Fig. 3
Vemurafenib-associated matrix remodeling impacts melanoma cell-state changes. a Single-cell RNA-seq violin plot showing expression of the MAPK gene signature in tumor, non-immune stromal, and immune cells. In all three cellular compartments, MAPK activity is significantly repressed in the V12d tumor cells but re-activated in the VPr tumor cells. Number of cells per group is given below the violin plots. b Single-cell RNA-seq violin plots showing the expression of Pdgfa and Tgfb1 in tumor cells split by treatment. Expression of stroma-recruiting factors is increased in untreated and progressing tumor cells as compared with regressing tumor cells. c Average shear wave velocity measurement plotted for C (n = 6) and VPr (n = 10) tumors, reflecting the stiffness of tumors. d, e Mass spectrometry of pyridinoline (PYD) and deoxypyridinoline (DPD) from C (n = 26) and VPr (n = 26) tumors. f Differential impact of stiffness on the melanoma differentiation signature in three Brafmut cell lines. Differentiation change from baseline score was derived using the expression of the eight genes from Fig. 2a (Ednrb, S100a1, Pmel, Lef1, Mlana, Tyrp1, Mc1r, Gpr143). Human melanoma-derived cell lines, A375 and Colo829, and murine BrafV600E; PTEN melanoma-derived cell line, MelNBR1, were used. MelNBR1 expressed only three of the eight genes (Pmel, Lef1, Mc1r). *p < 0.05, ***p < 0.001, ****p < 0.0001 by Wilcoxon rank-sum test in a; data are plotted as the mean ± SD for c–f. *p < 0.05, **p < 0.005, ***p < 0.0005, ****p < 0.00005 by t-test in c–f. C: control vehicle treated samples; IB: initial biopsy; V12d: 12-day vemurafenib treated samples; VPr: vemurafenib-progressed samples
