Monitoring the aging lung using genomics, proteomics and informatics

利用基因组学、蛋白质组学和信息学监测肺部老化

• 批准号: 10620762
• 负责人: Alexander Misharin
• 金额: $ 37.07万
• 依托单位: NORTHWESTERN UNIVERSITY AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-07-01 至 2025-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10620762
• 关键词: Acceleration; Aging; Alveolar Macrophages; Animals; Award; Biological; Biology; Biology of Aging; Brain; Cell Separation; Cell physiology; Cells; Collection; Complex; Coupled; DNA; Data; Data Set; Dimensions; Disease; Electronics; Environment; Flow Cytometry; Funding; Funding Opportunities; Genetic; Genetic study; Genomics; Genotype; Health; Human; Impairment; Infection; Influenza A virus; Informatics; Injury; Instruction; Intervention; Link; Longevity; Lung; Lung diseases; Machine Learning; Macrophage; Mass Spectrum Analysis; Membrane; Metabolism; Metformin; Methods; Microglia; Mitochondria; Modeling; Monitor; Mus; Muscle; Muscle satellite cell; Pathway interactions; Patients; Pharmaceutical Preparations; Pharmacology Study; Phenotype; Pneumonia; Population; Protein Biosynthesis; Proteins; Proteome; Proteomics; Protocols documentation; Publishing; RNA; Recovery; Research; Research Personnel; Sampling; Science; Signal Transduction; Skeletal Muscle; Sorting; Stress; Structure of parenchyma of lung; System; Technology; Tissue Harvesting; Tissues; aged; alveolar type II cell; biological adaptation to stress; brain tissue; data integration; healthspan; injury recovery; lung health; lung repair; mouse model; multiple omics; novel; pharmacologic; protein complex; protein folding; proteostasis; repaired; response; single-cell RNA sequencing; skeletal tissue; tissue injury; tissue mapping; tool; transcriptome sequencing; transcriptomics

ABSTRACT_CORE B The long-term health of the lung and other tissues is inextricably linked to the sustainability of the protein fold and its function. Fold and function are tightly coupled to the energetic health of the cell. This is achieved by the emerging paradigm of harmonization of cell function (DNA, RNA and protein) with protein homeostasis or proteostasis, a collection of integrated biological pathways that generate, maintain and repair the proteome. Efforts in the previous funding period revealed the importance of both proteostasis sensitive pathways and the mitochondria in management of the aging lung, pathways that are responsive to the life-span extending drug metformin that is thought to impact the function of mitochondrial complex I, and ISRIB, which our preliminary data suggests accelerates lung repair in a variety of injury models. In Core B, we will quantitatively track changes in proteostasis during recovery from influenza A-induced tissue injury using integrated bulk and single cell RNA-Seq, spatial transcriptomics and rigorous mass spectrometry (MS) approaches. We will apply these approaches to high quality flow cytometry sorted samples of lung, skeletal muscle and brain tissue from aged mice provided by Core C. Our computational groups at Northwestern and Scripps Research interact freely via shared electronic platforms. They will use these data to create a multi- dimensional understanding of the impaired recovery from influenza A infection in older animals. Core B will couple these powerful technologies with the genetic and pharmacologic studies the investigators propose to manipulate mitochondrial complex I function, the integrated stress response and ATF4 over the lifespan. We will support these important studies in aging biology by focusing on three Specific Aims: Aim 1: To provide bulk and single cell RNA-Seq and spatial transcriptomic data using flow-sorted cell populations and homogenized tissues provided by Core C. Aim 2: To provide mass spectroscopy analyses from flow-sorted cell populations obtained from the lung, brain and skeletal muscle of aged animals. Aim 3. To use advanced machine learning and system science tools to couple genetic and pharmacologic interventions during aging with multi-omic experimental data from aging animals. While the methods employed in this Core are inherently unbiased, we take advantage of the special expertise within this Core and the PPG to focus on proteostasis, macrophage biology and metabolism over the lifespan. By providing simultaneous RNA-Seq and proteomic analysis of alveolar type II cells, alveolar macrophages, Core B we will create a multi-omic genotype to phenotype map of tissue recovery after injury during aging that will be broadly applicable to other environmental challenges that limit healthspan.

摘要_核心 B 肺和其他组织的长期健康与蛋白质折叠的可持续性有着千丝万缕的联系 及其功能。折叠和功能与细胞的能量健康紧密相关。这是通过以下方式实现的 细胞功能（DNA、RNA 和蛋白质）与蛋白质稳态协调的新兴范式或 蛋白质稳态，生成、维持和修复蛋白质组的综合生物途径的集合。 上一个资助期的努力揭示了蛋白质稳态敏感途径和 线粒体管理衰老的肺部，对延长寿命的药物有反应的途径 二甲双胍被认为会影响线粒体复合物 I 和 ISRIB 的功能，我们初步 数据表明，可以加速各种损伤模型中的肺部修复。 在核心 B 中，我们将定量跟踪甲型流感诱导的组织恢复过程中蛋白质稳态的变化 使用集成的批量和单细胞 RNA-Seq、空间转录组学和严格的质谱分析来检测损伤 （MS）方法。我们将把这些方法应用于高质量流式细胞仪分选的肺、骨骼样本 Core C 提供的老年小鼠的肌肉和脑组织。我们西北大学和 斯克里普斯研究中心通过共享电子平台自由互动。他们将使用这些数据来创建一个多 对老年动物甲型流感感染恢复受损的维度理解。核心B将 将这些强大的技术与研究人员建议的遗传和药理学研究结合起来 在整个生命周期中操纵线粒体复合物 I 功能、综合应激反应和 ATF4。我们将 通过关注三个具体目标来支持衰老生物学的这些重要研究： 目标 1：使用流式排序提供批量和单细胞 RNA 测序和空间转录组数据 Core C 提供的细胞群和均质组织。 目标 2：对从以下来源获得的流式分选细胞群进行质谱分析 老年动物的肺、脑和骨骼肌。 目标 3. 使用先进的机器学习和系统科学工具将遗传和 利用衰老动物的多组学实验数据对衰老过程进行药物干预。 虽然本核心中采用的方法本质上是公正的，但我们利用了特殊的专业知识 在这个核心和 PPG 中，重点关注蛋白质稳态、巨噬细胞生物学和整个生命周期的新陈代谢。 通过同时提供肺泡 II 型细胞、肺泡巨噬细胞的 RNA 测序和蛋白质组学分析， 核心 B 我们将创建衰老过程中损伤后组织恢复的多组学基因型到表型图 将广泛适用于限制健康寿命的其他环境挑战。