Expression data from Synovial Sarcomas
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: cM-CM-)line brulard
PROVIDER: E-GEOD-40025 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Background: Synovial sarcoma (SS) occur in children as well as in adults, although metastatic events are much more common in the latter. Whereas the importance of the t(X;18) translocation in SS oncogenesis is well established, the genetic basis of SS metastasis is still poorly understood. We recently reported expression (CINSARC) and genomic (GI) prognostic signatures related to chromosome integrity in sarcomas and gastrointestinal stromal tumors (GISTs). Here we investigate whether these signatures can also predict outcomes in SS. Methods: One hundred primary untreated SS were selected for expression and genomic profiling in a training/validation approach. Results: CINSARC and GI have strong, independent and validated prognostic values (p<0.0001). Comparing expression profiles of tumors with or without metastasis, 14 genes common with the CINSARC signature were identified and the two top-ranked genes, KIF14 and CDCA2, were validated as prognostic markers in an independent cohort. Comparing genomic profiles of adult vs. pediatric SS, we show that metastasis is associated with genome complexity in both situations and that the adult genome is more frequently rearranged. Accordingly, pediatric patients with an even genomic profile do not develop metastasis. Conclusions: Metastasis development in SS is strongly associated with chromosome complexity, and CINSARC and GI are validated independent prognostic factors. The differences in metastasis frequency between adults and children are associated with genome instability, which is much more frequent in adults. GI is potentially the best overall biomarker, and clearly the most clinically relevant, considering that genome profiling from formalin fixed samples is already used in pathology. 34 Synovial Sarcomas hybridized to Agilent-026652 Whole Human Genome Microarray 4x44K
2014-08-09 | E-GEOD-40018 | biostudies-arrayexpress
Project description:Background: Synovial sarcoma (SS) occur in children as well as in adults, although metastatic events are much more common in the latter. Whereas the importance of the t(X;18) translocation in SS oncogenesis is well established, the genetic basis of SS metastasis is still poorly understood. We recently reported expression (CINSARC) and genomic (GI) prognostic signatures related to chromosome integrity in sarcomas and gastrointestinal stromal tumors (GISTs). Here we investigate whether these signatures can also predict outcomes in SS. Methods: One hundred primary untreated SS were selected for expression and genomic profiling in a training/validation approach. Results: CINSARC and GI have strong, independent and validated prognostic values (p<0.0001). Comparing expression profiles of tumors with or without metastasis, 14 genes common with the CINSARC signature were identified and the two top-ranked genes, KIF14 and CDCA2, were validated as prognostic markers in an independent cohort. Comparing genomic profiles of adult vs. pediatric SS, we show that metastasis is associated with genome complexity in both situations and that the adult genome is more frequently rearranged. Accordingly, pediatric patients with an even genomic profile do not develop metastasis. Conclusions: Metastasis development in SS is strongly associated with chromosome complexity, and CINSARC and GI are validated independent prognostic factors. The differences in metastasis frequency between adults and children are associated with genome instability, which is much more frequent in adults. GI is potentially the best overall biomarker, and clearly the most clinically relevant, considering that genome profiling from formalin fixed samples is already used in pathology. 58 Synovial Sarcomas hybridized to Agilent-014850 Whole Human Genome Microarray 4x44K G4112F
2014-08-09 | E-GEOD-40021 | biostudies-arrayexpress
Project description:The aim of the current study was to characterize the genetic adaptive pathways altered by exercise in veteran athletes and age-matched untrained individuals. Two groups of 50-60 year old males: competitive cyclists and untrained, minimally active individuals were examined. All participants completed an acut bout of submaximal endurance exercise and blood samples pre- and post-exercise were analyzed for gene expression changes utilizing genome-wide DNA microarray analysis. Our results indicate distinct differences in gene expression involving energy metabolism, lipids, insuling signaling and cardiovascular function between the two groups. These findings may lead to new insights into beneficial signaling pathways of healthy aging and help identify surrogate markers for monitoring exercise and training load. Blood samples from the control and athlete groups were analyzed at three time-points: T1 (before exercise); T2 (immediately after exercise) and T3 (24 hours after exercise). There were n = 4 samples in each of control and athlete group at T1 and T3; and n = 7 for control group and n = 8 for athlete group at T2. One athlete sample (Sample # 010201) at time - point T2 had a technical replicate.
2013-09-27 | E-GEOD-51216 | biostudies-arrayexpress
Project description:Androgen deprivation therapy remains the primary treatment modality for patients with metastatic prostate cancer but is uniformly marked by progression to castration-resistant prostate cancer (CRPC) after a period of regression. Continued activation of androgen receptor (AR) signaling is attributed as one of the most important mechanisms underlying failure of therapy. Recently, the discovery of constitutively active AR splice variants (AR-Vs) adds more credence to this idea. Expression of AR-Vs in metastases portends a rapid progression of the tumor. However, the precise role of the AR-Vs in CRPC still remains unknown. ARv567es is one of the two AR variants frequently found in human CRPC xenografts and metastases. Herein, we developed a probasin (Pb) promoter-driven ARv567es transgenic mouse, Pb-ARv567es, to evaluate the role of ARv567es in both autonomous prostate growth and progression to CRPC. We found that expression of ARv567es in the prostate results in epithelial hyperplasia by 16 weeks and invasive adenocarcinoma is evident by 1 year of age. The underlying genetic cellular events involved a cell cycle-related transcriptome and differential expression of a spectrum of genes that are critical for tumor initiation and progression. These findings indicate that ARv567es could induce tumorigenesis de novo and signifies the critical role of AR-Vs in CRPC. Thus, the Pb-ARv567es mouse could provide a novel model in which the role of AR variants in prostate cancer progression can be examined. Custom Agilent 44K whole mouse genome expression oligonucleotide microarrays were used to profile prostate tissue from probasin (Pb) promoter-driven ARv567es transgenic mice and control littermates. Total RNA was isolated and amplified prior to hybridization against a common reference pool of normal adult mouse tissues.
