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Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells [ATAC-seq]

ABSTRACT: Inactivation of the von Hippel-Lindau tumor suppressor leads to stabilization of HIF transcription factors and subsequent oncogenic HIF-2 signaling in ccRCC. However, little is known about the transcriptional mechanisms leading to dysregulation of HIF-2α mRNA in renal cancer. Epigenetic analysis of the EPAS1 locus (coding for HIF-2α) using ATAC-seq, ChIP-seq and RNA-seq revealed an oncogenic enhancer that maintains a HIF-dependent feed-forward circuit of HIF-2α regulation in renal tumor cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE255998 | GEO | 2025/12/15

REPOSITORIES: GEO

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Open chromatin, HIF binding and mRNA expression analysis in primary tubule and ccRCC cells [ChIP-seq]

Project description:Inactivation of the von Hippel-Lindau tumor suppressor leads to stabilization of HIF transcription factors and subsequent oncogenic HIF-2 signaling in ccRCC. However, little is known about the transcriptional mechanisms leading to dysregulation of HIF-2α mRNA in renal cancer. Epigenetic analysis of the EPAS1 locus (coding for HIF-2α) using ATAC-seq, ChIP-seq and RNA-seq revealed an oncogenic enhancer that maintains a HIF-dependent feed-forward circuit of HIF-2α regulation in renal tumor cells.

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Genome-wide mapping of Hif-1Î± binding sites in zebrafish [ChIP-seq]

Project description:Analysis of the binding sites of Hif-1Î± in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf by ChIP linked next generation sequencing. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1Î± binding to the genome, and provide a basis for analysis of the transcriptional response to genetically induced hypoxia in zebrafish. Analysis of the DNA binding sites of Hif-1Î± in both wild-type and von Hippel Lindau mutant zebrafish lines at 4dpf. The von Hippel Lindau mutant displays a systemic hypoxic response under normoxic conditions. Results show the extent of Hif-1Î± binding to the genome, and provide a basis for analysis of the dependency of the transcriptional response on Hif-1Î± in conditions of genetically induced hypoxia in zebrafish.

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Project description:Clear cell renal cell carcinoma is characterized by loss of function of the von Hippel-Lindau tumor suppressor gene (VHL) and unrestrained activation of hypoxia inducible transcription factors (HIF). Genetic and epigenetic determinants can impact on HIF pathways. A recent genome-wide association study identified single nucleotide polymorphisms (SNPs) in an intergenic region on chromosome 8 that modify the risk of developing renal cancer. The SNPs are located in a putative regulatory region between the oncogenes MYC and PVT1. Using capture C assay and genome editing we show that HIF-binding to this regulatory element is necessary to trans-activate MYC and PVT1 expression specifically in cells of renal tubular origins. Moreover, we demonstrate that the risk associated polymorphisms increase chromatin accessibility and activity as well as binding of HIF to the enhancer. These findings further strengthen the hypothesis that genetic variation at HIF-binding sites modulates the oncogenic transcriptional output of the VHL-HIF axis and provide a functional explanation for disease associated effects of SNPs in ccRCC.

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IGR_VHL_GE

Project description:VHL is a tumor suppressor gene involved in the oxygen-sensing pathway whose germline mutations predispose to distinct phenotypes. Heterozygous mutations predispose to von Hippel-Lindau disease characterized by the development of multiple tumors (including hemangioblastomas, renal cell carcinomas and pheochromocytomas)1-3. More recently, a specific VHL-R200W mutation was shown to be responsible for Chuvash Polycythemia in homozygous carriers whereas heterozygous individuals have no clinical manifestation4. We report here a family carrying, on the same allele, VHL mutations characteristics of the two types of disease (a Chuvash polycythemia-R200W mutation and a von Hippel-Lindau disease-R161Q mutation). Genotyping, modeling analysis and functional studies, including transcriptomic profile of the distinct mutants validated for the first time on direct HIF target genes, show a gradual capacity of the VHL mutants to regulate the hypoxia responsive pathway that correlate with the severity of the developed phenotype. Our study provide original results that illuminate genotype/phenotype correlations in von Hippel-Lindau disease.

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Project description:Kidney cancer accounts for more than 100,000 deaths per year world-wide. More than 80% are clear cell tumors (ccRCCs) and the majority are associated with loss of function of the von Hippel Lindau (pVHL) tumor suppressor resulting in upregulation of HIF-{alpha} subunits, and activation of HIF-dependent transcriptional pathways. Recent GWAS studies have discovered RCC-susceptibility loci both within EPAS1 (HIF-2{alpha}) and in an intergenic region of unknown function on 11q13.3. As part of an ongoing study to define the direct transcriptional targets of HIF-2 in renal cancer, we undertook a genome-wide analysis of HIF-2-binding sites in pVHL-defective 786-O cells (that lack functional HIF-1{alpha} due to a truncated transcript) using chromatin immunoprecipitation with antibodies directed against HIF-2{alpha} and its dimerization partner HIF-1{beta}, coupled to high-throughput sequencing (ChIP-seq). Amongst approximately 600 pangenomic HIF-2{beta} ChIP signals, we observed strong binding (ranked 12th by peak height) almost precisely coinciding with the RCC predisposition SNP rs7105934 on 11q13.3. We report binding of HIF-2{alpha} and HIF-1{beta} in 786-O clear cell renal carcinoma cells. 3 samples examined, HIF-2{alpha}, HIF-1{beta} and pre-immune control ChIP.

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Genome-wide mapping of Hif-1α binding sites in zebrafish [microarray]

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2016-03-22 | GSE70885 | GEO

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