Identification of robust mortality-associated neutrophil gene programs and cytokine responses using large-scale ARDS endotracheal aspirate scRNA-seq data

Myeloid dysregulation is involved in severe Acute Respiratory Distress Syndrome (ARDS), but the mechanistic understanding is still incomplete. We analyzed endotracheal aspirate (ETA) scRNA-seq data from 40 intubated patients (both COVID-19 and non-COVID-19) in the COMET cohort, to uncover cell types and gene programs associated with ARDS mortality. In cell-type-agnostic analyses, we identified neutrophils as a critical cell type prognostic for ARDS mortality. Subsequent analyses uncovered a mortality-associated neutrophil subpopulation characterized by upregulation of IFN-ɣ response and ferroptosis genes, and downregulation of TNF-ɑ response genes. These findings were validated across independent COVID-19 clinical cohorts. Analyses of in vitro data further suggested that gene programs active in the mortality-associated neutrophil subpopulation could be attributable to specific cytokine responses. Finally, we confirmed that this mortality-associated neutrophil subpopulation could be induced in rodents via influenza A or SARS-CoV-2 infections, providing insights for modeling this neutrophil phenotype for therapeutic development.