The function of Snf5, an epigenetic tumor suppressor

 描述（由申请人提供）：SNF 5（SMARCB 1/INI 1/BAF 47）是SWI/SNF染色质重塑复合物中与癌症相关的第一个亚基，发现其在几乎所有高度侵袭性儿科癌症恶性横纹肌样瘤和家族性癌症易感综合征病例中特异性突变。随后建立的小鼠模型表明，SNF 5的条件性失活导致100%的小鼠癌症快速发展。基因组测序研究显示，20%的人类癌症在编码SWI/SNF亚基的基因中携带突变，这与人类恶性肿瘤的广泛相关性最近出现。在目前的资助周期中，我们发现SNF 5缺陷型人类肿瘤的基因组非常简单，这表明SNF 5缺失的影响在本质上是表观遗传的。沿着这些路线，我们发现了SNF 5在建立启动子核小体占据中的作用;发现了SNF 5和Polycomb复合物之间的表观遗传拮抗作用;鉴定了细胞周期蛋白D1/CDK 4、Hedgehog和Wnt/β-连环蛋白途径作为其肿瘤抑制活性的靶点;并将我们的CDK 4发现转化为临床试验。为什么SNF 5介导的核小体定位在启动子和基因表达变化之间几乎没有相关性？SNF 5对SWI/SNF复合物的功能有何作用？此外，鉴于我们已经证明SNF 5缺失会导致特定的遗传依赖性，我们能否系统地识别SNF 5突变造成的漏洞？我们现在有大量的初步数据，开始解决这些问题。我们已经为SNF 5的支架和增强子靶向作用以及SNF 5在控制H3 K27乙酰化中的关键作用提供了证据。基于我们的初步发现，我们假设SNF 5的中心功能是将SWI/SNF复合物靶向谱系特异性增强子和超级增强子，在那里它调节核小体位置并促进H3 K27乙酰化以激活转录。我们进一步假设SNF 5缺失导致癌症是由于SNF 5缺陷细胞执行谱系特异性分化程序的能力受损。使用我们的基因工程功能丧失小鼠模型系统和我们的功能获得系统，其中我们将SNF 5重新引入SNF 5缺陷癌细胞系中，我们将定义SNF 5对控制核小体占用和增强子和超级增强子处的H3 K27乙酰化的贡献。我们还将使用这些模型来表征SNF 5在控制谱系特异性转录调控中的作用。最后，在我们最近成功鉴定其他SWI/SNF亚基突变的癌细胞系中的脆弱性的基础上，我们将系统地鉴定SNF 5缺失所产生的遗传脆弱性。相关性：SWI/SNF复合物突变发生在20%的人类癌症中。我们提出的研究旨在确定核心SWI/SNF亚基SNF 5突变驱动癌症的机制，并确定SNF 5缺失所带来的遗传脆弱性，这是潜在的治疗靶点。

 DESCRIPTION (provided by applicant): SNF5 (SMARCB1/INI1/BAF47) was the first subunit of the SWI/SNF chromatin remodeling complex linked to cancer when it was found to be specifically mutated in virtually all cases of the highly aggressive pediatric cancer malignant rhabdoid tumor and in a familial cancer predisposition syndrome. Mouse models subsequently established that conditional inactivation of SNF5 results in the rapid development of cancer in 100% of mice. Broad relevance to human malignancy has recently emerged as genome sequencing studies have revealed that 20% of all human cancers carry mutations in genes encoding SWI/SNF subunits. During the current funding cycle, we discovered that the genomes of SNF5-deficient human tumors are remarkably simple, suggesting that the effects of SNF5 loss are epigenetic in nature. Along these lines, we discovered a role for SNF5 in establishing nucleosome occupancy at promoters; discovered epigenetic antagonism between SNF5 and the Polycomb complexes; identified the Cyclin D1/CDK4, Hedgehog, and Wnt/ß-catenin pathways as targets of its tumor suppressor activity; and translated our CDK4 findings into a clinical trial However, major questions remain. Why is there little correlation between SNF5-mediated nucleosome positioning at promoters and changes in gene expression? What is the biochemical mechanism by which SNF5 contributes to the function of the SWI/SNF complex? Also, given that we have demonstrated that SNF5 loss leads to specific genetic dependencies, can we systematically identify vulnerabilities created by SNF5 mutation? We now have substantial preliminary data that begin to address these questions. We have generated evidence for scaffolding and enhancer-targeting roles for SNF5 as well as for a key role of SNF5 in controlling acetylation of H3K27. Based upon our preliminary findings, we hypothesize that a central function of SNF5 is to target the SWI/SNF complex to lineage-specific enhancers and super-enhancers, where it modulates nucleosome position and facilitates H3K27 acetylation to activate transcription. We further hypothesize that SNF5 loss drives cancer due to an impaired ability of SNF5-deficient cells to execute lineage-specific differentiation programs. Using our genetically engineered loss-of-function murine model systems and our gain-of-function systems in which we reintroduce SNF5 into SNF5-deficient cancer cell lines, we will define the contributions of SNF5 to control of nucleosome occupancy and H3K27 acetylation at enhancers and super-enhancers. We will also use these models to characterize roles for SNF5 in the control of lineage-specific transcriptional regulation. Lastly, building upon our recent successes in identifying vulnerabilities in cancer cell lines mutant for other SWI/SNF subunits, we will systematically identify genetic vulnerabilities created by SNF5 loss. Relevance: Mutations of the SWI/SNF complex occur in 20% of all human cancers. Our proposed studies are designed to define the mechanism by which mutation of the core SWI/SNF subunit SNF5 drives cancer and to identify genetic vulnerabilities conferred by SNF5 loss, which represent potential therapeutic targets.