Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptional regulation of cellular processes important in control of skeletal myogenesis by interferon-M-NM-3

ABSTRACT: The purpose of the study was to investigate the effect of IFN-M-NM-3 on transcriptomic profile of differentiating mouse C2C12 myogenic cells. Global gene expression was evaluated using the oligonucleotide whole mouse genome microarrays and was validated with real-time PCR method. Exogenous IFN-M-NM-3 (1 ng/ml) increased myoblast proliferation, but decreased cell viability, the fusion index and the cellular content of myosin heavy chain, MyHC in C2C12 cultures on the 3rd day of differentiation. IFN-M-NM-3 up-regulated genes were mainly involved in biological processes such as: cell cycle, regulation of cell proliferation, programmed cell death, inflammatory, vasculature development, regulation of cytokine, transmembrane receptor protein tyrosine kinase signaling pathway, and chemotaxis, whereas down-regulated genes contributed mainly to: regulation of transcription, cell-cell signaling, nitrogen compound biosynthetic process, transmembrane receptor protein ser/thr protein kinase signaling pathway, and regulation of Wnt receptor signaling pathway. IFN-M-NM-3 up-regulated the expression of cytokines/growth factors controlling cell proliferation (Cxcl10, Il15, Ccl2, Fgf7, Figf, Csf1, Vegfc, Hgf). Moreover, IFN-M-NM-3: i) down-regulated genes encoding factors that are anabolic for muscle cells (Fst, Igf-1); ii) inhibited pro-myogenic transcription (via Mef2a, Nfkb1, and Pparg); iii) decreased expression of genes controlling cell adhesion and sarcolemma/cytoskeleton organization; and iv) activated the proteolytic pathways: proteasomes and catepsins, leading to protein degradation and impaired myotube growth. Our data suggest that the effect of IFN-M-NM-3 on mygenesis is, at least partly, associated with the regulation of muscle cell secretom at the transcriptional level. To whom the correspondence should be addressed: Dr K. Grzelkowska-Kowalczyk; e-mail: k_grzel_kow@poczta.fm, tel/fax: (48 22) 847 24 52 After scanning of hybridized microarrays, quantitation of slide images was performed using Feature Extraction Software (Agilent) using default parameters and the raw data were exported to GeneSpring GX 12 (Agilent, Santa Clara, CA) and log2 transformed. For identification of genes significantly altered in cell compared with the control normal gene set, total detected entities were filtered by flags (present, marginal) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with IFNG (IFNG vs CTRL 1-4) was used t-test unpaired (p < 0.05) with multiple testing correction: Benjamini-Hochberg <0.05, all significant changes over fold change 2 were selected. Analysis of GO, GSEA and signaling pathway was carried out using GeneSpring GX 12 (Agilent) and the DAVID Classification System (p<0.05).

ORGANISM(S): Mus musculus

SUBMITTER: Zofia Wicik

PROVIDER: E-GEOD-53392 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:High-fat diet or exposure to saturated fatty acids affects skeletal muscle growth and function. The aim of the present study was to investigate the effect of palmitate on the transcriptomic profile of mouse C2C12 myoblasts. Global gene expression was evaluated using whole mouse genome oligonucleotide microarrays, and the results were validated through real-time PCR. A total of 4047genes were identified as differentially expressed, including 3492 down-regulated and 555 up-regulated genes during 48-h-exposure to palmitate (0.1 mmol/l). Functional classification showed the involvement of PA-regulated genes in several processes which regulate cell growth. In conclusion, palmitate modifies the expression of genes associated with: i) myoblast responsiveness to hormones and growth factors, ii) cytokine and growth factor expression, and iii) regulation of cell-cell cell-matrix communication. Such alterations can affect myoblast growth and differentiation, however further studies in this field are required. To whom the correspondence should be addressed: Dr K. Grzelkowska-Kowalczyk; e-mail: k_grzel_kow@poczta.fm, tel/fax: (48 22) 847 24 52 After scanning of hybridized microarrays, quantitation of slide images was performed using Feature Extraction Software (Agilent) using default parameters and the raw data were exported to GeneSpring GX 12 (Agilent, Santa Clara, CA) and log2 transformed. For identification of genes significantly altered in cell compared with the control normal gene set. Total detected entities were filtered by flags (detected, non detected) and error (coefficient of variation: CV < 50.0 percent) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with palmitate acid was used t-test unpaired (p < 0.05) with multiple testing correction: Benjamini-Hochberg <0.05, all significant changes over fold change 1.6 were selected.

