101
|
Fitzgerald E, Boardman JP, Drake AJ. Preterm Birth and the Risk of Neurodevelopmental Disorders - Is There a Role for Epigenetic Dysregulation? Curr Genomics 2018; 19:507-521. [PMID: 30386170 PMCID: PMC6158617 DOI: 10.2174/1389202919666171229144807] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/06/2017] [Accepted: 12/17/2017] [Indexed: 12/29/2022] Open
Abstract
Preterm Birth (PTB) accounts for approximately 11% of all births worldwide each year and is a profound physiological stressor in early life. The burden of neuropsychiatric and developmental impairment is high, with severity and prevalence correlated with gestational age at delivery. PTB is a major risk factor for the development of cerebral palsy, lower educational attainment and deficits in cognitive functioning, and individuals born preterm have higher rates of schizophrenia, autistic spectrum disorder and attention deficit/hyperactivity disorder. Factors such as gestational age at birth, systemic inflammation, respiratory morbidity, sub-optimal nutrition, and genetic vulnerability are associated with poor outcome after preterm birth, but the mechanisms linking these factors to adverse long term outcome are poorly understood. One potential mechanism linking PTB with neurodevelopmental effects is changes in the epigenome. Epigenetic processes can be defined as those leading to altered gene expression in the absence of a change in the underlying DNA sequence and include DNA methylation/hydroxymethylation and histone modifications. Such epigenetic modifications may be susceptible to environmental stimuli, and changes may persist long after the stimulus has ceased, providing a mechanism to explain the long-term consequences of acute exposures in early life. Many factors such as inflammation, fluctuating oxygenation and excitotoxicity which are known factors in PTB related brain injury, have also been implicated in epigenetic dysfunction. In this review, we will discuss the potential role of epigenetic dysregulation in mediating the effects of PTB on neurodevelopmental outcome, with specific emphasis on DNA methylation and the α-ketoglutarate dependent dioxygenase family of enzymes.
Collapse
Affiliation(s)
| | | | - Amanda J. Drake
- Address correspondence to this author at the University/BHF Centre for Cardiovascular Science, University of Edinburgh, The Queen’s Medical Research Institute, Edinburgh EH16 4TJ, UK; Tel: 44 131 2426748; Fax: 44 131 2426779; E-mail:
| |
Collapse
|
102
|
Pardo M, Cheng Y, Sitbon YH, Lowell JA, Grieco SF, Worthen RJ, Desse S, Barreda-Diaz A. Insulin growth factor 2 (IGF2) as an emergent target in psychiatric and neurological disorders. Review. Neurosci Res 2018; 149:1-13. [PMID: 30389571 DOI: 10.1016/j.neures.2018.10.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/05/2018] [Accepted: 10/29/2018] [Indexed: 12/23/2022]
Abstract
Insulin-like growth factor 2 (IGF2) is abundantly expressed in the central nervous system (CNS). Recent evidence highlights the role of IGF2 in the brain, sustained by data showing its alterations as a common feature across a variety of psychiatric and neurological disorders. Previous studies emphasize the potential role of IGF2 in psychiatric and neurological conditions as well as in memory impairments, targeting IGF2 as a pro-cognitive agent. New research on animal models supports that upcoming investigations should explore IGF2's strong promising role as a memory enhancer. The lack of effective treatments for cognitive disturbances as a result of psychiatric diseases lead to further explore IGF2 as a promising target for the development of new pharmacology for the treatment of memory dysfunctions. In this review, we aim at gathering all recent relevant studies and findings on the role of IGF2 in the development of psychiatric diseases that occur with cognitive problems.
Collapse
Affiliation(s)
- M Pardo
- University of Miami Miller School of Medicine, Department of Neurology, Miami, FL, USA.
| | - Y Cheng
- University of California Los Angeles, Neurology Department, Los Angeles, CA, USA.
| | - Y H Sitbon
- University of Miami Miller School of Medicine, Department of Molecular and Cellular Pharmacology, Miami, FL, USA.
| | - J A Lowell
- University of Miami, Department of Psychiatry & Behavioral Sciences, Miami, FL, USA.
| | - S F Grieco
- University of California, Department of Anatomy and Neurobiology, Irvine, CA, USA.
| | - R J Worthen
- University of Miami, Department of Psychiatry & Behavioral Sciences, Miami, FL, USA.
| | - S Desse
- University of Miami, Department of Psychiatry & Behavioral Sciences, Miami, FL, USA.
| | - A Barreda-Diaz
- University of Miami Miller School of Medicine, Department of Neurology, Miami, FL, USA.
| |
Collapse
|
103
|
Combining DNA methylation and RNA sequencing data of cancer for supervised knowledge extraction. BioData Min 2018; 11:22. [PMID: 30386434 PMCID: PMC6203208 DOI: 10.1186/s13040-018-0184-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 10/11/2018] [Indexed: 11/26/2022] Open
Abstract
Background In the Next Generation Sequencing (NGS) era a large amount of biological data is being sequenced, analyzed, and stored in many public databases, whose interoperability is often required to allow an enhanced accessibility. The combination of heterogeneous NGS genomic data is an open challenge: the analysis of data from different experiments is a fundamental practice for the study of diseases. In this work, we propose to combine DNA methylation and RNA sequencing NGS experiments at gene level for supervised knowledge extraction in cancer. Methods We retrieve DNA methylation and RNA sequencing datasets from The Cancer Genome Atlas (TCGA), focusing on the Breast Invasive Carcinoma (BRCA), the Thyroid Carcinoma (THCA), and the Kidney Renal Papillary Cell Carcinoma (KIRP). We combine the RNA sequencing gene expression values with the gene methylation quantity, as a new measure that we define for representing the methylation quantity associated to a gene. Additionally, we propose to analyze the combined data through tree- and rule-based classification algorithms (C4.5, Random Forest, RIPPER, and CAMUR). Results We extract more than 15,000 classification models (composed of gene sets), which allow to distinguish the tumoral samples from the normal ones with an average accuracy of 95%. From the integrated experiments we obtain about 5000 classification models that consider both the gene measures related to the RNA sequencing and the DNA methylation experiments. Conclusions We compare the sets of genes obtained from the classifications on RNA sequencing and DNA methylation data with the genes obtained from the integration of the two experiments. The comparison results in several genes that are in common among the single experiments and the integrated ones (733 for BRCA, 35 for KIRP, and 861 for THCA) and 509 genes that are in common among the different experiments. Finally, we investigate the possible relationships among the different analyzed tumors by extracting a core set of 13 genes that appear in all tumors. A preliminary functional analysis confirms the relation of part of those genes (5 out of 13 and 279 out of 509) with cancer, suggesting to focus further studies on the new individuated ones. Electronic supplementary material The online version of this article (10.1186/s13040-018-0184-6) contains supplementary material, which is available to authorized users.
Collapse
|
104
|
Nociti V, Santoro M, Quaranta D, Losavio FA, De Fino C, Giordano R, Palomba N, Rossini PM, Guerini FR, Clerici M, Caputo D, Mirabella M. BDNF rs6265 polymorphism methylation in Multiple Sclerosis: A possible marker of disease progression. PLoS One 2018; 13:e0206140. [PMID: 30352103 PMCID: PMC6198951 DOI: 10.1371/journal.pone.0206140] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 10/08/2018] [Indexed: 01/19/2023] Open
Abstract
INTRODUCTION Brain-Derived Neurotrophic Factor (BDNF) and its most common polymorphism Val66Met are known to have a role in Multiple Sclerosis (MS) pathogenesis. Evidence is accumulating that there is an involvement of DNA methylation in the regulation of BDNF expression. The aim of this study was to assess in blood samples of MS patients the correlation between the methylation status of the CpG site near BDNF-Val66Met polymorphism and the severity of the disease. METHODS We recruited 209 MS patients that were genotyped for the BDNF Val66Met polymorphism. For each patient we quantitatively measured the methylation level of cytosine included in the exonic CpG site that can be created or abolished by the Val66Met BDNF polymorphism. Furthermore, we analyzed the clinical history of each patient and determined the time elapsed since the onset of the disease and an EDSS score of 6.0. RESULTS The genetic analysis identified 122 (58.4%) subjects carrying the Val/Val genotype, 81 (38.8%) with Val/Met genotype, and 6 (2.8%) carrying the Met/Met genotype. When the endpoint of an EDSS score of 6 was taken into account by means of a survival analysis, 52 failures (i.e., reaching an EDSS score of 6) were reported. When the sample was stratified according to the percentage of the BDNF methylation, subjects falling below the median (median methylation = 81%) were at higher risk of failure (IRD = 0.016; 95%CI = 0.0050-0.0279; p = 0.004). CONCLUSIONS In patients with a high disease progression the hypomethylation of the BDNF gene could increase the secretion of the protective neurotrophin, so epigenetic modifications could be the organism response to limit a brain functional reserve loss. Our study suggests that the percentage of methylation of the BDNF gene could be used as a prognostic factor for disease progression toward a high disability in MS patient.
Collapse
Affiliation(s)
- Viviana Nociti
- Institute of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Davide Quaranta
- Institute of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Rome, Italy
| | - Francesco Antonio Losavio
- Institute of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Rome, Italy
| | - Chiara De Fino
- Institute of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rocco Giordano
- Institute of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Rome, Italy
| | - Nicole Palomba
- Institute of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Rome, Italy
| | - Paolo Maria Rossini
- Institute of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
| | | | - Massimiliano Mirabella
- Institute of Neurology, Fondazione Policlinico Universitario A. Gemelli IRCCS—Università Cattolica del Sacro Cuore, Rome, Italy
- * E-mail:
| |
Collapse
|
105
|
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.
