Gene expression profiling on FePro labeled bone marrow stromal cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Francesco Marincola
PROVIDER: E-GEOD-20431 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Superparamagnetic iron oxide nanoparticles labeling of bone marrow stromal (mesenchymal) cells does not affect their "stemness".
Balakumaran Arun A Pawelczyk Edyta E Ren Jiaqiang J Sworder Brian B Chaudhry Aneeka A Sabatino Marianna M Stroncek David D Frank Joseph A JA Robey Pamela G PG
PloS one 20100707 7
Superparamagnetic iron oxide nanoparticles (SPION) are increasingly used to label human bone marrow stromal cells (BMSCs, also called "mesenchymal stem cells") to monitor their fate by in vivo MRI, and by histology after Prussian blue (PB) staining. SPION-labeling appears to be safe as assessed by in vitro differentiation of BMSCs, however, we chose to resolve the question of the effect of labeling on maintaining the "stemness" of cells within the BMSC population in vivo. Assays performed includ ...[more]
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Project description:Abstract Background: Bone marrow stromal cells (BMSCs) are being used for immune modulatory, anti-inflammatory and tissue engineering applications, but the properties responsible for these effects are not completely understood. Human BMSCs were characterized to identify factors that might be responsible for their clinical effects and biomarkers for assessing their quality. Methods: Early passage BMSCs prepared from marrow aspirates of 4 healthy subjects were compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. The cells were analyzed with oligonucleotide expression microarrays with more than 35,000 probes. Results: BMSC gene expression signatures of BMSCs differed from those of hematopoietic stem cells (HSCs), hESCs and fibroblasts. Genes up-regulated in BMSCs were involved with cell movement, cell-to-cell signaling and interaction and proliferation. The BMSC up-regulated genes were most likely to belong to integrin signaling, integrin linked kinase (ILK) signaling, NFR2-mediated oxidative stress response, regulation of actin-based motility by Rho, actin cytoskeletal signaling, caveolar-mediated endocytosis, clathrin-mediated endocytosis and Wnt/beta catenin signaling pathways. Among the most highly up-regulated genes were structural extracellular (ECM) proteins: alpha1 and beta1 integrin chains, fibronectin, collagen type IIIalpha1, and collagen type Valpha1 and functional EMC proteins: connective tissue growth factor (CTGF) and transforming growth factor beta induced protein (TGFBI) and ADAM12. Conclusions: Global analysis of human BMSCs suggests that they are mobile, metabolically active, proliferative and interactive cells that make use of integrins and integrin signaling. They produce abundant ECM proteins; some of which may contribute to their clinical immune modulatory and anti-inflammatory effects. Seven samples from early passage BMSCs were prepared from marrow aspirates of healthy subjects and compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. Total RNA from a pool of PBMCs from six healthy subjects was extracted and amplified into aRNA to serve as a reference.
2011-09-20 | E-GEOD-24871 | biostudies-arrayexpress
Project description:Plerixafor (AMD3100) and G-CSF mobilize peripheral blood stem cells (PBSCs) by different mechanisms. A rhesus macaque model was used to compare plerixafor and G-CSF-mobilized CD34+ cells. Three PBSC concentrates were collected from 3 macaques treated with G-CSF, plerixafor, or plerixafor plus G-CSF. CD34+ cells were isolated by immunoselection and were analyzed by global gene and micro RNA (miR) expression microarrays. Unsupervised hierarchical clustering of the gene expression data separated the CD34+ cells into three groups based on mobilization regimen. Plerixafor-mobilized cells were enriched for B cells, T cells and mast cells genes and G-CSF-mobilized cells were enriched for neutrophils, and mononuclear phagocytes (MPs) genes. Genes up-regulated in plerixafor plus G-CSF-mobilized CD34+ cells included many that were not up-regulated by either agent alone. Two hematopoietic progenitor cell miR, miR-10 and miR-126, and a dendritic cell miR, miR-155, were up-regulated in G-CSF-mobilized CD34+ cells. A pre-B cell acute lymphocytic leukemia miR, miR-143-3p, and a T cell miR, miR-143-5p, were up-regulated in plerixafor plus G-CSF-mobilized cells. The composition of CD34+ cells is dependent on the mobilization protocol. Plerixafor-mobilized CD34+ cells include more B, T, and mast cell precursors while G-CSF-mobilized cells have more neutrophil and MP precursors. Three rhesus macaques were given all three mobilization protocols and PBSCs were collected from each of these three animals. Two monkeys were given plerixafor first, one was given G-CSF first and all three were given plerixafor plus G-CSF last. This resulted in 6 samples (CD34+ and CD34- cells from each of the 3 mobilizations) from each of the 3 individual animals (biological replicates).
