ArticleThe European respiratory journal2022
Profiling of lung SARS-CoV-2 and influenza virus infection dissects virus-specific host responses and gene signatures.
Article in The European respiratory journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Cytokine levels associated with favorable clinical outcome in the CAPSID randomized trial of convalescent plasma in patients with severe COVID-19.Frontiers in immunology · 2022Trial
- Single-cell and spatial transcriptomic profiling reveals distinct immune landscapes in murine lungs infected with H1N1 versus H5N1 influenza viruses.Journal of virology · 2026Article
- Review
- Progress in the Application of Machine Learning in the Field of Single-Cell and Spatial Transcriptomics.Genes · 2026Review
- Metatranscriptomics uncovers host immune and microbiome signatures specific to and shared between human metapneumovirus and respiratory syncytial virus infections in children.Virologica Sinica · 2026Article
- IFN alpha inducible protein 27 (IFI27) acts as a positive regulator of PACT-dependent PKR activation after RNA virus infections.PLoS pathogens · 2025Article
- COVID-19 Induces Greater NLRP3 Inflammasome Activation in Obese Patients than Other Chronic Illnesses: A Case-Control Study.International journal of molecular sciences · 2025Article
- Interferon-Stimulated Genes and Immune Metabolites as Broad-Spectrum Biomarkers for Viral Infections.Viruses · 2025Review
- Spatial-Omics Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Integrating spatial omics with routine haematoxylin and eosin in formalin-fixed paraffin-embedded: a step-by-step clinical workflow.F1000Research · 2025Review
- Novel Core Gene Signature Associated with Inflammation-to-Metaplasia Transition in Influenza A Virus-Infected Lungs.International journal of molecular sciences · 2024Article
- Omics-based profiles and biomarkers of respiratory infections: are we there yet?The European respiratory journal · 2024Article
- Article
- DiSignAtlas: an atlas of human and mouse disease signatures based on bulk and single-cell transcriptomics.Nucleic acids research · 2024Article
- Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies placental dysfunction signatures.Clinical & translational immunology · 2024Article
- The IFN-induced protein IFI27 binds MDA5 and counteracts its activation after SARS-CoV-2 infection.Frontiers in cellular and infection microbiology · 2024Article
- Ensemble modeling of SARS-CoV-2 immune dynamics in immunologically naïve rhesus macaques predicts that potent, early innate immune responses drive viral elimination.Frontiers in immunology · 2024Article
- Dual spatially resolved transcriptomics for human host-pathogen colocalization studies in FFPE tissue sections.Genome biology · 2023Article
- Spatial transcriptome atlas reveals pulmonary microstructure-specific COVID-19 gene signatures in cynomolgus macaques.Communications biology · 2023Article
- Spatial transcriptomics: recent developments and insights in respiratory research.Military Medical Research · 2023Review
Corrections and comments
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Authors and funding
21 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged in late 2019 has spread globally, causing a pandemic of respiratory illness designated coronavirus disease 2019 (COVID-19). A better definition of the pulmonary host response to SARS-CoV-2 infection is required to understand viral pathogenesis and to validate putative COVID-19 biomarkers that have been proposed in clinical studies.
methodsHere, we use targeted transcriptomics of formalin-fixed paraffin-embedded tissue using the NanoString GeoMX platform to generate an in-depth picture of the pulmonary transcriptional landscape of COVID-19, pandemic H1N1 influenza and uninfected control patients.
resultsHost transcriptomics showed a significant upregulation of genes associated with inflammation, type I interferon production, coagulation and angiogenesis in the lungs of COVID-19 patients compared to non-infected controls. SARS-CoV-2 was non-uniformly distributed in lungs (emphasising the advantages of spatial transcriptomics) with the areas of high viral load associated with an increased type I interferon response. Once the dominant cell type present in the sample, within patient correlations and patient-patient variation, had been controlled for, only a very limited number of genes were differentially expressed between the lungs of fatal influenza and COVID-19 patients. Strikingly, the interferon-associated gene
conclusionCollectively, these data demonstrate that spatial transcriptomics is a powerful tool to identify novel gene signatures within tissues, offering new insights into the pathogenesis of SARS-COV-2 to aid in patient triage and treatment.
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