A five-CpG DNA methylation score to predict metastatic-lethal outcomes in men treated with radical prostatectomy for localized prostate cancer

Abstract

Background: Prognostic biomarkers for localized prostate cancer (PCa) could improve personalized medicine. Our group previously identified a panel of differentially methylated CpGs in primary tumor tissue that predict disease aggressiveness, and here we further validate these biomarkers.

Methods: Pyrosequencing was used to assess CpG methylation of eight biomarkers previously identified using the HumanMethylation450 array; CpGs with strongly correlated (r >0.70) results were considered technically validated. Logistic regression incorporating the validated CpGs and Gleason sum was used to define and lock a final model to stratify men with metastatic-lethal versus non-recurrent PCa in a training dataset. Coefficients from the final model were then used to construct a DNA methylation score, which was evaluated by logistic regression and Receiver Operating Characteristic (ROC) curve analyses in an independent testing dataset.

Results: Five CpGs were technically validated and all were retained (P < 0.05) in the final model. The 5-CpG and Gleason sum coefficients were used to calculate a methylation score, which was higher in men with metastatic-lethal progression (P = 6.8 × 10^-6 ) in the testing dataset. For each unit increase in the score there was a four-fold increase in risk of metastatic-lethal events (odds ratio, OR = 4.0, 95%CI = 1.8-14.3). At 95% specificity, sensitivity was 74% for the score compared to 53% for Gleason sum alone. The score demonstrated better prediction performance (AUC = 0.91; pAUC = 0.037) compared to Gleason sum alone (AUC = 0.87; pAUC = 0.025).

Conclusions: The DNA methylation score improved upon Gleason sum for predicting metastatic-lethal progression and holds promise for risk stratification of men with aggressive tumors. This prognostic score warrants further evaluation as a tool for improving patient outcomes.

Keywords: DNA methylation score; biomarker validation; metastatic-lethal; prognostic; prostate cancer.

Figure 1

Box plots of the DNA methylation score in the UM testing dataset stratified by prostate cancer outcome status (no recurrence or metastatic‐lethal progression)

Figure 2

Receiver Operating Characteristic curves for predicting metastatic‐lethal versus non‐recurrent prostate cancer outcomes in the UM testing dataset. The dashed vertical line indicates 95% specificity, which corresponds to a sensitivity of 53% for Gleason sum alone compared to a sensitivity of 74% for the DNA methylation score. The red line shows the prediction performance of Gleason sum alone (AUC = 0.87; pAUC = 0.025), and the blue line shows the prediction performance of the DNA methylation score based on Gleason sum plus five CpGs (AUC = 0.91; pAUC = 0.037)