ArticleNature communications2025
Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19.
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 15 papers.
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Who cites it
15 citing papers in PubMed.
- Rapid progression of diffuse alveolar damage in ARDS: temporal alignment, composite phenotype, and physiological interpretation.Journal of intensive care · 2026Article
- Agentic AI for Spatial Omics.Immunology and cell biology · 2026Review
- Safety, feasibility, and exploratory biomarker findings of bone marrow-derived mesenchymal stromal cells in hospitalized severe COVID-19: a phase I/II randomized trial.Journal of thoracic disease · 2026Article
- Single-cell and spatial transcriptomic profiling reveals distinct immune landscapes in murine lungs infected with H1N1 versus H5N1 influenza viruses.Journal of virology · 2026Article
- SERPINE1 in ARDS: an emerging regulator of inflammation-coagulation-fibrinolysis crosstalk.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Review
- Spatial Immune Model of Alveolar Lung Infection (SIMALI) Identifies Structural Determinants of Lung Inflammation.Research square · 2026Article
- AI-driven big data analysis and predictive modeling of infectious disease immunity: from correlates to causal, multiscale understanding.Archives of microbiology · 2026Review
- Deciphering immune features and cellular heterogeneity in PRRSV infection via single-cell RNA sequencing.Journal of virology · 2026Article
- Spatial architecture of development and disease.Nature reviews. Genetics · 2026Review
- Dual-function cytokines as modulators of autophagy: reprogramming inflammatory resolution in severe COVID-19.Inflammation research : official journal of the European Histamine Research Society ... [et al.] · 2026Review
- Source-renewing ectopic ApoB-TRL lipolysis in non-resolving ARDS: a testable spatial hypothesis.Frontiers in immunology · 2026Article
- Osteopontin promoted cardiac inflammation through increased interleukin-12 in acute myocarditis.Molecular biomedicine · 2025Article
- Applications of Spatial Transcriptomics in Veterinary Medicine: A Scoping Review of Research, Diagnostics, and Treatment Strategies.International journal of molecular sciences · 2025Article
- Serum osteopontin as a prognostic biomarker in acute exacerbations of chronic obstructive pulmonary disease.Frontiers in immunology · 2025Article
- Single-Cell Sequencing Redefines Immune Heterogeneity and Communication Networks in ARDS: Toward Precision Therapeutics.International journal of genomics · 2025Review
Corrections and comments
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Authors and funding
29 authors.
Funding
Abstract
The most common cause of death due to COVID-19 remains respiratory failure. Yet, our understanding of the precise cellular and molecular changes underlying lung alveolar damage is limited. Here, we integrate single cell transcriptomic data of COVID-19 and donor lung tissue with spatial transcriptomic data stratifying histopathological stages of diffuse alveolar damage. We identify changes in cellular composition across progressive damage, including waves of molecularly distinct macrophages and depletion of epithelial and endothelial populations. Predicted markers of pathological states identify immunoregulatory signatures, including IFN-alpha and metallothionein signatures in early damage, and fibrosis-related collagens in late damage. Furthermore, we predict a fibrinolytic shutdown via endothelial upregulation of SERPINE1/PAI-1. Cell-cell interaction analysis revealed macrophage-derived SPP1/osteopontin signalling as a key regulator during early steps of alveolar damage. These results provide a comprehensive, spatially resolved atlas of alveolar damage progression in COVID-19, highlighting the cellular mechanisms underlying pro-inflammatory and pro-fibrotic pathways in severe disease.
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