Smoking increases the risk of many diseases and could act through changes in DNA methylation patterns. The aims of this study were to determine the association between smoking and DNA methylation throughout the genome at cytosine-phosphate-guanine (CpG) site level and genomic regions. A discovery cross-sectional epigenome-wide association study nested in the follow-up of the REGICOR cohort was designed and included 645 individuals. Blood DNA methylation was assessed using the Illumina HumanMethylation450 BeadChip. Smoking status was self-reported using a standardized questionnaire. We identified 66 differentially methylated CpG sites associated with smoking, located in 38 genes. In most of these CpG sites, we observed a trend among those quitting smoking to recover methylation levels typical of never smokers. A CpG site located in a novel smoking-associated gene (cg06394460 in LNX2) was hypomethylated in current smokers. Moreover, we validated two previously reported CpG sites (cg05886626 in THBS1, and cg24838345 in MTSS1) for their potential relation to atherosclerosis and cancer diseases, using several different approaches: CpG site methylation, gene expression, and plasma protein level determinations. Smoking was also associated with higher THBS1 gene expression but with lower levels of thrombospondin-1 in plasma. Finally, we identified differential methylation regions in 13 genes and in four non-coding RNAs. In summary, this study replicated previous findings and identified and validated a new CpG site located in LNX2 associated with smoking.

This work was supported by the following sources: Agència de Gestió Ajuts 464 Universitaris de Recerca (2014 SGR 240); the Spanish Ministry of Economy through 465 the Carlos III Health Institute (ISCIII-FIS-FEDER-ERDF PI11-01801, PI08-1327, PI05-466 1251, PI05-1297, PI02-0471, FIS99/0013-01, FIS96/0026-01, FIS93/0568, 467 FIS92/0009-05), and the Red de Investigación Cardiovascular (RD12/0042/0061, 468 RD12/0042/0013). The BAsicMAR study was funded by the Spanish Ministry of 469 Economy through the Carlos III Health Institute (ISCIII-FIS-FEDER-ERDF) PI12/01238 470 and RecerCaixa JJ086116. Sergi Sayols-Baixeras was funded by a contract from 471 Instituto de Salud Carlos III FEDER (IFI14/00007).