Epigenomic analysis of lung adenocarcinoma reveals novel DNA methylation patterns associated with smoking

Abstract

The importance of epigenetic regulation has been increasingly recognized in the development of cancer. In this study, we investigated the impact of smoking, a major risk factor of lung cancer, on DNA methylation by comparing the genome-wide DNA methylation patterns between lung adenocarcinoma samples from six smokers and six nonsmokers. We identified that smoking-induced DNA methylations were enriched in the calcium signaling and neuroactive ligand receptor signaling pathways, which are closely related to smoking-induced lung cancers. Interestingly, we discovered that two genes in the mitogen-activated protein kinase signaling pathway (RPS6KA3 and ARAF) were hypomethylated in smokers but not in nonsmokers. In addition, we found that the smoking-induced lung cancer-specific DNA methylations were mostly enriched in nuclear activities, including regulation of gene expression and chromatin remodeling. Moreover, the smoking-induced hypermethylation could only be seen in lung adenocarcinoma tissue but not in adjacent normal lung tissue. We also used differentially methylated DNA loci to construct a diagnostic model to distinguish smoking-associated lung cancer from nonsmoking lung cancer with a sensitivity of 88.9% and specificity of 83.2%. Our results provided novel evidence to support that smoking can cause dramatic changes in the DNA methylation landscape of lung cancer, suggesting that epigenetic regulation of specific oncogenic signaling pathways plays an important role in the development of lung cancer.

Keywords: epigenome; lung cancer; methylation; smoking; tumor suppressor gene.

Figure 1

Differences in global DNA methylation pattern in lung cancer between smokers and nonsmokers. The global DNA methylation pattern in normal lung tissues from smokers (SLT) was compared with that from nonsmokers (NSLT), producing 90 differentially methylated regions. The global DNA methylation pattern of lung tumor tissues from smokers (STT) was compared with that from nonsmokers (NSTT), resulting in 137 differentially methylated regions. Twenty-seven loci can be found in both result sets. The numbers of hypermethylation and hypomethylation loci are also shown. Abbreviation: vs, versus.

Figure 2

Hypothesized model of smoking-induced lung cancer based on our data.

Figure 3

Diagnostic model for classifying smoking-associated lung cancer and nonsmoking lung cancer. Notes: Classification accuracy is shown with the horizontal axis represents the individual samples grouped according to the disease class whereas the vertical axis represents the predicted classes. Black denotes nonsmokers and red denotes smokers. Abbreviations: PC, principal component; Sensit, sensitivity; specif, specificity.