeremy D. Coplan
- State University of New York Downstate Medical Center, New York City
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30
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Menke A, Binder EB. Epigenetic alterations in depression and antidepressant treatment. DIALOGUES IN CLINICAL NEUROSCIENCE 2015. [PMID: 25364288 PMCID: PMC4214180 DOI: 10.31887/dcns.2014.16.3/amenke] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Epigenetic modifications control chromatin structure and function, and thus mediate changes in gene expression, ultimately influencing protein levels. Recent research indicates that environmental events can induce epigenetic changes and, by this, contribute to long-term changes in neural circuits and endocrine systems associated with altered risk for stress-related psychiatric disorders such as major depression. In this review, we describe recent approaches investigating epigenetic modifications associated with altered risk for major depression or response to antidepressant drugs, both on the candidate gene levels as well as the genome-wide level. In this review we focus on DNA methylation, as this is the most investigated epigenetic change in depression research.
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Affiliation(s)
- Andreas Menke
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Elisabeth B Binder
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia, USA
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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.
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Affiliation(s)
- Schahram Akbarian
- Department of Psychiatry, Friedman Brain Institute Icahn School of Medicine at Mount Sinai, New York, USA
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32
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Feng J, Shao N, Szulwach KE, Vialou V, Huynh J, Zhong C, Le T, Ferguson D, Cahill ME, Li Y, Koo JW, Ribeiro E, Labonte B, Laitman BM, Estey D, Stockman V, Kennedy P, Couroussé T, Mensah I, Turecki G, Faull KF, Ming GL, Song H, Fan G, Casaccia P, Shen L, Jin P, Nestler EJ. Role of Tet1 and 5-hydroxymethylcytosine in cocaine action. Nat Neurosci 2015; 18:536-44. [PMID: 25774451 DOI: 10.1038/nn.3976] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/17/2015] [Indexed: 12/12/2022]
Abstract
Ten-eleven translocation (TET) enzymes mediate the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which is enriched in brain, and its ultimate DNA demethylation. However, the influence of TET and 5hmC on gene transcription in brain remains elusive. We found that ten-eleven translocation protein 1 (TET1) was downregulated in mouse nucleus accumbens (NAc), a key brain reward structure, by repeated cocaine administration, which enhanced behavioral responses to cocaine. We then identified 5hmC induction in putative enhancers and coding regions of genes that have pivotal roles in drug addiction. Such induction of 5hmC, which occurred similarly following TET1 knockdown alone, correlated with increased expression of these genes as well as with their alternative splicing in response to cocaine administration. In addition, 5hmC alterations at certain loci persisted for at least 1 month after cocaine exposure. Together, these reveal a previously unknown epigenetic mechanism of cocaine action and provide new insight into how 5hmC regulates transcription in brain in vivo.
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Affiliation(s)
- Jian Feng
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ningyi Shao
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Keith E Szulwach
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Vincent Vialou
- 1] Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA. [2] Institut National de la Santé et de la Recherhe Médicale (INSERM) U1130, CNRS UMR8246, UPMC UM18, Neuroscience Paris Seine, Paris, France
| | - Jimmy Huynh
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Chun Zhong
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Thuc Le
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Deveroux Ferguson
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Michael E Cahill
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yujing Li
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Ja Wook Koo
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Efrain Ribeiro
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benoit Labonte
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Benjamin M Laitman
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - David Estey
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Victoria Stockman
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Pamela Kennedy
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Thomas Couroussé
- Institut National de la Santé et de la Recherhe Médicale (INSERM) U1130, CNRS UMR8246, UPMC UM18, Neuroscience Paris Seine, Paris, France
| | - Isaac Mensah
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Gustavo Turecki
- The McGill Group for Suicide Studies, Douglas Hospital Research Centre, McGill University, Montreal, Canada
| | - Kym F Faull
- Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Guo-li Ming
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Hongjun Song
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Guoping Fan
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Patrizia Casaccia
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Li Shen
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Eric J Nestler
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Satterlee JS, Beckel-Mitchener A, Little R, Procaccini D, Rutter JL, Lossie AC. Neuroepigenomics: Resources, Obstacles, and Opportunities. NEUROEPIGENETICS 2015; 1:2-13. [PMID: 25722961 PMCID: PMC4337407 DOI: 10.1016/j.nepig.2014.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Long-lived post-mitotic cells, such as the majority of human neurons, must respond effectively to ongoing changes in neuronal stimulation or microenvironmental cues through transcriptional and epigenomic regulation of gene expression. The role of epigenomic regulation in neuronal function is of fundamental interest to the neuroscience community, as these types of studies have transformed our understanding of gene regulation in post-mitotic cells. This perspective article highlights many of the resources available to researchers interested in neuroepigenomic investigations and discusses some of the current obstacles and opportunities in neuroepigenomics.
