Severe Hypoxia Exerts Parallel and Cell-specific Regulation of Gene Expression and Alternative Splicing in Human Mesenchymal Stem CellsMesenchymal Stem Cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE55875 | GEO | 2014/03/14
SECONDARY ACCESSION(S): PRJNA241189
REPOSITORIES: GEO
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Project description:To identify the effects of hypoxia on stem cell populations, we subjected human mesenchymal stem cells to a pO2 of 4 mmHg and analyzed global gene expression and alternative splicing (AS) by genome-exon microarray. Hypoxia induced gene expression in human mesenchymal stem cells was measured at 24 hours after exposure to 0.5% oxygen or normal 21% oxygen. Three independent experiments were performed per condition (Hypoxia or Normoxia).
2014-03-14 | E-GEOD-55875 | biostudies-arrayexpress
Project description:The endosteum of the bone marrow provides a specialized hypoxic niche that may serve to preserve the integrity, pluripotency, longevity and stemness of resident mesenchymal stem cells (MSCs). To explore the molecular genetic consequences of such a niche we subjected human (h) MSCs to a pO2 of 4 mmHg and analyzed global gene expression and alternative splicing (AS) by genome-exon microarray and RT-qPCR, and phenotype by western blot and immunostaining.Out of 446 genes differentially regulated by >2.5-fold, down-regulated genes outnumbered up-regulated genes by 243:203. Exon analyses revealed 60 hypoxia-regulated AS events with splice indices (SI) >1.0 from 53 genes and a correlation between high SI and degree of transcript regulation. Parallel analyses of a publicly available AS study on human umbilical vein endothelial cells (HUVECs) showed that there was a strong cell-specific component with only 11 genes commonly regulated in hMSCs and HUVECs and 17 common differentially spliced genes. Only 3 genes were differentially responsive to hypoxia at the gene (>2.0) and AS levels in both cell types. Functional assignments revealed unique profiles of gene expression with complex regulation of differentiation, extracellular matrix, intermediate filament and metabolic marker genes. Antioxidant genes, striated muscle genes and insulin/IGF-1 signaling intermediates were down-regulated. There was a coordinate induction of 9 out of 12 acidic keratins that along with other epithelial and cell adhesion markers implies a partial mesenchymal to epithelial transition.We conclude that severe hypoxia confers a quiescent phenotype in hMSCs that is reflected by both the transcriptome profile and gene-specific changes of splicosome actions. The results reveal that severe hypoxia imposes markedly different patterns of gene regulation of MSCs compared with more moderate hypoxia. This is the first study to report hypoxia-regulation of AS in stem/progenitor cells and the first molecular genetic characterization of MSC in a hypoxia-induced quiescent immobile state.
| S-EPMC4234502 | biostudies-literature
Project description:Endothelial cells, and many other types of cells too, physiologically reside in low O2 environments (~ 2-13% O2 or 15-60 mmHg pO2; [PCN]) relevantly to atmospheric O2 (~ 21% or 160 mmHg pO2 at sea level) in vivo. Such PCN is critical for endothelial functions. The majority of our current knowledge regarding the cellular and signaling mechanisms governing endothelial functions, however, is built on endothelial models established under atmospheric O2 (~21% O2). Herein, we comapred the transcriptional profiles between HUVE and HUAE cells cultured and expanded under PCN (3% oxygen) and standard culture normoxia (21% O2).
2013-08-30 | GSE49958 | GEO
Project description:Endothelial cells, and many other types of cells too, physiologically reside in low O2 environments (~ 2-13% O2 or 15-60 mmHg pO2; [PCN]) relevantly to atmospheric O2 (~ 21% or 160 mmHg pO2 at sea level) in vivo. Such PCN is critical for endothelial functions. The majority of our current knowledge regarding the cellular and signaling mechanisms governing endothelial functions, however, is built on endothelial models established under atmospheric O2 (~21% O2). Herein, we comapred the transcriptional profiles between HUVE and HUAE cells cultured and expanded under PCN (3% oxygen) and standard culture normoxia (21% O2). We established human umbilical vein (HUVE) and artery (HUAE) endothelial cell cultures under PCN (3% O2; 20-25 days) and SCN (21% O2), and examined the global gene expression using Affymetrix U133 plus 2.0 microarray chips.
