Quantitative promoter hypermethylation analysis of cancer-related genes in salivary gland carcinomas

comparison with methylation-specific PCR technique and clinical significance

Eung Seok Lee, Jean Pierre Issa, Dianna B. Roberts, Michelle D. Williams, Randal S. Weber, Merrill S. Kies, Adel K. El-Naggar

Research output: Contribution to journalArticle

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Abstract

Purpose: To compare the methylation status of tumor-associated genes by quantitative pyrosequencing and qualitative methylation-specific PCR (MSP) techniques and to correlate the results with clinicopathologic features and patients outcome to determine which method might have greater clinical utility. Experimental Design: The hypermethylation status of the retinoid acid receptor (β2 (RARβ2), RAS association domain family 1A (RASSF1A), 0 6-methylguanine-DNA methyltransferase (MGMT), and E-cadherin genes was analyzed in five salivary carcinoma cell lines and 69 human salivary gland carcinoma specimens by pyrosequencing and MSP techniques. The two datasets were compared by linear regression. Correlations between methods and with clinicopathologic characteristics were assessed by Pearson's x2 test or the two-tailed Fisher exact test, as applicable, using cutoff points determined from the regression curves and empirical fitting. We also investigated the effect of demethylating agents on methylated genes in cell lines to assess their effect on the expression of these genes. Results: Overall, regression analysis indicated high degrees of correlation of the two methods for measurement of methylation for the RARb2, RASSF1A, and MGMT genes (adjusted R2 =0.319,0.835, and 0.178; P < 0.001, <0.001, and 0.0002, respectively) among the 69 tumors tested. However, the pyrosequencing technique yielded four more instances of methylation above background levels than MSP for RARβ2 and three more for RASSF1. Methylation of either RARβ2 and RASSF1A alone or both by pyrosequencing were correlated with tumor type (P = 0.027, 0.014, and 0.012, respectively). Methylation of RARβ2 alone and in combination with RASSF1A by pyrosequencing were also significantly correlated with tumor grade (P = 0.014 and 0.011, respectively) and 3-year survival (P = 0.002 and 0.004, respectively). The survival curves of patients who had hypermethylation at both RARβ2 and RASSF1A were significantly lower than those of patients who had hypermethylation at neither or just for the RASSF1A (P = 0.008 and 0.007, respectively). 5-Azadeoxycytidine treatment of methylated cell lines led to the reactivation of RARβ2 expression in only one of the five cell lines. Conclusions: (a) Although the methylation status of RARb2, RASSF1A, and MGMT genes by both techniques were significantly correlated, pyrosequencing is generally more sensitive and its results correlate better with the clinical variables than those of MSP. (b) The methylation level of the RARβ2 and/or RASSF1A by pyrosequencing is significantly associated with aggressive tumor phenotypes and patients survival.

Original languageEnglish
Pages (from-to)2664-2672
Number of pages9
JournalClinical Cancer Research
Volume14
Issue number9
DOIs
Publication statusPublished - 2008 May 1

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Neoplasm Genes
Salivary Glands
Methylation
Retinoids
Carcinoma
Polymerase Chain Reaction
Acids
Methyltransferases
Cell Line
Genes
decitabine
Neoplasms
Survival
DNA
Cadherins
Linear Models
Research Design
Regression Analysis
Phenotype
Gene Expression

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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Quantitative promoter hypermethylation analysis of cancer-related genes in salivary gland carcinomas : comparison with methylation-specific PCR technique and clinical significance. / Lee, Eung Seok; Issa, Jean Pierre; Roberts, Dianna B.; Williams, Michelle D.; Weber, Randal S.; Kies, Merrill S.; El-Naggar, Adel K.

In: Clinical Cancer Research, Vol. 14, No. 9, 01.05.2008, p. 2664-2672.

