The response of human melanocytic nevi to simulated solar radiation assessed by single-nucleus RNA sequencing of frozen tissue.

Exposure to excess UVR is associated with approximately three-quarters of the global burden of melanoma. Yet, much of what is known about the effects of UV on melanocytes comes from studies of cell lines, animal models, and ex vivo-cultured human skin. In this in vivo study of human melanocytic nevi, we describe a protocol that facilitates the characterization of the effects of simulated solar radiation on a wide array of cell types using RNA sequencing of single nuclei isolated from optimal cutting temperature-embedded frozen tissue. With no enrichment for rare cell types, our RNA sequencing of single nuclei data reveal the transcriptional diversity of melanocytes, keratinocytes of the epidermis and adnexa, lymphatic and vascular endothelium, fibroblasts, and immune cells of the skin. Differences in gene expression between interfollicular basilar and nevomelanocytes, including those involved in senescence, are delineated. Co-expression analysis identified changes elicited by simulated solar radiation in gene modules containing SERPINE2, and components of the IGF-1 signaling axis, in nevus cells, fibroblasts, and endothelial cells. These findings were corroborated by RNAscope analysis of formalin-fixed parafin-embedded samples, thereby providing valuable pharmacologic targets and biomarkers for clinical trials of melanoma prevention agents.