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Affiliation(s)
- John S. Satterlee
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Andrea Beckel-Mitchener
- National Institute on Mental Health (NIMH), Division of Neuroscience and Basic Behavioral Science, 6001 Executive Boulevard Bethesda, MD 20892-9641, USA
| | - Roger Little
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Dena Procaccini
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Joni L. Rutter
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Amy C. Lossie
- Office of Behavioral and Social Sciences Research (OBSSR), Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director/National Institutes of Health (NIH), 31 Center Drive, Bethesda, MD 20892, USA
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34
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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.
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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.
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35
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Roussos P, Mitchell AC, Voloudakis G, Fullard JF, Pothula VM, Tsang J, Stahl EA, Georgakopoulos A, Ruderfer DM, Charney A, Okada Y, Siminovitch KA, Worthington J, Padyukov L, Klareskog L, Gregersen PK, Plenge RM, Raychaudhuri S, Fromer M, Purcell SM, Brennand KJ, Robakis NK, Schadt EE, Akbarian S, Sklar P. A role for noncoding variation in schizophrenia. Cell Rep 2014; 9:1417-29. [PMID: 25453756 PMCID: PMC4255904 DOI: 10.1016/j.celrep.2014.10.015] [Citation(s) in RCA: 185] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/31/2014] [Accepted: 10/03/2014] [Indexed: 01/20/2023] Open
Abstract
A large portion of common variant loci associated with genetic risk for schizophrenia reside within noncoding sequence of unknown function. Here, we demonstrate promoter and enhancer enrichment in schizophrenia variants associated with expression quantitative trait loci (eQTL). The enrichment is greater when functional annotations derived from the human brain are used relative to peripheral tissues. Regulatory trait concordance analysis ranked genes within schizophrenia genome-wide significant loci for a potential functional role, based on colocalization of a risk SNP, eQTL, and regulatory element sequence. We identified potential physical interactions of noncontiguous proximal and distal regulatory elements. This was verified in prefrontal cortex and -induced pluripotent stem cell-derived neurons for the L-type calcium channel (CACNA1C) risk locus. Our findings point to a functional link between schizophrenia-associated noncoding SNPs and 3D genome architecture associated with chromosomal loopings and transcriptional regulation in the brain.
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Affiliation(s)
- Panos Roussos
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; James J. Peters VA Medical Center, Mental Illness Research Education and Clinical Center (MIRECC), 130 West Kingsbridge Road, Bronx, NY 10468, USA.
| | - Amanda C Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Georgios Voloudakis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John F Fullard
- 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
| | - Venu M Pothula
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan Tsang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eli A Stahl
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Douglas M Ruderfer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander Charney
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Yukinori Okada
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 230-0045, Japan; Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Katherine A Siminovitch
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Toronto General Research Institute, Toronto, ON M5G 2M9, Canada; Department of Medicine, University of Toronto, Toronto, ON M5S 2J7, Canada
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Musculoskeletal Research Centre, Institute for Inflammation and Repair, Manchester Academic Health Science Centre, University of Manchester, Manchester M13 9NT, UK; National Institute for Health Research, Manchester Musculoskeletal Biomedical Research Unit, Central Manchester University Hospitals National Health Service Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9NT, UK
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine (Solna), Karolinska Institutet, Stockholm 171 76, Sweden
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine (Solna), Karolinska Institutet, Stockholm 171 76, Sweden
| | - Peter K Gregersen
- The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, NY 11030, USA
| | - Robert M Plenge
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13 9NT, UK
| | - Menachem Fromer
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shaun M Purcell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, 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; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nikolaos K Robakis
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, 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; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pamela Sklar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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Menke A. Epigenetic alterations in depression and antidepressant treatment. DIALOGUES IN CLINICAL NEUROSCIENCE 2014; 16:395-404. [PMID: 25364288 PMCID: PMC4214180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 05/10/2024]
Abstract
Epigenetic modifications control chromatin structure and function, and thus mediate changes in gene expression, ultimately influencing protein levels. Recent research indicates that environmental events can induce epigenetic changes and, by this, contribute to long-term changes in neural circuits and endocrine systems associated with altered risk for stress-related psychiatric disorders such as major depression. In this review, we describe recent approaches investigating epigenetic modifications associated with altered risk for major depression or response to antidepressant drugs, both on the candidate gene levels as well as the genome-wide level. In this review we focus on DNA methylation, as this is the most investigated epigenetic change in depression research.
