A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation [RNA-seq]. A non-canonical SWI/SNF complex underlies synthetic lethality in cancers driven by BAF complex perturbation [RNA-seq]

Mammalian SWI/SNF chromatin remodeling complexes exist in three distinct, final-form assemblies: canonical BAF (cBAF), PBAF, and a newly characterized non-canonical complex, ncBAF. However, their complex-specific targeting on chromatin, functions and roles in disease remain largely unknown. Here, we comprehensively map complex assemblies on chromatin and find that ncBAF uniquely localizes to CTCF sites and promoters. We identified ncBAF subunits as major synthetic lethalities specific to human synovial sarcoma and malignant rhabdoid tumor, which share in common cBAF complex perturbation. Chemical degradation of the BRD9 subunit of ncBAF rapidly attenuates SS and MRT cell proliferation. Notably, in cBAF-perturbed cancers, ncBAF complexes retain their hallmark localization to CTCF sites and promoters, and maintain gene expression at retained mSWI/SNF sites to support cell proliferation in a manner distinct from fusion oncoprotein-mediated targeting. Taken together, these findings unmask the unique targeting and function of ncBAF complexes and present new cancer-specific therapeutic targets. Overall design: CRL7250 cells were treated in biological duplicate with either DMSO vehicle control , dBRD9 compound, or dBRD9 compound for 24h followed by lentiviral infection with construct containing V5-SS18-SSX1 to assess role of BRD9 in SS18-SSX1 gene activation. RNA-seq was performed in biological duplicate in SYO-1 synovial sarcoma cells upon chemical BRD9 degradation by dBRD9 compound or DMSO vehicle control at 3 days and 6 days to assess gene expression changes upon BRD9 perturbation. SYO-1 cells were lentivirally infected in biological duplicate with pGIPZ shControl, pGIPZ shBRD9, or pGIP shSMARCE1 to assess if BRD9 and SMARE1 knockdown are transcriptionally similar. RNA-seq was collected in biological duplicate from TTC1240 cells treated with either DMSO or dBRD9 as for SYO-1. To assess gene expression changes upon BRD9 loss, TTC1240 and MOLM-13 cells were treated with 250nM dBRD9 (1:10,000 dilution) or DMSO control for 7 days (TTC1240) or 6 days (MOLM-13) in duplicate.

哺乳动物SWI/SNF染色质重塑复合物（mammalian SWI/SNF chromatin remodeling complexes）存在三种不同的终末组装形式：经典BAF（canonical BAF, cBAF）、PBAF，以及新近鉴定的非经典复合物ncBAF（non-canonical complex, ncBAF）。然而，其复合物特异性的染色质靶向机制、生物学功能以及在疾病中的作用仍有待深入阐明。本研究中，我们全面绘制了染色质上的复合物组装图谱，发现ncBAF独特定位于CTCF结合位点与启动子区域。我们鉴定出ncBAF亚基是人类滑膜肉瘤与恶性横纹肌样瘤这两类共同存在cBAF复合物扰动的肿瘤所特有的主要合成致死靶点。对ncBAF的BRD9亚基进行化学降解可快速减弱滑膜肉瘤（SS）与恶性横纹肌样瘤（MRT）细胞的增殖能力。值得注意的是，在cBAF扰动的癌症中，ncBAF复合物仍保留其标志性的CTCF位点与启动子定位特征，并在保留的mSWI/SNF结合位点维持基因表达，以不同于融合癌蛋白介导的靶向方式支持细胞增殖。综上，这些研究结果揭示了ncBAF复合物独特的靶向机制与生物学功能，并为癌症治疗提供了全新的特异性治疗靶点。
整体实验设计：将CRL7250细胞设置生物学重复，分别以DMSO溶剂对照、dBRD9化合物、dBRD9化合物处理24小时，随后用携带V5-SS18-SSX1的慢病毒感染，以评估BRD9在SS18-SSX1基因激活中的作用。在SYO-1滑膜肉瘤细胞中，分别用dBRD9化合物或DMSO溶剂对照处理3天和6天以诱导BRD9化学降解，并设置生物学重复进行RNA测序（RNA sequencing, RNA-seq），以检测BRD9扰动后的基因表达变化。将SYO-1细胞以生物学重复的方式分别用pGIPZ shControl、pGIPZ shBRD9或pGIP shSMARCE1进行慢病毒感染，以评估BRD9与SMARCE1敲降后的转录谱相似性。我们同样从经DMSO或dBRD9处理的TTC1240细胞中收集了生物学重复样本进行RNA测序。为评估BRD9缺失后的基因表达变化，将TTC1240与MOLM-13细胞分别用250nM dBRD9（1:10000稀释）或DMSO对照处理，其中TTC1240处理7天、MOLM-13处理6天，均设置生物学重复。