Single-cell transcriptomics and epigenomics point to CD58/CD59-CD2 interactions in controlling primary melanoma growth and immunity

To uncover new molecules in melanoma immunological control, single-cell transcriptomic and epigenomic analyses are performed on human melanoma samples using the 10x Genomics technology. Melanoma samples were categorized as high, intermediate and low immune, based on the percentage of lymphocyte infiltration of the tumors. Single-cell transcriptomic analysis identified a number of different cell populations. Melanoma cells were categorized into nine subclusters with developmental trajectories from melanocytic cells to de-differentiated neural crest-like cells. An emphasis is put on the interaction of melanoma cells with T cells, analyzing possible ligand and receptor interactions. Apart from HLA molecules, a number of new ligand receptor interactions were identified. Single-cell ATAC-seq was used to identify open chromatin regions that might be involved in the immunological control of melanoma. Analysis of primary melanoma lesions that were processed after surgical excision. None of the patients received any treatment in advance nor were any metastatic outgrowths observed in the patients. Additionally, benign melanocytic nevi were processed and analysed within the same pipeline.