Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dll1 acts as a tumor suppressor in neural stem cells to induce an astroglial lineage-restricted glioblastoma

ABSTRACT: There is increasing evidence for tissue stem cells as potential source for cancers. However, the cellular and molecular mechanisms at the origin of this transformation remain elusive. Here we show that Delta-like1 (Dll1) mutation induces the oncogenic transformation of neural stem cell–derived neurospheres into oncogenic spheres capable of generating histological and molecular human glioblastoma (GBM)-like tumors upon subcutaneous and intracranial transplantations into nude mice. Serial transplantation assays suggest that Dll1 spheres tumorigenicity results from the oncogenic transformation of normal neural stem cell into GBM-producing stem cell. Compared differentiation of Dll1 vs. WT spheres shows the presence in Dll1 spheres of a subpopulation of cells which although fated to a glial lineage fail to differentiate terminally, in keeping with the astrocytic promoting function of Delta-Notch. This population of astrocyte progenitors proliferates actively and fails to down-regulate EGFR phosphorylation. These studies suggest that Dll1-induced tumorigenesis is restricted to the astrocytic lineage thereby providing a model for human GBM as well as an explanation for the duality of Notch signaling acting either as an oncogene or a tumor suppressor in stem/progenitor cells derived tumors, depending on the lineage commitment. Comparison between control (WT) and mutants (Dll1-3 and Dll1-5) cells was performed. Two biological replicates (n=3 each replicate) were used, and each replicate (n=3, total RNA pooled) was dye-swaped.

ORGANISM(S): Mus musculus

SUBMITTER: Randeep Rakwal

PROVIDER: E-GEOD-32293 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Activity of the mouse Notch ligand DLL1 is sensitive to C-terminal tagging in vivo

Project description:Objective DLL1 is a mammalian Notch ligand with essential functions during embryonic development. We tagged endogenous DLL1 in one homologous recombination step such that AcGFP-HA tagged DLL1 could be converted by Cre-mediated site-specific recombination into StrepFlag tagged DLL1. We anticipated that this should allow us to visualise DLL1 in living cells as well as allow for sorting and enrichment of DLL1-expressing cells and efficient purification of DLL1 protein complex. Results We generated constructs to express a DLL1 variant that carried C-terminal in frame an AcGFPHA tag flanked by loxP sites followed by a StrepFlag tag out of frame. Cre-mediated recombination removed AcGFP-HA and added StrepFlag in frame to DLL1. The AcGFPHAstopStrepFlag tag was added to the Dll1 cDNA to allow for tests in cultured cells in vitro and was introduced into endogenous DLL1 in mice using ES cells modified by homologous recombination. Tagged DLL1 protein was detected by antibodies against GFP and HA or Flag, respectively, both in CHO cell and embryo lysates. In CHO cells the AcGFP protein fused to DLL1 was functional. In vivo AcGFP expression was below the level of detection by direct fluorescence. However, the StrepFlag tag allowed us to specifically purify DLL1 complexes from embryo lysates. Homozygous mice expressing AcGFPHA or StrepFlag-tagged DLL1 revealed a vertebral column phenotype reminiscent of disturbances in AP polarity during somitogenesis, a process most sensitive to reduced DLL1 function. Thus, even small C-terminal tags can impinge on sensitive developmental processes requiring DLL1 activity.

2021-11-03 | PXD024680 | Pride

Dll1 marks early secretory progenitors in gut crypts that can revert to stem cells upon tissue damage

Project description:The introduction of GFP into the Dll1 locus has made it possible to isolate and study primary intestinal Dll1 positive cells, which constitute the secretory cell precursors of the intestine. Applying DNA array technology, we profiled the RNA changes of FACS-sorted Dll1_high/CD24_low, Dll1_high/CD24_medium and Dll1_high/CD24_high cells . We used cell fractions of intestines from Dll1-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Dll1 promoter. RNA was isolated from three FACS sorted cell populations: all are expressing Dll1-GFP at high levels, but are expressing different levels of Cd24 (low, medium and high). For this set two biological replicates were generated. One additional fraction was isolated from Lgr5-EGFP-ires-CreERT2 mice, expressing GFP under the control of the Lgr5 promoter. This cell fraction contains intestinal stem cells. Differentially labelled cRNA from these cell fractions was hybridized against a reference (RNA isolated from whole intestine) on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F).

