Bioinformatics analysis identified TCP1 and NOTCH1 as potential target molecules to overcome 5-fluorouracil resistance in cholangiocarcinoma.

Background: Late diagnosis and chemotherapy resistance, particularly to 5-fluorouracil (5-FU), contribute to the low survival rate in cholangiocarcinoma (CCA) patients. Identifying relevant genes and pathways, as well as novel targeted molecules, is crucial to overcoming 5-FU resistance and improving treatment outcomes for CCA patients.

Objectives: This study aimed to determine the potential molecules associated with 5-FU resistance in CCA cells.

Material and methods: Transcriptomic datasets from 4 stable 5-FU-resistant cell lines and their corresponding parental lines were retrieved from the Gene Expression Omnibus. A series of bioinformatics analyses were conducted to identify key genes upregulated in 5-FU-resistant cells compared to their parental counterparts. The expression levels of candidate genes identified through bioinformatics analysis were validated in CCA tissues and cell lines.

Results: Differential gene expression, protein-protein interaction, and Hub genes analysis revealed 8 genes that were significantly upregulated in 5-FU resistance cells compared to their parental cells. Six of the 8 genes, including TCP1, RPS6, RPS29, HSPA5, RPS15A, and NOTCH1, were upregulated in patient CCA tissues. Using real-time PCR, only the expression levels of NOTCH1 and TCP1 were significantly higher in the 5-FU insensitive CCA cell lines, KKU-213A and KKU-213B, than that of the 5-FU sensitive CCA cell line, KKU-055. A similar result was observed in stable 5-FU-resistant cell lines (KKU-213A-FR and KKU-213B-FR) compared to their parental cells.

Conclusions: The bioinformatic analysis and PCR results revealed that NOTCH1 and TCP1 might be associated with 5-FU resistance and serve as potential molecular targets to enhance 5-FU sensitivity in CCA cells.