Unknown,Transcriptomics,Genomics,Proteomics

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Irisin is a Pro-Myogenic Factor that Induces Skeletal Muscle Hypertrophy and Rescues Denervation-Induced Atrophy

ABSTRACT: C2C12 myoblasts were seeded at a density of 25,000 cells/cm2 in a 10cm cell culture dish and differentiated with low serum differentiation medium at 37 °C, 5% CO2 for 72h and further treated with either DB or recombinant Irisin protein (1000ng/ml) for 6h, 12h, 24h and 48h. Myotubes were resuspended in 2ml of TRIzol ® for each 10cm dish and RNA isolation was performed according to the manufacturer s protocol. Purified isolated RNA was then subjected to Illumina bead array sequencing and data analysis, as per in-house protocols (Sciencewerke, Singapore). Only genes that were upregulated or downregulated by 1.5-fold were considered significant. For genes that had multiple probes (with different accession number), only one probe with the highest upregulation or downregulation was taken into consideration.

ORGANISM(S): Mus musculus

SUBMITTER: MUSARRAT MAISHA REZA

PROVIDER: E-MTAB-6024 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Enhanced understanding of differential gene expression and biological pathways associated with distinct phases of intramembranous bone regeneration following femoral marrow ablation surgery will improve future advancements regarding osseointegration of joint replacement implants, biomaterials design, and bone tissue engineering. A rat femoral marrow ablation model was performed and genome-wide microarray data were obtained from samples at 1, 3, 5, 7, 10, 14, 28, and 56 days post-ablation, with intact bones serving as controls at Day 0. Bayesian model-based clustering produced eight distinct groups amongst 9,062 significant gene probe sets based on similar temporal expression profiles, which were further categorized into three major temporal classes of increased, variable, and decreased expression. Differential biological processes and pathways associated with each major temporal group were identified, and significantly expressed genes involved were visually represented by heat maps. It was determined that the increased expression group exclusively contains genes involved in pathways for matrix metalloproteinases (MMPs), Wnt signaling, TGF-Î² signaling, and inflammatory pathway. Only the variable expression group contains genes associated with glycolysis and gluconeogenesis, Notch Signaling Pathway, natural killer cell mediated cytotoxicity, and B cell receptor signaling pathway, among others. The decreased group exclusively consists of genes involved in heme biosynthesis, p53 signaling pathway, and hematopoietic cell lineage. Significant biological pathways and transcription factors expressed at each time point post-ablation were also identified. These data present the first temporal gene expression profiling analysis of the rat genome during intramembranous bone regeneration induced by femoral marrow ablation. In an Institutional Animal Care and Use Committee (IACUC) approved study, 27 adult male rats (Sprague Dawley, 400-425 g) were divided into nine groups: intact control (0 day), and 1, 3, 5, 7, 10, 14, 28, and 56 days post marrow ablation. Twenty-four animals received unilateral femoral ablation. At each time point, animals were killed in a carbon dioxide chamber, and whole femurs were harvested and denuded of soft tissue. For three samples per time point, both the distal and proximal ends of the femurs were cut off in order to exclude the epiphyses and growth plate regions. Diaphyseal marrow tissue and cells from the mid-shaft were flushed out using TrizolÂ®. Extracted RNA was homoginized and was prepared for hybridization. For each of the three samples per time point, gene expression was analyzed with GeneChipÂ® Rat Genome 230 2.0 Arrays (Affymetrix, Santa Clara, CA).

Dataset Information

Irisin is a Pro-Myogenic Factor that Induces Skeletal Muscle Hypertrophy and Rescues Denervation-Induced Atrophy

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