Impact of ZFAND3 knockdown on whole-genome gene expression in GBM cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE138618 | GEO | 2020/09/30
REPOSITORIES: GEO
Similar Datasets
Project description:Treating recurrent GBM is a clinical challenge due to its highly resistant and aggressive nature. In order to develop new therapeutic targets for recurrent GBM a better understanding of its molecular landscape is necessary. Here we used a cellular model, developed in our lab which generates paired primary and recurrent samples from GBM cell lines and primary patient samples hence allowing us to compare the molecular differences between the two populations. Total RNA seq analysis of parent and recurrent population of two cell lines and one patient sample revealed a significant upregulation of Extracellular matrix interaction in recurrent population. Since matrix stiffness plays a pivotal role in cell-ECM interaction and downstream signaling, we developed a system that mimicked the brain like substrate stiffness by using collagen coated polyacrylamide-based substrate whose stiffness can be modified from normal brain (0.5kPa) to tumorigenic (10kPa). Using these substrates, we were able to capture the morphological and physiological differences between parent and recurrent GBM which were not evident on plastic surfaces (~1 GPa). On 0.5kPa, unlike circular parent cells, recurrent GBM cells showed two morphologies (circular and elongated). The recurrent cells growing on 0.5kPa also showed higher proliferation, invasion, migration and in-vivo tumorigenicity in orthotropic GBM mouse model, compared to parent cells. Furthermore, recurrent cells exhibited elevated velocity irrespective of substrate stiffness, which indicated that recurrent cells may possess inherent differential mechanosignalling ability which was reflected by higher expression of ECM proteins like Collagen IVA, MMP2 and MMP9. Moreover, mice brain injected with recurrent cells grown on 0.5kPa substrate showed higher Young’s modulus values suggesting that recurrent cells conditioned on 0.5kPa make the surrounding ECM stiffer. Importantly, inhibition of EGFR signaling, that is amplified with tissue stiffening in GBM resulted in decreased invasion, migration and proliferation in 0.5kPa recurrent cells, but interestingly survival remained unaffected, highlighting the importance of mimicking the physiological stiffness of the brain mimicking clinical scenario. Total RNA seq analysis of parent and recurrent cells grown on plastic and 0.5kPa substrate identified PLEKHA7 as significantly upregulated gene specifically in 0.5kPa recurrent sample. Higher protein expression of PLEKHA7 in recurrent GBM as compared to primary GBM was validated in patient biopsies. Accordingly, PLEKHA7 knockdown reduced invasion and survival of recurrent GBM cells. Together, these data provides a model system that captures the differential mechanosensing signals of primary and recurrent GBM cells and identifies a novel potential target specific for recurrent GBM.
2023-06-29 | E-MTAB-11293 | biostudies-arrayexpress
Project description:Glioblastoma multiforme (GBM) is the most prevalent and deadliest adult brain tumor. To systematically characterize the pathways governing brain invasion, we developed a three-dimensional (3D) ex vivo organotypic invasion model with clinical relevance to GBM. We used this model to enrich for highly invasive GBM cell population. Using next-generation sequencing to transcriptomically profile highly invasive and poorly invasive GBM cell populations, we have identified a network of extracellular matrix (ECM) components, including multiple collagens and collagen-interacting proteins, which are upregulated by invading GBM cells and strongly correlate in expression with clinical glioma progression outcomes. We identify the interferon regulatory factor 3 (IRF3) as a direct transcriptional repressor of ECM factors in GBM and show that IRF3 acts as an endogenous suppressor of GBM invasion. Therapeutic activation of IRF3 by inhibiting casein kinase 2 (CK2) -- a negative regulator of IRF3 phosphorylation -- downregulated the expression of ECM factors and suppressed GBM invasion in ex vivo and in vivo models across a panel of patient-derived GBM cell lines representative of the main molecular GBM subtypes in the clinic. Our findings illustrate an integrated and systematic approach for the discovery of novel pathways regulating brain tumor invasion and provide a strong mechanistic insight into the notorious, yet poorly understood, invasion capacity of GBM tumors.
