Gene expression profile of murine proneural glioblastoma
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PROVIDER: PRJNA716179 | ENA |
REPOSITORIES: ENA
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Project description:Murine proneural (PN) glioblastomas were induced by lentiviral vector expressing PDGFB and shRNA targeting p53. Tumor tissues were isolaed from mice reaching end point stage. RNA was isolated using RNAeasy kit according to manufacturer's protocol. cDNA libraries were preaped using TruSeq RNA sample Prep kit (Illumina). RNA sequencing was performed using
2022-04-01 | GSE169286 | GEO
Project description:The determinants of the genetic complexity of Glioblastoma are poorly understood. We generated murine Glioblastomas by transforming glial progenitors in the adult brain with PDGF expression and PTEN deletion +/- p53 deletion. PDGF+PTEN-/- tumors developed additional deletions of specific genes in up to 100% of the tumors, whereas PDGF+PTEN-/-p53-/- tumors did not. Cross-species comparison with data from tCGA database and published in Verhaak, 2010, showed that consistent genetic deletions observed in mouse tumors were specific to human Proneural Glioblastoma. These findings show that the genetic alterations that accumulate during tumor progression are determined by the initiating genetic alterations and by the cellular context in which they occur. Murine gliomas were induced in vivo by retroviral mediated PDGF overexpression, PTEN deletion with or without p53 deletion using Cre/lox system. Tumors were subsequently harvested for sequencing and aCGH analysis. Paired liver DNA was used for hybridization. For PDGF+PTEN-/- tumors, different timepoints were obtained including 21, 35 days post tumor induction, as well as endstage tumors.
2014-01-17 | E-GEOD-36940 | biostudies-arrayexpress
Project description:The determinants of the genetic complexity of Glioblastoma are poorly understood. We generated murine Glioblastomas by transforming glial progenitors in the adult brain with PDGF expression and PTEN deletion +/- p53 deletion. PDGF+PTEN-/- tumors developed additional deletions of specific genes in up to 100% of the tumors, whereas PDGF+PTEN-/-p53-/- tumors did not. Cross-species comparison with data from tCGA database and published in Verhaak, 2010, showed that consistent genetic deletions observed in mouse tumors were specific to human Proneural Glioblastoma. These findings show that the genetic alterations that accumulate during tumor progression are determined by the initiating genetic alterations and by the cellular context in which they occur.
2014-01-17 | GSE36940 | GEO
Project description:To identify proneural, neural, classical and mesenchymal gene expression signature (Verhaak's classification) in human glioblastoma, a microarray analysis on 16 patient-derived glioblastoma stem cell cultures was performed.
2018-06-26 | E-MTAB-6408 | biostudies-arrayexpress
Project description:Glioblastoma (GBM) cells’ stemness-like features and lineage plasticity promote tumor progression. Here, we demonstrate that Clemastine, a drug for treating hay fever and allergy symptoms, effectively attenuated the stemness and suppressed the propagation of primary GBM cultures bearing PDGFRA amplification. We show that these effects of GBM cells were accompanied by altered gene expression profiling indicative of a more differentiated state of tumor cells, in resonating with Clemastine’s activity in promoting the differentiation of normal oligodendrocyte progenitors (OPCs) into mature oligodendrocyte. Functional assays for proteins that can be pharmacologically targeted by Clemastine, including histamine receptors, muscarinic receptors, and Emopamil binding protein (EBP), revealed the essential roles of these proteins in sustaining GBM cell propagation and suggested that Clemastine likely impairs tumor cells via targeting multiple pathways. Finally, we showed that a PDGFB-driven mouse glioma model, representing the proneural subtype GBMs, was similarly susceptible to Clemastine treatment. Collectively, these results identify pathways that are essential for maintaining the proneural progenitor features of GBMs, and suggest that non-oncology, low toxicity drugs with OPC differentiation promoting effects, such as Clemastine, can be exploited for targeting GBM cell’s progenitor property.
