Epigenetic profiling of human alveolar epithelial cells in health and disease

健康和疾病状态下人类肺泡上皮细胞的表观遗传学分析

• 批准号: 8505030
• 负责人: Zea Borok
• 金额: $ 64.21万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-09-23 至 2016-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8505030
• 关键词: Acetylation; Affect; Age; Alveolar; American; Asphyxia; Automobile Driving; Biological Models; Cause of Death; Cell Differentiation process; Cells; Cessation of life; Chromatin Remodeling Factor; Chromatin Structure; Chromosomes; Cicatrix; Complex; Cuboidal Cell; DNA Methylation; Data; Deposition; Development; Developmental Biology; Diagnosis; Differentiation and Growth; Disease; Dissection; Distal; Effector Cell; Epigenetic Process; Epithelial; Epithelial Cells; Etiology; Event; Fibroblasts; Fibrosis; Functional RNA; Gases; Gene Expression; Gene Expression Profile; Gene Expression Regulation; Genes; Genetic Transcription; Genomics; Goals; Growth Factor; Hamman-Rich syndrome; Health; Human; Immunofluorescence Immunologic; Immunohistochemistry; In Vitro; Injury; Knowledge; Location; Lung; Lung diseases; Maps; Mediating; Messenger RNA; Methylation; MicroRNAs; Modeling; Modification; Monitor; Morphology; Normal Cell; Pathogenesis; Patients; Pattern; Peripheral; Phenotype; Play; Polycomb; Population; Prevention; Prevention strategy; Process; Proliferating; Property; Public Health; Pulmonary Surfactants; Pulmonology; RNA Polymerase II; Regenerative Medicine; Regulation; Regulatory Pathway; Resolution; Respiratory Failure; Reverse Transcriptase Polymerase Chain Reaction; SMARCA4 gene; Serum; Source; System; Time; Tissues; Transcriptional Regulation; Transforming Growth Factor beta; Transplantation; United States; Validation; Woman; alveolar epithelium; base; bisulfite; cell type; chromatin immunoprecipitation; data integration; disorder prevention; epigenomics; epithelial to mesenchymal transition; genome-wide; histone modification; in vivo; insight; lung repair; men; prevent; progenitor; programs; response; response to injury; restoration; self-renewal; spatial relationship; transcription factor; treatment strategy

PROJECT SUMMARY: Idiopathic pulmonary fibrosis (IPF) is a fatal disease of unknown etiology characterized by progressive lung fibrosis. It leads to death within 5 years unless patients undergo a lung transplant. Up to 34,000 cases of IPF are diagnosed in the United States each year. IPF lungs are characterized by increased accumulation of (myo)fibroblasts, activated fibroblasts with a contractile phenotype that are believed to be key effector cells leading to matrix deposition. Although the source of (myo)fibroblasts has not been definitively established, recent studies suggest that a significant portion of these cells arise from alveolar epithelial cells (AEC), through the process of epithelial-to-mesenchymal transition (EMT). Numerous observations point to a key role for AEC in the initiation and development of IPF. Alveolar epithelium consists of cuboidal type 2 (AEC2) cells and long thin type 1 (AEC1) cells, each with distinct morphologies, functions, and patterns of gene expression. AEC2 are a major source of pulmonary surfactants. They are believed to both self-renew and serve as progenitors for AEC1 for restoration of epithelial integrity following injury. In contrast, AEC1 mediate gas exchange and are believed to be terminally differentiated and unable to proliferate. AEC have been shown to undergo EMT in vivo in response to transforming growth factor beta (TGF-¿), giving rise to (myo)fibroblasts. AEC differentiation can be recapitulated in vitro; in the absence of added growth factors, purified AEC2 differentiate into AEC1-like cells. In contrast, when treated with TGF-¿, AEC2 undergo EMT, producing (myo)fibroblasts. This unique model system allows the temporal dissection of events that drive differentiation in the peripheral lung under conditions of health and disease. This proposal aims to identify genome-wide transcriptional and epigenetic changes of human AEC2 at distinct time points as the cells transition to AEC1- like cells or to (myo)fibroblasts. For comparison, primary AEC2 and AEC1 cells from normal lungs, and AEC2 and (myo)fibroblasts from the lungs of IPF patients will be examined. The Specific Aims are: 1) Transcriptome profiling of human AEC2 during the transition to AEC1-like cells or (myo)fibroblasts. Primary cells from healthy lung (AEC2 and AEC1) and IPF lung (AEC2 and (myo)fibroblasts) will be similarly analyzed. 2) Epigenomic profiling of the cells from Aim 1, using genome-wide approaches to assess DNA methylation patterns, histone modifications, polycomb group complex occupancy, chromosome remodeling complex occupancy, and selected transcription factor occupancy. 3) Integration of the data from Aims 1 and 2 to model the temporal and spatial relationships between the various epigenetic modifications and transcription of mRNAs and small non- coding RNAs. 4) Validation of a subset of newly identified expression patterns, epigenetic control networks and regulatory pathways using independent cultures of AEC and (myo)fibroblasts. Knowledge of the transcriptional and epigenetic programs driving AEC (mis)differentiation will provide insights into potential new avenues for lung restoration and will help develop strategies to treat and ultimately prevent diseases such as IPF.

