HIF-binding Sites Research Articles

Whole genome profiling of short-term hypoxia induced genes and identification of HIF-1 binding sites provide insights into HIF-1 function in Caenorhabditis elegans.

Oxygen is essential to all the aerobic organisms. However, during normal development, disease and homeostasis, organisms are often challenged by hypoxia (oxygen deprivation). Hypoxia-inducible transcription factors (HIFs) are master regulators of hypoxia response and are evolutionarily conserved in metazoans. The homolog of HIF in the genetic model organism C. elegans is HIF-1. In this study, we aimed to understand short-term hypoxia response to identify HIF-1 downstream genes and identify HIF-1 direct targets in C. elegans. The central research questions were: (1) which genes are differentially expressed in response to short-term hypoxia? (2) Which of these changes in gene expression are dependent upon HIF-1 function? (3) Are any of these hif-1-dependent genes essential to survival in hypoxia? (4) Which genes are the direct targets of HIF-1? We combine whole genome gene expression analyses and chromatin immunoprecipitation sequencing (ChIP-seq) experiments to address these questions. In agreement with other published studies, we report that HIF-1-dependent hypoxia-responsive genes are involved in metabolism and stress response. Some HIF-1-dependent hypoxia-responsive genes like efk-1 and phy-2 dramatically impact survival in hypoxic conditions. Genes regulated by HIF-1 and hypoxia overlap with genes responsive to hydrogen sulfide, also overlap with genes regulated by DAF-16. The genomic regions that co-immunoprecipitate with HIF-1 are strongly enriched for genes involved in stress response. Further, some of these potential HIF-1 direct targets are differentially expressed under short-term hypoxia or are differentially regulated by mutations that enhance HIF-1 activity.

Abstract 14496: HIF2a Activation Reduces Pulmonary Angiogenesis and Promotes Vascular Remodeling in Pulmonary Arterial Hypertension by Suppressing Wnt7a Production in Pulmonary Endothelial Cells

Introduction: Dysfunctional angiogenesis and obliterative vasculopathy are hallmarks of pulmonary arterial hypertension (PAH). Inappropriate HIF1a/2a activation and insufficient Wnt7a production are associated with pulmonary artery endothelial cell (PAEC) dysfunction, suggesting that HIF1a/2a and Wnt7a may interact as part of a signaling axis to promote PAEC homeostasis. Hypothesis: HIF1a/2a overactivation suppresses Wnt7a expression in PAH PAECs. Methods: Healthy and PAH PMVECs were obtained from explanted lungs. Cobalt Chloride (CoCl2) was used to activate HIF. PMVECs were transfected with lentiviruses carrying HIF1a/2a constructs, followed by functional and molecular studies. Lungs from mice with endothelial-specific HIF1a/2a activation (Egln1 Tie2Cre ) and HIF2a deletion (EH2) were analyzed via single cell (sc) RNA-seq and confocal imaging. Results: Compared to controls, PAH lung tissue and PAECs demonstrated an inverse correlation between increased HIF1a/2a, and reduced Wnt7a expression. Treatment with CoCl2 for 24 hours resulted in a ~4-fold increase in Wnt7a transcription that was absent in PAH PMVECs. Lentivirus transfection of healthy PAEC demonstrated that HIF1a increased Wnt7a transcription while HIF2a significantly reduced Wnt7a transcription. In silico analysis of the Wnt7a gene locus demonstrated HIF binding sites at promoter-enhancer sequences suggesting that Wnt7a is a gene target of HIF signaling. In addition, ATAC-seq and ChIP-seq analysis of the Wnt7a gene locus in PAH PMVECs indicated a closed chromatin configuration, suggesting epigenetic repression. Lung scRNA-seq and RNAScope analysis of Egln1 Tie2Cre mice demonstrated a reduction of capillary EC, which was absent in EH2 mice, suggesting a HIF2a-dependent mechanism. Confocal and WB of lung tissues demonstrate that Wnt7a expression was significantly reduced in Egln1 Tie2Cre mice but preserved in EH2 mice. Conclusions: HIF2a and epigenetic repression contribute to PAEC dysfunction by suppressing Wnt7a-dependent angiogenesis in PAH. We speculate that Wnt7a may also be required to maintain the capillary EC phenotype in the lung and that restoring Wnt7a production could compensate for HIF-driven endothelial dysfunction in PAH.

