Fig. 4: Spatial transcriptomics and proteomics in tumors with mutated or WT desmosomes.

a, A total of 18 primary melanoma tumors underwent WES. Top, eight tumors were subjected to spatial transcriptomic analysis using NanoString GeoMx, covering a combined total of 48 ROIs. Bottom, the remaining ten tumors were subjected to IF analysis, in which the expression levels of the DSP protein were scored using quantitative fluorescence. b, Tissue cross-section with example ROIs shown. Each ROI is indicated by a circle boundary marked using a lowercase Roman numeral. ROIs are enriched for keratinocytes (i), mixed melanocytes and keratinocytes (ii) or melanocytes (iii). Fluorescent markers have been used to label nuclei (blue), immune cells (red), cancer cells (yellow) or keratinocytes (green). Gene expression profiling was performed once per slide with multiple ROIs. c, Average mRNA expression levels of desmosome genes in each ROI, stratified according to keratinocyte (n = 15) versus melanoma (n = 21) and mixed (n = 12) ROIs. In the box plots, the lower and upper box boundaries delineate the 25th and 75th percentiles, the middle line denotes the 50th percentile and the whiskers mark the 5th and 95th percentiles. Significance was determined using a two-sided, two-sample t-test (**P = 0.001, ****P < 10⁻¹³). d, Average mRNA expression levels of desmosome genes in each ROI, stratified according to keratinocyte (n = 15) versus melanoma (n = 21) and further subdivided based on whether ROIs are from tumors with WT (dark gray, n = 24) or mutant desmosomes (light gray, n = 12). In each category, the set of ROI values is summarized using a box plot, according to the convention used in c. Significance was determined using a two-sided, two-sample t-test (*P = 0.033). e, DSP IF of tumor MKD15 (right, desmosome WT) and MKD12 (left, mutated desmosome). Red indicates DSP expression, cyan represents JUP expression serving as a membrane mask and yellow represents SOX10 expression marking melanocytes. Each staining was performed once for ten individual tumor samples. f, Total DSP protein expression levels across ten human melanoma tumor-adjacent epidermis primary tumors. Samples are split according to desmosome mutational status (WT, mutated). Significance was determined using a two-sided Wilcoxon rank-sum test (*P = 0.042). g, Same as in f but for membrane-only DSP protein expression. Significance was determined using a two-sided Wilcoxon rank-sum test (*P = 0.018).