2023-10-04 | GSE186319 | GEO
Project description:Glioblastoma multiforme (GBM) is an aggressive, heterogeneous and highly vascularized brain tumor. GBM is thought to arise from glioblastoma stem-like cells (GSCs) which are characterized as being either proneural or mesenchymal. The former isolates of GSCs are tight sphere forming and slow growing while mesenchymal GSCs are lose sphere forming, fast growing, highly invasive and when dominant yield poorer patient prognosis. GSCs are known to be plastic in nature and can therefore evolve from a proneural to a mesenchymal state. Here, we observed that factors secreted by endothelial cells (which make up the brain vasculature) alter several properties of GSCs resulting in the acquisition of a more mesenchymal and invasive phenotype coupled with changes at the level of secretory and cellular proteome. Thus, using mass spectrometry, quantitative proteomic analysis and GO term filters, we identified several mesenchymal traits in proneural GSCs exposed to endothelial cell secretome. Specifically, proneural cells treated with the conditioned media derived from human umbilical vein endothelial cells (HUVEC) upregulated the expression of mesenchymal proteins such as CD44 and VIM, while downregulating the expression of the proneural proteins such as NOTCH1, activated NOTCH intracellular domain (NICD), SOX2 and NESTIN, which were validated using flow cytometry (FACS) and western blots (WB). Using DAVID analysis tool, we detected the features of cellular proteome indicative of the activation of NFkB, Wnt and several other pathways in the proneural cells treated with HUVEC conditioned media. Using conditioned media fractionation through several centrifugation steps we identified the extracellular vesicles (EV) sedimented at 100,000 x g using ultracentrifugation, as the source of activity in endothelial conditioned media capable of triggering mesenchymal shift in proneural GSCs. EVs are heterogeneous membrane structures containing multiple bioactive macromolecules, which have the ability to carry multiple bioactive proteins, transfer them to recipient cells and alter their function, signalling and biological programmes. We compared the effects of EVs, soluble fraction and unfractionated conditioned media in terms of their ability to trigger mesenchymal changes in the phenotype of proneural GSCs. Once the cultures were established, the culture medium was removed and replaced with HUVEC-derived material (conditioned media, supernatant or EV fraction) and responses evaluated over 7 days by microscopical analysis of sphere structures, and biochemically by following the aforementioned proneural or mesenchymal markers (WB, FACS). We observed an upregulation of mesenchymal proteins, as well as downregulation of the proneural proteins, mentioned above. These effects recapitulated those of unfractionated conditioned media and were absent from target cells exposed to EV-depleted conditioned media. The data analysis of EV proteome included canonical markers and pathways of cellular vesiculation as well as markers and pathways of interest with regards to the biological effects associated with treatment of GSC recipient cells. In this regard we observed several EV related tetraspanin markers, which were validated using western blot including CD9, CD63, CD81 and a purity control, BIP. Although we identified several potential effectors associated with endothelial cell EVs that could impact proneural cell phenotype, we focused on MMPs for at least three reasons: (i) evidence in the literature (see text) indicated that MMPs may induce differentiation programs in neural stem cells; (ii) MMPs in EV cargo were relatively abundant and have been implicated in various biological processes; (iii) MMPs released from endothelial cells could be functionally involved in disrupting proneural cell sphere structures that we observed in the presence of endothelial cell secretome. We noted the expressions of MMP1, MMP2, MMP11 and MP14 in our HUVEC-EV mass spectrometry dataset, the activity of which was validated using the MMP activity assay kit from abcam (ab112146). Using GO terms we also detected a signal for NFkB pathway activation in the proteome of endothelial (HUVEC) conditioned media-treated proneural GSCs. NFkB activation is regarded as hallmark of mesenchymal phenotype in GSCs and GBM cells. We validated that the upregulation of NFkB, was also true for the proneural cells treated with HUVEC derived EVs. Moreover, upon blocking MMP expression in proneural cells treated with endothelial cell EVs, we inhibited the activation of NFkB activity thereby documenting that the initial effects of MMPs trigger a shift in cellular phenotype toward NfkB activation and mesenchymal reprogramming. Briefly, we compared GO terms of GSC157 cells treated with their own or HUVEC-derived EVs. Validation of the NFkB pathway activation was analysed using WB and immunofluorescence for levels of NFkB and phosphor-NFkB.
2022-10-14 | PXD034819 | Pride
Project description:Glioblastoma (GBM) cells’ stemness-like features and lineage plasticity promote tumor progression. Here, we demonstrate that Clemastine, a drug for treating hay fever and allergy symptoms, effectively attenuated the stemness and suppressed the propagation of primary GBM cultures bearing PDGFRA amplification. We show that these effects of GBM cells were accompanied by altered gene expression profiling indicative of a more differentiated state of tumor cells, in resonating with Clemastine’s activity in promoting the differentiation of normal oligodendrocyte progenitors (OPCs) into mature oligodendrocyte. Functional assays for proteins that can be pharmacologically targeted by Clemastine, including histamine receptors, muscarinic receptors, and Emopamil binding protein (EBP), revealed the essential roles of these proteins in sustaining GBM cell propagation and suggested that Clemastine likely impairs tumor cells via targeting multiple pathways. Finally, we showed that a PDGFB-driven mouse glioma model, representing the proneural subtype GBMs, was similarly susceptible to Clemastine treatment. Collectively, these results identify pathways that are essential for maintaining the proneural progenitor features of GBMs, and suggest that non-oncology, low toxicity drugs with OPC differentiation promoting effects, such as Clemastine, can be exploited for targeting GBM cell’s progenitor property.
