1
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White JD, Minto MS, Willis C, Quach BC, Han S, Tao R, Deep-Soboslay A, Zillich L, Witt SH, Spanagel R, Hansson AC, Clark SL, van den Oord EJ, Hyde TM, Mayfield RD, Webb BT, Johnson EO, Kleinman JE, Bierut LJ, Hancock DB. Alcohol Use Disorder-Associated DNA Methylation in the Nucleus Accumbens and Dorsolateral Prefrontal Cortex. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2024; 4:100375. [PMID: 39399155 PMCID: PMC11470413 DOI: 10.1016/j.bpsgos.2024.100375] [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: 04/11/2024] [Revised: 07/02/2024] [Accepted: 07/31/2024] [Indexed: 10/15/2024] Open
Abstract
Background Alcohol use disorder (AUD) has a profound public health impact. However, understanding of the molecular mechanisms that underlie the development and progression of AUD remains limited. Here, we investigated AUD-associated DNA methylation changes within and across 2 addiction-relevant brain regions, the nucleus accumbens and dorsolateral prefrontal cortex. Methods Illumina HumanMethylation EPIC array data from 119 decedents (61 cases, 58 controls) were analyzed using robust linear regression with adjustment for technical and biological variables. Associations were characterized using integrative analyses of public annotation data and published genetic and epigenetic studies. We also tested for brain region-shared and brain region-specific associations using mixed-effects modeling and assessed implications of these results using public gene expression data from human brain. Results At a false discovery rate of ≤.05, we identified 105 unique AUD-associated CpGs (annotated to 120 genes) within and across brain regions. AUD-associated CpGs were enriched in histone marks that tag active promoters, and our strongest signals were specific to a single brain region. Some concordance was found between our results and those of earlier published alcohol use or dependence methylation studies. Of the 120 genes, 23 overlapped with previous genetic associations for substance use behaviors, some of which also overlapped with previous addiction-related methylation studies. Conclusions Our findings identify AUD-associated methylation signals and provide evidence of overlap with previous genetic and methylation studies. These signals may constitute predisposing genetic differences or robust methylation changes associated with AUD, although more work is needed to further disentangle the mechanisms that underlie these associations and their implications for AUD.
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Affiliation(s)
- Julie D. White
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Melyssa S. Minto
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Caryn Willis
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Bryan C. Quach
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Shizhong Han
- Lieber Institute for Brain Development, Baltimore, Maryland
| | - Ran Tao
- Lieber Institute for Brain Development, Baltimore, Maryland
| | | | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Stephanie H. Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Rainer Spanagel
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anita C. Hansson
- Institute of Psychopharmacology, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Shaunna L. Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University, College Station, Texas
| | - Edwin J.C.G. van den Oord
- Center for Biomarker Research and Precision Medicine, Virginia Commonwealth University, Richmond, Virgina
| | - Thomas M. Hyde
- Lieber Institute for Brain Development, Baltimore, Maryland
| | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, the University of Texas at Austin, Austin, Texas
| | - Bradley T. Webb
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
| | - Eric O. Johnson
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
- Fellow Program, RTI International, Research Triangle Park, North Carolina
| | | | - Laura J. Bierut
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, Missouri
| | - Dana B. Hancock
- GenOmics and Translational Research Center, RTI International, Research Triangle Park, North Carolina
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Zhou H, Gelernter J. Human genetics and epigenetics of alcohol use disorder. J Clin Invest 2024; 134:e172885. [PMID: 39145449 PMCID: PMC11324314 DOI: 10.1172/jci172885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024] Open
Abstract
Alcohol use disorder (AUD) is a prominent contributor to global morbidity and mortality. Its complex etiology involves genetics, epigenetics, and environmental factors. We review progress in understanding the genetics and epigenetics of AUD, summarizing the key findings. Advancements in technology over the decades have elevated research from early candidate gene studies to present-day genome-wide scans, unveiling numerous genetic and epigenetic risk factors for AUD. The latest GWAS on more than one million participants identified more than 100 genetic variants, and the largest epigenome-wide association studies (EWAS) in blood and brain samples have revealed tissue-specific epigenetic changes. Downstream analyses revealed enriched pathways, genetic correlations with other traits, transcriptome-wide association in brain tissues, and drug-gene interactions for AUD. We also discuss limitations and future directions, including increasing the power of GWAS and EWAS studies as well as expanding the diversity of populations included in these analyses. Larger samples, novel technologies, and analytic approaches are essential; these include whole-genome sequencing, multiomics, single-cell sequencing, spatial transcriptomics, deep-learning prediction of variant function, and integrated methods for disease risk prediction.
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Affiliation(s)
- Hang Zhou
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
- Department of Biomedical Informatics and Data Science
- Center for Brain and Mind Health
| | - Joel Gelernter
- Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, USA
- Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut, USA
- Department of Genetics, and
- Department of Neuroscience, Yale School of Medicine, New Haven, Connecticut, USA
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3
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Heidari N, Hajikarim-Hamedani A, Heidari A, Ghane Y, Ashabi G, Zarrindast MR, Sadat-Shirazi MS. Alcohol: Epigenome alteration and inter/transgenerational effect. Alcohol 2024; 117:27-41. [PMID: 38508286 DOI: 10.1016/j.alcohol.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024]
Abstract
While DNA serves as the fundamental genetic blueprint for an organism, it is not a static entity. Gene expression, the process by which genetic information is utilized to create functional products like proteins, can be modulated by a diverse range of environmental factors. Epigenetic mechanisms, including DNA methylation, histone modification, and microRNAs, play a pivotal role in mediating the intricate interplay between the environment and gene expression. Intriguingly, alterations in the epigenome have the potential to be inherited across generations. Alcohol use disorder (AUD) poses significant health issues worldwide. Alcohol has the capability to induce changes in the epigenome, which can be inherited by offspring, thus impacting them even in the absence of direct alcohol exposure. This review delves into the impact of alcohol on the epigenome, examining how its effects vary based on factors such as the age of exposure (adolescence or adulthood), the duration of exposure (chronic or acute), and the specific sample collected (brain, blood, or sperm). The literature underscores that alcohol exposure can elicit diverse effects on the epigenome during different life stages. Furthermore, compelling evidence from human and animal studies demonstrates that alcohol induces alterations in epigenome content, affecting both the brain and blood. Notably, rodent studies suggest that these epigenetic changes can result in lasting phenotype alterations that extend across at least two generations. In conclusion, the comprehensive literature analysis supports the notion that alcohol exposure induces lasting epigenetic alterations, influencing the behavior and health of future generations. This knowledge emphasizes the significance of addressing the potential transgenerational effects of alcohol and highlights the importance of preventive measures to minimize the adverse impact on offspring.
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Affiliation(s)
- Nazila Heidari
- School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Amirhossein Heidari
- Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Yekta Ghane
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ghorbangol Ashabi
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad-Reza Zarrindast
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Martínez-Rivera FJ, Holt LM, Minier-Toribio A, Estill M, Yeh SY, Tofani S, Futamura R, Browne CJ, Mews P, Shen L, Nestler EJ. Transcriptional characterization of cocaine withdrawal versus extinction within nucleus accumbens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584637. [PMID: 38559084 PMCID: PMC10980003 DOI: 10.1101/2024.03.12.584637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Substance use disorder is characterized by a maladaptive imbalance wherein drug seeking persists despite negative consequences or drug unavailability. This imbalance correlates with neurobiological alterations some of which are amplified during forced abstinence, thereby compromising the capacity of extinction-based approaches to prevent relapse. Cocaine use disorder (CUD) exemplifies this phenomenon in which neurobiological modifications hijack brain reward regions such as the nucleus accumbens (NAc) to manifest craving and withdrawal-like symptoms. While increasing evidence links transcriptional changes in the NAc to specific phases of addiction, genome-wide changes in gene expression during withdrawal vs. extinction (WD/Ext) have not been examined in a context- and NAc-subregion-specific manner. Here, we used cocaine self-administration (SA) in rats combined with RNA-sequencing (RNA-seq) of NAc subregions (core and shell) to transcriptionally profile the impact of experiencing withdrawal in the home cage or in the previous drug context or experiencing extinction training. As expected, home-cage withdrawal maintained drug seeking in the previous drug context, whereas extinction training reduced it. By contrast, withdrawal involving repetitive exposure to the previous drug context increased drug-seeking behavior. Bioinformatic analyses of RNA-seq data revealed gene expression patterns, networks, motifs, and biological functions specific to these behavioral conditions and NAc subregions. Comparing transcriptomic analysis of the NAc of patients with CUD highlighted conserved gene signatures, especially with rats that were repetitively exposed to the previous drug context. Collectively, these behavioral and transcriptional correlates of several withdrawal-extinction settings reveal fundamental and translational information about potential molecular mechanisms to attenuate drug-associated memories.
