Spatial anatomic and microanatomic diversity across human skin at single-cell resolution

Summary: Abstract Body: The spatial organization of human skin underlies its many critical functions, including barrier establishment and immune surveillance. While skin physiological differences across anatomic sites are well documented, the molecular programs and cell communication networks that govern this patterning are not well understood. Given the anatomic predilection of skin disease and that disruption of proper cell communication is a hallmark of disease, there is an unmet need to better understand the molecular mechanisms of anatomic site-specific skin function. To address this, we applied single-cell resolution spatial transcriptomics profiling via multiplexed error robust fluorescence in situ hybridization (MERFISH) to characterize the anatomic heterogeneity of the skin microenvironment across 114 samples representing 15 anatomic sites from 22 donors (ncells=889,421). We quantified cellular diversity across donor-matched anatomic sites and identified the spatially dynamic and stable cell types within them. Dynamic cell types such as sole-specific keratinocytes correlating with epidermal thickness and immune populations less abundant in the scalp reflected site-specific specialization. In contrast, the cellular composition of anatomic sites like the inguinal fold and buttocks was less diverse. We next defined 6 spatially resolved multicellular neighborhoods defined by cell-cell proximity, which varied in abundance across anatomic sites and provided a spatial framework for cell-cell interaction inference. Finally, we quantified spatially informed ligand-receptor interactions in each neighborhood and intersected them with interactions found in publicly available scRNA-seq data to describe cell-cell signaling networks, uncovering distinct epithelial-stromal and stromal-immune interactions across neighborhoods. In summary, these data provide a novel framework exploring the human skin microenvironment and serve as a comprehensive resource for understanding cellular neighborhoods in homeostasis that may be disrupted in skin diseases. Paula Restrepo¹, Alexis Wilder¹, Aubrey Houser¹, Abiha Kazmi¹, Mary G. Hren¹, Jesse Lewin¹, Andrew Ji¹ 1. Icahn School of Medicine at Mount Sinai, New York, NY, United States. Bioinformatics, Computational Biology, and Imaging