15q12 Variants, Sputum Gene Promoter Hypermethylation, and Lung Cancer Risk: A GWAS in Smokers

Lung cancer is the leading cause of cancer-related mortality in both sexes worldwide, mainly because of lack of established early screening strategies (1). The development of this disease over 30 to 40 years in smokers involves field cancerization, characterized as the acquisition of genetic and epigenetic changes in oncogenes and tumor suppressor genes throughout the lung epithelium (2). The epigenetic silencing of tumor suppressor genes by promoter hypermethylation has been recognized as a major and causal event for lung cancer initiation and progression (2). Moreover, the detection of gene methylation in exfoliated cells from the lungs of smokers provides an assessment of the extent of field cancerization and is a validated biomarker for predicting lung cancer risk (2–4). The precise mechanism by which cigarette carcinogens disrupt the capacity of lung cells to maintain the epigenetic code during DNA replication and repair is largely unknown. Thus, the identification of genetic determinants contributing to the propensity for acquiring gene methylation in lung epithelium of smokers should provide new insights into the mechanisms underlying epigenetic reprogramming during lung carcinogenesis. Importantly, these genetic loci may also contribute to the genetic component affecting the risk for lung cancer that includes risk loci identified in several lung cancer genome-wide association studies (GWAS [5]). Emerging evidence suggested that genome-wide landscaping of the sequence-dependent allele-specific methylation for nonimprinted genes may help pinpoint the functional regulatory polymorphisms that may influence the disease susceptibility (6). Most recently, Shi et al. (7) conducted a genome-wide assessment for methylation quantitative trait loci (meQTL) and found 34 304 cis-meQTLs, mostly localized to CpG sites outside of genes, promoters, and CpG islands, and 585 trans-meQTLs largely overrepresented in promoter CpG islands. A strong enrichment of these meQTL single nucleotide polymorphisms (SNPs) for DNase hypersensitive sites and sequences bound by CCCTC-binding factor (CTCF) or modified histones was also identified in cell lines, although the effect of methylation of these CpG sites on gene transcription regulation warrants future investigation (7). The etiology of tumor development likely requires the acquisition of the silencing of hundreds of critical genes by promoter methylation, with most gene silencing occurring independent of allele-specific methylation and/or meQTL (Leng et al., unpublished data). Previously, we conducted a candidate gene–based study that implicated genetic variation in DNA replication and apoptosis pathways in modifying the propensity for gene methylation in the aerodigestive tract of smokers (8). The current study extends this work by conducting a two-stage GWAS (9) using smokers from two geographically independent cohorts to identify low-penetrance alleles affecting the propensity for acquiring gene methylation in the lungs.