GABRA2 Alcohol Dependence Risk Allele is Associated with Reduced Expression of Chromosome 4p12 GABAA Subunit Genes in Human Neural Cultures

BackgroundGenetic variation in a region of chromosome 4p12 that includes the GABA(A) subunit gene GABRA2 has been reproducibly associated with alcohol dependence (AD). However, the molecular mechanisms underlying the association are unknown. This study examined correlates of invitro gene expression of the AD-associated GABRA2 rs279858*C-allele in human neural cells using an induced pluripotent stem cell (iPSC) model system. MethodsWe examined mRNA expression of chromosome 4p12 GABA(A) subunit genes (GABRG1, GABRA2, GABRA4, and GABRB1) in 36 human neural cell lines differentiated from iPSCs using quantitative polymerase chain reaction and next-generation RNA sequencing. mRNA expression in adult human brain was examined using the BrainCloud and BRAINEAC data sets. ResultsWe found significantly lower levels of GABRA2 mRNA in neural cell cultures derived from rs279858*C-allele carriers. Levels of GABRA2RNA were correlated with those of the other 3 chromosome 4p12 GABA(A) genes, but not other neural genes. Cluster analysis based on the relative RNA levels of the 4 chromosome 4p12 GABA(A) genes identified 2 distinct clusters of cell lines, a low-expression cluster associated with rs279858*C-allele carriers and a high-expression cluster enriched for the rs279858*T/T genotype. In contrast, there was no association of genotype with chromosome 4p12 GABA(A) gene expression in postmortem adult cortex in either the BrainCloud or BRAINEAC data sets. ConclusionsAD-associated variation in GABRA2 is associated with differential expression of the entire cluster of GABA(A) subunit genes on chromosome 4p12 in human iPSC-derived neural cell cultures. The absence of a parallel effect in postmortem human adult brain samples suggests that AD-associated genotype effects on GABA(A) expression, although not present in mature cortex, could have effects on regulation of the chromosome 4p12 GABA(A) cluster during neural development.