Abstract
Mass spectrometry-based discovery proteomics is an essential tool for the proximal readout of cellular drug action. Here, we apply a robust proteomic workflow to rapidly profile the proteomes of five lung cancer cell lines in response to more than 50 drugs. Integration of millions of quantitative protein–drug associations substantially improved the mechanism of action (MoA) deconvolution of single compounds. For example, MoA specificity increased after removal of proteins that frequently responded to drugs and the aggregation of proteome changes across cell lines resolved compound effects on proteostasis. We leveraged these findings to demonstrate efficient target identification of chemical protein degraders. Aggregating drug response across cell lines also revealed that one-quarter of compounds modulated the abundance of one of their known protein targets. Finally, the proteomic data led us to discover that inhibition of mitochondrial function is an off-target mechanism of the MAP2K1/2 inhibitor PD184352 and that the ALK inhibitor ceritinib modulates autophagy.
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Acknowledgements
We thank T. Huynh for help with compound plating and A. Vickers and S. Smith for assistance with imaging experiments.
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B.R., I.C.-T. and A.C conceived the study. B.R., Y.X. and A.L. designed experiments. B.R., O.U. and H.W. analyzed the proteomics data. B.R., J.D.B., X.M., R.B.F., M.C., Z.W. and L.Z. prepared samples. J.D.B., R.B.F., X.M., Z.W., L.Z. and R.B.F. performed imaging experiments. B.R. wrote the manuscript with input from all authors. N.S. performed cell viability experiments and B.A. and J.D.M. contributed reagents/compounds. B.R. and B.D.D. performed MS measurements. M.G., J.R.T., V.K., I.C.-T. and A.C. provided resources. B.R. and A.C. supervised the study. All authors read the manuscript and contributed to revisions.
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All authors are or were employees of Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA.
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Extended data
Extended Data Fig. 1 Proteome-wide mapping of drug-induced protein abundance changes in five cell lines.
a, The heatmap shows the pairwise Pearson correlations (color-coded from 0.95–1) of proteomes from one 96-well plate (the average pairwise Pearson R is 0.983; data is based on 96 biologically independent samples). b, To define MS1 mass-to-charge ratio (m/z) segments, the m/z ion intensity was recorded over a 120 min gradient, summed up and distributed into 1 Da bins (only z > 1 was considered). After calculating the percentage of intensity per 1 Da bin, the m/z range was distributed into segments such that the overall intensity in each segment is equal. The graph shows an example for the distribution of the ion density into three segments (S): S1 = m/z 350–525; S2 = m/z 525–695; S3 = m/z 695–1,200. c, Heatmap showing the number of regulated proteins per inhibitor and cell line (two-sided t-test with permutation-based FDR < 0.05; n = 12 (DMSO) and 3 (each inhibitor) biologically independent samples).
Extended Data Fig. 2 Improving single drug mechanism of action (MoA) deconvolution through pharmaco-proteomic context.
a, Global, drug-induced kinome reprograming visualized in a kinome tree. The bubbles represent individual kinases and their size reflects the number of inhibitor-cell line combinations their abundance was upregulated in (two-sided t-test with permutation-based FDR < 0.05; n = 9 (DMSO) and 3 (inhibitor) biologically independent samples). Among them are many kinases with known roles in lung cancer drug resistance (for example MET, AXL or RAF1). b, Expression of the drug efflux pump ABCB1 was significantly induced by LMK235 (iHDAC4/5) in 2030 cells. ABCB1 is known to bind and export structurally similar compounds (q value derived by permutation-based FDR correction of two-sided t-test derived P values; n = 11 (DMSO) and 3 (iHDAC4/5) biologically independent samples). c, Bar plot showing the number of proteins (two-sided t-test with permutation-based FDR < 0.05; n = 12 (DMSO) and 3 (inhibitor) biologically independent samples) which were exclusively regulated in a single cell line (bars facing down), or consistently across multiple cell lines (bars facing up; color code indicates the number of cell lines). Only the 10 inhibitors with the highest number of regulated proteins across the five cell lines are shown. d, The dot plots depict the log2(FC) of the same protein for different inhibitors (each inhibitor is a dot) in different cell lines (x-axis). The red dot shows Ribociclib (iCDK4/6) which is known to bind to CDK4. Summing up the log2(FC) for the same inhibitor across different cell lines (labeled with “sum”) increased signal-to-noise e, Examples for known drug targets which display outlier characteristics after aggregation of log2 fold changes across cell lines. The dots represent the summed log2(FC) of the same protein (labeled in the header) for different inhibitors. A red dot indicates an inhibitor which is known to bind to the labeled protein (5-FU = 5-fluorouracil).
