ArticleNature communications2025
Multimodal spatial transcriptomic characterization of mouse kidney injury and repair.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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.
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.
Who cites it
16 citing papers in PubMed.
- The GPX3-VCAM1 Axis Gates Pro-Fibrotic Tubule Cell Fate in Hyperuricemic Nephropathy.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Beyond cytoskeletal regulation: Rho-associated, coiled-coil-containing protein kinase 2 in kidney inflammation and fibrosis.Histology and histopathology · 2026Review
- Article
- Benchmarking cell type annotation in spatial transcriptomics: resolving cellular hierarchies, biological fidelity, and dynamic cell states.Research square · 2026Article
- CD38-activated macrophages drive age-related placental senescence by depleting NADNature communications · 2026Article
- Shared mechanisms of organ fibrosis.JCI insight · 2026Review
- Benchmarking cell type annotation in spatial transcriptomics: resolving cellular hierarchies, biological fidelity, and dynamic cell states.bioRxiv : the preprint server for biology · 2026Article
- Analysis of changes in glomerular lesions in children diagnosed with IgA nephropathy following immunosuppressive therapy.BMC nephrology · 2026Article
- Stem cell therapies to modulate harmful immune responses in kidney disease: progress toward clinical validation.Stem cells (Dayton, Ohio) · 2026Review
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- Dose-Dependent and Non-Autonomous Signaling in CAKUT: A Lineage-Specific Framework from Conditional Knockout Studies.Biomolecules · 2026Review
- A Multimodal Imaging Pipeline for the Discovery of Molecular Markers of Cellular Neighborhoods.bioRxiv : the preprint server for biology · 2026Article
- Uric acid-associated mechanisms of coronary artery calcification in diabetic kidney disease: evidence, hypotheses, and translational perspectives.Frontiers in cardiovascular medicine · 2026Review
- Spatial AI in cancer: mapping immune evasion topology through multi-modal omics and deep learning.Frontiers in oncology · 2026Review
- Mapping disease critical spatially variable gene programs by integrating spatial transcriptomics with human genetics.bioRxiv : the preprint server for biology · 2025Article
- Single-Cell and Spatial Transcriptomics in Renal Injury and Fibrosis Research.Kidney diseases (Basel, Switzerland)Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
The transition from acute kidney injury to chronic kidney disease is characterized by significant changes in the cellular composition and molecular interactions within the kidney. Utilizing high-resolution Xenium and whole transcriptome Visium spatial transcriptomics platforms, we analyze over a million cells on 12 male mouse kidneys across six stages of renal injury and repair. We define and validate 20 major kidney cell populations and delineate distinct cellular neighborhoods through this multimodal spatial analysis. We further reveal a specific fibro-inflammatory niche enriched in failed-repair proximal tubule cells, fibroblasts, and immune cells, with conserved neighborhood gene signatures across mouse and human. Within this niche, we predict Runx2 as a key upstream regulator, along with platelet-derived growth factor and integrin beta-2 signaling pathways shaping the fibrogenic microenvironment. Altogether, our study provides deep insights into the cellular and molecular dynamics during kidney injury and repair and establishes a comprehensive multimodal analytical framework applicable to other spatial omics studies.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.