Single-cell transcriptome reveals keratinocyte subclusters contributing to altered differentiation and inflammatory responses in atopic dermatitis

Atopic dermatitis (AD) is a common chronic inflammatory skin disease with heterogeneous and poorly understood mechanisms. We perform single-cell RNA sequencing of lesional (LAD) and non-lesional (NAD) skin from 42 AD patients and 23 healthy controls (HC). Keratinocytes (KCs) are the predominant disease-relevant cell type. In healthy skin, KC differentiation follows a linear trajectory from basal KCs through seven differentiated stages to terminal keratinized cells. In LAD, this process is disrupted, showing a reversed terminal transition mainly driven by DK7 cells. APOD, LYZ and SERPINB4 emerge as LAD-specific regulators linked to IL-13/IL-22 responses, ER stress and oxidative damage. Mitochondrial and ER dysfunction are specifically enriched in LAD DK6 cells, indicating a key pathogenic compartment. Spatial transcriptomics and cell-cell interaction analysis further identify LAD-specific TWEAK signaling from IL-13+ Th2/cycling T cells to Fn14+ basal/differentiated KCs. Here, we reveal disrupted KC differentiation and immune signaling circuits in AD, highlighting potential therapeutic targets. Our single-cell analysis of atopic dermatitis reveals disrupted epidermal differentiation and aberrant immune signaling, identifying key stressed keratinocyte populations and pathways that may serve as potential therapeutic targets.