Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

58 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Characterization of macrophage - cancer cell crosstalk in estrogen receptor positive and triple-negative breast cancer

ABSTRACT: We performed whole transcriptome sequencing of human monocytes that were co-cultured with estrogen receptor positive (ER+) or triple-negative (TNBC) breast cancer cell lines and studied the biological responses related to the differential gene activation in both cell types to understand how different cancer cells educate host cells to support tumor growth To characterize the differences in macrophage activation under the influence of either ER+ or TNBC breast cancer cells, we cultured freshly isolated human peripheral monocytes with two breast cancer cell lines (T47D, ER+ and MDA-MB-231, TNBC) in an in vitro transwell co-culture assay. The transwell setting allowed us to investigate the effect of soluble mediators on macrophage activation since direct cell contact of these cells was inhibited by a (PET) membrane (pore size 0.4âÎ¼m).

ORGANISM(S): Homo sapiens

SUBMITTER: Maija HollmÃ©n

PROVIDER: E-GEOD-75130 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Characterization of macrophage--cancer cell crosstalk in estrogen receptor positive and triple-negative breast cancer.

Hollmén Maija M Roudnicky Filip F Karaman Sinem S Detmar Michael M

Scientific reports 20150317

Tumor heterogeneity may broadly influence the activation of tumor-associated macrophages. We aimed to dissect how breast cancer cells of different molecular characteristics contribute to macrophage phenotype and function. Therefore, we performed whole transcriptome sequencing of human monocytes that were co-cultured with estrogen receptor positive (ER(+)) or triple-negative (TNBC) breast cancer cell lines and studied the biological responses related to the differential gene activation in both mo ...[more]

PMID: 25776849

Similar Datasets

Targeting the SIN3A-PF1 Interaction inhibits Epithelial to Mesenchymal Transition and Maintenance of a Stem Cell Phenotype in Triple Negative Breast Cancer (MNase-seq)

Project description:Triple negative breast cancer (TNBC) is characterized by a poorly differentiated phenotype and limited treatment options. Aberrant epigenetics in this subtype represent a potential therapeutic opportunity, but a better understanding of the mechanisms contributing to the TNBC pathogenesis is required. The SIN3 molecular scaffold performs a critical role in multiple cellular processes, including epigenetic regulation, and has been identified as a potential therapeutic target. Using a competitive peptide corresponding to the SIN3 interaction domain of MAD (Tat-SID), we investigated the functional consequences of selectively blocking the paired amphipathic helix (PAH2) domain of SIN3. Here, we report the identification of the SID-containing adaptor PF1 as a factor required for maintenance of the TNBC stem cell phenotype and epithelial to mesenchymal transition (EMT). Tat-SID peptide blocked the interaction between SIN3A and PF1, leading to epigenetic modulation and transcriptional downregulation of TNBC stem cell and EMT markers. Importantly, Tat-SID treatment led to a reduction in primary tumor growth and disseminated metastatic disease in vivo. In support of these findings, knockdown of PF1 expression phenocopied treatment with Tat-SID both in vitro and in vivo. These results demonstrate a critical role for a complex containing SIN3A and PF1 in TNBC and provide a rational for its therapeutic targeting. Mononucleosomes from MDA-MB-231 cells were isolated and ChIP with H3K4me3 antibody. DNA from Input and ChIP samples was purified and sequenced on Illumina Hiseq.

2015-11-02 | E-GEOD-73869 | biostudies-arrayexpress

human breast cancer cell line LC-MS/MS

Project description:Triple-negative breast cancer (TNBC) is the most aggressive type with poor prognosis among the breast cancers and has a high population of cancer stem cells (CSCs) which are main target to cure and inhibit TNBC. In this study, we analyzed the CSC-related proteome alteration by NEDD4 knockdown in CSC-abundant MDA-MB-231 cells by LC-MS/MS analysis.

2021-09-09 | PXD020585 | Pride

Gene expression analysis in CITED2 knockdown MDA-MB-231 human breast cancer cells.

Project description:The goal of this experiment is to explore the mechanism behind CITED2 (a non-DNA binding transcriptional co-activator) metastatic action by comparing gene expression changes between shScramble and shCITED2-expressing MDA-MB-231 cells.

2017-01-14 | E-MTAB-4267 | biostudies-arrayexpress

Differential transcript stability measurements in MDA-MB-231 vs. MDA-LM2 cells

Project description:We performed whole-genome stability measurements for MDA-MB-231 and its highly metastatic derivative MDA-LM2. Our goal was to identify post-transcriptonal regulons that are deregulated en route to higher metastatic capacity. Cells were pulsed with 4-thiouridine for 2 hours and then RNA was extracted at 0, 2, 4, and 7 hr time-points in quadruplicate from each cell line. 4sU labeling followed by RNA-seq was then used to measure the abundance of transcripts in each population. A decay rate was estimated based on the rate at which transcript abundance was reduced at these time-points.

