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Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line [RNA-seq]

ABSTRACT: Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line [RNA-seq]

PROVIDER: PRJNA1022070 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26212750_1.fastq.gz	Fastqsanger.gz
	SRR26212750_2.fastq.gz	Fastqsanger.gz
	SRR26212751_1.fastq.gz	Fastqsanger.gz
	SRR26212751_2.fastq.gz	Fastqsanger.gz
	SRR26212752_1.fastq.gz	Fastqsanger.gz

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Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line

Project description:Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line

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Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line [ATAC-seq]

Project description:Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line [ATAC-seq]

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Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line [ATAC-seq]

Project description:Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest and most metastatic cancers in human. PDACs respond poorly to therapies, partly due to cancer stem cells (CSCs) that self-renew, survive chemotherapies, metastasise and replenish the tumor. Factors secreted by tumor cells mediate autocrine/paracrine crosstalk with surrounding cells contributing to the stem cell niche but are still insufficiently characterised. Here we used quantitative SILAC proteomics to identify secreted factors enriched in CSC secretome compared to non-CSCs. Our data uncovered factors that mediate the crosstalk between CSCs and non-CSCs as well as genes mediating the gene expression circuitries regulating CSC proliferation.

2024-02-18 | GSE244326 | GEO

Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line [RNA-seq]

2024-02-18 | GSE244287 | GEO

Comparison of gene expression in CSCs (tumorspheres) vs non-CSCs (2D adherent condition) from A13A PDAC cell line

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-02-18 | GSE244327 | GEO

Tumorspheres from transformed fibroblasts highlight the great plasticity of differentiated tumorigenic cells

Project description:Tumors are heterogeneous tissues. A subpopulation of cells with stemness features (cancer stem cells: CSCs) has been implicated in tumor maintenance and progression. There is evidence that CSCs can originate from tumor cell dedifferentiation. Here we used in vitro transformed human fibroblasts (cen3tel cells) and the tumorsphere assay to search for and possibly characterize CSCs from differentiated transformed cells. To obtain tumorspheres, cen3tel cells were grown in the absence of serum and in the presence of growth factors. Sphere cells were analysed for the expression of specific genes and their genome wide gene expression profiles relative to cells grown in adhesion were determined by microarray analysis. Cen3tel cells formed spheres showing self-renewal capacity and Sox2 overexpression, suggesting that they contained a subset of cells with CSC-like features. Sphere cells displayed the deregulation of a c-MYC-miR-34a circuitry, likely associated with cell protection from apoptosis. Gene expression profiles of sphere cells revealed an extensive transcriptional reprogramming. Genes upregulated in tumorspheres identified processes related to tumorigenesis and stemness, such as chromatin organization, cholesterol biosynthetic pathway, apoptosis suppression, immunity and defense, interferon mediated immunity and cytokine and chemokine mediated signalling pathway. However, sphere cells were only slightly more tumorigenic in vivo than adherent cells. Our results indicate that tumorigenic cells obtained from differentiated human fibroblasts are highly plastic and can acquire cancer stem cells properties. However, tumorsphere cells are not the main tumorigenic population, highlighting a further level of complexity in tumor heterogeneity.

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Pancreatic ductal adenocarcinoma primary cultures enriched or not in cancer stem cells

Project description:RNA sequencing of pancreatic ductal adenocarcinoma (PDAC) primary cultures from five different patient-derived xenograft models grown either in adherent conditions selecting for non-CSCs or in CSC-enriching anchorage-independent sphere conditions. A and B are two biological duplicates, from the same patient-derived xenograft model of PDAC.

2015-11-01 | E-MTAB-3808 | biostudies-arrayexpress

Gene expression profiling of N87 and OE19 gastric cancer cell lines grown in 3D or 2D condition

Project description:A great deal of evidence indicates that solid and hematological tumors are driven and maintained by a minor cell compartment with stem cell properties. In this context, gastric cancer stem cells (GCSCs) are implicated in tumor aggressiveness, invasion, metastasis and therapy resistance. HER2 amplification/overexpression (HER2+) is found in about 20% of GCs. Although the anti-HER2 antibody trastuzumab has improved the outcomes of patients with HER2+ advanced disease, its benefits are usually transitory because of high HER2 heterogeneity and frequent co-existence of other oncogenic drivers associated with primary/acquired resistance. To identify potential drivers of trastuzumab resistance in GCSCs, we compare the gene expression profile of OE19 and N87 HER2+ GC cell lines cultured as gastrospheres, peculiar 3D cell cultures that allow detecting the in vitro enrichment of CSCs, versus their matched adherent cell (2D) counterparts. Comparison of the transcriptomic profiles of HER2+ GC cells cultured in 2D versus 3D conditions evidenced a significant enrichment of Fatty Acid Synthase (FASN) transcript among the genes upmodulated in 3D cell cultures. We found that the pharmacological blockade of HER2 and FASN targets CSCs and decreases tumor growth of HER2-positive GC models

2023-05-31 | GSE212442 | GEO

mRNA sequencing SUM159PT WT, Kod and KOs cells cultured in adherent or suspension (i.e. secondary tumorspheres) conditions.

Project description:mRNA sequencing SUM159PT WT, Kod and KOs cells cultured in adherent or suspension (i.e. secondary tumorspheres) conditions.

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Epigenome analysis of PDAC cancer stem cells and non-cancer stem cells

Project description:Most carcinomas, including pancreatic ductal adenocarcinoma (PDAC), are hierarchically organized with cancer stem cells (CSCs) residing at the top of the hierarchy and driving tumor progression, metastasis, and chemoresistance. Since CSCs and their more differentiated progenies (non-CSCs) share an identical genetic background, differences in epigenetics should account for the striking functional differences between these two populations of cells. Epigenetic mechanisms, such as DNA methylation, play an important role in maintaining pluripotency and regulating the differentiation of stem cells, but the role of DNA methylation in pancreatic CSCs remains unclear. Therefore, the objective of our study was to investigate the genome-wide DNA methylation profile of PDAC CSCs and to determine the importance of DNMT methyltransferases for CSC maintenance and tumorigenicity. Using high-throughput methylation analysis, we discovered that sorted CSCs have a higher level of DNA methylation, regardless of the heterogeneity or polyclonality of the CSC populations present in the tumors analyzed. Mechanistically, CSCs expressed higher DNMT1 levels than non-CSCs, and pharmacological or genetic targeting of DNMT1 in CSCs reduced their self-renewal and in vivo tumorigenic potential, highlighting DNMT1 as a potentially attractive therapeutic target.

2017-04-12 | GSE80241 | GEO

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