1
|
Ma J, Huang A, Yan K, Li Y, Sun X, Joehanes R, Huan T, Levy D, Liu C. Blood transcriptomic biomarkers of alcohol consumption and cardiovascular disease risk factors: the Framingham Heart Study. Hum Mol Genet 2023; 32:649-658. [PMID: 36130209 PMCID: PMC9896471 DOI: 10.1093/hmg/ddac237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/19/2022] [Accepted: 09/15/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The relations of alcohol consumption and gene expression remain to be elucidated. MATERIALS AND METHODS We examined cross-sectional associations between alcohol consumption and whole blood derived gene expression levels and between alcohol-associated genes and obesity, hypertension, and diabetes in 5531 Framingham Heart Study (FHS) participants. RESULTS We identified 25 alcohol-associated genes. We further showed cross-sectional associations of 16 alcohol-associated genes with obesity, nine genes with hypertension, and eight genes with diabetes at P < 0.002. For example, we observed decreased expression of PROK2 (β = -0.0018; 95%CI: -0.0021, -0.0007; P = 6.5e - 5) and PAX5 (β = -0.0014; 95%CI: -0.0021, -0.0007; P = 6.5e - 5) per 1 g/day increase in alcohol consumption. Consistent with our previous observation on the inverse association of alcohol consumption with obesity and positive association of alcohol consumption with hypertension, we found that PROK2 was positively associated with obesity (OR = 1.42; 95%CI: 1.17, 1.72; P = 4.5e - 4) and PAX5 was negatively associated with hypertension (OR = 0.73; 95%CI: 0.59, 0.89; P = 1.6e - 3). We also observed that alcohol consumption was positively associated with expression of ABCA13 (β = 0.0012; 95%CI: 0.0007, 0.0017; P = 1.3e - 6) and ABCA13 was positively associated with diabetes (OR = 2.57; 95%CI: 1.73, 3.84; P = 3.5e - 06); this finding, however, was inconsistent with our observation of an inverse association between alcohol consumption and diabetes. CONCLUSIONS We showed strong cross-sectional associations between alcohol consumption and expression levels of 25 genes in FHS participants. Nonetheless, complex relationships exist between alcohol-associated genes and CVD risk factors.
Collapse
Affiliation(s)
- Jiantao Ma
- Division of Nutrition Epidemiology and Data Science, Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111, USA
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Allen Huang
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02142, USA
| | - Kaiyu Yan
- Department of Biostatistics, Boston University, Boston, MA 02118, USA
| | - Yi Li
- Department of Biostatistics, Boston University, Boston, MA 02118, USA
| | - Xianbang Sun
- Department of Biostatistics, Boston University, Boston, MA 02118, USA
| | - Roby Joehanes
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tianxiao Huan
- Department of Ophthalmology and Visual Sciences, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA 01702, USA
| | - Chunyu Liu
- Department of Biostatistics, Boston University, Boston, MA 02118, USA
- Boston University’s and National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA 01702, USA
| |
Collapse
|
2
|
Cabrera-Mendoza B, Stertz L, Najera K, Selvaraj S, Teixeira AL, Meyer TD, Fries GR, Walss-Bass C. Within subject cross-tissue analyzes of epigenetic clocks in substance use disorder postmortem brain and blood. Am J Med Genet B Neuropsychiatr Genet 2023; 192:13-27. [PMID: 36056652 PMCID: PMC9742183 DOI: 10.1002/ajmg.b.32920] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/22/2022] [Accepted: 08/16/2022] [Indexed: 12/14/2022]
Abstract
There is a possible accelerated biological aging in patients with substance use disorders (SUD). The evaluation of epigenetic clocks, which are accurate estimators of biological aging based on DNA methylation changes, has been limited to blood tissue in patients with SUD. Consequently, the impact of biological aging in the brain of individuals with SUD remains unknown. In this study, we evaluated multiple epigenetic clocks (DNAmAge, DNAmAgeHannum, DNAmAgeSkinBlood, DNAmPhenoAge, DNAmGrimAge, and DNAmTL) in individuals with SUD (n = 42), including alcohol (n = 10), opioid (n = 19), and stimulant use disorder (n = 13), and controls (n = 10) in postmortem brain (prefrontal cortex) and blood tissue obtained from the same individuals. We found a higher DNAmPhenoAge (β = 0.191, p-value = 0.0104) and a nominally lower DNAmTL (β = -0.149, p-value = 0.0603) in blood from individuals with SUD compared to controls. SUD subgroup analysis showed a nominally lower brain DNAmTL in subjects with alcohol use disorder, compared to stimulant use disorder and controls (β = 0.0150, p-value = 0.087). Cross-tissue analyzes indicated a lower blood DNAmTL and a higher blood DNAmAge compared to their respective brain values in the SUD group. This study highlights the relevance of tissue specificity in biological aging studies and suggests that peripheral measures of epigenetic clocks in SUD may depend on the specific type of drug used.
Collapse
Affiliation(s)
- Brenda Cabrera-Mendoza
- PECEM, Faculty of Medicine, Universidad Nacional
Autónoma de México, Mexico City, 04510, Mexico
| | - Laura Stertz
- Louis A. Faillace, MD, Department of Psychiatry and
Behavioral Sciences, McGovern Medical School, University of Texas Health Science
Center at Houston, Houston, TX, 77054, USA
| | - Katherine Najera
- Louis A. Faillace, MD, Department of Psychiatry and
Behavioral Sciences, McGovern Medical School, University of Texas Health Science
Center at Houston, Houston, TX, 77054, USA
| | - Sudhakar Selvaraj
- Louis A. Faillace, MD, Department of Psychiatry and
Behavioral Sciences, McGovern Medical School, University of Texas Health Science
Center at Houston, Houston, TX, 77054, USA
| | - Antonio L. Teixeira
- Louis A. Faillace, MD, Department of Psychiatry and
Behavioral Sciences, McGovern Medical School, University of Texas Health Science
Center at Houston, Houston, TX, 77054, USA
| | - Thomas D. Meyer
- Louis A. Faillace, MD, Department of Psychiatry and
Behavioral Sciences, McGovern Medical School, University of Texas Health Science
Center at Houston, Houston, TX, 77054, USA
| | - Gabriel R. Fries
- Louis A. Faillace, MD, Department of Psychiatry and
Behavioral Sciences, McGovern Medical School, University of Texas Health Science
Center at Houston, Houston, TX, 77054, USA
- Center for Precision Health, School of Biomedical
Informatics, University of Texas Health Science Center at Houston, Houston, TX,
77054, USA
| | - Consuelo Walss-Bass
- Louis A. Faillace, MD, Department of Psychiatry and
Behavioral Sciences, McGovern Medical School, University of Texas Health Science
Center at Houston, Houston, TX, 77054, USA
| |
Collapse
|
3
|
Seyednejad SA, Sartor GC. Noncoding RNA therapeutics for substance use disorder. ADVANCES IN DRUG AND ALCOHOL RESEARCH 2022; 2:10807. [PMID: 36601439 PMCID: PMC9808746 DOI: 10.3389/adar.2022.10807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although noncoding RNAs (ncRNAs) have been shown to regulate maladaptive neuroadaptations that drive compulsive drug use, ncRNA-targeting therapeutics for substance use disorder (SUD) have yet to be clinically tested. Recent advances in RNA-based drugs have improved many therapeutic issues related to immune response, specificity, and delivery, leading to multiple successful clinical trials for other diseases. As the need for safe and effective treatments for SUD continues to grow, novel nucleic acid-based therapeutics represent an appealing approach to target ncRNA mechanisms in SUD. Here, we review ncRNA processes implicated in SUD, discuss recent therapeutic approaches for targeting ncRNAs, and highlight potential opportunities and challenges of ncRNA-targeting therapeutics for SUD.
