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

项目概要/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，代表着多种 复杂疾病的集合。 30-40年没有改变治疗策略后，过去2年 多项药物获得批准，包括最近批准的 FLT3 抑制剂、gilteritinib 和 BCL2 抑制剂， 维奈托克。虽然这两种药物的反应率令人鼓舞，但耐药性和复发率仍然很高 几乎所有患者都会遇到问题。在过去的十年中，我们执行了功能性蛋白质基因组学平台 直接应用于 AML 和其他血液恶性肿瘤患者的原始样本。使用这个 在这个平台上，我们总共研究了 2,500 多个主要患者标本。通过整合这些数据 具有广泛的蛋白质组学、磷酸化蛋白质组学、转录组学、基因组学、代谢组学、全基因组 CRISPR 通过屏幕和详细的临床注释，我们定义了潜在反应的生物标志物和机制 以及对 FLT3i 和 BCL2i 的早期和晚期耐药。因此，我们已经开始临床试验测试 可以减轻这些耐药机制的组合。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 联合治疗和/或通过序贯治疗缓解。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志物。以中央为基础 假设检查 AML 的整体蛋白质组学特征可提供药物反应的预测因子 并确定耐药性发展过程中的动态变化，产生机制 洞察产生新颖的、改进的药物组合。为了实现这些目标，临床前和临床 拟议的工作：在早期和晚期耐药细胞系模型上训练蛋白质组生物标志物 – 我们 将对一组表现出耐药性的细胞系进行蛋白质组学分析 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 一个大量的 AML 患者标本生物储存库，其中一部分来自接受过治疗的患者 FLT3i 或 BCL2i 作为护理标准或作为我们正在进行的临床试验的一部分。我们将测试我们的细胞系衍生 这些储存的患者标本中的生物标志物，我们还将使用尖端的蛋白质组学技术 能够以低输入材料来研究分级细胞群。敏感性生物标志物的临床验证 和耐药性——我们已经开展了测试 FLT3i 和 BCL2i 组合治疗 AML 的临床试验。我们将会有 获得这些试验中患者的前瞻性纵向样本。我们将进行蛋白质组学 对这些前瞻性样本进行分析，以评估我们的特征预测临床反应的能力。 总的来说，我们预计这些创新分析将对我们对 AML 生物学的理解产生重大影响， 新的、更有效的药物组合策略和预测生物标志物的成功临床转化。

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.