Alcohol-dose-dependent DNA methylation and expression in the nucleus accumbens identifies coordinated regulation of synaptic genes

Abstract

Alterations in DNA methylation have been associated with alcohol exposure and proposed to contribute to continued alcohol use; however, the molecular mechanisms involved remain obscure. We investigated the escalating effects of alcohol use on DNA methylation, gene expression and predicted neural effects in the nucleus accumbens of rhesus macaques that self-administered 4% alcohol for over 12 months. Using an exploratory approach to identify CpG-rich regions, followed by bisulfite sequencing, the methylation levels of 2.7 million CpGs were compared between seven low-binge drinkers and nine heavy–very heavy drinking subjects. We identified 17 significant differential methylation regions (DMRs), including 14 with methylation levels that were correlated with average daily alcohol consumption. The size of the DMRs ranged from 29 to 158 bp (mean=63.7), included 4–19 CpGs per DMR (mean=8.06) and spanned a range of average methylation values from 5 to 34%. Eight of the DMRs mapped to genes implicated in modulating synaptic plasticity. Six of the synaptic genes have not previously been linked to alcohol use. Validation studies of these eight DMRs using bisulfite amplicon sequencing and an expanded set of 30 subjects confirmed the significant alcohol-dose-associated methylation of the DMRs. Expression analysis of three of the DMR-associated genes, LRP5, GPR39 and JAKMIP1, revealed significant correlations between DMR methylation and whole-gene or alternative transcript expression, supporting a functional role in regulating gene expression. Together, these studies suggest that alcohol-associated synaptic remodeling may be regulated and coordinated at the level of DNA methylation.

Chronic ethanol consumption alters lamina propria leukocyte response to stimulation in a region‐dependent manner

“…We also reported region-specific changes in mucosal tissue gene expression and microbial composition with CD (22). Additional studies using this cohort of macaques have reported suppression of intracortical bone remodeling (23) as well as gene expression and DNA methylation pattern changes in the brain associated with CD (24)(25)(26). Here, we examined the impact of CD on the transcriptional profiles and functional responses of LPLs isolated from the duodenum, jejunum, ileum, and colon in presence or absence of phorbol myristate acetate (PMA) and ionomycin stimulation.…”

Studies using macaque monkeys to address excessive alcohol drinking and stress interactions

“…As noted in the previous section, gene regulation and expression by epigenetic alterations in chromatin structure, such as DNA methylation or acetylation may provide a cumulative record of genomic adaptations to chronic alcohol exposure. Using this approach, Cervera-Juanes and colleagues (2017) report that male rhesus macaques who met criteria for heavy or very heavy drinking status (Baker et al, 2014) had a greater proportion of CpG hypermethylation of synaptic genes. Importantly, the differentially regulated regions (DMRs) between heavy/very heavy and light/binge drinking monkeys were largely hypermethylated and correlated with average daily intake.…”

“…Importantly, the differentially regulated regions (DMRs) between heavy/very heavy and light/binge drinking monkeys were largely hypermethylated and correlated with average daily intake. Of the 17 DMRs that distinguished these two drinking phenotypes, eight were mapped to genes that regulate neurotransmitter release and receptor trafficking in a coordinated fashion (Cervera-Juanes et al, 2017). …”

“…Applying a standard protocol to assess the population distribution of daily alcohol drinking, given nearly unlimited access to 4% (w/v diluted in water) (Baker et al, 2014; Grant et al, 2008), has provided longitudinal self-administration and endocrine data from dozens of macaques that are conducive for studying adaptations in neurocircuitry that integrate genetic (Cervera-Juanes et al, 2017; Iancu et al, 2017) and neuroimaging techniques (Kroenke et al, 2013; 2014). Using this animal model, novel approaches to both genetic (Cervera-Juanes et al, 2016) and MRI connectivity studies can help address highly translational endocrine, neuroanatomical and behavioral measures of the temporal sequence and specific mediators of dysregulation in motivational circuitry associated with severity of AUDs.…”

Alcohol consumption is associated with widespread changes in blood DNA methylation: analysis of cross-sectional and longitudinal data

“…Although there is a plausible relationship between alcohol intake and altered one-carbon metabolism and DNA methylation (18-20), to our knowledge only one large methylome-wide association study (herein referred to as EWAS) of alcohol consumption has been conducted (21). Genes have been reported to be differentially methylated in alcohol abusers, but most evidence comes from studies that either had small sample size, were not specific to humans or were carried out using tissues other than blood (22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33). Molecular mechanisms such as DNA methylation may underlie or enhance a predisposition to addictions and substance abuse, including alcohol drinking (23, 27, 29, 31-34).…”