Longitudinal characterization of circulating neutrophils uncovers distinct phenotypes associated with disease severity in hospitalized COVID-19 patients

LaSalle, Thomas J.; Gonye, Anna L. K.; Freeman, Samuel S.; Kaplonek, Paulina; Gushterova, Irena; Kays, Kyle R.; Manakongtreecheep, Kasidet; Tantivit, Jessica; Rojas-Lopez, Maricarmen; Russo, Brian C.; Sharma, Nihaarika; Thomas, Molly F.; Lavin-Parsons, Kendall M.; Lilly, Brendan M.; Mckaig, Brenna N.; Charland, Nicole C.; Khanna, Hargun K.; Lodenstein, Carl L.; Margolin, Justin D.; Blaum, Emily M.; Lirofonis, Paola B.; Sonny, Abraham; Bhattacharyya, Roby P.; Parry, Blair Alden; Goldberg, Marcia B.; Alter, Galit; Filbin, Michael R.; Villani, Alexandra Chloe; Hacohen, Nir; Sade-Feldman, Moshe

Multiple studies have identified an association between neutrophils and COVID-19 disease severity; however, the mechanistic basis of this association remains incompletely understood. Here we collected 781 longitudinal blood samples from 306 hospitalized COVID-19+ patients, 78 COVID-19− acute respiratory distress syndrome patients, and 8 healthy controls, and performed bulk RNA-sequencing of enriched neutrophils, plasma proteomics, cfDNA measurements and high throughput antibody profiling assays to investigate the relationship between neutrophil states and disease severity or death. We identified dynamic switches between six distinct neutrophil subtypes using non-negative matrix factorization (NMF) clustering. At days 3 and 7 post-hospitalization, patients with severe disease had an enrichment of a granulocytic myeloid derived suppressor cell-like state gene expression signature, while non-severe patients with resolved disease were enriched for a progenitor-like immature neutrophil state signature. Severe disease was associated with gene sets related to neutrophil degranulation, neutrophil extracellular trap (NET) signatures, distinct metabolic signatures, and enhanced neutrophil activation and generation of reactive oxygen species (ROS). We found that the majority of patients had a transient interferon-stimulated gene signature upon presentation to the emergency department (ED) defined here as Day 0, regardless of disease severity, which persisted only in patients who subsequently died. Humoral responses were identified as potential drivers of neutrophil effector functions, as enhanced antibody-dependent neutrophil phagocytosis and reduced NETosis was associated with elevated SARS-CoV-2-specific IgG1-to-IgA1 ratios in plasma of severe patients who survived. In vitro experiments confirmed that while patient-derived IgG antibodies mostly drove neutrophil phagocytosis and ROS production in healthy donor neutrophils, patient-derived IgA antibodies induced a predominant NETosis response. Overall, our study demonstrates neutrophil dysregulation in severe COVID-19 and a potential role for IgA-dominant responses in driving neutrophil effector functions in severe disease and mortality.