Discovery and validation of 3 novel DNA methylation markers of prostate cancer prognosis.

About 15% of men experience prostate specific antigen recurrence after radical prostatectomy. A DNA methylation based molecular test could provide important information to predict which patients are most likely to experience recurrence. We performed a genome-wide scan to find aberrantly methylated loci in prostate cancer from patients with early recurrence, high Gleason score or advanced stage. We discovered 441 candidate methylation markers and further analyzed 62 candidates in a methylation microarray study of 304 frozen prostatectomy samples. Methylation of 25 markers was significantly changed in high Gleason score (8-10) vs low Gleason score (2-6) cancers. Methylation levels of the 3 marker candidates GPR7, ABHD9 and an expressed sequence tag on chromosome 3 (Chr3-EST) were significantly increased in patients who did vs did not experience early PSA recurrence (Bonferroni correction p<0.05). Furthermore, these markers were also informative when the sample set was restricted to 68 mid range Gleason score (6 or 7) samples only. We developed real-time polymerase chain reaction assays for ABHD9 and Chr3-EST, and measured methylation in paraffin embedded, formalin fixed prostatectomy samples from an independent set of 223 patients. Methylation of the 2 markers was significantly higher in patients with early PSA recurrence compared to that in patients who did not experience PSA recurrence. We report that methylation of the 3 novel markers GPR7, ABHD9 and Chr3-EST is significantly associated with prostate cancer prognosis. Incorporation of these methylation markers into clinical practice will result in more accurate prediction of which patients are likely to experience PSA recurrence.