Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CasID on RRM2 promoter region in neuroblastoma

ABSTRACT: dCas9-guided recruitment of the proximity ligation enzyme BirA* to the promoter region of RRM2 in SKNBE2c neuroblastoma cells.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

DISEASE(S): Neuroblastoma

SUBMITTER: Louis Delhaye

LAB HEAD: Sven Eyckerman

PROVIDER: PXD029630 | Pride | 2022-08-12

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

RRM2 enhances MYCN-driven neuroblastoma formation and acts as a synergistic target with CHK1 inhibition.

Nunes Carolina C Depestel Lisa L Mus Liselot L Keller Kaylee M KM Delhaye Louis L Louwagie Amber A Rishfi Muhammad M Whale Alex A Kara Neesha N Andrews Simon R SR Dela Cruz Filemon F You Daoqi D Siddiquee Armaan A Cologna Camila Takeno CT De Craemer Sam S Dolman Emmy E Bartenhagen Christoph C De Vloed Fanny F Sanders Ellen E Eggermont Aline A Bekaert Sarah-Lee SL Van Loocke Wouter W Bek Jan Willem JW Dewyn Givani G Loontiens Siebe S Van Isterdael Gert G Decaesteker Bieke B Tilleman Laurentijn L Van Nieuwerburgh Filip F Vermeirssen Vanessa V Van Neste Christophe C Ghesquiere Bart B Goossens Steven S Eyckerman Sven S De Preter Katleen K Fischer Matthias M Houseley Jon J Molenaar Jan J De Wilde Bram B Roberts Stephen S SS Durinck Kaat K Speleman Frank F

Science advances 20220713 28

High-risk neuroblastoma, a pediatric tumor originating from the sympathetic nervous system, has a low mutation load but highly recurrent somatic DNA copy number variants. Previously, segmental gains and/or amplifications allowed identification of drivers for neuroblastoma development. Using this approach, combined with gene dosage impact on expression and survival, we identified ribonucleotide reductase subunit M2 (RRM2) as a candidate dependency factor further supported by growth inhibition upo ...[more]

PMID: 35857500

Similar Datasets

Global gene expression profiling of Plasmodium falciparum in response to the anti-malarial drug pyronaridine

Project description:This SuperSeries is composed of the following subset Series: GSE30867: Pyronaridine and chloroquine responses in the K1 strain GSE30869: Comparison of developmental stage transcripts in the K1 strain Refer to individual Series

2011-08-01 | E-GEOD-31109 | biostudies-arrayexpress

Pyronaridine and chloroquine responses in the K1 strain

Project description:Pyronaridine (PN) and chloroquine (CQ) are structurally related anti-malarial drugs with primarily the same mode of action. However, PN is effective against several multidrug-resistant lines of Plasmodium falciparum, including CQ-resistant lines, suggestive of important operational differences between the two drugs. Synchronized trophozoite-stage cultures of P. falciparum strain K1 (CQ resistant) were exposed to 50% inhibitory concentrations (IC50) of PN and CQ, and parasites were harvested from culture after 4 and 24 hours exposure. Global transcriptional changes effected by drug treatment were investigated using DNA microarrays. Plasmodium falciparum in vitro cultures were synchronized to trophozoite stage (22-24h post infection) and exposed to either CQ or PN at IC50 concentrations. 18 sample pairs (drug treated/untreated) were analyzed; 9 for CQ and 9 for PN. All drug-treated samples were labelled with Cy5 and untreated controls were labelled with Cy3.