Collapse
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
| |
Collapse
|
106
|
Alfimova MV, Kondratiev NV, Golov AK, Golimbet VE. Methylation of the Reelin Gene Promoter in Peripheral Blood and Its Relationship with the Cognitive Function of Schizophrenia Patients. Mol Biol 2018. [DOI: 10.1134/s0026893318050023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
107
|
Guo JC, Yang YJ, Zheng XA, Jiang XL, Guo M, Wang XD, Gao YS, Fu LQ, Chen XS. CpG methylation of brain-derived the neurotrophic factor gene promoter as a potent diagnostic and prognostic biomarker for post-traumatic stress disorder. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:5101-5109. [PMID: 31949588 PMCID: PMC6962936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/15/2018] [Indexed: 06/10/2023]
Abstract
Posttraumatic stress disorder (PTSD) is a common response to traumatic events. Many PTSD patients recover in the next few months, but in a significant subgroup, the symptoms persist, often for years. The present study shows that brain-derived neurotrophic factor (BDNF) gene is related to the pathological mechanism of a variety of mental diseases. Here we investigate the effect of methylation of BDNF gene and different loci on the occurrence and development of PTSD. Initially, using case-control method, 322 PTSD patients as well as 215 normal controls were selected as the subjects. Following peripheral venous blood being collected from the subjects, genomic DNA was extracted. Methylation of the cytosine-guanine dinucleotide (CpG) island in BDNF gene promoter was then modified by bisulfite and detected through direct sequencing. Methylation of CpG in BDNF gene promoter was closely related to PTSD, and the methylation level of CpG in BDNF gene promoter may serve as a biomarker for PTSD diagnosis. Types of trauma of PTSD patients may have a certain effect on the methylation level of BDNF gene promoter. Methylation level of the BDNF promoter, depressive degree score, poor sleep quality score, early trauma score, mental stress score, and trauma type were closely related to the occurrence and development of PTSD. Taken together, our data support the notion that stressful life events may directly cause CpG methylation in the BDNF promoter of PTSD patients. Stress types may be associated with methylation levels of CpG1, CpG7, and CpG18 in the BDNF promoter of PTSD patients. These findings provide a new way for the diagnosis and treatment of PTSD.
Collapse
Affiliation(s)
- Jun-Cheng Guo
- Central South University Xiangya School of Medical Affiliated Haikou HospitalHaikou, Hainan Province, P. R. China
- Central South UniversityChangsha, P. R. China
| | - Yi-Jun Yang
- Central South University Xiangya School of Medical Affiliated Haikou HospitalHaikou, Hainan Province, P. R. China
| | - Xiao-Ai Zheng
- Psychological Research Center of Hainan General HospitalHaikou, Hainan Province, P. R. China
| | - Xiang-Ling Jiang
- Psychological Research Center of Hainan General HospitalHaikou, Hainan Province, P. R. China
| | - Min Guo
- Psychological Research Center of Hainan General HospitalHaikou, Hainan Province, P. R. China
| | - Xiao-Dan Wang
- School of Public Health, Hainan Medical CollegeHaikou 571199, Hainan Province, P. R. China
| | - Yun-Suo Gao
- Psychological Research Center of Hainan General HospitalHaikou, Hainan Province, P. R. China
| | - Lin-Qiu Fu
- Psychological Research Center of Hainan General HospitalHaikou, Hainan Province, P. R. China
| | - Xian-Shan Chen
- Psychological Research Center of Hainan General HospitalHaikou, Hainan Province, P. R. China
| |
Collapse
|
108
|
Davis E, Sethuraman S. Consistency of modularity clustering on random geometric graphs. ANN APPL PROBAB 2018. [DOI: 10.1214/17-aap1313] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
109
|
Reproductive period and epigenetic modifications of the oxidative phosphorylation pathway in the human prefrontal cortex. PLoS One 2018; 13:e0199073. [PMID: 30052629 PMCID: PMC6063396 DOI: 10.1371/journal.pone.0199073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 05/31/2018] [Indexed: 01/13/2023] Open
Abstract
PURPOSE Human females have a unique duration of post-reproductive longevity, during which sex-specific mechanisms ma influence later-life mechanisms of neuronal resilience and vulnerability. The maintenance of energy metabolism, through the oxidative phosphorylation (OXPHOS) apparatus, is essential for brain health. Given the known association between reproductive period (years from menarche to menopause) and cognitive aging, we examined the hypothesis that cumulative estrogen exposure across the lifetime may be associated with differential methylation of genes in the OXPHOS pathway. METHODS Using DNA methylation patterns in the post-mortem dorsolateral prefrontal cortex (DLPFC) of 426 women prospectively followed until death in the Religious Orders Study and Rush Memory and Aging Project, we examined the relationship between reproductive period (subtracting age at menarche from age at menopause) and DNA methylation of a published set of autosomal OXPHOS genes previously implicated in stroke susceptibility. We then performed an unsupervised analysis of methylation levels across the Hallmark pathways from the Molecular Signatures Database. RESULTS We observed a strong association between reproductive period and DNA methylation status across OXPHOS CpGs. We replicated this association between reproductive period and DNA methylation in a much larger set of OXPHOS genes in our unsupervised analysis. Here, reproductive period also showed associations with methylation in genes related to E2F, MYC and MTORC1 signaling, fatty acid metabolism and DNA repair. CONCLUSION This study provides evidence from both a supervised and unsupervised analyses, that lifetime cumulative endogenous steroid exposures may play a role in maintenance of post-menopausal cellular balance, including in brain tissue.
Collapse
|
110
|
Punzi G, Bharadwaj R, Ursini G. Neuroepigenetics of Schizophrenia. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 158:195-226. [PMID: 30072054 DOI: 10.1016/bs.pmbts.2018.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Schizophrenia is a complex disorder of the brain, where genetic variants explain only a portion of risk. Neuroepigenetic mechanisms may explain the remaining share of risk, as well as the transition from susceptibility to the actual disease. Here, we discuss the most recent findings in the field of brain epigenetics applied to the study of schizophrenia. Methylome studies have found several candidates exhibiting methylation modifications in association with the disorder, but genes affected do not always overlap. Notably, these studies converge in that genes within the schizophrenia risk loci or genes differentially methylated in patients affected with the disorder are dynamically regulated during early life. They also imply that schizophrenia-associated genetic variation may affect DNA methylation in fetal and adult brains. Histone modifications may help mediating the effect of genetic risk variants associated with schizophrenia, and regulating chromatin higher-order structure. The 3D-organization of chromatin in the brain creates physical interactions within chromosomes, so that schizophrenia-associated genetic variants can be linked with genes distant from their loci; this suggests that chromatin conformation matters in the mechanism of risk for the disorder. Non-coding RNAs provide a novel and complex mechanism of gene regulation potentially significant for schizophrenia, as proposed by research on specific microRNAs and long non-coding RNAs (lncRNAs). Finally, a recent study in epitranscriptomics identifies RNA methylation as a further epigenetic mechanism active in human brain and specifically in a portion of the transcriptome associated with schizophrenia susceptibility. These findings indicate that, as expected from the complexity of the brain and its development, several epigenetic mechanisms may intervene in the etiopathogenesis of schizophrenia. An understanding of their roles calls for research approaches integrating the investigation of different epigenetic mechanisms and of environmental and genetic risk, in the context of development.
Collapse
Affiliation(s)
- Giovanna Punzi
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Rahul Bharadwaj
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States
| | - Gianluca Ursini
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, United States; Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
| |
Collapse
|
111
|
Effects of Antipsychotic Drugs on the Epigenetic Modification of Brain-Derived Neurotrophic Factor Gene Expression in the Hippocampi of Chronic Restraint Stress Rats. Neural Plast 2018; 2018:2682037. [PMID: 29991943 PMCID: PMC6016229 DOI: 10.1155/2018/2682037] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 03/19/2018] [Accepted: 04/01/2018] [Indexed: 01/23/2023] Open
Abstract
Recent studies have shown that antipsychotic drugs have epigenetic effects. However, the effects of antipsychotic drugs on histone modification remain unclear. Therefore, we investigated the effects of antipsychotic drugs on the epigenetic modification of the BDNF gene in the rat hippocampus. Rats were subjected to chronic restraint stress (6 h/d for 21 d) and then were administered with either olanzapine (2 mg/kg) or haloperidol (1 mg/kg). The levels of histone H3 acetylation and MeCP2 binding at BDNF promoter IV were assessed with chromatin immunoprecipitation assays. The mRNA levels of total BDNF with exon IV, HDAC5, DNMT1, and DNMT3a were assessed with a quantitative RT-PCR procedure. Chronic restraint stress resulted in the downregulation of total and exon IV BDNF mRNA levels and a decrease in histone H3 acetylation and an increase in MeCP2 binding at BDNF promoter IV. Furthermore, there were robust increases in the expression of HDAC5 and DNMTs. Olanzapine administration largely prevented these changes. The administration of haloperidol had no effect. These findings suggest that the antipsychotic drug olanzapine induced histone modification of BDNF gene expression in the hippocampus and that these epigenetic alterations may represent one of the mechanisms underlying the actions of antipsychotic drugs.
