Proteogenomic characterization of early and late resistance mechanisms in acute myeloid leukemia

项目摘要/摘要 急性髓系白血病(AML)是最常见的血液系统恶性肿瘤之一，临床表现多样 复杂疾病的集合。在三四十年没有改变治疗策略之后，过去的两年 看到了几种药物的批准，包括最近批准的Flt3抑制剂吉特替尼和BCL2抑制剂， 维尼托克拉克斯。虽然对这两种药物的应答率都是令人鼓舞的，但耐药性和复发仍然存在。 对几乎所有的患者来说都是个问题。在过去的十年里，我们已经执行了一个功能蛋白质组学平台 直接应用于急性髓系白血病和其他血液系统恶性肿瘤患者的原始样本。使用这个 平台上，我们共同研究了2500多个初诊患者样本。通过集成这些数据 具有扩展的蛋白质组、磷酸蛋白质组、转录组、基因组、代谢组、全基因组CRISPR 筛查和详细的临床注释，我们定义了生物标记物和潜在的反应机制 以及对Flt3i和BCL2i的早期和晚期抗性。因此，我们已经开始临床试验测试 可能缓解这些抗性机制的组合。对于这个项目，我们的长期目标是 翻译Flt3i和BCL2i治疗方案，以便可以预先预防耐药性 联合和/或通过序贯疗法缓解。我们的近期目标是定义和 优化对这些药物的反应和耐药性的特定生物标记物。基于中环 假设检测AML的整体蛋白质组特征可预测药物反应 并确定了耐药发展过程中的动态变化、产生机制 洞察力，以产生新颖的、改进的药物组合。为了实现这些目标，临床前和临床 建议的工作：在早期和晚期耐药的细胞系模型上培训蛋白质基因组生物标记物-WE 将对一组表现出抗药性的细胞系进行蛋白质基因组学分析 类似于耐药的临床特征。验证存档患者样本材料中的签名-我们有 AML患者样本的大量生物库，其中一部分来自接受治疗的患者 Flt3i或BCL2i作为标准护理或作为我们正在进行的临床试验的一部分。我们将测试我们衍生的细胞系 在这些储存的患者样本中，我们还将使用尖端蛋白质组学技术 使低投入材料能够研究分离的细胞群体。敏感性生物标志物的临床验证 以及耐药性-我们已经开始了临床试验，测试Flt3i和BCL2i联合治疗急性髓细胞白血病。我们会有 在这些试验中获得患者的预期纵向标本。我们将进行蛋白质组学研究 对这些预期样本进行分析，以评估我们的签名预测临床反应的能力。 总体而言，我们预计这些创新的分析将对我们对AML生物学的理解产生重大影响， 随着新的、更有效的药物组合策略和预测性生物标志物的成功临床翻译。

PROJECT SUMMARY/ABSTRACT Acute myeloid leukemia (AML) is one of the most common hematologic malignancies, representing a diverse collection of complex diseases. After 30-40 years without change of treatment strategy, the past 2 years have seen several drug approvals, including recent approvals for the FLT3 inhibitor, gilteritinib, and the BCL2 inhibitor, venetoclax. While response rates to both of these agents are encouraging, drug resistance and relapse is still problematic for nearly all patients. For the past decade, we have executed a functional proteogenomics platform applied directly to primary samples from patients with AML and other hematologic malignancies. Using this platform, we have collectively studied over 2,500 primary patient specimens. Through integration of these data with expansive proteomic, phospho-proteomic, transcriptomic, genomic, metabolomic, genome-wide CRISPR screens, and detailed clinical annotations, we have defined biomarkers and mechanisms underlying response as well as early and late resistance to both FLT3i and BCL2i. Consequently, we have started clinical trials testing combinations that may mitigate these resistance mechanisms. For this project, our long-term goals are to translate FLT3i and BCL2i therapeutic regimens such that resistance can be prevented with up-front combinations and/or mitigated with sequential therapies. Our immediate goals are to define and optimize specific biomarkers of response and resistance to these agents. Based on the central hypothesis that examination of global proteomic features of AML provides predictors of drug response and also identifies the dynamic changes during development of drug resistance, yielding mechanistic insight to generate novel, improved drug combinations. To accomplish these goals, Preclinical and Clinical work is proposed: Training of proteogenomic biomarkers on cell line models of early and late resistance – We will perform proteogenomic analyses of a panel of cell lines that have been derived to exhibit drug resistance resembling clinical features of resistance. Validation of signatures in archival patient sample material – We have a substantial biorepository of specimens from AML patients, a subset of which are from patients treated with FLT3i or BCL2i as standard-of-care or as part of our ongoing clinical trials. We will test our cell line derived biomarkers in these banked patient specimens, and we will also use cutting edge proteomics technology that enables low input material to study fractionated cell populations. Clinical validation of biomarkers of sensitivity and resistance – We have opened clinical trials testing FLT3i and BCL2i combinations in AML. We will have access to prospective, longitudinal specimens from patients on these trials. We will perform proteogenomic analyses on these prospective specimens to evaluate the ability of our signatures to predict clinical responses. Cumulatively, we expect these innovative analyses to have a major impact on our understanding of AML biology, with successful clinical translation of new, more effective drug combination strategies and predictive biomarkers.