Multi-omics analysis of human skeletal muscle in response to acute exercise: initial insights from MoTrPAC

The Molecular Transducers of Physical Exercise Consortium (MoTrPAC) was established to deeply and systematically characterize the molecular basis of exercise through integrative, multi-omics analysis of tissues obtained from rats and human participants1. For the clinical study, sedentary participants were recruited and randomized into endurance exercise (EE), resistance exercise (RE) and control (CON) groups. Vastus lateralis muscle biopsies were collected before a sub maximal acute bout of either EE or RE and at one of several time points after following the acute bout (30min, 3.5h, and 24h). Tissue collection was performed in the CON group at the same time points, but without exercise. Muscle tissue samples were analyzed by ATAC-seq, transcriptomics, proteomics, phosphoproteomics and metabolomics, with the goal of identifying dynamic molecular changes in response to an acute bout of EE or RE including divergent molecular responses between the two modes of exercise.

Data QC and differential analysis for all omes were performed using limma and variancePartition packages in R2, respectively. For differential analysis, a linear mixed model was used with participant as the random effect, timepoint-exercise intervention as an interaction term and sex, age, clinical site, and BMI as covariates. Exercise intervention groups (EE and RE) were compared to matched timepoint CON values to identify significantly changed features.

Initial multi-omics analysis of an acute bout of exercise showed divergent behavior of different omes throughout the time course. Maximal changes in ATACseq, phosphoproteome and metabolome occur earlier (30min) than changes in the transcriptome (3.5h) and proteome (3.5h and 24h). Furthermore, the proportion of genes with annotated differentially accessible regions (DARs) based on ATACseq that are also differentially regulated genes (DEGs) in the RNAseq data overlap significantly, especially at the later time points (3.5h and 24h), suggesting a time delay between chromatin remodeling and gene expression. Additionally, PTM signature enrichment analysis, using PTM-SEA3 of the phosphoproteome data, shows enrichment of many kinase signatures, more pronounced after RE than EE. These include several MAPK kinase signatures following an acute bout of either exercise mode, consistent with prior findings4. Some overlap of omic dynamics is observed between changes in EE and RE; however, there is a considerable difference in magnitude of changes between modes of exercise, with RE resulting in a greater number of changed features. These MoTrPAC data provide initial insights into the multi-omic exercise responses in human skeletal muscle highlighting a dynamic and varied time course across the omes with common and specific signatures between EE and RE.