title: Genome-wide analysis of the nucleus accumbens identifies DNA methylation signals differentiating low/binge from heavy alcohol drinking.
abstract: Alcohol-use disorders encompass a range of drinking levels and behaviors, including low, binge, and heavy drinking. In this regard, investigating the neural state of individuals who chronically self-administer lower doses of alcohol may provide insight into mechanisms that prevent the escalation of alcohol use. DNA methylation is one of the epigenetic mechanisms that stabilizes adaptations in gene expression and has been associated with alcohol use. Thus, we investigated DNA methylation, gene expression, and the predicted neural effects in the nucleus accumbens core (NAcc) of male rhesus macaques categorized as "low" or "binge" drinkers, compared to "alcohol-naïve" and "heavy" drinkers based on drinking patterns during a 12-month alcohol self-administration protocol. Using genome-wide CpG-rich region enrichment and bisulfite sequencing, the methylation levels of 2.6 million CpGs were compared between alcohol-naïve (AN), low/binge (L/BD), and heavy/very heavy (H/VHD) drinking subjects (n = 24). Through regional clustering analysis, we identified nine significant differential methylation regions (DMRs) that specifically distinguished ANs and L/BDs, and then compared those DMRs among H/VHDs. The DMRs mapped to genes encoding ion channels, receptors, cell adhesion molecules, and cAMP, NF-κβ and Wnt signaling pathway proteins. Two of the DMRs, linked to PDE10A and PKD2L2, were also differentially methylated in H/VHDs, suggesting an alcohol-dose independent effect. However, two other DMRs, linked to the CCBE1 and FZD5 genes, had L/BD methylation levels that significantly differed from both ANs and H/VHDs. The remaining five DMRs also differentiated L/BDs and ANs. However, H/VHDs methylation levels were not distinguishable from either of the two groups. Functional validation of two DMRs, linked to FZD5 and PDE10A, support their role in regulating gene expression and exon usage, respectively. In summary, the findings demonstrate that L/BD is associated with unique DNA methylation signatures in the primate NAcc, and that the methylation signatures identify synaptic genes that may play a role in preventing the escalation of alcohol use.
authors.affiliation: Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA. Electronic address: cerveraj@ohsu.edu.
authors.forename: Rita
authors.initials: R
authors.lastname: Cervera-Juanes
authors.affiliation: Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA.
authors.forename: Larry J
authors.initials: LJ
authors.lastname: Wilhelm
authors.affiliation: Department of Public Health and Preventive Medicine, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: Byung
authors.initials: B
authors.lastname: Park
authors.affiliation: Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA.
authors.forename: Kathleen A
authors.initials: KA
authors.lastname: Grant
authors.affiliation: Division of Neurosciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA.
authors.forename: Betsy
authors.initials: B
authors.lastname: Ferguson
mesh_terms: D000428:Alcohol Drinking / Q000009:adverse effects / Q000235:genetics*; D000437:Alcoholism / Q000235:genetics*; D000818:Animals; D063425:Binge Drinking / Q000235:genetics*; D016000:Cluster Analysis; D018899:CpG Islands; D019175:DNA Methylation / Q000187:drug effects*; D004195:Disease Models, Animal; D044127:Epigenesis, Genetic / Q000187:drug effects*; D000431:Ethanol / Q000633:toxicity*; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D008253:Macaca mulatta; D008297:Male; D009714:Nucleus Accumbens / Q000187:drug effects* / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D015398:Signal Transduction / Q000235:genetics
chemical_list: D000431:Ethanol
keywords: Alcohol; DNA methylation; Differentially methylated regions; Exon-usage; Gene expression; Nonhuman primates