Elucidating early intestinal stem cell response to bacterial infection

Intestinal epithelial cells (IECs) in the small intestine sense and respond to microbial stimuli, maintain barrier integrity, and coordinate immune responses. However, the precise mechanisms by which IEC subsets, particularly Lgr5+ stem cells, detect and combat intracellular pathogens remain incompletely understood. Here, we used GFP-labeled Salmonella enterica to interrogate early epithelial responses by single-cell transcriptomic profiling of infected IECs. Our analysis revealed a robust infection signature dominated by antimicrobial peptide (AMP) gene induction, including defensin family members, specifically in Paneth cells, enterocytes, and stem/progenitor cell populations. Notably, Salmonella selectively targeted Lgr5+ intestinal stem cells at early time points, prompting an ASC-mediated inflammasome activation, essential for clearing infected stem cells and triggering their differentiation toward AMP-secreting lineages. Eliminating compromised stem cells from the pool simultaneously preserves crypt integrity and promotes tissue regeneration.

Mechanistically, ASC-driven inflammasome signalling activated a rapid transcriptional program favouring Paneth- and enterocyte-like phenotypes, reinforcing the epithelial barrier against the invading pathogen. Moreover, we observed that similar molecular signatures were dysregulated in intestinal tissues from patients with inflammatory bowel disease (IBD), underscoring the clinical relevance of this IEC-intrinsic defense pathway.

Our findings propose a novel innate immune mechanism whereby Lgr5+ stem cells harness ASC-mediated inflammasome pathways for epithelial remodelling to curb bacterial infection. This provides insights into how the intestinal epithelium orchestrates host defense while maintaining tissue integrity, offering a novel therapeutic target for conditions involving compromised epithelial barriers, including IBD.