Quantitation of promoter methylation of multiple genes in urine DNA and bladder cancer detection

Mohammad Obaidul Hoque, Shahnaz Begum, Ozlem Topaloglu, Aditi Chatterjee, Eli Rosenbaum, Wim Van Criekinge, William H. Westra, Mark P. Schoenberg, Marianna Zahurak, Steven N. Goodman, David Sidransky

Research output: Contribution to journalArticle

205 Citations (Scopus)

Abstract

Background: The noninvasive identification of bladder tumors may improve disease control and prevent disease progression. Aberrant promoter methylation (i.e., hypermethylation) is a major mechanism for silencing tumor suppressor genes and other cancer-associated genes in many human cancers, including bladder cancer. Methods: A quantitative fluorogenic real-time polymerase chain reaction (PCR) assay was used to examine primary tumor DNA and urine sediment DNA from 15 patients with bladder cancer and 25 control subjects for promoter hypermethylation of nine genes (APC, ARF, CDH1, GSTP1, MGMT, CDKN2A, RARβ2, RASSF1A, and TIMP3) to identify potential biomarkers for bladder cancer. We then used these markers to examine urine sediment DNA samples from an additional 160 patients with bladder cancers of various stages and grades and from an additional 69 age-matched control subjects. Data were analyzed on the basis of a prediction model and were internally validated using a jacknife procedure. All statistical tests were two-sided. Results: For all 15 patients with paired DNA samples, the promoter methylation pattern in urine matched that in the primary tumors. Four genes displayed 100% specificity. Of the 175 bladder cancer patients, 121 (69%, 95% confidence interval [CI] = 62% to 76%) displayed promoter methylation in at least one of these genes (CDKN2A, ARF, MGMT, and GSTP1), whereas all control subjects were negative for such methylation (100% specificity, 95% CI = 96% to 100%). A logistic prediction model using the methylation levels of all remaining five genes was developed and internally validated for subjects who were negative on the four-gene panel. This combined, two-stage predictor produced an internally validated ROC curve with an overall sensitivity of 82% (95% CI = 75 % to 87%) and specificity of 96% (95% CI = 90% to 99%). Conclusion: Testing a small panel of genes with the quantitative methylation-specific PCR assay in urine sediment DNA is a powerful noninvasive approach for the detection of bladder cancer. Larger independent confirmatory cohorts with longitudinal follow-up will be required in future studies to define the impact of this technology on early detection, prognosis, and disease monitoring before clinical application.

Original languageEnglish (US)
Pages (from-to)996-1004
Number of pages9
JournalJournal of the National Cancer Institute
Volume98
Issue number14
DOIs
StatePublished - Jul 19 2006
Externally publishedYes

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Urinary Bladder Neoplasms
Methylation
Urine
DNA
Genes
Confidence Intervals
APC Genes
p16 Genes
Neoplasm Genes
Tumor Suppressor Genes
ROC Curve
Disease Progression
Real-Time Polymerase Chain Reaction
Early Diagnosis
Neoplasms
Biomarkers
Logistic Models
Technology
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Hoque, M. O., Begum, S., Topaloglu, O., Chatterjee, A., Rosenbaum, E., Van Criekinge, W., ... Sidransky, D. (2006). Quantitation of promoter methylation of multiple genes in urine DNA and bladder cancer detection. Journal of the National Cancer Institute, 98(14), 996-1004. https://doi.org/10.1093/jnci/djj265

Quantitation of promoter methylation of multiple genes in urine DNA and bladder cancer detection. / Hoque, Mohammad Obaidul; Begum, Shahnaz; Topaloglu, Ozlem; Chatterjee, Aditi; Rosenbaum, Eli; Van Criekinge, Wim; Westra, William H.; Schoenberg, Mark P.; Zahurak, Marianna; Goodman, Steven N.; Sidransky, David.

In: Journal of the National Cancer Institute, Vol. 98, No. 14, 19.07.2006, p. 996-1004.

