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Liu Y, Koo JS, Zhang H. Chronic intermittent ethanol exposure-induced m6A modifications around mRNA stop codons of opioid receptor genes. Epigenetics 2024; 19:2294515. [PMID: 38118075 PMCID: PMC10761033 DOI: 10.1080/15592294.2023.2294515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Chronic alcohol consumption may alter mRNA methylation and expression levels of genes related to addiction and reward in the brain, potentially contributing to alcohol tolerance and dependence. Neuron-like (SH-SY5Y) and non-neuronal (SW620) cells were utilized as models to examine chronic intermittent ethanol (CIE) exposure-induced global m6A RNA methylation changes, as well as m6A mRNA methylation changes around the stop codon of three opioid receptor genes (OPRM1, OPRD1, and OPRK1), which are known to regulate pain, reward, and addiction behaviours. CIE exposure for three weeks significantly increased global RNA methylation levels in both SH-SY5Y (t = 3.98, P = 0.007) and SW620 (t = 2.24, P = 0.067) cells. However, a 3-week CIE exposure resulted in hypomethylation around mRNA stop codon regions of OPRM1 and OPRD1 in both cell lines [OPRM1(SH-SY5Y): t = -5.05, P = 0.0005; OPRM1(SW620): t = -3.19, P = 0.013; OPRD1(SH-SY5Y): t = -13.43, P < 0.00001; OPRD1(SW620): t = -4.00, P = 0.003]. Additionally, mRNA expression levels of OPRM1, OPRD1, and OPRK1 were downregulated (corresponding to mRNA hypomethylation) in both SH-SY5Y and SW620 cells after a 3-week CIE exposure. The present study demonstrated that chronic ethanol exposure altered global RNA methylation levels, as well as mRNA methylation and expression levels of opioid receptor genes in both neuron-like and non-neuronal cells. Our findings suggest a potential epitranscriptomic mechanism by which chronic alcohol consumption remodels the expression of reward-related and alcohol responsive genes in the brain, thus increasing the risk of alcohol use disorder development.Abbreviations: OPRM1: the μ-opioid receptor; OPRD1: the δ-opioid receptor; OPRK1: the κ-opioid receptor; CIE: chronic intermittent ethanol exposure; CIE+WD: chronic intermittent ethanol exposure followed by a 24-hr withdrawal; SH-SY5Y: human neuroblastoma cell Line; SW620: human colon carcinoma cell line; RT-qPCR: reverse transcription followed by quantitative polymerase reaction; MazF-RT-qPCR: MazF digestion followed by RT-qPCR.
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Affiliation(s)
- Ying Liu
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, USA
| | - Ji Sun Koo
- Department of Biology, Boston University, Boston, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, USA
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, Boston, USA
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Özkan-Kotiloğlu S, Kaya-Akyüzlü D, Güven E, Doğan Ö, Ağtaş-Ertan E, Özgür-İlhan İ. A case control study investigating the methylation levels of GHRL and GHSR genes in alcohol use disorder. Mol Biol Rep 2024; 51:663. [PMID: 38771494 DOI: 10.1007/s11033-024-09585-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
BACKGROUND Alcohol use disorder (AUD) is a relapsing disease described as excessive use of alcohol. Evidence of the role of DNA methylation in addiction is accumulating. Ghrelin is an important peptide known as appetite hormone and its role in addictive behavior has been identified. Here we aimed to determine the methylation levels of two crucial genes (GHRL and GHSR) in ghrelin signaling and further investigate the association between methylation ratios and plasma ghrelin levels. METHODS Individuals diagnosed with (n = 71) and without (n = 82) AUD were recruited in this study. DNA methylation levels were measured through methylation-sensitive high-resolution melting (MS-HRM). Acylated ghrelin levels were detected by ELISA. The GHRL rs696217 polymorphism was analyzed by the standard PCR-RFLP method. RESULTS GHRL was significantly hypermethylated (P < 0.0022) in AUD between 25 and 50% methylation than in control subjects but no significant changes of GHSR methylation were observed. Moreover, GHRL showed significant positive correlation of methylation ratio between 25 and 50% with age. A significant positive correlation between GHSR methylation and ghrelin levels in the AUD group was determined (P = 0.037). The level of GHRL methylation and the ghrelin levels showed a significant association in the control subjects (P = 0.042). CONCLUSION GHSR and GHRL methylation levels did not change significantly between control and AUD groups. However, GHRL and GHSR methylations seemed to have associations with plasma ghrelin levels in two groups. This is the first study investigating the DNA methylation of GHRL and GHSR genes in AUD.
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Affiliation(s)
- Selin Özkan-Kotiloğlu
- Department of Molecular Biology and Genetics, Faculty of Science and Art, Kırşehir Ahi Evran University, Kırşehir, Türkiye.
| | | | - Emine Güven
- Department of Biomedical Engineering, Faculty of Engineering, Düzce University, Düzce, Türkiye
- Neuroscience Institute, Morehouse School of Medicine, Atlanta, USA
| | - Özlem Doğan
- Department of Medical Biochemistry, Faculty of Medicine, Ankara University, Ankara, Türkiye
| | - Ece Ağtaş-Ertan
- Department of Mental Health and Diseases, Faculty of Medicine, Ankara University, Ankara, Türkiye
| | - İnci Özgür-İlhan
- Department of Mental Health and Diseases, Faculty of Medicine, Ankara University, Ankara, Türkiye
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Schuch JB, Bandeira CE, Junior JLS, Müller D, Charão MF, da Silva BS, Grevet EH, Kessler FHP, von Diemen L, Rovaris DL, Bau CHD. Global DNA methylation patterns in Alcohol Use Disorder. Genet Mol Biol 2024; 46:e20230139. [PMID: 38197733 PMCID: PMC10778554 DOI: 10.1590/1678-4685-gmb-2023-0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024] Open
Abstract
Alcohol Use Disorder (AUD) is a highly prevalent condition worldwide that produces a wide range of pathophysiological consequences, with a critical impact on health and social issues. Alcohol influences gene expression through epigenetic changes mainly through DNA methylation. In this sense, levels of 5-methylcytosine (5-mC), namely Global DNA methylation (GMe), which can be influenced by environmental and hormonal effects, represent a putative biological mechanism underlying alcohol effects. Our aim was to investigate the influence of AUD diagnosis and alcohol patterns (i.e., years of addiction, use in the last 30 days, and alcohol severity) on GMe levels. The sample consisted of 256 men diagnosed with AUD and 361 men without AUD. DNA samples from peripheral blood were used to assess GMe levels, measured through the levels of 5-mC using high-performance liquid chromatography. Results from multiple linear regression analysis indicated that the presence of AUD was associated with lower GMe levels (beta=-0.155, p=0.011). Other alcohol-related outcomes were not associated with DNA methylation. Our findings are consistent with the hypothesis that the impact of chronic and heavy alcohol use in GMe could be a potential mechanism mediating the multiple organ damages related to AUD.
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Affiliation(s)
- Jaqueline B. Schuch
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa em Álcool e Drogas, Porto Alegre, RS, Brazil
| | - Cibele E. Bandeira
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Fisiologia e Biofísica, São Paulo, SP, Brazil
| | - Jorge L. S. Junior
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Diana Müller
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
| | - Mariele F. Charão
- Universidade Feevale, Programa de Pós-Graduação em Toxicologia e Análises Toxicológicas, Novo Hamburgo, RS, Brazil
| | - Bruna S. da Silva
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Fisiologia e Biofísica, São Paulo, SP, Brazil
| | - Eugenio H. Grevet
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
| | - Felix H. P. Kessler
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa em Álcool e Drogas, Porto Alegre, RS, Brazil
| | - Lisia von Diemen
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Centro de Pesquisa em Álcool e Drogas, Porto Alegre, RS, Brazil
| | - Diego L. Rovaris
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Fisiologia e Biofísica, São Paulo, SP, Brazil
| | - Claiton H. D. Bau
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Psiquiatria, Programa de Pós-Graduação em Psiquiatria e Ciências do Comportamento, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Biociências, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Hospital de Clínicas de Porto Alegre, Programa de Psiquiatria do Desenvolvimento, Porto Alegre, RS, Brazil
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Naue J. Getting the chronological age out of DNA: using insights of age-dependent DNA methylation for forensic DNA applications. Genes Genomics 2023; 45:1239-1261. [PMID: 37253906 PMCID: PMC10504122 DOI: 10.1007/s13258-023-01392-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/15/2023] [Indexed: 06/01/2023]
Abstract
BACKGROUND DNA analysis for forensic investigations has a long tradition with important developments and optimizations since its first application. Traditionally, short tandem repeats analysis has been the most powerful method for the identification of individuals. However, in addition, epigenetic changes, i.e., DNA methylation, came into focus of forensic DNA research. Chronological age prediction is one promising application to allow for narrowing the pool of possible individuals who caused a trace, as well as to support the identification of unknown bodies and for age verification of living individuals. OBJECTIVE This review aims to provide an overview of the current knowledge, possibilities, and (current) limitations about DNA methylation-based chronological age prediction with emphasis on forensic application. METHODS The development, implementation and application of age prediction tools requires a deep understanding about the biological background, the analysis methods, the age-dependent DNA methylation markers, as well as the mathematical models for age prediction and their evaluation. Furthermore, additional influences can have an impact. Therefore, the literature was evaluated in respect to these diverse topics. CONCLUSION The numerous research efforts in recent years have led to a rapid change in our understanding of the application of DNA methylation for chronological age prediction, which is now on the way to implementation and validation. Knowledge of the various aspects leads to a better understanding and allows a more informed interpretation of DNAm quantification results, as well as the obtained results by the age prediction tools.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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Shankarappa B, Mahadevan J, Murthy P, Purushottam M, Viswanath B, Jain S, Devarbhavi H, Mysore Visweswariah A. Hypomethylation of Long Interspersed Nucleotide Elements and Aldehyde Dehydrogenase in Patients of Alcohol Use Disorder with Cirrhosis. DNA Cell Biol 2023. [PMID: 37367217 DOI: 10.1089/dna.2022.0669] [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: 06/28/2023] Open
Abstract
Alcohol use disorder (AUD) and cirrhosis are key outcomes of excessive alcohol use, and a genetic influence in these outcomes is increasingly recognized. While 80-90% of heavy alcohol users show evidence of fatty liver, only 10-20% progress to cirrhosis. There is currently no clear understanding of the causes of this difference in progression. The aim of this study is to evaluate genetics and epigenetics at the aldehyde dehydrogenase (ALDH2) locus in patients with AUD and liver complications. Study participants were inpatients from the clinical services of Gastroenterology and Psychiatry at St. John's Medical College Hospital (SJMCH) and the National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India. Men diagnosed as having AUD with cirrhosis (AUDC+ve, N = 136) and AUD without cirrhosis (AUDC-ve, N = 107) were assessed. FibroScan/sonographic evidence was used to rule out fibrosis in the AUDC-ve group. Genomic DNA was used for genotyping at the ALDH2 (rs2238151) locus. A subset of 89 samples was used for DNA methylation (AUDC+ve, N = 44; and AUDC-ve, N = 45) analysis at long interspersed nucleotide element 1 (LINE-1) and ALDH2 cytosine-phosphate-guanine (CpG) loci by pyrosequencing. ALDH2 DNA methylation was significantly lower in the AUDC+ve group compared with the AUDC-ve group (p < 0.001). Lower methylation was associated with a risk allele (T) of the ALDH2 locus (rs2238151) (p = 0.01). Global (LINE-1) DNA methylation levels were also significantly lower in the AUDC+ve group compared with the AUDC-ve group (p = 0.01). Compromised global methylation (LINE-1) and hypomethylation at the ALDH2 gene was observed in patients with cirrhosis compared with those without cirrhosis. DNA methylation could be explored as a biomarker for cirrhosis and liver complications.