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White JD, Minto MS, Willis C, Quach BC, Han S, Tao R, Deep-Soboslay A, Zillich L, Clark SL, van den Oord EJCG, Hyde TM, Mayfield RD, Webb BT, Johnson EO, Kleinman JE, Bierut LJ, Hancock DB. Alcohol Use Disorder-Associated DNA Methylation in the Nucleus Accumbens and Dorsolateral Prefrontal Cortex. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.17.23300238. [PMID: 38293028 PMCID: PMC10827272 DOI: 10.1101/2024.01.17.23300238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Alcohol use disorder (AUD) has a profound public health impact. However, understanding of the molecular mechanisms underlying the development and progression of AUD remain limited. Here, we interrogate AUD-associated DNA methylation (DNAm) changes within and across addiction-relevant brain regions: the nucleus accumbens (NAc) and dorsolateral prefrontal cortex (DLPFC). Methods Illumina HumanMethylation EPIC array data from 119 decedents of European ancestry (61 cases, 58 controls) were analyzed using robust linear regression, with adjustment for technical and biological variables. Associations were characterized using integrative analyses of public gene regulatory data and published genetic and epigenetic studies. We additionally tested for brain region-shared and -specific associations using mixed effects modeling and assessed implications of these results using public gene expression data. Results At a false discovery rate ≤ 0.05, we identified 53 CpGs significantly associated with AUD status for NAc and 31 CpGs for DLPFC. In a meta-analysis across the regions, we identified an additional 21 CpGs associated with AUD, for a total of 105 unique AUD-associated CpGs (120 genes). AUD-associated CpGs were enriched in histone marks that tag active promoters and our strongest signals were specific to a single brain region. Of the 120 genes, 23 overlapped with previous genetic associations for substance use behaviors; all others represent novel associations. Conclusions Our findings identify AUD-associated methylation signals, the majority of which are specific within NAc or DLPFC. Some signals may constitute predisposing genetic and epigenetic variation, though more work is needed to further disentangle the neurobiological gene regulatory differences associated with AUD.
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Affiliation(s)
- Julie D. White
- GenOmics and Translational Research Center, RTI International
| | | | - Caryn Willis
- GenOmics and Translational Research Center, RTI International
| | - Bryan C. Quach
- GenOmics and Translational Research Center, RTI International
| | | | - Ran Tao
- Lieber Institute for Brain Development (LIBD)
| | | | - Lea Zillich
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Shaunna L. Clark
- Department of Psychiatry & Behavioral Sciences, Texas A&M University
| | | | | | - R. Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin
| | - Bradley T. Webb
- GenOmics and Translational Research Center, RTI International
| | - Eric O. Johnson
- GenOmics and Translational Research Center, RTI International
- Fellow Program, RTI International
| | | | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine
| | - Dana B. Hancock
- GenOmics and Translational Research Center, RTI International
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6
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Refn MR, Andersen MM, Kampmann ML, Tfelt-Hansen J, Sørensen E, Larsen MH, Morling N, Børsting C, Pereira V. Longitudinal changes and variation in human DNA methylation analysed with the Illumina MethylationEPIC BeadChip assay and their implications on forensic age prediction. Sci Rep 2023; 13:21658. [PMID: 38066081 PMCID: PMC10709620 DOI: 10.1038/s41598-023-49064-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/04/2023] [Indexed: 12/18/2023] Open
Abstract
DNA methylation, a pivotal epigenetic modification, plays a crucial role in regulating gene expression and is known to undergo dynamic changes with age. The present study investigated epigenome-wide methylation profiles in 64 individuals over two time points, 15 years apart, using the Illumina EPIC850k arrays. A mixed-effects model identified 2821 age-associated differentially methylated CpG positions (aDMPs) with a median rate of change of 0.18% per year, consistent with a 10-15% change during a human lifespan. Significant variation in the baseline DNA methylation levels between individuals of similar ages as well as inconsistent direction of change with time across individuals were observed for all the aDMPs. Twenty-three of the 2821 aDMPs were previously incorporated into forensic age prediction models. These markers displayed larger changes in DNA methylation with age compared to all the aDMPs and less variation among individuals. Nevertheless, the forensic aDMPs also showed inter-individual variations in the direction of DNA methylation changes. Only cg16867657 in ELOVL2 exhibited a uniform direction of the age-related change among the investigated individuals, which supports the current knowledge that CpG sites in ELOVL2 are the best markers for age prediction.
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Affiliation(s)
- Mie Rath Refn
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark.
| | - Mikkel Meyer Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- The Department of Mathematical Sciences, Aalborg University, 9220, Aalborg, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Margit Hørup Larsen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, 2100, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100, Copenhagen, Denmark
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7
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Rungratanawanich W, Ballway JW, Wang X, Won KJ, Hardwick JP, Song BJ. Post-translational modifications of histone and non-histone proteins in epigenetic regulation and translational applications in alcohol-associated liver disease: Challenges and research opportunities. Pharmacol Ther 2023; 251:108547. [PMID: 37838219 DOI: 10.1016/j.pharmthera.2023.108547] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/30/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Epigenetic regulation is a process that takes place through adaptive cellular pathways influenced by environmental factors and metabolic changes to modulate gene activity with heritable phenotypic variations without altering the DNA sequences of many target genes. Epigenetic regulation can be facilitated by diverse mechanisms: many different types of post-translational modifications (PTMs) of histone and non-histone nuclear proteins, DNA methylation, altered levels of noncoding RNAs, incorporation of histone variants, nucleosomal positioning, chromatin remodeling, etc. These factors modulate chromatin structure and stability with or without the involvement of metabolic products, depending on the cellular context of target cells or environmental stimuli, such as intake of alcohol (ethanol) or Western-style high-fat diets. Alterations of epigenetics have been actively studied, since they are frequently associated with multiple disease states. Consequently, explorations of epigenetic regulation have recently shed light on the pathogenesis and progression of alcohol-associated disorders. In this review, we highlight the roles of various types of PTMs, including less-characterized modifications of nuclear histone and non-histone proteins, in the epigenetic regulation of alcohol-associated liver disease (ALD) and other disorders. We also describe challenges in characterizing specific PTMs and suggest future opportunities for basic and translational research to prevent or treat ALD and many other disease states.
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Affiliation(s)
- Wiramon Rungratanawanich
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Jacob W Ballway
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Xin Wang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kyoung-Jae Won
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, West Hollywood, CA, 90069, USA
| | - James P Hardwick
- Department of Integrative Medical Sciences, Northeast Ohio Medical University, Rootstown, OH 44272, USA.
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, 9000 Rockville Pike, Bethesda, MD 20892, USA.
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8
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Refn MR, Kampmann ML, Morling N, Tfelt-Hansen J, Børsting C, Pereira V. Prediction of chronological age and its applications in forensic casework: methods, current practices, and future perspectives. Forensic Sci Res 2023; 8:85-97. [PMID: 37621446 PMCID: PMC10445583 DOI: 10.1093/fsr/owad021] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/28/2023] [Indexed: 08/26/2023] Open
Abstract
Estimating an individual's age can be relevant in several areas primarily related to the clinical and forensic fields. In the latter, estimation of an individual's chronological age from biological material left by the perpetrator at a crime scene may provide helpful information for police investigation. Estimation of age is also beneficial in immigration cases, where age can affect the person's protection status under the law, or in disaster victim identification to narrow the list of potential missing persons. In the last decade, research has focused on establishing new approaches for age prediction in the forensic field. From the first forensic age estimations based on morphological inspections of macroscopic changes in bone and teeth, the focus has shifted to molecular methods for age estimation. These methods allow the use of samples from human biological material that does not contain morphological age features and can, in theory, be investigated in traces containing only small amounts of biological material. Molecular methods involving DNA analyses are the primary choice and estimation of DNA methylation levels at specific sites in the genome is the most promising tool. This review aims to provide an overview of the status of forensic age prediction using molecular methods, with particular focus in DNA methylation. The frequent challenges that impact forensic age prediction model development will be addressed, together with the importance of validation efforts within the forensic community.
