A Comprehensive Analysis of Type I Interferon Risk Gene Signatures in Systemic Lupus Erythematosus

Systemic lupus erythematosus (SLE) is a chronic, heterogeneous autoimmune disease influenced by various genetic and environmental factors, and recent advances have established type I interferons (IFN-I) as pivotal drivers. This study comprehensively characterises IFN-I risk gene signatures in SLE. The IFN-I-related genes were obtained from GSE185047, and then Mendelian randomisation analysis using data from the FinnGen cohort (705 SLE cases, 385 509 controls) was utilised as a discovery set to identify IFN-I related risk genes. Single-cell RNA sequencing (scRNA-seq) and external cohorts were used to validate the four key signatures. Univariate and multivariate linear regression models assessed associations between gene expression and clinical parameters. DNA methylation analysis further evaluated epigenetic dysregulation in SLE immune subsets. Thirty-eight IFN-I-related genes were identified, and Mendelian randomisation analysis revealed robust causal associations between four genes (HERC5, IFIT3, IFI44L and IFI6) and SLE risk, with no heterogeneity or pleiotropy. ScRNA-seq demonstrated significant upregulation of these gene signatures in SLE PBMCs and monocytes (except IFIT3 in monocytes), along with altered immune cell proportions-specifically, increased monocytes and decreased T cells. External validation confirmed elevated expression of all four genes in SLE, with high diagnostic accuracy. Clinically, increased expression of these genes correlated with SLEDAI, reduced lymphocyte counts and lower complement C4 levels. Furthermore, DNA hypomethylation of IFI44L was observed across multiple SLE immune subsets, indicating epigenetic dysregulation. This study establishes HERC5, IFIT3, IFI44L and IFI6 as causal IFN-I risk genes in SLE and identifies IFI44L hypomethylation as a key epigenetic driver of IFN-I pathway activation. These findings offer new insights into SLE pathogenesis and highlight potential diagnostic biomarkers and therapeutic targets.