The Lung DNA Virome in Health and Disease

翻译后摘要：肺DNA病毒在健康和疾病 我们生活在一个相互依存的关系与我们的居民微生物群，这强烈影响人类健康 和疾病微生物群落在不同的身体部位不同，并在每个部位有不同的结果。 人类和他们的微生物之间的关系已经被最广泛的研究为我们的细菌 但对人类病毒组，特别是呼吸道病毒组的了解要少得多。 在初步研究中，我们使用鸟枪宏基因组学来研究几个受试者组中的肺病毒组。 我们建立了有效的纯化病毒颗粒的方法和序列的计算方法， assembly & taxonomic assignment.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Tenoviruses（TTV），这是一种具有极端 我们发现了一组新的小型环状DNA病毒，与任何 先前描述的病毒（我们称之为“人类圆环相关病毒”; HCRV）。据了解，血液中的TTV TTV是在有效的宿主免疫控制下，但无论是控制TTV的细胞免疫反应， 已经研究了肺特异性调节。自从我们鉴定出肺特异性HCRV以来， 他们第一次来到这里。这些发现突出了当前知识的主要差距：肺及其组织如何与其他组织发生关系？ 无处不在的病毒群落相互作用并相互影响，特别是大量的小单 搁浅的DNA病毒吸烟是造成肺损伤的主要原因之一，它的影响是什么？这些是 病毒和宿主对它们的免疫应答导致肺损伤和/或炎症， 疾病？为了加速对肺部病毒组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：为进一步发展奠定基础，我们将（1）确定TTV的分布 （2）来自严重肺病受试者的呼吸道样品中的HCRV（“极端表型”）; 生成和查询肺病毒组宏基因组数据集，以获得更多共享的新型呼吸道DNA病毒 （3）开发一种新的“个性化”的T细胞免疫应答评估， 高变TTV，并接近HCRV免疫应答;（4）产生支气管肺泡病毒库， 代表肺部疾病的灌洗（BAL）标本，在第2阶段进行病毒组和免疫分析。 第2阶段（R33）3-5年：我们将（1）定义肺病毒组成分和病毒组之间的关系- 目标免疫反应，和肺部疾病的高度优先;（2）确定吸烟的影响 肺病毒组和血浆病毒组，以及病毒组靶向免疫反应;（3）定义了 HCRV、TTV及其他与肺相关的小DNA病毒。 该项目旨在将发现/假设生成科学与特定的 RFA HL-17-002中概述的假设检验研究，我们预计这些研究将为 肺内病毒组的性质以及在肺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.