Suppression of inflammation by a synthetic histone mimic (original) (raw)

Nature volume 468, pages 1119–1123 (2010)Cite this article

Subjects

Abstract

Interaction of pathogens with cells of the immune system results in activation of inflammatory gene expression. This response, although vital for immune defence, is frequently deleterious to the host due to the exaggerated production of inflammatory proteins. The scope of inflammatory responses reflects the activation state of signalling proteins upstream of inflammatory genes as well as signal-induced assembly of nuclear chromatin complexes that support mRNA expression1,2,3,4. Recognition of post-translationally modified histones by nuclear proteins that initiate mRNA transcription and support mRNA elongation is a critical step in the regulation of gene expression5,6,7,8,9,10. Here we present a novel pharmacological approach that targets inflammatory gene expression by interfering with the recognition of acetylated histones by the bromodomain and extra terminal domain (BET) family of proteins. We describe a synthetic compound (I-BET) that by ‘mimicking’ acetylated histones disrupts chromatin complexes responsible for the expression of key inflammatory genes in activated macrophages, and confers protection against lipopolysaccharide-induced endotoxic shock and bacteria-induced sepsis. Our findings suggest that synthetic compounds specifically targeting proteins that recognize post-translationally modified histones can serve as a new generation of immunomodulatory drugs.

This is a preview of subscription content, access via your institution

Access options

Subscribe to this journal

Receive 51 print issues and online access

$199.00 per year

only $3.90 per issue

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Additional access options:

Similar content being viewed by others

Accession codes

Primary accessions

Gene Expression Omnibus

Protein Data Bank

Data deposits

Crystal structure of the first bromodomain of human BRD4 in complex with I-BET inhibitor was deposited in the RCSB Protein Data Bank with PDB ID code 3P5O. Microarray and ChIP sequencing results were deposited in GEO with GEO accession codes GSE21764 and GSE21910, respectively.

