Transcriptomic and Genetic Endotyping of Exacerbation-Prone Asthmatics

项目总结/摘要 上呼吸道的人鼻病毒（HRV）感染是呼吸道感染的最强环境风险因素之一。 儿童哮喘恶化。然而，并不是所有的儿童都经历急性加重， HRV感染。事实上，哮喘人群分为易加重和难加重 患者患者细胞对病毒感染反应的变异性可以解释急性加重风险 在儿童哮喘患者中观察到的分层。鼻气道上皮是HRV感染的主要部位 和复制，提示鼻上皮对HRV反应的重要性。我们假设 哮喘气道病理生物学机制（内型）存在异质性，其中一些可能 容易恶化。支持这一点，我们发现鼻基因表达水平高的IL-13，一个标志物， 2型-高哮喘内型，与急性发作风险相关。呼吸道对病毒的反应 上皮细胞可能由气道上皮细胞的分子状态驱动。内源性免疫（IL-13） 和吸入的环境暴露（环境烟草烟雾（ETS））可以大大改变 气道上皮的转录组谱。此外，最近的研究发现， 影响气道基因表达易导致儿童哮喘恶化。因此，我们假设， 免疫和/或环境“致敏”的气道上皮以失调的方式对病毒应答 感染，导致遗传易感受试者的哮喘恶化。测试这些 目的1：确定是否2型细胞因子高和其他鼻分泌物 表达内型与易加重哮喘相关并可预测哮喘的发生 加重我们将对儿童的鼻气道刷拭物进行全转录组测序（WTS） 易加重（n=100）、难加重（n =100）的哮喘患者和健康对照受试者 （n=100）。我们将确定与急性加重相关的基因、途径和表达内型- 容易哮喘目的2：确定IL-13和ETS刺激如何改变鼻粘膜细胞的转录组反应。 上皮细胞（NEC）对HRV感染的反应，以及这些反应是否因易加重的哮喘状态而异。空气- 来自Aim 1供体的液体界面NEC培养物将用模拟刺激、IL-13、ETS、HRV-A、-C或 用IL-13或ETS致敏，然后用HRV-A或HRV-C感染。WTS基因表达数据来自 这些培养物将用于通过处理来识别差异表达的基因。治疗反应将 在协同/拮抗分析中进行分析，以鉴定受IL-13干扰的HRV感染应答 或ETS预处理。目的3：筛选体内气道上皮表达的数量性状基因座（eQTL） 易加重哮喘基因的变异。我们将确定基因变异， 免疫/环境刺激的气道上皮对HRV感染产生有害的上皮反应 （响应eQTL）。我们将确定eQTL/reQTL变异，赋予哮喘加重倾向的风险。

PROJECT SUMMARY/ABSTRACT Human rhinovirus (HRV) infection of the upper airways is one of the strongest environmental risk factors for childhood asthma exacerbations. However, not all children experience an acute exacerbation in response to HRV infection. In fact, the asthmatic population is stratified into exacerbation-prone and exacerbation-resistant patients. Variability in patient cellular responses to virus infection could explain the exacerbation risk stratification observed in childhood asthmatics. The nasal airway epithelium is the primary site of HRV infection and replication, suggesting the importance of nasal epithelial responses to HRV. We hypothesize that heterogeneity exists in asthmatic airway pathobiological mechanisms (endotypes), some of which may predispose to exacerbations. Supporting this we find that high nasal gene expression levels of IL-13, a marker of the type 2-high asthma endotype, are associated with exacerbation risk. The response to virus of the airway epithelium is likely driven by the molecular state of the airway epithelium. Both endogenous immune (IL-13) and inhaled environmental exposures (environmental tobacco smoke (ETS)) can greatly alter the transcriptome profile of the airway epithelium. Additionally, recent studies have found genetic variants that affect airway gene expression predispose to childhood asthma exacerbations. Therefore, we hypothesize that an immune and/or environmentally “primed” airway epithelium responds in a dysregulated way to viral infections, resulting in asthma exacerbations among genetically predisposed subjects. To test these hypotheses we propose the following aims: Aim 1: Determine if type 2 cytokine high and other nasal expression endotypes are associated with exacerbation-prone asthma and predict occurrence of asthma exacerbations. We will perform whole transcriptome sequencing (WTS) of nasal airway brushings from children with asthma that are exacerbation-prone (n=100), exacerbation-resistant (n=100), and healthy control subjects (n=100). We will identify genes, pathways, and expression endotypes that are associated with exacerbation- prone asthma. Aim 2: Determine how IL-13 and ETS stimuli modify the transcriptome response of nasal epithelial cells (NECs) to HRV infection and if these responses vary by exacerbation-prone asthma status. Air- liquid interface NEC cultures from Aim 1 donors will be treated with mock-stimulus, IL-13, ETS, HRV-A,-C or primed with IL-13 or ETS and then infected with HRV-A or -C. WTS gene expression data generated from these cultures will be used to identify differentially expressed genes by treatment. The treatment responses will be analyzed in a synergy/antagonism analysis to identify HRV infection responses that are perturbed by IL-13 or ETS pretreatment. Aim 3: We will identify in vivo airway epithelium expression quantitative trait loci (eQTL) variants in exacerbation-prone asthma genes. We will determine genetic variants that interact with immune/environmental stimulated airway epithelium to drive deleterious epithelial responses to HRV infection (response eQTLs). We will determine eQTL/reQTL variants that confer risk of exacerbation-prone asthma.