Pharmacologic inhibition of BAF chromatin remodeling complexes as a therapeutic approach to transcription factor-dependent cancers
Abstract The BRG/Brahma-associated factors (BAF or mSWI/SNF) family of chromatin remodeling complexes are critical regulators of gene expression and are major determinants of cancer and other diseases. Two paralog ATPases, SMARCA4 and SMARCA2 (BRG1 and BRM, respectively), provide the enzymatic activity required for chromatin remodeling. Here, we discover and characterize a novel series of compounds that potently and selectively inhibit SMARCA4/SMARCA2. Mutational and biochemical studies demonstrate that these inhibitors act through a unique mode of inhibition, distinct from reported SMARCA4/SMARCA2 inhibitors. Across a range of cancer cell lines, SMARCA4/SMARCA2 inhibition resulted in lineage-specific changes in chromatin accessibility at binding sites for key transcription factors (TFs). In uveal melanoma (UM), BAF inhibition resulted in loss of enhancer occupancy of SOX10 and MITF, two essential TFs, leading to down-regulation of the melanocytic gene expression program. In a mouse xenograft model of UM, SMARCA4/SMARCA2 inhibition was well tolerated and resulted in dose-dependent tumor regression correlating with pharmacodynamic modulation of BAF-target gene expression. These data provide the foundation for first-in-human studies of BAF ATPase inhibition as a novel therapeutic to treat TF-dependent cancers.
Authors
- Laura E. Zawadzke
- Kimberly D. Barnash (ORCID: https://orcid.org/0000-0002-0918-7188)
- David S. Millan (ORCID: https://orcid.org/0000-0001-5590-7273)
- GiNell Elliott
- Gromoslaw A. Smolen (ORCID: https://orcid.org/0000-0003-0136-4685)
- Ammar Adam
- Shawn Schiller
- Luis M. M. Soares
- David C.S. Huang (ORCID: https://orcid.org/0000-0002-3101-4873)
- Kana Ichikawa (ORCID: https://orcid.org/0000-0002-7170-1571)
- Yunji Davenport
- Carl P. Decicco
- Gabriel J. Sandoval
- Martin Hentemann
- Jeremy W. Setser (ORCID: https://orcid.org/0000-0002-2032-6740)
- Rishi G. Vaswani
- Salih Topal
- Katharine Feldman
- Jordana Muwanguzi
- Hong Fan (ORCID: https://orcid.org/0000-0002-3370-7833)
- David L. Lahr (ORCID: https://orcid.org/0000-0001-6283-0286)
- Richard C. Centore
- Johannes Voigt (ORCID: https://orcid.org/0009-0000-3912-8595)
- Steven F. Bellon
- Ryan G. Kruger
- Xueying Chen (ORCID: https://orcid.org/0000-0002-5167-3550)
- Zhifang Li (ORCID: https://orcid.org/0000-0001-8398-7338)
- Lan Xu (ORCID: https://orcid.org/0000-0003-0838-6473)
- Kevin Wilson (ORCID: https://orcid.org/0000-0003-4574-8250)
- Ho Man Chan (ORCID: https://orcid.org/0000-0002-1117-1230)
- Neville J. Anthony
Institutions
- Novartis (Switzerland) (CH)
- Crescent University (NG)
- Qarshi University (PK)
- BeiGene (China) (CN)
- Therapeutics Clinical Research (US)
- Exicure (United States) (US)
- HEM Technologies (United States) (US)
- SK Life Science (United States) (US)
- Epix Pharmaceuticals (United States) (US)
- Arrakis Therapeutics (United States) (US)
- Recludix Pharma (United States) (US)
- Nimbus (Italy) (IT)
- BioNTech (United States) (US)
- CTI BioPharma (Italy) (IT)
- Quaternary Research Association (GB)
- Flagship Pioneering (United States) (US)
- Foghorn Therapeutics (United States) (US)
- Novartis Institutes for BioMedical Research
- Orion Corporation (United Kingdom) (GB)
Publication Details
- Journal
- eLife
- Published
- 2025-09-29
- DOI
- https://doi.org/10.7554/elife.93478.2
- Primary Topic
- Chromatin Remodeling and Cancer
- Type
- article
- Field-Weighted Citation Impact
- 0.00