Effect of hypoxia on gene expression by human hepatocytes (HepG2) (original) (raw)
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Gene expression of the liver in response to chronic hypoxia
Physiological Genomics, 2010
Hypoxia is an important ecological, evolutionary, and biomedical stressor. While physiological acclimatization of mammals to hypoxia is well studied, the variation in gene expression that underlies acclimatization is not well studied. We acclimatized inbred mice for 32 days to hypoxic conditions that simulated altitudes of 1400, 3000, and 4500 m. We used oligonucleotide microarrays to measure changes in steady-state abundance of mRNA in the livers of these mice. Mice exposed to more severe hypoxia (simulated altitude of 4500 m) were smaller in mass and had higher hematocrit than mice exposed to less severe hypoxia. ANOVA and false discovery rate tests indicated that 580 genes were significantly differentially expressed in response to chronic hypoxia. Few of these 580 genes have previously been reported to respond to hypoxia. In contrast, many of these 580 genes belonged to same functional groups typically respond to acute hypoxia. That is, both chronic and acute hypoxia elicit chang...
Regulation of gene expression by hypoxia
Biochemical Journal, 2008
Hypoxia induces profound changes in the cellular gene expression profile. The discovery of a major transcription factor family activated by hypoxia, HIF (hypoxia-inducible factor), and the factors that contribute to HIF regulation have greatly enhanced our knowledge of the molecular aspects of the hypoxic response. However, in addition to HIF, other transcription factors and cellular pathways are activated by exposure to reduced oxygen. In the present review, we summarize the current knowledge of how additional hypoxia-responsive transcription factors integrate with HIF and how other cellular pathways such as chromatin remodelling, translation regulation and microRNA induction, contribute to the co-ordinated cellular response observed following hypoxic stress.
The Journal of Physiology, 1999
. Western blot analysis of HIF_1á expression in Hep3B cells Normoxic control was incubated for 4 h in an atmosphere of 20% Oµ, 5% COµ, balance Nµ. Hypoxia was induced by placing the cultures in an atmosphere of 3% Oµ, 5% COµ, balance Nµ for 4 or 24 h as indicated. Protein extraction and Western blotting were done as described in the Methods section. Reactive proteins were detected using the ECL system (Amersham).
Transcriptional Profiling Using RNA-Seq to Study Hypoxia-Mediated Gene Regulation
Methods in molecular biology (Clifton, N.J.), 2018
Exposing cells to a hypoxic environment leads to significant physiological and molecular alterations. Most of the hypoxic responses are regulated by the transcription factors known as hypoxia-inducible factors (HIFs). HIF1, a heterodimer of hypoxia-stabilized subunit HIF-1alpha and a constitutively expressed subunit HIF-1beta, serves as a key transcription factor that regulates gene expressions which are involved in cell growth, metabolism, and proliferation. The global expression patterns can be analyzed by utilizing RNA-Seq to understand the cellular alterations in hypoxia. This technique enables us to understand the comprehensive regulation of gene expression by specific factors or environmental stimuli. Here, we describe the complete process of studying hypoxia-mediated gene expression by using RNA-Seq, including the hypoxic treatment of cells, RNA isolation, RNA quality check, cDNA library preparation, and library quality check.
A microarray analysis of the hypoxia-induced modulation of gene expression in human adipocytes
Archives Of Physiology And Biochemistry, 2012
The effect of hypoxia on global gene expression in human adipocytes has been examined using DNA microarrays. Adipocytes (Zen-Bio, day 12 post-differentiation) were exposed to hypoxia (1% O 2 ) or 'normoxia' (21% O 2 ) for 24 h and extracted RNA probed with Agilent arrays containing 41,152 probes. A total of 1346 probes were differentially expressed (>2.0-fold change, P < 0.01) in response to hypoxia; 650 genes were up-regulated (including LEP, IL6, VEGF, ANGPTL4) and 650 down-regulated (including ADIPOQ, UCP2). Major genes not previously identified as hypoxiasensitive in adipocytes include AQP3, FABP3, FABP5 and PPARGC1A. Ingenuity analysis indicated that several pathways and functions were modulated by hypoxia, including glucose utilization, lipid oxidation and cell death. Network analysis indicated a down-regulation of p38/MAPK and PGC-1α signalling in the adipocytes. It is concluded that hypoxia has extensive effects on human adipocyte gene expression, consistent with low O 2 tension underlying adipose tissue dysfunction in obesity.
