Spatial gene expression and microenvironmental changes in the transition of nevus to melanoma

Imaging Mass Cytometry (IMC) was used to analyze nevus and melanoma slides, utilizing a custom panel of antibodies targeting structural, cell-defining, and immune cell markers. Tissue sections underwent deparaffinization, rehydration, epitope retrieval, and blocking before sequential incubation with metal-labeled antibodies and nuclear staining. IMC images were acquired using the Hyperion Imaging System, and pixel-based data analysis was performed using Seurat, clustering pixels based on shared nearest neighbors and assigning cell types based on upregulated proteins. The patient numbers correspond to the numbers used in the Visium data on GEO and the supplemental table in the article.