Fig. 6. Kdm4b and Znf217 protein levels predict differentiation state-specific sensitivity to JIB-04 and SP2509.

a Relative cell viability in WM115 cells (left), WM902B cells (middle), and A2058 cells (right) following treatment with indicated doses of the combination of vemurafenib and trametinib or vehicle (DMSO) in the presence of pools of four siRNAs targeting either KDM4A, KDM4B, KDM5A, or KDM5B for 96 h. Viability data for each treatment condition were normalized to cells treated with DMSO and the non-targeting (control) siRNA. Data are presented as mean values ± s.d. calculated across n = 3 biologically independent experiments. Statistical significance was determined by two-sided t test. b Relative cell viability in Cas9-positive A2058 cells following treatment with three different types of KDM1A lentiviral single guide RNA (sgRNA) for 96 h. Viability data were normalized to cells treated with non-targeting (control) sgRNA. Data are presented as mean values ± s.d. calculated across n = 4 biologically independent experiments. Statistical significance was determined by two-sided t test. c Two-sided Pearson’s correlation analysis of variations in the difference between Ngfr and Axl protein levels and Znf217 (left panels) or Kdm4b (right panels) in comparison with the rest of the measured proteome (shown as histograms) across BRAF-mutant melanoma cell lines. Protein data are extracted from the Cancer Cell Line Encyclopedia (CCLE) proteomics database (measured by multiplexed mass spectrometry) and z-scored across all of BRAF-mutant melanoma cell lines present in the database. d Two-sided Pearson’s correlation between the baseline fractions of Znf217^High cells and Kdm4b^High cells and the fractions of Ngfr^Low/Axl^High cells (top left), the fractions of Ngfr^High/Axl^Low cells (top right), sensitivity to SP2509 at 1 μM (bottom left), and sensitivity to the combination of JIB-04 (at 0.2 μM), vemurafenib (at 100 nM) and trametinib (at 10 nM) (bottom right), as evaluated by normalized growth rates following 5 days of treatment. Protein data were measured by immunofluorescence microscopy, quantified following single-cell analysis, and averaged across n = 3 biologically independent samples. e Two-sided Pearson’s correlation between responses (normalized growth rates) to SP2509 (top) or JIB-04 in combination with vemurafenib and trametinib (bottom), measured for each of the 21 melanoma cell lines (x-axis) and corresponding responses fitted by multi-linear regression (MLR) analysis of 14 cell lines (training set; shown in gray) or responses predicted by the trained models for the remaining seven cell lines (validation set; shown in blue or red). Source data are provided as a Source data file.