Epigenetic ConFUSION: SS18-SSX Fusion Rewires BAF Complex to Activate Bivalent Genes in Synovial Sarcoma
Authors: Marc A. Morgan, Ali Shilatifard
Journal: Cancer Cell (2018)

In this issue of Cancer Cell, McBride and colleagues report that the synovial sarcoma SS18-SSX fusion drives BAF complex recruitment to bivalent domains repressed by PRC2 complex to orchestrate aberrant transcriptional activation. Redistribution of BAF localization is a major driver of synovial sarcoma proliferation and presents a promising therapeutic target. In this issue of Cancer Cell, McBride and colleagues report that the synovial sarcoma SS18-SSX fusion drives BAF complex recruitment to bivalent domains repressed by PRC2 complex to orchestrate aberrant transcriptional activation. Redistribution of BAF localization is a major driver of synovial sarcoma proliferation and presents a promising therapeutic target. "Uninvited guests are often most welcome when they leave."-Aesop A group of friends (the BAF complex) has gathered for a dinner party, but on this particular evening, one member (SS18) has brought along an uninvited and problematic guest (SSX). One friend (BAF47) cannot abide this unwelcome newcomer's antics and leaves the party. The interloper hijacks the conversation and takes it to inappropriate areas (Bivalent Polycomb repressed genes). This derails the entire evening and leaves a lingering malignant mood. This allegorical scene describes molecular mechanisms for the intruding SS18-SSX fusion oncoprotein in synovial sarcoma, as revealed in this issue of Cancer Cell (McBride et al., 2018McBride M.J. Pulice J.L. Beird H.C. Ingram D.R. D'Avino A.R. Shern J.F. Charville G.W. Hornick J.L. Nakayama R.T. Garcia-Rivera E.M. et al.The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma.Cancer Cell. 2018; 33 (this issue): 1128-1141Abstract Full Text Full Text PDF PubMed Scopus (120) Google Scholar). Expelling the unwanted visitor, SS18-SSX, restores normal BAF complex function and reestablishes Polycomb repression of bivalent genes. Importantly, the authors reveal that eliminating SS18-SSX's deviant gain-of-function behavior is the primary requirement for halting synovial sarcoma proliferation, rather than restoring BAF47 (also known as SMARCB1, SNF5, or INI1) to the BAF complex. These findings shed new light onto synovial sarcoma pathogenesis and have important implications for the development of targeted therapies. Synovial sarcoma is a soft-tissue tumor characterized by a reciprocal t(X;18) translocation involving the SS18 gene and one of three related SSX genes (SSX1, SSX2, or SSX4) that occurs predominantly in young adults. SS18-SSX fusions contain most of the SS18 protein sequence followed by additional amino acids derived from SSX. SS18 normally participates as a component of the multi-subunit BAF (mammalian SWI/SNF) ATP-dependent chromatin-remodeling complex, thus implicating the deregulation of chromatin-based gene-regulatory systems as a central driver of synovial sarcoma pathogenesis (Kadoch and Crabtree, 2015Kadoch C. Crabtree G.R. Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics.Sci. Adv. 2015; 1: e1500447Crossref PubMed Scopus (472) Google Scholar). Despite SS18-SSX's status as a bona fide oncoprotein (Haldar et al., 2007Haldar M. Hancock J.D. Coffin C.M. Lessnick S.L. Capecchi M.R. A conditional mouse model of synovial sarcoma: insights into a myogenic origin.Cancer Cell. 2007; 11: 375-388Abstract Full Text Full Text PDF PubMed Scopus (230) Google Scholar), until recently it remained largely unknown how SS18-SSX drives synovial sarcoma formation. In 2013, Kadoch and Crabtree published their breakthrough discovery that SS18-SSX alters the composition of BAF complexes by evicting both wild-type SS18 and the tumor suppressor BAF47, thus earmarking them for proteolytic degradation (Kadoch and Crabtree, 2013Kadoch C. Crabtree G.R. Reversible disruption of mSWI/SNF (BAF) complexes by the SS18-SSX oncogenic fusion in synovial sarcoma.Cell. 2013; 153: 71-85Abstract Full Text Full Text PDF PubMed Scopus (317) Google Scholar). These biochemical alterations are accompanied by the transcriptional activation of oncogenic factors such as SOX2, which are normally targeted for repression by the Polycomb Repressive Complex 2 (PRC2). Importantly, removing SS18-SSX restores wild-type SS18 and BAF47 to the BAF complex and is sufficient to inhibit synovial sarcoma proliferation (Kadoch and Crabtree, 2013Kadoch