Single-Cell Multi-Omics Reveals Activation of the STAT3–PIM1 Axis in T Cell Subsets in Proteinase 3-ANCA-Positive Granulomatosis with Polyangiitis

Granulomatosis with polyangiitis (GPA) is an autoimmune disease marked by relapses and treatment-related morbidity. CD4⁺ T cells play a central role in GPA pathogenesis, but their molecular profile remains incompletely defined. This study aimed to characterize CD4⁺ T cells in proteinase 3-ANCA-positive GPA (PR3-GPA) patients using single-cell multi-omics to identify molecular signatures associated with disease activity. Peripheral blood mononuclear cells were obtained from PR3-GPA patients during active disease, remission, and healthy controls. Single-cell RNA sequencing and CITE-seq were used to define transcriptional and protein expression profiles of CD4⁺ T cell subsets. Findings were validated using RT-qPCR, flow cytometry–based assays, including phospho-flow cytometry, and in vitro inhibition assay. scRNA-seq and CITE-seq revealed upregulated PIM1 expression in CD4⁺ T cell subsets in active GPA compared to controls. Pim kinase inhibition reduced CD4⁺ T cell activation, proliferation, and cytokine production. These findings indicate that circulating CD4⁺ T cells in active PR3-GPA are characterized by activation of the STAT3–PIM1 axis, potentially driven by upstream IL-6 signaling.