title: DNA co-methylation modules in postmortem prefrontal cortex tissues of European Australians with alcohol use disorders.
abstract: DNA methylome alterations in the prefrontal cortex (PFC) may contribute to risk for alcohol use disorders (AUDs). We examined postmortem PFC DNA methylomes of 16 male and seven female pairs of AUD and control subjects using Illumina's HumanMethylation450 BeadChip assays. In male AUD subjects, 1,812 CpGs (1,099 genes) were differentially methylated (9.5 × 10(-9) ≤ Pnominal ≤ 7.2 × 10(-4), q < 0.05). In females, no CpGs were associated with AUDs after multiple testing correction (q > 0.05). Twenty-one AUD-associated co-methylation modules were identified in males by co-methylation analysis. The 1,812 CpGs were over-presented by two AUD-associated co-methylation modules (Mturquoise: 1,048 CpGs/683 genes; Mblue: 429 CpGs/304 genes) (Phyper ≤ 0.001). Biological processes enriched for genes in these two modules included neural development and transcriptional regulation. Genes mapped by CpGs in these two modules were enriched in genome-wide association study-identified genes with variants associated with four substance dependence phenotypes or five psychiatric disorders. Additionally, 106 of the 1,812 CpGs were mapped to 93 genes (e.g., AUD-associated genes GRIK3, GRIN2C, and GABRA1) with differential expression in postmortem PFC of male AUD subjects. Our study demonstrates that DNA methylation alterations in the PFC are associated with (and might result in) increased risk of AUDs, and there was a complex DNA methylation-gene expression relationship.
authors.affiliation: Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.|VA Medical Center, VA Connecticut Healthcare System, West Haven, CT, USA.
authors.forename: Fan
authors.initials: F
authors.lastname: Wang
authors.affiliation: Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.|VA Medical Center, VA Connecticut Healthcare System, West Haven, CT, USA.
authors.forename: Hongqin
authors.initials: H
authors.lastname: Xu
authors.affiliation: Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.|Department of Biostatistics, Yale University School of Public Health, New Haven, CT, USA.
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.affiliation: Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.|Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.|Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA.|VA Medical Center, VA Connecticut Healthcare System, West Haven, CT, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: Gelernter
authors.affiliation: Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.|VA Medical Center, VA Connecticut Healthcare System, West Haven, CT, USA.
authors.forename: Huiping
authors.initials: H
authors.lastname: Zhang
mesh_terms: D020751:Alcohol-Induced Disorders / Q000453:epidemiology / Q000235:genetics* / Q000473:pathology; D001344:Autopsy; D002874:Chromosome Mapping; D016000:Cluster Analysis; D018899:CpG Islands; D019175:DNA Methylation; D005260:Female; D020869:Gene Expression Profiling; D055106:Genome-Wide Association Study; D006801:Humans; D008297:Male; D017397:Prefrontal Cortex / Q000378:metabolism* / Q000473:pathology; D012737:Sex Factors; D014158:Transcription, Genetic; D044465:White People