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Systematic Analysis of Transcriptomic Profile of Renal Cell Carcinoma under Long-Term Hypoxia using Next-Generation Sequencing and Bioinformatics

ABSTRACT: Systematic Analysis of Transcriptomic Profile of Renal Cell Carcinoma under Long-Term Hypoxia using Next-Generation Sequencing and Bioinformatics

PROVIDER: PRJNA421706 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6363050.fastq.gz	Fastqsanger.gz
	SRR6363051.fastq.gz	Fastqsanger.gz
	SRR6363052.fastq.gz	Fastqsanger.gz
	SRR6363053.fastq.gz	Fastqsanger.gz
	SRR6363054.fastq.gz	Fastqsanger.gz

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Systematic Analysis of Transcriptomic Profile of Renal Cell Carcinoma under Long-Term Hypoxia using Next-Generation Sequencing and Bioinformatics

Project description:Patients with clear cell renal cell carcinoma (ccRCC) are often diagnosed with both von Hippel-Lindau (VHL) mutations and the constitutive activation of hypoxia-inducible factor-dependent signaling. In this study, we investigated the effects of long-term hypoxia in 786-O, a VHL-defective renal cell carcinoma cell line, to identify potential genes and microRNAs associated with tumor malignancy. The transcriptomic profiles of 786-O under normoxia, short-term hypoxia, and long-term hypoxia were analyzed using next-generation sequencing. The results showed that long-term hypoxia promoted the ability of colony formation and transwell migration compared to normoxia. In addition, the differentially expressed genes induced by long-term hypoxia were involved in various biological processes including cell proliferation, the tumor necrosis factor signaling pathway, basal cell carcinoma, and cancer pathways. The upregulated (L1CAM and FBN1) and downregulated (AUTS2, MAPT, AGT, and USH1C) genes in 786-O under long-term hypoxia were also observed in clinical ccRCC samples along with malignant grade. The expressions of these genes were significantly correlated with survival outcomes in patients with renal cancer. We also found that long-term hypoxia in 786-O resulted in decreased expressions of hsa-miR-100 and has-miR-378, and this effect was also observed in samples of metastatic ccRCC compared to samples of non-metastatic ccRCC. These findings may provide a new direction for the study of potential molecular mechanisms associated with the progression of ccRCC.

2017-12-12 | GSE107848 | GEO

Renal Cell Carcinoma: Hypoxia and Endocytosis

Project description:Hypoxia signature in Clear cell RCC A set of clear cell renal cell carcinomas were examined for the deregulation of hypoxia inducible and endocytosis regulated genes Tumor samples and Normal renal tissue GSE14762.rda contains an R data object

2009-02-09 | E-GEOD-14762 | biostudies-arrayexpress

Renal Cell Carcinoma: Hypoxia and Endocytosis

Project description:Hypoxia signature in Clear cell RCC A set of clear cell renal cell carcinomas were examined for the deregulation of hypoxia inducible and endocytosis regulated genes

2009-02-10 | GSE14762 | GEO

Systematic Analysis of Transcriptomic Profile of Renal Cell Carcinoma under Long-Term Hypoxia Using Next-Generation Sequencing and Bioinformatics.

Project description:Patients with clear cell renal cell carcinoma (ccRCC) are often diagnosed with both von Hippel-Lindau (VHL) mutations and the constitutive activation of hypoxia-inducible factor-dependent signaling. In this study, we investigated the effects of long-term hypoxia in 786-O, a VHL-defective renal cell carcinoma cell line, to identify potential genes and microRNAs associated with tumor malignancy. The transcriptomic profiles of 786-O under normoxia, short-term hypoxia and long-term hypoxia were analyzed using next-generation sequencing. The results showed that long-term hypoxia promoted the ability of colony formation and transwell migration compared to normoxia. In addition, the differentially expressed genes induced by long-term hypoxia were involved in various biological processes including cell proliferation, the tumor necrosis factor signaling pathway, basal cell carcinoma and cancer pathways. The upregulated (L1CAM and FBN1) and downregulated (AUTS2, MAPT, AGT and USH1C) genes in 786-O under long-term hypoxia were also observed in clinical ccRCC samples along with malignant grade. The expressions of these genes were significantly correlated with survival outcomes in patients with renal cancer. We also found that long-term hypoxia in 786-O resulted in decreased expressions of hsa-mir-100 and hsa-mir-378 and this effect was also observed in samples of metastatic ccRCC compared to samples of non-metastatic ccRCC. These findings may provide a new direction for the study of potential molecular mechanisms associated with the progression of ccRCC.

