DNA methylation signature of smoking in lung cancer is enriched for exposure signatures in newborn and adult blood

Abstract

Smoking impacts DNA methylation genome-wide in blood of newborns from maternal smoking during pregnancy and adults from personal smoking. We compared smoking-related DNA methylation in lung adenocarcinoma (61 never smokers, 91 current smokers, and 238 former smokers) quantified with the Illumina450k BeadArray in The Cancer Genome Atlas with published large consortium meta-analyses of newborn and adult blood. We assessed whether CpG sites related to smoking in blood from newborns and adults were enriched in the lung adenocarcinoma methylation signal. Testing CpGs differentially methylated by smoke exposure, we identified 296 in lung adenocarcinoma meeting a P < 10^-4 cutoff, while previous meta-analyses identified 3,042 in newborn blood, and 8,898 in adult blood meeting the same P < 10^-4 cutoff. Lung signals were highly enriched for those seen in newborn (24 overlapping CpGs, P_enrichment = 1.2 × 10^-18) and adult blood (66 overlapping CpGs, P_enrichment = 1.2 × 10^-48). The 105 genes annotated to CpGs differentially methylated in lung tumors, but not blood, were enriched for RNA processing ontologies. Some epigenetic alterations associated with cigarette smoke exposure are tissue specific, but others are common across tissues. These findings support the value of blood-based methylation biomarkers for assessing exposure effects in target tissues.

Figure 1

Enrichment for blood smoking associated DNA methylation signal in lung adenocarcinoma. Enrichment was evaluated by testing the overlap of smoking associated sites in lung adenocarcinoma of current smokers (red), recent former smokers (green), and longer former smokers (blue) that met P thresholds with smoking associated sites in blood. The threshold in adult and newborn blood meta-analyses was P < 10⁻⁴. In lung, a range of P thresholds from 0 to 1 were applied and plotted against Fisher’s test P-values.

Figure 2

Effect estimates of CpG sites with P < 10⁻⁴. (A) CpG sites that are both associated with current smoking in adult blood and current smoking status in lung adenocarcinoma (P < 10⁻⁴) relative to never smokers. (B) Effect estimates of CpG sites that are both associated with maternal smoking in newborn blood and current smoking status in lung adenocarcinoma (P < 10⁻⁴) relative to never smokers.

Figure 3

Adult blood smoking signal enrichment in lung stratified by cancer stage. Fisher’s enrichment test results comparing overlap of DNA methylation sites associated with current smoking in lung adenocarcinoma and sites in adult blood (P < 10⁻⁴), stratifying samples by cancer stage. The smoking signature in blood is most strongly enriched in stage I samples.