Dynamics of smoking-induced genome-wide methylation changes with time since smoking cessation

Abstract

Several studies have recently identified strong epigenetic signals related to tobacco smoking. However, an aspect that did not receive much attention is the evolution of epigenetic changes with time since smoking cessation. We conducted a series of epigenome-wide association studies to capture the dynamics of smoking-induced epigenetic changes after smoking cessation, using genome-wide methylation profiles obtained from blood samples in 745 women from 2 European populations. Two distinct classes of CpG sites were identified: sites whose methylation reverts to levels typical of never smokers within decades after smoking cessation, and sites remaining differentially methylated, even more than 35 years after smoking cessation. Our results suggest that the dynamics of methylation changes following smoking cessation are driven by a differential and site-specific magnitude of the smoking-induced alterations (with persistent sites being most affected) irrespective of the intensity and duration of smoking. Analyses of the link between methylation and expression levels revealed that methylation predominantly and remotely down-regulates gene expression. Among genes whose expression was associated with our candidate CpG sites, LRRN3 appeared to be particularly interesting as it was one of the few genes whose methylation and expression were directly associated, and the only gene in which both methylation and gene expression were found associated with smoking. Our study highlights persistent epigenetic markers of smoking, which can potentially be detected decades after cessation. Such historical signatures are promising biomarkers to refine individual risk profiling of smoking-induced chronic disease such as lung cancer.

The dynamics of smoking-related disturbed methylation: a two time-point study of methylation change in smokers, non-smokers and former smokers

“…Regarding overall rates of reversion of disturbed methylation over time, it is of debate as to whether the relative persistence of differential methylation following cessation for certain CpG sites is due to slower reversion rates, or comparable reversion rates but a larger initial disturbance in methylation [8,20]. Our results indicate the rate at which the methylation levels change in FS is related to the difference in methylation to NS, implying perhaps a type of exponential decay in the difference in methylation after cessation.…”

“…Previous evaluations of the effect of time since smoking cessation have revealed CpG sites that could be classified as reversible and sites that could be classified as persistently differentially methylated [8,[18][19][20]. Reversible sites are those that are differentially methylated between smokers and non-smokers but with the difference disappearing some time after cessation of smoking.…”

“…Reversible sites are those that are differentially methylated between smokers and non-smokers but with the difference disappearing some time after cessation of smoking. Persistently differentially methylated sites remain differentially methylated, perhaps indefinitely; this persistence has been observed even up to 35 years after cessation [20]. However, there is again a lack of longitudinal studies with regard to reversion of methylation levels; this lack impedes the identification of potential long-term biomarkers of smoking [11,21], and hinders insights into the increased risk for disease faced by former smokers decades after cessation [22,23].…”

The Effect of Different Case Definitions of Current Smoking on the Discovery of Smoking-Related Blood Gene Expression Signatures in Chronic Obstructive Pulmonary Disease

“…32 The study of Beineke et al 31 reported up-regulation of LRRN3, PID1, GPR15 and FUCA1 gene expression in the whole blood of current smokers with LRRN3 being the most statistically significant gene. In a recent study by Guida et al, 33 CpG sites at both LRRN3 and GPR15 were found to be hypomethylated in blood. LRRN3 is particularly interesting because it has been shown to be over-expressed in current smokers and in the study by Guida et al, 33 it was the only gene associated with smoking at the level of both methylation and gene expression.…”

“…In a recent study by Guida et al, 33 CpG sites at both LRRN3 and GPR15 were found to be hypomethylated in blood. LRRN3 is particularly interesting because it has been shown to be over-expressed in current smokers and in the study by Guida et al, 33 it was the only gene associated with smoking at the level of both methylation and gene expression. In genetic association studies, variants in PID1 have been associated with lung function in the Korean population.…”