Gene expression of HCT116 colorectal cancer cells after treament with Thymoquinone (TQ), 5-Fluorouracil (5-FU), Combination of the individual compounds (Combi) and the Hybrid compound (SARB).

Cancer stem cells (CSCs) residing in colorectal cancer tissues have tumorigenic capacity and contribute to chemotherapeutic resistance and disease relapse. It is well known that the survival of colorectal CSCs after 5-Fluorouracil (5-FU)-based therapy leads to cancer recurrence. Thus CSCs represent a promising drug target. Here, we designed and synthesized novel hybrid molecules linking 5-FU with the plant-derived compound thymoquinone (TQ) and tested the potential of individual compounds and their combination to eliminate colorectal CSCs. SARB hybrid showed augmented cytotoxicity against colorectal cancer cells. Data obtained via Nanostring nCounter Gene Expression Assay (Pan Cancer Pathway Panel). Nanostring analysis revealed a unique signature of dysregulated gene expression in response to the combination of TQ and 5-FU (Combi) and SARB treatment. Importantly, two principle stem cell regulatory pathways WNT/ß-Catenin and PI3K/AKT were found to be downregulated after hybrid treatment. In this study three biological replicates of each treatment and of the untreated control cells were included. HCT116 cells were treated for 24 h with the individual compounds, the combination of them and with the hybrid compound. We aimed to reveal differences in gene expression between treated and untreated cells as well as the differences on gene expression among different treatments.