Research output: Contribution to journalArticle

Hoque, MO, Begum, S, Topaloglu, O, Chatterjee, A, Rosenbaum, E, Van Criekinge, W, Westra, WH, Schoenberg, MP, Zahurak, M, Goodman, SN & Sidransky, D 2006, 'Quantitation of promoter methylation of multiple genes in urine DNA and bladder cancer detection', Journal of the National Cancer Institute, vol. 98, no. 14, pp. 996-1004. https://doi.org/10.1093/jnci/djj265
Hoque MO, Begum S, Topaloglu O, Chatterjee A, Rosenbaum E, Van Criekinge W et al. Quantitation of promoter methylation of multiple genes in urine DNA and bladder cancer detection. Journal of the National Cancer Institute. 2006 Jul 19;98(14):996-1004. https://doi.org/10.1093/jnci/djj265
Hoque, Mohammad Obaidul ; Begum, Shahnaz ; Topaloglu, Ozlem ; Chatterjee, Aditi ; Rosenbaum, Eli ; Van Criekinge, Wim ; Westra, William H. ; Schoenberg, Mark P. ; Zahurak, Marianna ; Goodman, Steven N. ; Sidransky, David. / Quantitation of promoter methylation of multiple genes in urine DNA and bladder cancer detection. In: Journal of the National Cancer Institute. 2006 ; Vol. 98, No. 14. pp. 996-1004.
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abstract = "Background: The noninvasive identification of bladder tumors may improve disease control and prevent disease progression. Aberrant promoter methylation (i.e., hypermethylation) is a major mechanism for silencing tumor suppressor genes and other cancer-associated genes in many human cancers, including bladder cancer. Methods: A quantitative fluorogenic real-time polymerase chain reaction (PCR) assay was used to examine primary tumor DNA and urine sediment DNA from 15 patients with bladder cancer and 25 control subjects for promoter hypermethylation of nine genes (APC, ARF, CDH1, GSTP1, MGMT, CDKN2A, RARβ2, RASSF1A, and TIMP3) to identify potential biomarkers for bladder cancer. We then used these markers to examine urine sediment DNA samples from an additional 160 patients with bladder cancers of various stages and grades and from an additional 69 age-matched control subjects. Data were analyzed on the basis of a prediction model and were internally validated using a jacknife procedure. All statistical tests were two-sided. Results: For all 15 patients with paired DNA samples, the promoter methylation pattern in urine matched that in the primary tumors. Four genes displayed 100{\%} specificity. Of the 175 bladder cancer patients, 121 (69{\%}, 95{\%} confidence interval [CI] = 62{\%} to 76{\%}) displayed promoter methylation in at least one of these genes (CDKN2A, ARF, MGMT, and GSTP1), whereas all control subjects were negative for such methylation (100{\%} specificity, 95{\%} CI = 96{\%} to 100{\%}). A logistic prediction model using the methylation levels of all remaining five genes was developed and internally validated for subjects who were negative on the four-gene panel. This combined, two-stage predictor produced an internally validated ROC curve with an overall sensitivity of 82{\%} (95{\%} CI = 75 {\%} to 87{\%}) and specificity of 96{\%} (95{\%} CI = 90{\%} to 99{\%}). Conclusion: Testing a small panel of genes with the quantitative methylation-specific PCR assay in urine sediment DNA is a powerful noninvasive approach for the detection of bladder cancer. Larger independent confirmatory cohorts with longitudinal follow-up will be required in future studies to define the impact of this technology on early detection, prognosis, and disease monitoring before clinical application.",
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AU - Begum, Shahnaz

AU - Topaloglu, Ozlem

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AU - Rosenbaum, Eli

AU - Van Criekinge, Wim

AU - Westra, William H.

AU - Schoenberg, Mark P.

AU - Zahurak, Marianna

AU - Goodman, Steven N.

