The function of Snf5, an epigenetic tumor suppressor

 描述(申请人提供)：SNF5(SMARCB1/INI1/BAF47)是SWI/SNF染色质重塑复合体的第一个亚基，与癌症有关，当时发现它在几乎所有高度侵袭性的儿科癌症、恶性横纹肌样瘤和家族性癌症易感综合征的病例中都发生了特异性突变。小鼠模型随后证实，SNF5的条件灭活会导致100%的小鼠癌症快速发展。最近，随着基因组测序研究显示，20%的人类癌症携带编码SWI/SNF亚单位的基因突变，与人类恶性肿瘤的广泛相关性已经出现。在当前的资金周期中，我们发现SNF5缺失的人类肿瘤的基因组非常简单，这表明SNF5缺失的影响本质上是表观遗传的。沿着这些思路，我们发现了SNF5在建立核小体在启动子上的占位方面的作用；发现了SNF5和Polycomb复合体之间的表观遗传拮抗作用；确定了Cyclin D1/CDK4、Hedgehog和Wnt/？catenin通路是其肿瘤抑制活性的靶点；并将我们的CDK4发现转化为临床试验，然而，主要问题仍然存在。为什么SNF5介导的核小体在启动子上的定位与基因表达的变化几乎没有相关性？SNF5参与SWI/SNF复合体功能的生化机制是什么？此外，鉴于我们已经证明SNF5缺失会导致特定的遗传依赖，我们能否系统地识别SNF5突变造成的漏洞？我们现在有了大量的初步数据，开始解决这些问题。我们已经为SNF5的支架和增强子靶向作用以及SNF5在控制H3K27乙酰化中的关键作用提供了证据。根据我们的初步发现，我们假设SNF5的一个中心功能是将SWI/SNF复合体靶向谱系特异性增强子和超级增强子，其中它调节核小体位置并促进H3K27乙酰化激活转录。我们进一步假设，SNF5缺失导致癌症的原因是SNF5缺失的细胞执行特定谱系分化程序的能力受损。使用我们的基因工程小鼠功能丧失模型系统和我们的功能获得系统，在这些系统中，我们将SNF5重新引入SNF5缺失的癌细胞系中，我们将确定SNF5在控制核小体占据和H3K27乙酰化增强剂和超级增强剂方面的贡献。我们还将使用这些模型来表征SNF5在控制谱系特异性转录调控中的作用。最后，在我们最近成功识别其他SWI/SNF亚单位突变的癌细胞中的脆弱性的基础上，我们将系统地识别SNF5缺失造成的遗传脆弱性。相关性：SWI/SNF复合体突变发生在20%的人类癌症中。我们建议的研究旨在确定核心SWI/SNF亚单位SNF5突变导致癌症的机制，并确定SNF5缺失带来的遗传脆弱性，这些都是潜在的治疗靶点。

 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.