Alcohol consumption is associated with widespread changes in blood DNA methylation: analysis of cross-sectional and longitudinal data

Abstract

Background: DNA methylation may be one of the mechanisms by which alcohol consumption is associated with the risk of disease. We conducted a large-scale, cross-sectional, genome-wide DNA methylation association study of alcohol consumption and a longitudinal analysis of repeated measurements taken several years apart. Methods:Using the Illumina Infinium HumanMethylation450 BeadChip, DNA methylation measures were determined using baseline peripheral blood samples from 5,606 adult Melbourne Collaborative Cohort Study (MCCS) participants. For a subset of 1,088 of them, these measures were repeated using blood samples collected at follow-up, a median of 11 years later. Associations between alcohol intake and blood DNA methylation were assessed using linear mixed-effects regression models adjusted for batch effects and potential confounders. Independent data from the LOLIPOP (N=4,042) and KORA (N=1,662) cohorts were used to replicate associations discovered in the MCCS.Results: Cross-sectional analyses identified 1,414 CpGs associated with alcohol intake at P<10 -7 , 1,243 of which had not been reported previously. Of these 1,243 novel associations, 1,078 were replicated (P<0.05) using LOLIPOP and KORA data. Using the MCCS data, we also replicated (P<0.05) 403 of 518 associations that had been reported previously. Interaction analyses suggested that associations were stronger for women, non-smokers, and participants genetically predisposed to consume less alcohol. Of the 1,414 CpGs, 530 were differentially methylated (P<0.05) in former compared with current drinkers. Longitudinal associations between the change in alcohol intake and the change in methylation were observed for 513 of the 1,414 cross-sectional associations. Conclusion:Our study indicates that, for middle-aged and older adults, alcohol intake is associated with widespread changes in DNA methylation across the genome. Longitudinal analyses showed that the methylation status of alcohol-associated CpGs may change with changes in alcohol consumption.

Smoking and blood DNA methylation: novel associations, replication of previous findings and assessment of reversibility

“…>4,000 CpGs identified with τ=1.5, which was substantially more that with the current smoking variable). Finally, the reversibility coefficients calculated in this study were substantially lower than those observed in our previous analysis of alcohol consumption, 20 which suggests that smoking-associated methylation marks might be more frequent but less persistent compared to alcohol-associated methylation changes.…”

“…Cell composition was estimated with the widely used Houseman algorithm [33, 34] and we did not assess sensitivity to the method used for deriving cell composition [39] . Additionally, we reported in a previous study that many differentially-methylated CpGs with respect to alcohol drinking are also associated with smoking, so it may be difficult to tease out the individual effects or joint influences on many of these CpGs across the genome [36] . Finally, we included who later developed cancer, which could give rise to collider bias given the strong association of smoking with cancer risk [24] , but, by assessing effect modification by case-control status, we found no evidence of such bias in our setting.…”

“…We also calculated a ‘reversibility coefficient’, expressed as a percentage and defined as the regression coefficient comparing ‘ former ’ to ‘ current ’ smokers divided by the coefficient comparing ‘ never ’ to ‘ current ’ smokers, as done previously. 20…”

“…For all associations with P<10 −7 in our cross-sectional EWAS we estimated the half-life τ that provided the best model fit for the CSI, as described previously. We also calculated a ‘reversibility coefficient’, expressed as a percentage and defined as the regression coefficient comparing ‘ former’ to ‘ current’ smokers divided by the coefficient comparing ‘ never’ to ‘ current’ smokers, as done previously [36] .…”

DNA Methylation Signature on Phosphatidylethanol, not Self-Reported Alcohol Consumption, Predicts Hazardous Alcohol Consumption in Two Distinct Populations

“…A large number of CpGs in the human leukocyte DNA methylome have recently been reported to have associations with dietary folate and alcohol intake 37 . Some CpGs have been found to be associated with alcohol consumption in different cell types, ethnic groups, and phenotypic assessments 29,30,38 . Among the reported CpGs for alcohol consumption, more than a dozen CpGs have been replicated.…”