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

以单细胞分辨率回溯脐带血中白血病典型体细胞改变

• 批准号: 10274321
• 负责人: Adam De Smith
• 金额: $ 68.18万
• 依托单位: UNIVERSITY OF MINNESOTA
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-08-01 至 2026-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10274321
• 关键词: 15 year old; Acute Lymphocytic Leukemia; Acute Myelocytic Leukemia; Acute leukemia; Architecture; Biological Assay; Birth; Birth Records; Blood; Blood Cells; Blood specimen; CBFA2T1 gene; CD34 gene; Cause of Death; Cells; Cesarean section; Child; Childhood Acute Lymphocytic Leukemia; Childhood Leukemia; Cohort Studies; DNA Sequence Alteration; Data; Development; Diagnostic; ETV6 gene; Eligibility Determination; Ethnic Origin; Etiology; Event; Face; Frequencies; Future; Gene Expression; Gene Expression Profile; Gene Fusion; Generations; Genetic; Genotype; Goals; Hematopoietic; Infant; Lesion; Light; MLL gene; Malignant Childhood Neoplasm; Measures; Morbidity - disease rate; Mutation; Natural History; Neonatal; Neonatal Screening; Newborn Infant; Parental Ages; Patients; Pediatric Oncology Group; Perinatal; Point Mutation; Population; Preleukemia; Prevention; Preventive; RUNX1 gene; Race; Resolution; Risk Factors; Sampling; Somatic Mutation; Surveys; Survivors; Testing; Umbilical Cord Blood; cell type; digital; disorder risk; driver mutation; epidemiology study; genetic risk factor; genome sequencing; high risk; in utero; indexing; individualized prevention; leukemia; leukemogenesis; prenatal; progenitor; risk prediction model; screening; sex; stem; transcriptome sequencing; transcriptomics; tumor; whole genome

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.

抽象的 急性白血病是最常见的儿童癌症，仍然是儿童死亡的主要原因之一 15岁以下。因此，预防仍然是最终目标。未来预防的重要组成部分 努力将涉及确定出生时携带普雷克米亚克隆的儿童。几种白血病发射遗传 病变已显示出产前出现。但是，许多其他白血病发病的病变还没有 出生时检查。还有几个关键问题要回答：1）哪些子类型和哪些比例 子宫里的儿童白血病发展？ 2）在preleukemia克隆中出现的原始特定细胞是什么？ 3）有些新生儿比其他新生儿更容易发育白血病发病的病变？在这个项目中，我们 将回答这些问题，重点是约70％的已知转运或点突变驱动器的患者 事件。该项目具有三个主要目标。目标1：确定产前的存在和克隆频率 出生时性白血病发病。我们将获得匹配的脐带血（CB）和诊断性白血病样本 〜250个儿童肿瘤学组项目中的儿童白血病患者：每个儿童研究。回溯 专注于〜182例易位/突变驱动亚型的患者。我们得出患者特定的体细胞突变 从肿瘤分析中，然后在流程的CB细胞中使用液滴数字PCR（DDPCR）来确认存在和 出生时和不同造血阶段的白血病发病病变的频率。我们还将使用DDPCR 可用新生的干血点的回溯病变（n〜45）。目标2：确定白血病的起源细胞 - 启动病变，从preleukemia到明显白血病的转录组发生变化，以及是否次要 跨儿童白血病亚型出现突变。在50名儿童白血病患者中 DDPCR是正的 每个患者特异性白血病发射事件，次要突变和基因表达的存在 单个细胞水平上的基因型和免疫性定义的种群。目标3：确定是否 PRELEUKEMIA克隆的存在和频率与白血病的已知危险因素相关。人群， 儿童白血病的围产期和遗传危险因素将通过父母的调查，出生记录， 和测序数据。对于总体和AML以及对于常见亚型，我们将测试 危险因素以及出生时preleukemia克隆的存在和克隆频率，如AIM 1所测量。 peleukemic基因组改变及其在新生儿血液中的频率的特定细胞将揭示 儿童白血病病因，对预防精确的努力具有重要意义。这项研究将确定 白血病发生所需的关键步骤，直接比较 PRELEUKEMIA CB到随后的成熟白血病。结果将为开发大型的平台提供一个平台 在健康的新生儿中对普雷卢克米亚克隆的规模种群测试，并将启用首次队列研究 检查从前再到明显的白血病的进展。