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Omar SA, Feng Y, Yu M, Eldin SAG, Eldenary ME, Shabala S, Allakhverdiev SI, Abdelfattah MH. Exogenous application of 5-azacitidin, royal jelly and folic acid regulate plant redox state, expression level of DNA methyltransferases and alleviate adverse effects of salinity stress on Vicia faba L. plants. Heliyon 2024; 10:e30934. [PMID: 38784551 PMCID: PMC11112330 DOI: 10.1016/j.heliyon.2024.e30934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/05/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
DNA methylation is one of induced changes under salinity stress causing reduction in the expression of several crucial genes required for normal plant's operation. Potential use of royal jelly (RJ), folic acid (FA) and 5-azacitidine (5-AZA) on two Egyptian faba bean varieties (Sakha-3 and Giza-716) grown under saline conditions was investigated. Salinity stress affects negatively on seeds germination (G %), mitotic index, membrane stability and induced a significant increase in chromosomal abnormalities (CAs). DNA methyltransferases genes (MT1 and MT2) were highly up-regulated (∼23 and 8 folds for MT1 and MT2 in shoots of Giza-716 stressed plants). On the other hand, down regulation of other studied stress related genes: superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), heat shock protein (HSP-17.9) and proline-rich protein (GPRP) were detected in stressed plants of both studied varieties. Treating plants with RJ and FA increase G%, chlorophyll content, improves membrane properties and reduces CAs compared to non-treated stressed plants. Exogenous application of 5-AZA, RJ and FA on salinity stressed plants was associated with a significant reduction in the transcription of MT1 and MT2 which was associated with significant up regulation in the expression of Cu/Zn-SOD, CAT, GR, GPRP and HSP-17.9 encoding genes. The Lowest expression of MT1 and MT2 were induced with 5-AZA treatment in both studied varieties. Exogenous application of the FA, RJ and 5-AZA modified the methylation state of stressed plants by regulation the expression of DNA methyltransferases, subsequently, modulated the expression of studied genes and could be proposed as a promising treatment to ameliorate hazardous effects of salt stress on different plants.
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Affiliation(s)
| | - Yingming Feng
- International Research Centre for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, China
| | - Min Yu
- International Research Centre for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, China
| | | | | | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, China
- School of Biological Science, University of Western Australia, Crawley, Australia
| | - Suleyman I. Allakhverdiev
- K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, Moscow, 127276, Russia
- Bahcesehir University, Istanbul, 34353, Turkey
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Ambroa-Conde A, Casares de Cal MA, Gómez-Tato A, Robinson O, Mosquera-Miguel A, de la Puente M, Ruiz-Ramírez J, Phillips C, Lareu MV, Freire-Aradas A. Inference of tobacco and alcohol consumption habits from DNA methylation analysis of blood. Forensic Sci Int Genet 2024; 70:103022. [PMID: 38309257 DOI: 10.1016/j.fsigen.2024.103022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/22/2023] [Accepted: 01/25/2024] [Indexed: 02/05/2024]
Abstract
DNA methylation has become a biomarker of great interest in the forensic and clinical fields. In criminal investigations, the study of this epigenetic marker has allowed the development of DNA intelligence tools providing information that can be useful for investigators, such as age prediction. Following a similar trend, when the origin of a sample in a criminal scenario is unknown, the inference of an individual's lifestyle such as tobacco use and alcohol consumption could provide relevant information to help in the identification of DNA donors at the crime scene. At the same time, in the clinical domain, prediction of these trends of consumption could allow the identification of people at risk or better identification of the causes of different pathologies. In the present study, DNA methylation data from the UK AIRWAVE study was used to build two binomial logistic models for the inference of smoking and drinking status. A total of 348 individuals (116 non-smokers, 116 former smokers and 116 smokers) plus a total of 237 individuals (79 non-drinkers, 79 moderate drinkers and 79 drinkers) were used for development of tobacco and alcohol consumption prediction models, respectively. The tobacco prediction model was composed of two CpGs (cg05575921 in AHRR and cg01940273) and the alcohol prediction model three CpGs (cg06690548 in SLC7A11, cg0886875 and cg21294714 in MIR4435-2HG), providing correct classifications of 86.49% and 74.26%, respectively. Validation of the models was performed using leave-one-out cross-validation. Additionally, two independent testing sets were also assessed for tobacco and alcohol consumption. Considering that the consumption of these substances could underlie accelerated epigenetic ageing patterns, the effect of these lifestyles on the prediction of age was evaluated. To do that, a quantile regression model based on previous studies was generated, and the potential effect of tobacco and alcohol consumption with the epigenetic age was assessed. The Wilcoxon test was used to evaluate the residuals generated by the model and no significant differences were observed between the categories analyzed.
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Affiliation(s)
- A Ambroa-Conde
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M A Casares de Cal
- CITMAga (Center for Mathematical Research and Technology of Galicia), University of Santiago de Compostela, Spain
| | - A Gómez-Tato
- CITMAga (Center for Mathematical Research and Technology of Galicia), University of Santiago de Compostela, Spain
| | - O Robinson
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - A Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - J Ruiz-Ramírez
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain
| | - A Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, Universidade de Santiago de Compostela, Spain.
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Schuch JB, Bandeira CE, Junior JLS, Müller D, Charão MF, da Silva BS, Grevet EH, Kessler FHP, von Diemen L, Rovaris DL, Bau CHD. Global DNA methylation patterns in Alcohol Use Disorder. Genet Mol Biol 2024; 46:e20230139. [PMID: 38197733 PMCID: PMC10778554 DOI: 10.1590/1678-4685-gmb-2023-0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024] Open
Abstract
Alcohol Use Disorder (AUD) is a highly prevalent condition worldwide that produces a wide range of pathophysiological consequences, with a critical impact on health and social issues. Alcohol influences gene expression through epigenetic changes mainly through DNA methylation. In this sense, levels of 5-methylcytosine (5-mC), namely Global DNA methylation (GMe), which can be influenced by environmental and hormonal effects, represent a putative biological mechanism underlying alcohol effects. Our aim was to investigate the influence of AUD diagnosis and alcohol patterns (i.e., years of addiction, use in the last 30 days, and alcohol severity) on GMe levels. The sample consisted of 256 men diagnosed with AUD and 361 men without AUD. DNA samples from peripheral blood were used to assess GMe levels, measured through the levels of 5-mC using high-performance liquid chromatography. Results from multiple linear regression analysis indicated that the presence of AUD was associated with lower GMe levels (beta=-0.155, p=0.011). Other alcohol-related outcomes were not associated with DNA methylation. Our findings are consistent with the hypothesis that the impact of chronic and heavy alcohol use in GMe could be a potential mechanism mediating the multiple organ damages related to AUD.
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Affiliation(s)
- Jaqueline B. Schuch
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa em Álcool e Drogas, Porto Alegre, RS, Brazil
| | - Cibele E. Bandeira
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Fisiologia e Biofísica, São Paulo, SP, Brazil
| | - Jorge L. S. Junior
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Diana Müller
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
| | - Mariele F. Charão
- Universidade Feevale, Programa de Pós-Graduação em Toxicologia e Análises Toxicológicas, Novo Hamburgo, RS, Brazil
| | - Bruna S. da Silva
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Fisiologia e Biofísica, São Paulo, SP, Brazil
| | - Eugenio H. Grevet
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
| | - Felix H. P. Kessler
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa em Álcool e Drogas, Porto Alegre, RS, Brazil
| | - Lisia von Diemen
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa em Álcool e Drogas, Porto Alegre, RS, Brazil
| | - Diego L. Rovaris
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Fisiologia e Biofísica, São Paulo, SP, Brazil
| | - Claiton H. D. Bau
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
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Hong X, Wu Z, Cao W, Lv J, Yu C, Huang T, Sun D, Liao C, Pang Y, Pang Z, Cong L, Wang H, Wu X, Liu Y, Gao W, Li L. Longitudinal Association of DNA Methylation With Type 2 Diabetes and Glycemic Traits: A 5-Year Cross-Lagged Twin Study. Diabetes 2022; 71:2804-2817. [PMID: 36170668 DOI: 10.2337/db22-0513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
Investigators of previous cross-sectional epigenome-wide association studies (EWAS) in adults have reported hundreds of 5'-cytosine-phosphate-guanine-3' (CpG) sites associated with type 2 diabetes mellitus (T2DM) and glycemic traits. However, the results from EWAS have been inconsistent, and longitudinal observations of these associations are scarce. Furthermore, few studies have investigated whether DNA methylation (DNAm) could be modified by smoking, drinking, and glycemic traits, which have broad impacts on genome-wide DNAm and result in altering the risk of T2DM. Twin studies provide a valuable tool for epigenetic studies, as twins are naturally matched for genetic information. In this study, we conducted a systematic literature search in PubMed and Embase for EWAS, and 214, 33, and 117 candidate CpG sites were selected for T2DM, HbA1c, and fasting blood glucose (FBG). Based on 1,070 twins from the Chinese National Twin Registry, 67, 17, and 16 CpG sites from previous studies were validated for T2DM, HbA1c, and FBG. Longitudinal review and blood sampling for phenotypic information and DNAm were conducted twice in 2013 and 2018 for 308 twins. A cross-lagged analysis was performed to examine the temporal relationship between DNAm and T2DM or glycemic traits in the longitudinal data. A total of 11 significant paths from T2DM to subsequent DNAm and 15 paths from DNAm to subsequent T2DM were detected, suggesting both directions of associations. For glycemic traits, we detected 17 cross-lagged associations from baseline glycemic traits to subsequent DNAm, and none were from the other cross-lagged direction, indicating that CpG sites may be the consequences, not the causes, of glycemic traits. Finally, a longitudinal mediation analysis was performed to explore the mediation effects of DNAm on the associations of smoking, drinking, and glycemic traits with T2DM. No significant mediations of DNAm in the associations linking smoking and drinking with T2DM were found. In contrast, our study suggested a potential role of DNAm of cg19693031, cg00574958, and cg04816311 in mediating the effect of altered glycemic traits on T2DM.
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Affiliation(s)
- Xuanming Hong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zhiyu Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Dianjianyi Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Chunxiao Liao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Yuanjie Pang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Zengchang Pang
- Qingdao Center for Disease Control and Prevention, Qingdao, China
| | - Liming Cong
- Zhejiang Center for Disease Control and Prevention, Hangzhou, China
| | - Hua Wang
- Jiangsu Center for Disease Control and Prevention, Nanjing, China
| | - Xianping Wu
- Sichuan Center for Disease Control and Prevention, Chengdu, China
| | - Yu Liu
- Heilongjiang Center for Disease Control and Prevention, Harbin, China
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
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5
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Gong H, Chen Y, Chen M, Li J, Zhang H, Yan S, Lv C. Advanced development and mechanism of sepsis-related acute respiratory distress syndrome. Front Med (Lausanne) 2022; 9:1043859. [PMID: 36452899 PMCID: PMC9701739 DOI: 10.3389/fmed.2022.1043859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2023] Open
Abstract
The introduction of the Sepsis 3.0 guidelines in 2016 improved our understanding of sepsis diagnosis and therapy. Personalized treatment strategies and nursing methods for sepsis patients are recommended in the "Save Sepsis Campaign" in 2021. However, mortality in sepsis patients remains high. Patients with sepsis-related acute respiratory distress syndrome account for around 30% of them, with fatality rates ranging from 30 to 40%. Pathological specimens from individuals with sepsis-related ARDS frequently demonstrate widespread alveolar damage, and investigations have revealed that pulmonary epithelial and pulmonary endothelial injury is the underlying cause. As a result, the purpose of this work is to evaluate the mechanism and research progress of pulmonary epithelial and pulmonary endothelial damage in sepsis-related ARDS, which may provide new directions for future research, diagnosis, and therapy.
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Affiliation(s)
- Huankai Gong
- Emergency and Trauma College, Hainan Medical University, Haikou, China
- Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou, China
| | - Yao Chen
- Department of Oncology, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Meiling Chen
- Emergency and Trauma College, Hainan Medical University, Haikou, China
- Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou, China
| | - Jiankang Li
- Emergency and Trauma College, Hainan Medical University, Haikou, China
- Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou, China
| | - Hong Zhang
- Emergency and Trauma College, Hainan Medical University, Haikou, China
- Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou, China
| | - Shijiao Yan
- Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, China
- School of Public Health, Hainan Medical University, Haikou, China
| | - Chuanzhu Lv
- Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou, China
- Research Unit of Island Emergency Medicine, Chinese Academy of Medical Sciences (No. 2019RU013), Hainan Medical University, Haikou, China
- Emergency Medicine Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
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Ferguson LB, Mayfield RD, Messing RO. RNA biomarkers for alcohol use disorder. Front Mol Neurosci 2022; 15:1032362. [PMID: 36407766 PMCID: PMC9673015 DOI: 10.3389/fnmol.2022.1032362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Alcohol use disorder (AUD) is highly prevalent and one of the leading causes of disability in the US and around the world. There are some molecular biomarkers of heavy alcohol use and liver damage which can suggest AUD, but these are lacking in sensitivity and specificity. AUD treatment involves psychosocial interventions and medications for managing alcohol withdrawal, assisting in abstinence and reduced drinking (naltrexone, acamprosate, disulfiram, and some off-label medications), and treating comorbid psychiatric conditions (e.g., depression and anxiety). It has been suggested that various patient groups within the heterogeneous AUD population would respond more favorably to specific treatment approaches. For example, there is some evidence that so-called reward-drinkers respond better to naltrexone than acamprosate. However, there are currently no objective molecular markers to separate patients into optimal treatment groups or any markers of treatment response. Objective molecular biomarkers could aid in AUD diagnosis and patient stratification, which could personalize treatment and improve outcomes through more targeted interventions. Biomarkers of treatment response could also improve AUD management and treatment development. Systems biology considers complex diseases and emergent behaviors as the outcome of interactions and crosstalk between biomolecular networks. A systems approach that uses transcriptomic (or other -omic data, e.g., methylome, proteome, metabolome) can capture genetic and environmental factors associated with AUD and potentially provide sensitive, specific, and objective biomarkers to guide patient stratification, prognosis of treatment response or relapse, and predict optimal treatments. This Review describes and highlights state-of-the-art research on employing transcriptomic data and artificial intelligence (AI) methods to serve as molecular biomarkers with the goal of improving the clinical management of AUD. Considerations about future directions are also discussed.
