Endurance exercise reduces the risk of metabolic diseases by improving skeletal muscle metabolism, particularly in individuals with overweight and obesity. As biological sex impacts glucose and fatty acid handling in skeletal muscle, we hypothesized sex differences at the transcriptomic and proteomic level in the acute response to exercise and after an 8-week exercise intervention.

We analyzed skeletal muscle biopsies from 25 sedentary subjects (16f/9m) with overweight and obesity using transcriptomics and proteomics at baseline, after acute exercise, and following an 8-week endurance training program. Regulation of sex-specific differences was studied in primary myotubes from the donors.

At baseline, differences were dominated by higher abundance of transcripts and proteins regulating glycogen degradation, glycolysis and other fast-twitch fiber type proteins in males. Females showed higher abundance of proteins regulating fatty acid uptake and storage. Differentially methylated CpG-sites potentially explained up to 60% of transcriptomic and 80% of proteomic sex differences. Acute exercise induced stress-responsive transcripts and plasma myoglobin predominantly in males. Both sexes adapted to 8-week endurance training by upregulating mitochondrial proteins involved in TCA cycle, oxidative phosphorylation, and β-oxidation. Training equalized fast-twitch fiber type protein levels, mainly by reducing them in males. In vivo sex differences in autosomal genes were poorly retained in myotubes but partially restored by sex hormone treatment.

In conclusion, the sex-specific molecular profiles underpin differences in glucose and fatty acid metabolism in female and male skeletal muscle. After just 8 weeks, training attenuates skeletal muscle sexual dimorphism towards a common metabolically beneficial response.