Functional interplay between SWI/SNF complexes underlies BRD9 dependency in SMARCB1-mutant cancers [ATAC-seq]

Genes encoding subunits of SWI/SNF (BAF) chromatin remodeling complexes are mutated in >20% of cancers. SWI/SNF complexes exist in three distinct families that each contribute to regulation of transcription, although the functional interactions between the families are not well understood. Rhabdoid tumors constitute an informative model system as these highly aggressive cancers are driven by inactivation of a single SWI/SNF subunit, SMARCB1, which is present in two SWI/SNF families (cBAF and PBAF) but not in the third (GBAF/ncBAF). We and others have shown that BRD9, a therapeutically targetable member of ncBAF, is essential specifically in SMARCB1-deficient cancers, suggesting key functional relationships between SMARCB1-containing complexes and BRD9/ncBAF. However, the mechanistic underpinnings of these relationships are poorly understood. Here, we demonstrate that genomic binding of BRD9 is largely dependent upon SMARCB1 such that the absence of SMARCB1 results in significantly reduced BRD9 binding. At select sites, however, we show that SMARCB1-loss results in gain of BRD9 binding and BRD9-dependent accessibility. We find that this gain is associated with expression of genes promoting cell migration. Our results define relationships between SWI/SNF complex families, elucidate mechanisms by which SMARCB1 loss drives oncogenesis, and provide mechanistic insight into the synthetic-lethal relationship between SMARCB1 and BRD9. n=3 ATAC-seq of control vs SMARCB1 induced G401 cells treated with DMSO or dBRD9-A

编码SWI/SNF（BAF）染色质重塑复合物亚基的基因在超过20%的癌症中发生突变。SWI/SNF复合物存在三个不同的家族，每个家族均参与转录调控，但各家族间的功能互作机制尚未被充分阐明。横纹肌样瘤（Rhabdoid tumors）是极具研究价值的模型系统：这类高侵袭性癌症由单个SWI/SNF亚基SMARCB1的失活驱动，而SMARCB1仅存在于两个SWI/SNF家族（cBAF与PBAF）中，并不存在于第三个家族（GBAF/ncBAF）内。我们与其他研究团队均已证实，BRD9——一种可被靶向治疗的ncBAF组分——仅在SMARCB1缺陷型癌症中发挥必需功能，这提示含SMARCB1的复合物与BRD9/ncBAF之间存在关键的功能关联。然而，这类关联的分子机制仍有待深入解析。本研究证实，BRD9的基因组结合位点在很大程度上依赖于SMARCB1的存在，即SMARCB1的缺失会显著降低BRD9的结合水平。但在部分特定位点，我们发现SMARCB1缺失反而会导致BRD9结合增强，且该过程依赖BRD9调控染色质开放状态。我们进一步发现，这类结合增强现象与促进细胞迁移的基因表达上调密切相关。本研究明确了SWI/SNF复合物家族间的相互关系，阐明了SMARCB1缺失驱动肿瘤发生的分子机制，并为SMARCB1与BRD9之间的合成致死关联提供了分子层面的洞见。本研究包含样本量n=3的实验：分别为经DMSO或dBRD9-A处理的对照组与SMARCB1诱导型G401细胞的转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing，ATAC-seq）分析。