Epigenome-wide association study in the European Prospective Investigation Into Cancer And Nutrition (EPIC-Turin) identifies novel genetic loci associated with smoking

Epigenetics Unit, Department of Surgery and Cancer, Imperial College London, W12 0NN, UK.
Human Molecular Genetics (Impact Factor: 6.68). 11/2012; 22(5). DOI: 10.1093/hmg/dds488
Source: PubMed

ABSTRACT A single cytosine–guanine dinucleotide (CpG) site within coagulation factor II (thrombin) receptor-like 3 (F2RL3) was recently found to be hypomethylated in peripheral blood genomic DNA from smokers compared with former and non-smokers.
We performed two epigenome-wide association studies (EWAS) nested in a prospective healthy cohort using the Illumina 450K
Methylation Beadchip. The two populations consisted of matched pairs of healthy individuals (n = 374), of which half went on to develop breast or colon cancer. The association was analysed between methylation and smoking
status, as well as cancer risk. In addition to the same locus in F2RL3, we report several loci that are hypomethylated in smokers compared with former and non-smokers, including an intragenic
region of the aryl hydrocarbon receptor repressor gene (AHRR; cg05575921, P = 2.31 × 10−15; effect size = 14–17%), an intergenic CpG island on 2q37.1 (cg21566642, P = 3.73 × 10−13; effect size = 12%) and a further intergenic region at 6p21.33 (cg06126421, P = 4.96 × 10−11, effect size = 7–8%). Bisulphite pyrosequencing validated six loci in a further independent population of healthy individuals
(n = 180). Methylation levels in AHRR were also significantly decreased (P < 0.001) and expression increased (P = 0.0047) in the lung tissue of current smokers compared with non-smokers. This was further validated in a mouse model of
smoke exposure. We observed an association with breast cancer risk for the 2q37.1 locus (P = 0.003, adjusted for the smoking status), but not for the other loci associated with smoking. These data show that smoking
has a direct effect on the epigenome in lung tissue, which is also detectable in peripheral blood DNA and may contribute to
cancer risk.

