A Comparative Analysis of the Transcriptome of Hypoxia and Inflammation in Swan 71 Human Trophophoblast Cells: Its Implications in Preeclampsia
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: gaurav bhatti
PROVIDER: E-GEOD-31679 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Chemical hypoxia by CoCl2 treatment and pro-inflammatory cytokines induced distinct changes in the transcriptome of Swan 71 human trophoblasts.
2011-11-15 | GSE31679 | GEO
Project description:The function of human circulating proangiogenic cells (PACs) has been described extensively. However, little focus has been placed on understanding how these cells differ in their functions in the presence of microenvironments mimicking vascular inflammation. We hypothesized that exposure to proinflammatory cytokines or the oxLDL, an autoantigen abundant in advanced atherosclerotic plaques, converts PACs into immune-modulating/proinflammatory cells. Hence, we examined the effect of oxLDL and inflammatory stimuli on their phenotype by use of a functional genomics model based on secretome and whole genome transcriptome profiling. PACs obtained from culturing a PBMC fraction in angiogenic medium were primed with DC differentiation cytokines for 3 days and then exposed to proinflammatory cytokines or oxLDL for 2 days. Under these conditions, PACs converted into APCs (APCcy and APCox, respectively), expressed maturation markers CD80 and CD83, and showed an up-regulation of CD86. APCcy and APCox induced a robust T cell BrdU incorporation. Despite a similar ability to induce lymphocyte proliferation, APCcy and APCox differed for the secretory pathway and mRNA expression. Analysis of the differentially expressed genes identified 4 gene "clusters", showing reciprocal modulation in APCcy vs. APCox justifying, according to functional genomics analyses, a different putative function of the cells in antigen processing. Together, these data show that treatment with inflammatory cytokines or oxLDL converts human PAC phenotype and function into that of APCs with similar lymphocyte-activating ability but distinct maturation degree and paracrine functions. PBMC-derived PACs were committed with GM-CSF and IL-4 to a dendritic phenotype, and then exposed to proinflammatory cytokines (IL-1β and TNF-α) or to the oxidized form of LDL (oxLDL). Functional assays and whole genome gene expression profiling were performed both on PACs (n=6) and or resulting cytokine- (APCcy, n=6) and oxLDL-induced APCs (APCox, n=6). RNA was reverse transcribed, labeled, and linearly amplified, and then hybridized to HumanHT-12 v.4 Expression BeadChip microarrays. To estimate technical variability, ≈20% of the samples (n=4) were hybridized in duplicate.
2015-06-30 | E-GEOD-60208 | biostudies-arrayexpress
Project description:Ewing's Sarcoma cell lines were made resistant to different IGF-1R drugs to investigate mechanisms and pathways modulated by the resistance. EWS TC-71 cell line was exposed to increasing concentration to three different anti-IGF-1R drugs (HAb AVE1642, TKI NVP-AEW541, HAb CP-751,871, cell lines named respectively as TC/AVE, TC/AEW or TC/CP) for at least six months. Expression profile of resistant cell variants was compared either singularly for each resistance or commonly vs. parental cell line. Two technical replicates for resistant variants and three biological replicated for parental cell were present.
2012-10-03 | E-GEOD-34027 | biostudies-arrayexpress
Project description:CD133 (Prominin-1) is considered the most important cancer stem cell (CSC)-associated marker identified so far, with increased expression in the CSC fraction of a large variety of human malignancies, including melanoma. Here we investigated the effects of CD133 down-regulation in vitro and in vivo in human metastatic melanoma. The average number of CD133 molecules on the cell surface of FEMX-I melanoma cells was decreased by 8.7-fold and 1.8-fold using two different short hairpin RNAs. Down-regulation of CD133, confirmed by immunocytochemistry, Western blotting, microarray analysis and RT-PCR, resulted in slower cell growth, reduced cell motility, and decreased capacity to form spheroids under stem cell-like growth conditions. Clonal analysis revealed that the reduction in growth rate was proportional to the extent of CD133 down-regulation. Monoclonal antibodies directed against two different epitopes of the CD133 protein induced a specific, dose-dependent cytotoxic effect in FEMX-I cells. The down-regulation of CD133 severely reduced the capacity of the cells to metastasize, particularly to the spinal cord. In the CD133 downregulated cells, microarray analysis revealed expression changes for only 143 annotated genes (76 up- and 67 down-regulated). Ten of the 76 up-regulated genes coded for Wnt inhibitors, suggesting an interaction between CD133 and the canonical Wnt pathway. We conclude that CD133, in addition to its role as a cancer stem cell marker, is an important therapeutic target for metastatic melanoma and, potentially, for other CD133-expressing cancer types. Two control experiments and two CD133 knockdown experiments.
