Ssx Drives Gain-Of-Function Baf Complex Chromatin Affinity And Genomic Targeting In Synovial Sarcoma

Synovial sarcoma (SS) is a soft-tissue malignancy driven by a recurrent chromosomal translocation (t(X;18)) that uniformly produces the SS18-SSX oncogenic fusion protein. SS18 is a core subunit of the mammalian SWI/SNF (BAF) complexes, which remodel nucleosomes in an ATP-dependent manner and antagonistically oppose gene-silencing activity of polycomb complexes to maintain transcriptional control throughout development and differentiation. We previously discovered that in SS, incorporation of the oncogenic SS18-SSX fusion into BAF complexes leads to eviction of the tumor-suppressor BAF47 (INI1/SMARCB1) subunit, and aberrant activation of polycomb target genes by displacement of H3K27me3-mediated repression. However, uncoupling the oncogenic consequences of two co-occurrent BAF complex perturbations, gain of 78- amino acids to SS18 and loss of BAF47 has remained a challenge for the field; understanding gain- versus loss-of-function properties of these molecular events is critical to the identification of effective targeted therapeutics for this patient population. Here we show that synovial sarcoma primary tumors and cell lines harbor a transcriptional signature markedly distinct from sarcomas such as malignant rhabdoid tumors, which are driven solely by biallelic loss of BAF47. Indeed, we show that SS18-SSX-containing BAF complexes exhibit distinct chromatin localization in that suppression of SS18-SSX results in a near complete genome-wide retargeting of BAF complexes. We find that SS18-SSX directs BAF complexes to polycomb-repressed sites to activate embryonic development and neuronal gene pathways hallmark to SS primary tumors. Strikingly, using biochemical affinity assays, we demonstrate that the SSX 78aa tail dramatically increases the affinity of BAF complexes for chromatin as well as their genomic footprint sizes upon ChIP-seq analyses. This is in stark contrast to the demonstrated decrease in chromatin affinity and genomic occupancy resulting from the loss of function of BAF47 in MRT. Moreover, using CRISPR/Cas9-mediated KO of BAF47 in SS cell lines, we show that the proliferative arrest of SS cell lines upon suppression of SS18-SSX is independent of the BAF47 reassembly into BAF complexes, thereby demonstrating a unique SSX-driven oncogenic mechanism distinct from BAF47 loss. Taken together, these studies uncover a novel functionality of the SSX tail that is required for SS oncogenesis, and inform the selection of appropriate targeted therapeutic agents for this gain-of-function BAF complex-driven cancer. Citation Format: Matthew J. McBride, John L. Pulice, Robert T. Nakayama, Nazar Mashtalir, Davis R. Ingram, Jack F. Shern, Javed Khan, Jason L. Hornick, Alexander J. Lazar, Cigall Kadoch. SSX drives gain-of-function BAF complex chromatin affinity and genomic targeting in synovial sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3875. doi:10.1158/1538-7445.AM2017-3875