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Affiliation(s)
- Bhagyalakshmi Shankarappa
- Department of Psychiatry, St. John's Medical College Hospital, Bangalore, India
- Molecular Genetics Laboratory, Department of Psychiatry, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Jayant Mahadevan
- Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Pratima Murthy
- Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Meera Purushottam
- Molecular Genetics Laboratory, Department of Psychiatry, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Biju Viswanath
- Molecular Genetics Laboratory, Department of Psychiatry, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
- Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Sanjeev Jain
- Molecular Genetics Laboratory, Department of Psychiatry, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
- Department of Psychiatry, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore, India
| | - Harshad Devarbhavi
- Department of Gastroenterology, St. John's Medical College Hospital, Bangalore, India
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Wang Z, Luo C, Zhou EW, Sandhu AF, Yuan X, Williams GE, Cheng J, Sinha B, Akbar M, Bhattacharya P, Zhou S, Song BJ, Wang X. Molecular Toxicology and Pathophysiology of Comorbid Alcohol Use Disorder and Post-Traumatic Stress Disorder Associated with Traumatic Brain Injury. Int J Mol Sci 2023; 24:ijms24108805. [PMID: 37240148 DOI: 10.3390/ijms24108805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The increasing comorbidity of alcohol use disorder (AUD) and post-traumatic stress disorder (PTSD) associated with traumatic brain injury (TBI) is a serious medical, economic, and social issue. However, the molecular toxicology and pathophysiological mechanisms of comorbid AUD and PTSD are not well understood and the identification of the comorbidity state markers is significantly challenging. This review summarizes the main characteristics of comorbidity between AUD and PTSD (AUD/PTSD) and highlights the significance of a comprehensive understanding of the molecular toxicology and pathophysiological mechanisms of AUD/PTSD, particularly following TBI, with a focus on the role of metabolomics, inflammation, neuroendocrine, signal transduction pathways, and genetic regulation. Instead of a separate disease state, a comprehensive examination of comorbid AUD and PTSD is emphasized by considering additive and synergistic interactions between the two diseases. Finally, we propose several hypotheses of molecular mechanisms for AUD/PTSD and discuss potential future research directions that may provide new insights and translational application opportunities.
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Affiliation(s)
- Zufeng Wang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Forensic Medicine, Soochow University, Suzhou 215006, China
| | - Chengliang Luo
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Department of Forensic Medicine, Soochow University, Suzhou 215006, China
| | - Edward W Zhou
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aaron F Sandhu
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaojing Yuan
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - George E Williams
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jialu Cheng
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Bharati Sinha
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mohammed Akbar
- Division of Neuroscience & Behavior, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD 20892, USA
| | - Pallab Bhattacharya
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, Gandhinagar 382355, Gujarat, India
| | - Shuanhu Zhou
- Harvard Medical School, Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD 20892, USA
| | - Xin Wang
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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Zou T, Shi D, Wang W, Chen G, Zhang X, Tian Y, Gong P. Identification of a New m6A Regulator-Related Methylation Signature for Predicting the Prognosis and Immune Microenvironment of Patients with Pancreatic Cancer. Mediators Inflamm 2023; 2023:5565054. [PMID: 37181810 PMCID: PMC10169250 DOI: 10.1155/2023/5565054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 02/21/2023] [Accepted: 03/31/2023] [Indexed: 05/16/2023] Open
Abstract
Pancreatic cancer (PC) is a malignant tumor of the digestive system that has a bad prognosis. N6-methyladenosine (m6A) is involved in a wide variety of biological activities due to the fact that it is the most common form of mRNA modification in mammals. Numerous research has accumulated evidence suggesting that a malfunction in the regulation of m6A RNA modification is associated with various illnesses, including cancers. However, its implications in PC remain poorly characterized. The methylation data, level 3 RNA sequencing data, and clinical information of PC patients were all retrieved from the TCGA datasets. Genes associated with m6A RNA methylation were compiled from the existing body of research and made available for download from the m6Avar database. The LASSO Cox regression method was used to construct a 4-gene methylation signature, which was then used to classify all PC patients included in the TCGA dataset into either a low- or high-risk group. In this study, based on the set criteria of |cor| > 0.4 and p value < 0.05. A total of 3507 gene methylation were identified to be regulated by m6A regulators. Based on the univariate Cox regression analysis and identified 3507 gene methylation, 858 gene methylation was significantly associated with the patient's prognosis. The multivariate Cox regression analysis identified four gene methylation (PCSK6, HSP90AA1, TPM3, and TTLL6) to construct a prognosis model. Survival assays indicated that the patients in the high-risk group tend to have a worse prognosis. ROC curves showed that our prognosis signature had a good prediction ability on patient survival. Immune assays suggested a different immune infiltration pattern in patients with high- and low-risk scores. Moreover, we found that two immune-related genes, CTLA4 and TIGIT, were downregulated in high-risk patients. We generated a unique methylation signature that is related to m6A regulators and is capable of accurately predicting the prognosis for patients with PC. The findings might prove useful for therapeutic customization and the process of making medical decisions.
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Affiliation(s)
- Tianle Zou
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, China
- College of Nursing, Shenzhen University Medical School, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Dan Shi
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Weiwei Wang
- Hepatobiliary Surgery, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Guoyong Chen
- Hepatobiliary Surgery, People's Hospital of Zhengzhou University and Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Xianbin Zhang
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, China
| | - Yu Tian
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, China
- School of Public Health, Benedictine University, Lisle, USA
| | - Peng Gong
- Department of General Surgery and Integrated Chinese and Western Medicine, Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Carson International Cancer Center, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong 518060, China
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8
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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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DNA Hypomethylation as a Potential Link between Excessive Alcohol Intake and Cardiometabolic Dysfunction in Morbidly Obese Adults. Biomedicines 2022; 10:biomedicines10081954. [PMID: 36009501 PMCID: PMC9406007 DOI: 10.3390/biomedicines10081954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/24/2022] Open
Abstract
A large percentage of obese patients in the United States suffer a comorbid substance use disorder, mainly alcohol use. Alcohol consumption interferes with the absorption of dietary methyl donors such as folate required for the one-carbon metabolism pathway and subsequently for DNA methylation. In this study, we assessed the association between alcohol consumption and DNA methylation in obese subjects. We obtained visceral adipose tissue (VAT) biopsies from bariatric patients. DNA methylation of 94 genes implicated in inflammation and immunity were analyzed in VAT in relation to alcohol consumption data obtained via questionnaires. Vasoreactivity was measured in the brachial artery and the VAT-isolated arterioles. Pro-inflammatory genes were significantly hypomethylated in the heavy drinking category correlating with higher levels of circulating inflammatory cytokines. Alcohol consumption correlated positively with body mass index (BMI), fat percentage, insulin resistance, impaired lipid profile, and systemic inflammation and negatively with plasma folate and vitamin B12, inflammatory gene DNA methylation, and vasoreactivity. In conclusion, these data suggest that alcohol intake is associated with lower DNA methylation and higher inflammation and cardiometabolic risk in obese individuals.
