Novel combination therapy for AML expressing mutant RUNX1

采用目前的治疗方案，高风险成人患者的长期缓解率 骨髓增生异常综合征（MDS）和急性髓性白血病（AML）为15- 25%。RUNX 1是DNA- 核心结合因子（CBF）复合物的结合亚基和主调节转录因子 与造血有关大多数突变体（mt）RUNX 1是错义、大缺失或截短- 突变，主要表现为功能丧失（LOF）突变。mtRUNX 1的存在赋予相对 MDS/AML患者的治疗耐药性和较差的生存率。生殖系突变和缺失 在RUNX 1中，引起高度渗透性（~40%）家族性血小板疾病，并倾向于演变为 MDS或AML。缺乏特异性靶向治疗，加上对标准治疗的耐药性， 对于表达体细胞或生殖细胞mtRUNX 1的MDS/AML的预后和结果较差。因此，我们认为， 对开发用于表达mtRUNX 1的MDS/AML的新型靶向疗法存在未满足的需求。我们 初步研究表明，RUNX 1的敲低在体外诱导显著更高的致死性， 表达mtRUNX 1与野生型（wt）RUNX 1的AML母细胞。利用RUNX 1的RNA-Seq签名 击倒和查询LINCS 1000-CMap（连接映射）数据集，我们发现 高三尖杉酯碱（HHT）是最高表达模拟物（EM）之一。与观察结果一致， mtRUNX 1的存在损害核糖体生物发生（RiBi），用HHT或其半合成的 抑制蛋白质翻译的类似物omacetaxine mepesuccinate（OM）优先发挥更多的作用， 在表达mtRUNX 1的AML模型中的体外致死率和体内功效。这是与 抑制RUNX 1及其靶点，以及减弱短寿命蛋白，包括c-Myc和 MCL-1。值得注意的是，OM和维奈托克（Ven）的联合治疗诱导了协同致死性，上级 在表达mtRUNX 1的AML异种移植模型中的体内功效。因此，我们的过度假设 提出的动机研究是OM和Ven的靶向组合将产生高缓解率 并提高生存率，与患者的特定遗传和基因表达特征相关。 表达mtRUNX 1的高危MDS/AML。拟议研究的具体目标是：目标1： OM和Ven联合治疗高风险MDS或AML表达患者的Ib/II期临床试验 mtRUNX1.目的2：确定OM和Ven联合治疗的疗效/耐药性的相关性， 包括遗传损伤结构（通过NextGen和scDNA测序），表观遗传和基因- MDS/AML中的表达特征（通过RNA-Seq、RPPA和CyTOF分析）和受损的RiBi特征 在Ib/II期试验中招募的患者的细胞。目的3：确定额外的临床前疗效 基于OM的与BET或CDK 9抑制剂的组合，以及与新靶向剂的组合， 针对通过体外蛋白质结构域特异性CRISPR-gRNA筛选提名的可药用命中。

With current treatment regimens, long-term remission rates for adult patients with high risk Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML) are 15-25%. RUNX1 is the DNA- binding subunit of the core-binding factor (CBF) complex and a master-regulator transcription factor involved in hematopoiesis. Majority of mutant (mt) RUNX1 are missense, large deletions or truncation- mutations, behaving mostly as loss of function (LOF) mutations. Presence of mtRUNX1 confers relative therapy-resistance and poorer survival in patients with MDS/AML. The germline mutations and deletions in RUNX1 cause the highly penetrant (~40%) Familial Platelet Disorder with a propensity to evolve into MDS or AML. Lack of specific targeted therapy, coupled with resistance to standard therapy may account for poorer prognosis and outcome in MDS/AML expressing somatic or germline mtRUNX1. Therefore, there is an unmet need to develop novel targeted therapies for MDS/AML expressing mtRUNX1. Our preliminary studies demonstrate that knockdown of RUNX1 induces significantly more in vitro lethality in AML blasts expressing mtRUNX1 versus wild type (wt) RUNX1. Utilizing RNA-Seq signature of RUNX1 knockdown and querying the LINCS1000-CMap (Connectivity-Mapping) datasets, we identified homoharringtonine (HHT) among the top expression mimickers (EMs). Consistent with observations that presence of mtRUNX1 impairs ribosomal biogenesis (RiBi), treatment with HHT or its semisynthetic analog omacetaxine mepesuccinate (OM), which inhibit protein translation, preferentially exerted more lethality in vitro and efficacy in vivo in models of AML expressing mtRUNX1. This was associated with repression of RUNX1 and its targets, as well as attenuation of short-lived proteins including c-Myc and MCL-1. Notably, co-treatment with OM and venetoclax (Ven) induced synergistic lethality and superior in vivo efficacy in xenograft models of AML expressing mtRUNX1. Therefore, our Overarching hypothesis motivating studies proposed is that targeted combination of OM and Ven will yield high remission rates and improved survival, correlating with specific genetic and gene-expression signatures in patients with high-risk MDS/AML expressing mtRUNX1. Specific aims of studies proposed are: AIM 1: To conduct a Phase Ib/II clinical trial of co-treatment with OM and Ven in patients with high risk MDS or AML expressing mtRUNX1. AIM 2: To determine correlates of efficacy/resistance to co-treatment with OM and Ven, including genetic-lesions architecture (via NextGen and scDNA sequencing), epigenetic and gene- expression signature (via RNA-Seq, RPPA and CyTOF analyses) and impaired RiBi features in MDS/AML cells of patients enrolled on the Phase Ib/II trial. AIM 3: To determine pre-clinical efficacy of additional OM-based combinations with BET or CDK9 inhibitor, as well as with novel targeted agents directed against druggable hits nominated through an in vitro protein domain-specific CRISPR-gRNA screen.