Collapse
Affiliation(s)
- Seyed Afshin Seyednejad
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
- Connecticut Institute for the Brain and Cognitive Sciences (CT IBACS), Storrs, CT, United States
| | - Gregory C. Sartor
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT, United States
- Connecticut Institute for the Brain and Cognitive Sciences (CT IBACS), Storrs, CT, United States
| |
Collapse
|
4
|
Yuan X, Cui H, Jin Y, Zhao W, Liu X, Wang Y, Ding J, Liu L, Wen J, Zhao G. Fatty acid metabolism-related genes are associated with flavor-presenting aldehydes in Chinese local chicken. Front Genet 2022; 13:902180. [PMID: 36035160 PMCID: PMC9412053 DOI: 10.3389/fgene.2022.902180] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Aldehydes are primary volatile organic compounds (VOCs) in local Chinese chicken meat and contribute green grass, fatty, citrus, and bitter almond aromas to chicken meat. To understand the genetic basis of these aldehyde VOC aromas, we used approximately 500 Chinese Jingxing Yellow (JXY) chickens to conduct genome-wide association studies (GWAS) on the flavor traits with the data of single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs). In total, 501 association variants (253 SNPs and 248 INDELs) were found to be suggestively (SNPs: p-value < 2.77e-06 and INDELs: p-value < 3.78e-05) associated with total aldehydes (the sum of nine aldehydes), hexanal, heptanal, benzaldehyde, (E,E)-2,4-nonadienal, octanal, (E)-2-decenal, nonanal, decanal, and octadecanal. Of them, six SNPs and 23 INDELs reached a genome-wide significance level (SNPs: p-value < 1.38e-07 and INDELs: p-value < 1.89e-06). Potential candidate aldehyde genes were functionally annotated for lipid metabolism, especially fatty acid-related pathways and phospholipid-related gene ontology (GO) terms. Moreover, the GWAS analysis of total aldehydes, hexanal, and nonanal generated the most significant signals, and phenotypic content differed between different genotypes at candidate gene-related loci. For total aldehydes and hexanal traits, candidate genes were annotated based on the significant and suggestive variants on chromosomes 3 and 8 with highly polymorphic linkage blocks. The following candidate genes were also identified: GALM, MAP4K3, GPCPD1, RPS6KA2, CRLS1, ASAP1, TRMT6, SDC1, PUM2, ALDH9A1, MGST3, GMEB1, MECR, LDLRAP1, GPAM and ACSL5. We also found that polyunsaturated fatty acids (PUFAs) (C18:2n6c linoleic acid and C18:3n3 linolenic acid) were significantly correlated with total aldehydes and hexanal contents. PUFAs are important aldehyde precursors, and consistently, our results suggested that candidate genes involved in fatty acid pathways and phospholipid GO terms were identified in association loci. This work provides an understanding of the genetic basis of aldehyde formation, which is a key flavor-forming compound.
Collapse
|
5
|
Denham AN, Drake J, Gavrilov M, Taylor ZN, Bacanu SA, Vladimirov VI. Long Non-Coding RNAs: The New Frontier into Understanding the Etiology of Alcohol Use Disorder. Noncoding RNA 2022; 8:ncrna8040059. [PMID: 36005827 PMCID: PMC9415279 DOI: 10.3390/ncrna8040059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/28/2022] Open
Abstract
Alcohol use disorder (AUD) is a complex, chronic, debilitating condition impacting millions worldwide. Genetic, environmental, and epigenetic factors are known to contribute to the development of AUD. Long non-coding RNAs (lncRNAs) are a class of regulatory RNAs, commonly referred to as the “dark matter” of the genome, with little to no protein-coding potential. LncRNAs have been implicated in numerous processes critical for cell survival, suggesting that they play important functional roles in regulating different cell processes. LncRNAs were also shown to display higher tissue specificity than protein-coding genes and have a higher abundance in the brain and central nervous system, demonstrating a possible role in the etiology of psychiatric disorders. Indeed, genetic (e.g., genome-wide association studies (GWAS)), molecular (e.g., expression quantitative trait loci (eQTL)) and epigenetic studies from postmortem brain tissues have identified a growing list of lncRNAs associated with neuropsychiatric and substance use disorders. Given that the expression patterns of lncRNAs have been associated with widespread changes in the transcriptome, including methylation, chromatin architecture, and activation or suppression of translational activity, the regulatory nature of lncRNAs may be ubiquitous and an innate component of gene regulation. In this review, we present a synopsis of the functional impact that lncRNAs may play in the etiology of AUD. We also discuss the classifications of lncRNAs, their known functional roles, and therapeutic advancements in the field of lncRNAs to further clarify the functional relationship between lncRNAs and AUD.
Collapse
Affiliation(s)
- Allie N. Denham
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- Correspondence:
| | - John Drake
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- MSCI Program, Texas A&M University, Bryan, TX 77807, USA
| | - Matthew Gavrilov
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
| | - Zachary N. Taylor
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA 23219, USA
- Departent of Psychiatry, Virginia Commonwealth University, Richmond, VA 23219, USA
| | - Vladimir I. Vladimirov
- Department of Psychiatry and Behavioral Sciences, Texas A&M University, Bryan, TX 77807, USA
- Department of Psychiatry, College of Medicine, University of Arizona Phoenix, Phoenix, AZ 85004, USA
- Departent of Psychiatry, Virginia Commonwealth University, Richmond, VA 23219, USA
- Texas A&M Institute for Neuroscience, College Station, Texas A&M University, College Station, TX 77843, USA
- Genetics Interdisciplinary Program, College Station, Texas A&M University, College Station, TX 77843, USA
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD 21205, USA
| |
Collapse
|
6
|
Liu Y, Zhang H. RNA m6A Modification Changes in Postmortem Nucleus Accumbens of Subjects with Alcohol Use Disorder: A Pilot Study. Genes (Basel) 2022; 13:958. [PMID: 35741720 PMCID: PMC9222907 DOI: 10.3390/genes13060958] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/25/2022] [Accepted: 05/26/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The nucleus accumbens (NAc) is a key brain structure mediating the rewarding effect of alcohol and drug abuse. Chronic alcohol consumption may alter RNA methylome (or epitranscriptome) in the NAc, leading to altered gene expression and thus behavioral neuroadaptation to alcohol. METHODS This pilot study profiled the epitranscriptomes of mRNAs, long noncoding RNAs (lncRNAs), and microRNAs (miRNAs) in postmortem NAc of three male Caucasian subjects with alcohol use disorder (AUD) and three matched male Caucasian control subjects using Arraystar's m6A-mRNA&lncRNA Epitranscriptomic Microarray assay. Differentially methylated (DM) RNAs and the function of DM RNAs were analyzed by biostatistics and bioinformatics programs. RESULTS 26 mRNAs were hypermethylated and three mRNAs were hypomethylated in the NAc of AUD subjects (≥2-fold changes and p ≤ 0.05). Most of these 29 DM mRNAs are involved in immune-related pathways (e.g., IL-17 signaling). Moreover, four lncRNAs were hypermethylated and one lncRNA was hypomethylated in the NAc of AUD subjects (≥2-fold changes and p ≤ 0.05). Additionally, three miRNAs were hypermethylated in the NAc of AUD subjects (≥2-fold changes and p ≤ 0.05). CONCLUSIONS This study revealed RNA methylomic changes in the NAc of AUD subjects, suggesting that chronic alcohol consumption may lead to AUD through epitranscriptomic RNA modifications. Our findings need to be replicated in a larger sample.
Collapse
Affiliation(s)
- Ying Liu
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA;
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University School of Medicine, Boston, MA 02118, USA;
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA
| |
Collapse
|
7
|
Lim Y, Beane-Ebel JE, Tanaka Y, Ning B, Husted CR, Henderson DC, Xiang Y, Park IH, Farrer LA, Zhang H. Exploration of alcohol use disorder-associated brain miRNA-mRNA regulatory networks. Transl Psychiatry 2021; 11:504. [PMID: 34601489 PMCID: PMC8487426 DOI: 10.1038/s41398-021-01635-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/17/2021] [Indexed: 02/08/2023] Open
Abstract
Transcriptomic changes in specific brain regions can influence the risk of alcohol use disorder (AUD), but the underlying mechanism is not fully understood. We investigated AUD-associated miRNA-mRNA regulatory networks in multiple brain regions by analyzing transcriptomic changes in two sets of postmortem brain tissue samples and ethanol-exposed human embryonic stem cell (hESC)-derived cortical interneurons. miRNA and mRNA transcriptomes were profiled in 192 tissue samples (Set 1) from eight brain regions (amygdala, caudate nucleus, cerebellum, hippocampus, nucleus accumbens, prefrontal cortex, putamen, and ventral tegmental area) of 12 AUD and 12 control European Australians. Nineteen differentially expressed miRNAs (fold-change>2.0 & P < 0.05) and 97 differentially expressed mRNAs (fold-change>2.0 & P < 0.001) were identified in one or multiple brain regions of AUD subjects. AUD-associated miRNA-mRNA regulatory networks in each brain region were constructed using differentially expressed and negatively correlated miRNA-mRNA pairs. AUD-relevant pathways (including CREB Signaling, IL-8 Signaling, and Axonal Guidance Signaling) were potentially regulated by AUD-associated brain miRNA-mRNA pairs. Moreover, miRNA and mRNA transcriptomes were mapped in additional 96 tissue samples (Set 2) from six of the above eight brain regions of eight AUD and eight control European Australians. Some of the AUD-associated miRNA-mRNA regulatory networks were confirmed. In addition, miRNA and mRNA transcriptomes were analyzed in hESC-derived cortical interneurons with or without ethanol exposure, and ethanol-influenced miRNA-mRNA regulatory networks were constructed. This study provided evidence that alcohol could induce concerted miRNA and mRNA expression changes in reward-related or alcohol-responsive brain regions. We concluded that altered brain miRNA-mRNA regulatory networks might contribute to AUD development.
