Fig 2: Mek and BET inhibitor combinations improve response and sensitize cells to Axl inhibition. (a) Phenotypic drug response for MEKi (selumetinib, 1.5 µM), BETi (JQ1, 0.2 µM), and AXLi (R428, 1 µM) in MDAMB231 cells. Proliferation (black) and Migration (grey) responses, represented by either % confluence of the entire well or of the wound respectively, were measured for varying single and combination treatments. Proliferation measurement was after 100 h and migration measurement was after 24 h. Mean ± standard deviation with n = 8. (b) Lysate levels in molecules/cell for RTKs when treated with control, MEKi, BETi, or MEKi + BETi in MDAMB231 cells. Points indicate experimental data (n = 12) and crosses indicate mean values. Asterisk indicates p < 0.01 and ·· indicates p < 0.05 determined by pairwise t tests with Bonferroni correction.

Fig 3: Model schematic. Axl (blue), Met (orange), EGFR (green), and Her2 (purple) receptors exist in one of three compartments: Cell surface (rs), intracellular (combined endosomal, lysosomal, nuclear) (ri), or freely circulating in the extracellular medium (rf). Psyn represents net protein synthesis, the sum of transcriptional and translational regulation, kdeg represents protein degradation from the internal compartment, kshed represents proteolytic shedding of cell surface extracellular domains, and kend and krec represent endocytosis and recycling to and from the internal protein pool (i.e., endosomes) respectively.

Fig 4: Quantitative experiments and parameter estimation define MDAMB231 cell basal state. (a) End point sample quantification for total lysate (left) and supernatant (right) samples for control treated MDAMB231 cells. mean ± standard deviation, n = 12. (b) Time-course measurement of total biotin labeled RTK (left) and internal biotin labeled RTK (right) samples for control treated MDAMB231 cells. mean ± standard deviation, n = 18. (c) Optimized posterior value from deterministic patternsearch algorithm for 100 start sites determined by latin hypercube sampling and ordered by increasing -log(posterior) values. (d) Parameter posterior distributions from adaptive metropolis algorithm. Data are summed from 4 independent chains, 100,000 iterations each, minus 20,000 step burn-in period. Psyn has units of molecules cell-1 min-1 and kdeg, kend, krec, and kshed have units of min-1. Blue—Axl, orange—Met, green—EGFR, purple—Her2.

Fig 5: Principal component analysis identifies separation of Mek and Erk inhibitors and cell type specific responses. (a) and (b) Scores and Loadings plots respectively for PCA analysis where mean parameter values were used as variables. (c) and (d) Scores and Loadings plots respectively for PCA analysis where predicted protein fold change values were used as variables. In Scores plots, circles indicate control treated samples, squares indicate Mek inhibitor treated samples, and diamonds indicate Erk inhibitor treated samples. Filled symbols indicate MDAMB231 cells while open symbols indicate SUM159 cells. In Loadings plots, variables are color coded by RTK (blue—Axl, orange—Met, green—EGFR, purple—Her2) and mechanistic processes are labeled accordingly.