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Identification of hypoxia-induced genes in human SGBS adipocytes by microarray analysis.

Geiger K, Leiherer A, Muendlein A, Stark N, Geller-Rhomberg S, Saely CH, Wabitsch M, Fraunberger P, Drexel H - PLoS ONE (2011)

Bottom Line: Therefore, we compared gene expression profiles of human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes under normoxic or hypoxic conditions to detect hypoxia-responsive genes in adipocytes by using whole human genome microarrays.Moreover in six of these eight genes we identified HIF response elements in the proximal promoters, specific for the HIF transcription factor family members HIF1A and HIF2A.In addition, the identified hypoxia-regulated genes are likely involved in the regulation of obesity, the incidence of type 2 diabetes, and the metabolic syndrome.

View Article: PubMed Central - PubMed

Affiliation: Vorarlberg Institute for Vascular Investigation and Treatment, Feldkirch, Austria.

ABSTRACT
Hypoxia in adipose tissue is suggested to be involved in the development of a chronic mild inflammation, which in obesity can further lead to insulin resistance. The effect of hypoxia on gene expression in adipocytes appears to play a central role in this inflammatory response observed in obesity. However, the global impact of hypoxia on transcriptional changes in human adipocytes is unclear. Therefore, we compared gene expression profiles of human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes under normoxic or hypoxic conditions to detect hypoxia-responsive genes in adipocytes by using whole human genome microarrays. Microarray analysis showed more than 500 significantly differentially regulated mRNAs after incubation of the cells under low oxygen levels. To gain further insight into the biological processes, hypoxia-regulated genes after 16 hours of hypoxia were classified according to their function. We identified an enrichment of genes involved in important biological processes such as glycolysis, response to hypoxia, regulation of cellular component movement, response to nutrient levels, regulation of cell migration, and transcription regulator activity. Real-time PCR confirmed eight genes to be consistently upregulated in response to 3, 6 and 16 hours of hypoxia. For adipocytes the hypoxia-induced regulation of these genes is shown here for the first time. Moreover in six of these eight genes we identified HIF response elements in the proximal promoters, specific for the HIF transcription factor family members HIF1A and HIF2A. In the present study, we demonstrated that hypoxia has an extensive effect on gene expression of SGBS adipocytes. In addition, the identified hypoxia-regulated genes are likely involved in the regulation of obesity, the incidence of type 2 diabetes, and the metabolic syndrome.

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Venn diagram of the hypoxia-regulated genes in human adipocytes.Microarray analysis resulted in 10 differentially regulated genes after 3 hours, 52 differentially regulated genes after 6 hours and 514 differentially regulated genes after 16 hours cultivation of the cells in a hypoxic environment (1% O2). In the intersection of the circles the number of genes commonly regulated to the corresponding time points is indicated. The genes included in this analysis showed at least a 2-fold change in the expression compared to the control with a p value <0.05.
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pone-0026465-g001: Venn diagram of the hypoxia-regulated genes in human adipocytes.Microarray analysis resulted in 10 differentially regulated genes after 3 hours, 52 differentially regulated genes after 6 hours and 514 differentially regulated genes after 16 hours cultivation of the cells in a hypoxic environment (1% O2). In the intersection of the circles the number of genes commonly regulated to the corresponding time points is indicated. The genes included in this analysis showed at least a 2-fold change in the expression compared to the control with a p value <0.05.

Mentions: Further analysis of the results obtained from the microarrays showed that 9 mRNAs were consistently differentially expressed at 3, 6 and 16 hours of 1% O2 (figure 1). These genes encode for adreno­medullin (ADM), ankyrin repeat domain 37 (ANKRD37), DNA-damage-inducible transcript 4 (DDIT4), lysine(K)-specific demethylase 3A (KDM3A), 6-phosphofructo-2-kinase/fructose-2,6-bip­hosphatase 4 (PFKFB4), protein phosphatase 1 regulatory (inhibitor) subunit 3C (PPP1R3C), vascular endothelial growth factor A (VEGFA), WD-repeat domain 73 (WDR73), and zink finger protein 395 (ZNF395). The transcriptional induction values of these genes obtained from the microarray data are shown in figure 2. Thereupon we analyzed proximal promoter sequences (-700 bp to +300 bp with respect to the transcription start site) of the corresponding genes, looking for transcription factor binding sites. Applying the F-Match tool integrated in the ExPlain software we used a predefined set of 561 human housekeeping genes, from which the set of 514 upregulated genes after 16h were excluded, as background and the PWM profile mentioned above for the calculation. The result was filtered according to their p-values (<0.007) and Yes/No ratio (>1.3) and ranked according to their Yes/No ratio which represents their abundance in the set of 9 genes (ADM, ANKRD37, DDIT4, KDM3A, PFKFB4, PPP1R3C, VEGFA, WDR73 and ZNF395) compared to the background. The 18 best hits among the matched PWMs and the graphical output of the corresponding consensus sequences are displayed in figure 3. At position two, five and fourteen, according to the ranking, we found PWMs representing hypoxia response.


Identification of hypoxia-induced genes in human SGBS adipocytes by microarray analysis.