2012-09-27 | E-GEOD-39915 | biostudies-arrayexpress

Glioma-propagating cells as an in vitro screening platform: PLK1 as a case study

Project description:Gliomas are the most devastating of primary adult malignant brain tumors. These tumors are highly infiltrative and can arise from cells with extensive self-renewal capability and chemoresistance, frequently termed glioma-propagating cells (GPCs). GPCs are thus the plausible culprits of tumor recurrence. Treatment strategies that eradicate GPCs will greatly improve disease outcome. Such findings support the use of GPCs as in vitro cellular systems for small molecule screening. However, the nuances in utilizing GPCs as a cellular screening platform are not trivial. These slow-growing cells are typically cultured as suspension, spheroid structures in serum-free condition supplemented with growth factors. Consequently, replenishment of growth factors throughout the screening period must occur to maintain cells in their undifferentiated state, as the more lineage-committed, differentiated cells are less tumorigenic. We will present a case study of a small molecule screen conducted with GPCs and explain how unique sphere activity assays were implemented to distinguish drug efficacies against the long-term, self-renewing fraction, as opposed to transient-amplifying progenitors, latter of which are detected in conventional viability assays. We identified Pololike kinase 1 as a regulator of GPC survival. Finally, we leveraged on public glioma databases to illustrate GPC contribution to disease progression and patient survival outcome. Total RNA from primary neurosphere culture of brain tumor specimens were hybridized in baseline condition. Specimens were obtained from 11 patients and replicate arrays were performed for all 11 neurosphere cultures.

2012-08-01 | E-GEOD-36782 | biostudies-arrayexpress

ST3GAL1-Associated Transcriptomic Program in Glioblastoma Tumor Growth, Invasion, and Prognosis

Project description:Cell surface sialylation confers many roles in cancer biology including cell proliferation, invasiveness, metastasis and angiogenesis. We show here that ST3Gal1 sialyltransferase marks a self-renewing cellular fraction. Depletion of ST3GAL1 abrogates glioma cell growth and tumorigenicity. In contrast, TGFb induces ST3GAL1 expression and correlates with the pattern of ST3Gal1 activation in patient tumors of the mesenchymal molecular subtype. To delineate the downstream events of ST3Gal1 signaling, we utilized a bioinformatical approach that leveraged on the greater statistical power of large patient databases, and subsequently verified our predictions in patient-derived glioma cells. We identify FoxM1, a major stem cell regulatory gene, as a downstream effector, and show that ST3Gal1 mediates the glioma phenotype through control of FoxM1 protein degradation Total RNA from primary neurosphere culture of brain tumor specimens were flow-sorted to identify Peanut Agglutinin(PNA) affinity. The fractions of different degress of PNA bound GPCs were hybridized on Illumina Human Ref-8v2 bead chips to study the impact of transcriptome pattern of PNA affinity. Specimens were obtained from 4 patients and replicate arrays were performed for all 4 neurosphere cultures.

2015-11-09 | E-GEOD-51411 | biostudies-arrayexpress

ST3GAL1-Associated Transcriptomic Program in Glioblastoma Tumor Growth, Invasion, and Prognosis

Project description:Cell surface sialylation confers many roles in cancer biology including cell proliferation, invasiveness, metastasis and angiogenesis. We show here that ST3Gal1 sialyltransferase marks a self-renewing cellular fraction. Depletion of ST3GAL1 abrogates glioma cell growth and tumorigenicity. In contrast, TGFb induces ST3GAL1 expression and correlates with the pattern of ST3Gal1 activation in patient tumors of the mesenchymal molecular subtype. To delineate the downstream events of ST3Gal1 signaling, we utilized a bioinformatical approach that leveraged on the greater statistical power of large patient databases, and subsequently verified our predictions in patient-derived glioma cells. We identify FoxM1, a major stem cell regulatory gene, as a downstream effector, and show that ST3Gal1 mediates the glioma phenotype through control of FoxM1 protein degradation Total RNA from primary neurosphere culture of brain tumor specimens non-treated and ST3GAL1 KD clones. The mRNAs of 5 unique glioma propagating cells (GPCs) were hybridized on Affymetrix HG-U133 Plus2 chips to study the transcriptomic impact of ST3GAL1 knock-down. Specimens were obtained from 5 glioma patients and replicate arrays were performed for all 5 neurosphere cultures.

