Desmosome mutations impact the tumor microenvironment to promote melanoma proliferation [Spatial transcriptomics]

Desmosomes are transmembrane protein complexes that contribute to cell-cell adhesion in epithelia and other tissues. Here, we report the discovery of frequent genetic alterations in the desmosome in human cancers, with the strongest signal seen in cutaneous melanoma where desmosomes are mutated in >70% of cases. In primary but not metastatic melanoma biopsies, the burden of coding mutations in desmosome genes associates with a strong reduction in desmosome gene expression. Analysis by spatial transcriptomics and protein immunofluorescence suggests that these expression decreases occur in keratinocytes in the microenvironment rather than in primary melanoma cells. In further support of a microenvironmental origin, we find that desmosome gene knockdown in keratinocytes yields markedly increased proliferation of adjacent melanoma cells in keratinocyte/melanoma co-cultures. Similar increases in melanoma proliferation are observed in media preconditioned by desmosome-deficient keratinocytes. Thus, gradual accumulation of desmosome mutations in neighboring cells may prime melanoma cells for neoplastic transformation. Formalin-fixed paraffin-embedded (FFPE) samples of 8 primary melanomas were chosen and sectioned (clinical information provided in Supplementary Table 2). One section was retained for the digital spatial profiling workflow to determine desmosome expression. Digital spatial profiling was performed using the GeoMX system as previously described (Merritt et al. 2020). Immunofluorescent visualization markers for keratinocytes (PanCK), melanoma cells (S100B, PMEL) and immune cells (CD45) were used to guide the selection of regions of interest (ROIs) containing either pure or mixed areas of each cell type (keratinocyte, melanocyte) followed by RNA profiling using the GeoMx human whole assay.