2009-12-04 | E-GEOD-16936 | biostudies-arrayexpress
Project description:Traditional Chinese Medicine (TCM) has been used for thousands of years to treat or prevent diseases, including cancer. Good manufacturing practices (GMP) and sophisticated product analysis (PhytomicsQC) to ensure consistency are now available allowing the assessment of its utility. Polychemical Medicines, like TCM, include chemicals with distinct tissue-dependent pharmacodynamic properties that result in tissue-specific bioactivity. Determining the mode of action of these mixtures was previously unsatisfactory; however, information rich RNA microarray technologies now allow for thorough mechanistic studies about complex mixtures effects. PHY906 is a long used four herb TCM formula employed as adjuvant to relieve side effects associated with chemotherapy. Animal studies documented a decrease in global toxicity and an increase in therapeutic effectiveness of chemotherapy when PHY906 was combined. Using a systems biology approach, we studied tumor tissue to identify reasons for the enhancement of the antitumor effect of Irinotecan by PHY-906 in a well-characterized pre-clinical model; PHY-906 and Irinotecan were administered orally to female BDF-1 mice bearing subcutaneous Colon 38 tumors. We observed that 1) individually PHY-906 and Irinotecan induce distinct alterations in tumor, liver and spleen; 2) PHY-906 alone predominantly induces repression of transcription and immune-suppression in tumors; 3) these effects are reverted in the presence of Irinotecan, with prevalent induction of pro-apoptotic and pro-inflammatory pathways that may favor tumor rejection. Most importantly, PHY-906 together with Irinotecan triggers unique changes not activated by each one alone suggesting that the combination creates a unique tissue-specific response. Four groups of BDF-1 mice bearing colon 38 tumors were treated with Phosphate Buffered Saline (PBS) (n=10), PHY-906 (n=10), Irinotecan (CPT-11, Camptosar(TM)) (n=10) or the combination PHY-906 and Irinotecan (n=10). Tumor (38 samples), spleen (38 samples), and liver (35 samples) tissues were removed and frozen for total RNA isolation and subsequent microarray hybridization. There were a total of 111 samples representing 12 treated tissue groups with 8 to 10 biological replicates each. A reference sample was generated from a pool of mixed normal mouse tissue.
2011-10-21 | E-GEOD-25192 | biostudies-arrayexpress
Project description:Using RNA interference to identify IRF4 target genes. Keywords: time series design Gene expression was analyzed using Lymphochip cDNA spotted arrays. Myeloma cell lines were infected with control (shluc, Cy3) or shIRF4 (Cy5) constructs, and changes in gene expression were monitored over time after induction of the shRNA with doxycyclin.
2008-07-07 | E-GEOD-8958 | biostudies-arrayexpress
Project description:Determine the biochemical cause of impaired development of Themis-deficient thymocytes. We isolated three thymocyte populations (three populations: CD4+CD8+CD5loCD69lo, CD4+CD8+CD5+CD69+, and CD4+CD8-CD24hiH2Klo) from Themis-deficient and WT mice. 8 or 9 individual biological replicates were analyzed for each population. An aliquot of cDNA from each sample was pooled and used as a reference.
2009-09-14 | E-GEOD-15246 | biostudies-arrayexpress
Project description:Abstract: Hematopoietic stem cells (HSCs) are used in transplantation therapy to reconstitute the hematopoietic system. Human cord blood (hCB) transplantation has emerged as an attractive alternative treatment option when traditional HSC sources are unavailable, however, the absolute number of hCB HSCs transplanted is significantly lower than bone marrow or mobilized peripheral blood stem cells (MPBSCs). We previously demonstrated that dimethyl-prostaglandin E2 (dmPGE2) increased HSCs in vertebrate models. Here, we describe preclinical analyses of the therapeutic potential of dmPGE2-treatment using human and non-human primate HSCs. dmPGE2 significantly increased total human hematopoietic colony formation in vitro and enhanced engraftment of unfractionated and CD34+ hCB following xenotransplantation. In non-human primate autologous transplantation, dmPGE2-treated CD34+ MPBSCs showed stable multilineage engraftment over one year post-infusion. Together, our analyses indicated that dmPGE2 mediates conserved responses in HSCs from human and non-human primates, and provided sufficient preclinical information to support proceeding to an FDA-approved phase 1 clinical trial. In order to identify the potential mechanism of action of dmPGE2 on gene expression and HSC function, and to possibly explain the muted response of rhesus CD34+ MPBSCs to dmPGE2 exposure, microarray gene expression analysis was conducted. Human and rhesus CD34+ MPBSCs were exposed to DMSO control or dmPGE2 at a dose of either 10 and 50 uM as described above, and processed for microarray analysis at 0, 2, 6, 12 and 24 hours post treatment. Four human donors contributed 8 to 10 samples each at varying time points and dosage for a total of 37 samples (2 samples were technical repeats). Six rhesus macaques contributed 3 to 9 samples each at varying time points and dosage for a total of 28 samples (4 samples were technical repeats). Pooled PBMC's from 6 donors aphereses were used as a reference sample.
