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DNA Methylation-Guided Prediction of Clinical Failure in High-Risk Prostate Cancer.

Litovkin K, Van Eynde A, Joniau S, Lerut E, Laenen A, Gevaert T, Gevaert O, Spahn M, Kneitz B, Gramme P, Helleputte T, Isebaert S, Haustermans K, Bollen M - PLoS ONE (2015)

Bottom Line: However, only GSTP1 methylation was significantly associated with CF in both independent high-risk PCa cohorts.Patients with either a low or high GSTP1 methylation level, as compared to the moderate methylation groups, were at a higher risk for CF in both the training (Hazard ratio [HR], 3.65; 95% CI, 1.65 to 8.07) and validation sets (HR, 4.27; 95% CI, 1.03 to 17.72) as well as in the combined cohort (HR, 2.74; 95% CI, 1.42 to 5.27) in multivariate analysis.Classification of primary high-risk tumors into three subtypes based on DNA methylation can be combined with clinico-pathological parameters for a more informative risk-stratification of these PCa patients.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Leuven, Belgium.

ABSTRACT

Background: Prostate cancer (PCa) is a very heterogeneous disease with respect to clinical outcome. This study explored differential DNA methylation in a priori selected genes to diagnose PCa and predict clinical failure (CF) in high-risk patients.

Methods: A quantitative multiplex, methylation-specific PCR assay was developed to assess promoter methylation of the APC, CCND2, GSTP1, PTGS2 and RARB genes in formalin-fixed, paraffin-embedded tissue samples from 42 patients with benign prostatic hyperplasia and radical prostatectomy specimens of patients with high-risk PCa, encompassing training and validation cohorts of 147 and 71 patients, respectively. Log-rank tests, univariate and multivariate Cox models were used to investigate the prognostic value of the DNA methylation.

Results: Hypermethylation of APC, CCND2, GSTP1, PTGS2 and RARB was highly cancer-specific. However, only GSTP1 methylation was significantly associated with CF in both independent high-risk PCa cohorts. Importantly, trichotomization into low, moderate and high GSTP1 methylation level subgroups was highly predictive for CF. Patients with either a low or high GSTP1 methylation level, as compared to the moderate methylation groups, were at a higher risk for CF in both the training (Hazard ratio [HR], 3.65; 95% CI, 1.65 to 8.07) and validation sets (HR, 4.27; 95% CI, 1.03 to 17.72) as well as in the combined cohort (HR, 2.74; 95% CI, 1.42 to 5.27) in multivariate analysis.

Conclusions: Classification of primary high-risk tumors into three subtypes based on DNA methylation can be combined with clinico-pathological parameters for a more informative risk-stratification of these PCa patients.

No MeSH data available.


Related in: MedlinePlus

Comparison of DNA-marker methylation in benign prostatic hyperplasia (BPH) and high-risk PCa.The methylation of RARB, GSTP1, APC, CCND2 and PTGS2 was determined by QM-MSP in radical prostatectomy samples from 42 patients with BPH and from 147 (PCa1) and 71 (PCa2) patients with high-risk PCa. The data are shown in dot plots for the indicated genes (A-E, left graphs). Methylation levels of every gene in each PCa cohort were significantly higher than in the BPH group, as determined by the Mann-Whitney U-test (*, P<0.001). Receiver-operating-characteristic (ROC) analysis the methylation markers to discern BHP from high-risk prostate cancer samples (A-E; middle, PCa1 and right, PCa2), using the data displayed in the dot plots was performed. Grey line, median; AUC, area under the curve.
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pone.0130651.g001: Comparison of DNA-marker methylation in benign prostatic hyperplasia (BPH) and high-risk PCa.The methylation of RARB, GSTP1, APC, CCND2 and PTGS2 was determined by QM-MSP in radical prostatectomy samples from 42 patients with BPH and from 147 (PCa1) and 71 (PCa2) patients with high-risk PCa. The data are shown in dot plots for the indicated genes (A-E, left graphs). Methylation levels of every gene in each PCa cohort were significantly higher than in the BPH group, as determined by the Mann-Whitney U-test (*, P<0.001). Receiver-operating-characteristic (ROC) analysis the methylation markers to discern BHP from high-risk prostate cancer samples (A-E; middle, PCa1 and right, PCa2), using the data displayed in the dot plots was performed. Grey line, median; AUC, area under the curve.

