Unknown,Transcriptomics,Genomics,Proteomics

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Human sarcoma cell lines and untransformed cells

ABSTRACT: This study was performed with an overall aim to compare gene expression prolife in human sarcoma cell lines and in primary untransformed cells. Individual Cell Lines were collected from ATCC, DSMZ, HPA Cultures, Clonetics, Wolfson Insitute for Biomedical Research Cell bank, UCL, London, U.K. or were a gift from other researchers.

ORGANISM(S): Homo sapiens

SUBMITTER: Stephen Henderson

PROVIDER: E-GEOD-39262 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:To determine a gene/molecular fingerprint of multiple myeloma (MM) endothelial cells (MMECs), also identifying some of the vascular mechanisms that govern the malignant progression from quiescent monoclonal gammopathy of undetermined significance (MGUS). A comparative gene expression profiling (GEP) was carried out on patient-derived MMECs and MGUS endothelial cells (MGECs) using the Affymetrix U133A Arrays. Expression of selective vascular markers were also validated by RT-PCR and immunoblotting analysis in primary cultures of ECs isolated from total bone marrow (BM)-mononuclear cells. Twenty-two genes were found differently expressed in MMECs compared to MGECs (with 14 down-regulated and 8 up-regulated), thus proving that molecular differences were maintained in vitro. Specific pathways analysis revealed transcriptional and protein expression changes for key regulators of extracellular matrix formation and bone remodeling, cell-adhesion, chemotaxis, angiogenesis, resistance to apoptosis, and cell-cycle regulation. Specifically, we focused on six of these genes (DIRAS3, SERPINF1, SRPX, BNIP3, IER3 and SEPW1), which were not previously functionally correlated to the overangiogenic phenotype of MMECs and disease activity. These data identified distinct EC gene expression profiles and some vascular phenotypes that could influence the remodeling of the BM-microenvironment in patients with active MM. A better understanding of the linkage between genetic and epigenetic events in MM tumor/ECs may contribute to the molecular classification of the disease, thereby identifying selective targets of more effective anti-vessel/stroma therapeutic strategies. Experiment Overall Design: This series of microarray experiments contains the gene expression profiles of five samples from HUVECs (Human Umbilical Vein Endothelial Cells) and five bone marrow ECs (endothelial cells) samples from newly diagnosed MGUS and MM patients, respectively. Centrifugation on Ficoll gradient of heparinized BM-aspirates was followed by polystyrene flask adherence to isolate stromal cells from plasma cells in suspension. Adherent stromal elements were first immunodepleted of macrophages and residual plasma cells with CD14 and CD38 monoclonal antibody (mAb)-coated flasks (mAbs were from Immunotech, Coulter, Marseilles, France), and then incubated with magnetic microbeads coated with Ulex europaeus-1 lectin. Freshly-isolated ECs were cultured in complete medium RPMI-1640 medium supplemented with 10% heat-inactivated FCS and 1% glutamine to allow cell spreading and growth. The purity and viability of EC cultures grown at least one passage (more than 97% viable cells) were assessed by fluorescence-activated cell sorting (FACS, FACS Canto II, Becton Dickinson, San Jose, CA) with double positivity for factor VIII-related antigen (FVIII-RA, a highly specific EC marker) and CD105 (or endoglyn, a molecule strongly expressed by ECs) as well as for CD14 and CD38 negativity. Analysis of mRNA transcripts for FVIII-RA, CD38, CD105 and IgH VDJ region was also performed by RT-PCR, and EC viability was assessed by trypan blue viable staining. HUVECs were purchased from Clonetics Biowhittaker (Walkersville, MD) and cultured in EGM-2MV media (Clonetics Biowhittaker). Five micrograms of total RNA was processed and, in accordance with the manufacturer's protocols, 15 micrograms of fragmented biotin-labelled cRNA were hybridized on GeneChip Human Genome U133A Arrays (Affymetrix Inc.). The arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix). The images were acquired using Affymetrix MicroArray Suite (MAS) 5.0 software and the probe level data converted to expression values using the Bioconductor function for the Robust Multi-Array average (RMA) procedure (Irizarry et al, 2003), in which perfect match intensities are background adjusted, quantile-quantile normalized and log2-transformed.

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Human sarcoma cell lines and untransformed cells

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