Novel combination therapy for AML expressing mutant RUNX1

在目前的治疗方案下，高危成人患者的长期缓解率 骨髓增生异常综合征(MDS)和急性髓系白血病(AML)占15%-25%。RUNX1是DNA- 核心结合因子(CBF)复合体的结合亚基和主调控转录因子 参与了造血。大多数突变(Mt)RUNX1是错误的、大的缺失或截断- 突变，主要表现为功能丧失(LOF)突变。MtRUNX1的存在使亲属 MDS/AML患者耐药且生存较差。生殖系突变和缺失 在RUNX1中导致高渗透性(~40%)家族性血小板紊乱并有演变为 MDS或AML。缺乏特定的靶向治疗，加上对标准治疗的抵抗可能是原因 MtRUNX1表达的MDS/AML患者预后和结局较差。因此， 对于表达mtRUNX1的MDS/AML，开发新的靶向治疗方法的需求尚未得到满足。我们的 初步研究表明，RUNX1基因的敲除在体外诱导了显著更高的杀伤力 表达mtRUNX1的AML细胞与野生型(Wt)RUNX1。利用RUNX1的RNA-Seq签名 击倒和查询LINCS1000-Cmap(连通性映射)数据集，我们发现 高三尖杉酯碱(HHT)是最常见的表达模拟物(EM)。与观察到的情况一致 MtRUNX1的存在损害核糖体生物发生(RIBI)，用HHT或其半合成治疗 类似的甲基丁二酸奥马西辛(OM)抑制蛋白质翻译，优先发挥更多 表达mtRUNX1的急性髓系白血病模型的体外致死性和体内疗效。这与 RUNX1及其靶点的抑制以及包括c-Myc和c-Myc在内的短寿命蛋白的衰减 MCL-1。值得注意的是，与OM和万乃馨(Ven)联合治疗可诱导协同致死性，且优于 表达mtRUNX1的AML异种移植模型的体内疗效。因此，我们的首要假设 提出的激励研究是，OM和VEN的靶向组合将产生高缓解率 并改善存活率，与特定的遗传和基因表达特征相关 表达mtRUNX1的高危MDS/AML。拟议研究的具体目标是：目标1：进行 OM和VEN联合治疗高危MDS或AML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/耐药性的相关因素， 包括遗传-损伤结构(通过NextGen和scDNA测序)、表观遗传和基因- MDS/AML的表达特征(通过RNA-Seq、RPPA和CyTOF分析)和受损的RIBI特征 参加Ib/II期试验的患者的细胞。目的3：确定其他药物的临床前疗效 基于OM的与BET或CDK9抑制剂的组合，以及与新的靶向药物的联合 对抗通过体外蛋白质结构域特异性CRISPR-gRNA筛选提名的可药物击中。

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.