Hypoxia dampens innate immune signalling at early time points and increases Zika virus RNA levels in iPSC-derived macrophages.

Type I interferons (IFNs) are the major host defence against viral infection and are induced following activation of cell surface or intracellular pattern recognition receptors, including retinoic-acid-inducible gene I (RIG-I)-like receptors (RLRs). All cellular processes are shaped by the microenvironment and one important factor is the local oxygen tension. The majority of published studies on IFN signalling are conducted under laboratory conditions of 18% oxygen (O2), that do not reflect the oxygen levels in most organs (1-5 % O2). We studied the effect of low oxygen on IFN induction and signalling in induced Pluripotent Stem Cell (iPSC)-derived macrophages as a model for tissue-resident macrophages and assessed the consequence for Zika virus (ZIKV) infection. Hypoxic conditions dampened the expression of interferon-stimulated genes (ISGs) following RLR stimulation or IFN treatment at early time points. RNA-sequencing and bio-informatic analysis uncovered several pathways including changes in transcription factor availability, the presence of HIF binding sites in promoter regions, and CpG content that may contribute to the reduced ISG expression. Hypoxic conditions increased the abundance of ZIKV RNA highlighting the importance of understanding how low oxygen conditions in the local microenvironment affect pathogen sensing and host defences.

Oxygen‐dependent regulation of β3‐adrenoceptor in the retina: Another piece in the puzzle of the pathological neovascularization

AbstractPurpose: Hypoxia‐inducible factor (HIF)‐1 is the major transcriptional regulator involved in the adaptive responses to hypoxia in health and disease. In the retina, HIF‐1 controls the hypoxia‐driven vascular proliferation by inducing the overexpression of neoangiogenic factors. The HIF‐1‐mediated neoangiogenesis is strongly promoted by β‐adrenoceptors overstimulation following the hypoxia‐driven surge of catecholamines. Among them, β3‐adrenoceptor (β3‐AR) appears strictly linked to hypoxia, resulting overexpressed in proliferating vessels parallelly with increased HIF‐1. However, whether β3‐AR undergoes HIF‐1 direct regulation remains to be established.Methods: The mouse model of oxygen‐induced retinopathy (OIR) was used to test the influence of the HIF‐1 stabilization with DMOG on the oxygen‐dependent modulation of β3‐AR expression in the retina. Hence, the mouse β3‐AR gene was analysed to search for putative HIF binding sites (HBSs), which then underwent in silico simulations to predict their suitability for the binding with HIF‐1. Finally, the oxygen‐dependent physical interaction of the best scored HBS with HIF‐1 was tested using ChIP‐qPCR in retinas of OIR mice and correlated with the β3‐AR gene expression.Results: In OIR retinas, β3‐AR expression inversely correlated with the oxygen tension. The inhibition of HIF‐1 drop under hyperoxia abolished the oxygen‐dependent β3‐AR modulation, indicating that β3‐AR expression might depend on HIF‐1 levels. The β3‐AR gene analysis and the HIF‐1 docking simulations revealed 6 possible HBS, of which HBS#1 resulted the most suitable region for HIF‐1 binding. The ChIP‐qPCR analysis on OIR retinas demonstrated the actual oxygen‐dependent HIF‐1/HBS#1 physical interaction, which correlated with the β3‐AR gene transactivation.Conclusions: This evidence allows to establish the β3‐AR as a member of the HIF‐1 target genes, thus paving the way to the further characterization of its role in oxygen‐dependent retinal abnormalities.

