Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genome-wide mapping of HIF-2 binding in 786-O clear cell renal carcinoma cells

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE34871 | GEO | 2012/02/01

SECONDARY ACCESSION(S): PRJNA150099

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Genome-wide mapping of HIF-2 binding in 786-O clear cell renal carcinoma cells

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.

2012-02-01 | E-GEOD-34871 | biostudies-arrayexpress

Array CGH analysis in primary human renal tumors, categorized by VHL genotype and HIF-alpha expression

Project description:Human renal cell carcinomas (RCC) have differential expression of HIF-1alpha and HIF-2alpha, depending on VHL genotype and other events. Here, we have divided a series of RCC samples based on HIF-alpha expression, in order to examine levels of genomic DNA aberration. Keywords: Patient Sample Study A total of 57 frozen RCC samples were stained for HIF-1alpha and HIF-2alpha, and genotyped for VHL. 10 VHL-deficient/HIF-1alpha+/HIF-2alpha+ and 11 VHL-deficient/HIF-2alpha+ tumors were selected for array CGH.

2008-12-27 | E-GEOD-13282 | biostudies-arrayexpress

Gene expression analysis in primary human renal tumors, categorized by VHL genotype and HIF-alpha expression

Project description:Human renal cell carcinomas (RCC) have differential expression of HIF-1alpha and HIF-2alpha, depending on VHL genotype and other events. Here, we have divided a series of RCC samples for HIF-alpha expression and VHL genotype, in order to define differentially expressed genes Keywords: Patient Sample Study A total of 57 frozen RCC samples were stained for HIF-1alpha and HIF-2alpha, and genotyped for VHL. 5 VHL WT/HIF-negative, 8 VHL-deficient/HIF-1alpha+/HIF-2alpha+ and 8 VHL-deficient/HIF-2alpha+ tumors were selected for microarray

2008-12-27 | E-GEOD-11904 | biostudies-arrayexpress

Array CGH analysis in primary human renal tumors, categorized by VHL genotype and HIF-alpha expression

2008-12-27 | GSE13282 | GEO

Gene expression analysis in primary human renal tumors, categorized by VHL genotype and HIF-alpha expression

2008-12-27 | GSE11904 | GEO

Gene expression analysis in renal cell carcinoma

Project description:Renal cell carcinoma (RCC) tumors express varying gene profiles, dependent on VHL and HIF status, as well as other events. Here we analyzed a series of RCC tumors for HIF-alpha expression and VHL genotype, in relation to overal gene expression profiles. Keywords: Patient sample study

2008-10-18 | GSE11985 | GEO

Transcriptome profiling of 786-O RCC cells transduced with control vector or PRDM16 lentivirus.

Project description:Recent large-scale data sets indicate the emerging importance of alterations of the epigenome in renal cell carcinoma (RCC). Analysis of transcriptomic data of patient samples including normal kidney, primary tumor, and metastatic tumor deposits demonstrates epigenetic silencing of the gene encoding the transcription factor PR domain-containing 16 (PRDM16). PRDM16 has a prominent role in adipocyte metabolism but is also highly expressed in the kidney. The role of PRDM16 in renal cancer has not been investigated. RNAseq analysis reveals that PRDM16 imparts a predominantly repressive effect on the RCC transcriptome including suppression of SEMA5B (semaphorin 5B), a target gene of hypoxia inducible factor (HIF). Collectively, our data uncover a novel epigenetic basis by which HIF target gene expression is amplified in kidney cancer. Moreover, they demonstrate a new mechanism by which PRDM16 exerts its tumor suppressive effects.

2020-03-20 | GSE130049 | GEO

High resolution genome-wide mapping of HIF binding sites by ChIP-seq

Project description:We report ChIP-Seq analysis of HIF-1 alpha, HIF-2 alpha, and HIF-1 beta binding in MCF-7 breast cancer cells Sample analysis compared to pre-immune serum chromatin immunoprecipitation

2011-04-05 | E-GEOD-28352 | biostudies-arrayexpress

RNA-seq analysis between mouse UPS tumors (KP) and mouse UPS tumors without HIF-2alpha (KPH2)

Project description:Purpose: determine RNA expression differences in an unbiased fashion between UPS tumors derived from LSL-KrasG12D;Trp53-/- (KP) mice, and UPS tumors derived from LSL-KrasG12D;Trp53-/-;Epas1-/- (KPH2) mice. Epas1 encodes HIF-2alpha protein. RNA-seq was performed on KP (n = 4) and KPH2 (n = 4) derived UPS tumors using Illumina HiSeq 2000.

2015-12-31 | E-GEOD-67672 | biostudies-arrayexpress

High resolution genome-wide mapping of HIF binding sites by ChIP-seq

Project description:We report ChIP-Seq analysis of HIF-1 alpha, HIF-2 alpha, and HIF-1 beta binding in MCF-7 breast cancer cells

2011-04-05 | GSE28352 | GEO