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MiRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MCF-7 cell line.

ABSTRACT: Intro: Spheroid culture especially on MCF-7 cell has been used as in vitro CSC model for anti-CSC drug discovery. Methods: Tumour spheroid of MCF-7 was generated and characterised for the biological features and CSCs characteristic comparing to the monolayer parental MCF-7 cells. Differential expression of miRNA between the spheroid and parental cells was evaluated using miRNA microarray expressions.

ORGANISM(S): synthetic construct Homo sapiens

PROVIDER: GSE68031 | GEO | 2020/09/20

REPOSITORIES: GEO

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miRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MCF-7 cell line

Project description:Intro: Spheroid culture especially on MCF-7 cell has been used as in vitro CSC model for anti-CSC drug discovery. The role of miRNAs in the regulation of mRNA specifically looking at the self-renewal capacity and the drug resistance of the spheroid-enriched CSCs models has not been evaluated. Therefore, a comprehensive profiling of the miRNAs will provide an insight into the regulatory mechanisms associated with breast cancer and CSCs. Methods: Tumour spheroid of MCF-7 was generated and characterised for the biological features and CSCs characteristic comparing to the monolayer parental MCF-7 cells. Differential expression of miRNA between the spheroid and parental cells was evaluated using next generation sequencing (NGS). The differentially expressed miRNAs were then subjected to target genes predictions, followed pathway analyses to better understand the mechanism associated with spheroid-enriched CSCs. Results: Spheroids generated from MCF-7 cell line under serum-free condition were found to be enriched with CSCs characteristics. miRNA-NGS analysis revealed 119 differentially expressed miRNAs between the spheroids and parental, with 24 up-regulated and 94 down-regulated. The gene ontology (GO) analysis showed that the predicted genes of the differentially expressed miRNAs were enriched in various biological processes. Pathway analysis revealed that the differentially expressed miRNAs and their target genes were associated with a variety of KEGG pathways, which could explain the self-renewal capability, and the higher drug resistance in spheroids when compared to parental.

2016-05-10 | GSE68246 | GEO

miRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MDA-MB-231 cell line.

Project description:cancer spheroid has been widely used as in vitro model of cancer stem cells (CSCs), yet little is known about their phenotypic characteristics and microRNAs (miRNAs) expression profiles. The objectives of this research were to evaluate the phenotypic characteristics of MDA-MB-231 spheroid-enriched cells for their CSCs properties and also to determine their miRNAs expression profile. Similar to our previously published MCF-7 spheroid, MDA-MB-231 spheroid also showed typical CSCs characteristics namely self-renewability, expression of putative CSCs-related surface markers and enhancement of drug resistance. From the miRNA profile, miR-15b, miR-34a, miR-148a, miR-628 and miR-196b were shown to be involved in CSCs-associated signalling pathways in both models of spheroids which highlights the involvement of these miRNAs in maintaining the CSCs features. In addition, unique clusters of miRNAs namely miR-205, miR-181a and miR-204 were found in basal-like spheroid whereas miR-125, miR-760, miR-30c and miR-136 were identified in luminal-like spheroid. Our results highlight the roles of miRNAs as well as providing novel perspectives of the relevant pathways underlying spheroid-enriched CSCs in breast cancer. Keywords: Breast

2016-11-17 | GSE75396 | GEO

Polymer thin film promotes tumor spheroid formation via JAK2-STAT3 signaling primed by fibronectin-integrin 5ɑ and sustained by LMO2-LDB1 complex

Project description:Cancer stem-like cells (CSCs) are considered as a tempting target due to their role in tumor progression. Although recent studies attempted to obtain and analyze patient-derived CSCs ex vivo, there are limitations in supplying diverse and large quantity of CSCs. Previously, functional polymer thin film (PTF) platform which induces cancer cells transformation into tumorigenic CSCs was invented. Here, we verified the functionality of polymer X, new PTF with a streamlined production process. Polymer X induced tumor spheroid formation and the spheroids showed increase in the expression of CSC-related genes. STAT3 phosphorylation was upregulated by fibronectin-integrin 5α-JAK2 axis and maintained by the cytosolic LMO2/LBD1 complex. In addition, STAT3 signaling was critical in spheroid formation on polymer X. By allowing the generation of CSCs from cancer cells, the PTF platform will enable to overcome the previous limitation of patient-derived CSC.

2022-12-09 | GSE213872 | GEO

Gene microarray data for HT-29 monolayer and spheroids

Project description:Colorectal cancers have a rare population of cells that express specific cell surface markers, and are referred to as cancer stem cells (CSC). Targeting CSCs, implicated in tumor relapse, is a paradigm shifting approach for colorectal cancer. We used gene microarray to analyze gene expression in HT-29, a colon cancer cell line, grown as monolayer and spheroid and identify metabolic pathways that are upregulated. HT-29 monolayer cells were grown in DMEM/F12 media supplemented with 10% FBS, and 1X Antibiotic-Antimycotic liquid (AA); and spheroids were grown in stem cell media [DMEM:F12, 1X AA, 1X B27, epidermal growth factors, and fibroblast growth factor for five days. Total RNA was isolated using the mirVana™ miRNA Isolation Kit according to the manufacturer's protocol. RNA intergrity was confirmed on the Nanodrop ND-1000 and analyzed with Agilent 2100 bioanalyzer. The arrays were scanned with the Affymetrix 3000 7G plus scanner.

