Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-SEQ of epithelioid mouse mesothelioma treated with or without CSF1R inhibitor

ABSTRACT: Mesothelioma arises in humans after prolonged chronic inflammation driven by the presence of inhaled asbestos fibres in the chest cavity. We have generated a genetically engineered mouse model of mesothelioma that combines CRE-mediated deletion of 3 disease-relevant tumour suppressor genes, namely Cdkn2a, Nf2 and p53, with a single intrapleural injection of asbestos. Tumours arising in these mice are heavily infiltrated by macrophages, which play. key roles in tumour development and are thought to create a permissive environment for tumour growth. We used a CSF1R inhibitor, AZD7507, to suppress macrophages, starting from day 60 post tumour initiation. This experiment analysed the overall tumour transcriptome in response to macrophage suppression

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Mus musculus

SUBMITTER: Daniel Murphy

PROVIDER: E-MTAB-12998 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Gene expression profiles in MexTAg transgenic mouse and wild type mouse asbestos-induced mesothelioma

Project description:Malignant mesothelioma is an aggressive tumour arising from the mesothelial cells lining the pleura, peritoneum or pericardium. The principal carcinogen associated with malignant mesothelioma is asbestos . A transgenic mouse model, denoted MexTAg, which encodes the Simian Virus 40 (SV40) large T antigen (TAg) downstream of the mesothelin promoter was developed. Inactivation of the tumour suppressors p53 and RB following binding to TAg results. In this model mesothelioma develops in the mesothelial cell compartment after the mice have been exposed to asbestos. The MexTAg transgenic mouse model of mesothelioma model enables analysis of the molecular events associated with asbestos induced mesothelioma and is utilised here to investigate the molecular dynamics of tumours induced in these mice, using gene expression patterns as a read out.

2016-01-30 | E-MTAB-3988 | biostudies-arrayexpress

Translational profiling shows aberrant translational regulation in primary mesothelioma cells compared to untransformed mesothelium control cells

Project description:Malignant mesothelioma (MpM) is an aggressive, fatal tumour, associated with asbestos exposure, for which there is no curative therapy and the mechanism of carcinogenesis is poorly understood. We use translational profiling to show that dysregulated post-transcriptional control makes a major contribution to aberrant cell growth in primary MpM cells, with elevated signalling through the mTOR axis activating mRNA translation initiation.

2020-11-10 | E-MTAB-8167 | biostudies-arrayexpress

Gene expression changes between primary mesothelioma tumour cells and commercially available cell lines, compared to normal primary mesothelial cells

Project description:Malignant mesothelioma (MM) is an aggressive, fatal tumour strongly associated with asbestos exposure. There is an urgent need to improve MM patient outcomes and this requires functionally validated pre-clinical models. Mesothelioma-derived cell lines provide an essential and robust tool widely used for candidate drug evaluation. Although a number of cell lines are commercially available, a detailed comparison of these lines with freshly-derived primary tumour cells to validate their suitability as pre-clinical models is lacking. Patient-derived primary mesothelioma cell lines were established and characterised by gene expression profiling. Molecular profiling revealed a significantly different transcriptome in commercially available compared with primary cell lines. Primary mesothelioma cell lines are more representative of the tumour close to its native state and show a degree of molecular diversity, thus capturing the disease heterogeneity in a patient cohort.

2018-02-01 | E-MTAB-6351 | biostudies-arrayexpress

In situ depletion of Nuak1 in murine colon tumours

Project description:The aim of the project is to determine the impact of NUAK1 depletion on the transcriptome of in situ colon tumours. Tumours were initiated in Villin-CRE-ER;APC-floxed;DI-shNUAK1 mice, followed by treatment for 1 week with dextran sodium sulphate. 68 days after tumour initiation, NUAK1 shRNAs were induced by doxycycline administration (via gavage), or left un-induced. 6 tumours were harvested from NUAK1 shRNA expressing mice and 6 from controls. RNA was isolated using Qiagen RNEasy and analyzed by Illumina paired-end RNA-SEQ

