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An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells

Abstract

The KDM5 family of histone demethylases catalyzes the demethylation of histone H3 on lysine 4 (H3K4) and is required for the survival of drug-tolerant persister cancer cells (DTPs). Here we report the discovery and characterization of the specific KDM5 inhibitor CPI-455. The crystal structure of KDM5A revealed the mechanism of inhibition of CPI-455 as well as the topological arrangements of protein domains that influence substrate binding. CPI-455 mediated KDM5 inhibition, elevated global levels of H3K4 trimethylation (H3K4me3) and decreased the number of DTPs in multiple cancer cell line models treated with standard chemotherapy or targeted agents. These findings show that pretreatment of cancer cells with a KDM5-specific inhibitor results in the ablation of a subpopulation of cancer cells that can serve as the founders for therapeutic relapse.

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Figure 1: Identification and characterization of a potent and selective KDM5 inhibitor with reversible activity in cells.
Figure 2: CPI-455 selectively affects H3K4 methylation in several cell models.
Figure 3: Crystal structure of KDM5A.
Figure 4: Inhibitor binding at the KDM5A active site.
Figure 5: KDM5 activity is increased in DTP models in vitro and in vivo.
Figure 6: KDM5 inhibition suppresses the emergence of drug-tolerant cells.

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Acknowledgements

We thank the Genentech Structural Biology Expression Group and J. Wu for additional protein expression and purification, as well as other members of the KDM5 team. We also thank J. Settleman for comments on the manuscript and B. Haley for short hairpin design. We thank Shamrock Structures, LLC, for diffraction data collection from beamline 08ID-1 at the Canadian Light Source, supported by the Natural Sciences and Engineering Research Council of Canada, the National Research Council Canada, the Canadian Institutes of Health Research, the Province of Saskatchewan, Western Economic Diversification Canada, and the University of Saskatchewan, and from beamline 5.0.2 of the Advanced Light Source. The Berkeley Center for Structural Biology is supported in part by the National Institutes of Health, National Institute of General Medical Sciences, and the Howard Hughes Medical Institute. The Advanced Light Source is supported by the Director, Office of Science and Office of Basic Energy Sciences, of the US Department of Energy under Contract No. DE-AC02-05CH11231.

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Contributions

M.V. and J.R.K. were involved in the crystallography efforts. V.S.G., A.G., K.E.W., P.G., W.M., E.M.F., F.L., S.O., A.G.C., Y.L., C.B., S.B., R.T.C., B.K.A. and J.-C.H. were involved in assay development, protein production, biochemical assays, and the development and execution of cell-based assays. F.L. made the KDM5A constructs. S.A., C.A.T., C.W., G.D.G., H.K., T.L., M.C. and R.P. were involved in the design and execution of DTP and ALDH assays. M.W., Y.Y., E.J. and G.V.H. were involved in the in vivo analysis of tumors in patients and mice. T.K.C., T.M.M., D.A. and J.B. participated in histone MS analysis. J.R.K., P.T. and M.C. contributed equally, oversaw all experiments and wrote the manuscript.

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Correspondence to James R Kiefer, Patrick Trojer or Marie Classon.

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Competing interests

V.S.G., S.A., K.E.W., W.M., J.B., S.O., C.B., S.B., R.T.C. and P.T. are employees and shareholders of Constellation Pharmaceutical Inc. P.G., F.L., J.-C.H. and B.K.A. are shareholders of Constellation Pharmaceutical Inc. All other authors are employees of Genentech Inc. and may hold stock in the Roche Group.

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Vinogradova, M., Gehling, V., Gustafson, A. et al. An inhibitor of KDM5 demethylases reduces survival of drug-tolerant cancer cells. Nat Chem Biol 12, 531–538 (2016). https://doi.org/10.1038/nchembio.2085

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