2014-07-24 | E-GEOD-49608 | 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

Detection and isolation of circulating tumor cells from breast cancer patients using CUB domain-containing protein 1 (CDCP1) Detection and isolation of circulating tumor cells from breast cancer patients using CUB domain-containing protein 1 (CDCP1) Detection and isolation of circulating tumor cells from breast cancer patients using CUB domain-containing protein 1 (CDCP1)

Project description:Circulating tumor cells (CTCs) and disseminated tumour cells with mesenchymal traits are difficult to detect by epithelial marker proteins. Particularly, triple negative breast cancers (TNBC) that are prone to therapy failure release a subpopulation of circulating tumour cells (CTCs) with mesenchymal traits. To provide tools that support their detection and analysis, the cell line BC-M1 established from disseminated tumour cells in the bone marrow of a breast cancer patient and a bone metastasis subline of MDA-MB-231 were analysed. Mass spectrometry analysis revealed high levels of CUB domain-containing protein 1 (CDCP1) in BC-M1. CDCP1 was found in other carcinoma cell lines (MDA-MB-231, MDA-MB-468) and other DTC cell lines (LC-M1, PC-E1) as well. Peripheral blood mononuclear cells were virtually negative for CDCP1 by Western Blot and immunofluorescent staining. Presence of CDCP1 in CTCs was confirmed by CellSearch. Here, CDCP1 positive CTCs were detected in eight of 30 analysed breast cancer patients. For the isolation of CTCs from the blood of breast cancer patients, we established a sandwich magnetic-activated cell sorting (MACS). The extracellular domain of CDCP1 served for cell catching and the cytoplasmic domain of CDCP1 for immunofluorescent detection of CDCP1 in CTCs. We showed that the MACS approach is suitable for the isolation of EpCam/keratin negative breast cancer cells from the blood and isolated CDCP1 positive CTCs from breast cancer patients by MACS. Hence, our approach is particularly suited for the detection and isolation of CTCs from TNBC when low EpCam or keratin levels limit the application of conventional approaches.

2023-03-20 | PXD035203 | Pride

Intact extracellular vesicle cross-linking on vesicles derived from MDA-MB-231 and LM2 cells

Project description:The development of any pharmaceutical requires characterization of the compound, usually be several techniques. Therefore, characterizing the protein content and biochemical state of EVs is of great importance for their useif they are to be used as biopharmaceuticals. Structural characterization of proteins in EVs remains a great challenge even for state-of-the-art technologies such as super-resolution and electron microscopy, partly due to the biophysical and biochemical heterogeneity of EVs. Here we overcome some of these challenges by using cross-linking mass spectrometry (XL-MS) to structurally characterize protein complexes and the interactome of intact EVs, at an unprecedented resolution of up to 30Å. By applying XL-MS to intact EVs derived from two metastatic breast cancer cell lines (MDA-MB-231 and LM2), we validate the presence of active forms of protein complexes that are known to play a role metastasis, revealing for example previously uncharacterized regions of Moesin. Moreover, a cross-linking data-driven molecular docking supports novel conformations of ANXA2 in LM2 EVs.

2022-11-08 | PXD029591 | Pride

Proteomic analysis of proteome of THP-1 macrophages incubated with Paracoccidioides brasiliensis yeast cells alive or heat-killed

Project description:Paracoccidioides spp. is the etiological agent of Paracoccidioidomycosis (PCM), a systemicinfection with wide distribution in Latin America. Macrophages are very important cells during the response to infection by Paracoccidoides brasiliensis and understanding the interaction between the fungus and immune cells is very relevant for understanding the disease. In this study, we performed a proteomic analysis to assess the consequences of P. brasiliensis yeast infection on the THP-1 macrophage proteome and to verify whether there are differences between the proteome of cells infected with the live fungus. We identified 443 upregulated and 2247 downregulated proteins in macrophages infected with live P. brasiliensis yeasts, compared to uninfected macrophages. Proteins differentially expressed in cells infected are related to metabolism and energy production, protein synthesis and processing, transcription, cell cycle, DNA processing, cell signaling, oxidative stress, immune response, among other processes . Proteomic analysis revealed that P. brasiliensis, causes metabolic alterations in infected cells, drastically affecting energy production pathways. In addition, macrophages showed many upregulated, mostly downregulated, immune system proteins. Thus, the present work contributes to elucidate the changes that occur in immune cells in response to infection by P. brasiliensis and may help to better understand PCM.

2023-10-23 | PXD043727 | Pride

The melanoma cell line MDA-MB-435 adhesome in long-term culture and its comparison to the adhesome upon integrin αV knockdown

Project description:Using mass spectrometry–based proteomics, we analysed the components of integrin adhesion complexes of MDA-MB-435S cells and two MDA-MB-435S-derived integrin αV-specific shRNA-expressing cell clones. Among integrins, we detected αV and β5 integrin subunits in the MDA-MB-435S adhesome, thus showing that in long term culture these cells use preferentially integrin αVβ5 for adhesion. Our data represents the first published adhesome of αVβ5 integrin heterodimer.

2020-02-17 | PXD016837 | Pride

Identification of nutrient dependend PIK3C2B regulators

Project description:To identify factors responsible for the differential localization and activity of PIK3C2Bin the presence or absence of serum mitogens we took a quantitative functional proteomics approach based on stable isotope labeling of amino acids in cell culture (SILAC). Genome-engineered HEK293T cells endogenously expressing eGFP-PI3KC15were cultured in serum-containing or serum-deprived media containing heavy or light amino acids, and subjected to affinity capture using a GFP trap matrix and LC-MS/MS

2019-10-02 | PXD014533 | 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