Single-Cell Transcriptome Profiles of Foxl1-Lineage Cells Along the Intestinal Crypt-Villus Axis

Intestinal epithelial cells rely on a complex array of stromal signals to determine their fate and function along the crypt-villus axis, but the precise cellular sources and combinations of signals at each position remain poorly defined.

We generated an atlas of Foxl1-lineage cells along the crypt-villus axis using single-cell RNA sequencing integrated with in situ hybridization, immunofluorescence, and reporter mouse models.

We identify 4 spatially distinct Foxl1-lineage subepithelial populations: crypt, villus-base, villus-mid and villus-tip, that segregate into 2 related pairs. Crypt and villus-mid Foxl1-lineage cells share a low platelet-derived growth factor receptor α transcriptional program enriched for canonical Wnts and R-spondins, consistent with regenerative signaling functions. In contrast, villus-base and villus-tip Foxl1-lineage cells are platelet-derived growth factor receptor α-high and express noncanonical Wnt5a and bone morphogenetic protein ligands. Crypt Foxl1-lineage cells are additionally enriched for extracellular matrix proteins and complement components, whereas villus-base Foxl1-lineage cells express contractility-associated genes, suggesting a role in villus architecture. Villus-mid Foxl1-lineage cells display signatures of immune regulation and inflammation, whereas villus-tip Foxl1-lineage cells are specialized for regulation of ribonucleoprotein complexes and nutrient sensing.

This atlas provides a foundational resource for understanding how diverse stromal populations coordinate signaling niches and influence intestinal epithelial homeostasis.