Single-cell multi-omics sequencing reveals the immunological disturbance underlying Kawasaki disease.

Introduction: Kawasaki disease (KD) is an acute autoimmune vasculitis that predominantly affects children under 5 years of age. Although immune dysregulation is considered central to KD pathogenesis, the cellular heterogeneity and regulatory mechanisms underlying this process remain incompletely understood. Single-cell multi-omics technologies provide an opportunity to characterize immune alterations at high resolution. Methods: Peripheral blood mononuclear cells (PBMCs) were obtained from two children with typical KD and two age-matched healthy controls. Integrated single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) were performed to characterize immune cell composition, transcriptional profiles, and chromatin accessibility. Comparative analyses were conducted to identify altered immune cell subsets and dysregulated signaling pathways in KD. Results: Children with KD exhibited marked immune dysregulation, characterized by altered proportions and functional states of multiple PBMC subsets, including T cells, B cells, and natural killer (NK) cells. Notably, specific NK cell subsets were associated with the pathogenesis of intravenous immunoglobulin (IVIG)-resistant KD. Pathway analyses revealed significant dysregulation of toll-like receptor signaling, B cell and T cell receptor signaling, Th17 and Th1/Th2 differentiation, NK cell-mediated cytotoxicity, and platelet activation pathways. Discussion: By integrating scRNA-seq and scATAC-seq data, this study delineates the heterogeneity of immune cell populations in KD at the single-cell level. The findings highlight coordinated immune and platelet activation pathways that may contribute to KD-associated inflammation and IVIG resistance. These results provide mechanistic insights into KD immunopathogenesis and suggest potential cellular and molecular targets for therapeutic intervention.