Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

82 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Suppression of HSF1 activity by wildtype p53 creates a driving force for p53 loss-of-heterozygosity

ABSTRACT: p53LOH in murine CRC organoids de-represses HSF1 activity and triggers mutp53-driven invasion.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Mus musculus

SUBMITTER: Ramona Schulz-Heddergott

PROVIDER: E-MTAB-10416 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of mouse colon to investigate how suppression of HSF1 activity by wildtype p53 creates a driving force for p53 loss-of-heterozygosity

Project description:Mice with colonic tumors (chemically induced by AOM/DSS) were treated with Nutlin or control vehicle solution to analyze p53 target gene expression in vivo.

2021-04-20 | E-MTAB-10041 | biostudies-arrayexpress

Enhancement of colorectal cancer therapy through interruption of the HSF1-HSP90 axis by p53 activation or cell cycle inhibition

Project description:The heat-shock protein 90 (HSP90) is a promising target in cancer therapy, but its inhibitors' clinical trial failures are partly due to a compensatory heat-shock response (HSR) mediated by heat-shock factor 1 (HSF1). We previously showed that wildtype p53 reduces HSR by repressing HSF1 via a p21-CDK4/6-MAPK-HSF1 axis. Here, we explore if simultaneous p53 activation or cell cycle inhibition can disrupt the HSF1-HSR axis and enhance HSP90 inhibitors' efficiency. mRNA sequencing was performed on HCT116 cells treated for 24 hours with DMSO, 50 nM Ganetespib, 1 µM RG-7388, or their combination. We found that the p53 activator Idasanutlin suppresses HSF1-HSR activity in HSP90 inhibitor-based therapies, synergistically reducing cell viability and accelerating cell death in p53-proficient colorectal cancer (CRC) cells and organoids. Combination therapy upregulates p53 pathways, apoptosis, and inflammation. In a CRC mouse model, dual HSF1-HSP90 inhibition represses tumor growth and alters immune cell composition. CDK4/6 inhibition under HSP90 inhibition mimics HSR repression in p53-proficient CRC cells. In p53-deficient CRC cells and p53-mutated organoids, combined HSP90 and CDK4/6 inhibition suppresses HSF1-HSR and reduces cancer growth, offering a p53-independent strategy for CRC treatment. In conclusion, we present new options to improve HSP90-based therapies for enhanced CRC treatment.

2025-03-28 | E-MTAB-14877 | biostudies-arrayexpress

RNA-seq of MOLM-13 acute myeloid leukemia cell line treated with single and combination 5-Azacytidine and CB-5083

Project description:MOLM-13 acute myeloid leukemia cells were treated with 7 µM 5-Azacytidine (Cayman Chemical 11164), or 450 nM CB-5083 (Cayman Chemical 19311), or in combination, or 0.1% DMSO as control. Treatments were conducted for 48 hours.

2023-04-22 | E-MTAB-12848 | biostudies-arrayexpress

RNA-seq analysis of human forebrain organoids irradiated with moderate to high doses of ionizing radiation

Project description:Prenatal irradiation can cause neurodevelopmental defects which are characterized by a reduction in brain size (microcephaly). The underlying molecular mechanisms in humans have so far not been studied. Here, we leveraged human forebrain organoids as a model for human embryonic brain development to investigate time- and dose-dependent effects of radiation on organoid growth. For this, organoids of 14 days and 56 days old were irradiated with acute X-ray doses of 0.5 Gy or 2 Gy and compared to controls. Using bulk RNA-seq at different early (6 h and 24 h) and late (14 days) time points after irradiation, we investigated mechanisms of radiation-induced growth defects which resulted from activation of the DNA damage response (cell cycle arrest, DNA repair, apoptosis), premature differentiation and the coordinated repression of primary microcephaly genes.