Mentions: Next, the promoter methylation of APC, CCND2, GSTP1, PTGS2 and RARB was quantified in FFPE prostate tissue samples, using the QM-MSP procedure. Samples were derived from the transurethral resection or adenomectomy specimens of 42 patients with BPH and the radical prostatectomy specimens of 218 patients with high-risk PCa. The PCa patients comprised two groups, further denoted as the PCa1 or training cohort (n = 147) and PCa2 or validation (n = 71) cohort. In the BPH cohort, the average methylation level of these marker genes did not exceed 2% (Fig 1, Table B in S1 File). However, a much higher degree of CpG methylation was detected for all genes in both high-risk PCa cohorts, indicating a cancer-specific methylation of the selected markers (Fig 1, Table C and D in S1 File). With a methylation cutoff value of 1 or 2%, GSTP1 showed the highest sensitivity in PCa1 (0.99) and PCa2 (0.97) cohorts, at a specificity of 1.00 for the five single markers (Table E in S1 File). Other combinations of marker genes did not further improve the sensitivity without decreasing the specificity (Table E in S1 File). To further assess the accuracy in discriminating high-risk PCa from BPH, receiver-operating-characteristics (ROC) analysis for each of the single markers was performed and the area under the curve (AUC) was calculated (Fig 1). The AUCs ranged from 0.85 (PTGS2) to 0.99 (GSTP1), confirming cancer-specific methylation, with GSTP1 methylation as the best classifier.


DNA Methylation-Guided Prediction of Clinical Failure in High-Risk Prostate Cancer.

Litovkin K, Van Eynde A, Joniau S, Lerut E, Laenen A, Gevaert T, Gevaert O, Spahn M, Kneitz B, Gramme P, Helleputte T, Isebaert S, Haustermans K, Bollen M - PLoS ONE (2015)

Comparison of DNA-marker methylation in benign prostatic hyperplasia (BPH) and high-risk PCa.The methylation of RARB, GSTP1, APC, CCND2 and PTGS2 was determined by QM-MSP in radical prostatectomy samples from 42 patients with BPH and from 147 (PCa1) and 71 (PCa2) patients with high-risk PCa. The data are shown in dot plots for the indicated genes (A-E, left graphs). Methylation levels of every gene in each PCa cohort were significantly higher than in the BPH group, as determined by the Mann-Whitney U-test (*, P<0.001). Receiver-operating-characteristic (ROC) analysis the methylation markers to discern BHP from high-risk prostate cancer samples (A-E; middle, PCa1 and right, PCa2), using the data displayed in the dot plots was performed. Grey line, median; AUC, area under the curve.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4472347&req=5