Collapse
|
112
|
Larsen K, Kristensen KK, Callesen H. DNA methyltransferases and tRNA methyltransferase DNMT2 in developing pig brain - expression and promoter methylation. GENE REPORTS 2018. [DOI: 10.1016/j.genrep.2018.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
113
|
|
114
|
Hemerich D, van Setten J, Tragante V, Asselbergs FW. Integrative Bioinformatics Approaches for Identification of Drug Targets in Hypertension. Front Cardiovasc Med 2018; 5:25. [PMID: 29670885 PMCID: PMC5894467 DOI: 10.3389/fcvm.2018.00025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/12/2018] [Indexed: 01/11/2023] Open
Abstract
High blood pressure or hypertension is an established risk factor for a myriad of cardiovascular diseases. Genome-wide association studies have successfully found over nine hundred loci that contribute to blood pressure. However, the mechanisms through which these loci contribute to disease are still relatively undetermined as less than 10% of hypertension-associated variants are located in coding regions. Phenotypic cell-type specificity analyses and expression quantitative trait loci show predominant vascular and cardiac tissue involvement for blood pressure-associated variants. Maps of chromosomal conformation and expression quantitative trait loci (eQTL) in critical tissues identified 2,424 genes interacting with blood pressure-associated loci, of which 517 are druggable. Integrating genome, regulome and transcriptome information in relevant cell-types could help to functionally annotate blood pressure associated loci and identify drug targets.
Collapse
Affiliation(s)
- Daiane Hemerich
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | - Jessica van Setten
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Vinicius Tragante
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands.,Durrer Center for Cardiovascular Research, Netherlands Heart Institute, Utrecht, Netherlands.,Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London, United Kingdom.,Farr Institute of Health Informatics Research and Institute of Health Informatics, University College London, London, United Kingdom
| |
Collapse
|
115
|
Hu Z, Yang Y, Zhao Y, Yu H, Ying X, Zhou D, Zhong J, Zheng Z, Liu J, Pan R, Zhang W, Cheng F, Duan S. APOE hypermethylation is associated with autism spectrum disorder in a Chinese population. Exp Ther Med 2018; 15:4749-4754. [PMID: 29844799 PMCID: PMC5958870 DOI: 10.3892/etm.2018.6069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/01/2018] [Indexed: 12/27/2022] Open
Abstract
Abnormal apolipoprotein E (APOE) methylation has been demonstrated to be associated with Alzheimer's disease, which may have overlapping mechanisms with autism spectrum disorder (ASD). Thus, the purpose of the present study was to assess the possible link between APOE methylation and ASD. Genomic DNA was extracted from peripheral blood and subjected to a methylation assay. SYBR green-based quantitative methylation-specific polymerase chain reaction analysis was used to measure APOE methylation in 62 pediatric patients with ASD and 73 age-matched healthy subjects. The APOE methylation in each sample was expressed as a percentage of methylation of a reference (PMR). The results indicated that APOE methylation in pediatric patients with ASD was significantly higher than that in the healthy controls (median PMR, 33 vs. 11%; P=2.36×10−10). Receiver operating characteristic curve demonstrated that PMR of 15.4% was the optimal cut-off for predicting ASD (area under curve, 0.817; sensitivity, 93.5%; specificity, 72.6%; P=2.36×10−10). In summary, the present results indicated that APOE hypermethylation in peripheral blood DNA may be used as a diagnostic biomarker for ASD.
Collapse
Affiliation(s)
- Zhenyu Hu
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yong Yang
- Zhejiang Provincial Key Laboratory of Pathophysiology, Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Yuanzhi Zhao
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Hang Yu
- Zhejiang Provincial Key Laboratory of Pathophysiology, Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Xiuru Ying
- Zhejiang Provincial Key Laboratory of Pathophysiology, Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Dongsheng Zhou
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhong
- Zhejiang Provincial Key Laboratory of Pathophysiology, Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Zhonghua Zheng
- Zhejiang Provincial Key Laboratory of Pathophysiology, Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jing Liu
- Zhejiang Provincial Key Laboratory of Pathophysiology, Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Ranran Pan
- Zhejiang Provincial Key Laboratory of Pathophysiology, Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Wenwu Zhang
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Fang Cheng
- Department of Child Psychiatry, Ningbo Kangning Hospital, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, Medical Genetics Center, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| |
Collapse
|
116
|
Peedicayil J, Kumar A. Epigenetic Drugs for Mood Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:151-174. [PMID: 29933949 DOI: 10.1016/bs.pmbts.2018.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There is increasing evidence that changes in epigenetic mechanisms of gene expression are involved in the pathogenesis of mood disorders. Such evidence stems from studies conducted on postmortem brain tissues and peripheral cells or tissues of patients with mood disorders. This article describes and discusses the epigenetic changes in the mood disorders (major depressive disorder and bipolar disorder) found to date. The article also describes and discusses preclinical drug trials of epigenetic drugs for treating mood disorders. In addition, nonrandomized and randomized controlled trials of nutritional drugs with effects on epigenetic mechanisms of gene expression in patients with major depressive disorder and bipolar disorder are discussed. Trials of epigenetic drugs and nutritional drugs with epigenetic effects are showing promising results for the treatment of mood disorders. Thus, epigenetic drugs and nutritional drugs with epigenetic effects could be useful in the treatment of patients with these disorders.
Collapse
|
117
|
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.
Collapse
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
| |
Collapse
|
118
|
Chromosomal Conformations and Epigenomic Regulation in Schizophrenia. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:21-40. [PMID: 29933951 DOI: 10.1016/bs.pmbts.2017.11.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chromosomal conformations, including promoter-enhancer loops, provide a critical regulatory layer for the transcriptional machinery. Therefore, schizophrenia, a common psychiatric disorder associated with broad changes in neuronal gene expression in prefrontal cortex and other brain regions implicated in psychosis, could be associated with alterations in higher-order chromatin. Here, we review early studies on spatial genome organization in the schizophrenia postmortem brain and discuss how integrative approaches using cell culture and animal model systems could gain deeper insight into the potential roles of higher-order chromatin for the neurobiology of and novel treatment avenues for common psychiatric disease.
Collapse
|
119
|
DNA redox modulations and global DNA methylation in bipolar disorder: Effects of sex, smoking and illness state. Psychiatry Res 2018; 261:589-596. [PMID: 29407727 DOI: 10.1016/j.psychres.2017.12.051] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 11/22/2017] [Accepted: 12/18/2017] [Indexed: 01/20/2023]
Abstract
DNA redox modulations and methylation have been associated with bipolar disorder (BD) pathophysiology. We aimed to investigate DNA redox modulation and global DNA methylation and demethylation levels in patients with BD during euthymia, mania or depression in comparison to non-psychiatric controls. The roles of sex and smoking as susceptibility factors for DNA redox modulations and global DNA methylation and demethylation were also explored. Levels of 5-methylcytosine (5-mC), 5-hydroxymethylcytosine (5-hmC) and 8-hydroxy-2'-deoxyguanosine (8-OHdG) were assessed in DNA samples of 75 patients with DSM-IV BD type I (37 euthymic, 18 manic, 20 depressive) in comparison to 60 non-psychiatric controls. Levels of 5-mC and 5-hmC were assessed using Dot Blot as a screening process, and verified using ELISA. Levels of 8-OHdG were assessed using ELISA. The levels of 8-OHdG significantly differed among non-psychiatric control, euthymia, mania and depression groups [F (3,110) = 2.771, p = 0.046], whereas there were no alterations in the levels of 5-hmC and 5-mC. Linear regression analyses revealed the significant effects of smoking (p = 0.031) and sex (p = 0.012) as well as state of illness on the levels of 8-OHdG (p = 0.025) in patients with BD. Our results suggest that levels of 8-OHdG may be affected by sex, illness states and smoking in BD.
Collapse
|
120
|
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.
Collapse
|
121
|
Ovenden ES, McGregor NW, Emsley RA, Warnich L. DNA methylation and antipsychotic treatment mechanisms in schizophrenia: Progress and future directions. Prog Neuropsychopharmacol Biol Psychiatry 2018; 81:38-49. [PMID: 29017764 DOI: 10.1016/j.pnpbp.2017.10.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 10/01/2017] [Accepted: 10/04/2017] [Indexed: 12/15/2022]
Abstract
Antipsychotic response in schizophrenia is a complex, multifactorial trait influenced by pharmacogenetic factors. With genetic studies thus far providing little biological insight or clinical utility, the field of pharmacoepigenomics has emerged to tackle the so-called "missing heritability" of drug response in disease. Research on psychiatric disorders has only recently started to assess the link between epigenetic alterations and treatment outcomes. DNA methylation, the best characterised epigenetic mechanism to date, is discussed here in the context of schizophrenia and antipsychotic treatment outcomes. The majority of published studies have assessed the influence of antipsychotics on methylation levels in specific neurotransmitter-associated candidate genes or at the genome-wide level. While these studies illustrate the epigenetic modifications associated with antipsychotics, very few have assessed clinical outcomes and the potential of differential DNA methylation profiles as predictors of antipsychotic response. Results from other psychiatric disorder studies, such as depression and bipolar disorder, provide insight into what may be achieved by schizophrenia pharmacoepigenomics. Other aspects that should be addressed in future research include methodological challenges, such as tissue specificity, and the influence of genetic variation on differential methylation patterns.
