Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution

The intestinal epithelium plays a critical role in health and disease, yet the impact of microenvironmental cues in diseased contexts, such as inflammatory bowel disease (IBD), remains poorly defined. To address this gap, we first benchmarked human colonic organoid injury models against IBD tissue and established a disease-relevant model of inflammation using inflammatory cytokines. Using this system, we built a dictionary of epithelial responses to 79 secreted niche factors at single cell resolution via donor-pooled, multiplexed single cell RNA-sequencing. The comprehensive nature of our atlas allowed us to map relationships between perturbations, infer the function of less characterized ligands, and identify cell type-specific perturbed pathways. Finally, we established the relevance of organoid-derived gene programs by mapping them to single cell and spatial atlases of human IBD tissue. Our resource offers a global view of epithelial responses to microenvironmental cues, offering insights into epithelial homeostasis and repair mechanisms in IBD.