Monitoring the aging lung using genomics, proteomics and informatics

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密不可分 以及它的功能。折叠和功能与细胞的能量健康紧密相连。这是通过 细胞功能(DNA、RNA和蛋白质)与蛋白质动态平衡协调的新兴范例 蛋白质平衡，一组产生、维持和修复蛋白质组的综合生物途径。 上一次资助期间的努力揭示了蛋白质调节敏感途径和 线粒体在衰老肺的管理中，对延长寿命的药物反应的途径 二甲双胍被认为影响线粒体复合体I的功能，以及ISRIB，我们的初步研究 数据表明，在各种损伤模型中，加速肺修复。 在核心B中，我们将定量跟踪从甲型流感诱导的组织中恢复过程中蛋白质平衡的变化 用整体和单细胞RNA-Seq、空间转录组分和严格质谱学研究损伤 (Ms)接近。我们将把这些方法应用于高质量的流式细胞术分选的肺、骨骼样本 由Core C提供的老龄小鼠的肌肉和脑组织。我们在西北大学和 斯克里普斯研究公司通过共享的电子平台自由互动。他们将使用这些数据来创建多个- 对老年动物从甲型流感感染中恢复受损的维度的理解。核心B将 将这些强大的技术与研究人员建议进行的遗传和药理学研究结合起来 操纵线粒体复合体I的功能，整合的应激反应和ATF4在整个生命周期。我们会 通过关注三个具体目标来支持这些关于衰老生物学的重要研究： 目标1：使用流分类提供批量和单细胞RNA-Seq和空间转录数据 由Core C提供的细胞群体和均质组织。 目的2：提供流动分选细胞群的质谱分析 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 衰老过程中的药物干预：来自老龄动物的多组学实验数据。 虽然在这个核心中使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内，专注于蛋白质平衡、巨噬细胞生物学和整个生命周期的新陈代谢。 通过提供肺泡II型细胞、肺泡巨噬细胞、 我们将创建衰老过程中损伤后组织恢复的多组基因到表型图谱 将广泛适用于限制健康寿命的其他环境挑战。

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.