Expression data from untreated vs. BMP4-treated cultured wild-type and MuSK null muscle cells (myoblasts and myotubes)
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE59567 | GEO | 2015/08/03
SECONDARY ACCESSION(S): PRJNA255646
REPOSITORIES: GEO
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Project description:Bone morphogenic proteins (BMPs) function in virtually all tissues with cell-type specific outcomes. Since there are a relatively small number of BMP receptors this exquisite signaling specificity requires additional molecules to regulate the output of this pathway. We demonstrated that the receptor tyrosine kinase MuSK that is selectively expressed in muscle and plays a critical role in synapse formation and maintenance binds to BMP4 and related BMPs. Since BMPs regulate the transcription of a set of genes, we performed microarrays for wild-type and MuSK null muscle cells to test if MuSK regulates BMP responses in muscle cells. We shought to determine if MuSK regulates BMP responses in muscle cells and if the cell context made any difference in MuSK regulation of BMP pathway. To test this, expression profiles of untreated vs. BMP4-treated undifferentiated myoblast and differentiated myotube cultures were generated for both wild-type and MuSK-null genotypes. All conditions were done in triplicates. In total 24 arrays were analyzed.
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Project description:Myofiber size regulation is critical in health, disease, and aging. MuSK (muscle-specific kinase) is a BMP (bone morphogenetic protein) co-receptor that promotes and shapes BMP signaling that is expressed at all neuromuscular junctions and is also present extrasynaptically in the slow soleus muscle. To investigate the role of the MuSK-BMP pathway in vivo we generated mice lacking the BMP-binding MuSK Ig3 domain. These ∆Ig3-MuSK mice are viable and fertile with innervation levels comparable to wild type. In 3-month-old mice myofibers are smaller in the slow soleus, but not in the fast TA. Here we use bulk RNA-seq to perform transcriptomic analysis of slow and fast mouse muscle. RNAseq analysis revealed soleus-selective decreases in RNA metabolism and protein synthesis pathways as well as dysregulation of IGF1 pathway components. Moreover, Akt-mTOR signaling is reduced in soleus but not TA. We propose that the MuSK-BMP pathway acts extrasynaptically to maintain myofiber size in slow muscle by promoting protein synthetic pathways including the IGF1-Akt-mTOR signaling. These results reveal a novel mechanism for regulating myofiber size in slow muscle and introduce the MuSK-BMP pathway as a target for promoting muscle growth and combatting atrophy.
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Project description:Satellite cells play an important role in post-natal growth and regeneration of skeletal muscle. They can be defined as a population adult muscle stem cells based on their self renewal capability and ability to differentiate into skeletal muscle fibers. Functional Retinoblastoma protein (pRb) is essential for the process of skeletal muscle differentiation in satellite cell derived primary myoblasts. Furthermore, the biochemical function of pRb is largely associated with its ability to interact with chromatin modifying factors such as histone deacetylases (HDACs) and histone methyltransferases thus inhibiting transcription of target gene promoters. Hence, expression profiling of pRb null primary myoblasts and myotubes will provide a global picture of the downstream targets of pRb transcriptional regulation in relation to cell cycle control, apoptosis inhibition, and muscle differentiation. Keywords: other
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Project description:During the last decade, skeletal muscle-secreted proteins have been identified with important roles in intercellular communications. To investigate whether muscle-derived exosomes participate in this molecular dialog, we determined and compared the protein contents of the exosome-like vesicles (ELVs) released from C2C12 murine myoblasts during proliferation (ELV-MB), and after differentiation into myotubes (ELV-MT). Using a proteomic approach combined with electron microscopy, western-blot and bioinformatic analyses, we compared the protein repertoires within ELV-MB and ELV-MT. RAW files were processed using MaxQuant [28] version 1.3.0.3. Spectra were searched against the Uniprot database (August 2012 version, Mus musculus taxonomy 10090, 86644 sequences, Bos taurus taxonomy 9913, 34280 sequences and Equus caballus taxonomy 9796, 24299 sequences) and the frequently observed contaminants database (notably containing protein sequences from serum proteins) embedded in MaxQuant. Trypsin was chosen as the enzyme and 2 missed cleavages were allowed. Precursor mass error tolerances were set respectively at 20 ppm and 6 ppm for first and main searches. Fragment mass error tolerance was set to 0.5 Da. Peptide modifications allowed during the search were: trioxidation (C, fixed), acetyl (N-ter, variable), dioxidation (M, variable), oxidation (M, variable) and deamidation (NQ, variable). Minimum peptide length was set to 7 amino acids. Minimum number of peptides, razor+unique peptides and unique peptides were set respectively to 2, 2 and1. Maximum false discovery rates - calculated by employing a reverse database strategy - were set to 0.01 at peptide and protein levels.
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Project description:Bone morphogenetic proteins (BMPs) are members of the TGF-β superfamily of growth factors. They are known for their roles in regulation of osteogenesis and developmental processes and, in recent years, evidence has accumulated of their crucial functions in tumor biology. BMP4, in particular, has been implicated in breast cancer. However, little is known about BMP target genes in the context of tumor. We therefore explored the effects of BMP4 treatment on global gene transcription in five breast cancer cell lines during a 6-point time series. Data analysis included hierarchical clustering of differentially expressed genes, gene ontology enrichment analyses and model based clustering of temporal data. BMP4 had a strong effect on gene expression. The cellular functions most strongly affected were regulation of transcription and development. The observed transcriptional response, as well as its functional outcome, followed a temporal sequence, with regulation of gene expression and signal transduction leading to changes in metabolism and cell proliferation. Hierarchical clustering revealed distinct differences in the response of individual cell lines to BMP4, but also highlighted a synexpression group of genes. Finally, this study provides a list of potential novel BMP target genes relevant in breast cancer. Two-condition experiment, vehicle-treated vs. BMP4-treated. Five cell lines were tested at six time points each, what makes a total of 30 samples. RNA samples from three biological replicates were pooled before hybridization.
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