AUTHOR=Gay-Mimbrera Jesus , Gómez-Arias Pedro Jesús , Álvarez-Heredia Pablo , Batista-Duharte Alexander , Rivera-Ruiz Irene , Aguilar-Luque Macarena , Juan-Cencerrado Miguel , Mochón-Jiménez Carmen , Cebrián-García Álvaro , Andújar-Pulido Eloísa , Pérez-Alegre Mónica , Pera Alejandra , Ruano Juan 

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

JOURNAL=Frontiers in Immunology

VOLUME=Volume 16 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2025.1565241

DOI=10.3389/fimmu.2025.1565241

ISSN=1664-3224

ABSTRACT=IntroductionAlopecia 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.MethodsWe 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.ResultsIn 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.DiscussionOur 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.