Expression data from CD34+ hematopoietic progenitor cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE20505 | GEO | 2010/02/24
SECONDARY ACCESSION(S): PRJNA125091
REPOSITORIES: GEO
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Project description:Gene transfer vectors based on gamma-retroviruses target actively transcribing genes indicating that the cellular gene expression profile can be predictive of their integration pattern. Therefore, different culture conditions leading to different transcriptional activity may translate into differences in the profile of targeted genes in cells transduced with these vectors. Recent data from two gene therapy trials for SCID-X1 conducted in France and the UK suggested that small differences between in vitro stimulation conditions could explain the disparity in the frequency of common integrations sites observed in the two studies. We set out to compare the transcriptional activity of human CD34+ bone marrow-derived cells cultured under the French (S1) or British (S2) culture conditions. RNA was extracted from human CD34+ bone marrow-derived cells from 3 donors stimulated under the French (S1) conditions (X-vivo 10, 4% fetal calf serum, 300 ng/ml stem cell factor [SCF], 100 ng/ml thrombopoietin [TPO], 60 ng/ml interleukin-3 [IL3], and 300 ng/ml Flt3 ligand [FL]) and under the British (S2) conditions (X-vivo 10, 1% human serum albumin, 300 ng/ml SCF, 100 ng/ml TPO, 20 ng/ml IL3, and 300 ng/ml FL). Extracted RNA was amplified with random hexamer primer reverse transcription strategy. Lastly, amplified RNA was labeled and hybridized to HG U133 Plus 2.0 Affymetrix microarrays. Four time points during cytokine stimulation were analyzed, corresponding to 0 hr and three transduction time points in the French and British SCID-X1 gene therapy clinical trials (48 h, 72 h, and 96 h). Samples are referred to as donor, stimulation condition, and time point (e.g., Don 1 S1-48 for donor 1 of 3, S1 stimulation conditions, and 48 h after stimulation was begun).
2010-03-09 | E-GEOD-20505 | biostudies-arrayexpress
Project description:We examined if pediatric AMLs rank-ordered according to C/EBPδ expression showed the activation of similar pathways. AML samples were dichotomized into groups including the upper quartile (Q1) and the lower three quartiles (Q2-4) according to their C/EBPδ expression values. Moreover, AML samples were associated to French-American-British (FAB) classification.
2016-06-21 | GSE75461 | GEO
Project description:Subcutaneous abdominal adipose tissue was obtained from female subjects undergoing plastic surgery in agreement with French laws on biomedical research. Stromal cells prepared from WAT were cultured for 13 days in a chemically defined medium. At day 13, 60–80% of cells were differentiated into lipid droplet-containing adipocytes. The cells were infected at a m.o.i. of 200 for 6 h. The day after infection, cells were treated with the following drugs at 1 µM unless otherwise indicated: rosiglitazone (BRL49653, Smith Kline and French, Harlow, UK) and 9-cis-RA (Sigma). Cells were harvested after 48 h of treatment. PPAR agonists and 9-cis-RA were prepared in dimethylsulfoxide, and the remaining compounds were diluted in medium. Dimethylsulfoxide or medium was added to control cells) to obtain the same concentration as in compound-treated conditions. Human subcutaneous abdominal adipose tissue was obtained from female subjects undergoing plastic surgery in agreement with French laws on biomedical research. In brief, on 100 ml of tissue, all visible fibrous material and blood vessels were discarded. Adipose tissue was subjected to collagenase digestion. After centrifugations, stromal cells were suspended in Dulbecco's modified Eagle's medium (DMEM)/Ham's F-12 medium supplemented with 10% fetal calf serum (FCS) and antibiotics. Cells were seeded at 30,000 cells/cm2. After 20h incubation, the medium was changed to a chemically defined differentiation medium, consisting of DMEM/Ham's F-12 supplemented with biotin (33 5mol/l), panthotenate (17 5mol/l), insulin (66 nmol/l), triiodothyronine (1 nmol/l), cortisol (100 nmol/l), transferrin (100 ng/ml), (50 5g/ml) gentamicin and (0.2u/ml) penicillin/streptomycin