2023-10-04 | GSE186392 | GEO
Project description:The AVAglio and RTOG-0825 randomized, placebo-controlled phase III trials in newly diagnosed glioblastoma reported prolonged progression-free survival (PFS), but not overall survival (OS), with the addition of bevacizumab to radiotherapy/temozolomide. To establish whether certain patient subgroups derived OS benefit from the addition of bevacizumab to first-line standard-of-care therapy, AVAglio patients were retrospectively evaluated for molecular subtype, and bevacizumab efficacy assessed for each patient subgroup. A multivariate analysis accounting for prognostic covariates revealed that bevacizumab conferred a significant OS advantage versus placebo for patients with Proneural IDH1 wild-type tumors (17.1 v 12.8 months, respectively; hazard ratio, 0.43; 95% CI, 0.26 to 0.73; P = .002). This analysis also revealed an interaction between the Proneural subtype biomarker and treatment arm (P = .023). The group of patients with Mesenchymal and Proneural tumors derived a PFS benefit from bevacizumab, compared with placebo; however, this translated to an OS benefit in the Proneural subset only. Retrospective analysis of AVAglio data suggests that patients with IDH1 wild-type Proneural glioblastoma may derive OS benefit from first-line bevacizumab treatment. The predictive value of the Proneural subtype observed in AVAglio should be validated in an independent dataset. A total of 349 (bevacizumab arm, n = 171; placebo arm, n = 178) pretreatment specimens from AVAglio patients (total n = 921) were available for biomarker analysis. Samples were profiled for gene expression and isocitrate dehydrogenase 1 (IDH1) mutation status and classified into previously identified molecular subtypes. PFS and OS were assessed within each subtype.
2016-07-06 | E-GEOD-84010 | biostudies-arrayexpress
Project description:The AVAglio and RTOG-0825 randomized, placebo-controlled phase III trials in newly diagnosed glioblastoma reported prolonged progression-free survival (PFS), but not overall survival (OS), with the addition of bevacizumab to radiotherapy/temozolomide. To establish whether certain patient subgroups derived OS benefit from the addition of bevacizumab to first-line standard-of-care therapy, AVAglio patients were retrospectively evaluated for molecular subtype, and bevacizumab efficacy assessed for each patient subgroup. A multivariate analysis accounting for prognostic covariates revealed that bevacizumab conferred a significant OS advantage versus placebo for patients with Proneural IDH1 wild-type tumors (17.1 v 12.8 months, respectively; hazard ratio, 0.43; 95% CI, 0.26 to 0.73; P = .002). This analysis also revealed an interaction between the Proneural subtype biomarker and treatment arm (P = .023). The group of patients with Mesenchymal and Proneural tumors derived a PFS benefit from bevacizumab, compared with placebo; however, this translated to an OS benefit in the Proneural subset only. Retrospective analysis of AVAglio data suggests that patients with IDH1 wild-type Proneural glioblastoma may derive OS benefit from first-line bevacizumab treatment. The predictive value of the Proneural subtype observed in AVAglio should be validated in an independent dataset.
2016-07-06 | GSE84010 | GEO
Project description:SUMMARY Despite numerous genome-wide association studies involving glioblastoma (GBM), few therapeutic targets have been identified for this disease. Using patient derived glioma sphere cultures (GSCs), we have found that a subset of the proneural (PN) GSCs undergo transition to a mesenchymal (MES) state in a TNFa/NFkB dependent manner with an associated enrichment of CD44 sub-populations and radio-resistant phenotypes. To the contrary, MES GSCs exhibit constitutive NFkB activation, CD44 enrichment and radio-resistance. Patients whose tumors exhibit a higher MES metagene, increased expression of CD44, or activated NFkB were associated with poor radiation response and shorter survival. Our results indicate that NFkB activation mediated MES differentiation and radiation resistance presents an attractive therapeutic target for GBM. SIGNIFICANCE In this study, we show plasticity between the proneural (PN) and mesenchymal (MES) transcriptome signatures observed in glioblastoma (GBM). Specifically, we show that PN glioma sphere cultures (GSCs) can be induced to a MES state with an associated enrichment of CD44 expressing cells and a gain of radio-resistance, which we implicate as NFkB- dependent. Newly diagnosed GBM samples show a direct correlation between radiation response, higher MES metagene, CD44 expression, and NFkB activation. This correlation is also observed in the subset of GBM samples that do not exhibit IDH1 mutation, a favorable prognostic marker. Our results uncover a previously unknown link between subtype plasticity that is regulated by NFkB. Inhibition of NFkB activation can directly impact radio-resistance and presents an attractive therapeutic target for GBM. 4 treatments
2013-08-15 | E-GEOD-49162 | biostudies-arrayexpress