Genome‐wide and digital polymerase chain reaction epigenetic assessments of alcohol consumption

Abstract

The lack of readily employable biomarkers of alcohol consumption is a problem for clinicians and researchers. In 2014, we published a preliminary DNA methylation signature of heavy alcohol consumption that remits as a function of abstinence. Herein, we present new genome-wide methylation findings from a cohort of additional subjects and a meta-analysis of the data. Using DNA from 47 consecutive heavy drinkers admitted for alcohol detoxification in the context of alcohol treatment and 47 abstinent controls, we replicate the 2014 results and show that 21,221 CpG residues are differentially methylated in active heavy drinkers. Meta-analysis of all data from the 448,058 probes common to the two methylation platforms shows a similarly profound signature with confirmation of findings from other groups. Principal components analyses show that genome-wide methylation changes in response to alcohol consumption load on two major factors with one component accounting at least 50% of the total variance in both smokers and nonsmoking alcoholics. Using data from the arrays, we derive a panel of five methylation probes that classifies use status with a receiver operator characteristic area under the curve (AUC) of 0.97. Finally, using droplet digital polymerase chain reaction (PCR), we convert these array-based findings to two marker assays with an AUC of 0.95 and a four marker set AUC of 0.98. We conclude that DNA methylation assessments are capable of quantifying alcohol use status and suggest that readily employable digital PCR approaches for substance consumption may find widespread use in alcohol-related research and patient care.

A DNA Methylation Signature of Addiction in T Cells and Its Reversal With DHEA Intervention

“…To further explore the relation of our findings to recent finding in the literature we overlapped our significantly differentially methylated CpGs (healthy control vs. placebo at baeline) to those of two other studies which measured DNA methylation in alcohol users using the same Illumina 450K arrays. We found ( Figures 6A,B ) a significant overlap between our findings and those of others ( Liu et al, 2018 ; Philibert et al, 2018 ) suggesting a common DNA methylation landscape across addiction to different substances.…”

“…(A) A significant overlap was observed between our list of differentially methylated CpGs and a list of alcohol use markers found by Liu et al (2018) . (B) A significant overlap was observed between our list of differentially methylated CpGs and a list of alcohol use markers found by Philibert et al (2018) . Significance was assessed by the Fisher hyper-geometric test.…”

Epigenetic Biomarkers for Environmental Exposures and Personalized Breast Cancer Prevention

“…Although DNA methylation loci associated with numerous exposures have been identified, most have not been demonstrated to be able to act as markers. The exceptions, CpG markers for current smoking and current heavy alcohol intake, were identified in cohorts that used questionnaires that assessed detailed current and previous use, including type, quantity, frequency, and duration of use, age when first started using, and age when quitting (if applicable) [37,40,59,60]. Identification of epigenetic markers for additional personal exposures that may be associated with breast cancer risk would also require a robust characterization of the exposure and data analysis for potential associations with the peripheral blood epigenome.…”

“…Remarkably, methylation of CDC42BPB (cg04987734) was shown to be able to classify individuals with respect to heavy alcohol consumption from non-drinkers with an AUC of 0.88. A combination of this marker with one and three additional CpG markers increased the AUC to 0.95 and 0.98, respectively [59]. In an intervention study, after a mean of 21 days of inpatient enforced abstinence, the methylation status of cg04987734 began to revert to baseline values [62].…”

“…DNA methylation has been shown to be associated with various other environmental exposures, including aging [41,42], BMI [43][44][45][46][47][48][49], physical activity and inactivity [50,51], air pollution [52][53][54], stress [55,56], depression [57], and alcohol [58][59][60][61] (Table 1). Remarkably, methylation of CDC42BPB (cg04987734) was shown to be able to classify individuals with respect to heavy alcohol consumption from non-drinkers with an AUC of 0.88.…”