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
- 14 September 2015
- journal article
- research article
- Published by American Association for Cancer Research (AACR) in Cancer Research
- Vol. 75 (18), 3865-3878
- https://doi.org/10.1158/0008-5472.can-14-3798
Abstract
The SWI/SNF multisubunit complex modulates chromatin structure through the activity of two mutually exclusive catalytic subunits, SMARCA2 and SMARCA4, which both contain a bromodomain and an ATPase domain. Using RNAi, cancer-specific vulnerabilities have been identified in SWI/SNF-mutant tumors, including SMARCA4-deficient lung cancer; however, the contribution of conserved, druggable protein domains to this anticancer phenotype is unknown. Here, we functionally deconstruct the SMARCA2/4 paralog dependence of cancer cells using bioinformatics, genetic, and pharmacologic tools. We evaluate a selective SMARCA2/4 bromodomain inhibitor (PFI-3) and characterize its activity in chromatin-binding and cell-functional assays focusing on cells with altered SWI/SNF complex (e.g., lung, synovial sarcoma, leukemia, and rhabdoid tumors). We demonstrate that PFI-3 is a potent, cell-permeable probe capable of displacing ectopically expressed, GFP-tagged SMARCA2-bromodomain from chromatin, yet contrary to target knockdown, the inhibitor fails to display an antiproliferative phenotype. Mechanistically, the lack of pharmacologic efficacy is reconciled by the failure of bromodomain inhibition to displace endogenous, full-length SMARCA2 from chromatin as determined by in situ cell extraction, chromatin immunoprecipitation, and target gene expression studies. Furthermore, using inducible RNAi and cDNA complementation (bromodomain- and ATPase-dead constructs), we unequivocally identify the ATPase domain, and not the bromodomain of SMARCA2, as the relevant therapeutic target with the catalytic activity suppressing defined transcriptional programs. Taken together, our complementary genetic and pharmacologic studies exemplify a general strategy for multidomain protein drug-target validation and in case of SMARCA2/4 highlight the potential for drugging the more challenging helicase/ATPase domain to deliver on the promise of synthetic-lethality therapy. Cancer Res; 75(18); 3865–78. ©2015 AACR.Keywords
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This publication has 50 references indexed in Scilit:
- Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancyNature Genetics, 2013
- Reversible Disruption of mSWI/SNF (BAF) Complexes by the SS18-SSX Oncogenic Fusion in Synovial SarcomaCell, 2013
- Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain FamilyCell, 2012
- Snf2-family proteins: chromatin remodellers for any occasionCurrent Opinion in Chemical Biology, 2011
- RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemiaNature, 2011
- Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinomaNature, 2011
- Epigenetic Antagonism between Polycomb and SWI/SNF Complexes during Oncogenic TransformationCancer Cell, 2010
- ARID1AMutations in Endometriosis-Associated Ovarian CarcinomasThe New England Journal of Medicine, 2010
- Frequent BRG1/SMARCA4-inactivating mutations in human lung cancer cell linesHuman Mutation, 2008
- Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cellsGenome Research, 2008