Upregulation of interferon-γ response genes in monocytes and T cells identified by single-cell transcriptomics in patients with anti-citrullinated peptide antibody-positive early rheumatoid arthritis

Introduction: Our aim was to investigate the insufficiently understood differences in the immune system between anti-citrullinated peptide antibody (ACPA)-positive (ACPA⁺) and ACPA-negative (ACPA^-) early rheumatoid arthritis (eRA) patients. Methods: We performed multiple cytokine assays using sera from drug-naïve ACPA⁺ and ACPA^- eRA patients. Additionally, we conducted single-cell RNA sequencing of CD45⁺ cells from peripheral blood samples to analyze and compare the distribution and functional characteristics of the cell subsets based on the ACPA status. Results: Serum concentrations of interferon-γ (IFN-γ) and interleukin (IL)-12 were higher in ACPA⁺ eRA than in ACPA^- eRA. Single-cell transcriptome analysis of 37,318 cells identified 17 distinct cell types and revealed the expansion of IL1B⁺ proinflammatory monocytes, IL7R⁺ T cells, and CD8⁺ CCL4⁺ T cells in ACPA⁺ eRA. Furthermore, we observed an enrichment of IFN-γ response genes in nearly all monocytes and T cells of ACPA⁺ eRA subsets. Heightened interactions between IFN-γ and IFN-γ receptors were observed in ACPA⁺ eRA, particularly between monocytes and T cells. We examined IFITM2 and IFITM3 as potential key markers in ACPA⁺ eRA given their pronounced upregulation and association with the IFN response. Specifically, the expression of these genes was elevated in IL1B⁺ proinflammatory monocytes (likely M1 monocytes), correlating with serum IFN-γ levels. Discussion: Compared to ACPA^- eRA, ACPA⁺ eRA showed higher serum IFN-γ and IL-12 levels, upregulated IFN-γ response genes, and enhanced IFN-γ-driven monocyte-T cell interactions. These distinct immune features of the peripheral circulation in ACPA⁺ eRA suggest a role for type 1 helper T cell-related immunity in its pathogenesis.