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

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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.