Neutrophils have altered response to acute respiratory viral infection in sputum of patients with rheumatoid arthritis

Background: Rheumatoid arthritis (RA) has been shown to pathologically modify the human lung environment. Individuals with RA have been shown to have higher incidence of respiratory infections and worse resultant patient outcomes. Objective: We investigated whether single-cell transcriptional signals within sputum distinguished healthy lungs from those of patients with RA before and after infection. Methods: Flex single-cell RNA sequencing protocol. Cells were clustered via transcriptomic signal, and cell types were identified via canonic markers. Differentially expressed genes within cell types between disease state and timepoints were grouped into coexpressed gene modules, and their relative expression and putative functions were described. Results: A total of 5 female donors (2 healthy and 3 with RA) were included. A mean of 5,773 cells per donor were captured, resulting in a total of 23,094 high-quality cells included in this study. The samples comprised 5 major cell types: 2 distinct macrophage populations, a neutrophil population, and minor populations of both B and T cells. There were no statistically significant differences in proportion of cell types between samples from healthy donors and those from patients with RA or between baseline and postinfection timepoints. However, gene modules of significantly differentially expressed genes between groups revealed transcriptional differences between groups that were associated with neutrophil function, including NETosis and inflammatory responses. Conclusion: Immune cell proportions in donors with RA and in healthy donors are similar both before and after infection. However, transcriptional differences within lung neutrophils persist up to 30 days following respiratory infection.