Neutrophil proteomics identifies temporal changes and hallmarks of delayed recovery in COVID19

RationaleNeutrophils are important in the pathophysiology of COVID19 but the molecular changes contributing to altered neutrophil phenotypes following SARS-CoV-2 infection are not fully understood. ObjectivesTo use quantitative mass spectrometry-based proteomics to explore neutrophil phenotypes following acute SARS-CoV-2 infection and during recovery. MethodsProspective observational study of hospitalised patients with PCR-confirmed SARS-CoV-2 infection (May 2020-December 2020). Patients were enrolled within 96 hours of admission, with longitudinal sampling up to 29 days. Control groups comprised non-COVID19 acute lower respiratory tract infection (LRTI) and age-matched non-infected controls. Neutrophils isolated from peripheral blood were processed for mass spectrometry. COVID19 severity and recovery were defined using the WHO ordinal scale. Measurements and Main Results84 COVID19 patients were included and compared to 91 LRTI patients and 42 controls. 5,800 neutrophil proteins were identified and 1,748 proteins were significantly different (q-value<0.05) in neutrophils from COVID19 patients compared to those of non-infected controls, including a robust interferon response at baseline, which was lost in severe patients one week after enrolment. Neutrophil changes associated with COVID19 disease severity and prolonged illness were characterized and candidate targets for modulation of neutrophil function were identified. Delayed recovery from COVID19 was associated with changes in metabolic and signalling proteins, complement, chemokine and leukotriene receptors, integrins and inhibitory receptors. ConclusionsSARS-CoV-2 infection results in the sustained presence of recirculating neutrophils with distinct metabolic profiles and altered capacities to respond to migratory signals and cues from other immune cells, pathogens or cytokines. Scientific Knowledge on the SubjectInflammation is the primary driver of morbidity and mortality in severe COVID19. Type I interferon responses, T-cell exhaustion, cytokine storm, emergency myelopoiesis, myeloid compartment dysregulation and procoagulant pathway activation are well established contributors to COVID19 disease severity. Neutrophils play an important role in COVID19, with elevated neutrophil-to-lymphocyte ratios and the emergence of a circulating immature neutrophil population in individuals with severe symptoms. Neutrophil infiltration in the lungs coupled with the release of neutrophil extracellular traps has also been reported in severe and fatal COVID19. The aim of this study was to quantitatively map the proteomes of peripheral blood neutrophils from a cohort of hospitalised COVID19 patients to understand how SARS-CoV-2 infection changes neutrophil phenotypes and functional capacity. What this study adds to the fieldHigh-resolution mass spectrometry was used to characterise the proteomes of peripheral blood neutrophils from >200 individuals at different stages of disease. This work has comprehensively mapped neutrophil molecular changes associated with mild and severe COVID19 and identified significant quantitative changes in more than 1700 proteins in neutrophils from patients hospitalised with COVID19 versus patients with non-COVID19 acute respiratory infections. The study identifies neutrophil protein signatures associated with COVID19 disease severity. The data also show that alterations in neutrophil proteomes can persist in fully recovered patients and identify distinct neutrophil proteomes in recovered versus non recovered patients. Our study provides novel insights into neutrophil responses during acute COVID19 and reveals that altered neutrophil phenotypes persist in convalescent COVID19 patients.