• DEPP1
• depression
• diabetes
• glucose metabolism
• mPFC
• synaptic protein

• 2017ZX09301013 National Key Special Project of Science and Technology for Innovation Drugs of China
• BK20192005 Leading Technology Foundation Research Project of Jiangsu Province
• 2021-I2M-5-011 CAMS Innovation Fund for Medical Sciences

• FAM66C
• bioinformatics analysis
• biomarkers
• hypoxia
• long non-coding RNAs
• molecular subtypes
• transcription factors
• tumor microenvironment

Acute or chronic irreversible respiratory failure may occur in patients undergoing pneumonectomy. Aim of this study was to determine transcriptome expression changes after experimental pneumonectomy in swine model. Experimental left pneumonectomy was performed in five pigs under general anaesthesia. Both the resected and the remaining lung, after 60 post-operative completely uneventful days, underwent genome-wide bulk RNA-Sequencing (RNA-Seq).

Histological analysis showed dilation of air spaces and rupture of interalveolar septa. In addition, mild inflammation, no fibrosis, radial stretch of the bronchus, strong enlargement of airspaces and thinning of the blood supply were observed. Bioinformatic analyses of bulk RNA-Seq data identified 553 Differentially Expressed Genes (DEGs) at adjusted P-value below 0.001, between pre- and post-pneumonectomy. The top 10 up-regulated DEGs were Edn1, Areg, Havcr2, Gadd45g, Depp1, Cldn4, Atf3, Myc, Gadd45b, Socs3; the top 10 down-regulated DEGs were Obscn, Cdkn2b, ENSSSCG00000015738, Prrt2, Amer1, Flrt3, Efnb2, Tox3, Znf793, Znf365. Leveraging digital cytometry tools, no difference in cellular abundance was found between the two experimental groups, while the analysis of cell type-specific gene expression patterns highlighted a striking predominance of macrophage-specific genes among the DEGs. DAVID-based gene ontology analysis showed a significant enrichment of “Extrinsic apoptotic signaling pathway” (FDR q = 7.60 × 10^− 3) and “Response to insulin” (FDR q = 7.60 × 10^− 3) genes, along with an enrichment of genes involved as “Negative regulators of DDX58/IFIH1 signaling” (FDR q = 7.50 × 10^− 4) found by querying the REACTOME pathway database. Gene network analyses indicated a general dysregulation of gene inter-connections.

This translational genomics study highlighted the existence both of individual genes, mostly dysregulated in certain cellular populations (e.g., macrophages), and gene-networks involved in pulmonary reaction after left pneumonectomy. Their involvement in lung homeostasis is largely supported by previous studies, carried out both in humans and in other animal models (under homeostatic or disease-related conditions), that adopted candidate-gene approaches. Overall, the present findings represent a preliminary assessment for future, more focused, studies on compensatory lung adaptation, pulmonary regeneration and functional reload.

The online version contains supplementary material available at 10.1186/s12864-021-08171-3.

• Differentially expressed genes
• Experimental Pneumonectomy
• Genome-wide expression
• Lung
• Pig
• Pulmonary regeneration
• RNA-Seq
• Transcriptomics
• Translational genomics

Glioblastoma is one of the most aggressive and deadliest malignant tumors. Acquired resistance decreases the effectiveness of bevacizumab in glioblastoma treatment and thus increases the mortality rate in patients with glioblastoma. In this study, the potential targets of pentagamavunone-1 (PGV-1), a curcumin analog, were explored as a complementary treatment to bevacizumab in glioblastoma therapy.

Target prediction, data collection, and analysis were conducted using the similarity ensemble approach (SEA), SwissTargetPrediction, STRING DB, and Gene Expression Omnibus (GEO) datasets. Gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were conducted using Webgestalt and DAVID, respectively. Hub genes were selected based on the highest degree scores using the CytoHubba. Analysis of genetic alterations and gene expression as well as Kaplan–Meier survival analysis of selected genes were conducted with cBioportal and GEPIA. Immune infiltration correlations between selected genes and immune cells were analyzed with database TIMER 2.0.