2013-08-30 | E-GEOD-49958 | biostudies-arrayexpress
Project description:In order to study the gene expression profile in C57Bl/10 mouse blood, we exposed three different groups of animals. First was exposed to PO2 21% or normoxia. The second was exposed to chronic hypoxia (from PO2 21% to PO2 8%) and the third was also exposed to the same chronic hypoxia (CH) protocol but followed by two weeks under normoxia, and called as recovery group. The blood was extracted from inferior vena cava, the RNA was extracted, amplified and hybridized to Affimetrix MOE 430 V2.o chip. The results were analyzed using Partek Genome suite software. Using two fold cuttoff and 0% FDR parameters, we observed genes 512 diferentially expressed, of which one gene was up-regulated in both hypoxic and recovery condition, 202 were up-regulated during CH and then down-regulated after the recovery, 18 genes were down-regulated afteh CH and the up-regulated after recovery, ans finally 9 genes were down-regulated in both CH and recovery conditions.
2012-05-26 | GSE17728 | GEO
Project description:BACKGROUND:Multiple neurological diseases result from a pathological hypoxia in the brain, resulting in various motor, sensory or cognitive sequelae. Understanding the response of neural stem cells (NSCs) and differentiated neurons to hypoxia will help better treat such diseases. METHODS:We exposed mouse embryonic primary neurons (PN) and neural stem cells to 1% O2 in vitro. RESULTS:Both cell types survived and retained their immunocyto-chemical markers, and neurons showed no obvious morphological changes. Microarray analysis showed that the number of genes with significantly altered expression levels was almost five-fold higher in NSCs compared to PN. NSCs displayed a clear block in G1/S phase of the cell cycle and a number of down-regulated cytokine genes. Various growth factors (e.g. neural growth factor, prolactin), involved in survival and proliferation, genes of the Notch pathway, and genes involved in glial differentiation, and cell-matrix adhesion were up-regulated. PN displayed a down-regulation of a number of genes involved in neuron-specific functions, in particular, transmitter-related (e.g. synaptic transmission, neurotransmitter transport and release, learning, adult behavior). CONCLUSIONS:We conclude that hypoxia 1-down-regulates genes involved in multiple neuronal functions which can negatively impact learning and memory; 2-induces a cell cycle block in NSCs; 3-can precondition NSC towards a particular differentiation potential while maintaining them fully undifferentiated.
| S-EPMC3858017 | biostudies-literature
Project description:In order to study the gene expression profile in C57Bl/10 mouse blood, we exposed three different groups of animals. First was exposed to PO2 21% or normoxia. The second was exposed to chronic hypoxia (from PO2 21% to PO2 8%) and the third was also exposed to the same chronic hypoxia (CH) protocol but followed by two weeks under normoxia, and called as recovery group. The blood was extracted from inferior vena cava, the RNA was extracted, amplified and hybridized to Affimetrix MOE 430 V2.o chip. The results were analyzed using Partek Genome suite software. Using two fold cuttoff and 0% FDR parameters, we observed genes 512 diferentially expressed, of which one gene was up-regulated in both hypoxic and recovery condition, 202 were up-regulated during CH and then down-regulated after the recovery, 18 genes were down-regulated afteh CH and the up-regulated after recovery, ans finally 9 genes were down-regulated in both CH and recovery conditions. Each group of C57Bl/10 mouse had 4 individuals and they were divided into three different groups of animals. First was exposed to PO2 21% or normoxia for 14 days. The second was exposed to chronic hypoxia (from PO2 21% to PO2 8%) and the third was also exposed to the same chronic hypoxia (CH) protocol but followed by two weeks under normoxia, and called as recovery group. After the exposure period, the animals were anaesthetized with a mix of Ketamine (100 mg/mL) and xylasine (20 mg/mL) in a proportion of 1:1. A incison was made on abdominal area and from kidneis and liver area of inferior vena cava venus blood was collected The blood was extracted from inferior vena cava. Then, the RNA was extracted, amplified and hybridized to Affimetrix MOE 430 V2.o chip. The results were analyzed using Partek Genome suite software. Using two fold cuttoff and 0% FDR parameters, we observed genes 512 diferentially expressed, of which one gene was up-regulated in both hypoxic and recovery condition, 202 were up-regulated during CH and then down-regulated after the recovery, 18 genes were down-regulated afteh CH and the up-regulated after recovery, ans finally 9 genes were down-regulated in both CH and recovery conditions.
