Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk

Abstract

Bromodomain-containing proteins of the BET family recognize histone lysine acetylation and mediate transcriptional activation of target genes such as the MYC oncogene. Pharmacological inhibitors of BET domains promise therapeutic benefits in a variety of cancers. We performed a high-diversity chemical compound screen for agents capable of modulating BRD4-dependent heterochromatization of a generic reporter in human cells. In addition to known and new compounds targeting BRD4, we identified small molecules that mimic BRD4 inhibition without direct engagement. One such compound was a potent inhibitor of the second bromodomain of TAF1. Using this inhibitor, we discovered that TAF1 synergizes with BRD4 to control proliferation of cancer cells, making TAF1 an attractive epigenetic target in cancers driven by MYC.

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Figure 1: Generation of a reporter cell line for the inhibition of BRD4.
Figure 2: Screening for functional BRD4 inhibitors.
Figure 3: Molecular and cellular characterization of CeMMEC1 and CeMMEC2.
Figure 4: TAF1 synergizes with BRD4 to mediate transcriptional control.

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Acknowledgements

Research in the Kubicek laboratory is supported by the Austrian Federal Ministry of Science, Research and Economy; the National Foundation for Research, Technology, and Development; the Marie Curie Career Integration Grant EPICAL; and the JDRF. This project was supported by SFB grant F4710 of the Austrian Science Fund (FWF). S.S. acknowledges support by JDRF postdoctoral fellowship 3-PDF-2014-206-A-N “Reprogramming by Loss of Function”. J.B., C.T., O.F. and S.M. are funded by the Structural Genomics Consortium, a registered charity (number 1097737) that receives funds from AbbVie, Bayer, Boehringer Ingelheim, the Canada Foundation for Innovation, the Canadian Institutes for Health Research, Genome Canada, GlaxoSmithKline, Janssen, Lilly Canada, the Novartis Research Foundation, the Ontario Ministry of Economic Development and Innovation, Pfizer, Takeda and the Wellcome Trust (092809/Z/10/Z). We thank all the members of the BioOptic Facility of the Research Institute of Molecular Pathology (IMP) and the Institute of Molecular Biotechnology GmbH (IMBA) for their help with cell sorting; S. Gresko and V. Ivanov (Enamine Ltd) for compound synthesis; J.E. Bradner (Dana-Farber Cancer Institute) for an initial batch of JQ1 and for library compounds; and K.M. Pugh (Target Discovery Institute; Oxford) for help with analytical chemistry. Dedicated to S.L. Schreiber on the occasion of his 60th birthday.

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S.S. and S. Kubicek conceived the project, designed experiments, analyzed data and wrote the manuscript with input from all co-authors; S.S. and C.-H.L. performed high-throughput screens and analyzed data; S.S., C.T., B.K., J.B., O.F., S. Knapp and S.M. performed biochemical binding studies and analyzed data; F.K. generated and analyzed molecular modeling data; P.R., T.P., M.S., C.B. and J.Z. generated and analyzed transcriptomics data; K.V.M.H. and G.S.-F. performed analytical chemistry and co-wrote the manuscript.

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Correspondence to Stefan Kubicek.

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S.S. and S. Kubicek have filed a patent application (EP16155781) with claims derived from work described in this manuscript.

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Supplementary Results, Supplementary Figures 1–7 and Supplementary Tables 1–3. (PDF 7996 kb)

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Sdelci, S., Lardeau, CH., Tallant, C. et al. Mapping the chemical chromatin reactivation landscape identifies BRD4-TAF1 cross-talk. Nat Chem Biol 12, 504–510 (2016). https://doi.org/10.1038/nchembio.2080

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