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Updated: Aug 6, 2026
08:23
Using Human Intestinal Organoids to Understand the Small Intestine Epithelium at the Single Cell Transcriptional Level
Published on: June 28, 2024
Single-Cell Transcriptome Profiles of Foxl1-Lineage Cells Along the Intestinal Crypt-Villus Axis
Amal Gharbi1, Noa Corem1, Sharona Elgavish2
1Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.
Cellular and Molecular Gastroenterology and Hepatology
|July 16, 2026
Summary
This study maps distinct Foxl1-lineage stromal cell populations in the intestine. These cells, identified by their location, exhibit unique signaling roles influencing epithelial cell fate and intestinal homeostasis.
Area of Science:
- Gastroenterology
- Developmental Biology
- Cell Biology
Background:
- Intestinal epithelial cells require stromal signals for fate and function along the crypt-villus axis.
- The precise sources and combinations of these signals remain poorly understood.
Purpose of the Study:
- To generate a detailed atlas of Foxl1-lineage cells along the intestinal crypt-villus axis.
- To characterize the spatial distribution and functional signatures of these subepithelial cell populations.
Main Methods:
- Single-cell RNA sequencing of Foxl1-lineage cells.
- Integration with in situ hybridization, immunofluorescence, and reporter mouse models.
- Spatial mapping along the crypt-villus axis.
Main Results:
- Identification of 4 distinct Foxl1-lineage populations: crypt, villus-base, villus-mid, and villus-tip.
- Segregation into two related pairs with distinct signaling profiles (e.g., Wnts, BMPs, PDGFRA expression).
- Specific functions assigned: regenerative signaling, villus architecture, immune regulation, nutrient sensing.
Conclusions:
- A comprehensive atlas of intestinal Foxl1-lineage stromal cells was created.
- This resource elucidates how diverse stromal populations create signaling niches.
- Provides foundational knowledge for understanding intestinal epithelial homeostasis.
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