MYCN and HIF-1 directly regulate TET1 expression to control 5-hmC gains and enhance neuroblastoma cell migration in hypoxia

ABSTRACT Ten-Eleven-Translocation 5-methylcytosine dioxygenases 1–3 (TET1-3) convert 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC), using oxygen as a co-substrate. Contrary to expectations, hypoxia induces 5-hmC gains in MYCN-amplified neuroblastoma (NB) cells via upregulation of TET1. Here, we show that MYCN directly controls TET1 expression in normoxia, and in hypoxia, HIF-1 augments TET1 expression and TET1 protein stability. Through gene-editing, we identify two MYCN and HIF-1 binding sites within TET1 that regulate gene expression. Bioinformatic analyses of 5-hmC distribution and RNA-sequencing data from hypoxic cells implicate hypoxia-regulated genes important for cell migration, including CXCR4. We show that hypoxic cells lacking the two MYCN/HIF-1 binding sites within TET1 migrate slower than controls. Treatment of MYCN-amplified NB cells with a CXCR4 antagonist results in slower migration under hypoxic conditions, suggesting that inclusion of a CXCR4 antagonist into NB treatment regimens could be beneficial for children with MYCN-amplified NBs.

HIF-1-Dependent Induction of β3 Adrenoceptor: Evidence from the Mouse Retina.

A major player in the homeostatic response to hypoxia is the hypoxia-inducible factor (HIF)-1 that transactivates a number of genes involved in neovessel proliferation in response to low oxygen tension. In the retina, hypoxia overstimulates β-adrenoceptors (β-ARs) which play a key role in the formation of pathogenic blood vessels. Among β-ARs, β3-AR expression is increased in proliferating vessels in concomitance with increased levels of HIF-1α and vascular endothelial growth factor (VEGF). Whether, similarly to VEGF, hypoxia-induced β3-AR upregulation is driven by HIF-1 is still unknown. We used the mouse model of oxygen-induced retinopathy (OIR), an acknowledged model of retinal angiogenesis, to verify the hypothesis of β3-AR transcriptional regulation by HIF-1. Investigation of β3-AR regulation over OIR progression revealed that the expression profile of β3-AR depends on oxygen tension, similar to VEGF. The additional evidence that HIF-1α stabilization decouples β3-AR expression from oxygen levels further indicates that HIF-1 regulates the expression of the β3-AR gene in the retina. Bioinformatics predicted the presence of six HIF-1 binding sites (HBS #1-6) upstream and inside the mouse β3-AR gene. Among these, HBS #1 has been identified as the most suitable HBS for HIF-1 binding. Chromatin immunoprecipitation-qPCR demonstrated an effective binding of HIF-1 to HBS #1 indicating the existence of a physical interaction between HIF-1 and the β3-AR gene. The additional finding that β3-AR gene expression is concomitantly activated indicates the possibility that HIF-1 transactivates the β3-AR gene. Our results are indicative of β3-AR involvement in HIF-1-mediated response to hypoxia.

Polymorphisms in the hypoxia inducible factor binding site of the macrophage migration inhibitory factor gene promoter in schizophrenia.

Macrophage migration inhibitory factor (MIF) is a multifunctional cytokine that promotes neurogenesis and neuroprotection. MIF is predominantly expressed in astrocytes in the brain. The serum MIF level and microsatellites/single nucleotide polymorphisms (SNPs) in the MIF gene promoter region are known to be associated with schizophrenia (SCZ). Interestingly, previous studies reported that hypoxia, an environmental risk factor for SCZ, induced MIF expression through binding of the hypoxia inducible factor (HIF)-1 to the hypoxia response element (HRE) in the MIF promoter. We investigated the involvement of MIF in SCZ while focusing on the HIF pathway. First, we conducted an association study of the SNP rs17004038 (C>A) in the HRE of the MIF promoter between 1758 patients with SCZ and 1507 controls. Next, we investigated the effect of hypoxia on MIF expression in primary cultured astrocytes derived from neonatal mice forebrain. SNP rs17004038 was significantly associated with SCZ (p = 0.0424, odds ratio = 1.445), indicating that this SNP in the HRE of the MIF promoter was a genetic risk factor for SCZ. Hypoxia induced MIF mRNA expression and MIF protein production and increased HIF-1 binding to the MIF promoter, while the activity of the MIF promoter was suppressed by mutations in the HRE and by deletion of the HRE in astrocytes. These results suggest that SNP rs17004038 in the HRE of the MIF promoter was significantly associated with SCZ and may be involved in the pathophysiology of SCZ via suppression of hypoxia and HIF pathway-induced MIF expression.

