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1.
American Journal of Respiratory and Critical Care Medicine ; 205(1), 2022.
Article in English | EMBASE | ID: covidwho-1927902

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.

2.
PubMed; 2020.
Preprint in English | PubMed | ID: ppcovidwho-333583

ABSTRACT

While SARS-CoV-2 infection has pleiotropic and systemic effects in some patients, many others experience milder symptoms. We sought a holistic understanding of the severe/mild distinction in COVID-19 pathology, and its origins. We performed a whole-blood preserving single-cell analysis protocol to integrate contributions from all major cell types including neutrophils, monocytes, platelets, lymphocytes and the contents of serum. Patients with mild COVID-19 disease display a coordinated pattern of interferon-stimulated gene (ISG) expression across every cell population and these cells are systemically absent in patients with severe disease. Severe COVID-19 patients also paradoxically produce very high anti-SARS-CoV-2 antibody titers and have lower viral load as compared to mild disease. Examination of the serum from severe patients demonstrates that they uniquely produce antibodies with multiple patterns of specificity against interferon-stimulated cells and that those antibodies functionally block the production of the mild disease-associated ISG-expressing cells. Overzealous and auto-directed antibody responses pit the immune system against itself in many COVID-19 patients and this defines targets for immunotherapies to allow immune systems to provide viral defense. ONE SENTENCE SUMMARY: In severe COVID-19 patients, the immune system fails to generate cells that define mild disease;antibodies in their serum actively prevents the successful production of those cells.

3.
PubMed; 2021.
Preprint in English | PubMed | ID: ppcovidwho-297038

ABSTRACT

Secondary bacterial infections, including ventilator-associated pneumonia (VAP), lead to worse clinical outcomes and increased mortality following viral respiratory infections. Critically ill patients with coronavirus disease 2019 (COVID-19) face an elevated risk of VAP, although susceptibility varies widely. Because mechanisms underlying VAP predisposition remained unknown, we assessed lower respiratory tract host immune responses and microbiome dynamics in 36 patients, including 28 COVID-19 patients, 15 of whom developed VAP, and eight critically ill controls. We employed a combination of tracheal aspirate bulk and single cell RNA sequencing (scRNA-seq). Two days before VAP onset, a lower respiratory transcriptional signature of bacterial infection was observed, characterized by increased expression of neutrophil degranulation, toll-like receptor and cytokine signaling pathways. When assessed at an earlier time point following endotracheal intubation, more than two weeks prior to VAP onset, we observed a striking early impairment in antibacterial innate and adaptive immune signaling that markedly differed from COVID-19 patients who did not develop VAP. scRNA-seq further demonstrated suppressed immune signaling across monocytes/macrophages, neutrophils and T cells. While viral load did not differ at an early post-intubation timepoint, impaired SARS-CoV-2 clearance and persistent interferon signaling characterized the patients who later developed VAP. Longitudinal metatranscriptomic analysis revealed disruption of lung microbiome community composition in patients who developed VAP, providing a connection between dysregulated immune signaling and outgrowth of opportunistic pathogens. Together, these findings demonstrate that COVID-19 patients who develop VAP have impaired antibacterial immune defense weeks before secondary infection onset. One sentence summary: COVID-19 patients with secondary bacterial pneumonia have impaired immune signaling and lung microbiome changes weeks before onset.

5.
American Journal of Respiratory and Critical Care Medicine ; 203(9), 2021.
Article in English | EMBASE | ID: covidwho-1277339

ABSTRACT

Background: The coronavirus disease 2019 (COVID-19) pandemic has led to a rapid increase in the incidence of acute respiratory distress syndrome (ARDS). The distinct features of pulmonary biology in COVID-19 ARDS compared to other causes of ARDS, including other lower respiratory tract infections (LRTIs), are not well understood. Methods: Tracheal aspirates (TA) and plasma were collected within five days of intubation from mechanically ventilated adults admitted to one of two academic medical centers. ARDS and LRTI diagnoses and were verified by study physicians. Subjects were excluded if they received immunosuppression. TA from subjects with COVID-ARDS was compared to gene expression in TA from subjects with other causes of ARDS (OtherARDS) or mechanically ventilated control subjects without evidence of pulmonary pathology (NoARDS). Plasma concentrations of IL-6, IL-8, and protein C also were compared between these groups. Upstream regulator and pathway analysis was performed on significantly differentially expressed genes with Ingenuity Pathway Analysis (IPA). Subgroup analyses were performed to compare gene expression in COVID to ARDS associated with other viral LRTIs and bacterial LRTIs. The association of interferon-stimulated gene expression with SARS-CoV2 viral load was compared to the same association in nasopharyngeal swabs in a cohort of subjects with mild SARS-CoV2. Results: TA sequencing was available from 15 subjects with COVID, 32 subjects with other causes of ARDS (OtherARDS), and 5 mechanically ventilated subjects without evidence of pulmonary pathology (NoARDS). 696 genes were differentially expressed between COVID and OtherARDS (Figure 1A). IL-6, IL-8, B-cell receptor, and hypoxia inducible factor-1a signaling were attenuated in COVID compared to OtherARDS. Peroxisome proliferator-activated receptor (PPAR) and PTEN signaling were higher in COVID compared to OtherARDS (Figure 1B). Plasma levels of IL-6, IL-8, and protein C were not significantly different between COVID and OtherARDS. In subgroup analyses, IL-8 signaling was higher in COVID compared to viral LRTI, but lower than bacterial LRTI. Type I/III interferon was higher in COVID compared to bacterial ARDS, but lower compared to viral ARDS (Figure 1C). Compared to nasopharyngeal swabs from subjects with mild COVID-19, expression of several interferon stimulated genes was less strongly correlated with SARS-CoV2 viral load in TA (Figure 1D). IPA identified several candidate medications to treat COVID-19, including dexamethasone, G-CSF, and etanercept. Conclusions: TA sequencing identifies unique features of the host response in COVID-19. These differentially expressed pathways may represent potential therapeutic targets. An impaired interferon response in the lung may increase susceptibility to severe SARS-COV2.

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