Complexity of the neutrophil transcriptome in early and severe rheumatoid arthritis: a role for microRNAs?

Neutrophils are innate immune cells that drive the progression of rheumatoid arthritis through the release of reactive oxygen species, neutrophil extracellular traps, and proteases that damage host tissues. Neutrophil activation is regulated, in part, by dynamic changes in gene expression. In this study, we have used RNAseq to measure the transcriptomes of neutrophils from people with severe, methotrexate-refractory rheumatoid arthritis and healthy controls. We identified a dynamic gene expression profile in people with severe rheumatoid arthritis. This is dominated by a type-I interferon-induced gene expression signature as well as activation of genes regulating neutrophil degranulation, neutrophil extracellular trap production, response to reactive oxygen species, and oxidative stress. While we did not detect significantly elevated levels of interferon-alpha in rheumatoid arthritis blood sera, we identified increased expression in rheumatoid arthritis neutrophils of miR-96-5p and miR-183-5p, which regulate activation of the interferon pathway as members of the miR-183C cluster. We also detected significantly elevated neutrophil extracellular trap debris in rheumatoid arthritis blood sera (P < 0.05). Using gene set variation analysis, we explored the heterogeneity of neutrophil gene expression in rheumatoid arthritis and identified subsets of patients with gene expression profiles reflecting enhanced neutrophil degranulation and cytotoxicity, tissue inflammation, or activation by interferons. Comparison with published single-cell RNAseq datasets identified rheumatoid arthritis transcriptomes where neutrophils were polarized by genes relating to early or late cell maturity, with significant genes in each polarized state being regulated by miR-146a-5p, miR-155-5p, miR-183-5p, or miR-96-5p. Overall, our study demonstrates the heterogeneity of the rheumatoid arthritis neutrophil transcriptome and proposes microRNA-driven mechanisms for regulating the activated neutrophil phenotype in rheumatoid arthritis.