We found 374 targets of PGV-1, 1139 differentially expressed genes (DEGs) from bevacizumab-resistant-glioblastoma cells. A Venn diagram analysis using these two sets of data resulted in 21 genes that were identified as potential targets of PGV-1 against bevacizumab resistance (PBR). PBR regulated the metabolism of xenobiotics by cytochrome P450. Seven potential therapeutic PBR, namely GSTM1, AKR1C3, AKR1C4, PTGS2, ADAM10, AKR1B1, and HSD17B110 were found to have genetic alterations in 1.2%–30% of patients with glioblastoma. Analysis using the GEPIA database showed that the mRNA expression of ADAM10, AKR1B1, and HSD17B10 was significantly upregulated in glioblastoma patients. Kaplan–Meier survival analysis showed that only patients with low mRNA expression of AKR1B1 had significantly better overall survival than the patients in the high mRNA group. We also found a correlation between PBR and immune cells and thus revealed the potential of PGV-1 as an immunotherapeutic agent via targeting of PBR.

This study highlighted seven PBR, namely, GSTM1, AKR1C3, AKR1C4, PTGS2, ADAM10, AKR1B1, and HSD17B110. This study also emphasized the potential of PBR as a target for immunotherapy with PGV-1. Further validation of the results of this study is required for the development of PGV-1 as an adjunct to immunotherapy for glioblastoma to counteract bevacizumab resistance.

• ADAM10, a disintegrant and metalloproteinase 10
• AKRs, Aldo keto reductases
• Bevacizumab resistance
• Bioinformatics
• CAFs, Cancer-associated fibroblasts
• COX-2, cyclooxigenase-2
• DEGs, differentially expressed genes
• DT, Direct targets of PGV-1
• GSTM1, glutathione S-transferase mu 1
• GSTP1, glutathione S-transferase Pi-1
• Glioblastoma
• HSD17B10, Human type 10 17beta-hydroxysteroid dehydrogenase
• Immunotherapy
• KEGG, Kyoto Encyclopedia of Genes and Genomes
• PBR, potential therapeutic target genes of PGV-1 against bevacizumab resistance glioblastoma
• PGV-1
• PGV-1, Pentagamavunon-1
• PTGS2, prostaglandin-endoperoxide synthase 2
• ROS, reactive oxygen species
• SEA, Similarity ensemble approach
• Target prediction
• VEGF, vascular endothelial growth factor
• Webgestalt, WEB-based GEne SeT AnaLysis Toolkit

• decidual protein induced by progesterone (DEPP)
• hypoxia
• hypoxia responsive element (HRE)
• retina
• retinal pigment epithelium (RPE)

• Basis Functions
• Bayesian Modeling
• Functional Regression
• Imaging Genetics
• Markov chain Monte Carlo
• Probability Density Function

• R01 CA160736 NCI NIH HHS
• R01 CA178744 NCI NIH HHS
• R01 CA194391 NCI NIH HHS

• A-kinase anchor protein 4 (AKAP4)
• epithelial-to-mesenchymal transition (EMT)
• gastric cancer
• hypoxia

• decidualization
• insulin
• liver
• reactive oxygen species

Baicalin is a natural flavonoid glycoside which has potent anti-tumor and antioxidant activity in cancer cells. In the present study, we found that baicalin treatment significantly induced senescence in colon cancer cells. Furthermore, baicalin upregulated the expression of decidual protein induced by progesterone (DEPP) in HCT116 colon cancer cells, which accompanied with the activation of Ras/Raf/MEK/ERK and p16^INK4A/Rb signaling pathways. Meanwhile, these phenomena also appeared under the anti-oxidation effect exerted by baicalin. In addition, ectopic expression of DEPP in HCT116 cells significantly induced the activity of senescence-associated β-galactosidase (SA-β-Gal) in tumor cells regulated by Ras/Raf/MEK/ERK signaling pathway. Knockdown of DEPP by RNA interference efficiently counteracted the baicalin-mediated growth inhibition, senescence and cell cycle arrest in cancer cells. Importantly, in a xenograft mouse model of human colon cancer, we further confirmed that baicalin treatment dramatically inhibited tumor growth, which was due to the induction of tumor cellular senescence via the upregulation of DEPP and the activation of Ras/Raf/MEK/ERK signaling in vivo. In addition to baicalin treatment, we found that the hypoxia-response protein DEPP functions as a positive regulator involving the regulations of Ras/Raf/MEK/ERK signaling pathway and inhibition of human colon cancer by other anti-oxidative drugs, such as curcumin and sulforaphane, resulting in tumor cellular senescence. These results collectively suggest that baicalin upregulates the expression of DEPP and activates its downstream Ras/Raf/MEK/ERK and p16^INK4A/Rb pathways by acting as an antioxidant, leading to senescence in colon cancer cells.

