Epigenetic predicators of asthma in neonates

新生儿哮喘的表观遗传预测因素

基本信息

批准号：
7935439
负责人：
Donata Vercelli
金额：
$ 47.24万
依托单位：
UNIVERSITY OF ARIZONA
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-30 至 2012-02-29
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7935439
关键词：
Address Adult Affect Age Allergens Area Asthma Automobile Driving Biological Markers Birth Blood Cells Blood donor Blood specimen Candidate Disease Gene Child Childhood Asthma CpG dinucleotide DNA Methylation Development Diagnosis Disease Effectiveness Enrollment Epidemic Epigenetic Process Exposure to Future Gene Expression Genes Health Immune Individual Infant Life Measurement Measures Methylation Mothers Nature Neonatal Nursery Schools Pattern Play Population Pregnancy Prevention Preventive Principal Investigator Process Promoter Regions Prospective Studies Quality of life Recurrence Reducing Agents Resolution Reverse Transcriptase Polymerase Chain Reaction Role Sampling Testing Tobacco smoke Umbilical Cord Blood United States Validation Wheezing bisulfite early childhood emerging adult environmental agent genome-wide improved mRNA Expression neonate programs promoter public health relevance research study

项目摘要

DESCRIPTION (provided by applicant): This application addresses broad Challenge Area (03) Biomarker discovery and validation, and specific Challenge Topic, 03-OD-101: Use of epigenetic signatures in blood cells to predict disease. Asthma can currently be managed but not really cured. Therefore, prevention would be an ideal approach to this disease. Obviously, availability of asthma predictors detectable in early life, or even better at birth, would greatly improve the effectiveness of prevention by identifying those individuals within the population for whom more drastic, and therefore less easy to implement, preventive measures might be most justified and useful. Because asthma typically begins in early life, and the asthma status of the child is strongly related to that of the mother, the overall hypothesis driving this application is that signatures detectable in the epigenome, and more specifically, in the methylome, at birth can serve as predictors of asthma status later in life. To test this hypothesis, we propose to assess genome-wide patterns of DNA methylation, a robust and quantifiable epigenetic mark. Our analysis will focus on cord blood samples isolated from children enrolled in the longitudinal Infant Immune Study (IIS), and already available. The longitudinal nature of the IIS study offers a unique opportunity to address and answer questions about early epigenetic predictors of asthma. Indeed, the cord blood donors have now reached age 5-8 yrs, an age at which a firm diagnosis of asthma can be established. Results for the most robust candidate genes will be quantitatively validated by bisulfite sequencing and measurements of candidate gene expression levels. Specific Aim 1 To identify candidate epigenetic predictors of asthma by interrogating the methylome of cord blood cells isolated from neonates who have or have not become asthmatic by age 5 yrs. We will perform genome-wide comparisons of promoter DNA methylation patterns in cord blood cells isolated from neonates enrolled in the IIS study (n=20 per group), and we will use asthma status at age 5 yrs to anchor and interpret these results. Each group will contain equal numbers of samples from neonates whose mothers were or were not asthmatic during pregnancy. These experiments will yield candidate epigenetic predictors of asthma, which will be validated in Aim 2. Specific Aim 2 To validate the candidate epigenetic predictors of asthma identified in Aim 1 by using quantitative high resolution bisulfite sequencing and gene expression assessments. We will implement a stringent strategy to filter and further explore the putative epigenetic predictors of asthma identified in Aim 1. Genes found to be differentially methylated by genome-wide promoter methylation arrays (at least 10) will be biologically validated by measuring levels of DNA methylation at promoter regions and individual CpG dinucleotides (by bisulfite sequencing) and levels of mRNA expression (by RT-PCR). These analyses will include the 40 initial samples and 40 additional ones. Genes showing a functionally concordant pattern of differential epigenetic changes and expression (e.g., genes that are more intensely expressed and hypomethylated) correlated with subsequent development of asthma in the child will be considered as bona fide neonatal epigenetic predictors of asthma, and will be proposed for future prospective studies. PUBLIC HEALTH RELEVANCE: This application addresses broad Challenge Area (03) Biomarker discovery and validation, and specific Challenge Topic, 03-OD-101: Use of epigenetic signatures in blood cells to predict disease. Asthma can currently be managed but not really cured. Therefore, prevention would be an ideal approach to this disease. Obviously, availability of asthma predictors detectable in early life, or even better at birth, would greatly improve the effectiveness of prevention by identifying those individuals within the population for whom more drastic, and therefore less easy to implement, preventive measures might be most justified and useful. Because asthma typically begins in early life, and the asthma status of the child is strongly related to that of the mother, the overall hypothesis driving this application is that signatures detectable in the epigenome, and more specifically, in the methylome, at birth can serve as predictors of asthma status later in life. To test this hypothesis, we propose to assess genome-wide patterns of promoter DNA methylation, a robust and quantifiable epigenetic mark. Our analysis will focus on cord blood samples (n=40) isolated from children enrolled in the longitudinal Infant Immune Study (IIS), and already available. The longitudinal nature of the IIS study offers a unique opportunity to address and answer questions about early epigenetic predictors of asthma. Indeed, the cord blood donors have now reached age 5-8 yrs, an age at which a firm diagnosis of asthma can be established. Results for the most robust candidate genes will be quantitatively validated by bisulfite sequencing and measurements of candidate gene expression levels, extending the analysis to 40 additional samples. Genes showing a functionally concordant pattern of differential epigenetic changes and expression (e.g., genes that are more intensely expressed and hypomethylated) correlated with subsequent development of asthma in the child will be considered as bona fide neonatal epigenetic predictors of asthma, and will be proposed for future prospective studies.

