The SS18-SSX fusion oncoprotein hijacks BAF complex targeting and function to drive synovial sarcoma [ATAC-seq]

Synovial sarcoma (SS) is defined by the hallmark SS18-SSX fusion oncoprotein, which renders BAF complexes aberrant in two manners: gain of SSX to the SS18 subunit and concomitant loss of BAF47 subunit assembly. Here we demonstrate that SS18-SSX globally hijacks BAF complexes on chromatin to activate a SS transcriptional signature we define using primary tumors and cell lines. Specifically, SS18-SSX retargets BAF complexes from enhancers to broad polycomb domains to oppose PRC2-mediated repression and activate bivalent genes. Upon suppression of SS18-SSX, reassembly of BAF47 restores enhancer activation, but is not required for proliferative arrest. These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations. Overall design: Synovial sarcoma cell lines (Aska) were lentivirally infected with either an shControl or a shSSX vector, selected for 48 hours with puromycin, then grown for 5 days, at which point cells were harvested for ATAC-seq preparation. CRL7250 fibroblast cell line was lentivirally infected with either a V5-SS18 or V5-SS18-SSX expressing vector, selected for 48 hours with puromycin, then grown for 5 days, at which point cells were harvested for ATAC-seq preparation. The processed data was generated on merged biological duplicate experiments and linked to the corresponding *rep1 sample records.

滑膜肉瘤（Synovial Sarcoma, SS）以标志性的SS18-SSX融合癌蛋白（SS18-SSX fusion oncoprotein）为特征，该蛋白通过两种途径使BAF复合物（BAF Complex）出现功能异常：一是将SSX融合至SS18亚基，二是伴随BAF47亚基组装的缺失。本研究证实，SS18-SSX可在染色质（chromatin）层面全局性劫持BAF复合物，从而激活我们通过原发性肿瘤与细胞系鉴定的滑膜肉瘤特征性转录谱。具体而言，SS18-SSX将BAF复合物从增强子（enhancer）区域重定位至宽泛的多梳蛋白结构域（polycomb domains），以此拮抗多梳抑制复合体2（PRC2）介导的基因沉默并激活二价基因（bivalent genes）。当抑制SS18-SSX表达后，BAF47的重新组装可恢复增强子的激活活性，但这对于细胞增殖阻滞并非必需。上述研究结果阐明了SS18-SSX在染色质层面的全局性劫持机制，并明确了两种同步发生的BAF复合物异常各自的独立功能贡献。

实验设计：滑膜肉瘤细胞系（Aska）分别经携带shControl或shSSX载体的慢病毒（lentivirus）感染，以嘌呤霉素（puromycin）筛选48小时后继续培养5天，随后收集细胞用于转座酶可及性测序（ATAC-seq）文库制备。CRL7250成纤维细胞系分别经携带V5-SS18或V5-SS18-SSX表达载体的慢病毒感染，以嘌呤霉素筛选48小时后继续培养5天，随后收集细胞用于ATAC-seq文库制备。本研究的经处理数据由合并的生物学重复（biological duplicate）实验生成，并与对应的*rep1样本记录相关联。