Molecular Determinants of Usual Interstitial Pneumonia (UIP)

普通间质性肺炎 (UIP) 的分子决定因素

• 批准号: 10440715
• 负责人: David Albert Schwartz
• 金额: $ 72.59万
• 依托单位: UNIVERSITY OF COLORADO DENVER
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-04-01 至 2027-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10440715
• 关键词: Address; Affect; Antigens; Asbestosis; Binding; Biological; Biological Assay; Biology; Cell Nucleus; Cells; Characteristics; Chromatin; Chronic; Clinical; Complication; Data; Development; Disease; Distal; Dominant Genetic Conditions; Drug Targeting; Elements; Enhancers; Epigenetic Process; Epithelial; Etiology; Exposure to; Extrinsic allergic alveolitis; Fibroblasts; Fibrosis; Gene Expression; Gene Expression Profile; Genes; Genetic Transcription; Genotype; Goals; Heterogeneity; Immunohistochemistry; In Situ Hybridization; In Vitro; Individual; Interstitial Lung Diseases; Interstitial Pneumonia; Investigation; Lead; Lung; Lung diseases; MUC5B gene; Methods; Molecular; Molecular Profiling; Morphology; Pathogenesis; Pathogenicity; Pathologic; Pathway interactions; Patients; Pattern; Pharmaceutical Preparations; Phenotype; Publishing; Pulmonary Fibrosis; Quantitative Trait Loci; Regulator Genes; Regulatory Pathway; Reporting; Research; Rheumatoid Arthritis; Risk Factors; Small Nuclear RNA; Structure of parenchyma of lung; Testing; Transcription Factor 3; Transcriptional Regulation; Transposase; Usual Interstitial Pneumonia; Variant; airway epithelium; cell type; combinatorial; disease phenotype; endoplasmic reticulum stress; epigenetic regulation; gain of function; gene regulatory network; genetic risk factor; genetic variant; idiopathic pulmonary fibrosis; indexing; multiple omics; novel; promoter; radiological imaging; risk variant; transcription regulatory network; transcriptome sequencing

ABSTRACT: The overall goal of this proposal is to understand how the gain-of-function MUC5B promoter variant affects transcriptional regulation and gene expression that are common to clinically distinct types of usual interstitial pneumonia (UIP). UIP was initially described as a morphologic entity, however, recently has been defined using specific pathologic and radiographic criteria. While UIP is characteristic of idiopathic pulmonary fibrosis (IPF), these pathologic and radiographic patterns of chronic fibrosing interstitial pneumonia are also typical of chronic hypersensitivity pneumonitis (CHP), rheumatoid arthritis-associated interstitial lung disease (RA-ILD), asbestosis, and several drug-induced lung diseases. The gain-of-function promoter variant in MUC5B (rs35705950) is the dominant risk factor for IPF, is present in >50% of affected patients, and has also been reported to be the dominant genetic risk variant for the development of CHP and RA-ILD. However, while IPF is by definition idiopathic, CHP develops following repeated exposure to organic antigens, and RA-ILD is a complication of rheumatoid arthritis. We proposed by understanding the relationship between the MUC5B promoter variant, transcriptional regulation, and gene expression in IPF, CHP, and RA-ILD, we will be able to identify the common molecular elements that are critical to the development of UIP. The two critical questions that we plan to address are: 1) what are the common molecular features of UIP, irrespective of clinical context, and 2) does MUC5B promoter variant have a unique molecular signature common to UIP? The hypothesis we plan to test is that the gain-of-function MUC5B promoter variant drives cell-specific chromatin accessibility and gene expression that define UIP. In Aim 1, we will use single nucleus RNA sequencing (snRNA-seq) to identify the cell-specific transcriptional profiles for IPF, CHP, and RA-ILD, and determine the relationship of the common cell-specific transcriptional profiles of UIP to the MUC5B promoter variant. In Aim 2, we will use a combinatorial indexing single nucleus assay for transposase-accessible chromatin (snATAC-seq) to identify the cell-specific chromatin accessibility profiles for IPF, CHP, and RA-ILD, and determine the relationship of the common cell-specific chromatin accessibility profiles of UIP to the MUC5B promoter variant. In Aim 3, we will perform integrative analyses of the MUC5B promoter genotype, snRNA-seq, and snATAC-seq data using single-cell expression QTL, multi-omic and network inference methods to identify UIP-specific gene regulatory networks with key drivers of UIP in specific cell types. In Aim 4, we will validate the transcriptional features that are common to MUC5B-associated UIP by determining the relationship of these key genes to the pathogenic heterogeneity of UIP and relevant in vitro biology. In aggregate, we will characterize regulatory effects of MUC5B on cell-specific transcriptional profiles and networks in UIP, launching investigation of novel pathogenic mechanisms and drug targets for these incurable diseases.

摘要：该提案的总体目标是了解功能障碍MUC5B启动子如何 变体会影响转录调控和基因表达，而临床上不同类型的通常 间质性肺炎（UIP）。 UIP最初被描述为形态学实体，但是最近已经 使用特定的病理和影像学标准定义。 uip是特发性肺的特征 纤维化（IPF），这些慢性纤维间肺肺炎的病理和放射学模式也是 典型的慢性超敏性肺炎（CHP），类风湿关节炎相关的间质性肺部疾病 （RA-ild），石棉病和几种药物诱导的肺部疾病。 MUC5B中功能启动子的增长启动子变体 （RS35705950）是IPF的主要危险因素，> 50％的患者中存在，也是 据报道是CHP和RA-ILD发展的主要遗传风险变异。但是，虽然IPF是 根据定义，特发性，CHP在反复接触有机抗原之后会发展出来，而Ra-ild是 类风湿关节炎的并发症。我们通过了解MUC5B之间的关系提出 IPF，CHP和RA-ILD中的启动子变体，转录调控和基因表达，我们将能够 确定对UIP开发至关重要的常见分子元素。两个关键问题 我们计划解决的是：1）UIP的常见分子特征是什么，无论临床环境如何， 2）MUC5B启动子变体是否具有UIP共有的独特分子签名？我们的假设 计划测试的是功能获得的MUC5B启动子变体驱动细胞特异性染色质 定义UIP的可访问性和基因表达。在AIM 1中，我们将使用单核RNA测序 （snRNA-seq）确定IPF，CHP和RA-ILD的细胞特异性转录曲线，并确定 UIP的常见细胞特异性转录谱与MUC5B启动子变体的关系。在AIM 2中， 我们将使用组合索引单核测定法进行转座酶可访问的染色质（SNATAC-SEQ） 识别IPF，CHP和RA-ILD的细胞特异性染色质可及性配置文件，并确定 UIP与MUC5B启动子变体的常见细胞特异性染色质可及性分布的关系。 在AIM 3中，我们将对MUC5B启动子基因型，SNRNA-SEQ和SNATAC-SEQ进行综合分析 使用单细胞表达式QTL，多摩变和网络推理方法来识别UIP特异性基因的数据 特定细胞类型中具有UIP的关键驱动因素的监管网络。在AIM 4中，我们将验证转录 通过确定这些关键基因与MUC5B相关的UIP常见的特征 UIP的致病异质性和相关的体外生物学。总体而言，我们将表征监管 MUC5B对UIP中细胞特异性转录曲线和网络的影响，启动了新型的研究 这些无法治愈的疾病的致病机制和药物靶标。