1
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Sportelli L, Eisenberg DP, Passiatore R, D'Ambrosio E, Antonucci LA, Bettina JS, Chen Q, Goldman AL, Gregory MD, Griffiths K, Hyde TM, Kleinman JE, Pardiñas AF, Parihar M, Popolizio T, Rampino A, Shin JH, Veronese M, Ulrich WS, Zink CF, Bertolino A, Howes OD, Berman KF, Weinberger DR, Pergola G. Dopamine signaling enriched striatal gene set predicts striatal dopamine synthesis and physiological activity in vivo. Nat Commun 2024; 15:3342. [PMID: 38688917 PMCID: PMC11061310 DOI: 10.1038/s41467-024-47456-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/22/2024] [Indexed: 05/02/2024] Open
Abstract
The polygenic architecture of schizophrenia implicates several molecular pathways involved in synaptic function. However, it is unclear how polygenic risk funnels through these pathways to translate into syndromic illness. Using tensor decomposition, we analyze gene co-expression in the caudate nucleus, hippocampus, and dorsolateral prefrontal cortex of post-mortem brain samples from 358 individuals. We identify a set of genes predominantly expressed in the caudate nucleus and associated with both clinical state and genetic risk for schizophrenia that shows dopaminergic selectivity. A higher polygenic risk score for schizophrenia parsed by this set of genes predicts greater dopamine synthesis in the striatum and greater striatal activation during reward anticipation. These results translate dopamine-linked genetic risk variation into in vivo neurochemical and hemodynamic phenotypes in the striatum that have long been implicated in the pathophysiology of schizophrenia.
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Affiliation(s)
- Leonardo Sportelli
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Daniel P Eisenberg
- Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, NIH, DHHS, Bethesda, MD, USA
| | - Roberta Passiatore
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Enrico D'Ambrosio
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Linda A Antonucci
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Jasmine S Bettina
- Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, NIH, DHHS, Bethesda, MD, USA
| | - Qiang Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Aaron L Goldman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Michael D Gregory
- Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, NIH, DHHS, Bethesda, MD, USA
| | - Kira Griffiths
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
- Holmusk Technologies, New York, NY, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Madhur Parihar
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Teresa Popolizio
- Radiology Department, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Antonio Rampino
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Azienda Ospedaliero Universitaria Consorziale Policlinico, Bari, Italy
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Mattia Veronese
- Department of Information Engineering, University of Padua, Padua, Italy
- Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - William S Ulrich
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Caroline F Zink
- Baltimore Research and Education Foundation, Baltimore, MD, USA
| | - Alessandro Bertolino
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Azienda Ospedaliero Universitaria Consorziale Policlinico, Bari, Italy
| | - Oliver D Howes
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Karen F Berman
- Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, NIH, DHHS, Bethesda, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Giulio Pergola
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA.
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy.
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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2
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Shastri GG, Sudre G, Ahn K, Jung B, Kolachana B, Auluck PK, Elnitski L, Marenco S, Shaw P. Cortico-striatal differences in the epigenome in attention-deficit/ hyperactivity disorder. Transl Psychiatry 2024; 14:189. [PMID: 38605038 PMCID: PMC11009227 DOI: 10.1038/s41398-024-02896-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/20/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
While epigenetic modifications have been implicated in ADHD through studies of peripheral tissue, to date there has been no examination of the epigenome of the brain in the disorder. To address this gap, we mapped the methylome of the caudate nucleus and anterior cingulate cortex in post-mortem tissue from fifty-eight individuals with or without ADHD. While no single probe showed adjusted significance in differential methylation, several differentially methylated regions emerged. These regions implicated genes involved in developmental processes including neurogenesis and the differentiation of oligodendrocytes and glial cells. We demonstrate a significant association between differentially methylated genes in the caudate and genes implicated by GWAS not only in ADHD but also in autistic spectrum, obsessive compulsive and bipolar affective disorders through GWAS. Using transcriptomic data available on the same subjects, we found modest correlations between the methylation and expression of genes. In conclusion, this study of the cortico-striatal methylome points to gene and gene pathways involved in neurodevelopment, consistent with studies of common and rare genetic variation, as well as the post-mortem transcriptome in ADHD.
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Affiliation(s)
- Gauri G Shastri
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Gustavo Sudre
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Kwangmi Ahn
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Benjamin Jung
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Bhaskar Kolachana
- Human Brain Collection Core, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Pavan K Auluck
- Human Brain Collection Core, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Laura Elnitski
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA
| | - Stefano Marenco
- Human Brain Collection Core, National Institute of Mental Health, NIH, Bethesda, MD, 20892, USA
| | - Philip Shaw
- Social and Behavioral Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, 20892, USA.
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3
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Wang S, Deng X, Wu Y, Wu Y, Zhou S, Yang J, Huang Y. Understanding the pathogenesis of brain arteriovenous malformation: genetic variations, epigenetics, signaling pathways, and immune inflammation. Hum Genet 2023; 142:1633-1649. [PMID: 37768356 DOI: 10.1007/s00439-023-02605-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/10/2023] [Indexed: 09/29/2023]
Abstract
Brain arteriovenous malformation (BAVM) is a rare but serious cerebrovascular disease whose pathogenesis has not been fully elucidated. Studies have found that epigenetic regulation, genetic variation and their signaling pathways, immune inflammation, may be the cause of BAVM the main reason. This review comprehensively analyzes the key pathways and inflammatory factors related to BAVMs, and explores their interplay with epigenetic regulation and genetics. Studies have found that epigenetic regulation such as DNA methylation, non-coding RNAs and m6A RNA modification can regulate endothelial cell proliferation, apoptosis, migration and damage repair of vascular malformations through different target gene pathways. Gene defects such as KRAS, ACVRL1 and EPHB4 lead to a disordered vascular environment, which may promote abnormal proliferation of blood vessels through ERK, NOTCH, mTOR, Wnt and other pathways. PDGF-B and PDGFR-β were responsible for the recruitment of vascular adventitial cells and smooth muscle cells in the extracellular matrix environment of blood vessels, and played an important role in the pathological process of BAVM. Recent single-cell sequencing data revealed the diversity of various cell types within BAVM, as well as the heterogeneous expression of vascular-associated antigens, while neutrophils, macrophages and cytokines such as IL-6, IL-1, TNF-α, and IL-17A in BAVM tissue were significantly increased. Currently, there are no specific drugs targeting BAVMs, and biomarkers for BAVM formation, bleeding, and recurrence are lacking clinically. Therefore, further studies on molecular biological mechanisms will help to gain insight into the pathogenesis of BAVM and develop potential therapeutic strategies.
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Affiliation(s)
- Shiyi Wang
- Department of Neurology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, Zhejiang, China
| | - Xinpeng Deng
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, Zhejiang, China
| | - Yuefei Wu
- Department of Neurology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, Zhejiang, China
| | - Yiwen Wu
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, Zhejiang, China
| | - Shengjun Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, Zhejiang, China
| | - Jianhong Yang
- Department of Neurology, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, Zhejiang, China.
| | - Yi Huang
- Department of Neurosurgery, The First Affiliated Hospital of Ningbo University, Ningbo, 315010, Zhejiang, China.
- Key Laboratory of Precision Medicine for Atherosclerotic Diseases of Zhejiang Province, Ningbo, 315010, Zhejiang, China.
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4
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Zhu Z, Chen X, Zhang S, Yu R, Qi C, Cheng L, Zhang X. Leveraging molecular quantitative trait loci to comprehend complex diseases/traits from the omics perspective. Hum Genet 2023; 142:1543-1560. [PMID: 37755483 DOI: 10.1007/s00439-023-02602-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023]
Abstract
Comprehending the molecular basis of quantitative genetic variation is a principal goal for complex diseases or traits. Molecular quantitative trait loci (molQTLs) have made it possible to investigate the effects of genetic variants hiding behind large-scale omics data. A deeper understanding of molQTL is urgently required in light of the multi-dimensionalization of omics data to more fully elucidate the pertinent biological mechanisms. Herein, we reviewed molQTLs with the corresponding resource from the omics perspective and further discussed the integrative strategy of GWAS-molQTL to infer their causal effects. Subsequently, we described the opportunities and challenges encountered by molQTL. The case studies showed that molQTL is essential for complex diseases and traits, whether single- or multi-omics QTLs. Overall, we highlighted the functional significance of genetic variants to employ the discovery of molQTL in complex diseases and traits.
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Affiliation(s)
- Zijun Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xinyu Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Rui Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Changlu Qi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China.
| | - Xue Zhang
- NHC Key Laboratory of Molecular Probe and Targeted Diagnosis and Therapy, Harbin Medical University, Harbin, 150028, Heilongjiang, China
- McKusick-Zhang Center for Genetic Medicine, State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China
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5
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Pergola G, Parihar M, Sportelli L, Bharadwaj R, Borcuk C, Radulescu E, Bellantuono L, Blasi G, Chen Q, Kleinman JE, Wang Y, Sripathy SR, Maher BJ, Monaco A, Rossi F, Shin JH, Hyde TM, Bertolino A, Weinberger DR. Consensus molecular environment of schizophrenia risk genes in coexpression networks shifting across age and brain regions. SCIENCE ADVANCES 2023; 9:eade2812. [PMID: 37058565 PMCID: PMC10104472 DOI: 10.1126/sciadv.ade2812] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
Schizophrenia is a neurodevelopmental brain disorder whose genetic risk is associated with shifting clinical phenomena across the life span. We investigated the convergence of putative schizophrenia risk genes in brain coexpression networks in postmortem human prefrontal cortex (DLPFC), hippocampus, caudate nucleus, and dentate gyrus granule cells, parsed by specific age periods (total N = 833). The results support an early prefrontal involvement in the biology underlying schizophrenia and reveal a dynamic interplay of regions in which age parsing explains more variance in schizophrenia risk compared to lumping all age periods together. Across multiple data sources and publications, we identify 28 genes that are the most consistently found partners in modules enriched for schizophrenia risk genes in DLPFC; twenty-three are previously unidentified associations with schizophrenia. In iPSC-derived neurons, the relationship of these genes with schizophrenia risk genes is maintained. The genetic architecture of schizophrenia is embedded in shifting coexpression patterns across brain regions and time, potentially underwriting its shifting clinical presentation.
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Affiliation(s)
- Giulio Pergola
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Madhur Parihar
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Leonardo Sportelli
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Rahul Bharadwaj
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Christopher Borcuk
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Eugenia Radulescu
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Loredana Bellantuono
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Istituto Nazionale di Fisica Nucleare, Bari, Italy
| | - Giuseppe Blasi
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Azienda Ospedaliero Universitaria Consorziale Policlinico, Bari, Italy
| | - Qiang Chen
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yanhong Wang
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Srinidhi Rao Sripathy
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Brady J. Maher
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alfonso Monaco
- Istituto Nazionale di Fisica Nucleare, Bari, Italy
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Fabiana Rossi
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
| | - Joo Heon Shin
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alessandro Bertolino
- Group of Psychiatric Neuroscience, Department of Translational Biomedicine and Neuroscience, University of Bari Aldo Moro, Bari, Italy
- Azienda Ospedaliero Universitaria Consorziale Policlinico, Bari, Italy
| | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, USA
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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6
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Trangle SS, Rosenberg T, Parnas H, Levy G, Bar E, Marco A, Barak B. In individuals with Williams syndrome, dysregulation of methylation in non-coding regions of neuronal and oligodendrocyte DNA is associated with pathology and cortical development. Mol Psychiatry 2023; 28:1112-1127. [PMID: 36577841 DOI: 10.1038/s41380-022-01921-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 12/29/2022]
Abstract
Williams syndrome (WS) is a neurodevelopmental disorder caused by a heterozygous micro-deletion in the WS critical region (WSCR) and is characterized by hyper-sociability and neurocognitive abnormalities. Nonetheless, whether and to what extent WSCR deletion leads to epigenetic modifications in the brain and induces pathological outcomes remains largely unknown. By examining DNA methylation in frontal cortex, we revealed genome-wide disruption in the methylome of individuals with WS, as compared to typically developed (TD) controls. Surprisingly, differentially methylated sites were predominantly annotated as introns and intergenic loci and were found to be highly enriched around binding sites for transcription factors that regulate neuronal development, plasticity and cognition. Moreover, by utilizing enhancer-promoter interactome data, we confirmed that most of these loci function as active enhancers in the human brain or as target genes of transcriptional networks associated with myelination, oligodendrocyte (OL) differentiation, cognition and social behavior. Cell type-specific methylation analysis revealed aberrant patterns in the methylation of active enhancers in neurons and OLs, and important neuron-glia interactions that might be impaired in individuals with WS. Finally, comparison of methylation profiles from blood samples of individuals with WS and healthy controls, along with other data collected in this study, identified putative targets of endophenotypes associated with WS, which can be used to define brain-risk loci for WS outside the WSCR locus, as well as for other associated pathologies. In conclusion, our study illuminates the brain methylome landscape of individuals with WS and sheds light on how these aberrations might be involved in social behavior and physiological abnormalities. By extension, these results may lead to better diagnostics and more refined therapeutic targets for WS.
