ARID2 promotes clear cell renal cell carcinoma in the absence of functional PBRM1 [ARID2 ChIP-seq]

Subunits of SWI/SNF chromatin remodeling complexes are frequently mutated in human malignancies. The PBAF complex is composed of multiple subunits, including the putative tumor suppressor proteins PBRM1 (BAF180) and ARID2 (BAF200) that are unique to this SWI/SNF complex. PBRM1 is mutated in various cancers, with a high mutation frequency in clear cell renal cell carcinoma (ccRCC). Here, we integrate RNA-seq, ARID2 and histone mark ChIP-seq, and ATAC-seq data to show that PBAF acts to enhance or repress gene expression depending on the genomic context. At baseline, ARID2 binds to areas of open chromatin at both active enhancers and promoters. Depletion of PBRM1 leads to attenuated and redistributed ARID2 chromatin binding that correlates significantly with gene expression changes. At enhancers, ARID2 binding loss leads to diminishment of the histone mark H3K4me1 and gene downregulation. Alternatively, at a subset of promoters, ARID2 binding loss derepresses gene expression. Interestingly, ARID2, which remains bound to other PBAF subunits after loss of PBRM1, is essential for many of the pro-tumorigenic transcriptional changes observed after loss of PBRM1, whereas other core SWI/SNF components are dispensable. Upon loss of PBRM1, ARID2 positively regulates cancer-related genes and pathways, including the cancer stem cell marker ALDH1A1 and ­­­EG­F signaling, to stimulate tumor cell growth. Therefore, ARID2 is crucial for maintaining the transformed state of PBRM1-deficient ccRCC cells. In total, this study suggests a novel mechanism of transcriptional control by PBRM1, whereby its loss alters the chromatin distribution of the residual PBAF complex leading to altered transcription that promotes tumorigenesis.

SWI/SNF染色质重塑复合物（SWI/SNF chromatin remodeling complexes）的亚基在人类恶性肿瘤中频发突变。PBAF复合物由多个亚基组成，包含该SWI/SNF复合物特有的推定肿瘤抑制蛋白PBRM1（BAF180）与ARID2（BAF200）。PBRM1在多种癌症中发生突变，其中透明细胞肾细胞癌（clear cell renal cell carcinoma, ccRCC）的突变频率较高。本研究整合RNA-seq、ARID2与组蛋白标记（histone mark）ChIP-seq及ATAC-seq数据，证实PBAF可根据基因组背景正向或负向调控基因表达。在基础状态下，ARID2结合于活性增强子与启动子区域的开放染色质（open chromatin）。敲低PBRM1会导致ARID2的染色质结合能力减弱且分布重排，该变化与基因表达改变显著相关。在增强子区域，ARID2结合缺失会导致组蛋白标记H3K4me1水平降低并引发基因表达下调（gene downregulation）；而在部分启动子区域，ARID2结合缺失则会解除对基因表达的抑制。值得注意的是，在PBRM1缺失后仍能与其他PBAF亚基结合的ARID2，对PBRM1缺失后观察到的多种促肿瘤发生（pro-tumorigenic）转录变化（transcriptional changes）至关重要，而其他核心SWI/SNF组分（core SWI/SNF components）则并非必需。PBRM1缺失后，ARID2可正向调控癌症相关基因与通路，包括癌症干细胞标记（cancer stem cell marker）ALDH1A1与EGF信号通路（EGF signaling），从而促进肿瘤细胞增殖。因此，ARID2对维持PBRM1缺陷型（PBRM1-deficient）ccRCC细胞的转化状态（transformed state）至关重要。综上，本研究揭示了PBRM1介导转录调控的全新机制：PBRM1缺失会改变残留PBAF复合物的染色质分布，进而引发转录改变并促进肿瘤发生。