The Lung DNA Virome in Health and Disease

摘要：健康与疾病中的肺DNA病毒体 我们与我们居住的微生物群生活在一种相互依赖的关系中，这强烈地影响着人类的健康 和疾病。微生物群落在不同的身体部位是不同的，并且在每个部位都有不同的后果。 对于我们的细菌来说，人类与微生物之间的关系得到了最广泛的研究 但人们对人类病毒体的了解要少得多，特别是在呼吸道。 在初步研究中，我们使用鸟枪式元基因组学研究了几组受试者的肺病毒群。 我们建立了有效的病毒颗粒纯化方法和序列计算方法 装配和分类分配。这揭示了噬菌体和动物细胞病毒的多样性。最突出的是， 我们在肺中发现了高水平的扭矩TenoVirus(TTV)，这是一类具有极端 高度变异性，我们鉴定了一组新的小环状DNA病毒，与任何 以前描述的病毒(我们称之为“人类环状病毒”；HCRV)。众所周知，血液中的TTV 处于有效的宿主免疫控制之下，但既不是控制TTV的细胞免疫反应，也不是 对肺的特异性调节进行了研究。对肺部特异的HCRV一无所知，因为我们发现 他们是第一次来这里。这些发现突显了当前知识中的主要差距：肺和它的 无处不在的病毒群落相互作用和影响，特别是丰富的小单个 搁浅的DNA病毒？吸烟是导致肺损伤的主要原因，它的影响是什么？是这些吗？ 病毒和宿主对它们的免疫反应导致肺损伤和/或炎症，从而驱动肺 疾病？为促进对肺部病毒及其与肺部健康和疾病的关系的了解，我们将： 第1阶段(R61)第1-2年：为了为进一步发展奠定基础，我们将(1)定义TTV的分布 严重肺部疾病患者呼吸道样本中的&HCRV(“极端表型”)；(2) 为共享的其他新的呼吸道DNA病毒生成和询问肺病毒元基因组数据集 (3)开发了一种新的对T细胞免疫反应的“个性化”评估 高变量TTV，以及对HCRV免疫应答的探讨；(4)生成支气管肺泡库 代表高度优先的肺部疾病的灌洗(BAL)标本，用于第二阶段的病毒和免疫分析。 第2阶段(R33)3-5年：我们将(1)定义肺病毒组分和病毒组分之间的关系- 靶向免疫反应，以及高度优先的肺部疾病；(2)确定吸烟对 肺病毒体和血浆病毒体，以及病毒靶向免疫反应；(3)定义了 HCRV、TTV和其他与肺部相关的小型DNA病毒。 这个项目被设计成一个发现/假设生成科学以及具体的 RFA HL-17-002中概述的假设检验研究，我们预计这将为 肺内病毒的性质，以及在肺部健康和疾病中的作用。

Abstract: The Lung DNA Virome in Health and Disease We live in an interdependent relationship with our resident microbiota, which strongly influence human health and disease. Microbial communities differ at different body sites, and have distinctive consequences at each. The relationship between humans and their microbes has been most extensively studied for our bacterial communities but far less is known about the human virome, particularly in the respiratory tract. In preliminary studies, we used shotgun metagenomics to investigate the lung virome in several subject groups. We established efficient methods for purification of viral particles and computational methods for sequence assembly & taxonomic assignment. This revealed a diversity of phage & animal cell viruses. Most prominently, we discovered high levels in lung of Torque Tenoviruses (TTV), a family of small DNA viruses with extreme hypervariability, and we identified a novel group of small circular DNA viruses with limited homology to any previously described viruses (which we term “human circo-related virus”; HCRV). It is known that TTV in blood is under potent host immune control, but neither cellular immune responses that control TTV in general nor lung-specific regulation have been investigated. Nothing is known about lung-specific HCRV since we identify them here for the first time. These findings highlight major gaps in current knowledge: How do the lung and its ubiquitous communities of viruses interact and affect each other, particularly the abundant small single stranded DNA viruses? What is the influence of cigarette smoking, a principal cause of lung injury? Are these viruses and host immune response to them contributing to lung injury and/or inflammation that drive lung diseases? To accelerate understanding of the lung virome and relationship to lung health & disease, we will: Phase 1 (R61) Years 1-2: To set the stage for further advancement, we will (1) Define the distribution of TTV & HCRV in respiratory tract samples from severely ill lung disease subjects (“extreme phenotype”); (2) Generate & interrogate lung virome metagenomic datasets for additional novel respiratory DNA viruses shared among individuals; (3) Develop a novel “personalized” assessment of T cell immune responses to hypervariable TTV, and approach to HCRV immune responses; (4) Generate a repository of bronchoalveolar lavage (BAL) specimens representing lung diseases of high priority for virome & immune analysis in Phase 2. Phase 2 (R33) Years 3-5: We will (1) Define the relationship between lung virome constituents & virome- targeted immune responses, and pulmonary diseases of high priority; (2) Determine the impact of smoking on the lung virome and plasma virome, & virome-targeted immune responses; (3) Define the molecular virology of HCRV, TTV & other small DNA viruses relevant to the lung. This project is designed to be a combination of discovery/hypothesis-generating science as well as specific hypothesis-testing studies as outlined in RFA HL-17-002, which we anticipate will provide novel insight into the nature of the virome within the lungs, and role in lung health and disease.