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Affiliation(s)
- Sari Schokoroy Trangle
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Tali Rosenberg
- Neuro-Epigenetics Laboratory, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Hadar Parnas
- Neuro-Epigenetics Laboratory, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel
| | - Gilad Levy
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Ela Bar
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel.,The School of Neurobiology, Biochemistry & Biophysics, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Asaf Marco
- Neuro-Epigenetics Laboratory, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, 7610001, Israel.
| | - Boaz Barak
- The School of Psychological Sciences, Faculty of Social Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel. .,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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7
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Gene Expression and Epigenetic Regulation in the Prefrontal Cortex of Schizophrenia. Genes (Basel) 2023; 14:genes14020243. [PMID: 36833173 PMCID: PMC9957055 DOI: 10.3390/genes14020243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/03/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Schizophrenia pathogenesis remains challenging to define; however, there is strong evidence that the interaction of genetic and environmental factors causes the disorder. This paper focuses on transcriptional abnormalities in the prefrontal cortex (PFC), a key anatomical structure that determines functional outcomes in schizophrenia. This review summarises genetic and epigenetic data from human studies to understand the etiological and clinical heterogeneity of schizophrenia. Gene expression studies using microarray and sequencing technologies reported the aberrant transcription of numerous genes in the PFC in patients with schizophrenia. Altered gene expression in schizophrenia is related to several biological pathways and networks (synaptic function, neurotransmission, signalling, myelination, immune/inflammatory mechanisms, energy production and response to oxidative stress). Studies investigating mechanisms driving these transcriptional abnormalities focused on alternations in transcription factors, gene promoter elements, DNA methylation, posttranslational histone modifications or posttranscriptional regulation of gene expression mediated by non-coding RNAs.
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8
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McKinney BC, McClain LL, Hensler CM, Wei Y, Klei L, Lewis DA, Devlin B, Wang J, Ding Y, Sweet RA. Schizophrenia-associated differential DNA methylation in brain is distributed across the genome and annotated to MAD1L1, a locus at which DNA methylation and transcription phenotypes share genetic variation with schizophrenia risk. Transl Psychiatry 2022; 12:340. [PMID: 35987687 PMCID: PMC9392724 DOI: 10.1038/s41398-022-02071-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/21/2022] [Accepted: 07/15/2022] [Indexed: 11/09/2022] Open
Abstract
DNA methylation (DNAm), the addition of a methyl group to a cytosine in DNA, plays an important role in the regulation of gene expression. Single-nucleotide polymorphisms (SNPs) associated with schizophrenia (SZ) by genome-wide association studies (GWAS) often influence local DNAm levels. Thus, DNAm alterations, acting through effects on gene expression, represent one potential mechanism by which SZ-associated SNPs confer risk. In this study, we investigated genome-wide DNAm in postmortem superior temporal gyrus from 44 subjects with SZ and 44 non-psychiatric comparison subjects using Illumina Infinium MethylationEPIC BeadChip microarrays, and extracted cell-type-specific methylation signals by applying tensor composition analysis. We identified SZ-associated differential methylation at 242 sites, and 44 regions containing two or more sites (FDR cutoff of q = 0.1) and determined a subset of these were cell-type specific. We found mitotic arrest deficient 1-like 1 (MAD1L1), a gene within an established GWAS risk locus, harbored robust SZ-associated differential methylation. We investigated the potential role of MAD1L1 DNAm in conferring SZ risk by assessing for colocalization among quantitative trait loci for methylation and gene transcripts (mQTLs and tQTLs) in brain tissue and GWAS signal at the locus using multiple-trait-colocalization analysis. We found that mQTLs and tQTLs colocalized with the GWAS signal (posterior probability >0.8). Our findings suggest that alterations in MAD1L1 methylation and transcription may mediate risk for SZ at the MAD1L1-containing locus. Future studies to identify how SZ-associated differential methylation affects MAD1L1 biological function are indicated.
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Affiliation(s)
- Brandon C McKinney
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Lora L McClain
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Christopher M Hensler
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yue Wei
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - David A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jiebiao Wang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ying Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert A Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Translational Neuroscience Program, Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA.
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9
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Alameda L, Trotta G, Quigley H, Rodriguez V, Gadelrab R, Dwir D, Dempster E, Wong CCY, Forti MD. Can epigenetics shine a light on the biological pathways underlying major mental disorders? Psychol Med 2022; 52:1645-1665. [PMID: 35193719 PMCID: PMC9280283 DOI: 10.1017/s0033291721005559] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 11/30/2021] [Accepted: 12/29/2021] [Indexed: 12/27/2022]
Abstract
A significant proportion of the global burden of disease can be attributed to mental illness. Despite important advances in identifying risk factors for mental health conditions, the biological processing underlying causal pathways to disease onset remain poorly understood. This represents a limitation to implement effective prevention and the development of novel pharmacological treatments. Epigenetic mechanisms have emerged as mediators of environmental and genetic risk factors which might play a role in disease onset, including childhood adversity (CA) and cannabis use (CU). Particularly, human research exploring DNA methylation has provided new and promising insights into the role of biological pathways implicated in the aetio-pathogenesis of psychiatric conditions, including: monoaminergic (Serotonin and Dopamine), GABAergic, glutamatergic, neurogenesis, inflammatory and immune response and oxidative stress. While these epigenetic changes have been often studied as disease-specific, similarly to the investigation of environmental risk factors, they are often transdiagnostic. Therefore, we aim to review the existing literature on DNA methylation from human studies of psychiatric diseases (i) to identify epigenetic modifications mapping onto biological pathways either transdiagnostically or specifically related to psychiatric diseases such as Eating Disorders, Post-traumatic Stress Disorder, Bipolar and Psychotic Disorder, Depression, Autism Spectrum Disorder and Anxiety Disorder, and (ii) to investigate a convergence between some of these epigenetic modifications and the exposure to known risk factors for psychiatric disorders such as CA and CU, as well as to other epigenetic confounders in psychiatry research.
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Affiliation(s)
- Luis Alameda
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Departamento de Psiquiatría, Centro Investigación Biomedica en Red de Salud Mental (CIBERSAM), Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Sevilla, Spain
| | - Giulia Trotta
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - Harriet Quigley
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Victoria Rodriguez
- Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Romayne Gadelrab
- Centre for Affective Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Daniella Dwir
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Emma Dempster
- University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, UK
| | - Chloe C. Y. Wong
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
| | - Marta Di Forti
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, King's College London, London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
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10
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Wagh VV, Vyas P, Agrawal S, Pachpor TA, Paralikar V, Khare SP. Peripheral Blood-Based Gene Expression Studies in Schizophrenia: A Systematic Review. Front Genet 2021; 12:736483. [PMID: 34721526 PMCID: PMC8548640 DOI: 10.3389/fgene.2021.736483] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/31/2021] [Indexed: 12/19/2022] Open
Abstract
Schizophrenia is a disorder that is characterized by delusions, hallucinations, disorganized speech or behavior, and socio-occupational impairment. The duration of observation and variability in symptoms can make the accurate diagnosis difficult. Identification of biomarkers for schizophrenia (SCZ) can help in early diagnosis, ascertaining the diagnosis, and development of effective treatment strategies. Here we review peripheral blood-based gene expression studies for identification of gene expression biomarkers for SCZ. A literature search was carried out in PubMed and Web of Science databases for blood-based gene expression studies in SCZ. A list of differentially expressed genes (DEGs) was compiled and analyzed for overlap with genetic markers, differences based on drug status of the participants, functional enrichment, and for effect of antipsychotics. This literature survey identified 61 gene expression studies. Seventeen out of these studies were based on expression microarrays. A comparative analysis of the DEGs (n = 227) from microarray studies revealed differences between drug-naive and drug-treated SCZ participants. We found that of the 227 DEGs, 11 genes (ACOT7, AGO2, DISC1, LDB1, RUNX3, SIGIRR, SLC18A1, NRG1, CHRNB2, PRKAB2, and ZNF74) also showed genetic and epigenetic changes associated with SCZ. Functional enrichment analysis of the DEGs revealed dysregulation of proline and 4-hydroxyproline metabolism. Also, arginine and proline metabolism was the most functionally enriched pathway for SCZ in our analysis. Follow-up studies identified effect of antipsychotic treatment on peripheral blood gene expression. Of the 27 genes compiled from the follow-up studies AKT1, DISC1, HP, and EIF2D had no effect on their expression status as a result of antipsychotic treatment. Despite the differences in the nature of the study, ethnicity of the population, and the gene expression analysis method used, we identified several coherent observations. An overlap, though limited, of genetic, epigenetic and gene expression changes supports interplay of genetic and environmental factors in SCZ. The studies validate the use of blood as a surrogate tissue for biomarker analysis. We conclude that well-designed cohort studies across diverse populations, use of high-throughput sequencing technology, and use of artificial intelligence (AI) based computational analysis will significantly improve our understanding and diagnostic capabilities for this complex disorder.
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Affiliation(s)
- Vipul Vilas Wagh
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Parin Vyas
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
| | - Suchita Agrawal
- The Psychiatry Unit, KEM Hospital and KEM Hospital Research Centre, Pune, India
| | | | - Vasudeo Paralikar
- The Psychiatry Unit, KEM Hospital and KEM Hospital Research Centre, Pune, India
| | - Satyajeet P Khare
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Pune, India
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11
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Srivastava A, Dada O, Qian J, Al-Chalabi N, Fatemi AB, Gerretsen P, Graff A, De Luca V. Epigenetics of Schizophrenia. Psychiatry Res 2021; 305:114218. [PMID: 34638051 DOI: 10.1016/j.psychres.2021.114218] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/07/2021] [Accepted: 09/20/2021] [Indexed: 12/31/2022]
Abstract
Schizophrenia (SCZ) is a chronic psychotic disorder that contributes significantly to disability, affecting behavior, thought, and cognition. It has long been known that there is a heritable component to schizophrenia; studies in both the pre-genomic and post-genomic era, however, have failed to elucidate fully the genetic basis for this complex disease. Epigenetic processes - broadly, those which contribute to changes in gene expression without altering the genetic code itself - may help to understand better the mechanisms leading to development of SCZ. The objective of this review is to synthesize current knowledge of the epigenetic mechanisms involved in schizophrenia. Specifically, DNA methylation studies in both peripheral and post-mortem brain samples in SCZ are reviewed, as are epigenetic mechanisms including histone modification. The promising role of non-coding RNA including micro-RNA (miRNA) and its role as a potential diagnostic and therapeutic biomarker is outlined, as are epigenetic age acceleration and telomere shortening. Finally, we discuss limitations in current knowledge and propose future research directions.
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Affiliation(s)
| | | | | | | | | | | | - Ariel Graff
- Department of Psychiatry, University of Toronto
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12
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Shen L, Lv X, Huang H, Li M, Huai C, Wu X, Wu H, Ma J, Chen L, Wang T, Tan J, Sun Y, Li L, Shi Y, Yang C, Cai L, Lu Y, Zhang Y, Weng S, Tai S, Zhang N, He L, Wan C, Qin S. Genome-wide analysis of DNA methylation in 106 schizophrenia family trios in Han Chinese. EBioMedicine 2021; 72:103609. [PMID: 34628353 PMCID: PMC8511801 DOI: 10.1016/j.ebiom.2021.103609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 09/05/2021] [Accepted: 09/17/2021] [Indexed: 12/26/2022] Open
Abstract
Background Schizophrenia (SCZ) is a severe psychiatric disorder that affects approximately 0.75% of the global population. Both genetic and environmental factors contribute to development of SCZ. SCZ tends to run in family while both genetic and environmental factor contribute to its etiology. Much evidence suggested that alterations in DNA methylations occurred in SCZ patients. Methods To investigate potential inheritable pattern of DNA methylation in SCZ family, we performed a genome-wide analysis of DNA methylation of peripheral blood samples from 106 Chinese SCZ family trios. Genome-wide DNA methylations were quantified by Agilent 1 × 244 k Human Methylation Microarray. Findings In this study, we proposed a loci inheritance frequency model that allows characterization of differential methylated regions as SCZ biomarkers. Based on this model, 112 hypermethylated and 125 hypomethylated regions were identified. Additionally, 121 hypermethylated and 139 hypomethylated genes were annotated. The results of functional enrichment analysis indicated that multiple differentially methylated genes (DMGs) involved in Notch/HH/Wnt signaling, MAPK signaling, GPCR signaling, immune response signaling. Notably, a number of hypomethylated genes were significantly enriched in cerebral cortex and functionally enriched in nervous system development. Interpretation Our findings not only validated previously discovered risk genes of SCZ but also identified novel candidate DMGs in SCZ. These results may further the understanding of altered DNA methylations in SCZ.
