Mapping mesenchymal diversity in the developing human intestine and organoids

Area of Science:

• Developmental Biology
• Gastroenterology
• Single-cell Genomics

Background:

• Mesenchymal cell organization in the developing human intestine is vital but poorly understood.
• Spatiotemporal information on intestinal fibroblasts and stroma is lacking.

Purpose of the Study:

• To create a comprehensive, tissue-scale spatial map of the developing human small intestine.
• To define and characterize mesenchymal populations and their anatomical distribution.
• To establish molecular markers for distinct mesenchymal cell types.

Main Methods:

• Utilized single-cell RNA-sequencing data to design a custom Xenium spatial transcriptomics gene panel.
• Focused analysis on developing mesenchyme populations (fibroblasts/stroma).
• Applied spatial transcriptomics to map cell populations within the lamina propria and submucosa.

Main Results:

• Defined 5 distinct mesenchymal populations: subepithelial cells (SEC), lamina propria fibroblasts (LPF), submucosal fibroblasts (SMF), smooth muscle cells (SMC), and CXCL13+ fibroblasts.
• Revealed dynamic spatial remodeling of fibroblast communities during intestinal development.
• Established molecular markers to differentiate these mesenchymal populations.

Conclusions:

• The study provides a high-resolution spatial atlas of the developing human intestinal mesenchyme.
• This resource enables benchmarking of human intestinal organoids derived from pluripotent stem cells.
• The atlas facilitates spatial dissection of intestinal stromal signaling for modeling development, regeneration, and disease.