CpG Sites Associated with Cigarette Smoking: Analysis of Epigenome-Wide Data from the Sister Study

Abstract

Background: Smoking increases the risk of many diseases, and it is also linked to blood DNA methylation changes that may be important in disease etiology.Objectives: We sought to identify novel CpG sites associated with cigarette smoking.Methods: We used two epigenome-wide data sets from the Sister Study to identify and confirm CpG sites associated with smoking. One included 908 women with methylation measurements at 27,578 CpG sites using the HumanMethylation27 BeadChip; the other included 200 women with methylation measurements for 473,844 CpG sites using the HumanMethylation450 BeadChip. Significant CpGs from the second data set that were not included in the 27K assay were validated by pyrosequencing in a subset of 476 samples from the first data set.Results: Our study successfully confirmed smoking associations for 9 previously established CpGs and identified 2 potentially novel CpGs: cg26764244 in GNG12 (p = 9.0 × 10–10) and cg22335340 in PTPN6 (p = 2.9 × 10–05). We also found strong evidence of an association between smoking status and cg02657160 in CPOX (p = 7.3 × 10–7), which has not been previously reported. All 12 CpGs were undermethylated in current smokers and showed an increasing percentage of methylation in former and never-smokers.Conclusions: We identified 2 potentially novel smoking related CpG sites, and provided independent replication of 10 previously reported CpGs sites related to smoking, one of which is situated in the gene CPOX. The corresponding enzyme is involved in heme biosynthesis, and smoking is known to increase heme production. Our study extends the evidence base for smoking-related changes in DNA methylation.Citation: Harlid S, Xu Z, Panduri V, Sandler DP, Taylor JA. 2014. CpG sites associated with cigarette smoking: analysis of epigenome-wide data from the Sister Study. Environ Health Perspect 122:673–678; http://dx.doi.org/10.1289/ehp.1307480

The DNA methylation profile of activated human natural killer cells

“…The authors show that smoking-associated alterations of a CD3 lymphocyte subtype explain the reports by multiple authors of tobacco-associated DNA methylation alterations at the GPR15 locus. Because it is possible that tobacco smoking activates NK cells, we examined whether the long list of loci reported to have altered methylation associated with smoking 77 might also be found as DMSs indicative of NK activation. We observed that change in methylation of the AHRR locus is both a marker of NK activation and smoking 78 and that several other DMSs associated with NK activation that we found here have been reported by others to be associated with smoking, including: MYO1G (cg07826859), NCF4 (cg02532700), and GPR68 (cg05875421).…”

The Influences of Genetic and Environmental Factors on Methylome-Wide Association Studies for Human Diseases

“…Recent MWAS studies have identified and replicated smoking-related DNAm sites in samples of European ancestry [50, 51, 53]. The most significant smoking-related DNAm sites are hypomethylated among smokers [53, 54, 58]. Several studies also reported an inverse association between pack-years and DNA methylation, and a positive association between time since quitting smoking and DNA methylation [51, 55, 58, 62].…”

Gene promoter methylation and DNA repair capacity in monozygotic twins with discordant smoking habits

“…Smokerelated changes in DNA methylation have also been detected in blood cells [18][19][20][21] and in newborns [37] in recent epigenomewide association studies on DNA methylation and smoking habits. Even though only a relatively low number of CpG sites attained the high statistical significance required to be identified as differently methylated in such untargeted studies, this does not rule out the possibility that smoking could elicit milder effects also in other genes, which may be important when critical genes are affected.…”

“…Altered methylation of cancer-related genes is, in fact, frequently observed in lung tumors of smokers [8][9][10][11], and a progressive accumulation of epigenetic alterations is also observed in the respiratory epithelium of cancer-free heavy smokers [12][13][14] and in exfoliated cells of smokers sputum [15]. Moreover, changes in the methylation profile of cancer related genes have been observed in plasma DNA from cancer-free heavy smokers [16,17], and smoking-related changes in methylation at a number of CpG sites have been identified in epigenome-wide investigations in blood cells of subjects with different smoking habits [18][19][20][21].…”