Expression data from HTR-8/Svneo side population (SP) and non-side population (NSP) cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Tetsunori Inagaki
PROVIDER: E-GEOD-61547 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Immature cell populations, including stem cells and progenitor cells, can be found in “side-population (SP)” cells. Although SP cells isolated from some adult tissues have been reported elsewhere, isolation and characterization of human trophoblast SP cells remained to be reported. We used microarrays to detail the global program of gene expression underlying cell differentiation and identified up-regulated genes of SP cells. HTR-8/SVneo SP cells or NSP cells were isolated using a cell sorter for RNA extraction and hybridization on Affymetrix microarrays. To obtain many SP or NSP cells, we cultured a large amount of HTR-8/SVneo cells (1×10^7 cells). The cells were labeled with 2.5µg/ml Hoechst 33342 dye (Molecular Probes, Eugene, OR) for 120 minutes at 37 ℃, either alone or in combination with 50 µmol/L verapamil (Sigma-Aldrich, ST Louis, MO). Finally, the cells were then passed through EPICS ALTRA HyPerSort (Beckman Coulter, Fullerton, CA) using dual wavelength analysis (blue, 424-444 nm; red, 675 nm) after excitation with 350 nm UV light.
2011-03-12 | E-GEOD-27909 | biostudies-arrayexpress
Project description:We are currently studying the mechanisms that confer tumour initiating potential upon SP, and as part of this work, we undertook gene profiling studies comparing expression between SP and non-SP cells, initially focusing on the most common soft tissue sarcoma, malignant fibrous histiocytoma (or MFH) Sarcomas contain a subpopulation of cells which exclude Hoechst dye (SP cells) and are enriched for tumor initiating potential. The persistence of SP cells could be responsible for relapse or a failed response to therapy. Expression profiles were compared between the SP and non-SP cells from malignant fibrous histiocytoma (MFH) tumors using microarray. The Hedgehog and Notch pathways were activated in SP cells. Blocking these pathways in MFH xenografts established in NOD-SCID mice depleted the abundance of SP cells and reduced tumor growth. Intriguingly, treatment also substantially inhibited the potential for successful secondary transplantation. The data provides support that SP cells act as tumor initiating cells in sarcomas and suggests targeting the SP as an enticing approach for sarcoma therapy. In this study, we studied six MFH tumours, and identified a number of signaling pathways that were consistently activated in the SP population compared to the non-SP population.
2012-01-17 | E-GEOD-32375 | biostudies-arrayexpress
Project description:SPARC is a matricellular glycoprotein that plays critical roles in the pathologies associated with obesity and diabetes, as well as tumorigenesis. The objective of this study was to investigate the role of SPARC in the process of trophoblast invasion which shares many similarities with tumor cells invasion. Our results reveals that hormones, cell adhesion molecules, ECM molecules, growth factors and cytokines all are mediated by SPARC in EVT invasion. HTR-8/SVneo cells were transfected with SPARC siRNA or a 25-nucleotide universal negative control siRNA using Lipofectamine 2000 according to the manufacturer’s protocol. Seventy-two hours after transfection, cells were harvested and RNA was isolated using standard procedures.
2012-04-27 | E-GEOD-37639 | biostudies-arrayexpress
Project description:Malignant pleural mesothelioma (MPM), which is associated with occupational asbestos exposure, is a deadly disease with no effective treatments due mainly to its high resistance to anti-cancer drugs. The molecular mechanisms responsible for its chemotherapeutic resistance are complicated and undefined. However, the presence of side population cells (SP cells) in tumors is a well-accepted explanation for their anti-cancer drug resistance. To identify SP cell-specific gene expression signature, microarray technique has been employed. Our data show differential gene expression profiles between SP and non-SP cells of H2714 mesothelioma cells. SP cells over-expressed genes associated with cancer stem cell (CSC) and drug resistance: DUSP6, SPRY2 and IL6, as well as multi-pathways, including the cancer stem cell-associated pathways Notch and c-Kit. Therefore, we believe that targeting CSC-specific genes and pathways in SP cells may hold the key to the discovery of effective treatments for reversing chemotherapeutic resistance to MPM treatment. 4 samples
2011-11-18 | E-GEOD-33734 | biostudies-arrayexpress
Project description:Abnormal trophoblast invasion is associated with the most common and most severe complications of human pregnancy. The biology of invasion, as well as the etiology of abnormal invasion remains poorly understood. The aim of this study was to characterize the transcriptome of the HTR-8/SVneo human cytotrophoblast cell line which displays well characterized invasive and non-invasive behaviors, and to correlate the activity of the transcriptome with nuclear matrix attachment and cell phenotype. Interestingly comparison of the transcriptome did not reveal an obvious significant difference between the transcriptomes of invasive and non-invasive HTR cells. In contrast, comparison of the MARs on chromosomes 14-18 revealed an increased number of MARs associated with an invasive phenotype. These attachment areas were more likely to be associated with silent (rather than actively transcribed) genes. DNA extraction with a 2 M NaCl solution followed by restriction digestion with EcoR1 facilitates the separation of matrix bound DNA from non matrix bound DNA. Genomic CGH arrays were used to map the relative differences between attached (scaffold/matrix) and non-attached (loop) portions of the genome in non-invasive (proliferative) and invasive trophoblasts. The matrix association was assessed relative to gene expression measured on Illumina expression beadchips.
