Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA289758 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We treated nine lines of breast cancer cells with conditioned medium derived from NAF and CAF to study the paracrine interaction beetween stroma and tumor. Gene expression profiles for breast cancer cell lines are reported after 72h of treatment with conditioned medium derived from NAF and CAF or with control media.
2016-11-01 | GSE70884 | GEO
Project description:Conditioned medium experiments carried out in our laboratory with CAFs derived from HER2-positive patients showed a significant capacity to promote resistance to trastuzumab plus pertuzumab therapies in two HER2-positive breast cancer cell lines (BCCLs), even in the presence of docetaxel. In order to elucidate the components of CAF-conditioned medium that would be relevant in the promotion of BCCL resistance, we performed a multi-omics strategy to identify miRNAs, cytokines, transcription factors and/or kinases in the secretome that target specific objectives in cancer cells. The combination of miRNA analysis, label-free LC-MS/MS quantification and cytokine arrays to explore the secretome of CAFs under treatment conditions revealed several up- and down-regulated candidates. We discuss the potential role of some of the most interesting candidates in generating resistance in HER2-positive breast cancer
2022-01-26 | PXD025556 | Pride
Project description:Using genome-wide approaches, we have identified groups of genes modulated by CAF-secreted factors from human breast cancer cell lines grown in different CAF-conditioned medium. The genes modulated by CAF secreted factors were characterized by a specific DNA methylation pattern: hypermethylation at transcription start site (TSS) and shore regions. Approximately 60% of them exhibited a methylation-dependent expression level and 20% of them were also dependent on the methyl-CpG-binding protein domain 2. Thus, these specific DNA methylation patterns were linked to an epigenetic control of their expression, upon CAF-secreted factors. We have therefore identified some molecular events defining the responsiveness of groups of genes to stromal cell contents in human breast tumors.
2018-02-22 | GSE95461 | GEO
Project description:Using genome-wide approaches we have identified groups of genes modulated by CAF-secreted factors from human breast cancer cell lines grown in different CAF-conditioned medium. The genes modulated by CAF secreted factors were characterized by a specific DNA methylation pattern: hypermethylation at transcription start site (TSS) and shore regions. Approximately 60% of them exhibited a methylation-dependent expression level and 20% of them were also dependent on the methyl-CpG-binding protein domain 2. Thus, these specific DNA methylation patterns were linked to an epigenetic control of their expression, upon CAF-secreted factors. We have therefore identified some molecular events defining the responsiveness of groups of genes to stromal cell contents in human breast tumors.
2018-02-22 | GSE95460 | GEO
Project description:To investigate whether conditioned medium (CM) from cancer cell culture impacts dynamic changes of the transcriptome in myotubes differentiated from hMuSC, we ran RNA sequencing from differentiated hMuSC that were treated by multiple breast cancer cell lines-conditioned medium. Among 14208 readable mRNAs, MCF-7 CM treatment induced significant changes in 2680 genes, MB-468 CM caused significant changes in 2674 genes, and SKBR-3 CM resulted in significant changes in 1823 genes in myotubes from differentiated hMuSC, compared to control group, respectively. Among them, 961 genes had significant upregulation or downregulation presented in differentiated myotubes over all 3 breast cancer cell lines CMs
2023-05-03 | GSE206662 | GEO
Project description:Introduction: Ampullary cancer is a relatively rare entity and usually treated by pancreatoduodenectomy followed by adjuvant therapy. The intestinal subtype is associated with markedly improved prognosis after resection. Only few cell lines are available for in vitro studies of ampullary cancer and they have not been collectively characterized. Methods: We characterized available ampullary cancer cell lines by subtype maker expression, epithelial-mesenchymal transition (EMT) features, growth and invasion, drug sensitivity and response to cancer-associated fibroblast conditioned medium (CAF-CM). Results: On the basis of EMT features, subtype marker expression, growth, invasion and drug sensitivity three types of cell lines could be distinguished: mesenchymal-like, pancreatobiliary-like and intestinal-like. In response to CAF-CM, enhanced growth, EMT induction as well as suppression of intestinal differentiation markers were observed, but in a heterogenous pattern. Also proteomic analysis of the CAF response distinguished intestinal-like from other cell lines. Discussion: Most of the available AMPAC cell lines seem to reflect a poorly differentiated pancreatobiliary or mesenchymal-like phenotype, consistent with their origin. We suggest that the best cell line model for intestinal-like AMPAC is the SNU869 cell line, while others seem to reflect aggressive AMPAC subtypes.
