Differential Transcriptomic Responses to MRQ 74 and MRQ 76 Rice Extracts in HT-29 Cells; Implications for Apoptosis and Cell Cycle Regulation

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, and resistance to conventional chemotherapy necessitates exploration of alternative bioactive compounds. Malaysian fragrant rice varieties MRQ 74 and MRQ 76 have demonstrated cytotoxic and pro-apoptotic effects in HT-29 colorectal adenocarcinoma cells; however, their global molecular mechanisms remain unclear. Transcriptomic profiling was performed using RNA sequencing (RNA-seq) to characterize gene expression changes in HT-29 cells treated with MRQ 74 3UP, MRQ 76 3P, and 5-fluorouracil (5-FU) for 24-h and 48-h. Differentially expressed genes (DEGs) were identified using |log₂FC| ≥ 1 and adjusted p-value ≤ 0.05. Functional enrichment analyses were conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Selected apoptosis- and cell cycle-related genes were validated by qRT-PCR. High-quality sequencing data (>97% clean reads; >94% Q30; >96% mapping rate) confirmed robust transcriptomic profiling. At 24-h, MRQ 74 predominantly activated immune-related pathways, including antigen processing and cytokine signalling, whereas MRQ 76 induced modest replication-associated responses. By 48-h, MRQ 76 demonstrated marked suppression of DNA replication and cell cycle regulatory genes, with significant enrichment of DNA replication and cytokine–cytokine receptor interaction pathways. In contrast, MRQ 74 maintained sustained immunomodulatory and cell adhesion pathway enrichment. 5-FU induced extensive and progressive transcriptional disruption, reflecting broad cytotoxic stress. qRT-PCR validation confirmed concordant expression trends for key apoptotic regulators. Hence, MRQ 74 and MRQ 76 exert distinct, time-dependent molecular effects in HT-29 cells, with MRQ 74 primarily modulating immune-associated pathways and MRQ 76 targeting proliferative machinery. These findings provide transcriptomic evidence supporting the potential of rice-derived bioactive as complementary anticancer agents in CRC.