The Altered DNA Methylome as a Determinant of Variable Disease Progression in IPF

DNA 甲基化组的改变是 IPF 疾病进展的决定因素

• 批准号: 8903517
• 负责人: STEVEN K HUANG
• 金额: $ 43.62万
• 依托单位: UNIVERSITY OF MICHIGAN AT ANN ARBOR
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2016-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8903517
• 关键词: Accounting; Cells; Cessation of life; Characteristics; Clinical; Clinical Course of Disease; Clinical Data; Clinical Markers; Complex; DNA; DNA Methylation; DNA Methyltransferase; DNA Modification Methylases; Data; Development; Diagnosis; Dinoprostone; Disease; Disease Progression; Effector Cell; Epigenetic Process; Exhibits; Fibroblasts; Fibrosis; Future; Gene Expression; Gene Expression Profile; Genes; Genetic; Genomic DNA; Goals; Hamman-Rich syndrome; Health; Heterogeneity; Impairment; Incidence; Individual; Knowledge; Lung; Lung diseases; Mediator of activation protein; Methylation; Mission; Modeling; Modification; Molecular; Molecular Profiling; Natural History; Nature; Pathogenesis; Pathway interactions; Patients; Pattern; Production; Public Health; Publishing; Relative (related person); Research; Respiratory physiology; Severity of illness; Signal Transduction; Technology; Tissue-Specific Gene Expression; Transforming Growth Factors; United States; United States National Institutes of Health; Work; clinical phenotype; effective therapy; epigenomics; extracellular; fibrogenesis; genome-wide; improved; innovation; insight; knowledge base; methylome; next generation; novel; outcome forecast; overexpression; response; therapeutic target; transcriptomics; treatment strategy

DESCRIPTION (provided by applicant): Idiopathic pulmonary fibrosis (IPF) is a devastating lung disease with no known effective therapy. Despite the dismal median survival, the prognosis of individual patients is variable and unpredictable, with some patients remaining stable and others deteriorating rapidly. The mechanisms that account for the variability in patients' clinical disease course are unknown. Fibroblasts are the main effector cell in fibrosis, and their relentless and exuberant activity is felt to contribute to the progressive nature of IPF. IPF fibroblasts exhibit gene expression changes that persist in culture even after multiple cell passages, suggesting that epigenetic modifications may be responsible for some of these gene expression differences. Alterations in DNA methylation of select genes have been identified in IPF fibroblasts, but a global assessment of the DNA methylomic abnormalities in IPF and their contribution to disease progression has never been assessed. The objectives of this project are to explore how genome-wide DNA methylomic and transcriptomic changes in IPF cells contribute to the clinical variability in IPF and determine how specific anti- and profibrotic mediators, prostaglandin E2 (PGE2) and transforming growth factor (TGF)-�1 respectively, contribute to altered DNA methylation patterns in IPF. The central hypothesis is that fibroblasts of IPF patients acquire distinct alterations in the DNA methylome in response to multiple extracellular signals, and that these distinct patterns of methylation contribute to both the heterogeneous gene expression profiles of fibroblasts and variable rates of clinical progression in IPF patients. This project has two specific aims: 1) examine how DNA methylomic changes in IPF fibroblasts contribute to both variable fibroblast gene expression patterns and clinical disease progression, and 2) understand the mechanisms by which PGE2 and TGF-�1 regulate DNA methyltransferases (DNMTs) and DNA methylation patterns and how they may contribute to differences in DNA methylation and gene expression of IPF fibroblasts. Fibroblasts from IPF and nonfibrotic lungs will be examined for methylation differences using the Illumina HumanMethylation450 Bead-Chip Array. Differentially methylated genes will be correlated with differential gene expression and longitudinal clinical disease progression. In Aim 2, the effects o PGE2 and TGF-�1 on DNA methylation and DNA methylation machinery will be examined in normal and IPF fibroblasts. The approach is innovative because it will utilize nonbiased, "next-generation" technologies to correlate whole genomic DNA methylation patterns with longitudinal clinical data from IPF patients and delineate mechanisms that regulate DNA methylation machinery and specific DNA methylation patterns. This project is significant because it will establish DNA methylation as a mechanism that contributes to differential gene expression, altered fibroblast function, and ultimately clinical disease progression, offer insight into how DN methylation patterns may be regulated, and identify novel pathways that may be candidates for future therapeutic targeting.

描述（由申请人提供）：特发性肺纤维化（IPF）是一种毁灭性的肺部疾病，目前尚无已知的有效治疗方法。尽管中位生存期令人沮丧，但个体患者的预后是可变的和不可预测的，一些患者保持稳定，另一些患者迅速恶化。解释患者临床表现变异性的机制 病程不明。成纤维细胞是纤维化中的主要效应细胞，其持续和旺盛的活性被认为有助于IPF的进行性。IPF成纤维细胞表现出即使在多次细胞传代后仍在培养物中持续存在的基因表达变化，这表明表观遗传修饰可能是造成这些基因表达差异的原因。已在IPF成纤维细胞中确定了选定基因的DNA甲基化改变，但从未对IPF中的DNA甲基化异常及其对疾病进展的贡献进行过全面评估。该项目的目标是探索IPF细胞中全基因组DNA甲基化组和转录组的变化如何影响IPF的临床变异性，并确定特异性抗纤维化和促纤维化介质前列腺素E2（PGE 2）和转化生长因子（TGF）-β 1分别如何影响IPF中DNA甲基化模式的改变。中心假设是IPF患者的成纤维细胞响应于多种细胞外信号而获得DNA甲基化组的不同改变，并且这些不同的甲基化模式有助于成纤维细胞的异质性基因表达谱和IPF患者临床进展的可变速率。该项目有两个具体目标：1）研究IPF成纤维细胞中的DNA甲基化变化如何有助于可变的成纤维细胞基因表达模式和临床疾病进展，以及2）了解PGE 2和TGF-β 1调节DNA甲基转移酶（DNMT）和DNA甲基化模式的机制，以及它们如何有助于IPF成纤维细胞DNA甲基化和基因表达的差异。将使用Illumina HumanMethylation 450微珠芯片阵列检查IPF和非纤维化肺的成纤维细胞的甲基化差异。差异甲基化基因将与差异基因表达和纵向临床疾病进展相关。在目标2中，将在正常和IPF成纤维细胞中检测PGE 2和TGF-β 1对DNA甲基化和DNA甲基化机制的影响。该方法具有创新性，因为它将利用无偏倚的“下一代”技术将全基因组DNA甲基化模式与IPF患者的纵向临床数据相关联，并描述调节DNA甲基化机制和特定DNA甲基化模式的机制。该项目具有重要意义，因为它将建立DNA甲基化作为一种机制，有助于差异基因表达，改变成纤维细胞功能，并最终导致临床疾病进展，提供对DN甲基化模式如何调节的见解，并确定可能成为未来治疗靶向候选者的新途径。