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: 10264175
• 负责人: Zhen Yan
• 金额: $ 52.18万
• 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 2023-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10264175
• 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; Regulator Genes; 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; 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 定期锻炼（身体活动）是促进健康和对抗非健康的最有效的干预措施 然而，我们对导致传染性疾病（NCD）的分子的了解非常有限。 运动的好处并不明确。美国国立卫生研究院共同基金项目“身体活动的分子传感器”。 Consortium (MoTrPAC)”是一项大规模发现研究，旨在了解分子反应 运动训练，发布了第一批多组学数据，包括RNA-seq、Reduced 代表性亚硫酸氢盐测序、蛋白质组学、磷酸化蛋白质组学、乙酰蛋白质组学以及靶向和 非靶向代谢组学，来自大鼠急性发作后不同时间点收集的 5 个组织 这些努力为阐明分子传感器奠定了坚实的耐力基础。 我们最近在四个领域取得了重大进展，这使我们准备好探索这些领域。 数据并以前所未有的方式阐明机制具体来说，1）我们获得了类似的结果。 急性和长期耐力运动后小鼠 4 个组织的时间进程、转录组学数据 开发了机器学习能力，用于挖掘多组学数据，以识别监管因素 介导运动益处；2) 我们已经完善了 CRISPR/Cas9 介导的基因编辑，以产生损失- 功能敲入小鼠以及产生组织特异性、可诱导的功能获得转基因的技术 小鼠；3) 我们已经在小鼠中建立了全面的表型分析；4) 我们已经成功地进行了 阐明细胞外超氧化物歧化酶（EcSOD）的调节和功能的经验，EcSOD是一种体液 在骨骼肌中表达并通过耐力运动促进的因素，在调节健康益处和 我们勇敢地说，运动耐力可以促进一种物质的表达和释放。 来自一种或多种组织/器官的一种或多种体液因子，其对于调节 为此，我们建议运动对健康的好处。 1）通过基于机器学习的多组学建模来识别身体活动的候选分子传感器。 2) 使用 CRISPR/Cas9 生成功能缺失的敲入和组织特异性、功能获得的转基因小鼠 介导的基因编辑和转基因。 3) 阐明体力活动的候选分子传感器在运动对健康的益处中的作用。 实验设计和模型系统在概念和技术上都具有创新性。 显着提高对运动引起的适应的机制理解，具有巨大的潜在影响 关于非传染性疾病治疗方法的未来发展。