The gene differential expression analysis of TFE3 rearranged renal cell carcinoma UOK120 cell line after knocking down PRCC-TFE3 fusion gene

TFE3 rearranged renal cell carcinoma (TFE3-rRCC), previously known as Xp11.2 translocation renal cell carcinoma (Xp11.2 tRCC), is a relatively rare type of renal cell carcinoma, accounting for about 1-4% of adult cases. To date, 23 subtypes of TFE3-rRCC have been identified, among which the NONO-TFE3 (UOK109 cell line) and PRCC-TFE3 (UOK120 cell line) fusion are two of the more common subtypes. In the UOK109 and UOK120 cell line, we knocked down the TFE3 fusion gene and attempted to study the important role this fusion gene plays in tumor initiation, progression, and metastasis through various mechanisms by analyzing differential gene expression Overall design: We hypothesize that the TFE3 fusion protein regulates the quantity and function of lysosomes by affecting genes related to the lysosomal pathway. By performing RNA-seq on UOK109 and UOK120 cells before and after interfering with TFE3, we confirmed this hypothesis. Analysis of differentially expressed genes (DEGs) (fold change >1.5, p<0.05) revealed that compared to the shNC group, the shTFE3 group of UOK109 cells enriched 516 upregulated genes and 117 downregulated genes, while the shTFE3 group of UOK120 cells enriched 175 upregulated genes and 338 downregulated genes. Further GO and KEGG enrichment analysis of DEGs showed that genes related to lysosomes and autophagy were affected in both UOK109 and UOK120 cells, and they were all in pathways with downregulated differential expression