• chemosensitivity
• gene expression profile
• glioma
• prognosis

• GBM
• HIF
• chemotherapy
• hypoxia
• invasion

Neuroblastoma is the most common solid tumor in childhood and develops from undifferentiated progenitor cells of the sympathetic nervous system. In neuronal tumor cells DNA-damaging chemotherapeutic agents activate the transcription factor FOXO3 which regulates the formation of reactive oxygen species (ROS) and cell death as well as a longevity program associated with therapy resistance.

We demonstrated before that C10ORF10/DEPP, a transcriptional target of FOXO3, localizes to peroxisomes and mitochondria and impairs cellular ROS detoxification. In the present study, we investigated the impact of FOXO3 and DEPP on the regulation of autophagy. Autophagy serves to reduce oxidative damage as it triggers a self-degradative process for the removal of aggregated or misfolded proteins and damaged organelles.

The effect of FOXO3 and DEPP on autophagy induction was analyzed using live cell fluorescence microscopy and immunoblot analyses of SH-EP cells transfected with a plasmid for EYFP-LC3 and with siRNAs specific for LC3, respectively. ROS steady-state levels were measured with reduced MitoTrackerRed CM-H2XROS. Cellular apoptosis was analyzed by flow cytometry and the caspase 3/7 assay.

We report for the first time that DEPP induces ROS accumulation and thereby mediates the formation of autophagosomes as inhibition of ROS formation by N-acetyl-cysteine completely blocks autophagy. We further demonstrate that H₂O₂-treatment triggers autophagy-induction by FOXO3-mediated DEPP expression. Importantly, knockdown of DEPP was sufficient to efficiently inhibit autophagy-induction under different stress conditions such as serum starvation and genotoxic stress, suggesting that DEPP expression is critical for the initiation of autophagy in neuroblastoma. FOXO3-triggered autophagy partially protects neuroblastoma cells from cell death. Consistent with this concept, we demonstrate that inhibition of autophagy by LC3-knockdown significantly increased etoposide- and doxorubicin-induced apoptosis. These results were also confirmed by the use of the autophagy-inhibitor chloroquine that significantly enhanced the chemotherapeutic effect of etoposide and doxorubicin in neuronal tumor cells.

Targeting FOXO3/DEPP-triggered autophagy is a promising strategy to sensitize neuroblastoma cells to chemotherapy.

The online version of this article (doi:10.1186/s12943-017-0661-4) contains supplementary material, which is available to authorized users.

• Autophagy
• DEPP
• FOXO3
• Reactive oxygen species

• Analysis
• ELISA
• Gene
• Glioblastoma multiforme
• IGFBP-2 and IGFBP-3
• Immunohistochemistry
• Plasma

• Adult
• Aged
• Aged, 80 and over
• Aging/metabolism
• Biomarkers, Tumor/metabolism
• Blood Chemical Analysis
• Brain/metabolism
• Brain/pathology
• Brain Neoplasms/metabolism
• Brain Neoplasms/pathology
• Enzyme-Linked Immunosorbent Assay
• Female
• Glioblastoma/metabolism
• Glioblastoma/pathology
• Humans
• Immunohistochemistry
• Insulin-Like Growth Factor Binding Protein 2/metabolism
• Insulin-Like Growth Factor Binding Protein 3/metabolism
• Kaplan-Meier Estimate
• Male
• Middle Aged
• Sex Characteristics
• Tumor Burden

FOXO transcription factors control cellular levels of reactive oxygen species (ROS) which critically contribute to cell survival and cell death in neuroblastoma. In the present study we investigated the regulation of C10orf10/DEPP by the transcription factor FOXO3. As a physiological function of C10orf10/DEPP has not been described so far we analyzed its effects on cellular ROS detoxification and death sensitization in human neuroblastoma cells.

