TGM2, HMGA2, FXYD3, and LGALS4 genes as biomarkers in acquired oxaliplatin resistance of human colorectal cancer: A systems biology approach

Abstract

Acquired resistance to oxaliplatin is considered as the primary reason for failure in colorectal cancer (CRC) therapy. Identifying the underlying resistance mechanisms may improve CRC treatment. The present study aims to identify the key genes involved in acquired oxaliplatin-resistant in CRC by confirming the oxaliplatin resistance index (OX-RI). To this aim, two public microarray datasets regarding oxaliplatin-resistant CRC cells with different OX-RI, GSE42387, and GSE76092 were downloaded from GEO database to identify differentially expressed genes (DEGs). The results indicated that the OX-RI affects the gene expression pattern significantly. Then, 54 common DEGs in both datasets including 18 up- and 36 down-regulated genes were identified. Protein-protein interaction (PPI) analysis revealed 13 up- (MAGEA6,TGM2,MAGEA4,SCHIP1,ECI2,CD33,AKAP12,MAGEA12,CALD1,WFDC2,VSNL1,HMGA2, andMAGEA2B) and 12 down-regulated (PDZK1IP1,FXYD3,ALDH2,CEACAM6,QPRT,GRB10,TM4SF4,LGALS4,ALDH3A1,USH1C,KCNE3, andCA12) hub genes. In the next step, two novel up-regulated hub genes includingECI2andSCHIP1were identified to be related to oxaliplatin resistance. Functional enrichment and pathway analysis indicated that metabolic pathways, proliferation, and epithelial-mesenchymal transition may play dominant roles in CRC progression and oxaliplatin resistance. In the next procedure, two in vitro oxaliplatin-resistant sub-lines including HCT116/OX-R4.3 and HCT116/OX-R10 cells with OX-IR 3.93 and 10.06 were established, respectively. The results indicated the up-regulation ofTGM2andHMGA2in HCT116/OX-R10 cells with high OX-RI and down-regulation ofFXYD3,LGALS4, andECI2in both cell types. Based on the results,TGM2,HMGA2,FXYD3, andLGALS4genes are related to oxaliplatin-resistant CRC and may serve as novel therapeutic targets.