Profiling Transcription Initiation in Peripheral Leukocytes Reveals Severity-Associated Cis-Regulatory Elements in Critical COVID-19

Abstract

The contribution of transcription factors (TFs) and gene regulatory programs in the immune response to COVID-19 and their relationship to disease outcome is not fully understood. Analysis of genome-wide changes in transcription at both promoter-proximal and distal cis-regulatory DNA elements, collectively termed the 'active cistrome,' offers an unbiased assessment of TF activity identifying key pathways regulated in homeostasis or disease. Here, we profiled the active cistrome from peripheral leukocytes of critically ill COVID-19 patients to identify major regulatory programs and their dynamics during SARS-CoV-2 associated acute respiratory distress syndrome (ARDS). We identified TF motifs that track the severity of COVID-19 lung injury, disease resolution, and outcome. We used unbiased clustering to reveal distinct cistrome subsets delineating the regulation of pathways, cell types, and the combinatorial activity of TFs. We found critical roles for regulatory networks driven by stimulus and lineage determining TFs, showing that STAT and E2F/MYB regulatory programs targeting myeloid cells are activated in patients with poor disease outcomes and associated with single nucleotide genetic variants implicated in COVID-19 susceptibility. Integration with single-cell RNA-seq found that STAT and E2F/MYB activation converged in specific neutrophils subset found in patients with severe disease. Collectively we demonstrate that cistrome analysis facilitates insight into disease mechanisms and provides an unbiased approach to evaluate global changes in transcription factor activity and stratify patient disease severity.

Delineating COVID-19 immunological features using single-cell RNA sequencing

“…19 Lam et al stratified patients by measuring lung injury with a modified Murray score that assigns a score between 0 and 4 based on five criteria. 20 Lee et al used NEWS standard to stratify the disease status and found that type I interferons (IFNs) exacerbate inflammation in severe infections. 9 Since the classification systems from the WHO and NHCC have similar guidelines, we expect the results to be comparable between similar infection severities.…”

Pharmacological inhibition of bromodomain and extra-terminal proteins induces an NRF-2-mediated antiviral state that is subverted by SARS-CoV-2 infection

“…For this purpose, we performed global TF activity profiling using the bulk RNA-seq dataset, which was collected in parallel with ATAC-seq data to identify TFs with significantly regulated gene module scores across our experimental groups. SARS-CoV-2 infection of Calu-3 cells induced activity of the inflammatory TF families (STATs, IRFs, and NFκB-1) ( Fig 6A ), whose signalling is associated with severe COVID-19 cases [ 63 ]. JQ-1 treatment in the presence of SARS-CoV-2 infection suppressed the activity of these inflammatory TF families, suggesting an anti-inflammatory effect of JQ-1 ( Fig 6A ).…”

Pharmacological inhibition of bromodomain and extra-terminal proteins induces NRF-2-mediated inhibition of SARS-CoV-2 replication and is subject to viral antagonism

“…SARS-CoV-2 infection of Calu-3 cells induced activity of the inflammatory TF families (STATs, IRFs, and NFκB-1) (Fig. 6A), whose signalling is associated with severe COVID-19 cases (Lam et al, 2021). JQ-1 treatment in the presence of SARS-CoV-2 infection suppressed the activity of these inflammatory TF families, suggesting an anti-inflammatory effect of JQ-1 (Fig.…”

“…Irrespective of the infection status, JQ-1 treatment suppressed activity of the TF families that regulate cell cycle and proliferation (E2F & MYB), whose synergistic signalling is associated with severe lung injury in COVID-19 cases (Lam et al, 2021). This is in line with JQ-1-mediated dysregulation of cell cycle-regulating genes (Fig.…”