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10
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Zindler T, Frieling H, Fliedner L, Veer IM, Neyazi A, Awasthi S, Ripke S, Walter H, Friedel E. How alcohol makes the epigenetic clock tick faster and the clock reversing effect of abstinence. Addict Biol 2022; 27:e13198. [DOI: 10.1111/adb.13198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 11/29/2022]
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
| | - Lena Fliedner
- Charité–Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of Health, Charité Campus Mitte (CCM) Berlin Germany
| | - Ilya M. Veer
- Charité–Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of Health, Charité Campus Mitte (CCM) Berlin Germany
| | - Alexandra Neyazi
- Department of Psychiatry, Social Psychiatry and Psychotherapy Hannover Medical School Hannover Germany
| | - Swapnil Awasthi
- Charité–Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of Health, Charité Campus Mitte (CCM) Berlin Germany
| | - Stephan Ripke
- Charité–Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of Health, Charité Campus Mitte (CCM) Berlin Germany
| | - Henrik Walter
- Charité–Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of Health, Charité Campus Mitte (CCM) Berlin Germany
| | - Eva Friedel
- Charité–Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt‐Universität zu Berlin, and Berlin Institute of Health, Charité Campus Mitte (CCM) Berlin Germany
- Berlin Institute of Health (BIH) Berlin Germany
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11
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Dragic D, Chang SL, Ennour-Idrissi K, Durocher F, Severi G, Diorio C. Association between alcohol consumption and DNA methylation in blood: a systematic review of observational studies. Epigenomics 2022; 14:793-810. [PMID: 35762294 DOI: 10.2217/epi-2022-0055] [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: 11/21/2022] Open
Abstract
Aim: We systematically reviewed and evaluated current literature on alcohol consumption and DNA methylation (DNAm) at the genome-wide and probe-wise level in blood of adults. Materials & methods: Five databases (PubMed, Embase, Web of Science, CINAHL and PsycInfo) were searched until 20 December 2020. Studies assessing the effect of alcohol dependence on DNAm were not eligible. Results: 11 cross-sectional studies were included with 88 to 9643 participants. Overall, all studies had a risk of bias criteria unclear or unmet. Epigenome-wide association studies identified between 0 and 5458 differentially methylated positions, and 15 were observed in at least four studies. Conclusion: Potential methylation markers for alcohol consumption have been identified, but further validation in large cohorts is needed.
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Affiliation(s)
- Dzevka Dragic
- Department of Social & Preventive Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada.,Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome & Heredity" team, Gustave Roussy, Villejuif, 94807, France
| | - Sue-Ling Chang
- Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada
| | - Kaoutar Ennour-Idrissi
- Department of Social & Preventive Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada.,Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Department of Molecular Biology, Medical Biochemistry & Pathology, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Francine Durocher
- Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada
| | - Gianluca Severi
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome & Heredity" team, Gustave Roussy, Villejuif, 94807, France.,Department of Statistics, Computer Science & Applications "G. Parenti" (DISIA), University of Florence, Florence, 50134, Italy
| | - Caroline Diorio
- Department of Social & Preventive Medicine, Faculty of Medicine, Université Laval, Quebec, QC, G1V 0A6, Canada.,Cancer Research Center, CHU de Québec Research Center, Oncology division, Quebec, QC, G1R 3S3, Canada.,Deschênes-Fabia Center for Breast Diseases, Saint-Sacrement Hospital, Quebec, QC, G1S 4L8, Canada
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12
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Bøstrand SM, Vaher K, de Nooij L, Harris MA, Cole JH, Cox SR, Marioni RE, McCartney DL, Walker RM, McIntosh AM, Evans KL, Whalley HC, Wootton RE, Clarke TK. Associations between alcohol use and accelerated biological ageing. Addict Biol 2022; 27:e13100. [PMID: 34636470 PMCID: PMC7614236 DOI: 10.1111/adb.13100] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 08/31/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022]
Abstract
Harmful alcohol use is a leading cause of premature death and is associated with age-related disease. Biological ageing is highly variable between individuals and may deviate from chronological ageing, suggesting that biomarkers of biological ageing (derived from DNA methylation or brain structural measures) may be clinically relevant. Here, we investigated the relationships between alcohol phenotypes and both brain and DNA methylation age estimates. First, using data from UK Biobank and Generation Scotland, we tested the association between alcohol consumption (units/week) or hazardous use (Alcohol Use Disorders Identification Test [AUDIT] scores) and accelerated brain and epigenetic ageing in 20,258 and 8051 individuals, respectively. Second, we used Mendelian randomisation (MR) to test for a causal effect of alcohol consumption levels and alcohol use disorder (AUD) on biological ageing. Alcohol use showed a consistent positive association with higher predicted brain age (AUDIT-C: β = 0.053, p = 3.16 × 10-13 ; AUDIT-P: β = 0.052, p = 1.6 × 10-13 ; total AUDIT score: β = 0.062, p = 5.52 × 10-16 ; units/week: β = 0.078, p = 2.20 × 10-16 ), and two DNA methylation-based estimates of ageing, GrimAge (units/week: β = 0.053, p = 1.48 × 10-7 ) and PhenoAge (units/week: β = 0.077, p = 2.18x10-10 ). MR analyses revealed limited evidence for a causal effect of AUD on accelerated brain ageing (β = 0.118, p = 0.044). However, this result should be interpreted cautiously as the significant effect was driven by a single genetic variant. We found no evidence for a causal effect of alcohol consumption levels on accelerated biological ageing. Future studies investigating the mechanisms associating alcohol use with accelerated biological ageing are warranted.
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Affiliation(s)
- Sunniva M.K. Bøstrand
- Division of Psychiatry, Royal Edinburgh Hospital, The University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, UK
| | - Kadi Vaher
- Division of Psychiatry, Royal Edinburgh Hospital, The University of Edinburgh, Edinburgh, UK
- MRC Centre for Reproductive Health, The Queen’s Medical Research Institute, The University of Edinburgh, Edinburgh, UK
| | - Laura de Nooij
- Division of Psychiatry, Royal Edinburgh Hospital, The University of Edinburgh, Edinburgh, UK
| | - Matthew A. Harris
- Division of Psychiatry, Royal Edinburgh Hospital, The University of Edinburgh, Edinburgh, UK
| | - James H. Cole
- Centre for Medical Image Computing, Department of Computer Science, University College London, London, UK
- Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London, UK
- Dementia Research Centre, Institute of Neurology, University College London, London, UK
| | - Simon R. Cox
- Department of Psychology, The University of Edinburgh, Edinburgh, UK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, The University of Edinburgh, Edinburgh, UK
| | - Andrew M. McIntosh
- Division of Psychiatry, Royal Edinburgh Hospital, The University of Edinburgh, Edinburgh, UK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Heather C. Whalley
- Division of Psychiatry, Royal Edinburgh Hospital, The University of Edinburgh, Edinburgh, UK
| | - Robyn E. Wootton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Psychological Science, University of Bristol, Bristol, UK
| | - Toni-Kim Clarke
- Division of Psychiatry, Royal Edinburgh Hospital, The University of Edinburgh, Edinburgh, UK
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13
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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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14
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Babkina AS, Khadzhiyeva MB, Ostrova IV, Ryzhkov IA, Golubev AM. Global DNA Methylation Of Brain Neurons In Acute Poisoning With Clozapine And Its Combination With Alcohol: An Experimental Study. RUSSIAN OPEN MEDICAL JOURNAL 2021. [DOI: 10.15275/rusomj.2021.0306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Background — Acute poisoning with atypical neuroleptic clozapine is characterized by rapid progression, high risk of death and severe neurological manifestations. Neurotoxic effects of this pharmaceutical drug have also been reported at therapeutic doses. The pathogenesis of brain damage in acute clozapine poisoning is not fully understood. Changes in DNA methylation level may play an important role in the mechanisms of drug neurotoxicity. The available data on the effect of clozapine on brain cell DNA provide a rationale for studying the epigenetic aspects of the pathogenesis of acute poisoning with this neuroleptic agent. The objective of our study was to evaluate the global DNA methylation level in rat brain neurons in acute poisoning with clozapine and its combination with ethanol. Material and methods — Clozapine – 150 mg/kg in 2.0 ml of normal saline solution, or clozapine – 150 mg/kg in 2.0 ml of 40% ethanol were administered via a gastric tube to adult male Wistar rats (n=21) under anesthesia with sevoflurane. In the control group, saline was administered via a gastric tube. Animals were euthanized four hours after drug administration. Autopsy was performed with the collection of brain samples for histochemical examination and determination of the DNA methylation level using the fluorometric method. To detect DNA in sections of paraffin-embedded tissue, we used the Feulgen staining. The TUNEL method was employed to detect DNA fragmentation. Results — An increase in the level of global DNA methylation in brain neurons was found in the clozapine and clozapine+ethanol groups. The average level of methylated DNA in the clozapine+ethanol group was higher than in the control group or clozapine group (2.56±0.31 vs. 1.35±0.1, p=0.007 and 1.70±0.33, p=0.044, respectively). An increase in the mean optical density of the cortical neuron nuclei was observed in the clozapine+ethanol group compared with the control group and clozapine group. DNA fragmentation was not detected in any experimental group. Conclusion — Acute poisoning with clozapine in combination with alcohol caused an increase in the global DNA methylation level in brain neurons, which may have played a significant role in the pathogenesis of acute clozapine poisoning and could be an important factor in the neurotoxicity of this medication.
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Affiliation(s)
- Anastasiya S. Babkina
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Maryam B. Khadzhiyeva
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Irina V. Ostrova
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Ivan A. Ryzhkov
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - Arkady M. Golubev
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
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15
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Liu L, Yang X, Zhao F, Gao C, Zhang N, Bao J, Li K, Zhang X, Lu X, Ruan Y, Zhong S. Hypermethylation of the OPRM1 and ALDH2 promoter regions in Chinese Han males with alcohol use disorder in Yunnan Province. THE AMERICAN JOURNAL OF DRUG AND ALCOHOL ABUSE 2021; 47:694-703. [PMID: 34582308 DOI: 10.1080/00952990.2021.1973486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Alcohol use disorder (AUD) is one of the most serious public health problems worldwide. The OPRM1 and ALDH2 genes are important factors in the reward and alcohol metabolism pathways, and their DNA methylation patterns are closely related to AUD and are population-specific. Chinese Han people are the most populous ethnic group in the world, and this group experiences severe AUD. No epigenetic study on OPRM1 and ALDH2 has been performed in Chinese Han patients with AUD. OBJECTIVES To investigate whether methylation patterns of OPRM1 and ALDH2 are associated with susceptibility to AUD in Chinese Han males. METHODS DNA methylation of the OPRM1 and ALDH2 promoters was studied in Chinese Han males with AUD in Yunnan Province (N = 50 controls, N = 90 individuals with AUD) using the bisulfite pyrosequencing method. RESULTS In the AUD group, compared with the control group, OPRM1 was hypermethylated(p < .01) but there was no significant difference in the methylation level of ALDH2 (p > .05). 9 CpG sites of OPRM1 (p < .05) and 2 CpG sites of ALDH2 (p > .01) were hypermethylated. Smoking promoted AUD-mediated hypermethylation of OPRM1, in which 3 CpG sites showed significant hypermethylation (p < .01). Age had no significant effect on the DNA methylation levels of these two genes. CONCLUSIONS Our study demonstrates that DNA hypermethylation of the OPRM1 and ALDH2 promoter regions is associated with an increased risk of AUD, which may help to explain the pathogenesis and progression of AUD.