Collapse
Affiliation(s)
- Ellen S Ovenden
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Nathaniel W McGregor
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Robin A Emsley
- Department of Psychiatry, Stellenbosch University, Tygerberg 7505, South Africa
| | - Louise Warnich
- Department of Genetics, Stellenbosch University, Stellenbosch 7600, South Africa.
| |
Collapse
|
122
|
Adriani W, Romano E, Pucci M, Pascale E, Cerniglia L, Cimino S, Tambelli R, Curatolo P, Granstrem O, Maccarrone M, Laviola G, D'Addario C. Potential for diagnosis versus therapy monitoring of attention deficit hyperactivity disorder: a new epigenetic biomarker interacting with both genotype and auto-immunity. Eur Child Adolesc Psychiatry 2018; 27:241-252. [PMID: 28822049 DOI: 10.1007/s00787-017-1040-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022]
Abstract
In view of the need for easily accessible biomarkers, we evaluated in ADHD children the epigenetic status of the 5'-untranslated region (UTR) in the SLC6A3 gene, coding for human dopamine transporter (DAT). We analysed buccal swabs and sera from 30 children who met DSM-IV-TR criteria for ADHD, assigned to treatment according to severity. Methylation levels at six-selected CpG sites (among which, a CGGCGGCGG and a CGCG motif), alone or in combination with serum titers in auto-antibodies against dopamine transporter (DAT aAbs), were analysed for correlation with CGAS scores (by clinicians) and Conners' scales (by parents), collected at recruitment and after 6 weeks. In addition, we characterized the DAT genotype, i.e., the variable number tandem repeat (VNTR) polymorphisms at the 3'-UTR of the gene. DAT methylation levels were greatly reduced in ADHD patients compared to control, healthy children. Within patients carrying at least one DAT 9 allele (DAT 9/x), methylation at positions CpG2 and/or CpG6 correlated with recovery, as evident from delta-CGAS scores as well as delta Conners' scales ('inattentive' and 'hyperactive' subscales). Moreover, hypermethylation at CpG1 position denoted severity, specifically for those patients carrying a DAT 10/10 genotype. Intriguingly, high serum DAT-aAbs titers appeared to corroborate indications from high CpG1 versus high CpG2/CpG6 levels, likewise denoting severity versus recovery in DAT 10/10 versus 9/x patients, respectively. These profiles suggest that DAT 5'UTR epigenetics plus serum aAbs can serve as suitable biomarkers, to confirm ADHD diagnosis and/or to predict the efficacy of treatment.
Collapse
Affiliation(s)
- Walter Adriani
- Center for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Building 19 Floor D Room 5, viale Regina Elena 299, 00161, Rome, Italy. .,Faculty of Psychology, Università Telematica Internazionale "Uninettuno", Rome, Italy.
| | - Emilia Romano
- Center for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Building 19 Floor D Room 5, viale Regina Elena 299, 00161, Rome, Italy
| | - Mariangela Pucci
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Esterina Pascale
- Medico-Surgical Sciences and Biotechnologies, "Sapienza" University of Rome, Rome, Italy
| | - Luca Cerniglia
- Faculty of Psychology, Università Telematica Internazionale "Uninettuno", Rome, Italy
| | - Silvia Cimino
- Dynamic and Clinical Psychology Department, "Sapienza" University of Rome, Rome, Italy
| | - Renata Tambelli
- Dynamic and Clinical Psychology Department, "Sapienza" University of Rome, Rome, Italy
| | - Paolo Curatolo
- Pediatric Neurology Unit, Department of System Medicine, "Tor Vergata" University of Rome, Rome, Italy
| | | | - Mauro Maccarrone
- Department of Medicine, "Campus Bio-Medico" University of Rome, Rome, Italy.,European Center for Brain Research, IRCCS "Santa Lucia", Rome, Italy
| | - Giovanni Laviola
- Center for Behavioural Sciences and Mental Health, Istituto Superiore di Sanità, Building 19 Floor D Room 5, viale Regina Elena 299, 00161, Rome, Italy
| | - Claudio D'Addario
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy.,European Center for Brain Research, IRCCS "Santa Lucia", Rome, Italy
| |
Collapse
|
123
|
Jones MJ, Moore SR, Kobor MS. Principles and Challenges of Applying Epigenetic Epidemiology to Psychology. Annu Rev Psychol 2018; 69:459-485. [DOI: 10.1146/annurev-psych-122414-033653] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Meaghan J. Jones
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Sarah R. Moore
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
| | - Michael S. Kobor
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital, Vancouver, British Columbia V6H 3N1, Canada;, ,
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6H 3N1, Canada
- Human Early Learning Partnership, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
124
|
Mitchell AC, Javidfar B, Pothula V, Ibi D, Shen EY, Peter CJ, Bicks L, Fehr T, Jiang Y, Brennand KJ, Neve RL, Gonzalez-Maeso J, Akbarian S. MEF2C transcription factor is associated with the genetic and epigenetic risk architecture of schizophrenia and improves cognition in mice. Mol Psychiatry 2018; 23:123-132. [PMID: 28115742 PMCID: PMC5966823 DOI: 10.1038/mp.2016.254] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 10/30/2016] [Accepted: 12/06/2016] [Indexed: 12/20/2022]
Abstract
Large-scale consortia mapping the genomic risk architectures of schizophrenia provide vast amounts of molecular information, with largely unexplored therapeutic potential. We harnessed publically available information from the Psychiatric Genomics Consortium, and report myocyte enhancer factor 2C (MEF2C) motif enrichment in sequences surrounding the top scoring single-nucleotide polymorphisms within risk loci contributing by individual small effect to disease heritability. Chromatin profiling at base-pair resolution in neuronal nucleosomes extracted from prefrontal cortex of 34 subjects, including 17 cases diagnosed with schizophrenia, revealed MEF2C motif enrichment within cis-regulatory sequences, including neuron-specific promoters and superenhancers, affected by histone H3K4 hypermethylation in disease cases. Vector-induced short- and long-term Mef2c upregulation in mouse prefrontal projection neurons consistently resulted in enhanced cognitive performance in working memory and object recognition paradigms at baseline and after psychotogenic drug challenge, in conjunction with remodeling of local connectivity. Neuronal genome tagging in vivo by Mef2c-Dam adenine methyltransferase fusion protein confirmed the link between cognitive enhancement and MEF2C occupancy at promoters harboring canonical and variant MEF2C motifs. The multilayered integrative approaches presented here provide a roadmap to uncover the therapeutic potential of transcriptional regulators for schizophrenia and related disorders.
Collapse
Affiliation(s)
- Amanda C. Mitchell
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Behnam Javidfar
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Venu Pothula
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Daisuke Ibi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Erica Y. Shen
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Cyril J. Peter
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Lucy Bicks
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Tristan Fehr
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Yan Jiang
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kristen J. Brennand
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Rachael L. Neve
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge MA02139, USA
| | - Javier Gonzalez-Maeso
- Department of Physiology and Biophysics, Virginia Commonwealth University Medical School, Richmond, Virginia 23298, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| |
Collapse
|
125
|
Pisanu C, Katsila T, Patrinos GP, Squassina A. Recent trends on the role of epigenomics, metabolomics and noncoding RNAs in rationalizing mood stabilizing treatment. Pharmacogenomics 2018; 19:129-143. [DOI: 10.2217/pgs-2017-0111] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mood stabilizers are the cornerstone in treatment of mood disorders, but their use is characterized by high interindividual variability. This feature has stimulated intensive research to identify predictive biomarkers of response and disentangle the molecular bases of their clinical efficacy. Nevertheless, findings from studies conducted so far have only explained a small proportion of the observed variability, suggesting that factors other than DNA variants could be involved. A growing body of research has been focusing on the role of epigenetics and metabolomics in response to mood stabilizers, especially lithium salts. Studies from these approaches have provided new insights into the molecular networks and processes involved in the mechanism of action of mood stabilizers, promoting a systems-level multiomics synergy. In this article, we reviewed the literature investigating the involvement of epigenetic mechanisms, noncoding RNAs and metabolomic modifications in bipolar disorder and the mechanism of action and clinical efficacy of mood stabilizers.
Collapse
Affiliation(s)
- Claudia Pisanu
- Department of Biomedical Sciences, Section of Neuroscience & Clinical Pharmacology, University of Cagliari, Italy
- Department of Neuroscience, Unit of Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Theodora Katsila
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece
| | - George P Patrinos
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece
- Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience & Clinical Pharmacology, University of Cagliari, Italy
- Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| |
Collapse
|
126
|
Chan RF, Shabalin AA, Xie LY, Adkins DE, Zhao M, Turecki G, Clark SL, Aberg KA, van den Oord EJCG. Enrichment methods provide a feasible approach to comprehensive and adequately powered investigations of the brain methylome. Nucleic Acids Res 2017; 45:e97. [PMID: 28334972 PMCID: PMC5499761 DOI: 10.1093/nar/gkx143] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 02/20/2017] [Indexed: 12/19/2022] Open
Abstract
Methylome-wide association studies are typically performed using microarray technologies that only assay a very small fraction of the CG methylome and entirely miss two forms of methylation that are common in brain and likely of particular relevance for neuroscience and psychiatric disorders. The alternative is to use whole genome bisulfite (WGB) sequencing but this approach is not yet practically feasible with sample sizes required for adequate statistical power. We argue for revisiting methylation enrichment methods that, provided optimal protocols are used, enable comprehensive, adequately powered and cost-effective genome-wide investigations of the brain methylome. To support our claim we use data showing that enrichment methods approximate the sensitivity obtained with WGB methods and with slightly better specificity. However, this performance is achieved at <5% of the reagent costs. Furthermore, because many more samples can be sequenced simultaneously, projects can be completed about 15 times faster. Currently the only viable option available for comprehensive brain methylome studies, enrichment methods may be critical for moving the field forward.
