Ewing sarcoma is a cancer of children and young adults characterized by the critical translocation-associated fusion oncoprotein EWSR1::FLI1. EWSR1::FLI1 targets characteristic genetic loci where it mediates aberrant chromatin and the establishment of de novo enhancers. Ewing sarcoma thus provides a model to interrogate mechanisms underlying chromatin dysregulation in tumorigenesis. Previously, we developed a high-throughput chromatin-based screening platform based on the de novo enhancers and demonstrated its utility in identifying small molecules capable of altering chromatin accessibility. Here, we report the identification of MS0621, a molecule with previously uncharacterized mechanism of action, as a small molecule modulator of chromatin state at sites of aberrant chromatin accessibility at EWSR1::FLI1-bound loci. MS0621 suppresses cellular proliferation of Ewing sarcoma cell lines by cell cycle arrest. Proteomic studies demonstrate that MS0621 associates with EWSR1::FLI1, RNA binding and splicing proteins, as well as chromatin regulatory proteins. Surprisingly, interactions with chromatin and many RNA-binding proteins, including EWSR1::FLI1 and its known interactors, were RNA-independent. Our findings suggest that MS0621 affects EWSR1::FLI1-mediated chromatin activity by interacting with and altering the activity of RNA splicing machinery and chromatin modulating factors. Genetic modulation of these proteins similarly inhibits proliferation and alters chromatin in Ewing sarcoma cells. The use of an oncogene-associated chromatin signature as a target allows for a direct approach to screen for unrecognized modulators of epigenetic machinery and provides a framework for using chromatin-based assays for future therapeutic discovery efforts.
尤文肉瘤是一种儿童和青少年癌症,其特征是与关键易位相关的融合肿瘤蛋白 EWSR1::FLI1。EWSR1::FLI1以特征性遗传位点为靶点,在这些位点上介导异常染色质和新生增强子的建立。因此,尤文肉瘤为研究肿瘤发生过程中染色质失调的机制提供了一个模型。在此之前,我们基于新生增强子开发了一种基于染色质的高通量筛选平台,并证明了它在鉴定能够改变染色质可及性的小分子方面的实用性。在这里,我们报告了 MS0621 的鉴定结果,这是一种具有之前未表征的作用机制的分子,是 EWSR1::FLI1 结合位点染色质可及性异常位点染色质状态的小分子调节剂。MS0621 通过抑制细胞周期来抑制尤文肉瘤细胞系的细胞增殖。蛋白质组学研究表明,MS0621 能与 EWSR1::FLI1、RNA 结合蛋白、剪接蛋白以及染色质调控蛋白结合。令人惊讶的是,MS0621与染色质和许多RNA结合蛋白(包括EWSR1::FLI1及其已知的相互作用因子)的相互作用与RNA无关。我们的研究结果表明,MS0621通过与RNA剪接机制和染色质调节因子相互作用并改变其活性,从而影响EWSR1::FLI1介导的染色质活性。对这些蛋白的基因调控同样会抑制尤文肉瘤细胞的增殖并改变其染色质。使用癌基因相关染色质特征作为靶标,可以直接筛选出尚未认识到的表观遗传机制调节因子,并为未来使用基于染色质的检测方法发现治疗方法提供了一个框架。