2010-06-22 | E-GEOD-17501 | biostudies-arrayexpress
Project description:Purpose: To explore the side population (SP) in pancreatic ductal adenocarcinoma (PDAC) for its gene expression profile and its association to cancer stem cells (CSC) and to evaluate the value of genes from its gene signature on patient survival. Experimental design: Side and main population (MP) cells were isolated from 11 human PDAC resection specimens using fluorescence-activated cell sorting (FACS) after Hoechst incubation. Total RNA was extracted for whole-genome analysis. A gene signature for the purified SP (pSP; depleted from immune/endothelial CD45+/CD31+ cells) was developed and validated with the nCounter system on expression data of 78 primary PDAC using Cox regression analyses for disease-free and overall survival. Results: An SP was identified in all PDAC samples. Whole-genome expression profiling of pSP revealed upregulation of genes related to therapy-resistance and of CSC-associated genes and pathways. A pSP signature of 32 up- or downregulated genes was capable of discriminating SP from MP in an independent set of 10 PDAC samples, and some contributing genes had a prognostic value in a separate series of 78 patients who underwent surgery for PDAC. Conclusion: Pancreatic cancer contains an SP with chemo-resistant and CSC-associated molecular characteristics. Genes from a newly defined pSP gene signature are related to survival of patients who undergo surgical resection for pancreatic cancer, and might therefore represent potential therapeutic targets. Microarray analysis was performed on SP and MP samples from 11 different human PDAC samples.
2014-09-26 | E-GEOD-42404 | biostudies-arrayexpress
Project description:Presence of key hypoxic regulators, HIF-1α or HIF-2α, in tumors is associated with disease progression and poor patient prognosis. Hypoxia massively activates several genes including the one encoding BCRP transport protein that proffers the multidrug resistance to cancer cells through the xenobiotic efflux and, moreover, is a determinant of side population (SP) that associates with cancer stem-like phenotype. As the natural medicine comes to the fore, it is instinctive to look for natural agents possessing powerful features against cancer resistance. Hypericin, pleiotropic agent found in Hypericum plants, is good example, as it is BCRP substrate and potential inhibitor, as well as SP- and HIF-modulator. Here, we showed that hypericin efficiently accumulates in hypoxic cancer cells, degrades HIF-1/2α and together with hypoxia decreases BCRP efflux, thus diminishes SP population. On the contrary, this seemingly favorable result was accompanied by stimulated migration of this minor population of cancer cells that preserved SP phenotype. Since hypoxia unexpectedly decreased BCRP level and SP fraction, we also compared the SP and nonSP proteomes and their changes under hypoxia in A549 cell line. We identified differences especially among protein groups connected to the epithelial-mesenchymal transition, although major changes were related to hypoxia, as upregulation of many proteins, including serpin E1, PLOD2 and LOXL2, that ultimately contribute to the initiation of the metastatic cascade, were detected. Altogether, this study represents another piece of puzzle that clarify the innate and hypoxia-triggered resistance of cancer cells and highlights the ambivalent role of natural agents in biology of these cells.
2023-05-04 | PXD038740 | Pride
Project description:Pituitary adenomas cause significant endocrine and mass-related morbidity. Not much is known about mechanisms underlying pituitary tumor pathogenesis. We searched for a side population (SP) in pituitary tumor, representing cells with high efflux capacity and potentially enriching for cancer/tumor stem cells (CSC/TSC). Human pituitary adenomas contain a SP irrespective of hormonal phenotype. This adenoma SP, as well as the further purified SP (pSP) depleted from endothelial and immune cells, enriches for cells that express ‘tumor stemness’ markers and signaling pathways, including epithelial-mesenchymal transition (EMT)-linked factors. The adenomas were found to contain self-renewing sphere-forming cells, considered a property of TSC. The sphere-initiating cells were retrieved in the pSP. Because benign pituitary adenomas do not grow in vitro and failed to expand in immunodeficient mice, the pituitary tumor cell line AtT20 was further used. We identified a SP in this cell line and found it more tumorigenic than the main population (MP). Of the two EMT-regulatory pathways tested, inhibition of Cxcr4 signaling reduced EMT-linked cell motility in vitro as well as xenograft tumor growth, whereas activation of TGFβ had no effect. The tumor pSP showed upregulated expression of the pituitary stem cell marker SOX2. Pituitaries from dopamine receptor D2 knockout (Drd2-/-) mice bearing prolactinomas, contain more pSP, Sox2+ and colony-forming cells than wildtype glands. In conclusion, we detected a SP in pituitary tumors and identified TSC-associated characteristics. Our study may contribute to a better understanding of pituitary tumor pathogenesis and lead to new therapeutic targets. We determined gene expression profiles for 5 human pituitary adenoma samples (all NF-A type). The samples were obtained immediately after transsphenoidal resection (by the neurosurgeon Dr. van Loon, Division Neurosurgery, University Hospitals Leuven). Informed consent was received from the patients. Hormonal phenotype was determined by the Department of Imaging and Pathology (University Hospitals Leuven). For each sample, CD31¯/CD45¯ SP (purified SP or pSP) and pMP cells were sorted by FACS. Separate assays were run subsequently for the two fractions. As such we present data from 10 microarrays.
