Proteogenomics of dysregulated protein interaction networks in MTB infection

描述（由申请人提供）：雾化结核分枝杆菌（MTB）很容易在人与人之间传播。分枝杆菌感染远端肺泡，在那里它们在面对先天反应时不受约束地复制。随着适应性T细胞免疫的发展，结核分枝杆菌的生长得到控制，但不能根除杆菌。T细胞与MTB感染的抗原呈递细胞（APC）之间的相互作用是机体逃避/抵抗宿主免疫以建立潜伏感染的核心。为了响应RFA-HL-10-015“TB潜伏期和再激活机制的系统生物学方法”，我们将蛋白质组学、计算机科学、生物信息学、遗传流行病学、流行病学、免疫学、肺生物学和肺医学领域的多学科专家团队聚集在一起，以获得一组独特的流行病学和临床特征良好的人群，这些人在美国具有MTB暴露、感染和疾病谱。乌干达和南非，以便应用新的系统生物学方法潜伏MTB感染。最近的研究表明，旨在鉴定蛋白质-蛋白质相互作用网络的蛋白质组学方法可以鉴定在疾病发病机制中起作用的功能亚网络。我们建议将这种方法应用于人类潜伏性MTB感染（LTBI）的分析，并将蛋白质组学结果与使用人类遗传和系统化学/细胞因子方法的平行研究联系起来，以了解MTB的发病机制。该提议的一般假设是，蛋白质组学种子识别出区分结核分枝杆菌感染和疾病不同阶段人群的蛋白质亚网络，并提供了从LTBI到活动性结核进展的机制。目的1：确定家庭中严重暴露于MTB但未感染的人与未进展为疾病的LTBI患者和发展为TB的人的单核吞噬细胞和CD4+ T细胞中蛋白-蛋白相互作用亚网络失调。目的2：确定蛋白-蛋白相互作用子网络与全基因组和靶向基因分析之间的关系，以及在与目的1相同的人群中通过多重化学/细胞因子测定检测到的外周化学/细胞因子反应。目的3：确定目的1和目的2中分析的蛋白-蛋白相互作用和化疗/细胞因子亚网络中哪一个与LTBI患者的肺CD4+ T细胞和巨噬细胞最相关。该提案结合了美国、乌干达和南非流行病学特征良好的结核分枝杆菌感染者的独特临床标本（外周血、血浆、支气管肺泡灌洗液标本），以及使用蛋白质组学、遗传流行病学和细胞因子生物学的专家，采用多学科系统生物学方法研究LTBI及其向活动性结核的进展。

DESCRIPTION (provided by applicant): Aerosolized Mycobacterium tuberculosis (MTB) is readily transmitted from person to person. Mycobacteria infect the distal alveoli where they replicate unfettered in the face of innate responses. As adaptive T cell immunity develops, MTB growth is controlled but bacilli are not eradicated. The interactions between T cells and MTB infected antigen presenting cells (APC) are central for the organism to evade/resist host immunity to establish latent infection. In this application in response to RFA-HL-10-015 "Systems Biology Approach to the Mechanisms of TB Latency and Reactivation" we bring together a multidisciplinary team of experts in proteomics, computer science, bioinformatics, genetic epidemiology, epidemiology, immunology, lung biology and pulmonary medicine coupled to access to a unique set of cohorts of epidemiologically and clinically well characterized persons with the spectrum of MTB exposure, infection and disease in the US, Uganda and S. Africa, in order to apply novel systems biology approaches to latent MTB infection. Recent studies suggest that proteomic approaches aimed at identifying protein-protein interaction networks result in the identification of functional sub-networks with a role in disease pathogenesis. We propose to apply this approach to the analysis of latent MTB infection (LTBI) in humans, and to link proteomic results with parallel studies using human genetic and systemic chemo-/cytokine approaches to understanding MTB pathogenesis. The general hypothesis of this proposal is that proteomic seeds identify sub-networks of proteins that differentiate persons at different stages of MTB infection and disease, and provide insight into the mechanism(s) responsible for progression from LTBI to active TB. The aims are: Aim 1: To determine dysregulated protein-protein interaction sub-networks in mononuclear phagocytes and CD4+ T cells of persons in households heavily exposed to MTB who do not become infected compared to those with LTBI who do not progress to disease and those who develop TB. Aim 2: To determine the relationship between protein-protein interaction sub-networks to whole genome and targeted gene analyses, and peripheral chemo-/cytokine responses detected by multiplex chemo-/cytokine assays in the same population as in Aim 1. Aim 3: To determine which of the protein-protein interaction and chemo-/cytokine sub-networks analyzed in Aims 1 and 2 are most relevant for lung CD4+ T cells and macrophages from persons with LTBI. This proposal combines access to unique clinical specimens (peripheral blood cells, plasma, broncho- alveolar lavage specimens) from epidemiologically well characterized persons with MTB infection in US, Uganda and South Africa with experts in the use of proteomics, genetic epidemiology and cytokine biology for a multidisciplinary systems biology approach to LTBI and its progression to active TB. PUBLIC HEALTH RELEVANCE: Systems biology is ideally suited to analyze the complex interaction between humans and M. tuberculosis (MTB), the cause of tuberculosis (TB), and is particularly powerful when applied to tissues from persons in different stages of MTB exposure, infection and disease. Using systems biology to find key host proteins disturbed by MTB exposure or infection allows us to identify persons at risk for progression to active TB and find out what we need to be naturally or through vaccination protected against TB.