The effect of DEPP on cellular ROS was measured by catalase activity assay and live cell fluorescence microscopy using the ROS-sensitive dye reduced MitoTracker Red CM-H2XROS. The cellular localization of DEPP was determined by confocal microscopy of EYFP-tagged DEPP, fluorescent peroxisomal- and mitochondrial probes and co-immunoprecipitation of the PEX7 receptor.

We report for the first time that DEPP regulates ROS detoxification and localizes to peroxisomes and mitochondria in neuroblastoma cells. FOXO3-mediated apoptosis involves a biphasic ROS accumulation. Knockdown of DEPP prevented the primary and secondary ROS wave during FOXO3 activation and attenuated FOXO3- and H₂O₂-induced apoptosis. Conditional overexpression of DEPP elevates cellular ROS levels and sensitizes to H₂O₂ and etoposide-induced cell death. In neuronal cells, cellular ROS are mainly detoxified in peroxisomes by the enzyme CAT/catalase. As DEPP contains a peroxisomal-targeting-signal-type-2 (PTS2) sequence at its N-terminus that allows binding to the PEX7 receptor and import into peroxisomes, we analyzed the effect of DEPP on cellular detoxification by measuring enzyme activity of catalase. Catalase activity was reduced in DEPP-overexpressing cells and significantly increased in DEPP-knockdown cells. DEPP directly interacts with the PEX7 receptor and localizes to the peroxisomal compartment. In parallel, the expression of the transcription factor peroxisome proliferator-activated receptor gamma (PPARG), a critical regulator of catalase enzyme activity, was strongly upregulated in DEPP-knockdown cells.

The combined data indicate that in neuroblastoma DEPP localizes to peroxisomes and mitochondria and impairs cellular ROS detoxification, which sensitizes tumor cells to ROS-induced cell death.

The online version of this article (doi:10.1186/1476-4598-13-224) contains supplementary material, which is available to authorized users.

Breast cancer is a common malignant tumor, which severely threatens the health of women with an increasing incidence in many countries. Here, we identified C10orf10 as a novel differentially expression gene using expression microarray screening. The expression analysis indicated that C10orf10 was frequently decreased in human breast cancers compared to noncancerous breast tissues (81/95, P = 0.0063). Kaplan-Meier analysis indicated that patients with low C10orf10 expression showed a poorer prognosis both in mRNA (n = 1115, P = 0.0013) and protein (n = 100, P = 0.003) levels. Univariate and multivariate analysis showed that the C10orf10 expression was an independent prognostic factor for overall survival of breast cancer patients. Further analysis revealed that low expression of C10orf10 was an unfavorable factor for the prognosis of the patients who were luminal A, luminal B, Her2+ subtypes, at histological grade 2, lymph node negative and ER positive. Our data provided the first evidence that C10orf10 expression was frequently decreased in breast cancer tissues, and low expression of C10orf10 may be an important prognostic factor for poorer survival time of breast cancer patients.

