DNA methylation and sensitivity to antimetabolites in cancer cell lines

Abstract

Abstract. The prediction of the cellular direction of metabolic pathways toward either DNA synthesis or DNA methylation is crucial for determining the susceptibility of cancers to antimetabolites such as fluorouracil (5-FU). We genotyped the methylenetetrahydrofolate reductase (MTHFR) gene in NCI-60 cancer cell lines, and identified the methylation status of 24 tumor suppressor genes using methylation-specific multiplex ligation-dependent probe amplification. The susceptibility of the cancer cell lines to seven antimetabolites was then determined. Cells homozygous for CC at MTHFR-A1298C were significantly more sensitive to cyclocytidine, cytarabine (AraC) and floxuridine than those with AA or AC (p=0.0215, p=0.0166, and p=0.0323, respectively), and carried more methylated tumor suppressor genes (p=0.0313). Among the 12 tumor suppressor genes which were methylated in >25% of cancer cell lines, the methylation status of TIMP3, APC and IGSF4 significantly correlated with sensitivity to pyrimidine synthesis inhibitors. In particular, cells with methylated TIMP3 had reduced mRNA levels and were significantly more sensitive to aphidicolin-glycinate, AraC and 5-FU than cells with unmethylated TIMP3. We speculate that MTHFR-A1298C homozygous CC might direct the methylation rather than the synthesis of DNA, and result in the methylation of several tumor suppressor genes such as TIMP3. These genes could be useful biological markers for predicting the efficacy of antimetabolites.

Predicting clinical outcome of 5-fluorouracil-based chemotherapy for colon cancer patients: is the CpG island methylator phenotype the 5-fluorouracilresponsive subgroup?

“…31 Moreover, a recent in vitro study showed that cancer cell lines with methylated TIMP3 were more sensitive to 5-FU. 32 Aside from having high intracellular folate concentrations, another possible explanation for CIMP+ tumors showing better response to 5-FU is because of the silencing of critical genes. One candidate for this is the methylationinduced silencing of the dihydropyrimidine dehydrogenase gene (DPYD).…”

Pharmacogenomic Discovery Using Cell-Based Models

“…Studies using these cells have successfully identified polymorphisms in candidate genes associated with drug response in vitro (Le Morvan et al, 2006;Jarjanazi et al, 2008;Puyo et al, 2008;Sasaki et al, 2008). Methylation of certain promoter CpG islands predicts toxicity to antimetabolites and alkylating agents in the NCI-60 lines (Shen et al, 2007;Sasaki et al, 2008).…”

“…Studies using these cells have successfully identified polymorphisms in candidate genes associated with drug response in vitro (Le Morvan et al, 2006;Jarjanazi et al, 2008;Puyo et al, 2008;Sasaki et al, 2008). Methylation of certain promoter CpG islands predicts toxicity to antimetabolites and alkylating agents in the NCI-60 lines (Shen et al, 2007;Sasaki et al, 2008). Like HapMap LCLs, the NCI-60 panel has been important in examining the role of genetic variation in membrane transporters on sensitivity to chemotherapeutics (Huang et al, , 2005bSzaká cs et al, 2004;Liu et al, 2007a;Okabe et al, 2008;Pham et al, 2009).…”

The Use of Genomic Information to Optimize Cancer Chemotherapy

“…Studies using these cell lines have successfully identified polymorphisms in candidate genes associated with drug response in vitro (54-57) . Methylation of certain promoter CpG islands predicts toxicity to antimetabolites and alkylating agents in the NCI-60 lines (57, 58) . In addition, relationships between sensitivity to a panel of EGFR inhibitors and EGFR amplification, EGFR mutations and EGFR mRNA expression have been studied (59) .…”