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Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors

Abstract

It is generally assumed that recurrent mutations within a given cancer driver gene elicit similar drug responses. Cancer genome studies have identified recurrent but divergent missense mutations affecting the substrate-recognition domain of the ubiquitin ligase adaptor SPOP in endometrial and prostate cancers. The therapeutic implications of these mutations remain incompletely understood. Here we analyzed changes in the ubiquitin landscape induced by endometrial cancer–associated SPOP mutations and identified BRD2, BRD3 and BRD4 proteins (BETs) as SPOP–CUL3 substrates that are preferentially degraded by endometrial cancer–associated SPOP mutants. The resulting reduction of BET protein levels sensitized cancer cells to BET inhibitors. Conversely, prostate cancer–specific SPOP mutations resulted in impaired degradation of BETs, promoting their resistance to pharmacologic inhibition. These results uncover an oncogenomics paradox, whereby mutations mapping to the same domain evoke opposing drug susceptibilities. Specifically, we provide a molecular rationale for the use of BET inhibitors to treat patients with endometrial but not prostate cancer who harbor SPOP mutations.

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Figure 1: Endometrial cancer– and prostate cancer–associated SPOP mutants induce opposing effects on BET protein levels.
Figure 2: BET proteins are bona fide substrates of wild-type SPOP.
Figure 3: BET proteins are differentially ubiquitinated and degraded by endometrial cancer– and prostate cancer–specific SPOP mutants.
Figure 4: Cancer-type-specific SPOP mutants alter BET inhibitor sensitivity in an opposing manner.
Figure 5: Downregulation of FOSL1 sensitizes Ishikawa cells to JQ1 treatment.
Figure 6: Endometrial cancer–associated SPOP mutants sensitize cells to JQ1 treatment in vivo.

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Acknowledgements

We thank M. Losa, M. Storz, P. Schraml, S. Dettwiler and F. Prutek for help with tissue handling and histology assistance. We thank Q. Zhong for his help with the next-generation sequencing bioinformatics pipeline. We thank all members of the IRB animal core facility for technical assistance and the animal work. We thank E. Samartzis and K. Dedes (University Hospital Zurich) for providing AN3CA, HEC1A, HEC1B, HEC116, SNG-II, EFE184 and KLE cell lines. We thank the Oregon Health & Science University (OHSU) and the Cooperative Human Tissue Network (CHTN) for the tissue repository. We also thank all members of the laboratory for scientific discussions. J.-P.P.T. is funded by a Swiss National Science Foundation Professorship (PP00P3_150645) grant, a Swiss Cancer League (KSL-3654-02-2015) grant, a grant by the Jubiläumsstiftung Swiss Life AG and a grant by the Vontobel Stiftung. The Swiss National Science Foundation (310030B_160312/1), the European Research Council (268930), SystemsX IPhD (2013/128), Krebsforschungs Schweiz (KFS-3498-08-2014) and a GRL grant from the Korean government fund M.P. This work was also funded in part by a grant to P.J.W. provided by Oncosuisse (KLS-3384-02-2014-R) and the Foundation for Research in Science and the Humanities at the University of Zurich (SWF).

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Contributions

J.-P.P.T. originally developed the concept, further elaborated on it and designed the experiments together with H.J., G.E.T. and N.D.U. H.J., G.E.T., A.R., J.-P.P.T., N.D.U., T.S., S.N., A.U. and R.I.E. performed experiments and analyzed the data. H.J., G.C., G.E.T. and T.B. performed tumor xenograft experiments in immune-deficient mice. M.L., H.J. and J.-P.P.T. performed immunohistochemical experiments and analysis. P.J.W., P.S., H.M. and E.B. provided endometrial and prostate cancer samples with annotation for SPOP mutation status. D.G.M., M.E.C., A.B., B.J.N.W. and R.R.B. provided SPOP-mutant endometrial cancer samples. C.M.B., G.V.K., A.R. and L.C. analyzed genomic and RNA-seq data. J.-P.P.T., L.A.G., S.A.C., M.P., C.V.C., F.B. and P.J.W. provided funding and resources. J.-P.P.T., H.J. and G.E.T. interpreted the data and wrote the paper. H.J. and G.E.T. contributed equally to this work.

Corresponding author

Correspondence to Jean-Philippe P Theurillat.

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Competing interests

L.A.G. is a paid consultant of the following pharmaceutical companies: Novartis Foundation Medicine, Boehringer INgelheim and Millennium/Takeda. The authors declare no additional competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–11. (PDF 5869 kb)

Supplementary Table 1

Proteome and KGG Datasets. (XLSX 17362 kb)

Supplementary Table 2

RNA sequencing Datasets. (XLSX 6884 kb)

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Janouskova, H., El Tekle, G., Bellini, E. et al. Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors. Nat Med 23, 1046–1054 (2017). https://doi.org/10.1038/nm.4372

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