Abstract
The addressable pocket of a protein is often not functionally relevant in disease. This is true for the multidomain, bromodomain-containing transcriptional regulator TRIM24. TRIM24 has been posited as a dependency in numerous cancers, yet potent and selective ligands for the TRIM24 bromodomain do not exert effective anti-proliferative responses. We therefore repositioned these probes as targeting features for heterobifunctional protein degraders. Recruitment of the VHL E3 ubiquitin ligase by dTRIM24 elicits potent and selective degradation of TRIM24. Using dTRIM24 to probe TRIM24 function, we characterize the dynamic genome-wide consequences of TRIM24 loss on chromatin localization and gene control. Further, we identify TRIM24 as a novel dependency in acute leukemia. Pairwise study of TRIM24 degradation versus bromodomain inhibition reveals enhanced anti-proliferative response from degradation. We offer dTRIM24 as a chemical probe of an emerging cancer dependency, and establish a path forward for numerous selective yet ineffectual ligands for proteins of therapeutic interest.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$29.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Change history
08 August 2018
In the version of this article originally published, numbered compounds were not linked correctly to their respective compound pages. The error has been corrected in the HTML version of this paper.
References
Bradner, J. E., Hnisz, D. & Young, R. A. Transcriptional addiction in cancer. Cell 168, 629–643 (2017).
Darnell, J. E. Jr. Transcription factors as targets for cancer therapy. Nat. Rev. Cancer 2, 740–749 (2002).
Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067–1073 (2010).
Vangamudi, B. et al. The SMARCA2/4 ATPase domain surpasses the bromodomain as a drug target in SWI/SNF-mutant cancers: Insights from cDNA rescue and PFI-3 inhibitor studies. Cancer. Res. 75, 3865–3878 (2015).
Le Douarin, B. et al. The N-terminal part of TIF1, a putative mediator of the ligand-dependent activation function (AF-2) of nuclear receptors, is fused to B-raf in the oncogenic protein T18. EMBO J. 14, 2020–2033 (1995).
Meroni, G. & Diez-Roux, G. TRIM/RBCC, a novel class of ‘single protein RING finger’ E3 ubiquitin ligases. BioEssays 27, 1147–1157 (2005).
Reymond, A. et al. The tripartite motif family identifies cell compartments. EMBO J. 20, 2140–2151 (2001).
Allton, K. et al. Trim24 targets endogenous p53 for degradation. Proc. Natl. Acad. Sci. USA 106, 11612–11616 (2009).
Jain, A. K., Allton, K., Duncan, A. D. & Barton, M. C. TRIM24 is a p53-induced E3-ubiquitin ligase that undergoes ATM-mediated phosphorylation and autodegradation during DNA damage. Mol. Cell. Biol. 34, 2695–2709 (2014).
Khetchoumian, K. et al. Loss of Trim24 (Tif1alpha) gene function confers oncogenic activity to retinoic acid receptor alpha. Nat. Genet. 39, 1500–1506 (2007).
Le Douarin, B. et al. A possible involvement of TIF1 alpha and TIF1 beta in the epigenetic control of transcription by nuclear receptors. EMBO J. 15, 6701–6715 (1996).
Tsai, W. W. et al. TRIM24 links a non-canonical histone signature to breast cancer. Nature 468, 927–932 (2010).
Cui, Z. et al. TRIM24 overexpression is common in locally advanced head and neck squamous cell carcinoma and correlates with aggressive malignant phenotypes. PLoS ONE 8, e63887 (2013).
Groner, A. C. et al. TRIM24 is an oncogenic transcriptional activator in prostate cancer. Cancer Cell 29, 846–858 (2016).
Li, H. et al. Overexpression of TRIM24 correlates with tumor progression in non-small cell lung cancer. PLoS ONE 7, e37657 (2012).
Liu, X. et al. Overexpression of TRIM24 is associated with the onset and progress of human hepatocellular carcinoma. PLoS ONE 9, e85462 (2014).
Wang, J. et al. Knockdown of tripartite motif containing 24 by lentivirus suppresses cell growth and induces apoptosis in human colorectal cancer cells. Oncol. Res. 22, 39–45 (2014).
Pathiraja, T. N. et al. TRIM24 links glucose metabolism with transformation of human mammary epithelial cells. Oncogene 34, 2836–2845 (2015).