Project description:Background: Follistatin (FS) is an activin-binding glycoprotein, known for its antagonistic action on the TGF-M-NM-2 super-family of cytokines. It has ability to prevent muscle atrophy and to stimulate muscle growth through binding of myostatin (GDF8). FS does not cause these changes only by inhibition of GDF8 but this mechanism is still not well elucidated. In order to identify GDF8-dependent and GDF8-independent action of FS, we performed comprehensive transcriptomic analysis of differentiating C2C12 mouse myoblasts. Results: To evaluate influence of FS-288 (200ng/ml) on differentiating C2C12 myoblasts was used immunofluorescence analysis of MyHC protein expression in the culture and counting of the number and type of myotubes. Differentiating myoblasts treated with FS showed increase in number and size of myotubes. Microarray studies performed by us identified 30 genes oppositely regulated by FS and GDF8. Analyses of the transcriptomic profiles showed that FS has highly significant influence, associated with GDF8 binding, on the regulation of cell cycle, transport processes, cell communication, cell adhesion, cell motion, developmental processes and binding functions. The signalling pathways that may play a primary role in the myogenesis stimulation by FS are associated with TGF-M-NM-2, Delta-Notch and Wnt signalling pathways, integrin and actin cytoskeleton signalling and adipogenesis regulation. Changes in expression of Hgf, Sort1, Trdn, Stmn2, Hdac1 genes, significantly involved in the process of myoblasts differentiation were validated with Real-Time PCR method. Conclusions: Our results implicate which aspects of transcriptional regulation of myogenesis process by FS could have significant and protective influence. We have shown that FS activity is associated not only with GDF8 binding but also with inhibited expression of genes involved in TGF-M-NM-2 signalling and by regulating of genes associated with vesicle transport apoptosis signalling pathway, inflammatory pathways and adipogenesis expression. Our analysis showed that follistatin GDF8-independent on differentiating myotubes involves regulation of localization processes, cell-matrix adhesion, mRNA processing, apoptosis, fatty acid metabolic processes, SNAP receptor activity functions and partial regulation of transcription processes. These results give a new and complete image of the follistatin role in the muscle cell differentiation and indicate target genes for FS which in the future may be a good therapeutic approach. After scanning of hybridized microarrays, quantitation of slide images were performed using Feature Extraction Software 10.7.3.1 (Agilent) using default parameters. Normalized raw data was exported to GeneSpring GX 11.0.5 (Agilent, Santa Clara, CA). For identification of genes significantly altered in cells treated with FSl compared with untreated cells. T total detected entities were filtered by flags (present, marginal) and error (coefficient of variation: CV < 50.0 percent) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with FS(FS vs. CTRL 1-4) was used t-test unpaired (p < 0.05) with multiple testing correction: Benjamini-Hochberg <0.05, all significant changes over fold change 1.6 were selected. Analysis of GO, GSEA and signaling pathway was carried out using GeneSpring GX 12 (Agilent) and the DAVID, KEEG and PANTHER Classification System (p<0.01). In the analysis of signaling pathways using GeneSpring GX 12 (Agilent) and Ariadne Pathway Studio.

