Mapping Development of the Human Intestinal Niche at Single-Cell Resolution

Highlights

• Cell diversity in the developing human intestine was interrogated using scRNA-seq

• PGDFRA^HI/F3^HI/DLL1^HI mesenchyme lines the epithelium and expresses NRG1

• EGF, a common in vitro niche factor, is not abundant in the crypt domain

• Compared with EGF, NRG1 increases cellular diversity in enteroid culture

Summary

The human intestinal stem cell niche supports self-renewal and epithelial function, but little is known about its development. We used single-cell mRNA sequencing with in situ validation approaches to interrogate human intestinal development from 7–21 weeks post conception, assigning molecular identities and spatial locations to cells and factors that comprise the niche. Smooth muscle cells of the muscularis mucosa, in close proximity to proliferative crypts, are a source of WNT and RSPONDIN ligands, whereas EGF is expressed far from crypts in the villus epithelium. Instead, an PDGFRA^HI/F3^HI/DLL1^HI mesenchymal population lines the crypt-villus axis and is the source of the epidermal growth factor (EGF) family member NEUREGULIN1 (NRG1). In developing intestine enteroid cultures, NRG1, but not EGF, permitted increased cellular diversity via differentiation of secretory lineages. This work highlights the complexities of intestinal EGF/ERBB signaling and delineates key niche cells and signals of the developing intestine.