Cloning of the Human MORG1 Promoter: Differential Regulation by Hypoxia and Prolyl-Hydroxylase Inhibitors.

MAPK-organizer 1 (MORG1) is a molecular scaffold for prolyl-hydroxylase-3 containing a domain (PHD3) protein linking MORG1 to mechanisms of adaptation in hypoxic conditions. In this paper, we report the cloning of the promoter region of the murine and human MORG1 gene. Among other transcriptional factors binding sites, we identified that both (mouse and human) promoter regions contained several putative hypoxia-inducible factor binding motifs. Analyses of the human MORG1 promoter by reporter assays revealed that hypoxia and pharmacological inhibitors of prolyl-hydroxylases under in vitro conditions in HEK 293 cells differentially regulate the MORG1 promoter reporter activity. The exposure of the cells to 10% hypoxia showed inhibition of MORG1 promotor activity at 6 and 12 h, but stimulation after 24 h while treated with prolyl-hydroxylase inhibitors led to a time-independent MORG1 promoter activation. Mutational analyses of the individual HIF binding sites on human MORG1 promoter suggest that the binding sites work in a complex corporation because single mutations were not sufficient to abolish completely the MORG1 reporter activation by PHD inhibitors. Our data provide the first evidence that not only MORG1 regulate HIF stabilization through a PHD complex, but also that, vice versa, HIFs control MORG1 expression directly or indirectly by a complex regulatory mechanism.

Hypoxic Regulation of Gene Transcription and Chromatin: Cause and Effect.

Cellular responses to low oxygen (hypoxia) are fundamental to normal physiology and to the pathology of many common diseases. Hypoxia-inducible factor (HIF) is central to this by enhancing the transcriptional activity of many hundreds of genes. The cellular response to HIF is cell-type-specific and is largely governed by the pre-existing epigenetic landscape. Prior to activation, HIF-binding sites and the promoters of HIF-target genes are already accessible, in contact with each other through chromatin looping and display markers of activity. However, hypoxia also modulates the epigenetic environment, both in parallel to and as a consequence of HIF activation. This occurs through a combination of oxygen-sensitive changes in enzyme activity, transcriptional activation of epigenetic modifiers, and localized recruitment to chromatin by HIF and activated RNApol2. These hypoxic changes in the chromatin environment may both contribute to and occur as a consequence of transcriptional regulation. Nevertheless, they have the capacity to both modulate and extend the transcriptional response to hypoxia.

HIF-1 directly induces TET3 expression to enhance 5-hmC density and induce erythroid gene expression in hypoxia

AbstractIn mammalian cells, cytosines found within cytosine guanine dinucleotides can be methylated to 5-methylcytosine (5-mC) by DNA methyltransferases and further oxidized by the Ten-eleven translocation dioxygenase (TET) enzymes to 5-hydroxymethylcytosine (5-hmC). We have previously shown that hematopoietic stem and progenitor cells (HSPCs) with TET2 mutations have aberrant 5-hmC distribution and less erythroid differentiation potential. However, these experiments were performed under standard tissue culture conditions with 21% oxygen (O2), whereas HSPCs in human bone marrow reside in ∼1% O2. Therefore, to model human erythropoiesis more accurately, we compared 5-hmC distribution and gene expression in hypoxic vs normoxic conditions. Despite TET enzymes having limited O2 as a substrate in hypoxia, 5-hmC peaks were more numerous and pronounced than in normoxia. Among the TET genes, TET3 was upregulated specifically in hypoxia. We identified 2 HIF-1 binding sites in TET3 by chromatin immunoprecipitation of HIF-1α followed by sequencing, and TET3 upregulation was abrogated with deletion of both sites, indicating that TET3 is a direct HIF-1 target. Finally, we showed that loss of one or both of these HIF-1 binding sites in K562 cells disrupted erythroid differentiation in hypoxia and lowered cell viability. This work provides a molecular link between O2 availability, epigenetic modification of chromatin, and erythroid differentiation.