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Affiliation(s)
- Laura B. Ferguson
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX, United States,Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX, United States,Department of Neuroscience, University of Texas at Austin, Austin, TX, United States,*Correspondence: Laura B. Ferguson,
| | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX, United States,Department of Neuroscience, University of Texas at Austin, Austin, TX, United States
| | - Robert O. Messing
- Waggoner Center for Alcohol and Addiction Research, University of Texas at Austin, Austin, TX, United States,Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX, United States,Department of Neuroscience, University of Texas at Austin, Austin, TX, United States
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Alcohol-Induced Oxidative Stress and the Role of Antioxidants in Alcohol Use Disorder: A Systematic Review. Antioxidants (Basel) 2022; 11:antiox11071374. [PMID: 35883865 PMCID: PMC9311529 DOI: 10.3390/antiox11071374] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/06/2022] [Accepted: 07/11/2022] [Indexed: 12/12/2022] Open
Abstract
Alcohol use disorder (AUD) is a highly prevalent, comorbid, and disabling disorder. The underlying mechanism of ethanol neurotoxicity and the involvement of oxidative stress is still not fully elucidated. However, ethanol metabolism has been associated with increased oxidative stress through alcohol dehydrogenase, the microsomal ethanol oxidation system, and catalase metabolic pathways. We searched the PubMed and genome-wide association studies (GWAS) catalog databases to review the literature systematically and summarized the findings focusing on AUD and alcohol abstinence in relation to oxidative stress. In addition, we reviewed the ClinicalTrials.gov resource of the US National Library of Medicine to identify all ongoing and completed clinical trials that include therapeutic interventions based on antioxidants. The retrieved clinical and preclinical studies show that oxidative stress impacts AUD through genetics, alcohol metabolism, inflammation, and neurodegeneration.
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Unlocking the potential of forensic traces: Analytical approaches to generate investigative leads. Sci Justice 2022; 62:310-326. [PMID: 35598924 DOI: 10.1016/j.scijus.2022.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 03/17/2022] [Accepted: 03/19/2022] [Indexed: 11/21/2022]
Abstract
Forensic investigation involves gathering the information necessary to understand the criminal events as well as linking objects or individuals to an item, location or other individual(s) for investigative purposes. For years techniques such as presumptive chemical tests, DNA profiling or fingermark analysis have been of great value to this process. However, these techniques have their limitations, whether it is a lack of confidence in the results obtained due to cross-reactivity, subjectivity and low sensitivity; or because they are dependent on holding reference samples in a pre-existing database. There is currently a need to devise new ways to gather as much information as possible from a single trace, particularly from biological traces commonly encountered in forensic casework. This review outlines the most recent advancements in the forensic analysis of biological fluids, fingermarks and hair. Special emphasis is placed on analytical methods that can expand the information obtained from the trace beyond what is achieved in the usual practices. Special attention is paid to those methods that accurately determine the nature of the sample, as well as how long it has been at the crime scene, along with individualising information regarding the donor source of the trace.
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Clark SL, Chan RF, Zhao M, Xie LY, Copeland WE, Penninx BW, Aberg KA, van den Oord EJ. Dual methylation and hydroxymethylation study of alcohol use disorder. Addict Biol 2022; 27:e13114. [PMID: 34791764 PMCID: PMC8891051 DOI: 10.1111/adb.13114] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 09/16/2021] [Accepted: 10/30/2021] [Indexed: 12/11/2022]
Abstract
Using an integrative, multi-tissue design, we sought to characterize methylation and hydroxymethylation changes in blood and brain associated with alcohol use disorder (AUD). First, we used epigenomic deconvolution to perform cell-type-specific methylome-wide association studies within subpopulations of granulocytes/T-cells/B-cells/monocytes in 1132 blood samples. Blood findings were then examined for overlap with AUD-related associations with methylation and hydroxymethylation in 50 human post-mortem brain samples. Follow-up analyses investigated if overlapping findings mediated AUD-associated transcription changes in the same brain samples. Lastly, we replicated our blood findings in an independent sample of 412 individuals and aimed to replicate published alcohol methylation findings using our results. Cell-type-specific analyses in blood identified methylome-wide significant associations in monocytes and T-cells. The monocyte findings were significantly enriched for AUD-related methylation and hydroxymethylation in brain. Hydroxymethylation in specific sites mediated AUD-associated transcription in the same brain samples. As part of the most comprehensive methylation study of AUD to date, this work involved the first cell-type-specific methylation study of AUD conducted in blood, identifying and replicating a finding in DLGAP1 that may be a blood-based biomarker of AUD. In this first study to consider the role of hydroxymethylation in AUD, we found evidence for a novel mechanism for cognitive deficits associated with AUD. Our results suggest promising new avenues for AUD research.
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Affiliation(s)
| | - Robin F. Chan
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University
| | - Min Zhao
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University
| | - Lin Y. Xie
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University
| | | | - Brenda W.J.H. Penninx
- Department of Psychiatry, University of Vermont,Department of Psychiatry, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Karolina A. Aberg
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University
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10
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Kaplan G, Xu H, Abreu K, Feng J. DNA Epigenetics in Addiction Susceptibility. Front Genet 2022; 13:806685. [PMID: 35145550 PMCID: PMC8821887 DOI: 10.3389/fgene.2022.806685] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/06/2022] [Indexed: 12/22/2022] Open
Abstract
Addiction is a chronically relapsing neuropsychiatric disease that occurs in some, but not all, individuals who use substances of abuse. Relatively little is known about the mechanisms which contribute to individual differences in susceptibility to addiction. Neural gene expression regulation underlies the pathogenesis of addiction, which is mediated by epigenetic mechanisms, such as DNA modifications. A growing body of work has demonstrated distinct DNA epigenetic signatures in brain reward regions that may be associated with addiction susceptibility. Furthermore, factors that influence addiction susceptibility are also known to have a DNA epigenetic basis. In the present review, we discuss the notion that addiction susceptibility has an underlying DNA epigenetic basis. We focus on major phenotypes of addiction susceptibility and review evidence of cell type-specific, time dependent, and sex biased effects of drug use. We highlight the role of DNA epigenetics in these diverse processes and propose its contribution to addiction susceptibility differences. Given the prevalence and lack of effective treatments for addiction, elucidating the DNA epigenetic mechanism of addiction vulnerability may represent an expeditious approach to relieving the addiction disease burden.
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11
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Lohoff FW, Roy A, Jung J, Longley M, Rosoff DB, Luo A, O'Connell E, Sorcher JL, Sun H, Schwandt M, Hodgkinson CA, Goldman D, Momenan R, McIntosh AM, Adams MJ, Walker RM, Evans KL, Porteous D, Smith AK, Lee J, Muench C, Charlet K, Clarke TK, Kaminsky ZA. Epigenome-wide association study and multi-tissue replication of individuals with alcohol use disorder: evidence for abnormal glucocorticoid signaling pathway gene regulation. Mol Psychiatry 2021; 26:2224-2237. [PMID: 32398718 PMCID: PMC7658001 DOI: 10.1038/s41380-020-0734-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/13/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022]
Abstract
Alcohol use disorder (AUD) is a chronic debilitating disorder with limited treatment options and poorly defined pathophysiology. There are substantial genetic and epigenetic components; however, the underlying mechanisms contributing to AUD remain largely unknown. We conducted the largest DNA methylation epigenome-wide association study (EWAS) analyses currently available for AUD (total N = 625) and employed a top hit replication (N = 4798) using a cross-tissue/cross-phenotypic approach with the goal of identifying novel epigenetic targets relevant to AUD. Results show that a network of differentially methylated regions in glucocorticoid signaling and inflammation-related genes were associated with alcohol use behaviors. A top probe consistently associated across all cohorts was located in the long non-coding RNA growth arrest specific five gene (GAS5) (p < 10-24). GAS5 has been implicated in regulating transcriptional activity of the glucocorticoid receptor and has multiple functions related to apoptosis, immune function and various cancers. Endophenotypic analyses using peripheral cortisol levels and neuroimaging paradigms showed that methylomic variation in GAS5 network-related probes were associated with stress phenotypes. Postmortem brain analyses documented increased GAS5 expression in the amygdala of individuals with AUD. Our data suggest that alcohol use is associated with differential methylation in the glucocorticoid system that might influence stress and inflammatory reactivity and subsequently risk for AUD.
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Affiliation(s)
- Falk W Lohoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA.
| | - Arunima Roy
- Royal's Institute of Mental Health Research, University of Ottawa, Ottawa, Canada
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Martha Longley
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Daniel B Rosoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Audrey Luo
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Emma O'Connell
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Jill L Sorcher
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Hui Sun
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Melanie Schwandt
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Colin A Hodgkinson
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - David Goldman
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Reza Momenan
- Clinical Neuroimaging Research Core, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Andrew M McIntosh
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Mark J Adams
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Rosie M Walker
- Medical Genetic Section, Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Medical Genetic Section, Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
| | - David Porteous
- Medical Genetic Section, Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, Georgia, USA
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Jisoo Lee
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Christine Muench
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Katrin Charlet
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA
| | - Toni-Kim Clarke
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Zachary A Kaminsky
- Royal's Institute of Mental Health Research, University of Ottawa, Ottawa, Canada
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12
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Abstract
OBJECTIVES Recent evidence from the fields of microbiology and immunology, as well as a small number of human sepsis studies, suggest that epigenetic regulation may play a central role in the pathogenesis of sepsis. The term "epigenetics" refers to regulatory mechanisms that control gene expression but are not related to changes in DNA sequence. These include DNA methylation, histone modifications, and regulation of transcription via non-coding RNAs. Epigenetic modifications, occurring in response to external stressors, lead to changes in gene expression, and thus lie at the intersection between genetics and the environment. In this review, we examine data from in vitro studies, animal studies, and the existing human sepsis studies in epigenetics to demonstrate that epigenetic mechanisms are likely central to the pathogenesis of sepsis and that epigenetic therapies may have potential in the treatment of sepsis and its associated organ failures. DATA SOURCES Online search of published scientific literature via Pubmed using the term "epigenetics" in combination with the terms "sepsis", "infection", "bacterial infection", "viral infection", "critical illness", "acute respiratory distress syndrome", and "acute lung injury". STUDY SELECTION Articles were chosen for inclusion based on their relevance to sepsis, acute inflammation, sepsis-related immune suppression, and sepsis-related organ failure. Reference lists were reviewed to identify additional relevant articles. DATA EXTRACTION Relevant data was extracted and synthesized for narrative review. DATA SYNTHESIS Epigenetic regulation is a key determinant of gene expression in sepsis. At the onset of infection, host-pathogen interactions often result in epigenetic alterations to host cells that favor pathogen survival. In parallel, the host inflammatory response is characterized by epigenetic modifications in key regulatory genes, including tumor necrosis factor and interleukin-1β. In human sepsis patients, multiple epigenetic modifying enzymes show differential expression in early sepsis, suggesting a role for epigenetics in coordinating the response to infection. In the later stages of sepsis, epigenetic modifications accompany endotoxin tolerance and the immune-suppressed state. In animal models, treatment with epigenetic modifiers can mitigate the effects of sepsis and improve survival as well as reverse sepsis-associated organ injury. CONCLUSIONS Epigenetic modifications are associated with key phases of sepsis, from the host-pathogen interaction, to acute inflammation, to immune suppression. Epigenetic markers show promise in the diagnosis and prognosis of sepsis and epigenetic modifying agents show promise as therapeutic tools in animal models of sepsis. Human studies in the area of epigenetics are sorely lacking and should be a priority for sepsis researchers.
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13
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Lu M, Xueying Q, Hexiang P, Wenjing G, Hägg S, Weihua C, Chunxiao L, Canqing Y, Jun L, Zengchang P, Liming C, Hua W, Xianping W, Yunzhang W, Liming L. Genome-wide associations between alcohol consumption and blood DNA methylation: evidence from twin study. Epigenomics 2021; 13:939-951. [PMID: 33993705 DOI: 10.2217/epi-2021-0039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Alcohol intake alters DNA methylation profiles and methylation might mediate the association between alcohol and disease, but limited number of positive CpG sites repeatedly replicated. Materials & methods: In total, 57 monozygotic (MZ) twin pairs discordant for alcohol drinking from the Chinese National Twin Registry and 158 MZ and dizygotic twin pairs in the Swedish Adoption/Twin Study of Aging were evaluated. DNA methylation was detected using the Infinium HumanMethylation450 BeadChip. Results: Among candidate CpG sites, cg07326074 was significantly correlated with drinking after adjusting for covariates in MZ twins in both datasets but not in the entire sample or dizygotic twins. Conclusion: The hypermethylation of cg07326074, located in the tumor-promoting gene C16orf59, was associated with alcohol consumption.
