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Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML

Nature Chemical Biology volume 8, pages 905–912 (2012)Cite this article

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Abstract

Occurrence of the BCR-ABLT315I gatekeeper mutation is among the most pressing challenges in the therapy of chronic myeloid leukemia (CML). Several BCR-ABL inhibitors have multiple targets and pleiotropic effects that could be exploited for their synergistic potential. Testing combinations of such kinase inhibitors identified a strong synergy between danusertib and bosutinib that exclusively affected CML cells harboring BCR-ABLT315I. To elucidate the underlying mechanisms, we applied a systems-level approach comprising phosphoproteomics, transcriptomics and chemical proteomics. Data integration revealed that both compounds targeted Mapk pathways downstream of BCR-ABL, resulting in impaired activity of c-Myc. Using pharmacological validation, we assessed that the relative contributions of danusertib and bosutinib could be mimicked individually by Mapk inhibitors and collectively by downregulation of c-Myc through Brd4 inhibition. Thus, integration of genome- and proteome-wide technologies enabled the elucidation of the mechanism by which a new drug synergy targets the dependency of BCR-ABLT315I CML cells on c-Myc through nonobvious off targets.

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Figure 1: Danusertib and bosutinib synergize specifically in BCR-ABLT315I cells.
Figure 2: Quantitative chemical proteomics reveals target spectra of eight clinical BCR-ABL kinase inhibitors and indicates impairment of MAPK signaling resulting from off-target effects of danusertib and bosutinib.
Figure 3: Transcriptome-wide analysis indicates global downregulation of c-Myc target genes after combinatorial treatment with danusertib and bosutinib.
Figure 4: Quantitative phosphoproteomics highlights the impact of drug combination on the MAPK signaling network and the functional relevance of inhibition of MEK and ERK.
Figure 5: Combination of danusertib and bosutinib interferes on a post-translational level with c-Myc transcriptional activity.

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Acknowledgements

We thank J. Bradner (Dana Faber Cancer Institute–Harvard Medical School) for providing JQ1S and JQ1R and R. Giambruno, C. Tan, J. Bigenzahn and O. Hantschel for skillful advice and help. We also thank J. Lehar for inspiring discussions and S. Nijman and O. Hantschel for carefully reading this manuscript. We thank Cell Signaling Technology for allowing reproduction of the kinome map. We acknowledge L. Brecker for measuring NMR spectra. The present work was, in part, financed by the 'GEN-AU' initiative of the Austrian Federal Ministry for Science and Research (PLACEBO GZ BMWF-70.081/0018-II/1a/2008) as well as the Austrian Science Fund (P 24321-B21).

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Author notes

  1. Uwe Rix & Scott M Carlson

    Present address: Present addresses: Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA (U.R.) and Department of Biology, Stanford University, Stanford, California, USA (S.M.C.).,

  2. Georg E Winter and Uwe Rix: These authors contributed equally to this work.

Authors and Affiliations

  1. CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria

    Georg E Winter, Uwe Rix, Florian Grebien, Manuela Gridling, André C Müller, Florian P Breitwieser, Jacques Colinge, Keiryn L Bennett & Giulio Superti-Furga

  2. Department of Biological Engineering and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA

    Scott M Carlson & Forest M White

  3. Department of Internal Medicine I, Division of Hematology and Hemostaseology, Medical University of Vienna, Vienna, Austria

    Karoline V Gleixner & Peter Valent

  4. Clinical Institute for Medical and Chemical Laboratory Diagnostics, Medical University of Vienna, Vienna, Austria

    Martin Bilban

  5. Ludwig Boltzmann Cluster Oncology, Vienna, Austria

    Peter Valent

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Contributions

G.E.W. designed and performed the experiments, analyzed and interpreted the data, performed statistical analyses, made the figures and wrote the manuscript. U.R. designed and performed the experiments, analyzed and interpreted the data, performed statistical analyses, made the figures and wrote the manuscript. S.M.C. performed phosphoproteomics studies and analyzed and interpreted the resulting data. K.V.G. performed experiments in primary human samples and analyzed and interpreted the data. F.G. performed fluorescence-activated cell sorting analysis and helped perform colony formation assays. M.G. carried out immunoblot experiments. A.C.M. performed pre-phosphoproteomic screening studies and analyzed quantitative drug pulldowns by mass spectrometry. F.P.B. analyzed quantitative proteomics data and performed bioinformatic experiments. M.B. performed microarray experiments. J.C. analyzed chemical proteomics experimental data and performed bioinformatic analysis. P.V. planned experiments, contributed patient samples and gave advice on the research. K.L.B. planned experiments and analyzed chemical proteomics experiments. F.M.W. planned experiments and analyzed phosphoproteomics data. G.S.-F. conceived of the experimental strategy with G.E.W. and U.R., had overall responsibility for the research and wrote and edited the manuscript.

Corresponding author

Correspondence to Giulio Superti-Furga.

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Winter, G., Rix, U., Carlson, S. et al. Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML. Nat Chem Biol 8, 905–912 (2012). https://doi.org/10.1038/nchembio.1085

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