Validation Study of Genes with Hypermethylated Promoter Regions Associated with Prostate Cancer Recurrence

Abstract

Background One challenge in prostate cancer (PCa) is distinguishing indolent from aggressive disease at diagnosis. DNA promoter hypermethylation is a frequent epigenetic event in PCa, but few studies of DNA methylation in relation to features of more aggressive tumors or PCa recurrence have been completed. Methods We used the Infinium® HumanMethylation450 BeadChip to assess DNA methylation in tumor tissue from 407 patients with clinically localized PCa who underwent radical prostatectomy. Recurrence status was determined by follow-up patient surveys, medical record review, and linkage with the SEER registry. The methylation status of 14 genes for which promoter hypermethylation was previously correlated with advanced disease or biochemical recurrence was evaluated. Average methylation level for promoter region CpGs in patients who recurred compared to those with no evidence of recurrence was analyzed. For two genes with differential methylation, time to recurrence was examined. Results During an average follow-up of 11.7 years, 104 (26%) patients recurred. Significant promoter hypermethylation in at least 50% of CpG sites in two genes, ABHD9 and HOXD3, was found in tumors from patients who recurred compared to those without recurrence. Evidence was strongest for HOXD3 (lowest P = 9.46x10−6), with higher average methylation across promoter region CpGs associated with reduced recurrence-free survival (P = 2×10−4). DNA methylation profiles did not differ by recurrence status for the other genes. Conclusions These results validate the association between promoter hypermethylation of ADHB9 and HOXD3 and PCa recurrence. Impact Tumor DNA methylation profiling may help distinguish PCa patients at higher risk for disease recurrence.

A DNA Hypermethylation Profile Independently Predicts Biochemical Recurrence Following Radical Prostatectomy

“…In recent years, other variable DNA methylation alterations in neoplastic tissue samples have been also associated with the prediction of PSA recurrence after RP [10,17,18,19,20,21,22,23,24]. These studies have identified new potential tumor markers including methylation of PITX2 , HOXD3 , APC , TGFβ2 , RASSF1A , ANEP , PCDH10 , ZNF132 , TDRD1 , AOX1 , C1orf114 , GAS6 , HAPLN3 , KLF8 , MOB3B , CCND2 , PTGS2 , RARB , SRD5A2 and CYP11A1 , thus emerging as new predictors of BCR particularly in high-risk clinically localized disease.…”

Prognostic DNA Methylation Markers for Prostate Cancer

“…Another study [ 16 ], using qMSP on 592 RP specimens, reported a significant association between ABHD9 hypermethylation and PC progression (BCR or clinical recurrence) in univariate, but not in multivariate analysis ( Table 2 ). Finally, a more recent study [ 58 ] investigated the methylation status in RP specimens from 407 PC patients using the Illumina Infinium HumanMethylation450 BeadChip (Illumina 450K array), which interrogates >450,000 CpG sites in the human genome. Here, ABDH9 hypermethylation was not found to be significantly associated with time to progression ( Table 2 ), however in this study, progression was very broadly defined as either BCR (PSA ≥ 0.2 ng/mL), receipt of secondary treatment, positive imaging results, prostate bed or lymph node biopsy showing tumor content, diagnosis of tumor recurrence, or PC-specific death.…”

“…The Illumina 450K methylation array was recently used to analyze methylation of 407 RP specimens, using a broad spectrum of clinical end points for progression [ 58 ]. When analyzed as a dichotomized variable, HOXD3 methylation was found significantly associated with progression in univariate log-rank analysis as well as in multivariate analysis adjusting for age, Gleason score, pre-operative PSA, and pathological tumor stage ( Table 2 ).…”

“…When analyzed as a dichotomized variable, HOXD3 methylation was found significantly associated with progression in univariate log-rank analysis as well as in multivariate analysis adjusting for age, Gleason score, pre-operative PSA, and pathological tumor stage ( Table 2 ). However, the median time for progression-free survival was very long in the low (19.4 years) as well as in the high methylation group (17.0 years) [ 58 ].…”

Molecular markers to guide primary radical treatment selection in localized prostate cancer

“…Leung et al investigating post-radiotherapy changes in PC3 cells identified a panel of 6 upregulated and 16 downregulated miRNAs involved in diverse signaling pathway modulation and suggested that these might potentially be useful as radiotherapy biomarkers [90]. Methylation markers have also been shown to be promising biomarkers in surgically treated men, but a search of the literature for this review did not identify any predictive biomarker studies in clinical cohorts of EBRT-treated men but some promising work in cell lines [91][92][93]. As such, this review has not discussed epigenetic markers in any detail because of the significant paucity of evidence in the literature other than in RPtreated cohorts.…”