Dual methylation and hydroxymethylation study of alcohol use disorder

Abstract

Using an integrative, multi-tissue design, we sought to characterize methylation and hydroxymethylation changes in blood and brain associated with alcohol use disorder (AUD). First, we used epigenomic deconvolution to perform cell-type-specific methylome-wide association studies within subpopulations of granulocytes/T-cells/ B-cells/monocytes in 1132 blood samples. Blood findings were then examined for overlap with AUD-related associations with methylation and hydroxymethylation in 50 human post-mortem brain samples. Follow-up analyses investigated if overlapping findings mediated AUD-associated transcription changes in the same brain samples. Lastly, we replicated our blood findings in an independent sample of 412 individuals and aimed to replicate published alcohol methylation findings using our results. Celltype-specific analyses in blood identified methylome-wide significant associations in monocytes and T-cells. The monocyte findings were significantly enriched for AUD-

Alcohol Use Disorder-Associated DNA Methylation in the Nucleus Accumbens and Dorsolateral Prefrontal Cortex

“…Of the three studies that assayed methylation in brain tissues 7,9,10 , we identified one CpG with look-up significance and three annotated genes that overlapped with our results. cg00402668 (intergenic) reached look-up significance in the DLPFC EWAS and was among the top 20 sites with AUD-associated hydroxymethylation in BA10 from Clark et al 10 .…”

“…. We did not observe significant enrichment between our results and those from Clark et al (Table S9) 10 .…”

“…We selected previous EWAS with large sample sizes (defined below), results reported by probe or coordinates, and DNAm assayed from blood or brain tissues. Three selected studies tested for associations with alcohol abuse, dependence, or use disorder in brain tissues 7,9,10 (n ≥ 46), and two tested for associations with alcohol consumption in blood 33,34 (n > 5,000). First, we performed a “look-up” of previously reported sites in our results.…”

“…Most studies have used the Illumina 450K or EPIC (∼850K CpG sites) arrays, with AUD-associated differential DNAm found within Brodmann Area 9 (BA9; including parts of the dorsolateral and medial prefrontal cortex) 5,6 , the precuneus 7 , Brodmann Area 10 (anterior-most portion of the prefrontal cortex) 8 , caudate nucleus 9 , and ventral striatum 9 . Another recent study assayed both 5mC methylation and hydroxymethylation from the BA10 region of 50 decedents using methyl-CG binding domain sequencing, resulting in near-complete coverage of the 28 million possible methylation sites in the genome; no methylome-wide significant sites were found 10 . No overlapping sites have been reported across these studies, which is not surprising given the highly context-specific nature of DNAm, different analytic strategies, and small sample sizes.…”

Is DNA methylation in the brain a mechanism of alcohol use disorder?

“…While exploratory methylome-wide analyses in the human brain found no global differences between alcohol dependent and control subjects ( Manzardo et al, 2012 ; Clark et al, 2022 ), the focused approaches were more successful. The authors tested the hypothesis that methylation of prodynorphin (Pdyn) CpG-SNPs in the PFC is associated with alcohol misuse ( Taqi et al, 2011 ).…”