The transcriptomes, intercellular coupling and ontogeny of submucosal stromal lineages in the mouse small intestine
June 21
The submucosal compartment orchestrates essential digestive physiology, yet its stromal composition remains incompletely defined. Through single-cell RNA sequencing of the murine small intestine we resolved two putative secretory-supportive stromal lineages and a previously unrecognized submucosal sensor mesenchymal lineage. Using inducible Cre-lox lineage reporters and adeno-associated–vector delivery of photoconvertible tags, we delineated their three-dimensional architectures and mucosa-directed projections, uncovering extensive gap-junctional coupling among all lineages and an unexpected intimate association with enterochromaffin cells. Further transcriptomic profiling at early postnatal stages, combined with clonal barcoding, revealed that lineage identity arises via an initial binary fate bifurcation at the first post-mitotic division, followed by progressive phenotypic diversification, mirroring the developmental logic previously described for the myenteric mesenchyme. We propose a unified morphogenetic framework for stromal diversification across the gut wall. These data provide comprehensive molecular, developmental and architectural insight into submucosal stromal cells, opening avenues to probe their physiological roles, network dynamics and contribution to intestinal regeneration.