Evidence map›Paper›PMID 39019149›Full record

ArticleThe Journal of investigative dermatology2025

Integrated Single-Cell Analysis Reveals Spatially and Temporally Dynamic Heterogeneity in Fibroblast States during Wound Healing.

Axel A Almet, Yingzi Liu, Qing Nie, Maksim V Plikus

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The Journal of investigative dermatology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
27citing papers in PubMed, 1 pooled it
–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

27 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  7. Macrophage-Fibroblast Crosstalk Shapes Wound Repair Signaling In Vitro.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026
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  19. Loss of MFAP5 and Its Effect on Skin Homeostasis and Wound Healing.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Axel A AlmetDepartment of Mathematics, University of California, Irvine, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA.
Yingzi LiuDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA.
Qing NieDepartment of Mathematics, University of California, Irvine, Irvine, California, USA; NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA. Electronic address: qnie@uci.edu.
Maksim V PlikusNSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, Irvine, California, USA; Department of Developmental and Cell Biology, University of California, Irvine, Irvine, California, USA; Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, California, USA. Electronic address: plikus@uci.edu.

Funding

UCI P30 Skin Center Systems Biology CoreP30AR075047 · NIAMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI ANDERSEN, BOGI, GANESAN, ANAND K · 2019 to 2025
$5.1M
Multiscale Models of Wound Cell Plasticity for RegenerationU01AR073159 · NIAMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI DAI, XING, NIE, QING · 2018 to 2022
$3.5M
Tissue Size and Precision Control in Growing Hair FolliclesR01AR079150 · NIAMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI Qing Nie, Maksim V Plikus · 2022 to 2026
$2.7M
Leveraging immune-fibroblast interactions for biomaterial induced skin regenerationR01AR079470 · NIAMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI SCUMPIA, PHILIP · 2021 to 2025
$2.6M
Development of tools for analyzing cell-cell communication using spatial transcriptomic dataR01GM152494 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI Zixuan Cang, Qing Nie · 2024 to 2026
$1.0M
NIAMS NIH HHS P30 AR075047NIAMS NIH HHS R01 AR079150NIAMS NIH HHS R01 AR079470NIAMS NIH HHS U01 AR073159NIGMS NIH HHS R01 GM152494
6 · The paper itself

Abstract

Wound healing is a dynamic process over temporal and spatial scales. Key to repair outcomes are fibroblasts; yet, how they modulate healing across time and in different wound regions remains incompletely understood. By integrating single-cell RNA-sequencing datasets of mouse skin and wounds, we infer that fibroblasts are the most transcriptionally dynamic skin-resident cells, evolving during postnatal skin maturation and rapidly after injury toward distinct late scar states. We show that transcriptional dynamics in fibroblasts are largely driven by genes encoding extracellular matrix and signaling factors. Lineage trajectory inference and spatial gene mapping reveal that Prg4-expressing fibroblasts transiently emerge along early wound edges. Within days, they become replaced by long-lasting and likely noninterconverting fibroblast populations, including Col25a1-expressing and Pamr1-expressing fibroblasts that occupy subepidermal and deep scar regions, respectively, where they engage in reciprocal signaling with immune cells. Signaling inference shows that fibroblast-immune crosstalk repeatedly uses some signaling pathways across wound healing time, whereas use of other signaling pathways is time and space limited. Collectively, we uncovered high transcriptional plasticity by wound fibroblasts, with early states transiently forming distinct microniches along wound edges and in the fascia, followed by stable states that stratify scar tissue into molecularly dissimilar upper and lower layers.

Indexed as

CicatrixFibroblastsSkinWound HealingAnimalsDisease Models, AnimalExtracellular MatrixMiceSignal TransductionSingle-Cell AnalysisData integrationFibroblastsScarSingle-cell RNA sequencingWound healing

Identifiers

PMID39019149
PMCPMC12324929

What OpenQuestion holds

Textmetadata
LicenceTDM
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.