pone.0130651.g001: Comparison of DNA-marker methylation in benign prostatic hyperplasia (BPH) and high-risk PCa.The methylation of RARB, GSTP1, APC, CCND2 and PTGS2 was determined by QM-MSP in radical prostatectomy samples from 42 patients with BPH and from 147 (PCa1) and 71 (PCa2) patients with high-risk PCa. The data are shown in dot plots for the indicated genes (A-E, left graphs). Methylation levels of every gene in each PCa cohort were significantly higher than in the BPH group, as determined by the Mann-Whitney U-test (*, P<0.001). Receiver-operating-characteristic (ROC) analysis the methylation markers to discern BHP from high-risk prostate cancer samples (A-E; middle, PCa1 and right, PCa2), using the data displayed in the dot plots was performed. Grey line, median; AUC, area under the curve.
Mentions: Next, the promoter methylation of APC, CCND2, GSTP1, PTGS2 and RARB was quantified in FFPE prostate tissue samples, using the QM-MSP procedure. Samples were derived from the transurethral resection or adenomectomy specimens of 42 patients with BPH and the radical prostatectomy specimens of 218 patients with high-risk PCa. The PCa patients comprised two groups, further denoted as the PCa1 or training cohort (n = 147) and PCa2 or validation (n = 71) cohort. In the BPH cohort, the average methylation level of these marker genes did not exceed 2% (Fig 1, Table B in S1 File). However, a much higher degree of CpG methylation was detected for all genes in both high-risk PCa cohorts, indicating a cancer-specific methylation of the selected markers (Fig 1, Table C and D in S1 File). With a methylation cutoff value of 1 or 2%, GSTP1 showed the highest sensitivity in PCa1 (0.99) and PCa2 (0.97) cohorts, at a specificity of 1.00 for the five single markers (Table E in S1 File). Other combinations of marker genes did not further improve the sensitivity without decreasing the specificity (Table E in S1 File). To further assess the accuracy in discriminating high-risk PCa from BPH, receiver-operating-characteristics (ROC) analysis for each of the single markers was performed and the area under the curve (AUC) was calculated (Fig 1). The AUCs ranged from 0.85 (PTGS2) to 0.99 (GSTP1), confirming cancer-specific methylation, with GSTP1 methylation as the best classifier.

Bottom Line: However, only GSTP1 methylation was significantly associated with CF in both independent high-risk PCa cohorts.Patients with either a low or high GSTP1 methylation level, as compared to the moderate methylation groups, were at a higher risk for CF in both the training (Hazard ratio [HR], 3.65; 95% CI, 1.65 to 8.07) and validation sets (HR, 4.27; 95% CI, 1.03 to 17.72) as well as in the combined cohort (HR, 2.74; 95% CI, 1.42 to 5.27) in multivariate analysis.Classification of primary high-risk tumors into three subtypes based on DNA methylation can be combined with clinico-pathological parameters for a more informative risk-stratification of these PCa patients.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Biosignaling & Therapeutics, KU Leuven Department of Cellular and Molecular Medicine, University of Leuven, Leuven, Belgium.

ABSTRACT

Background: Prostate cancer (PCa) is a very heterogeneous disease with respect to clinical outcome. This study explored differential DNA methylation in a priori selected genes to diagnose PCa and predict clinical failure (CF) in high-risk patients.

Methods: A quantitative multiplex, methylation-specific PCR assay was developed to assess promoter methylation of the APC, CCND2, GSTP1, PTGS2 and RARB genes in formalin-fixed, paraffin-embedded tissue samples from 42 patients with benign prostatic hyperplasia and radical prostatectomy specimens of patients with high-risk PCa, encompassing training and validation cohorts of 147 and 71 patients, respectively. Log-rank tests, univariate and multivariate Cox models were used to investigate the prognostic value of the DNA methylation.

Results: Hypermethylation of APC, CCND2, GSTP1, PTGS2 and RARB was highly cancer-specific. However, only GSTP1 methylation was significantly associated with CF in both independent high-risk PCa cohorts. Importantly, trichotomization into low, moderate and high GSTP1 methylation level subgroups was highly predictive for CF. Patients with either a low or high GSTP1 methylation level, as compared to the moderate methylation groups, were at a higher risk for CF in both the training (Hazard ratio [HR], 3.65; 95% CI, 1.65 to 8.07) and validation sets (HR, 4.27; 95% CI, 1.03 to 17.72) as well as in the combined cohort (HR, 2.74; 95% CI, 1.42 to 5.27) in multivariate analysis.

Conclusions: Classification of primary high-risk tumors into three subtypes based on DNA methylation can be combined with clinico-pathological parameters for a more informative risk-stratification of these PCa patients.

No MeSH data available.


Related in: MedlinePlus