Transcriptome profiling of a mouse model of alveolar soft part sarcoma
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ABSTRACT:
PROVIDER: PRJNA237513 | ENA |
REPOSITORIES: ENA
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Project description:Alveolar soft-part sarcoma (ASPS) is an extremely rare, highly vascular soft tissue sarcoma affecting predominantly adolescents and young adults. In an attempt to gain insight into the pathobiology of this enigmatic tumor, we performed the first genome-wide gene expression profiling study.
2009-01-01 | GSE13433 | GEO
Project description:In order to dtermine how well a mouse genetic model of alveolar soft part sarcoma (ASPS) mimics the human disease, five human ASPS tumor samples and three normal skeletal muscle samples were profiled by RNAseq and compared to samples from five mouse tumors induced by expression of ASPSCR1-TFE3 and three normal mouse skeletal muscle samples, also profiled by RNAseq.
2014-11-26 | GSE54729 | GEO
Project description:In order to dtermine how well a mouse genetic model of alveolar soft part sarcoma (ASPS) mimics the human disease, five human ASPS tumor samples and three normal skeletal muscle samples were profiled by RNAseq and compared to samples from five mouse tumors induced by expression of ASPSCR1-TFE3 and three normal mouse skeletal muscle samples, also profiled by RNAseq. The reference was really comparing 5 human ASPS tumors to 5 mouse tumors that histologically mimic ASPS, but using skeletal muscle controls (3 from each species) as a sounding board for differential expression.
2014-11-26 | E-GEOD-54729 | biostudies-arrayexpress
Project description:Gene expression profiles of the mouse model for alveolar soft part sarcoma
| PRJNA342090 | ENA
Project description:Alveolar soft-part sarcoma (ASPS) is an extremely rare, highly vascular soft tissue sarcoma affecting predominantly adolescents and young adults. In an attempt to gain insight into the pathobiology of this enigmatic tumor, we performed the first genome-wide gene expression profiling study. Experiment Overall Design: For seven patients with confirmed primary or metastatic ASPS, RNA samples were isolated immediately following surgery, reverse transcribed to cDNA and each sample hybridized to duplicate high-density human U133 plus 2.0 microarrays. Array data was then analyzed relative to arrays hybridized to universal RNA to generate an unbiased transcriptome. Subsequent gene ontology analysis was used to identify transcripts with therapeutic or diagnostic potential. A subset of the most interesting genes was then validated using quantitative RT-PCR and immunohistochemistry.
2009-01-14 | E-GEOD-13433 | biostudies-arrayexpress
Project description:Alveolar soft part sarcoma (ASPS) is a soft tissue sarcoma with poor prognosis. We analysed primary and metastatic ASPS samples to elucidate candidate molecular pathways involved in tumor pathogenesis. Differential gene expression analysis revealed the neural origin for ASPS and implication of fusion genes expression in the pathogenesis of ASPS.
2013-04-12 | GSE45257 | GEO
Project description:Alveolar soft part sarcoma (ASPS) is a slowly growing but highly metastatic sarcoma that affects adolescents and young adults. Its characteristic alveolar structure is constituted by tumor cell nests and abundant vascular network that is responsible for metastatic activities at the initial stage. Here we have generated a new ex vivo mouse model for ASPS that well recapitulates angiogenic and metastatic phenotypes. In mouse ASPS the tumor cells frequently show tumor intravasation, and the intravascular tumor cells were present as organoid structures covered with hemangiopericytes, which is also the case in human ASPS. High expression of GPNMB, a transcriptional target of ASPSCR1-TFE3, was observed at the intravasation. ASPS tumor cells showed the enhanced activity of transendothelial migration and the activity was inhibited by silencing of Gpnmb, indicating that GPNMB plays an important role in tumor intravasation, one of key steps in cancer metastasis. The present model also enabled to evaluate the function of TFE/MITF family transcription factors, and ASPSCR1-TFEB also possessed definitive but less oncogenic activity than that of ASPSCR1-TFE3. Collectively, our new mouse model is a useful tool to understand oncogenic, angiogenic and metastatic mechanisms of ASPS, to identify important motif within the ASPSCR1-TFE3 fusion protein and to provide a novel therapeutic strategy. We used microarrays to detail the global programme of gene expression in mouse ASPS.
2017-03-07 | GSE86501 | GEO
Project description:Alveolar soft part sarcoma (ASPS) is a soft tissue sarcoma with poor prognosis. We analysed primary and metastatic ASPS samples to elucidate candidate molecular pathways involved in tumor pathogenesis. Differential gene expression analysis revealed the neural origin for ASPS and implication of fusion genes expression in the pathogenesis of ASPS. Total RNA was extracted, cleaned up, and eluted using the RNeasy MiniKit and RNeasy MinElute Cleanup Kit, respectively (Qiagen), according to the manufacturer’s protocol. The total RNA yield per sample ranged from 191ng to 2ug. cDNA-mediated annealing, selection, ligation, and extension (DASL) expression assay (Illumina) was performed as per manufacturer’s instructions on a panel comprising 24,526 probes for a total of 18,631 genes (Human Ref-8 Expression; BeadChip).
2013-04-12 | E-GEOD-45257 | biostudies-arrayexpress
Project description:Alveolar soft part sarcoma (ASPS) is a rare soft part malignancy affecting adolescents and young adult. ASPS is characterized by its alveolar structure consisting of tumor cells and highly integrated vascular network, and its high metastatic potential indicates the importance of the prominent angiogenic activity of ASPS. Here we find that the expression of ASPSCR1-TFE3, the fusion transcription factor causatively associated with ASPS, is dispensable for in vitro tumor maintenance but required for in vivo tumor development via angiogenesis. ASPSCR1-TFE3 frequently associates with active enhancers including super-enhancers (SE) upon its DNA binding, and the loss of its expression induces dynamic modification of SE distribution related to genes belonging to the angiogenesis pathway. Using epigenomic CRISPR/dCas9 screening, we identify Pdgfb, Rab27a, Sytl2, and Vwf as critical target genes associated with reduced enhancer activities due to the ASPSCR1-TFE3 loss. ASPSCR1-TFE3 thus orchestrates higher ordered angiogenesis via enhanced intracellular trafficking of angiogenic factors.
2023-01-20 | GSE215316 | GEO
Project description:Alveolar soft part sarcoma (ASPS) is a rare soft part malignancy affecting adolescents and young adult. ASPS is characterized by its alveolar structure consisting of tumor cells and highly integrated vascular network, and its high metastatic potential indicates the importance of the prominent angiogenic activity of ASPS. Here we find that the expression of ASPSCR1-TFE3, the fusion transcription factor causatively associated with ASPS, is dispensable for in vitro tumor maintenance but required for in vivo tumor development via angiogenesis. ASPSCR1-TFE3 frequently associates with active enhancers including super-enhancers (SE) upon its DNA binding, and the loss of its expression induces dynamic modification of SE distribution related to genes belonging to the angiogenesis pathway. Using epigenomic CRISPR/dCas9 screening, we identify Pdgfb, Rab27a, Sytl2, and Vwf as critical target genes associated with reduced enhancer activities due to the ASPSCR1-TFE3 loss. ASPSCR1-TFE3 thus orchestrates higher ordered angiogenesis via enhanced intracellular trafficking of angiogenic factors.
2023-01-16 | GSE189163 | GEO