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: 8153846
• 负责人: Zea Borok
• 金额: $ 66.84万
• 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/8153846
• 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; 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; men; prevent; progenitor; programs; repaired; response; response to injury; restoration; self-renewal; spatial relationship; transcription factor; treatment strategy

DESCRIPTION (provided by applicant): 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-2), 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-2, 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. PUBLIC HEALTH RELEVANCE: Nobody knows why each year up to 34,000 Americans develop idiopathic pulmonary fibrosis, "IPF", a lethal disease in which the lungs are slowly destroyed by scar tissue, ultimately resulting in suffocation. Evidence suggests that in patients with IPF, certain lung cells differentiate into scar tissue instead of growing normally. Using a unique system of cultured human lung cells, we will examine how the information that is layered on top of the genes ("epigenetic" information) makes lung cells grow in normal as well as abnormal ways, with the objective to develop new treatment and prevention strategies for IPF and other lung diseases.

描述（由申请人提供）：特发性肺纤维化（IPF）是一种致命病因的致命疾病，其特征是进行性肺纤维化。除非患者接受肺移植，否则它会在5年内导致死亡。每年在美国诊断出多达34,000例IPF病例。 IPF肺的特征是（MYO）成纤维细胞的积累增加，具有收缩表型的活化成纤维细胞，据信被认为是导致基质沉积的关键效应细胞。尽管尚未确定（MYO）成纤维细胞的来源，但最近的研究表明，这些细胞的很大一部分来自牙槽上皮细胞（AEC），这是通过上皮 - 间质转变（EMT）的过程。许多观察结果表明，AEC在IPF的启动和开发中的关键作用。牙槽上皮由Cuboidal 2型（AEC2）细胞和长薄型1（AEC1）细胞组成，每个细胞具有不同的形态，功能和基因表达的模式。 AEC2是肺表面活性剂的主要来源。据信它们既可以自我更新，又是AEC1恢复受伤后上皮完整性的祖细胞。相比之下，AEC1介导了气体交换，被认为是最终区分且无法扩散的。已显示AEC会响应转化生长因子β（TGF-2）而在体内进行EMT，从而导致（MyO）成纤维细胞。可以在体外概括AEC分化；在没有附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-2处理时，AEC2会经历EMT，产生（MYO）成纤维细胞。这种独特的模型系统允许在健康和疾病条件下驱动周围肺部分化的事件的时间解剖。该建议旨在确定人AEC2在不同时间点的全基因组转录和表观遗传变化，因为细胞过渡到AEC1-like细胞或（myo）成纤维细胞。为了进行比较，将检查来自正常肺的初级AEC2和AEC1细胞，以及来自IPF患者肺的AEC2和（MyO）成纤维细胞。具体目的是：1）在过渡到AEC1样细胞或（MyO）成纤维细胞的转录组分析。将类似地分析来自健康肺（AEC2和AEC1）和IPF肺（AEC2和（MYO）成纤维细胞）的原代细胞。 2）细胞从AIM 1中对细胞的表观分析，采用全基因组的方法来评估DNA甲基化模式，组蛋白修饰，Polycomb组复杂占用，染色体重塑复杂占用率和选定的转录因子占用率。 3）从目标1和2的数据集成，以建模各种表观遗传修饰与mRNA和小型非编码RNA之间的时间和空间关系。 4）使用AEC和（myo）成纤维细胞的独立培养物的新确定的表达模式，表观遗传控制网络和调节途径的验证。了解驱动AEC（MIS）分化的转录和表观遗传学计划的知识将为潜在的肺部修复新途径提供见解，并将有助于制定治疗并最终预防IPF等疾病的策略。 公共卫生相关性：没有人知道为什么每年多达34,000名美国人会出现特发性肺纤维化，即“ IPF”，这是一种致命的疾病，其中肺部被疤痕组织缓慢破坏，最终导致窒息。有证据表明，在IPF患者中，某些肺细胞分化为疤痕组织，而不是正常生长。使用独特的培养的人肺细胞系统，我们将研究如何在基因之上分层的信息（“表观遗传学”信息）使肺细胞以正常和异常方式生长，并目的是为IPF和其他肺部疾病制定新的治疗方法和预防策略。