Collapse
Affiliation(s)
- Yolpanhchana Lim
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- The Bioinformatics Program, Boston University Graduate School of Arts and Sciences, Boston, MA, USA
| | - Jennifer E Beane-Ebel
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Yoshiaki Tanaka
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- Department of Medicine, Maisonneuve-Rosemont Hospital Research Center, University of Montreal, Montreal, QC, H1T 2M4, Canada
| | - Boting Ning
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Christopher R Husted
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - David C Henderson
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Yangfei Xiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - In-Hyun Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Lindsay A Farrer
- Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Departments of Neurology and Ophthalmology, Boston University School of Medicine, Boston, MA, USA
- Departments of Biostatistics and Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA.
- Departments of Biostatistics and Epidemiology, Boston University School of Public Health, Boston, MA, USA.
| |
Collapse
|
8
|
Bountress KE, Vladimirov V, McMichael G, Taylor ZN, Hardiman G, Chung D, Adams ZW, Danielson CK, Amstadter AB. Gene Expression Differences Between Young Adults Based on Trauma History and Post-traumatic Stress Disorder. Front Psychiatry 2021; 12:581093. [PMID: 33897478 PMCID: PMC8060466 DOI: 10.3389/fpsyt.2021.581093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 03/15/2021] [Indexed: 11/29/2022] Open
Abstract
Background: The purpose of this study was to identify gene expression differences associated with post-traumatic stress disorder (PTSD) and trauma exposure (TE) in a three-group study design comprised of those with and without trauma exposure and PTSD. Methods: We conducted gene expression and gene network analyses in a sample (n = 45) composed of female subjects of European Ancestry (EA) with PTSD, TE without PTSD, and controls. Results: We identified 283 genes differentially expressed between PTSD-TE groups. In an independent sample of Veterans (n = 78) a small minority of these genes were also differentially expressed. We identified 7 gene network modules significantly associated with PTSD and TE (Bonferroni corrected p ≤ 0.05), which at a false discovery rate (FDR) of q ≤ 0.2, were significantly enriched for biological pathways involved in focal adhesion, neuroactive ligand receptor interaction, and immune related processes among others. Conclusions: This study uses gene network analyses to identify significant gene modules associated with PTSD, TE, and controls. On an individual gene level, we identified a large number of differentially expressed genes between PTSD-TE groups, a minority of which were also differentially expressed in the independent sample. We also demonstrate a lack of network module preservation between PTSD and TE, suggesting that the molecular signature of PTSD and trauma are likely independent of each other. Our results provide a basis for the identification of likely disease pathways and biomarkers involved in the etiology of PTSD.
Collapse
Affiliation(s)
- Kaitlin E. Bountress
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
| | - Vladimir Vladimirov
- Department of Psychiatry and Behavioral Sciences, College of Medicine Texas A&M University, Richmond, VA, United States
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, United States
| | - Gowon McMichael
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
| | - Z. Nathan Taylor
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
| | - Gary Hardiman
- Institute for Global Food Security, Queens University Belfast, Belfast, United Kingdom
| | - Dongjun Chung
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Zachary W. Adams
- Department of Psychiatry, Indiana University of Medicine, Indianapolis, IN, United States
| | - Carla Kmett Danielson
- National Crime Victim Research and Treatment Center, Medical University of South Carolina, Charleston, SC, United States
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Ananda B. Amstadter
- Virginia Institute for Psychiatry and Behavioral Genetics, Virginia Commonwealth University (VCU), Richmond, VA, United States
| |
Collapse
|
9
|
Drake J, McMichael GO, Vornholt ES, Cresswell K, Williamson V, Chatzinakos C, Mamdani M, Hariharan S, Kendler KS, Kalsi G, Riley BP, Dozmorov M, Miles MF, Bacanu S, Vladimirov VI. Assessing the Role of Long Noncoding RNA in Nucleus Accumbens in Subjects With Alcohol Dependence. Alcohol Clin Exp Res 2020; 44:2468-2480. [PMID: 33067813 PMCID: PMC7756309 DOI: 10.1111/acer.14479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/01/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Long noncoding RNA (lncRNA) have been implicated in the etiology of alcohol use. Since lncRNA provide another layer of complexity to the transcriptome, assessing their expression in the brain is the first critical step toward understanding lncRNA functions in alcohol use and addiction. Thus, we sought to profile lncRNA expression in the nucleus accumbens (NAc) in a large postmortem alcohol brain sample. METHODS LncRNA and protein-coding gene (PCG) expressions in the NAc from 41 subjects with alcohol dependence (AD) and 41 controls were assessed via a regression model. Weighted gene coexpression network analysis was used to identify lncRNA and PCG networks (i.e., modules) significantly correlated with AD. Within the significant modules, key network genes (i.e., hubs) were also identified. The lncRNA and PCG hubs were correlated via Pearson correlations to elucidate the potential biological functions of lncRNA. The lncRNA and PCG hubs were further integrated with GWAS data to identify expression quantitative trait loci (eQTL). RESULTS At Bonferroni adj. p-value ≤ 0.05, we identified 19 lncRNA and 5 PCG significant modules, which were enriched for neuronal and immune-related processes. In these modules, we further identified 86 and 315 PCG and lncRNA hubs, respectively. At false discovery rate (FDR) of 10%, the correlation analyses between the lncRNA and PCG hubs revealed 3,125 positive and 1,860 negative correlations. Integration of hubs with genotype data identified 243 eQTLs affecting the expression of 39 and 204 PCG and lncRNA hubs, respectively. CONCLUSIONS Our study identified lncRNA and gene networks significantly associated with AD in the NAc, coordinated lncRNA and mRNA coexpression changes, highlighting potentially regulatory functions for the lncRNA, and our genetic (cis-eQTL) analysis provides novel insights into the etiological mechanisms of AD.
Collapse
Affiliation(s)
- John Drake
- From the Center for Integrative Life Sciences Education (JD)Virginia Commonwealth UniversityRichmondVirginia
| | - Gowon O. McMichael
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Eric Sean Vornholt
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Kellen Cresswell
- Department of Biostatistics(KC, MD)Virginia Commonwealth UniversityRichmondVirginia
| | - Vernell Williamson
- Department of Pathology(VW)Virginia Commonwealth UniversityRichmondVirginia
| | - Chris Chatzinakos
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Mohammed Mamdani
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Siddharth Hariharan
- Summer Research Fellowship(SH)School of MedicineVirginia Commonwealth UniversityRichmondVirginia
| | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Human and Molecular Genetics(KSK, BPR)Virginia Commonwealth UniversityRichmondVirginia
| | - Gursharan Kalsi
- Department of Social, Genetic and Developmental Psychiatry(GK)Institute of PsychiatryLondonUK
| | - Brien P. Riley
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Human and Molecular Genetics(KSK, BPR)Virginia Commonwealth UniversityRichmondVirginia
| | - Mikhail Dozmorov
- Department of Biostatistics(KC, MD)Virginia Commonwealth UniversityRichmondVirginia
| | - Michael F. Miles
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Pharmacology and Toxicology(MFM)Virginia Commonwealth UniversityRichmondVirginia
| | - Silviu‐Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
| | - Vladimir I. Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics(GOM, ESV, CC, MM, KSK, BPR, MFM, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Department of Psychiatry(KSK, BPR, S‐AB, VIV)Virginia Commonwealth UniversityRichmondVirginia
- Center for Biomarker Research and Personalized Medicine(VIV)Virginia Commonwealth UniversityRichmondVirginia
- Lieber Institute for Brain Development(VIV)Johns Hopkins UniversityBaltimoreMaryland
| |
Collapse
|
10
|
Casanova Ferrer F, Pascual M, Hidalgo MR, Malmierca-Merlo P, Guerri C, García-García F. Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. Genes (Basel) 2020; 11:E1106. [PMID: 32967293 PMCID: PMC7564639 DOI: 10.3390/genes11091106] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/13/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
The abuse of alcohol, one of the most popular psychoactive substances, can cause several pathological and psychological consequences, including alcohol use disorder (AUD). An impaired ability to stop or control alcohol intake despite adverse health or social consequences characterize AUD. While AUDs predominantly occur in men, growing evidence suggests the existence of distinct cognitive and biological consequences of alcohol dependence in women. The molecular and physiological mechanisms participating in these differential effects remain unknown. Transcriptomic technology permits the detection of the biological mechanisms responsible for such sex-based differences, which supports the subsequent development of novel personalized therapeutics to treat AUD. We conducted a systematic review and meta-analysis of transcriptomics studies regarding alcohol dependence in humans with representation from both sexes. For each study, we processed and analyzed transcriptomic data to obtain a functional profile of pathways and biological functions and then integrated the resulting data by meta-analysis to characterize any sex-based transcriptomic differences associated with AUD. Global results of the transcriptomic analysis revealed the association of decreased tissue regeneration, embryo malformations, altered intracellular transport, and increased rate of RNA and protein replacement with female AUD patients. Meanwhile, our analysis indicated that increased inflammatory response and blood pressure and a reduction in DNA repair capabilities are associated with male AUD patients. In summary, our functional meta-analysis of transcriptomic studies provides evidence for differential biological mechanisms of AUD patients of differing sex.
