Serial monitoring of circulating cell-free tumor DNA as measured by duplex sequencing in older patients with acute myeloid leukemia who receive azacitidine+venetoclax +/- immune checkpoint blockade

摘要 IDH 1和IDH 2突变存在于15%至20%的新诊断的AML病例中。他们是 与致癌代谢物2-羟基戊二酸的产生和独特的克隆景观相关。IDH 在过去十年中，靶向抑制剂已被成功开发，但原发性或继发性耐药性 仍然非常普遍。耐药是由多种机制驱动的，包括同种型开关、IDH 继发性点突变，RTK突变（如RAS）的获得，或IDH阴性的发展 克隆确定患者耐药性的驱动机制对于制定策略至关重要， 预防和治疗进展。我们的研究小组已经证明，IDH突变的存在诱导了一种新的免疫应答。 细胞中的“BRCAness表型”和对PARP抑制剂的敏感性。这些体外和体内研究结果如下： Olaparib在IDH突变的AML和MDS中的II期研究（PRIME研究，CTEP#10264）。为 在接受奥拉帕尼治疗的患者中，我们预计会看到类似的耐药机制模式， IDH抑制剂，为了优化我们的治疗，我们需要有一个清晰的图片克隆的复杂性， 治疗的不同点。常规的“批量测序”可以提供一些信息，但是测序水平不高。 数据的粒度可能不是在所有情况下都足够。单细胞测序可以克服这些限制 新一代平台，如Tapestri平台，允许集成和可靠的工作流程， 可以处理大量的样品。最近，已经开发了多组学方法， 伴随的免疫表型，这允许通过允许集中于不同的免疫表型来进一步细化结果。 细胞亚群 在本研究中，我们利用单细胞DNA测序和多组学方法来评估克隆 奥拉帕尼治疗前和治疗期间的结构。除了让我们更深入地了解 奥拉帕尼，这种方法将帮助我们确定原发性和继发性耐药奥拉帕尼的机制， 人口因此，这将指导我们未来的战略，以克服这些阻力。二是 将SCS数据与临床缓解相关联，并评价SCS是否有可能用作以下疾病的生物标志物： 多中心试验中的缓解情况。 2

ABSTRACT IDH1 and IDH2 mutations are present in 15 to 20% of newly diagnosed cases of AML. They are associated with the production of the onco-metabolite 2-Hydroxyglutarate and a distinctive clonal landscape. IDH targeted inhibitors have been developed with success over the last decade but primary or secondary resistances remain extremely common. Resistance is driven by a variety of mechanisms including isotype switch, IDH secondary point mutation, acquisition of RTK mutation (such as RAS), or the development of IDH negative clones. Identifying the mechanisms driving resistance in a patient is crucial to be able to develop strategies to prevent and treat progressions. Our group has demonstrated that the presence IDH mutation induces a “BRCAness phenotype” in cells and a sensitivity to PARP inhibitors. These in vitro and in vivo findings were translated in a phase 2 study of Olaparib in IDH mutated AML and MDS (the PRIME study, CTEP #10264). For patients treated with Olaparib, we expect to see a similar pattern of resistance mechanisms as the one seen with IDH inhibitors and in order to optimize our therapies, we need to have a clear picture of the clonal complexity at the different points of the treatment. Conventional “Bulk sequencing” can provide some information but the level of granularity of the data may not be sufficient in all cases. Single cell sequencing may overcome these limitations and the new generation of platforms, such as the Tapestri platform, allow integrated and reliable workflows that can process a large volume of samples. More recently, multi-omics approaches have been developed with concomitant immunophenotyping and this allows to refine even more the results by allowing to focus on different cellular subsets. In this proposal, we use Single Cell DNA Sequencing and multi-omics approach to evaluate the clonal architecture before and during treatment with olaparib. Besides giving us more insights on the mode of action of olaparib, this approach will help us define the mechanisms of primary and secondary resistance to olaparib in this population. Consequently, this will guide our future strategies to overcome these resistances. Second, we will correlate SCS data with clinical response and evaluate if SCS has the potential to be used as a biomarker of response in a multicenter trial setting. 2