Why Certain Repurposed Drugs Are Unlikely to Be Effective Antivirals to Treat SARS-CoV-2 Infections

Most repurposed drugs have proved ineffective for treating COVID-19. We evaluated median effective and toxic concentrations (EC50, CC50) of 49 drugs, mostly from previous clinical trials, in Vero cells. Ratios of reported unbound peak plasma concentrations, (Cmax)/EC50, were used to predict the potential in vivo efficacy. The 20 drugs with the highest ratios were retested in human Calu-3 and Caco-2 cells, and their CC50 was determined in an expanded panel of cell lines. Many of the 20 drugs with the highest ratios were inactive in human Calu-3 and Caco-2 cells. Antivirals effective in controlled clinical trials had unbound Cmax/EC50 ≥ 6.8 in Calu-3 or Caco-2 cells. EC50 of nucleoside analogs were cell dependent. This approach and earlier availability of more relevant cultures could have reduced the number of unwarranted clinical trials.

Substrate-dependent metabolomic signatures of myeloperoxidase activity in airway epithelial cells: Implications for early cystic fibrosis lung disease

Myeloperoxidase (MPO) is released by neutrophils in inflamed tissues. MPO oxidizes chloride, bromide, and thiocyanate to produce hypochlorous acid (HOCl), hypobromous acid (HOBr), and hypothiocyanous acid (HOSCN), respectively. These oxidants are toxic to pathogens, but may also react with host cells to elicit biological activity and potential toxicity. In cystic fibrosis (CF) and related diseases, increased neutrophil inflammation leads to increased airway MPO and airway epithelial cell (AEC) exposure to its oxidants. In this study, we investigated how equal dose-rate exposures of MPO-derived oxidants differentially impact the metabolome of human AECs (BEAS-2B cells). We utilized enzymatic oxidant production with rate-limiting glucose oxidase (GOX) coupled to MPO, and chloride, bromide (Br-), or thiocyanate (SCN-) as substrates. AECs exposed to GOX/MPO/SCN- (favoring HOSCN) were viable after 24 h, while exposure to GOX/MPO (favoring HOCl) or GOX/MPO/Br- (favoring HOBr) developed cytotoxicity after 6 h. Cell glutathione and peroxiredoxin-3 oxidation were insufficient to explain these differences. However, untargeted metabolomics revealed GOX/MPO and GOX/MPO/Br- diverged significantly from GOX/MPO/SCN- for dozens of metabolites. We noted methionine sulfoxide and dehydromethionine were significantly increased in GOX/MPO- or GOX/MPO/Br--treated cells, and analyzed them as potential biomarkers of lung damage in bronchoalveolar lavage fluid from 5-year-olds with CF (n = 27). Both metabolites were associated with increasing bronchiectasis, neutrophils, and MPO activity. This suggests MPO production of HOCl and/or HOBr may contribute to inflammatory lung damage in early CF. In summary, our in vitro model enabled unbiased identification of exposure-specific metabolite products which may serve as biomarkers of lung damage in vivo. Continued research with this exposure model may yield additional oxidant-specific biomarkers and reveal explicit mechanisms of oxidant byproduct formation and cellular redox signaling.

Inactivation of SARS-CoV-2 and COVID-19 Patient Samples for Contemporary Immunology and Metabolomics Studies

Due to the severity of COVID-19 disease, the U.S. Centers for Disease Control and Prevention and World Health Organization recommend that manipulation of active viral cultures of SARS-CoV-2 and respiratory secretions from COVID-19 patients be performed in biosafety level (BSL)3 laboratories. Therefore, it is imperative to develop viral inactivation procedures that permit samples to be transferred to lower containment levels (BSL2), while maintaining the fidelity of complex downstream assays to expedite the development of medical countermeasures. In this study, we demonstrate optimal conditions for complete viral inactivation following fixation of infected cells with commonly used reagents for flow cytometry, UVC inactivation in sera and respiratory secretions for protein and Ab detection, heat inactivation following cDNA amplification for droplet-based single-cell mRNA sequencing, and extraction with an organic solvent for metabolomic studies. Thus, we provide a suite of viral inactivation protocols for downstream contemporary assays that facilitate sample transfer to BSL2, providing a conceptual framework for rapid initiation of high-fidelity research as the COVID-19 pandemic continues.

Transcriptional reprogramming drives neutrophil phenotype and function in chronic lung disease

Rationale

Neutrophils are often considered the first line of defense against bacterial infections. In cystic fibrosis (CF), massive neutrophil presence is concomitant with phenotypical changes and prolonged bacterial infections. Here, we sought to determine whether this paradox was dependent on transcriptional reprogramming of airway neutrophils.

Methods

Blood neutrophils were transmigrated in an in vitro model recapitulating the in vivo phenotype of CF airway neutrophils. Blood and airway neutrophils from the in vitro model and from CF patients were analyzed by flow cytometry, microarrays and RNA sequencing, as well as used for bacterial killing assays.

Results

Airway neutrophils in vivo and in vitro showed increased total RNA content and profound shifts in their transcriptional profile for survival, anabolic, and antimicrobial genes. Furthermore, transcriptional blockade by α-amanitin in airway neutrophils in vitro and ex vivo fully restored their bacterial killing capacity.

Conclusions

These findings show that some canonical functions in neutrophils, including bacterial clearance, depend on the active repression of RNA transcription, which can be modulated by the local microenvironment at the site of inflammation, challenging the paradigm holding these cells as terminally differentiated.

Single-Step Purification of Sputum Extracellular vesicles from Cystic Fibrosis patients using aF4-MALS

Rationale

Patients with cystic fibrosis (CF) present a large amount of respiratory damage caused in large part by chronic neutrophil influx into the lung. Neutrophils recruited to the lumen of the CF lung actively exocytose neutrophil elastase (NE) and other damaging molecules. Airway NE levels correlate strongly with disease severity in patients with CF. We previously showed that extracellular vesicles (EVs) from patients with other lung diseases carry NE and promote emphysema in a mouse model (Genschmer et al. 2019). Here, we hypothesized that airway NE also compartmentalizes within EVs in CF patients.

Methods

To avoid potential aggregation and purification biases, we gently sorted EVs from CF sputum samples using asymmetrical flow field flow fractionation (aF4). Sputum EV fractions were then subjected to analysis by multi-angle light scattering, nanoparticle tracking analysis and flow cytometry.

Results

Multi-angle light scattering and nanoparticle tracking analyses demonstrate the presence of EVs of different sizes ranging from 40–500 nm, with a concentration of ~5 × 107 EVs/mL. EVs were separated by size with aF4 and downstream flow cytometry analysis showed that discrete subfractions concentrate NE on their surface, but that NE burden was not proportional to size.

Conclusions

Our data show that there are discrete subtypes of EVs released by neutrophils carrying various amounts of NE on their surface. These findings provide evidence for a role of EVs in promoting inflammation in the lungs of patients with CF.