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Affiliation(s)
- Lu Shen
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaoying Lv
- DCH Technologies Inc, Cambridge, MA 02142, USA
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences (SIBS), Chinese Academy of Sciences, Shanghai 200031, PR China; Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Mo Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Cong Huai
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Xi Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Hao Wu
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Jingsong Ma
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Luan Chen
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Ting Wang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Jie Tan
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Yidan Sun
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Lixing Li
- Department of General Surgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yi Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Chao Yang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Lei Cai
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Yana Lu
- Wuxi Mental Health Center, Nanjing Medical University, Wuxi 214151, China
| | - Yan Zhang
- The Second People's Hospital of Lishui, Lishui 323020, China
| | - Saizheng Weng
- Fuzhou Neuro-psychiatric hospital, Fujian Medical University, Fuzhou 350026, China
| | - Shaobin Tai
- The Second People's Hospital of Huangshan, Huangshan 245021, China
| | - Na Zhang
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China
| | - Lin He
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China; Department of General Surgery, School of Medicine, Shanghai General Hospital, Shanghai Jiao Tong University, Shanghai, China; Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
| | - Chunling Wan
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China.
| | - Shengying Qin
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200030, PR China.
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13
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Buck JM, Yu L, Knopik VS, Stitzel JA. DNA methylome perturbations: an epigenetic basis for the emergingly heritable neurodevelopmental abnormalities associated with maternal smoking and maternal nicotine exposure†. Biol Reprod 2021; 105:644-666. [PMID: 34270696 PMCID: PMC8444709 DOI: 10.1093/biolre/ioab138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/29/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Maternal smoking during pregnancy is associated with an ensemble of neurodevelopmental consequences in children and therefore constitutes a pressing public health concern. Adding to this burden, contemporary epidemiological and especially animal model research suggests that grandmaternal smoking is similarly associated with neurodevelopmental abnormalities in grandchildren, indicative of intergenerational transmission of the neurodevelopmental impacts of maternal smoking. Probing the mechanistic bases of neurodevelopmental anomalies in the children of maternal smokers and the intergenerational transmission thereof, emerging research intimates that epigenetic changes, namely DNA methylome perturbations, are key factors. Altogether, these findings warrant future research to fully elucidate the etiology of neurodevelopmental impairments in the children and grandchildren of maternal smokers and underscore the clear potential thereof to benefit public health by informing the development and implementation of preventative measures, prophylactics, and treatments. To this end, the present review aims to encapsulate the burgeoning evidence linking maternal smoking to intergenerational epigenetic inheritance of neurodevelopmental abnormalities, to identify the strengths and weaknesses thereof, and to highlight areas of emphasis for future human and animal model research therein.
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Affiliation(s)
- Jordan M Buck
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado, Boulder, Boulder, CO, USA
| | - Li Yu
- Department of Human Development and Family Studies, Purdue University, West Lafayette, IN, USA
| | - Valerie S Knopik
- Department of Human Development and Family Studies, Purdue University, West Lafayette, IN, USA
| | - Jerry A Stitzel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado, Boulder, Boulder, CO, USA
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14
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Berdenis van Berlekom A, Notman N, Sneeboer MAM, Snijders GJLJ, Houtepen LC, Nispeling DM, He Y, Dracheva S, Hol EM, Kahn RS, de Witte LD, Boks MP. DNA methylation differences in cortical grey and white matter in schizophrenia. Epigenomics 2021; 13:1157-1169. [PMID: 34323598 PMCID: PMC8386513 DOI: 10.2217/epi-2021-0077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/09/2021] [Indexed: 01/27/2023] Open
Abstract
Aim: Identify grey- and white-matter-specific DNA-methylation differences between schizophrenia (SCZ) patients and controls in postmortem brain cortical tissue. Materials & methods: Grey and white matter were separated from postmortem brain tissue of the superior temporal and medial frontal gyrus from SCZ (n = 10) and control (n = 11) cases. Genome-wide DNA-methylation analysis was performed using the Infinium EPIC Methylation Array (Illumina, CA, USA). Results: Four differentially methylated regions associated with SCZ status and tissue type (grey vs white matter) were identified within or near KLF9, SFXN1, SPRED2 and ALS2CL genes. Gene-expression analysis showed differential expression of KLF9 and SFXN1 in SCZ. Conclusion: Our data show distinct differences in DNA methylation between grey and white matter that are unique to SCZ, providing new leads to unravel the pathogenesis of SCZ.
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Affiliation(s)
- Amber Berdenis van Berlekom
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Nina Notman
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Marjolein AM Sneeboer
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Gijsje JLJ Snijders
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lotte C Houtepen
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Danny M Nispeling
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Yujie He
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | | | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research, Education, & Clinical Center (VISN 2 South), James J Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Elly M Hol
- Department of Translational Neuroscience, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - René S Kahn
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Mental Illness Research, Education, & Clinical Center (VISN 2 South), James J Peters VA Medical Center, Bronx, NY, 10468, USA
| | - Lot D de Witte
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Marco P Boks
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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15
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Hidden Role of Gut Microbiome Dysbiosis in Schizophrenia: Antipsychotics or Psychobiotics as Therapeutics? Int J Mol Sci 2021; 22:ijms22147671. [PMID: 34299291 PMCID: PMC8307070 DOI: 10.3390/ijms22147671] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 02/06/2023] Open
Abstract
Schizophrenia is a chronic, heterogeneous neurodevelopmental disorder that has complex symptoms and uncertain etiology. Mounting evidence indicates the involvement of genetics and epigenetic disturbances, alteration in gut microbiome, immune system abnormalities, and environmental influence in the disease, but a single root cause and mechanism involved has yet to be conclusively determined. Consequently, the identification of diagnostic markers and the development of psychotic drugs for the treatment of schizophrenia faces a high failure rate. This article surveys the etiology of schizophrenia with a particular focus on gut microbiota regulation and the microbial signaling system that correlates with the brain through the vagus nerve, enteric nervous system, immune system, and production of postbiotics. Gut microbially produced molecules may lay the groundwork for further investigations into the role of gut microbiota dysbiosis and the pathophysiology of schizophrenia. Current treatment of schizophrenia is limited to psychotherapy and antipsychotic drugs that have significant side effects. Therefore, alternative therapeutic options merit exploration. The use of psychobiotics alone or in combination with antipsychotics may promote the development of novel therapeutic strategies. In view of the individual gut microbiome structure and personalized response to antipsychotic drugs, a tailored and targeted manipulation of gut microbial diversity naturally by novel prebiotics (non-digestible fiber) may be a successful alternative therapeutic for the treatment of schizophrenia patients.
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16
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Munawar N, Ahsan K, Muhammad K, Ahmad A, Anwar MA, Shah I, Al Ameri AK, Al Mughairbi F. Hidden Role of Gut Microbiome Dysbiosis in Schizophrenia: Antipsychotics or Psychobiotics as Therapeutics? Int J Mol Sci 2021. [DOI: https://doi.org/10.3390/ijms22147671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Schizophrenia is a chronic, heterogeneous neurodevelopmental disorder that has complex symptoms and uncertain etiology. Mounting evidence indicates the involvement of genetics and epigenetic disturbances, alteration in gut microbiome, immune system abnormalities, and environmental influence in the disease, but a single root cause and mechanism involved has yet to be conclusively determined. Consequently, the identification of diagnostic markers and the development of psychotic drugs for the treatment of schizophrenia faces a high failure rate. This article surveys the etiology of schizophrenia with a particular focus on gut microbiota regulation and the microbial signaling system that correlates with the brain through the vagus nerve, enteric nervous system, immune system, and production of postbiotics. Gut microbially produced molecules may lay the groundwork for further investigations into the role of gut microbiota dysbiosis and the pathophysiology of schizophrenia. Current treatment of schizophrenia is limited to psychotherapy and antipsychotic drugs that have significant side effects. Therefore, alternative therapeutic options merit exploration. The use of psychobiotics alone or in combination with antipsychotics may promote the development of novel therapeutic strategies. In view of the individual gut microbiome structure and personalized response to antipsychotic drugs, a tailored and targeted manipulation of gut microbial diversity naturally by novel prebiotics (non-digestible fiber) may be a successful alternative therapeutic for the treatment of schizophrenia patients.
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17
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Richetto J, Meyer U. Epigenetic Modifications in Schizophrenia and Related Disorders: Molecular Scars of Environmental Exposures and Source of Phenotypic Variability. Biol Psychiatry 2021; 89:215-226. [PMID: 32381277 DOI: 10.1016/j.biopsych.2020.03.008] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/19/2020] [Accepted: 03/16/2020] [Indexed: 12/18/2022]
Abstract
Epigenetic modifications are increasingly recognized to play a role in the etiology and pathophysiology of schizophrenia and other psychiatric disorders with developmental origins. Here, we summarize clinical and preclinical findings of epigenetic alterations in schizophrenia and relevant disease models and discuss their putative origin. Recent findings suggest that certain schizophrenia risk loci can influence stochastic variation in gene expression through epigenetic processes, highlighting the intricate interaction between genetic and epigenetic control of neurodevelopmental trajectories. In addition, a substantial portion of epigenetic alterations in schizophrenia and related disorders may be acquired through environmental factors and may be manifested as molecular "scars." Some of these scars can influence brain functions throughout the entire lifespan and may even be transmitted across generations via epigenetic germline inheritance. Epigenetic modifications, whether caused by genetic or environmental factors, are plausible molecular sources of phenotypic heterogeneity and offer a target for therapeutic interventions. The further elucidation of epigenetic modifications thus may increase our knowledge regarding schizophrenia's heterogeneous etiology and pathophysiology and, in the long term, may advance personalized treatments through the use of biomarker-guided epigenetic interventions.
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Affiliation(s)
- Juliet Richetto
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, and Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.
| | - Urs Meyer
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, and Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland
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18
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Starnawska A, Demontis D. Role of DNA Methylation in Mediating Genetic Risk of Psychiatric Disorders. Front Psychiatry 2021; 12:596821. [PMID: 33868039 PMCID: PMC8049112 DOI: 10.3389/fpsyt.2021.596821] [Citation(s) in RCA: 9] [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: 08/20/2020] [Accepted: 02/16/2021] [Indexed: 12/28/2022] Open
Abstract
Psychiatric disorders are common, complex, and heritable conditions estimated to be the leading cause of disability worldwide. The last decade of research in genomics of psychiatry, performed by multinational, and multicenter collaborative efforts on hundreds of thousands of mental disorder cases and controls, provided invaluable insight into the genetic risk variants of these conditions. With increasing cohort sizes, more risk variants are predicted to be identified in the near future, but there appears to be a knowledge gap in understanding how these variants contribute to the pathophysiology of psychiatric disorders. Majority of the identified common risk single-nucleotide polymorphisms (SNPs) are non-coding but are enriched in regulatory regions of the genome. It is therefore of great interest to study the impact of identified psychiatric disorders' risk SNPs on DNA methylation, the best studied epigenetic modification, playing a pivotal role in the regulation of transcriptomic processes, brain development, and functioning. This work outlines the mechanisms through which risk SNPs can impact DNA methylation levels and provides a summary of current evidence on the role of DNA methylation in mediating the genetic risk of psychiatric disorders.
