GSBS Student Publications


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

UMMS Affiliation

Graduate School of Biomedical Sciences; Laboratory of Molecular Pharmacology



Document Type


Medical Subject Headings

Base Sequence; Cadherins; Cell Line, Tumor; Cluster Analysis; CpG Islands; *DNA Methylation; Gene Expression Regulation, Neoplastic; Gene Silencing; Humans; Molecular Sequence Data; *Oligonucleotide Array Sequence Analysis; Polymerase Chain Reaction; *Promoter Regions, Genetic; Sequence Analysis, DNA; Sequence Homology, Nucleic Acid


Life Sciences | Medicine and Health Sciences


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 approximately 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.

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Citation: Mol Cancer Ther. 2007 Feb;6(2):391-403. Epub 2007 Feb 1. Link to article on publisher's site

DOI of Published Version


Related Resources

Link to Article in PubMed

Journal Title

Molecular cancer therapeutics

PubMed ID