Project description:Ewing Sarcoma is caused by a pathognomonic genomic translocation that places an N-terminal EWSR1 gene in approximation with one of several ETS genes (typically FLI1). This aberration, in turn, alters the transcriptional regulation of more than five hundred genes and perturbs a number of critical pathways that promote oncogenesis, cell growth, invasion, and metastasis. Among them, translocation-mediated up-regulation of the insulin-like growth factor receptor 1 (IGF-1R) and mammalian target of rapamycin (mTOR) are of particular importance since they work in concert to facilitate IGF-1R expression and ligand-induced activation, respectively, of proven importance in ES transformation. When used as a single agent in Ewing sarcoma therapy, IGF-1R or mTOR inhibition leads to rapid counter-regulatory effects that blunt the intended therapeutic purpose. Therefore, identify new mechanisms of resistance that are used by Ewing sarcoma to evade cell death to single-agent IGF-1R inhibition might suggest a number of therapeutic combinations that could improve its clinical activity. TC32 and TC71 ES clones with acquired resistance to OSI-906 or NVP-ADW-742 were generated by maintaining the corresponding parental cell lines with increasing concentrations of the agents (up to 2.3 Î¼M for OSI-906, 1.5 Î¼M for NVP-ADW-742) for 7 months. All parental and acquired drug resistant cell lines were tested twice per year for mycoplasma contamination using the MycoAlert Detection Kit (Lonza Group Ltd.) according to the manufacturerâs protocol and validated using short-tandem repeat fingerprinting with an AmpFLSTR Identifier kit as previously described. Herein, we determine subtle differences in acquired mechanism of resistance by two promising small molecule inhibitors of IGF-1R/IR-Î±. OSI-906, which inhibits IGF-1R and IR, and NVP-ADW-742, which inhibits only IGF-1R, were evaluated using in vitro assays to decipher the mechanism(s) by which IGF-1R inhibition induces drug resistance in Ewing sarcoma cells. The preparation of extracted proteins from sensitive and acquired resistant Ewing sarcoma cells to OSI-906 and NVP-ADW-742 for reverse-phase protein lysate array (RPPA) analysis were prepared using the same array. Lysates were processed, spotted onto nitrocellulose-coated FAST slides, probed with 115 validated primary antibodies, and detected using a DakoCytomation-catalyzed system with secondary antibodies. MicroVigene software program (VigeneTech) was used for automated spot identification, background correction, and individual spot-intensity determination. Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were media-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal â log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between sensitive and resistant cell lines to drug treatments. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs). Biostatistical analyses comparing two groups were performed using an unpaired t-test with Gaussian distribution followed by the Welch correction. To distinguish between treatment groups, we used one-way ANOVA with the Geisser-Greenhouse correction. Differences with p values <0.05 were considered significant. Within clustered image maps (CIM), unsupervised double hierarchical clustering used the Pearson correlation distance and Wardâs linkage method as the clustering algorithm to link entities (proteins) and samples.

Project description:Wnt/M-NM-2-catenin signaling is involved in various aspects of skeletal muscle development and regeneration. In addition, Wnt3a and M-NM-2-catenin are required for muscle-specific gene transcription in embryonic carcinoma cells and satellite-cell proliferation during adult skeletal muscle regeneration. Downstream targets of canonical Wnt signaling are cyclin D1 and c-myc. However, both target genes are suppressed during differentiation of mouse myoblast cells, C2C12. Underlying molecular mechanisms of M-NM-2-catenin signaling during myogenic differentiation remain unknown. Using C2C12 cells, we examined intracellular signaling and gene transcription during myoblast proliferation and differentiation. We confirmed that several Wnt signaling components, including Wnt9a, Sfrp2 and porcupine, were consistently upregulated in differentiating C2C12 cells. Troponin T-positive myotubes were decreased by Wnt3a overexpression, but not Wnt4. TOP/FOP reporter assays revealed that co-expression with Wnt4 reduced Wnt3a-induced luciferase activity, suggesting that Wnt4 signaling counteracted Wnt3a signaling in myoblasts. FH535, a small-molecule inhibitor of M-NM-2-catenin/Tcf complex formation, reduced basal M-NM-2-catenin in cytoplasm and decreased myoblast proliferation. K252a, a protein kinase inhibitor, increased membrane-bound M-NM-2-catenin and enhanced myoblast fusion. Treatments with K252a or Wnt4 resulted in increased cytoplasmic vesicles containing phosphorylated M-NM-2-catenin (Tyr654) during myogenic differentiation. These results suggest that various Wnt ligands control subcellular M-NM-2-catenin localization, which regulate myoblast proliferation and myotube formation. Wnt signaling via M-NM-2-catenin likely acts as a molecular switch that regulates the transition from cell proliferation to myogenic differentiation. Control cells (day 0) prior to differentiation induction with n=4; differentiated for two days with n=3; differentiated for four days with n=3.

