Gene expression profiles of intestinal organoids under collagen/Matrigel culture and 5-fluorouracil treatment in human

In this study, we examined how 5-fluorouracil (5-FU) treatment modulates transcriptional programs in human intestinal organoids cultured in Matrigel or collagen matrices. By comparing Matrigel-embedded and collagen-embedded organoids under control and 5-FU–treated conditions, we identified ECM-dependent and treatment-specific gene expression changes associated with cellular stress responses, epithelial regeneration, and matrix-driven phenotypic differences. Overall design: To evaluate how extracellular matrix (ECM) environments influence chemotherapeutic stress responses, organoids in each ECM condition were either left untreated (CTRL) or treated with 5-fluorouracil (5-FU). This generated a 2 × 2 factorial design comprising four experimental groups: MG_Control, MG_5FU, COL_Control, and COL_5FU, with three biological replicates per condition (n = 3).