Backtracking Leukemia-Typical Somatic Alterations in Cord Blood at Single-cell Resolution

摘要 急性白血病是儿童最常见的癌症，也是导致儿童死亡的主要原因之一。 未满15周岁。因此，预防仍然是最终目标。未来预防措施的重要组成部分 这些努力将涉及识别出生时携带白血病前期克隆的儿童。几种引发白血病的基因 已有研究表明，损害发生在产前；然而，许多其他引发白血病的损害还没有出现。 在出生时进行检查。几个关键问题仍有待回答：1)什么亚型和多大比例 儿童白血病发生在子宫中？2)产生白血病前期克隆的特定细胞(S)是什么？ 3)一些新生儿比其他新生儿更容易发生白血病引发的损害吗？在这个项目中，我们 将回答这些问题，重点是~70%的已知易位或点突变驱动因素患者 事件。这个项目有三个主要目标。目的1：确定产前的存在和克隆性频率 白血病在出生时就会引发损害。我们将从以下地点获取匹配的脐带血(CB)和诊断白血病样本 儿童肿瘤学小组项目：每个儿童研究中的约250名儿童白血病患者。回溯将 关注约182名易位/突变驱动亚型患者。我们得出了患者特有的体细胞突变 然后在流式分选的CB细胞中使用液滴数字聚合酶链式反应(DdPCR)来确认存在和 在出生时和不同的造血期引发白血病的损害的频率。我们还将使用ddPCR来 可用新生儿干血斑的回溯病变(N~45)。目的2：确定白血病的起源细胞-- 起始病变，从白血病前期到显性白血病的转录变化，以及继发性 突变发生在产前，发生在儿童白血病亚型中。在50例儿童白血病患者中 DdPCR为阳性，我们将对流式分选的细胞群体进行单细胞靶序列检测，以同时检测 每个患者特异性白血病启动事件、继发突变和基因表达的存在 在单个细胞水平上由基因和免疫表型定义的群体。目标3：确定是否 白血病前期克隆的存在和频率与白血病的已知危险因素相关。人口统计数据， 儿童白血病的围产期和遗传危险因素将通过父母调查、出生记录、 和测序数据。对于总体ALL和AML以及公共子类型，我们将测试它们之间的关联 风险因素和出生时白血病前期克隆的存在和克隆频率，如在目标1中测量的。 白血病前期基因组改变的特定起源细胞及其在新生儿血液中的频率将有助于揭示 儿童白血病病因学，并对精准预防工作具有重要意义。这项研究将确定 通过直接比较白血病发生的遗传和转录结构所需的关键步骤 白血病前期的慢性粒细胞白血病到随后的全面白血病。成果将为大型企业的发展提供平台。 对健康新生儿进行白血病前期克隆的规模人群测试，将使第一次队列研究成为可能 检查从白血病前期到临床白血病的进展。

Abstract Acute leukemia is the most common childhood cancer, and remains one of the leading causes of death in children under 15 years of age. Prevention, therefore, remains the ultimate goal. An essential part of future preventive efforts will involve identifying children harboring preleukemic clones at birth. Several leukemia-initiating genetic lesions have been shown to arise prenatally; however, many other leukemia-initiating lesions have not been examined at birth. Several critical questions remain to be answered: 1) What subtypes and what proportion of childhood leukemia develops in utero? 2) What is the specific cell(s) of origin in which preleukemic clones arise? and 3) Are some newborns more prone to developing leukemia-initiating lesions than others? In this project, we will answer these questions, with a focus on the ~70% of patients with known translocation or point mutation driver events. This project has three main aims. Aim 1: To identify the presence and clonal frequency of prenatal leukemia-initiating lesions at birth. We will obtain matched cord blood (CB) and diagnostic leukemia samples from ~250 childhood leukemia patients in the Children’s Oncology Group Project:Every Child study. Backtracking will focus on ~182 patients with translocation/mutation-driven subtypes. We derive patient-specific somatic mutations from tumor profiling, then use droplet digital PCR (ddPCR) in flow-sorted CB cells to confirm the presence and frequency of leukemia-initiating lesions at birth, and at different hematopoietic stages. We will also use ddPCR to backtrack lesions in available newborn dried bloodspots (N ~45). Aim 2: To determine the cell of origin of leukemia- initiating lesions, the transcriptomic changes from preleukemia to overt leukemia, and whether secondary mutations arise prenatally, across childhood leukemia subtypes. In 50 childhood leukemia patients where CB ddPCR is positive we will conduct single-cell TARGET-seq on flow-sorted cell populations to simultaneously detect the presence of each patient-specific leukemia-initiating events, secondary mutations, and gene expression in genotypically- and immunophenotypically-defined populations at a single cell level. Aim 3: To determine whether the presence and frequency of preleukemic clones correlate with known risk factors for leukemia. Demographic, perinatal, and genetic risk factors for childhood leukemia will be obtained through parental survey, birth records, and sequencing data. For overall ALL and AML, and for common subtypes, we will test for association between risk factors and the presence and clonal frequency of preleukemic clones at birth, as measured in Aim 1. Identifying a specific cell of origin of preleukemic genomic alterations, and their frequency in neonatal blood, will shed light on childhood leukemia etiology and have important implications for precision prevention efforts. This study will identify key steps required for leukemogenesis by directly comparing the genetic and transcriptomic architecture of preleukemic CB to the subsequent full-blown leukemia. Results will provide a platform for development of large- scale population testing of preleukemic clones in healthy newborns and will enable the first cohort studies examining progression from pre- to overt leukemia.