Systems genetics analysis of the LXS recombinant inbred mouse strains:Genetic and molecular insights into acute ethanol tolerance.

Richard A Radcliffe,Beth Bennett,Laura M Saba,Shi Wen,Pratyaydipta Rudra,Colin Larson,Robin Dowell,Phillip A Richmond,Aaron T Odell,Katerina Kechris

doi:10.1371/journal.pone.0240253

Abstract

We have been using the Inbred Long- and Short-Sleep mouse strains (ILS, ISS) and a recombinant inbred panel derived from them, the LXS, to investigate the genetic underpinnings of acute ethanol tolerance which is considered to be a risk factor for alcohol use disorders (AUDs). Here, we have used RNA-seq to examine the transcriptome of whole brain in 40 of the LXS strains 8 hours after a saline or ethanol "pretreatment" as in previous behavioral studies. Approximately 1/3 of the 14,184 expressed genes were significantly heritable and many were unique to the pretreatment. Several thousand cis- and trans-eQTLs were mapped; a portion of these also were unique to pretreatment. Ethanol pretreatment caused differential expression (DE) of 1,230 genes. Gene Ontology (GO) enrichment analysis suggested involvement in numerous biological processes including astrocyte differentiation, histone acetylation, mRNA splicing, and neuron projection development. Genetic correlation analysis identified hundreds of genes that were correlated to the behaviors. GO analysis indicated that these genes are involved in gene expression, chromosome organization, and protein transport, among others. The expression profiles of the DE genes and genes correlated to AFT in the ethanol pretreatment group (AFT-Et) were found to be similar to profiles of HDAC inhibitors. Hdac1, a cis-regulated gene that is located at the peak of a previously mapped QTL for AFT-Et, was correlated to 437 genes, most of which were also correlated to AFT-Et. GO analysis of these genes identified several enriched biological process terms including neuron-neuron synaptic transmission and potassium transport. In summary, the results suggest widespread genetic effects on gene expression, including effects that are pretreatment-specific. A number of candidate genes and biological functions were identified that could be mediating the behavioral responses. The most prominent of these was Hdac1 which may be regulating genes associated with glutamatergic signaling and potassium conductance.

Highlights

It has been well established that genetics is a contributing factor to the development of alcohol use disorders (AUDs), yet knowledge of the underlying genetic variants is limited [1]
Acute functional tolerance (AFT) was first described by Mellanby [8] who observed that intoxicated dogs were more ataxic on the rising limb of ethanol distribution than they were at the same blood ethanol concentration (BEC) on the falling limb indicating the presence of AFT
Using a moderately conservative filtering procedure, we found that 13,460 and 14,170 out of 38,087 Ensembl genes were expressed in the saline and ethanol cohorts, respectively

Summary

Introduction

It has been well established that genetics is a contributing factor to the development of alcohol use disorders (AUDs), yet knowledge of the underlying genetic variants is limited [1]. The genetic analysis of human AUDs is complicated by a number of factors including low penetrance, population heterogeneity, poor control or lack of understanding of relevant nongenetic factors, and the likelihood that dozens if not hundreds of small effect genes are involved [2]. To some extent, these issues can be mitigated through the study of endophenotypes; i.e., intermediate traits that are heritable, biologically plausible, and predictive of the condition [3]. AFT has been postulated to be an important factor in the genetic relationship between acute sensitivity and AUD risk, this has not been firmly established [7, 13, 14]

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