Evidence map›Paper›PMID 40777494›Full record

ArticlebioRxiv : the preprint server for biology2025

Mapping mesenchymal diversity in the developing human intestine and organoids.

Kelli F Johnson, Xiangning Dong, Yu-Hwai Tsai, Angeline Wu, Sydney G Clark, Sha Huang, Rachel K Zwick, Ian Glass, Katherine D Walton, Ophir D Klein and 1 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Kelli F JohnsonDepartment of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.ORCID 0000-0002-2407-2039
Xiangning DongDepartment of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
Yu-Hwai TsaiDepartment of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
Angeline WuDepartment of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
Sydney G ClarkDepartment of Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
Sha HuangDepartment of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
Rachel K ZwickDepartment of Cell Biology, NYU Grossman School of Medicine, New York, NY, USA; Regenerative Medicine Institute, NYU Grossman School of Medicine, New York, NY, USA.
Ian GlassDepartment of Pediatrics, Genetic Medicine, University of Washington, Seattle, WA 98195, USA.
Katherine D WaltonDepartment of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
Ophir D KleinProgram in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA, USA.ORCID 0000-0002-6254-7082
Jason R SpenceDepartment of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.ORCID 0000-0001-7869-3992

Funding

XenograftP30CA046592 · NCI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Alexey I Nesvizhskii · 1988 to 2026
$178.2M
University of Michigan Center for Gastrointestinal ResearchP30DK034933 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI OMARY, BISHR · 1986 to 2021
$22.5M
LABORATORY OF DEVELOPMENTAL BIOLOGYR24HD000836 · NICHD · UNIVERSITY OF WASHINGTON · PI Ian Amos Glass · 1995 to 2026
$16.9M
Niche support of human intestinal stem cellsU01DK103141 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI SPENCE, JASON · 2014 to 2023
$3.9M
Mechanisms of Hedgehog Regulation of Intestinal Villus MorphogenesisR01DK121166 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI WALTON, KATHERINE DEMPSEY · 2019 to 2023
$1.8M
Human iPSC intestine mimetics with integrated mesenchymal, endothelial and enteric nervous tissueR01DK137806 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Jason Spence · 2024 to 2026
$1.5M
Interrogating sub-epithelial cell heterogeneity in the developing human intestinal stem cell nicheF32DK138694 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Kelli Johnson · 2024 to 2026
$234k
NCI NIH HHS P30 CA046592NICHD NIH HHS R24 HD000836NIDDK NIH HHS F32 DK138694NIDDK NIH HHS P30 DK034933NIDDK NIH HHS R01 DK121166NIDDK NIH HHS R01 DK137806NIDDK NIH HHS U01 DK103141
6 · The paper itself

Abstract

The organization of diverse mesenchymal populations during human intestinal development is critical for tissue architecture and function yet remains poorly defined. To construct a comprehensive, tissue-scale map of the developing human small intestine, we leveraged single-cell RNA-sequencing data to build a custom Xenium spatial transcriptomics gene panel covering the diversity of cell types in the human intestine. Analysis was focused on the developing mesenchyme populations (also referred to as fibroblasts or stroma) given the lack of spatiotemporal information about these cell populations. We defined 5 broad mesenchymal populations occupying discrete anatomical locations within the lamina propria and submucosa - the subepithelial cells (SEC), lamina propria fibroblasts (LPF), submucosal fibroblasts (SMF), smooth muscle cells (SMC), and

Indexed as

developmentfibroblasthumanintestinemesenchymesingle-cell sequencingspatial transcriptomicsXenium

Identifiers

PMID40777494
PMCPMC12330706

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.