Genetic Dissection of Acute Ethanol Responsive Gene Networks in Prefrontal Cortex: Functional and Mechanistic Implications

Abstract

BackgroundIndividual differences in initial sensitivity to ethanol are strongly related to the heritable risk of alcoholism in humans. To elucidate key molecular networks that modulate ethanol sensitivity we performed the first systems genetics analysis of ethanol-responsive gene expression in brain regions of the mesocorticolimbic reward circuit (prefrontal cortex, nucleus accumbens, and ventral midbrain) across a highly diverse family of 27 isogenic mouse strains (BXD panel) before and after treatment with ethanol.ResultsAcute ethanol altered the expression of ∼2,750 genes in one or more regions and 400 transcripts were jointly modulated in all three. Ethanol-responsive gene networks were extracted with a powerful graph theoretical method that efficiently summarized ethanol's effects. These networks correlated with acute behavioral responses to ethanol and other drugs of abuse. As predicted, networks were heavily populated by genes controlling synaptic transmission and neuroplasticity.Several of the most densely interconnected network hubs, including Kcnma1 and Gsk3β, are known to influence behavioral or physiological responses to ethanol, validating our overall approach. Other major hub genes like Grm3, Pten and Nrg3 represent novel targets of ethanol effects. Networks were under strong genetic control by variants that we mapped to a small number of chromosomal loci. Using a novel combination of genetic, bioinformatic and network-based approaches, we identified high priority cis-regulatory candidate genes, including Scn1b, Gria1, Sncb and Nell2.ConclusionsThe ethanol-responsive gene networks identified here represent a previously uncharacterized intermediate phenotype between DNA variation and ethanol sensitivity in mice. Networks involved in synaptic transmission were strongly regulated by ethanol and could contribute to behavioral plasticity seen with chronic ethanol. Our novel finding that hub genes and a small number of loci exert major influence over the ethanol response of gene networks could have important implications for future studies regarding the mechanisms and treatment of alcohol use disorders.

KCNN Genes that Encode Small-Conductance Ca2+-Activated K+ Channels Influence Alcohol and Drug Addiction

“…Studies on correlations for Kcnn1-3 gene expression in NAc were completed using microarray datasets produced from BXD RI strains treated with either saline (Wolen et al, 2012) or the CIE protocol (Miles, Smith, Lopez, Becker and Williams, unpublished data). Tissue punch dissections, RNA isolation, and hybridization/scanning procedures with Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Cat #900497) were performed as described previously (Wolen et al, 2012).…”

“…Tissue punch dissections, RNA isolation, and hybridization/scanning procedures with Affymetrix Mouse Genome 430 2.0 arrays (Affymetrix, Cat #900497) were performed as described previously (Wolen et al, 2012). Full presentation and discussion of the BXD CIE microarray data will be reported elsewhere (Miles, Smith, Lopez, Becker and Williams, manuscript in preparation).…”

“…First, we conducted a linear regression analysis of Kcnn1 (probe set 1419617_at), Kcnn2 (1448927_at), and Kcnn3 (1421632_at) RMA levels in the NAc of alcohol-naive (saline treated) BXD RI mice from a previous study (Wolen et al, 2012) and baseline alcohol intake values from a separate cohort of corresponding BXD RI strains in the CIE-drinking model (as described above). Next, we conducted a linear regression analysis of NAc Kcnn1-3 RMA levels from air-exposed BXD RI mice and alcohol intake values from the 4-h session on day 4 of a binge alcohol drinking (DID) procedure (Jones, Lu and Williams, unpublished observation, GeneNetwork record ID 13565).…”

“…First, we correlated NAc Kcnn1-3 RMA values obtained from alcohol-naive mice (Wolen et al, 2012) with baseline drinking data obtained from corresponding BXD RI strains of mice in the present study (n = 14 strains; 106 total mice). Transcript levels of each KCNN gene in the NAc varied across the BXD strains (Kcnn1: 7.58 ± 0.114 (mean transcript expression levels ± SD), 1.53-fold range; Kcnn2: 9.59 ± 0.099, 1.30-fold range; Kcnn3: 7.46 ± 0.112, 1.44-fold range; Figure 1a).…”

Integrative epigenetic profiling analysis identifies DNA methylation changes associated with chronic alcohol consumption

“…This link between gene interactions and alcoholism-related pathways is evident in the association between AR (androgen receptor) and NCOR1 (nuclear receptor co-repressor 1). AR is known to have a modulating effect on craving during withdrawal in men [37], whereas NCOR1 is an established alcohol candidate gene whose expression in the mouse prefrontal cortex is responsive to ethanol treatment [38]. It has been demonstrated that NCOR1 directly interact with AR, suppressing AR transcription [39].…”