Transcriptomics and metabolomics reveal the changes of regulatory mechanisms of osteosarcoma under different culture methods in vitro
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ABSTRACT:
PROVIDER: PRJNA828155 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18819429_1.fastq.gz | Fastqsanger.gz | |||
| SRR18819429_2.fastq.gz | Fastqsanger.gz | |||
| SRR18819430_1.fastq.gz | Fastqsanger.gz | |||
| SRR18819430_2.fastq.gz | Fastqsanger.gz | |||
| SRR18819431_1.fastq.gz | Fastqsanger.gz |
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Project description:The purpose of this study was to reveal the differences in transcriptional and metabolic levels between osteosarcoma 2D cells, 3D cells, 3D cell printed tissue, isolated tissue, and transplanted tumor in vivo
2022-12-28 | GSE201050 | GEO
Project description:BackgroundRecently, increasing attention has been drawn to the impact of the tumor microenvironment (TME) on the occurrence and progression of malignant tumors. A variety of 3D culture techniques have been used to simulate TME in vitro. The purpose of this study was to reveal the differences in transcriptional and metabolic levels between osteosarcoma (OS) 2D cells, 3D cells, 3D cell-printed tissue, isolated tissue, and transplanted tumor tissue in vivo.MethodsWe cultured the OS Saos-2 cell line under different culture methods as 2D cells, 3D cells, 3D cell-printed tissue and isolated tissue for 14 days and transplanted tumors in vivo as a control group. Through transcriptomic and metabonomic analyses, we determined the changes in gene expression and metabolites in OS tissues under different culture methods.ResultsAt the transcriptional level, 166 differentially expressed genes were found, including the SMAD family, ID family, BMP family and other related genes, and they were enriched in the TGF-β signaling pathway, complement and coagulation cascades, signaling pathways regulating pluripotency of stem cells, Hippo signaling pathway, ferroptosis, cGMP-PKG signaling pathway and other pathways. At the metabolic level, 362 metabolites were significantly changed and enriched in metabolic pathways such as the Fc Epsilon RI signaling pathway, histidine metabolism, primary bile acid biosynthesis, steroid biosynthesis, protein digestion and absorption, ferroptosis, and arachidonic acid metabolism. After integrating the transcriptome and metabolomics data, it was found that 44 metabolic pathways were changed, and the significantly enriched pathways were ferroptosis and pyrimidine metabolism.ConclusionDifferent culture methods affect the gene expression and metabolite generation of OS Saos-2 cells. Moreover, the cell and tissue culture method in vitro cannot completely simulate TME in vivo, and the ferroptosis and pyrimidine metabolism pathways mediate the functional changes of OS Saos-2 cells in different microenvironments.
| S-EPMC9762085 | biostudies-literature
Project description:We performed copy number analysis of high-grade osteosarcoma samples. in order to detect osteosarcoma drivers, we integrated these data with genome-wide gene expression data. We performed two different methods - a non-paired and a paired integrative analysis.
2012-03-28 | GSE33153 | GEO
Project description:We performed copy number analysis of high-grade osteosarcoma samples. in order to detect osteosarcoma drivers, we integrated these data with genome-wide gene expression data. We performed two different methods - a non-paired and a paired integrative analysis. Copy number analysis was performed on 32 pre-treatment high-grade osteosarcoma diagnostic biopsies, of which 29 overlapped with the 84 samples used for gene expression analyses.
2012-03-27 | E-GEOD-33153 | biostudies-arrayexpress
Project description:We performed genome-wide gene expression data of high-grade osteosarcoma samples. In order to detect osteosarcoma drivers, we integrated these data with copy number data. We performed two different methods - a non-paired and a paired integrative analysis.
2012-03-28 | GSE33382 | GEO
Project description:SaOS2 osteosarcoma cells were cultured with or without atorvastatin (10 µM) for 6, 15 or 24h (2 biological replcates). RNA were isolated and hybridized to RNG microarrays. Background Osteosarcoma is the most common primary tumor of bone. The rapid development of metastatic lesions and resistance to chemotherapy remain major mechanisms responsible for the failure of treatments and poor survival rate for patients. Methods We previously showed that the HMGCoA reductase inhibitors statins exhibit anti-tumoral effects on osteosarcoma cells. Here, using microarray analysis, we identify cyr61/CCN1 as a new target of statins. Modulations of expression of cyr61 were performed in human and murine osteosarcoma cell lines to investigate in vitro cell viability, migratory potential and invasiveness. Cyr61 expression was evaluated in 231 tissue cores from osteosarcoma patients using tissue microarray. Tumor behavior and metastases occurence were analysed by IM injection of modified osteosarcoma cells to BALB/c mice. Results Transcriptome comparisons revealed that statins down-regulate cyr61 expression in SaOS2 cells. Cyr61 silencing in human and murine osteosarcoma cell lines enhanced cell death, but reduced cell migration and cell invasion compared to parental cells whereas cyr61 overexpression had opposite effects. Tissue microarray analysis demonstrated that cyr61 protein expression is higher in human osteosarcoma compared to normal bone tissue and is further increased in metastatic tissues. In vivo, cyr61 overexpression in osteosarcoma cells enhanced lung metastases development whereas cyr61 silencing strongly reduced metastases in mice. Conclusion The results reveal that cyr61 expression increases with tumor grade in human osteosarcoma and demonstrate that cyr61 silencing inhibits in vitro osteosarcoma cell invasion and migration as well as in vivo lung metastases in mice. These data provide a novel molecular target for therapeutic intervention in metastatic osteosarcoma.
