ABSTRACT
Introduction: Dexamethasone decreases mortality in patients with severe COVID-19. The effects of dexamethasone on inflammation and repair in patients with severe COVID-19 are not well understood. We integrated tracheal aspirate (TA) and peripheral blood bulk/single-cell RNA sequencing to study the effect of dexamethasone on patients with COVID-19 ARDS. Methods: We studied selected patients from a cohort of adults with COVID-19 admitted to three hospitals in San Francisco, California from April 2020 to February 2021. Immunosuppression was not used to treat COVID-19 ARDS at these hospitals prior to July 2020, but was routinely used in these patients after this date. For this analysis, we included patients who were mechanically ventilated for COVID-19 ARDS for whom sequencing samples were available within four days of intubation. We excluded patients who received steroids prior to July 2020, subjects who received immunosuppression other than dexamethasone (e.g., tocilizumab) prior to sample collection, and chronically immunosuppressed subjects. We compared bulk RNASeq from TA and single cell RNASeq from TA and whole blood from subjects who received dexamethasone to subjects who did not receive dexamethasone. In addition, we studied the effect of dexamethasone on peripheral blood cytokine concentrations to confirm the effects of observed changes in gene expression. Results: TA bulk RNASeq was available from 20 subjects (six dexamethasone, 14 non-dexamethasone). There was no significant difference in age, sex, smoking, or BMI between groups. After correcting for multiple comparisons, 947 genes were differentially expressed in TA from subjects who received dexamethasone. Ingenuity Pathway Analysis predicted decreased activation of interferon, JAK/STAT, and NLRP12 signaling in subjects who received dexamethasone (Figure 1A). TA scRNASeq samples were available from ten dexamethasone-treated subjects and nine non-dexamethasone subjects. Whole blood scRNAseq samples were available for seven dexamethasone and eight non-dexamethasone subjects (Figure 1B). Eight subjects (three treated with dexamethasone) had both TA and whole blood scRNAseq samples available for analysis. Dexamethasone had distinct effects on the proportions of immune cells in tracheal aspirates and whole blood (Figure 1C). In 36 dexamethasone vs 42 non-dexamethasone subjects, treatment with dexamethasone was associated with significantly increased concentrations of IL-10 and decreased concentrations of IL-6 (Figure 1D). Conclusions: Dexamethasone decreases pro-inflammatory gene expression in the respiratory tract and peripheral blood of patients with COVID-19 ARDS. The effect of dexamethasone on specific cell populations may be distinct in the respiratory tract and peripheral blood.
ABSTRACT
Rationale: SARS-CoV-2, the virus that causes COVID-19, exhibits an ACE2-dependent airway epithelial tropism, and exploits host cell proteins to replicate and evade detection. The impact of asthma on COVID-19 susceptibility and severity is unclear. We sought to discover how genes encoding SARS-CoV-2-associated host proteins are expressed in primary human bronchial epithelial cells (HBECs), and how these genes are regulated by cytokines important in asthma. Methods: We compiled a list of 342 SARS-CoV-2-associated genes. We cultured primary HBECs at air-liquid interface in the absence of cytokine, or with interleukin (IL)-13, IL-17, interferon (IFN)-α, or IFN-γ. We used bulk RNA-seq and single cell RNA-sequencing to identify changes in gene expression. We correlated cytokine-regulated changes in SARS-CoV-2-associated transcripts on cytokine exposure in vitro with gene expression changes in transcriptomic profiling datasets derived from individuals with mild-to-moderate asthma and chronic obstructive pulmonary disease (COPD). Results: Transcripts encoding 332 of 342 (97%) SARS-CoV-2-associated proteins were detected in HBECs (≥1 RPM in 50% samples);85 (26%) were regulated by at least one cytokine (>1.5-fold change, FDR < 0.05). 21 and 19 of the 41 IL-13 responsive, SARS-CoV-2-associated genes identified in HBECs correlated with type 2 inflammatory gene signature scores in transcriptomic profiling datasets derived from individuals with mild-to-moderate asthma and COPD (p < 0.05);few IL-17 or interferon-responsive genes were correlated with their respective signatures in either dataset. Single cell RNA-sequencing revealed that 143 of the 332 (43%) SARS-CoV-2-associated transcripts detected in HBECs were differentially expressed between cell types (FDR < 0.05). 11 SARS-CoV-2-associated genes were modulated by IL-13 in a cell type-specific manner (>1.25-fold change, FDR < 0.05). Conclusions: Many genes encoding proteins associated with SARS-CoV-2 infection are expressed in HBECs, with substantial differences among cell subsets. IL-13 induces extensive changes in the expression of SARS-CoV-2-related genes that correlated with a measure of type-2 inflammation in vivo, providing a plausible basis for differences in outcome of COVID-19 in individuals with asthma.