Hierarchical clustering of the 845 genes significantly altered in at least one condition was performed and is shown in Figure 2A. The variability in the expression patterns among the 3 resistant phenotypes suggested in the Venn diagram was evident in the clus tering as well. Clustering was also per formed for the genes significantly differentially altered in resistant cell lines developed through cisplatin expo sure, doxorubicin exposure, and paclitaxel exposure. Again, the heat maps showed that the cell lines exhibited little overlap in gene expression changes following the development of resis tance to the different drugs. In order to validate the microarray results, we selected a number of highly differentially expressed genes present in Table 1 for validation by RT PCR.

Nineteen genes whose expression patterns were confirmed by RT PCR are shown in Figure 3A,B. ABCB1 was found highly overexpressed, with increases of over 1,000 fold in OV90D and OV90P cells, while the increase in cisplatin resistant OV90C cells was approximately 15 fold. Similarly XAGE1D expression was also increased 1,000 fold in OV90P cells compare to the OV90 cells. For the other SH-4-54 ic50 genes analyzed, such as the GAGE family genes, CD96, and VSIG1, the expression levels were increased significantly in various drug resistant cells. In addition, we validated several genes found downregulated in drug resistance. CCL26 was found downregulated more than 200 fold in all three resistant phenotypes compared to drug sensitive cells. RHOU and MAF1 were decreased over 2,000 fold in OV90 P cells.

The other genes analyzed, SPOCK2, RFTN1, PRSS8, MSMB, ECAT11, CDH26, CDH11, CD9, and CD44 were all decreased to various levels in the drug resis tant cells. As further validation, we investigated the protein expres sion levels of selected candidates by immunoblotting. We found PTC-209 HBr ic50 five genes whose protein level changed significantly in the drug resistant cell lines. Consistent with our RT PCR findings, the P glycoprotein, a well studied protein which has been implicated in multi drug resistance, was found elevated in all three drug resistant cell lines, including OV90C, in spite of a relatively small increase in mRNA levels observed in cis platin cell lines. On the other hand, the CCL26, PRSS8, and MSMB proteins were found to be sig nificantly decreased in all three drug resistant cell lines. The SPOCK2 protein was only found decreased in the paclitaxel resistant lines. Pathway analysis of drug resistance In order to gain some insight into the possible mechan isms important in the development of resistance to these drugs, we performed pathway analysis using the genes that were found significantly differentially expressed in each resistance phenotype.