TY - JOUR
KW - Cell Lineage
KW - Cellular imaging
KW - intestinal stem cells
KW - Physiology
KW - RNA sequencing
AU - Kelli F. Johnson
AU - Xiangning Dong
AU - Yu-Hwai Tsai
AU - Angeline Wu
AU - Sydney G. Clark
AU - Abigail Vallie
AU - Sha Huang
AU - Charlie J. Childs
AU - Rachel K. Zwick
AU - Ian Glass
AU - Katherine D. Walton
AU - Ophir D. Klein
AU - Jason R. Spence
AB - The organization of diverse mesenchymal populations during human small intestinal development is critical for tissue architecture and function yet remains poorly defined. Here, to construct a comprehensive, tissue-scale map of the developing human small intestine at single cell resolution, we leveraged single-cell RNA-sequencing data to build a Xenium spatial transcriptomics gene panel covering the cell diversity of the human small intestine. We defined five subpopulations occupying discrete anatomical locations within the lamina propria and submucosa—the subepithelial cells, lamina propria fibroblasts, submucosal fibroblasts, smooth muscle cells and CXCL13+ fibroblasts. Our data establish molecular markers to distinguish these populations in both sequencing and imaging data. We leverage this high-resolution atlas to interrogate cell–cell signalling, benchmark pluripotent stem cell-derived human intestinal organoids and to demonstrate how this resource can incorporate relative spatial organization into tissue analysis, with broad implications for modelling development, regeneration and disease.
BT - Nature Cell Biology
DA - 2026-07-22
DO - 10.1038/s41556-026-02027-2
LA - en
N2 - The organization of diverse mesenchymal populations during human small intestinal development is critical for tissue architecture and function yet remains poorly defined. Here, to construct a comprehensive, tissue-scale map of the developing human small intestine at single cell resolution, we leveraged single-cell RNA-sequencing data to build a Xenium spatial transcriptomics gene panel covering the cell diversity of the human small intestine. We defined five subpopulations occupying discrete anatomical locations within the lamina propria and submucosa—the subepithelial cells, lamina propria fibroblasts, submucosal fibroblasts, smooth muscle cells and CXCL13+ fibroblasts. Our data establish molecular markers to distinguish these populations in both sequencing and imaging data. We leverage this high-resolution atlas to interrogate cell–cell signalling, benchmark pluripotent stem cell-derived human intestinal organoids and to demonstrate how this resource can incorporate relative spatial organization into tissue analysis, with broad implications for modelling development, regeneration and disease.
PY - 2026
SP - 1
EP - 13
T2 - Nature Cell Biology
TI - Mapping mesenchymal diversity in the human small intestine and organoids
UR - https://www.nature.com/articles/s41556-026-02027-2
Y2 - 2026-07-23
SN - 1476-4679
ER -