# Anatomic and functional characterization of the intestinal crypt-villus niche

> **NIH NIH U01** · DANA-FARBER CANCER INST · 2021 · $419,650

## Abstract

Project Description
 Intestinal epithelial integrity, turnover, and function require signals from the underlying mesenchyme.
The new focus of the Intestinal Stem Cell Consortium (ISCC) of the NIDDK and NIAID is to investigate in
depth the mesenchymal cells that provide crucial support, their organization within the tissue, and their
molecular signatures, including essential secreted factors. The PI has been a member of the Consortium
for the last 4 years and this application is made in response to RFA-DK-18-507, a Limited Competition to
renew the ISCC Research Centers. Although recent progress in the field implicates various cell populations
(CD34+, Foxl1+, PDGFRA+, Gli1+) as key niche elements, their precise identities, overlap, and contributions
remain uncertain. By integrated consideration of high-resolution whole-mount confocal microscopy and
ensemble and single-cell (sc) RNA-seq analysis of well-defined cell populations isolated by flow cytometry,
we have identified three distinct mesenchymal cell types as leading candidates for essential niche
functions. Over the last 2 years, our sharing of data on these telocytes and two distinct (anatomic and
molecular) PDGFRAlo cell populations has stimulated one important stream of investigation in several ISCC
laboratories. Building on this experience and community, and following productive completion of all Aims
from the current award period, we propose three lines of investigation. Specific Aim 1 will generate
detailed molecular, anatomic, and functional maps of mouse stromal cell populations, with three purposes:
(a) to identify the sources of Wnt, BMP, EGF, and other key mesenchymal signals at high spatial
resolution, (b) to establish robust and reproducible culture conditions for selected important mesenchymal
cell types, and (c) to inform identification and validation of the corresponding functional human cell
populations. These studies consider the whole small intestine as a unit, and Aim 2 will advance purpose
(c) further by considering each gut region (duodenum, jejunum, ileum, and ascending and descending
colon) separately. Both Aims will integrate high-resolution anatomic and molecular analyses to generate
accurate 3D maps, superimposed with assessments of mesenchymal cell functions conducted in
collaboration with other ISCC groups. Aim 3 addresses an urgent need in the field and the specific RFA
call to generate new Cre-driver and fluorescent reporter mice. Based on extensive molecular profiling in
Aims 1 and 2, we will identify novel cell type-specific loci and use CRISPR/Cas9 editing to insert reporter
constructs in up to 3 such loci. Each Aim involves extensive collaboration with ISCC laboratories under the
umbrella of a comprehensive Collaborative Management Plan. In addition, we will contribute and adopt
standardized protocols and share data, protocols, reagents, and mouse strains with ISCC investigators.

## Key facts

- **NIH application ID:** 10237318
- **Project number:** 5U01DK103152-08
- **Recipient organization:** DANA-FARBER CANCER INST
- **Principal Investigator:** Ramesh A Shivdasani
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $419,650
- **Award type:** 5
- **Project period:** 2014-09-01 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10237318

## Citation

> US National Institutes of Health, RePORTER application 10237318, Anatomic and functional characterization of the intestinal crypt-villus niche (5U01DK103152-08). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10237318. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*