Bennett, J. et al. Discovery of a chemical tool inhibitor targeting the bromodomains of TRIM24 and BRPF. J. Med. Chem. 59, 1642–1647 (2016).
Palmer, W. S. et al. Structure-guided design of IACS-9571, a selective high-affinity dual TRIM24-BRPF1 bromodomain inhibitor. J. Med. Chem. 59, 1440–1454 (2016).
Zhan, Y. et al. Development of novel cellular histone-binding and chromatin-displacement assays for bromodomain drug discovery. Epigenetics Chromatin 8, 37 (2015).
Winter, G. E. et al. DRUG DEVELOPMENT. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science 348, 1376–1381 (2015).
Bondeson, D. P. et al. Catalytic in vivo protein knockdown by small-molecule PROTACs. Nat. Chem. Biol. 11, 611–617 (2015).
Lu, J. et al. Hijacking the E3 ubiquitin ligase cereblon to efficiently target BRD4. Chem. Biol. 22, 755–763 (2015).
Zengerle, M., Chan, K.-H. & Ciulli, A. Selective small molecule induced degradation of the BET bromodomain protein BRD4. ACS Chem. Biol. 10, 1770–1777 (2015).
Gadd, M. S. et al. Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat. Chem. Biol. 13, 514–521 (2017).
Crews, C. M. et al. Compounds and methods for the inhibition of vcb e3 ubiquitin ligase. Patent WO 2013106646 (2013).
Buckley, D. L. et al. HaloPROTACS: use of small molecule PROTACs to induce degradation of HaloTag fusion proteins. ACS Chem. Biol. 10, 1831–1837 (2015).
Huang, H.-T. et al. A chemoproteomic approach to query the degradable kinome using a multi-kinase degrader. Cell Chem. Biol. 25, 88–99 (2017).
Douglass, E. F. Jr, Miller, C. J., Sparer, G., Shapiro, H. & Spiegel, D. A. A comprehensive mathematical model for three-body binding equilibria. J. Am. Chem. Soc. 135, 6092–6099 (2013).
Soucy, T. A. et al. An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer. Nature 458, 732–736 (2009).
Barretina, J. et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity. Nature 483, 603–607 (2012).
Cheung, H. W. et al. Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. Proc. Natl. Acad. Sci. USA 108, 12372–12377 (2011).
Shao, D. D. et al. ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Res. 23, 665–678 (2012).
Shi, J. et al. Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains. Nat. Biotechnol. 33, 661–667 (2015).
Remillard, D. et al. Degradation of the BAF complex factor BRD9 by heterobifunctional ligands. Angew. Chem. Int. Ed. Eng. 56, 5738–5743 (2017).
Orlando, D. A. et al. Quantitative ChIP-Seq normalization reveals global modulation of the epigenome. Cell Rep. 9, 1163–1170 (2014).
Chapuy, B. et al. Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma. Cancer Cell 24, 777–790 (2013).
Herquel, B. et al. Transcription cofactors TRIM24, TRIM28, and TRIM33 associate to form regulatory complexes that suppress murine hepatocellular carcinoma. Proc. Natl. Acad. Sci. USA 108, 8212–8217 (2011).
Herquel, B. et al. Trim24-repressed VL30 retrotransposons regulate gene expression by producing noncoding RNA. Nat. Struct. Mol. Biol. 20, 339–346 (2013).
Tisserand, J. et al. Tripartite motif 24 (Trim24/Tif1α) tumor suppressor protein is a novel negative regulator of interferon (IFN)/signal transducers and activators of transcription (STAT) signaling pathway acting through retinoic acid receptor α (Rarα) inhibition. J. Biol. Chem. 286, 33369–33379 (2011).
Gaboli, M. et al. Mzf1 controls cell proliferation and tumorigenesis. Genes Dev. 15, 1625–1630 (2001).
Grossmann, V. et al. Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype. Blood 118, 6153–6163 (2011).
Kewitz, S. & Staege, M. S. Expression and regulation of the endogenous retrovirus 3 in Hodgkin’s lymphoma cells. Front. Oncol. 3, 179 (2013).
Lasorella, A., Benezra, R. & Iavarone, A. The ID proteins: master regulators of cancer stem cells and tumour aggressiveness. Nat. Rev. Cancer 14, 77–91 (2014).