描述（由申请人提供）：本申请涉及广泛的挑战领域 (03) 生物标志物发现和验证，以及具体的挑战主题 03-OD-101：利用血细胞中的表观遗传特征来预测疾病。哮喘目前可以得到控制，但尚未真正治愈。因此，预防是治疗这种疾病的理想方法。显然，在生命早期，甚至在出生时就可以检测到哮喘预测因子，可以通过识别人群中那些更严格、因此更不易实施的预防措施可能是最合理的个体，从而大大提高预防的有效性。有用。由于哮喘通常始于生命早期，并且儿童的哮喘状况与母亲的哮喘状况密切相关，因此推动该应用的总体假设是，出生时在表观基因组中，更具体地说，在甲基化组中可检测到的特征可以服务作为晚年哮喘状况的预测因子。为了检验这一假设，我们建议评估 DNA 甲基化的全基因组模式，这是一种强大且可量化的表观遗传标记。我们的分析将重点关注从参加纵向婴儿免疫研究 (IIS) 的儿童中分离出来的脐带血样本，这些样本已经可用。 IIS 研究的纵向性质为解决和回答有关哮喘早期表观遗传预测因子的问题提供了独特的机会。事实上，脐带血捐献者现在已经达到了 5 至 8 岁的年龄，在这个年龄就可以对哮喘做出明确的诊断。最稳健的候选基因的结果将通过亚硫酸氢盐测序和候选基因表达水平的测量来定量验证。具体目标 1 通过检测从 5 岁时患或未患哮喘的新生儿中分离出的脐带血细胞的甲基化组，确定哮喘的候选表观遗传预测因子。我们将对参加 IIS 研究的新生儿（每组 n=20）分离的脐带血细胞中的启动子 DNA 甲基化模式进行全基因组比较，并且我们将使用 5 岁时的哮喘状况来锚定和解释这些结果。每组将包含相同数量的新生儿样本，这些新生儿的母亲在怀孕期间患有或未患有哮喘。这些实验将产生哮喘的候选表观遗传预测因子，这些预测因子将在目标 2 中得到验证。具体目标 2 通过使用定量高分辨率亚硫酸氢盐测序和基因表达评估来验证目标 1 中确定的哮喘候选表观遗传预测因子。我们将实施严格的策略来过滤并进一步探索目标 1 中确定的哮喘的假定表观遗传预测因子。通过全基因组启动子甲基化阵列（至少 10 个）发现差异甲基化的基因将通过测量 DNA 甲基化水平进行生物学验证启动子区域和单个 CpG 二核苷酸（通过亚硫酸氢盐测序）以及 mRNA 表达水平（通过 RT-PCR）。这些分析将包括 40 个初始样本和 40 个附加样本。显示出与儿童哮喘后续发展相关的差异表观遗传变化和表达的功能一致模式（例如，表达更强烈和低甲基化的基因）的基因将被视为真正的哮喘新生儿表观遗传预测因子，并将被提议用于未来的前瞻性研究。公共健康相关性：该应用解决了广泛的挑战领域 (03) 生物标志物的发现和验证，以及具体的挑战主题 03-OD-101：利用血细胞中的表观遗传特征来预测疾病。哮喘目前可以得到控制，但尚未真正治愈。因此，预防是治疗这种疾病的理想方法。显然，在生命早期，甚至在出生时就可以检测到哮喘预测因子，可以通过识别人群中那些更严格、因此更不易实施的预防措施可能是最合理的个体，从而大大提高预防的有效性。有用。由于哮喘通常始于生命早期，并且儿童的哮喘状况与母亲的哮喘状况密切相关，因此推动该应用的总体假设是，出生时在表观基因组中，更具体地说，在甲基化组中可检测到的特征可以服务作为晚年哮喘状况的预测因子。为了检验这一假设，我们建议评估启动子 DNA 甲基化的全基因组模式，这是一种强大且可量化的表观遗传标记。我们的分析将重点关注从参加纵向婴儿免疫研究 (IIS) 的儿童中分离出来的脐带血样本 (n=40)，并且这些样本已经可用。 IIS 研究的纵向性质为解决和回答有关哮喘早期表观遗传预测因素的问题提供了独特的机会。事实上，脐带血捐献者现在已经达到了 5 至 8 岁的年龄，在这个年龄就可以对哮喘做出明确的诊断。最稳健的候选基因的结果将通过亚硫酸氢盐测序和候选基因表达水平的测量进行定量验证，从而将分析扩展到 40 个额外的样本。显示出与儿童哮喘后续发展相关的差异表观遗传变化和表达的功能一致模式（例如，表达更强烈和低甲基化的基因）的基因将被视为真正的哮喘新生儿表观遗传预测因子，并将被提议用于未来的前瞻性研究。