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Affiliation(s)
- Meng Lu
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Qin Xueying
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China.,Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Peng Hexiang
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Gao Wenjing
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Sara Hägg
- Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Cao Weihua
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Li Chunxiao
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Yu Canqing
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Lv Jun
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
| | - Pang Zengchang
- Qingdao Center for Disease Control & Prevention, Qingdao 266033, PR China
| | - Cong Liming
- Zhejiang Center for Disease Control & Prevention, Hangzhou 310051, PR China
| | - Wang Hua
- Jiangsu Center for Disease Control & Prevention, Nanjing 210009, PR China
| | - Wu Xianping
- Sichuan Center for Disease Control & Prevention, Chengdu 610041, PR China
| | - Wang Yunzhang
- Department of Medical Epidemiology & Biostatistics, Karolinska Institute, 171 76 Stockholm, Sweden
| | - Li Liming
- Department of Epidemiology & Biostatistics, School of Public Health, Peking University, Beijing 100191, PR China
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14
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Soundararajan S, Agrawal A, Purushottam M, Anand SD, Shankarappa B, Sharma P, Jain S, Murthy P. Changes in DNA methylation persist over time in males with severe alcohol use disorder-A longitudinal follow-up study. Am J Med Genet B Neuropsychiatr Genet 2021; 186:183-192. [PMID: 33491855 DOI: 10.1002/ajmg.b.32833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 12/25/2022]
Abstract
Treatment strategies for alcohol use disorder (AUD) aim for abstinence or harm reduction. While deranged biochemical parameters reverse with alcohol abstinence, whether molecular changes at the epigenetic level reverse is not clearly understood. We investigated whether the reduction from high alcohol use reflects DNA methylation at the gene-specific and global level. In subjects seeking treatment for severe AUD, we assessed gene-specific (aldehyde dehydrogenase [ALDH2]/methylene tetrahydrofolate reductase [MTHFR]) and global (long interspersed elements [LINE-1]) methylation across three-time points (baseline, after detoxification and at an early remission period of 3 months), in peripheral blood leukocytes. We observed that both gene-specific and global DNA methylation did not change over time, irrespective of the drinking status at 3 months (52% abstained from alcohol). Further, we also compared DNA methylation in AUD subjects with healthy controls. At baseline, there was a significantly higher gene-specific DNA methylation (ALDH2: p < .001 and MTHFR: p = .001) and a significant lower global methylation (LINE-1: p = .014) in AUD as compared to controls. Our results suggest that epigenetic changes at the DNA methylation level associated with severe AUD persist for at least 3 months of treatment.
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Affiliation(s)
- Soundarya Soundararajan
- Department of Clinical Neurosciences, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Centre for Addiction Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meera Purushottam
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Shravanthi Daphne Anand
- Centre for Addiction Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Bhagyalakshmi Shankarappa
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Priyamvada Sharma
- Centre for Addiction Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Department of Clinical Pharmacology and Neurotoxicology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Sanjeev Jain
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Pratima Murthy
- Centre for Addiction Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
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15
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Johnstone AL, Andrade NS, Barbier E, Khomtchouk BB, Rienas CA, Lowe K, Van Booven DJ, Domi E, Esanov R, Vilca S, Tapocik JD, Rodriguez K, Maryanski D, Keogh MC, Meinhardt MW, Sommer WH, Heilig M, Zeier Z, Wahlestedt C. Dysregulation of the histone demethylase KDM6B in alcohol dependence is associated with epigenetic regulation of inflammatory signaling pathways. Addict Biol 2021; 26:e12816. [PMID: 31373129 PMCID: PMC7757263 DOI: 10.1111/adb.12816] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/28/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
Epigenetic enzymes oversee long‐term changes in gene expression by integrating genetic and environmental cues. While there are hundreds of enzymes that control histone and DNA modifications, their potential roles in substance abuse and alcohol dependence remain underexplored. A few recent studies have suggested that epigenetic processes could underlie transcriptomic and behavioral hallmarks of alcohol addiction. In the present study, we sought to identify epigenetic enzymes in the brain that are dysregulated during protracted abstinence as a consequence of chronic and intermittent alcohol exposure. Through quantitative mRNA expression analysis of over 100 epigenetic enzymes, we identified 11 that are significantly altered in alcohol‐dependent rats compared with controls. Follow‐up studies of one of these enzymes, the histone demethylase KDM6B, showed that this enzyme exhibits region‐specific dysregulation in the prefrontal cortex and nucleus accumbens of alcohol‐dependent rats. KDM6B was also upregulated in the human alcoholic brain. Upregulation of KDM6B protein in alcohol‐dependent rats was accompanied by a decrease of trimethylation levels at histone H3, lysine 27 (H3K27me3), consistent with the known demethylase specificity of KDM6B. Subsequent epigenetic (chromatin immunoprecipitation [ChIP]–sequencing) analysis showed that alcohol‐induced changes in H3K27me3 were significantly enriched at genes in the IL‐6 signaling pathway, consistent with the well‐characterized role of KDM6B in modulation of inflammatory responses. Knockdown of KDM6B in cultured microglial cells diminished IL‐6 induction in response to an inflammatory stimulus. Our findings implicate a novel KDM6B‐mediated epigenetic signaling pathway integrated with inflammatory signaling pathways that are known to underlie the development of alcohol addiction.
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Affiliation(s)
- Andrea L. Johnstone
- Center for Therapeutic Innovation University of Miami Miller School of Medicine Miami Florida USA
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of Medicine Miami Florida USA
- Division of Product Development EpiCypher, Inc Durham North Carolina USA
| | - Nadja S. Andrade
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of Medicine Miami Florida USA
| | - Estelle Barbier
- Department of Clinical and Experimental Medicine, Division of Cell Biology, Faculty of Health Sciences Linköping University Linköping Sweden
| | - Bohdan B. Khomtchouk
- Center for Therapeutic Innovation University of Miami Miller School of Medicine Miami Florida USA
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of Medicine Miami Florida USA
- Department of Medicine, Section of Computational Biomedicine and Biomedical Data Science, Institute for Genomics and Systems Biology University of Chicago Chicago IL USA
| | - Christopher A. Rienas
- Center for Therapeutic Innovation University of Miami Miller School of Medicine Miami Florida USA
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of Medicine Miami Florida USA
| | - Kenneth Lowe
- Center for Therapeutic Innovation University of Miami Miller School of Medicine Miami Florida USA
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of Medicine Miami Florida USA
| | - Derek J. Van Booven
- John P. Hussman Institute for Human Genomics University of Miami Miller School of Medicine Miami Florida USA
| | - Esi Domi
- Department of Clinical and Experimental Medicine, Division of Cell Biology, Faculty of Health Sciences Linköping University Linköping Sweden
| | - Rustam Esanov
- Center for Therapeutic Innovation University of Miami Miller School of Medicine Miami Florida USA
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of Medicine Miami Florida USA
| | - Samara Vilca
- Center for Therapeutic Innovation University of Miami Miller School of Medicine Miami Florida USA
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of Medicine Miami Florida USA
| | - Jenica D. Tapocik
- Laboratory of Clinical and Translational Studies, National Institute on Alcohol Abuse and Alcoholism National Institutes of Health Bethesda Maryland USA
| | - Keli Rodriguez
- Division of Product Development EpiCypher, Inc Durham North Carolina USA
| | - Danielle Maryanski
- Division of Product Development EpiCypher, Inc Durham North Carolina USA
| | | | - Marcus W. Meinhardt
- Department of Psychopharmacology Central Institute of Mental Health, Heidelberg University Mannheim Germany
| | - Wolfgang H. Sommer
- Department of Psychopharmacology Central Institute of Mental Health, Heidelberg University Mannheim Germany
| | - Markus Heilig
- Department of Clinical and Experimental Medicine, Division of Cell Biology, Faculty of Health Sciences Linköping University Linköping Sweden
| | - Zane Zeier
- Center for Therapeutic Innovation University of Miami Miller School of Medicine Miami Florida USA
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of Medicine Miami Florida USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation University of Miami Miller School of Medicine Miami Florida USA
- Department of Psychiatry and Behavioral Sciences University of Miami Miller School of Medicine Miami Florida USA
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16
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Stephenson M, Bollepalli S, Cazaly E, Salvatore JE, Barr P, Rose RJ, Dick D, Kaprio J, Ollikainen M. Associations of Alcohol Consumption With Epigenome-Wide DNA Methylation and Epigenetic Age Acceleration: Individual-Level and Co-twin Comparison Analyses. Alcohol Clin Exp Res 2020; 45:318-328. [PMID: 33277923 DOI: 10.1111/acer.14528] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND DNA methylation may play a role in the progression from normative to problematic drinking and underlie adverse health outcomes associated with alcohol misuse. We examined the association between alcohol consumption and DNA methylation patterns using 3 approaches: a conventional epigenome-wide association study (EWAS); a co-twin comparison design, which controls for genetic and environmental influences that twins share; and a regression of age acceleration, defined as a discrepancy between chronological age and DNA methylation age, on alcohol consumption. METHODS Participants came from the Finnish Twin Cohorts (FinnTwin12/FinnTwin16; N = 1,004; 55% female; average age = 23 years). Individuals reported the number of alcoholic beverages consumed in the past week, and epigenome-wide DNA methylation was assessed in whole blood using the Infinium HumanMethylation450 BeadChip. RESULTS In the EWAS, alcohol consumption was significantly related to methylation at 24 CpG sites. When evaluating whether differences between twin siblings (185 monozygotic pairs) in alcohol consumption predicted differences in DNA methylation, co-twin comparisons replicated 4 CpG sites from the EWAS and identified 23 additional sites. However, when we examined qualitative differences in drinking patterns between twins (heavy drinker vs. light drinker/abstainer or moderate drinker vs. abstainer; 44 pairs), methylation patterns did not significantly differ within twin pairs. Finally, individuals who reported higher alcohol consumption also exhibited greater age acceleration, though results were no longer significant after controlling for genetic and environmental influences shared by co-twins. CONCLUSIONS Our analyses offer insight into the associations between epigenetic variation and levels of alcohol consumption in young adulthood.
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Affiliation(s)
- Mallory Stephenson
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland
| | - Emma Cazaly
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland
| | - Jessica E Salvatore
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia.,Virginia Institute for Psychiatric and Behavioral Genetics, (JES), Virginia Commonwealth University, Richmond, Virginia
| | - Peter Barr
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia
| | - Richard J Rose
- Department of Psychological and Brain Sciences, (RJR), Indiana University, Bloomington, Indiana
| | - Danielle Dick
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia.,Department of Human and Molecular Genetics, (DD), Virginia Commonwealth University, Richmond, Virginia
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland.,Department of Public Health, (JK, MO), University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland.,Department of Public Health, (JK, MO), University of Helsinki, Helsinki, Finland
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17
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Shu C, Justice AC, Zhang X, Marconi VC, Hancock DB, Johnson EO, Xu K. DNA methylation biomarker selected by an ensemble machine learning approach predicts mortality risk in an HIV-positive veteran population. Epigenetics 2020; 16:741-753. [PMID: 33092459 PMCID: PMC8216205 DOI: 10.1080/15592294.2020.1824097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Background: With the improved life expectancy of people living with HIV (PLWH), identifying vulnerable subpopulations at high mortality risk is important. Evidences showed that DNA methylation (DNAm) is associated with mortality in non-HIV populations. Here, we established a panel of DNAm biomarkers that can predict mortality risk among PLWH. Methods: 1,081 HIV-positive participants from the Veterans Ageing Cohort Study (VACS) were divided into training (N = 460), validation (N = 114), and testing (N = 507) sets. VACS index was used as a measure of mortality risk among PLWH. Model training and fine-tuning were conducted using the ensemble method in the training and validation sets and prediction performance was assessed in the testing set. The survival analysis comparing the predicted high and low mortality risk groups and the Gene Ontology enrichment analysis of the predictive CpG sites were performed. Results: We selected a panel of 393 CpGs for the ensemble prediction model that showed excellent performance in predicting high mortality risk with an auROC of 0.809 (95%CI: 0.767,0.851) and a balanced accuracy of 0.653 (95%CI: 0.611, 0.693) in the testing set. The high mortality risk group was significantly associated with 10-year mortality (hazard ratio = 1.79, p = 4E-05) compared with low risk group. These 393 CpGs were located in 280 genes enriched in immune and inflammation response pathways. Conclusions: We identified a panel of DNAm features associated with mortality risk in PLWH. These DNAm features may serve as predictive biomarkers for mortality risk among PLWH. Abbreviations: AUC: Area Under Curve; CI: Confidence interval; DMR: differentially methylated region; DNA: Deoxyribonucleic acid; DNAm: DNA methylation; DAVID: Database for Annotation, Visualization, and Integrated Discovery; EWA: epigenome-wide association; FDR: False discovery rate; FWER: Family-wise error rate; GLMNET: elastic-net-regularized generalized linear models; GO: Gene ontology; HIV: Human immunodeficiency virus; HM450K: Human Methylation 450 K BeadChip; k-NN: k-nearest neighbours; NK: Natural killer; PC: Principal component; PLWH: people living with HIV; QC: Quality control; SVM: Support Vector Machines; VACS: Veterans Ageing Cohort Study; XGBoost: Extreme Gradient Boosting Tree
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Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- Connecticut Veteran Healthcare System, West Haven, CT, USA.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Vincent C Marconi
- Division of Infectious Disease, Emory University School of Medicine, Atlanta, GA, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
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18
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Stephen JM, Solis I, Janowich J, Stern M, Frenzel MR, Eastman JA, Mills MS, Embury CM, Coolidge NM, Heinrichs-Graham E, Mayer A, Liu J, Wang YP, Wilson TW, Calhoun VD. The Developmental Chronnecto-Genomics (Dev-CoG) study: A multimodal study on the developing brain. Neuroimage 2020; 225:117438. [PMID: 33039623 DOI: 10.1016/j.neuroimage.2020.117438] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/07/2020] [Accepted: 10/05/2020] [Indexed: 01/10/2023] Open
Abstract
Brain development has largely been studied through unimodal analysis of neuroimaging data, providing independent results for structural and functional data. However, structure clearly impacts function and vice versa, pointing to the need for performing multimodal data collection and analysis to improve our understanding of brain development, and to further inform models of typical and atypical brain development across the lifespan. Ultimately, such models should also incorporate genetic and epigenetic mechanisms underlying brain structure and function, although currently this area is poorly specified. To this end, we are reporting here a multi-site, multi-modal dataset that captures cognitive function, brain structure and function, and genetic and epigenetic measures to better quantify the factors that influence brain development in children originally aged 9-14 years. Data collection for the Developmental Chronnecto-Genomics (Dev-CoG) study (http://devcog.mrn.org/) includes cognitive, emotional, and social performance scales, structural and functional MRI, diffusion MRI, magnetoencephalography (MEG), and saliva collection for DNA analysis of single nucleotide polymorphisms (SNPs) and DNA methylation patterns. Across two sites (The Mind Research Network and the University of Nebraska Medical Center), data from over 200 participants were collected and these children were re-tested annually for at least 3 years. The data collection protocol, sample demographics, and data quality measures for the dataset are presented here. The sample will be made freely available through the collaborative informatics and neuroimaging suite (COINS) database at the conclusion of the study.
