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）：此申请解决了广泛的挑战区域（03）生物标志物发现和验证以及特定的挑战主题，03-OD-101：使用血细胞中的表观遗传签名来预测疾病。目前可以管理哮喘，但无法真正治愈。因此，预防将是这种疾病的理想方法。显然，通过确定人们在人群中确定更为剧烈且易于实施的人群中的那些人，预防措施可能是最合理和有用的，可以在早期或出生时可以检测到的哮喘预测能力，甚至可以在出生时更好地提高预防的有效性。因为哮喘通常从早期开始，并且儿童的哮喘状况与母亲的哮喘状况密切相关，因此推动这种应用的总体假设是表观基因组中可检测到的签名，更具体地说，在甲基甲基体中，出生时可以作为生命后期哮喘地位的预测指标。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，这是一种健壮且可量化的表观遗传标记。我们的分析将集中在纵向婴儿免疫研究（IIS）的儿童中分离出的脐带血样本，并且已经可用。 IIS研究的纵向性质提供了一个独特的机会，可以解决有关哮喘早期表观遗传预测因子的问题和问题。实际上，绳索献血者现在已经达到5 - 8年的年龄，在这个年龄可以建立哮喘的牢固诊断。最坚固的候选基因的结果将通过甲硫酸盐测序和候选基因表达水平的测量来定量验证。特定的目标1通过询问从患有或尚未哮喘的新生儿中分离出的脐带血细胞的甲基甲基甲基化的哮喘的表观遗传预测因子。我们将对从IIS研究中入学的新生儿（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的比较，我们将在5岁时使用哮喘状态来锚定和解释这些结果。每组将包含来自母亲在怀孕期间或不是哮喘的新生儿的相等数量的样本。这些实验将产生哮喘的候选表观遗传预测因子，该预测将在AIM 2中进行验证。特定的目标2通过使用定量的高分辨率Bisulfite bisulfite测序和基因表达评估来验证AIM 1鉴定的哮喘的表观遗传预测指标。我们将实施一个严格的策略来过滤和进一步探索目标1中鉴定出的哮喘的推定表观遗传预测因子。被发现是通过全基因组启动子甲基化阵列差异化甲基化的基因（至少10个），将通过测量启动子和单个CPG dinucletides的DNA甲基化水平在生物学上验证（通过BISCRNA的级别）（biscrna）和级别（biSulna）级别（biscrna）和级别（biSulna crcrna cre）和级别。这些分析将包括40个初始样本和40个样本。与差异表观遗传变化和表达的功能一致的基因（例如，更强烈表达和甲基化的基因）与儿童随后的哮喘发育相关，将被视为哮喘的善良新生儿表观遗传学预测因子，并将提议拟议的前瞻性研究。公共卫生相关性：该应用程序解决了广泛的挑战领域（03）生物标志物发现和验证以及特定的挑战主题，03-OD-101：使用血细胞中表观遗传签名的使用来预测疾病。目前可以管理哮喘，但无法真正治愈。因此，预防将是这种疾病的理想方法。显然，通过确定人们在人群中确定更为剧烈且易于实施的人群中的那些人，预防措施可能是最合理和有用的，可以在早期或出生时可以检测到的哮喘预测能力，甚至可以在出生时更好地提高预防的有效性。因为哮喘通常从早期开始，并且儿童的哮喘状况与母亲的哮喘状况密切相关，因此推动这种应用的总体假设是表观基因组中可检测到的签名，更具体地说，在甲基甲基体中，出生时可以作为生命后期哮喘地位的预测指标。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，这是一种健壮且可量化的表观遗传标记。我们的分析将集中在纵向婴儿免疫研究（IIS）的儿童中分离出的脐带血样本（n = 40），并且已经可用。 IIS研究的纵向性质提供了一个独特的机会，可以解决有关哮喘早期表观遗传预测因子的问题和问题。实际上，绳索献血者现在已经达到5 - 8年的年龄，在这个年龄可以建立哮喘的牢固诊断。最强大的候选基因的结果将通过亚硫酸盐测序和候选基因表达水平的测量来定量验证，从而将分析扩展到40个其他样本。与差异表观遗传变化和表达的功能一致的基因（例如，更强烈表达和甲基化的基因）与儿童随后的哮喘发育相关，将被视为哮喘的善良新生儿表观遗传学预测因子，并将提议拟议的前瞻性研究。