Lung Hybrid Neutrophils and Subsequent Extracellular Traps Are Protective In COVID-19-Associated Pulmonary Aspergillosis

Background. COVID-19-associated pulmonary aspergillosis (CAPA) is a severe superinfection with the fungus Aspergillus frequently affecting critically ill COVID-19 patients. Pathophysiological insight, key to improve diagnostic and immunomodulatory therapeutic options, is lacking. Methods. We performed single-cell RNA sequencing (scRNA-seq) on 37 bronchoalveolar lavage (BAL) samples from 37 critically ill COVID-19 patients. Three groups were defined: patients who did not develop aspergillosis (COVID-19-only, n=22), CAPA patients with sampling < 5 days after CAPA diagnosis (early CAPA, n=6) and CAPA patients with sampling 5-11 days after CAPA diagnosis (late CAPA, n=9). All CAPA patients had probable/proven CAPA according to the 2020 ECMM/ISHAM consensus criteria. Additionally, we assessed neutrophil extracellular trap (NET) levels in a separate cohort of 33 biobanked COVID-19-only BAL samples and 24 early CAPA samples. Results. A total of 69008 cells passed quality filtering. CAPA patients had significantly lower BAL neutrophil proportions than COVID-19-only patients, particularly in early CAPA (Fig. 1A). Pseudotime inference revealed two neutrophil trajectories: a regular maturation trajectory, and a trajectory giving rise to "hybrid" neutrophils which express genes encoding proteins with antigen-presenting functions (Fig. 1B). The latter trajectory was dominant in CAPA patients (Fig. 1C). NETosis analyses revealed significantly higher levels of citrullinated histone H3 DNA complexes (H3Cit-DNA) in CAPA patients (Fig. 2A). This explains the low CAPA BAL neutrophil proportions, as neutrophils that underwent NETosis are no longer detected via scRNA-seq. CAPA patients with the lowest H3Cit-DNA levels had significantly decreased survival rates (Fig. 2B). Panel (A): BALF neutrophil proportions as analyzed by single-cell RNA sequencing using the Seurat R package are significantly lower in CAPA patients compared to COVID-19-only patients. Patients with early CAPA have significantly lower BALF neutrophil proportions than patients with late CAPA. Macrophage/monocyte and epithelial cell proportions are reciprocally increased in CAPA patients compared to COVID-19-only patients. P-values shown for differences between the pooled CAPA patients and the COVID-19-only patients. P-values were calculated using a generalized linear model correcting for age, Charlson Comorbidity Index at hospital admission, and administration of corticosteroids (prednisone equivalent dose 20 mg or higher) within 48 hours of BALF sampling. Panel (B): Two trajectories are defined using pseudotime inference calculated using the Slingshot R package: a trajectory dominant in COVID-19-only patients with regular maturation of progenitor neutrophils, and a trajectory dominant in CAPA patients with maturation towards a 'hybrid neutrophil' state, with neutrophils expression genes encoding proteins with functions in antigen presentation. Subsequently, the hybrid neutrophil proportion is significantly higher in CAPA patients compared to COVID-19-only patients, and is significantly higher in patients with early CAPA than those with late CAPA. The mature neutrophil proportion is reciprocally reduced in CAPA patients. P-values shown for differences between the pooled CAPA patients and the COVID-19-only patients. P-values were calculated using a generalized linear model correcting for age, Charlson Comorbidity Index at hospital admission, and administration of corticosteroids (prednisone equivalent dose 20 mg or higher) within 48 hours of BALF sampling. Panel (A): Myeloperoxidase (MPO) DNA levels were analyzed as measure for general NET-formation, while citrullinated histone H3 bound DNA (H3Cit-DNA) levels were analyzed as more specific PAD4-dependent NET-formation, in BALF samples from early CAPA and COVID-19-only patients. A trend towards higher MPO-DNA levels was found in early CAPA patients, while H3Cit-DNA levels were significantly higher in early CAPA compared to COVID-19-only patients. P-values calculated using Mann-Whitney U test. Panel (B): Kaplan-Meier analy is of patients with NETosis analyses, divided in early CAPA and COVID-19-only patients and subdivided according to H3Cit-DNA levels (cut-off at 20000 ng/mL for early CAPA and at 8000 ng/mL for COVID-19-only). Log-rank test was used to compare survival distributions. For the comparison early CAPA (low H3Cit-DNA) versus early CAPA (high H3Cit-DNA), the log-rank p-value was 0.033. Conclusion. CAPA patients display extremely high levels of released NETs in the lower respiratory tract, associated with a shift from the normal neutrophil maturation process towards "hybrid neutrophil" formation, probably upon encountering the fungus. In contrast to high NETosis contributing to mortality in severe COVID-19, CAPA patients likely require these NETs to survive aspergillosis. BAL NET levels hold promise as a tool to guide diagnosis, prognosis and treatment in these patients.

