Fig. 6: Molecular and functional characterization of acquired BRAF + MEK inhibitor resistance in patient PID028.

a Patient PID028’s clinical course (see Supplementary patient case PID028). b PCY-based cellular and morphological sample composition over time. c Genomic alterations at diagnosis (FB103), first relapse (FB209) and second relapse (FB261). d PCY-based ex vivo response to dabrafenib + trametinib in longitudinal MSE samples. Dots represent technical replicates (n = 4 for drugs, n = 16 for DMSO). e Dose-response to dabrafenib + trametinib at relapse to targeted therapy (FB215). Dots represent technical replicates (n = 3), lines and shaded areas indicate the mean and 95% confidence interval per concentration. f Fraction of phospho-ERK (pERK) positive tumor cells in response to different doses of dabrafenib + trametinib. Dots represent technical replicates (n = 3 per concentration and n = 17 for DMSO). Exact P values are provided in the Source Data. g Comparison of gene expression of FACS-purified tumor cells from diagnosis (FB103) and relapse to targeted therapy (FB215). Highlighted genes are implicated in acquired resistance to this therapy in melanoma⁵⁶. h Drug-target-proximal gene network for dabrafenib and trametinib. Green dots correspond to compounds, all other nodes represent genes. Color indicates log2 fold change of dabrafenib + trametinib vs DMSO in FACS-purified tumor cells from sample FB215. Enrichment visualized by mosaic plot (insert), P value from right-tailed hypergeometric test. i Change in DUSP6 levels after exposure to dabrafenib + trametinib across five additional samples measured by DRUG-seq. Values represent average expression across four replicate wells. P value from paired two-sided Wilcoxon test. j Comparison of in situ and ex vivo transcriptional adaptation of tumor cells to dabrafenib + trametinib. X axis corresponds to log2 fold change of gene expression in tumor cells taken at diagnosis (FB103) vs relapse (FB215), and y axis to log2 fold change of gene expression of tumor cells (FB215) treated ex vivo with dabrafenib + trametinib relative to DMSO. Regression line with 95% confidence bands, Pearson’s R, and corresponding P value (two-sided t test) are indicated. P values in (d) and (f) from two-sided Student’s t test comparing treatment to control, no adjustment for multiple testing. All box plots as in Fig. 3e.