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Affiliation(s)
- Mie Rath Refn
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Department of Cardiology, The Heart Centre, Copenhagen University Hospital, Rigshospitalet, Copenhagen , Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vania Pereira
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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James LM, Georgopoulos AP. Risk assessment of substance use disorders based on the human leukocyte antigen (HLA). Sci Rep 2023; 13:8545. [PMID: 37237010 DOI: 10.1038/s41598-023-35305-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Substance use disorders (SUDs) are common and costly conditions that are partially attributable to genetic factors. In light of immune system influences on neural and behavioral aspects of addiction, the present study evaluated the influence of genes involved in the human immune response, human leukocyte antigen (HLA), on SUDs. We used an immunogenetic epidemiological approach to evaluate associations between the population frequencies of 127 HLA alleles and the population prevalences of six SUDs (alcohol, amphetamine, cannabis, cocaine, opioid, and "other" dependence) in 14 countries of Continental Western Europe to identify immunogenetic profiles of each SUD and evaluate their associations. The findings revealed two primary groupings of SUDs based on their immunogenetic profiles: one group comprised cannabis and cocaine, whereas the other group comprised alcohol, amphetamines, opioids, and "other" dependence. Since each individual possesses 12 HLA alleles, the population HLA-SUD scores were subsequently used to estimate individual risk for each SUD. Overall, the findings highlight similarities and differences in immunogenetic profiles of SUDs that may influence the prevalence and co-occurrence of problematic SUDs and may contribute to assessment of SUD risk of an individual on the basis of their HLA genetic makeup.
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Affiliation(s)
- Lisa M James
- The HLA Research Group, Brain Sciences Center (11B), Department of Veterans Affairs Health Care System, Minneapolis VAHCS, One Veterans Drive, Minneapolis, MN, 55417, USA.
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
- Department of Psychiatry, University of Minnesota Medical School, Minneapolis, MN, 55455, USA.
| | - Apostolos P Georgopoulos
- The HLA Research Group, Brain Sciences Center (11B), Department of Veterans Affairs Health Care System, Minneapolis VAHCS, One Veterans Drive, Minneapolis, MN, 55417, USA
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
- Department of Psychiatry, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
- Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
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10
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Arfmann W, Achenbach J, Meyer-Bockenkamp F, Proskynitopoulos PJ, Groh A, Muschler MAN, Glahn A, Hagemeier L, Preuss V, Klintschar M, Frieling H, Rhein M. Comparing DRD2 Promoter Methylation Between Blood and Brain in Alcohol Dependence. Alcohol Alcohol 2023; 58:216-223. [PMID: 36747480 DOI: 10.1093/alcalc/agad005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 02/08/2023] Open
Abstract
AIMS The dopamine receptor D2 (DRD2) is substantially involved in several forms of addiction. In addition to genetic polymorphisms, epigenetic mechanisms have emerged as an important means of regulation. Previously, DRD2 hypo- and hyper-methylation have been observed in alcohol use disorder (AUD). Blood samples are commonly used as a surrogate marker of epigenetic alterations in epigenetic research, but few specific comparisons between blood and brain tissue samples in AUD exist. METHODS We used post-mortem brain tissue samples of 17 deceased patients with AUD and 31 deceased controls to investigate the relationship between blood and brain methylation of the DRD2 promoter. RESULTS When investigating individual cytosine methylation sites (CpG), several significant differences were found in the nucleus accumbens and hippocampus in the study population. Investigating binding sites with significant differences in methylation levels revealed hypomethylated CpGs targeting mainly activating transcription factors. CONCLUSION These findings support an altered transcription of the DRD2 gene in AUD specimens with a consecutively changed reward response in the brain. While methylation between specific brain regions and blood is comparable, our study further suggests that blood methylation cannot provide meaningful perspectives on DRD2 promoter methylation in the brain.
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Affiliation(s)
- Wiebke Arfmann
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Johannes Achenbach
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
- Department of Anesthesiology and Intensive Care Medicine, Pain Clinic, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Fiona Meyer-Bockenkamp
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Phileas J Proskynitopoulos
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Adrian Groh
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Marc A N Muschler
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Alexander Glahn
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Lars Hagemeier
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Vanessa Preuss
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Michael Klintschar
- Institute of Legal Medicine, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Helge Frieling
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Mathias Rhein
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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Domi E, Barchiesi R, Barbier E. Epigenetic Dysregulation in Alcohol-Associated Behaviors: Preclinical and Clinical Evidence. Curr Top Behav Neurosci 2023. [PMID: 36717533 DOI: 10.1007/7854_2022_410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Alcohol use disorder (AUD) is characterized by loss of control over intake and drinking despite harmful consequences. At a molecular level, AUD is associated with long-term neuroadaptations in key brain regions that are involved in reward processing and decision-making. Over the last decades, a great effort has been made to understand the neurobiological basis underlying AUD. Epigenetic mechanisms have emerged as an important mechanism in the regulation of long-term alcohol-induced gene expression changes. Here, we review the literature supporting a role for epigenetic processes in AUD. We particularly focused on the three most studied epigenetic mechanisms: DNA methylation, Histone modification and non-coding RNAs. Clinical studies indicate an association between AUD and DNA methylation both at the gene and global levels. Using behavioral paradigms that mimic some of the characteristics of AUD, preclinical studies demonstrate that changes in epigenetic mechanisms can functionally impact alcohol-associated behaviors. While many studies support a therapeutic potential for targeting epigenetic enzymes, more research is needed to fully understand their role in AUD. Identification of brain circuits underlying alcohol-associated behaviors has made major advances in recent years. However, there are very few studies that investigate how epigenetic mechanisms can affect these circuits or impact the neuronal ensembles that promote alcohol-associated behaviors. Studies that focus on the role of circuit-specific and cell-specific epigenetic changes for clinically relevant alcohol behaviors may provide new insights on the functional role of epigenetic processes in AUD.
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Affiliation(s)
- Esi Domi
- Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience, Linköping University, Linköping, Sweden
- School of Pharmacy, Pharmacology Unit, Center for Neuroscience, University of Camerino, Camerino, Italy
| | - Riccardo Barchiesi
- Department of Neuroscience, Waggoner Center for Alcohol and Alcohol Addiction Research, University of Texas at Austin, Austin, TX, USA
| | - Estelle Barbier
- Department of Biomedical and Clinical Sciences, Center for Social and Affective Neuroscience, Linköping University, Linköping, Sweden.
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12
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Jarczak J, Miszczak M, Radwanska K. Is DNA methylation in the brain a mechanism of alcohol use disorder? Front Behav Neurosci 2023; 17:957203. [PMID: 36778133 PMCID: PMC9908583 DOI: 10.3389/fnbeh.2023.957203] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 01/09/2023] [Indexed: 01/27/2023] Open
Abstract
Alcohol use disorder (AUD) is a worldwide problem. Unfortunately, the molecular mechanisms of alcohol misuse are still poorly understood, therefore successful therapeutic approaches are limited. Accumulating data indicate that the tendency for compulsive alcohol use is inherited, suggesting a genetic background as an important factor. However, the probability to develop AUD is also affected by life experience and environmental factors. Therefore, the epigenetic modifications that are altered over lifetime likely contribute to increased risk of alcohol misuse. Here, we review the literature looking for the link between DNA methylation in the brain, a common epigenetic modification, and AUD-related behaviors in humans, mice and rats. We sum up the main findings, identify the existing gaps in our knowledge and indicate future directions of the research.