and ciglitazone (1 5g/ml) the first 3 days. Cells then received the same medium without ciglitazone which was changed every 3rd day. At day 13, 60 80% of cells were differentiated into lipid droplet-containing adipocytes. The full-length human PGC-1alpha; cDNA was cloned into the pAdEasy parent plasmid. Recombination between the pAdEasy and pAdTrack vectors and production of the PGC-1alpha; adenovirus was performed at the Laboratoire de Therapie Genique de Nantes. The virus contains, in tandem, the green fluorescent protein (GFP) gene and the PGC-1alpha; cDNA downstream of separate cytomegalovirus promoters. An adenovirus containing only the GFP gene was used as control. Viral titers were 1011 infectious particles per ml. For experiments with agonist treatments, cells were infected with PGC1alpha; adenovirus at a m.o.i. of 200 for 6 h. The day after infection, cells were treated as indicated in text and figure legends with the following drugs at 1 5M unless otherwise indicated: rosiglitazone (BRL49653, Smith Kline and French) and 9-cis-retinoic acid (Sigma). Cells were harvested after 48 h of treatment. PPAR agonists and 9-cis-RA were prepared in dimethylsulfoxide then diluted in medium. A similar dimethylsulfoxide was added to control cells as in drug-treated cells. Total RNA was extracted using the Qiagen RNeasy kit (Qiagen, Courtaboeuf, France, RNA concentration and integrity were assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Massy France). In order to compare microarray experiments, we used a common reference pool which was generated by mixing equal amounts of total RNA extracted from control samples. One 5g of total RNA from each total RNA sample preparation was amplified by MessageAmp RNA Kit (Ambion, Huntington, Cambridgeshire, UK) and amplified RNA quality checked using Agilent 2100 Bioanalyser (Agilent Technologies, Massy France). 35g of amplified RNA was labeled with cyanin dyes (Cy) using the CyScribe First-Strand cDNA labeling kit (Amersham Biosciences, Orsay, France). Amplified RNA from the reference pool was labelled with Cy3 and those from the testing samples were labelled with Cy5. The labelled cDNA mixtures were hybridized according to the protocol described at http://cmgm.stanford.edu/pbrown/protocols/index.After scanning the arrays, the images were analyzed using Genepix Pro 5.1 software and entered into SMD. Keywords: treatment comparison
2007-12-10 | GSE5184 | GEO
Project description:Recombinant adeno-associated virus (AAV)-based vectors are used clinically for gene transfer and persist as extrachromosomal episomes. A small fraction of vector genomes can integrate into the host genome, but the theoretical risk of tumorigenesis may depend on vector regulatory features. A mouse model was used to investigate long-term kinetics and integration profiles of an AAV serotype 5 (AAV5) vector that mimics key features of valoctocogene roxaparvovec (AAV5-hFVIII-SQ), a gene therapy for severe hemophilia A. The majority (95%) of vector genome reads identified by target enrichment sequencing were derived from episomes, and mean integration frequency was 2.70 (standard deviation, 1.24) integrations per 1000 cells. Longitudinal integration analysis suggested AAV5 vector integrations occur primarily within 1 week, at low frequency, and their abundance was stable over time. Integration profiles were polyclonal, and only 5.46% of integrations had a common integration site order ≥5, suggesting random distributions when looking at a 50-kb genomic window. No integrations were associated with clonal expansion. Integrations were enriched near transcription start sites of genes highly expressed in the liver (P = 1x10−4) and less enriched for genes with low or no liver expression. We found no evidence of tumorigenesis or fibrosis caused by the vector integrations.
2024-02-01 | GSE254503 | GEO
Project description:A Cartes dM-^RIdentite des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net) | IntegraChipTM BAC pangenomic arrays (IntegraGen, Evry, France) : 59 ACTs samples including adrenocortical carcinomas (n=21) and adenomas (n=38) | Submitter : Olivia Barreau <olivia.barreau@inserm.fr> | Project leader : Jerome Bertherat <jerome.bertherat@inserm.fr>.