Independence of HIF1a and androgen signaling pathways in prostate cancer

BackgroundTherapeutic targeting of the androgen signaling pathway is a mainstay treatment for prostate cancer. Although initially effective, resistance to androgen targeted therapies develops followed by disease progression to castrate-resistant prostate cancer (CRPC). Hypoxia and HIF1a have been implicated in the development of resistance to androgen targeted therapies and progression to CRCP. The interplay between the androgen and hypoxia/HIF1a signaling axes was investigated.MethodsIn vitro stable expression of HIF1a was established in the LNCaP cell line by physiological induction or retroviral transduction. Tumor xenografts with stable expression of HIF1a were established in castrated and non-castrated mouse models. Gene expression analysis identified transcriptional changes in response to androgen treatment, hypoxia and HIF1a. The binding sites of the AR and HIF transcription factors were identified using ChIP-seq.ResultsAndrogen and HIF1a signaling promoted proliferation in vitro and enhanced tumor growth in vivo. The stable expression of HIF1a in vivo restored tumor growth in the absence of endogenous androgens. Hypoxia reduced AR binding sites whereas HIF binding sites were increased with androgen treatment under hypoxia. Gene expression analysis identified seven genes that were upregulated both by AR and HIF1a, of which six were prognostic.ConclusionsThe oncogenic AR, hypoxia and HIF1a pathways support prostate cancer development through independent signaling pathways and transcriptomic profiles. AR and hypoxia/HIF1a signaling pathways independently promote prostate cancer progression and therapeutic targeting of both pathways simultaneously is warranted.

How to catch a HIF-the work of Gregg Semenza's lab on hypoxia-inducible factor 1.

How to catch a HIF-the work of Gregg Semenza's lab on hypoxia-inducible factor 1.

HIF1/2-exerted control over glycolytic gene expression is not functionally relevant for glycolysis in human leukemic stem/progenitor cells

BackgroundHypoxia-inducible factors (HIF)1 and 2 are transcription factors that regulate the homeostatic response to low oxygen conditions. Since data related to the importance of HIF1 and 2 in hematopoietic stem and progenitors is conflicting, we investigated the chromatin binding profiles of HIF1 and HIF2 and linked that to transcriptional networks and the cellular metabolic state.MethodsGenome-wide ChIPseq and ChIP-PCR experiments were performed to identify HIF1 and HIF2 binding sites in human acute myeloid leukemia (AML) cells and healthy CD34+ hematopoietic stem/progenitor cells. Transcriptome studies were performed to identify gene expression changes induced by hypoxia or by overexpression of oxygen-insensitive HIF1 and HIF2 mutants. Metabolism studies were performed by 1D-NMR, and glucose consumption and lactate production levels were determined by spectrophotometric enzyme assays. CRISPR-CAS9-mediated HIF1, HIF2, and ARNT−/− lines were generated to study the functional consequences upon loss of HIF signaling, in vitro and in vivo upon transplantation of knockout lines in xenograft mice.ResultsGenome-wide ChIP-seq and transcriptome studies revealed that overlapping HIF1- and HIF2-controlled loci were highly enriched for various processes including metabolism, particularly glucose metabolism, but also for chromatin organization, cellular response to stress and G protein-coupled receptor signaling. ChIP-qPCR validation studies confirmed that glycolysis-related genes but not genes related to the TCA cycle or glutaminolysis were controlled by both HIF1 and HIF2 in leukemic cell lines and primary AMLs, while in healthy human CD34+ cells these loci were predominantly controlled by HIF1 and not HIF2. However, and in contrast to our initial hypotheses, CRISPR/Cas9-mediated knockout of HIF signaling did not affect growth, internal metabolite concentrations, glucose consumption or lactate production under hypoxia, not even in vivo upon transplantation of knockout cells into xenograft mice.ConclusionThese data indicate that, while HIFs exert control over glycolysis but not OxPHOS gene expression in human leukemic cells, this is not critically important for their metabolic state. In contrast, inhibition of BCR-ABL did impact on glucose consumption and lactate production regardless of the presence of HIFs. These data indicate that oncogene-mediated control over glycolysis can occur independently of hypoxic signaling modules.

