ArticleCell reports. Medicine2023
Dynamic activity in cis-regulatory elements of leukocytes identifies transcription factor activation and stratifies COVID-19 severity in ICU patients.
Article in Cell reports. Medicine, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT07673250 (Personalized Ventilator Settings for Patients on ECMO), which is not on this map. Cited by 13 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.
Personalized Ventilator Settings for Patients on ECMO (PEEPECMO)
Who cites it
13 citing papers in PubMed, 18 citations in OpenAlex.
- Spatial transcriptomics unveils the in situ cellular and molecular hallmarks of the lung in fatal COVID-19.Nature communications · 2026Article
- Profiling active RNA polymerase II transcription start sites from total RNA by capped small RNA sequencing (csRNA-seq).Nature protocols · 2026Review
- Hyaluronan Ameliorates Viral Pneumonia in Mice and Humans by Inhibiting Transcription Factor E2F1.American journal of respiratory cell and molecular biology · 2026Article
- Network-informed deconvolution of bulk immune gene co-expression reveals single-cell programs and spatial organization.Frontiers in immunology · 2026Article
- Epigenomic landscapes define differential Janus kinases inhibitor sensitivity in IFN-γ-primed human macrophages.iScience · 2025Article
- ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets.Frontiers in bioinformatics · 2025Article
- Article
- Efficient small fragment sequencing of human, cattle, and bison miRNA, small RNA, or csRNA-seq libraries using AVITI.BMC genomics · 2024Article
- Enhancers associated with unstable RNAs are rare in plants.Nature plants · 2024Article
- Article
- Efficient small fragment sequencing of human, cow, and bison miRNA, small RNA or csRNA-seq libraries using AVITI.bioRxiv : the preprint server for biology · 2024Article
- The Role of the Nuclear Factor-Kappa B (NF-κB) Pathway in SARS-CoV-2 Infection.Pathogens (Basel, Switzerland) · 2024Review
- Enhancers associated with unstable RNAs are rare in plants.bioRxiv : the preprint server for biology · 2023Article
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Authors and funding
26 authors at 8 institutions in 1 country.
Funding
Abstract
Transcription factor programs mediating the immune response to coronavirus disease 2019 (COVID-19) are not fully understood. Capturing active transcription initiation from cis-regulatory elements such as enhancers and promoters by capped small RNA sequencing (csRNA-seq), in contrast to capturing steady-state transcripts by conventional RNA-seq, allows unbiased identification of the underlying transcription factor activity and regulatory pathways. Here, we profile transcription initiation in critically ill COVID-19 patients, identifying transcription factor motifs that correlate with clinical lung injury and disease severity. Unbiased clustering reveals distinct subsets of cis-regulatory elements that delineate the cell type, pathway-specific, and combinatorial transcription factor activity. We find evidence of critical roles of regulatory networks, showing that STAT/BCL6 and E2F/MYB regulatory programs from myeloid cell populations are activated in patients with poor disease outcomes and associated with COVID-19 susceptibility genetic variants. More broadly, we demonstrate how capturing acute, disease-mediated changes in transcription initiation can provide insight into the underlying molecular mechanisms and stratify patient disease severity.
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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.