Chromatin Regulation by mSWI/SNF (BAF) Chromatin Remodeling Complexes in Synovial Sarcoma

Abstract

The defining hallmark of a cancerous cell is unchecked and uncontrolled proliferative capacity leading to the build up of biomass, a tumor. Tumor exome sequencing has revealed gene mutations within biological processes that are recurrent both within and across cancer subtypes. A few of these biological processes, such as DNA methylation, histone modifications and chromatin remodeling, are directly involved in controlling chromatin architecture for the regulation of gene expression. The accumulation of genetic alterations to these regulators of chromatin structure underscores their contribution to oncogenic transformation and/or progression. Of these chromatin regulators, the genes encoding the 12-15 subunit members of mammalian SWI/SNF (BAF) protein complexes, which remodel nucleosomes in an ATP-dependent manner, are recurrently mutated in over 20% of all human cancers. The aggressive, soft tissue tumor synovial sarcoma has a hallmark chromosomal translocation forming the SS18-SSX fusion protein. Since SS18 is a core subunit of BAF complexes, the SS18-SSX fusion retains the ability to assemble and results in the eviction of the BAF47 (SMARCB1) subunit member, which is a known tumor suppressor. Since these two alterations to BAF complexes, gain of the SS18- SSX fusion and loss of BAF47, occur in a concurrent manner, we do not know how each event alters transcriptional regulation and their individual contributions to oncogenic cell proliferation in synovial sarcoma. To explore this, we used genome-wide approaches to capture the localization of BAF complexes, chromatin accessibility and transcriptional output in synovial sarcoma cell line models and primary tumor samples. From this, we determined that SS18-SSX-containing BAF complexes are recruited away from enhancers and to broad polycomb domains resulting in loss of the repressive H3K27me3 histone modification to establish a transcriptional profile distinct from other BAF47-null malignancies. Furthermore, proliferation assays and transcriptional analysis in synovial sarcoma cells with loss of BAF47 expression by gene knockout revealed oncogenic growth is dependent on gain of the SS18-SSX fusion and is independent of BAF47 eviction. Since the gained localization of BAF complexes by SS18-SSX is the event driving growth, we next used a series of biochemical approaches to elucidate the molecular nature by which the 78 amino acid SSX tail of the fusion directs novel targeting on chromatin. We found that the evolutionarily conserved 33 amino acids on the C-terminus of SSX are sufficient for engaging nucleosomes to direct chromatin localization and drive proliferation in synovial sarcoma. This 33 amino acid SSX tail contains a basic patch that is responsible for engaging the acidic patch of nucleosomes and an acidic patch that preferentially binds the non-acetylated tail of histone H4. Each of these regions of SSX, the basic and acidic patches, is necessary for oncogenic chromatin targeting, gene activation and proliferation. The culmination of this work demonstrates that BAF complexes act in a novel gain-of-function manner to drive proliferation in synovial sarcoma due to addition of the SSX tail, which is a newly characterized chromatin binder through direct engagements with transcriptionally repressed nucleosomes.