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 IDH1和IDH2突变存在于15%到20%的新诊断的AML病例中。他们是 与肿瘤代谢物2-羟基戊二酸的产生和独特的克隆景观有关。IDH 在过去的十年中，靶向抑制剂的开发取得了成功，但一次或二次抵抗 仍然非常普遍。抗性是由多种机制驱动的，包括同型开关，IDH 继发性点突变、获得RTK突变(如RAS)或发展为IDH阴性 克隆人。确定患者耐药的驱动机制对于制定治疗策略至关重要。 预防和治疗进展。我们的团队已经证明了IDH突变的存在会诱导 细胞中的“BRCAness表型”和对PARP抑制剂的敏感性。这些体外和体内的研究结果是 在IDH突变的急性髓系白血病和MDS中对奥拉帕利的第2阶段研究中翻译的(主要研究，CTEP#10264)。为 接受奥拉帕利治疗的患者，我们希望看到类似于使用奥拉帕利治疗的耐药机制的模式 IDH抑制剂，为了优化我们的治疗，我们需要对克隆的复杂性有一个清晰的了解 治疗的不同点。传统的“批量测序”可以提供一些信息，但 数据的粒度可能并不是在所有情况下都足够。单细胞测序可能会克服这些限制 新一代平台，如Tapestri平台，允许集成且可靠的工作流 可以处理大量的样品。最近，多种组学方法被开发出来， 随之而来的免疫表型鉴定，这允许通过专注于不同的 细胞子集。 在本方案中，我们使用单细胞DNA测序和多组学方法来评估克隆 奥拉帕利治疗前和治疗期间的结构。除了让我们更深入地了解 Olaparib，这一方法将有助于我们确定在本研究中对olaparib的原发和继发耐药机制 人口。因此，这将指导我们未来克服这些阻力的战略。第二，我们将 将SCS数据与临床反应相关联，并评估SCS是否有可能被用作 多中心试验环境中的反应。 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