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Affiliation(s)
- J M Stephen
- The Mind Research Network a division of Lovelace Biomedical Research Institute, Albuquerque, NM, United States.
| | - I Solis
- The Mind Research Network a division of Lovelace Biomedical Research Institute, Albuquerque, NM, United States; Department of Psychology, University of New Mexico, Albuquerque, NM, United States
| | - J Janowich
- The Mind Research Network a division of Lovelace Biomedical Research Institute, Albuquerque, NM, United States; Department of Psychology, University of New Mexico, Albuquerque, NM, United States
| | - M Stern
- The Mind Research Network a division of Lovelace Biomedical Research Institute, Albuquerque, NM, United States; Department of Psychology, University of New Mexico, Albuquerque, NM, United States
| | - M R Frenzel
- University of Nebraska Medical Center, Omaha, NE, United States
| | - J A Eastman
- University of Nebraska Medical Center, Omaha, NE, United States
| | - M S Mills
- University of Nebraska Medical Center, Omaha, NE, United States
| | - C M Embury
- University of Nebraska Medical Center, Omaha, NE, United States
| | - N M Coolidge
- University of Nebraska Medical Center, Omaha, NE, United States
| | | | - A Mayer
- The Mind Research Network a division of Lovelace Biomedical Research Institute, Albuquerque, NM, United States
| | - J Liu
- The Mind Research Network a division of Lovelace Biomedical Research Institute, Albuquerque, NM, United States
| | - Y P Wang
- Tulane University, New Orleans, LA, United States
| | - T W Wilson
- University of Nebraska Medical Center, Omaha, NE, United States
| | - V D Calhoun
- The Mind Research Network a division of Lovelace Biomedical Research Institute, Albuquerque, NM, United States; Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, United States; Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, GA, United States
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19
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Shu C, Justice AC, Zhang X, Wang Z, Hancock DB, Johnson EO, Xu K. DNA methylation mediates the effect of cocaine use on HIV severity. Clin Epigenetics 2020; 12:140. [PMID: 32928285 PMCID: PMC7491141 DOI: 10.1186/s13148-020-00934-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background Cocaine use accelerates human immunodeficiency virus (HIV) progression and worsens HIV outcomes. We assessed whether DNA methylation in blood mediates the association between cocaine use and HIV severity in a veteran population. Methods We analyzed 1435 HIV-positive participants from the Veterans Aging Cohort Study Biomarker Cohort (VACS-BC). HIV severity was measured by the Veteran Aging Cohort Study (VACS) index. We assessed the effect of cocaine use on VACS index and mortality among the HIV-positive participants. We selected candidate mediators that were associated with both persistent cocaine use and VACS index by epigenome-wide association (EWA) scans at a liberal p value cutoff of 0.001. Mediation analysis of the candidate CpG sites between cocaine’s effect and the VACS index was conducted, and the joint mediation effect of multiple CpGs was estimated. A two-step epigenetic Mendelian randomization (MR) analysis was conducted as validation. Results More frequent cocaine use was significantly associated with a higher VACS index (β = 1.00, p = 2.7E−04), and cocaine use increased the risk of 10-year mortality (hazard ratio = 1.10, p = 0.011) with adjustment for confounding factors. Fifteen candidate mediator CpGs were selected from the EWA scan. Twelve of these CpGs showed significant mediation effects, with each explaining 11.3–29.5% of the variation. The mediation effects for 3 of the 12 CpGs were validated by the two-step epigenetic MR analysis. The joint mediation effect of the 12 CpGs accounted for 47.2% of cocaine’s effect on HIV severity. Genes harboring these 12 CpGs are involved in the antiviral response (IFIT3, IFITM1, NLRC5, PLSCR1, PARP9) and HIV progression (CX3CR1, MX1). Conclusions We identified 12 DNA methylation CpG sites that appear to play a mediation role in the association between cocaine use and HIV severity.
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Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- Connecticut Veteran Healthcare System, West Haven, CT, USA.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA. .,Connecticut Veteran Healthcare System, West Haven, CT, USA.
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20
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Mulder RH, Walton E, Neumann A, Houtepen LC, Felix JF, Bakermans-Kranenburg MJ, Suderman M, Tiemeier H, van IJzendoorn MH, Relton CL, Cecil CAM. Epigenomics of being bullied: changes in DNA methylation following bullying exposure. Epigenetics 2020; 15:750-764. [PMID: 31992121 PMCID: PMC7574379 DOI: 10.1080/15592294.2020.1719303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bullying among children is ubiquitous and associated with pervasive mental health problems. However, little is known about the biological pathways that change after exposure to bullying. Epigenome-wide changes in DNA methylation in peripheral blood were studied from pre- to post measurement of bullying exposure, in a longitudinal study of the population-based Generation R Study and Avon Longitudinal Study of Parents and Children (combined n = 1,352). Linear mixed-model results were meta-analysed to estimate how DNA methylation changed as a function of exposure to bullying. Sensitivity analyses including co-occurring child characteristics and risks were performed, as well as a Gene Ontology analysis. A candidate follow-up was employed for CpG (cytosine-phosphate-guanine) sites annotated to 5-HTT and NR3C1. One site, cg17312179, showed small changes in DNA methylation associated to bullying exposure (b = -2.67e-03, SE = 4.97e-04, p = 7.17e-08). This site is annotated to RAB14, an oncogene related to Golgi apparatus functioning, and its methylation levels decreased for exposed but increased for non-exposed. This result was consistent across sensitivity analyses. Enriched Gene Ontology pathways for differentially methylated sites included cardiac function and neurodevelopmental processes. Top CpG sites tended to have overall low levels of DNA methylation, decreasing in exposed, increasing in non-exposed individuals. There were no gene-wide corrected findings for 5-HTT and NR3C1. This is the first study to identify changes in DNA methylation associated with bullying exposure at the epigenome-wide significance level. Consistent with other population-based studies, we do not find evidence for strong associations between bullying exposure and DNA methylation.
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Affiliation(s)
- Rosa H Mulder
- Institute of Education and Child Studies, Leiden University , Leiden, The Netherlands.,Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands
| | - Esther Walton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol , Bristol, UK.,Department of Psychology, University of Bath , Bath, UK
| | - Alexander Neumann
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Generation R Study Group, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Lady Davis Institute for Medical Research, Jewish General Hospital , Montreal, Qc, Canada
| | - Lotte C Houtepen
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol , Bristol, UK
| | - Janine F Felix
- Generation R Study Group, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands
| | | | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol , Bristol, UK
| | - Henning Tiemeier
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Department of Social and Behavioral Science, Harvard TH Chan School of Public Health , Boston, MA, USA
| | - Marinus H van IJzendoorn
- Department of Psychology, Education and Child Studies, Erasmus University Rotterdam , Rotterdam, The Netherlands.,School of Clinical Medicine, University of Cambridge , Cambridge, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol , Bristol, UK
| | - Charlotte A M Cecil
- Department of Child and Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam , Rotterdam, The Netherlands.,Department of Psychology, Institute of Psychology, Psychiatry & Neuroscience, King's College London , London, UK
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21
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ALDH3B2 Polymorphism Is Associated with Colorectal Cancer Susceptibility. JOURNAL OF ONCOLOGY 2020; 2020:5179635. [PMID: 32377192 PMCID: PMC7199530 DOI: 10.1155/2020/5179635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 11/21/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022]
Abstract
Colorectal cancer (CRC) is the 5th leading cancer in China. Alcohol consumption has been reported to be one of the risk factors of CRC. However, it remains unclear whether genetic variants of alcohol metabolic genes are associated with CRC risk. In this study, we tested the coding variants in the alcohol metabolic genes and the risk of CRC, by using 485 cases and 516 controls. A total of 16 germline coding variants in 10 alcohol metabolic genes were genotyped. We identified that rs3741178 in ALDH3B2 was significantly associated with CRC risk with odds ratio being 2.13 (95% CI: 1.24–3.68, P=0.0064). Further functional annotation suggested that this variant may damage the protein function of ALDH3B2. Our results suggested that ALDH3B2 in the alcohol metabolism pathway contributed to the development of CRC, which may contribute to the prevention of this disease in the future.
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22
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Zhao Y, Ge Y, Zheng ZL. Brain Imaging-Guided Analysis Reveals DNA Methylation Profiles Correlated with Insular Surface Area and Alcohol Use Disorder. Alcohol Clin Exp Res 2019; 43:628-639. [PMID: 30830696 PMCID: PMC6443499 DOI: 10.1111/acer.13971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/26/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Alcohol use disorder (AUD) is a wide-spread, heritable brain disease, but few studies have linked genetic variants or epigenetic factors to brain structures related to AUD in humans, due to many factors including the high-dimensional nature of imaging and genomic data. METHODS To provide potential insights into the links among epigenetic regulation, brain structure, and AUD, we have performed an integrative analysis of brain structural imaging and blood DNA methylome data from 52 AUD and 58 healthy control (HC) subjects collected in the Nathan Kline Institute-Rockland Sample. RESULTS We first found that AUD subjects had significantly larger insular surface area than HC in both left and right hemispheres. We then found that 7,827 DNA methylation probes on the HumanMethylation450K BeadChip had significant correlations with the right insular surface area (false discovery rate [FDR] < 0.05). Furthermore, we showed that 44 of the insular surface area-correlated methylation probes were also strongly correlated with AUD status (FDR < 0.05). These AUD-correlated probes are annotated to 36 protein-coding genes, with 16 genes (44%) having been reported by others to be related to AUD or alcohol response, including TAS2R16 and PER2. The remaining 20 genes, in particular ARHGAP22, might represent novel genes involved in AUD or responsive to alcohol. CONCLUSIONS We have identified 36 insular surface area- and AUD-correlated protein-coding genes that are either known to be AUD- or alcohol-related or not yet reported by prior studies. Therefore, our study suggests that the brain imaging-guided epigenetic analysis has a potential of identifying possible epigenetic mechanisms involved in AUD.