• Breast Neoplasms/metabolism
• Breast Neoplasms/mortality
• Breast Neoplasms/pathology
• Case-Control Studies
• Female
• Gene Expression
• Humans
• Intracellular Signaling Peptides and Proteins
• Kaplan-Meier Estimate
• Lymphatic Metastasis
• Prognosis
• Proportional Hazards Models
• Proteins/genetics
• Proteins/metabolism

• DMEM = Dulbecco's modified Eagle's medium
• FBS = fetal bovine serum
• GBM = glioblastoma
• HRP = horseradish peroxidase
• IFN = interferon
• IGF = insulin-like growth factor
• IGFBP = IGF binding protein
• IGFBP-3
• IHC = immunohistochemistry
• IR = insulin receptor
• KPS = Karnofsky Performance Scale
• LI = labeling index
• MTT = 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
• OD = optical density
• STAT-1
• STAT-1 = signal transducer and activator of transcription 1
• TGFβ = transforming growth factor–β
• biomarker
• glioblastoma
• oncology
• prognosis
• qPCR = quantitative polymerase chain reaction
• shRNA = short hairpin RNA

While the effects of hypoxia on gene expression have been investigated in the CNS to some extent, we currently do not know what role epigenetics plays in the transcription of many genes during such hypoxic stress. To start understanding the role of epigenetic changes during hypoxia, we investigated the long-term effect of hypoxia on gene expression and DNA methylation in hippocampal neuronal cells. Primary murine hippocampal neuronal cells were cultured for 7 days. Hypoxic stress of 1% O2, 5% CO2 for 24 hours was applied on Day 3, conditions we found to maximize cellular hypoxic stress response without inducing cell death. Cells were returned to normoxia for 4 days following the period of hypoxic stress. On Day 7, Methyl-Sensitive Cut Counting (MSCC) was used to identify a genome-wide methylation profile of the hippocampal cell lines to assess methylation changes resulting from hypoxia. RNA-Seq was also done on Day 7 to analyze changes in gene transcription. Phenotypic analysis showed that neuronal processes were significantly shorter after 1 day of hypoxia, but there was a catch-up growth of these processes after return to normoxia. Transcriptome profiling using RNA-Seq revealed 369 differentially expressed genes with 225 being upregulated, many of which form networks shown to affect CNS development and function. Importantly, the expression level of 59 genes could be correlated to the changes in DNA methylation in their promoter regions. CpG islands, in particular, had a strong tendency to remain hypomethylated long after hypoxic stress was removed. From this study, we conclude that short-term, sub-lethal hypoxia results in long-lasting changes to genome wide DNA methylation status and that some of these changes can be highly correlated with transcriptional modulation in a number of genes involved in functional pathways that have been previously implicated in neural growth and development.

• biomarkers
• gene databases
• glioblastoma multiforme
• gliomas
• immunohistochemistry

• Algorithms
• Biomarkers, Tumor/metabolism
• Brain/metabolism
• Brain Neoplasms/metabolism
• Brain Neoplasms/pathology
• Calcium-Binding Proteins/metabolism
• Case-Control Studies
• Extracellular Matrix Proteins/metabolism
• Gene Expression Profiling
• Gene Expression Regulation, Neoplastic
• Glioma/metabolism
• Glioma/pathology
• Humans
• Membrane Proteins/metabolism
• Neoplasm Grading
• Nerve Tissue Proteins/metabolism
• Oligonucleotide Array Sequence Analysis
• Prognosis

• P20 GM103456 NIGMS NIH HHS
• P20 GM103636 NIGMS NIH HHS
• 1P20GM103636 NIGMS NIH HHS
• 8P20GM103456-09 NIGMS NIH HHS

• Cyclin G2
• DNA damage
• PML
• PP2A B'γ
• γH2AX

Glioblastoma multiforme, the most common type of primary brain tumor in adults, is driven by cells with neural stem (NS) cell characteristics. Using derivation methods developed for NS cells, it is possible to expand tumorigenic stem cells continuously in vitro. Although these glioblastoma-derived neural stem (GNS) cells are highly similar to normal NS cells, they harbor mutations typical of gliomas and initiate authentic tumors following orthotopic xenotransplantation. Here, we analyzed GNS and NS cell transcriptomes to identify gene expression alterations underlying the disease phenotype.

Sensitive measurements of gene expression were obtained by high-throughput sequencing of transcript tags (Tag-seq) on adherent GNS cell lines from three glioblastoma cases and two normal NS cell lines. Validation by quantitative real-time PCR was performed on 82 differentially expressed genes across a panel of 16 GNS and 6 NS cell lines. The molecular basis and prognostic relevance of expression differences were investigated by genetic characterization of GNS cells and comparison with public data for 867 glioma biopsies.