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Affiliation(s)
- Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, China.,Forensic biology identification laboratory, Judicial Identification Center of Kunming Medical University, Kunming, China
| | - Xiaopei Yang
- School of Forensic Medicine, Kunming Medical University, Kunming, China.,Department of basic medicine, Chuxiong Medical and Pharmaceutical College, Chuxiong, China
| | - Fei Zhao
- School of Forensic Medicine, Kunming Medical University, Kunming, China.,Forensic Lab 1, Jiangxi Shenzhou Judicial Identification Center, Nanchang, China
| | - Changqing Gao
- Children's mental department, The Mental Hospital of Yunnan Province, Kunming, China.,Children's mental department, Alcohol and Drug Dependence Treatment Department, Mental Health Center Affiliated With Kunming Medical University, Kunming, China
| | - Ning Zhang
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Jianjun Bao
- Alcohol and Drug Dependence Treatment Department, The Mental Hospital of Yunnan Province, Kunming, China.,Alcohol and Drug Dependence Treatment Department, Mental Health Center Affiliated With Kunming Medical University, Kunming, China
| | - Kuan Li
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Xulan Zhang
- Alcohol and Drug Dependence Treatment Department, The Mental Hospital of Yunnan Province, Kunming, China.,Alcohol and Drug Dependence Treatment Department, Mental Health Center Affiliated With Kunming Medical University, Kunming, China
| | - Xiaoxiao Lu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Ye Ruan
- Alcohol and Drug Dependence Treatment Department, The Mental Hospital of Yunnan Province, Kunming, China.,Alcohol and Drug Dependence Treatment Department, Mental Health Center Affiliated With Kunming Medical University, Kunming, China
| | - Shurong Zhong
- School of Forensic Medicine, Kunming Medical University, Kunming, China.,Forensic biology identification laboratory, Judicial Identification Center of Kunming Medical University, Kunming, China
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16
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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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17
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Soundararajan S, Agrawal A, Purushottam M, Anand SD, Shankarappa B, Sharma P, Jain S, Murthy P. Changes in DNA methylation persist over time in males with severe alcohol use disorder-A longitudinal follow-up study. Am J Med Genet B Neuropsychiatr Genet 2021; 186:183-192. [PMID: 33491855 DOI: 10.1002/ajmg.b.32833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 12/31/2020] [Accepted: 01/08/2021] [Indexed: 12/25/2022]
Abstract
Treatment strategies for alcohol use disorder (AUD) aim for abstinence or harm reduction. While deranged biochemical parameters reverse with alcohol abstinence, whether molecular changes at the epigenetic level reverse is not clearly understood. We investigated whether the reduction from high alcohol use reflects DNA methylation at the gene-specific and global level. In subjects seeking treatment for severe AUD, we assessed gene-specific (aldehyde dehydrogenase [ALDH2]/methylene tetrahydrofolate reductase [MTHFR]) and global (long interspersed elements [LINE-1]) methylation across three-time points (baseline, after detoxification and at an early remission period of 3 months), in peripheral blood leukocytes. We observed that both gene-specific and global DNA methylation did not change over time, irrespective of the drinking status at 3 months (52% abstained from alcohol). Further, we also compared DNA methylation in AUD subjects with healthy controls. At baseline, there was a significantly higher gene-specific DNA methylation (ALDH2: p < .001 and MTHFR: p = .001) and a significant lower global methylation (LINE-1: p = .014) in AUD as compared to controls. Our results suggest that epigenetic changes at the DNA methylation level associated with severe AUD persist for at least 3 months of treatment.
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Affiliation(s)
- Soundarya Soundararajan
- Department of Clinical Neurosciences, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Centre for Addiction Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Meera Purushottam
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Shravanthi Daphne Anand
- Centre for Addiction Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Bhagyalakshmi Shankarappa
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Priyamvada Sharma
- Centre for Addiction Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Department of Clinical Pharmacology and Neurotoxicology, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Sanjeev Jain
- Molecular Genetics Laboratory, Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
| | - Pratima Murthy
- Centre for Addiction Medicine, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India.,Department of Psychiatry, National Institute of Mental Health and Neuro Sciences (NIMHANS), Bengaluru, India
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18
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Dugué PA, Wilson R, Lehne B, Jayasekara H, Wang X, Jung CH, Joo JE, Makalic E, Schmidt DF, Baglietto L, Severi G, Gieger C, Ladwig KH, Peters A, Kooner JS, Southey MC, English DR, Waldenberger M, Chambers JC, Giles GG, Milne RL. Alcohol consumption is associated with widespread changes in blood DNA methylation: Analysis of cross-sectional and longitudinal data. Addict Biol 2021; 26:e12855. [PMID: 31789449 DOI: 10.1111/adb.12855] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 09/29/2019] [Accepted: 11/04/2019] [Indexed: 12/26/2022]
Abstract
DNA methylation may be one of the mechanisms by which alcohol consumption is associated with the risk of disease. We conducted a large-scale, cross-sectional, genome-wide DNA methylation association study of alcohol consumption and a longitudinal analysis of repeated measurements taken several years apart. Using the Illumina HumanMethylation450 BeadChip, DNA methylation was measured in blood samples from 5606 Melbourne Collaborative Cohort Study (MCCS) participants. For 1088 of them, these measures were repeated using blood samples collected a median of 11 years later. Associations between alcohol intake and blood DNA methylation were assessed using linear mixed-effects regression models. Independent data from the London Life Sciences Prospective Population (LOLIPOP) (N = 4042) and Cooperative Health Research in the Augsburg Region (KORA) (N = 1662) cohorts were used to replicate associations discovered in the MCCS. Cross-sectional analyses identified 1414 CpGs associated with alcohol intake at P < 10-7 , 1243 of which had not been reported previously. Of these novel associations, 1078 were replicated (P < .05) using LOLIPOP and KORA data. Using the MCCS data, we also replicated 403 of 518 previously reported associations. Interaction analyses suggested that associations were stronger for women, non-smokers, and participants genetically predisposed to consume less alcohol. Of the 1414 CpGs, 530 were differentially methylated (P < .05) in former compared with current drinkers. Longitudinal associations between the change in alcohol intake and the change in methylation were observed for 513 of the 1414 cross-sectional associations. Our study indicates that alcohol intake is associated with widespread changes in DNA methylation across the genome. Longitudinal analyses showed that the methylation status of alcohol-associated CpGs may change with alcohol consumption changes in adulthood.
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Affiliation(s)
- Pierre-Antoine Dugué
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Harindra Jayasekara
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Xiaochuan Wang
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
| | - Chol-Hee Jung
- Melbourne Bioinformatics, The University of Melbourne, Parkville, VIC, Australia
| | - JiHoon E Joo
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, Australia
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Daniel F Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Laura Baglietto
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Gianluca Severi
- CESP, INSERM U1018, Univ. Paris-Sud, UVSQ, Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
| | - Karl-Heinz Ladwig
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Klinik und Poliklinik für Psychosomatische Medizin und Psychotherapie des Klinikums Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, Middlesex, UK
- Imperial College Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Melissa C Southey
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Dallas R English
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Munich, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, Middlesex, UK
- Imperial College Healthcare NHS Trust, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Graham G Giles
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
| | - Roger L Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, Australia
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Stephenson M, Bollepalli S, Cazaly E, Salvatore JE, Barr P, Rose RJ, Dick D, Kaprio J, Ollikainen M. Associations of Alcohol Consumption With Epigenome-Wide DNA Methylation and Epigenetic Age Acceleration: Individual-Level and Co-twin Comparison Analyses. Alcohol Clin Exp Res 2020; 45:318-328. [PMID: 33277923 DOI: 10.1111/acer.14528] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND DNA methylation may play a role in the progression from normative to problematic drinking and underlie adverse health outcomes associated with alcohol misuse. We examined the association between alcohol consumption and DNA methylation patterns using 3 approaches: a conventional epigenome-wide association study (EWAS); a co-twin comparison design, which controls for genetic and environmental influences that twins share; and a regression of age acceleration, defined as a discrepancy between chronological age and DNA methylation age, on alcohol consumption. METHODS Participants came from the Finnish Twin Cohorts (FinnTwin12/FinnTwin16; N = 1,004; 55% female; average age = 23 years). Individuals reported the number of alcoholic beverages consumed in the past week, and epigenome-wide DNA methylation was assessed in whole blood using the Infinium HumanMethylation450 BeadChip. RESULTS In the EWAS, alcohol consumption was significantly related to methylation at 24 CpG sites. When evaluating whether differences between twin siblings (185 monozygotic pairs) in alcohol consumption predicted differences in DNA methylation, co-twin comparisons replicated 4 CpG sites from the EWAS and identified 23 additional sites. However, when we examined qualitative differences in drinking patterns between twins (heavy drinker vs. light drinker/abstainer or moderate drinker vs. abstainer; 44 pairs), methylation patterns did not significantly differ within twin pairs. Finally, individuals who reported higher alcohol consumption also exhibited greater age acceleration, though results were no longer significant after controlling for genetic and environmental influences shared by co-twins. CONCLUSIONS Our analyses offer insight into the associations between epigenetic variation and levels of alcohol consumption in young adulthood.