Extended Data Fig. 3 Proteomic binning of compounds by MoA.
a, Waterfall plot showing all cell line aggregated log2(FC) outliers (> 3 s.d.; 52 inhibitors; n = 12 (DMSO) and 3 (inhibitor) biologically independent samples) for the PIK3C3 inhibitor PIK-III (ranked by magnitude of protein log2(FC)). The protein SQSTM1 (also known as p62; marked in red), which is a known marker for autophagy modulation was strongly and consistently upregulated in response to PIK-III (iPIK3C3) treatment. b, Indicated cell lines were treated with inhibitors for 24 h (30 μM CQ, 3 μM iALK, 10 μM iCAMK2 or DMSO) and stained for endogenous SQSTM1 (p62, green fluorescence). Cell nuclei were stained using Hoechst (blue). Chloroquine (CQ) and PIK-III (iPIK3C3) served as positive controls. Dots represent extracted, background corrected and normalized intensity values for autophagosome puncta from four individual wells (center line represents the median). c, Chemoproteomic kinase selectivity profiling of iALK and iCAMK2 using pan-kinase beads in A549 cell lysate. EC50 values were derived from a dose–response curve based on eight doses (n = one replicate; four-parameter nonlinear regression fit). The dot plot shows the -log10 EC50 values for kinases competed by iCAMK2 (left) and iALK (right). Red dots represent protein kinase competed by both compounds, whereas grey dots represent unique protein kinases. iCAMK2 also competed six subunits of the PRKA (AMPKA) complex (marked in purple). d, Calu6 cells were treated with increasing doses of the indicated compounds for 16 h and stained for SQSTM1 (p62). Puncta representing autophagosomes were automatically extracted and quantified. PF-562271 is a known inhibitor of the kinases PTK2, PTK2B and FER which are also targets of iALK and iCAMK2. A full list of tested compounds and curve fitting parameters in all five cell lines can be found in Supplementary Data 4.
Extended Data Fig. 4 Using differential proteome changes of pharmacologically related compounds to identify off-target MoAs.
a, Volcano plots comparing iMEK I and iMEK II in A549 and Calu1 cells (q value derived by permutation-based FDR correction of two-sided t-test P values; n = 9 (DMSO for A549), 12 (DMSO for Calu6) and 3 (inhibitors) biologically independent samples; proteins with FDR < 0.1 are shown in black; mitochondrial ribosome subunits are labeled). The mitochondrial translation machinery was strongly downregulated by iMEK II but not iMEK I in A549 and Calu6 cells. b, Aggregation analysis for iMEK I (> 3 s.d.; 53 inhibitors; 5 cell lines; outlier for < 3 compounds). Data is based on n = 12 (DMSO) and 3 (inhibitor) biologically independent samples. Two subunits of the mitochondrial ribosomes are highlighted in red.
Supplementary information
Supplementary Information
Supplementary Figs. 1–3 and Note.
Supplementary Data 1
Table 1: Compound names including target/MoA annotation. Table 2: Matrix containing CTG-derived compound EC50 values per inhibitor and cell line and corresponding canonical doses used for proteome profiling. Table 3: Position of compounds on plates per cell line. This annotation can be used to map inhibitors to the individual LFQ values of the datasets in Tables 3–7. Tables 4–8: Protein quantification data and quantification/regulation statistics for individual cell lines A549, Calu1, Calu6, 2030 and 2122. Table 9: Valid values per sample for each cell line. Table 10: Matrix showing the number of regulated proteins per inhibitor and cell line (FDR < 0.05).