2015-04-01 | E-GEOD-65433 | biostudies-arrayexpress

Gene microarray data for HT-29 monolayer and spheroids

2015-04-01 | GSE65433 | GEO

Gene expression profile at single cell level of BT-549 TNBC Spheroid cultures with inducible expression of CTL or MUC1 targeting knockdown

Project description:The MUC1-C protein evolved in mammals for adaptation of barrier tissues to loss of homeostasis. Prolonged activation of MUC1-C in settings of chronic inflammation promotes lineage plasticity, epigenetic reprogramming and the cancer stem cell (CSC) state. The effects of MUC1-C on the metabolism of CSCs remain unexplored. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of BT-549 spheroid cultures with and without knockdown of MUC1 to examine the effects of MUC1 on CSC renewal and metbolic states.

2023-11-08 | GSE230308 | GEO

Expression data for cultured NCI-H1299 parental and spheroid cells as well as their derived xenograft models

Project description:Current approaches to the preclinical investigation for novel cancer therapies rely heavily on the use of traditional cancer cell lines maintained in serum-containing conditions. The discrepancy between promising preclinical efficacy and clinical outcome of most novel anticancer agents emphasizes a need for developing predictive preclinical models that preserve the integrity of original patient tumors, including cancer stem cell (CSC) compartment. In this study, we isolate and characterize CSCs from a non-small cell lung cancer cell line, NCI-H1299, by selectively propagating the cells in a stem-cell culture condition. Isolated CSCs proliferated as nonadherent spheroids, displayed capacity to differentiate and self-renew and exhibited higher tumorigenic potential compared to the parental cells. The gene expression profiles of NCI-H1299 parental cells (serum-containing medium), CSCs (stem-cell medium), and xenograft tumor derived from both cell types were studied by Affymetrix array analysis

2010-07-30 | E-GEOD-21612 | biostudies-arrayexpress

Gene expression of C28/I2 cells in monolayer and spheroid culture

Project description:Here we described the transcriptional differences of chondrocytes in monolayer and spheroid cultures.

2023-04-18 | GSE224598 | GEO

Crosstalk between the STAT3, NF-kB and Notch signaling pathways in glioblastoma stem cells

Project description:In this study, we describe a novel relationship between glioblastoma CSCs and the Notch pathway, which involves the constitutive activation of STAT3 and NF-κB signaling. We demonstrate that adherent glioma CSCs exhibit characteristics previously described for CSCs grown in suspension culture. The expression of CD133, Sox2 and Nestin increased when compared to glioma cells grown in monolayer, and the adherent CSCs were ~100 times more tumorigenic in vivo than monolayer cultured glioma cells. We also found that while the STAT3 and NF-κB signaling pathways are constitutively activated in glioma lines, these pathways are dramatically activated in glioma CSCs. Treatment with STAT3 inhibitors led to a loss of nuclear activation of STAT3 signaling and suppression of growth in both monolayer and CSC conditions. There was a markedly greater growth suppressive effect on glioma CSCs, suggesting that targeted therapy of these key pathways in glioma CSCs may be possible. To further investigate potential biomarkers in glioma CSCs, microarray analysis was performed and revealed deregulation of the Notch signaling pathway. This constitutive activation of STAT3, NF-κB, and Notch pathways in glioma CSCs helps identify novel therapeutic targets for the treatment of glioma. GBM6 cells were continuously maintained as subcutaneous xenografts in NSG mice, and monolayer and CSC cultures were derived from freshly harvested tumor tissue. A total of 6 samples were subjected to microarray analysis, with three biological replicates for each experimental condition.

2013-06-19 | E-GEOD-48079 | biostudies-arrayexpress

Proteome profiling of myogenic differentiation of alveolar mucosa multipotent mesenchymal stromal cells revealed an unexpected deviation between 2D monolayer and 3D spheroid model cultures.

Project description:Recently, it has been proposed to employ three-dimensional cultivation of cell in spheroids that contributes more proper physiological conditions in matrix extracellular space architecture and cell morphology accompanied by appropriate intracellular biomechanical organization of cytoskeleton and energy generation apparatus adaptation. In this research we presented the data of proteome survey for cells growing in monolayer and in spheroids that were induced in myogenic way of differentiation and reached terminal stage in seven days. Semi-quantitative profiling of the dynamic changes in proteins abundance depicted strict advantage of spheroid manner cultivation in contrast to monolayer. Cells cultured in spheroid were significantly enriched in proteins of mitochondria biogenesis, respiratory chain proteins, extracellular proteins and cytoskeleton. Most of signal transducers involved in active proliferation and early stages of differentiation were inhibited in spheroid cultures unlike monolayer. The obtained data were broadly consistent with known molecular mechanisms of myogenesis in transcripts level and reflected strong advantage of spheroid cultivation conditions.

2021-11-15 | PXD015410 | Pride

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