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13
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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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14
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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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15
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Gelernter J, Polimanti R. Genetics of substance use disorders in the era of big data. Nat Rev Genet 2021; 22:712-729. [PMID: 34211176 PMCID: PMC9210391 DOI: 10.1038/s41576-021-00377-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/07/2021] [Indexed: 02/06/2023]
Abstract
Substance use disorders (SUDs) are conditions in which the use of legal or illegal substances, such as nicotine, alcohol or opioids, results in clinical and functional impairment. SUDs and, more generally, substance use are genetically complex traits that are enormously costly on an individual and societal basis. The past few years have seen remarkable progress in our understanding of the genetics, and therefore the biology, of substance use and abuse. Various studies - including of well-defined phenotypes in deeply phenotyped samples, as well as broadly defined phenotypes in meta-analysis and biobank samples - have revealed multiple risk loci for these common traits. A key emerging insight from this work establishes a biological and genetic distinction between quantity and/or frequency measures of substance use (which may involve low levels of use without dependence), versus symptoms related to physical dependence.
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Affiliation(s)
- Joel Gelernter
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA.
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA.
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine, West Haven, CT, USA
- Department of Psychiatry, Veterans Affairs Connecticut Healthcare Center, West Haven, CT, USA
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16
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Longley MJ, Lee J, Jung J, Lohoff FW. Epigenetics of alcohol use disorder-A review of recent advances in DNA methylation profiling. Addict Biol 2021; 26:e13006. [PMID: 33538087 PMCID: PMC8596445 DOI: 10.1111/adb.13006] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 01/05/2021] [Accepted: 01/09/2021] [Indexed: 12/13/2022]
Abstract
Alcohol use disorder (AUD) is a major contributor to morbidity and mortality worldwide. Although there is a heritable component, the etiology of AUD is complex and can involve environmental exposures like trauma and can be associated with many different patterns of alcohol consumption. Epigenetic modifications, which can mediate the influence of genetic variants and environmental variables on gene expression, have emerged as an important area of AUD research. Over the past decade, the number of studies investigating AUD and DNA methylation, a form of epigenetic modification, has grown rapidly. Yet we are still far from understanding how DNA methylation contributes to or reflects aspects of AUD. In this paper, we reviewed studies of DNA methylation and AUD and discussed how the field has evolved. We found that global DNA and candidate DNA methylation studies did not produce replicable results. To assess whether findings of epigenome-wide association studies (EWAS) were replicated, we aggregated significant findings across studies and identified 184 genes and 15 gene ontological pathways that were differentially methylated in at least two studies and four genes and three gene ontological pathways that were differentially methylated in three studies. These genes and pathways repeatedly found enrichment of immune processes, which is in line with recent developments suggesting that the immune system may be altered in AUD. Finally, we assess the current limitations of studies of DNA methylation and AUD and make recommendations on how to design future studies to resolve outstanding questions.
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Affiliation(s)
- Martha J. Longley
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Jisoo Lee
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
| | - Falk W. Lohoff
- Section on Clinical Genomics and Experimental TherapeuticsNational Institute on Alcohol Abuse and Alcoholism, National Institutes of HealthBethesdaMarylandUSA
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17
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Piniewska-Róg D, Heidegger A, Pośpiech E, Xavier C, Pisarek A, Jarosz A, Woźniak A, Wojtas M, Phillips C, Kayser M, Parson W, Branicki W. Impact of excessive alcohol abuse on age prediction using the VISAGE enhanced tool for epigenetic age estimation in blood. Int J Legal Med 2021; 135:2209-2219. [PMID: 34405265 PMCID: PMC8523459 DOI: 10.1007/s00414-021-02665-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022]
Abstract
DNA methylation-based clocks provide the most accurate age estimates with practical implications for clinical and forensic genetics. However, the effects of external factors that may influence the estimates are poorly studied. Here, we evaluated the effect of alcohol consumption on epigenetic age prediction in a cohort of extreme alcohol abusers. Blood samples from deceased alcohol abusers and age- and sex-matched controls were analyzed using the VISAGE enhanced tool for age prediction from somatic tissues that enables examination of 44 CpGs within eight age markers. Significantly altered DNA methylation was recorded for alcohol abusers in MIR29B2CHG. This resulted in a mean predicted age of 1.4 years higher compared to the controls and this trend increased in older individuals. The association of alcohol abuse with epigenetic age acceleration, as determined by the prediction analysis performed based on MIR29B2CHG, was small but significant (β = 0.190; P-value = 0.007). However, the observed alteration in DNA methylation of MIR29B2CHG had a non-significant effect on age estimation with the VISAGE age prediction model. The mean absolute error in the alcohol-abusing cohort was 3.1 years, compared to 3.3 years in the control group. At the same time, upregulation of MIR29B2CHG expression may have a biological function, which merits further studies.
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Affiliation(s)
- Danuta Piniewska-Róg
- Jagiellonian University Medical College, Faculty of Medicine, Department of Forensic Medicine, Grzegórzecka 16, 31-531, Krakow, Poland
| | - Antonia Heidegger
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020, Innsbruck, Austria
| | - Ewelina Pośpiech
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020, Innsbruck, Austria
| | - Aleksandra Pisarek
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland
| | - Agata Jarosz
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland
| | - Anna Woźniak
- Central Forensic Laboratory of the Police, Aleje Ujazdowskie 7, 00-583, Warsaw, Poland
| | - Marta Wojtas
- Jagiellonian University Medical College, Faculty of Medicine, Department of Forensic Medicine, Grzegórzecka 16, 31-531, Krakow, Poland
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, R/ San Francisco s/n, 15782, Santiago de Compostela, Spain
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, 6020, Innsbruck, Austria
- Forensic Science Program, The Pennsylvania State University, 13 Thomas Building, University Park, PA, 16802, USA
| | - Wojciech Branicki
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-348, Krakow, Poland.
- Central Forensic Laboratory of the Police, Aleje Ujazdowskie 7, 00-583, Warsaw, Poland.
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18
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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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19
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Shu C, Sosnowski DW, Tao R, Deep-Soboslay A, Kleinman JE, Hyde TM, Jaffe AE, Sabunciyan S, Maher BS. Epigenome-wide study of brain DNA methylation following acute opioid intoxication. Drug Alcohol Depend 2021; 221:108658. [PMID: 33667780 PMCID: PMC8026744 DOI: 10.1016/j.drugalcdep.2021.108658] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/01/2021] [Accepted: 02/18/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND Opioid abuse poses significant risk to individuals in the United States and epigenetic changes are a leading potential biomarker of opioid abuse. Current evidence, however, is mostly limited to candidate gene analysis in whole blood. To clarify the association between opioid abuse and DNA methylation, we conducted an epigenome-wide analysis of DNA methylation in brain samples of individuals who died from acute opioid intoxication and group-matched controls. METHODS Tissue samples were extracted from the dorsolateral prefrontal cortex of 153 deceased individuals (Mage = 35.42; 62 % male; 77 % European ancestry). The study included 72 opioid samples, 53 psychiatric controls, and 28 normal controls. The epigenome-wide analysis was implemented using the Illumina MethylationEPIC BeadChip; analyses adjusted for sociodemographic characteristics, negative control principal components, ancestry principal components, cellular composition, and surrogate variables. Horvath's epigenetic age and Levine's PhenoAge were calculated, and gene set enrichment analyses were performed. RESULTS Although no CpG sites survived false-discovery rate correction for multiple testing, 13 sites surpassed a relaxed significance threshold (p < 1.0 × 10-5). One of these sites was located within Netrin-1, a gene implicated in kappa opioid receptor activity. There was an association between opioid use and accelerated PhenoAge (b = 2.24, se = 1.11, p = .045). Gene set enrichment analyses revealed enrichment of differential methylation in GO and KEGG pathways broadly related to substance use. CONCLUSIONS Netrin-1 may be associated with opioid overdose, and future research with larger samples across stages of opioid use will elucidate the complex genomics of opioid abuse.
