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

描述(申请人提供)：与吸烟相关的最早异常是在小气道上皮(SAE)，气道腔内衬里的基细胞、柱状细胞、分泌细胞和纤毛细胞是第六代。基底细胞(BC)具有干/祖细胞的功能，分化的上皮细胞提供屏障功能。吸烟障碍表现为分化不良，伴有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-细胞连接改变。其后果是粘蛋白产生增加，粘液纤毛清除效率低下，导致病原体定植和炎性细胞募集，进一步扰乱肺结构。这项提议的核心 认识到SAE是慢性阻塞性肺疾病(COPD)发病的始动部位，BC在COPD的SAE紊乱中起关键作用。虽然在了解SAE和BC在健康和疾病方面的生物学方面取得了进展，但重点一直放在单基因和单途径的贡献上。组学技术使人们认识到许多基因参与了SAE对吸烟的反应和COPD的发病机制，并且这些基因的表达可以被基因组、表观基因组和miRNA改变。我们的建议基于：(1)我们从SAE的刷检样本中提纯BC的能力；以及(2)我们对161名具有良好特征的队列受试者的SAE转录组的分析，这些受试者包括不吸烟者、健康吸烟者和COPD吸烟者，所有这些受试者都具有人口统计学、肺功能、HRCT胸部成像和全基因组SNP阵列，其中SAE通过支气管镜检查和刷检在1年内(0、3、6和12个月)重复采样4次。对这些样本进行从头网络恢复分析，我们确定了9组相连的HUB基因(模块)，包括273个HUB基因和10条区分COPD和吸烟的重要途径。我们建议在这个网络的基础上分析遗传、表观遗传和miRNA表达的变异性对关键转录组模块、枢纽和连接性的影响，这些影响定义了SAE生物学如何随着COPD的发展而变得混乱。目的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分化中枢和连接的影响。目的2.验证SAE COPD转录组的模块、中枢和连接性受BC生物学控制的假说。目的3.验证这样一种假设，即改变区分COPD的SAE中枢将对表征紊乱的SAE COPD分化转录组的相关基因产生显著影响。我们的成果将是确定潜在的中枢药物靶点，以逆转和/或预防以COPD SAE为特征的无序生物学。

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.