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

基本信息

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
项目类别：
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

项目摘要

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，并且仍然是儿童死亡的主要原因之一因此，预防仍然是未来预防的重要组成部分。将涉及识别出生时携带白血病前期克隆的儿童。病变已被证明是在产前出现的；然而，许多其他白血病起始病变尚未被证实。出生时进行检查。仍有几个关键问题需要回答：1）什么亚型以及比例是多少。儿童白血病在子宫内发生？ 2) 白血病前期克隆产生的特定细胞来源是什么？ 3) 是否有些新生儿比其他新生儿更容易出现白血病起始病变？将回答这些问题，重点关注约 70% 具有已知易位或点突变驱动因素的患者该项目有三个主要目标 1：确定产前克隆的存在和频率。我们将从出生时的白血病起始病变中获得匹配的脐带血（CB）和诊断性白血病样本。儿童肿瘤学小组项目：每个儿童研究中约有 250 名儿童白血病患者。重点关注约 182 名易位/突变驱动亚型的患者，我们推导出患者特异性体细胞突变。从肿瘤分析中获得，然后在流式分选的 CB 细胞中使用液滴数字 PCR (ddPCR) 来确认其存在和我们还将使用 ddPCR 来确定出生时和不同造血阶段白血病起始病变的频率。目标 2：确定白血病的起源细胞。起始病变、从白血病前期到明显白血病的转录组变化，以及是否是继发性的在 50 名患有 CB 的儿童白血病患者中，突变发生在产前。 ddPCR 呈阳性，我们将对流式分选的细胞群进行单细胞 TARGET-seq，以同时检测每个患者特异性白血病起始事件、继发突变和基因表达的存在目标 3：确定单细胞水平上基因型和免疫表型定义的群体。白血病前期克隆的存在和频率与已知的白血病危险因素相关。将通过父母调查、出生记录、对于总体 ALL 和 AML 以及常见亚型，我们将测试之间的关联。风险因素以及出生时白血病前期克隆的存在和克隆频率，如目标 1 中所测量。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揭示这项研究将确定儿童白血病的病因并对精准预防工作具有重要意义。通过直接比较遗传和转录组结构来确定白血病发生所需的关键步骤白血病前期的CB到随后的成熟白血病的结果将为大的发展提供一个平台。对健康新生儿的白血病前期克隆进行大规模群体测试，并将开展第一批队列研究检查从前期白血病到明显白血病的进展。