Bioinformatic analysis and experimental verification reveal expansion of monocyte subsets with an interferon signature in systemic lupus erythematosus patients

Abstract

Background: Systemic lupus erythematosus (SLE) is a complex autoimmune disorder characterized by chronic inflammation and multi-organ damage. A central factor in SLE pathogenesis is the excessive production of type I interferon (IFN-I), which drives immune dysregulation. Monocytes, key components of the immune system, significantly contribute to IFN-I production. However, their specific roles in SLE remain incompletely understood.

Methods: This study utilized bioinformatics and statistical analyses, including robust rank aggregation (RRA), DESeq2, and limma, to analyze transcriptome data from peripheral blood mononuclear cells (PBMCs) and monocytes of SLE patients and healthy controls. Single-cell RNA sequencing (scRNA-seq) data were processed using the Seurat R package to identify and characterize monocyte subsets with a strong IFN-driven gene signature. Flow cytometry was employed to validate key findings, using markers such as CD14, SIGLEC1, and IRF7 to confirm monocyte subset composition.

Results: Our research has found that monocytes in SLE undergo IFN-driven transcriptional reprogramming, with the upregulation of key interferon signature genes (ISGs), forming the SLE-Related Monocyte Signature (SLERRAsignature). Moreover, the composition of mononuclear phagocyte subsets in SLE patients changes, with an increase trend in the proportion of the CD14Mono8 subset in the flare group. The differentially expressed genes (DEGs) in 13 mononuclear phagocyte subsets of SLE are mainly ISGs, and the expression of ISGs is higher in severe patients. We identified SIGLEC1⁺IRF7⁺ monocytes among these subsets and for the first time discovered this group of cells in the peripheral blood of healthy individuals. In SLE, the enrichment score of the gene set representing SIGLEC1⁺IRF7⁺ monocytes is positively correlated with the severity of SLE. Finally, flow cytometry confirmed that the frequency of CD14⁺SIGLEC1⁺IRF7⁺ monocytes in PBMCs was higher in SLE compared with healthy controls.

Conclusions: Our study found that the expansion of IFN-I-producing monocyte subsets, particularly the CD14⁺SIGLEC1⁺IRF7⁺ subset, plays a crucial role in SLE pathogenesis. This subset may serve as a potential biomarker and therapeutic target for managing SLE.

Keywords: CD14+SIGLEC1+IRF7+ monocytes; Interferon-stimulated genes; Single-cell RNA sequencing; Systemic lupus erythematosus; Type I interferon.