Research output: Contribution to journalArticle

Lee, Eung Seok ; Issa, Jean Pierre ; Roberts, Dianna B. ; Williams, Michelle D. ; Weber, Randal S. ; Kies, Merrill S. ; El-Naggar, Adel K. / Quantitative promoter hypermethylation analysis of cancer-related genes in salivary gland carcinomas : comparison with methylation-specific PCR technique and clinical significance. In: Clinical Cancer Research. 2008 ; Vol. 14, No. 9. pp. 2664-2672.
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abstract = "Purpose: To compare the methylation status of tumor-associated genes by quantitative pyrosequencing and qualitative methylation-specific PCR (MSP) techniques and to correlate the results with clinicopathologic features and patients outcome to determine which method might have greater clinical utility. Experimental Design: The hypermethylation status of the retinoid acid receptor (β2 (RARβ2), RAS association domain family 1A (RASSF1A), 0 6-methylguanine-DNA methyltransferase (MGMT), and E-cadherin genes was analyzed in five salivary carcinoma cell lines and 69 human salivary gland carcinoma specimens by pyrosequencing and MSP techniques. The two datasets were compared by linear regression. Correlations between methods and with clinicopathologic characteristics were assessed by Pearson's x2 test or the two-tailed Fisher exact test, as applicable, using cutoff points determined from the regression curves and empirical fitting. We also investigated the effect of demethylating agents on methylated genes in cell lines to assess their effect on the expression of these genes. Results: Overall, regression analysis indicated high degrees of correlation of the two methods for measurement of methylation for the RARb2, RASSF1A, and MGMT genes (adjusted R2 =0.319,0.835, and 0.178; P < 0.001, <0.001, and 0.0002, respectively) among the 69 tumors tested. However, the pyrosequencing technique yielded four more instances of methylation above background levels than MSP for RARβ2 and three more for RASSF1. Methylation of either RARβ2 and RASSF1A alone or both by pyrosequencing were correlated with tumor type (P = 0.027, 0.014, and 0.012, respectively). Methylation of RARβ2 alone and in combination with RASSF1A by pyrosequencing were also significantly correlated with tumor grade (P = 0.014 and 0.011, respectively) and 3-year survival (P = 0.002 and 0.004, respectively). The survival curves of patients who had hypermethylation at both RARβ2 and RASSF1A were significantly lower than those of patients who had hypermethylation at neither or just for the RASSF1A (P = 0.008 and 0.007, respectively). 5-Azadeoxycytidine treatment of methylated cell lines led to the reactivation of RARβ2 expression in only one of the five cell lines. Conclusions: (a) Although the methylation status of RARb2, RASSF1A, and MGMT genes by both techniques were significantly correlated, pyrosequencing is generally more sensitive and its results correlate better with the clinical variables than those of MSP. (b) The methylation level of the RARβ2 and/or RASSF1A by pyrosequencing is significantly associated with aggressive tumor phenotypes and patients survival.",
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T1 - Quantitative promoter hypermethylation analysis of cancer-related genes in salivary gland carcinomas

T2 - comparison with methylation-specific PCR technique and clinical significance

AU - Lee, Eung Seok

AU - Issa, Jean Pierre

AU - Roberts, Dianna B.

AU - Williams, Michelle D.

AU - Weber, Randal S.

AU - Kies, Merrill S.

AU - El-Naggar, Adel K.

