Human skin provides vital protection from water loss and from external insult through structural adaptations and interplay with the innate and adaptive immune systems. The skin develops and functions in an aquatic environment in utero but rapidly adapts to a contrasting set of physical and pathogenic challenges after birth. The changes that take place across this complex multicellular system during development and upon perturbation by immune-mediated inflammatory diseases are poorly understood. A detailed study will facilitate the development of therapeutic interventions for inflammatory skin disease.

We generated a comprehensive atlas of human skin in early prenatal life, in adulthood, and during inflammatory skin disease by profiling the transcriptomes of more than 500,000 single cells. We analyzed human embryonic skin between 7 and 10 post-conception weeks, healthy adult skin surplus from mammoplasty surgery, and skin biopsies from patients affected by atopic dermatitis (AD) and psoriasis, two common inflammatory skin diseases. Additionally, we performed single-cell T cell receptor analysis to assess T cell clonality in disease. Validation experiments were conducted at the protein level and used mass cytometry, flow cytometry, and immunostaining in situ of skin biopsies from healthy skin and patients with AD and psoriasis, including a cohort of AD patients before and during treatment with oral methotrexate.

Thirty-four cell states were identified in healthy human skin across the collective dataset, with dynamic changes in the nature and abundance of single-cell gene expression profiles identified across embryonic and adult life and upon perturbation during inflammatory skin disease. This resource can be accessed via an interactive browsable web portal, https://developmentcellatlas.ncl.ac.uk/datasets/hca_skin_portal. Analyses revealed that the immune system of first-trimester embryonic skin consists mainly of innate lymphocytes and macrophages. In adult skin, we defined two inferred trajectories for keratinocyte differentiation and the presence of endothelial cells that formed dilated postcapillary venules. We revealed a migratory dendritic cell (DC) signature in healthy adult skin that is conserved in murine DCs. The migratory DC signature was also evident in the developing human thymus and additional disease states. We identified clonally expanded disease-associated cytotoxic T cells (Tc IL13/IL22 cells) in lesional AD and Tc17/T helper 17 (T_H17) cells in lesional psoriasis. We demonstrated the reemergence of prenatal cellular programs mediated by Mac2 macrophages via the chemokine CXCL8 interacting with the venular capillary marker ACKR1 on VE3 vascular endothelial cells in diseased skin. This interaction is implicated in lymphocyte recruitment and angiogenesis. We identified and validated in situ the expansion of Mac2 and VE3 in lesional AD and lesional psoriasis skin, their close apposition in AD and psoriasis tissue, and their reduction in AD skin during methotrexate treatment, which aligned with an improvement in the clinical severity of disease in this patient cohort.

Our single-cell atlas of human skin from prenatal life, healthy adults, and AD and psoriasis patients highlights the dynamic nature of cutaneous homeostasis and immunity. Our study provides insights into perturbed and co-opted developmental cellular programs in inflammatory skin disease. These results may provide potential future translational targets to improve the diagnosis and molecular classification of these diseases and to guide treatment strategies.

We used single …