Integrated single-cell chromatin and transcriptomic analyses of peripheral immune cells in patients with alopecia areata

Introduction Alopecia areata (AA) is an autoimmune disorder characterized by non-scarring hair loss ranging from mild, self-limiting episodes to severe and chronic forms. While prior research has primarily focused on lesional skin, the contribution of systemic immune cells remains underexplored. Methods We performed integrated single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on peripheral blood mononuclear cells (PBMCs) from patients with mild and severe AA, as well as healthy controls. A total of 32,453 high-quality cells were analyzed across 36 immune cell subtypes. Results In AA patients, especially those with severe disease, we observed increased transcriptional heterogeneity, cytokine and chemokine pathway activation, and upregulation of antigen-presentation machinery enriched in TH1, TH2, and TH17 signatures. Chromatin accessibility profiling revealed 42,248 significant peaks with pronounced epigenetic remodeling in CD14 + monocytes, NK cells, and CD8 + T cells. Mild AA showed early immune regulatory failure, with elevated exhaustion markers in double-negative T cells and increased apoptosis in myeloid populations. Pseudotime and transcription factor analyses indicated altered differentiation trajectories, and inferred cell-cell communication networks highlighted monocytes, NK cells, and memory T cells as key signaling hubs. Discussion Our results provide the first integrated single-cell chromatin and transcriptomic map of peripheral immune dysregulation in AA. These findings uncover systemic alterations associated with disease severity and identify candidate pathways for immune modulation and therapeutic targeting.