Primary Sjögren's syndrome (pSS) is a chronic autoimmune disorder characterized by exocrine gland dysfunction and systemic inflammation. Dysregulated interferon-gamma (IFN-γ) signaling is implicated in pSS pathogenesis, yet the comprehensive molecular and cellular mechanisms underlying this process remain elusive. This study sought to identify key IFN-gamma-associated diagnostic genes and delineate their roles in immune dysregulation

Transcriptomic data from a training cohort and an independent cohort were analyzed. Key genes were further screened through machine learning (ML) algorithms, ROC curve analysis, and differential expression assessment. A diagnostic model and nomogram were constructed and validated. Furthermore, immune infiltration, pathway enrichment, and regulatory networks were analyzed. In addition, single-cell RNA sequencing (scRNA-seq) was performed to delineate cellular heterogeneity, trajectory, and cell-cell communication. Ultimately, the expression of key genes was corroborated via reverse transcription-quantitative PCR (RT-qPCR).

Four key genes (HERC6, IL15, CD58, PTGS2) were identified. The diagnostic model and nomogram achieved high diagnostic accuracy. Immune profiling revealed a profoundly dysregulated immune microenvironment in pSS, with widespread metabolic and signaling pathway alterations. Pathway enrichment analysis delineated both distinct and shared functional roles for the key genes. Furthermore, analysis of scRNA-seq positioned macrophages as potential central orchestrators in pSS pathogenesis, exhibiting developmental arrest in pseudotime trajectories and enriched early differentiation states. In addition, macrophages also displayed intensified cell-cell communication networks. Additionally, RT-qPCR confirmed significant upregulation of HERC6, IL15, and PTGS2 in pSS patients. 

This study established an IFN-gamma-centered diagnostic model for pSS, and macrophages were implicated as potential pivotal drivers of immune dysregulation via altered differentiation, enhanced intercellular signaling, and IFN-gamma-driven gene expression. These results provided novel grasp of pSS pathogenesis and potential therapeutic targets.