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Affiliation(s)
- Chang Shu
- Department of Pediatrics, Columbia University Irving Medical Center, United States; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, United States
| | - David W Sosnowski
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, United States.
| | - Ran Tao
- Lieber Institute for Brain Development, United States
| | | | - Joel E Kleinman
- Lieber Institute for Brain Development, United States; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, United States
| | - Thomas M Hyde
- Lieber Institute for Brain Development, United States
| | - Andrew E Jaffe
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, United States; Lieber Institute for Brain Development, United States
| | | | - Brion S Maher
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, United States
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20
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Baumgarten N, Hecker D, Karunanithi S, Schmidt F, List M, Schulz MH. EpiRegio: analysis and retrieval of regulatory elements linked to genes. Nucleic Acids Res 2020; 48:W193-W199. [PMID: 32459338 PMCID: PMC7319550 DOI: 10.1093/nar/gkaa382] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/21/2020] [Accepted: 05/04/2020] [Indexed: 12/26/2022] Open
Abstract
A current challenge in genomics is to interpret non-coding regions and their role in transcriptional regulation of possibly distant target genes. Genome-wide association studies show that a large part of genomic variants are found in those non-coding regions, but their mechanisms of gene regulation are often unknown. An additional challenge is to reliably identify the target genes of the regulatory regions, which is an essential step in understanding their impact on gene expression. Here we present the EpiRegio web server, a resource of regulatory elements (REMs). REMs are genomic regions that exhibit variations in their chromatin accessibility profile associated with changes in expression of their target genes. EpiRegio incorporates both epigenomic and gene expression data for various human primary cell types and tissues, providing an integrated view of REMs in the genome. Our web server allows the analysis of genes and their associated REMs, including the REM's activity and its estimated cell type-specific contribution to its target gene's expression. Further, it is possible to explore genomic regions for their regulatory potential, investigate overlapping REMs and by that the dissection of regions of large epigenomic complexity. EpiRegio allows programmatic access through a REST API and is freely available at https://epiregio.de/.
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Affiliation(s)
- Nina Baumgarten
- Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Dennis Hecker
- Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
| | - Sivarajan Karunanithi
- Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
| | - Florian Schmidt
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
- Genome Institute of Singapore, 60 Biopolis Street, Genome, 02-01, 138672, Singapore
| | - Markus List
- Big Data in BioMedicine Group, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Marcel H Schulz
- Institute for Cardiovascular Regeneration, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University Hospital, 60590 Frankfurt am Main, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
- Cluster of Excellence, Multimodal Computing and Interaction, Saarland Informatics Campus, 66123 Saarbrücken, Germany
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21
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Zindler T, Frieling H, Neyazi A, Bleich S, Friedel E. Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies. BMC Bioinformatics 2020; 21:271. [PMID: 32605541 PMCID: PMC7328269 DOI: 10.1186/s12859-020-03559-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/26/2020] [Indexed: 12/04/2022] Open
Abstract
Background Systematic technical effects—also called batch effects—are a considerable challenge when analyzing DNA methylation (DNAm) microarray data, because they can lead to false results when confounded with the variable of interest. Methods to correct these batch effects are error-prone, as previous findings have shown. Results Here, we demonstrate how using the R function ComBat to correct simulated Infinium HumanMethylation450 BeadChip (450 K) and Infinium MethylationEPIC BeadChip Kit (EPIC) DNAm data can lead to a large number of false positive results under certain conditions. We further provide a detailed assessment of the consequences for the highly relevant problem of p-value inflation with subsequent false positive findings after application of the frequently used ComBat method. Using ComBat to correct for batch effects in randomly generated samples produced alarming numbers of false discovery rate (FDR) and Bonferroni-corrected (BF) false positive results in unbalanced as well as in balanced sample distributions in terms of the relation between the outcome of interest variable and the technical position of the sample during the probe measurement. Both sample size and number of batch factors (e.g. number of chips) were systematically simulated to assess the probability of false positive findings. The effect of sample size was simulated using n = 48 up to n = 768 randomly generated samples. Increasing the number of corrected factors led to an exponential increase in the number of false positive signals. Increasing the number of samples reduced, but did not completely prevent, this effect. Conclusions Using the approach described, we demonstrate, that using ComBat for batch correction in DNAm data can lead to false positive results under certain conditions and sample distributions. Our results are thus contrary to previous publications, considering a balanced sample distribution as unproblematic when using ComBat. We do not claim completeness in terms of reporting all technical conditions and possible solutions of the occurring problems as we approach the problem from a clinician’s perspective and not from that of a computer scientist. With our approach of simulating data, we provide readers with a simple method to assess the probability of false positive findings in DNAm microarray data analysis pipelines.
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Affiliation(s)
- Tristan Zindler
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany.
| | - Helge Frieling
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Alexandra Neyazi
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Stefan Bleich
- Department of Psychiatry, Social Psychiatry and Psychotherapy, Hannover Medical School, Hannover, Germany
| | - Eva Friedel
- Department of Psychiatry and Psychotherapy, Charité Campus Mitte (CCM), Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health (BIH), 10178, Berlin, Germany
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22
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Friedel E, Walter H, Veer IM, Zimmermann US, Heinz A, Frieling H, Zindler T. Impact of Long‐Term Alcohol Consumption and Relapse on Genome‐Wide DNA Methylation Changes in Alcohol‐Dependent Subjects: A Longitudinal Study. Alcohol Clin Exp Res 2020; 44:1356-1365. [DOI: 10.1111/acer.14354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Eva Friedel
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthCharité Campus Mitte (CCM) Berlin Germany
- Berlin Institute of Health (BIH) Berlin Germany
| | - Henrik Walter
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthCharité Campus Mitte (CCM) Berlin Germany
| | - Ilya M. Veer
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthCharité Campus Mitte (CCM) Berlin Germany
| | - Ulrich S. Zimmermann
- Department of Addiction Medicine and Psychotherapykbo Isar‐Amper‐Klinikum Munich Germany
| | - Andreas Heinz
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of HealthCharité Campus Mitte (CCM) Berlin Germany
| | - Helge Frieling
- Department of Psychiatry, Social Psychiatry and PsychotherapyHannover Medical School Hannover Germany
| | - Tristan Zindler
- Department of Psychiatry, Social Psychiatry and PsychotherapyHannover Medical School Hannover Germany
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Twin Research in the Post-Genomic Era: Dissecting the Pathophysiological Effects of Adversity and the Social Environment. Int J Mol Sci 2020; 21:ijms21093142. [PMID: 32365612 PMCID: PMC7247668 DOI: 10.3390/ijms21093142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 11/29/2022] Open
Abstract
The role of twins in research is evolving as we move further into the post-genomic era. With the re-definition of what a gene is, it is becoming clear that biological family members who share a specific genetic variant may well not have a similar risk for future disease. This has somewhat invalidated the prior rationale for twin studies. Case co-twin study designs, however, are slowly emerging as the ideal tool to identify both environmentally induced epigenetic marks and epigenetic disease-associated processes. Here, we propose that twin lives are not as identical as commonly assumed and that the case co-twin study design can be used to investigate the effects of the adult social environment. We present the elements in the (social) environment that are likely to affect the epigenome and measures in which twins may diverge. Using data from the German TwinLife registry, we confirm divergence in both the events that occur and the salience for the individual start as early as age 11. Case co-twin studies allow for the exploitation of these divergences, permitting the investigation of the role of not only the adult social environment, but also the salience of an event or environment for the individual, in determining lifelong health trajectories. In cases like social adversity where it is clearly not possible to perform a randomised-controlled trial, we propose that the case co-twin study design is the most rigorous manner with which to investigate epigenetic mechanisms encoding environmental exposure. The role of the case co-twin design will continue to evolve, as we argue that it will permit causal inference from observational data.
