Extended Data Fig. 3: MCSP+ melanoma DCC display different phenotypes during metastatic colonization.
a, Schematic overview of analyzed patient samples and exclusion criteria. The number of patients and cells are depicted in black and blue, respectively. b-d, UMAP of scRNA-seq data of LN-derived small and large MCSP+MT+ cells (n = 170 cells) and MCSP+MT- cells (n = 23 cells) from melanoma patients, LN-derived MCSP+ cells from nonmelanoma patients (n = 9 cells) and cultured human melanocytes (n = 14 cells) with Seurat. Cells are annotated by their patient origin (melanoma, nonmelanoma patient) and cell type (melanocyte, MCSP/MT-status) (b), gene expression inferred CNA (c) or expression of marker genes for immune cells (PTPRC/CD45) and cells of melanocytic origin (MLANA) (d). e, scRNA-seq data (see panel d) integrated into skin and LN of the Human Cell Atlas (Tabula sapiens). Each cell type retrieved from the Human Cell Atlas (n = 33 cell types) was downsampled to contain 50 cells. Each cell is colored by its assigned cluster or cell type. f, g, Stability of DCC cluster assignment (Fig. 3a, n = 164 cells) using Seurat was assessed by comparison with multiple alternative clustering methods and variable parameter combination. Consensus heatmap (f) and its quantification (g). The box plots (g) show consensus scores of cell pairs within Seurat clusters and consensus scores of cell pairs between different Seurat clusters. Boxes represent the median, lower quartile, and upper quartile, with whiskers extending to the minimum and maximum values within 1.5 times the interquartile range. h, Silhoutte score analysis for DCC clusters. i, AUCell scores based on published melanoma subtype marker gene sets 26,27,28,29,30,31,32,33,34 averaged over DCC clusters.
