Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA261112 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Glioblastoma is the most aggressive and lethal malignant brain tumor. miRNA expression profiling could be useful in improving the classification of tumors and predicting their behavior. In this study, the miRNA expression patterns in glioblastoma tumor tissues and adjacent normal tissues were identified through expression profiling of a patient with glioblastoma. The results will hopefully enhance our understandings of the epigentic changes in glioblastoma progression and provide candidates for miRNAs-based targeting tharapy. A paired miRNAs tumor tissues and adjacent tissues of a glioblastoma patient was used in this study. miRNAs were isolated using miRNeasy FFPE Kit (Qiagen). Profiling was established by applying the Agilent human miRNA Microarray (8 M-CM-^W 60K, v16.0) (Agilent Technologies).
2014-09-17 | E-GEOD-61445 | biostudies-arrayexpress
Project description:Glioblastoma is the most aggressive and lethal malignant brain tumor. miRNA expression profiling could be useful in improving the classification of tumors and predicting their behavior. In this study, the miRNA expression patterns in glioblastoma tumor tissues and adjacent normal tissues were identified through expression profiling of a patient with glioblastoma. The results will hopefully enhance our understandings of the epigentic changes in glioblastoma progression and provide candidates for miRNAs-based targeting tharapy.
2014-09-17 | GSE61445 | GEO
Project description:To investigate differential gene expression, we analyzed the entire transcriptomes of tumor and matched normal brain tissues obtained from a patient who had glioblastoma multiforme. We extracted and sequenced the mRNA using Illumina GA2 platform. The raw data was analyzed using our recently developed program called RNASEQR, as well as ERANGE, MapSplice, SpliceMap, and TopHat. Tumor and matched control brain tissues were obtained from a Han-Chinese patient.
2011-10-30 | E-GEOD-33328 | biostudies-arrayexpress
Project description:Differentially expressed miRNAs in colon cancer tissues vs normal colon tissues
| PRJNA231746 | ENA
Project description:Intra-tumor genetic heterogeneity comes from whole chromosome and/or focal copy number variations (CNVs). We investigated the impact of whole chromosome CNVs on gene expression by performing single-cell RNA sequencing on a chromosomally unstable glioblastoma cancer stem cell (CSC) line and a control normal, diploid neural stem cell (NSC) line. From the gene expression data, we computationally inferred large-scale CNVs in single cells. We find that gene expression across large genomic regions scales proportionally to whole chromosome copy number in chromosomally unstable CSCs. Also, we find that the differential expression of most genes between normal NSCs and glioblastoma CSCs is largely accounted for by copy number alterations. However, we identify 269 genes whose differential expression in glioblastoma CSCs relative to normal NSCs is independent of copy number. Moreover, a gene signature derived from the subset of genes that are differential expressed independent of copy number in glioblastoma CSCs correlates with tumor grade and is prognostic for patient survival. In conclusion, this study demonstrates the utility of single-cell RNA sequencing when analyzing chromosomally unstable cells.
2019-06-05 | GSE132172 | GEO
Project description:To investigate differential gene expression, we analyzed the entire transcriptomes of tumor and matched normal brain tissues obtained from a patient who had glioblastoma multiforme. We extracted and sequenced the mRNA using Illumina GA2 platform. The raw data was analyzed using our recently developed program called RNASEQR, as well as ERANGE, MapSplice, SpliceMap, and TopHat.
2011-10-30 | GSE33328 | GEO
Project description:glioblastoma(GBM) tissues: Tumor tissues(C) vs. Normal tissues(N)
| PRJNA431408 | ENA
Project description:Formalin fixed paraffin embedded (FFPE) primary-recurrent Glioblastoma (pGBM-rGBM) matched patient samples and normal tissue adjacent to tumor (NAT) were analyzed by shotgun DDA proteomics. The proteomic profiles of pGBM-rGBM pairs revealed differentially expressed proteins in rGBM samples, which in future could be used for potential therapeutic interventions.