| S-EPMC5751259 | biostudies-literature

Profiling and Bioinformatics Analyses of Differential Circular RNA Expression in Glioblastoma Multiforme Cells under Hypoxia

Project description:Background: The hypoxia microenvironment is highly associated with GBM’s malignant phenotypes. CircRNAs were reported involved in GBM’s biological characteristics and regulated by HIF-1α. However, the differential expression profile and role of circRNAs in GBM cells under hypoxia are still unclear. Methods: The expression profiles of circRNAs in LN229 and T98G under hypoxia were explored via circRNA sequencing analysis. Those circRNAs significantly dysregulated both in LN229 and T98G, and could be found in circBase were selected and validated by qRT-PCR, RNase R digestion reaction and Sanger sequencing. Normal cell line and fresh GBM tissues were also used for qRT-PCR validation. The roles of differentially expressed circRNAs were evaluated by bioinformatics analyses. Results: There were 672 dysregulated circRNAs in LN229 and 698 dysregulated circRNAs in T98G. GO analysis indicated that the alteration of circRNAs expression related to GBM cell’s biogenesis and metabolism. KEGG analysis demonstrated that TGF-β signaling pathway, HIF-1 signaling pathway and metabolism related signaling pathway were closely associated with differentially expressed circRNAs under hypoxia. The 6 selected and dysregulated circRNAs both in LN229 and T98G including hsa_circ_0000745, hsa_circ_0020093, hsa_circ_0020094, hsa_circ_0000943, hsa_circ_0004874 and hsa_circ_0002359 were validated by qRT-PCR. HIF-1α centered circRNA-miRNA-mRNA networks analysis showed that the 6 validated circRNAs could cross-talk with 11 related miRNAs. Conclusion: The circRNA expressions are dysregulated in GBM cell under hypoxia. The 6 validated circRNAs could participate in GBM’s development and progression when hypoxia occurs. They might be the candidates for prognostic markers and adjuvant therapeutics of GBM in the future.

2024-12-28 | GSE192678 | GEO

Effect of hypoxia on gene expression among HK-2 cells and 786-0 cells

Project description:Although both of renal interstitial fibrosis (RIF) and renal carcinoma (RCC) are in hypoxic microenvironments, they underwent several contrary pathologicall changes. To investigate the potent targets in the RIF and RCC through transcriptome alterations of hypoxia compared with normoxia, we established hypoxia cell culture models, primarily simulating hypoxia microenvironments in RIF and RCC. By bioinformatics analysis, a certain number of significant differentially expressed genes (DEGs) among RIF and RCC were recognized. We then performed gene expression profiling analysis using data obtained from RNA-seqencing of 2 different cells cultured in hypoxia and normoxia.

2023-11-15 | GSE225253 | GEO

Profiling and Bioinformatics Analyses of Differential Circular RNA Expression in Glioblastoma Multiforme Cells under Hypoxia

Project description:Profiling and Bioinformatics Analyses of Differential Circular RNA Expression in Glioblastoma Multiforme Cells under Hypoxia

| PRJNA792596 | ENA

Renal Cell Carcinoma (Renca) Extracellular Vesicles under Hypoxia and Normoxia

Project description:Extracellular vesicles (EVs) represent a diverse group of small membrane-encapsulated particles and provide a universal molecular cell-cell communication system. Hypoxia is a typical condition in solid tumors, and cancer-derived EVs support growth and invasion of tissues by tumor cells. EVs were purified from cell culture medium by ultracentrifugation followed by size exclusion chromatography with Exo-spin™ columns (Cell Guidance Systems Ltd). We performed proteomic analysis of five hypoxia/normoxia pairs of EV samples; each of these replicates for either hypoxia or normoxia was analyzed in duplicates. Obtained data were compared with proteomics analysis of corresponding cell culture media supernatants (SN) after EV removal with 100 000 g ultracentrifugation. We found that exposure of tumor cells to hypoxia (1% oxygen) induced EV secretion, altered EV sizes, and led to notable changes in the EV protein cargo in comparison to normoxia.

2022-02-16 | PXD023546 | Pride

Genome-wide maps of HIF1a binding sites in ccRCC cell line under hypoxia condition

Project description:We report the application of chromatin immunoprecipitation and next generation sequencing technology for HIF1a binding sites at genome wide level in a RCC (renal cell carcinoma) cell line under hypoxia conditions. We found HIF1a binding sites in Caki-2 cell line under hypoxia conditions. Especially, we found HIF1a bind to SPOP under hypoxia condition, which was further validated.

2014-03-27 | GSE54327 | GEO

Genome-wide maps of HIF1a binding sites in ccRCC cell line under hypoxia condition

2014-03-27 | E-GEOD-54327 | biostudies-arrayexpress