C. Crabtree G.R. Reversible disruption of mSWI/SNF (BAF) complexes by the SS18-SSX oncogenic fusion in synovial sarcoma.Cell. 2013; 153: 71-85Abstract Full Text Full Text PDF PubMed Scopus (317) Google Scholar), thus making SS18-SSX an attractive therapeutic target because of its involvement in both tumor initiation and tumor maintenance. In their current study, McBride and colleagues use patient-derived cell lines to demonstrate that SS18-SSX containing BAF complexes aberrantly target to bivalent genes normally occupied and repressed by PRC2 (Figure 1). This mis-recruitment causes loss of the PRC2 catalytic product, histone H3 lysine 27 trimethylation (H3K27me3), and ultimately drives inappropriate gene activation. Concurrently, SS18-SSX-orchestrated redistribution of BAF binding results in a loss of BAF complexes from distal enhancer regulatory sequences due to BAF47 eviction. Thus, SS18-SSX globally rewires BAF-controlled gene regulation through an epigenetic retargeting mechanism. Notably, transcriptomic analysis revealed that myogenic progenitor marker genes PAX3 and PAX7, as well as SOX2 and MYC oncogenes, are major components of the SS18-SSX-driven transcriptional signature. The authors also show that synovial sarcomas are transcriptionally heterogeneous and cluster into two subtypes that express either high levels of MYC or high levels of PAX7, suggesting a developmental window for the initiation of oncogenesis. These findings provide important new insight into the cellular origin of synovial sarcoma, because previous studies of SS18-SSX tumorigenicity within the PAX3/7-positive lineages in mice were precluded by embryonic lethality (Haldar et al., 2007Haldar M. Hancock J.D. Coffin C.M. Lessnick S.L. Capecchi M.R. A conditional mouse model of synovial sarcoma: insights into a myogenic origin.Cancer Cell. 2007; 11: 375-388Abstract Full Text Full Text PDF PubMed Scopus (230) Google Scholar). Generally, BAF complexes occupy active promoters and enhancers, whereas PRC2 complexes bind to transcriptionally silent genes. Hence, the binding pattern of these complexes is largely mutually exclusive. Moreover, BAF activity can evict PRC2 complexes from chromatin, and antagonism between these complexes has been demonstrated in both developmental and oncogenic contexts (Kadoch and Crabtree, 2015Kadoch C. Crabtree G.R. Mammalian SWI/SNF chromatin remodeling complexes and cancer: Mechanistic insights gained from human genomics.Sci. Adv. 2015; 1: e1500447Crossref PubMed Scopus (472) Google Scholar, Wilson et al., 2010Wilson B.G. Wang X. Shen X. McKenna E.S. Lemieux M.E. Cho Y.J. Koellhoffer E.C. Pomeroy S.L. Orkin S.H. Roberts C.W.M. Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation.Cancer Cell. 2010; 18: 316-328Abstract Full Text Full Text PDF PubMed Scopus (452) Google Scholar). In cells lacking SS18-SSX, these loci contain both H3K27me3, the catalytic product of PRC2, and histone H3 lysine 4 trimethylation (H3K4me3), the catalytic product of the MLL2/COMPASS family of enzymes (Hu et al., 2013Hu D. Garruss A.S. Gao X. Morgan M.A. Cook M. Smith E.R. Shilatifard A. The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells.Nat. Struct. Mol. Biol. 2013; 20: 1093-1097Crossref PubMed Scopus (129) Google Scholar). This bivalent chromatin state is associated with developmentally regulated genes, however, during embryonic stem cell differentiation, H3K4me3 is not required for rapid bivalent gene activation (Hu et al., 2013Hu D. Garruss A.S. Gao X. Morgan M.A. Cook M. Smith E.R. Shilatifard A. The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells.Nat. Struct. Mol. Biol. 2013; 20: 1093-1097Crossref PubMed Scopus (129) Google Scholar). McBride et al. identify co-occupancy of BAF and PRC2 complexes as a unique chromatin signature of synovial sarcoma. The SS18-SSX fusion does not alter H3K4me3, but gene activation by SS18-SSX is proportional to H3K4me3 levels at bivalent promoters. Notably, these differences in H3K4me3 levels account for the heterogeneous expression of genes such as PAX7 and MYC between synovial sarcoma subtypes. These findings shed light onto the function of bivalent chromatin in synovial sarcoma and suggest that the respective presence or absence of H3K27me3 determines whether a gene is repressed or active (on/off switch), whereas H3K4me3 levels dictate the potential output levels of active genes (rheostat/potentiometer). Although MLL2/COMPASS is required for H3K4 methylation on bivalent