2011-08-01 | E-GEOD-30867 | biostudies-arrayexpress

Genomic binding profiles of ERa in MCF-7 and T47D control or enhancer588-targeted cells

Project description:Estrogen Receptor a (ERa) bindning to DNA was profiled by ChIP-seq in MCF-7 and T47D cells transduced with either control sgRNA, or sgRNA targeting a specific enhancer region (enhancer588). ERa in MCF-7 and T47D control or enhancer588-targeted cells

2015-12-14 | E-GEOD-75779 | biostudies-arrayexpress

Crosstalk between very different family members: How STAT3 activating IL6-type cytokines inhibit the IFNg-like responses of IL27 in hepatocellular carcinoma cells

Project description:Interleukin-27 (IL27) is a type-I-cytokine of the IL6/IL12 family predominantly secreted by activated macrophages and dendritic cells. Best understood are the effects of IL27 on immune cells where it has been described to have pro- or anti-inflammatory properties, either promoting TH1 responses or suppressing TH1 and TH2 responses. The action on other cell types is less well studied. In the liver, IL27 expression was observed to be upregulated in patients with hepatitis B, and sera of hepatocellular carcinoma (HCC) patients contain significantly elevated levels of IL27 compared to healthy controls or patients with hepatitis and/or liver cirrhosis. We previously reported interferon-gamma-like antiviral activity of IL27 in hepatic cells. Here we further studied the effects of IL27 on HCC cells in comparison to other cytokines. We were especially interested in the relevance of the IL27-induced STAT3 activation. Thus we compared its response with those induced by IFNg (STAT1-dominated response) or IL6-type cytokines (IL6, Hyper-IL6 or OSM) (STAT3-dominated response). We find that in hepatocytes, IL27 induces an IFNg-like, STAT1-dependent transcriptional response, but we do not find an effective STAT3-dependent response. The availability of STAT1 seems critical in the shaping of the IL27 response, as the siRNA knock-down of STAT1 revealed its ability to induce the acute-phase protein gamma-fibrinogen, a typical IL6 family characteristic. Moreover, we describe a crosstalk between the signaling of IL6-type cytokines and IL27: responses to the gp130-engaging cytokine IL27 (but not those to IFNs) can be inhibited by IL6-type cytokine pre-stimulation, likely by a SOCS3-mediated mechanism. This experiment represents microarray analysis of three hepatocellular carcinoma cell lines treated with IL-27, IFNg, hyper-IL6 or OSM in combination with shRNA knockdown of STAT3.

2017-07-05 | E-MTAB-4570 | biostudies-arrayexpress

The effect on gene expression by the knockdown of lincRNAs

Project description:To evaluate the effect on gene expression by lincRNAs, we knocked down three lincRNAs and evaluated the gene expression by microarray analysis. Gene expression was measured in Hep3B cells transfected with siRNAs targeting the indicated lincRNAs or negative control siRNA and infected with adenovirus expressing p53 (Ad-p53) or LacZ (Ad-LacZ).

2012-08-01 | E-GEOD-39773 | biostudies-arrayexpress

Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1M-NM-1 in the regulation of the hypoxic gene program

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

2014-06-16 | E-GEOD-51191 | biostudies-arrayexpress

IRF4, a master transcription factor, regulates genes involved in BCR signaling, antigen processing and presentation, and GC development [expression array]

Project description:Interferon regulatory factor 4 (IRF4) is a master transcription factor required for the maturation of germinal center B cells that eventually develop into antibody secreting plasma cells and memory B cells. IRF4-deficient mice exhibit a profound reduction in serum immunoglobulin levels. In spite of wealth of the information relating to IRF4 and B cell biology, little is known about the intricate molecular details of the role of this transcription factor during B cell development. We therefore examined the genome-wide targets of IRF4 by ChIP-chip analysis in GC derived BL2 Burkittâs lymphoma cells. ChIP studies were further supplemented by whole genome expression analysis after shRNA-mediated knockdown of IRF4. Our study revealed that IRF4 regulates expression of genes important for a) BCR signaling b) antigen processing and presentation by MHC. In addition we found that IRF4 possibly in some way involved to regulate LTA, LTB and CXCR5 those involved in immune system development, particularly light zone development related genes such as FDC clustering regulating and IL21R and IL10 who are involved in B cell development.. On the other hand, IRF4 suppressesd genes in the oxidative phosphorylation pathway. Our findings illuminate hitherto unexplored roles of IRF4 in GC B cell development. BL2 Burkitt's lymphoma-derived B cells were infected with lentivirus expressing shRNA for IRF4 or control, and total RNA was subjected to Illumina BeadsExpression Arrays analysis.

