• Developed a novel 3D co-culture model of human small intestinal organoids and MSCs to study regenerative effects in a physiologically relevant setting.
• Busulfan treatment induced transcriptomic and proteomic changes in intestinal organoids, affecting pathways related to epithelial-mesenchymal transition, proliferation, and apoptosis.
• Co-culture with MSCs reversed busulfan-induced changes, restoring proliferation and reducing apoptosis in damaged intestinal epithelium.
• This co-culture system provides a valuable tool for investigating molecular mechanisms of MSC therapy and optimizing MSC use in HSCT patients.