Temporal dynamics of the multi-omic response to endurance exercise training

Regular exercise offers substantial health benefits, reducing mortality risk and the incidence of numerous chronic diseases. These benefits stem from molecular and cellular adaptations across multiple organ systems. While various 'omics' approaches have been used to study these adaptations, most investigations have focused on single time points, limited tissue types (often skeletal muscle, heart, or blood), or a single sex. To obtain a comprehensive understanding of exercise's effects, a whole-organism, multi-omic analysis is crucial. The Molecular Transducers of Physical Activity Consortium (MoTrPAC) aims to build a molecular map of the exercise response across multiple tissues. This study presents the first whole-organism multi-omic map of temporal effects from endurance exercise training in male and female rats, providing insights enabled by the MoTrPAC data resource.

Previous research using 'omics' techniques has often been limited in scope, focusing on a single tissue (e.g., skeletal muscle, heart, or blood), a single 'ome' (e.g., transcriptomics), or a single sex. These studies have provided valuable information, but a comprehensive, organism-wide perspective is lacking. This study builds upon previous findings, offering a more complete view by employing a multi-tissue, multi-omic, and longitudinal approach.

Six-month-old male and female Fischer 344 rats underwent progressive treadmill endurance training for 1, 2, 4, or 8 weeks. Tissues (whole blood, plasma, and 18 solid tissues) were collected 48 hours post-training. A wide range of molecular assays were conducted, including transcriptomics, proteomics (global protein expression, phosphorylation, acetylation, ubiquitination), metabolomics, lipidomics, epigenomics (DNA methylation and chromatin accessibility), and immunomics. Differential analysis identified thousands of training-regulated features across tissues and 'omes'. Pathway enrichment analysis was used to determine biological pathways affected by training. Transcription factor and phosphosignaling activity were inferred using relevant data. Graphical clustering was employed to identify features with similar temporal responses. Finally, the findings were compared to existing human studies and disease ontology annotations to assess translational value.

The study generated a vast dataset encompassing 9,466 assays across 19 tissues and 25 molecular platforms. Thousands of shared and tissue-specific molecular alterations were observed, with notable sex differences. Key findings include: * **Widespread molecular changes:** The study revealed extensive training-induced changes in multiple tissues and 'omes', demonstrating the organism-wide nature of adaptations to endurance training. * **Tissue-specific responses:** Many tissue-specific adaptations were identified, with notable differences in responses across tissues. For example, the lung showed immune cell recruitment and remodeling, while the liver showed cofactor and cholesterol biosynthesis changes. * **Multi-tissue responses:** Significant numbers of genes were differentially regulated in multiple tissues. Lung and white adipose tissue shared a significant number of genes, mainly related to immune responses. Heart and gastrocnemius exhibited shared genes associated with mitochondrial metabolism. Twenty-two genes were consistently regulated across all six tissues examined, demonstrating a common response to exercise training. * **Heat shock response:** The study revealed a robust and ubiquitous up-regulation of heat shock proteins (HSPs) across tissues, likely contributing to cytoprotection. * **Transcription factor activity:** Analysis of transcription factors revealed tissue-specific enrichments. In the blood, haematopoietic-associated transcription factors were enriched, while the heart and skeletal muscle showed enrichment of Mef2 family transcription factors. * **Phosphosignaling changes:** Extensive changes in phosphorylation signatures were observed across many tissues, including key kinases such as AKT1, mTOR, and MAPK. The liver showed increased phosphosignatures related to hepatic regeneration. * **Mitochondrial adaptation:** Mitochondrial biogenesis was observed in skeletal muscle, heart, and liver, reflecting the well-known effects of exercise on energy metabolism. * **Sex differences:** Significant sex differences were identified across various tissues and 'omes', underscoring the importance of considering sex in exercise responses. * **Immune response:** The study demonstrated sex-specific immune responses to exercise. In males, brown and white adipose tissue showed increased immune cell activity at week 8, while the small intestine showed reduced inflammatory responses in both sexes. * **Metabolic changes:** Extensive metabolic changes were observed across tissues, including changes in lipid metabolism, carbohydrate metabolism, and amino acid metabolism. The liver showed significant changes in lipid-related compounds and increased abundance and acetylation of proteins in the peroxisome. * **Translational relevance:** The rat data showed significant overlap with findings from human studies of exercise training, enhancing the translational potential of this work.

This large-scale multi-omic study provides a comprehensive map of molecular adaptations to endurance exercise training in rats. The findings support the well-established health benefits of exercise by revealing the underlying molecular mechanisms across multiple tissues and 'omes'. The discovery of shared responses across tissues and 'omes', as well as tissue-specific and sex-specific responses, highlights the complexity and interconnectedness of exercise-induced adaptations. The prominent up-regulation of heat shock proteins suggests a protective role against tissue damage. Sex differences in immune responses highlight the need for sex-specific exercise guidelines and research. The observed metabolic changes may shed light on the mechanisms by which exercise improves liver health and reduces the risk of chronic diseases such as non-alcoholic fatty liver disease and inflammatory bowel disease. The extensive overlap with human data enhances the translational value of these findings.

This study provides a comprehensive, organism-wide, multi-omic map of the temporal response to endurance exercise training in rats. The data revealed thousands of molecular changes across various tissues and 'omes', highlighting tissue-specific and sex-specific adaptations. The findings offer valuable insights into the mechanisms underlying exercise-induced health benefits and provide a valuable resource for future research exploring the effects of exercise on human health and disease.

The study's limitations include the use of a rat model, the collection of samples 48 hours post-exercise (excluding acute responses), the analysis of bulk tissue samples instead of single-cell analysis, limited 'omic' characterization in some tissues, and the absence of certain platforms, such as microbiome profiling. Additionally, many findings are hypothesis-generating and require further validation.