Abstract 373: Regulation of Hypoxia by Chromatin Reader Protein Kinase C Binding Protein 1 (PRKCBP1)

PRKCBP1 (also known as RACK7 and Zmynd8) is a polyvalent chromatin reader known to cooperatively bind acetylated and methylated nucleosomes. Recently it has been shown to regulate transcription and cancer progression by coordinating histone methylation modifications affecting enhancer and promoter regions of genes. The role of PRKCBP1 in the cardiac myocardium is unexplored. Hypoxia-inducible factor 1α (HIF-1α) upregulation and stabilization is a common feature of both cancer and myocardial ischemia, promoting cellular functions such as proliferation, glucose metabolism and angiogenesis. Here we investigated the mechanism by which PRKCBP1 modulates the cardiac hypoxic response. We hypothesize that PRKCBP1 inhibits the HIF-1 response in the hypoxic heart by reducing enhancer activity of HIF-1 target genes and altering availability of HIF-1 binding sites. We have found that in transgenic mice with a mutation that increases HIF-induced expression of PRKCBP, the effect of induced oxygen-stable HIF is markedly diminished. These mice did not exhibit the typical HIF-1 over-expression phenotype of dilated vessels, increased heart size and reduced ventricular function. Semi-quantitative rtPCR analysis of mouse neonatal cardiomyocytes transfected with CMV-driven expression plasmids for PRKCBP1 and oxygen-stable HIF-1α showed striking reduction of multiple HIF-1 target genes such as PDK1 (45% reduction relative to Ehbp1) compared to the HIF-1α plasmid alone. RNAi mediated knockdown of PRKCBP1 removed this negative regulation (65% increase). Analysis of human PRKCBP1 and HIF-1α ChIP-seq data indicate that PRKCBP1 binds to the enhancer of 78% of HIF-1 regulated genes. ATAC-seq data suggest that PRKCBP1 affects genome-wide chromatin accessibility, with loci-specific modifications at numerous HIF-1 target genes, such as EGLN3. These data suggest that PRKCBP1 may be acting both by modulating enhancer activity in cis - to HIF-1 target genes and by preventing HIF-1 binding to hypoxia response elements of target genes. We have discovered a new regulator of HIF-1 action that modifies the hypoxic response, likely through chromatin remodeling. This new form of regulation may modify the pathophysiology of ischemia and provide new targets for therapy.

Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements

Cyprinus carpio is world’s most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (−4,900 to +100) sequences of 31,466 protein coding genes was downloaded from “Gene” and “RefSeq” databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes.

Regulation of glyceraldehyde-3-phosphate dehydrogenase by hypoxia inducible factor 1 in the white shrimp Litopenaeus vannamei during hypoxia and reoxygenation

