Spatial Transcriptomics Identifies Characteristic Immunological Niches in Atopic Dermatitis

ABSTRACT Background Atopic dermatitis (AD) is primarily driven by a Type 2 immune response, with T helper (T H 2) cells producing IL‐4 and IL‐13, thereby promoting inflammation, itch, and a compromised skin barrier. Yet, the spatial organization of pathogenic immune cells and their interactions with stromal and epithelial compartments in human AD skin remain incompletely understood. Methods We performed 10× Genomics Visium spatial transcriptomics on FFPE skin biopsies from patients with AD ( n = 6), psoriasis ( n = 2), and healthy controls ( n = 5). Data were integrated with AD single‐cell RNA sequencing (scRNA‐seq) datasets and complemented by imaging mass cytometry (IMC) and multiplex immunofluorescence (IF) to validate the spatial localization of immune cells. Cell–cell communication analysis revealed putative signaling interactions within immune niches. Results Spatial clustering resolved tissue compartments and demonstrated transcriptional dysregulation in keratinocytes in AD and psoriasis. AD lesions showed a conserved spatial organization of immune aggregates within the superficial dermis. Integration of scRNA‐seq signatures revealed spatially organized co‐localization of T cells and mature migratory dendritic cells (mmDCs). We developed a ring‐based neighborhood analysis to characterize the cellular organization of the immune‐stromal niches, revealing T cell‐enriched regions surrounded by inflammatory fibroblasts and activated keratinocytes. Intercellular communication analysis further identified putative signaling within mmDC‐T cell niches that may promote pathogenic T cell recruitment and activation. Application of tertiary lymphoid structure (TLS) signatures indicated the presence of TLS‐like regions. IMC and IF validated the close spatial proximity between activated T H 2 cells and mmDCs. Conclusion AD lesions contain spatially organized TLS‐like immune niches at the dermal‐epidermal junction, characterized by the close association of T cells and mmDCs and coordinated interactions with surrounding stromal and epithelial compartments. These mmDC‐T cell niches may represent potential targets for future therapeutic strategies aimed at disrupting persistent local inflammatory pathways and improving long‐term disease control.