Collapse
Affiliation(s)
- Franc Casanova Ferrer
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain; (F.C.F.); (M.R.H.); (P.M.-M.)
- Hospital Clinico Research Foundation, INCLIVA, 46010 Valencia, Spain
| | - María Pascual
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, 46010 Valencia, Spain;
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center (CIPF), 46012 Valencia, Spain;
| | - Marta R. Hidalgo
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain; (F.C.F.); (M.R.H.); (P.M.-M.)
| | - Pablo Malmierca-Merlo
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain; (F.C.F.); (M.R.H.); (P.M.-M.)
- Atos Research Innovation (ARI), 28037 Madrid, Spain
| | - Consuelo Guerri
- Department of Molecular and Cellular Pathology of Alcohol, Príncipe Felipe Research Center (CIPF), 46012 Valencia, Spain;
| | - Francisco García-García
- Bioinformatics and Biostatistics Unit, Principe Felipe Research Center (CIPF), 46012 Valencia, Spain; (F.C.F.); (M.R.H.); (P.M.-M.)
- Spanish National Bioinformatics Institute, ELIXIR-Spain (INB, ELIXIR-ES), 46012 Valencia, Spain
| |
Collapse
|
11
|
Lin H, Wang F, Rosato AJ, Farrer LA, Henderson DC, Zhang H. Prefrontal cortex eQTLs/mQTLs enriched in genetic variants associated with alcohol use disorder and other diseases. Epigenomics 2020; 12:789-800. [PMID: 32496132 DOI: 10.2217/epi-2019-0270] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aim: This study aimed to investigate the function of genome-wide association study (GWAS)-identified variants associated with alcohol use disorder (AUD)/comorbid psychiatric disorders. Materials & methods: Genome-wide genotype, transcriptome and DNA methylome data were obtained from postmortem prefrontal cortex (PFC) of 48 Caucasians (24 AUD cases/24 controls). Expression/methylation quantitative trait loci (eQTL/mQTL) were identified and their enrichment in GWAS signals for the above disorders were analyzed. Results: PFC cis-eQTLs (923 from cases+controls, 27 from cases and 98 from controls) and cis-mQTLs (9,932 from cases+controls, 264 from cases and 695 from controls) were enriched in GWAS-identified genetic variants for the above disorders. Cis-eQTLs from AUD cases were mapped to morphine addiction-related genes. Conclusion: PFC cis-eQTLs/cis-mQTLs influence gene expression/DNA methylation patterns, thus increasing the disease risk.
Collapse
Affiliation(s)
- Honghuang Lin
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, MA, USA.,Boston University's & National Heart, Lung & Blood Institute's Framingham Heart Study, MA, USA
| | - Fan Wang
- Department of Cardiovascular & Metabolic Sciences, Cleveland Clinic Lerner Research Institute, OH, USA
| | - Andrew J Rosato
- Department of Psychiatry, Boston University School of Medicine, MA, USA
| | - Lindsay A Farrer
- Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, MA, USA
| | - David C Henderson
- Department of Psychiatry, Boston University School of Medicine, MA, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University School of Medicine, MA, USA.,Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, MA, USA
| |
Collapse
|
12
|
Dai Y, Hu R, Pei G, Zhang H, Zhao Z, Jia P. Diverse types of genomic evidence converge on alcohol use disorder risk genes. J Med Genet 2020; 57:733-743. [PMID: 32170004 DOI: 10.1136/jmedgenet-2019-106490] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 01/08/2020] [Accepted: 02/10/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND Alcohol use disorder (AUD) is one of the most common forms of substance use disorders with a strong contribution of genetic (50%-60%) and environmental factors. Genome-wide association studies (GWAS) have identified a number of AUD-associated variants, including those in alcohol metabolism genes. These genetic variants may modulate gene expression, making individuals more susceptible to AUD. A long-term alcohol consumption can also change the transcriptome patterns of subjects via epigenetic modulations. METHODS To explore the interactive effect of genetic and epigenetic factors on AUD, we conducted a secondary analysis by integrating GWAS, CNV, brain transcriptome and DNA methylation data to unravel novel AUD-associated genes/variants. We applied the mega-analysis of OR (MegaOR) method to prioritise AUD candidate genes (AUDgenes). RESULTS We identified a consensus set of 206 AUDgenes based on the multi-omics data. We demonstrated that these AUDgenes tend to interact with each other more frequent than chance expectation. Functional annotation analysis indicated that these AUDgenes were involved in substance dependence, synaptic transmission, glial cell proliferation and enriched in neuronal and liver cells. We obtained a multidimensional evidence that AUD is a polygenic disorder influenced by both genetic and epigenetic factors as well as the interaction of them. CONCLUSION We characterised multidimensional evidence of genetic, epigenetic and transcriptomic data in AUD. We found that 206 AUD associated genes were highly expressed in liver, brain cerebellum, frontal cortex, hippocampus and pituitary. Our studies provides important insights into the molecular mechanism of AUD and potential target genes for AUD treatment.
Collapse
Affiliation(s)
- Yulin Dai
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Ruifeng Hu
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Guangsheng Pei
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Huiping Zhang
- Department of Psychiatry, Boston University School of Medicine, Boston, Massachusetts, USA.,Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, Massachusetts, USA
| | - Zhongming Zhao
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Peilin Jia
- School of Biomedical Science, University of Texas Health Science Center at Houston, Houston, Texas, USA
| |
Collapse
|
13
|
Ferguson LB, Patil S, Moskowitz BA, Ponomarev I, Harris RA, Mayfield RD, Messing RO. A Pathway-Based Genomic Approach to Identify Medications: Application to Alcohol Use Disorder. Brain Sci 2019; 9:brainsci9120381. [PMID: 31888299 PMCID: PMC6956180 DOI: 10.3390/brainsci9120381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/31/2022] Open
Abstract
Chronic, excessive alcohol use alters brain gene expression patterns, which could be important for initiating, maintaining, or progressing the addicted state. It has been proposed that pharmaceuticals with opposing effects on gene expression could treat alcohol use disorder (AUD). Computational strategies comparing gene expression signatures of disease to those of pharmaceuticals show promise for nominating novel treatments. We reasoned that it may be sufficient for a treatment to target the biological pathway rather than lists of individual genes perturbed by AUD. We analyzed published and unpublished transcriptomic data using gene set enrichment of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways to identify biological pathways disrupted in AUD brain and by compounds in the Library of Network-based Cellular Signatures (LINCS L1000) and Connectivity Map (CMap) databases. Several pathways were consistently disrupted in AUD brain, including an up-regulation of genes within the Complement and Coagulation Cascade, Focal Adhesion, Systemic Lupus Erythematosus, and MAPK signaling, and a down-regulation of genes within the Oxidative Phosphorylation pathway, strengthening evidence for their importance in AUD. Over 200 compounds targeted genes within those pathways in an opposing manner, more than twenty of which have already been shown to affect alcohol consumption, providing confidence in our approach. We created a user-friendly web-interface that researchers can use to identify drugs that target pathways of interest or nominate mechanism of action for drugs. This study demonstrates a unique systems pharmacology approach that can nominate pharmaceuticals that target pathways disrupted in disease states such as AUD and identify compounds that could be repurposed for AUD if sufficient evidence is attained in preclinical studies.
Collapse
Affiliation(s)
- Laura B. Ferguson
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Shruti Patil
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
| | - Bailey A. Moskowitz
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Igor Ponomarev
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA;
| | - Robert A. Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
| | - Roy D. Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
| | - Robert O. Messing
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712, USA; (L.B.F.); (S.P.); (B.A.M.); (R.A.H.); (R.D.M.)
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Neurology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
- Correspondence: ; Tel.: +1-512-471-1735
| |
Collapse
|
14
|
Starski P, Peyton L, Oliveros A, Heppelmann CJ, Dasari S, Choi DS. Proteomic Profile of a Chronic Binge Ethanol Exposure Model. J Proteome Res 2019; 18:3492-3502. [PMID: 31329447 DOI: 10.1021/acs.jproteome.9b00394] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chronic binge alcohol drinking is known to increase risky decision through pathological impulsive behaviors. Recently, we established a novel rodent model of ethanol-induced waiting impulsivity using 5-choice serial reaction time task (5-CSRTT) in mice. However, molecular mechanisms underlying the chronic binge ethanol-induced waiting impulsivity is not well characterized. Among brain regions involved in impulsivity, the anterior cingulate cortex (ACC) is a major neural substrate for mediating the 5-CSRTT-based waiting impulsivity. Thus, we sought to determine the ACC proteomic profile using label-free proteomics of mice exhibiting ethanol-induced impulsivity. Ingenuity pathway analysis revealed that impulsivity-related proteins involved in ion channel complexes such as KCNIP3 (potassium voltage-gated channel interacting protein 3) and CACNG2 (calcium voltage-gated channel auxiliary subunit gamma 2) are downregulated in the ACC. We identified significant protein expression changes in the mechanistic target of rapamycin (mTOR) canonical pathway between control and ethanol-induced impulsive mice. Impulsive mice showed over 60% of proteins involved in the mTOR canonical pathway have been altered. This pathway has been previously implicated in the neuroadaptation in drugs of abuse and impulsivity. We found substantial changes in the protein levels involved in neurological disorders such as schizophrenia and Alzheimer's disease. Our findings provide a neuroproteomic profile of ethanol-induced impulsive mice.