2021-08-06 | MSV000087947 | MassIVE
Project description:Background: Newer 3D culturing approaches are a promising way to better mimic the in vivo tumor microenvironment and to study the interactions between the heterogeneous cell populations of glioblastoma multiforme. Like many other tumors, glioblastoma uses extracellular vesicles as an intercellular communication system to prepare surrounding tissue for invasive tumor growth. However, little is known about the effects of 3D culture on extracellular vesicles. The aim of this study was to comprehensively characterise extracellular vesicles in 3D organoid models and compare them to conventional 2D cell culture systems.Methods: Primary glioblastoma cells were cultured as 2D and 3D organoid models. Extracellular vesicles were obtained by precipitation and immunoaffinity, with the latter allowing targeted isolation of the CD9/CD63/CD81 vesicle subpopulation. Comprehensive vesicle characterisation was performed and miRNA expression profiles were generated by smallRNA-sequencing. In silico analysis of differentially regulated miRNAs was performed to identify mRNA targets and corresponding signaling pathways. The tumor cell media and extracellular vesicle proteome were analysed by high-resolution mass spectrometry.Results: We observed an increased concentration of extracellular vesicles in 3D organoid cultures. Differential gene expression analysis further revealed the regulation of twelve miRNAs in 3D tumor organoid cultures (with nine miRNAs down and three miRNAs upregulated). MiR-23a-3p, known to be involved in glioblastoma invasion, was significantly increased in 3D. MiR-7-5p, which counteracts glioblastoma malignancy, was significantly decreased. Moreover, we identified four miRNAs (miR- 323a-3p, miR-382-5p, miR-370-3p, miR-134-5p) located within the DLK1-DIO3 domain, a cancer associated genomic region, suggesting a possible importance of this region in glioblastoma progression. Overrepresentation analysis identified alterations of extracellular vesicle cargo in 3D organoids, including representation of several miRNA targets and proteins primarily implicated in the immune response.Conclusion: Our results show that 3D glioblastoma organoid models secrete extracellular vesicles with an altered cargo compared to corresponding conventional 2D cultures. Extracellular vesicles from 3D cultures were found to contain signaling molecules associated with the immune regulatory signaling pathways and as such could potentially change the surrounding microenvironment towards tumor progression and immunosuppressive conditions. These findings suggest the use of 3D glioblastoma models for further clinical biomarker studies as well as investigation of new therapeutic options.
2024-04-09 | PXD047328 | Pride
Project description:Abstract:
Despite intensive treatments including temozolomide (TMZ) administration, glioblastoma patient prognosis remains dismal and innovative therapeutic strategies are urgently needed. A systems pharmacology approach was undertaken to investigate TMZ pharmacokinetics‐pharmacodynamics (PK‐PD) incorporating the effect of local pH, tumor spatial configuration and micro‐environment. A hybrid mathematical framework was designed coupling ordinary differential equations describing the intracellular reactions, with a spatial cellular automaton to individualize the cells. A differential drug impact on tumor and healthy cells at constant extracellular pH was computationally demonstrated as TMZ‐induced DNA damage was larger in tumor cells as compared to normal cells due to less acidic intracellular pH in cancer cells. Optimality of TMZ efficacy defined as maximum difference between damage in tumor and healthy cells was reached for extracellular pH between 6.8 and 7.5. Next, TMZ PK‐PD in a solid tumor was demonstrated to highly depend on its spatial configuration as spread cancer cells or fragmented tumors presented higher TMZ‐induced damage as compared to compact tumor spheroid. Simulations highlighted that smaller tumors were less acidic than bigger ones allowing for faster TMZ activation and their closer distance to blood capillaries allowed for better drug penetration. For model parameters corresponding to U87 glioma cells, inter‐cell variability in TMZ uptake play no role regarding the mean drug‐induced damage in the whole cell population whereas this quantity was increased by inter‐cell variability in TMZ efflux which was thus a disadvantage in terms of drug resistance. Overall, this study revealed pH as a new potential target to significantly improve TMZ antitumor efficacy.
Change the value of pH for different cases.
2019-09-30 | MODEL1909300003 | BioModels