title: 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 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.
authors.affiliation: Epigenetics Unit, Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK.
authors.forename: Natalie S
authors.initials: NS
authors.lastname: Shenker
authors.forename: Silvia
authors.initials: S
authors.lastname: Polidoro
authors.forename: Karin
authors.initials: K
authors.lastname: van Veldhoven
authors.forename: Carlotta
authors.initials: C
authors.lastname: Sacerdote
authors.forename: Fulvio
authors.initials: F
authors.lastname: Ricceri
authors.forename: Mark A
authors.initials: MA
authors.lastname: Birrell
authors.forename: Maria G
authors.initials: MG
authors.lastname: Belvisi
authors.forename: Robert
authors.initials: R
authors.lastname: Brown
authors.forename: Paolo
authors.initials: P
authors.lastname: Vineis
authors.forename: James M
authors.initials: JM
authors.lastname: Flanagan
mesh_terms: D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics*; D016022:Case-Control Studies; D003110:Colonic Neoplasms / Q000235:genetics*; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D057890:Epigenomics; D005260:Female; D055106:Genome-Wide Association Study; D006801:Humans; D008168:Lung / Q000378:metabolism / Q000473:pathology; D008297:Male; D051379:Mice; D009752:Nutritional Status; D018179:Receptors, Thrombin / Q000235:genetics*; D012097:Repressor Proteins / Q000235:genetics*; D012907:Smoking / Q000235:genetics* / Q000378:metabolism / Q000473:pathology
chemical_list: D051792:Basic Helix-Loop-Helix Proteins; D018179:Receptors, Thrombin; D012097:Repressor Proteins; C492162:AHRR protein, human; C112908:protease-activated receptor 4