Differentially expressed genes and microRNAs in bladder carcinoma cell line 5637 and T24 detected by RNA sequencing

Bladder carcinoma is a common malignancy with complicated treatment methods due to its heterogeneity. In this study, we focused on two bladder carcinoma cell lines, 5637 and T24, to compare their differences from the transcriptome level. RNA sequencing was used to generate the transcriptome data of the two cell line and the control cell line SV-HUC-1. Differentially expressed genes (DEGs) and differentially expressed microRNAs (miRNAs) of cell line 5637 and T24 were screened. Their annotation and analyses were conducted using gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) to predict their possible functions and pathways involved. Number of DEGs specific in cell line 5637, specific in cell line T24 and in both the cell lines was 880, 1512 and 1412, respectively. Number of differentially expressed miRNAs of the three categories was 7, 20 and 18, respectively. These DEGs and miRNAs participated in different biological processes and pathways, among which some were further verified by qRT-PCR. Interferon-stimulated genes (ISGs), including STAT1, TMEM173 and OAS3, were down-regulated in cell line 5637 compared to SV-HUC-1. NDOR1 and NDUFV1, genes related to mitochondrial metabolism, were up-regulated in cell line T24. miR-4257, miR-6733 and gene WNT9A and WNT10A were down-regulated in both the cell lines. Thus cell line 5637 might have lower chemotherapy resistance while T24 might exhibit abnormal mitochondrial metabolism. These results uncovered major differences between cell line 5637 and T24, which indicated the two cell lines, should be selectively used in bladder carcinoma research.