Collapse
Affiliation(s)
- Robin F Chan
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Andrey A Shabalin
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Lin Y Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Daniel E Adkins
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Gustavo Turecki
- Douglas Mental Health University Institute and McGill University, Montréal, Québec H4H 1R3, Canada
| | - Shaunna L Clark
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Karolina A Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Edwin J C G van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA
| |
Collapse
|
127
|
Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
|
128
|
Javidfar B, Park R, Kassim BS, Bicks LK, Akbarian S. The epigenomics of schizophrenia, in the mouse. Am J Med Genet B Neuropsychiatr Genet 2017; 174:631-640. [PMID: 28699694 PMCID: PMC5573750 DOI: 10.1002/ajmg.b.32566] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 05/04/2017] [Accepted: 06/12/2017] [Indexed: 01/02/2023]
Abstract
Large-scale consortia including the Psychiatric Genomics Consortium, the Common Minds Consortium, BrainSeq and PsychENCODE, and many other studies taken together provide increasingly detailed insights into the genetic and epigenetic risk architectures of schizophrenia (SCZ) and offer vast amounts of molecular information, but with largely unexplored therapeutic potential. Here we discuss how epigenomic studies in human brain could guide animal work to test the impact of disease-associated alterations in chromatin structure and function on cognition and behavior. For example, transcription factors such as MYOCYTE-SPECIFIC ENHANCER FACTOR 2C (MEF2C), or multiple regulators of the open chromatin mark, methyl-histone H3-lysine 4, are associated with the genetic risk architectures of common psychiatric disease and alterations in chromatin structure and function in diseased brain tissue. Importantly, these molecules also affect cognition and behavior in genetically engineered mice, including virus-mediated expression changes in prefrontal cortex (PFC) and other key nodes in the circuitry underlying psychosis. Therefore, preclinical and small laboratory animal work could target genomic sequences affected by chromatin alterations in SCZ. To this end, in vivo editing of enhancer and other regulatory non-coding DNA by RNA-guided nucleases including CRISPR-Cas, and designer transcription factors, could be expected to deliver pipelines for novel therapeutic approaches aimed at improving cognitive dysfunction and other core symptoms of SCZ.
Collapse
Affiliation(s)
| | | | | | - Lucy K. Bicks
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai; New York New York
| | - Schahram Akbarian
- Department of Psychiatry; Friedman Brain Institute; Icahn School of Medicine at Mount Sinai; New York New York
| |
Collapse
|
129
|
Wang Y, Teschendorff AE, Widschwendter M, Wang S. Accounting for differential variability in detecting differentially methylated regions. Brief Bioinform 2017; 20:47-57. [DOI: 10.1093/bib/bbx097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 12/11/2022] Open
Affiliation(s)
- Ya Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Andrew E Teschendorff
- Department of Women's Cancer, University College London, London, UK
- CAS Key Lab of Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Statistical Cancer Genomics, UCL Cancer Institute, University College London, London, UK
| | | | - Shuang Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| |
Collapse
|
130
|
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.
Collapse
|
131
|
Cheah SY, McLeay R, Wockner LF, Lawford BR, Young RM, Morris CP, Voisey J. Expression and methylation of BDNF in the human brain in schizophrenia. World J Biol Psychiatry 2017; 18:392-400. [PMID: 27712141 DOI: 10.1080/15622975.2016.1245443] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVES To examine the combined effect of the BDNF Val66Met (rs6265) polymorphism and BDNF DNA methylation on transcriptional regulation of the BDNF gene. METHODS DNA methylation profiles were generated for CpG sites proximal to Val66Met, within BDNF promoter I and exon V for prefrontal cortex samples from 25 schizophrenia and 25 control subjects. Val66Met genotypes and BDNF mRNA expression data were generated by transcriptome sequencing. Expression, methylation and genotype data were correlated and examined for association with schizophrenia. RESULTS There was 43% more of the BDNF V-VIII-IX transcript in schizophrenia samples. BDNF mRNA expression and DNA methylation of seven CpG sites were not associated with schizophrenia after accounting for age and PMI effects. BDNF mRNA expression and DNA methylation were not altered by Val66Met after accounting for age and PMI effects. DNA methylation of one CpG site had a marginally significant positive correlation with mRNA expression in schizophrenia subjects. CONCLUSIONS Schizophrenia risk was not associated with differential BDNF mRNA expression and DNA methylation. A larger age-matched cohort with comprehensive clinical history is required to accurately identify the effects of genotype, mRNA expression and DNA methylation on schizophrenia risk.
Collapse
Affiliation(s)
- Sern-Yih Cheah
- a School of Biomedical Sciences, Institute of Health and Biomedical Innovation , Queensland University of Technology , Kelvin Grove , Queensland , Australia
| | - Robert McLeay
- a School of Biomedical Sciences, Institute of Health and Biomedical Innovation , Queensland University of Technology , Kelvin Grove , Queensland , Australia
| | - Leesa F Wockner
- b Queensland Institute of Medical Research, Royal Brisbane Hospital , Brisbane , Queensland , Australia
| | - Bruce R Lawford
- a School of Biomedical Sciences, Institute of Health and Biomedical Innovation , Queensland University of Technology , Kelvin Grove , Queensland , Australia.,c Discipline of Psychiatry , Royal Brisbane and Women's Hospital , Herston , Queensland , Australia
| | - Ross McD Young
- a School of Biomedical Sciences, Institute of Health and Biomedical Innovation , Queensland University of Technology , Kelvin Grove , Queensland , Australia
| | - Charles P Morris
- a School of Biomedical Sciences, Institute of Health and Biomedical Innovation , Queensland University of Technology , Kelvin Grove , Queensland , Australia
| | - Joanne Voisey
- a School of Biomedical Sciences, Institute of Health and Biomedical Innovation , Queensland University of Technology , Kelvin Grove , Queensland , Australia
| |
Collapse
|
132
|
BECon: a tool for interpreting DNA methylation findings from blood in the context of brain. Transl Psychiatry 2017; 7:e1187. [PMID: 28763057 PMCID: PMC5611738 DOI: 10.1038/tp.2017.171] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/14/2017] [Accepted: 06/17/2017] [Indexed: 12/11/2022] Open
Abstract
Tissue differences are one of the largest contributors to variability in the human DNA methylome. Despite the tissue-specific nature of DNA methylation, the inaccessibility of human brain samples necessitates the frequent use of surrogate tissues such as blood, in studies of associations between DNA methylation and brain function and health. Results from studies of surrogate tissues in humans are difficult to interpret in this context, as the connection between blood-brain DNA methylation is tenuous and not well-documented. Here, we aimed to provide a resource to the community to aid interpretation of blood-based DNA methylation results in the context of brain tissue. We used paired samples from 16 individuals from three brain regions and whole blood, run on the Illumina 450 K Human Methylation Array to quantify the concordance of DNA methylation between tissues. From these data, we have made available metrics on: the variability of cytosine-phosphate-guanine dinucleotides (CpGs) in our blood and brain samples, the concordance of CpGs between blood and brain, and estimations of how strongly a CpG is affected by cell composition in both blood and brain through the web application BECon (Blood-Brain Epigenetic Concordance; https://redgar598.shinyapps.io/BECon/). We anticipate that BECon will enable biological interpretation of blood-based human DNA methylation results, in the context of brain.
Collapse
|
133
|
Chaumette B, Kebir O, Krebs MO. [Genetics and epigenetics of schizophrenia and other psychoses]. Biol Aujourdhui 2017; 211:69-82. [PMID: 28682228 DOI: 10.1051/jbio/2017015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Indexed: 06/07/2023]
Abstract
Schizophrenia and other psychoses are categorical psychiatric diagnoses corresponding to frequent and heterogeneous disorders. Their physiopathology still remains largely unknown despite numerous recent advances. In particular, the last decade has identified different types of genetic variants, thanks to emergence of high-throughput methods. These methods allow both the identification of rare variants with a large effect such as punctual mutations or copy-number variants and the identification of frequent variants with a limited effect such as polymorphisms. Many impacted genes have been identified showing a very high genetic heterogeneity of psychoses. These genes are overrepresented in synaptic and neurotransmission pathways. Only a small fraction of psychoses could be easily explained by genetics but this screening in clinical practice is important as it can lead to therapeutic challenge or genetic counselling. Nowadays, it is clear that the pathophysiology of the psychoses can only be understood by an integrative approach taking into account the interaction between genes and environment. This interaction could be mediated by the epigenome defined as the modification of gene expression without changes in DNA sequence. Epigenome is stable but could be modified by environmental factors. Several epigenetic mechanisms have been studied in psychosis, in particular the DNA methylation, the modification of histones and the microRNA. All of these mechanisms are under regulation by genetic factors and variants in these epigenetic-involved genes and cofactors have been also associated with schizophrenia. Thus, pathophysiology of psychosis is complex and morestudiesare needed before definitive conclusions. Altogether, the recent advances in the genetics and epigenetics of psychosis are promising and could open the way to a recategorization of these disorders as well as the identification of new therapeutic targets.