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Xu K, Montalvo‐Ortiz JL, Zhang X, Southwick SM, Krystal JH, Pietrzak RH, Gelernter J. Epigenome‐Wide
DNA
Methylation Association Analysis Identified Novel Loci in Peripheral Cells for Alcohol Consumption Among European American Male Veterans. Alcohol Clin Exp Res 2019; 43:2111-2121. [PMID: 31386212 DOI: 10.1111/acer.14168] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/25/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Ke Xu
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
| | - Janitza L. Montalvo‐Ortiz
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
| | - Xinyu Zhang
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
| | - Steven M. Southwick
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
- Clinical Neurosciences Division U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder West Haven Connecticut
| | - John H. Krystal
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
- Clinical Neurosciences Division U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder West Haven Connecticut
| | - Robert H. Pietrzak
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
- Clinical Neurosciences Division U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder West Haven Connecticut
| | - Joel Gelernter
- Department of Psychiatry Yale School of Medicine New Haven Connecticut
- VA Connecticut Healthcare System West Haven Connecticut
- Clinical Neurosciences Division U.S. Department of Veterans Affairs National Center of Posttraumatic Stress Disorder West Haven Connecticut
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25
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Lunde‐Young R, Ramirez J, Naik V, Orzabal M, Lee J, Konganti K, Hillhouse A, Threadgill D, Ramadoss J. Hippocampal transcriptome reveals novel targets of FASD pathogenesis. Brain Behav 2019; 9:e01334. [PMID: 31140755 PMCID: PMC6625466 DOI: 10.1002/brb3.1334] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/01/2019] [Accepted: 05/06/2019] [Indexed: 01/26/2023] Open
Abstract
INTRODUCTION Prenatal alcohol exposure can contribute to fetal alcohol spectrum disorders (FASD), characterized by a myriad of developmental impairments affecting behavior and cognition. Studies show that many of these functional impairments are associated with the hippocampus, a structure exhibiting exquisite vulnerability to developmental alcohol exposure and critically implicated in learning and memory; however, mechanisms underlying alcohol-induced hippocampal deficits remain poorly understood. By utilizing a high-throughput RNA-sequencing (RNA-seq) approach to address the neurobiological and molecular basis of prenatal alcohol-induced hippocampal functional deficits, we hypothesized that chronic binge prenatal alcohol exposure alters gene expression and global molecular pathways in the fetal hippocampus. METHODS Timed-pregnant Sprague-Dawley rats were randomly assigned to a pair-fed control (PF) or binge alcohol (ALC) treatment group on gestational day (GD) 4. ALC dams acclimatized from GDs 5-10 with a daily treatment of 4.5 g/kg alcohol and subsequently received 6 g/kg on GDs 11-20. PF dams received a once daily maltose dextrin gavage on GDs 5-20, isocalorically matching ALC counterparts. On GD 21, bilateral hippocampi were dissected, flash frozen, and stored at -80° C. Total RNA was then isolated from homogenized tissues. Samples were normalized to ~4nM and pooled equally. Sequencing was performed by Illumina NextSeq 500 on a 75 cycle, single-end sequencing run. RESULTS RNA-seq identified 13,388 genes, of these, 76 genes showed a significant difference (p < 0.05, log2 fold change ≥2) in expression between the PF and ALC groups. Forty-nine genes showed sex-dependent dysregulation; IPA analysis showed among female offspring, dysregulated pathways included proline and citrulline biosynthesis, whereas in males, xenobiotic metabolism signaling and alaninine biosynthesis etc. were altered. CONCLUSION We conclude that chronic binge alcohol exposure during pregnancy dysregulates fetal hippocampal gene expression in a sex-specific manner. Identification of subtle, transcriptome-level dysregulation in hippocampal molecular pathways offers potential mechanistic insights underlying FASD pathogenesis.
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Affiliation(s)
- Raine Lunde‐Young
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Josue Ramirez
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Vishal Naik
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Marcus Orzabal
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Jehoon Lee
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Kranti Konganti
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Andrew Hillhouse
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - David Threadgill
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
| | - Jayanth Ramadoss
- Department of Veterinary Physiology and Pharmacology, College of Veterinary Medicine and Biomedical SciencesTexas A&M UniversityCollege StationTexas
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26
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Wilson LE, Xu Z, Harlid S, White AJ, Troester MA, Sandler DP, Taylor JA. Alcohol and DNA Methylation: An Epigenome-Wide Association Study in Blood and Normal Breast Tissue. Am J Epidemiol 2019; 188:1055-1065. [PMID: 30938765 DOI: 10.1093/aje/kwz032] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 02/01/2019] [Accepted: 02/04/2019] [Indexed: 12/12/2022] Open
Abstract
The biological mechanisms driving associations between alcohol consumption and chronic diseases might include epigenetic modification of DNA methylation. We explored the hypothesis that alcohol consumption is associated with methylation in an epigenome-wide association study of blood and normal breast tissue DNA. Infinium HumanMethylation450 BeadChip (Illumina Inc., San Diego, California) array data on blood DNA methylation was examined in a discovery set of 2,878 non-Hispanic white women from the Sister Study (United States, 2004-2015) who provided detailed questionnaire information on lifetime alcohol use. Robust linear regression modeling was used to identify significant associations (false discovery rate of Q < 0.05) between the number of alcoholic drinks per week and DNA methylation at 5,458 cytosine-phosphate-guanine (CpG) sites. Associations were replicated (P < 0.05) for 677 CpGs in an independent set of 187 blood DNA samples from the Sister Study and for 628 CpGs in an independent set of 171 normal breast DNA samples; 1,207 CpGs were replicated in either blood or normal breast, with 98 CpGs replicated in both tissues. Individual gene effects were notable for phosphoglycerate dehydrogenase (PGHDH), peptidyl-prolyl cis-trans isomerase (PPIF), solute carrier 15 (SLC15), solute carrier family 43 member 1 (SLC43A1), and solute carrier family 7 member 11 (SLC7A11). We also found that high alcohol consumption was associated with significantly lower global methylation as measured by the average of CpGs on the entire array.
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Affiliation(s)
- Lauren E Wilson
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
- Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Zongli Xu
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Sophia Harlid
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
- Department of Radiation Sciences, Oncology, Umea University, Umea, Sweden
| | - Alexandra J White
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
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27
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Bidwell LC, Karoly HC, Thayer RE, Claus ED, Bryan AD, Weiland BJ, YorkWilliams S, Hutchison KE. DRD2 promoter methylation and measures of alcohol reward: functional activation of reward circuits and clinical severity. Addict Biol 2019; 24:539-548. [PMID: 29464814 DOI: 10.1111/adb.12614] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 01/02/2018] [Accepted: 01/24/2018] [Indexed: 12/13/2022]
Abstract
Studies have identified strong associations between D2 receptor binding potential and neural responses to rewarding stimuli and substance use. Thus, D2 receptor perturbations are central to theoretical models of the pathophysiology of substance dependence, and epigenetic changes may represent one of the fundamental molecular mechanisms impacting the effects of alcohol exposure on the brain. We hypothesized that epigenetic alterations in the promoter region of the dopamine D2 receptor (DRD2) gene would be associated with cue-elicited activation of neural reward regions, as well as severity of alcohol use behavior. The current study leveraged functional neuroimaging (fMRI) during an alcohol reward paradigm (n = 383) to test associations among DRD2 promoter methylation in peripheral tissue, signal change in the striatum during the presentation of alcohol cues, and severity of alcohol use disorder (AUD). Controlling for age, DRD2 promoter methylation was positively associated with responses to alcohol cues in the right accumbens (partial r = 0.144, P = 0.005), left putamen (partial r = 0.133, P = 0.009), right putamen (partial r = 0.106, P = 0.039), left caudate (partial r = 0.117, P = 0.022), and right caudate (partial r = 0.133, P = 0.009), suggesting that DRD2 methylation was positively associated with robust activation in the striatum in response to reward cues. DRD2 methylation was also positively associated with clinical metrics of AUD severity. Specifically, controlling for age, DRD2 methylation was associated with Alcohol Use Disorders Identification Test total (partial r = 0.140, P = 0.002); Impaired Control Scale total (partial r = 0.097, P = 0.044) and Alcohol Dependence Scale total (partial r = 0.152, P = 0.001). Thus, DRD2 methylation may be a critical mechanism linking D2 receptors with functional striatal brain changes and clinical severity among alcohol users.
