Abstract NG05: Chromatin accessibility underlies the tumor-suppression role of BAF (mSWI/SNF) complexes in many malignancies
Authors: Hodges Courtney , Hargreaves Diana , Miller Erik , Crabtree Gerald R. 
Published: August 2015

Abstract
The mammalian SWI/SNF (mSWI/SNF or BAF) complex is an ATP-dependent chromatin remodeler long thought to be a tumor suppressor because it is frequently inactivated in cell lines. It was definitively identified as a tumor suppressor in malignant rhabdoid tumors (MRTs), an aggressive pediatric cancer. In most of these tumors, the dedicated BAF subunit SMARCB1 (BAF47) undergoes loss-of-heterozygosity, with no other large-scale chromosomal instability, leading to the conclusion that the tumor-suppression mechanism in MRTs is “epigenetic” in nature, meaning that it leads to changes in gene expression without necessarily altering other sequences of DNA. However, these tumors account for a small fraction of all cancers containing mutations in BAF subunits, and other evidence implicates the BAF complex in DNA repair processes, making its tumor-suppression mechanism uncertain. We sought to determine the applicability of this epigenetic model of tumor suppression in the large number of other cancers bearing BAF subunit mutations. To answer this question, we analyzed exome sequencing and genomic copy-number data derived from 5,659 patient samples, together representing 22 cancer types and over 4,500,000 genetic alterations, to compare the genomic states of tumors with BAF subunit defects against similar tumors that lacked such defects. We find that BAF subunits collectively are mutated significantly more frequently than expected in 19 of the 22 cancer types examined, far more than expected. The increase in BAF subunit mutations was statistically robust, both in samples with low mutation rates (e.g., lower-grade glioma), as well as those with high rates (e.g., melanoma, tumors of the lung), indicating that mutation of the complex is under positive selection in the vast majority of cancers. We also performed an analysis of copy-number variation of BAF subunits in each cancer, and find recurrent patterns of biallelic deletions and amplifications. In many malignancies, mutation and biallelic deletion of BAF subunits occurs at rates comparable to or higher than well-known tumor suppressors, such as TP53, PTEN, and RB1.
In the majority of cancer types, tumors with BAF subunit defects have higher mutational rates than cancers of the same tissue lacking such defects. By reconstructing the mutational processes active in each patient sample, we find that excess mutations in BAF-deficient cancers represent the signatures of defective mismatch repair, cytidine deamination, UV-damage response, DNA end joining, Pol epsilon function, and other enzymatic processes acting on DNA. In four cancer types where ChIP-seq tracks were available for the healthy cell type of origin, we tracked the locations of over 280,000 mutations, and find that excess mutations in BAF-deficient tumors are biased towards regions of elevated H3K36me3 and low H3K27me3 in their corresponding non-cancerous tissues. We hypothesized that these mutations resulted from inaccessibility for repair and maintenance factors when a BAF subunit is defective. We tested this hypothesis using topoisomerase II alpha binding as representative of enzymes that require access to DNA, and find that rapid conditional deletion of the BAF ATPase Brg led to an increase in genome-wide deposition of H3K27me3 at Brg-dependent topoisomerase II alpha sites from an initial low state, contributing to loss of enzyme accessibility at its target sites.
Our data indicate that the tumor suppressive functions of BAF complexes arise from their contribution to maintaining genomic stability by providing access to DNA for repair and maintenance mechanisms. Consistent with this conclusion, we examined levels of P53 and phospho-P53 in mouse embryonic fibroblasts expressing a tamoxifen-inducible deletion of Brg, the ATPase of the BAF complex. Deletion of Brg causes a significant increase in the levels of P53 and phospho-P53 following DNA damage by a panel of conditions, confirming that genomic stability and DNA repair is compromised upon loss of BAF activity. Our data are consistent with a general model, wherein DNA accessibility is maintained at a steady state arising from a balance between silencing factors and factors (including the BAF complex) that maintain accessibility. Many repair and maintenance factors operate on DNA that require at least transient accessibility, making the BAF complex an upstream contributor to several activities. When BAF activity is compromised, the equilibrium is shifted towards a state that is less accessible to repair enzymes. This disruption of normal repair and maintenance function leads to accumulation of mutations. Our analysis of 5,659 patient genomes indicates that this is the mechanism of tumor suppression under positive selection in the majority of human malignancies.
Citation Format: Courtney Hodges, Diana Hargreaves, Erik Miller, Gerald R. Crabtree. Chromatin accessibility underlies the tumor-suppression role of BAF (mSWI/SNF) complexes in many malignancies. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr NG05. doi:10.1158/1538-7445.AM2015-NG05