Transcriptome analysis revealed major differences correlated with glioma histological grade, and identified misregulated genes of known significance in glioblastoma as well as novel candidates, including genes associated with other malignancies or glioma-related pathways. This analysis further detected several long non-coding RNAs with expression profiles similar to neighboring genes implicated in cancer. Quantitative PCR validation showed excellent agreement with Tag-seq data (median Pearson r = 0.91) and discerned a gene set robustly distinguishing GNS from NS cells across the 22 lines. These expression alterations include oncogene and tumor suppressor changes not detected by microarray profiling of tumor tissue samples, and facilitated the identification of a GNS expression signature strongly associated with patient survival (P = 1e-6, Cox model).

These results support the utility of GNS cell cultures as a model system for studying the molecular processes driving glioblastoma and the use of NS cells as reference controls. The association between a GNS expression signature and survival is consistent with the hypothesis that a cancer stem cell component drives tumor growth. We anticipate that analysis of normal and malignant stem cells will be an important complement to large-scale profiling of primary tumors.

AIM: To study short dsRNA oligonucleotides (siRNA) as a potent tool for artificially modulating gene expression of N-Myc down regulated gene 1 (NDRG1) gene induced under different physiological conditions (Normoxia and hypoxia) modulating NDRG1 transcription, mRNA stability and translation.

METHODS: A cell line established from a patient with glioblastoma multiforme. Plasmid DNA for transfections was prepared with the Endofree Plasmid Maxi kit. From plates containing 5 × 10⁷ cells, nuclear extracts were prepared according to previous protocols. The pSUPER-NDRG1 vectors were designed, two sequences were selected from the human NDRG1 cDNA (5’-GCATTATTGGCATGGGAAC-3’ and 5’-ATGCAGAGTAACGTGGAAG-3’. reverse transcription polymerase chain reaction was performed using primers designed using published information on β-actin and hypoxia-inducible factor (HIF)-1α mRNA sequences in GenBank. NDRG1 mRNA and protein level expression results under different conditions of hypoxia or reoxygenation were compared to aerobic control conditions using the Mann-Whitney U test. Reoxygenation values were also compared to the NDRG1 levels after 24 h of hypoxia (P < 0.05 was considered significant).

RESULTS: siRNA- and iodoacetate (IAA)-mediated downregulation of NDRG1 mRNA and protein expression in vitro in human glioblastoma cell lines showed a nearly complete inhibition of NDRG1 expression when compared to the results obtained due to the inhibitory role of glycolysis inhibitor IAA. Hypoxia responsive elements bound by nuclear HIF-1 in human glioblastoma cells in vitro under different oxygenation conditions and the clearly enhanced binding of nuclear extracts from glioblastoma cell samples exposed to extreme hypoxic conditions confirmed the HIF-1 Western blotting results.

CONCLUSION: NDRG1 represents an additional diagnostic marker for brain tumor detection, due to the role of hypoxia in regulating this gene, and it can represent a potential target for tumor treatment in human glioblastoma. The siRNA method can represent an elegant alternative to modulate the expression of the hypoxia induced NDRG1 gene and can help to monitor the development of the cancer disease treatment outcome through monitoring the expression of this gene in the patients undergoing the different therapeutic treatment alternatives available nowadays.

• N-Myc down regulated gene 1
• Short dsRNA oligonucleotides
• Human cancer diseases
• Brain cancer
• Radiotherapy

• Adenosine Triphosphate/metabolism
• Brain Neoplasms/enzymology
• Brain Neoplasms/pathology
• Brain Neoplasms/surgery
• Cell Death
• Cell Hypoxia
• Cell Proliferation
• Cell Survival
• Cyclin G2/metabolism
• Female
• G1 Phase
• Glioblastoma/enzymology
• Glioblastoma/pathology
• Glioblastoma/surgery
• Humans
• Male
• Middle Aged
• Multivariate Analysis
• Neoplastic Stem Cells/enzymology
• Neoplastic Stem Cells/pathology
• Prognosis
• Proportional Hazards Models
• Protein Phosphatase 2/antagonists & inhibitors
• Protein Phosphatase 2/metabolism
• Protein Subunits/antagonists & inhibitors
• Protein Subunits/metabolism
• S Phase