2010-05-18 | E-GEOD-13144 | biostudies-arrayexpress
Project description:To evaluate the role of HIF1α in modulating the m6A abundance, we conducted m6A sequencing in the Kasumi-1 cell line treated with CoCl2 and echinomycin. CoCl2 can mediate the stabilization of HIF1α protein. Echinomycin is a small-molecule inhibitor of HIF1α, which functions through sequence-specific binding to HRE to competitively inhibit HIF1α binding to its target genes. The m6A sequencing results of the Kasumi-1 cell line treated with CoCl2 and non-treated control were uploaded previously (GSE168778). The differential m6A peaks analysis between CoCl2 + echinomycin group and CoCl2 group was performed.
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Project description:Acute lung injury (ALI) or acute respiratory distress syndrome (ARDS) is a severe syndrome affecting more than 200,000 patients annually in the U.S. New studies are needed to understand the biological and clinical mechanisms that impair alveolar epithelial function. Also, innovative therapies are needed for the resolution of pulmonary edema in ARDS. We and other investigators have reported that bone marrow derived mesenchymal stem cells (MSCs) are effective in preclinical models of ALI due to their ability to secrete several paracrine factors that can regulate lung endothelial and epithelial permeability, including growth factors, anti-inflammatory cytokines, and antimicrobial peptides. So in this study we will test the therapeutic value of human MSCs in an in vitro model of acute lung injury induced by pro-inflammatory cytokines. We will identify differentially expressed genes in primary cultures of human alveolar epithelial type II cells and human bone marrow derived mesenchymal stem cells using Affymetrix gene expression arrays. Human mesenchymal stem cells (MSCs) and human alveolar epithelial type II cells were co-cultured in a transwell system. The cells were stimulated with cytomix (a combination of different pro-inflammatory cytokines) under different conditions. Cells were harvested for Affymetrix gene expression arrays. Total 25 samples are analyzed, 3~5 replicates are included.
2015-07-08 | E-GEOD-68610 | biostudies-arrayexpress
Project description:The Mexican axolotl provides a powerful model to investigate mechanisms of tissue regeneration. A recent chemical screen found that HDAC inhibitor romidepsin, administered for only 1-minute post amputation (1 MPA), blocks axolotl tail regeneration. Here, we tested the potential for cobalt chloride (CoCl2), a chemical stabilizer of HIF1a and inducer of hypoxia, to rescue romidepsin-inhibition of tail regeneration. Tail regeneration was partially rescued when embryos with amputated tails were co-treated with romidepsin and CoCl2. However, extending the CoCl2 dosage window either inhibited regeneration (CoCl2:0-30 MPA) or was lethal (CoCl2:0-24 hours post amputation; HPA). CoCl2:0-30 MPA caused tissue damage, tissue loss, and cell death at the distal tail tip, and blocked regeneration. In contrast, CoCl2 treatment of non-amputated embryos or CoCl2:60-90 MPA treatment of amputated embryos did not affect wound healing or inhibit tail regeneration. To further investigate the contrasting effects of CoCl2, microarray analysis was performed to identify differentially expressed genes at 3 HPA. CoCl2-romidepsin:1 MPA treatment significantly increased the expression of transcription factors associated with appendage regeneration, while CoCl2:0-30 MPA significantly increased expression of hemoglobin and platelet-specific transcripts, consistent with hemorrhage and an impaired hemostatic response. Also, CoCl2:0-30 MPA significantly increased expression of hypoxia inducible genes, including genes that encode Hif1a interacting proteins and heat shock proteins (HSP); in contrast, genes encoding TGFB signaling components were significantly downregulated. Using additional chemical inhibitors of tail regeneration, we identified transcriptional responses associated with HSP90 activity and TGFB signaling. Notably, geldanamcin decreased transcription of matrix metalloproteinases and sustained muscle-specific gene expression, suggesting a role for HSP90 in regulating extracellular matrix remodeling and muscle dedifferentiation. Our study shows the power of using chemical tools to precisely identify temporal windows within which critical biological processes are enacted during tissue regeneration.
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Project description:Osteoarthritis (OA) is a joint condition associated with articular cartilage loss, low-grade synovitis and alterations in subchondral bone and periarticular tissues. In OA, the interest for mesenchymal stem cell (MSC)-EV therapeutic applications has increased. We have assessed the immunomodulary properties of adipose-derived MSCs (AD-MSCs) microvesicles (MV) and exosomes (EX) in interleukin (IL)-1β stimulated OA chondrocytes and cartilage explants and characterized them by mass spectrometry in order to uncover novel mediators in (AD-MSC)-EV immunomodulation.
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Project description:To investigate differentially expressed lncRNAs in C2C12 myotubes with/without CoCl2 treatment, we used mouse lncRNA microarray to examine the expression of lncRNAs in C2C12 myotubes and C2C12 myotubes with CoCl2 treatment.
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Project description:To investigate differentially expressed circRNAs in C2C12 myotubes with/without CoCl2 treatment, we used mouse circRNA microarray to examine the expression of circRNAs in C2C12 myotubes and C2C12 myotubes with CoCl2 treatment.
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