2016-03-14 | PXD002657 | Pride
Project description:Invasive Lobular Carcinoma (ILC) is an under-studied yet common subtype of breast cancer. A key feature of ILC tumours, due to their single-file invasive growth pattern, is a high stromal content and in particular, an abundance of cancer-associated fibroblasts (CAFs). We identified that IL-6 secreted from primary ILC patient-derived CAFs drives STAT3 activation in ILC cell lines and found that IL6, STAT3, pSTAT3 and subsequent downstream gene expression induced by IL-6 within CAF conditioned media is upregulated in ILC tumours compared to Invasive Ductal Carcinoma tumours, the most common subtype of breast cancer. This dataset contains 3`-mRNAseq data from ILC cell lines (SUM44PE and MDA-MB-134VI) and patient-derived organoids (HCI-013 and HCI-018) stimulated with either recombinant human IL-6 (10 ng/ml) for 24 hours or 1 week or SUM44PE cells stimulated with CAF conditioned media (CAF CM)collected from ED26 primary ILC CAFs (characterised here: doi.org/10.3390/cancers14040904) +/- an IL-6 neutralising antibody. RNA was extracted using Qiagen RNeasy mini-kit and libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen Inc, #015).
2024-10-11 | GSE276108 | GEO
Project description:Interactions between epithelial cells and their associated stroma, mainly the fibroblasts therein have been implicated in breast malignancy. Our aim was to verify the effect of soluble factors resulting from the co-culture of normal (NAF) or associated breast cancer fibroblasts (CAF) with a normal (MCF-10A) or a metastatic (MDA-MB231) breast epithelial cell line on fibroblast gene expression profiles. Fibroblast primary cultures were established and co-culture of these cell types separated by inserts, which allow the passage of soluble factors, was performed. Total RNA was extracted, amplified and subjected to microarray gene expression profiling using microarrays in which 4,608 ORESTES (open reading frame expressed sequence tags) were spotted. Differentially expressed genes, at a False Discovery Ratio (FDR) less then 0.01 and fold variation greater than 2, were selected. CAF molecular signature was characterized by down regulation of 62% (29/47) of genes as compared to NAF, represented mainly by those related to vesicular transport, cytoskeleton plasticity and cell motility. CAF responded to co-culture with MCF-10A cells by up regulation of 63.5% (89/140) of genes, including those involved with cytoskeleton remodelling, lipid synthesis and members of the PI3K pathway. Contrarywise, MDA-MB231 cells affected the gene expression profile of CAF by down regulation of 65% (102/156) of genes, including those associated to tumor suppression and antiangiogenic potential. Up regulated genes, were mainly implicated with cell cycle progression and proliferation. NAF signature was altered by MDA-MB231 presence resulting in down regulation of suppressor genes, integrins and angiogenic factors, but it was modestly affected by MCF-10A. Keywords: Fibroblasts transcriptome altered by breast cell lines
2006-09-10 | GSE4708 | GEO
Project description:Introduction: Ampullary cancer is a relatively rare entity and usually treated by pancreatoduodenectomy followed by adjuvant therapy. The intestinal subtype is associated with markedly improved prognosis after resection. Only few cell lines are available for in vitro studies of ampullary cancer and they have not been collectively characterized. Methods: We characterized available ampullary cancer cell lines by subtype maker expression, epithelial-mesenchymal transition (EMT) features, growth and invasion, drug sensitivity and response to cancer-associated fibroblast conditioned medium (CAF-CM). Results: On the basis of EMT features, subtype marker expression, growth, invasion and drug sensitivity three types of cell lines could be distinguished: mesenchymal-like, pancreatobiliary-like and intestinal-like. In response to CAF-CM, enhanced growth, EMT induction as well as suppression of intestinal differentiation markers were observed, but in a heterogenous pattern. Also proteomic analysis of the CAF response distinguished intestinal-like from other cell lines. Discussion: Most of the available AMPAC cell lines seem to reflect a poorly differentiated pancreatobiliary or mesenchymal-like phenotype, consistent with their origin. We suggest that the best cell line model for intestinal-like AMPAC is the SNU869 cell line, while others seem to reflect aggressive AMPAC subtypes.
2017-03-29 | MSV000080802 | MassIVE
Project description:Gene expression profiling of monocyte-derived macrophage polarised by triple-negative breast cancer cell conditioned medium
2016-12-28 | GSE92927 | GEO