Single cell RNA-seq from primary ccRCC-patient-derived cell cultures on the 10X genomics platform
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE200207 | GEO | 2022/11/15
REPOSITORIES: GEO
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Project description:The cellular response to low oxygen supply is mediated by hypoxia-inducible factors (HIF). Under hypoxic conditions, HIF is stabilized and target genes are induced. Under normoxia, however, HIF is ubiquitinated through the von Hippel-Lindau protein (VHL), which results in proteasomal degradation. HIF activation leads to induction of genes involved in erythropoiesis, angiogenesis, and cell survival. Furthermore, HIF orchestrates a metabolic shift from oxidative phosphorylation to glycolysis to facilitate ATP production under low oxygen conditions. We used microarrays to detail gene expression changes in kidneys with stable HIF activation in renal tubules, which was achieved by tubule-specific VHL ablation. Three week old Pax8-rtTA;LC-1;Vhl-floxed mice (n=4) and control littermates (n=4) were treated with doxycyline in drinking water for two weeks and put back on normal drinking water for one week. Six weeks old mice were sacrificed and kidneys harvested. Total RNA was extracted and hybridized on Affymetrix microarrays.
2014-01-17 | E-GEOD-54172 | biostudies-arrayexpress
Project description:Microarrray experiments were performed in order to identify genes whose expression is altered under hypoxic conditions and to determine whether these changes are dependant on the p53 and HIF tanscription factors. In order to determine HIF dependance, isogenic RCC4 cell lines were used that were either wildtype of null for vhl, the gene responsible for degrading HIF under normoxic conditions. In order to determine p53 dependance, isogenic HCT116 and H1299 cell lines that were wildtype or null for p53 were used. Gene expression was measured after exposure of cells in monolayer culture to hypoxia (<0.01% O2) for various times. Keywords: hypoxia, time course, genetic modification, cell line comparison
2006-03-07 | GSE4186 | GEO
Project description:Changes in mRNA abundance upon HIF activation and/or hypoxia in VHL-defective kidney cancer cell were analysed. Sequencing of the 5′ ends of mRNAs (5′ end-Seq) was applied to VHL-defective kidney cancer cell lines with or without reintroduction of VHL and/or with hypoxic incubation (1% O2 for 24h) to analyse the abundance of mRNAs resolved by their transcription start sites. In addition, the contribution of HIF pathway was confirmed using 786-O cells in which HIF1B was inactivated.
2022-05-14 | E-MTAB-10688 | biostudies-arrayexpress
Project description:Investigation whether hypoxic stabilization of HIF-1alpha quantitatively or qualitatively modifies the gene expression pattern induced by poly I:C, a TLR ligand that does not induce normoxic HIF-1alpha stabilization on its own (non-HIF-1alpha-stabilizing TLR ligand). Keywords: Comparison of single and combined treatment Bone marrow derived Dendritic Cells from mice were stimulated under normoxic or hypoxic conditions for 16h with media or poly I:C. Total cellular RNA was harvested, labeled and hybridised to Affymetrix Mouse Gene ST 1.0 GeneChips. Cel files were normalized with RMA.
2011-06-28 | E-GEOD-24995 | biostudies-arrayexpress
Project description:VHL loss is the most common genetic alteration event in ccRCC, but its effect on epigenetic landscape has not been elucidated previously. By performing histone modifications (H3K27ac, H3K4me1, H3K4me3) from ccRCC cell lines, we describe the genome-wide cis-regulatory landscapes of VHL-deficient ccRCC tumors. We show that ccRCCs exhibit a pervasive gain of enhancers around hypoxic and metabolic transcriptional targets.
2017-08-22 | GSE86091 | GEO
Project description:VHL loss is the most common genetic alteration event in ccRCC, but its effect on epigenetic landscape has not been elucidated previously. By performing histone modifications (H3K27ac, H3K4me1, H3K4me3) from ccRCC cell lines, we describe the genome-wide cis-regulatory landscapes of VHL-deficient ccRCC tumors. We show that ccRCCs exhibit a pervasive gain of enhancers around hypoxic and metabolic transcriptional targets.
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Project description:HIF-2alpha is essential for (VHL-/-) ccRCC subcutaneous tumor growth in mice, and in tumor cell lines, its inhibition results in increased ROS accumulation, tumor cell death and responsiveness to radiation treatment. We have utilized transcriptional profiling to screen for putative HIF-2alpha targets genes that serve an anti-oxidant and, thus, cell survival function. A498 ccRCC cell line was treated with control siRNA or mixture of two HIF-2alpha specific siRNA for 48 hours, and RNA was harvested. 4 independent experiments were performed, and expression was compared between control and HIF-2alpha knockdown groups. 8 total samples were applied to Affymetrix Human Gene 1.0 ST Arrays. We performed two-class paired analysis using Significance Analysis of Microarrays (SAM) software to compare expression in the CT (control siRNA) and H2 (Hif2-alpha siRNA) groups.
2009-08-27 | E-GEOD-16622 | biostudies-arrayexpress
Project description:HIF-2alpha is essential for (VHL-/-) ccRCC subcutaneous tumor growth in mice, and in tumor cell lines, its inhibition results in increased ROS accumulation, tumor cell death and responsiveness to radiation treatment. We have utilized transcriptional profiling to screen for putative HIF-2alpha targets genes that serve an anti-oxidant and, thus, cell survival function. A498 ccRCC cell line was treated with control siRNA or mixture of two HIF-2alpha specific siRNA for 48 hours, and RNA was harvested. 4 independent experiments were performed, and expression was compared between control and HIF-2alpha knockdown groups.
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Project description:Analysis of the binding sites of Hif-1α 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-1α 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-1α 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-1α binding to the genome, and provide a basis for analysis of the dependency of the transcriptional response on Hif-1α in conditions of genetically induced hypoxia in zebrafish.
2016-03-22 | E-GEOD-70727 | biostudies-arrayexpress
Project description:Investigation whether hypoxic stabilization of HIF-1alpha quantitatively or qualitatively modifies the gene expression pattern induced by poly I:C, a TLR ligand that does not induce normoxic HIF-1alpha stabilization on its own (non-HIF-1alpha-stabilizing TLR ligand). Keywords: Comparison of single and combined treatment
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