Collapse
Affiliation(s)
- Boris Chaumette
- Montreal Neurological Institute and Hospital, Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Oussama Kebir
- INSERM, U894, Laboratoire "Physiopathologie des maladies psychiatriques", Centre de Psychiatrie et Neurosciences, Université Paris Descartes, Sorbonne Paris Cité, 102-108 rue de la Santé, 75014 Paris, France Institut de Psychiatrie-GDR 3557, Centre Hospitalier Sainte-Anne, Paris, France
| | - Marie-Odile Krebs
- INSERM, U894, Laboratoire "Physiopathologie des maladies psychiatriques", Centre de Psychiatrie et Neurosciences, Université Paris Descartes, Sorbonne Paris Cité, 102-108 rue de la Santé, 75014 Paris, France Institut de Psychiatrie-GDR 3557, Centre Hospitalier Sainte-Anne, Paris, France
| |
Collapse
|
134
|
|
135
|
Delgado-Morales R, Agís-Balboa RC, Esteller M, Berdasco M. Epigenetic mechanisms during ageing and neurogenesis as novel therapeutic avenues in human brain disorders. Clin Epigenetics 2017; 9:67. [PMID: 28670349 PMCID: PMC5493012 DOI: 10.1186/s13148-017-0365-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 06/11/2017] [Indexed: 12/26/2022] Open
Abstract
Ageing is the main risk factor for human neurological disorders. Among the diverse molecular pathways that govern ageing, epigenetics can guide age-associated decline in part by regulating gene expression and also through the modulation of genomic instability and high-order chromatin architecture. Epigenetic mechanisms are involved in the regulation of neural differentiation as well as in functional processes related to memory consolidation, learning or cognition during healthy lifespan. On the other side of the coin, many neurodegenerative diseases are associated with epigenetic dysregulation. The reversible nature of epigenetic factors and, especially, their role as mediators between the genome and the environment make them exciting candidates as therapeutic targets. Rather than providing a broad description of the pathways epigenetically deregulated in human neurological disorders, in this review, we have focused on the potential use of epigenetic enzymes as druggable targets to ameliorate neural decline during normal ageing and especially in neurological disorders. We will firstly discuss recent progress that supports a key role of epigenetic regulation during healthy ageing with an emphasis on the role of epigenetic regulation in adult neurogenesis. Then, we will focus on epigenetic alterations associated with ageing-related human disorders of the central nervous system. We will discuss examples in the context of psychiatric disorders, including schizophrenia and posttraumatic stress disorders, and also dementia or Alzheimer's disease as the most frequent neurodegenerative disease. Finally, methodological limitations and future perspectives are discussed.
Collapse
Affiliation(s)
- Raúl Delgado-Morales
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908L'Hospitalet, Barcelona, Catalonia Spain.,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
| | - Roberto Carlos Agís-Balboa
- Psychiatric Diseases Research Group, Galicia Sur Health Research Institute, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, CIBERSAM, Vigo, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908L'Hospitalet, Barcelona, Catalonia Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - María Berdasco
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), 3rd Floor, Hospital Duran i Reynals, Av. Gran Via 199-203, 08908L'Hospitalet, Barcelona, Catalonia Spain
| |
Collapse
|
136
|
D'Addario C, Shchetynsky K, Pucci M, Cifani C, Gunnar A, Vukojević V, Padyukov L, Terenius L. Genetic variation and epigenetic modification of the prodynorphin gene in peripheral blood cells in alcoholism. Prog Neuropsychopharmacol Biol Psychiatry 2017; 76:195-203. [PMID: 28336495 DOI: 10.1016/j.pnpbp.2017.03.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/28/2017] [Accepted: 03/19/2017] [Indexed: 12/31/2022]
Abstract
Dynorphins are critically involved in the development, maintenance and relapse of alcoholism. Alcohol-induced changes in the prodynorphin gene expression may be influenced by both gene polymorphisms and epigenetic modifications. The present study of human alcoholics aims to evaluate DNA methylation patterns in the prodynorphin gene (PDYN) promoter and to identify single nucleotide polymorphisms (SNPs) associated with alcohol dependence and with altered DNA methylation. Genomic DNA was isolated from peripheral blood cells of alcoholics and healthy controls, and DNA methylation was studied in the PDYN promoter by bisulfite pyrosequencing. In alcoholics, DNA methylation increased in three of the seven CpG sites investigated, as well as in the average of the seven CpG sites. Data stratification showed lower increase in DNA methylation levels in individuals reporting craving and with higher levels of alcohol consumption. Association with alcoholism was observed for rs2235751 and the presence of the minor allele G was associated with reduced DNA methylation at PDYN promoter in females and younger subjects. Genetic and epigenetic factors within PDYN are related to risk for alcoholism, providing further evidence of its involvement on ethanol effects. These results might be of relevance for developing new biomarkers to predict disease trajectories and therapeutic outcome.
Collapse
Affiliation(s)
- Claudio D'Addario
- Karolinska Institutet, Department of Clinical Neuroscience, Center for Molecular Medicine, Stockholm, Sweden; Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Italy.
| | - Klementy Shchetynsky
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Mariangela Pucci
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | - Carlo Cifani
- School of Pharmacy, University of Camerino, Italy
| | - Agneta Gunnar
- Karolinska Institutet, Department of Clinical Neuroscience, Center for Molecular Medicine, Stockholm, Sweden
| | - Vladana Vukojević
- Karolinska Institutet, Department of Clinical Neuroscience, Center for Molecular Medicine, Stockholm, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Lars Terenius
- Karolinska Institutet, Department of Clinical Neuroscience, Center for Molecular Medicine, Stockholm, Sweden
| |
Collapse
|
137
|
Massart R, Suderman M, Mongrain V, Szyf M. DNA methylation and transcription onset in the brain. Epigenomics 2017; 9:797-809. [DOI: 10.2217/epi-2016-0184] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: The goal of this study was to test the state of methylation of transcription start positions in DNA that are actively involved in transcription. Materials & methods: We used sequential ChIP-bisulfite-sequencing with an antibody to RNpolII-PS5 to map the state of methylation of actively transcribing transcription start sites (TSS). Results: TSS that RNApolII-PS5 physically bind to, are ubiquitously unmethylated. TSS that appear to be both heavily methylated and transcriptionally active are truly a mixture of unmethylated TSS with bound RNApolII-PS5 in some nuclei and unbound methylated TSS in other nuclei. Conclusion: TSS DNA methylation is universally inconsistent with transcription onset and could therefore serve as a digital count of the fraction of nuclei with methylation-silenced TSS.
Collapse
Affiliation(s)
- Renaud Massart
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Inserm U955 Interventional NeuroPsychology Team, Ecole Normale Supérieure, PSL Research University
| | - Matthew Suderman
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- McGill Centre for Bioinformatics, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0B1, Canada
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | - Valerie Mongrain
- Department of Neuroscience, Université de Montréal & Research Center, Hôpital du Sacré-Coeur de Montréal, 5400 Gouin West blvd., Montreal, Quebec H4J1C5, Canada
| | - Moshe Szyf
- Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec, Canada
- Sackler Program for Epigenetics & Psychobiology, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
138
|
Jokinen J, Boström AE, Chatzittofis A, Ciuculete DM, Öberg KG, Flanagan JN, Arver S, Schiöth HB. Methylation of HPA axis related genes in men with hypersexual disorder. Psychoneuroendocrinology 2017; 80:67-73. [PMID: 28319850 DOI: 10.1016/j.psyneuen.2017.03.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/26/2017] [Accepted: 03/03/2017] [Indexed: 12/21/2022]
Abstract
Hypersexual Disorder (HD) defined as non-paraphilic sexual desire disorder with components of compulsivity, impulsivity and behavioral addiction, and proposed as a diagnosis in the DSM 5, shares some overlapping features with substance use disorder including common neurotransmitter systems and dysregulated hypothalamic-pituitary-adrenal (HPA) axis function. In this study, comprising 67 HD male patients and 39 male healthy volunteers, we aimed to identify HPA-axis coupled CpG-sites, in which modifications of the epigenetic profile are associated with hypersexuality. The genome-wide methylation pattern was measured in whole blood using the Illumina Infinium Methylation EPIC BeadChip, measuring the methylation state of over 850K CpG sites. Prior to analysis, the global DNA methylation pattern was pre-processed according to standard protocols and adjusted for white blood cell type heterogeneity. We included CpG sites located within 2000bp of the transcriptional start site of the following HPA-axis coupled genes: Corticotropin releasing hormone (CRH), corticotropin releasing hormone binding protein (CRHBP), corticotropin releasing hormone receptor 1 (CRHR1), corticotropin releasing hormone receptor 2 (CRHR2), FKBP5 and the glucocorticoid receptor (NR3C1). We performed multiple linear regression models of methylation M-values to a categorical variable of hypersexuality, adjusting for depression, dexamethasone non-suppression status, Childhood Trauma Questionnaire total score and plasma levels of TNF-alpha and IL-6. Of 76 tested individual CpG sites, four were nominally significant (p<0.05), associated with the genes CRH, CRHR2 and NR3C1. Cg23409074-located 48bp upstream of the transcription start site of the CRH gene - was significantly hypomethylated in hypersexual patients after corrections for multiple testing using the FDR-method. Methylation levels of cg23409074 were positively correlated with gene expression of the CRH gene in an independent cohort of 11 healthy male subjects. The methylation levels at the identified CRH site, cg23409074, were significantly correlated between blood and four different brain regions. CRH is an important integrator of neuroendocrine stress responses in the brain, with a key role in the addiction processes. Our results show epigenetic changes in the CRH gene related to hypersexual disorder in men.
