Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

77 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ΔNp63α expression induces loss of cell adhesion in triple-negative breast cancer cells

ABSTRACT: Transcription profiling of MDA-MB-468 cells with inducible expression of p63 isoforms Tap63α and ∆Np63α. Expression of p63 isoforms was induced by tetracycline, cells were harvested 24 hours after treatment in three biological replicates.

ORGANISM(S): Homo sapiens

SUBMITTER: Marta Nekulova

PROVIDER: E-MTAB-3761 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Estrogen receptor β role in tumour suppression of triple negative breast cancer

Project description:Breast cancer (BC) is the most common cancer in women worldwide, and is classified in multiple subtypes, including the so called triple-negative BC (TNBC). This is characterized by lack of estrogen receptor alpha (ERα), progesterone receptor (PR) and epidermal growth factor receptor 2 (HER2/neu), that represent common targets for BC treatment. Their absence limits the number of therapies that may be applied for TNBC treatment, suggesting the need to identify novel therapeutic targets against this disease. Several studies reported that the beta ER subtype (ERβ) is expressed in a sizeable fraction of TNBCs where its presence correlates with improved patient outcome. We evaluated ERβ expression in TNBC tissues by immunohistochemistry using two validated antibodies, demonstrating presence of this protein in 28% of samples. To investigate, in this context, the role of this estrogen receptor in TNBC biology, ERβ-expressing cell lines, representing different TNBC subtypes, were generated. Cellular and functional assays confirmed the antiproliferative activity of ERβ in TNBCs. Interaction proteomics revealed in BC nuclei the presence of several protein complexes associated with this receptor involved in chromatin remodeling, miRNA maturation and mRNA transcription. Transcriptome analyses pointed out tumor subtype-specific signaling pathways deregulation. Interestingly, among these the cholesterol biosynthesis pathway was commonly downregulated in all cell lines tested. Global analyses of ERβ binding to the genome showed its recruitment to regulatory sites of Sterol Regulatory Element-Binding Protein 1 (SREBP1), indicating a direct regulation of this pathway by the receptor. These findings suggest that drugs targeting components of cholesterol biosynthesis pathway may be new potential therapeutic options for TNBC treatment.

2019-12-03 | E-MTAB-8055 | biostudies-arrayexpress

Transcriptional profiling of triple-negative breast cancer cell lines treated with OTX015

Project description:In order to determine the impact on transcription of the novel bromodomain inhibitor OTX015, we treated two triple-negative breast cancer cell lines (MDA-MB-231 and MDA-MB-468) treated with the compound at 24 hours.

2018-01-16 | E-MTAB-3862 | biostudies-arrayexpress

Microarray analyses of microRNA expressions in comparison with immortal healthy mammary epithelial cells, breast cancer cells, and long-term-cultured breast cancer stem cells

Project description:RNA extraction and microarray analysis total RNA from immortalized normal mammary epithelial cells (184A1, MCF-12A), breast cancer cells (MDA-MB-231, MCF-7, MDA-MB-468, SK-BR-3), BCSC (MDA-MB-231SC, MCF-7SC, XM322, XM607). MDA-MB-231SC and MCF-7SC originating from breast cancer cell lines; XM322 and XM607 derived from clinical specimens which had been described in previous submission (E-MTAB-5057). The miRNA profiling was performed using Agilent miRNA array. Microarray experiments were conducted according to the manufacturer's instructions. To select the differentially expressed genes, we used threshold values of ≥ 2 and ≤ −2-fold change and a Benjamini-Hochberg corrected p value of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of Cluster 3.0 software then further analyzed with hierarchical clustering with average linkage (genes which value more than 100 were evaluated).

2017-12-01 | E-MTAB-5584 | biostudies-arrayexpress

Transcriptome analysis of Wnt3a-treated triple-negative breast cancer cell lines.

Project description:We analyzed the transcriptome of two different triple negative breast cancer (TNBC) cell lines to define a comprehensive list of Wnt target genes. Cells were treated with Wnt3a for 6h, 12h or 24h. We found up-regulated and down-regulated genes in response to Wnt3a treatment. They are involved in the Wnt pathway itself, and also in TGFM-CM-^_, p53 and Hedgehog pathways. Thorough characterization of these novel potential Wnt target genes may reveal new regulators of the canonical Wnt pathway. The comparison of our list of Wnt target genes with those published in other cellular contexts confirms the notion that Wnt target genes are tissue-, cell line- and treatment-specific. Cells were seeded in six-well plates, serum starved overnight then treated with Wnt3a for the indicated times (6, 12 and 24 hours). Triplicates for each condition were included in the experiment.