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Affiliation(s)
- Anna Starnawska
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine (CGPM), Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark.,Center for Genomics and Personalized Medicine (CGPM), Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
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19
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Kikuchi M, Nakazawa T, Kinoshita M, Yamamori H, Yasuda Y, Fujimoto M, Hashimoto R, Numata S. Methylation Analysis in Monozygotic Twins With Treatment-Resistant Schizophrenia and Discordant Responses to Clozapine. Front Psychiatry 2021; 12:734606. [PMID: 34616320 PMCID: PMC8488120 DOI: 10.3389/fpsyt.2021.734606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Schizophrenia is a mental illness that involves both genetic and environmental factors. Clozapine, an atypical antipsychotic, is a well-established therapy for treatment-resistant schizophrenia. In this study, we focused on a set of monozygotic twins with treatment-resistant schizophrenia in which one twin effectively responded to clozapine treatment and the other did not. Our previous study generated neurons from induced pluripotent stem (iPS) cells derived from these patients and compared the transcriptome profiles between mock- and clozapine-treated neurons. In this study, we performed genome-wide DNA methylation profiling to investigate the mechanisms underlying gene expression changes. First, we extracted the differentially methylated sites from each twin based on statistical analysis. Then, we combined the DNA methylation profiling with transcriptome profiling from our previous RNA-seq data. Among the genes with altered methylation and expression, we found the different proportions of the genes related to neuronal and synaptic functions between the clozapine responder and non-responder (35.7 and 6.7%, respectively). This trend was observed even when the basal differences between the responder and non-responder was excluded. These results suggest that effective clozapine action may correct the abnormalities of neuronal and synapse functions in schizophrenia via changes in methylation.
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Affiliation(s)
- Masataka Kikuchi
- Department of Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Takanobu Nakazawa
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Makoto Kinoshita
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hidenaga Yamamori
- Department of Pathology of Mental Diseases, National Center of Neurology and Psychiatry, National Institute of Mental Health, Tokyo, Japan.,Department of Psychiatry, Graduate School of Medicine, Osaka University, Osaka, Japan.,Japan Community Health Care Organization Osaka Hospital, Osaka, Japan
| | - Yuka Yasuda
- Department of Pathology of Mental Diseases, National Center of Neurology and Psychiatry, National Institute of Mental Health, Tokyo, Japan.,Medical Corporation Foster, Osaka, Japan
| | - Michiko Fujimoto
- Department of Pathology of Mental Diseases, National Center of Neurology and Psychiatry, National Institute of Mental Health, Tokyo, Japan.,Department of Psychiatry, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Center of Neurology and Psychiatry, National Institute of Mental Health, Tokyo, Japan
| | - Shusuke Numata
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
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20
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Lin D, Chen J, Duan K, Perrone-Bizzozero N, Sui J, Calhoun V, Liu J. Network modules linking expression and methylation in prefrontal cortex of schizophrenia. Epigenetics 2020; 16:876-893. [PMID: 33079616 PMCID: PMC8331039 DOI: 10.1080/15592294.2020.1827718] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tremendous work has demonstrated the critical roles of genetics, epigenetics as well as their interplay in brain transcriptional regulations in the pathology of schizophrenia (SZ). There is great success currently in the dissection of the genetic components underlying risk-conferring transcriptomic networks. However, the study of regulating effect of epigenetics in the etiopathogenesis of SZ still faces many challenges. In this work, we investigated DNA methylation and gene expression from the dorsolateral prefrontal cortex (DLPFC) region of schizophrenia patients and healthy controls using weighted correlation network approach. We identified and replicated two expression and two methylation modules significantly associated with SZ. Among them, one pair of expression and methylation modules were significantly overlapped in the module genes which were significantly enriched in astrocyte-associated functional pathways, and specifically expressed in astrocytes. Another two linked expression-methylation module pairs were involved ageing process with module genes mostly related to oligodendrocyte development and myelination, and specifically expressed in oligodendrocytes. Further examination of underlying quantitative trait loci (QTLs) showed significant enrichment in genetic risk of most psychiatric disorders for expression QTLs but not for methylation QTLs. These results support the coherence between methylation and gene expression at the network level, and suggest a combinatorial effect of genetics and epigenetics in regulating gene expression networks specific to glia cells in relation to SZ and ageing process.
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Affiliation(s)
- Dongdong Lin
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): {Georgia State University, Georgia Institute of Technology, and Emory University}, Atlanta, USA
| | - Jiayu Chen
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): {Georgia State University, Georgia Institute of Technology, and Emory University}, Atlanta, USA
| | - Kuaikuai Duan
- Department of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, USA
| | - Nora Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico, Albuquerque, NM, USA.,Department of Psychiatry, University of New Mexico, Albuquerque, NM, USA
| | - Jing Sui
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): {Georgia State University, Georgia Institute of Technology, and Emory University}, Atlanta, USA
| | - Vince Calhoun
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): {Georgia State University, Georgia Institute of Technology, and Emory University}, Atlanta, USA.,Department of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, USA.,Department of Psychology, Georgia State University, Atlanta, USA.,Department of Computer Science, Georgia State University, Atlanta, USA
| | - Jingyu Liu
- Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS): {Georgia State University, Georgia Institute of Technology, and Emory University}, Atlanta, USA.,Department of Computer Science, Georgia State University, Atlanta, USA
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21
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Smigielski L, Jagannath V, Rössler W, Walitza S, Grünblatt E. Epigenetic mechanisms in schizophrenia and other psychotic disorders: a systematic review of empirical human findings. Mol Psychiatry 2020; 25:1718-1748. [PMID: 31907379 DOI: 10.1038/s41380-019-0601-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 11/05/2019] [Accepted: 11/07/2019] [Indexed: 12/26/2022]
Abstract
Schizophrenia and other psychotic disorders are highly debilitating psychiatric conditions that lack a clear etiology and exhibit polygenic inheritance underlain by pleiotropic genes. The prevailing explanation points to the interplay between predisposing genes and environmental exposure. Accumulated evidence suggests that epigenetic regulation of the genome may mediate dynamic gene-environment interactions at the molecular level by modulating the expression of psychiatric phenotypes through transcription factors. This systematic review summarizes the current knowledge linking schizophrenia and other psychotic disorders to epigenetics, based on PubMed and Web of Science database searches conducted according to the PRISMA guidelines. Three groups of mechanisms in case-control studies of human tissue (i.e., postmortem brain and bio-fluids) were considered: DNA methylation, histone modifications, and non-coding miRNAs. From the initial pool of 3,204 records, 152 studies met our inclusion criteria (11,815/11,528, 233/219, and 2,091/1,827 cases/controls for each group, respectively). Many of the findings revealed associations with epigenetic modulations of genes regulating neurotransmission, neurodevelopment, and immune function, as well as differential miRNA expression (e.g., upregulated miR-34a, miR-7, and miR-181b). Overall, actual evidence moderately supports an association between epigenetics and schizophrenia and other psychotic disorders. However, heterogeneous results and cross-tissue extrapolations call for future work. Integrating epigenetics into systems biology may critically enhance research on psychosis and thus our understanding of the disorder. This may have implications for psychiatry in risk stratification, early recognition, diagnostics, precision medicine, and other interventional approaches targeting epigenetic fingerprints.
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Affiliation(s)
- Lukasz Smigielski
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland. .,The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.
| | - Vinita Jagannath
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland.,Merck Sharp & Dohme (MSD) R&D Innovation Centre, London, UK
| | - Wulf Rössler
- The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Department of Psychiatry, Psychotherapy and Psychosomatics, University Hospital of Psychiatry, University of Zurich, Zurich, Switzerland.,Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin, Berlin, Germany.,Laboratory of Neuroscience, Institute of Psychiatry, Universidade de São Paulo, São Paulo, Brazil
| | - Susanne Walitza
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland.,The Zurich Program for Sustainable Development of Mental Health Services (ZInEP), University Hospital of Psychiatry Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
| | - Edna Grünblatt
- Department of Child and Adolescent Psychiatry and Psychotherapy, University Hospital of Psychiatry Zurich, University of Zurich, Zurich, Switzerland.,Neuroscience Center Zurich, University of Zurich and ETH Zurich, Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
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22
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Wu Y, Li X, Liu J, Luo XJ, Yao YG. SZDB2.0: an updated comprehensive resource for schizophrenia research. Hum Genet 2020; 139:1285-1297. [DOI: 10.1007/s00439-020-02171-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/25/2020] [Indexed: 12/11/2022]
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23
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van Mierlo HC, Schot A, Boks MPM, de Witte LD. The association between schizophrenia and the immune system: Review of the evidence from unbiased 'omic-studies'. Schizophr Res 2020; 217:114-123. [PMID: 31130400 DOI: 10.1016/j.schres.2019.05.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/17/2019] [Accepted: 05/18/2019] [Indexed: 01/04/2023]
Abstract
A role for immune processes in the pathogenesis of schizophrenia has been suggested by genetic and epidemiological studies, as well as cross-sectional studies on blood and brain samples. However, results are heterogeneous, which is likely caused by low samples sizes, insufficient control of confounders that influence immune processes, and potentially publication bias. Large hypothesis-free 'omic' studies partially circumvent these problems and could provide further evidence for a role of immune pathways in schizophrenia. In this review we assessed whether the largest genome, transcriptome and methylome studies in schizophrenia to date support a link with the immune system. We constructed an overview of the schizophrenia-associated genes and transcripts that were identified in these large 'omic' studies. We then performed a hypothesis-driven analysis to examine the association and enrichment of immune system-related genes and transcripts in these datasets. Additionally, we reviewed secondary analyses that were previously performed on these 'omic' studies. Except for the link between complement factor 4 (C4), we found limited evidence for a role of microglia and immune processes among genetic risk variants. Transcriptome and methylome studies point towards alterations in immune system related genes, pathways and cells. This includes changes in microglia, as well as complement, nuclear factor-κB, toll-like receptor and interferon signaling pathways. Many of these associated immune-related genes and pathways have been shown to be involved in neurodevelopment and neuronal functioning. Additional replication of these findings is needed, but once further conformation is provided, these findings could be a potentially interesting target for future therapies.
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Affiliation(s)
- Hans C van Mierlo
- Department of Psychiatry, UMC Utrecht Brain Center, 3508GA Utrecht, the Netherlands
| | - Aron Schot
- Department of Psychiatry, UMC Utrecht Brain Center, 3508GA Utrecht, the Netherlands
| | - Marco P M Boks
- Department of Psychiatry, UMC Utrecht Brain Center, 3508GA Utrecht, the Netherlands
| | - Lot D de Witte
- Department of Psychiatry, Icahn School of Medicine, New York, United States of America; Mental Illness Research, Education and Clinical Center (MIRECC), James J Peters VA Medical Center, Bronx, NY, United States of America.
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24
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Egervari G, Kozlenkov A, Dracheva S, Hurd YL. Molecular windows into the human brain for psychiatric disorders. Mol Psychiatry 2019; 24:653-673. [PMID: 29955163 PMCID: PMC6310674 DOI: 10.1038/s41380-018-0125-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 05/14/2018] [Accepted: 06/05/2018] [Indexed: 12/20/2022]
Abstract
Delineating the pathophysiology of psychiatric disorders has been extremely challenging but technological advances in recent decades have facilitated a deeper interrogation of molecular processes in the human brain. Initial candidate gene expression studies of the postmortem brain have evolved into genome wide profiling of the transcriptome and the epigenome, a critical regulator of gene expression. Here, we review the potential and challenges of direct molecular characterization of the postmortem human brain, and provide a brief overview of recent transcriptional and epigenetic studies with respect to neuropsychiatric disorders. Such information can now be leveraged and integrated with the growing number of genome-wide association databases to provide a functional context of trait-associated genetic variants linked to psychiatric illnesses and related phenotypes. While it is clear that the field is still developing and challenges remain to be surmounted, these recent advances nevertheless hold tremendous promise for delineating the neurobiological underpinnings of mental diseases and accelerating the development of novel medication strategies.
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Affiliation(s)
- Gabor Egervari
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- Epigenetics Institute and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alexey Kozlenkov
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Stella Dracheva
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA
- James J. Peters VA Medical Center, Bronx, NY, USA
| | - Yasmin L Hurd
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Addiction Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, School of Medicine at Mount Sinai, New York, NY, USA.
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25
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Okazaki S, Otsuka I, Numata S, Horai T, Mouri K, Boku S, Ohmori T, Sora I, Hishimoto A. Epigenetic clock analysis of blood samples from Japanese schizophrenia patients. NPJ SCHIZOPHRENIA 2019; 5:4. [PMID: 30814520 PMCID: PMC6393510 DOI: 10.1038/s41537-019-0072-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/07/2019] [Indexed: 01/01/2023]
Abstract
The accelerated aging hypothesis of schizophrenia (SCZ) has been proposed. DNA methylation profiles were developed for determining “epigenetic age.” Here, we assessed intrinsic and extrinsic epigenetic age acceleration (IEAA and EEAA, respectively) in SCZ. We examined two independent cohorts of Japanese ancestry. The first cohort consisted of 80 patients with SCZ under long-term or repeated hospitalization and 40 controls, with the economical DNA pooling technique. The second cohort consisted of 24 medication-free patients with SCZ and 23 controls. Blood of SCZ subjects exhibited decreased EEAA in the first cohort (p = 0.0162), but not in the second cohort. IEAA did not differ in either cohort. We performed replication analyses using publicly available datasets from European ancestry (three blood and one brain datasets). One blood dataset showed increased EEAA in SCZ (p = 0.0228). Overall, our results provide evidence for decreased EEAA in SCZ associated with hospitalization in the Japanese population.