2011-02-22 | GSE24401 | GEO
Project description:In order to study the molecular mechanism of Agrimol B compound in inhibiting osteosarcoma cells, we established HOS cell line and intervened with Agrimol B for 24 hours.
2024-08-04 | GSE218856 | GEO
Project description:SaOS2 osteosarcoma cells were cultured with or without atorvastatin (10 µM) for 6, 15 or 24h (2 biological replcates). RNA were isolated and hybridized to RNG microarrays. Background Osteosarcoma is the most common primary tumor of bone. The rapid development of metastatic lesions and resistance to chemotherapy remain major mechanisms responsible for the failure of treatments and poor survival rate for patients. Methods We previously showed that the HMGCoA reductase inhibitors statins exhibit anti-tumoral effects on osteosarcoma cells. Here, using microarray analysis, we identify cyr61/CCN1 as a new target of statins. Modulations of expression of cyr61 were performed in human and murine osteosarcoma cell lines to investigate in vitro cell viability, migratory potential and invasiveness. Cyr61 expression was evaluated in 231 tissue cores from osteosarcoma patients using tissue microarray. Tumor behavior and metastases occurence were analysed by IM injection of modified osteosarcoma cells to BALB/c mice. Results Transcriptome comparisons revealed that statins down-regulate cyr61 expression in SaOS2 cells. Cyr61 silencing in human and murine osteosarcoma cell lines enhanced cell death, but reduced cell migration and cell invasion compared to parental cells whereas cyr61 overexpression had opposite effects. Tissue microarray analysis demonstrated that cyr61 protein expression is higher in human osteosarcoma compared to normal bone tissue and is further increased in metastatic tissues. In vivo, cyr61 overexpression in osteosarcoma cells enhanced lung metastases development whereas cyr61 silencing strongly reduced metastases in mice. Conclusion The results reveal that cyr61 expression increases with tumor grade in human osteosarcoma and demonstrate that cyr61 silencing inhibits in vitro osteosarcoma cell invasion and migration as well as in vivo lung metastases in mice. These data provide a novel molecular target for therapeutic intervention in metastatic osteosarcoma. Dye balance-experiment comparing atorvastatin versus untreated cells at 6, 15 and 24 hours using 2 biological replicates.
2011-02-22 | E-GEOD-24401 | biostudies-arrayexpress
Project description:We performed genome-wide gene expression data of high-grade osteosarcoma samples. In order to detect osteosarcoma drivers, we integrated these data with copy number data. We performed two different methods - a non-paired and a paired integrative analysis. Genome-wide gene expression analysis was performed on 84 pre-treatment high-grade osteosarcoma diagnostic biopsies, of which 29 overlapped with the 32 samples used for copy number analysis. Two different sets of control samples were used for comparison: osteoblasts (n=3) and mesenchymal stem cells (n=12, GEO accession number GSE28974).
2012-03-27 | E-GEOD-33382 | biostudies-arrayexpress
Project description:Global warming and human activities have led to an increased frequency of hypoxia in coastal regions. Hypoxia not only affects the growth and development of scallops but can also cause death, posing a significant challenge to the health and sustainability of aquaculture. Its effects on scallop growth and immune system have been widely reported, but studies on the effects of hypoxic stress on the metabolism of Yesso scallop Mizuhopecten yessoensis are not fully understood. Additionally, the molecular mechanisms of hypoxic stress on damage to the Yesso scallop are still limited. In this study, we deploy high-throughput RNA sequencing (RNA-Seq) and non-targeted liquid chromatography-mass spectrometry (LC-MS) based metabolomics analysis to investigate the alterations in key genes and metabolites in scallops after 24 hours of hypoxia stress (DO: 1 ± 0.1 mg/L). A total of 704 differentially expressed genes (DEGs) and 302 differentially expressed metabolites (DEMs) were identified in the gill tissues of Yesso scallops under hypoxic conditions, respectively. DEGs and DEMs were involved in energy metabolism, antioxidant responses, immune responses, and inflammatory responses, as well as processes of cell apoptosis and cell proliferation. KEGG enrichment analysis shows that the mTOR signaling pathway is a significantly enriched pathway shared by DEGs and DEMs. These findings suggest that Yesso scallops cope with acute hypoxic stress by changing energy metabolism, inhibiting cell apoptosis and proliferation, and increasing immune defense strategies. Overall, the results of this study provide a new understanding of how Yesso scallops respond to hypoxia and provide target genes for the selection and breeding of low-oxygen-tolerant scallops.
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