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Affiliation(s)
- Yihong Zhao
- Department of Child and Adolescent Psychiatry, NYU Langone Medical Center, New York, NY 10016, USA
- Center for Behavioral Science Research, Department of Health Policy & Health Services Research, Boston University, Boston, MA 02118, USA
| | - Yongchao Ge
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhi-Liang Zheng
- Department of Biological Sciences, Lehman College, City University of New York, Bronx, NY 10468, USA
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23
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Wolf EJ, Logue MW, Morrison FG, Wilcox ES, Stone A, Schichman SA, McGlinchey RE, Milberg WP, Miller MW. Posttraumatic psychopathology and the pace of the epigenetic clock: a longitudinal investigation. Psychol Med 2019; 49:791-800. [PMID: 29897034 PMCID: PMC6292741 DOI: 10.1017/s0033291718001411] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Posttraumatic stress disorder (PTSD) and stress/trauma exposure are cross-sectionally associated with advanced DNA methylation age relative to chronological age. However, longitudinal inquiry and examination of associations between advanced DNA methylation age and a broader range of psychiatric disorders is lacking. The aim of this study was to examine if PTSD, depression, generalized anxiety, and alcohol-use disorders predicted acceleration of DNA methylation age over time (i.e. an increasing pace, or rate of advancement, of the epigenetic clock). METHODS Genome-wide DNA methylation and a comprehensive set of psychiatric symptoms and diagnoses were assessed in 179 Iraq/Afghanistan war veterans who completed two assessments over the course of approximately 2 years. Two DNA methylation age indices (Horvath and Hannum), each a weighted index of an array of genome-wide DNA methylation probes, were quantified. The pace of the epigenetic clock was operationalized as change in DNA methylation age as a function of time between assessments. RESULTS Analyses revealed that alcohol-use disorders (p = 0.001) and PTSD avoidance and numbing symptoms (p = 0.02) at Time 1 were associated with an increasing pace of the epigenetic clock over time, per the Horvath (but not the Hannum) index of cellular aging. CONCLUSIONS This is the first study to suggest that posttraumatic psychopathology is longitudinally associated with a quickened pace of the epigenetic clock. Results raise the possibility that accelerated cellular aging is a common biological consequence of stress-related psychopathology, which carries implications for identifying mechanisms of stress-related cellular aging and developing interventions to slow its pace.
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Affiliation(s)
- Erika J. Wolf
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
| | - Mark W. Logue
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
- Biomedical Genetics, Boston University School of Medicine
| | - Filomene G. Morrison
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
| | | | - Annjanette Stone
- Pharmacogenomics Analysis Laboratory, Research Service, Central
Arkansas Veterans Healthcare System
| | - Steven A. Schichman
- Pharmacogenomics Analysis Laboratory, Research Service, Central
Arkansas Veterans Healthcare System
| | - Regina E. McGlinchey
- Geriatric Research Educational and Clinical Center and Translational
Research Center for TBI and Stress Disorders, VA Boston Healthcare System
- Department of Psychiatry, Harvard Medical School
| | - William P. Milberg
- Geriatric Research Educational and Clinical Center and Translational
Research Center for TBI and Stress Disorders, VA Boston Healthcare System
- Department of Psychiatry, Harvard Medical School
| | - Mark W. Miller
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
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24
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Braun PR, Han S, Hing B, Nagahama Y, Gaul LN, Heinzman JT, Grossbach AJ, Close L, Dlouhy BJ, Howard MA, Kawasaki H, Potash JB, Shinozaki G. Genome-wide DNA methylation comparison between live human brain and peripheral tissues within individuals. Transl Psychiatry 2019; 9:47. [PMID: 30705257 PMCID: PMC6355837 DOI: 10.1038/s41398-019-0376-y] [Citation(s) in RCA: 239] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 12/10/2018] [Accepted: 01/02/2019] [Indexed: 12/24/2022] Open
Abstract
Differential DNA methylation in the brain is associated with many psychiatric diseases, but access to brain tissues is essentially limited to postmortem samples. The use of surrogate tissues has become common in identifying methylation changes associated with psychiatric disease. In this study, we determined the extent to which peripheral tissues can be used as surrogates for DNA methylation in the brain. Blood, saliva, buccal, and live brain tissue samples from 27 patients with medically intractable epilepsy undergoing brain resection were collected (age range 5-61 years). Genome-wide methylation was assessed with the Infinium HumanMethylation450 (n = 12) and HumanMethylationEPIC BeadChip arrays (n = 21). For the EPIC methylation data averaged for each CpG across subjects, the saliva-brain correlation (r = 0.90) was higher than that for blood-brain (r = 0.86) and buccal-brain (r = 0.85) comparisons. However, within individual CpGs, blood had the highest proportion of CpGs correlated to brain at nominally significant levels (20.8%), as compared to buccal tissue (17.4%) and saliva (15.1%). For each CpG and each gene, levels of brain-peripheral tissue correlation varied widely. This indicates that to determine the most useful surrogate tissue for representing brain DNA methylation, the patterns specific to the genomic region of interest must be considered. To assist in that objective, we have developed a website, IMAGE-CpG, that allows researchers to interrogate DNA methylation levels and degree of cross-tissue correlation in user-defined locations across the genome.
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Affiliation(s)
- Patricia R Braun
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52246, USA
- Department of Psychiatry and Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Shizhong Han
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52246, USA
- Department of Psychiatry and Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Benjamin Hing
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Yasunori Nagahama
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Lindsey N Gaul
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Jonathan T Heinzman
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Andrew J Grossbach
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
- Department of Neurological Surgery, Ohio State University, Columbus, OH, 43203, USA
| | - Liesl Close
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Brian J Dlouhy
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Matthew A Howard
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - Hiroto Kawasaki
- Department of Neurosurgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
| | - James B Potash
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, IA, 52246, USA
- Department of Psychiatry and Behavioral Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Gen Shinozaki
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA.
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA.
- Interdisciplinary Graduate Program for Neuroscience, University of Iowa Carver College of Medicine, Iowa City, IA, 52246, USA.
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25
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Methamphetamine (MA) Use Induces Specific Changes in LINE-1 Partial Methylation Patterns, Which Are Associated with MA-Induced Paranoia: a Multivariate and Neuronal Network Study. Mol Neurobiol 2018; 56:4258-4272. [PMID: 30302724 DOI: 10.1007/s12035-018-1371-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/27/2018] [Indexed: 12/29/2022]
Abstract
The use of psychoactive substances, including methamphetamine (MA) may cause changes in DNA methylation. The aim of this study was to examine the effects of MA use on long interspersed element-1 (LINE-1) methylation patterns in association with MA-induced paranoia. This study recruited 123 normal controls and 974 MA users, 302 with and 672 without MA-induced paranoia. The Semi-Structured Assessment for Drug Dependence and Alcoholism was used to assess demographic and substance use variables. Patterns of LINE-1 methylation were assessed in peripheral blood mononuclear cells and a combined bisulfite restriction analysis (COBRA) was used to estimate overall LINE-1 methylation (mC) while COBRA classified LINE-alleles into four patterns based on the methylation status of two CpG dinucleotides on each strand from 5' to 3', namely two methylated (mCmC) and two unmethylated (uCuC) CpGs and two types of partially methylated loci (mCuC that is 5'm with 3'u and uCmC that is 5'u with 3'm CpGs). MA users showed higher % mCuC and % mCuC + uCmC levels than controls. Use of solvents and opioids, but not cannabis and alcohol dependence, significantly lowered % uCmC levels, while current smoking significantly increased % uCuC levels. MA-induced paranoia was strongly associated with changes in LINE-1 partial methylation patterns (lowered % uCmC), heavy MA use, lower age at onset of MA use, and alcohol dependence. Women who took contraceptives showed significantly lower LINE-1 % mC and % mCmC and higher % uCuC levels than women without contraceptive use and men. The results show that MA-induced changes in LINE-1 partial methylation patterns are associated with MA-induced paranoia and could explain in part the pathophysiology of this type of psychosis. It is argued that MA-induced neuro-oxidative pathways may have altered LINE-1 partial methylation patterns, which in turn may regulate neuro-oxidative and immune pathways, which may increase risk to develop MA-induced paranoia.
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26
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Lohoff FW, Sorcher JL, Rosen AD, Mauro KL, Fanelli RR, Momenan R, Hodgkinson CA, Vendruscolo LF, Koob GF, Schwandt M, George DT, Jones IS, Holmes A, Zhou Z, Xu MJ, Gao B, Sun H, Phillips MJ, Muench C, Kaminsky ZA. Methylomic profiling and replication implicates deregulation of PCSK9 in alcohol use disorder. Mol Psychiatry 2018; 23:1900-1910. [PMID: 28848234 PMCID: PMC5832488 DOI: 10.1038/mp.2017.168] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/25/2017] [Accepted: 06/23/2017] [Indexed: 01/08/2023]
Abstract
Alcohol use disorder (AUD) is a common and chronic disorder with substantial effects on personal and public health. The underlying pathophysiology is poorly understood but strong evidence suggests significant roles of both genetic and epigenetic components. Given that alcohol affects many organ systems, we performed a cross-tissue and cross-phenotypic analysis of genome-wide methylomic variation in AUD using samples from 3 discovery, 4 replication, and 2 translational cohorts. We identified a differentially methylated region in the promoter of the proprotein convertase subtilisin/kexin 9 (PCSK9) gene that was associated with disease phenotypes. Biological validation showed that PCSK9 promoter methylation is conserved across tissues and positively correlated with expression. Replication in AUD datasets confirmed PCSK9 hypomethylation and a translational mouse model of AUD showed that alcohol exposure leads to PCSK9 downregulation. PCSK9 is primarily expressed in the liver and regulates low-density lipoprotein cholesterol (LDL-C). Our finding of alcohol-induced epigenetic regulation of PCSK9 represents one of the underlying mechanisms between the well-known effects of alcohol on lipid metabolism and cardiovascular risk, with light alcohol use generally being protective while chronic heavy use has detrimental health outcomes.
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Affiliation(s)
- Falk W. Lohoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD,Corresponding Author: Falk W. Lohoff, M.D., Chief, Section on Clinical Genomics and Experimental Therapeutics (CGET), Lasker Clinical Research Scholar, National Institute on Alcohol Abuse and Alcoholism (NIAAA), National Institutes of Health, 10 Center Drive (10CRC/2-2352), Bethesda, MD 20892-1540, Office: 301-827-1542,
| | - Jill L. Sorcher
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Allison D. Rosen
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Kelsey L. Mauro
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Rebecca R. Fanelli
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Reza Momenan
- Section on Brain and Electrophysiology and Imaging, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Colin A. Hodgkinson
- Laboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Leandro F. Vendruscolo
- Neurobiology of Addiction Section, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD
| | - George F. Koob
- Neurobiology of Addiction Section, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD
| | - Melanie Schwandt
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - David T. George
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Ilenna S. Jones
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Andrew Holmes
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Zhou Zhou
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Ming-Jiang Xu
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Hui Sun
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Monte J. Phillips
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Christine Muench
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD
| | - Zachary A. Kaminsky
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD,Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
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27
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Mahna D, Puri S, Sharma S. DNA methylation signatures: Biomarkers of drug and alcohol abuse. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 777:19-28. [DOI: 10.1016/j.mrrev.2018.06.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/22/2018] [Accepted: 06/18/2018] [Indexed: 01/08/2023]
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28
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Ramoz N, Gorwood P. Aspects génétiques de l’alcoolo-dépendance. Presse Med 2018; 47:547-553. [DOI: 10.1016/j.lpm.2017.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 07/12/2017] [Indexed: 12/31/2022] Open
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Liu C, Jiao C, Wang K, Yuan N. DNA Methylation and Psychiatric Disorders. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:175-232. [PMID: 29933950 DOI: 10.1016/bs.pmbts.2018.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA methylation has been an important area of research in the study of molecular mechanism to psychiatric disorders. Recent evidence has suggested that abnormalities in global methylation, methylation of genes, and pathways could play a role in the etiology of many forms of mental illness. In this article, we review the mechanisms of DNA methylation, including the genetic and environmental factors affecting methylation changes. We report and discuss major findings regarding DNA methylation in psychiatric patients, both within the context of global methylation studies and gene-specific methylation studies. Finally, we discuss issues surrounding data quality improvement, the limitations of current methylation analysis methods, and the possibility of using DNA methylation-based treatment for psychiatric disorders in the future.
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Affiliation(s)
- Chunyu Liu
- University of Illinois, Chicago, IL, United States; School of Life Science, Central South University, Changsha, China.
| | - Chuan Jiao
- School of Life Science, Central South University, Changsha, China
| | - Kangli Wang
- School of Life Science, Central South University, Changsha, China
| | - Ning Yuan
- Hunan Brain Hospital, Changsha, China
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30
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A DNA methylation biomarker of alcohol consumption. Mol Psychiatry 2018; 23:422-433. [PMID: 27843151 PMCID: PMC5575985 DOI: 10.1038/mp.2016.192] [Citation(s) in RCA: 228] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 09/05/2016] [Accepted: 09/14/2016] [Indexed: 12/11/2022]
Abstract
The lack of reliable measures of alcohol intake is a major obstacle to the diagnosis and treatment of alcohol-related diseases. Epigenetic modifications such as DNA methylation may provide novel biomarkers of alcohol use. To examine this possibility, we performed an epigenome-wide association study of methylation of cytosine-phosphate-guanine dinucleotide (CpG) sites in relation to alcohol intake in 13 population-based cohorts (ntotal=13 317; 54% women; mean age across cohorts 42-76 years) using whole blood (9643 European and 2423 African ancestries) or monocyte-derived DNA (588 European, 263 African and 400 Hispanic ancestry) samples. We performed meta-analysis and variable selection in whole-blood samples of people of European ancestry (n=6926) and identified 144 CpGs that provided substantial discrimination (area under the curve=0.90-0.99) for current heavy alcohol intake (⩾42 g per day in men and ⩾28 g per day in women) in four replication cohorts. The ancestry-stratified meta-analysis in whole blood identified 328 (9643 European ancestry samples) and 165 (2423 African ancestry samples) alcohol-related CpGs at Bonferroni-adjusted P<1 × 10-7. Analysis of the monocyte-derived DNA (n=1251) identified 62 alcohol-related CpGs at P<1 × 10-7. In whole-blood samples of people of European ancestry, we detected differential methylation in two neurotransmitter receptor genes, the γ-Aminobutyric acid-A receptor delta and γ-aminobutyric acid B receptor subunit 1; their differential methylation was associated with expression levels of a number of genes involved in immune function. In conclusion, we have identified a robust alcohol-related DNA methylation signature and shown the potential utility of DNA methylation as a clinically useful diagnostic test to detect current heavy alcohol consumption.