Collapse
Affiliation(s)
- Jussi Jokinen
- Department of Clinical Neuroscience/Psychiatry, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Sciences/Psychiatry, Umeå University, Umeå, Sweden.
| | | | - Andreas Chatzittofis
- Department of Clinical Neuroscience/Psychiatry, Karolinska Institutet, Stockholm, Sweden; Medical School, University of Cyprus, Nicosia, Cyprus
| | | | | | - John N Flanagan
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Stefan Arver
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| |
Collapse
|
139
|
Agrawal R, Kalmady SV, Venkatasubramanian G. In SilicoModel-driven Assessment of the Effects of Brain-derived Neurotrophic Factor Deficiency on Glutamate and Gamma-Aminobutyric Acid: Implications for Understanding Schizophrenia Pathophysiology. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2017; 15:115-125. [PMID: 28449558 PMCID: PMC5426484 DOI: 10.9758/cpn.2017.15.2.115] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/15/2016] [Accepted: 08/17/2016] [Indexed: 01/14/2023]
Abstract
Objective Deficient brain-derived neurotrophic factor (BDNF) is one of the important mechanisms underlying the neuroplasticity abnormalities in schizophrenia. Aberration in BDNF signaling pathways directly or circuitously influences neurotransmitters like glutamate and gamma-aminobutyric acid (GABA). For the first time, this study attempts to construct and simulate the BDNF-neurotransmitter network in order to assess the effects of BDNF deficiency on glutamate and GABA. Methods Using CellDesigner, we modeled BDNF interactions with calcium influx via N-methyl-D-aspartate receptor (NMDAR)- Calmodulin activation; synthesis of GABA via cell cycle regulators protein kinase B, glycogen synthase kinase and β-catenin; transportation of glutamate and GABA. Steady state stability, perturbation time-course simulation and sensitivity analysis were performed in COPASI after assigning the kinetic functions, optimizing the unknown parameters using random search and genetic algorithm. Results Study observations suggest that increased glutamate in hippocampus, similar to that seen in schizophrenia, could potentially be contributed by indirect pathway originated from BDNF. Deficient BDNF could suppress Glutamate decarboxylase 67-mediated GABA synthesis. Further, deficient BDNF corresponded to impaired transport via vesicular glutamate transporter, thereby further increasing the intracellular glutamate in GABAergic and glutamatergic cells. BDNF also altered calcium dependent neuroplasticity via NMDAR modulation. Sensitivity analysis showed that Calmodulin, cAMP response element-binding protein (CREB) and CREB regulated transcription coactivator-1 played significant role in this network. Conclusion The study presents in silicoquantitative model of biochemical network constituting the key signaling molecules implicated in schizophrenia pathogenesis. It provides mechanistic insights into putative contribution of deficient BNDF towards alterations in neurotransmitters and neuroplasticity that are consistent with current understanding of the disorder.
Collapse
Affiliation(s)
- Rimjhim Agrawal
- Translational Psychiatry Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, India
| | - Sunil Vasu Kalmady
- Translational Psychiatry Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, India
| | - Ganesan Venkatasubramanian
- Translational Psychiatry Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neuro Sciences, Bangalore, India
| |
Collapse
|
140
|
Bayraktar G, Kreutz MR. Neuronal DNA Methyltransferases: Epigenetic Mediators between Synaptic Activity and Gene Expression? Neuroscientist 2017; 24:171-185. [PMID: 28513272 PMCID: PMC5846851 DOI: 10.1177/1073858417707457] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
DNMT3A and 3B are the main de novo DNA methyltransferases (DNMTs) in the brain that introduce new methylation marks to non-methylated DNA in postmitotic neurons. DNA methylation is a key epigenetic mark that is known to regulate important cellular processes in neuronal development and brain plasticity. Accumulating evidence disclosed rapid and dynamic changes in DNA methylation of plasticity-relevant genes that are important for learning and memory formation. To understand how DNMTs contribute to brain function and how they are regulated by neuronal activity is a prerequisite for a deeper appreciation of activity-dependent gene expression in health and disease. This review discusses the functional role of de novo methyltransferases and in particular DNMT3A1 in the adult brain with special emphasis on synaptic plasticity, memory formation, and brain disorders.
Collapse
Affiliation(s)
- Gonca Bayraktar
- 1 RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany
| | - Michael R Kreutz
- 1 RG Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg, Germany.,2 Leibniz Group "Dendritic Organelles and Synaptic Function", ZMNH, Magdeburg, Germany
| |
Collapse
|
141
|
Swathy B, Banerjee M. Understanding epigenetics of schizophrenia in the backdrop of its antipsychotic drug therapy. Epigenomics 2017; 9:721-736. [DOI: 10.2217/epi-2016-0106] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The diatheses of gene and environment interaction in schizophrenia (SCZ) are becoming increasingly evident. Genetic and epigenetic backgrounds are being considered in stratifying and addressing phenotypic variation and drug response in SCZ. But how much of these epigenetic alterations are the primary contributing factor, toward disease pathogenesis and drug response, needs further clarity. Evidence indicates that antipsychotic drugs can also alter the epigenetic homeostasis thereby inducing pharmacoepigenomic effects. We re-examine the context of epigenetics in disease pathogenesis and antipsychotic drug therapy in SCZ to understand how much of these observations act as real indicators of the disease or therapeutic response. We propose that epigenetic viewpoint in SCZ needs to be critically examined under the genetic, epigenetic and pharmacoepigenetic background.
Collapse
Affiliation(s)
- Babu Swathy
- Human Molecular Genetics Laboratory, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, India
| | - Moinak Banerjee
- Human Molecular Genetics Laboratory, Rajiv Gandhi Center for Biotechnology, Thiruvananthapuram, India
| |
Collapse
|
142
|
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.
Collapse
|
143
|
Thippeswamy H, Paul P, Purushottam M, Philip M, Jain S, Chandra PS. Estrogen pathway related genes and their association with risk of postpartum psychosis: A case control study. Asian J Psychiatr 2017; 26:82-85. [PMID: 28483099 DOI: 10.1016/j.ajp.2017.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/07/2017] [Accepted: 01/16/2017] [Indexed: 02/08/2023]
Affiliation(s)
- Harish Thippeswamy
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, 560029, India.
| | - Pradip Paul
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, 560029, India.
| | | | - Mariamma Philip
- Department of Biostatistics, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, 560029, India.
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, 560029, India.
| | - Prabha S Chandra
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, 560029, India.
| |
Collapse
|
144
|
Perkovic MN, Erjavec GN, Strac DS, Uzun S, Kozumplik O, Pivac N. Theranostic Biomarkers for Schizophrenia. Int J Mol Sci 2017; 18:E733. [PMID: 28358316 PMCID: PMC5412319 DOI: 10.3390/ijms18040733] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 12/14/2022] Open
Abstract
Schizophrenia is a highly heritable, chronic, severe, disabling neurodevelopmental brain disorder with a heterogeneous genetic and neurobiological background, which is still poorly understood. To allow better diagnostic procedures and therapeutic strategies in schizophrenia patients, use of easy accessible biomarkers is suggested. The most frequently used biomarkers in schizophrenia are those associated with the neuroimmune and neuroendocrine system, metabolism, different neurotransmitter systems and neurotrophic factors. However, there are still no validated and reliable biomarkers in clinical use for schizophrenia. This review will address potential biomarkers in schizophrenia. It will discuss biomarkers in schizophrenia and propose the use of specific blood-based panels that will include a set of markers associated with immune processes, metabolic disorders, and neuroendocrine/neurotrophin/neurotransmitter alterations. The combination of different markers, or complex multi-marker panels, might help in the discrimination of patients with different underlying pathologies and in the better classification of the more homogenous groups. Therefore, the development of the diagnostic, prognostic and theranostic biomarkers is an urgent and an unmet need in psychiatry, with the aim of improving diagnosis, therapy monitoring, prediction of treatment outcome and focus on the personal medicine approach in order to improve the quality of life in patients with schizophrenia and decrease health costs worldwide.
Collapse
Affiliation(s)
| | | | - Dubravka Svob Strac
- Rudjer Boskovic Institute, Division of Molecular Medicine, 10000 Zagreb, Croatia.
| | - Suzana Uzun
- Clinic for Psychiatry Vrapce, 10090 Zagreb, Croatia.
| | | | - Nela Pivac
- Rudjer Boskovic Institute, Division of Molecular Medicine, 10000 Zagreb, Croatia.
| |
Collapse
|
145
|
Glad CAM, Andersson-Assarsson JC, Berglund P, Bergthorsdottir R, Ragnarsson O, Johannsson G. Reduced DNA methylation and psychopathology following endogenous hypercortisolism - a genome-wide study. Sci Rep 2017; 7:44445. [PMID: 28300138 PMCID: PMC5353706 DOI: 10.1038/srep44445] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/08/2017] [Indexed: 01/21/2023] Open
Abstract
Patients with Cushing’s Syndrome (CS) in remission were used as a model to test the hypothesis that long-standing excessive cortisol exposure induces changes in DNA methylation that are associated with persisting neuropsychological consequences. Genome-wide DNA methylation was assessed in 48 women with CS in long-term remission (cases) and 16 controls matched for age, gender and education. The Fatigue impact scale and the comprehensive psychopathological rating scale were used to evaluate fatigue, depression and anxiety. Cases had lower average global DNA methylation than controls (81.2% vs 82.7%; p = 0.002). Four hundred and sixty-one differentially methylated regions, containing 3,246 probes mapping to 337 genes were identified. After adjustment for age and smoking, 731 probes in 236 genes were associated with psychopathology (fatigue, depression and/or anxiety). Twenty-four gene ontology terms were associated with psychopathology; terms related to retinoic acid receptor signalling were the most common (adjusted p = 0.0007). One gene in particular, COL11A2, was associated with fatigue following a false discovery rate correction. Our findings indicate that hypomethylation of FKBP5 and retinoic acid receptor related genes serve a potential mechanistic explanation for long-lasting GC-induced psychopathology.
