Evaluating splicing modulators for therapeutic impact in cohesin-mutant myeloid malignancies

骨髓增生异常综合征（MDS）和急性髓性白血病（AML）是造血干细胞和祖细胞突变的克隆性疾病，其特征在于异常分化和增殖状态，并与影响转录因子、表观遗传调节因子、染色质修饰剂和剪接基因的突变和重排相关。在13%的原发性AML患者、21%的继发性AML患者和11%的MDS患者中，粘着蛋白复合物STAG 2、SMC 1、SMC 3、RAD 21及其调节剂PDS 5和NIPBL的核心组分共同发生突变，这些突变与较差的总生存期相关。粘着蛋白基因的突变几乎总是互斥的、杂合的、预测的功能丧失突变，其被认为是在从克隆造血向MDS进展的早期获得的。先前的工作发现，髓系恶性肿瘤中常见的粘附素突变破坏了RNA剪接，使细胞对广谱剪接抑制剂高度敏感。我们建议使用最先进的方法来表征新生转录，RNA加工和RNA-蛋白质相互作用测定，以确定介导这种脆弱性的异常RNA种类，并探索原发性粘附素突变患者样本对剪接调节的敏感性。我们假设粘连蛋白复合物突变导致RNA生物合成和剪接的改变，并可作为粘连蛋白突变型MDS和AML患者的治疗弱点。我们提出以下具体目标：1：表征粘连蛋白突变对原发性患者样本中RNA生物合成的影响2：确定粘连蛋白突变对原发性AML细胞对剪接调节H3 B-8800和E71073的敏感性的影响：使用eCLIP-Seq表征cohesin复合物和SF 3B复合物之间相互作用的性质我们期望利用来自无偏蛋白质组学研究、基因组规模的功能遗传筛选和药物敏感性测定的广泛数据，来确定针对cohesin突变型癌症患者的新治疗方法，并发现这些遗传驱动因子的新转化机制。这些研究的结果有可能在未来几年内直接导致一项或多项临床试验。

Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML) are clonal diseases of mutated hematopoietic stem and progenitor cells characterized by abnormal differentiation and proliferative states, and associated with mutations and rearrangements affecting transcription factors, epigenetic regulators, chromatin modifiers and splicing genes. The core components of the cohesin complex STAG2, SMC1, SMC3, RAD21, as well as its modulators PDS5 and NIPBL are collectively mutated in 13% of patients with de novo AML, 21% of patients with secondary AML, and 11% of patients with MDS where they are associated with poor overall survival. Mutations in the cohesin genes are nearly always mutually exclusive, heterozygous, predicted loss-of-function mutations, which are thought to be acquired early during the progression from clonal hematopoiesis to MDS. Previous work discovered that cohesin mutations common in myeloid malignancies disrupt RNA splicing and render cells highly sensitive to broad-spectrum splicing inhibitors. We propose to use state-of-the-art approaches to characterize nascent transcription, RNA processing and RNA-protein interaction assays to define the aberrant RNA species that mediate this vulnerability and explore sensitivity of primary cohesin-mutant patient samples to splicing modulation. We hypothesize that cohesin complex mutations lead to altered RNA biogenesis and splicing and can serve as a therapeutic vulnerability in patients with cohesin-mutant MDS and AML.We propose the following specific Aims:1: Characterize the effect of cohesin mutations on RNA biogenesis in primary patient samples2: Determine the effect of cohesin mutations on sensitivity of primary AML cells to splicing modulation H3B-8800 und E71073: Characterize the nature of the interaction between the cohesin complex and SF3B complex using eCLIP-SeqWe expect to leverage extensive data from unbiased proteomic studies, genome-scale functional genetic screens, and drug sensitivity assays to identify new therapeutic approaches for patients with cohesin mutant cancers and to discover novel mechanisms of transformation by these genetic drivers. The findings fromthese studies have the potential to lead directly to one or more clinical trials within the next several years.