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Affiliation(s)
- Andreas Menke
- Department of Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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37
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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.
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Gamo NJ, Sawa A. Human stem cells and surrogate tissues for basic and translational study of mental disorders. Biol Psychiatry 2014; 75:918-9. [PMID: 24862565 PMCID: PMC4302385 DOI: 10.1016/j.biopsych.2014.03.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 03/14/2014] [Indexed: 12/28/2022]
Affiliation(s)
| | - Akira Sawa
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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39
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The role of DNA methylation in stress-related psychiatric disorders. Neuropharmacology 2014; 80:115-32. [DOI: 10.1016/j.neuropharm.2014.01.013] [Citation(s) in RCA: 219] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/19/2013] [Accepted: 01/09/2014] [Indexed: 02/06/2023]
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40
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Sprooten E, Knowles EE, McKay DR, Göring HH, Curran JE, Kent JW, Carless MA, Dyer TD, Drigalenko EI, Olvera RL, Fox PT, Almasy L, Duggirala R, Kochunov P, Blangero J, Glahn DC. Common genetic variants and gene expression associated with white matter microstructure in the human brain. Neuroimage 2014; 97:252-61. [PMID: 24736177 DOI: 10.1016/j.neuroimage.2014.04.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 03/29/2014] [Accepted: 04/07/2014] [Indexed: 12/29/2022] Open
Abstract
Identifying genes that contribute to white matter microstructure should provide insights into the neurobiological processes that regulate white matter development, plasticity and pathology. We detected five significant SNPs using genome-wide association analysis on a global measure of fractional anisotropy in 776 individuals from large extended pedigrees. Genetic correlations and genome-wide association results indicated that the genetic signal was largely homogeneous across white matter regions. Using RNA transcripts derived from lymphocytes in the same individuals, we identified two genes (GNA13 and CCDC91) that are likely to be cis-regulated by top SNPs, and whose expression levels were also genetically correlated with fractional anisotropy. A transcript of HTR7 was phenotypically associated with FA, and was associated with an intronic genome-wide significant SNP. These results encourage further research in the mechanisms by which GNA13, HTR7 and CCDC91 influence brain structure, and emphasize a role for g-protein signaling in the development and maintenance of white matter microstructure in health and disease.
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Affiliation(s)
- Emma Sprooten
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, New Haven, CT, USA; Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, 200 Retreat Avenue, CT, USA.
| | - Emma E Knowles
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, New Haven, CT, USA; Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, 200 Retreat Avenue, CT, USA
| | - D Reese McKay
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, New Haven, CT, USA; Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, 200 Retreat Avenue, CT, USA
| | - Harald H Göring
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, USA
| | - Joanne E Curran
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, USA
| | - Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, USA
| | - Melanie A Carless
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, USA
| | - Thomas D Dyer
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, USA
| | - Eugene I Drigalenko
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, USA
| | - Rene L Olvera
- Department of Psychiatry, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX, USA
| | - Peter T Fox
- Research Imaging Institute, University of Texas Health Science Center San Antonio, 8403 Floyd Curl Drive, San Antonio, TX, USA; South Texas Veterans Health System, 7400 Merton Minter, San Antonio, TX 78229, USA
| | - Laura Almasy
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, USA
| | - Ravi Duggirala
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, USA
| | - Peter Kochunov
- Maryland Psychiatric Research Center, Department of Psychiatry, University of Maryland School of Medicine, Baltimore, MD, USA
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, PO Box 760549, San Antonio, TX, USA
| | - David C Glahn
- Department of Psychiatry, Yale University School of Medicine, 300 George Street, New Haven, CT, USA; Olin Neuropsychiatry Research Center, Institute of Living, Hartford Hospital, 200 Retreat Avenue, CT, USA
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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.
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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
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