Machine learning-based multi-omics modeling and CRISPR/Cas9-mediated gene editing in elucidating molecular transducer of physical activity

基于机器学习的多组学建模和 CRISPR/Cas9 介导的基因编辑阐明身体活动的分子转导器

• 批准号: 10413230
• 负责人: Zhen Yan
• 金额: $ 8.46万
• 依托单位: UNIVERSITY OF VIRGINIA
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-30 至 2022-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10413230
• 关键词: Acute; Animals; Area; Biological; Biological Models; Blood Circulation; Brain; CRISPR/Cas technology; Cardiac; Cardiovascular system; Cessation of life; Cognition; Consumption; Data; Development; Disease; Endocrine; Exercise; Experimental Designs; Experimental Models; Fatty acid glycerol esters; Fibrinogen; Foundations; Funding; Future; Gene Transfer Techniques; Generations; Genes; Health; Health Benefit; Health Promotion; Health protection; Heart; Hippocampus (Brain); Human; Hypothalamic structure; Knock-in; Knock-in Mouse; Ligands; Liver; Liver Circulation; Longitudinal Studies; Machine Learning; Mediating; Metabolic; Metabolism; Metals; Mining; Modeling; Molecular; Multiomic Data; Mus; Muscle; Mutation; Neurodegenerative Disorders; Organ; Phenotype; Physical activity; Prevention; Proteins; Proteomics; Psyche structure; Rattus; Regulation; Research Design; Role; Site; Skeletal Muscle; Solid; Superoxide Dismutase; Techniques; Tetanus Helper Peptide; Time; Tissues; Transducers; Transgenes; Transgenic Mice; United States National Institutes of Health; autocrine; base; bisulfite sequencing; cognitive function; design; effective intervention; endurance exercise; exercise capacity; exercise training; experience; extracellular; gain of function; gene regulatory network; improved; innovation; loss of function; mental function; metabolomics; multidisciplinary; multiple omics; paracrine; phenotypic data; phosphoproteomics; pre-clinical; prevent; programs; receptor; response; skeletal; therapeutic development; therapeutically effective; transcriptome sequencing; transcriptomics

ABSTRACT Regular exercise (physical activity) is the most effective intervention that promotes health and combats non- communicable disease (NCD). However, our understanding of the molecule(s) responsible for the superb benefits of exercise is obscure. The NIH Common Fund project “Molecular Transducers of Physical Activity Consortium (MoTrPAC)” is a large-scale discovery study designed to understand the molecular responses to exercise training, which has released the first batch of multi-omics data, including RNA-seq, Reduced Representation Bisulfite Sequencing, proteomics, phosphoproteomics, acetylproteomics, and targeted and untargeted metabolomics, from 5 tissues collected at different time points in rats following an acute bout of endurance exercise. These endeavors have laid a solid foundation for elucidation of the molecular transducer of physical activity. We have recently made significant progress in four areas, which poised us to explore these data and elucidate the mechanism(s) in an unprecedented manner. Specifically, 1) We have obtained similar time-course, transcriptomics data in 4 tissues in mice following acute and long-term endurance exercise and developed machine learning capability for mining the multi-omics data for identification of regulatory factors that mediate the exercise benefits; 2) We have perfected CRISPR/Cas9-mediated gene editing for generation of loss- of-function knock-in mice as well as techniques to generate tissue-specific, inducible gain-of-function transgenic mice; 3) We have established comprehensive phenotypic analysis in mice; and 4) We have had a successful experience in elucidating the regulation and function of extracellular superoxide dismutase (EcSOD), a humoral factor expressed in skeletal muscle and promoted by endurance exercise, in mediating the health benefits and protection against diseases. We hypothesize that endurance exercise promotes expression and release of one or more humoral factors from one or multiple tissues/organs, which is sufficient and necessary mediating the health benefits of exercise. To this end, we propose 1) Identify candidate molecular transducers of physical activity by machine learning-based multi-omics modeling. 2) Generate loss-of-function knock-in and tissue-specific, gain-of-function transgenic mice using CRISPR/Cas9- mediated gene editing and transgenesis. 3) Elucidate the role of the candidate molecular transducers of physical activity in health benefits of exercise. The experimental design and model systems are both conceptually and technically innovative. The findings will significantly improve the mechanistic understanding of exercise-induced adaptations with great potential impact on the future development of therapeutics for NCD.

抽象的 定期运动（体育锻炼）是促进健康的最有效干预措施，并与非 - 传染病（NCD）。但是，我们对负责精湛的分子的理解 运动的好处是晦涩的。 NIH共同基金项目“体育锻炼的分子传感器 财团（MOTRPAC）”是一项大规模发现研究，旨在了解分子反应 锻炼训练已发布了包括RNA-seq在内的第一批多摩斯数据，减少了 代表硫酸盐测序，蛋白质组学，磷酸蛋白质组学，乙酰蛋白质组学和靶向和靶向 未靶向的代谢组学，来自在急性回合后在大鼠不同时间点收集的5个组织 耐力运动。这些努力为阐明分子传感器的稳固基础 体育锻炼。我们最近在四个领域取得了重大进展，这使我们毒化了这些 数据并以前所未有的方式阐明机制。具体来说，1）我们获得了相似的 急性和长期耐力运动和长期耐力运动后，小鼠4组织中的转录组学数据以及 开发的机器学习能力用于挖掘多摩斯数据，以识别监管因素 调解运动益处； 2）我们已经完善了CRISPR/CAS9介导的基因编辑，以产生损失 - 功能敲击小鼠以及产生组织特异性，功能障碍的转基因的技术 小鼠； 3）我们已经在小鼠中建立了全面的表型分析； 4）我们取得了成功 阐明细胞外超氧化物歧化酶（ECSOD）的调节和功能的经验，一种 在骨骼肌中表达的因素，并通过耐力运动促进，调解健康益处和 防止疾病。我们假设耐力运动促进了一个 或来自一个或多次/器官的更多体液因素，这足以介导 运动的健康益处。为此，我们提出了 1）通过基于机器学习的多词建模来确定候选体育活动的分子传感器。 2）使用CRISPR/CAS9-产生功能损失的敲入和组织特异性的转基因小鼠。 介导的基因编辑和转基因。 3）阐明了候选人体育活动中候选分子传感器在运动中的健康益处中的作用。 实验设计和模型系统在概念和技术上都是创新的。调查结果会 显着提高对运动引起的适应的机械理解，并具有很大的潜在影响 关于NCD理论的未来发展。