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

摘要 有规律的锻炼(体力活动)是促进健康和对抗非 传染病(NCD)。但是，我们对分子(S)的理解是高超的 锻炼的好处是不清楚的。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” 协会(MoTrPAC)是一项大规模的发现研究，旨在了解 运动训练，已经发布了包括RNA-seq在内的第一批多组学数据，减少了 代表亚硫酸盐测序、蛋白质组学、磷酸蛋白质组学、乙酰化蛋白质组学，以及靶向和 非靶向代谢组学，从大鼠急性发作后不同时间点收集的5个组织 耐力锻炼。这些工作为进一步阐明分子传感器奠定了坚实的基础。 体力活动。我们最近在四个领域取得了重大进展，这使我们准备探索这些领域 数据，并以前所未有的方式阐明其机理(S)。具体地说，1)我们获得了类似的 急性和长期耐力运动后小鼠4种组织的时程、转录和转录数据 开发了机器学习能力，用于挖掘多组学数据，以识别 2)我们完善了CRISPR/Cas9介导的基因编辑，用于产生丢失- 功能敲入小鼠以及产生组织特异性的、可诱导的功能获得转基因技术 3)我们已经在小鼠身上建立了全面的表型分析；4)我们已经成功地 体液细胞外超氧化物歧化酶(EcSOD)的调节和功能研究体会 在骨骼肌中表达并由耐力运动促进的因子，在调节健康益处和 对疾病的保护。我们假设耐力运动可以促进一种物质的表达和释放 或来自一个或多个组织/器官的体液因子，这是充分和必要的调解 锻炼对健康的好处。为此，我们建议 1)采用基于机器学习的多组学建模方法，识别生理活动的候选分子换能器。 2)利用CRISPR/Cas9获得功能缺失、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)阐明运动的候选分子转导系统在运动对健康益处中的作用。 实验设计和模型系统在概念和技术上都是创新的。调查结果将 显著提高对运动诱导适应的机制理解，具有巨大的潜在影响 关于NCD治疗学的未来发展。

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.