Epigenome-wide association study in the European Prospective Investigation into Cancer and Nutrition (EPIC-Turin) identifies novel genetic loci associated with smoking
ABSTRACT A single CpG site within F2RL3 was recently found to be hypomethylated in peripheral blood genomic DNA from smokers compared to 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 to former and non-smokers, including an intragenic region of the aryl hydrocarbon receptor repressor gene (AHRR; cg05575921, p=2.31x10(-15); effect size = 14%-17%), an intergenic CpG island on 2q37.1 (cg21566642, p=3.73x10(-13); effect size = 12%), and a further intergenic region at 6p21.33 (cg06126421, p=4.96x10(-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 to 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 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.
SourceAvailable from: PubMed Central[Show abstract] [Hide abstract]
ABSTRACT: Epigenetics plays an important role in regulating gene expression, and can be modified by environmental factors and physiological conditions. Studying epigenetics is a promising approach to potentially improving the diagnosis, prevention and treatment of human diseases, and to providing personalized medical care. However, the role of epigenetics in the development of diseases is not clear because epigenetic markers may be both mediators and outcomes of human diseases. It is particularly complicated to study pharmacoepigenetics, as medication use may modify the epigenetic profile. To address the challenges facing pharmacoepigenetic research of human diseases, we developed a novel design to rapidly identify, contact, and recruit participants and collect specimens for longitudinal studies of pharmacoepigenetics. Using data in real-time from electronic medical record systems, we can identify patients recently start on new medications and who also have a blood test. Prior to disposal of the leftover blood by the clinical laboratory, we are able to contact and recruit these patients, enabling us to use both their leftover baseline blood sample as well as leftover specimens at future tests. With treatment-naïve and follow-up specimens, this system is able to study both epigenetic markers associated with disease without treatment effect as well as treatment-related epigenetic changes.
[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.Mutation Research/Genetic Toxicology and Environmental Mutagenesis 01/2015; DOI:10.1016/j.mrgentox.2015.01.006 · 2.48 Impact Factor
[Show abstract] [Hide abstract]
ABSTRACT: Maternal smoking during pregnancy has been found to influence newborn DNA methylation in genes involved in fundamental developmental processes. It is pertinent to understand the degree to which the offspring methylome is sensitive to the intensity and duration of prenatal smoking. An investigation of the persistence of offspring methylation associated with maternal smoking, and the relative roles of the intra-uterine and postnatal environment, is also warranted. In the Avon Longitudinal Study of Parents and Children, we investigated associations between prenatal exposure to maternal smoking and offspring DNA methylation at multiple time points in approximately 800 mother-offspring pairs. In cord blood, methylation at 15 CpG sites in seven gene regions (AHRR, MYO1G, GFI1, CYP1A1, CNTNAP2, KLF13 and ATP9A) was associated with maternal smoking and a dose-dependent response was observed in relation to smoking duration and intensity. Longitudinal analysis of blood DNA methylation in serial samples at birth, age 7 and age 17 years demonstrated that some CpG sites showed reversibility of methylation (GFI1, KLF13 and ATP9A) whereas others showed persistently perturbed patterns (AHRR, MYO1G, CYP1A1 and CNTNAP2). Of those showing persistence, we explored the effect of postnatal smoke exposure and found that the major contribution to altered methylation was attributed to a critical window of in-utero exposure. A comparison of paternal and maternal smoking and offspring methylation showed consistently stronger maternal associations, providing further evidence for causal intra-uterine mechanisms. These findings highlight the sensitivity of the methylome to maternal smoking during early development and the long-term impact of such exposure. © The Author 2014. Published by Oxford University Press.Human Molecular Genetics 12/2014; DOI:10.1093/hmg/ddu739 · 6.68 Impact Factor