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Kong LM, Zeng JY, Zheng WB, Shen ZW, Wu RH. Effects of Acute Alcohol Consumption on the Human Brain: Diffusional Kurtosis Imaging and Arterial Spin-Labeling Study. AJNR Am J Neuroradiol 2019; 40:641-647. [PMID: 30872417 DOI: 10.3174/ajnr.a5992] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 01/22/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND AND PURPOSE Brain function and microstructure are affected by alcohol consumption. Until recently, the effect of alcohol on neural mechanisms has not been fully elucidated. Our aim was to explore the acute effects of alcohol on healthy human brains by diffusional kurtosis imaging and 3D arterial spin-labeling and elucidate structural and functional changes in the brain on acute alcohol intake. MATERIALS AND METHODS Conventional MR imaging, diffusional kurtosis imaging, and 3D arterial spin-labeling were performed on 24 healthy volunteers before and 0.5 and 1 hour after drinking alcohol. Participants were divided into 2 groups according to the response to alcohol: blushing (n = 12) and unblushing (n = 12) groups. Twenty brain regions were analyzed. RESULTS Diffusional kurtosis imaging revealed an increase in mean kurtosis and fractional anisotropy at 0.5 hour post-alcohol intake in most brain regions, whereas mean diffusion was decreased in several brain regions at 1 hour after drinking. 3D arterial spin-labeling showed increased cerebral blood flow in most brain regions, particularly in the frontal regions. However, perfusion in the anterior commissure decreased. Regional changes in the brain correlated with various behavioral performances with respect to blush response and sex. In general, blushing individuals and men are more sensitive to alcohol with acute effects. CONCLUSIONS Physiologic and microstructural alterations in the brain on alcohol consumption were examined. Brain areas with blood flow alteration detected by 3D arterial spin-labeling were highly consistent with susceptible areas detected by diffusional kurtosis imaging. The current study provides new insight into the effects of alcohol on the brain and behavioral performance in different blush response and sex populations.
Collapse
Affiliation(s)
- L M Kong
- From the Department of Radiology (L.M.K., J.Y.Z., W.B.Z., Z.W.S., R.H.W.), the Second Affiliated Hospital, Medical College of Shantou University, Shantou, China
| | - J Y Zeng
- From the Department of Radiology (L.M.K., J.Y.Z., W.B.Z., Z.W.S., R.H.W.), the Second Affiliated Hospital, Medical College of Shantou University, Shantou, China
| | - W B Zheng
- From the Department of Radiology (L.M.K., J.Y.Z., W.B.Z., Z.W.S., R.H.W.), the Second Affiliated Hospital, Medical College of Shantou University, Shantou, China
| | - Z W Shen
- From the Department of Radiology (L.M.K., J.Y.Z., W.B.Z., Z.W.S., R.H.W.), the Second Affiliated Hospital, Medical College of Shantou University, Shantou, China
| | - R H Wu
- From the Department of Radiology (L.M.K., J.Y.Z., W.B.Z., Z.W.S., R.H.W.), the Second Affiliated Hospital, Medical College of Shantou University, Shantou, China .,China Provincial Key Laboratory of Medical Molecular Imaging (R.H.W.), Guangdong, Shantou, China
| |
Collapse
|
17
|
De Sa Nogueira D, Merienne K, Befort K. Neuroepigenetics and addictive behaviors: Where do we stand? Neurosci Biobehav Rev 2018; 106:58-72. [PMID: 30205119 DOI: 10.1016/j.neubiorev.2018.08.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 07/28/2018] [Accepted: 08/29/2018] [Indexed: 12/21/2022]
Abstract
Substance use disorders involve long-term changes in the brain that lead to compulsive drug seeking, craving, and a high probability of relapse. Recent findings have highlighted the role of epigenetic regulations in controlling chromatin access and regulation of gene expression following exposure to drugs of abuse. In the present review, we focus on data investigating genome-wide epigenetic modifications in the brain of addicted patients or in rodent models exposed to drugs of abuse, with a particular focus on DNA methylation and histone modifications associated with transcriptional studies. We highlight critical factors for epigenomic studies in addiction. We discuss new findings related to psychostimulants, alcohol, opiate, nicotine and cannabinoids. We examine the possible transmission of these changes across generations. We highlight developing tools, specifically those that allow investigation of structural reorganization of the chromatin. These have the potential to increase our understanding of alteration of chromatin architecture at gene regulatory regions. Neuroepigenetic mechanisms involved in addictive behaviors could explain persistent phenotypic effects of drugs and, in particular, vulnerability to relapse.
Collapse
Affiliation(s)
- David De Sa Nogueira
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, CNRS, Université de Strasbourg, Team 3 « Abuse of Drugs and Neuroadaptations », Faculté de Psychologie, 12 rue Goethe, F-67000, France
| | - Karine Merienne
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, CNRS, Université de Strasbourg, Team 1 « Dynamics of Memory and Epigenetics », Faculté de Psychologie, 12 rue Goethe, F-67000, France
| | - Katia Befort
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, CNRS, Université de Strasbourg, Team 3 « Abuse of Drugs and Neuroadaptations », Faculté de Psychologie, 12 rue Goethe, F-67000, France.
| |
Collapse
|
18
|
Proanthocyanidins prevent ethanol-induced cognitive impairment by suppressing oxidative and inflammatory stress in adult rat brain. Neuroreport 2018; 28:980-986. [PMID: 28877101 DOI: 10.1097/wnr.0000000000000867] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Excessive chronic alcohol consumption enhances brain oxidative and inflammatory stress, resulting in cognitive deficit. This study investigated the potential alleviating effects of proanthocyanidins (PACs) on ethanol-induced cognitive impairment and stress in brain regions including the prefrontal cortex, hippocampus, and amygdala. Adult male rats were administered saline, PACs, ethanol, or combinations of ethanol with different doses of PACs for 8 weeks. Then, the Morris water-maze test was performed. Thiobarbituric acid-reactive substances, superoxide dismutase activity, total antioxidant capacity, and nitric oxide were chosen as parameters of oxidative stress, whereas tumor necrosis factor-α and interleukin-1β chosen as parameters of inflammatory stress. The results indicated that ethanol led to cognitive impairment along with enhanced oxidative and inflammatory stress in brain regions, whereas PACs per se had no significant effects. Moreover, coadministration with PACs in ethanol-treated rats dose dependently rescued cognitive impairment accompanied by suppressed oxidative and inflammatory stress in brain regions. Thus, the protective effects of PACs on ethanol-induced cognitive impairments may be because of their antioxidant and anti-inflammatory activities.
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
Warden AS, Mayfield RD. Gene expression profiling in the human alcoholic brain. Neuropharmacology 2017; 122:161-174. [PMID: 28254370 DOI: 10.1016/j.neuropharm.2017.02.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 01/12/2023]
Abstract
Long-term alcohol use causes widespread changes in gene expression in the human brain. Aberrant gene expression changes likely contribute to the progression from occasional alcohol use to alcohol use disorder (including alcohol dependence). Transcriptome studies have identified individual gene candidates that are linked to alcohol-dependence phenotypes. The use of bioinformatics techniques to examine expression datasets has provided novel systems-level approaches to transcriptome profiling in human postmortem brain. These analytical advances, along with recent developments in next-generation sequencing technology, have been instrumental in detecting both known and novel coding and non-coding RNAs, alternative splicing events, and cell-type specific changes that may contribute to alcohol-related pathologies. This review offers an integrated perspective on alcohol-responsive transcriptional changes in the human brain underlying the regulatory gene networks that contribute to alcohol dependence. This article is part of the Special Issue entitled "Alcoholism".
