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A chemical-genetic screen reveals a mechanism of resistance to PI3K inhibitors in cancer

Nature Chemical Biology volume 7, pages 787–793 (2011)Cite this article

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Abstract

Linking the molecular aberrations of cancer to drug responses could guide treatment choice and identify new therapeutic applications. However, there has been no systematic approach for analyzing gene-drug interactions in human cells. Here we establish a multiplexed assay to study the cellular fitness of a panel of engineered isogenic cancer cells in response to a collection of drugs, enabling the systematic analysis of thousands of gene-drug interactions. Applying this approach to breast cancer revealed various synthetic-lethal interactions and drug-resistance mechanisms, some of which were known, thereby validating the method. NOTCH pathway activation, which occurs frequently in breast cancer, unexpectedly conferred resistance to phosphoinositide 3-kinase (PI3K) inhibitors, which are currently undergoing clinical trials in breast cancer patients. NOTCH1 and downstream induction of c-MYC over-rode the dependency of cells on the PI3K-mTOR pathway for proliferation. These data reveal a new mechanism of resistance to PI3K inhibitors with direct clinical implications.

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Figure 1: Barcode screen setup, detection and performance.
Figure 2: Combinatorial breast cancer gene small compound screen.
Figure 3: NOTCH activation renders breast cancer cells resistant to PI3K-mTORC1 inhibition.
Figure 4: c-MYC induction confers resistance to PI3K-mTOR inhibition.

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Acknowledgements

We thank the T. Berg, A. Harutyunyan, U. Rix and G. Hofbauer for technical assistance; F. Ganglberger, B. Eizinger and P. Markt for assisting in data analysis; and H. Pickersgill, M. Creyghton and G. Superti-Furga for critical reading and suggestions. We are grateful to T. Golub and C. Yu for support and discussions in the early phases of the project; and to A. D'Andrea, H. Dolznig, C. Tabin, T. Brummelkamp, R. Bernards, P. Eichhorn, D. Peeper, W. Hahn, R. Conaway, J. Conaway, R. Weinberg, I. Screpanti, J. Zhao, R. Hynes, Y. Xiong, R. Basch, B. Vogelstein, D. Bulavin, P. Yaswen, R. Kopan, M. Parker, J. Bradner and D. Root for providing reagents. We thank Luminex for providing reagents and support. This work was made possible by research grants from the Austrian Science Fund (FWF, P21768-B13) and the Vienna Science and Technology Fund (WWTF, LS09-009).

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Author notes

  1. Iris Z Uras and Bianca V Gapp: 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

    Markus K Muellner, Iris Z Uras, Bianca V Gapp, Claudia Kerzendorfer, Michal Smida, Hannelore Lechtermann, Nils Craig-Mueller, Jacques Colinge, Gerhard Duernberger & Sebastian M B Nijman

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Contributions

S.M.B.N. and M.K.M. conceived the study, designed experiments, analyzed data and wrote the manuscript. M.K.M. and S.M.B.N., with help from I.Z.U. and N.C.-M., set up the multiplexing assay. B.V.G., I.Z.U and M.K.M. created and characterized the isogenic cell lines. J.C. and G.D. designed the analysis platform and database infrastructure for the screen. G.D. and M.K.M. analyzed the screening data and wrote R code to identify hits. M.K.M. performed the majority of experiments. C.K., M.S., H.L. and S.M.B.N. performed and helped with additional experiments.

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Correspondence to Sebastian M B Nijman.

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Muellner, M., Uras, I., Gapp, B. et al. A chemical-genetic screen reveals a mechanism of resistance to PI3K inhibitors in cancer. Nat Chem Biol 7, 787–793 (2011). https://doi.org/10.1038/nchembio.695

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