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31
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Savarese AM, Lasek AW. Transcriptional Regulators as Targets for Alcohol Pharmacotherapies. Handb Exp Pharmacol 2018; 248:505-533. [PMID: 29594350 PMCID: PMC6242703 DOI: 10.1007/164_2018_101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Alcohol use disorder (AUD) is a chronic relapsing brain disease that currently afflicts over 15 million adults in the United States. Despite its prevalence, there are only three FDA-approved medications for AUD treatment, all of which show limited efficacy. Because of their ability to alter expression of a large number of genes, often with great cell-type and brain-region specificity, transcription factors and epigenetic modifiers serve as promising new targets for the development of AUD treatments aimed at the neural circuitry that underlies chronic alcohol abuse. In this chapter, we will discuss transcriptional regulators that can be targeted pharmacologically and have shown some efficacy in attenuating alcohol consumption when targeted. Specifically, the transcription factors cyclic AMP-responsive element binding protein (CREB), peroxisome proliferator-activated receptors (PPARs), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), and glucocorticoid receptor (GR), as well as the epigenetic enzymes, the DNA methyltransferases (DNMTs) and histone deacetylases (HDACs), will be discussed.
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Affiliation(s)
| | - Amy W. Lasek
- Department of Psychiatry, University of Illinois at Chicago,Corresponding author: 1601 West Taylor Street, MC 912, Chicago, IL 60612, Tel: (312) 355-1593,
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Chen J, Hutchison KE, Bryan AD, Filbey FM, Calhoun VD, Claus ED, Lin D, Sui J, Du Y, Liu J. Opposite Epigenetic Associations With Alcohol Use and Exercise Intervention. Front Psychiatry 2018; 9:594. [PMID: 30498460 PMCID: PMC6249510 DOI: 10.3389/fpsyt.2018.00594] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 10/26/2018] [Indexed: 12/31/2022] Open
Abstract
Alcohol use disorder (AUD) is a devastating public health problem in which both genetic and environmental factors play a role. Growing evidence supports that epigenetic regulation is one major mechanism in neuroadaptation that contributes to development of AUD. Meanwhile, epigenetic patterns can be modified by various stimuli including exercise. Thus, it is an intriguing question whether exercise can lead to methylation changes that are opposite to those related to drinking. We herein conducted a comparative study to explore this issue. Three cohorts were profiled for DNA methylation (DNAm), including a longitudinal exercise intervention cohort (53 healthy participants profiled at baseline and after a 12-months exercise intervention), a cross-sectional case-control cohort (81 hazardous drinkers and 81 healthy controls matched in age and sex), and a cross-sectional binge drinking cohort (281 drinkers). We identified 906 methylation sites showing significant DNAm differences between drinkers and controls in the case-control cohort, as well as, associations with drinking behavior in the drinking cohort. In parallel, 341 sites were identified for significant DNAm alterations between baseline and follow-up in the exercise cohort. Thirty-two sites overlapped between these two set of findings, of which 15 sites showed opposite directions of DNAm associations between exercise and drinking. Annotated genes of these 15 sites were enriched in signaling pathways related to synaptic plasticity. In addition, the identified methylation sites significantly associated with impaired control over drinking, suggesting relevance to neural function. Collectively, the current findings provide preliminary evidence that exercise has the potential to partially reverse DNAm differences associated with drinking at some CpG sites, motivating rigorously designed longitudinal studies to better characterize epigenetic effects with respect to prevention and intervention of AUD.
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Affiliation(s)
- Jiayu Chen
- The Mind Research Network, Albuquerque, NM, United States
| | - Kent E Hutchison
- The Mind Research Network, Albuquerque, NM, United States.,Department of Psychology and Neuroscience, University of Colorado at Boulder, Boulder, CO, United States
| | - Angela D Bryan
- Department of Psychology and Neuroscience, University of Colorado at Boulder, Boulder, CO, United States
| | - Francesca M Filbey
- Center for BrainHealth, School of Behavioral and Brain Sciences, University of Texas at Dallas, Dallas, TX, United States
| | - Vince D Calhoun
- The Mind Research Network, Albuquerque, NM, United States.,Department of Electrical Engineering, University of New Mexico, Albuquerque, NM, United States
| | - Eric D Claus
- The Mind Research Network, Albuquerque, NM, United States
| | - Dongdong Lin
- The Mind Research Network, Albuquerque, NM, United States
| | - Jing Sui
- The Mind Research Network, Albuquerque, NM, United States.,Brainnetome Center and National Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Yuhui Du
- The Mind Research Network, Albuquerque, NM, United States.,School of Computer & Information Technology, Shanxi University, Taiyuan, China
| | - Jingyu Liu
- The Mind Research Network, Albuquerque, NM, United States.,Department of Electrical Engineering, University of New Mexico, Albuquerque, NM, United States
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Abstract
Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Room Ee1051, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
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Prom-Wormley EC, Ebejer J, Dick DM, Bowers MS. The genetic epidemiology of substance use disorder: A review. Drug Alcohol Depend 2017; 180:241-259. [PMID: 28938182 PMCID: PMC5911369 DOI: 10.1016/j.drugalcdep.2017.06.040] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND Substance use disorder (SUD) remains a significant public health issue. A greater understanding of how genes and environment interact to regulate phenotypes comprising SUD will facilitate directed treatments and prevention. METHODS The literature studying the neurobiological correlates of SUD with a focus on the genetic and environmental influences underlying these mechanisms was reviewed. Results from twin/family, human genetic association, gene-environment interaction, epigenetic literature, phenome-wide association studies are summarized for alcohol, nicotine, cannabinoids, cocaine, and opioids. RESULTS There are substantial genetic influences on SUD that are expected to influence multiple neurotransmission pathways, and these influences are particularly important within the dopaminergic system. Genetic influences involved in other aspects of SUD etiology including drug processing and metabolism are also identified. Studies of gene-environment interaction emphasize the importance of environmental context in SUD. Epigenetic studies indicate drug-specific changes in gene expression as well as differences in gene expression related to the use of multiple substances. Further, gene expression is expected to differ by stage of SUD such as substance initiation versus chronic substance use. While a substantial literature has developed for alcohol and nicotine use disorders, there is comparatively less information for other commonly abused substances. CONCLUSIONS A better understanding of genetically-mediated mechanisms involved in the neurobiology of SUD provides increased opportunity to develop behavioral and biologically based treatment and prevention of SUD.
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Affiliation(s)
- Elizabeth C Prom-Wormley
- Dvision of Epidemiology, Department of Family Medicine and Population Health, Virginia Commonwealth University, PO Box 980212, Richmond, VA 23298-0212, USA.
| | - Jane Ebejer
- School of Cognitive Behavioural and Social Sciences, University of New England, Armidale, NSW 2350, Australia
| | - Danielle M Dick
- Department of Psychology, Virginia Commonwealth University, PO Box 842509, Richmond, VA 23284-2509, USA
| | - M Scott Bowers
- Faulk Center for Molecular Therapeutics, Biomedical Engeneering, Northwestern University, Evanston, IL 60201, USA
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35
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Brückmann C, Islam SA, MacIsaac JL, Morin AM, Karle KN, Di Santo A, Wüst R, Lang I, Batra A, Kobor MS, Nieratschker V. DNA methylation signatures of chronic alcohol dependence in purified CD3 + T-cells of patients undergoing alcohol treatment. Sci Rep 2017; 7:6605. [PMID: 28747766 PMCID: PMC5529570 DOI: 10.1038/s41598-017-06847-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/19/2017] [Indexed: 02/07/2023] Open
Abstract
Several studies have shown an association of alcohol dependence with DNA methylation (DNAm), suggesting that environmentally-induced changes on epigenomic variation may play an important role in alcohol dependence. In the present study, we analysed genome-wide DNAm profiles of purified CD3+ T-cells from pre- and post-treatment alcohol dependent patients, as well as closely matched healthy controls. We identified 59 differentially methylated CpG sites comparing patients prior to treatment with healthy controls and were able to confirm 8 of those sites in additional analyses for differentially methylated regions. Comparing patients before and after a 3-week alcohol treatment program we revealed another unique set of 48 differentially methylated CpG sites. Additionally, we found that the mean global DNAm was significantly lower in patients prior to treatment compared to controls, but reverted back to levels similar to controls after treatment. We validated top-ranked hits derived from the epigenome-wide analysis by pyrosequencing and further replicated two of them in an independent cohort and confirmed differential DNAm of HECW2 and SRPK3 in whole blood. This study is the first to show widespread DNAm variation in a disease-relevant blood cell type and implicates HECW2 and SRPK3 DNAm as promising blood-based candidates to follow up in future studies.
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Affiliation(s)
- Christof Brückmann
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Tuebingen, Germany
| | - Sumaiya A Islam
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
| | - Alexander M Morin
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
| | - Kathrin N Karle
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Tuebingen, Germany
| | - Adriana Di Santo
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Tuebingen, Germany
| | - Richard Wüst
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Tuebingen, Germany.,Department of Neurodegenerative Disease, Hertie-Institute for Clinical Brain Research, Tuebingen, Germany
| | - Immanuel Lang
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Tuebingen, Germany
| | - Anil Batra
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Tuebingen, Germany
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada.,Human Early Learning Partnership, University of British Columbia, Vancouver, British Columbia, Canada.,Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Vanessa Nieratschker
- Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen, Tuebingen, Germany.
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36
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Do C, Shearer A, Suzuki M, Terry MB, Gelernter J, Greally JM, Tycko B. Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era. Genome Biol 2017. [PMID: 28629478 PMCID: PMC5477265 DOI: 10.1186/s13059-017-1250-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Studies on genetic-epigenetic interactions, including the mapping of methylation quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation (hap-ASM), have become a major focus in the post-genome-wide-association-study (GWAS) era. Such maps can nominate regulatory sequence variants that underlie GWAS signals for common diseases, ranging from neuropsychiatric disorders to cancers. Conversely, mQTLs need to be filtered out when searching for non-genetic effects in epigenome-wide association studies (EWAS). Sequence variants in CCCTC-binding factor (CTCF) and transcription factor binding sites have been mechanistically linked to mQTLs and hap-ASM. Identifying these sites can point to disease-associated transcriptional pathways, with implications for targeted treatment and prevention.
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Affiliation(s)
- Catherine Do
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Alyssa Shearer
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Masako Suzuki
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mary Beth Terry
- Department of Epidemiology, Columbia University Mailman School of Public Health, and Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, 10032, USA
| | - Joel Gelernter
- Departments of Psychiatry, Genetics, and Neurobiology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - John M Greally
- Center for Epigenomics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Benjamin Tycko
- Institute for Cancer Genetics, Herbert Irving Comprehensive Cancer Center, Taub Institute for Research on Alzheimer's disease and the Aging Brain, New York, NY, 10032, USA. .,Department of Pathology and Cell Biology, Columbia University, New York, NY, 10032, USA.
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37
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Abstract
酒精性肝病(alcoholic liver disease, ALD)是一种慢性肝脏疾病, 包括肝脂肪变性、酒精性脂肪性肝炎、肝硬化、肝细胞癌和肝衰竭. 许多因素被认为能促进ALD的发展, 特别是氧化应激, 在酒精代谢期间活性氧物质的产生, 来自内脏脂肪组织的脂肪因子和来自肠道的内毒素等. 目前, ALD的发病机制已被广泛研究, 精确的机制尚待阐明. 在我国随着人类生活水平提高和生活方式的改变, 人群中的嗜酒者的比率逐年上升, 乙醇也已成为导致肝脏损害的第二大原因. 因此, ALD相关治疗也受到人们的广泛关注. 在本文中, 我们就ALD的发病机制、治疗等方面的最新研究进展作一综述.
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Tulisiak CT, Harris RA, Ponomarev I. DNA modifications in models of alcohol use disorders. Alcohol 2017; 60:19-30. [PMID: 27865607 DOI: 10.1016/j.alcohol.2016.11.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/03/2016] [Accepted: 11/05/2016] [Indexed: 02/07/2023]
Abstract
Chronic alcohol use and abuse result in widespread changes to gene expression, some of which contribute to the development of alcohol-use disorders (AUD). Gene expression is controlled, in part, by a group of regulatory systems often referred to as epigenetic factors, which includes, among other mechanisms, chemical marks made on the histone proteins around which genomic DNA is wound to form chromatin, and on nucleotides of the DNA itself. In particular, alcohol has been shown to perturb the epigenetic machinery, leading to changes in gene expression and cellular functions characteristic of AUD and, ultimately, to altered behavior. DNA modifications in particular are seeing increasing research in the context of alcohol use and abuse. To date, studies of DNA modifications in AUD have primarily looked at global methylation profiles in human brain and blood, gene-specific methylation profiles in animal models, methylation changes associated with prenatal ethanol exposure, and the potential therapeutic abilities of DNA methyltransferase inhibitors. Future studies may be aimed at identifying changes to more recently discovered DNA modifications, utilizing new methods to discriminate methylation profiles between cell types, thus clarifying how alcohol influences the methylomes of cell-type populations and how this may affect downstream processes. These studies and more in-depth probing of DNA methylation will be key to determining whether DNA-level epigenetic regulation plays a causative role in AUD and can thus be targeted for treatment of the disorder.
