Pharmacogenomic dissection of resistance to thymidylate synthase inhibitors

Chemoresistance is a major obstacle for successful cancer treatment. Gene a mplification and altered expression are the main genetic mechanisms of tumo r chemoresistance. Previously, only a limited number of genes were analyzed in each individual study using traditional molecular methods such as North ern and Southern blotting. In this study, the global gene expression patter ns of 1176 genes in a panel of five thymidylate synthase (TS) inhibitor [ra ltitrexed (TDX) and 5-fluorouracil (5-FU)] resistant and sensitive parent c ell lines were investigated using cDNA array technology. Only 28 of 1176 ge nes were altered >1.5-fold among resistant cells, with 2 genes (TS and YES1 ) consistently higher in the panel. TS mRNA and protein were consistently o verexpressed in all drug-resistant tumor cell lines compared with the sensi tive parent cell lines. Southern blot and FISH analysis demonstrated that t he TS gene was amplified in 5-FU- and TDX-resistant cell lines, YES1 mRNA a nd protein were overexpressed in four drug-resistant tumor cell lines but w ere not overexpressed in the lymphoblast cell line W1L2(TDX), although the YES1 gene was highly amplified in these cells. The fact that W1L2 has high level (> 10-fold) resistance to TS inhibitor in the absence of high YES1 ex pression leads to a conclusion that YES1 has no direct role in this drug re sistance process. By narrowing the search from 1176 to 2 genes, the analysi s of in vitro TDX and 5-FU resistance becomes more straightforward for conf irmatory studies. These data provide encouragement that comprehensive trans cript analysis will aid the quest for more enlightened therapeutics.