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Affiliation(s)
- Satoshi Okazaki
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shusuke Numata
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Tadasu Horai
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Kentaro Mouri
- Department of Internal Medicine, Division of Biosignal Pathophysiology, Kobe University Graduate School of Medicine, Kobe, Japan.,Medical Center for Student's Health Service, Kobe University, Kobe, Japan
| | - Shuken Boku
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tetsuro Ohmori
- Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Ichiro Sora
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.
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26
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Migdalska-Richards A, Mill J. Epigenetic studies of schizophrenia: current status and future directions. Curr Opin Behav Sci 2019. [DOI: 10.1016/j.cobeha.2018.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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DNA methylation in the human frontal cortex reveals a putative mechanism for age-by-disease interactions. Transl Psychiatry 2019; 9:39. [PMID: 30696804 PMCID: PMC6351569 DOI: 10.1038/s41398-019-0372-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 12/02/2018] [Accepted: 12/09/2018] [Indexed: 12/19/2022] Open
Abstract
A consistent gene set undergoes age-associated expression changes in the human cerebral cortex, and our Age-by-Disease Model posits that these changes contribute to psychiatric diseases by "pushing" the expression of disease-associated genes in disease-promoting directions. DNA methylation (DNAm) is an attractive candidate mechanism for age-associated gene expression changes. We used the Illumina HumanMethylation450 array to characterize genome-wide DNAm in the postmortem orbital frontal cortex from 20 younger (<42 years) and 19 older (>60 years) subjects. DNAm data were integrated with existing normal brain aging expression data and sets of psychiatric disease risk genes to test the hypothesis that age-associated DNAm changes contribute to age-associated gene expression changes and, by extension, susceptibility to psychiatric diseases. We found that age-associated differentially methylated regions (aDMRs) are common, robust, bidirectional, concentrated in CpG island shelves and sea, depleted in CpG islands, and enriched among genes undergoing age-associated expression changes (OR = 2.30, p = 1.69 × 10-27). We found the aDMRs are enriched among genetic association-based risk genes for schizophrenia, Alzheimer's disease (AD), and major depressive disorder (MDD) (OR = 2.51, p = 0.00015; OR = 2.38, p = 0.036; and OR = 3.08, p = 0.018, respectively) as well as expression-based MDD-associated genes (OR = 1.48, p = 0.00012). Similar patterns of enrichment were found for aDMRs that correlate with local gene expression. These results were replicated in a large publically-available dataset, and confirmed by meta-analysis of the two datasets. Our findings suggest DNAm is a molecular mechanism for age-associated gene expression changes and support a role for DNAm in age-by-disease interactions through preferential targeting of disease-associated genes.
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28
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Matrisciano F, Dong E, Nicoletti F, Guidotti A. Epigenetic Alterations in Prenatal Stress Mice as an Endophenotype Model for Schizophrenia: Role of Metabotropic Glutamate 2/3 Receptors. Front Mol Neurosci 2018; 11:423. [PMID: 30564095 PMCID: PMC6289213 DOI: 10.3389/fnmol.2018.00423] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/30/2018] [Indexed: 01/13/2023] Open
Abstract
Mice subjected to prenatal restraint stress (PRS mice) showed biochemical and behavioral abnormalities consistent with a schizophrenia-like phenotype (Matrisciano et al., 2016). PRS mice are characterized by increased DNA-methyltransferase 1 (DNMT1) and ten-eleven methylcytosine dioxygenase 1 (TET1) expression levels and exhibit an enrichment of 5-methylcytosine (5MC) and 5-hydroxymethylcytosine (5HMC) at neocortical GABAergic and glutamatergic gene promoters. Activation of group II metabotropic glutamate receptors (mGlu2 and−3 receptors) showed a potential epigenetically-induced antipsychotic activity by reversing the molecular and behavioral changes observed in PRS mice. This effect was most likely caused by the increase in the expression of growth arrest and DNA damage 45-β (Gadd45-β) protein, a molecular player of DNA demethylation, induced by the activation of mGlu2/3 receptors. This effect was mimicked by clozapine and valproate but not by haloperidol. Treatment with the selective mGlu2/3 receptors agonist LY379268 also increased the amount of Gadd45-β bound to specific promoter regions of reelin, BDNF, and GAD67. A meta-analysis of several clinical trials showed that treatment with an orthosteric mGlu2/3 receptor agonist improved both positive and negative symptoms of schizophrenia, but only in patients who were early-in-disease and had not been treated with atypical antipsychotic drugs (Kinon et al., 2015). Our findings show that PRS mice are valuable model for the study of epigenetic mechanisms involved in the pathogenesis of schizophrenia and support the hypothesis that pharmacological modulation of mGlu2/3 receptors could impact the early phase of schizophrenia and related neurodevelopmental disorders by regulating epigenetic processes that lie at the core of the disorders.
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Affiliation(s)
- Francesco Matrisciano
- Department of Psychiatry, Psychiatric Institute, College of Medicine, University of Illinois Chicago, Chicago, IL, United States
| | - Erbo Dong
- Department of Psychiatry, Center for Alcohol Research in Epigenetics College of Medicine, University of Illinois Chicago, Chicago, IL, United States
| | - Ferdinando Nicoletti
- Department of Physiology and Pharmacology, University of Rome "Sapienza", Rome, Italy.,IRCCS, Neuromed, Pozzilli, Italy
| | - Alessandro Guidotti
- Department of Psychiatry, Psychiatric Institute, College of Medicine, University of Illinois Chicago, Chicago, IL, United States.,Department of Psychiatry, Center for Alcohol Research in Epigenetics College of Medicine, University of Illinois Chicago, Chicago, IL, United States
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29
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Kondratyev N, Golov A, Alfimova M, Lezheiko T, Golimbet V. Prediction of smoking by multiplex bisulfite PCR with long amplicons considering allele-specific effects on DNA methylation. Clin Epigenetics 2018; 10:130. [PMID: 30352621 PMCID: PMC6199807 DOI: 10.1186/s13148-018-0565-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 10/10/2018] [Indexed: 12/13/2022] Open
Abstract
Background Methylation of DNA is associated with a variety of biological processes. With whole-genome studies of DNA methylation, it became possible to determine a set of genomic sites where DNA methylation is associated with a specific phenotype. A method is needed that allows detailed follow-up studies of the sites, including taking into account genetic information. Bisulfite PCR is a natural choice for this kind of task, but multiplexing is one of the most important problems impeding its implementation. To address this task, we took advantage of a recently published method based on Pacbio sequencing of long bisulfite PCR products (single-molecule real-time bisulfite sequencing, SMRT-BS) and tested the validity of the improved methodology with a smoking phenotype. Results Herein, we describe the “panhandle” modification of the method, which permits a more robust PCR with multiple targets. We applied this technique to determine smoking by DNA methylation in 71 healthy people and 83 schizophrenia patients (n = 50 smokers and n = 104 non-smokers, Russians of the Moscow region). We used five targets known to be influenced by smoking (regions of genes AHRR, ALPPL2, IER3, GNG12, and GFI1). We discovered significant allele-specific methylation effects in the AHRR and IER3 regions and assessed how this information could be exploited to improve the prediction of smoking based on the collected DNA methylation data. We found no significant difference in the methylation profiles of selected targets in relation to schizophrenia suggesting that smoking affects methylation at the studied genomic sites in healthy people and schizophrenia patients in a similar way. Conclusions We determined that SMRT-BS with “panhandle” modification performs well in the described setting. Additional information regarding methylation and allele-specific effects could improve the predictive accuracy of DNA methylation-based models, which could be valuable for both basic research and clinical applications. Electronic supplementary material The online version of this article (10.1186/s13148-018-0565-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nikolay Kondratyev
- Clinical Genetics Laboratory, Mental Health Research Center, Moscow, Russia.
| | - Arkady Golov
- Clinical Genetics Laboratory, Mental Health Research Center, Moscow, Russia
| | - Margarita Alfimova
- Clinical Genetics Laboratory, Mental Health Research Center, Moscow, Russia
| | - Tatiana Lezheiko
- Clinical Genetics Laboratory, Mental Health Research Center, Moscow, Russia
| | - Vera Golimbet
- Clinical Genetics Laboratory, Mental Health Research Center, Moscow, Russia
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30
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Liu J, Chen J, Perrone-Bizzozero N, Calhoun VD. A Perspective of the Cross-Tissue Interplay of Genetics, Epigenetics, and Transcriptomics, and Their Relation to Brain Based Phenotypes in Schizophrenia. Front Genet 2018; 9:343. [PMID: 30190726 PMCID: PMC6115489 DOI: 10.3389/fgene.2018.00343] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 08/09/2018] [Indexed: 12/11/2022] Open
Abstract
Genetic association studies of psychiatric disorders have provided unprecedented insight into disease risk profiles with high confidence. Yet, the next research challenge is how to translate this rich information into mechanisms of disease, and further help interventions and treatments. Given other comprehensive reviews elsewhere, here we want to discuss the research approaches that integrate information across various tissue types. Taking schizophrenia as an example, the tissues, cells, or organisms being investigated include postmortem brain tissues or neurons, peripheral blood and saliva, in vivo brain imaging, and in vitro cell lines, particularly human induced pluripotent stem cells (iPSC) and iPSC derived neurons. There is a wealth of information on the molecular signatures including genetics, epigenetics, and transcriptomics of various tissues, along with neuronal phenotypic measurements including neuronal morphometry and function, together with brain imaging and other techniques that provide data from various spatial temporal points of disease development. Through consistent or complementary processes across tissues, such as cross-tissue methylation quantitative trait loci (QTL) and expression QTL effects, systemic integration of such information holds the promise to put the pieces of puzzle together for a more complete view of schizophrenia disease pathogenesis.
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Affiliation(s)
- Jingyu Liu
- Mind Research Network, Lovelace Biomedical and Environmental Research Institute, Albuquerque, NM, United States
- Department of Neurosciences, University of New Mexico, Albuquerque, NM, United States
| | - Jiayu Chen
- Mind Research Network, Lovelace Biomedical and Environmental Research Institute, Albuquerque, NM, United States
| | - Nora Perrone-Bizzozero
- Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, United States
| | - Vince D. Calhoun
- Mind Research Network, Lovelace Biomedical and Environmental Research Institute, Albuquerque, NM, United States
- Department of Neurosciences, University of New Mexico, Albuquerque, NM, United States
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31
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Boks MP, Houtepen LC, Xu Z, He Y, Ursini G, Maihofer AX, Rajarajan P, Yu Q, Xu H, Wu Y, Wang S, Shi JP, Hulshoff Pol HE, Strengman E, Rutten BPF, Jaffe AE, Kleinman JE, Baker DG, Hol EM, Akbarian S, Nievergelt CM, De Witte LD, Vinkers CH, Weinberger DR, Yu J, Kahn RS. Genetic vulnerability to DUSP22 promoter hypermethylation is involved in the relation between in utero famine exposure and schizophrenia. NPJ SCHIZOPHRENIA 2018; 4:16. [PMID: 30131491 PMCID: PMC6104043 DOI: 10.1038/s41537-018-0058-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 01/27/2023]
Abstract
Epigenetic changes may account for the doubled risk to develop schizophrenia in individuals exposed to famine in utero. We therefore investigated DNA methylation in a unique sample of patients and healthy individuals conceived during the great famine in China. Subsequently, we examined two case-control samples without famine exposure in whole blood and brain tissue. To shed light on the causality of the relation between famine exposure and DNA methylation, we exposed human fibroblasts to nutritional deprivation. In the famine-exposed schizophrenia patients, we found significant hypermethylation of the dual specificity phosphatase 22 (DUSP22) gene promoter (Chr6:291687-293285) (N = 153, p = 0.01). In this sample, DUSP22 methylation was also significantly higher in patients independent of famine exposure (p = 0.025), suggesting that hypermethylation of DUSP22 is also more generally involved in schizophrenia risk. Similarly, DUSP22 methylation was also higher in two separate case-control samples not exposed to famine using DNA from whole blood (N = 64, p = 0.03) and postmortem brains (N = 214, p = 0.007). DUSP22 methylation showed strong genetic regulation across chromosomes by a region on chromosome 16 which was consistent with new 3D genome interaction data. The presence of a direct link between famine and DUSP22 transcription was supported by data from cultured human fibroblasts that showed increased methylation (p = 0.048) and expression (p = 0.019) in response to nutritional deprivation (N = 10). These results highlight an epigenetic locus that is genetically regulated across chromosomes and that is involved in the response to early-life exposure to famine and that is relevant for a major psychiatric disorder.
