RNA Sequencing in COVID-19 patients identifies neutrophil activation biomarkers as a promising diagnostic platform for infections

Abstract

Infection with the SARS-CoV2 virus can vary from asymptomatic, or flu-like with moderate disease, up to critically severe. Severe disease, termed COVID-19, involves acute respiratory deterioration that is frequently fatal. To understand the highly variable presentation, and identify biomarkers for disease severity, blood RNA from COVID-19 patient in an intensive care unit was analyzed by whole transcriptome RNA sequencing. Both SARS-CoV2 infection and the severity of COVID-19 syndrome were associated with up to 25-fold increased expression of neutrophil-related transcripts, such as neutrophil defensin 1 (DEFA1), and 3-5-fold reductions in T cell related transcripts such as the T cell receptor (TCR). The DEFA1 RNA level detected SARS-CoV2 viremia with 95.5% sensitivity, when viremia was measured by ddPCR of whole blood RNA. Purified CD15+ neutrophils from COVID-19 patients were increased in abundance and showed striking increases in nuclear DNA staining by DAPI. Concurrently, they showed >10-fold higher elastase activity than normal controls, and correcting for their increased abundance, still showed 5-fold higher elastase activity per cell. Despite higher CD15+ neutrophil elastase activity, elastase activity was extremely low in plasma from the same patients. Collectively, the data supports the model that increased neutrophil and decreased T cell activity is associated with increased COVID-19 severity, and suggests that blood DEFA1 RNA levels and neutrophil elastase activity, both involved in neutrophil extracellular traps (NETs), may be informative biomarkers of host immune activity after viral infection.

Human genetic variants associated with COVID-19 severity are enriched in immune and epithelium regulatory networks

“…CCR5 was downstream TGs in this regulatory network, and it encoded a protein on the surface of white blood cells that is involved in the immune system 29 . We found that 2 TGs (CCR5, CXCR6) of the 15 immune TGs were also differentially expressed in blood samples of fatal COVID-19 patients 30 ( 𝑃 ≤ 0.014 ), which supported that our reconstructed sub-regulatory networks of immune cells were significantly associated with severity of COVID-19. In COVID-19 severity associated epithelium regulatory network, there were totally 16 TFs, 24 REs and 10 TGs associated with 42 SNPs (Figure 2B).…”

Human Genetic Variants Associated with COVID-19 Severity are Enriched in Immune and Epithelium Regulatory Networks

“…C–C Motif Chemokine Receptor 5 ( CCR5 ) was one of the downstream TGs in this regulatory network, and it encoded a protein on the surface of white blood cells that are involved in the immune system (Jiao et al 2019 ). We found that two TGs ( CCR5 and C-X-C Motif Chemokine Receptor 6 ( CXCR6 )) of the 15 immune TGs were also differentially expressed in blood samples of fatal COVID-19 patients (Wargodsky et al 2022 ) ( ), which proved that our reconstructed regulatory networks of immune cells were significantly associated with severity of COVID-19. In the COVID-19 severity-associated regulatory network in epithelium cells, there were 16 TFs, 24 REs, and 10 TGs that were associated with 42 SNPs (Fig.…”

Assessment of plasma Catestatin in COVID-19 reveals a hitherto unknown inflammatory activity with impact on morbidity-mortality

“…This includes an imbalanced innate host response to the SARS-CoV-2 with an aberrant activation of PMNs ( 23 ), and with unusually high release of pro-inflammatory cytokines ( 24 ). A recently reported comparison of circulatory levels of neutrophils secretory proteins showed that defensin DEFA1 level is higher in severe than in mild COVID patients ( 25 , 26 ). Similar data were published for the antimicrobial peptide LL-37 ( 26 ).…”

“…A recently reported comparison of circulatory levels of neutrophils secretory proteins showed that defensin DEFA1 level is higher in severe than in mild COVID patients ( 25 , 26 ). Similar data were published for the antimicrobial peptide LL-37 ( 26 ).…”