Collapse
Affiliation(s)
- Anna S Warden
- Institute for Neuroscience, The University of Texas at Austin, 1 University Station, C7000, Austin, TX 78712, USA; Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA
| | - R Dayne Mayfield
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, 2500 Speedway, A4800, Austin, TX 78712, USA.
| |
Collapse
|
21
|
Wang Z, Song J, Zhang L, Huang S, Bao L, Chen F, Zhao X. Increased expression of microRNA-378a-5p in acute ethanol exposure of rat cardiomyocytes. Cell Stress Chaperones 2017; 22:245-252. [PMID: 28160209 PMCID: PMC5352598 DOI: 10.1007/s12192-016-0760-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/18/2016] [Accepted: 12/22/2016] [Indexed: 12/12/2022] Open
Abstract
Alcohol abuse is a risk factor for a distinct form of congestive heart failure, known as alcoholic cardiomyopathy (ACM). Here, we investigate how microRNAs may participate in the induction of cardiomyocyte apoptosis associated with ethanol exposure in vitro. Increasing the concentrations of ethanol to primary rat cardiomyocytes resulted in elevated apoptosis assessed by annexin V and propidium iodide staining, and reduced expression of an enzyme for alcohol detoxification aldehyde dehydrogenase 2 (ALDH2). These ethanol effects were accompanied by a substantial elevation of miR-378a-5p. Driving miR-378a-5p overexpression in cardiomyocytes decreased ALDH2. The specific interaction of miR-378a-5p with the 3'UTR of ALDH2 was examined by luciferase reporter assays, and we found that miR-378a-5p activity depends on a complementary base pairing at the 3'-UTR region of ALDH2 mRNA. Finally, ethanol-induced apoptosis in cardiomyocytes was attenuated in the presence of anti-miR378a-5p. Collectively, these data implicate a likely involvement of miR-378a-5p in the stimulation of cardiomyocyte apoptosis through ALDH2 gene suppression, which might play a potential role in the pathogenesis of ACM.
Collapse
Affiliation(s)
- Zhongkai Wang
- Department of Cardiovasology, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Jingwen Song
- Department of Cardiovasology, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Liang Zhang
- Department of Cardiovasology, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Songqun Huang
- Department of Cardiovasology, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Lizhi Bao
- Department of Cardiovasology, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai, 200433, China
| | - Feng Chen
- Department of Cardiovasology, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai, 200433, China.
| | - Xianxian Zhao
- Department of Cardiovasology, Changhai Hospital, Second Military Medical University, 168 Changhai Road, Shanghai, 200433, China.
| |
Collapse
|
22
|
Walter NAR, Denmark DL, Kozell LB, Buck KJ. A Systems Approach Implicates a Brain Mitochondrial Oxidative Homeostasis Co-expression Network in Genetic Vulnerability to Alcohol Withdrawal. Front Genet 2017; 7:218. [PMID: 28096806 PMCID: PMC5206817 DOI: 10.3389/fgene.2016.00218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 12/08/2016] [Indexed: 12/31/2022] Open
Abstract
Genetic factors significantly affect vulnerability to alcohol dependence (alcoholism). We previously identified quantitative trait loci on distal mouse chromosome 1 with large effects on predisposition to alcohol physiological dependence and associated withdrawal following both chronic and acute alcohol exposure in mice (Alcdp1 and Alcw1, respectively). We fine-mapped these loci to a 1.1–1.7 Mb interval syntenic with human 1q23.2-23.3. Alcw1/Alcdp1 interval genes show remarkable genetic variation among mice derived from the C57BL/6J and DBA/2J strains, the two most widely studied genetic animal models for alcohol-related traits. Here, we report the creation of a novel recombinant Alcw1/Alcdp1 congenic model (R2) in which the Alcw1/Alcdp1 interval from a donor C57BL/6J strain is introgressed onto a uniform, inbred DBA/2J genetic background. As expected, R2 mice demonstrate significantly less severe alcohol withdrawal compared to wild-type littermates. Additionally, comparing R2 and background strain animals, as well as reciprocal congenic (R8) and appropriate background strain animals, we assessed Alcw1/Alcdp1 dependent brain gene expression using microarray and quantitative PCR analyses. To our knowledge this includes the first Weighted Gene Co-expression Network Analysis using reciprocal congenic models. Importantly, this allows detection of co-expression patterns limited to one or common to both genetic backgrounds with high or low predisposition to alcohol withdrawal severity. The gene expression patterns (modules) in common contain genes related to oxidative phosphorylation, building upon human and animal model studies that implicate involvement of oxidative phosphorylation in alcohol use disorders (AUDs). Finally, we demonstrate that administration of N-acetylcysteine, an FDA-approved antioxidant, significantly reduces symptoms of alcohol withdrawal (convulsions) in mice, thus validating a phenotypic role for this network. Taken together, these studies support the importance of mitochondrial oxidative homeostasis in alcohol withdrawal and identify this network as a valuable therapeutic target in human AUDs.
Collapse
Affiliation(s)
- Nicole A R Walter
- Research and Development, Portland Veterans Affairs Medical Center, PortlandOR, USA; Department of Behavioral Neuroscience, School of Medicine, Oregon Health and Science University, PortlandOR, USA
| | - DeAunne L Denmark
- Research and Development, Portland Veterans Affairs Medical Center, PortlandOR, USA; Department of Behavioral Neuroscience, School of Medicine, Oregon Health and Science University, PortlandOR, USA
| | - Laura B Kozell
- Research and Development, Portland Veterans Affairs Medical Center, PortlandOR, USA; Department of Behavioral Neuroscience, School of Medicine, Oregon Health and Science University, PortlandOR, USA
| | - Kari J Buck
- Research and Development, Portland Veterans Affairs Medical Center, PortlandOR, USA; Department of Behavioral Neuroscience, School of Medicine, Oregon Health and Science University, PortlandOR, USA
| |
Collapse
|
23
|
Chan D, McGraw S, Klein K, Wallock LM, Konermann C, Plass C, Chan P, Robaire B, Jacob RA, Greenwood CMT, Trasler JM. Stability of the human sperm DNA methylome to folic acid fortification and short-term supplementation. Hum Reprod 2016; 32:272-283. [PMID: 27994001 DOI: 10.1093/humrep/dew308] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 10/26/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022] Open
Abstract
STUDY QUESTION Do short-term and long-term exposures to low-dose folic acid supplementation alter DNA methylation in sperm? SUMMARY ANSWER No alterations in sperm DNA methylation patterns were found following the administration of low-dose folic acid supplements of 400 μg/day for 90 days (short-term exposure) or when pre-fortification of food with folic acid and post-fortification sperm samples (long-term exposure) were compared. WHAT IS KNOWN ALREADY Excess dietary folate may be detrimental to health and DNA methylation profiles due to folate's role in one-carbon metabolism and the formation of S-adenosyl methionine, the universal methyl donor. DNA methylation patterns are established in developing male germ cells and have been suggested to be affected by high-dose (5 mg/day) folic acid supplementation. STUDY DESIGN, SIZE, DURATION This is a control versus treatment study where genome-wide sperm DNA methylation patterns were examined prior to fortification of food (1996-1997) in men with no history of infertility at baseline and following 90-day exposure to placebo (n = 9) or supplement containing 400 μg folic acid/day (n = 10). Additionally, pre-fortification sperm DNA methylation profiles (n = 19) were compared with those of a group of post-fortification (post-2004) men (n = 8) who had been exposed for several years to dietary folic acid fortification. PARTICIPANTS/MATERIALS, SETTING, METHODS Blood and seminal plasma folate levels were measured in participants before and following the 90-day treatment with placebo or supplement. Sperm DNA methylation was assessed using the whole-genome and genome-wide techniques, MassArray epityper, restriction landmark genomic scanning, methyl-CpG immunoprecipitation and Illumina HumanMethylation450 Bead Array. MAIN RESULTS AND THE ROLE OF CHANCE Following treatment, supplemented individuals had significantly higher levels of blood and seminal plasma folates compared to placebo. Initial first-generation genome-wide analyses of sperm DNA methylation showed little evidence of changes when comparing pre- and post-treatment samples. With Illumina HumanMethylation450 BeadChip arrays, no significant changes were observed in individual probes following low-level supplementation; when compared with those of the post-fortification cohort, there were also few differences in methylation despite exposure to years of fortified foods. LARGE SCALE DATA Illumina HumanMethylation450 BeadChip data from this study have been submitted to the NCBI Gene Expression Omnibus under the accession number GSE89781. LIMITATIONS, REASONS FOR CAUTION This study was limited to the number of participants available in each cohort, in particular those who were not exposed to early (pre-1998) fortification of food with folic acid. While genome-wide DNA methylation was assessed with several techniques that targeted genic and CpG-rich regions, intergenic regions were less well interrogated. WIDER IMPLICATIONS OF THE FINDINGS Overall, our findings provide evidence that short-term exposure to low-dose folic acid supplements of 400 μg/day, over a period of 3 months, a duration of time that might occur during infertility treatments, has no major impact on the sperm DNA methylome. STUDY FUNDING/COMPETING INTERESTS This work was supported by a grant to J.M.T. from the Canadian Institutes of Health Research (CIHR: MOP-89944). The authors have no conflicts of interest to declare.