PLoS ONE, 2014
Hypoxia is one of the most important features of the tumor microenvironment, exerting an adverse effect on tumor aggressiveness and patient prognosis. Two types of hypoxia may occur within the tumor mass, chronic (prolonged) and cycling (transient, intermittent) hypoxia. Cycling hypoxia has been shown to induce aggressive tumor cell phenotype and radioresistance more significantly than chronic hypoxia, though little is known about the molecular mechanisms underlying this phenomenon. The aim of this study was to delineate the molecular response to both types of hypoxia induced experimentally in tumor cells, with a focus on cycling hypoxia. We analyzed in vitro gene expression profile in three human cancer cell lines (melanoma, ovarian cancer, and prostate cancer) exposed to experimental chronic or transient hypoxia conditions. As expected, the cell-type specific variability in response to hypoxia was significant. However, the expression of 240 probe sets was altered in all 3 cell lines. We found that gene expression profiles induced by both types of hypoxia were qualitatively similar and strongly depend on the cell type. Cycling hypoxia altered the expression of fewer genes than chronic hypoxia (6,132 vs. 8,635 probe sets, FDR adjusted p,0.05), and with lower fold changes. However, the expression of some of these genes was significantly more affected by cycling hypoxia than by prolonged hypoxia, such as IL8, PLAU, and epidermal growth factor (EGF) pathway-related genes (AREG, HBEGF, and EPHA2). These transcripts were, in most cases, validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Our results indicate that experimental cycling hypoxia exerts similar, although less intense effects, on the examined cancer cell lines than its chronic counterpart. Nonetheless, we identified genes and molecular pathways that seem to be preferentially regulated by cyclic hypoxia.
Hypoxia-inducible gene expression
Respiration physiology, 1995
When oxygen is lacking the cellular production of some hormones, cytokines and glycolytic enzymes can be dramatically increased by a hypoxia-induced increase in the expression of the respective genes that encode for these proteins. The most progress in understanding how the transcription of genes is increased under hypoxic conditions has been made by studying the hypoxia-inducible expression of the erythropoietin gene. Elucidating the oxygen sensitive enhancer elements of the erythropoietin gene has prompted studies on other oxygen-regulated genes. The transcription-regulating proteins that are induced with hypoxia bind to closely related regulatory DNA sequences that control the expression of the genes for erythropoietin, the vascular endothelial growth factor and a number of glycolytic enzymes. It became evident that the hypoxia-inducible enhancer may be part of a widespread oxygen-sensing mechanism acting in a wide variety of mammalian cells. Comparison with the oxygen sensor sys...
Regulation of gene expression by hypoxia: A molecular approach
Respiration Physiology, 1997
Oxygen is a strict requirement for cell function. The cellular mechanisms by which organisms detect and respond to changes in oxygen tension remain a major unanswered question in pulmonary physiology. Part of the difficulty in addressing this question is due to the limited scope of experiments that can be performed in vivo. In the past few years, several laboratories have begun to make progress in this area, using a variety of cell culture model systems and sophisticated genetic manipulations. Here, we review the current state of knowledge of regulation of gene expression by hypoxia, and describe novel experimental approaches that promise to broaden our understanding of how cells and whole organisms respond to alterations in O 2 tension.
Decoding the secreted inflammatory response of primary human hepatocytes to hypoxic stress in vitro
Annals of Translational Medicine
Background: The cellular and molecular response of liver cells to hypoxic stress is not fully understood. We used computational modeling to gain insights into the inflammatory response of primary human hepatocytes (HC) to hypoxic stress in vitro. Methods: Primary HC from cancer patients were exposed to hypoxia (1% O 2) or normoxia (21% O 2) for 1-48 h, and the cell supernatants were assayed for 21 inflammatory mediators. Data were analyzed by Two-Way ANOVA, Dynamic Bayesian Network (DBN) inference, Dynamic Network Analysis (DyNA), and Time-interval Principal Component Analysis (TI-PCA). Results: The chemokines MCP-1/CCL2 and IP-10/CXCL10, along with the cytokines interleukin (IL)-2 and IL-15 were altered significantly over time in hypoxic vs. normoxic HC. DBN inference suggested central, coordinating roles for MCP-1 and IL-8 in regulating a largely conserved inflammatory program in both hypoxic and normoxic HC. DyNA likewise suggested similar network trajectories of decreasing complexity over time in both hypoxic and normoxic HC, though with differential connectivity of MCP-1, IP-10, IL-8, and Eotaxin. TI-PCA pointed to IL-1β as a central characteristic of inflammation in hypoxic HC across all time intervals, along with IL-15 and IL-10, vs. Eotaxin, IL-7, IL-10, IL-15, and IL-17A in normoxic HC. Conclusions: Thus, diverse human HC appear to respond in a largely conserved fashion to cell culture stress, with distinct characteristics based on the presence or absence of hypoxia.
Hypoxia induces hexokinase II gene expression in human lung cell line A549
American Journal of Physiology-Lung Cellular and Molecular Physiology, 2000
During adaptation to hypoxic and hyperoxic conditions, the genes involved in glucose metabolism are upregulated. To probe involvement of the transcription factor hypoxia-induced factor-1 (HIF-1) in hexokinase (HK) II expression in human pulmonary cells, A549 cells and small-airway epithelial cells (SAECs) were exposed to stimuli such as hypoxia, deferoxamine (DFO), and metal ions. The largest increase in HK-II (20-fold for mRNA and 2.5-fold for enzymatic activity) was observed in A549 cells when exposed to DFO. All stimuli selectively increased the 5.5-kb rather than 4-kb transcript in A549 cells. Cycloheximide and actinomycin D inhibited these responses. In addition, cells were transfected with luciferase reporter constructs driven by the full-length HK-II 5′-regulatory region (4.0 kb) or various deletions of that region. A549 cells transfected with the 4.0-kb construct and exposed to hypoxia or DFO increased their luciferase activity 7- and 10-fold, respectively, indicating that H...