Identifying Clinically Relevant Drug Resistance Genes In Drug-Induced Resistant Cancer Cell Lines

Resistance to chemotherapy is a major problem of cancer treatment. To identify molecular signatures of drug resistance, extensive studies have been done based on transcriptional profiles of drug-resistant cell lines often established by continuously exposing cancer-derived cell lines to drug treatment in vitro over a period of time.Differentially expressed genes(DEGs) between parental and drug–induced resistant cells were frequently regarded as drug resistance genes. However, findings of such studies can be hardly translated into clinical practice. It has been recognized that genes identified from drug–induced resistant cell models may simply represent drug-induced transcriptional changes that may be irrelevant to resistance mechanisms. Therefore, it is necessary to evaluate the clinical relevance of genes identified in cell models.Another problem is that, in microarray or RNA-sequencing experiments that compare two types of cell lines, usually only two or three technical replicates are generated. The Fold change(FC) method is frequently applied to select DEGs in such small-scale cell line experiments. However, genes that are highly expressed in both cells can hardly reach large FCs Moreover, genes with low expression levels in both cell types may reach large FCs owing simply to measurement variations,resulting in false positives. In contrast, the average difference(AD) method can identify genes that are highly expressed in both cells and show large absolute differences, even if the FCs in their expression levels are small. Hence, it is necessary to leverage its value in detecting drug resistance genes in small-scale cell line experiments.In this study, we defined DEGs between pre-chemotherapy colorectal cancer(CRC) tissue samples of non-responders and responders for 5-fluorouracil(5-FU)and oxaliplatin(L-OHP)-based therapy as clinically relevant drug resistance genes(CRG5-FU/L-OHP). Taking CRG5-FU/L-OHP as reference, we evaluated the clinical relevance of several types of genes derived from HCT116 CRC cells with resistance to 5-fluorouracil and oxaliplatin, respectively. The results revealed that(1)DEGs between parental and resistant cells mainly reflect drug treatment response rather than resistance;(2)DEGs between parental and resistant cells, when both were treated with the corresponding drug for a certain time(eg:24 h), were significantly consistent with the CRG5-FU/L-OHP as well as the DEGs between the post-chemotherapy CRC specimens of responders and non-responders;(3)Compared with FC method, AD method identified genes significantly consistent with CRG5-FU/L-OHP were highly expressed in both cells. This study suggests a novel strategy to extract clinically relevant drug resistance genes from both drug-induced resistant cell models and post-chemotherapy cancer tissue specimens.