2015-08-04 | E-GEOD-62870 | biostudies-arrayexpress
Project description:Pituitary adenomas cause significant endocrine and mass-related morbidity. Not much is known about mechanisms underlying pituitary tumor pathogenesis.We searched for a side population (SP) in pituitary tumor, representing cells with high efflux capacity and potentially enriching for cancer/tumor stem cells (CSC/TSC). Human pituitary adenomas contain a SP irrespective of hormonal phenotype. This adenoma SP, as well as the further purified SP (pSP) depleted from endothelial and immune cells, enriches for cells that express ‘tumor stemness’ markers and signaling pathways, including epithelial-mesenchymal transition (EMT)-linked factors. The adenomas were found to contain self-renewing sphere-forming cells, considered a property of TSC. The sphere-initiating cells were retrieved in the pSP.Because benign pituitary adenomas do not grow in vitro and failed to expand in immunodeficient mice, the pituitary tumor cell line AtT20 was further used. We identified a SP in this cell line and found it more tumorigenic than the main population (MP). Of the two EMT-regulatory pathways tested, inhibition of Cxcr4 signaling reduced EMT-linked cell motility in vitro as well as xenograft tumor growth, whereas activation of TGFβ had no effect.The tumor pSP showed upregulated expression of the pituitary stem cell marker SOX2. Pituitaries from dopamine receptor D2 knockout (Drd2-/-) mice bearing prolactinomas, contain more pSP, Sox2+ and colony-forming cells than wildtype glands.In conclusion, we detected a SP in pituitary tumors and identified TSC-associated characteristics. Our study may contribute to a better understanding of pituitary tumor pathogenesis and lead to new therapeutic targets. We determined gene expression profiles for 9 human pituitary adenoma samples (5 x NF-A; 4 x GH-A). The samples were obtained immediately after transsphenoidal resection (by the neurosurgeon Dr. van Loon, Division Neurosurgery, University Hospitals Leuven). Informed consent was received from the patients. Hormonal phenotype was determined by the Department of Imaging and Pathology (University Hospitals Leuven). For each sample, total SP and MP cells were sorted by FACS. Separate assays were run subsequently for the two fractions. As such we present data from 18 microarrays.
2015-08-04 | E-GEOD-62866 | biostudies-arrayexpress
Project description:Intratumoral heterogeneity is a major barrier against effective cancer therapy. Human malignant mesothelioma (HMM) that is closely associated with asbestos exposure is extremely heterogeneous in morphology and molecular phenotype. Contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous populations in cancers remains largely undetermined. The present study was performed to investigate underlying molecular mechanisms for the emergence of intratumoral heterogeneity by identifying the global microRNA expression profile of distinct subpopulations of MS1 cell line, a HMM cell line. More aggressive cancer cells could be enriched by side population (SP) assay in HMM [20]. The sorted SP and NSP subpopulations were subjected to the microarray analysis of miRNA expression to investigate differentially altered miRNA genes defining tumor heterogeneity in HMM. Total RNAs were isolated from the sorted subpopulations of HMM cells, SP and non-SP fractions. The expression profile of miRNAs was evaluated using Affymetrix GeneChip miRNA Arrays. After data extraction and normalization, the microRNAs defining the cell subpopulations were determined using bioinformatics softwares. A total of 95 miRNAs including 42 up-regulated and 53 down-regulated were identified based on the criteria of 2 fold difference and a p-value < 0.05. Functional ontology of the dysregulated miRNAs revealed that a large number of target genes were categorized into the regulation of various cellular processes, including cell proliferation, programmed cell death, cell migration, cellular response to stress, and stem cell maintenance. The data show that microRNAs are significantly involved in the generation and maintenance of intratumoral heterogeneity and their regulation could be an effective strategy to eradicate a more aggressive cancer cell subpopulation. This is the first to report the profile of miRNA expression in CSCs in HMM by using side population assay assisted with flow cytometry. It will be valuable to understand the regulatory function of HMM CSC miRNAs in generation and maintenance of intratumoral heterogeneity. Total RNAs were isolated from the sorted subpopulations of HMM cells, SP and non-SP fractions. (no replicates)
2016-06-15 | E-GEOD-69910 | biostudies-arrayexpress