2011-04-18 | E-MTAB-659 | biostudies-arrayexpress
Project description:We compared the expression profiles of papillary thyroid tumors from the Chernobyl Tissues Bank (CTB) with tumors from French patients with no history of exposure to radiations. Keywords: papillary thyroid cancer vs. patient-matched healthy adjacent thyroid thyroid papillary cancer vs. patient-matched adjacent nontumor thyroid tissues. -14 tumors from France -12 tumors from Ukraine
2007-07-11 | E-GEOD-3950 | biostudies-arrayexpress
Project description:<p>The Human Genetic Cell Repository (HGCR) is sponsored by the <a href="http://www.nigms.nih.gov/" target="_blank">National Institute of General Medical Sciences (NIGMS)</a> with the mission of supplying scientists with the materials for accelerating disease gene discovery and functional studies. The resources available include highly-characterized, contaminant-free fibroblast cell lines, transformed lymphoblastoid cell lines (LCLs), and DNA samples derived from these cultures. While the Repository has a major emphasis on inherited diseases, it also contains large collections of cell lines gathered from populations around the world that are intended for use in facilitating the understanding of human variation. Prominent among these resources is the CEPH Reference Family collection contributed by the Centre d'Etude du Polymorphisme Humain (<a href="http://landru.cephb.fr/" target="_blank">CEPH</a>), Foundation Jean Dausset, Paris, France. The CEPH collection includes families collected by R. White (Utah), J. Dausset (French), J. Gusella (Venezuelan), and J. Egeland (Amish). There are a total of 809 individuals accounting for 832 pedigree positions in the reference families. Family relationships for the 61 reference families were verified at Coriell and approved by CEPH. In an effort to enhance the value of this cell culture resource available from the Repository, the Coriell Genotyping and Microarray Center used the Affymetrix Genome-Wide Human SNP Array 6.0 platform to genotype 181 samples from the NIGMS HGCR CEPH collection. Included are thirteen families from the United States (Amish Pedigree 884 and Utah Pedigrees 1331, 1356, 1400, 1416, 1424, 1427, 1477, and 1582), France (Pedigrees 35 and 66), and Venezuela (Pedigrees 102 and 104). Twelve of the families consist of 3 generations and one family consists of 2 generations. Pedigree charts and sample descriptions are available on the Repository catalog website (see below).</p>
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Project description:Our laboratory has identified the Growth Hormone Receptor (GHR) as a candidate oncogenic pathway involved in GBM oncogenicity. In order to study further the role of GHR in GBM, we have generated GHR overexpressing patient-derived cell lines (PDCL) from PDCL established by GlioTEx team (Institut du Cerveau et de la Moelle, Paris, France). An analysis of the global proteome of each variant was then undertaken. The wild-type (GHR WT) and constitutively activated (GHR CA) GHR expression vectors were generous gifts from Mike Waters and Peter Brooks (University of Queensland, Australia). The constitutively activated GHR vector was generated by fusing the transmembrane and cytoplasmic domains of rabbit GHR (to ensure the absence of human GH stimulation) to Jun zippers in order to achieve GH-independent forced dimerization in absence of the extracellular domain. The control GFP vector was obtained from Addgene . These vectors were then inserted in lentiviral vectors. Cells were transduced with multiplicity of infection of 20 and transduced cells were selected with puromycin.
2022-06-23 | PXD004969 | Pride
Project description:DNA transposon-based gene delivery vectors represent a promising new branch of randomly integrating vector development for gene therapy. For the side-by-side evaluation of the piggyBac and Sleeping Beauty systems - the only DNA transposons currently employed in clinical trials - during therapeutic intervention, we treated the mouse model of Tyrosinemia type I. with liver-targeted gene delivery using both transposon vectors. For genome-wide mapping of transposon insertion sites we developed a new Next Generation Sequencing procedure called Streptavidin-Based Enrichment Sequencing, which allowed us to identify approximately 1 million integration sites for both systems. We revealed that a high proportion of piggyBac integrations are clustered in hot regions and found that they are frequently recurring at the same genomic positions among treated animals, indicating that the genome-wide distribution of Sleeping Beauty-generated integrations is closer to random. We also revealed that the piggyBac transposase protein exhibits prolonged activity, which predicts the risk of oncogenesis by generating chromosomal double-strand breaks. Safety concerns associated with prolonged transpositional activity draw attention to the importance of squeezing the active state of the transposase enzymes into a narrower time window.
2023-03-09 | GSE212895 | GEO
Project description:Infection by Hepatitis B Virus (HBV) is the main risk factor for Hepatocellular Carcinoma (HCC) worldwide. HBV can directly drive carcinogenesis through integrations in human genome. This integrative analysis of a French cohort of 190 patients mainly coming from Europe and Africa provides a deep characterization of HBV integrations, in relation with viral and host genomics and clinical features. Clonal HBV integrations directly contribute to HCC development through alterations of cancer driver genes, either at distance when co-localizing with copy number alterations, either locally through viral Enhancers. Together, this analysis gives new insights on HBV-associated driver mechanisms involved in hepato-carcinogenesis.
| EGAS00001004629 | EGA