References

  1. Medzhitov, R. & Horng, T. Transcriptional control of the inflammatory response. Nature Rev. Immunol. 9, 692–703 (2009)
    Article CAS Google Scholar
  2. Smale, S. T. Selective transcription in response to an inflammatory stimulus. Cell 140, 833–844 (2010)
    Article CAS Google Scholar
  3. Natoli, G. Control of NF-κB-dependent transcriptional responses by chromatin organization. Cold Spring Harb. Perspect. Biol. 1, a000224 (2009)
    Article Google Scholar
  4. Maniatis, T. & Reed, R. An extensive network of coupling among gene expression machines. Nature 416, 499–506 (2002)
    Article ADS CAS Google Scholar
  5. Hargreaves, D. C., Horng, T. & Medzhitov, R. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 138, 129–145 (2009)
    Article CAS Google Scholar
  6. LeRoy, G., Rickards, B. & Flint, S. J. The double bromodomain proteins Brd2 and Brd3 couple histone acetylation to transcription. Mol. Cell 30, 51–60 (2008)
    Article CAS Google Scholar
  7. Jang, M. K. et al. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. Mol. Cell 19, 523–534 (2005)
    Article CAS Google Scholar
  8. Yang, Z. et al. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol. Cell 19, 535–545 (2005)
    Article CAS Google Scholar
  9. Taverna, S. D., Li, H., Ruthenburg, A. J., Allis, C. D. & Patel, D. J. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nature Struct. Mol. Biol. 14, 1025–1040 (2007)
    Article CAS Google Scholar
  10. Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074–1080 (2001)
    Article CAS Google Scholar
  11. Ruthenburg, A. J., Li, H., Patel, D. J. & Allis, C. D. Multivalent engagement of chromatin modifications by linked binding modules. Nature Rev. Mol. Cell Biol. 8, 983–994 (2007)
    Article CAS Google Scholar
  12. Huang, H. et al. Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails. BMC Struct. Biol. 7, 57 (2007)
    Article Google Scholar
  13. Liu, Y. et al. Structural basis and binding properties of the second bromodomain of Brd4 with acetylated histone tails. Biochemistry 47, 6403–6417 (2008)
    Article CAS Google Scholar
  14. Vollmuth, F., Blankenfeldt, W. & Geyer, M. Structures of the dual bromodomains of the P-TEFb-activating protein Brd4 at atomic resolution. J. Biol. Chem. 284, 36547–36556 (2009)
    Article CAS Google Scholar
  15. Gavrilin, M. A. et al. Pyrin critical to macrophage IL-1β response to Francisella challenge. J. Immunol. 182, 7982–7989 (2009)
    Article CAS Google Scholar
  16. Hagen, F. S. et al. Expression and characterization of recombinant human acyloxyacyl hydrolase, a leukocyte enzyme that deacylates bacterial lipopolysaccharides. Biochemistry 30, 8415–8423 (1991)
    Article CAS Google Scholar
  17. Huang, B., Yang, X. D., Zhou, M. M., Ozato, K. & Chen, L. F. Brd4 coactivates transcriptional activation of NF-κB via specific binding to acetylated RelA. Mol. Cell. Biol. 29, 1375–1387 (2009)
    Article CAS Google Scholar
  18. Jiang, Y. W. et al. Mammalian mediator of transcriptional regulation and its possible role as an end-point of signal transduction pathways. Proc. Natl Acad. Sci. USA 95, 8538–8543 (1998)
    Article ADS CAS Google Scholar
  19. Denis, G. V. et al. Identification of transcription complexes that contain the double bromodomain protein Brd2 and chromatin remodeling machines. J. Proteome Res. 5, 502–511 (2006)
    Article CAS Google Scholar
  20. Nishiyama, A., Dey, A., Miyazaki, J. & Ozato, K. Brd4 is required for recovery from antimicrotubule drug-induced mitotic arrest: preservation of acetylated chromatin. Mol. Biol. Cell 17, 814–823 (2006)
    Article CAS Google Scholar
  21. Marshall, N. F., Peng, J., Xie, Z. & Price, D. H. Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J. Biol. Chem. 271, 27176–27183 (1996)
    Article CAS Google Scholar
  22. Sims, R. J., III, Belotserkovskaya, R. & Reinberg, D. Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18, 2437–2468 (2004)
    Article CAS Google Scholar
  23. Ramirez-Carrozzi, V. R. et al. Selective and antagonistic functions of SWI/SNF and Mi-2β nucleosome remodeling complexes during an inflammatory response. Genes Dev. 20, 282–296 (2006)
    Article CAS Google Scholar
  24. Ramirez-Carrozzi, V. R. et al. A unifying model for the selective regulation of inducible transcription by CpG islands and nucleosome remodeling. Cell 138, 114–128 (2009)
    Article CAS Google Scholar
  25. Lee, T. I., Johnstone, S. E. & Young, R. A. Chromatin immunoprecipitation and microarray-based analysis of protein location. Nature Protocols 1, 729–748 (2006)
    Article CAS Google Scholar
  26. Goldberg, A. D. et al. Distinct factors control histone variant H3.3 localization at specific genomic regions. Cell 140, 678–691 (2010)
    Article CAS Google Scholar
  27. Rittirsch, D., Huber-Lang, M. S., Flierl, M. A. & Ward, P. A. Immunodesign of experimental sepsis by cecal ligation and puncture. Nature Protocols 4, 31–36 (2008)
    Article Google Scholar

Download references

Acknowledgements

We would like to acknowledge R. Grimley and C. Patel for supplying FRET data and R. Woodward, C. Delves, E. Jones and P. Holmes for protein production. J. Witherington, N. Smithers, S. Baddeley, J. Seal and L. Cutler provided compound selectivity and pharmacokinetics data. G. Krysa, O. Mirguet and R. Gosmini contributed to the discovery, development and characterization of the compound. We thank R. Anthony and S. McCleary for assistance with animal models, R. Gejman for bioinformatics analysis of gene expression kinetics and A. Santana and T. Chapman for technical assistance. We would like to thank C. Nathan, R. Medzhitov, S. Rudensky and S. Smale for helpful discussions and S. Sampath for his contribution to the concept of ‘histone mimicry’. R.C. is supported by an NIH KL2 Career Development Award and I.M. is supported by the American Italian Cancer Foundation. K.L.J. is supported by the National Health and Medical Research Council of Australia and is currently a Rockefeller University Women in Science Fellow.

Author information

Author notes

  1. Edwige Nicodeme, Kate L. Jeffrey, Uwe Schaefer and Soren Beinke: These authors contributed equally to this work.

Authors and Affiliations

  1. Centre de Recherche GSK, 27 Avenue du Québec, 91140, Villebon Sur Yvette, France
    Edwige Nicodeme, Hervé Coste & Jorge Kirilovsky
  2. Laboratory of Lymphocyte Signaling, The Rockefeller University, 1230 York Avenue, New York, 10065, New York, USA
    Kate L. Jeffrey, Uwe Schaefer, Rohit Chandwani, Ivan Marazzi & Alexander Tarakhovsky
  3. Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
    Soren Beinke, Jose M. Lora, Rab K. Prinjha & Kevin Lee
  4. Genomics Resource Center, The Rockefeller University, 1230 York Avenue, New York, 10065, New York, USA
    Scott Dewell
  5. GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
    Chun-wa Chung, Paul Wilson & Julia White
  6. Laboratory of Virology and Infectious Disease, The Rockefeller University, 1230 York Avenue, New York, 10065, New York, USA
    Charles M. Rice