Love, C. et al. The genetic landscape of mutations in Burkitt lymphoma. Nat. Genet. 44, 1321–1325 (2012).
Perrotti, D. et al. Overexpression of the zinc finger protein MZF1 inhibits hematopoietic development from embryonic stem cells: correlation with negative regulation of CD34 and c-myb promoter activity. Mol. Cell. Biol. 15, 6075–6087 (1995).
Richter, J. et al. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat. Genet. 44, 1316–1320 (2012).
Schmitz, R. et al. Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics. Nature 490, 116–120 (2012).
Ludtke, S. J., Baldwin, P. R. & Chiu, W. EMAN: semiautomated software for high-resolution single-particle reconstructions. J. Struct. Biol. 128, 82–97 (1999).
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta. Crystallogr. D. Biol. Crystallogr. 60, 2126–2132 (2004).
Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013).
Zhang, Y. et al., Model-based analysis of ChIP-Seq, Genome Biol. 9, R137 (2008).
Acknowledgements
We thank the members of the Bradner and Gray labs for engaging scientific conversations. We also thank J. Wang (Dana-Farber Cancer Institute) for her help with chemical characterization. Lastly, we would like to thank S.A. Armstrong and K. Stegmaier (Dana-Farber Cancer Institute) for kindly providing us with materials. This research was supported by a Starr Cancer Consortium Grant (J.E.B.) and NIH/NCI P01CA066996 (J.E.B.). L.N.G is supported by an NSF GRFP fellowship (2016222867). D.L.B. was supported by the Claudia Adams Barr Program in Innovative Basic Cancer Research and is a Merck Fellow of the Damon Runyon Cancer Research Foundation (DRG-2196-14). Quantitative proteomics studies were performed by R. Kunz of the Thermo Fisher Scientific Center for Multiplexed Proteomics at Harvard Medical School.
Author information
Authors and Affiliations
Contributions
L.N.G. designed and performed experiments, analyzed data, and wrote the manuscript. D.L.B. designed experiments, designed and synthesized molecules, and edited the manuscript. M.A.L. performed ChIP-Rx and analyzed genomic data. J.M.R. analyzed genomic data. J.P., C.J.O., and T.G.S. designed and performed biochemical assays. G.E.W. and M.A.E. designed and performed CRISPR–Cas9 screens. M.X. performed computational and statistical analyses. S.D.-P. and H.-S.S. performed structural analysis. N.P.K. guided experimental analyses. J.A.P. provided technical advice and data interpretation and edited the manuscript. J.Q. aided in the formulation of the chemical degradation strategy. J.E.B. and N.S.G. designed the experimental strategy, wrote the manuscript, and held overall responsibility for the study.
Corresponding authors
Ethics declarations
Competing interests
D.L.B. and J.P. are now employees of Novartis. N.S.G. is a Scientific Founder and member of the Scientific Advisory Board of C4 Therapeutics. J.E.B. is a Scientific Founder of C4 Therapeutics. J.E.B. is now an executive and shareholder in Novartis AG.
Additional information
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–13 and Supplementary Note
Supplementary Dataset 1
dTRIM24 proteomics MCF-7
Supplementary Dataset 2
dTRIM24 proteomics MOLM-13
Rights and permissions
About this article
Cite this article
Gechijian, L.N., Buckley, D.L., Lawlor, M.A. et al. Functional TRIM24 degrader via conjugation of ineffectual bromodomain and VHL ligands. Nat Chem Biol 14, 405–412 (2018). https://doi.org/10.1038/s41589-018-0010-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/s41589-018-0010-y
This article is cited by
-
Targeting bromodomain-containing proteins: research advances of drug discovery
Molecular Biomedicine (2023)
-
Beyond canonical PROTAC: biological targeted protein degradation (bioTPD)
Biomaterials Research (2023)
-
Readout of histone methylation by Trim24 locally restricts chromatin opening by p53
Nature Structural & Molecular Biology (2023)
-
TRIM24 is critical for the cellular response to DNA double-strand breaks through regulating the recruitment of MRN complex
Oncogene (2023)
-
Bioinspired PROTAC-induced macrophage fate determination alleviates atherosclerosis
Acta Pharmacologica Sinica (2023)