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Affiliation(s)
- Christopher T Tulisiak
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA; The College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, A1900, Austin, TX 78712, USA
| | - Igor Ponomarev
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA; The College of Pharmacy, The University of Texas at Austin, 2409 University Avenue, A1900, Austin, TX 78712, USA.
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Pathak H, Frieling H, Bleich S, Glahn A, Heberlein A, Haschemi Nassab M, Hillemacher T, Burkert A, Rhein M. Promoter Polymorphism rs886205 Genotype Interacts With DNA Methylation of the ALDH2 Regulatory Region in Alcohol Dependence. Alcohol Alcohol 2017; 52:269-276. [PMID: 28430929 DOI: 10.1093/alcalc/agw106] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/30/2016] [Indexed: 12/28/2022] Open
Abstract
AIMS Aldehyde dehydrogenase 2 (ALDH2) protects cells from ethanol toxicity by metabolizing acetaldehyde. We studied the single nucleotide polymorphism (SNP) rs886205s located between a negative and a positive regulating promoter element in the ALDH2 gene. The negative regulatory region was already associated with differential DNA methylation in the two allele variations of rs886205 SNP. Another CpG island, in the positive regulatory region of the ALDH2 promoter, extends through the SNP rs886205 and a nuclear receptor response element. METHODS We assessed rs886305 genotype and DNA methylation using bisulfite sequencing in a cohort of 83 male alcohol-dependent patients undergoing detoxification treatment (Days 1, 7 and 14) and in 33 male age-matched controls. Luciferase reporter assays were performed to address the functional significance of genotype and methylation. RESULTS We observed a higher methylation in alcohol-dependent patients compared to controls. Patients with AA (n = 52) or GG/GA (n = 31) genotype differed significantly in baseline methylation levels as well as in methylation kinetics during withdrawal. AA carriers display an increase in methylation from low baseline levels while GG/GA showed the inverse pattern. The reporter gene assays corroborate these data by showing a significant effect of genotype on ALDH2 expression as well as an interaction between genotype and methylation. CONCLUSION Our results describe a new regulatory role of rs886205 in the methylation of ALDH2 promoter region and provide additional insight into the complex regulation of ALDH2 under the condition of alcohol dependence. SHORT SUMMARY Genetic variations have been described to influence DNA promoter methylation of various genes. We investigated the association between the polymorphism rs886205, located on ALDH2 promoter and methylation kinetics of the neighboring CpG island in alcohol-dependent patients. Luciferase reporter assays showed functional significance of genotype, methylation and a genotype-epigenotype interaction in vitro.
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Affiliation(s)
- Hansi Pathak
- Laboratory for Molecular Neuroscience, Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
- Center for Addiction Research (CARe), Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Helge Frieling
- Laboratory for Molecular Neuroscience, Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
- Center for Addiction Research (CARe), Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Stefan Bleich
- Laboratory for Molecular Neuroscience, Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
- Center for Addiction Research (CARe), Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Alexander Glahn
- Center for Addiction Research (CARe), Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Annemarie Heberlein
- Center for Addiction Research (CARe), Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Mani Haschemi Nassab
- Laboratory for Molecular Neuroscience, Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
- Center for Addiction Research (CARe), Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Thomas Hillemacher
- Center for Addiction Research (CARe), Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Alexandra Burkert
- Laboratory for Molecular Neuroscience, Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
| | - Mathias Rhein
- Laboratory for Molecular Neuroscience, Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
- Center for Addiction Research (CARe), Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School (MHH), 30625 Hannover, Germany
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40
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Vrettou M, Granholm L, Todkar A, Nilsson KW, Wallén-Mackenzie Å, Nylander I, Comasco E. Ethanol affects limbic and striatal presynaptic glutamatergic and DNA methylation gene expression in outbred rats exposed to early-life stress. Addict Biol 2017; 22:369-380. [PMID: 26610727 DOI: 10.1111/adb.12331] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 09/10/2015] [Accepted: 10/20/2015] [Indexed: 12/12/2022]
Abstract
Alcohol use disorder is the outcome of both genetic and environmental influences and their interaction via epigenetic mechanisms. The neurotransmitter glutamate is an important regulator of reward circuits and implicated in adaptive changes induced by ethanol intake. The present study aimed at investigating corticolimbic and corticostriatal genetic signatures focusing on the glutamatergic phenotype in relation to early-life stress (ELS) and consequent adult ethanol consumption. A rodent maternal separation model was employed to mimic ELS, and a free-choice paradigm was used to assess ethanol intake in adulthood. Gene expression levels of the Vesicular Glutamate Transporters (Vglut) 1, 2 and 3, as well as two key regulators of DNA methylation, DNA (cytosine-5)-methyltransferase 1 (Dnmt1) and methyl-CpG-binding protein 2 (Mecp2), were analyzed. Brain regions of interest were the ventral tegmental area (VTA), nucleus accumbens (Acb), medial prefrontal cortex (mPFC) and dorsal striatum (dStr), all involved in mediating aspects of ethanol reward. Region-specific Vglut, Dnmt1 and Mecp2 expression patterns were observed. ELS was associated with down-regulated expression of Vglut2 in the VTA and mPFC. Rats exposed to ELS were more sensitive to ethanol-induced changes in Vglut expression in the VTA, Acb, and dStr and in Dnmt1 and Mecp2 expression in the striatal regions. These findings suggest long-term glutamatergic and DNA methylation neuroadaptations as a consequence of ELS, and show an association between voluntary drinking in non-preferring, non-dependent, rodents and different Vglut, Dnmt1 and Mecp2 expression depending on early-life history.
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Affiliation(s)
- Maria Vrettou
- Department of Neuroscience; Uppsala University; Uppsala Sweden
| | - Linnea Granholm
- Department of Pharmaceutical Biosciences; Uppsala University; Uppsala Sweden
| | | | - Kent W. Nilsson
- Västerås Centre for Clinical Research; Uppsala University; Västerås Sweden
| | - Åsa Wallén-Mackenzie
- Department of Organismal Biology/Comparative Physiology; Uppsala University; Uppsala Sweden
| | - Ingrid Nylander
- Department of Pharmaceutical Biosciences; Uppsala University; Uppsala Sweden
| | - Erika Comasco
- Department of Neuroscience; Uppsala University; Uppsala Sweden
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41
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Drug Addiction and DNA Modifications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 978:105-125. [DOI: 10.1007/978-3-319-53889-1_6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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42
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Sugimoto K, Takei Y. Pathogenesis of alcoholic liver disease. Hepatol Res 2017; 47:70-79. [PMID: 27138729 DOI: 10.1111/hepr.12736] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 04/26/2016] [Accepted: 04/29/2016] [Indexed: 02/06/2023]
Abstract
Alcoholic liver disease (ALD) has become one of the most critical health problems in many countries, including Japan. Liver injury in ALD ranges from steatosis and steatohepatitis to fibrosis, cirrhosis, and hepatocellular carcinoma. Many factors are thought to contribute to the development and progression of ALD, particularly insulin resistance, generation of reactive oxygen species during alcohol metabolism, adipokines from visceral adipose tissue, and endotoxin derived from the gut. Although the pathogenesis of ALD has been widely investigated, the precise mechanisms are yet to be elucidated and many questions remain. This article reviews the possible mechanisms for the development of ALD identified to date.
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Affiliation(s)
- Kazushi Sugimoto
- Department of Gastroenterology and Hepatology, Mie University School of Medicine, Tsu, Mie, Japan
| | - Yoshiyuki Takei
- Department of Gastroenterology and Hepatology, Mie University School of Medicine, Tsu, Mie, Japan
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43
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Zhang H, Gelernter J. Review: DNA methylation and alcohol use disorders: Progress and challenges. Am J Addict 2016; 26:502-515. [PMID: 27759945 DOI: 10.1111/ajad.12465] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 09/17/2016] [Accepted: 10/02/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND AND OBJECTIVES Risk for alcohol use disorders (AUDs) is influenced by gene-environment interactions. Environmental factors can affect gene expression through epigenetic mechanisms such as DNA methylation. This review outlines the findings regarding the association of DNA methylation and AUDs. METHODS We searched PubMed (by April 2016) and identified 29 studies that examined the association of DNA methylation and AUDs. We also evaluated the methods used in these studies. RESULTS Two studies demonstrated elevated global (repetitive element) DNA methylation levels in AUD subjects. Fifteen candidate gene studies showed hypermethylation of promoter regions of six genes (AVP, DNMT3B, HERP, HTR3A, OPRM1, and SNCA) or hypomethylation of the GDAP1 promoter region in AUD subjects. Five genome-wide DNA methylation studies demonstrated widespread DNA methylation changes across the genome in AUD subjects. Six studies showed significant correlations of DNA methylation with gene expression in AUD subjects. Three studies revealed interactive effects of genetic variation and DNA methylation on susceptibility to AUDs. Most studies analyzed AUD-associated DNA methylation changes in the peripheral blood; a few studies examined DNA methylation changes in postmortem brains of AUD subjects. DISCUSSION AND CONCLUSIONS Chronic alcohol consumption may result in DNA methylation changes, leading to neuroadaptations that may underlie some of the mechanisms of AUD risk and persistence. Future studies are needed to confirm the few existing results, and then to elucidate whether DNA methylation changes are the cause or consequence of AUDs. SCIENTIFIC SIGNIFICANCE DNA methylation profiles may be used to assess AUD status or monitor AUD treatment response. (Am J Addict 2017;26:502-515).
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Affiliation(s)
- Huiping Zhang
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.,VA Connecticut Healthcare System, West Haven, Connecticut
| | - Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut.,VA Connecticut Healthcare System, West Haven, Connecticut.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut.,Department of Neurobiology, Yale University School of Medicine, New Haven, Connecticut
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44
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Jangra A, Sriram CS, Pandey S, Choubey P, Rajput P, Saroha B, Bezbaruah BK, Lahkar M. Epigenetic Modifications, Alcoholic Brain and Potential Drug Targets. Ann Neurosci 2016; 23:246-260. [PMID: 27780992 PMCID: PMC5075742 DOI: 10.1159/000449486] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/25/2016] [Indexed: 12/19/2022] Open
Abstract
Acute and chronic alcohol exposure evidently influences epigenetic changes, both transiently and permanently, and these changes in turn influence a variety of cells and organ systems throughout the body. Many of the alcohol-induced epigenetic modifications can contribute to cellular adaptations that ultimately lead to behavioral tolerance and alcohol dependence. The persistence of behavioral changes demonstrates that long-lasting changes in gene expression, within particular regions of the brain, may contribute importantly to the addiction phenotype. The research activities over the past years have demonstrated a crucial role of epigenetic mechanisms in causing long lasting and transient changes in the expression of several genes in diverse tissues, including brain. This has stimulated recent research work that is aimed at characterizing the influence of epigenetic regulatory events in mediating the long lasting and transient effects of alcohol abuse on the brain in humans and animal models of alcohol addiction. In this study, we update our current understanding of the impact of alcohol exposure on epigenetic mechanisms in the brain and refurbish the knowledge of epigenetics in the direction of new drugs development.
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Affiliation(s)
- Ashok Jangra
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, India
| | - Chandra Shaker Sriram
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, India
| | - Suryanarayan Pandey
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, India
| | - Priyansha Choubey
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, India
| | - Prabha Rajput
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, India
| | - Babita Saroha
- Department of Biotechnology, University Institute of Engineering and Technology (UIET), Maharshi Dayanand University, Rohtak, India
| | - Babul Kumar Bezbaruah
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, India
- Department of Pharmacology, Gauhati Medical College, Narkachal Hilltop, Bhangagarh, Guwahati, India
| | - Mangala Lahkar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Guwahati, India
- Department of Pharmacology, Gauhati Medical College, Narkachal Hilltop, Bhangagarh, Guwahati, India
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45
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Kim YY, Roubal I, Lee YS, Kim JS, Hoang M, Mathiyakom N, Kim Y. Alcohol-Induced Molecular Dysregulation in Human Embryonic Stem Cell-Derived Neural Precursor Cells. PLoS One 2016; 11:e0163812. [PMID: 27682028 PMCID: PMC5040434 DOI: 10.1371/journal.pone.0163812] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/14/2016] [Indexed: 01/08/2023] Open
Abstract
Adverse effect of alcohol on neural function has been well documented. Especially, the teratogenic effect of alcohol on neurodevelopment during embryogenesis has been demonstrated in various models, which could be a pathologic basis for fetal alcohol spectrum disorders (FASDs). While the developmental defects from alcohol abuse during gestation have been described, the specific mechanisms by which alcohol mediates these injuries have yet to be determined. Recent studies have shown that alcohol has significant effect on molecular and cellular regulatory mechanisms in embryonic stem cell (ESC) differentiation including genes involved in neural development. To test our hypothesis that alcohol induces molecular alterations during neural differentiation we have derived neural precursor cells from pluripotent human ESCs in the presence or absence of ethanol treatment. Genome-wide transcriptomic profiling identified molecular alterations induced by ethanol exposure during neural differentiation of hESCs into neural rosettes and neural precursor cell populations. The Database for Annotation, Visualization and Integrated Discovery (DAVID) functional analysis on significantly altered genes showed potential ethanol’s effect on JAK-STAT signaling pathway, neuroactive ligand-receptor interaction, Toll-like receptor (TLR) signaling pathway, cytokine-cytokine receptor interaction and regulation of autophagy. We have further quantitatively verified ethanol-induced alterations of selected candidate genes. Among verified genes we further examined the expression of P2RX3, which is associated with nociception, a peripheral pain response. We found ethanol significantly reduced the level of P2RX3 in undifferentiated hESCs, but induced the level of P2RX3 mRNA and protein in hESC-derived NPCs. Our result suggests ethanol-induced dysregulation of P2RX3 along with alterations in molecules involved in neural activity such as neuroactive ligand-receptor interaction may be a molecular event associated with alcohol-related peripheral neuropathy of an enhanced nociceptive response.
