Abstract

Triple-negative breast cancer (TNBC) is a heterogeneous and clinically aggressive disease for which there is no targeted therapy1,2,3. BET bromodomain inhibitors, which have shown efficacy in several models of cancer4,5,6, have not been evaluated in TNBC. These inhibitors displace BET bromodomain proteins such as BRD4 from chromatin by competing with their acetyl-lysine recognition modules, leading to inhibition of oncogenic transcriptional programs7,8,9. Here we report the preferential sensitivity of TNBCs to BET bromodomain inhibition in vitro and in vivo, establishing a rationale for clinical investigation and further motivation to understand mechanisms of resistance. In paired cell lines selected for acquired resistance to BET inhibition from previously sensitive TNBCs, we failed to identify gatekeeper mutations, new driver events or drug pump activation. BET-resistant TNBC cells remain dependent on wild-type BRD4, which supports transcription and cell proliferation in a bromodomain-independent manner. Proteomic studies of resistant TNBC identify strong association with MED1 and hyper-phosphorylation of BRD4 attributable to decreased activity of PP2A, identified here as a principal BRD4 serine phosphatase. Together, these studies provide a rationale for BET inhibition in TNBC and present mechanism-based combination strategies to anticipate clinical drug resistance.

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Primary accessions

Gene Expression Omnibus

Data deposits

RNA-seq, ChIP-seq, and Chem-seq data have been deposited in the NCBI GEO database with the accession number GSE63584.

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Acknowledgements

We thank D. Silver and members of the Polyak and Bradner laboratories for their critical reading of this manuscript and useful discussions. We thank G. Brown for help with creating the word cloud figures. This work was supported by the NIH DF/HCC SPORE in Breast Cancer CA168504 (K.P., E.P.W., I.E.K., D.D., W.T.B., and J.E.B.), CA080111 (K.P. and M.B.), and CA103867 (C.M.C.), Susan G. Komen Foundation (S.S.), CPRIT RP110471 and RP140367 (C.M.C), Welch Foundation (C.M.C.), US Department of Defense CDMRP BC122003 (S.X.L.) and CA120184 (C.Y.L.), Princess Margaret Cancer Foundation (H.H.H.), Canada Foundation for Innovation and Ontario Research Fund CFI32372 (H.H.H.), NSERC discovery grant RGPIN-2015-04658 (H.H.H.), and the Harvard Ludwig Center for Cancer Research (J.E.B., M.B. and K.P.).

Author information

Author notes

    • Shaokun Shu
    • , Charles Y. Lin
    • , Housheng Hansen He
    •  & Robert M. Witwicki

    These authors contributed equally to this work.

Affiliations

  1. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA

    • Shaokun Shu
    • , Charles Y. Lin
    • , Housheng Hansen He
    • , Robert M. Witwicki
    • , Doris P. Tabassum
    • , Justin M. Roberts
    • , Michalina Janiszewska
    • , Sung Jin Huh
    • , Jeremy Ryan
    • , Ernest Doherty
    • , Daniel G. Stover
    • , Muhammad B. Ekram
    • , Guillermo Peluffo
    • , Jonathan Brown
    • , Ian E. Krop
    • , Deborah Dillon
    • , Michael McKeown
    • , Christopher Ott
    • , Jun Qi
    • , Min Ni
    • , Eric P. Winer
    • , Antony Letai
    • , Henry W. Long
    • , Myles Brown
    • , James E. Bradner
    •  & Kornelia Polyak
  2. Department of Medicine, Brigham and Women’s Hospital, and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Shaokun Shu
    • , Charles Y. Lin
    • , Housheng Hansen He
    • , Robert M. Witwicki
    • , Michalina Janiszewska
    • , Sung Jin Huh
    • , Jeremy Ryan
    • , Daniel G. Stover
    • , Muhammad B. Ekram
    • , Guillermo Peluffo
    • , Jonathan Brown
    • , Ian E. Krop
    • , Michael McKeown
    • , Christopher Ott
    • , Jun Qi
    • , Min Ni
    • , Eric P. Winer
    • , Antony Letai
    • , William T. Barry
    • , Myles Brown
    • , James E. Bradner
    •  & Kornelia Polyak
  3. Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, and Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts 02115, USA

    • Housheng Hansen He
    • , Hao Guo
    • , William T. Barry
    • , X. Shirley Liu
    •  & Clifford A. Meyer
  4. Princess Margaret Cancer Center/University Health Network, Toronto, Ontario M5G1L7, Canada

    • Housheng Hansen He
    •  & Yi Liang
  5. Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G2M9, Canada

    • Housheng Hansen He
  6. Harvard University, Cambridge, Massachusetts 02138, USA

    • Ernest Doherty
  7. Cancer Research UK, Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK

    • Hisham Mohammed
    • , Clive D’Santos
    •  & Jason S. Carroll
  8. Department of Pathology, Brigham and Women’s Hospital, and Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Deborah Dillon
  9. Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA

    • Prakash K. Rao
    • , Melissa Duarte
    • , Henry W. Long
    • , Myles Brown
    • , X. Shirley Liu
    •  & Kornelia Polyak
  10. Simmons Comprehensive Cancer Center, Departments of Biochemistry and Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA

    • Shwu-Yuan Wu
    •  & Cheng-Ming Chiang
  11. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA

    • Lars Anders
    •  & Richard A. Young
  12. Broad Institute, Cambridge, Massachusetts 02142, USA

    • X. Shirley Liu
    • , James E. Bradner
    •  & Kornelia Polyak

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Contributions

S.S. performed cell culture, xenograft, ChIP-seq, and RNA-seq experiments, and data analyses. C.Y.L. and C.A.M. performed genomic data analyses. H.H.H. helped with ChIP-seq and RNA-seq experiments and data analyses. R.M.W. performed cell culture, ChIP-seq experiments and data analyses. J.M.R. performed synergy studies. D.P.T. helped with immunofluorescence staining. M.J. and S.J.H. helped with confocal microscopy and image quantification. Y.L. helped with BRD4 ChIP-seq. M.B.E. and G.P. helped with cell cycle studies. E.D. helped with generating and testing BRD4 mutants. J.B. and L.A. performed Chem-seq. H.M., C.D. and J.S.C. conducted proteomic experiments and data analyses. C.O. and M.M. performed drug sensitivity screens. J.Q. synthesized BBI compounds. M.N. generated shRNA constructs. D.D., I.E.K. and E.P.W. generated the TMA and linked to clinical data. H.G., D.G.S. and W.T.B. performed TMA and statistical analyses. J.R. and A.L. performed BH3 profiling and data analyses. C.-M.C. and S.-Y.W. provided phospho-BRD4 antibody. P.K.R. and M.D. generated RNA-seq libraries. K.P. supervised with help from J.E.B., X.S.L., M.B., R.A.Y. and H.L. All authors helped to design the study and write the manuscript.

Competing interests

J.E.B. and R.A.Y. are founders of Syros Pharmaceuticals, J.E.B. is the founder of Tensha Therapeutics. K.P. receives research support from and is a consultant for Novartis Oncology.

Corresponding authors

Correspondence to James E. Bradner or Kornelia Polyak.

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https://doi.org/10.1038/nature16508

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