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Affiliation(s)
- M P Boks
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands.
| | - L C Houtepen
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Z Xu
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Y He
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - G Ursini
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, USA
| | - A X Maihofer
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, USA.,VA Center of Excellence for Stress and Mental Health, San Diego, CA, USA.,Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - P Rajarajan
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Q Yu
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - H Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - Y Wu
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - S Wang
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - J P Shi
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - H E Hulshoff Pol
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - E Strengman
- Molecular Pathology, Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - B P F Rutten
- School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - A E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, USA
| | - J E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, USA
| | - D G Baker
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, USA.,VA Center of Excellence for Stress and Mental Health, San Diego, CA, USA.,Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - E M Hol
- Brain Center Rudolf Magnus, Department of Translational Neuroscience, University Medical Center Utrecht, Utrecht, The Netherlands
| | - S Akbarian
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
| | - C M Nievergelt
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, USA.,VA Center of Excellence for Stress and Mental Health, San Diego, CA, USA.,Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - L D De Witte
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - C H Vinkers
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands
| | - D R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, USA
| | - J Yu
- Department of Epidemiology and Health Statistics, School of Public Health, Jilin University, Changchun, China
| | - R S Kahn
- Brain Center Rudolf Magnus, Department of Psychiatry, University Medical Center Utrecht, Utrecht, The Netherlands.,Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, USA
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32
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Punzi G, Bharadwaj R, Ursini G. Neuroepigenetics of Schizophrenia. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:195-226. [PMID: 30072054 DOI: 10.1016/bs.pmbts.2018.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Schizophrenia is a complex disorder of the brain, where genetic variants explain only a portion of risk. Neuroepigenetic mechanisms may explain the remaining share of risk, as well as the transition from susceptibility to the actual disease. Here, we discuss the most recent findings in the field of brain epigenetics applied to the study of schizophrenia. Methylome studies have found several candidates exhibiting methylation modifications in association with the disorder, but genes affected do not always overlap. Notably, these studies converge in that genes within the schizophrenia risk loci or genes differentially methylated in patients affected with the disorder are dynamically regulated during early life. They also imply that schizophrenia-associated genetic variation may affect DNA methylation in fetal and adult brains. Histone modifications may help mediating the effect of genetic risk variants associated with schizophrenia, and regulating chromatin higher-order structure. The 3D-organization of chromatin in the brain creates physical interactions within chromosomes, so that schizophrenia-associated genetic variants can be linked with genes distant from their loci; this suggests that chromatin conformation matters in the mechanism of risk for the disorder. Non-coding RNAs provide a novel and complex mechanism of gene regulation potentially significant for schizophrenia, as proposed by research on specific microRNAs and long non-coding RNAs (lncRNAs). Finally, a recent study in epitranscriptomics identifies RNA methylation as a further epigenetic mechanism active in human brain and specifically in a portion of the transcriptome associated with schizophrenia susceptibility. These findings indicate that, as expected from the complexity of the brain and its development, several epigenetic mechanisms may intervene in the etiopathogenesis of schizophrenia. An understanding of their roles calls for research approaches integrating the investigation of different epigenetic mechanisms and of environmental and genetic risk, in the context of development.
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Affiliation(s)
- Giovanna Punzi
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Rahul Bharadwaj
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Gianluca Ursini
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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Liu J, Zhao W, Ware EB, Turner ST, Mosley TH, Smith JA. DNA methylation in the APOE genomic region is associated with cognitive function in African Americans. BMC Med Genomics 2018; 11:43. [PMID: 29739406 PMCID: PMC5941603 DOI: 10.1186/s12920-018-0363-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/26/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genetic variations in apolipoprotein E (APOE) and proximal genes (PVRL2, TOMM40, and APOC1) are associated with cognitive function and dementia, particularly Alzheimer's disease. Epigenetic mechanisms such as DNA methylation play a central role in the regulation of gene expression. Recent studies have found evidence that DNA methylation may contribute to the pathogenesis of dementia, but its association with cognitive function in populations without dementia remains unclear. METHODS We assessed DNA methylation levels of 48 CpG sites in the APOE genomic region in peripheral blood leukocytes collected from 289 African Americans (mean age = 67 years) from the Genetic Epidemiology Network of Arteriopathy (GENOA) study. Using linear regression, we examined the relationship between methylation in the APOE genomic region and multiple cognitive measures including learning, memory, processing speed, concentration, language and global cognitive function. RESULTS We identified eight CpG sites in three genes (PVRL2, TOMM40, and APOE) that showed an inverse association between methylation level and delayed recall, a measure of memory, after adjusting for age and sex (False Discovery Rate q-value < 0.1). All eight CpGs are located in either CpG islands (CGIs) or CGI shelves, and six of them are in promoter regions. Education and APOE ε4 carrier status significantly modified the effect of methylation in cg08583001 (PVRL2) and cg22024783 (TOMM40), respectively. Together, methylation of the eight CpGs explained an additional 8.7% of the variance in delayed recall, after adjustment for age, sex, education, and APOE ε4 carrier status. Methylation was not significantly associated with any other cognitive measures. CONCLUSIONS Our results suggest that methylation levels at multiple CpGs in the APOE genomic region are inversely associated with delayed recall during normal cognitive aging, even after accounting for known genetic predictors for cognition. Our findings highlight the important role of epigenetic mechanisms in influencing cognitive performance, and suggest that changes in blood methylation may be an early indicator of individuals at risk for dementia as well as potential targets for intervention in asymptomatic populations.
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Affiliation(s)
- Jiaxuan Liu
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, 4602 SPH Tower, Ann Arbor, MI 48109-2029 USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, 4602 SPH Tower, Ann Arbor, MI 48109-2029 USA
| | - Erin B. Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104 USA
| | - Stephen T. Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55905 USA
| | - Thomas H. Mosley
- Department of Neurology, University of Mississippi Medical Center, Jackson, MS 39126 USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, 4602 SPH Tower, Ann Arbor, MI 48109-2029 USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104 USA
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Liu C, Jiao C, Wang K, Yuan N. DNA Methylation and Psychiatric Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:175-232. [PMID: 29933950 DOI: 10.1016/bs.pmbts.2018.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA methylation has been an important area of research in the study of molecular mechanism to psychiatric disorders. Recent evidence has suggested that abnormalities in global methylation, methylation of genes, and pathways could play a role in the etiology of many forms of mental illness. In this article, we review the mechanisms of DNA methylation, including the genetic and environmental factors affecting methylation changes. We report and discuss major findings regarding DNA methylation in psychiatric patients, both within the context of global methylation studies and gene-specific methylation studies. Finally, we discuss issues surrounding data quality improvement, the limitations of current methylation analysis methods, and the possibility of using DNA methylation-based treatment for psychiatric disorders in the future.
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Affiliation(s)
- Chunyu Liu
- University of Illinois, Chicago, IL, United States; School of Life Science, Central South University, Changsha, China.
| | - Chuan Jiao
- School of Life Science, Central South University, Changsha, China
| | - Kangli Wang
- School of Life Science, Central South University, Changsha, China
| | - Ning Yuan
- Hunan Brain Hospital, Changsha, China
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35
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Lin D, Chen J, Perrone-Bizzozero N, Bustillo JR, Du Y, Calhoun VD, Liu J. Characterization of cross-tissue genetic-epigenetic effects and their patterns in schizophrenia. Genome Med 2018; 10:13. [PMID: 29482655 PMCID: PMC5828480 DOI: 10.1186/s13073-018-0519-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/09/2018] [Indexed: 01/14/2023] Open
Abstract
Background One of the major challenges in current psychiatric epigenetic studies is the tissue specificity of epigenetic changes since access to brain samples is limited. Peripheral tissues have been studied as surrogates but the knowledge of cross-tissue genetic-epigenetic characteristics remains largely unknown. In this work, we conducted a comprehensive investigation of genetic influence on DNA methylation across brain and peripheral tissues with the aim to characterize cross-tissue genetic-epigenetic effects and their roles in the pathophysiology of psychiatric disorders. Methods Genome-wide methylation quantitative trait loci (meQTLs) from brain prefrontal cortex, whole blood, and saliva were identified separately and compared. Focusing on cis-acting effects, we tested the enrichment of cross-tissue meQTLs among cross-tissue expression QTLs and genetic risk loci of various diseases, including major psychiatric disorders. CpGs targeted by cross-tissue meQTLs were also tested for genomic distribution and functional enrichment as well as their contribution to methylation correlation across tissues. Finally, a consensus co-methylation network analysis on the cross-tissue meQTL targeted CpGs was performed on data of the three tissues collected from schizophrenia patients and controls. Results We found a significant overlap of cis meQTLs (45–73 %) and targeted CpG sites (31–68 %) among tissues. The majority of cross-tissue meQTLs showed consistent signs of cis-acting effects across tissues. They were significantly enriched in genetic risk loci of various diseases, especially schizophrenia, and also enriched in cross-tissue expression QTLs. Compared to CpG sites not targeted by any meQTLs, cross-tissue targeted CpGs were more distributed in CpG island shores and enhancer regions, and more likely had strong correlation with methylation levels across tissues. The targeted CpGs were also annotated to genes enriched in multiple psychiatric disorders and neurodevelopment-related pathways. Finally, we identified one co-methylation network shared between brain and blood showing significant schizophrenia association (p = 5.5 × 10−6). Conclusions Our results demonstrate prevalent cross-tissue meQTL effects and their contribution to the correlation of CpG methylation across tissues, while at the same time a large portion of meQTLs show tissue-specific characteristics, especially in brain. Significant enrichment of cross-tissue meQTLs in expression QTLs and genetic risk loci of schizophrenia suggests the potential of these cross-tissue meQTLs for studying the genetic effect on schizophrenia. The study provides compelling motivation for a well-designed experiment to further validate the use of surrogate tissues in the study of psychiatric disorders. Electronic supplementary material The online version of this article (10.1186/s13073-018-0519-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dongdong Lin
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute, Albuquerque, NM, 87106, USA
| | - Jiayu Chen
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute, Albuquerque, NM, 87106, USA
| | - Nora Perrone-Bizzozero
- Department of Neurosciences, University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Psychiatry, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Juan R Bustillo
- Department of Neurosciences, University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Psychiatry, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Yuhui Du
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute, Albuquerque, NM, 87106, USA
| | - Vince D Calhoun
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute, Albuquerque, NM, 87106, USA.,Department of Neurosciences, University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Jingyu Liu
- The Mind Research Network and Lovelace Biomedical and Environmental Research Institute, Albuquerque, NM, 87106, USA. .,Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, 87131, USA.
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36
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Kondratiev NV, Alfimova MV, Golimbet VE. [A search of target regions for association studies between DNA methylation and cognitive impairment in schizophrenia]. Zh Nevrol Psikhiatr Im S S Korsakova 2018; 117:72-75. [PMID: 28884721 DOI: 10.17116/jnevro20171178172-75] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AIM To develop a strategy for the search for candidate genes and targets for epigenetic studies of cognitive impairments in patients with schizophrenia. MATERIAL AND METHODS A search for literature on epigenetics of schizophrenia and cognitive functions was performed. Single nucleotide polymorphisms (SNPs) that can create or abolish a site for DNA methylation or transcription factor sites were determined using a custom script. RESULTS AND CONCLUSION Eight candidate genes, including BDNF, COMT, RELN, SNRPN, PSMA4, FAM63B, IL-1RAP, MAD1L1, as well as 750 targets in CpG islands in the linkage regions identified in GWAS of schizophrenia and 406 targets in SNV located within transcription factor binding sites were selected.
