Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
- Dana Farber Cancer Institute, United States
- University of Pennsylvania, United States
- University College Dublin, Ireland
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Netherlands
- Dana-Farber Cancer Institute, United States
- German Cancer Consortium (DKTK), Germany
- Cold Spring Harbor Laboratory, United States
Abstract
Synovial sarcoma tumours contain a characteristic fusion protein, SS18-SSX, which drives disease development. Targeting oncogenic fusion proteins presents an attractive therapeutic opportunity. However, SS18-SSX has proven intractable for therapeutic intervention. Using a domain-focused CRISPR screen we identified the bromodomain of BRD9 as a critical functional dependency in synovial sarcoma. BRD9 is a component of SS18-SSX containing BAF complexes in synovial sarcoma cells; and integration of BRD9 into these complexes is critical for cell growth. Moreover BRD9 and SS18-SSX co-localize extensively on the synovial sarcoma genome. Remarkably, synovial sarcoma cells are highly sensitive to a novel small molecule degrader of BRD9, while other sarcoma subtypes are unaffected. Degradation of BRD9 induces downregulation of oncogenic transcriptional programs and inhibits tumour progression in vivo. We demonstrate that BRD9 supports oncogenic mechanisms underlying the SS18-SSX fusion in synovial sarcoma and highlight targeted degradation of BRD9 as a potential therapeutic opportunity in this disease.
Data availability
All next-generation sequencing datasets generated in association with this work have been deposited in the Gene Expression Omnibus (GEO) under accession number GSE113229
-
Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcomaNCBI Gene Expression Omnibus, GSE113229.
Article and author information
Author details
Funding
National Cancer Institute (CA176745)
- Scott A Armstrong
Alex's Lemonade Stand Foundation for Childhood Cancer
- Scott A Armstrong
European Molecular Biology Organization (ALTF-1235-2015)
- Gerard L Brien
Irish Cancer Society (CRF18BRI)
- Gerard L Brien
National Cancer Institute (CA066996)
- Scott A Armstrong
National Cancer Institute (CA204915)
- Scott A Armstrong
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All mouse experiments were performed according to approved institutional animal care and use committee (IACUC) protocols at the Dana Farber Cancer Institute.
Copyright
© 2018, Brien et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 9,644
- views
-
- 1,653
- downloads
-
- 134
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma
eLife 7:e41305.
https://doi.org/10.7554/eLife.41305
Further reading
-
- Biochemistry and Chemical Biology
Class-B1 G-protein-coupled receptors (GPCRs) are an important family of clinically relevant drug targets that remain difficult to investigate via high-throughput screening and in animal models. Here, we engineered PAClight1P78A, a novel genetically encoded sensor based on a class-B1 GPCR (the human PAC1 receptor, hmPAC1R) endowed with high dynamic range (ΔF/F0 = 1100%), excellent ligand selectivity, and rapid activation kinetics (τON = 1.15 s). To showcase the utility of this tool for in vitro applications, we thoroughly characterized and compared its expression, brightness and performance between PAClight1P78A-transfected and stably expressing cells. Demonstrating its use in animal models, we show robust expression and fluorescence responses upon exogenous ligand application ex vivo and in vivo in mice, as well as in living zebrafish larvae. Thus, the new GPCR-based sensor can be used for a wide range of applications across the life sciences empowering both basic research and drug development efforts.
-
- Biochemistry and Chemical Biology
- Structural Biology and Molecular Biophysics
Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis in crystallo with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.
