Transcriptome profiling by RNA sequencing reveals novel targets of Gemini nano curcumin on p53-mutant HT-29 colorectal cancer cells

• Published in: Journal of Genetic Engineering and Biotechnology Vol. 23; no. 4; p. 100548
• Main Authors: Azeez, Hewa Jalal, Karimzadeh, Raheleh, Babaei, Esmaeil
• Format: Journal Article
• Language: English
• Published: Elsevier Inc 01.12.2025
• Subjects: Colorectal cancer; Differentially expressed genes (DEG); Gemini curcumin; Gene ontology; HT-29 cells; RNA sequencing; Gene ontology; RNA sequencing; Gemini curcumin; Differentially expressed genes (DEG); HT-29 cells; Colorectal cancer
• ISSN: 1687-157X
• DOI: 10.1016/j.jgeb.2025.100548

Colorectal cancer is considered as an aggressive tumor with high mortality in the world. It has been shown that Gemini Nano-Curcumin (Gemini-Cur) affects viability of colorectal cancer cells. Nevertheless, the cellular and molecular mechanisms underlying its toxicity are debatable. Here, we planned to untangle the potential novel targets for nanocurcumin on p53-mutant HT-29 cancer cells by employing RNA sequencing. After cultivation, HT-29 cell were incubated with appropriate doses of Gemini-Cur for 24 h. Total RNA was extracted, cDNA library was constructed and sequenced. The DESeq2 tool were employed to normalize reads and detect differentially expressed genes (DEGs). The enrichR tool was employed to do Gene Ontology (GO) & identify biological processes (BP), cellular components (CC) and molecular functions (MF) that are impacted in the condition. The PPI network was constructed of 1200 DEGs using STRING, visualized by Cytoacape and analyzed with MCODE. After DEGs screening, 1309 genes between untreated and treated cancer cells were obtained including 479 upregulated with P-value < 0.05 & log2 FC > 1) as well as 63 downregulated genes with P-value < 0.05 and log2 FC < −1). Then, DEGs were assigned to 207 GO terms including numerous cellular pathways such as endoplasmic reticulum (ER)-related processes. Finally, 542 up and downregulated genes were mapped to 67 reactome pathways. The pathway analysis illustrated that Gemini-Cur modulates numerous pathways including ER stress response- and transporter-related genes. Using MCODE, Three modules were significantly identified with scores ≥ 1 and nodes ≥ 1. Our data reveal that nanocurcumin might affects HT-29 colorectal cancer cells through modulating different pathways such as endoplasmic reticulum response, and transporter-related genes. More studies necessitate to unravel the molecular mechanisms and proteins involved in these pathways that could be considered as novel therapeutic targets in colorectal cancer.