AUTHOR=Andrade-Brito Diego E. , Núñez-Ríos Diana L. , Martínez-Magaña José Jaime , Nagamatsu Sheila T. , Rompala Gregory , Zillich Lea , Witt Stephanie H. , Clark Shaunna L. , Lattig Maria C. , Montalvo-Ortiz Janitza L. , Alvarez Victor E. , Benedek David , Che Alicia , Cruz Dianne A. , Davis David A. , Girgenti Matthew J. , Hoffman Ellen , Holtzheimer Paul E. , Huber Bertrand R. , Kaye Alfred , Keane Terence M. , Krystal John H. , Labadorf Adam T. , Logue Mark W. , Marx Brian , Mash Deborah , McKee Ann , Miller Mark W. , Montalvo-Ortiz Janitza , Noller Crystal , Schnurr Paula , Scott William K. , Stein Thor , Ursano Robert , Williamson Douglas E. , Wolf Erika J. , Young Keith A.
TITLE=Neuronal-specific methylome and hydroxymethylome analysis reveal significant loci associated with alcohol use disorder
JOURNAL=Frontiers in Genetics
VOLUME=15
YEAR=2024
URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2024.1345410
DOI=10.3389/fgene.2024.1345410
ISSN=1664-8021
ABSTRACT=Background: Alcohol use disorder (AUD) is a complex condition associated with adverse health consequences that affect millions of individuals worldwide. Epigenetic modifications, including DNA methylation (5 mC), have been associated with AUD and other alcohol-related traits. Epigenome-wide association studies (EWAS) have identified differentially methylated genes associated with AUD in human peripheral and brain tissue. More recently, epigenetic studies of AUD have also evaluated DNA hydroxymethylation (5 hmC) in the human brain. However, most of the epigenetic work in postmortem brain tissue has examined bulk tissue. In this study, we investigated neuronal-specific 5 mC and 5 hmC alterations at CpG sites associated with AUD in the human orbitofrontal cortex (OFC).
Methods: Neuronal nuclei from the OFC were evaluated in 34 human postmortem brain samples (10 AUD, 24 non-AUD). Reduced representation oxidative bisulfite sequencing was used to assess 5 mC and 5 hmC at the genome-wide level. Differential 5 mC and 5 hmC were evaluated using the methylKit R package and significance was set at false discovery rate < 0.05 and differential methylation > 2. Functional enrichment analyses were performed, and gene-level convergence was evaluated in an independent dataset that assessed 5 mC and 5 hmC of AUD in bulk cortical tissue.
Results: We identified 417 5 mC and 363 5hmC significant differential CpG sites associated with AUD, with 59% in gene promoters. Some of the identified genes have been previously implicated in alcohol consumption, including SYK, DNMT3A for 5 mC, GAD1, DLX1, DLX2, for 5 hmC and GATA4 in both. Convergence with a previous AUD 5 mC and 5 hmC study was observed for 28 genes. We also identified 5 and 35 differential regions for 5 mC and 5 hmC, respectively. Lastly, GWAS enrichment analysis showed an association with AUD for differential 5 mC genes.
Discussion: This study reveals neuronal-specific methylome and hydroxymethylome dysregulation associated with AUD, identifying both previously reported and potentially novel gene associations with AUD. Our findings provide new insights into the epigenomic dysregulation of AUD in the human brain.