Decreased DNase activity in severe COVID-19 correlates with increased circulating NET burden C. Martens1

Background: COVID-19 represents a perfect storm for release of neutrophil extracellular traps (NETs) and resultant pathology from immunothrombosis. Levels of NETs in circulation are regulated by endogenous plasma DNases, which have been shown to be reduced in various diseases including myocardial infarction and sepsis. We previously reported elevated NET biomarkers in admission samples from our first wave study cohort. Aim(s): To characterize DNase activity and biomarkers of released NETs in the context of COVID-19 immunothrombosis. Method(s): With ethical permission and informed consent, we prospectively collected citrated platelet-poor plasma samples from patients admitted to the COVID ward (55 patients) or intensive care unit (216 patients) from March 2020-December 2021 as part of the COntAGIouS trial at UZ Leuven in Belgium (NCT04327750), with special attention paid to sample preparation and storage to preserve NET fragments and DNase activity. Consecutive samples were obtained within 48 hours of admission, between days 6-8, and upon hospital or ICU discharge. Analysis was batch-performed for MPO, MPO-DNA, PF4, sP-selectin, citrullinated histones, DNase activity, VWF:Ag, and FVIII:Ag levels. Result(s): In ICU patients, MPO, VWF, sP-selectin, and NET biomarkers were elevated throughout hospitalization, peaking at day 6-8 after admission, whereas PF4 and FVIII remained highly elevated through the time of ICU discharge. DNase activity was decreased in admission samples, normalized at day 6-8, and strongly increased at the time of discharge, indicating a potential compensatory mechanism. DNase activity was negatively correlated with MPO-DNA values (r = -0.29, p = 0.0013). sPselectin and NET levels were significantly higher in admission samples for patients who experienced a thrombotic event in the period during hospitalization, including pulmonary embolism, DVT, myocardial infarction, and/or stroke. Conclusion(s): Elevated NET levels and decreased DNase activity in plasma are correlated in severe COVID-19, together with elevated markers of thrombotic risk. Approaches to restore DNase activity in plasma may be beneficial in COVID-19-associated immunothrombosis.

The kallikrein-kinin system in bronchoalveolar lavage fluid from patients with COVID-19

Background : Markers of both inflammation and coagulation are linked to clinical outcome in coronavirus disease 2019 (COVID-19). Binding of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to the angiotensin-converting enzyme 2 receptor, which is involved in kinin breakdown, interferes with the kallikreinkinin pathway. This could result in increased vascular permeability, fluid excess in the lungs and pulmonary edema. Furthermore, the kallikrein-kinin pathway links coagulation and inflammation through its interactions with the contact activation pathway of coagulation via factor XII and with neutrophil extracellular traps (NETs). These insights could help to explain the clinical presentation of COVID-19 pneumonia with pulmonary coagulopathy and the high incidence of thromboembolic complications in COVID-19. Aims : Given the lack of clinical evidence to support this hypothesis, we studied the kallikrein-kinin system in bronchoalveolar lavage (BAL) fluid. Methods : In BAL fluid samples from patients with or without COVID-19, we performed in-depth analyses of kinin peptides (bradykinin, Lys-bradykinin, Lys-bradykinin-(1-8), bradykinin-(1-8), bradykinin-(1-7), and bradykinin-(1-5)) using a liquid chromatography with tandem mass spectrometry assay, along with measurements of plasma and tissue kallikrein hydrolytic activity and myeloperoxidase (MPO)-DNA complexes as a biomarker for NETs. Informed consent and ethical approval were obtained. Results : We observed higher levels of the most downstream kinin peptide bradykinin-(1-5) (Figure 1), higher tissue kallikrein activity (Figure 2), and higher levels of MPO-DNA complexes (699.0 ng/mL [66.0-142621.0], median [range], n = 21 vs 70.5 [9.9-960.0], n = 19;P < 0.001) in BAL fluid from patients with COVID-19 compared to those in BAL fluid from patients without COVID-19. Conclusions : Our data support the hypothesis that SARS-CoV-2 induces dysregulation of the kallikrein-kinin system, which contributes to thromboinflammation in COVID-19. These findings encourage the investigation of drugs that target the kallikrein-kinin system as a potential treatment option for patients with COVID-19.