2018-02-19 | E-MTAB-6265 | biostudies-arrayexpress

Chromosomal aberration of asbestos-induced malignant mesothelioma in rats

2012-08-14 | GSE36577 | GEO

Chromosomal aberration of asbestos-induced malignant mesothelioma in rats

Project description:Exposure to asbestos is a risk for malignant mesothelioma in humans. We carried out array comparative genomic hybridization (CGH) analysis in a rat model by repeated intraperitoneal injections of three types of asbestos including chrysotile, crocidolite and amosite. We found a common chromosomal deletion mapped to the chromosome 5q32 locus, containing the genes encoding tumour suppressor genes CDKN2A/2B/ARF. Homozygous deletion of CDKN2A/2B/ARF was observed in the majority (92.6%) of the rat MM samples. Carcinogenesis protocol was performed using specific pathogen-free male and female F1 hybrid rats between Fischer344 and Brown-Norway strains. A total of 27 tumor samples were profiled on Agilent 244A aCGH arrays according to manufacturer's instructions for the screening purpose.

2012-08-13 | E-GEOD-36577 | biostudies-arrayexpress

Genexpression of murine mesothelioma cell lines AC29 and AB1

Project description:RNA from two murine mesothelioma cell lines (AC29 and AB1) was extracted and hybridized to Affymetrix Microarrays to compare gene expression. Both mesothelioma cell lines were established following intraperitoneal introduction of crocidolite (asbestos) fibers (Davis et al. 1992) in CBA mice (AC29 cell line), and BALB/c mice (AB1).

2017-03-29 | GSE97150 | GEO

Gene changes in response to asbestos and carbon nanotube exposure in the pleural cavity, measured using microarrays.

Project description:Exposure to asbestos fibres causes profound pathological changes in the pleural cavity and can result in the development of a fatal tumour, malignant mesothelioma (MM). Due to their structural similarities there is concern that carbon nanotubes (CNTs) may present a similar inhalation hazard. However the underlying mechanisms leading to fibre-mediated mesothelioma development are not yet fully understood. To investigate the molecular changes which occur at the mesothelium as a consequence of direct exposure to fibres, short and long asbestos fibres (SFA and LFA) and short and long CNTs (NTS and NTL) were instilled directly into the pleural cavity in mice. After 12 weeks RNA was extracted from the diaphragm and microarray analysis was performed on all of the treatment groups compared to a 0.5% BSA/saline control. Concurrent histopatholgical investigations were performed and revealed that exposure to fibres resulted in responses that were dependent upon the length of the fibres, but not on fibre type. In response to NTL and LFA there was acute inflammation and fibrosis on the parietal pleura; no inflammatory changes were detected histologically after exposure to SFA and NTS. Furthermore, changes in the mTOR signalling pathway were observed. Thus, this study served to illustrate which pathways are involved in the development of fibre-mediated toxicity, and demonstrated that pleural lesions induced by long asbestos fibres and long CNT exhibit a common pro-oncogenic molecular signature.

2017-11-20 | GSE51636 | GEO

Differential susceptibility of human pleural and peritoneal mesothelial cells to asbestos exposure

Project description:We hypothesize that the observed differences in incidences of pleural and peritoneal malignant mesothelioma (MM) are the result of differences in the direct response of these cell types to asbestos rather than to differences mediated by the in vivo microenvironment. To test this hypothesis, we characterized cellular responses to asbestos in a controlled environment using high-throughput RNA sequence and other assays.

2015-03-02 | GSE63966 | GEO

Transcriptome analysis of mesothelioma induced by intraperitoneal injections of asbestos in rats

Project description:Human malignant mesothelioma (MM) is an aggressive tumor strongly associated with asbestos exposure. SM patients generally have poorer prognosis compared to EM patients. To identify potential genes accounting for the differential prognosis between these two subtypes, we compared the microarray gene expression profiles of rat SM and EM tissues induced by intraperitoneal injections of 3 types of asbestos (chrysotile,crocidolite and amosite).

2014-06-04 | GSE48298 | GEO

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