2012-06-24 | E-GEOD-27126 | biostudies-arrayexpress
Project description:CpG DNA interacts with TLR9 to stimulate a broadly protective innate immune response. This study uses bioinformatic network analysis of microarray data to identify the genes and regulatory networks triggered by CpG ODN. CpG treatment induced significant gene up-regulation (p < 0.00001) in the spleen within 30 min, peaking with the activation of >500 genes at 3 hr, and declining progressively thereafter. There were reproducible changes in the pattern of gene expression over time. This was mediated by a small group of “major inducers” (IL1A, IL1B, TNF, IFNG) whose activity was modulated by several “minor inducers” (NFKB1, IL6, IL15, IL18, STAT1, STAT2). The subsequent decline in gene activation was mediated by “suppressors” (MYC, IL1RN, SOCS1, SOCS3, NFKBIA, IL10, FOS) that actively down-regulated gene expression and targeted both major and minor inducers. Thus, the regulation of TLR9 dependent gene activation involves multiple waves of stimulation mediated by a small number of “major” and “minor” inducers followed by the active inhibition of gene expression by “suppressors”. Keywords: time series design Endotoxin-free phosphorothioate ODN were synthesized at the CBER core facility (FDA, Bethesda, MD) as previously described. Mice were injected intraperitoneal (i.p.) with 400 ìg of an equimolar mixture of CpG ODNs 1555 (GCTAGACGTTAGCGT) and 1466 (TCAACGTTGA) or control ODNs 1612 (GCTAGATGTTAGCGT) and 1471 (TCAAGCTTGA). Spleens were surgically removed from mice under sterile conditions after 0.5, 1, 3, 9, 24 hr, and/or 72 hr, diced, and stored at -800 C in RNAlater (Qiagen, Valencia, CA). Data from 4 independent experiments/time point and 4-6 untreated controls were used for all statistical analyses. Reproducibility was established by comparing gene expression profiles among similarly treated mice from independent experiments in mAdb (referenced above). Expression analyses were performed using BRB ArrayTools (Biometric Research Branch, NCI). Data were background corrected, flagged values were removed, spots in which both signals were <100 were filtered out, ratios were log base 2 transformed and lowess intensity dependent normalization was used to adjust for differences in labeling intensities of the Cy3 and Cy5 dyes (Yang et al., 2002). Analysis was restricted to genes present on >70% of the arrays after filtering. The gene expression profile of all treatment groups was compared to that of the control groups.
2009-04-01 | E-GEOD-11202 | biostudies-arrayexpress
Project description:Administration of tamoxifen (TAM) as breast cancer adjuvant therapy is associated with a 50% reduction in breast cancer risk and an increase in endometrial cancer risk. To investigate underlying mechanisms, we documented TAM-induced gene expression changes in cultured normal human mammary epithelial cell (NHMEC) strains (numbered 5, 16 and 40) established from tissue taken at reduction mammoplasty from three different individuals. Cells exposed to 0 and 10 uM TAM for 48 hours were evaluated for survival, TAM-DNA adduct formation by TAM-DNA chemiluminescence immunoassay (CIA), and gene expression changes using DNA-oligonucleotide microarray and real time reverse transcriptase-PCR (RT-PCR). At 48 hr, cells exposed to 10 uM TAM were 78% viable, respectively, and there were no measurable TAM-DNA adducts (limit of detection [LOD] = 0.3 adducts/10^8 nucleotides). For microarray analysis, RNA was extracted from cells exposed on three occasions to 10 uM TAM and the corresponding oligonucleotide probes were labeled with fluorescent dyes and hybridized to NCI microarrays (>20,000 human genes). Expression changes of > 3-fold were considered significant, and by these criteria, thirteen genes were up-regulated and one was down-related in NHMEC strain 16, seventeen genes were up-regulated in strain 05, and eleven genes were up-regulated in strain and 40. Elements that were up-regulated in all three cell strains included several interferon-induced genes (IFITM1, IFIT1, IFNA1, MXI and GIP3), and a potassium ion channel (KCNJ1). No significant expression changes were found for genes related to estrogen or xenobiotic metabolism. RT-PCR revealed TAM-induced up-regulation of the five genes of interest, and interferon á (IFNA1), in all three NHMEC strains, with the exception of GIP3 and MX1, which were unchanged in strain 40. The magnitude of TAM-induced up-regulation ranked: strain 16 > strain 05> strain 40. The consistent induction of interferon-related genes in all three NHMEC strains suggests that, in addition to hormonal effects, TAM exposure may enhance immune response, through interferon induction, in normal breast tissue. RNA was extracted from three cell strains (NHMEC 98016, 98040 and 99005) and exposed on three separate occasions to 10 uM TAM. Comparisons were made using 16 arrays with 8 dye swaps for cell strain NHMEC 99005, 9 arrays with 4 dye swaps for NHMEC 98016, and 12 arrays with 6 dye swaps for NHMEC 98040.
