ArticleJCI insight2023
Spatial transcriptomic characterization of COVID-19 pneumonitis identifies immune circuits related to tissue injury.
Article in JCI insight, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
What it found
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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.
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Who cites it
28 citing papers in PubMed, 30 citations in OpenAlex.
- Insights Into Spatial Transcriptomics: Exploring Recent Technical Developments and Their Diverse Applications.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Spatial Immune Model of Alveolar Lung Infection (SIMALI) Identifies Structural Determinants of Lung Inflammation.Research square · 2026Article
- Early innate immune signatures correlate with Ad26.COV2.S vaccine durability and protective efficacy.bioRxiv : the preprint server for biology · 2026Article
- Current status and future perspectives on the mechanistic and pathophysiological understanding of long COVID.Communications medicine · 2026Article
- Tissue resident memory T cells populate the human uveal tract.Scientific reports · 2026Article
- Spatiotemporal immune dynamics in lung cancer progression and treatment.Breathe (Sheffield, England) · 2026Review
- Advances in Spatial Transcriptomics for Infectious Disease Research: Insight for Vaccine Development.Vaccines · 2026Review
- Spatial information matters: are traditional imputation methods effective for spatial transcriptomics data?Briefings in bioinformatics · 2026Article
- Multi-omics to study chronic respiratory diseases and viral infections.European respiratory review : an official journal of the European Respiratory Society · 2026Review
- A Human Immuno-Lung Organoid Model to Study Macrophage-Mediated Lung Cell Senescence Upon SARS-CoV-2 Infection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Applications of Spatial Transcriptomics in Veterinary Medicine: A Scoping Review of Research, Diagnostics, and Treatment Strategies.International journal of molecular sciences · 2025Article
- OPG and BAFF as predictive biomarkers of the severity of SARS-CoV-2 infection.Journal of cellular and molecular medicine · 2025Article
- Single-Cell Sequencing Redefines Immune Heterogeneity and Communication Networks in ARDS: Toward Precision Therapeutics.International journal of genomics · 2025Review
- Human vascularized macrophage-islet organoids to model immune-mediated pancreatic β cell pyroptosis upon viral infection.Cell stem cell · 2024Article
- Human Vascularized Macrophage-Islet Organoids to Model Immune-Mediated Pancreatic β cell Pyroptosis upon Viral Infection.bioRxiv : the preprint server for biology · 2024Article
- Compartmentalization of the inflammatory response during bacterial sepsis and severe COVID-19.Journal of intensive medicine · 2024Review
- Spatial Transcriptomics: A Powerful Tool in Disease Understanding and Drug Discovery.Theranostics · 2024Review
- Effects of PGK1 on immunoinfiltration by integrated single-cell and bulk RNA-sequencing analysis in sepsis.Frontiers in immunology · 2024Article
- Single cell spatial analysis reveals inflammatory foci of immature neutrophil and CD8 T cells in COVID-19 lungs.Nature communications · 2023Article
- SARS-CoV-2 niches in human placenta revealed by spatial transcriptomics.Med (New York, N.Y.) · 2023Article
Corrections and comments
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Authors and funding
16 authors at 4 institutions in 2 countries.
Funding
Abstract
Severe lung damage resulting from COVID-19 involves complex interactions between diverse populations of immune and stromal cells. In this study, we used a spatial transcriptomics approach to delineate the cells, pathways, and genes present across the spectrum of histopathological damage in COVID-19-affected lung tissue. We applied correlation network-based approaches to deconvolve gene expression data from 46 areas of interest covering more than 62,000 cells within well-preserved lung samples from 3 patients. Despite substantial interpatient heterogeneity, we discovered evidence for a common immune-cell signaling circuit in areas of severe tissue that involves crosstalk between cytotoxic lymphocytes and pro-inflammatory macrophages. Expression of IFNG by cytotoxic lymphocytes was associated with induction of chemokines, including CXCL9, CXCL10, and CXCL11, which are known to promote the recruitment of CXCR3+ immune cells. The TNF superfamily members BAFF (TNFSF13B) and TRAIL (TNFSF10) were consistently upregulated in the areas with severe tissue damage. We used published spatial and single-cell SARS-CoV-2 data sets to validate our findings in the lung tissue from additional cohorts of patients with COVID-19. The resulting model of severe COVID-19 immune-mediated tissue pathology may inform future therapeutic strategies.
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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.