Supplementary Data 2
Table 1: Count of significant regulation for each protein per cell line and across the entire dataset (two-sided t-test with permutation-based FDR < 0.05; n = 12 (DMSO) and 3 (inhibitor) biologically independent samples). This singles out frequently responding proteins which are less likely to be compound specific. Table 2: Brefeldin A-regulated proteins in 2122 cells (two-sided t-test with permutation-based FDR < 0.05; n = 10 (DMSO) and 3 (brefeldin A) biologically independent samples). Frequent responders are indicated in red (including Reactome pathway enrichment based on 226 frequent responders; statistical framework based on String database v11.0). Specific proteins are colored green (including Reactome pathway enrichment based on 228 proteins remaining after subtraction of frequent responders; statistical framework based on String database v11.0). Table 3: Global aggregation analysis (AA). Individual log2(FC) for a given protein are summed up and compared to the summed log2(FC) of that protein across the remaining 52 inhibitors (n = 12 (DMSO) and 3 (inhibitor) biologically independent samples). Only sum log2(FC) values that deviate three standard deviations from the mean of the sum log2(FC) of the remaining 52 inhibitors are included. The user can filter based on the number of cell lines the protein was found in, the log2(FC) mean across cell lines and on the number of compounds that also show outlier behavior for the respective protein. Table 4: ‘Leave one out’ analysis to quantify the robustness of aggregation analysis. The table shows the R2 value (based on Pearson R correlation) of remaining aggregated log2(FC) after one cell line has been removed (n = 12 (DMSO) and 3 (inhibitor) biologically independent samples). Table 5: Filtered aggregation analysis (AA) for tanespimycin (iHSP90). Tables 6–10: Protein quantification data and quantification/regulation statistics for TL12–186 and TL13–27 in individual cell lines A549, Calu1, Calu6, 2030 and 2122 (two-sided t-test with permutation-based FDR control; n = 4 biologically independent samples). Table 11: Aggregation analysis (AA) for TL12–186 without TL13–27. Table 12: Aggregation analysis (AA) for TL12–186 with TL13–27. Table 13: Aggregation analysis (AA) for indisulam. Tables 14–18: Protein quantification data and quantification/regulation statistics for indisulam in individual cell lines A549, Calu1, Calu6, 2030 and 2122 (two-sided t-test with permutation-based FDR control; n = 4 biologically independent samples).
Supplementary Data 3
Table 1: L-1000 dataset annotation (20 overlapping compounds in A549; n = 1 replicate). Table 2: Combined L-1000 dataset in A549. Table 3: Correlation of z-scored abundance changes (536 overlapping genes) for single inhibitors between L-1000 and proteome profiling. Table 4: Combined proteome dataset of overlapping compounds in A549 (>50% valid values). Table 5: Azacitidine mRNA dataset and overlap with other datasets.
Supplementary Data 4
Table 1: Dose-resolved kinome selectivity profiling of iCAMK2 using pan-kinase beads and A549 cells (curve fit is based on eight doses; n = 1 replicate). Table 2: Dose-resolved kinome selectivity profiling of iALK using pan-kinase beads and A549 cells (curve fit is based on eight doses; n = 1 replicate). Table 3: Kinome targets of iALK and iCAMK2 including curve fitting parameters (curve fit is based on eight doses; n = 1 replicate). Table 4: Summary table for imaging-based quantification of SQSTM1 (p62) and MAP1LC3B (LC3) puncta in five cell lines A549, Calu1, Calu6, 2030 and 2122. All data have been acquired in a dose-dependent fashion and the table contains the individual curve fitting parameters. Tables 5–14: Extended curve characteristics for p62 and LC3 in individual cell lines.
Supplementary Data 5
Table 1: Global Reactome pathway enrichment across cell lines and inhibitors. The underlying protein quantification data are based on n = 12 (DMSO) and 3 (inhibitor) biologically independent samples. For pathway enrichment, GVSE was performed. The final list of proteins used as input for pathway enrichment was n(A549) = 6,738, n(Calu1) = 7,036, n(Calu6) = 7,163, n(2030) = 6,807, n(2122) = 6,092. P values were calculated using two-sided moderated t-statistics and corrected for multiple comparisons using a false discovery rate. Table 2: Dose-resolved kinome selectivity profiling of MEK inhibitors PD184352 and PD0325901 using pan-kinase beads and A549 cells (curve fit is based on eight doses; n = 1 replicate).
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Ruprecht, B., Di Bernardo, J., Wang, Z. et al. A mass spectrometry-based proteome map of drug action in lung cancer cell lines. Nat Chem Biol 16, 1111–1119 (2020). https://doi.org/10.1038/s41589-020-0572-3
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DOI: https://doi.org/10.1038/s41589-020-0572-3
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