1 Follower
  • Source
    • "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]. The mechanism(s) by which tobacco smoke could affect DNA methylation is not elucidated. "
    [Show abstract] [Hide abstract]
    ABSTRACT: The influence of DNA repair capacity, plasma nutrients and tobacco smoke exposure on DNA methylation was investigated in blood cells of twenty-one couples of monozygotic twins with discordant smoking habits. All study subjects had previously been characterized for mutagen sensitivity with challenge assays with ionizing radiation in peripheral blood lymphocytes. Plasma levels of folic acid, vitamin B12 and homocysteine were also available from a previous investigation. In this work DNA methylation in the promoter region of a panel of ten genes involved in cell cycle control, differentiation, apoptosis and DNA repair (p16, FHIT, RAR, CDH1, DAPK1, hTERT, RASSF1A, MGMT, BRCA1 and PALB2) was assessed in the same batches of cells isolated for previous studies, using the methylation-sensitive high-resolution melting technique. Fairly similar profiles of gene promoter methylation were observed within co-twins compared to unrelated subjects (p=1.23×10(-7)), with no significant difference related to smoking habits (p=0.23). In a regression analysis the methylation index of study subjects, used as synthetic descriptor of overall promoter methylation, displayed a significant inverse correlation with radiation-induced micronuclei (p=0.021) and plasma folic acid level (p=0.007) both in smokers and in non-smokers. The observed association between repair of radiation-induced DNA damage and promoter methylation suggests the involvement of the DNA repair machinery in DNA modification. Data also highlight the possible modulating effect of folate deficiency on DNA methylation and the strong influence of familiarity on the individual epigenetic profile. Copyright © 2015 Elsevier B.V. All rights reserved.
    Mutation Research/Genetic Toxicology and Environmental Mutagenesis 01/2015; 779. DOI:10.1016/j.mrgentox.2015.01.006 · 2.48 Impact Factor
  • Source
    • "There is evidence that the leading risk factors for lung cancer, tobacco smoke and air pollution, can influence DNA methylation in the lungs and in blood. A study nested within the EPIC cohort reported hypomethylation of F2RL3, AHRR and two intergenic regions in the blood of smokers in comparison to non-smokers [92]. A follow-up study from the same group demonstrated that four loci, including AHRR, may serve as blood-based markers of tobacco smoke exposure [93]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Epigenetic epidemiology includes the study of variation in epigenetic traits and the risk of disease in populations. Its application to the field of cancer has provided insight into how lifestyle and environmental factors influence the epigenome and how epigenetic events may be involved in carcinogenesis. Furthermore, it has the potential to bring benefit to patients through the identification of diagnostic markers that enable the early detection of disease and prognostic markers that can inform upon appropriate treatment strategies. However, there are a number of challenges associated with the conduct of such studies, and with the identification of biomarkers that can be applied to the clinical setting. In this review, we delineate the challenges faced in the design of epigenetic epidemiology studies in cancer, including the suitability of blood as a surrogate tissue and the capture of genome-wide DNA methylation. We describe how epigenetic epidemiology has brought insight into risk factors associated with lung, breast, colorectal and bladder cancer and review relevant research. We discuss recent findings on the identification of epigenetic diagnostic and prognostic biomarkers for these cancers.
    Biochemical and Biophysical Research Communications 08/2014; 455(1-2). DOI:10.1016/j.bbrc.2014.08.002 · 2.28 Impact Factor
  • Source
    • "GWAS-based PCs, the top 10 methylation-based PCs pick up some age-associated methylation (10 –26 < P < 10 –7 , Supplementary Table S2), and their inclusion as covariates can thus reduce power to detect association with age. Sets of PCs that are based on CpG sites close to SNPs may be better proxies for genetic variation and thus somewhat less associated with age (as demonstrated in Supplementary Table S2), and methods such as SVA will avoid this issue entirely; this is consistent with the pattern shown in Figure 2. In contrast, because only a few CpG sites associate with smoking, the PCs do not proxy for association between methylation and smoking (P > 0.005 for all PCs tested); in this case, all of the methylation-based PC-based methods perform similarly well, as in Figure 3. Similarly, adjustment via GC led to somewhat reduced significance in the smoking analysis (Fig. 3), but not the large reduction observed in the age analysis (Fig. 2); this is likely because thousands of CpG sites across the genome have been shown to associate with age [Alisch et al., 2012; Christensen et al., 2009; Numata et al., 2012; Rakyan et al., 2010; Teschendorff et al., 2010], while only a handful have been associated with smoking [Breitling et al., 2011, 2012; Shenker et al., 2013; Sun et al., 2013; Wan et al., 2012]. "
    [Show abstract] [Hide abstract]
    ABSTRACT: DNA methylation is an important epigenetic mechanism that has been linked to complex diseases and is of great interest to researchers as a potential link between genome, environment, and disease. As the scale of DNA methylation association studies approaches that of genome-wide association studies, issues such as population stratification will need to be addressed. It is well-documented that failure to adjust for population stratification can lead to false positives in genetic association studies, but population stratification is often unaccounted for in DNA methylation studies. Here, we propose several approaches to correct for population stratification using principal components (PCs) from different subsets of genome-wide methylation data. We first illustrate the potential for confounding due to population stratification by demonstrating widespread associations between DNA methylation and race in 388 individuals (365 African American and 23 Caucasian). We subsequently evaluate the performance of our PC-based approaches and other methods in adjusting for confounding due to population stratification. Our simulations show that (1) all of the methods considered are effective at removing inflation due to population stratification, and (2) maximum power can be obtained with single-nucleotide polymorphism (SNP)-based PCs, followed by methylation-based PCs, which outperform both surrogate variable analysis and genomic control. Among our different approaches to computing methylation-based PCs, we find that PCs based on CpG sites chosen for their potential to proxy nearby SNPs can provide a powerful and computationally efficient approach to adjust for population stratification in DNA methylation studies when genome-wide SNP data are unavailable.
    Genetic Epidemiology 04/2014; 38(3). DOI:10.1002/gepi.21789 · 2.95 Impact Factor
Show more