Abstract
Aberrant promoter hypermethylation and associated gene silencing are epigenetic hallmarks of tumorigenesis. It has been suggested that aberrant DNA methylation can affect the sensitivity of cancers to antineoplastic agents by altering expression of genes critical to drug response. To study this issue, we used bisulfite PCR to assess DNA methylation of 32 promoter-associated CpG islands in human cancer cell lines from the National Cancer Institute (NCI) drug-screening panel (NCI-60 panel). The frequency of aberrant hypermethylation of these islands ranged from 2% to 81% in NCI-60 cancer cells, and provided a database that can be analyzed for the sensitivity to approximately 30,000 drugs tested in this panel. By correlating drug activity with DNA methylation, we identified a list of methylation markers that predict sensitivity to chemotherapeutic drugs. Among them, hypermethylation of the p53 homologue p73 and associated gene silencing was strongly correlated with sensitivity to alkylating agents. We used small interfering RNA to down-regulate p73 expression in multiple cell lines, including the resistant cell lines TK10 (renal cancer) and SKMEL28 (melanoma). Down-regulating p73 substantially increased sensitivity to commonly used alkylating agents, including cisplatin, indicating that epigenetic silencing of p73 directly modulates drug sensitivity. Our results confirm that epigenetic profiles are useful in identifying molecular mediators for cancer drug sensitivity (pharmaco-epigenomics).
Highlights
The National Cancer Institute (NCI) has established a panel of cell lines (NCI-60) and used it to screen compounds for anticancer activity over the last decades [1]
As a proof of principle, by correlating DNA methylation with drug response, we show that p73 methylation and silencing of this gene predicts sensitivity to alkylating agents, and down-regulation of p73 gene expression by small interfering RNA sensitized the resistant cell lines to several alkylating agents tested
The methylation profile of NCI-60 cell lines was determined by testing the methylation status of 32 CpG islands
Summary
The NCI has established a panel of cell lines (NCI-60) and used it to screen compounds for anticancer activity over the last decades [1]. At this moment, the NCI-60 cells constitute the most extensively and diversely characterized cell panel anywhere, and several databases have been generated based on these cell lines, such as drug activity database for >30,000 chemically defined compounds, expression profile of >8,000 different genes, and selected genetic changes [2]. Genome-wide gene expression profiling of the NCI-60 cell lines [3] identified strong associations between selected gene expression and chemosensitivity in this panel, suggesting that gene-drug interactions may be useful for predicting the responsiveness of cancer cells to anticancer agents.
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