Integrated analysis of single-cell RNA-seq and bulk RNA-seq reveal macrophage subpopulation characteristics and the role of STAT1 in rheumatoid arthritis

BACKGROUND: Rheumatoid arthritis (RA) represents a persistent systemic autoimmune disorder characterized by chronic inflammation and significant disability. Macrophage heterogeneity plays a crucial role in the progression of RA, but the molecular characteristics and regulatory mechanisms of its subsets have not yet been fully elucidated. METHODS: In this study, we integrated single-cell RNA sequencing (scRNA-seq) data and bulk RNA sequencing (bulk RNA-seq) data, and employed multiple strategies for analysis and identification of the heterogeneity of macrophages in RA. We identified STAT1 as a key gene through a combined approach utilizing LASSO regression and random forest models. The differential expression of STAT1 was subsequently validated in an adjuvant-induced arthritis (AIA) rat model. Furthermore, functional experiments were performed to investigate the association of STAT1 with autophagy and ferroptosis pathways. RESULTS: macrophages were concentrated in inflammatory pathways. Moreover, bulk RNA-seq and animal models further confirmed the upregulated expression of STAT1 in RA. Functional experiments demonstrated that STAT1 activation upregulated synovial LC3 and ACSL4, while downregulating p62 and GPX4. Treatment with fludarabine (Flu) reversed these changes, suggesting that STAT1 may contribute to RA pathogenesis by modulating autophagy and ferroptosis pathways. CONCLUSIONS: This study elucidated the heterogeneity and functional characteristics of macrophage subsets in RA synovial tissue through scRNA-seq and bulk RNA sequencing, and suggested that STAT1 and its downstream signaling pathways may serve as potential therapeutic targets for RA.