2014-09-11 | E-GEOD-61303 | biostudies-arrayexpress
Project description:To determine Sigma 54 (SigL) reglons in Bacillus thuringiensis HD73 strain, A sigLmutant, HD(M-NM-^TsigL::kan), was constructed with insertion of kanamycin resistance gene cassete. We have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between mutant and wild-type strains. 2 ml samples were separately harvested from B. thuringiensis HD73 and HD(M-NM-^TsigL::kan) strains grown in SchaefferM-bM-^@M-^Ys sporulation medium (SSM) at stages T7 of stationary phase (7 hours after the end of the exponential phase). Three independent repeats were performed for each stain.
2013-06-29 | E-GEOD-48410 | biostudies-arrayexpress
Project description:In the current report, we report that ThbZIP1 is a direct target gene of the ThABF1 transcription factor. There are three ABRE motifs in the promoter of ThbZIP1, Yeast one-hybrid (Y1H) assays showed that a ABF protein, ThABF1, specifically binds to the ABRE motifs. The interaction between ThABF1 and the promoter of ThbZIP1 was further confirmed by transient expression assays in tobacco leaves. Chromatin Immunoprecipitation (ChIP) results suggested that binding of ThABF1 to ABRE motifs in the promoter of ThbZIP1 occurs in vivo in Tamarix hispida to regulate the expression of ThbZIP1. Moreover, ThABF1 and ThbZIP1 share similar expression patterns in response to salt, drought, ABA, methyl viologen (MV) and cold stress. Microarray analyses results showed there were 1,662 and 1,609 genes that were significantly upregulated or downregulated, respectively, under ABA stress conditions. ThbZIP1 regulated the genes via binding to the C-, G- or A-box motifs in their promoter sequences. Based on these data, the results suggested a regulatory network model mediated by ThbZIP1, under abiotic stress conditions, ThABF1 regulates the expression of ThbZIP1, and the activated ThbZIP1 binds to bZIP recognition sequences or other motifs to regulate the expression of genes containing these motifs in their promoters. Differentially expression genes of ThbZIP1-overexpression plants and wild type of Columbia Arabidopsis thaliana were measured under ABA stressed and normal condition for 3 hours, respectively. Two independent experiments were performed at each treatment using different plants for each experiment.
2014-11-01 | E-GEOD-62888 | biostudies-arrayexpress
Project description:Alkaline hemicellulytic bacteria Bacillus sp. N16-5 has abroad substrate spectrum and exhibits great growth ability on complex carbohydrates. In order to get insight into its carbohydrate utilization mechanism, global transcriptional profiles were separately determined for growth on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan, pectin and carboxymethyl cellulose by using one-color microarrays. Substrate induced gene expression was measured when culture was grown on glucose, fructose, mannose, galactose, arabinose, xylose, galactomannan, xylan and CMC to mid-logarithmic phase.
2014-06-17 | E-GEOD-38276 | biostudies-arrayexpress
Project description:Neuroblastoma is the most common extracranial solid malignancy derived from neural crest cells. Better elucidation of the mechanisms underlying the aggressive progression of neuroblastoma is needed for improving the therapeutic efficiencies. Since previous studies indicate that histone H2A type 2-B (H2AB), a histone H2A variant locating at chromosome 1q21.2 region, is up-regulated in neural progenitor cells and early motor neurons, we hypothesized that H2AB might participate in the progression of neuroblastoma. We employed the human whole genome microarray expression profiling as a discovery platform to analyze the transcriptome profiling changes of human neuroblastoma SH-SY5Y cells in response to stable over-expression of H2AB. The results showed that stable over-expression of H2AB led to altered expression of 514 human mRNAs, including 249 up-regulated genes and 265 down-regulated genes. Then we found the possible roles of these differentially regulated mRNAs in selected pathways including cell cycle/proliferation, apoptosis, and cytokine/chemokine responses by Bioinformatic analysis. Furthermore, we validated the microarray results by real-time RT-PCR with high identity. Overall, our results provided fundamental information about the transcriptomic changes in response to H2AB over-expression in human neuroblastoma cells, and these findings will help us to understand the pathogenesis of neuroblastoma. Total RNA of cells stably transfected with empty vector or H2AB was extracted using the TRIZOL Reagent according to the manufacturer's instructions. Gene expression profiling was performed for each RNA sample separately on the Agilent Whole Human Genome Oligo Microarray 4M-CM-^W44K at Shanghai Technology Corporation (Shanghai, China), in which GeneChip microarray service was certificated by Agilent.
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2014-11-06 | E-GEOD-63024 | biostudies-arrayexpress