2025-01-07 | E-MTAB-14150 | biostudies-arrayexpress

RNA-seq of adenoid cystic carcinoma (ACC) ACCX11 cells compared to normal salivary glands

Project description:PDX-derived ACCX11 adenoid cystic carcinoma cells were compared to normal salivary gland (NSG) controls.

2023-12-01 | E-MTAB-12978 | biostudies-arrayexpress

Transcriptome changes triggered by the loss of function of gene Mppcs in genome-edited Marchantia polymorpha plants

Project description:In the present study, Marchantia polymorpha Mppcs loss of function mutants were generated through CRISPR/cas9 mediated genome-editing. To assess whether the knockout of MpPCS gene affects the transcription of M. polymorpha nuclear genes in unstressed condition, the Mppcs-2 knockout mutant and Cam2 wild-type transcriptomes were compared by RNA-Seq.

2022-08-29 | E-MTAB-11885 | biostudies-arrayexpress

Transcriptome changes in leaves of the DEFENSE NO DEATH 1 (DND1) silenced potato plants

Project description:Silencing of DND1 in potato leads to resistance to late blight, powdery mildew and Botrytis cinerea. At the same time, however, it reduces plant growth and causes leaf necrosis. To get knowledge on the molecular events behind the pleiotropic effect of DND1 downregulation in potato transcriptome analysis were performed on three DND1 silenced lines in comparison with the potato cultivar ‘Désirée’ as a wild-type.

2024-10-22 | E-MTAB-13824 | biostudies-arrayexpress

ChIP-seq of MYB in adenoid cystic carcinoma (ACC) ACCX11 cells

Project description:Chromatin immunoprecipitation was carried out using an anti-MYB antibody in PDX-derived ACCX11 adenoid cystic carcinoma cells. Input samples were extracted prior to the addition of antibody.

2023-12-01 | E-MTAB-12976 | biostudies-arrayexpress

Root transcriptomic response of three potato cultivars (Desirée, Innovator, Mozart) to salt stress (NaCl=125mM) after 6h and 24h

Project description:This experiment aims to compare the transcriptomic response of three potato potato cultivars to salt stress. Plants were grown in hydroponic conditions (0.5MS +0.05MES) with long day light cycle (16h/8h). Roots were collected at ZT10 (time point 6h) and the following day at ZT4 (time point 24h). Three biological replicates were used and each biological replicate is composed of the roots of three plants. Tissues were flash-frozen in liquid nitrogen and subsequently ground with a mortar. RNA was extracted with FavorPrep™ Plant Total RNA Mini Kit from FAVORGEN. DNA was degraded in the column with RNase-free DNase I (Roche).

2025-03-13 | E-MTAB-14181 | biostudies-arrayexpress

Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny

Project description:Although Lgr5+ intestinal stem cells have been expanded in vitro as organoids, homogeneous culture of these cells has not been possible so far. Here we show that two small molecules, CHIR99021 and valproic acid, synergistically maintain self-renewal of mouse Lgr5+ intestinal stem cells, resulting in nearly homogeneous cultures. The colony-forming efficiency of cells from these cultures is ~100-fold greater than that of cells cultured in the absence of CHIR99021 and valproic acid, and multilineage differentiation ability is preserved. We made use of these homogeneous cultures to identify conditions employing simultaneous modulation of Wnt and Notch signaling to direct lineage differentiation into mature enterocytes, goblet cells and Paneth cells. Expansion in these culture conditions may be feasible for Lgr5+ cells from the mouse stomach and colon and from the human small intestine. These methods provide new tools for the study and application of multiple intestinal epithelial cell types. Total RNA was isolated from two independently established wild-type mouse small intestinal organoid lines after culture for 6 days in control condition or in the presence of CHIR99021, Valproic Acid (VPA) or both compounds. cRNA was labeled with Cy5 and hybridized against Cy3 labeled cRNA from control organoids (as an internal reference) on 4X44K Agilent Whole Mouse Genome dual colour Microarrays (G4122F), resulting in eight individual arrays.

2013-11-22 | E-GEOD-51539 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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