ArticleThe Journal of experimental medicine2021
Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19.
Article in The Journal of experimental medicine, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers, 2 of them syntheses that pooled it.
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
147 citing papers in PubMed, 2 syntheses or guidelines pooled it, 226 citations in OpenAlex.
- A consensus immune dysregulation framework for sepsis and critical illnesses.Nature medicine · 2025Guideline
- Systemic cytokines drive conserved severity-associated myeloid responses across bacterial and viral infections.Communications biology · 2025Pooled it
- Spleen tyrosine kinase inhibition restores myeloid homeostasis in COVID-19.Science advances · 2023Trial
- PhenoMapR: scalable mapping of sample phenotypes to single-cell, spatial, and bulk transcriptomics data.bioRxiv : the preprint server for biology · 2026Article
- Innate immunity: current understandings and future perspectives.Signal transduction and targeted therapy · 2026Review
- Natural killer (NK) cells with downregulated activating receptors and IL-10 production promote Trypanosoma cruzi T-cell responses in subjects in the Chronic phase of Trypanosoma cruzi infection: An exploratory immunological analysis.PLoS neglected tropical diseases · 2026Article
- Quantitative molecular cartography of emergency myelopoiesis reveals conserved modules of hematopoietic activation.Cell stem cell · 2026Article
- Comparison between a conventional tool and deep learning models for RNA velocity analysis of scRNA-Seq data.Molecular genetics and genomics : MGG · 2026Article
- Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information.Nucleic acids research · 2026Article
- A comprehensive benchmarking study on computational tools for cross-omics label transfer from single-cell RNA to ATAC data.G3 (Bethesda, Md.) · 2026Article
- Discovery of key regulators in classical monocyte phenotypes linked to COVID-19 severity using single-cell multi-omics sequencing.iScience · 2026Article
- Aryl hydrocarbon receptor activation alters emergency hematopoiesis during influenza A virus infection.Toxicological sciences : an official journal of the Society of Toxicology · 2026Article
- Embeddings from language models are good learners for single-cell data analysis.Patterns (New York, N.Y.) · 2026Article
- Interferon stimulation and NKG2D expression drive enhanced natural killer cell antibody-dependent cellular cytotoxicity against viral infections.Journal of leukocyte biology · 2026Article
- Exploring phenotype-related single-cells through attention-enhanced representation learning.Genome medicine · 2026Article
- Integrated humoral and inflammatory signatures predict outcomes in severe COVID-19: a 14-day longitudinal analysis.Clinical & translational immunology · 2026Article
- Interferon-mediated NK cell activation increases cytolytic activity against T follicular helper cells and limits antibody response to SARS-CoV-2.Nature immunology · 2025Article
- Bone marrow-derived emergency monopoiesis drives brain-lung axis injury after traumatic brain injury via IL-1.Journal of neuroinflammation · 2025Article
- Single-Cell Transcriptomics Identifies Novel Prognostic Signatures in HNSCC Immunotherapy Response.Cancer science · 2025Article
- Mapping NK cell diversity in response to COVID-19 and mRNA vaccination.Scientific reports · 2025Article
87 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
22 authors at 3 institutions in 1 country.
Funding
Abstract
Our understanding of protective versus pathological immune responses to SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is limited by inadequate profiling of patients at the extremes of the disease severity spectrum. Here, we performed multi-omic single-cell immune profiling of 64 COVID-19 patients across the full range of disease severity, from outpatients with mild disease to fatal cases. Our transcriptomic, epigenomic, and proteomic analyses revealed widespread dysfunction of peripheral innate immunity in severe and fatal COVID-19, including prominent hyperactivation signatures in neutrophils and NK cells. We also identified chromatin accessibility changes at NF-κB binding sites within cytokine gene loci as a potential mechanism for the striking lack of pro-inflammatory cytokine production observed in monocytes in severe and fatal COVID-19. We further demonstrated that emergency myelopoiesis is a prominent feature of fatal COVID-19. Collectively, our results reveal disease severity-associated immune phenotypes in COVID-19 and identify pathogenesis-associated pathways that are potential targets for therapeutic intervention.
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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 Socratic graph.