Deep Visual Proteomics advances human colon organoid models by revealing a switch to an in vivo-like phenotype upon xenotransplantation

Intestinal epithelial damage predisposes to chronic disorders like inflammatory bowel disease. The organoid model allows cultivation, expansion and analysis of primary intestinal epithelial cells and has been instrumental in studying epithelial behavior in homeostasis and disease. Recent advances in organoid transplantation allow studying human epithelial cell behavior within the intestinal tissue context. However, it remained unclear how organoid transplantation into the colon affects epithelial phenotypes, which is key to assessing the model’s suitability to study human epithelial cells. We employed Deep Visual Proteomics, integrating AI-guided cell classification, laser microdissection, and an improved proteomics pipeline to study the human colon. This created an in-depth cell type-resolved proteomics resource of human intestinal epithelial cells within human tissue, in vitro organoids, and the murine colon post-xenotransplantation. Our findings reveal that in vitro conditions induce a proliferative organoid phenotype, which was reversible upon transplantation and adjustment of organoid culturing conditions.