Project description:GDF8 (myostatin) is a unique cytokine strongly affecting the skeletal muscle phenotype in human and animals. The aim of the present study was to elucidate the molecular mechanism of myostatin influence on the differentiation of mouse C2C12 myoblasts, using the global-transcriptome analysis with the DNA microarray technique. Treatment with exogenous GDF8 strongly affected the growth and development of C2C12 mouse myoblasts. This was manifested by the inhibition of proliferation and differentiation as well as the impairment of cell fusion. DNA microarray analysis revealed 778 genes regulated by GDF8 in differentiating myoblasts (543 down-regulated and 235 up-regulated). Ontological analysis revealed their involvement in 17 types of biological processes, 10 types of molecular functions and 68 different signaling pathways. The effect of GDF8 was mainly mediated by the disruption of the cell cycle, calcium and insulin signaling pathways and expression of cytoskeletal and muscle specific proteins. The identified key-genes that could play a role as GDF8 targets in differentiating myoblasts are: Mef2, Hgf, Ilb1, Itgb1, Edn1, Ppargc1a. After scanning of hybridized microarrays, quantitation of slide images was performed using Feature Extraction Software (Agilent) using default parameters. The raw data were normalized by Loess normalization method, and then the normalized raw data was exported to GeneSpring GX 11.0.5 (Agilent, Santa Clara, CA). For identification of genes significantly altered in cell compared with the control normal gene set, total detected entities were filtered by flags (present, marginal) to remove very low signal entities and to select reproducible signal values of entities among the replicated experiments, respectively. In statistical analysis, separated for experiment with myoblasts treated with GDF8 ([C2C12]-[GDF8]1-4) was used t-test unpaired (p < 0.05) and fold change over 1.6. Analysis of GO and signaling pathway was carried out using GeneSpring GX 12 (Agilent), KEGG and PANTHER Classification System (http://www.pantherdb.org/). In the analysis of signaling pathways using Panther, a total of 68 cellular pathways were identified.

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Project description:This dataset details the time-dependent response of human Huh7 hepatoma cells to type I and type III IFN. Despite activating similar signaling cascades, the type I and type III interferons (IFNs) differ in their ability to antagonize viral replication. However, it is not clear whether these cytokines induce unique antiviral states, particularly in the liver, where the clinically important hepatitis B and C viruses cause persistent infection. Here, microarray-based gene expression analysis is combined with mechanistic studies of signaling pathways to dynamically characterize the transcriptional responses induced by these cytokines in Huh7 hepatoma cells and primary human hepatocytes. Type I and III IFNs differed greatly in their level of interferon-stimulated gene (ISG) induction with a clearly detectable hierarchy (IFN-M-NM-2 > IFN-M-NM-1 > IFN-M-NM-;3 > IFN-M-NM-;1 > IFN-M-NM-;2). This hierarchy resulted in widely varying numbers of differentially expressed genes when quantified using common statistical thresholds, even though individual IFNs did not appear to regulate unique sets of genes. The kinetic profiles of IFN-induced gene expression were also qualitatively similar with the important exception of IFN-M-NM-1. While stimulation with either IFN-M-NM-2 or IFN-M-NM-;s resulted in a similar long-lasting ISG induction, IFN-M-NM-1 signaling peaked early after stimulation then declined due to a negative feedback mechanism. The quantitative expression hierarchy and unique kinetics of IFN-M-NM-1 suggest different roles for individual IFNs in the immune response, and help explain previously observed differences in antiviral activity. Huh7 cells were seeded into 6-well plates at the density of 3x10^5 cells/well and cultured overnight before stimulation with either 500 U/ml of IFN-M-NM-1 or IFN-M-NM-2, or 10 ng/ml of IFN-M-NM-;1, IFN-M-NM-;2, or IFN-M-NM-;3. Total RNA was harvested and isolated at 0.5, 1, 2, 4, 6, 12 and 24 hours post-incubation using RNeasy Mini Kit (Qiagen) following the Affymetrix GeneChip protocol of the Keck Affymetrix Resource facility at Yale University. IFN incubation at each time point was performed in duplicate. All subsequent processing, hybridization to the Illumina HumanHT-12 microarray, and quality control analyses were carried out by the Yale Center for Genome Analysis using standard protocols.

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Transcriptional regulation of cellular processes important in control of skeletal myogenesis by interferon-M-NM-3

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