Figure 2.

Changes of melanoma expression signatures with PT. Melanoma short-term cultures were analyzed by single-cell RNA-seq and subjected to PT analysis using Wanderlust algorithm. (A) Stromal and pigmentation signature. (B) AXL and MITF signatures show a virtually bipolar characteristics with high levels of AXL in the NRAS-mut cells and low levels in the BRAF-mut and wt/wt cells, respectively, also indicated by the plus and minus signs. MITF shows opposite characteristics. (C) Gene expression levels of cyclin-dependent kinases CDK6 and CDK2 show bipolar, CDK1 central symmetrical activation patterns, respectively. (D) Mean expression of genes attributed to poised (TssP) promoters decreased with PT, while that with active (TssA) promoters increased. (E) Expression of genes related to cell cycle and oxidative phosphorylation (oxphos) both increased with PT, however, in a bimodal way with a delay of cell cycle activity and a plateau phase of oxphos. Gene sets were taken from gene ontology [26] and hallmarks of cancer [25] repositories and from two further studies on stromal and MITF/AXL signatures, respectively [13,27]. (F) ABC-transporter genes are selectively expressed across the melanoma cells in agreement with [12].