2009-01-29 | E-GEOD-13476 | biostudies-arrayexpress
Project description:HGF has been reported to have both positive and negative effects on carcinogenesis. Here we show that the loss of c-Met signaling in hepatocytes enhanced rather than suppressed the early stages of chemical hepatocarcinogenesis. c-Met conditional knockout mice (c-metfl/fl, AlbCre+/-; MetLivKO) treated with N-nitrosodiethylamine (DEN) developed significantly more and bigger tumors and with a shorter latency as compared with control (wt/wt, AlbCre+/-; Cre-Ctrl) mice. Accelerated tumor development was associated with increased rate of cell proliferation and prolonged activation of epidermal growth factor receptor (EGFR) signaling. MetLivKO livers treated with DEN also displayed elevated lipid peroxidation, decreased ratio of reduced glutathione (GSH) to oxidized glutathione (GSSG), and upregulation of superoxide dismutase 1 (Sod1) and heat shock protein 70 (Hsp70), all consistent with increased oxidative stress. Likewise, gene expression profiling performed at 3 and 5 months after DEN treatment revealed upregulation of genes associated with cell proliferation and stress responses in c-Met mutant livers. The negative effects of c-Met-deficiency were reversed by chronic oral administration of anti-oxidant N-acetylcysteine (NAC). NAC blocked the EGFR activation and reduced the DEN-initiated hepatocarcinogenesis to the levels of Cre-Ctrl mice. These results argue that intact HGF/c-Met signaling is essential for maintaining normal redox homeostasis in the liver and has tumor suppressor effect(s) during the early stages of DEN-induced hepatocarcinogenesis. Keywords: compound treatment design To address a role for c-Met in liver carcinogenesis, we employed a hepatocyte specific c-Met conditional knockout mouse model generated in our laboratory. Mice received a single intraperitoneal injection of 10 µg/g body weight of N-nitrosodiethylamine (DEN) (Sigma-Aldrich, Inc., St. Louis, MO, USA) at 14 days of age. Livers were examined at 3 and 5 months after DEN injection. Expression profiling was conducted on five animals from each genotype per time point. Total RNA pooled from five wild-type B6/129 strain mouse livers was used as universal hybridization reference. All experiments were performed in duplicates following a dye-swapping design. Arrays were scanned with a GenePix 4000A scanner (Axon Instruments Ltd., Burlingame, CA) in a way to achieve optimal signal intensity at both channels with less than 1% saturated spots. After excluding the invalid features, all arrays were normalized to the 50th percentile of the median signal intensity using the mAdb data analysis suite (http://nciarray.nci.nih.gov/). Unsupervised cluster analysis was performed with the Cluster and TreeView programs (http://rana.lbl.gov/EisenSoftware.htm). The BRB ArrayTools V3.3.0 software package (Biometric Research Branch, National Cancer Institute; http://linus.nci.nih.gov/BRB-ArrayTools.html) was used for the supervised comparison. Differentially expressed genes were selected using a univariate 2-sample t-test (P<0.001) with a random variance model (15). Functional classification of the significant genes was based on the Gene Ontology (GO) annotations (www.geneontology.org).
2008-08-09 | E-GEOD-8747 | biostudies-arrayexpress
Project description:Human embryonic stem (hES) cells have unique features: self-renewal ability and pluripotency. They can be continuously cultured in undifferentiated state and give rise to cells and tissues of all three germ layers. Thus hES cells provide a resource not only for cell replacement therapy but also for studying human developmental biology. We aimed to identify the unique signature of miRNAs in human embryonic stem cells. Keywords: cell type comparison design We performed microRNA expression profiling on 3 passages from 2 different hES cell lines (WA09 (H9) and BG01v) and 4 passages from 1 hES cell line (TE06 (I6)), EBs samples derived from WA09 cells at 4 different time points with replicates, and 5 types of adult cells (HUVEC, HMVEC, UASMC NHA, and LFB).
2009-04-17 | E-GEOD-12229 | biostudies-arrayexpress