Hypoxia is a frequent source of stress in the estuarine habitat of the white shrimp Litopenaeus vannamei. During hypoxia, L. vannamei gill cells rely more heavily on anaerobic glycolysis to obtain ATP. This is mediated by transcriptional up-regulation of glycolytic enzymes including glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The hypoxia inducible factor 1 (HIF-1) is an important transcriptional activator of several glycolytic enzymes during hypoxia in diverse animals, including crustaceans. In this work, we cloned and sequenced a fragment corresponding to the 5′ flank of the GAPDH gene and identified a putative HIF-1 binding site, as well as sites for other transcription factors involved in the hypoxia signaling pathway. To investigate the role of HIF-1 in GAPDH regulation, we simultaneously injected double-stranded RNA (dsRNA) into shrimp to silence HIF-1α and HIF-1β under normoxia, hypoxia, and hypoxia followed by reoxygenation, and then measured gill HIF-1α, HIF-1β expression, GAPDH expression and activity, and glucose and lactate concentrations at 0, 3, 24 and 48 h. During normoxia, HIF-1 silencing induced up-regulation of GAPDH transcripts and activity, suggesting that expression is down-regulated via HIF-1 under these conditions. In contrast, HIF-1 silencing during hypoxia abolished the increases in GAPDH expression and activity, glucose and lactate concentrations. Finally, HIF-1 silencing during hypoxia-reoxygenation prevented the increase in GAPDH expression, however, those changes were not reflected in GAPDH activity and lactate accumulation. Altogether, these results indicate that GAPDH and glycolysis are transcriptionally regulated by HIF-1 in gills of white shrimp.

A RASSF1A-HIF1\u03b1 loop drives Warburg effect in cancer and pulmonary hypertension

Hypoxia signaling plays a major role in non-malignant and malignant hyperproliferative diseases. Pulmonary hypertension (PH), a hypoxia-driven vascular disease, is characterized by a glycolytic switch similar to the Warburg effect in cancer. Ras association domain family 1A (RASSF1A) is a scaffold protein that acts as a tumour suppressor. Here we show that hypoxia promotes stabilization of RASSF1A through NOX-1- and protein kinase C- dependent phosphorylation. In parallel, hypoxia inducible factor-1 α (HIF-1α) activates RASSF1A transcription via HIF-binding sites in the RASSF1A promoter region. Vice versa, RASSF1A binds to HIF-1α, blocks its prolyl-hydroxylation and proteasomal degradation, and thus enhances the activation of the glycolytic switch. We find that this mechanism operates in experimental hypoxia-induced PH, which is blocked in RASSF1A knockout mice, in human primary PH vascular cells, and in a subset of human lung cancer cells. We conclude that RASSF1A-HIF-1α forms a feedforward loop driving hypoxia signaling in PH and cancer.

MicroRNA-668 represses MTP18 to preserve mitochondrial dynamics in ischemic acute kidney injury

The pathogenesis of ischemic diseases remains unclear. Here we demonstrate the induction of microRNA-668 (miR-668) in ischemic acute kidney injury (AKI) in human patients, mice, and renal tubular cells. The induction was HIF-1 dependent, as HIF-1 deficiency in cells and kidney proximal tubules attenuated miR-668 expression. We further identified a functional HIF-1 binding site in the miR-668 gene promoter. Anti-miR-668 increased apoptosis in renal tubular cells and enhanced ischemic AKI in mice, whereas miR-668 mimic was protective. Mechanistically, anti-miR-668 induced mitochondrial fragmentation, whereas miR-668 blocked mitochondrial fragmentation during hypoxia. We analyzed miR-668 target genes through immunoprecipitation of microRNA-induced silencing complexes followed by RNA deep sequencing and identified 124 protein-coding genes as likely targets of miR-668. Among these genes, only mitochondrial protein 18 kDa (MTP18) has been implicated in mitochondrial dynamics. In renal cells and mouse kidneys, miR-668 mimic suppressed MTP18, whereas anti-miR-668 increased MTP18 expression. Luciferase microRNA target reporter assay further verified MTP18 as a direct target of miR-668. In renal tubular cells, knockdown of MTP18 suppressed mitochondrial fragmentation and apoptosis. Together, the results suggest that miR-668 is induced via HIF-1 in ischemic AKI and that, upon induction, miR-668 represses MTP18 to preserve mitochondrial dynamics for renal tubular cell survival and kidney protection.

HIF 1 inhibits StAR transcription and testosterone synthesis in murine Leydig cells.

