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Detailed DNA methylation profiles of the E-cadherin promoter in the NCI-60 cancer cells

^{1 1}Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland; ²Gene Logic, Gaithersburg, Maryland; ³Science Applications International Corporation-Frederick, Inc., National Cancer Institute at Frederick, Frederick, Maryland; and ⁴Epigenetics Unit, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland

^* To whom correspondence should be addressed. E-mail: wcr{at}mail.nih.gov.

	Abstract

E-cadherin (E-cad) is a transmembrane adhesion glycoprotein, the expression of which is often reduced in invasive or metastatic tumors. To assess E-cad's distribution among different types of cancer cells, we used bisulfite-sequencing for detailed, base-by-base measurement of CpG methylation in E-cad's promoter region in the NCI-60 cell lines. The mean methylation levels of the cell lines were distributed bimodally, with values pushed toward either the high or low end of the methylation scale. The 38 epithelial cell lines showed substantially lower (28%) mean methylation levels compared with the nonepithelial cell lines (58%). The CpG site at -143 with respect to the transcriptional start was commonly methylated at intermediate levels, even in cell lines with low overall DNA methylation. We also profiled the NCI-60 cell lines using Affymetrix U133 microarrays and found E-cad expression to be correlated with E-cad methylation at highly statistically significant levels. Above a threshold of 20% to 30% mean methylation, the expression of E-cad was effectively silenced. Overall, this study provides a type of detailed analysis of methylation that can also be applied to other cancer-related genes. As has been shown in recent years, DNA methylation status can serve as a biomarker for use in choosing therapy. [Mol Cancer Ther 2007;6(2):391-403]

Key Words: methylation, E-cadherin, NCI60, NCI-60, bisulfite-sequencing, cell line, cancer, microarray

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