Validation of differential GDAP1 DNA methylation in alcohol dependence and its potential function as a biomarker for disease severity and therapy outcome

Abstract

Alcohol dependence is a severe disorder contributing substantially to the global burden of disease. Despite the detrimental consequences of chronic alcohol abuse and dependence, effective prevention strategies as well as treatment options are largely missing to date. Accumulating evidence suggests that gene-environment interactions, including epigenetic mechanisms, play a role in the etiology of alcohol dependence. A recent epigenome-wide study reported widespread alterations of DNA methylation patterns in alcohol dependent patients compared to control individuals. In the present study, we validate and replicate one of the top findings from this previous investigation in an independent cohort: the hypomethylation of GDAP1 in patients. To our knowledge, this is the first independent replication of an epigenome-wide finding in alcohol dependence. Furthermore, the AUDIT as well as the GSI score were negatively associated with GDAP1 methylation and we found a trend toward a negative association between GDAP1 methylation and the years of alcohol dependency, pointing toward a potential role of GDAP1 hypomethylation as biomarker for disease severity. In addition, we show that the hypomethylation of GDAP1 in patients reverses during a short-term alcohol treatment program, suggesting that GDAP1 DNA methylation could also serve as a potential biomarker for treatment outcome. Our data add to the growing body of knowledge on epigenetic effects in alcohol dependence and support GDAP1 as a novel candidate gene implicated in this disorder. As the role of GDAP1 in alcohol dependence is unknown, this novel candidate gene should be followed up in future studies.

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

“…Methylation at the second most powerfully predictive site used in our three marker assay set, cg02583484, was the second‐ranked probe in the 2016 Liu meta‐analyses. Finally, methylation at cg23779890, one of the loci for which we were unable to construct a ddPCR assay, has been independently shown to be associated with alcohol use status by Nieratschker and colleagues, as well as Liu and colleagues work (Brückmann et al, ; Liu et al, ). Hence, there is reason for optimism.…”

“…Third, and most importantly, the reversion curve for methylation status as a function of abstinence needs to be established. Reversion of substance‐induced changes has already been documented for both cigarette and alcohol‐associated methylation changes (Bauer et al, ; Brückmann et al, ; Philibert et al, ; Philibert et al, ; Wilson et al, ). However, this preliminary understanding of the reversion process is woefully short of the knowledge base needed to monitor the effectiveness and guide the improvement of existing therapies.…”

“…In 2014, we published the first genome‐wide study on the relationship of alcohol consumption to heavy alcohol consumption (Philibert et al, ). Since that time, these findings have been partially reproduced at the single and genome‐wide level (Brückmann, Di Santo, Karle, Batra, & Nieratschker, ; Liu et al, ). In this communication, we confirm and extend those prior findings and reduce the methylation assessment process to a set of digital polymerase chain reaction (PCR) assays.…”

Emerging Role of Epigenetic Mechanisms in Alcohol Addiction

“…Recent studies have begun to combine genome‐wide analysis of DNA methylation with that of intriguing phenotypic metrics. For instance, a recent study confirmed a genomewide report of hypomethylation at the ganglioside‐induced differentiation‐associated protein 1 ( GDAP1 ) gene and further found that GDAP1 DNA methylation was significantly associated with severity of patient with AUD (Brückmann et al., ). Another recent study examined DNA methylation in monozygotic twins with discordant AUD status and complemented this work with personality evaluation and MRI imaging during an impulsiveness task (Ruggeri et al., ).…”

Optimizing the chances of success in the search for epigenetic biomarkers: Embracing genetic variation

“…Unfortunately, this type of approach resulted in the inclusion of individuals who used substances at an earlier point in their life, but may have become abstinent for as many as 10–20 years. Since subsequent analyses have clearly shown that methylation signatures associated with substance use consumption may revert, sometimes rather rapidly, to baseline values (Bauer et al, ; Brückmann, Di Santo, Karle, Batra, & Nieratschker, ; Philibert et al, ), this lack of understanding resulted in the inclusion of individuals whose methylation signatures may have more resembled the “unaffecteds” in the “affected” category. Subsequent appreciation of the pliability of the methylome has led to improvements in both the chronological and quantitative consumption phenotyping of subjects used in epigenetic studies.…”