AU - Sidransky, David

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N2 - Background: The noninvasive identification of bladder tumors may improve disease control and prevent disease progression. Aberrant promoter methylation (i.e., hypermethylation) is a major mechanism for silencing tumor suppressor genes and other cancer-associated genes in many human cancers, including bladder cancer. Methods: A quantitative fluorogenic real-time polymerase chain reaction (PCR) assay was used to examine primary tumor DNA and urine sediment DNA from 15 patients with bladder cancer and 25 control subjects for promoter hypermethylation of nine genes (APC, ARF, CDH1, GSTP1, MGMT, CDKN2A, RARβ2, RASSF1A, and TIMP3) to identify potential biomarkers for bladder cancer. We then used these markers to examine urine sediment DNA samples from an additional 160 patients with bladder cancers of various stages and grades and from an additional 69 age-matched control subjects. Data were analyzed on the basis of a prediction model and were internally validated using a jacknife procedure. All statistical tests were two-sided. Results: For all 15 patients with paired DNA samples, the promoter methylation pattern in urine matched that in the primary tumors. Four genes displayed 100% specificity. Of the 175 bladder cancer patients, 121 (69%, 95% confidence interval [CI] = 62% to 76%) displayed promoter methylation in at least one of these genes (CDKN2A, ARF, MGMT, and GSTP1), whereas all control subjects were negative for such methylation (100% specificity, 95% CI = 96% to 100%). A logistic prediction model using the methylation levels of all remaining five genes was developed and internally validated for subjects who were negative on the four-gene panel. This combined, two-stage predictor produced an internally validated ROC curve with an overall sensitivity of 82% (95% CI = 75 % to 87%) and specificity of 96% (95% CI = 90% to 99%). Conclusion: Testing a small panel of genes with the quantitative methylation-specific PCR assay in urine sediment DNA is a powerful noninvasive approach for the detection of bladder cancer. Larger independent confirmatory cohorts with longitudinal follow-up will be required in future studies to define the impact of this technology on early detection, prognosis, and disease monitoring before clinical application.

AB - Background: The noninvasive identification of bladder tumors may improve disease control and prevent disease progression. Aberrant promoter methylation (i.e., hypermethylation) is a major mechanism for silencing tumor suppressor genes and other cancer-associated genes in many human cancers, including bladder cancer. Methods: A quantitative fluorogenic real-time polymerase chain reaction (PCR) assay was used to examine primary tumor DNA and urine sediment DNA from 15 patients with bladder cancer and 25 control subjects for promoter hypermethylation of nine genes (APC, ARF, CDH1, GSTP1, MGMT, CDKN2A, RARβ2, RASSF1A, and TIMP3) to identify potential biomarkers for bladder cancer. We then used these markers to examine urine sediment DNA samples from an additional 160 patients with bladder cancers of various stages and grades and from an additional 69 age-matched control subjects. Data were analyzed on the basis of a prediction model and were internally validated using a jacknife procedure. All statistical tests were two-sided. Results: For all 15 patients with paired DNA samples, the promoter methylation pattern in urine matched that in the primary tumors. Four genes displayed 100% specificity. Of the 175 bladder cancer patients, 121 (69%, 95% confidence interval [CI] = 62% to 76%) displayed promoter methylation in at least one of these genes (CDKN2A, ARF, MGMT, and GSTP1), whereas all control subjects were negative for such methylation (100% specificity, 95% CI = 96% to 100%). A logistic prediction model using the methylation levels of all remaining five genes was developed and internally validated for subjects who were negative on the four-gene panel. This combined, two-stage predictor produced an internally validated ROC curve with an overall sensitivity of 82% (95% CI = 75 % to 87%) and specificity of 96% (95% CI = 90% to 99%). Conclusion: Testing a small panel of genes with the quantitative methylation-specific PCR assay in urine sediment DNA is a powerful noninvasive approach for the detection of bladder cancer. Larger independent confirmatory cohorts with longitudinal follow-up will be required in future studies to define the impact of this technology on early detection, prognosis, and disease monitoring before clinical application.

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