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Epigenomic and transcriptomic changes associate with skeletal muscle stem cells to myotube differentiation.

ABSTRACT: It is well established that differentiation of muscle stem cells to myotubes is associated with significant changes in transcriptional landscape orchestrated by distinct transcription factor networks and such a dramatic change is likely coincident with changes in chromatin accessibility. We utilized this technique to map chromatin accessibility and transcriptome changes at single cell upon differentiation of human muscle stem cells. Results of these studies showed that integrated ATAC-seq and RNA-seq identified 18 subclusters of cells. Subclusters 0, 2-5, 7, 9, 12 and 18 are part of one group of cells, whereas subclusters 1, 6, and 17 formed another subgroup. Subclusters 14 and 10 formed another group, whereas 11, 13 and 15 formed another group. Subcluster 8 formed another distinct group. Thus cells in hMuSCs could be subgrouped into five major clusters. These studies demonstrate heterogeneity in skeletal muscle cell population.

ORGANISM(S): Homo sapiens

PROVIDER: GSE208248 | GEO | 2023/05/03

REPOSITORIES: GEO

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Project description:Microgravity has a dramatic impact on human physiology, illustrated in particular with skeletal muscle impairment. A thorough understanding of the mechanisms leading to loss of muscle mass and structural disorders is necessary for the definition of efficient clinical and spaceflight countermeasures. We investigated the effects of long-term bed rest on transcriptome of soleus (SOL) and vastus lateralis (VL) muscles in healthy women (BRC group, n=8), and the potential beneficial impact of protein supplementation (BRN group, n=8) and of a combined resistance and aerobic training (BRE group, n=8). Gene expression profiles were obtained using an in-house made microarray containing 6681 muscles-relevant genes. A two-class statistical analysis was applied on the 2103 genes with consolidated expression. We identified 472 and 207 modified genes, respectively for SOL and VL in BRC group. Further clustering approaches, identifying relevant biological mechanisms or pathways, underlined five main subclusters. Three are composed almost of upregulated genes involved mainly in nucleic acid and protein metabolism, and two composed almost of downregulated genes involved in energy metabolism. Exercise countermeasure demonstrated a drastic compensatory effect, decreasing the number of differentially-expressed genes by 89 and 96% in SOL and VL. In contrast, nutrition countermeasure had a moderate effect and decreased the number of differentially-expressed genes by 40 and 25% in SOL and VL. Our results allowed reporting a systematic, global and comprehensive view of long-term woman muscle atrophy and brought new lights and insights for space environment and for women who undergo a long-term clinical bed rest. Biological samples were collected from Pre- and Post- bed rest (BR) soleus and vastus lateralis biopsies of each subject from the three groups (bed rest only: BRC; Exercise: BRE; Nutrition: BRN). six technical replicate values (2 duplicate hybridizations âa et bâ to chips with triplicate spots âxxxâ) were obtained for each skeletal muscle sample. Thus for each subject, 12 expression measurements (6 before BR and 6 after BR) were obtained for each muscle.

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Epigenomic and transcriptomic changes associate with skeletal muscle stem cells to myotube differentiation.

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