Stem cells actively suppress regenerative plasticity in human colon

Insights into intestinal stem cell functioning during homeostasis and repair have been predominantly derived from genetic mouse models. This is in stark contrast to the largely unexplored situation in the human gut, where the underlying mechanisms and stimuli that induce regeneration are poorly understood. Here, we developed genetic strategies to characterize fluorescently labelled LGR5+ stem cells in normal human colon organoids. In parallel, we made diphtheria toxin-mediated cell type ablation compatible with human cells, thereby enabling in-depth interrogation of the sequence of events during depletion and reappearance of stem cells. Following LGR5+ stem cell depletion, most of the remaining epithelial cells entered a regenerative state characterized by fetal-like expression programs. Strikingly, this regenerative response was already initiated before stem cell loss, indicative of active communication between functional stem cells and progeny during homeostasis. We identified inactivation of retinoid X receptor (RXR) as a crucial trigger to initiate the regenerative response in colonocytes, with human colon stem cells being the producer of the RXR stimulus retinoic acid. Thus, stem cell-derived retinoic acid actively suppresses the regenerative state in colonocytes, explaining how surviving cells sense stem cell loss.