Geiger K, Leiherer A, Muendlein A, Stark N, Geller-Rhomberg S, Saely CH, Wabitsch M, Fraunberger P, Drexel H - PLoS ONE (2011)

Venn diagram of the hypoxia-regulated genes in human adipocytes.Microarray analysis resulted in 10 differentially regulated genes after 3 hours, 52 differentially regulated genes after 6 hours and 514 differentially regulated genes after 16 hours cultivation of the cells in a hypoxic environment (1% O2). In the intersection of the circles the number of genes commonly regulated to the corresponding time points is indicated. The genes included in this analysis showed at least a 2-fold change in the expression compared to the control with a p value <0.05.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3198480&req=5

pone-0026465-g001: Venn diagram of the hypoxia-regulated genes in human adipocytes.Microarray analysis resulted in 10 differentially regulated genes after 3 hours, 52 differentially regulated genes after 6 hours and 514 differentially regulated genes after 16 hours cultivation of the cells in a hypoxic environment (1% O2). In the intersection of the circles the number of genes commonly regulated to the corresponding time points is indicated. The genes included in this analysis showed at least a 2-fold change in the expression compared to the control with a p value <0.05.
Mentions: Further analysis of the results obtained from the microarrays showed that 9 mRNAs were consistently differentially expressed at 3, 6 and 16 hours of 1% O2 (figure 1). These genes encode for adreno­medullin (ADM), ankyrin repeat domain 37 (ANKRD37), DNA-damage-inducible transcript 4 (DDIT4), lysine(K)-specific demethylase 3A (KDM3A), 6-phosphofructo-2-kinase/fructose-2,6-bip­hosphatase 4 (PFKFB4), protein phosphatase 1 regulatory (inhibitor) subunit 3C (PPP1R3C), vascular endothelial growth factor A (VEGFA), WD-repeat domain 73 (WDR73), and zink finger protein 395 (ZNF395). The transcriptional induction values of these genes obtained from the microarray data are shown in figure 2. Thereupon we analyzed proximal promoter sequences (-700 bp to +300 bp with respect to the transcription start site) of the corresponding genes, looking for transcription factor binding sites. Applying the F-Match tool integrated in the ExPlain software we used a predefined set of 561 human housekeeping genes, from which the set of 514 upregulated genes after 16h were excluded, as background and the PWM profile mentioned above for the calculation. The result was filtered according to their p-values (<0.007) and Yes/No ratio (>1.3) and ranked according to their Yes/No ratio which represents their abundance in the set of 9 genes (ADM, ANKRD37, DDIT4, KDM3A, PFKFB4, PPP1R3C, VEGFA, WDR73 and ZNF395) compared to the background. The 18 best hits among the matched PWMs and the graphical output of the corresponding consensus sequences are displayed in figure 3. At position two, five and fourteen, according to the ranking, we found PWMs representing hypoxia response.

Bottom Line: Therefore, we compared gene expression profiles of human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes under normoxic or hypoxic conditions to detect hypoxia-responsive genes in adipocytes by using whole human genome microarrays.Moreover in six of these eight genes we identified HIF response elements in the proximal promoters, specific for the HIF transcription factor family members HIF1A and HIF2A.In addition, the identified hypoxia-regulated genes are likely involved in the regulation of obesity, the incidence of type 2 diabetes, and the metabolic syndrome.

View Article: PubMed Central - PubMed

Affiliation: Vorarlberg Institute for Vascular Investigation and Treatment, Feldkirch, Austria.

ABSTRACT
Hypoxia in adipose tissue is suggested to be involved in the development of a chronic mild inflammation, which in obesity can further lead to insulin resistance. The effect of hypoxia on gene expression in adipocytes appears to play a central role in this inflammatory response observed in obesity. However, the global impact of hypoxia on transcriptional changes in human adipocytes is unclear. Therefore, we compared gene expression profiles of human Simpson-Golabi-Behmel syndrome (SGBS) adipocytes under normoxic or hypoxic conditions to detect hypoxia-responsive genes in adipocytes by using whole human genome microarrays. Microarray analysis showed more than 500 significantly differentially regulated mRNAs after incubation of the cells under low oxygen levels. To gain further insight into the biological processes, hypoxia-regulated genes after 16 hours of hypoxia were classified according to their function. We identified an enrichment of genes involved in important biological processes such as glycolysis, response to hypoxia, regulation of cellular component movement, response to nutrient levels, regulation of cell migration, and transcription regulator activity. Real-time PCR confirmed eight genes to be consistently upregulated in response to 3, 6 and 16 hours of hypoxia. For adipocytes the hypoxia-induced regulation of these genes is shown here for the first time. Moreover in six of these eight genes we identified HIF response elements in the proximal promoters, specific for the HIF transcription factor family members HIF1A and HIF2A. In the present study, we demonstrated that hypoxia has an extensive effect on gene expression of SGBS adipocytes. In addition, the identified hypoxia-regulated genes are likely involved in the regulation of obesity, the incidence of type 2 diabetes, and the metabolic syndrome.

Show MeSH
Related in: MedlinePlus