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Affiliation(s)
- Mallory Stephenson
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland
| | - Emma Cazaly
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland
| | - Jessica E Salvatore
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia.,Virginia Institute for Psychiatric and Behavioral Genetics, (JES), Virginia Commonwealth University, Richmond, Virginia
| | - Peter Barr
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia
| | - Richard J Rose
- Department of Psychological and Brain Sciences, (RJR), Indiana University, Bloomington, Indiana
| | - Danielle Dick
- From the, Department of Psychology, (MS, JES, PB, DD), Virginia Commonwealth University, Richmond, Virginia.,Department of Human and Molecular Genetics, (DD), Virginia Commonwealth University, Richmond, Virginia
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland.,Department of Public Health, (JK, MO), University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), (SB, EC, JK, MO), University of Helsinki, Helsinki, Finland.,Department of Public Health, (JK, MO), University of Helsinki, Helsinki, Finland
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20
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Spence JP, Lai D, Reiter JL, Cao S, Bell RL, Williams KE, Liang T. Epigenetic changes on rat chromosome 4 contribute to disparate alcohol drinking behavior in alcohol-preferring and -nonpreferring rats. Alcohol 2020; 89:103-112. [PMID: 32798691 PMCID: PMC7722131 DOI: 10.1016/j.alcohol.2020.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/24/2020] [Accepted: 08/09/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND Paternal alcohol abuse is a well-recognized risk factor for the development of an alcohol use disorder (AUD). In addition to genetic and environmental risk factors, heritable epigenetic factors also have been proposed to play a key role in the development of AUD. However, it is not clear whether epigenetic factors contribute to the genetic inheritance in families affected by AUD. We used reciprocal crosses of the alcohol-preferring (P) and -nonpreferring (NP) rat lines to test whether epigenetic factors also impacted alcohol drinking in up to two generations of offspring. METHODS F1 offspring derived by reciprocal breeding of P and NP rats were tested for differences in alcohol consumption using a free-choice protocol of 10% ethanol, 20% ethanol, and water that were available concurrently. In a separate experiment, an F2 population was tested for alcohol consumption not only due to genetic differences. These rats were generated from inbred P (iP) and iNP rat lines that were reciprocally bred to produce genetically identical F1 offspring that remained alcohol-naïve. Intercrosses of the F1 generation animals produced the F2 generation. Alcohol consumption was then assessed in the F2 generation using a standard two-bottle choice protocol, and was analyzed using genome-wide linkage analysis. Alcohol consumption measures were also analyzed for sex differences. RESULTS Average alcohol consumption was higher in the F1 offspring of P vs. NP sires and in the F2 offspring of F0 iP vs. iNP grandsires. Linkage analyses showed the maximum LOD scores for alcohol consumption in both male and female offspring were on chromosome 4 (Chr 4). The LOD score for both sexes considered together was higher when the grandsire was iP vs. iNP (5.0 vs. 3.35, respectively). Furthermore, the F2 population displayed enhanced alcohol consumption when the P alleles from the F0 sire were present. CONCLUSIONS These results demonstrate that epigenetic and/or non-genetic factors mapping to rat chromosome 4 contribute to a transgenerational paternal effect on alcohol consumption in the P and NP rat model of AUD.
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Affiliation(s)
- John Paul Spence
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Dongbing Lai
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Jill L Reiter
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Sha Cao
- Department of Biostatistics, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Richard L Bell
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Kent E Williams
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States
| | - Tiebing Liang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, United States.
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21
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Shu C, Justice AC, Zhang X, Wang Z, Hancock DB, Johnson EO, Xu K. DNA methylation mediates the effect of cocaine use on HIV severity. Clin Epigenetics 2020; 12:140. [PMID: 32928285 PMCID: PMC7491141 DOI: 10.1186/s13148-020-00934-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022] Open
Abstract
Background Cocaine use accelerates human immunodeficiency virus (HIV) progression and worsens HIV outcomes. We assessed whether DNA methylation in blood mediates the association between cocaine use and HIV severity in a veteran population. Methods We analyzed 1435 HIV-positive participants from the Veterans Aging Cohort Study Biomarker Cohort (VACS-BC). HIV severity was measured by the Veteran Aging Cohort Study (VACS) index. We assessed the effect of cocaine use on VACS index and mortality among the HIV-positive participants. We selected candidate mediators that were associated with both persistent cocaine use and VACS index by epigenome-wide association (EWA) scans at a liberal p value cutoff of 0.001. Mediation analysis of the candidate CpG sites between cocaine’s effect and the VACS index was conducted, and the joint mediation effect of multiple CpGs was estimated. A two-step epigenetic Mendelian randomization (MR) analysis was conducted as validation. Results More frequent cocaine use was significantly associated with a higher VACS index (β = 1.00, p = 2.7E−04), and cocaine use increased the risk of 10-year mortality (hazard ratio = 1.10, p = 0.011) with adjustment for confounding factors. Fifteen candidate mediator CpGs were selected from the EWA scan. Twelve of these CpGs showed significant mediation effects, with each explaining 11.3–29.5% of the variation. The mediation effects for 3 of the 12 CpGs were validated by the two-step epigenetic MR analysis. The joint mediation effect of the 12 CpGs accounted for 47.2% of cocaine’s effect on HIV severity. Genes harboring these 12 CpGs are involved in the antiviral response (IFIT3, IFITM1, NLRC5, PLSCR1, PARP9) and HIV progression (CX3CR1, MX1). Conclusions We identified 12 DNA methylation CpG sites that appear to play a mediation role in the association between cocaine use and HIV severity.
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Affiliation(s)
- Chang Shu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Amy C Justice
- Connecticut Veteran Healthcare System, West Haven, CT, USA.,Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Xinyu Zhang
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA.,Connecticut Veteran Healthcare System, West Haven, CT, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, NC, USA.,Fellow Program, RTI International, Research Triangle Park, NC, USA
| | - Ke Xu
- Department of Psychiatry, Yale School of Medicine, New Haven, CT, USA. .,Connecticut Veteran Healthcare System, West Haven, CT, USA.
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22
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Chen J, Zang Z, Braun U, Schwarz K, Harneit A, Kremer T, Ma R, Schweiger J, Moessnang C, Geiger L, Cao H, Degenhardt F, Nöthen MM, Tost H, Meyer-Lindenberg A, Schwarz E. Association of a Reproducible Epigenetic Risk Profile for Schizophrenia With Brain Methylation and Function. JAMA Psychiatry 2020; 77:628-636. [PMID: 32049268 PMCID: PMC7042900 DOI: 10.1001/jamapsychiatry.2019.4792] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
IMPORTANCE Schizophrenia is a severe mental disorder in which epigenetic mechanisms may contribute to illness risk. Epigenetic profiles can be derived from blood cells, but to our knowledge, it is unknown whether these predict established brain alterations associated with schizophrenia. OBJECTIVE To identify an epigenetic signature (quantified as polymethylation score [PMS]) of schizophrenia using machine learning applied to genome-wide blood DNA-methylation data; evaluate whether differences in blood-derived PMS are mirrored in data from postmortem brain samples; test whether the PMS is associated with alterations of dorsolateral prefrontal cortex hippocampal (DLPFC-HC) connectivity during working memory in healthy controls (HC); explore the association between interactions between polygenic and epigenetic risk with DLPFC-HC connectivity; and test the specificity of the signature compared with other serious psychiatric disorders. DESIGN, SETTING, AND PARTICIPANTS In this case-control study conducted from 2008 to 2018 in sites in Germany, the United Kingdom, the United States, and Australia, blood DNA-methylation data from 2230 whole-blood samples from 6 independent cohorts comprising HC (1238 [55.5%]) and participants with schizophrenia (803 [36.0%]), bipolar disorder (39 [1.7%]), major depressive disorder 35 [1.6%]), and autism (27 [1.2%]), and first-degree relatives of all patient groups (88 [3.9%]) were analyzed. DNA-methylation data were further explored from 244 postmortem DLPFC samples from 136 HC and 108 patients with schizophrenia. Neuroimaging and genome-wide association data were available for 393 HC. The latter data was used to calculate a polygenic risk score (PRS) for schizophrenia. The data were analyzed in 2019. MAIN OUTCOMES AND MEASURES The accuracy of schizophrenia control classification based on machine learning using epigenetic data; association of schizophrenia PMS scores with DLPFC-HC connectivity; and association of the interaction between PRS and PMS with DLPFC-HC connectivity. RESULTS This study included 7488 participants (4395 men [58.7%]), of whom 3158 (2230 men [70.6%]) received a diagnosis of schizophrenia. The PMS signature was associated with schizophrenia across 3 independent data sets (area under the curve [AUC] from 0.69 to 0.78; P value from 0.049 to 1.24 × 10-7) and data from postmortem DLPFC samples (AUC = 0.63; P = 1.42 × 10-4), but not with major depressive disorder (AUC = 0.51; P = .16), autism (AUC = 0.53; P = .66), or bipolar disorder (AUC = 0.58; P = .21). Pathways contributing most to the classification included synaptic processes. Healthy controls with schizophrenia-like PMS showed significantly altered DLPFC-HC connectivity (validation methylation/magnetic resonance imaging, t < -3.81; P for familywise error, <.04; validation magnetic resonance imaging, t < -3.54; P for familywise error, <.02), mirroring the lack of functional decoupling in schizophrenia. There was no significant association of the interaction between PMS and PRS with DLPFC-HC connectivity (P > .19). CONCLUSIONS AND RELEVANCE We identified a reproducible blood DNA-methylation signature specific for schizophrenia that was correlated with altered functional DLPFC-HC coupling during working memory and mapped to methylation differences found in DLPFC postmortem samples. This indicates a possible epigenetic contribution to a schizophrenia intermediate phenotype and suggests that PMS could be of interest to be studied in the context of multimodal biomarkers for disease stratification and treatment personalization.