Weight adjusted prophylactic to intermediate dosed thromboprophylaxis in COVID-19

Background : COVID-19 is frequently associated with venous thromboembolism (VTE), and the use of thromboprophylaxis has been suggested to improve hospitalized patients ' outcomes. We, therefore, intensified our thromboprophylactic protocol starting March 31st. Aims : We aimed to validate the implementation of an intensified thromboprophylactic protocol by reporting VTE incidence and safety while awaiting randomized controlled trials. Methods : On March 31st, 2020, we implemented an intensified thromboprophylactic protocol based on weight and disease severity (50 IU anti-Xa LMWH/kg, once daily at the ward, twice daily at the intensive care unit (ICU)). ICU patients were monitored daily with anti-Xa serum levels. Full therapeutic doses were restricted to patients with a prior indication for therapeutic anticoagulation or confirmed VTE. As early reports demonstrated high VTE incidence, screening with duplex ultrasound became standard of care in our center as soon as logistically possible. We excluded patients with a prior indication for therapeutic anticoagulation and incidental findings of COVID-19 for analysis. The ethical committee has approved this observational study. Results : We analyzed 412 symptomatic and confirmed Covid-19 cases, of which 116 were admitted to the ICU. All symptomatic VTE cases were reported, and 20% of all patients (38% of ICU patients) received screening with venous ultrasound. In 219 patients who received the standard dose of LMWH, 16 patients (7.3%) had VTE, 10 of which were symptomatic (4.6%) (Figure 1). In 193 patients who received intensified thromboprophylaxis, there were no symptomatic VTE cases, three incidental DVT cases (1.6%), and one incidental pulmonary embolism (0.5%). Interestingly, rates of major bleeding were low (Figure 2). Conclusions : In a large cohort of hospitalized patients with COVID-19, we report no symptomatic VTE after implementing systematic thromboprophylaxis with weight-adjusted prophylactic (ward) to intermediate (ICU), but not therapeutic doses of LMWH. This strategy was associated with a low risk of major bleeding.

Monocyte-driven atypical cytokine storm and aberrant neutrophil activation as key mediators of COVID-19 disease severity.

Epidemiological and clinical reports indicate that SARS-CoV-2 virulence hinges upon the triggering of an aberrant host immune response, more so than on direct virus-induced cellular damage. To elucidate the immunopathology underlying COVID-19 severity, we perform cytokine and multiplex immune profiling in COVID-19 patients. We show that hypercytokinemia in COVID-19 differs from the interferon-gamma-driven cytokine storm in macrophage activation syndrome, and is more pronounced in critical versus mild-moderate COVID-19. Systems modelling of cytokine levels paired with deep-immune profiling shows that classical monocytes drive this hyper-inflammatory phenotype and that a reduction in T-lymphocytes correlates with disease severity, with CD8+ cells being disproportionately affected. Antigen presenting machinery expression is also reduced in critical disease. Furthermore, we report that neutrophils contribute to disease severity and local tissue damage by amplification of hypercytokinemia and the formation of neutrophil extracellular traps. Together our findings suggest a myeloid-driven immunopathology, in which hyperactivated neutrophils and an ineffective adaptive immune system act as mediators of COVID-19 disease severity.

High dimensional profiling identifies specific immune types along the recovery trajectories of critically ill COVID19 patients.

The COVID-19 pandemic poses a major burden on healthcare and economic systems across the globe. Even though a majority of the population develops only minor symptoms upon SARS-CoV-2 infection, a significant number are hospitalized at intensive care units (ICU) requiring critical care. While insights into the early stages of the disease are rapidly expanding, the dynamic immunological processes occurring in critically ill patients throughout their recovery at ICU are far less understood. Here, we have analysed whole blood samples serially collected from 40 surviving COVID-19 patients throughout their recovery in ICU using high-dimensional cytometry by time-of-flight (CyTOF) and cytokine multiplexing. Based on the neutrophil-to-lymphocyte ratio (NLR), we defined four sequential immunotypes during recovery that correlated to various clinical parameters, including the level of respiratory support at concomitant sampling times. We identified classical monocytes as the first immune cell type to recover by restoration of HLA-DR-positivity and the reduction of immunosuppressive CD163 + monocytes, followed by the recovery of CD8 + and CD4 + T cell and non-classical monocyte populations. The identified immunotypes also correlated to aberrant cytokine and acute-phase reactant levels. Finally, integrative analysis of cytokines and immune cell profiles showed a shift from an initially dysregulated immune response to a more coordinated immunogenic interplay, highlighting the importance of longitudinal sampling to understand the pathophysiology underlying recovery from severe COVID-19.