title: GABRA2 Alcohol Dependence Risk Allele is Associated with Reduced Expression of Chromosome 4p12 GABAA Subunit Genes in Human Neural Cultures.
abstract: BACKGROUND
  Genetic variation in a region of chromosome 4p12 that includes the GABAA 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 in vitro gene expression of the AD-associated GABRA2 rs279858*C-allele in human neural cells using an induced pluripotent stem cell (iPSC) model system.
  
  
  METHODS
  We examined mRNA expression of chromosome 4p12 GABAA 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.
  
  
  RESULTS
  We found significantly lower levels of GABRA2 mRNA in neural cell cultures derived from rs279858*C-allele carriers. Levels of GABRA2 RNA were correlated with those of the other 3 chromosome 4p12 GABAA genes, but not other neural genes. Cluster analysis based on the relative RNA levels of the 4 chromosome 4p12 GABAA 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 GABAA gene expression in postmortem adult cortex in either the BrainCloud or BRAINEAC data sets.
  
  
  CONCLUSIONS
  AD-associated variation in GABRA2 is associated with differential expression of the entire cluster of GABAA 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 GABAA expression, although not present in mature cortex, could have effects on regulation of the chromosome 4p12 GABAA cluster during neural development.
authors.affiliation: Alcohol Research Center, Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut.|Department of Neuroscience, University of Connecticut Health Center, University of Connecticut School of Medicine, Farmington, Connecticut.
authors.forename: Richard
authors.initials: R
authors.lastname: Lieberman
authors.affiliation: Center for Studies of Addiction, Department of Psychiatry, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, Pennsylvania.|VISN4 MIRECC, Philadelphia VAMC, Philadelphia, Pennsylvania.
authors.forename: Henry R
authors.initials: HR
authors.lastname: Kranzler
authors.affiliation: Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut.
authors.forename: Pujan
authors.initials: P
authors.lastname: Joshi
authors.affiliation: Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut.|Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut.
authors.forename: Dong-Guk
authors.initials: DG
authors.lastname: Shin
authors.affiliation: Alcohol Research Center, Department of Psychiatry, University of Connecticut School of Medicine, Farmington, Connecticut.|Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Covault
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D000437:Alcoholism / Q000175:diagnosis / Q000235:genetics*; D000483:Alleles; D002460:Cell Line; D002478:Cells, Cultured; D002894:Chromosomes, Human, Pair 4 / Q000235:genetics* / Q000378:metabolism; D005260:Female; D005786:Gene Expression Regulation; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D058953:Neural Stem Cells / Q000502:physiology*; D009474:Neurons / Q000502:physiology; D021122:Protein Subunits / Q000096:biosynthesis / Q000235:genetics; D011963:Receptors, GABA-A / Q000235:genetics*; D055815:Young Adult
chemical_list: C484841:GABRA2 protein, human; D021122:Protein Subunits; D011963:Receptors, GABA-A
keywords: Alcohol Dependence; GABAA Receptor; GABRA2; Gene Expression; Induced Pluripotent Stem Cells