2025
Journal of Inflammation Research

Single-Cell Transcriptomics Reveals CCL3+ Classical Monocyte Subset Linked to Autoimmune Pathogenesis

Authors:

Heng Xu, Kai Yuan, Guangyao Chen, Jing Luo, Aimin Yan, Huaijuan Huang, Xinbo Yu, Qingwen Tao, Guangrui Huang, Anlong Xu

Keywords:

autoimmune diseases; single-cell RNA sequencing; CCL3+ classical monocytes; mononuclear phagocytes; primary Sjogren’s syndrome

Abstract:

Objective: The diverse differentiation states of mononuclear macrophages are closely associated with the pathogenesis of autoimmune diseases. This study integrates single-cell RNA sequencing data from six autoimmune diseases to characterize shared and disease-specific alterations in mononuclear macrophages, with the aim of enhancing our understanding of the immune landscape in autoimmune diseases and refining clinical treatment strategies.

Methods: We collected single-cell RNA-sequencing data of autoimmune diseases including primary Sjogren’s syndrome (pSS), Behçet’s disease (BD), juvenile dermatomyositis (JDM), rheumatoid arthritis (RA), relapsing-remitting multiple sclerosis (RRMS), and systemic lupus erythematosus (SLE). We performed scRNA-seq analysis on 350,043 peripheral blood immune cells from autoimmune diseases patients and healthy controls, followed by validations with flow cytometry, immunohistochemical staining, and immunofluorescence.

Results: Fifteen mononuclear phagocyte subpopulations were clustered from peripheral blood mononuclear cells (PBMCs), we identified a new subpopulation named CCL3⁺ classical monocytes (cMo) that is co-amplified in multiple autoimmune diseases (BD, JDM, pSS, RRMS, SLE). The CCL3⁺ cMo cells are characterized by high M1-like score, exhibiting strong inflammatory characteristics and high chemotaxis toward other monocytes. In addition, CCL3⁺ cMo cells upregulated antigen presentation-related signaling pathways, and the cytotoxic CD8⁺ T or memory CD8⁺ T cells were strongly perturbed by their signaling crosstalk.

Conclusion: This study delineates a comprehensive landscape of mononuclear phagocyte heterogeneity in autoimmune diseases and reveals CCL3⁺ cMo as a commonly amplified immune subset associated with multiple autoimmune diseases. These findings highlight its potential role in disease mechanisms and nominate CCL3⁺ cMo as a candidate therapeutic target.