2017-10-01 | GSE87535 | GEO
Project description:Most patients affected by Glioblastoma multiforme (GBM) experience a recurrence of the disease because of the spreading of tumor-initiating cells (TICs) beyond surgical boundary. Unveiling and targeting molecular mechanisms causing this process is a logic goal to impair GBM killing ability. In an orthotopic xenograph model, we have noticed that GBM TICs isolated from several patients may fall into two classes of invasive behavior: nodular or diffuse. In order to identify genes responsible for the diffusive type of invasion, we have compared by genome expression analysis, cultured GBM TICs belonging to the two classes. This analysis allowed us to identify a small group of regulated genes in the diffusive type of GBM TICs. The gene ontology process of cell adhesion and the localization of the gene product functions to the plasmamembrane resulted significantly associated to this gene set. Real time RT-PCR and immunofluorescence analyses performed for a selected subgroup of regulated genes/gene products confirmed the results obtained by the expression analysis. Some of the genes that we found upregulated in our screening were already proven to be involved in Glioma cell invasion supporting our study. However, we have also identified genes that were not previously implicated in this process. To assess whether these are required to sustain TICs GBM invasion, we silenced a subset of them and evaluated in Boyden chamber the invasive ability of the cells. Our study provides novel target genes to be evaluated for the inhibition of GBM diffusion within the SNC. As we observed that GBM TICs may fall into two classes of M-bM-^@M-^\in vivoM-bM-^@M-^] invasive behavior in mouse orthotopic transplantation: expansive or highly diffusive, resulting in the hostM-bM-^@M-^Ys white and gray matters substitution, we decided to identify genes associated with the latter phenotype by microarray analysis. Three replicates of each class were analyzed.
2012-09-11 | E-GEOD-16805 | biostudies-arrayexpress
Project description:Glioblastoma (GBM) is the most aggressive cancer in brain and contains a high mortality ratedue to lack of effective treatment strategy. Molecular mechanisms of GBM characteristic invasive growth are urgently need to improve the poor prognosis. Via single nuclear-sequences of primary and recurrent GBM samples, level of the M3 muscarinic acetylcholine receptor (CHRM3) was significantly higher in recurrent samples. Moreover, immunohistochemical staining of an array of glioma samples showed that high levels of CHRM3 is correlated to poor prognosis of glioma, consistent with The Cancer Genome Atlas (TCGA) database. Knockdown of CHRM3 retarded glioma cell growth and invasion. In vivo assay of orthotopic glioma animal model indicated that inhibition of CHRM3 significantly suppressed glioma progression with prolonged survival time. Transcriptome analysis revealed that CHRM3 knockdown significantly reduced array of classic factors involved in cancer invasive growth including MMP1/MMP3/MMP10/MMP12 and CXCL1/CXCL5/CXCL8. Taken together, our study identified that CHRM3 is a new and important factor of GBM progression via regulation of multiple oncogenic genes and these results provide a new biomarker for prognosis and therapy of GBM patients.
2022-12-10 | GSE220083 | GEO
Project description:Background. Glioblastoma (GBM) is the most lethal form of brain tumors in human adults, and hypoxia is a common microenvironment in this disease. Circular RNAs (circRNAs) are identified as regulators in cancers including GBM. However, the specific roles of circRNAs in GBM under hypoxic condition remains elusive. Methods. RNA-seq was employed to investigate the expression profile of circRNAs in U87 cells under normoxia and hypoxia. Two circRNAs spliced from the same parental gene, named as circPLOD2a and circPLOD2b, were identified as hypoxia-responsive circRNAs, whose circular structures were verified by, qRT-PCR, RNase R digesting and Sanger sequencing in U87. Knockdown and overexpression of circPLOD2a/b in GBM cells were used to investigate the biological functions of these two circRNAs on tumor progression. Fluorescence in situ hybridization, RNA-pull down, mass spectrometry and RNA immunoprecipitation assays were conducted to explore the interactions between circPLOD2a/b, human antigen R (HuR), xin actin binding repeat containing 1 (XIRP1). Results. CircPLOD2a/b were significantly up-regulated in hypoxic GBM cells and directly induced by HIF1α under hypoxia. Overexpression of circPLOD2a/b enhance GBM cell invasion and migration, which could be inhibited by circPOD2a/b knockdown. Mechanistically, circPLOD2a/b competitively bind to HuR, inhibiting the interaction between HuR and XIRP1, thus promoting the tumor aggressiveness in GBM both in vitro and in vivo through down-regulating XIRP1. Conclusions. Hypoxia-induced circPLOD2a/b were identified as key regulators of migration and invasion in GBM cells, and act as oncogenic circRNAs to attenuate the interaction between HuR and XIRP1, which may be potential therapeutic strategy for GBM treatment.