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Affiliation(s)
- Junfang Chen
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Zhenxiang Zang
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Urs Braun
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Kristina Schwarz
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Anais Harneit
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Thomas Kremer
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ren Ma
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Janina Schweiger
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carolin Moessnang
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Lena Geiger
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Han Cao
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Franziska Degenhardt
- School of Medicine & University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Markus M. Nöthen
- School of Medicine & University Hospital Bonn, Institute of Human Genetics, University of Bonn, Bonn, Germany,Life & Brain Center, Department of Genomics, University of Bonn, Bonn, Germany
| | - Heike Tost
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Andreas Meyer-Lindenberg
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Emanuel Schwarz
- Central Institute of Mental Health, Department of Psychiatry and Psychotherapy, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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23
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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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24
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Liu J, Wan Y, Li S, Qiu H, Jiang Y, Ma X, Zhou S, Cheng W. Identification of aberrantly methylated differentially expressed genes and associated pathways in endometrial cancer using integrated bioinformatic analysis. Cancer Med 2020; 9:3522-3536. [PMID: 32170852 PMCID: PMC7221444 DOI: 10.1002/cam4.2956] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/21/2020] [Accepted: 02/19/2020] [Indexed: 12/14/2022] Open
Abstract
Endometrial cancer (EC) is a fatal female reproductive tumor. Bioinformatic tools are increasingly developed to screen out molecular targets related to EC. In this study, http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17025 and http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40032 were obtained from Gene Expression Omnibus (GEO). “limma” package and Venn diagram tool were used to identify hub genes. FunRich was used for functional analysis. Retrieval of Interacting Genes Database (STRING) was used to analyze protein‐protein interaction (PPI) complex. Cancer Genome Atlas (TCGA), GEPIA, immunohistochemistry staining, and ROC curve analysis were carried out for validation. Univariate and multivariate regression analyses were performed to predict the risk score. Compound muscle action potential (CMap) was used to find potential drugs. GSEA was also done. We retrieved seven oncogenes which were upregulated and hypomethylated and 12 tumor suppressor genes (TSGs) which were downregulated and hypermethylated. The upregulated and hypomethylated genes were strikingly enriched in term “immune response” while the downregulated and hypermethylated genes were mainly focused on term “aromatic compound catabolic process.” TCGA and GEPIA were used to screen out EDNRB, CDO1, NDN, PLCD1, ROR2, ESPL1, PRAME, and PTTG1. Among them, ESPL1 and ROR2 were identified by Cox regression analysis and were used to construct prognostic risk model. The result showed that ESPL1 was a negative independent prognostic factor. Cmap identified aminoglutethimide, luteolin, sulfadimethoxine, and maprotiline had correlation with EC. GSEA results showed that “hedgehog signaling pathway” was enriched. This research inferred potential aberrantly methylated DEGs and dysregulated pathways may participate in EC development and firstly reported eight hub genes, including EDNRB, CDO1, NDN, PLCD1, ROR2, ESPL1, PRAME, and PTTG1 that could be used to predict EC prognosis. Aminoglutethimide and luteolin may be used to fight against EC.
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Affiliation(s)
- JinHui Liu
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - YiCong Wan
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Siyue Li
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - HuaiDe Qiu
- Center of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yi Jiang
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoling Ma
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - ShuLin Zhou
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - WenJun Cheng
- Department of Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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25
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An analysis of the effect of mu-opioid receptor gene (OPRM1) promoter region DNA methylation on the response of naltrexone treatment of alcohol dependence. THE PHARMACOGENOMICS JOURNAL 2020; 20:672-680. [PMID: 32029903 PMCID: PMC7415483 DOI: 10.1038/s41397-020-0158-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 01/22/2020] [Accepted: 01/27/2020] [Indexed: 12/17/2022]
Abstract
This study explored the effect of OPRM1 promoter region DNA methylation on the outcome of treatment with the opioid antagonist naltrexone (NTX) for alcohol dependence (AD). Ninety-three patients with DSM-IV AD [41 African Americans (AAs) and 52 European Americans (EAs)] received double-blind treatment with NTX or placebo for at least three months. Relapse to heavy drinking was assessed during the first 13 weeks of the trial. Peripheral blood methylation levels of 33 CpG units in the OPRM1 promoter region were quantified using Sequenom EpiTYPER technology. Bayesian logistic regression was used to analyze the effects of NTX treatment, CpG methylation, CpG methylation×NTX treatment, and age on AD relapse. The Random Forest machine learning algorithm was applied to select AD relapse predictors. No significant effect of individual OPRM1 promoter CpG units on AD relapse was observed in either AAs or EAs. Age was significantly associated with AD relapse in EAs, among whom older subjects had a lower relapse rate. Random forest analyses revealed that the prediction rate for AD relapse reached 66.0% with five top variables (age and four CpG units; ranked by their importance to AD relapse) in the prediction model. These findings suggest that methylation levels of individual OPRM1 promoter CpG units do not contribute significantly to inter-individual variation in NTX response. However, the age of subjects in combination with a cluster of specific OPRM1 promoter CpG units may affect NTX treatment outcome. Additional studies of OPRM1 DNA methylation changes during and after NTX treatment of AD are needed.
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26
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Luo A, Jung J, Longley M, Rosoff DB, Charlet K, Muench C, Lee J, Hodgkinson CA, Goldman D, Horvath S, Kaminsky ZA, Lohoff FW. Epigenetic aging is accelerated in alcohol use disorder and regulated by genetic variation in APOL2. Neuropsychopharmacology 2020; 45:327-336. [PMID: 31466081 PMCID: PMC6901591 DOI: 10.1038/s41386-019-0500-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/06/2019] [Accepted: 08/12/2019] [Indexed: 12/31/2022]
Abstract
To investigate the potential role of alcohol use disorder (AUD) in aging processes, we employed Levine's epigenetic clock (DNAm PhenoAge) to estimate DNA methylation age in 331 individuals with AUD and 201 healthy controls (HC). We evaluated the effects of heavy, chronic alcohol consumption on epigenetic age acceleration (EAA) using clinical biomarkers, including liver function test enzymes (LFTs) and clinical measures. To characterize potential underlying genetic variation contributing to EAA in AUD, we performed genome-wide association studies (GWAS) on EAA, including pathway analyses. We followed up on relevant top findings with in silico expression quantitative trait loci (eQTL) analyses for biological function using the BRAINEAC database. There was a 2.22-year age acceleration in AUD compared to controls after adjusting for gender and blood cell composition (p = 1.85 × 10-5). This association remained significant after adjusting for race, body mass index, and smoking status (1.38 years, p = 0.02). Secondary analyses showed more pronounced EAA in individuals with more severe AUD-associated phenotypes, including elevated gamma-glutamyl transferase (GGT) and alanine aminotransferase (ALT), and higher number of heavy drinking days (all ps < 0.05). The genome-wide meta-analysis of EAA in AUD revealed a significant single nucleotide polymorphism (SNP), rs916264 (p = 5.43 × 10-8), in apolipoprotein L2 (APOL2) at the genome-wide level. The minor allele A of rs916264 was associated with EAA and with increased mRNA expression in hippocampus (p = 0.0015). Our data demonstrate EAA in AUD and suggest that disease severity further accelerates epigenetic aging. EAA was associated with genetic variation in APOL2, suggesting potential novel biological mechanisms for age acceleration in AUD.
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Affiliation(s)
- Audrey Luo
- 0000 0001 2297 5165grid.94365.3dSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Jeesun Jung
- 0000 0001 2297 5165grid.94365.3dSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Martha Longley
- 0000 0001 2297 5165grid.94365.3dSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Daniel B. Rosoff
- 0000 0001 2297 5165grid.94365.3dSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Katrin Charlet
- 0000 0001 2297 5165grid.94365.3dSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA ,0000 0001 2218 4662grid.6363.0Department of Psychiatry and Psychotherapy, Charite – Universitaetsmedizin Berlin, Berlin, Germany
| | - Christine Muench
- 0000 0001 2297 5165grid.94365.3dSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Jisoo Lee
- 0000 0001 2297 5165grid.94365.3dSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Colin A. Hodgkinson
- 0000 0001 2297 5165grid.94365.3dLaboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - David Goldman
- 0000 0001 2297 5165grid.94365.3dLaboratory of Neurogenetics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Steve Horvath
- 0000 0000 9632 6718grid.19006.3eDepartment of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA ,0000 0000 9632 6718grid.19006.3eDepartment of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA USA
| | - Zachary A. Kaminsky
- 0000 0001 2182 2255grid.28046.38The Royal’s Institute of Mental Health Research, University of Ottawa, Ottawa, ON Canada
| | - Falk W. Lohoff
- 0000 0001 2297 5165grid.94365.3dSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
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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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Martínez-Rodríguez TY, Rey-Buitrago M. Physiological, molecular and genetic aspects of alpha-synuclein and its correlation with high alcohol consumption. REVISTA DE LA FACULTAD DE MEDICINA 2019. [DOI: 10.15446/revfacmed.v67n3.69962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Introduction: Significant changes in the expression of α-synuclein (SNCA) can be seen in subjects with high alcohol consumption, altering neuroprotection and causing changes in the reward system.Objective: To present state-of-the-art studies on the physiological, molecular and genetic aspects of SNCA related to high alcohol consumption.Materials and methods: A search of records published from 2007 to 2017 was carried out in PUBMED, ScienceDirect and Cochrane with the terms alpha-synuclein, alcoholism, genetic polymorphism, gene expression, DNA methylation and molecular biology.Results: The search yielded 1 331 references, of which 51 full-texts were selected. The results describe the current evidence of the physiological and pathological aspects of α-synuclein (SNCA) and the genetic and epigenetic changes related to its expression in people with high alcohol consumption.Conclusions: The evidence suggests that a differential expression of α-synuclein (SNCA) is found in subjects with high alcohol consumption, as a result of modifications in the genetic and epigenetic mechanisms, leading to physipathological neuroadaptations. SNCA is a promising marker in the field of alcoholism research; therefore, more studies are required in this regard, taking into account the genetic heterogeneity of each population.