2012-05-25 | E-GEOD-17728 | biostudies-arrayexpress
Project description:Alternative RNA splicing analysis in Hep3B cell cultured under 21% (N1,3,5) or 1.2% (H2,4,6) oxygen Hypoxia is a common characteristic of many solid tumors. The hypoxic microenvironment stabilizes hypoxia-inducible transcription factor 1α (HIF1α) and 2α (HIF2α) to activate gene transcription, which promotes tumor cell survival. 95% of human genes are alternatively spliced, producing RNA isoforms that code functionally distinct proteins. Thus, effective hypoxia response requires increased HIF target gene transcription as well as proper RNA splicing of these HIF target genes. However, it is unclear if and how hypoxia regulates RNA splicing of HIF target genes. This study determined the effects of hypoxia on alternative splicing (AS) of HIF and non-HIF target genes in Hep3B cells and characterized the role of HIF in regulating AS of HIF induced genes. The results indicated that hypoxia generally promotes exon inclusion for hypoxia-induced, but reduces exon inclusion for hypoxia reduced genes. Mechanistically, HIF activity, but not hypoxia per se is found to be necessary and sufficient to increase exon inclusion of several HIF target genes including pyruvate dehydrogenase kinase 1 (PDK1). PDK1 splicing reporters confirmed that transcriptional activation by HIF is sufficient to increase exon inclusion of PDK1 splicing reporter. In contrast, transcriptional activation of the PDK1 minigene by other transcription factor in the absence of endogenous HIF target gene activation fails to alter PDK1 RNA splicing, demonstrating a novel role of HIF target gene(s) in regulating RNA splicing of HIF target genes. Implications:This study demonstrates a novel function of HIF in regulating RNA splicing of HIF target genes.
2014-05-14 | GSE57613 | GEO
Project description:Alternative RNA splicing analysis in Hep3B cell cultured under 21% (N1,3,5) or 1.2% (H2,4,6) oxygen Hypoxia is a common characteristic of many solid tumors. The hypoxic microenvironment stabilizes hypoxia-inducible transcription factor 1? (HIF1?) and 2? (HIF2?) to activate gene transcription, which promotes tumor cell survival. 95% of human genes are alternatively spliced, producing RNA isoforms that code functionally distinct proteins. Thus, effective hypoxia response requires increased HIF target gene transcription as well as proper RNA splicing of these HIF target genes. However, it is unclear if and how hypoxia regulates RNA splicing of HIF target genes. This study determined the effects of hypoxia on alternative splicing (AS) of HIF and non-HIF target genes in Hep3B cells and characterized the role of HIF in regulating AS of HIF induced genes. The results indicated that hypoxia generally promotes exon inclusion for hypoxia-induced, but reduces exon inclusion for hypoxia reduced genes. Mechanistically, HIF activity, but not hypoxia per se is found to be necessary and sufficient to increase exon inclusion of several HIF target genes including pyruvate dehydrogenase kinase 1 (PDK1). PDK1 splicing reporters confirmed that transcriptional activation by HIF is sufficient to increase exon inclusion of PDK1 splicing reporter. In contrast, transcriptional activation of the PDK1 minigene by other transcription factor in the absence of endogenous HIF target gene activation fails to alter PDK1 RNA splicing, demonstrating a novel role of HIF target gene(s) in regulating RNA splicing of HIF target genes. Implications:This study demonstrates a novel function of HIF in regulating RNA splicing of HIF target genes. We analyzed total RNA from Hep3B cells cultured under 21% (N1,3,5) or 1.2% (H2,4,6) oxygen using the Affymetrix Human Exon 1.0 ST platform. Array data was processed by Altanalyze software version 2.0.7. Techinical replicates were performed for Nx and Hx treated Hep3B cells
2014-05-14 | E-GEOD-57613 | biostudies-arrayexpress
Project description:Brain transcriptome at 0h, 1h, 3h, 6h, 12h, 24h, 48h after hypoxia stress Large yellow croakers (body weight at 90-100 g) were purchased from the mariculture farm in Ningde, Fuzhou, China. The fish were maintained at 25 °C in aerated water tanks (dissolved oxygen concentration: 7.8±0.5 mg per liter) with a flow through seawater supply. After 7 days of acclimation, these fish were used for the following experiments. Hypoxic time-course experiments were conducted at 25 °C using published method 30, by bubbling nitrogen gas into an aquarium. The desired pO2 was controlled by using dissolved oxygen meter (, Canada). At the onset of the time course, the oxygen content of the tank was lowered from an aerated pO2 of 100% (7.8 mg per liter) down to 20% (1.6±0.2 mg per liter) over a 30-min period. At the 1-, 3-, 6-, 12-, 24-, and 48-h time points, fish were sampled and sequenced.
2015-04-17 | E-GEOD-57608 | biostudies-arrayexpress