2023-10-23 | GSE245634 | GEO
Project description:Background. Glioblastoma (GBM) is the most lethal form of brain tumors in human adults, and hypoxia is a common microenvironment in this disease. Circular RNAs (circRNAs) are identified as regulators in cancers including GBM. However, the specific roles of circRNAs in GBM under hypoxic condition remains elusive. Methods. RNA-seq was employed to investigate the expression profile of circRNAs in U87 cells under normoxia and hypoxia. Two circRNAs spliced from the same parental gene, named as circPLOD2a and circPLOD2b, were identified as hypoxia-responsive circRNAs, whose circular structures were verified by, qRT-PCR, RNase R digesting and Sanger sequencing in U87. Knockdown and overexpression of circPLOD2a/b in GBM cells were used to investigate the biological functions of these two circRNAs on tumor progression. Fluorescence in situ hybridization, RNA-pull down, mass spectrometry and RNA immunoprecipitation assays were conducted to explore the interactions between circPLOD2a/b, human antigen R (HuR), xin actin binding repeat containing 1 (XIRP1). Results. CircPLOD2a/b were significantly up-regulated in hypoxic GBM cells and directly induced by HIF1α under hypoxia. Overexpression of circPLOD2a/b enhance GBM cell invasion and migration, which could be inhibited by circPOD2a/b knockdown. Mechanistically, circPLOD2a/b competitively bind to HuR, inhibiting the interaction between HuR and XIRP1, thus promoting the tumor aggressiveness in GBM both in vitro and in vivo through down-regulating XIRP1. Conclusions. Hypoxia-induced circPLOD2a/b were identified as key regulators of migration and invasion in GBM cells, and act as oncogenic circRNAs to attenuate the interaction between HuR and XIRP1, which may be potential therapeutic strategy for GBM treatment.
2023-10-23 | GSE245635 | GEO
Project description:Impact of ZFAND3 knockdown on whole-genome gene expression in GBM cells
| PRJNA576588 | ENA
Project description:Recent advances in glioblastoma (GBM) studies provide a comprehensive catalog of its genetic aberrations and cellular heterogeneity. However, a solid understanding of genotype-based analysis of cancer pathway dependency and actionable target identification is required to transform GBM treatment into a personalized era. Here, we generated a spectrum of mutant iPSCs harboring frequent GBM mutations with CRISPR/Cas9 and profiled the organoids (LEGO: Laboratory Engineered Glioblastoma Organoid) derived from these iPSCs temporally on transcriptome, methylome, metabolome, lipidome, proteome, and phospho-proteome levels. We found that LEGOs form brain tumors in vivo and recapitulate critical features of human GBM. The multi-omics analysis discovered essential milestones driven by genetic heterogeneity during GBM progressions, such as lineage alteration, methylome rewriting, and metabolome/lipidome reprogramming, in concordance with altered pathway activity and drug response. This study provides a tool and research path to realizing genome-based personalized GBM therapy using novel advanced models.
2022-09-17 | ST002284 | MetabolomicsWorkbench
Project description:Most patients affected by Glioblastoma multiforme (GBM) experience a recurrence of the disease because of the spreading of tumor-initiating cells (TICs) beyond surgical boundary. Unveiling and targeting molecular mechanisms causing this process is a logic goal to impair GBM killing ability. In an orthotopic xenograph model, we have noticed that GBM TICs isolated from several patients may fall into two classes of invasive behavior: nodular or diffuse. In order to identify genes responsible for the diffusive type of invasion, we have compared by genome expression analysis, cultured GBM TICs belonging to the two classes. This analysis allowed us to identify a small group of regulated genes in the diffusive type of GBM TICs. The gene ontology process of cell adhesion and the localization of the gene product functions to the plasmamembrane resulted significantly associated to this gene set. Real time RT-PCR and immunofluorescence analyses performed for a selected subgroup of regulated genes/gene products confirmed the results obtained by the expression analysis. Some of the genes that we found upregulated in our screening were already proven to be involved in Glioma cell invasion supporting our study. However, we have also identified genes that were not previously implicated in this process. To assess whether these are required to sustain TICs GBM invasion, we silenced a subset of them and evaluated in Boyden chamber the invasive ability of the cells. Our study provides novel target genes to be evaluated for the inhibition of GBM diffusion within the SNC.
2012-09-11 | GSE16805 | GEO
Project description:BET inhibitor UM-002 reduces GBM proliferation and invasion
| PRJNA723881 | ENA