Authors

  1. Edwige Nicodeme
    You can also search for this author inPubMed Google Scholar
  2. Kate L. Jeffrey
    You can also search for this author inPubMed Google Scholar
  3. Uwe Schaefer
    You can also search for this author inPubMed Google Scholar
  4. Soren Beinke
    You can also search for this author inPubMed Google Scholar
  5. Scott Dewell
    You can also search for this author inPubMed Google Scholar
  6. Chun-wa Chung
    You can also search for this author inPubMed Google Scholar
  7. Rohit Chandwani
    You can also search for this author inPubMed Google Scholar
  8. Ivan Marazzi
    You can also search for this author inPubMed Google Scholar
  9. Paul Wilson
    You can also search for this author inPubMed Google Scholar
  10. Hervé Coste
    You can also search for this author inPubMed Google Scholar
  11. Julia White
    You can also search for this author inPubMed Google Scholar
  12. Jorge Kirilovsky
    You can also search for this author inPubMed Google Scholar
  13. Charles M. Rice
    You can also search for this author inPubMed Google Scholar
  14. Jose M. Lora
    You can also search for this author inPubMed Google Scholar
  15. Rab K. Prinjha
    You can also search for this author inPubMed Google Scholar
  16. Kevin Lee
    You can also search for this author inPubMed Google Scholar
  17. Alexander Tarakhovsky
    You can also search for this author inPubMed Google Scholar

Contributions

E.N. identified, characterized and optimized the compound for in vivo experiments; K.L.J., U.S. and S.B. contributed equally to design, execution and analysis of in vitro and in vivo experiments. S.D. performed bioinformatics analysis of ChIP sequencing data; C.-w.C. performed crystallography, ITC, SPR and thermal shift assays; R.C. performed quantitative analysis of epigenetic states of the LPS-inducible genes; I.M. optimized BRD2 and BRD3 profiling of the LPS-inducible genes; P.W. performed bioinformatics analysis of gene expression in LPS-stimulated macrophages. H.C., J.W. and J.K. discovered, characterised and optimised the compound for in vivo experiments. C.M.R. was involved in studies of inflammatory responses. J.M.L., R.K.P. and K.L. contributed to the initiation and development of the studies on pharmacological targeting of proteins that recognize post-translationally modified histones. A.T. conceived and supervised this study, and wrote the final manuscript.

Corresponding authors

Correspondence toKevin Lee or Alexander Tarakhovsky.

Ethics declarations

Competing interests

E.N., S.B., C.-w.C., P.W., H.C., J.W., J.K., J.M.L., R.K.P. and K.L. are employees of GlaxoSmithKline. Research support, excluding salaries to the members of The Rockefeller University, but including protein analysis and compound synthesizing equipment, supplies and other expense, was provided by GlaxoSmithKline.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-14 with legends, Supplementary Tables 1-3, Supplementary Methods and additional references. (PDF 3565 kb)

PowerPoint slides

Rights and permissions

About this article

Cite this article

Nicodeme, E., Jeffrey, K., Schaefer, U. et al. Suppression of inflammation by a synthetic histone mimic.Nature 468, 1119–1123 (2010). https://doi.org/10.1038/nature09589

Download citation

This article is cited by

Editorial Summary

Histone mimics target BET bromodomains

Small molecules that perturb chromatin proteins are an emerging focus of current biomedical research. Two groups reporting in this issue have targeted bromodomain-containing BET proteins that bind acetylated lysine residues during gene activation, arriving at cell-permeable small molecule compounds with similar structures based on fused triazole-diazepine rings. James Bradner and colleagues report the development of a compound named JQ1. The BET protein BRD4, with two bromodomains, is implicated in human squamous cell carcinoma. JQ1 inhibits the growth of BRD4-dependent tumours in mouse models. Alexander Tarakhovsky and colleagues' inhibitor, I-BET, is shown to interfere with the binding of certain BET family members to acetylated histones. It inhibits activation of pro-inflammatory genes in macrophages and has immunomodulatory activity in a mouse model of inflammatory disease.

Associated content

Reader's block

Nature News & Views 22 Dec 2010