Prostate tumor DNA methylation is associated with cigarette smoking and adverse prostate cancer outcomes

Abstract

Background: DNA methylation has been hypothesized as a mechanism for explaining the association between smoking and adverse prostate cancer (PCa) outcomes. This study was aimed at assessing whether smoking is associated with prostate tumor DNA methylation and whether these alterations may explain in part the association of smoking with PCa recurrence and mortality.

Methods: A total of 523 men had radical prostatectomy as their primary treatment, detailed smoking history data, long-term follow-up for PCa outcomes, and tumor tissue profiled for DNA methylation. Ninety percent of the men also had matched tumor gene expression data. A methylome-wide analysis was conducted to identify differentially methylated regions (DMRs) by smoking status. To select potential functionally relevant DMRs, their correlation with the messenger RNA (mRNA) expression of corresponding genes was evaluated. Finally, a smoking-related methylation score based on the top-ranked DMRs was created to assess its association with PCa outcomes.

Results: Forty DMRs were associated with smoking status, and 10 of these were strongly correlated with mRNA expression (aldehyde oxidase 1 [AOX1], claudin 5 [CLDN5], early B-cell factor 1 [EBF1], homeobox A7 [HOXA7], lectin galactoside-binding soluble 3 [LGALS3], microtubule-associated protein τ [MAPT], protocadherin γ A [PCDHGA]/protocadherin γ B [PCDHGB], paraoxonase 3 [PON3], synaptonemal complex protein 2 like [SYCP2L], and zinc finger and SCAN domain containing 12 [ZSCAN12]). Men who were in the highest tertile for the smoking-methylation score derived from these DMRs had a higher risk of recurrence (odds ratio [OR], 2.29; 95% confidence interval [CI], 1.42-3.72) and lethal disease (OR, 4.21; 95% CI, 1.65-11.78) in comparison with men in the lower 2 tertiles.

Conclusions: This integrative molecular epidemiology study supports the hypothesis that smoking-associated tumor DNA methylation changes may explain at least part of the association between smoking and adverse PCa outcomes. Future studies are warranted to confirm these findings and understand the implications for improving patient outcomes. Cancer 2016;122:2168-77. © 2016 American Cancer Society.

Keywords: DNA methylation; epigenetics; prostate cancer; prostate cancer outcomes; smoking.

Figure 1. Differential methylation by smoking status at prostate cancer diagnosis

Figure 1A illustrates differential methylation comparing current versus never smokers. Figure 1B illustrates differential methylation comparing men who smoked ≥20 pack-years versus never smokers. Figure 1C illustrates differential methylation comparing former versus never smokers. Each CpG site is plotted as a point. Points to the right of zero on the x-axis indicate that the CpG is more methylated in smokers compared to nonsmokers and those to the left of zero are less methylated in smokers compared to nonsmokers. Blue points indicate comparisons with FDR<0.05 and red dots are those with an FDR<0.05 and at least a 10% difference in methylation beta between smokers and nonsmokers. There were no significantly differentially methylated CpG sites in former versus never smokers.

Figure 2. Top two differentially methylated regions (DMRs) by chromosome, gene location and CpG island relationship

This figure shows the two top-ranked DMRs by chromosome, ENSEMBLE gene location, and CpG island relationship (CGI). β-values for each CpG in the DMR are plotted with current smokers in red and never smokers in blue. The solid line shows the mean beta-value across the CpGs in current vs. never smokers.