Hypoxia-inducible factor-1 (HIF1) is a critical transcription factor involved in cell response to hypoxia. Under physiological conditions, its a subunit is rapidly degraded in most tissues except testes. HIF1 is stably expressed in Leydig cells, which are the main source of testosterone for male, and might bind to the promoter region of steroidogenic acute regulatory protein (Star), which is necessary for the testosterone synthesis, according to software analysis. This study aims to identify the binding sites of HIF1 on Star promoter and its transcriptional regulation of Star to affect testosterone synthesis. Testosterone level and steroid synthesis-related proteins were determined in male Balb/C mice exposed to hypoxia (8% O2). While HIF1 was upregulated, the testosterone level was significantly decreased. This was further confirmed by in vitro experiments with rat primary Leydig cells or TM3 cells exposed to hypoxia (1% O2), CoCl2 or DFX to raise HIF1. The decline of testosterone was reversed by pregnenolone but not cAMP, indicating the cholesterol transport disorder as the main cause. In agreement, StAR expression level was decreased in response to HIF1, while 3b-hydroxysteroid dehydrogenase, 17b-hydroxysteroid dehydrogenase and p450scc did not exhibit significant changes. By ChIP, EMSA supershift and dual-luciferase reporter assays, HIF1 was found to bind to the Star promoter region and repress the expression of StAR. Mutation assays identified three HIF1-binding sites on mouse Star promoter. These findings indicate that HIF1 represses Star transcription through directly binding to the Star promoter at -2082/-2078, -2064/-2060 and -1910/-1906, leading to the negative regulation of testosterone synthesis.

Abstract LB-239: Studying effects of disease associated polymorphism on a transcriptional pathway: A case study in renal cell cancer

Abstract Genome-wide association studies (GWAS) are an important way of identifying germline polymorphisms that are associated with a specific trait or disease. However, characterizing the functional effects of disease-associated variants is challenging since many are located in intergenic regions of the genome. We have established a methodological framework to study the functional effects of disease-associated polymorphisms by examining their effect on disease- specific transcriptional pathways. Based on the most recent meta-analysis of GWAS in renal cell cancer (RCC), we show that RCC- associated polymorphisms are statistically enriched for binding sites of the transcriptional enhancer, hypoxia-inducible factor (HIF), as identified by ChIP-seq analysis in kidney cancer cells. HIF orchestrates a major transcriptional pathway and is constitutively activated in kidney cancer through loss of the von Hippel-Lindau (VHL) tumor suppressor. At these loci, RCC-associated polymorphisms quantitatively affect HIF binding in allele-specific assays as well as expression of the HIF target genes in eQTL analysis. Furthermore, the association between HIF-binding sites and GWAS signal extends to loci below conventional levels of genome-wide significance thereby implicating these sub-threshold loci in the pathogenesis of RCC. In addition we also observe enrichment of RCC-associated polymorphisms close to, but not directly overlapping HIF-binding sites suggesting that they may alter HIF-target gene expression by mechanisms other than directly affecting HIF-binding. As well as emphasizing the importance of the HIF transcriptional pathway in kidney cancer, this analysis helps distinguish HIF key targets that help drive the pathogenesis of RCC from those that are simply co-activated as a consequence of pathway activation. Although focused on the HIF pathway in kidney cancer, this work also forms a paradigm for studying the effect of non-coding variants linked to other cancers originating from other tissue types. Financial support: The Ludwig Institute for Cancer Research, Cancer Research UK (A16016), National Institute for Health Research (NIHR-RP-2016-06-004), the Wellcome Trust (088182/Z/09/Z, 078333/Z/05/Z, WT091857MA), the Deanship of Scientific Research (DSR), Department of Nephrology and Hypertension, Universitätsklinikum Erlangen und Friedrich-Alexander-University Erlangen- Nürnberg, Ulmenweg 18, 91054 Erlangen, Germany. King Abdulaziz University, Ministry of High Education for Saudi Arabia. High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics is funded by the Wellcome Trust (090532/Z/09/Z). Citation Format: Virginia Schmid, David Mole. Studying effects of disease associated polymorphism on a transcriptional pathway: A case study in renal cell cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-239.