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A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response

Abstract

The jumonji (JMJ) family of histone demethylases are Fe2+- and α-ketoglutarate-dependent oxygenases that are essential components of regulatory transcriptional chromatin complexes1,2,3,4. These enzymes demethylate lysine residues in histones in a methylation-state and sequence-specific context5. Considerable effort has been devoted to gaining a mechanistic understanding of the roles of histone lysine demethylases in eukaryotic transcription, genome integrity and epigenetic inheritance2,4,6, as well as in development, physiology and disease3,7. However, because of the absence of any selective inhibitors, the relevance of the demethylase activity of JMJ enzymes in regulating cellular responses remains poorly understood. Here we present a structure-guided small-molecule and chemoproteomics approach to elucidating the functional role of the H3K27me3-specific demethylase subfamily (KDM6 subfamily members JMJD3 and UTX)8. The liganded structures of human and mouse JMJD3 provide novel insight into the specificity determinants for cofactor, substrate and inhibitor recognition by the KDM6 subfamily of demethylases. We exploited these structural features to generate the first small-molecule catalytic site inhibitor that is selective for the H3K27me3-specific JMJ subfamily. We demonstrate that this inhibitor binds in a novel manner and reduces lipopolysaccharide-induced proinflammatory cytokine production by human primary macrophages, a process that depends on both JMJD3 and UTX. Our results resolve the ambiguity associated with the catalytic function of H3K27-specific JMJs in regulating disease-relevant inflammatory responses and provide encouragement for designing small-molecule inhibitors to allow selective pharmacological intervention across the JMJ family.

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Figure 1: Structure of the H3K27me3-derived peptide bound to mouse JMJD3.
Figure 2: Structure of the inhibitor GSK-J1 bound in the catalytic pocket of human JMJD3.
Figure 3: GSK-J1 is selective for H3K27 demethylases of the KDM6 subfamily and specifically binds to endogenous JMJD3.
Figure 4: GSK-J1 inhibits TNF-α production by human primary macrophages in an H3K27-dependent manner.

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Primary accessions

Protein Data Bank

Data deposits

Crystal structures of JMJD3 have been deposited in the Protein Data Bank under accession numbers 4EZ4 (mouse JMJD3–NOG–Ni2+), 4EYU (mouse JMJD3–NOG–Ni2+), 4EZH (mouse JMJD3–H3K27me3–Ni2+), 2XUE (human JMJD3–α-ketoglutarate–Fe2+) and 4ASK (human JMJD3–GSK-J1–Co2+).

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Acknowledgements

We thank the following colleagues for their help and advice in preparing the manuscript: A. Argyrou, S. Atkinson, M. Barker, M. Campbell, L. Gordon, R. Gregory, R. Grimley, P. Humphreys, P. Jeffrey, A. Kucik, B. Leavens, C. Lewis, V. Ludbrook, R. Prinjha, S. Ratcliffe, C. Sharp, D. Thomas, D. Tough and M. Woodrow. Help was also provided by N. Burgess-Brown, S. Ng, J. Dunford, A. Kawamura, N. Rose and M. Daniel. D.J.P. was supported by funds from the Starr Foundation, the Abby Rockefeller Mauze Trust and the Maloris Foundation. The Structural Genomics Consortium is a registered charity (number 1097737) that receives funds from the Canadian Institutes for Health Research, the Canada Foundation for Innovation, Genome Canada, GlaxoSmithKline, Lilly Canada, the Novartis Research Foundation, Pfizer, Takeda, the Ontario Ministry of Economic Development and Innovation, and the Wellcome Trust. This study was supported by the National Institute for Health and Research (NIHR) Biomedical Research Unit, Oxford. Thanks also to M. Boesche and the Cellzome biochemistry and mass spectrometry teams for assistance with the chemoproteomics experiments. Finally, we acknowledge additional contributions from members of Platform Technology Sciences and the Epinova DPU and the JMJD3 programme team for supporting this research.

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L.K., C.-w.C., J.L., Z.C., G.D., U.O., D.J.P., K.C., K.L. and D.M.W. defined the research, interpreted the data and wrote the manuscript. All authors performed the experiments, analysed the data and/or contributed to the scientific discussion.

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Correspondence to David M. Wilson.

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The authors declare no competing financial interests.

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This file contains Supplementary Figures 1-24, Supplementary Text, Supplementary Tables 1-6 and Supplementary Methods 1-7. (PDF 4821 kb)

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Kruidenier, L., Chung, Cw., Cheng, Z. et al. A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response. Nature 488, 404–408 (2012). https://doi.org/10.1038/nature11262

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