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Spotlight on Molecular Profiling

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

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

Requests for reprints: William C. Reinhold, Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, Building 37, Room 5056, Bethesda, MD 20892-4255. Phone: 301-496-9572; Fax: 301-402-0752. 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]

Grant support: In part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research, and in part by the NCI under contract no. NO1-CO-12400.

The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

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⁵ See http://dtp.nci.nih.gov/.

⁶ U. Shankavaram, W. Reinhold, S. Nishizuka, et al. Transcript and protein expression profiles of the NCI-60 cancer cell panel: an integromic microarray analysis. Mol Cancer Ther 2006. Submitted for publication.

⁷ S. Kim, manuscript in preparation.

⁸ Available from: http://www.ncbi.nlm.nih.gov/entrez/.

⁹ Available from: http://molbio.info.nih.gov.

¹⁰ Available from: http://www.r-project.org/.

¹¹ Supplementary material for this article is available at Molecular Cancer Therapeutics Online (http://mct.aacrjournals.org/).

¹² Reinhold et al., in preparation.

¹³ Reinhold et al., manuscript in in preparation.

Received 10/ 3/06; revised 11/27/06; accepted 12/19/06.

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