Targeting DCAF5 suppresses SMARCB1-mutant cancer via stabilizing SWI/SNF. Targeting DCAF5 suppresses SMARCB1-mutant cancer via stabilizing SWI/SNF

While oncogenes can potentially be inhibited with small molecules, the loss of tumor suppressors is more common and presents a conundrum for precision therapy because the proteins are no longer present. SMARCB1-mutant cancers epitomize this challenge because these highly lethal cancers are driven by inactivation of a single gene, a subunit of SWI/SNF chromatin remodeling complexes. To generate mechanistic insight into the consequences of SMARCB1 mutation and to seek vulnerabilities, we contributed 16 SMARCB1-mutant cell lines to a near-genomewide CRISPR screen as part of the Cancer Dependency Map1-3. Here we report that the little-studied gene DCAF5 (DDB1-CUL4 Associated Factor 5) is a specific dependency in SMARCB1-mutant cancers. We show that DCAF5 serves a quality control function for SWI/SNF complexes and in the absence of SMARCB1 DCAF5 causes degradation of incompletely assembled SWI/SNF complexes. Upon inhibition of DCAF5 SMARCB1-deficient SWI/SNF complexes re-accumulate, bind to target loci, and restore gene expression to levels sufficient to fully reverse the cancer state, including in a xenograft mouse model. Consequently, cancer results not from the loss of SMARCB1 function per se but rather from DCAF5-mediated degradation of SWI/SNF complexes. These data indicate that therapeutic targeting of DCAF5 may be sufficient to restore substantial SWI/SNF function and reverse cancer phenotypes caused by SMARCB1 loss. Overall design: ATAC-seq in G401 cells: shCTRL(n=3), shDCAF5(n=3) ATAC-Seq performed in triplicate in G401 cells treated with the combination of shDCAF5 with ATPase inhibitor BRM014 (1uM) with proper controls. Reprocessed ATAC-Seq data in triplicate for G401s with and without SMARCB1 added back Re-analysed Samples GSE210632/PRJNA866528 and processed data files: GSM6433872 SRX16881727 SAMN30167975 2112966_GFP_ATAC_n1.free* GSM6433873 SRX16881728 SAMN30167974 2118889_GFP_ATAC_n2.free* GSM6433874 SRX16881729 SAMN30167973 2161067_GFP_ATAC_n3.free* GSM6433875 SRX16881730 SAMN30167972 2112968_SMARCB1_ATAC_n1.free* GSM6433876 SRX16881719 SAMN30167971 2118891_SMARCB1_ATAC_n2.free* GSM6433877 SRX16881720 SAMN30167970 2161068_SMARCB1_ATAC_n3.free*

尽管癌基因可通过小分子化合物实现抑制，但肿瘤抑制基因的缺失更为普遍，且给精准治疗带来了棘手难题——此类肿瘤抑制蛋白本身已不复存在。SMARCB1突变型癌症正是这类挑战的典型范例：这类致死性极强的癌症由单个基因的失活驱动，该基因是SWI/SNF染色质重塑复合物（SWI/SNF chromatin remodeling complexes）的一个亚基。为深入解析SMARCB1突变所引发的分子机制并探寻治疗脆弱位点，我们作为《癌症依赖性图谱（Cancer Dependency Map）》1-3的研究组成员，提交了16株SMARCB1突变细胞系用于近全基因组CRISPR筛选。
本研究首次证实，此前鲜有研究的基因DCAF5（DDB1-CUL4 Associated Factor 5）是SMARCB1突变型癌症的特异性依赖基因。我们发现，DCAF5对SWI/SNF复合物行使质量控制功能；在SMARCB1缺失的背景下，DCAF5会介导未完全组装的SWI/SNF复合物发生降解。抑制DCAF5后，SMARCB1缺陷型SWI/SNF复合物会重新积累并结合至靶位点，同时将基因表达恢复至足以完全逆转癌症表型的水平，这一效应在异种移植小鼠模型中同样得到验证。据此，癌症的发生并非源于SMARCB1功能本身的缺失，而是源于DCAF5介导的SWI/SNF复合物降解。上述研究数据表明，靶向DCAF5的治疗策略足以恢复SWI/SNF的核心功能，并逆转由SMARCB1缺失引发的癌症表型。
实验整体设计：
G401细胞的ATAC测序（ATAC-seq）：对照短发夹RNA组（shCTRL，n=3）、DCAF5靶向短发夹RNA组（shDCAF5，n=3）；对经shDCAF5联合ATP酶抑制剂BRM014（1μM）处理的G401细胞进行三次重复ATAC测序，并设置相应对照。对恢复或敲除SMARCB1的G401细胞进行三次重复ATAC测序数据的重新分析。同时重新分析公开数据集GSE210632/PRJNA866528中的样本及其处理后的数据文件：
GSM6433872 SRX16881727 SAMN30167975 2112966_GFP_ATAC_n1.free*
GSM6433873 SRX16881728 SAMN30167974 2118889_GFP_ATAC_n2.free*
GSM6433874 SRX16881729 SAMN30167973 2161067_GFP_ATAC_n3.free*
GSM6433875 SRX16881730 SAMN30167972 2112968_SMARCB1_ATAC_n1.free*
GSM6433876 SRX16881719 SAMN30167971 2118891_SMARCB1_ATAC_n2.free*
GSM6433877 SRX16881720 SAMN30167970 2161068_SMARCB1_ATAC_n3.free*