2015-01-24 | E-GEOD-65238 | biostudies-arrayexpress

Estrogen Receptor beta (ERβ) interactome in triple negative breast cancer cells nuclei

Project description:Breast cancer (BC) is the second most common type of cancer in women and one of the leading causes of cancer-related deaths worldwide. BC classification is based on the detection of three main histological markers: estrogen receptor alpha (ERα), progesterone receptor (PR) and the amplification of epidermal growth factor receptor 2 (HER2/neu). A specific BC subtype, named triple-negative BC (TNBC), lacks the aforementioned markers but a fraction of them express the estrogen receptor beta (ERβ). To investigate the functional role of ERβ in these tumors, interaction proteomics coupled to mass spectrometry (MS) was applied to deeply characterize the nuclear interactors partners in MDA-MD-468 and HCC1806 TNBC cells.

2019-12-03 | PXD014468 | Pride

Large-Scale Analysis of Breast Cancer-Related Conformational Changes in Proteins using SILAC-SPROX

Project description:Proteomic methods for disease state characterization and biomarker discovery have traditionally utilized quantitative mass spectrometry methods to identify proteins with altered expression levels in disease states. Here we report on the large-scale use of protein folding stability measurements to characterize different subtypes of breast cancer using the Stable Isotope Labeling with Amino Acids in Cell Culture and Stability of Proteins from Rates of Oxidation (SILAC-SPROX) technique. Protein folding stability differences were studied in a comparison of two luminal breast cancer subtypes, luminal-A and -B (i.e., MCF-7 and BT-474 cells, respectively), and in a comparison of a luminal-A and basal subtype of the disease (i.e., MCF-7 and MDA-MB-468 cells, respectively). The 242 and 445 protein hits identified with altered stabilities in these comparative analyses, included a large fraction with no significant expression level changes. This suggests thermodynamic stability measurements create a new avenue for protein biomarker discovery. A number of the identified protein hits are known from other biochemical studies to play a role in tumorigenesis and cancer progression. This not only substantiates the biological significance of the protein hits identified using the SILAC-SPROX approach, but it also helps elucidate the molecular basis for their dysregulation and/or dysfunction in cancer.

2017-07-10 | PXD006703 | Pride

Clinical and prognostic relevance of squalene epoxidase in breast cancer

Project description:All cell lines were purchased from ATCC (LGC Standards S.r.l., Milan, Italy), except T-47D and MDA-MB-468 that were obtained from the National Cancer Institute Developmental Therapeutics Program (Frederick, MD). Six untreated breast cancer cell lines grown according to the growth protocol reported below

2015-07-28 | E-GEOD-71395 | biostudies-arrayexpress

Transcriptional pathway signatures for the Aurora inhibitor Danusertib

Project description:Treatment with Aurora inhibitors has been shown to induce diverse biological responses in different tumor cell lines, in part depending on their p53 status. To characterize at the transcriptional level the effects of Danusertib we analyzed by microarray different tumor cell lines, with WT or mutant p53 status, that showed differential cell cycle response upon drug treatment. We analyzed the effects of Danusertib treatment in different tumor cell lines derived from ovary (A2780, p53WT), breast (MCF-7, p53WT and MDA-MB-468, p53 mut) and colon carcinoma (HCT116, p53 WT and Colo205, p53 mut). Cell line were treated (TRT) or left unreated (CTRL) for 24 hrs with 1 uM Danusertib.

2011-09-19 | E-GEOD-24547 | biostudies-arrayexpress

A panel of breast cell lines

Project description:RNA expression patterns of breast cell lines were compared with a breast cell line mixed reference. Gene expression profiles of 52 individual breast cell lines relative to a breast cell line reference mix containing equal amounts of 10 breast cell lines.

2013-02-22 | E-GEOD-44552 | biostudies-arrayexpress

Gene Expression Microarrays data from human breast cancer cell lines MDA-MB-468 and SkBr3 treated for 48h with 1mM and 4mM of Metformin with non-treated control samples

Project description:This study was designed to investigate the Metformin mode of action in different subtypes of breast cancer using cell and molecular, and systems biology techniques. To that end, several concentrations of Metformin have been used. Besides, five different breast cancer cell lines representing the five breast cancer phenotypes have been employed in this study. These cell lines were BT-474, MCF-7, MDA-MB-231, MDA-MB-468, and SkBr3 as representative for (Luminal B, Luminal A, Claudin-low, Basal-like, and HER2) subtypes respectively. Interestingly, Metformin treatment significantly reduced cancer cell viability and proliferation while inducing cell apoptosis and enhanced cell necrosis of the Basal-like (MDA-MB-468), although, the less sensitive subtype is HER2 (SkBr3).

2019-03-07 | E-MTAB-7737 | 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