PY - 2008/5/1

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N2 - Purpose: To compare the methylation status of tumor-associated genes by quantitative pyrosequencing and qualitative methylation-specific PCR (MSP) techniques and to correlate the results with clinicopathologic features and patients outcome to determine which method might have greater clinical utility. Experimental Design: The hypermethylation status of the retinoid acid receptor (β2 (RARβ2), RAS association domain family 1A (RASSF1A), 0 6-methylguanine-DNA methyltransferase (MGMT), and E-cadherin genes was analyzed in five salivary carcinoma cell lines and 69 human salivary gland carcinoma specimens by pyrosequencing and MSP techniques. The two datasets were compared by linear regression. Correlations between methods and with clinicopathologic characteristics were assessed by Pearson's x2 test or the two-tailed Fisher exact test, as applicable, using cutoff points determined from the regression curves and empirical fitting. We also investigated the effect of demethylating agents on methylated genes in cell lines to assess their effect on the expression of these genes. Results: Overall, regression analysis indicated high degrees of correlation of the two methods for measurement of methylation for the RARb2, RASSF1A, and MGMT genes (adjusted R2 =0.319,0.835, and 0.178; P < 0.001, <0.001, and 0.0002, respectively) among the 69 tumors tested. However, the pyrosequencing technique yielded four more instances of methylation above background levels than MSP for RARβ2 and three more for RASSF1. Methylation of either RARβ2 and RASSF1A alone or both by pyrosequencing were correlated with tumor type (P = 0.027, 0.014, and 0.012, respectively). Methylation of RARβ2 alone and in combination with RASSF1A by pyrosequencing were also significantly correlated with tumor grade (P = 0.014 and 0.011, respectively) and 3-year survival (P = 0.002 and 0.004, respectively). The survival curves of patients who had hypermethylation at both RARβ2 and RASSF1A were significantly lower than those of patients who had hypermethylation at neither or just for the RASSF1A (P = 0.008 and 0.007, respectively). 5-Azadeoxycytidine treatment of methylated cell lines led to the reactivation of RARβ2 expression in only one of the five cell lines. Conclusions: (a) Although the methylation status of RARb2, RASSF1A, and MGMT genes by both techniques were significantly correlated, pyrosequencing is generally more sensitive and its results correlate better with the clinical variables than those of MSP. (b) The methylation level of the RARβ2 and/or RASSF1A by pyrosequencing is significantly associated with aggressive tumor phenotypes and patients survival.

AB - Purpose: To compare the methylation status of tumor-associated genes by quantitative pyrosequencing and qualitative methylation-specific PCR (MSP) techniques and to correlate the results with clinicopathologic features and patients outcome to determine which method might have greater clinical utility. Experimental Design: The hypermethylation status of the retinoid acid receptor (β2 (RARβ2), RAS association domain family 1A (RASSF1A), 0 6-methylguanine-DNA methyltransferase (MGMT), and E-cadherin genes was analyzed in five salivary carcinoma cell lines and 69 human salivary gland carcinoma specimens by pyrosequencing and MSP techniques. The two datasets were compared by linear regression. Correlations between methods and with clinicopathologic characteristics were assessed by Pearson's x2 test or the two-tailed Fisher exact test, as applicable, using cutoff points determined from the regression curves and empirical fitting. We also investigated the effect of demethylating agents on methylated genes in cell lines to assess their effect on the expression of these genes. Results: Overall, regression analysis indicated high degrees of correlation of the two methods for measurement of methylation for the RARb2, RASSF1A, and MGMT genes (adjusted R2 =0.319,0.835, and 0.178; P < 0.001, <0.001, and 0.0002, respectively) among the 69 tumors tested. However, the pyrosequencing technique yielded four more instances of methylation above background levels than MSP for RARβ2 and three more for RASSF1. Methylation of either RARβ2 and RASSF1A alone or both by pyrosequencing were correlated with tumor type (P = 0.027, 0.014, and 0.012, respectively). Methylation of RARβ2 alone and in combination with RASSF1A by pyrosequencing were also significantly correlated with tumor grade (P = 0.014 and 0.011, respectively) and 3-year survival (P = 0.002 and 0.004, respectively). The survival curves of patients who had hypermethylation at both RARβ2 and RASSF1A were significantly lower than those of patients who had hypermethylation at neither or just for the RASSF1A (P = 0.008 and 0.007, respectively). 5-Azadeoxycytidine treatment of methylated cell lines led to the reactivation of RARβ2 expression in only one of the five cell lines. Conclusions: (a) Although the methylation status of RARb2, RASSF1A, and MGMT genes by both techniques were significantly correlated, pyrosequencing is generally more sensitive and its results correlate better with the clinical variables than those of MSP. (b) The methylation level of the RARβ2 and/or RASSF1A by pyrosequencing is significantly associated with aggressive tumor phenotypes and patients survival.

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