The interface of transcription, DNA damage and epigenetics: A therapeutic vulnerability of the EWS-FLI1 transcription factor

转录、DNA 损伤和表观遗传学的界面：EWS-FLI1 转录因子的治疗脆弱性

• 批准号: 10718793
• 负责人: Patrick J Grohar
• 金额: $ 50.57万
• 依托单位: CHILDREN'S HOSP OF PHILADELPHIA
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-06-01 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10718793
• 关键词: Binding; Biological Assay; Biology; Cell Nucleolus; Cell Nucleus; Cell Proliferation; Cell Survival; Cells; Chimeric Proteins; Chromatin; Chromatin Structure; Clinic; Clinical; Clinical Data; Clinical Trials; Combined Modality Therapy; Cytoprotection; DNA; DNA Binding; DNA Binding Agent; DNA Damage; DNA Minor Groove Binding; Data; Dependence; Development; Disease; Dose; Doxorubicin; Drug resistance; EWS-FLI1 fusion protein; EWSR1 gene; Enhancers; Epigenetic Process; Etoposide; Ewings sarcoma; FLI1 Transcription Factor; Genes; Genetic Transcription; Genome; Goals; Heat-Shock Proteins 70; Impairment; Malignant Neoplasms; Microsatellite Repeats; Modeling; Mutation; Normal Cell; Nucleotides; Oncogenes; Oncogenic; Output; Patient-Focused Outcomes; Patients; Pharmaceutical Preparations; Phase Transition; Poison; Proteins; Proteomics; Recovery; Recurrence; Relapse; Reporting; Response Elements; Site; Testing; Therapeutic; Toxic effect; Translating; Treatment Efficacy; Ultraviolet Rays; actinomycin; cell type; driver mutation; effective therapy; epigenetic silencing; global run on sequencing; improved; improved outcome; in vivo; inhibitor; insight; irinotecan; novel; novel strategies; patient derived xenograft model; pre-clinical; recruit; research clinical testing; resistance mechanism; response; success; targeted agent; targeted treatment; transcription factor; tumor; tumor growth

There is an urgent need to develop novel approaches to target oncogenic transcription factors. Ewing sarcoma (ES) is emblematic of this need. It has been known for more than 25 years that ES is absolutely dependent on the EWS-FLI1 transcription factor for cell survival. EWS-FLI1 is the only recurrent mutation of ES (>20% of tumors) and the dependence of the cells on this protein has been established by multiple independent studies. Our overarching goal is to identify and clinically translate compounds that inhibit EWS- FLI1 to improve outcomes for patients with Ewing sarcoma. Consistent with this goal, we have identified the minor groove DNA binding compound trabectedin as an inhibitor of EWS-FLI1. We have moved this compound into the clinic in combination with low dose irinotecan and have seen striking clinical responses. However, some patients progress while on therapy. Other patients have required dose reductions due to toxicity that limits the efficacy of the therapy. Therefore, in this study, we propose that a deeper understanding of the mechanisms of activity and drug resistance will improve the therapy. We hypothesize that while these compounds poison EWS-FLI1 by mechanisms that we have defined, they also alter chromatin structure and cellular state in such a way that poises the cell for recovery. More precisely, we have shown that trabectedin redistributes EWS-FLI1 in the nucleus to the nucleolus to trigger an epigenetic switch to alter chromatin accessibility at the EWS-FLI1 driven GGAA microsatellite enhancer. However, here we propose that additional epigenetic DNA damage response mechanisms, identified by unbiased approaches, leaves the chromatin poised for recovery. Additionally, we have shown that redistribution of EWS-FLI1 to the nucleolus stabilizes the fusion protein thus providing a reserve pool that facilitates transcriptional recovery. Therefore, the goal of this study is to directly target these poised states to improve the activity of the compound, limit toxicity, and restrict mechanisms of resistance. Importantly, these approaches should improve the toxicity profile because they focus on EWS-FLI1 which is only found in Ewing sarcoma cells and its downstream GGAA microsatellite enhancer which has no known function in normal cells. If successful, the study will yield a novel mechanistically focused combination therapy for relapsed Ewing sarcoma patients that will build on the preliminary success of trabectedin/irinotecan. In addition, the study will provide important insight into the use of DNA binding compounds as inhibitors of oncogenic transcription factors. Finally, it will yield a novel “trapping” approach to target phase transitioned transcription factors.

迫切需要开发新的方法来靶向致癌转录因子。尤因 肉瘤(ES)就是这种需求的象征。25年来，人们已经知道ES是绝对的 依赖于EWS-FLI1转录因子的细胞存活。EWS-FLI1是唯一一个反复发生的突变 ES(&gt；20%的肿瘤)和细胞对这种蛋白的依赖性已经通过多个 独立研究。我们的首要目标是识别并在临床上翻译抑制EWS的化合物- FLI1用于改善尤文肉瘤患者的预后。与这一目标一致，我们已经确定了 小槽DNA结合化合物曲贝替丁作为EWS-FLI1的抑制剂。我们已经把这件事 复方与小剂量伊立替康联合应用于临床，取得了显著的临床疗效。 然而，一些患者在接受治疗时会出现进展。其他患者由于以下原因而要求减少剂量 限制治疗效果的毒性。因此，在这项研究中，我们提出了更深入的理解 了解其作用机制和耐药机制将有助于提高治疗效果。我们假设，虽然这些 化合物通过我们定义的机制毒害EWS-FLI1，它们还改变染色质结构和 以这种方式使细胞处于平衡状态，以供恢复。更准确地说，我们已经证明了 将EWS-FLI1在细胞核中重新分布到核仁，以触发表观遗传开关来改变染色质 EWS-FLI1驱动的GGAA微卫星增强子的可及性。然而，在这里，我们建议增加 通过无偏见的方法确定的表观遗传DNA损伤反应机制，使染色质 准备好恢复了。此外，我们还表明，EWS-FLI1重新分布到核仁上可以稳定 因此，融合蛋白提供了促进转录恢复的储备池。因此，这一目标是 研究是直接针对这些平衡状态来提高化合物的活性，限制毒性和限制 抗性机制。重要的是，这些方法应该会改善毒性分布，因为它们 关注仅在尤文肉瘤细胞及其下游GGAA微卫星中发现的EWS-FLI1 在正常细胞中未知功能的增强子。如果成功，这项研究将产生一部小说 机械聚焦联合疗法治疗复发的尤因肉瘤患者将建立在 曲贝替丁/伊立替康的初步成功。此外，这项研究将为使用 作为致癌转录因子抑制物的DNA结合化合物。最后，它将产生一部小说《陷阱》 靶向相变转录因子的研究进展。