Gnai1+ stromal cells regulate intestinal goblet and Paneth cell differentiation through c-Jun signaling

Combining single-cell and spatial transcriptomics for mapping different intestinal segments is still relatively absented, and the subtypes of intestinal stromal cells and their downstream signling also remain obscure. Our study provides a comprehensive view of 18 identified cell types across five mouse intestinal segments using single-cell RNA sequencing (scRNA-seq). Integrating scRNA-seq with spatial transcriptomics reveals gene profiles along both segmental and crypt-villus spatial dimensions, including cell characteristics, interactions, signaling networks, extracellular matrix contributions, and functional coordination. Not only the different subtypes of intestinal immune cells were analyzed, but also a subtype of Pdgfra-high stromal cells, Gnai1+ stromal cells, was identified. These cells can support intestinal morphology and regulate the activities of goblet cells, Paneth cells, and intestinal stem cells via the activation of c-Jun and Wnt signaling. Thus, we have compiled a publicly available single-cell and spatial transcriptomics resource covering five intestinal segments to facilitate further research, particularly on stromal cell populations and intestinal microenvironment homeostasis.