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37
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Tomioka Y, Numata S, Kinoshita M, Umehara H, Watanabe SY, Nakataki M, Iwayama Y, Toyota T, Ikeda M, Yamamori H, Shimodera S, Tajima A, Hashimoto R, Iwata N, Yoshikawa T, Ohmori T. Decreased serum pyridoxal levels in schizophrenia: meta-analysis and Mendelian randomization analysis. J Psychiatry Neurosci 2018; 43:170053. [PMID: 29402374 PMCID: PMC5915240 DOI: 10.1503/jpn.170053] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 08/21/2017] [Accepted: 10/22/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Alterations in one-carbon metabolism have been associated with schizophrenia, and vitamin B6 is one of the key components in this pathway. METHODS We first conducted a case-control study of serum pyridoxal levels and schizophrenia in a large Japanese cohort (n = 1276). Subsequently, we conducted a meta-analysis of association studies (n = 2125). Second, we investigated whether rs4654748, which was identified in a genome-wide association study as a vitamin B6-related single nucleotide polymorphism, was genetically implicated in patients with schizophrenia in the Japanese population (n = 10 689). Finally, we assessed the effect of serum pyridoxal levels on schizophrenia risk using a Mendelian randomization (MR) approach. RESULTS Serum pyridoxal levels were significantly lower in patients with schizophrenia than in controls, not only in our cohort, but also in the pooled data set of the meta-analysis of association studies (standardized mean difference -0.48, 95% confidence interval [CI] -0.57 to -0.39, p = 9.8 × 10-24). We failed to find a significant association between rs4654748 and schizophrenia. Furthermore, an MR analysis failed to find a causal relationship between pyridoxal levels and schizophrenia risk (odds ratio 0.99, 95% CI 0.65-1.51, p = 0.96). LIMITATIONS Food consumption and medications may have affected serum pyridoxal levels in our cross-sectional study. Sample size, number of instrumental variables and substantial heterogeneity among patients with schizophrenia are limitations of an MR analysis. CONCLUSION We found decreased serum pyridoxal levels in patients with schizophrenia in this observational study. However, we failed to obtain data supporting a causal relationship between pyridoxal levels and schizophrenia risk using the MR approach.
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Affiliation(s)
- Yukiko Tomioka
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Shusuke Numata
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Makoto Kinoshita
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Hidehiro Umehara
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Shin-Ya Watanabe
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Masahito Nakataki
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Yoshimi Iwayama
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Tomoko Toyota
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Masashi Ikeda
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Hidenaga Yamamori
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Shinji Shimodera
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Atsushi Tajima
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Ryota Hashimoto
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Nakao Iwata
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Takeo Yoshikawa
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
| | - Tetsuro Ohmori
- From the Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan (Tomioka, Numata, Kinoshita, Umehara, Watanabe, Nakataki, Ohmori); the Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Saitama, Japan (Iwayama, Toyota, Yoshikawa); the Department of Psychiatry, School of Medicine, Fujita Health University, Aichi, Japan (Ikeda, Iwata); the Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan (Yamamori, Hashimoto); the Department of Neuropsychiatry, Kochi Medical School, Kochi University, Kochi, Japan (Shimodera); the Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Ishikawa, Japan (Tajima); and the Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Osaka, Japan (Hashimoto)
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Viana J, Hannon E, Dempster E, Pidsley R, Macdonald R, Knox O, Spiers H, Troakes C, Al-Saraj S, Turecki G, Schalkwyk LC, Mill J. Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions. Hum Mol Genet 2017; 26:210-225. [PMID: 28011714 PMCID: PMC5351932 DOI: 10.1093/hmg/ddw373] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/26/2016] [Indexed: 01/29/2023] Open
Abstract
Genetic association studies provide evidence for a substantial polygenic component to schizophrenia, although the neurobiological mechanisms underlying the disorder remain largely undefined. Building on recent studies supporting a role for developmentally regulated epigenetic variation in the molecular aetiology of schizophrenia, this study aimed to identify epigenetic variation associated with both a diagnosis of schizophrenia and elevated polygenic risk burden for the disease across multiple brain regions. Genome-wide DNA methylation was quantified in 262 post-mortem brain samples, representing tissue from four brain regions (prefrontal cortex, striatum, hippocampus and cerebellum) from 41 schizophrenia patients and 47 controls. We identified multiple disease-associated and polygenic risk score-associated differentially methylated positions and regions, which are not enriched in genomic regions identified in genetic studies of schizophrenia and do not reflect direct genetic effects on DNA methylation. Our study represents the first analysis of epigenetic variation associated with schizophrenia across multiple brain regions and highlights the utility of polygenic risk scores for identifying molecular pathways associated with aetiological variation in complex disease.
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Affiliation(s)
- Joana Viana
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma Dempster
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ruth Pidsley
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Ruby Macdonald
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Olivia Knox
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Helen Spiers
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Claire Troakes
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Safa Al-Saraj
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
| | - Gustavo Turecki
- Douglas Mental Health Institute, McGill University, Montreal, QC, Canada and
| | | | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK.,Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
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Gulchina Y, Xu SJ, Snyder MA, Elefant F, Gao WJ. Epigenetic mechanisms underlying NMDA receptor hypofunction in the prefrontal cortex of juvenile animals in the MAM model for schizophrenia. J Neurochem 2017. [PMID: 28628228 DOI: 10.1111/jnc.14101] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Schizophrenia (SCZ) is characterized not only by psychosis, but also by working memory and executive functioning deficiencies, processes that rely on the prefrontal cortex (PFC). Because these cognitive impairments emerge prior to psychosis onset, we investigated synaptic function during development in the neurodevelopmental methylazoxymethanol (MAM) model for SCZ. Specifically, we hypothesize that N-methyl-D-aspartate receptor (NMDAR) hypofunction is attributable to reductions in the NR2B subunit through aberrant epigenetic regulation of gene expression, resulting in deficient synaptic physiology and PFC-dependent cognitive dysfunction, a hallmark of SCZ. Using western blot and whole-cell patch-clamp electrophysiology, we found that the levels of synaptic NR2B protein are significantly decreased in juvenile MAM animals, and the function of NMDARs is substantially compromised. Both NMDA-mEPSCs and synaptic NMDA-eEPSCs are significantly reduced in prelimbic PFC (plPFC). This protein loss during the juvenile period is correlated with an aberrant increase in enrichment of the epigenetic transcriptional repressor RE1-silencing transcription factor (REST) and the repressive histone marker H3K27me3 at the Grin2b promoter, as assayed by ChIP-quantitative polymerase chain reaction. Glutamate hypofunction has been a prominent hypothesis in the understanding of SCZ pathology; however, little attention has been given to the NMDAR system in the developing PFC in models for SCZ. Our work is the first to confirm that NMDAR hypofunction is a feature of early postnatal development, with epigenetic hyper-repression of the Grin2b promoter being a contributing factor. The selective loss of NR2B protein and subsequent synaptic dysfunction weakens plPFC function during development and may underlie early cognitive impairments in SCZ models and patients. Read the Editorial Highlight for this article on page 264.
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Affiliation(s)
- Yelena Gulchina
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Song-Jun Xu
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Melissa A Snyder
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Felice Elefant
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Wen-Jun Gao
- Department of Neurobiology and Anatomy, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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40
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Epigenomics of Major Depressive Disorders and Schizophrenia: Early Life Decides. Int J Mol Sci 2017; 18:ijms18081711. [PMID: 28777307 PMCID: PMC5578101 DOI: 10.3390/ijms18081711] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/31/2017] [Accepted: 08/02/2017] [Indexed: 12/13/2022] Open
Abstract
Brain development is guided by the interactions between the genetic blueprint and the environment. Epigenetic mechanisms, especially DNA methylation, can mediate these interactions and may also trigger long-lasting adaptations in developmental programs that increase the risk of major depressive disorders (MDD) and schizophrenia (SCZ). Early life adversity is a major risk factor for MDD/SCZ and can trigger persistent genome-wide changes in DNA methylation at genes important to early, but also to mature, brain function, including neural proliferation, differentiation, and synaptic plasticity, among others. Moreover, genetic variations controlling dynamic DNA methylation in early life are thought to influence later epigenomic changes in SCZ. This finding corroborates the high genetic load and a neurodevelopmental origin of SCZ and shows that epigenetic responses to the environment are, at least in part, genetically controlled. Interestingly, genetic variants influencing DNA methylation are also enriched in risk variants from genome-wide association studies (GWAS) on SCZ supporting a role in neurodevelopment. Overall, epigenomic responses to early life adversity appear to be controlled to different degrees by genetics in MDD/SCZ, even though the potential reversibility of epigenomic processes may offer new hope for timely therapeutic interventions in MDD/SCZ.
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41
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Rethinking the Epigenetic Framework to Unravel the Molecular Pathology of Schizophrenia. Int J Mol Sci 2017; 18:ijms18040790. [PMID: 28387726 PMCID: PMC5412374 DOI: 10.3390/ijms18040790] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 03/23/2017] [Accepted: 04/04/2017] [Indexed: 12/26/2022] Open
Abstract
Schizophrenia is a complex mental disorder whose causes are still far from being known. Although researchers have focused on genetic or environmental contributions to the disease, we still lack a scientific framework that joins molecular and clinical findings. Epigenetic can explain how environmental variables may affect gene expression without modifying the DNA sequence. In fact, neuroepigenomics represents an effort to unify the research available on the molecular pathology of mental diseases, which has been carried out through several approaches ranging from interrogating single DNA methylation events and hydroxymethylation patterns, to epigenome-wide association studies, as well as studying post-translational modifications of histones, or nucleosomal positioning. The high dependence on tissues with epigenetic marks compels scientists to refine their sampling procedures, and in this review, we will focus on findings obtained from brain tissue. Despite our efforts, we still need to refine our hypothesis generation process to obtain real knowledge from a neuroepigenomic framework, to avoid the creation of more noise on this innovative point of view; this may help us to definitively unravel the molecular pathology of severe mental illnesses, such as schizophrenia.
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Effect of Clozapine on DNA Methylation in Peripheral Leukocytes from Patients with Treatment-Resistant Schizophrenia. Int J Mol Sci 2017; 18:ijms18030632. [PMID: 28335437 PMCID: PMC5372645 DOI: 10.3390/ijms18030632] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/10/2017] [Accepted: 03/10/2017] [Indexed: 02/06/2023] Open
Abstract
Clozapine is an atypical antipsychotic, that is established as the treatment of choice for treatment-resistant schizophrenia (SCZ). To date, no study investigating comprehensive DNA methylation changes in SCZ patients treated with chronic clozapine has been reported. The purpose of the present study is to reveal the effects of clozapine on DNA methylation in treatment-resistant SCZ. We conducted a genome-wide DNA methylation profiling in peripheral leukocytes (485,764 CpG dinucleotides) from treatment-resistant SCZ patients treated with clozapine (n = 21) in a longitudinal study. Significant changes in DNA methylation were observed at 29,134 sites after one year of treatment with clozapine, and these genes were enriched for “cell substrate adhesion” and “cell matrix adhesion” gene ontology (GO) terms. Furthermore, DNA methylation changes in the CREBBP (CREB binding protein) gene were significantly correlated with the clinical improvements. Our findings provide insights into the action of clozapine in treatment-resistant SCZ.
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McKinney B, Ding Y, Lewis DA, Sweet RA. DNA methylation as a putative mechanism for reduced dendritic spine density in the superior temporal gyrus of subjects with schizophrenia. Transl Psychiatry 2017; 7:e1032. [PMID: 28195572 PMCID: PMC5438028 DOI: 10.1038/tp.2016.297] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 11/13/2016] [Indexed: 01/11/2023] Open
Abstract
Reduced dendritic spine density (DSD) in cortical layer 3 of the superior temporal gyrus (STG), and multiple other brain regions, is consistently observed in postmortem studies of schizophrenia (SZ). Elucidating the molecular mechanisms of this intermediate phenotype holds promise for understanding SZ pathophysiology, identifying SZ treatment targets and developing animal models. DNA methylation (DNAm), the addition of a methyl group to a cytosine nucleotide, regulates gene transcription and is a strong candidate for such a mechanism. We tested the hypothesis that DNAm correlates with DSD in the human STG and that this relationship is disrupted in SZ. We used the Illumina Infinium HumanMethylation450 Beadchip Array to quantify DNAm on a genome-wide scale in the postmortem STG from 22 SZ subjects and matched non-psychiatric control (NPC) subjects; DSD measures were available for 17 of the 22 subject pairs. We found DNAm to correlate with DSD at more sites than expected by chance in NPC, but not SZ, subjects. In addition, we show that the slopes of the linear DNAm-DSD correlations differed between SZ and NPC subjects at more sites than expected by chance. From these data, we identified 2 candidate genes for mediating DSD abnormalities in SZ: brain-specific angiogenesis inhibitor 1-associated protein 2 (BAIAP2) and discs large, Drosophila, homolog of, 1 (DLG1). Together, these data suggest that altered DNAm in SZ may be a mechanism for SZ-related DSD reductions.
