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

骨髓增生异常综合征（MDS）和急性髓系白血病（AML）是造血干细胞和祖细胞突变的克隆性疾病，其特征是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、染色质修饰因子和剪接基因的突变和重排有关。黏结蛋白复合物的核心成分STAG2、SMC1、SMC3、RAD21及其调节剂PDS5和NIPBL在13%的新发AML患者、21%的继发性AML患者和11%的MDS患者中共同发生突变，这些突变与较差的总生存率相关。黏结蛋白基因的突变几乎总是互斥的、杂合的、可预测的功能丧失突变，这些突变被认为是在从克隆造血到MDS的早期过程中获得的。先前的研究发现，髓系恶性肿瘤中常见的黏结蛋白突变会破坏RNA剪接，并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-蛋白相互作用分析，以定义介导这种脆弱性的异常RNA物种，并探索初级内聚蛋白突变患者样本对剪接调节的敏感性。我们假设内聚蛋白复合物突变导致RNA生物发生和剪接改变，并可作为内聚蛋白突变MDS和AML患者的治疗脆弱性。我们提出以下具体目标：1：表征黏结蛋白突变对原发患者样本中RNA生物发生的影响2：确定黏结蛋白突变对原发AML细胞对剪接调节H3B-8800和E71073敏感性的影响。我们期望利用来自无偏倚的蛋白质组学研究、基因组规模的功能遗传筛选和药物敏感性分析的大量数据，为黏合蛋白突变型癌症患者确定新的治疗方法，并发现这些遗传驱动因素转化的新机制。这些研究的发现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.