Integrative-omics Network Model of the Disordered COPD Small Airway Epithelium

描述（由申请人提供）：与吸烟相关的最早异常发生在小气道上皮（SAE）中，即第6代气道腔内衬的基底细胞、柱状细胞、分泌细胞和纤毛细胞。基底细胞（BC）作为干细胞/祖细胞发挥功能，其产生提供屏障功能的分化的上皮细胞。吸烟障碍SAE分化，伴BC增生和鳞状化生，分泌细胞增多，纤毛细胞减少和紊乱，细胞间连接渗漏改变。其结果是粘蛋白产生增加和粘膜纤毛清除效率低下，导致病原体定植和炎症细胞的募集，进一步扰乱肺结构。本建议的核心 是认识到SAE是慢性阻塞性肺疾病（COPD）发病的起始部位，BC在COPD SAE紊乱中起关键作用。虽然在了解健康和疾病中SAE和BC的生物学方面取得了进展，但重点是单个基因和途径的贡献。组学技术已经认识到许多基因参与SAE对吸烟和COPD发病机制的反应，并且这些基因的表达可以通过基因组、表观基因组和miRNA修饰。我们的建议基于：（1）我们从SAE的刷样中纯化BC的能力;以及（2）我们对161例受试者（包括非吸烟者、健康吸烟者和COPD吸烟者）的SAE转录组进行了分析，所有受试者均具有人口统计学、肺功能、HRCT胸部成像和全基因组SNP阵列，SAE在1年内通过支气管镜检查和刷牙4次重复采样（0、3、6和12个月）。使用这些样本的从头网络恢复分析，我们确定了9组连接的枢纽基因（模块），包括273个枢纽基因和10个区分COPD与吸烟的重要途径。我们建议在此网络的基础上分析遗传、表观遗传和miRNA表达变异性对关键转录组模块、枢纽和连接性的影响，这些模块、枢纽和连接性定义了SAE生物学如何随着COPD的发展而变得紊乱。目标1.评估基因组、表观基因组（甲基化）和miRNA表达的变异性对SAE转录组COPD分化的枢纽和连接的影响。目标二。检查SAE COPD转录组特征性模块、枢纽和连接性由BC生物学主导的假设。目标3。检验区分COPD的SAE中心的修饰将对表征紊乱的SAE COPD分化转录组的相关基因产生显著影响的假设。我们的交付成果将是确定潜在的中心药物靶点，以逆转和/或预防COPD SAE特征性的生物学紊乱。

DESCRIPTION (provided by applicant): The earliest abnormalities associated with smoking are in the small airway epithelium (SAE), the basal, columnar, secretory and ciliated cells lining the airway lumen e 6th generations. The basal cells (BC) function as stem/progenitors that give rise to the differentiated epithelial cells that provide barrier function. Smoking disorders SAE differentiation, with BC hyperplasia and squamous metaplasia, more secretory cells, fewer and disordered ciliated cells, and altered leaky cell-cell junctions. The consequences are increased mucin production and inefficient mucociliary clearance, resulting in pathogen colonization and recruitment of inflammatory cells that further disorder lung architecture. Central to this proposal is the recognition that the SAE is the site initiating the pathogenesis of chronic obstructive pulmonary disease (COPD), and that BC play a critical role in the SAE disordering in COPD. While progress has been made in understanding the biology of the SAE and BC in health and disease, the focus has been on the contribution of single genes and pathways. Omics technology has led to the recognition that many genes are involved in the responses of the SAE to smoking and to COPD pathogenesis, and that the expression of these genes can be modified by the genome, epigenome, and miRNA. Our proposal is based on: (1) our ability to purify BC from brushed samples of the SAE; and (2) our analysis of the SAE transcriptome of a well characterized cohort of 161 subjects, including nonsmokers, healthy smokers and COPD smokers, all with demographic, lung function, HRCT chest imaging and genome-wide SNP arrays, with the SAE repeatedly sampled by bronchoscopy and brushing 4 times over 1 yr (0, 3, 6 and 12 months). Using de novo network recovery analysis of these samples, we identified 9 groups of connected hub genes (modules) comprised of 273 hub genes and 10 significant pathways that differentiate COPD from smoking. We propose to build on this network to analyze the influence of genetic, epigenetic and miRNA expression variability on key transcriptome modules, hubs and connectivities that de- fine how SAE biology becomes disordered with the development of COPD. Aim 1. To assess the effects of variability of genome, epigenome (methylation) and miRNA expression on the SAE transcriptome COPD-differentiated hubs and connections. Aim 2. To examine the hypothesis that the modules, hubs and connectivities that characterize the SAE COPD transcriptome are dominated by BC biology. Aim 3. To test the hypothesis that modification of the SAE hubs that differentiate COPD will have significant consequences on the connected genes that characterize the disordered SAE COPD-differentiated transcriptome. Our deliverable will be the identification of potential hub drug targets to reverse and/or prevent the disordered biology that characterizes the COPD SAE.