Genomic signatures for detection of upper respiratory viral infections

描述(由申请人提供)： 这项工作的总体目标是通过精心设计的职业发展活动和定向翻译研究的组合，确立候选人作为独立科学研究人员的地位。该项目旨在确定宿主基因表达模式，能够准确地对急性上呼吸道病毒感染(URI)进行分类，并根据URI在美国退伍军人群体中预测最终的疾病严重程度。这项工作是一个独特的机会，可以利用DARPA资助的年轻、健康个人呼吸道病毒挑战研究中收集的数据作为起点，根据退伍军人事务卫生系统的使命，确定在更脆弱的人群中人类对感染反应的启动和演变。本申请的目的是测试和改进(在必要时)基因组签名对更多样化的老年退伍军人群体的适用性，这些老年退伍军人的健康状况更有可能因年龄和可能改变基因组反应性质的多种共病而复杂化。这将通过以下具体目标来实现：目标1.通过使用体外模型，获得定义老龄化人口中上呼吸道病毒感染的宿主基因签名。我们将分离并感染人类外周血单个核细胞感染流感病毒，以开发表征感染的基因特征。这些PBMC将从稳定的、非急性感染的个体中分离出来，这些个体是从我们长期护理和康复中心的美国退伍军人中挑选出来的。然后在体外将PBMC暴露于活的呼吸道病毒(流感、HRV、RSV)或细菌(肺炎链球菌、支原体或大肠杆菌)，并在多个时间点分离宿主RNA并通过基因芯片检测基因表达。然后将通过标准方法以及我们先前为此目的开发的改进的稀疏潜在因子分析来分析基因组签名。目标2.登记和描述患有URI的美国退伍军人队列我们将通过两个主要门户网站识别美国退伍军人中的流感样疾病病例。第一个将是在生活在DVAMC ECRC的个人中识别ILI病例。第二个是通过DVAMC急诊部捕捉出现ILI的个人。在这两种情况下，我们都将在提交时获得用于微阵列分析的外周血液RNA，以及用于微生物学和血清学诊断的标准样本。这些人将被跟踪每天的症状评分报告-通过研究人员的每日探访在ECRC住院的患者，以及通过每天的电话访问登记在急诊室的门诊患者。参加ECRC的受试者还将在整个病程中每天抽血进行RNA分离和微阵列分析，以及细胞因子的表达，以表征宿主反应的演变。目的3.评估URI基因签名在老龄化人口中的表现。我们将评估我们之前对年轻、健康志愿者进行的研究中确定的基因组签名的性能，以及b)通过我们的体外感染特定目标1的模型，将这些签名应用于已出现特定目标2中定义的微生物证实的流感感染的个人。目的4.评估新的针对老龄化人口的基因签名(S)。我们将根据AIM 2中登记的流感感染者的数据得出新的基因签名。考虑到人群中的潜在差异，我们将交叉验证ECRC患者得出的签名与ED登记患者得出的签名，反之亦然。此外，我们将利用陈述时基因签名的变异来建立最终疾病严重程度的基因组预测模型。

DESCRIPTION (provided by applicant): The overall goal of this endeavor is to establish the Candidate as an independent scientific investigator through a carefully designed combination of career development activities and directed translational research. This project aims to define patterns of host gene expression which are capable of accurately classifying acute upper respiratory viral infection (URI) as well as predicting eventual disease severity from URIs in a population of US Veterans. This work represents a unique opportunity to utilize data collected as a part of DARPA- funded respiratory viral challenge studies in young, healthy individuals as a starting point to define the initiation nd evolution of the human response to infection in a more vulnerable population in keeping with the mission of the Veterans Affairs Health System. The objective of this application is to test and refine (where necessary) the applicability of genomic signatures to a more varied population of older Veterans whose health status is more likely to be complicated by age and multiple comorbidities which may alter the nature of the genomic response. This will be accomplished through the following Specific Aims: Aim 1. Derive host gene signatures that define upper respiratory viral infection in an aging population through use of an in vitro model. We will isolae and infect human Peripheral Blood Mononuclear Cells with influenza viruses in order to develop gene signatures which characterize infection. These PBMCs will be isolated from stable, non-acutely infected individuals selected from a population of US Veterans living in our Extended Care and Rehabilitation Center. The PBMCs will then be exposed in vitro to live respiratory viruses (Influenza, HRV, RSV) or bacteria (Streptococcus pneumoniae, Mycoplasma, or E. coli), and host RNA will be isolated at multiple timepoints and assayed by microarray for gene expression. Genomic signatures will then be analyzed through standard methods as well as by the modified sparse latent factor analysis we have previously developed for this purpose. Aim 2. Enroll and characterize a cohort of US Veterans with URI We will identify cases of Influenza-like illness in US Veterans through two major portals. The first will be to identify cases of ILI among individuals living in the DVAMC ECRC. The second will be to capture individuals presenting with ILI through the DVAMC Emergency Department. In both cases we will obtain peripheral blood RNA for microarray analysis at the time of presentation as well as standard samples for both microbiological and serological diagnosis. These individuals will be followed with daily symptom score reporting - inpatients in the ECRC through daily visits from study staff, and outpatients enrolled in the ED through daily phone interviews. Subjects enrolled in the ECRC will also have blood drawn daily throughout the course of disease for RNA isolation and microarray analysis as well as cytokine expression in order to characterize the evolution of the host response. Aim 3. Evaluate performance of URI gene signatures in an aging population. We will evaluate the performance of our genomic signatures identified a) in our previous studies with young, healthy volunteers and b) through our in vitro model of infection in Specific Aim 1 through application of these signatures to individuals who have presented with microbiologically proven Influenza infection as defined in Specific Aim 2. Aim 4. Evaluate new gene signature(s) specific to an aging population. We will derive new gene signatures based upon the data from Influenza infected individuals enrolled in Aim 2. Given potential differences in the populations, we will the cross-validate signatures derived from ECRC patients on signatures derived from ED-enrolled patients and vice versa. Furthermore, we will utilize variations in gene signatures at the time of presentation to build a genomic prediction model for eventual disease severity.