DNA methylation signatures of chronic alcohol dependence in purified CD3+ T-cells of patients undergoing alcohol treatment

Several studies have shown an association of alcohol dependence with DNA methylation, suggesting that environmentally-induced changes on epigenomic variation may play an important role in alcohol dependence. In the present study, we analyzed genome-wide DNA methylation profiles of purified CD3+ T-cells from pre- and post-treatment alcohol dependent patients, as well as closely matched healthy controls. We identified 59 differentially methylated CpG sites comparing patients prior to treatment with healthy controls and were able to confirm 8 of those sites in additional analyses for differentially methylated regions. Comparing patients before and after a 3-week alcohol treatment program we revealed another unique set of 48 differentially methylated CpG sites. Additionally, we found that the mean global DNA methylation was significantly lower in patients prior to treatment compared to controls, but reverted back to levels similar to controls after treatment. We validated top-ranked hits derived from the epigenome-wide analysis by pyrosequencing and further replicated two of them in an independent cohort and confirmed differential DNA methylation of HECW2 and SRPK3 in whole blood. This study is the first to show widespread DNAm variation in a disease-relevant blood cell type and implicates HECW2 and SRPK3 DNAm as promising candidates to follow up in future studies. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain genome-wide DNA methylation from purified CD3+ T-cells of a well-characterized cohort of long-term chronic alcohol dependent (AD) patients participating in a clinical 3-week alcohol treatment program, along with the profiles of closely matched healthy controls. These measures were used to identify AD-associated DNA methylation signatures in T-lymphocytes, assess intevention-related changes in DNA methylation, and test for replication of AD-associated differential DNA methylation in an independent cohort.