domains (Hu et al., 2013Hu D. Garruss A.S. Gao X. Morgan M.A. Cook M. Smith E.R. Shilatifard A. The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells.Nat. Struct. Mol. Biol. 2013; 20: 1093-1097Crossref PubMed Scopus (129) Google Scholar), it is Set1A/COMPASS that appears to be required for proper expression (Cao et al., 2017Cao K. Collings C.K. Marshall S.A. Morgan M.A. Rendleman E.J. Wang L. Sze C.C. Sun T. Bartom E.T. Shilatifard A. SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression.Genes Dev. 2017; 31: 787-801Crossref PubMed Scopus (34) Google Scholar). It will be interesting to determine whether removal of Set1A/COMPASS in cells carrying SS18-SSX fusions results in the loss of targeted activation. The effect of SS18-SSX on the BAF complex is multifaceted and comprises both the incorporation of SSX protein sequences into the BAF complex and the concurrent eviction of BAF47. These biochemical alterations are accompanied by a gain of BAF binding at broad PRC2-bound bivalent loci and a concomitant loss of BAF from distal enhancers. Given BAF47's established function as a tumor suppressor, the authors disentangle these effects using CRISPR/Cas9-mediated genetic knockouts. Strikingly, even in the absence of BAF47, removal of SS18-SSX is sufficient to halt synovial sarcoma proliferation, demonstrating that restoring BAF47 into the BAF complex and BAF binding to distal enhancers is not a requirement for blocking synovial sarcoma proliferation. These experiments strongly suggest that the SS18-SSX oncogene gain-of-function activity that targets BAF to PRC2 sites is the major mechanism involved in synovial sarcoma pathogenesis. PRC2 plays a complex role in cancer and functions as either a tumor promoter or a tumor suppressor, depending on the context. Many tumor types express high levels of PRC2 or contain hyperactivating point mutations. Conversely, certain tumor types contain loss-of-function PRC2 mutations or express inhibitory oncohistones (Morgan and Shilatifard, 2015Morgan M.A. Shilatifard A. Chromatin signatures of cancer.Genes Dev. 2015; 29: 238-249Crossref PubMed Scopus (146) Google Scholar). Here, McBride et al. point to locus-specific inhibition of PRC2 activity as a central driving feature of synovial sarcoma pathogenesis. Consistent with this, the authors find that a small-molecule PRC2 catalytic inhibitor does not impair synovial sarcoma proliferation. By contrast, KDM2B-containing PRC1.1 complexes were recently demonstrated to be a cancer dependency in synovial sarcoma (Banito et al., 2018Banito A. Li X. Laporte A.N. Roe J.S. Sanchez-Vega F. Huang C.H. Dancsok A.R. Hatzi K. Chen C.C. Tschaharganeh D.F. et al.The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma.Cancer Cell. 2018; 33: 527-541.e8Abstract Full Text Full Text PDF PubMed Scopus (65) Google Scholar), implying that these complexes are functionally divergent in this tumor context. This recent discovery by McBride and colleagues (Figure 1) points to several directions for future studies of the BAF complex in synovial sarcoma. First, what is the structural basis of SS18-SSX-induced redistribution of the BAF complex? Does the SSX carboxy terminal tail recognize a specific feature of bivalent genes, and what is its binding substrate? Second, what is the relationship between PRC1 and PRC2 in synovial sarcoma? Given the intricate cross-regulation between these complexes (Piunti and Shilatifard, 2016Piunti A. Shilatifard A. Epigenetic balance of gene expression by Polycomb and COMPASS families.Science. 2016; 352: aad9780Crossref PubMed Scopus (282) Google Scholar) and the divergence in their requirements in synovial sarcoma, this will become an important area for future work. Finally, what roles do the Set1A/COMPASS and MLL2/COMPASS family members play in controlling bivalent gene activation through SS18-SSX, and can their specific catalytic inhibition be leveraged as a targeted therapeutic for synovial sarcoma? The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial SarcomaMcBride et al.Cancer CellMay 31, 2018In BriefIncorporation of the synovial sarcoma SS18-SSX fusion into BAF complexes results in concomitant eviction of BAF47. McBride et al. show that SS18-SSX retargets BAF complexes from enhancers to polycomb domains to oppose PRC2-mediated repression. Reincorporation of BAF47 upon suppression of SS18-SSX restores enhancer activation but is not required for proliferative arrest. Full-Text PDF Open Archive