项目摘要：特发性肺纤维化 (IPF) 是一种病因不明的致命疾病，其特征是 由进行性肺纤维化引起。除非患者接受肺移植，否则会导致 5 年内死亡。最多 美国每年诊断出 34,000 例 IPF 病例。 IPF 肺部的特点是增加 （肌）成纤维细胞的积累，具有收缩表型的活化成纤维细胞被认为是关键 效应细胞导致基质沉积。尽管（肌）成纤维细胞的来源尚未明确 最近的研究表明，这些细胞的很大一部分来自肺泡上皮细胞 （AEC），通过上皮间质转化（EMT）过程。许多观察结果表明 AEC 在 IPF 的发起和发展中发挥着关键作用。肺泡上皮由 2 型立方形组成 (AEC2) 细胞和细长 1 型 (AEC1) 细胞，每种细胞具有不同的形态、功能和模式 基因表达。 AEC2 是肺表面活性物质的主要来源。人们相信它们既能自我更新，又能 作为 AEC1 的祖细胞，用于损伤后恢复上皮完整性。相反，AEC1 介导 气体交换，并被认为是终末分化且无法增殖。 AEC已显示 体内对转化生长因子β (TGF-¿) 进行 EMT 反应，产生（肌）成纤维细胞。 AEC分化可以在体外重现；在没有添加生长因子的情况下，纯化的 AEC2 分化为 AEC1 样细胞。相反，当用 TGF-¿ 处理时，AEC2 经历 EMT，产生 （肌）成纤维细胞。这种独特的模型系统允许对驱动分化的事件进行时间剖析 健康和疾病条件下的周围肺。该提案旨在识别全基因组范围 当细胞转变为 AEC1 时，人类 AEC2 在不同时间点的转录和表观遗传变化 像细胞或（肌）成纤维细胞。为了进行比较，来自正常肺的原代 AEC2 和 AEC1 细胞，以及来自正常肺的 AEC2 将检查 IPF 患者肺部的（肌）成纤维细胞。具体目标是：1）转录组 人类 AEC2 在向 AEC1 样细胞或（肌）成纤维细胞转变过程中的分析。来自健康的原代细胞 肺（AEC2 和 AEC1）和 IPF 肺（AEC2 和（肌）成纤维细胞）将进行类似分析。 2）表观基因组 使用全基因组方法评估 DNA 甲基化模式、组蛋白，对目标 1 中的细胞进行分析 修饰、多梳群复合体占据、染色体重塑复合体占据，以及 选择的转录因子占据。 3) 整合目标 1 和 2 的数据来建模时间和 各种表观遗传修饰和 mRNA 转录以及小非基因之间的空间关系 编码RNA。 4) 验证新识别的表达模式、表观遗传控制网络和 使用 AEC 和（肌）成纤维细胞的独立培养物的调节途径。转录知识 驱动 AEC（错误）分化的表观遗传计划将为潜在的新途径提供见解 肺部恢复并将有助于制定治疗和最终预防 IPF 等疾病的策略。