Collapse
Affiliation(s)
- D Chan
- Departments of Pediatrics and of Human Genetics of McGill University, Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Glen Site, 1001 Décarie Boulevard Block E- Room EM0.2236 Montreal, QC H4A 3J1, Canada
| | - S McGraw
- Department of Obstetrics and Gynaecology, Biochemistry and Molecular Medicine of Université de Montréal, Research Center of the Sainte-Justine University Hospital, Montreal, QC H3T 1C5, Canada
| | - K Klein
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada
| | - L M Wallock
- Department of Biological Sciences, Diablo Valley College, Pleasant Hill, CA 94523, USA
| | - C Konermann
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - C Plass
- Department of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - P Chan
- Royal Victoria Hospital of the McGill University Health Centre and Department of Surgery, McGill University, Montréal, QC H4A 3J1, Canada
| | - B Robaire
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3A 0G4, Canada
| | - R A Jacob
- USDA, Agricultural Research Service, Western Human Nutrition Research Center, Davis, CA 95616, USA
| | - C M T Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada.,Departments of Oncology, Epidemiology, Biostatistics and Occupational Health, and Human Genetics, McGill University, Montréal, QC H4A 3J1, Canada
| | - J M Trasler
- Departments of Pediatrics and of Human Genetics of McGill University, Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Glen Site, 1001 Décarie Boulevard Block E- Room EM0.2236 Montreal, QC H4A 3J1, Canada .,Department of Pharmacology and Therapeutics, McGill University, Montréal, QC H3A 0G4, Canada
| |
Collapse
|
24
|
Darlington TM, McCarthy RD, Cox RJ, Miyamoto-Ditmon J, Gallego X, Ehringer MA. Voluntary wheel running reduces voluntary consumption of ethanol in mice: identification of candidate genes through striatal gene expression profiling. GENES BRAIN AND BEHAVIOR 2016; 15:474-90. [PMID: 27063791 DOI: 10.1111/gbb.12294] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/11/2016] [Accepted: 04/06/2016] [Indexed: 01/10/2023]
Abstract
Hedonic substitution, where wheel running reduces voluntary ethanol consumption, has been observed in prior studies. Here, we replicate and expand on previous work showing that mice decrease voluntary ethanol consumption and preference when given access to a running wheel. While earlier work has been limited mainly to behavioral studies, here we assess the underlying molecular mechanisms that may account for this interaction. From four groups of female C57BL/6J mice (control, access to two-bottle choice ethanol, access to a running wheel, and access to both two-bottle choice ethanol and a running wheel), mRNA-sequencing of the striatum identified differential gene expression. Many genes in ethanol preference quantitative trait loci were differentially expressed due to running. Furthermore, we conducted Weighted Gene Co-expression Network Analysis and identified gene networks corresponding to each effect behavioral group. Candidate genes for mediating the behavioral interaction between ethanol consumption and wheel running include multiple potassium channel genes, Oprm1, Prkcg, Stxbp1, Crhr1, Gabra3, Slc6a13, Stx1b, Pomc, Rassf5 and Camta2. After observing an overlap of many genes and functional groups previously identified in studies of initial sensitivity to ethanol, we hypothesized that wheel running may induce a change in sensitivity, thereby affecting ethanol consumption. A behavioral study examining Loss of Righting Reflex to ethanol following exercise trended toward supporting this hypothesis. These data provide a rich resource for future studies that may better characterize the observed transcriptional changes in gene networks in response to ethanol consumption and wheel running.
Collapse
Affiliation(s)
- T M Darlington
- Institute for Behavioral Genetics, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA.,Current address: Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - R D McCarthy
- Institute for Behavioral Genetics, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - R J Cox
- Institute for Behavioral Genetics, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - J Miyamoto-Ditmon
- Institute for Behavioral Genetics, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - X Gallego
- Institute for Behavioral Genetics, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| | - M A Ehringer
- Institute for Behavioral Genetics, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA
| |
Collapse
|
25
|
Luo C, Liu J, Dey DK, Chen K. Canonical variate regression. Biostatistics 2016; 17:468-83. [PMID: 26861909 DOI: 10.1093/biostatistics/kxw001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 01/01/2016] [Indexed: 11/13/2022] Open
Abstract
In many fields, multi-view datasets, measuring multiple distinct but interrelated sets of characteristics on the same set of subjects, together with data on certain outcomes or phenotypes, are routinely collected. The objective in such a problem is often two-fold: both to explore the association structures of multiple sets of measurements and to develop a parsimonious model for predicting the future outcomes. We study a unified canonical variate regression framework to tackle the two problems simultaneously. The proposed criterion integrates multiple canonical correlation analysis with predictive modeling, balancing between the association strength of the canonical variates and their joint predictive power on the outcomes. Moreover, the proposed criterion seeks multiple sets of canonical variates simultaneously to enable the examination of their joint effects on the outcomes, and is able to handle multivariate and non-Gaussian outcomes. An efficient algorithm based on variable splitting and Lagrangian multipliers is proposed. Simulation studies show the superior performance of the proposed approach. We demonstrate the effectiveness of the proposed approach in an [Formula: see text] intercross mice study and an alcohol dependence study.
Collapse
Affiliation(s)
- Chongliang Luo
- Department of Statistics, University of Connecticut, Storrs, CT 06269, USA
| | - Jin Liu
- Centre for Quantitative Medicine, Duke-NUS Graduate Medical School, Singapore 169856, Singapore
| | - Dipak K Dey
- Department of Statistics, University of Connecticut, Storrs, CT 06269, USA
| | - Kun Chen
- Department of Statistics, University of Connecticut, Storrs, CT 06269, USA
| |
Collapse
|
26
|
DNA co-methylation modules in postmortem prefrontal cortex tissues of European Australians with alcohol use disorders. Sci Rep 2016; 6:19430. [PMID: 26763658 PMCID: PMC4725922 DOI: 10.1038/srep19430] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 12/14/2015] [Indexed: 02/03/2023] Open
Abstract
DNA methylome alterations in the prefrontal cortex (PFC) may contribute to risk for alcohol use disorders (AUDs). We examined postmortem PFC DNA methylomes of 16 male and seven female pairs of AUD and control subjects using Illumina's HumanMethylation450 BeadChip assays. In male AUD subjects, 1,812 CpGs (1,099 genes) were differentially methylated (9.5 × 10(-9) ≤ Pnominal ≤ 7.2 × 10(-4), q < 0.05). In females, no CpGs were associated with AUDs after multiple testing correction (q > 0.05). Twenty-one AUD-associated co-methylation modules were identified in males by co-methylation analysis. The 1,812 CpGs were over-presented by two AUD-associated co-methylation modules (Mturquoise: 1,048 CpGs/683 genes; Mblue: 429 CpGs/304 genes) (Phyper ≤ 0.001). Biological processes enriched for genes in these two modules included neural development and transcriptional regulation. Genes mapped by CpGs in these two modules were enriched in genome-wide association study-identified genes with variants associated with four substance dependence phenotypes or five psychiatric disorders. Additionally, 106 of the 1,812 CpGs were mapped to 93 genes (e.g., AUD-associated genes GRIK3, GRIN2C, and GABRA1) with differential expression in postmortem PFC of male AUD subjects. Our study demonstrates that DNA methylation alterations in the PFC are associated with (and might result in) increased risk of AUDs, and there was a complex DNA methylation-gene expression relationship.
Collapse
|
27
|
Webb A, Papp AC, Curtis A, Newman LC, Pietrzak M, Seweryn M, Handelman SK, Rempala GA, Wang D, Graziosa E, Tyndale RF, Lerman C, Kelsoe JR, Mash DC, Sadee W. RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles. BMC Genomics 2015; 16:990. [PMID: 26597164 PMCID: PMC4657279 DOI: 10.1186/s12864-015-2207-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 11/12/2015] [Indexed: 01/03/2023] Open
Abstract
Background We used RNA sequencing to analyze transcript profiles of ten autopsy brain regions from ten subjects. RNA sequencing techniques were designed to detect both coding and non-coding RNA, splice isoform composition, and allelic expression. Brain regions were selected from five subjects with a documented history of smoking and five non-smokers. Paired-end RNA sequencing was performed on SOLiD instruments to a depth of >40 million reads, using linearly amplified, ribosomally depleted RNA. Sequencing libraries were prepared with both poly-dT and random hexamer primers to detect all RNA classes, including long non-coding (lncRNA), intronic and intergenic transcripts, and transcripts lacking poly-A tails, providing additional data not previously available. The study was designed to generate a database of the complete transcriptomes in brain region for gene network analyses and discovery of regulatory variants. Results Of 20,318 protein coding and 18,080 lncRNA genes annotated from GENCODE and lncipedia, 12 thousand protein coding and 2 thousand lncRNA transcripts were detectable at a conservative threshold. Of the aligned reads, 52 % were exonic, 34 % intronic and 14 % intergenic. A majority of protein coding genes (65 %) was expressed in all regions, whereas ncRNAs displayed a more restricted distribution. Profiles of RNA isoforms varied across brain regions and subjects at multiple gene loci, with neurexin 3 (NRXN3) a prominent example. Allelic RNA ratios deviating from unity were identified in > 400 genes, detectable in both protein-coding and non-coding genes, indicating the presence of cis-acting regulatory variants. Mathematical modeling was used to identify RNAs stably expressed in all brain regions (serving as potential markers for normalizing expression levels), linked to basic cellular functions. An initial analysis of differential expression analysis between smokers and nonsmokers implicated a number of genes, several previously associated with nicotine exposure. Conclusions RNA sequencing identifies distinct and consistent differences in gene expression between brain regions, with non-coding RNA displaying greater diversity between brain regions than mRNAs. Numerous RNAs exhibit robust allele selective expression, proving a means for discovery of cis-acting regulatory factors with potential clinical relevance. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2207-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Amy Webb
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA. .,Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
| | - Audrey C Papp
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
| | - Amanda Curtis
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
| | - Leslie C Newman
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
| | - Maciej Pietrzak
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA. .,Division of Biostatistics, College of Public Health, and Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, USA.
