Juvenile xanthogranuloma (JXG) is the most common non-Langerhans cell histiocytic disorder in children. Nevertheless, its pathogenesis remains poorly understood. This study aims to elucidate the key cellular components and molecular mechanisms driving JXG lesion formation through transcriptomic profiling.

Pathological specimens from JXG lesions and adjacent normal skin were subjected to bulk RNA-seq (11 lesions, 9 controls) and scRNA-seq (2 lesions, 2 controls). Differentially expressed genes (DEGs) and enrichment analyses were performed on bulk data, while scRNA-seq data were processed using Seurat for cell clustering and annotation. Single-cell regulatory network inference and clustering (SCENIC) and regulon analyses quantified regulon activity differences, and CellChat decoded cell–cell communication. TF regulon activity associated with pathway-specific DEGs was assessed via AUCell. Developmental trajectories and signature genes of macrophages were inferred using Monocle 3.

4656 DEGs were identified in differential expression analysis. KEGG enrichment showed significant over-representation of the cytokine–cytokine receptor interaction (CCRI) pathway, which included 158 DEGs (CCRI-DEGs). In immune-cell clusters, the M6 regulon module displayed higher activity in JXG than in NOR lesions. CellChat analysis revealed robust immune–fibroblast crosstalk, with SPP1-mediated signaling markedly more pronounced in JXG. Almost all CCRI-DEG-specific TF regulons were highly and concordantly expressed in macrophage subsets. Trajectory inference resolved two major macrophage branches, and the distribution of the track-gene signature SPP1 closely mirrored that of the CCRI-DEG-specific TF regulons.

Cytokine-mediated interactions within macrophages play a pivotal role in the pathogenesis of JXG, and SPP1⁺ macrophages appeared to constitute a key cellular driver of disease initiation and progression.