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Affiliation(s)
- B McKinney
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Translational Neuroscience Program, University of Pittsburgh, Pittsburgh, PA, USA
| | - Y Ding
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - D A Lewis
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Translational Neuroscience Program, University of Pittsburgh, Pittsburgh, PA, USA,Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - R A Sweet
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA,Translational Neuroscience Program, University of Pittsburgh, Pittsburgh, PA, USA,Department of Neurology, University of Pittsburgh, Pittsburgh, PA, USA,Mental Illness Research, Education, and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA, USA,Department of Psychiatry, Neurology and VISN 4 Mental Illness Research, Education and Clinical Center (MIRECC), Biomedical Science Tower, Room W-1645, 3811 O'Hara Street, Pittsburgh, PA 15213, USA. E-mail:
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Abstract
Schizophrenia is a highly heritable psychiatric condition that displays a complex phenotype. A multitude of genetic susceptibility loci have now been identified, but these fail to explain the high heritability estimates of schizophrenia. In addition, epidemiologically relevant environmental risk factors for schizophrenia may lead to permanent changes in brain function. In conjunction with genetic liability, these environmental risk factors-likely through epigenetic mechanisms-may give rise to schizophrenia, a clinical syndrome characterized by florid psychotic symptoms and moderate to severe cognitive impairment. These pathophysiological features point to the involvement of epigenetic processes. Recently, a wave of studies examining aberrant DNA modifications in schizophrenia was published. This chapter aims to comprehensively review the current findings, from both candidate gene studies and genome-wide approaches, on DNA methylation changes in schizophrenia.
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45
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The Future is The Past: Methylation QTLs in Schizophrenia. Genes (Basel) 2016; 7:genes7120104. [PMID: 27886132 PMCID: PMC5192480 DOI: 10.3390/genes7120104] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 11/13/2016] [Accepted: 11/16/2016] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) have remarkably advanced insight into the genetic basis of schizophrenia (SCZ). Still, most of the functional variance in disease risk remains unexplained. Hence, there is a growing need to map genetic variability-to-genes-to-functions for understanding the pathophysiology of SCZ and the development of better treatments. Genetic variation can regulate various cellular functions including DNA methylation, an epigenetic mark with important roles in transcription and the mediation of environmental influences. Methylation quantitative trait loci (meQTLs) are derived by mapping levels of DNA methylation in genetically different, genotyped individuals and define loci at which DNA methylation is influenced by genetic variation. Recent evidence points to an abundance of meQTLs in brain tissues whose functional contributions to development and mental diseases are still poorly understood. Interestingly, fetal meQTLs reside in regulatory domains affecting methylome reconfiguration during early brain development and are enriched in loci identified by GWAS for SCZ. Moreover, fetal meQTLs are preserved in the adult brain and could trace early epigenomic deregulation during vulnerable periods. Overall, these findings highlight the role of fetal meQTLs in the genetic risk for and in the possible neurodevelopmental origin of SCZ.
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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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Berkowicz SR, Featherby TJ, Whisstock JC, Bird PI. Mice Lacking Brinp2 or Brinp3, or Both, Exhibit Behaviors Consistent with Neurodevelopmental Disorders. Front Behav Neurosci 2016; 10:196. [PMID: 27826231 PMCID: PMC5079073 DOI: 10.3389/fnbeh.2016.00196] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/29/2016] [Indexed: 12/31/2022] Open
Abstract
Background:Brinps 1–3, and Astrotactins (Astn) 1 and 2, are members of the Membrane Attack Complex/Perforin (MACPF) superfamily that are predominantly expressed in the mammalian brain during development. Genetic variation at the human BRINP2/ASTN1 and BRINP1/ASTN2 loci has been implicated in neurodevelopmental disorders. We, and others, have previously shown that Brinp1−/− mice exhibit behavior reminiscent of autism spectrum disorder (ASD) and attention deficit hyperactivity disorder (ADHD). Method: We created Brinp2−/− mice and Brinp3−/− mice via the Cre-mediated LoxP system to investigate the effect of gene deletion on anatomy and behavior. Additionally, Brinp2−/−Brinp3−/− double knock-out mice were generated by interbreeding Brinp2−/− and Brinp3−/− mice. Genomic validation was carried out for each knock-out line, followed by histological, weight and behavioral examination. Brinp1−/−Brinp2−/−Brinp3−/− triple knock-out mice were also generated by crossing Brinp2/3 double knock-out mice with previously generated Brinp1−/− mice, and examined by weight and histological analysis. Results:Brinp2−/− and Brinp3−/− mice differ in their behavior: Brinp2−/− mice are hyperactive, whereas Brinp3−/− mice exhibit marked changes in anxiety-response on the elevated plus maze. Brinp3−/− mice also show evidence of altered sociability. Both Brinp2−/− and Brinp3−/− mice have normal short-term memory, olfactory responses, pre-pulse inhibition, and motor learning. The double knock-out mice show behaviors of Brinp2−/− and Brinp3−/− mice, without evidence of new or exacerbated phenotypes. Conclusion:Brinp3 is important in moderation of anxiety, with potential relevance to anxiety disorders. Brinp2 dysfunction resulting in hyperactivity may be relevant to the association of ADHD with chromosome locus 1q25.2. Brinp2−/− and Brinp3−/− genes do not compensate in the mammalian brain and likely have distinct molecular or cell-type specific functions.
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Affiliation(s)
- Susan R Berkowicz
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University Clayton, VIC, Australia
| | - Travis J Featherby
- Melbourne Brain Centre, Florey Neuroscience Institute Parkville, VIC, Australia
| | - James C Whisstock
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash UniversityClayton, VIC, Australia; ARC Centre of Excellence in Advanced Molecular Imaging, Monash UniversityClayton, VIC, Australia
| | - Phillip I Bird
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University Clayton, VIC, Australia
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48
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van de Leemput J, Hess JL, Glatt SJ, Tsuang MT. Genetics of Schizophrenia: Historical Insights and Prevailing Evidence. ADVANCES IN GENETICS 2016; 96:99-141. [PMID: 27968732 DOI: 10.1016/bs.adgen.2016.08.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Schizophrenia's (SZ's) heritability and familial transmission have been known for several decades; however, despite the clear evidence for a genetic component, it has been very difficult to pinpoint specific causative genes. Even so genetic studies have taught us a lot, even in the pregenomic era, about the molecular underpinnings and disease-relevant pathways. Recurring themes emerged revealing the involvement of neurodevelopmental processes, glutamate regulation, and immune system differential activation in SZ etiology. The recent emergence of epigenetic studies aimed at shedding light on the biological mechanisms underlying SZ has provided another layer of information in the investigation of gene and environment interactions. However, this epigenetic insight also brings forth another layer of complexity to the (epi)genomic landscape such as interactions between genetic variants, epigenetic marks-including cross-talk between DNA methylation and histone modification processes-, gene expression regulation, and environmental influences. In this review, we seek to synthesize perspectives, including limitations and obstacles yet to overcome, from genetic and epigenetic literature on SZ through a qualitative review of risk factors and prevailing hypotheses. Encouraged by the findings of both genetic and epigenetic studies to date, as well as the continued development of new technologies to collect and interpret large-scale studies, we are left with a positive outlook for the future of elucidating the molecular genetic mechanisms underlying SZ and other complex neuropsychiatric disorders.
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Affiliation(s)
- J van de Leemput
- University of California, San Diego, La Jolla, CA, United States
| | - J L Hess
- SUNY Upstate Medical University, Syracuse, NY, United States
| | - S J Glatt
- SUNY Upstate Medical University, Syracuse, NY, United States
| | - M T Tsuang
- University of California, San Diego, La Jolla, CA, United States
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Montano C, Taub MA, Jaffe A, Briem E, Feinberg JI, Trygvadottir R, Idrizi A, Runarsson A, Berndsen B, Gur RC, Moore TM, Perry RT, Fugman D, Sabunciyan S, Yolken RH, Hyde TM, Kleinman JE, Sobell JL, Pato CN, Pato MT, Go RC, Nimgaonkar V, Weinberger DR, Braff D, Gur RE, Fallin MD, Feinberg AP. Association of DNA Methylation Differences With Schizophrenia in an Epigenome-Wide Association Study. JAMA Psychiatry 2016; 73:506-14. [PMID: 27074206 PMCID: PMC6353566 DOI: 10.1001/jamapsychiatry.2016.0144] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
IMPORTANCE DNA methylation may play an important role in schizophrenia (SZ), either directly as a mechanism of pathogenesis or as a biomarker of risk. OBJECTIVE To scan genome-wide DNA methylation data to identify differentially methylated CpGs between SZ cases and controls. DESIGN, SETTING, AND PARTICIPANTS Epigenome-wide association study begun in 2008 using DNA methylation levels of 456 513 CpG loci measured on the Infinium HumanMethylation450 array (Illumina) in a consortium of case-control studies for initial discovery and in an independent replication set. Primary analyses used general linear regression, adjusting for age, sex, race/ethnicity, smoking, batch, and cell type heterogeneity. The discovery set contained 689 SZ cases and 645 controls (n = 1334), from 3 multisite consortia: the Consortium on the Genetics of Endophenotypes in Schizophrenia, the Project among African-Americans To Explore Risks for Schizophrenia, and the Multiplex Multigenerational Family Study of Schizophrenia. The replication set contained 247 SZ cases and 250 controls (n = 497) from the Genomic Psychiatry Cohort. MAIN OUTCOMES AND MEASURES Identification of differentially methylated positions across the genome in SZ cases compared with controls. RESULTS Of the 689 case participants in the discovery set, 477 (69%) were men and 258 (37%) were non-African American; of the 645 controls, 273 (42%) were men and 419 (65%) were non-African American. In our replication set, cases/controls were 76% male and 100% non-African American. We identified SZ-associated methylation differences at 923 CpGs in the discovery set (false discovery rate, <0.2). Of these, 625 showed changes in the same direction including 172 with P < .05 in the replication set. Some replicated differentially methylated positions are located in a top-ranked SZ region from genome-wide association study analyses. CONCLUSIONS AND RELEVANCE This analysis identified 172 replicated new associations with SZ after careful correction for cell type heterogeneity and other potential confounders. The overlap with previous genome-wide association study data can provide potential insights into the functional relevance of genetic signals for SZ.
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Affiliation(s)
- Carolina Montano
- Medical Scientist Training Program and Predoctoral Training Program in Human Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland,Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Margaret A. Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Andrew Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Eirikur Briem
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jason I. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rakel Trygvadottir
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Adrian Idrizi
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Arni Runarsson
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Birna Berndsen
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ruben C. Gur
- Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Tyler M. Moore
- Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Rodney T. Perry
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham
| | - Doug Fugman
- Rutgers University Cell and DNA Repository, Piscataway, New Jersey
| | - Sarven Sabunciyan
- Stanley Division of Developmental Neurovirology, Johns Hopkins, School of Medicine, Baltimore, Maryland
| | - Robert H. Yolken
- Stanley Division of Developmental Neurovirology, Johns Hopkins, School of Medicine, Baltimore, Maryland
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Joel E. Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - Janet L. Sobell
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine of University of Southern California, Los Angeles
| | - Carlos N. Pato
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine of University of Southern California, Los Angeles
| | - Michele T. Pato
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine of University of Southern California, Los Angeles
| | - Rodney C. Go
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham
| | | | - Daniel R. Weinberger
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, Maryland
| | - David Braff
- Department of Psychiatry, University of California San Diego School of Medicine, La Jolla,VISN22, Mental Illness Research, Education, and Clinical Center, VA Veterans Affairs San Diego Healthcare System, San Diego, California
| | - Raquel E. Gur
- Neuropsychiatry Section, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Margaret Daniele Fallin
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Andrew P. Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland,Departments of Medicine and Biomedical Engineering, Johns Hopkins University School of Medicine and Whiting School of Engineering, Baltimore, Maryland
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Abstract
Despite a lack of recent progress in the treatment of schizophrenia, our understanding of its genetic and environmental causes has considerably improved, and their relationship to aberrant patterns of neurodevelopment has become clearer. This raises the possibility that 'disease-modifying' strategies could alter the course to - and of - this debilitating disorder, rather than simply alleviating symptoms. A promising window for course-altering intervention is around the time of the first episode of psychosis, especially in young people at risk of transition to schizophrenia. Indeed, studies performed in both individuals at risk of developing schizophrenia and rodent models for schizophrenia suggest that pre-diagnostic pharmacotherapy and psychosocial or cognitive-behavioural interventions can delay or moderate the emergence of psychosis. Of particular interest are 'hybrid' strategies that both relieve presenting symptoms and reduce the risk of transition to schizophrenia or another psychiatric disorder. This Review aims to provide a broad-based consideration of the challenges and opportunities inherent in efforts to alter the course of schizophrenia.
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