| | - Michal Seweryn
- Division of Biostatistics, College of Public Health, and Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, USA.
| | - Samuel K Handelman
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA.
| | - Grzegorz A Rempala
- Division of Biostatistics, College of Public Health, and Mathematical Biosciences Institute, The Ohio State University, Columbus, OH, USA.
| | - Daqing Wang
- Thermo Fisher Scientific, South San Francisco, CA, 94080, USA.
| | - Erica Graziosa
- Thermo Fisher Scientific, South San Francisco, CA, 94080, USA.
| | - Rachel F Tyndale
- Center for Addiction and Mental Health and Departments of Psychiatry and Pharmacology & Toxicology, University of Toronto, Toronto, Ontario, Canada.
| | - Caryn Lerman
- Department of Psychiatry, Annenberg School for Communication, and Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, USA.
| | - John R Kelsoe
- Department of Psychiatry, Laboratory of Psychiatric Genomics, University of California, San Diego, USA. .,VA San Diego Healthcare System, La Jolla, San Diego, CA, USA.
| | - Deborah C Mash
- Department of Neurology, Miller School of Medicine, University of Miami, Miami, FL, 33136, USA.
| | - Wolfgang Sadee
- Center for Pharmacogenomics, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA. .,Departments of Pharmacology, College of Medicine; Colleges of Pharmacy and Environmental Health Sciences, The Ohio State University, Columbus, OH, USA. .,Departments of Psychiatry, College of Medicine; Colleges of Pharmacy and Environmental Health Sciences, The Ohio State University, Columbus, OH, USA. .,Departments of Human Genetics/Internal Medicine, College of Medicine; Colleges of Pharmacy and Environmental Health Sciences, The Ohio State University, 5078 Graves Hall, 333 W. 10th Avenue, Columbus, OH, 43210, USA.
| |
Collapse
|
28
|
Mamdani M, Williamson V, McMichael GO, Blevins T, Aliev F, Adkins A, Hack L, Bigdeli T, D. van der Vaart A, Web BT, Bacanu SA, Kalsi G, Kendler KS, Miles MF, Dick D, Riley BP, Dumur C, Vladimirov VI. Integrating mRNA and miRNA Weighted Gene Co-Expression Networks with eQTLs in the Nucleus Accumbens of Subjects with Alcohol Dependence. PLoS One 2015; 10:e0137671. [PMID: 26381263 PMCID: PMC4575063 DOI: 10.1371/journal.pone.0137671] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 08/05/2015] [Indexed: 11/18/2022] Open
Abstract
Alcohol consumption is known to lead to gene expression changes in the brain. After performing weighted gene co-expression network analyses (WGCNA) on genome-wide mRNA and microRNA (miRNA) expression in Nucleus Accumbens (NAc) of subjects with alcohol dependence (AD; N = 18) and of matched controls (N = 18), six mRNA and three miRNA modules significantly correlated with AD were identified (Bonferoni-adj. p≤ 0.05). Cell-type-specific transcriptome analyses revealed two of the mRNA modules to be enriched for neuronal specific marker genes and downregulated in AD, whereas the remaining four mRNA modules were enriched for astrocyte and microglial specific marker genes and upregulated in AD. Gene set enrichment analysis demonstrated that neuronal specific modules were enriched for genes involved in oxidative phosphorylation, mitochondrial dysfunction and MAPK signaling. Glial-specific modules were predominantly enriched for genes involved in processes related to immune functions, i.e. cytokine signaling (all adj. p≤ 0.05). In mRNA and miRNA modules, 461 and 25 candidate hub genes were identified, respectively. In contrast to the expected biological functions of miRNAs, correlation analyses between mRNA and miRNA hub genes revealed a higher number of positive than negative correlations (χ2 test p≤ 0.0001). Integration of hub gene expression with genome-wide genotypic data resulted in 591 mRNA cis-eQTLs and 62 miRNA cis-eQTLs. mRNA cis-eQTLs were significantly enriched for AD diagnosis and AD symptom counts (adj. p = 0.014 and p = 0.024, respectively) in AD GWAS signals in a large, independent genetic sample from the Collaborative Study on Genetics of Alcohol (COGA). In conclusion, our study identified putative gene network hubs coordinating mRNA and miRNA co-expression changes in the NAc of AD subjects, and our genetic (cis-eQTL) analysis provides novel insights into the etiological mechanisms of AD.
Collapse
Affiliation(s)
- Mohammed Mamdani
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Vernell Williamson
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Gowon O. McMichael
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Tana Blevins
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Fazil Aliev
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Amy Adkins
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Laura Hack
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Tim Bigdeli
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Andrew D. van der Vaart
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Bradley Todd Web
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Silviu-Alin Bacanu
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Gursharan Kalsi
- Department of Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, London SE5 8AF, United Kingdom
| | | | - Kenneth S. Kendler
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Michael F. Miles
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Pharmacology & Toxicology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Danielle Dick
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Brien P. Riley
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Human & Molecular Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Catherine Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Vladimir I. Vladimirov
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth University, Richmond, VA, United States of America
- Department of Psychiatry, Virginia Commonwealth University, Richmond, VA, United States of America
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University, Richmond, VA, United States of America
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, United States of America
| |
Collapse
|
29
|
Xiang Y, Kim KY, Gelernter J, Park IH, Zhang H. Ethanol upregulates NMDA receptor subunit gene expression in human embryonic stem cell-derived cortical neurons. PLoS One 2015; 10:e0134907. [PMID: 26266540 PMCID: PMC4534442 DOI: 10.1371/journal.pone.0134907] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 07/16/2015] [Indexed: 01/16/2023] Open
Abstract
Chronic alcohol consumption may result in sustained gene expression alterations in the brain, leading to alcohol abuse or dependence. Because of ethical concerns of using live human brain cells in research, this hypothesis cannot be tested directly in live human brains. In the present study, we used human embryonic stem cell (hESC)-derived cortical neurons as in vitro cellular models to investigate alcohol-induced expression changes of genes involved in alcohol metabolism (ALDH2), anti-apoptosis (BCL2 and CCND2), neurotransmission (NMDA receptor subunit genes: GRIN1, GRIN2A, GRIN2B, and GRIN2D), calcium channel activity (ITPR2), or transcriptional repression (JARID2). hESCs were differentiated into cortical neurons, which were characterized by immunostaining using antibodies against cortical neuron-specific biomarkers. Ethanol-induced gene expression changes were determined by reverse-transcription quantitative polymerase chain reaction (RT-qPCR). After a 7-day ethanol (50 mM) exposure followed by a 24-hour ethanol withdrawal treatment, five of the above nine genes (including all four NMDA receptor subunit genes) were highly upregulated (GRIN1: 1.93-fold, P = 0.003; GRIN2A: 1.40-fold, P = 0.003; GRIN2B: 1.75-fold, P = 0.002; GRIN2D: 1.86-fold, P = 0.048; BCL2: 1.34-fold, P = 0.031), and the results of GRIN1, GRIN2A, and GRIN2B survived multiple comparison correction. Our findings suggest that alcohol responsive genes, particularly NMDA receptor genes, play an important role in regulating neuronal function and mediating chronic alcohol consumption-induced neuroadaptations.
Collapse
Affiliation(s)
- Yangfei Xiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | - Kun-Yong Kim
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
| | - Joel Gelernter
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States of America
- Department of Neurobiology, Yale University School of Medicine, New Haven, CT, United States of America
- VA Medical Center, VA Connecticut Healthcare System, West Haven, CT, United States of America
| | - In-Hyun Park
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States of America
- * E-mail: (HZ); (IHP)
| | - Huiping Zhang
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States of America
- VA Medical Center, VA Connecticut Healthcare System, West Haven, CT, United States of America
- * E-mail: (HZ); (IHP)
| |
Collapse
|