Transcription factors associated with regulation of transcriptome in human thigh and calf muscles at baseline and after six days of disuse

Disuse has a negative impact on the postural muscles of the trunk and legs. Different leg muscles demonstrate a differentiated and conservative response to disuse, in terms of a decrease in muscle mass, strength, aerobic performance, and changes in gene expression. We aimed to identify transcription factors regulating gene expression at baseline and after disuse in human m. soleus – a “slow” muscle with a strong postural function, and “mixed“ m. vastus lateralis. Biopsies were taken from these muscles prior to and after 6 days of strict disuse (dry immersion). The enriched transcription factor binding sites (and corresponding factors) in the individual promoter regions of co-expressed genes were examined using the positional weight matrix approach. The baseline transcriptomic profiles and the disuse-induced changes (RNA-seq) differ significantly between muscles. In particular, the specific and significant response to disuse in m. soleus was found to be strongly related to the suppression of genes regulating the mitochondrial energy metabolism, the activation of the inflammatory response and the ubiquitin-proteasome system. This response is associated with the proinflammatory transcription factors such as families IRF, STAT, and other. The validity of approximately two-thirds of the predicted transcription factors was indirectly confirmed by the analysis of their function described in the literature. These identified transcription factors appear to be promising candidates for future targeted studies that mechanistically investigate gene expression regulation in various muscles at baseline, following disuse or inactivity. Overall design: Ten males participated in a 7-day dry immersion (DI, ages 25–38 years; median height 1.78 m [interquartile range 1.71–1.79 m]; body mass 70 kg [64–74 kg]; and body mass index 24 kg/m² [21–24 kg/m²]). Muscle samples were taken using a Bergström needle with aspiration under local anesthesia (2 ml of 2% lidocaine) from the medial part of m. vastus lateralis (Vas) and m. soleus (Sol) muscles of the left leg 14 days before the start of DI (prior to any familiarization protocols and physiological tests, which did not included in the paper) and 6 days after the start of 7-day DI (at 10:00, 3 hours after a standardized light breakfast: 5.2 g protein, 2.7 g fat, 55 g carbohydrates, 1253 kJ). Strand-specific RNA libraries were prepared using the NEBNext Ultra II RNA kit (New England Biolabs, USA) and single-end sequencing was done by a NextSeq 550 analyzer (Illumina, USA).