Genome-wide association between DNA methylation and fiber type composition in skeletal muscle
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ABSTRACT:
PROVIDER: PRJNA595969 | ENA |
REPOSITORIES: ENA
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Project description:Association study between gene expression and fiber type composition in skeletal muscle
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2016-04-01 | E-GEOD-67803 | biostudies-arrayexpress
Project description:Skeletal muscle is a heterogeneous tissue consisting of blood vessels, connective tissue, and muscle fibers. The last are highly adaptive and can change their molecular composition depending on external and internal factors, such as exercise, age, and disease. Thus, examination of the skeletal muscles at the fiber type level is essential to detect potential alterations. Therefore, we established a protocol in which myosin heavy chain isoform immunolabeled muscle fibers were laser microdissected and separately investigated by mass spectrometry to develop advanced proteomic profiles of all murine skeletal muscle fiber types. Our in-depth mass spectrometric analysis revealed unique fiber type protein profiles, confirming fiber type-specific metabolic properties and revealing a more versatile function of type IIx fibers. Furthermore, we found that multiple myopathy-associated proteins were enriched in type I and IIa fibers. To further optimize the assignment of fiber types based on the protein profile, we developed a hypothesis-free machine-learning approach (available at: https://github.com/mpc-bioinformatics/FiPSPi), identified a discriminative peptide panel, and confirmed our panel using a public data set.
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Project description:Skeletal muscle is a complex heterogeneous tissue comprised of diverse muscle fiber and non-fiber cell types that, in addition to movement, influences other systems such as immunity, metabolism and cognition. We investigated gene expression patterns of resident human skeletal muscle cells using both single-cell RNA-seq and RNA-seq of single muscle fiber dissections from vastus lateralis. We generated transcriptome profiles of the major multinucleated human skeletal muscle fiber-types as well as 11 human skeletal muscle mononuclear cell types, including immune, endothelial, pericyte and satellite cells. We delineated two fibro-adipogenic progenitor cell subtypes that may contribute to heterotopic ossification and muscular dystrophy fibrosis under pathological conditions. An important application of cell type signatures is for computational deconvolution of cell type specific gene expression changes using data from bulk transcriptome experiments. Analysis of transcriptome data from a 12 week resistance exercise training study using these human skeletal muscle cell-type signatures revealed significant changes in specific mononuclear cell-type proportions related to age, sex, acute exercise and training. This characterization of human skeletal muscle cell types will resolve cell-type specific changes in large-scale physical activity muscle transcriptome studies and can further the understanding of the diverse effects of exercise and the pathophysiology of muscle disease.
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Project description:Skeletal muscle is composed of both slow-twich oxidative myofibers and fast-twitch glycolytic myofibers that differentially impact muscle metabolism, function, and eventually whole-body physiology. In the present study, we find that the mesodermal transcription factor T-box 15 (Tbx15) is highly and specifically expressed in glycolytic myofibers. Ablation of Tbx15 in vivo leads to a decrease in muscle size due to a decrease in the number of glycolytic fibers, associated with a small increase in the number of oxidative fibers. This shift in fiber composition results in muscles with slower myofiber contraction and relaxation, and also results in decreased whole-body oxygen consumption, decreased spontaneous activity, increased adiposity, and glucose intolerance. In order to identify genes regulated by Tbx15, we utilized C2C12 myoblasts with either a stable retroviral over-expression or stable lentiviral knockdown of Tbx15. RNA was extracted and biotin labelled complementary RNA (cRNA) was prepared from three independent transfections of the four stable C2C12 myoblast cell lines: shTbx15, shGFP, pBABE-Empty-puro, pBABE-Tbx15-puro. Cells were collected at 90% confluency, and subjected to microarray analysis. Affymetrix M430 2.0 Chips were used.
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