Extended Data Fig. 10: Characterization of drug-response variation across 27 MCF7 strains.

a, Unsupervised hierarchical clustering of 27 MCF7 strains, based on their response to all 321 compounds in the primary screen. Groups of strains expected to cluster together based on their evolutionary history are highlighted, as in Fig. 1. b, Pie chart of the classification of the screened compounds based on their differential activity. The response to each active compound was defined as ‘consistent’ if viability change was <−50% for all strains, ‘variable’ if viability change was <−50% for some strains and >−20% for other strains, or ‘intermediate’ if viability change was in between these values. Classification was performed using a two-strain threshold. c, Pie charts as in b excluding strains Q and M that were generally more drug resistant. Classification was performed using a one-strain or a two-strain threshold (left and right charts, respectively). d, Pie charts as in b using an activity threshold of viability change <−80%. Classification was performed using a one-strain threshold, either including all strains (left) or excluding strains Q and M (right). e, The number of gene-level CNAs shared by each number of MCF7 strains. Red, copy number gains; blue copy number losses. f, The number of non-silent point mutations shared by each number of MCF7 strains. The 10 naturally occurring connectivity map strains were averaged and considered as a single sample. g, The correlation between proliferation rate (shown as doubling time) and the number of non-silent protein-coding mutations, across naturally occurring MCF7 strains (n = 10). Spearman’s ρ and P values indicate the strength and significance of the correlation, respectively. The 10 naturally occurring CMap strains were averaged and considered as a single sample. h, The correlation between proliferation rate (shown as doubling time) and the fraction of subclonal mutations, across naturally occurring MCF7 strains (n = 10). Spearman’s ρ and P values indicate the strength and significance of the correlation, respectively. The 10 naturally occurring CMap strains were averaged and considered as a single sample. i, The number of differentially expressed genes identified in all possible pairwise comparisons of MCF7 strains, using a twofold change cutoff. The 10 naturally occurring CMap strains were averaged and considered as a single sample. j, Pie charts of the classification of the screened compounds based on their differential activity. The response to each active compound was defined as consistent if viability change was <−50% for all strains, variable if viability change was <−50% for some strains and >−20% for other strains, or intermediate if viability change was in between these values. Classification was performed using a one-strain or a two-strain resistance threshold (top and bottom charts, respectively). The 10 naturally occurring CMap strains were averaged and considered as a single sample. k, The dose–response curves for ten compounds are shown. For each compound, eight concentrations were tested in each strain. Two sensitive strains and two insensitive strains are plotted. Each data point represents the mean of two replicates. Nutlin-3, a compound that had no toxicity against any of the strains in the primary screen, was included as negative control. Romidepsin, a compound that killed all strains very efficiently in the primary screen was included as positive control and turned out to be differentially active at lower concentrations. l, The Pearson’s correlation of the two compound screen replicates across the MCF7 strains. m, Strains more sensitive to proteasome inhibitors exhibit higher proteasome activity. The chymotrypsin-like activity of the proteasome was measured in three sensitive and three insensitive strains. Data are mean ± s.d., one-tailed t-test, n = 4 replicate wells. n, Western blots of the relative protein expression levels of the proteasome 19S complex members PSMC2 and PSMD1 in three sensitive and three insensitive strains. The expression of α-tubulin was used for normalization. The experiment was repeated once, with n = 3 strains per group. For gel source data, see Supplementary Fig. 1. o, Quantification of the relative expression of PSMC2 and PSMD1. Data are mean ± s.d., one-tailed t-test, n = 3 strains per group. p, Upregulation of the KEGG cell cycle signature in strains sensitive to the cell cycle inhibitor CDK/CRK inhibitor (n = 3) compared to insensitive strains (n = 12). q, Upregulation of mTOR signalling in strains sensitive to the PI3K inhibitor PP-121 (n = 11) compared to insensitive strains (n = 5). r, Downregulation of the genes that are downregulated when ALK is knocked down in strains sensitive to the ALK inhibitor TAE-684 (n = 4) compared to insensitive strains (n = 15). s, Upregulation of IL-6–JAK–STAT3 signalling in strains sensitive to the STAT inhibitor nifuroxazide (n = 9) compared to insensitive strains (n = 6). t, Upregulation of the genes that are upregulated when AKT is overexpressed in strains sensitive to the AKT inhibitor triciribine (n = 2) compared to insensitive strains (n = 8). u, Upregulation of hypoxia signalling in strains sensitive to the HSP inhibitor 17-AAG (n = 3) compared to insensitive strains (n = 15). v, Downregulation of xenobiotic metabolism signatures in strains M and Q (n = 2), which exhibited an increased resistance to most compounds compared to the other strains (n = 25). w, Upregulation of the early and late oestrogen response signatures, in strains most sensitive to the ER inhibitor tamoxifen (n = 5) compared to the least sensitive strains (n = 5). x, Sensitivity to oestrogen depletion and to tamoxifen is associated with the copy number status of ESR1. Heat maps represent the relative viability in oestrogen-depleted medium (top) and in response to tamoxifen (at 16.6 μM; bottom).