DataSheet_1_Severe COVID-19 patients display hyper-activated NK cells and NK cell-platelet aggregates.pdf

COVID-19 is characterised by a broad spectrum of clinical and pathological features. Natural killer (NK) cells play an important role in innate immune responses to viral infections. Here, we analysed the phenotype and activity of NK cells in the blood of COVID-19 patients using flow cytometry, single-cell RNA-sequencing (scRNA-seq), and a cytotoxic killing assay. In the plasma of patients, we quantified the main cytokines and chemokines. Our cohort comprises COVID-19 patients hospitalised in a low-care ward unit (WARD), patients with severe COVID-19 disease symptoms hospitalised in intensive care units (ICU), and post-COVID-19 patients, who were discharged from hospital six weeks earlier. NK cells from hospitalised COVID-19 patients displayed an activated phenotype with substantial differences between WARD and ICU patients and the timing when samples were taken post-onset of symptoms. While NK cells from COVID-19 patients at an early stage of infection showed increased expression of the cytotoxic molecules perforin and granzyme A and B, NK cells from patients at later stages of COVID-19 presented enhanced levels of IFN-γ and TNF-α which were measured ex vivo in the absence of usual in vitro stimulation. These activated NK cells were phenotyped as CD49a+CD69a+CD107a+ cells, and their emergence in patients correlated to the number of neutrophils, and plasma IL-15, a key cytokine in NK cell activation. Despite lower amounts of cytotoxic molecules in NK cells of patients with severe symptoms, majority of COVID-19 patients displayed a normal cytotoxic killing of Raji tumour target cells. In vitro stimulation of patients blood cells by IL-12+IL-18 revealed a defective IFN-γ production in NK cells of ICU patients only, indicative of an exhausted phenotype. ScRNA-seq revealed, predominantly in patients with severe COVID-19 disease symptoms, the emergence of an NK cell subset with a platelet gene signature that we identified by flow and imaging cytometry as aggregates of NK cells with CD42a+CD62P+ activated platelets. Post-COVID-19 patients show slow recovery of NK cell frequencies and phenotype. Our study points to substantial changes in NK cell phenotype during COVID-19 disease and forms a basis to explore the contribution of platelet-NK cell aggregates to antiviral immunity against SARS-CoV-2 and disease pathology.</p

MOESM1 of Potentially modifiable respiratory variables contributing to outcome in ICU patients without ARDS: a secondary analysis of PRoVENT

Additional file 1. List of PRoVENT network collaborators. Table S1 Univariable analysis of factors associated with in-hospital mortality in patients without ARDS receiving mechanical ventilation. Table S2 Analysis of factors associated with ICU mortality in patients without ARDS receiving mechanical ventilation. Table S3 Analysis of factors associated with ICU mortality in patients without ARDS receiving mechanical ventilation considering driving pressure in the model instead of maximum airway pressure. Table S4 Analysis of factors associated with in-hospital mortality in patients without ARDS receiving mechanical ventilation considering driving pressure in the model instead of maximum airway pressure. Table S5 Analysis of factors associated with in-hospital mortality in patients without ARDS receiving mechanical ventilation considering maximum airway pressure in the subset of 343 patients in whom driving pressure could be reliably measured. Table S6 Analysis of factors associated with ICU mortality in patients without ARDS receiving mechanical ventilation considering maximum airway pressure in the subset of 343 patients in whom driving pressure could be reliably measured. Figure S1 Odds ratio of ICU mortality according to increases in one standard deviation of Pmax and in the patients at risk and not at risk of ARDS