Advancing biological and clinical applications of genomic Minimal Residual Disease detection in AML

摘要 急性骨髓性白血病（AML）每年影响美国超过20，000名成人患者， 超过11,000人过早死亡标准AML治疗包括化疗诱导，以实现 白血病减积，随后进行几个周期的单独巩固化疗和/或随后进行 异基因骨髓移植这种AML的一般治疗方法是风险适应性依赖 主要基于已确立的预后因素，包括AML的类型、年龄、基因突变和 细胞遗传学结果尽管尽了最大的努力，AML在大多数患者中仍然无法治愈。一 AML治愈的主要障碍是疾病复发，尽管在以下治疗中达到临床完全缓解（CR） 标准化疗方案。因此，重要的是识别和准确 测量AML患者缓解期间持续存在的残留AML，因为这种残留疾病可能 复发的根源。关于AML复发的几个重要问题仅处于令人满意的早期阶段。 答案，包括i）如何最好地测量AML中的微小残留病（MRD），ii）是否所有MRD都是 实际上是由残留疾病引起的，或者更确切地说，如最近的数据所表明的，包括白血病、前 白血病和年龄相关的克隆性造血，iii）什么构成AML复发的细胞来源，iv）如果 使用新的治疗方法可以更好地靶向这种引起复发的细胞，以及v）在什么情况下 这种情况是MRD预后的，并可用于MRD风险适应性AML临床管理。 由于缺乏合适的技术来可靠地回答上述相关问题，我们 优化的液滴数字PCR（ddPCR），一种用于检测基因组MRD的新型超高灵敏度检测方法， 急性髓细胞白血病在最近发表的一项详细研究中（Parkin et al，JCI 2017），我们发现AML经常复发， 来自缓解期骨髓中的罕见细胞，基于突变分析，这些细胞类似于AML原始细胞 诊断时发现。我们证明了检测AML相关基因突变的可行性， 频率低至0.002%，也提供了重要的新的预后见解。 在本申请中，我们提出了突变MRD和异常细胞的完整表征， 使用复杂的细胞分选和单细胞免疫分析相结合， 转录组分析与小鼠异种移植和离体集落形成测定互补。预期 这些发现将改善携带AML相关基因突变的细胞的功能特征， 尝试识别并更好地描述AML复发的来源。使用来自两个临床的AML样品， 验证队列，我们将定义基于ddPCR的MRD评估的预后效用。总体而言，数据将 为未来实时基因组MRD指导的AML临床试验奠定基础， 改善AML的巩固和维持治疗以及最终的生存结局。

ABSTRACT Acute myelogenous leukemia (AML) affects more than 20,000 adult patients in the US per year causing greater than 11,000 untimely deaths. Standard AML therapy comprises chemotherapy induction to achieve leukemia debulking, followed by a few cycles of consolidation chemotherapy alone and/or followed by allogeneic bone marrow transplantation. This general therapeutic approach to AML is risk-adapted relying principally on well-established prognostic factors, including the type of AML, age, gene mutations and cytogenetic results. Despite best efforts, AML remains incurable in the majority of afflicted patients. A principle barrier to AML cure is disease relapse despite achieving a clinical complete remission (CR) following standard chemotherapy regimens. Of substantial interest therefore, is the identification and accurate measurement of residual AML that persists during remission in AML patients, as such residual disease is likely the source of relapse. Several important questions about AML relapse are only in early stages of satisfactory answers, including i) how to best measure minimal residual disease (MRD) in AML, ii) whether all MRD is indeed caused by residual disease or rather as suggested by recent data comprises a mixture of leukemia, pre- leukemia and age-related clonal hematopoiesis, iii) what constitutes the cellular source of relapse in AML, iv) if such relapse-causing cells can be better targeted using novel therapeutic approaches, and v) under what circumstances is MRD prognostic and useful for MRD risk-adapted AML clinical management. Given lack of well-suited techniques to reliably answer the relevant questions detailed above, we have optimized droplet digital PCR (ddPCR), a novel ultra-high sensitivity assay for detecting genomic MRD in AML. In a detailed recently published study (Parkin et al, JCI 2017) we found that AML frequently relapses from rare cells residing in remission marrows that based on mutation analysis resemble AML blast cells detected at diagnosis. We demonstrated the feasibility for detecting AML-associated gene mutations at allele frequencies as low as 0.002% and have also provided important novel prognostic insights. In this application, we are proposing complete characterization of mutational MRD and aberrant cellular clusters in AML remission bone marrows using a combination of sophisticated cell sorting and single cell transcriptome analyses complemented with mouse xenografting and ex vivo colony forming assays. Anticipated findings will improve the functional characterization of cells that carry AML-associated gene mutations in an attempt to identify and better characterize the source(s) of AML relapse. Using AML samples from two clinical validation cohorts, we will define the prognostic utility of ddPCR-based MRD assessments. Overall, data will lay the foundation for future real-time genomic MRD-guided clinical AML trials aiming at monitoring and improving consolidation and maintenance therapy and ultimately survival outcome in AML.