Profiling and Bioinformatics Analyses of Differential Circular RNA Expression in Glioblastoma Multiforme Cells under Hypoxia
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA792596 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Background: The hypoxia microenvironment is highly associated with GBM’s malignant phenotypes. CircRNAs were reported involved in GBM’s biological characteristics and regulated by HIF-1α. However, the differential expression profile and role of circRNAs in GBM cells under hypoxia are still unclear. Methods: The expression profiles of circRNAs in LN229 and T98G under hypoxia were explored via circRNA sequencing analysis. Those circRNAs significantly dysregulated both in LN229 and T98G, and could be found in circBase were selected and validated by qRT-PCR, RNase R digestion reaction and Sanger sequencing. Normal cell line and fresh GBM tissues were also used for qRT-PCR validation. The roles of differentially expressed circRNAs were evaluated by bioinformatics analyses. Results: There were 672 dysregulated circRNAs in LN229 and 698 dysregulated circRNAs in T98G. GO analysis indicated that the alteration of circRNAs expression related to GBM cell’s biogenesis and metabolism. KEGG analysis demonstrated that TGF-β signaling pathway, HIF-1 signaling pathway and metabolism related signaling pathway were closely associated with differentially expressed circRNAs under hypoxia. The 6 selected and dysregulated circRNAs both in LN229 and T98G including hsa_circ_0000745, hsa_circ_0020093, hsa_circ_0020094, hsa_circ_0000943, hsa_circ_0004874 and hsa_circ_0002359 were validated by qRT-PCR. HIF-1α centered circRNA-miRNA-mRNA networks analysis showed that the 6 validated circRNAs could cross-talk with 11 related miRNAs. Conclusion: The circRNA expressions are dysregulated in GBM cell under hypoxia. The 6 validated circRNAs could participate in GBM’s development and progression when hypoxia occurs. They might be the candidates for prognostic markers and adjuvant therapeutics of GBM in the future.
2024-12-28 | GSE192678 | GEO
Project description:The purpose of this study is to determine whether the combination of two agents, INC280 and bevacizumab, is safe and effective when administered to patients with Glioblastoma Multiforme (GBM) who have progressed after receiving prior therapy or who have unresectable GBM.
| 2185625 | ecrin-mdr-crc
Project description:Quantitative analysis of human glioblastoma multiforme (GBM) using Tandem Mass Tags (TMT) reagent. Mass spectra comprised with global proteome and phosphoproteome with standard channel.
2020-07-06 | PXD015545 | Pride
Project description:TCGA Analysis of RNA Expression for Glioblastoma Multiforme Using Affymetrix HT_HG-U133A gabri-00003 Assay Type: Gene Expression Provider: Affymetrix Array Designs: HT_HG-U133A Organism: Homo sapiens (ncbitax) Tissue Sites: Brain Material Types: synthetic_RNA, organism_part, solid_tumor, total_RNA, cell Disease States: GLIOBLASTOMA MULTIFORME, NOT SPECIFIED
2015-05-14 | E-GEOD-68850 | biostudies-arrayexpress
Project description:Congenital glioblastoma multiforme (cGBM) historically has been considered an aggressive tumor of infancy requiring extensive chemotherapy to achieve cure. We report on 4 patients at our institution with cGBMs who were treated with surgery and chemotherapy (carboplatin and etoposide every 21 days for 2-6 cycles). Four of four patients are progression free at a median time of 27.5 months (22-103 months). To characterize the molecular biology of cGBM, we compared the gene expression profiles of 3 cGBMs to 12 pediatric and 6 primary adult glioblastomas collected at our institution. Unsupervised hierarchical clustering showed cGBMs grouped together with other high-grade gliomas. cGBMs demonstrated marked similarity to both pediatric and adult GBMs, with only a total of 31 differentially expressed genes identified (FDR < 0.05). Unique molecular features of congenital GBMs identified included over-expression of multiple genes involved in glucose metabolism and tissue hypoxia pathways. Four tyrosine kinases were also mong the up-regulated genes (RET, RASGRF2, EFNA5, ALK). Thus, at our institution congenital GBMs, while similar both histologically and molecularly to other GBMs, appear to have a good prognosis with surgery in combination with relatively moderate chemotherapy. Further study is needed to determine if the few gene expression differences that were identified may contribute to the better survival seen in these tumors compared to pediatric or adult GBMs. Key Words: glioblastoma; congenital; pediatric; gene expression; microarray Molecular profiling of 18 AT/RT patient tumor samples was performed using Affymetrix U133 Plus2 GeneChips. Data were background corrected and normalized using gcRMA (as implemented in Bioconductor). Unsupervised agglomerative hierarchical clustering was performed to identify subsets of AT/RTs with similar gene expression. Limma (moderated t-tests; Bioconductor) was used to identify signature genes for each cluster. Bioinformatics web tool DAVID was used to identify enriched biological processes for each cluster. Survival was analyzed using Kaplan-Meier curves and Cox Hazard Ratio. Bioinformatics tools Gene Set Enrichment (GSEA) and Ingenuity Pathways Analysis were also used to gain further insight into cluster differences.
2012-05-20 | E-GEOD-32374 | biostudies-arrayexpress
Project description:Human Glioblastoma Multiforme tumors taken before dendritic cell vaccination, the recurrent tumors taken after vaccination and control GBM tumors from non vaccinated patients. Keywords: Disease State Analysis
2009-04-03 | GSE11100 | GEO
Project description:TCGA Analysis of RNA Expression for Glioblastoma Multiforme Using Affymetrix HT_HG-U133A
2015-05-14 | GSE68850 | GEO
Project description:TCGA Analysis of RNA Expression for Glioblastoma Multiforme Using Affymetrix HT_HG-U133A
2016-05-27 | GSE81934 | GEO
Project description:Copy number analysis of human GBM samples were performed, and a high frequency of deletions of the PTPRD gene on chromosome 9p23-24.1 were identified. Keywords: SNP microarray, glioblastoma multiforme, copy number, amplification, deletion
2009-01-05 | GSE13021 | GEO
Project description:Copy number analysis of human GBM samples were performed, and a high frequency of deletions of the PTPRD gene on chromosome 9p23-24.1 were identified. Keywords: SNP microarray, glioblastoma multiforme, copy number, amplification, deletion Genomic DNA from 58 GBM tumor samples were hybridized to Affymetrix 250K NspI Gene Chip Arrays and analyzed by dChip using the hg17 genome assembly.
2009-01-04 | E-GEOD-13021 | biostudies-arrayexpress