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Affiliation(s)
| | - Hollis C. Karoly
- Department of Psychology & NeuroscienceUniversity of Colorado Boulder Boulder CO USA
| | - Rachel E. Thayer
- Department of Psychology & NeuroscienceUniversity of Colorado Boulder Boulder CO USA
| | | | - Angela D. Bryan
- Institute of Cognitive ScienceUniversity of Colorado Boulder Boulder CO USA
- Department of Psychology & NeuroscienceUniversity of Colorado Boulder Boulder CO USA
| | - Barbara J. Weiland
- Institute of Cognitive ScienceUniversity of Colorado Boulder Boulder CO USA
| | - Sophie YorkWilliams
- Department of Psychology & NeuroscienceUniversity of Colorado Boulder Boulder CO USA
| | - Kent E. Hutchison
- Institute of Cognitive ScienceUniversity of Colorado Boulder Boulder CO USA
- Department of Psychology & NeuroscienceUniversity of Colorado Boulder Boulder CO USA
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28
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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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29
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Karoly HC, Ellingson JM, Hutchison KE. Interactions between TLR4 methylation and alcohol consumption on subjective responses to an alcohol infusion. Alcohol Alcohol 2018; 53:650-658. [PMID: 29982285 PMCID: PMC6203129 DOI: 10.1093/alcalc/agy046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/04/2018] [Accepted: 06/06/2018] [Indexed: 01/16/2023] Open
Abstract
AIMS Converging evidence has implicated perturbed inflammatory signaling in alcohol use disorders (AUDs), and both animal and human studies suggest that alcohol-induced inflammatory signaling is mediated by Toll-Like Receptor 4 (TLR4). We previously demonstrated that TLR4 is hypermethylated in subjects with AUD compared to control individuals. Examining the relationship between TLR4 methylation and subjective alcohol responses could shed light on the role of TLR4 in promoting AUDs, thereby highlighting its potential as a treatment target. SHORT SUMMARY Significant interactions were demonstrated between Toll-like Receptor 4 (TLR4) methylation and human alcohol consumption patterns, such that greater methylation was associated with decreased positive and negative self-reported arousal during an alcohol infusion among light-to-moderate drinkers, but increased self-reported positive arousal and physiological arousal (i.e. systolic blood pressure) among heavy drinkers. METHODS Latent growth models were used to examine the relationship between TLR4 methylation and subjective responses and physiological measures of arousal during an alcohol infusion across 222 drinkers. RESULTS We observed significant interactions of TLR4 methylation and alcohol use (drinks per week) on intercepts for self-report and physiological arousal measures. Specifically, light-to-moderate drinkers had positive associations between methylation and stimulation and tension (r's = 0.21-0.24), and heavy drinkers had negative associations (r's = -0.15 to -0.21). There were also significant interaction effects on changes in tension (β = 0.31, P < 0.01), systolic blood pressure (β = 0.74, P < 0.01) and marginal effects on stimulation (β = 0.15, P = 0.07) during the infusion, such that methylation was associated with decreased arousal among light-to-moderate drinkers (r's = -0.12 to -0.25) but stable or increased arousal among heavy drinkers (r's = 0.05-0.19). CONCLUSIONS Findings suggest that the relationship between TLR4 methylation and subjective and physiological arousal during acute alcohol intoxication depends upon on self-reported alcohol use. These data demonstrate the influence of TLR4 on subjective responses to alcohol, thereby supporting the need for further research on its potential as a pharmacological treatment target.
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Affiliation(s)
- Hollis C Karoly
- Department of Psychology and Neuroscience, University of Colorado Boulder, UCB 344, Boulder, CO, USA
| | - Jarrod M Ellingson
- Department of Psychology and Neuroscience, University of Colorado Boulder, UCB 344, Boulder, CO, USA
| | - Kent E Hutchison
- Department of Psychology and Neuroscience, University of Colorado Boulder, UCB 344, Boulder, CO, USA
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De Sa Nogueira D, Merienne K, Befort K. Neuroepigenetics and addictive behaviors: Where do we stand? Neurosci Biobehav Rev 2018; 106:58-72. [PMID: 30205119 DOI: 10.1016/j.neubiorev.2018.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/28/2018] [Accepted: 08/29/2018] [Indexed: 12/21/2022]
Abstract
Substance use disorders involve long-term changes in the brain that lead to compulsive drug seeking, craving, and a high probability of relapse. Recent findings have highlighted the role of epigenetic regulations in controlling chromatin access and regulation of gene expression following exposure to drugs of abuse. In the present review, we focus on data investigating genome-wide epigenetic modifications in the brain of addicted patients or in rodent models exposed to drugs of abuse, with a particular focus on DNA methylation and histone modifications associated with transcriptional studies. We highlight critical factors for epigenomic studies in addiction. We discuss new findings related to psychostimulants, alcohol, opiate, nicotine and cannabinoids. We examine the possible transmission of these changes across generations. We highlight developing tools, specifically those that allow investigation of structural reorganization of the chromatin. These have the potential to increase our understanding of alteration of chromatin architecture at gene regulatory regions. Neuroepigenetic mechanisms involved in addictive behaviors could explain persistent phenotypic effects of drugs and, in particular, vulnerability to relapse.
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Affiliation(s)
- David De Sa Nogueira
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, CNRS, Université de Strasbourg, Team 3 « Abuse of Drugs and Neuroadaptations », Faculté de Psychologie, 12 rue Goethe, F-67000, France
| | - Karine Merienne
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, CNRS, Université de Strasbourg, Team 1 « Dynamics of Memory and Epigenetics », Faculté de Psychologie, 12 rue Goethe, F-67000, France
| | - Katia Befort
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, CNRS, Université de Strasbourg, Team 3 « Abuse of Drugs and Neuroadaptations », Faculté de Psychologie, 12 rue Goethe, F-67000, France.
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31
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Lax E, Szyf M. The Role of DNA Methylation in Drug Addiction: Implications for Diagnostic and Therapeutics. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 157:93-104. [PMID: 29933958 DOI: 10.1016/bs.pmbts.2018.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Drug addiction is a devastating health problem that is a very heavy burden on the individual affected and the society in general. Recent research defines addiction as a neurobehavioral disorder. Underpinning biological mechanisms of drug addiction are abnormal neuronal and brain activity following acute and repeated drug exposure. Abnormal gene expression is found in reward and decision-making brain regions of addicts and in animal models and is possibly responsible for changes in brain function. DNA methylation is an epigenetic modification that regulates gene expression. Global and site-specific changes in DNA methylation are observed in addiction. Here, we discuss recent findings on the involvement of DNA methylation in drug addiction from animal and human studies. We also propose future directions for utilizing DNA methylation-based approaches for diagnosis, therapeutics, and evaluation of response to therapy in drug addiction.
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Affiliation(s)
- Elad Lax
- Department of Pharmacology and Therapeutics, McGill University Medical School, Montreal, QC, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University Medical School, Montreal, QC, Canada.
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32
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Vadigepalli R, Hoek JB. Introduction to the Virtual Issue Alcohol and Epigenetic Regulation: Do the Products of Alcohol Metabolism Drive Epigenetic Control of Gene Expression in Alcohol-Related Disorders? Alcohol Clin Exp Res 2018. [PMID: 29532481 DOI: 10.1111/acer.13630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rajanikanth Vadigepalli
- Department of Pathology, Anatomy & Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Jan B Hoek
- Department of Pathology, Anatomy & Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
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33
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Karoly HC, Thayer RE, Hagerty SL, Hutchison KE. TLR4 Methylation Moderates the Relationship Between Alcohol Use Severity and Gray Matter Loss. J Stud Alcohol Drugs 2018; 78:696-705. [PMID: 28930057 DOI: 10.15288/jsad.2017.78.696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
OBJECTIVE Alcohol use disorders (AUDs) are associated with decreased gray matter, and neuroinflammation is one mechanism through which alcohol may confer such damage, given that heavy alcohol use may promote neural damage via activation of toll-like receptor 4 (TLR4)-mediated inflammatory signaling cascades. We previously demonstrated that TLR4 is differentially methylated in AUD compared with control subjects, and the present study aims to extend this work by examining whether TLR4 methylation moderates the relationship between alcohol use and gray matter. METHOD We examined TLR4 methylation and gray matter thickness in a large sample (N = 707; 441 males) of adults (ages 18-56) reporting a range of AUD severity (mean Alcohol Use Disorders Identification Test score = 13.18; SD = 8.02). We used a series of ordinary least squares multiple regression equations to regress gray matter in four bilateral brain regions (precuneus, lateral orbitofrontal, inferior parietal, and superior temporal) on alcohol use, TLR4 methylation, and their interaction, controlling for demographic, psychological, and other substance use variables. RESULTS After we corrected for multiple tests, a significant Alcohol × TLR4 Methylation interaction emerged in the equations modeling left precuneus and right inferior parietal gray matter. Follow-up analyses examining the nature of these interactions demonstrated a significant negative association between alcohol and precuneus and inferior parietal gray matter in individuals with low TLR4 methylation, but no relationship between alcohol and gray matter in the high methylation group. CONCLUSIONS These findings suggest that TLR4 methylation may be protective against the damage conferred by alcohol on precuneus and inferior parietal gray matter, thereby implicating TLR4 for further investigation as a possible AUD treatment target.
