On the relationships in rhesus macaques between chronic ethanol consumption and the brain transcriptome

Abstract

This is the first description of the relationship between chronic ethanol self-administration and the brain transcriptome in a non-human primate (rhesus macaque). Thirty-one male animals self-administered ethanol on a daily basis for over 12 months. Gene transcription was quantified with RNA-Seq in the central nucleus of the amygdala (CeA) and cortical Area 32. We constructed coexpression and cosplicing networks, and we identified areas of preservation and areas of differentiation between regions and network types. Correlations between intake and transcription included largely distinct gene sets and annotation categories across brain regions and between expression and splicing; positive and negative correlations were also associated with distinct annotation groups. Membrane, synaptic and splicing annotation categories were over-represented in the modules (gene clusters) enriched in positive correlations (CeA); our cosplicing analysis further identified the genes affected only at the exon inclusion level. In the CeA coexpression network, we identified Rab6b, Cdk18 and Igsf21 among the intake-correlated hubs, while in the Area 32, we identified a distinct hub set that included Ppp3r1 and Myeov2. Overall, the data illustrate that excessive ethanol self-administration is associated with broad expression and splicing mechanisms that involve membrane and synapse genes.

Keywords: RNA-Seq; addiction; cosplicing; ethanol; network analysis; non-human primate.

Figure 1

Network structure as quantified by hub identity is distinct across brain regions and network types. (a) CeA coexpression versus cosplicing network hubs. (b) Area 32 coexpression versus cosplicing network hubs. (c) Coexpression, Area 32 versus CeA. (d) Cosplicing, Area 32 versus CeA

Figure 2

Consumption-correlated genes cluster in a module (light cyan) significantly enriched in synapse and membrane annotations. (a) Positively (red) and negatively (blue) correlated genes. (b) Genes annotated with synapse part are colored in cyan, genes annotated with membrane part are colored in green, and genes with both annotations are colored in purple. Node size is proportional to module connectivity. For visual clarity, only edges with adjacency values over 0.1 are depicted

Figure 3

Overlap of three groups of genes correlated to ethanol consumption in the CeA: (1) gene expression negatively correlated to consumption, (2) gene expression positively correlated to consumption, (3) gene splicing correlated to consumption. Correlations at the splicing versus expression level are largely distinct