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Affiliation(s)
- Yi Young Kim
- Laboratory of Stem Cell & Cancer Epigenetic Research, School of Dentistry, University of California Los Angeles, 10833 Le Conte Avenue, 73–041 CHS, Los Angeles, CA, 90095, United States of America
| | - Ivan Roubal
- Laboratory of Stem Cell & Cancer Epigenetic Research, School of Dentistry, University of California Los Angeles, 10833 Le Conte Avenue, 73–041 CHS, Los Angeles, CA, 90095, United States of America
| | - Youn Soo Lee
- Laboratory of Stem Cell & Cancer Epigenetic Research, School of Dentistry, University of California Los Angeles, 10833 Le Conte Avenue, 73–041 CHS, Los Angeles, CA, 90095, United States of America
| | - Jin Seok Kim
- Laboratory of Stem Cell & Cancer Epigenetic Research, School of Dentistry, University of California Los Angeles, 10833 Le Conte Avenue, 73–041 CHS, Los Angeles, CA, 90095, United States of America
| | - Michael Hoang
- Laboratory of Stem Cell & Cancer Epigenetic Research, School of Dentistry, University of California Los Angeles, 10833 Le Conte Avenue, 73–041 CHS, Los Angeles, CA, 90095, United States of America
| | - Nathan Mathiyakom
- Laboratory of Stem Cell & Cancer Epigenetic Research, School of Dentistry, University of California Los Angeles, 10833 Le Conte Avenue, 73–041 CHS, Los Angeles, CA, 90095, United States of America
| | - Yong Kim
- Laboratory of Stem Cell & Cancer Epigenetic Research, School of Dentistry, University of California Los Angeles, 10833 Le Conte Avenue, 73–041 CHS, Los Angeles, CA, 90095, United States of America
- Center for Oral and Head/Neck Oncology Research Center, Division of Oral Biology & Medicine, UCLA School of Dentistry, 10833 Le Conte Avenue, 73–022 CHS, Los Angeles, CA, 90095, United States of America
- UCLA’s Jonsson Comprehensive Cancer Center, 8–684 Factor Building, Box 951781, Los Angeles, CA, 90095, United States of America
- UCLA Broad Stem Cell Research Center, Box 957357, Los Angeles, CA, 90095, United States of America
- * E-mail:
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Abstract
The main characteristic of alcohol use disorder is the consumption of large quantities of alcohol despite the negative consequences. The transition from the moderate use of alcohol to excessive, uncontrolled alcohol consumption results from neuroadaptations that cause aberrant motivational learning and memory processes. Here, we examine studies that have combined molecular and behavioural approaches in rodents to elucidate the molecular mechanisms that keep the social intake of alcohol in check, which we term 'stop pathways', and the neuroadaptations that underlie the transition from moderate to uncontrolled, excessive alcohol intake, which we term 'go pathways'. We also discuss post-transcriptional, genetic and epigenetic alterations that underlie both types of pathways.
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Affiliation(s)
- Dorit Ron
- Corresponding author: Dorit Ron, 675 Nelson Rising Lane, BOX 0663, San Francisco, CA 94143-0663,
| | - Segev Barak
- Department of Neurology, University of California, San Francisco, San Francisco, CA 94143, USA
- School of Psychological Sciences and Sagol School of Neuroscience, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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47
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Hagerty SL, Bidwell LC, Harlaar N, Hutchison KE. An Exploratory Association Study of Alcohol Use Disorder and DNA Methylation. Alcohol Clin Exp Res 2016; 40:1633-40. [PMID: 27388583 DOI: 10.1111/acer.13138] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/20/2016] [Indexed: 11/30/2022]
Abstract
BACKGROUND Epigenetic factors, including DNA methylation, play an important role in the etiology of alcohol use disorders (AUDs). Noncandidate-based methylome-wide studies leveraging multiple tissue types are needed in order to identify a set of CpG targets that reliably differentiate AUD patients from controls and strongly correlate across brain tissue and more commonly collected tissue types (e.g., buccal cells). METHODS Postmortem precuneus brain tissue samples were collected from 49 alcohol-dependent (AD) cases and 47 controls (sample I), and DNA was extracted from precuneus and putamen brain tissue and buccal cells in 24 postmortem subjects (sample II). Methylation levels were analyzed at over 450,000 CpG sites in both samples. CpGs that demonstrated significant methylation differences between cases and controls were advanced for further analysis with the goal of identifying CpGs that also demonstrated consistent methylation correlations across tissue type. RESULTS In the primary analysis, 244 hypomethylated and 188 hypermethylated CpGs met a priori criteria for both significant methylation differences between cases and controls as well as significant correlation across brain and buccal cell tissue types, employing stringent Bonferroni p-value correction. Many of these CpGs were involved in gene networks related to lipid metabolism, immune response, inflammatory response/disease, and gastro-intestinal disease. CONCLUSIONS More than 400 CpGs demonstrated differences in methylation between AD cases and controls and showed significant correlation across tissue types. Several genes and pathways (e.g., inflammation and immune functioning) that have been previously associated with AUD were identified in the current analyses.
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Affiliation(s)
- Sarah L Hagerty
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
| | - L Cinnamon Bidwell
- Institute of Cognitive Science, University of Colorado Boulder, Boulder, Colorado
| | - Nicole Harlaar
- The Kempe Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kent E Hutchison
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
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48
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Portales-Casamar E, Lussier AA, Jones MJ, MacIsaac JL, Edgar RD, Mah SM, Barhdadi A, Provost S, Lemieux-Perreault LP, Cynader MS, Chudley AE, Dubé MP, Reynolds JN, Pavlidis P, Kobor MS. DNA methylation signature of human fetal alcohol spectrum disorder. Epigenetics Chromatin 2016; 9:25. [PMID: 27358653 PMCID: PMC4926300 DOI: 10.1186/s13072-016-0074-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/17/2016] [Indexed: 02/06/2023] Open
Abstract
Background Prenatal alcohol exposure is the leading preventable cause of behavioral and cognitive deficits, which may affect between 2 and 5 % of children in North America. While the underlying mechanisms of alcohol’s effects on development remain relatively unknown, emerging evidence implicates epigenetic mechanisms in mediating the range of symptoms observed in children with fetal alcohol spectrum disorder (FASD). Thus, we investigated the effects of prenatal alcohol exposure on genome-wide DNA methylation in the NeuroDevNet FASD cohort, the largest cohort of human FASD samples to date. Methods Genome-wide DNA methylation patterns of buccal epithelial cells (BECs) were analyzed using the Illumina HumanMethylation450 array in a Canadian cohort of 206 children (110 FASD and 96 controls). Genotyping was performed in parallel using the Infinium HumanOmni2.5-Quad v1.0 BeadChip. Results After correcting for the effects of genetic background, we found 658 significantly differentially methylated sites between FASD cases and controls, with 41 displaying differences in percent methylation change >5 %. Furthermore, 101 differentially methylated regions containing two or more CpGs were also identified, overlapping with 95 different genes. The majority of differentially methylated genes were highly expressed at the level of mRNA in brain samples from the Allen Brain Atlas, and independent DNA methylation data from cortical brain samples showed high correlations with BEC DNA methylation patterns. Finally, overrepresentation analysis of genes with up-methylated CpGs revealed a significant enrichment for neurodevelopmental processes and diseases, such as anxiety, epilepsy, and autism spectrum disorders. Conclusions These findings suggested that prenatal alcohol exposure is associated with distinct DNA methylation patterns in children and adolescents, raising the possibility of an epigenetic biomarker of FASD. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0074-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Alexandre A Lussier
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Meaghan J Jones
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Rachel D Edgar
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Sarah M Mah
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada
| | - Amina Barhdadi
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Université de Montréal, Montreal, QC Canada
| | - Sylvie Provost
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Université de Montréal, Montreal, QC Canada
| | | | - Max S Cynader
- Brain Research Centre, University of British Columbia, Vancouver, BC Canada
| | - Albert E Chudley
- Department of Pediatrics and Child Health, Faculty of Medicine, University of Manitoba, Winnipeg, MB Canada.,Department of Biochemistry and Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg, MB Canada
| | - Marie-Pierre Dubé
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute, Université de Montréal, Montreal, QC Canada.,Faculty of Medicine, Université de Montréal, Montreal, QC Canada
| | - James N Reynolds
- Centre for Neuroscience Studies, Queen's University, Kingston, ON Canada
| | - Paul Pavlidis
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC Canada
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, BC Canada.,Human Early Learning Partnership, School of Population and Public Health, University of British Columbia, Vancouver, British Columbia Canada
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Xu YH, Wang LL, Shi L, Lei JP, Miao Q, Liu TQ, Hao W, Lu L, Zhang RL. The association of HTR3A mRNA expression and craving in Han Chinese alcohol-dependent patients: a preliminary study. THE AMERICAN JOURNAL OF DRUG AND ALCOHOL ABUSE 2016; 42:316-24. [PMID: 27144979 DOI: 10.3109/00952990.2016.1160098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Ya-Hui Xu
- Department of Addiction, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan Province, China
| | - Lin-Lin Wang
- Department of Psychology, Ninth People Hospital of Zhengzhou, Zhengzhou, Henan Province, China
| | - Le Shi
- Peking University Sixth Hospital/Institute of Mental Health and Key Laboratory of Mental Health and National Institute on Drug Dependence, Peking University, Beijing, China
| | - Jin-Ping Lei
- People Hospital of Cangzhou, Cangzhou, Hebei Province, China
| | - Qin Miao
- Department of Addiction, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan Province, China
| | - Tie-Qiao Liu
- Mental Health Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Wei Hao
- Mental Health Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Lin Lu
- Peking University Sixth Hospital/Institute of Mental Health and Key Laboratory of Mental Health and National Institute on Drug Dependence, Peking University, Beijing, China
| | - Rui-Ling Zhang
- Department of Addiction, Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan Province, China
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Brückmann C, Di Santo A, Karle KN, Batra A, Nieratschker V. Validation of differential GDAP1 DNA methylation in alcohol dependence and its potential function as a biomarker for disease severity and therapy outcome. Epigenetics 2016; 11:456-63. [PMID: 27128683 DOI: 10.1080/15592294.2016.1179411] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Alcohol dependence is a severe disorder contributing substantially to the global burden of disease. Despite the detrimental consequences of chronic alcohol abuse and dependence, effective prevention strategies as well as treatment options are largely missing to date. Accumulating evidence suggests that gene-environment interactions, including epigenetic mechanisms, play a role in the etiology of alcohol dependence. A recent epigenome-wide study reported widespread alterations of DNA methylation patterns in alcohol dependent patients compared to control individuals. In the present study, we validate and replicate one of the top findings from this previous investigation in an independent cohort: the hypomethylation of GDAP1 in patients. To our knowledge, this is the first independent replication of an epigenome-wide finding in alcohol dependence. Furthermore, the AUDIT as well as the GSI score were negatively associated with GDAP1 methylation and we found a trend toward a negative association between GDAP1 methylation and the years of alcohol dependency, pointing toward a potential role of GDAP1 hypomethylation as biomarker for disease severity. In addition, we show that the hypomethylation of GDAP1 in patients reverses during a short-term alcohol treatment program, suggesting that GDAP1 DNA methylation could also serve as a potential biomarker for treatment outcome. Our data add to the growing body of knowledge on epigenetic effects in alcohol dependence and support GDAP1 as a novel candidate gene implicated in this disorder. As the role of GDAP1 in alcohol dependence is unknown, this novel candidate gene should be followed up in future studies.
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Affiliation(s)
- Christof Brückmann
- a Department of Psychiatry and Psychotherapy , University Hospital of Tuebingen , Tuebingen , Germany
| | - Adriana Di Santo
- a Department of Psychiatry and Psychotherapy , University Hospital of Tuebingen , Tuebingen , Germany
| | - Kathrin Nora Karle
- a Department of Psychiatry and Psychotherapy , University Hospital of Tuebingen , Tuebingen , Germany
| | - Anil Batra
- b Section for Addiction Medicine and Addiction Research, Department of Psychiatry and Psychotherapy, University Hospital of Tuebingen , Tuebingen , Germany
| | - Vanessa Nieratschker
- a Department of Psychiatry and Psychotherapy , University Hospital of Tuebingen , Tuebingen , Germany
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