Collapse
Affiliation(s)
- Camilla A M Glad
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine at Sahlgrenska Academy, University of Gothenburg and Department of Endocrinology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Johanna C Andersson-Assarsson
- Department of Molecular and Clinical Medicine, Institute of Medicine at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Peter Berglund
- Institute of Neuroscience and Physiology at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Ragnhildur Bergthorsdottir
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine at Sahlgrenska Academy, University of Gothenburg and Department of Endocrinology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Oskar Ragnarsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine at Sahlgrenska Academy, University of Gothenburg and Department of Endocrinology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Gudmundur Johannsson
- Department of Internal Medicine and Clinical Nutrition, Institute of Medicine at Sahlgrenska Academy, University of Gothenburg and Department of Endocrinology, Sahlgrenska University Hospital, Gothenburg, Sweden
| |
Collapse
|
146
|
Weaver ICG, Korgan AC, Lee K, Wheeler RV, Hundert AS, Goguen D. Stress and the Emerging Roles of Chromatin Remodeling in Signal Integration and Stable Transmission of Reversible Phenotypes. Front Behav Neurosci 2017; 11:41. [PMID: 28360846 PMCID: PMC5350110 DOI: 10.3389/fnbeh.2017.00041] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 02/24/2017] [Indexed: 01/02/2023] Open
Abstract
The influence of early life experience and degree of parental-infant attachment on emotional development in children and adolescents has been comprehensively studied. Structural and mechanistic insight into the biological foundation and maintenance of mammalian defensive systems (metabolic, immune, nervous and behavioral) is slowly advancing through the emerging field of developmental molecular (epi)genetics. Initial evidence revealed that differential nurture early in life generates stable differences in offspring hypothalamic-pituitary-adrenal (HPA) regulation, in part, through chromatin remodeling and changes in DNA methylation of specific genes expressed in the brain, revealing physical, biochemical and molecular paths for the epidemiological concept of gene-environment interactions. Herein, a primary molecular mechanism underpinning the early developmental programming and lifelong maintenance of defensive (emotional) responses in the offspring is the alteration of chromatin domains of specific genomic regions from a condensed state (heterochromatin) to a transcriptionally accessible state (euchromatin). Conversely, DNA methylation promotes the formation of heterochromatin, which is essential for gene silencing, genomic integrity and chromosome segregation. Therefore, inter-individual differences in chromatin modifications and DNA methylation marks hold great potential for assessing the impact of both early life experience and effectiveness of intervention programs—from guided psychosocial strategies focused on changing behavior to pharmacological treatments that target chromatin remodeling and DNA methylation enzymes to dietary approaches that alter cellular pools of metabolic intermediates and methyl donors to affect nutrient bioavailability and metabolism. In this review article, we discuss the potential molecular mechanism(s) of gene regulation associated with chromatin modeling and programming of endocrine (e.g., HPA and metabolic or cardiovascular) and behavioral (e.g., fearfulness, vigilance) responses to stress, including alterations in DNA methylation and the role of DNA repair machinery. From parental history (e.g., drugs, housing, illness, nutrition, socialization) to maternal-offspring exchanges of nutrition, microbiota, antibodies and stimulation, the nature of nurture provides not only mechanistic insight into how experiences propagate from external to internal variables, but also identifies a composite therapeutic target, chromatin modeling, for gestational/prenatal stress, adolescent anxiety/depression and adult-onset neuropsychiatric disease.
Collapse
Affiliation(s)
- Ian C G Weaver
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Austin C Korgan
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Kristen Lee
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Ryan V Wheeler
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Amos S Hundert
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| | - Donna Goguen
- Department of Psychology and Neuroscience, and Department of Psychiatry, Dalhousie University Halifax, NS, Canada
| |
Collapse
|
147
|
Dubovsky SL. The Limitations of Genetic Testing in Psychiatry. PSYCHOTHERAPY AND PSYCHOSOMATICS 2017; 85:129-35. [PMID: 27043036 DOI: 10.1159/000443512] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 12/20/2015] [Indexed: 11/19/2022]
Affiliation(s)
- Steven L Dubovsky
- Department of Psychiatry, State University of New York at Buffalo, Buffalo, N.Y., and Departments of Psychiatry and Medicine, University of Colorado, Denver, Colo., USA
| |
Collapse
|
148
|
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.
Collapse
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:
| |
Collapse
|
149
|
Vitale AM, Matigian NA, Cristino AS, Nones K, Ravishankar S, Bellette B, Fan Y, Wood SA, Wolvetang E, Mackay-Sim A. DNA methylation in schizophrenia in different patient-derived cell types. NPJ SCHIZOPHRENIA 2017; 3:6. [PMID: 28560252 PMCID: PMC5441549 DOI: 10.1038/s41537-016-0006-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 11/11/2016] [Accepted: 12/02/2016] [Indexed: 12/21/2022]
Abstract
DNA methylation of gene promoter regions represses transcription and is a mechanism via which environmental risk factors could affect cells during development in individuals at risk for schizophrenia. We investigated DNA methylation in patient-derived cells that might shed light on early development in schizophrenia. Induced pluripotent stem cells may reflect a “ground state” upon which developmental and environmental influences would be minimal. Olfactory neurosphere-derived cells are an adult-derived neuro-ectodermal stem cell modified by developmental and environmental influences. Fibroblasts provide a non-neural control for life-long developmental and environmental influences. Genome-wide profiling of DNA methylation and gene expression was done in these three cell types from the same individuals. All cell types had distinct, statistically significant schizophrenia-associated differences in DNA methylation and linked gene expression, with Gene Ontology analysis showing that the differentially affected genes clustered in networks associated with cell growth, proliferation, and movement, functions known to be affected in schizophrenia patient-derived cells. Only five gene loci were differentially methylated in all three cell types. Understanding the role of epigenetics in cell function in the brain in schizophrenia is likely to be complicated by similar cell type differences in intrinsic and environmentally induced epigenetic regulation. Schizophrenia-associated differences in the DNA methylation status of patient-derived cells suggest it could affect early brain development. Mechanisms that control gene expression without altering the genetic code, such as DNA methylation, could explain how environmental risk factors contribute to schizophrenia in genetically susceptible individuals. Alan Mackay-Sim and colleagues from Griffith University, Australia, carried out genome-wide comparisons of DNA methylation in induced pluripotent stem (iPS) cells, olfactory neurosphere-derived cells and fibroblasts from patients and controls. Differences in the DNA methylation pattern between patient and control iPS cells, which could reflect what happens in the embryo, suggest a disease-associated effect very early on in development. Only five genes were differentially methylated in all three patient-derived cell types compared to controls. None of these genes has previously been associated with schizophrenia and may represent new targets for future research.
Collapse
Affiliation(s)
- Alejandra M Vitale
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD Australia.,Instituto de Biologia y Medicina Experimental-IBYME-CONICET, Buenos Aires, Argentina
| | - Nicholas A Matigian
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD Australia.,The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD Australia
| | - Alexandre S Cristino
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD Australia
| | - Katia Nones
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD Australia
| | - Sugandha Ravishankar
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD Australia
| | - Bernadette Bellette
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD Australia
| | - Yongjun Fan
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD Australia
| | - Stephen A Wood
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD Australia
| | - Ernst Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD Australia
| | - Alan Mackay-Sim
- Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD Australia
| |
Collapse
|
150
|
Kundakovic M, Jiang Y, Kavanagh DH, Dincer A, Brown L, Pothula V, Zharovsky E, Park R, Jacobov R, Magro I, Kassim B, Wiseman J, Dang K, Sieberts SK, Roussos P, Fromer M, Harris B, Lipska BK, Peters MA, Sklar P, Akbarian S. Practical Guidelines for High-Resolution Epigenomic Profiling of Nucleosomal Histones in Postmortem Human Brain Tissue. Biol Psychiatry 2017; 81:162-170. [PMID: 27113501 PMCID: PMC5017897 DOI: 10.1016/j.biopsych.2016.03.1048] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/28/2016] [Accepted: 03/01/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND The nervous system may include more than 100 residue-specific posttranslational modifications of histones forming the nucleosome core that are often regulated in cell-type-specific manner. On a genome-wide scale, some of the histone posttranslational modification landscapes show significant overlap with the genetic risk architecture for several psychiatric disorders, fueling PsychENCODE and other large-scale efforts to comprehensively map neuronal and nonneuronal epigenomes in hundreds of specimens. However, practical guidelines for efficient generation of histone chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) datasets from postmortem brains are needed. METHODS Protocols and quality controls are given for the following: 1) extraction, purification, and NeuN neuronal marker immunotagging of nuclei from adult human cerebral cortex; 2) fluorescence-activated nuclei sorting; 3) preparation of chromatin by micrococcal nuclease digest; 4) ChIP for open chromatin-associated histone methylation and acetylation; and 5) generation and sequencing of ChIP-seq libraries. RESULTS We present a ChIP-seq pipeline for epigenome mapping in the neuronal and nonneuronal nuclei from the postmortem brain. This includes a stepwise system of quality controls and user-friendly data presentation platforms. CONCLUSIONS Our practical guidelines will be useful for projects aimed at histone posttranslational modification mapping in chromatin extracted from hundreds of postmortem brain samples in cell-type-specific manner.
Collapse
Affiliation(s)
- Marija Kundakovic
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yan Jiang
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - David H Kavanagh
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Aslihan Dincer
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Leanne Brown
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Venu Pothula
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Elizabeth Zharovsky
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Royce Park
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Rivka Jacobov
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Isabelle Magro
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bibi Kassim
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jennifer Wiseman
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | | | - Panos Roussos
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Menachem Fromer
- Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brent Harris
- Department of Neurology, Georgetown University Medical Center, Washington, DC; Human Brain Collection Core, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | - Barbara K Lipska
- Human Brain Collection Core, Division of Intramural Research Programs, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland
| | | | - Pamela Sklar
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York; Friedman Brain Institute, and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Schahram Akbarian
- Departments of Psychiatry and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.
| |
Collapse
|