2015-11-09 | E-GEOD-51395 | biostudies-arrayexpress

Dll1 acts as a tumor suppressor in neural stem cells to induce an astroglial lineage-restricted glioblastoma

Project description:There is increasing evidence for tissue stem cells as potential source for cancers. However, the cellular and molecular mechanisms at the origin of this transformation remain elusive. Here we show that Delta-like1 (Dll1) mutation induces the oncogenic transformation of neural stem cell–derived neurospheres into oncogenic spheres capable of generating histological and molecular human glioblastoma (GBM)-like tumors upon subcutaneous and intracranial transplantations into nude mice. Serial transplantation assays suggest that Dll1 spheres tumorigenicity results from the oncogenic transformation of normal neural stem cell into GBM-producing stem cell. Compared differentiation of Dll1 vs. WT spheres shows the presence in Dll1 spheres of a subpopulation of cells which although fated to a glial lineage fail to differentiate terminally, in keeping with the astrocytic promoting function of Delta-Notch. This population of astrocyte progenitors proliferates actively and fails to down-regulate EGFR phosphorylation. These studies suggest that Dll1-induced tumorigenesis is restricted to the astrocytic lineage thereby providing a model for human GBM as well as an explanation for the duality of Notch signaling acting either as an oncogene or a tumor suppressor in stem/progenitor cells derived tumors, depending on the lineage commitment.

2011-09-24 | GSE32293 | GEO

ST3GAL1-Associated Transcriptomic Program in Glioblastoma Tumor Growth, Invasion, and Prognosis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-11-07 | E-GEOD-51413 | biostudies-arrayexpress

Expression analysis of big neurospheres generated in vitro

Project description:Expression analysis of neurospheres generated in vitro treated by potassium chloride (KCl) and norepinephrine Neurospheres generated in vitro were treated with norepinephrine or potassium chloride. Gene expression analysis was then carried out to identify genes that are up or down regulated due to chemical treatment.

2015-06-12 | E-GEOD-67304 | biostudies-arrayexpress

Expression analysis of neurospheres generated in vitro

Project description:Neurospheres generated in vitro were treated with non-epinephrine or potassium chloride. Gene expression analysis was then carried out to identify genes that are up or down regulated due to chemical treatement. The microarray data for the neurosphere samples was generated at Queensland Brain Institute. Briefly, RNA was isolated from neurospheres generated in presence of either N (norepinephrine) or K (potassium chloride)and converted to cDNA using Applause WT-Amp ST kit (NuGEN). Fragmentation and biotin labelling of the cDNA was carried out using Encore Biotin module (NuGEN) for Affymetrix GeneChip Mouse Gene 1.0 ST arrays. Labelled cDNA was hybridised to arrays in an oven at 45M-BM-0C. Hybridised arrays were scanned using the Affymetrix GeneChip Scanner and the scanned data (.CEL files) was transferred to the Partek Genomics Suite and data analysis was carried out as described in Narayanan RK, Mangelsdorf M, Panwar A, Butler TJ, Noakes PG, et al. (2013).

2014-06-20 | E-GEOD-57440 | biostudies-arrayexpress

Functional genomics of glioblastoma: from epigenetics to proteomic investigation of tumor-initiating cell secretome

Project description:The main objectives of the project are as follows: 1) Deciphering the TIC specific secretome signature. The secretome collected from four different TICs and their corresponding differentiated cell cultures will be subjected to label-free quantitative proteomic analysis to identify a TIC specific secretome signature. 2) Validation and functional characterization of selected molecules from TIC specific secretome signature. Selected molecules based on the level of regulation and literature information will be validated at the level of transcript and protein. The importance of a set of validated proteins will be studied both in vitro using neurosphere cultures and angiogenesis assays, and in vivo using an intracranial glioma model in nude mice 3) Characterizing of GBM specific serum proteome signature. Using label-free quantitative proteomics, we will compare the serum proteome of tumor bearing mice (xenotransplantated with TICs), early after tumor establisment and after the tumor has reached its maximum size.We will also explore by targeted quantitative proteomics whether the level of “specific” TIC-secreted proteins is increased in the serum of TIC initiated GBM bearing mice and verify, using the same strategy, proteins found to be differentially expressed in serum in both mice groups. These studies will reveal whether TIC-secreted proteins (and/or other GBM-derived proteins) can be retrieved in serum and thus be considered as candidate biomarkers of GBM.

2022-06-07 | PXD032958 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data