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Affiliation(s)
- Hollis C Karoly
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
| | - Rachel E Thayer
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
| | - Sarah L Hagerty
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
| | - Kent E Hutchison
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, Colorado
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Ragia G, Manolopoulos VG. From Homer and Hippocrates to modern personalized medicine: is there a role for pharmacoepigenomics in the treatment of alcohol addiction? Pharmacogenomics 2018; 19:513-516. [PMID: 29580163 DOI: 10.2217/pgs-2018-0025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
From the earliest times to the present, alcohol has evolved as part of life and culture. For most adults, moderate alcohol use is harmless, however, it lies at one end of a range that moves through alcohol abuse to alcohol addiction. Alcohol addiction is a serious and chronic psychiatric disorder that, on top of its heavy consequences on health, also brings significant social and economic losses to individuals and society at large. Pharmacotherapy of alcohol addiction exists, but its effectiveness varies significantly among individuals. Genomic and nongenomic factors are significant contributors to interindividual variation in the clinical presentation of alcohol problems and the response to a given treatment. In addition, emerging evidence suggests pharmacoepigenomics of alcohol addiction as a novel promising area for improvement of alcohol addiction management.
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Affiliation(s)
- Georgia Ragia
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Dragana Campus, 68100 Alexandroupolis, Greece.,DNALEX S.A., Leontaridou 2, Alexandroupolis, Greece
| | - Vangelis G Manolopoulos
- Laboratory of Pharmacology, Medical School, Democritus University of Thrace, Dragana Campus, 68100 Alexandroupolis, Greece.,Pharmacology & Pharmacogenetics Unit, Academic General Hospital of Evros, Alexandroupolis, Greece
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35
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De Nys S, Duca RC, Nawrot T, Hoet P, Van Meerbeek B, Van Landuyt KL, Godderis L. Temporal variability of global DNA methylation and hydroxymethylation in buccal cells of healthy adults: Association with air pollution. ENVIRONMENT INTERNATIONAL 2018; 111:301-308. [PMID: 29217223 DOI: 10.1016/j.envint.2017.11.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/11/2017] [Accepted: 11/02/2017] [Indexed: 05/17/2023]
Abstract
BACKGROUND Epigenetic changes, such as DNA methylation, are observed in response to environmental exposure and in the development of several chronic diseases. Consequently, DNA methylation alterations might serve as indicators of early effects. In this context, the aim of this study was to assess the temporal variability of global DNA methylation and hydroxymethylation levels in buccal cells from healthy adult volunteers. METHODS Global DNA methylation (%5mdC) and hydroxymethylation (%5hmdC) levels in human buccal cells, collected from 26 healthy adults at different time points, were quantified by UPLC-MS/MS. Associations between %5mdC and %5hmdC, respectively, and short-term exposure (1-7days) to air pollutants PM2.5 and PM10 were tested with mixed-effects models including various covariates. RESULTS/DISCUSSION Dynamic short-term changes in DNA methylation and hydroxymethylation levels in buccal cells were observed, which were inversely associated with exposure to PM2.5 and PM10. An IQR increase in PM2.5 over a 7-day moving average period was significantly associated with a decrease of -1.47% (-1.74%, -1.20%) and -0.043% (-0.054%, -0.032%) in %5mdC and %5hmdC, respectively. Likewise, for PM10, a decrease of -1.42% (-1.70, -1.13) and -0.040% (-0.051%, -0.028%) was observed. CONCLUSION Global DNA methylation and hydroxymethylatation varied over a time period of three weeks. The observed temporal variability was associated with exposure to ambient PM2.5 and PM10 levels. This should be taken into account when interpreting epigenetic alterations in buccal cells.
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Affiliation(s)
- Siemon De Nys
- KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven (UZ Leuven), Dentistry, Leuven, Belgium
| | - Radu-Corneliu Duca
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium
| | - Tim Nawrot
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium; Centre for Environmental Sciences, Hasselt University, Belgium
| | - Peter Hoet
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium
| | - Bart Van Meerbeek
- KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven (UZ Leuven), Dentistry, Leuven, Belgium
| | - Kirsten L Van Landuyt
- KU Leuven (University of Leuven), Department of Oral Health Sciences, BIOMAT & University Hospitals Leuven (UZ Leuven), Dentistry, Leuven, Belgium
| | - Lode Godderis
- Environment and Health, Department of Public Health and Primary Care, KU Leuven (University of Leuven), Kapucijnenvoer 35, 3000 Leuven, Belgium; IDEWE, External Service for Prevention and Protection at Work, Heverlee, Belgium.
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36
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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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37
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Schmitz J, Kumsta R, Moser D, Güntürkün O, Ocklenburg S. KIAA0319 promoter DNA methylation predicts dichotic listening performance in forced-attention conditions. Behav Brain Res 2018; 337:1-7. [DOI: 10.1016/j.bbr.2017.09.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/19/2017] [Accepted: 09/22/2017] [Indexed: 12/21/2022]
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38
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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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Chastain LG, Sarkar DK. Alcohol effects on the epigenome in the germline: Role in the inheritance of alcohol-related pathology. Alcohol 2017; 60:53-66. [PMID: 28431793 DOI: 10.1016/j.alcohol.2016.12.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 12/04/2016] [Accepted: 12/30/2016] [Indexed: 12/18/2022]
Abstract
Excessive alcohol exposure has severe health consequences, and clinical and animal studies have demonstrated that disruptions in the epigenome of somatic cells, such as those in brain, are an important factor in the development of alcohol-related pathologies, such as alcohol-use disorders (AUDs) and fetal alcohol spectrum disorders (FASDs). It is also well known that alcohol-related health problems are passed down across generations in human populations, but the complete mechanisms for this phenomenon are currently unknown. Recent studies in animal models have suggested that epigenetic factors are also responsible for the transmission of alcohol-related pathologies across generations. Alcohol exposure has been shown to induce changes in the epigenome of sperm of exposed male animals, and these epimutations are inherited in the offspring. This paper reviews evidence for multigenerational and transgenerational epigenetic inheritance of alcohol-related pathology through the germline. We also review the literature on the epigenetic effects of alcohol exposure on somatic cells in brain, and its contribution to AUDs and FASDs. We note gaps in knowledge in this field, such as the lack of clinical studies in human populations and the lack of data on epigenetic inheritance via the female germline, and we suggest future research directions.
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Affiliation(s)
- Lucy G Chastain
- The Endocrine Program, Department of Animal Sciences, Rutgers, The State University of New Jersey, 67 Poultry Lane, New Brunswick, NJ 08901, USA
| | - Dipak K Sarkar
- The Endocrine Program, Department of Animal Sciences, Rutgers, The State University of New Jersey, 67 Poultry Lane, New Brunswick, NJ 08901, USA.
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40
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Berkel TDM, Pandey SC. Emerging Role of Epigenetic Mechanisms in Alcohol Addiction. Alcohol Clin Exp Res 2017; 41:666-680. [PMID: 28111764 DOI: 10.1111/acer.13338] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/09/2017] [Indexed: 12/15/2022]
Abstract
Alcohol use disorder (AUD) is a complex brain disorder with an array of persistent behavioral and neurochemical manifestations. Both genetic and environmental factors are known to contribute to the development of AUD, and recent studies on alcohol exposure and subsequent changes in gene expression suggest the importance of epigenetic mechanisms. In particular, histone modifications and DNA methylation have emerged as important regulators of gene expression and associated phenotypes of AUD. Given the therapeutic potential of epigenetic targets, this review aims to summarize the role of epigenetic regulation in our current understanding of AUD by evaluating known epigenetic signatures of brain regions critical to addictive behaviors in both animal and human studies throughout various stages of AUD. More specifically, the effects of acute and chronic alcohol exposure, tolerance, and postexposure withdrawal on epigenetically induced changes to gene expression and synaptic plasticity within key brain regions and the associated behavioral phenotypes have been discussed. Understanding the contribution of epigenetic regulation to crucial signaling pathways may prove vital for future development of novel biomarkers and treatment agents in ameliorating or preventing AUD.
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Affiliation(s)
- Tiffani D M Berkel
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois.,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois.,Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois.,Department of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, Illinois
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