• K08 CA130985 NCI NIH HHS
• K08CA130985 NCI NIH HHS

• Adult
• Antineoplastic Agents, Alkylating/therapeutic use
• Brain Neoplasms/drug therapy
• Brain Neoplasms/genetics
• Brain Neoplasms/pathology
• Cell Survival/drug effects
• Computational Biology
• Databases, Genetic
• Drug Resistance, Neoplasm/genetics
• Female
• Gene Expression Regulation, Neoplastic/genetics
• Glioblastoma/drug therapy
• Glioblastoma/genetics
• Glioblastoma/pathology
• Humans
• Male
• Microarray Analysis
• Middle Aged
• Oligonucleotide Array Sequence Analysis
• Semustine/therapeutic use
• Signal Transduction/drug effects

• Cell Cycle Proteins
• Endothelial Cells/metabolism
• Endothelium, Vascular/cytology
• Female
• Forkhead Box Protein O1
• Forkhead Box Protein O3
• Forkhead Transcription Factors/physiology
• Gene Expression Regulation
• Humans
• Hypoxia/genetics
• Intracellular Signaling Peptides and Proteins
• Promoter Regions, Genetic
• Proteins/genetics
• Transcription Factors/physiology
• Transcription, Genetic

• Astrocytes/cytology
• Astrocytes/drug effects
• Bone Morphogenetic Protein 2/pharmacology
• Cell Differentiation/drug effects
• Cell Hypoxia/drug effects
• Cell Proliferation/drug effects
• Child
• Down-Regulation/drug effects
• Gene Silencing/drug effects
• Glioma/pathology
• Humans
• Hypoxia-Inducible Factor 1, alpha Subunit/genetics
• Hypoxia-Inducible Factor 1, alpha Subunit/metabolism
• Mitosis/drug effects
• Neoplastic Stem Cells/pathology
• Oxygen/pharmacology
• Signal Transduction/drug effects
• Smad Proteins/metabolism
• Tumor Suppressor Protein p53/metabolism

Hypoxia-inducible factor (HIF) controls an extensive range of adaptive responses to hypoxia. To better understand this transcriptional cascade we performed genome-wide chromatin immunoprecipitation using antibodies to two major HIF-α subunits, and correlated the results with genome-wide transcript profiling. Within a tiled promoter array we identified 546 and 143 sequences that bound, respectively, to HIF-1α or HIF-2α at high stringency. Analysis of these sequences confirmed an identical core binding motif for HIF-1α and HIF-2α (RCGTG) but demonstrated that binding to this motif was highly selective, with binding enriched at distinct regions both upstream and downstream of the transcriptional start. Comparison of HIF-promoter binding data with bidirectional HIF-dependent changes in transcript expression indicated that whereas a substantial proportion of positive responses (>20% across all significantly regulated genes) are direct, HIF-dependent gene suppression is almost entirely indirect. Comparison of HIF-1α- versus HIF-2α-binding sites revealed that whereas some loci bound HIF-1α in isolation, many bound both isoforms with similar affinity. Despite high-affinity binding to multiple promoters, HIF-2α contributed to few, if any, of the transcriptional responses to acute hypoxia at these loci. Given emerging evidence for biologically distinct functions of HIF-1α versus HIF-2α understanding the mechanisms restricting HIF-2α activity will be of interest.

• Animals
• Brain/blood supply
• Brain Neoplasms/metabolism
• Brain Neoplasms/pathology
• Cell Line, Tumor
• Endothelium, Vascular/cytology
• Endothelium, Vascular/metabolism
• Glioma/metabolism
• Glioma/pathology
• Glucose Transport Proteins, Facilitative/metabolism
• Hypoxia
• Rats
• Vascular Endothelial Growth Factor A/physiology