Single-cell and spatial transcriptomic analysis of homeostatic adult human skin

Epidermal homeostasis is governed by a balance between keratinocyte proliferation and differentiation with contributions from cell-cell interactions, but conserved or divergent mechanisms governing this equilibrium across species, and how an imbalance contributes to skin disease, are largely undefined. To address these questions, human skin single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST) data were integrated and compared to mouse skin data. Human skin cell type annotation was improved by using matched ST data, highlighting the importance of spatial context in cell type identity, and ST refined cellular communication inference. In cross-species analyses, we identified a human spinous keratinocyte subpopulation that exhibited proliferative capacity and a heavy-metal processing signature, which was absent in mouse and may account for species differences in epidermal thickness. This human subpopulation was expanded in psoriasis and zinc-deficiency dermatitis, attesting to disease relevance and suggesting a paradigm of subpopulation dysfunction as a hallmark of disease. To assess additional potential subpopulation drivers of skin diseases, we performed cell-of-origin enrichment analysis within genodermatoses, nominating pathogenic cell subpopulations and their communication pathways, which highlighted multiple potential therapeutic targets. This integrated dataset is encompassed in a publicly available web resource to aid mechanistic and translational studies of normal and diseased skin. Overall design: Human skin samples were fresh frozen and sectioned at 10um thickness onto spatial transcriptomics (ST) slides for mRNA capture, followed by library preparation and sequencing