Bacterial serine protease EspP induces differentiation and expansion of enteroendocrine cells in human colonoids

EspP is a potent serine protease that functions as a cytotoxin and is secreted by enterohemorrhagic Escherichia coli (EHEC). This bacterial toxin can cause significant colonic epithelial damage and mimic the pathophysiology of EHEC infection on human colonic organoids. However, transcriptomic changes within the intestinal epithelial cells and impacts on cell proliferation and differentiation are largely unknown. Here, using human colonic organoids, we defined the molecular and cellular changes that occur in response to acute EspP exposure, independent of microbiota, stroma, and immune cells. We performed droplet-based single cell RNA-sequencing to determine changes in epithelial cell lineages in response to EspP and demonstrated that there is a disruption in proliferation and a preferential differentiation of enteroendocrine cells (EECs). Higher resolution clustering revealed that the de novo EECs were primarily enterochromaffin or EEC progenitors. Interestingly, EECs induced from EspP treatment displayed an immune profile, expressing cytokines and chemokines associated with macrophage or neutrophil recruitment. These findings demonstrate that EspP, a potent EHEC cytotoxin, stimulates transcriptomic changes previously attributed to the whole bug infection and highlights the significance of crypts-based proliferative cells and secretory cell differentiation as major colonic responses to bacterial pathogens.