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Koller G, Zill P, Soyka M, Adorjan K, Weiss C, Kern A, Nguyen-Thien ML, Kamp F, Proebstl L, Krause D, Ruhdorfer S, Bergmann W, Preuss UW. Short-term changes in global methylation and hydroxymethylation during alcohol detoxification. Eur Neuropsychopharmacol 2019; 29:897-903. [PMID: 31133368 DOI: 10.1016/j.euroneuro.2019.05.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 05/07/2019] [Accepted: 05/11/2019] [Indexed: 12/21/2022]
Abstract
Alcohol dependence is a common public health problem and epigenetics may offer new aspects in understanding the biological and genetic underpinnings and improve treatment of this complex disease. Supposedly, methylation and hydroxymethylation are altered in brain tissues and in synapse-related genes due to chronic alcohol intake and during withdrawal. To assess potential epigenetic changes after cessation of chronic alcohol intake, we compared 23 alcohol-dependent individuals during inpatient alcohol detoxification with 13 carefully matched controls. Blood samples were taken on the day of admission, after one and after two weeks at the end of inpatient treatment. Genome-wide global methylation and global DNA hydroxymethylation were compared across groups. There were significant differences in global methylation across time from admission to one and two weeks of inpatient withdrawal (p < 0.001). These findings were paralleled to changes in global DNA hydroxymethylation across time when age was employed as a cofactor (p < 0.001). Several potentially influencing variables like severity of withdrawal, dose of withdrawal medication and alcohol intake before admission did not yield significant influence on epigenetic changes. The results confirm previous findings of significant alterations of epigenetic patterns during alcohol intoxication and present for the first time hydroxymethylation changes in these individuals.
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Affiliation(s)
- Gabriele Koller
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany.
| | - Peter Zill
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Michael Soyka
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany; Medical Park Chiemseeblick, Bernau am Chiemsee, Germany
| | - Kristina Adorjan
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Claudia Weiss
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Antonia Kern
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Mai-Ly Nguyen-Thien
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Felicia Kamp
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Lisa Proebstl
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Daniela Krause
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Sarah Ruhdorfer
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Wilhelm Bergmann
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Nussbaumstraße 7, D - 80336 Munich, Germany
| | - Ulrich W Preuss
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany; Vitos-Klinik Psychiatrie und Psychotherapie Herborn, Herborn, Germany
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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: 13] [Impact Index Per Article: 2.6] [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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Muench C, Luo A, Charlet K, Lee J, Rosoff DB, Sun H, Fede SJ, Jung J, Momenan R, Lohoff FW. Lack of Association Between Serotonin Transporter Gene (SLC6A4) Promoter Methylation and Amygdala Response During Negative Emotion Processing in Individuals With Alcohol Dependence. Alcohol Alcohol 2019; 54:209-215. [PMID: 31008507 DOI: 10.1093/alcalc/agz032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/20/2019] [Accepted: 03/25/2019] [Indexed: 11/12/2022] Open
Abstract
AIMS Differences in DNA methylation of the serotonin transporter gene (SLC6A4) have been shown to alter SLC6A4 expression and predict brain functions in healthy individuals. This study investigated the association between SLC6A4 promoter methylation and threat-related amygdala activation in individuals with alcohol dependence (AD). METHODS Methylation of the SLC6A4 promoter region was assessed using peripheral blood DNA from 45 individuals with AD and 45 healthy controls (HCs). All participants completed an emotional face matching task in a 3-T magnetic resonance imaging (MRI) scanner. RESULTS Results did not reveal any association between SLC6A4 promoter methylation variation and threat-related amygdala activation in HCs or individuals with AD. Furthermore, methylation in the promoter region of SLC6A4 did not significantly differ between the groups. CONCLUSIONS Our results do not replicate a previous finding that increased methylation in the promoter region of SLC6A4 is associated with threat-related amygdala activation in healthy individuals and further show that there is no such association in individuals with AD. Given that the number of imaging epigenetics studies on SLC6A4 is very limited to date, these inconsistent results indicate that future research is needed to clarify its association with amygdala reactivity in both healthy and clinical populations.
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Affiliation(s)
- Christine Muench
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 10 Center Drive (10CRC), Bethesda, MD, USA
| | - Audrey Luo
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 10 Center Drive (10CRC), Bethesda, MD, USA
| | - Katrin Charlet
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 10 Center Drive (10CRC), Bethesda, MD, USA.,Department of Psychiatry and Psychotherapy, Charité-Universitätsmedizin Berlin, Charitéplatz 1, Berlin, Germany
| | - Jisoo Lee
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 10 Center Drive (10CRC), Bethesda, MD, USA
| | - Daniel B Rosoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 10 Center Drive (10CRC), Bethesda, MD, USA
| | - Hui Sun
- Office of the Clinical Director, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 10 Center Drive (10CRC), Bethesda, MD, USA
| | - Samantha J Fede
- Clinical NeuroImaging Research Core, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 10 Center Drive (10CRC), Bethesda, MD, USA
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 10 Center Drive (10CRC), Bethesda, MD, USA
| | - Reza Momenan
- Clinical NeuroImaging Research Core, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 10 Center Drive (10CRC), Bethesda, MD, USA
| | - Falk W Lohoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, 10 Center Drive (10CRC), Bethesda, MD, USA
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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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Wolf EJ, Logue MW, Morrison FG, Wilcox ES, Stone A, Schichman SA, McGlinchey RE, Milberg WP, Miller MW. Posttraumatic psychopathology and the pace of the epigenetic clock: a longitudinal investigation. Psychol Med 2019; 49:791-800. [PMID: 29897034 PMCID: PMC6292741 DOI: 10.1017/s0033291718001411] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
BACKGROUND Posttraumatic stress disorder (PTSD) and stress/trauma exposure are cross-sectionally associated with advanced DNA methylation age relative to chronological age. However, longitudinal inquiry and examination of associations between advanced DNA methylation age and a broader range of psychiatric disorders is lacking. The aim of this study was to examine if PTSD, depression, generalized anxiety, and alcohol-use disorders predicted acceleration of DNA methylation age over time (i.e. an increasing pace, or rate of advancement, of the epigenetic clock). METHODS Genome-wide DNA methylation and a comprehensive set of psychiatric symptoms and diagnoses were assessed in 179 Iraq/Afghanistan war veterans who completed two assessments over the course of approximately 2 years. Two DNA methylation age indices (Horvath and Hannum), each a weighted index of an array of genome-wide DNA methylation probes, were quantified. The pace of the epigenetic clock was operationalized as change in DNA methylation age as a function of time between assessments. RESULTS Analyses revealed that alcohol-use disorders (p = 0.001) and PTSD avoidance and numbing symptoms (p = 0.02) at Time 1 were associated with an increasing pace of the epigenetic clock over time, per the Horvath (but not the Hannum) index of cellular aging. CONCLUSIONS This is the first study to suggest that posttraumatic psychopathology is longitudinally associated with a quickened pace of the epigenetic clock. Results raise the possibility that accelerated cellular aging is a common biological consequence of stress-related psychopathology, which carries implications for identifying mechanisms of stress-related cellular aging and developing interventions to slow its pace.
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Affiliation(s)
- Erika J. Wolf
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
| | - Mark W. Logue
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
- Biomedical Genetics, Boston University School of Medicine
| | - Filomene G. Morrison
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
| | | | - Annjanette Stone
- Pharmacogenomics Analysis Laboratory, Research Service, Central
Arkansas Veterans Healthcare System
| | - Steven A. Schichman
- Pharmacogenomics Analysis Laboratory, Research Service, Central
Arkansas Veterans Healthcare System
| | - Regina E. McGlinchey
- Geriatric Research Educational and Clinical Center and Translational
Research Center for TBI and Stress Disorders, VA Boston Healthcare System
- Department of Psychiatry, Harvard Medical School
| | - William P. Milberg
- Geriatric Research Educational and Clinical Center and Translational
Research Center for TBI and Stress Disorders, VA Boston Healthcare System
- Department of Psychiatry, Harvard Medical School
| | - Mark W. Miller
- National Center for PTSD at VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
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Methamphetamine (MA) Use Induces Specific Changes in LINE-1 Partial Methylation Patterns, Which Are Associated with MA-Induced Paranoia: a Multivariate and Neuronal Network Study. Mol Neurobiol 2018; 56:4258-4272. [PMID: 30302724 DOI: 10.1007/s12035-018-1371-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/27/2018] [Indexed: 12/29/2022]
Abstract
The use of psychoactive substances, including methamphetamine (MA) may cause changes in DNA methylation. The aim of this study was to examine the effects of MA use on long interspersed element-1 (LINE-1) methylation patterns in association with MA-induced paranoia. This study recruited 123 normal controls and 974 MA users, 302 with and 672 without MA-induced paranoia. The Semi-Structured Assessment for Drug Dependence and Alcoholism was used to assess demographic and substance use variables. Patterns of LINE-1 methylation were assessed in peripheral blood mononuclear cells and a combined bisulfite restriction analysis (COBRA) was used to estimate overall LINE-1 methylation (mC) while COBRA classified LINE-alleles into four patterns based on the methylation status of two CpG dinucleotides on each strand from 5' to 3', namely two methylated (mCmC) and two unmethylated (uCuC) CpGs and two types of partially methylated loci (mCuC that is 5'm with 3'u and uCmC that is 5'u with 3'm CpGs). MA users showed higher % mCuC and % mCuC + uCmC levels than controls. Use of solvents and opioids, but not cannabis and alcohol dependence, significantly lowered % uCmC levels, while current smoking significantly increased % uCuC levels. MA-induced paranoia was strongly associated with changes in LINE-1 partial methylation patterns (lowered % uCmC), heavy MA use, lower age at onset of MA use, and alcohol dependence. Women who took contraceptives showed significantly lower LINE-1 % mC and % mCmC and higher % uCuC levels than women without contraceptive use and men. The results show that MA-induced changes in LINE-1 partial methylation patterns are associated with MA-induced paranoia and could explain in part the pathophysiology of this type of psychosis. It is argued that MA-induced neuro-oxidative pathways may have altered LINE-1 partial methylation patterns, which in turn may regulate neuro-oxidative and immune pathways, which may increase risk to develop MA-induced paranoia.