2015-12-15 | E-GEOD-64269 | biostudies-arrayexpress

Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function [Rnase-Seq]

Project description:The epithelium lining the epididymis in the male reproductive tract maintains a luminal environment that promotes sperm cell maturation. This process is dependent on the coordinated expression of many genes that encode proteins with a role in epithelial transport. We previously generated genome-wide maps of open chromatin in primary human fetal epididymis epithelial cells to identify potential regulatory elements controlling coordinated gene expression in the epididymis epithelium. Subsequent in silico analysis identified transcription factor binding sites (TFBS) that were over-represented in the HEE open chromatin, include the motif for paired box 2 (PAX2). PAX2 is a critical transcriptional regulator of urogenital tract development, which is well studied in the kidney but is unexplored in the epididymis. Due to the limited lifespan of primary HEE cells in culture we investigated the role of PAX2 in an immortalized HEE cell line (REP). First, REP cells were evaluated by DNase-seq and their open chromatin map overlapped that of primary HEE cells at ~ 65% of sites. Moreover, the PAX2-binding motif was again identified as an overrepresented TFBS within intergenic open chromatin, though on fewer chromosomes than in the primary HEE cells. To identify PAX2-target genes in REP cells, RNA-seq analysis was performed after siRNA-mediated depletion of PAX2 in comparison to a non-targeting siRNA. In response to PAX2-represssion, 3142 transcripts were differentially expressed (1334 up-regulated and 1808 down-regulated). Novel PAX2 targets included multiple genes encoding proteins with a predicted function in the epididymis epithelium. mRNA profile of control and PAX2 knockdown REP cells

2015-01-07 | E-GEOD-59781 | biostudies-arrayexpress

The effect on gene expression by p53 family members and the knockdown of AKR1B10

Project description:To evaluate the effect on gene expression by p53 family members and AKR1B10, we overexpressed p53 family members in H1299 cells or knocked down AKR1B10 in HCT116 cells and evaluated the gene expression by microarray analysis. Gene expression was measured in H1299 cells infected with adenovirus expressing p53, p63g and p73b, and in HCT116 cells transfected with siRNAs targeting AKR1B10 and then treated with adriamycin.

2013-10-31 | E-GEOD-47096 | biostudies-arrayexpress

Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1M-NM-1 in the regulation of the hypoxic gene program [microarray: kD_AP1]

Project description:Skeletal muscle tissue shows an extraordinary cellular plasticity, but the underlying molecular mechanisms are still poorly understood. Here we use a combination of experimental and computational approaches to unravel the complex transcriptional network of muscle cell plasticity centered on the peroxisome proliferator-activated receptor M-NM-3 coactivator 1M-NM-1 (PGC-1M-NM-1), a regulatory nexus in endurance training adaptation. By integrating data on genome-wide binding of PGC-1M-NM-1 and gene expression upon PGC-1M-NM-1 over-expression with comprehensive computational prediction of transcription factor binding sites (TFBSs), we uncover a hitherto underestimated number of transcription factor partners involved in mediating PGC-1M-NM-1 action. In particular, principal component analysis of TFBSs at PGC-1M-NM-1 binding regions predicts that, besides the well-known role of the estrogen-related receptor M-NM-1 (ERRM-NM-1), the activator protein-1 complex (AP-1) plays a major role in regulating the PGC-1M-NM-1-controlled gene program of hypoxia response. Our findings thus reveal the complex transcriptional network of muscle cell plasticity controlled by PGC-1M-NM-1. We used microarrays to detect changes in gene expression in C2C12 cells following PGC-1alpha over-expression and either Atf3, Fos, Jun or control knockdown. We used 2 biological replicates for each condition.

2014-06-16 | E-GEOD-51190 | biostudies-arrayexpress

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