Microarray-based detection and expression analysis of new genes associated with drug resistance in ovarian cancer cell lines

Abstract

PurposeThe present study is to discover a new genes associated with drug resistance development in ovarian cancer.MethodsWe used microarray analysis to determine alterations in the level of expression of genes in cisplatin- (CisPt), doxorubicin- (Dox), topotecan- (Top), and paclitaxel- (Pac) resistant variants of W1 and A2780 ovarian cancer cell lines. Immunohistochemistry assay was used to determine protein expression in ovarian cancer patients.ResultsWe observed alterations in the expression of 22 genes that were common to all three cell lines that were resistant to the same cytostatic drug. The level of expression of 13 genes was upregulated and that of nine genes was downregulated. In the CisPt-resistant cell line, we observed downregulated expression of ABCC6, BST2, ERAP2 and MCTP1; in the Pac-resistant cell line, we observe upregulated expression of ABCB1, EPHA7 and RUNDC3B and downregulated expression of LIPG, MCTP1, NSBP1, PCDH9, PTPRK and SEMA3A. The expression levels of three genes, ABCB1, ABCB4 and IFI16, were upregulated in the Dox-resistant cell lines. In the Top-resistant cell lines, we observed increased expression levels of ABCG2, HERC5, IFIH1, MYOT, S100A3, SAMD4A, SPP1 and TGFBI and decreased expression levels of MCTP1 and PTPRK. The expression of EPHA7, IFI16, SPP1 and TGFBI was confirmed at protein level in analyzed ovarian cancer patients..ConclusionsThe expression profiles of the investigated cell lines indicated that new candidate genes are related to the development of resistance to the cytostatic drugs that are used in first- and second-line chemotherapy of ovarian cancer.

In vitroevolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells

“…ABCB1 amplifications are associated with clinical resistance to PTX (54). PTX-R4 and R5 showed structural variants on chromosome 1, and PTX-R4 show an amplification event on chromosome 17 that encompassed a variety of ABC transporters (ABCA5, 6,8,9,10). No compelling candidate genes were found in CNVs for PTX-R6.…”

“…Current advancement of DNA microarrays, proteomics technology and RNA-sequencing have contributed to the discovery of drug resistance genes and provided new avenues and potential clues to develop new targeted therapies to overcome the drug resistance (7)(8)(9). Gene expression has been more commonly used to predict resistance associated genes (10), however, gene expression data cannot account for mutations which affect protein activity or genetic heterogeneity among patients.…”

The significance of microRNA genes expression in ovarian cancer cell lines resistant to cytotoxic drugs

“…Differentially expressed miRNAs were used as a query for searching target genes in the following databases: for predicted targets-DIANA, Miranda, PicTar, TargetScan, and for experimentally validated targets-miRTAR, miRwalk [42]. To determine the actual expression value of target genes, mRNA transcriptomic data from our published experiment were used [43][44][45]. Obtained fold change values for mRNA were assigned to target genes data table.…”

“…Targets with expression levels of between 5-and 0.2-fold (up/down regulation between 5 and -5) those of the controls were considered 'not significant (NS)' when the target gene lists were constructed. For analysis of target genes expression we used our microarray data that were published previously [43][44][45]. From target genes analysis we excluded miRNAs expressed only in W1PR2 cell line, because we do not possess mRNA microarray data for this cell line.…”

“…For further analysis we selected genes involved in drug resistance, extracellular matrix and cancer stem cell biology using a following key words in GO Data Base: response to drug, drug transport, extracellular space, extracellular matrix, collagen containing extracellular matrix, stem cell, because previously we described changes in expression of genes from these groups in investigated drug resistance cell lines (43)(44)(45). Using this criteria we did not found targets for the following miRNA: miR-100, miR-10a, miR-143, miR-193a-5p, miR-199a-3p, miR-199b-3p, miR-4269 and miR-99a.…”