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Abstract
OBJECTIVE Addiction co-occurs with distinct pathological personality traits, other psychiatric disorders or symptoms and cognitive impairment, which are known as dual disorders or co-occurring disorders. This symptomatic high concurrency suggests that both conditions are in some ways causally linked. Research is ongoing to identify distinctive neurobehavioral mechanisms and endophenotypes that predispose individuals to compulsive drug use and other mental disorders. Research is also providing new revelations about the diverse effects of substances on individuals, including differences according to sex. Today we know that the same substance may give rise to different behavioral, affective, cognitive, and sensory effects across different individuals. METHODS This state-of the art review tends to address the concept of precision psychiatry and dual disorders. The PubMed database was searched for the last 15 years to identify those articles that reported neurobiological perspectives on dual disorders, addiction and other mental disorders, precision medicine, and precision psychiatry. RESULTS There has been considerable progress made in recent years in relation to the study of addiction and dual disorders. The concept of dual disorders attempts to capture not only the persistence of substance use and substance seeking but also the evident vulnerability of specific subpopulations to switch from controlled to compulsive drug use. Precision medicine is focused on identifying this individual vulnerability to illness as much as the individual response to treatment. Psychiatry is fully committed to this goal. Regarding addiction, essential precision medicine advances will be possible if concerted efforts are made in the discovery of biological variations and environmental factors that contribute to individual vulnerability to addictive disorders and dual disorders, together with the identification of moderators of treatment response. CONCLUSIONS Here we survey the discoveries, future research directions, and translational relevance of the concept of precision psychiatry for dual disorders. The review may offer new perspectives on this issue and highlight a new way to see and to think about dual disorders.
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Affiliation(s)
- Nestor Szerman
- a Servicio de Psiquiatría , Hospital Universitario Gregorio Marañon , Madrid , Spain
| | - Lola Peris
- b Research Unit and Dual Disorders Program, Centre Neuchâtelois de Psychiatrie (CNP) , Neuchâtel , Switzerland
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36
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Rosen AD, Robertson KD, Hlady RA, Muench C, Lee J, Philibert R, Horvath S, Kaminsky ZA, Lohoff FW. DNA methylation age is accelerated in alcohol dependence. Transl Psychiatry 2018; 8:182. [PMID: 30185790 PMCID: PMC6125381 DOI: 10.1038/s41398-018-0233-4] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 06/25/2018] [Accepted: 07/14/2018] [Indexed: 12/12/2022] Open
Abstract
Alcohol dependence (ALC) is a chronic, relapsing disorder that increases the burden of chronic disease and significantly contributes to numerous premature deaths each year. Previous research suggests that chronic, heavy alcohol consumption is associated with differential DNA methylation patterns. In addition, DNA methylation levels at certain CpG sites have been correlated with age. We used an epigenetic clock to investigate the potential role of excessive alcohol consumption in epigenetic aging. We explored this question in five independent cohorts, including DNA methylation data derived from datasets from blood (n = 129, n = 329), liver (n = 92, n = 49), and postmortem prefrontal cortex (n = 46). One blood dataset and one liver tissue dataset of individuals with ALC exhibited positive age acceleration (p < 0.0001 and p = 0.0069, respectively), whereas the other blood and liver tissue datasets both exhibited trends of positive age acceleration that were not significant (p = 0.83 and p = 0.57, respectively). Prefrontal cortex tissue exhibited a trend of negative age acceleration (p = 0.19). These results suggest that excessive alcohol consumption may be associated with epigenetic aging in a tissue-specific manner and warrants further investigation using multiple tissue samples from the same individuals.
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Affiliation(s)
- Allison D. Rosen
- 0000 0004 0481 4802grid.420085.bSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Keith D. Robertson
- 0000 0004 0459 167Xgrid.66875.3aDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Ryan A. Hlady
- 0000 0004 0459 167Xgrid.66875.3aDepartment of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN USA
| | - Christine Muench
- 0000 0004 0481 4802grid.420085.bSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Jisoo Lee
- 0000 0004 0481 4802grid.420085.bSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
| | - Robert Philibert
- 0000 0004 1936 8294grid.214572.7Department of Psychiatry, University of Iowa, Iowa City, IA USA
| | - Steve Horvath
- 0000 0000 9632 6718grid.19006.3eDepartment of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA USA ,0000 0000 9632 6718grid.19006.3eDepartment of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA USA
| | - Zachary A. Kaminsky
- 0000 0001 2171 9311grid.21107.35Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD USA ,0000 0001 2171 9311grid.21107.35Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Falk W. Lohoff
- 0000 0004 0481 4802grid.420085.bSection on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD USA
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Scott MS. Commentary: Perspectives on alcohol-related gene and environment interplay in diverse populations. Am J Addict 2018; 26:526-531. [PMID: 28745447 DOI: 10.1111/ajad.12584] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/26/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Racial/ethnic groups comprise more than 20% of the U.S. population, but many experience disproportionately high risk for alcohol misuse, often resulting in higher rates of alcohol-associated consequences. Completion of mapping the human genome has launched rapidly evolving research methods aimed at improved understanding of genetic contribution to disease. Despite decades of research on the influence of genetic and environmental risks on alcohol use disorders and outcomes, few studies have included racial/ethnic subpopulations in sufficient numbers to allow for proper statistical analysis. METHODS The papers in this special issue help to elucidate current knowledge on the etiology of genetic and environmental contributors and potential moderators of alcohol use and associated problems among racial/ethnic populations. The lack of racial/ethnic diversity across many genetic studies contributes to challenges in interpretation of findings and eventually applications to precision medicine. RESULTS Proposed approaches to overcome disparities in racial/ethnic participant recruitment in genetic studies include methods to address population stratification in allele frequency, improve transparency in subjects' consenting to participate, and engaging interdisciplinary research teams and community involvement to improve recruitment of racial/ethnic minorities. DISCUSSION AND CONCLUSIONS The reviews presented underscore various gaps in our knowledge of the genetic influences on alcohol use disorders due to the failure to include racially and ethnically diverse populations in genetic and epigenetic study samples. New directions are suggested to overcome the resulting research challenges and ultimately to inform future personalized intervention approaches for racial/ethnic populations. SCIENTIFIC SIGNIFICANCE Inclusion of heterogeneous populations in genomic research will provide a better comprehension of possible unique genetic factors in the broader general population that may be missed due to exclusion of unique and common variants that may be present in racial/ethnic populations. (Am J Addict 2017;26:526-531).
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Affiliation(s)
- Marcia S Scott
- National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
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Chartier KG, Hesselbrock MN, Hesselbrock VM. Conclusion: Special issue on genetic and alcohol use disorder research with diverse racial/ethnic groups: Key findings and potential next steps. Am J Addict 2018; 26:532-537. [PMID: 28745446 DOI: 10.1111/ajad.12585] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/09/2017] [Accepted: 06/26/2017] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND AND OBJECTIVES This special issue brings together papers focusing on a wide range of topics relevant to the research and understanding of the role of race/ethnicity and genetic variation for the susceptibility of developing an alcohol use disorder (AUD). METHODS The key findings from the issue's 10 articles are reviewed and organized here around three topics: I: addictive behaviors and potential environmental influences; II: a focus on four racial/ethnic groups; and III: special methodologies. RESULTS Several potential next steps in improving effective research strategies are highlighted: (1) implementing best practices for outreach and community engagement may reduce reluctance to participate; (2) recruiting adequately sized and racially/ethnically diverse samples will require new collaborations with investigators who successfully work in diverse communities; (3) identifying and assessing environmental influences that are both unique to, and common among, racial/ethnic groups may inform preventions for AUD; (4) use of standardized measures will facilitate the generation of larger samples and meta-analysis of research findings; and (5) use of better analytic approaches and experimental methods will improve replication in gene finding research and help advance new areas of research. CONCLUSIONS Genetic research of AUD in diverse racial/ethnic populations is advancing. The articles in this issue examined the general theme of including diverse population groups in genetic studies and offered potential strategies for addressing some common problems. SCIENTIFIC SIGNIFICANCE Greater inclusion of diverse racial/ethnic populations in this research is important to ensure that the benefits of new knowledge and technology are equally shared. (Am J Addict 2017;26:532-537).
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Affiliation(s)
- Karen G Chartier
- School of Social Work, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Michie N Hesselbrock
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut
| | - Victor M Hesselbrock
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut
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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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Chartier KG, Hesselbrock MN, Hesselbrock VM. Introduction: Special issue on genetic research of alcohol use disorder in diverse racial/ethnic populations. Am J Addict 2017; 26:422-423. [PMID: 28672076 DOI: 10.1111/ajad.12576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 05/20/2017] [Indexed: 11/29/2022] Open
Abstract
This special issue of The American Journal on Addictions is an extension of a workshop held at the Research Society on Alcoholism (2015) highlighting several important issues related to studies of the genetic bases of alcohol use disorder among racially/ethnically diverse populations. While not exhaustive in their coverage, the papers in this special issue focus on three important topics: (1) the importance of considering the social and environmental context in genetic analyses; (2) social and cultural considerations for engaging diverse communities in genetic research; and (3) methodologies related to phenotype development for use with racially/ethnically diverse populations. A brief overview of each paper included in these three sections is presented. The issue concludes with additional considerations for genetic research with racially/ethnically diverse population groups along with a commentary. (Am J Addict 2017;26:422-423).
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Affiliation(s)
- Karen G Chartier
- School of Social Work, Virginia Commonwealth University, Richmond, Virginia.,Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia
| | - Michie N Hesselbrock
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut
| | - Victor M Hesselbrock
- Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut
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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: 66] [Impact Index Per Article: 9.4] [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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