Ontology highlight
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PROVIDER: PRJNA976921 | ENA |
REPOSITORIES: ENA
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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
Project description:Transcriptome analysis of murine foetal NSCs (E14) after short-term (48 hours) and long-term (13 days) hypoxic (3% oxygen) culture compared to normoxic culture (21% oxygen) We focused on whole-transcriptome analyses using gene chip microarrays to compare expression profiles of NSCs cultured at hypoxic conditions to those of normoxic cells. Therefore, we used NSCs derived from the mesencephalon and the cortex and cultured them for short- and long-term at hypoxia/normoxia.
2016-04-09 | GSE80070 | GEO
Project description:Endocrine therapies targeting the proliferative effect of 17β-estradiol (17βE2) through estrogen receptor α (ERα) are the most effective systemic treatment of ERα-positive breast cancer. However, most breast tumors initially responsive to these therapies develop resistance through a molecular mechanism that is not yet fully understood. The long-term estrogen-deprived (LTED) MCF7 cell model has been proposed to recapitulate acquired resistance to aromatase inhibitors (AIs) in postmenopausal women. To elucidate this resistance, genomic, transcriptomic and molecular data were integrated into the time course of MCF7-LTED adaptation. Dynamic and widespread genomic changes were observed, including amplification of the ESR1 locus consequently linked to an increase in ERα. Dynamic transcriptomic profiles were also observed that correlated significantly with genomic changes and were influenced by transcription factors known to be involved in acquired resistance or cell proliferation (e.g. IRF1 and E2F1, respectively) but, notably, not by canonical ERα transcriptional function. Consistently, at the molecular level, activation of growth factor signaling pathways by EGFR/ERBB/AKT and a switch from phospho-Ser118 (pS118)- to pS167-ERα were observed during MCF7-LTED adaptation. Evaluation of relevant clinical settings identified significant associations between MCF7-LTED and breast tumor transcriptome profiles that characterize ERα-negative status, early response to letrozole and recurrence after tamoxifen treatment. This study proposes a mechanism for acquired resistance to estrogen deprivation that is coordinated across biological levels and independent of canonical ERα function. LTED (long term estrogen deprived) cell line was generated from MCF-7 cells by long-term culture under estrogen deprivated conditions. And RNA samples were obtained after 3, 15, 30, 90, 120, 150 and 180 days.
2010-09-01 | E-GEOD-20361 | biostudies-arrayexpress
Project description:This study explores the long-term adaptation mechanisms of lymphoma cells subjected to hypoxic conditions, with an emphasis on the HBL2 and Ramos cell lines under normoxia and 1% O2 environments. The research methodology encompassed lysing cells using a buffer containing sodium deoxycholate and TEAB, followed by protein quantification via a BCA assay. Subsequent steps involved protein digestion with trypsin, labelling with TMTpro™ 16plex Label Reagent Set for quantitative analysis, peptide fractionation, and LC-MS/MS analysis. The analytical process was supported by Proteome Discoverer 2.4 for protein identification and quantification. Experimental groups were categorized into "HBL2 normoxia," "HBL2 1% O2 adaptation," "Ramos normoxia," and "Ramos 1% O2 adaptation," conducted in triplicates to ensure reliability. This meticulous approach facilitated the delineation of unique proteomic landscapes indicative of hypoxia adaptation, unveiling cellular strategies employed by lymphoma cells to navigate low oxygen conditions. The findings advance our comprehension of how hypoxia influences cancer progression and potentially opens new avenues for targeting hypoxic niches within tumors.
2025-02-27 | PXD050227 | Pride
Project description:Adaptation to hypoxia is mediated through a coordinated transcriptional response driven largely by Hypoxia-Inducible Factor 1 (HIF-1). The direct transcriptional targets of HIF-1 play important roles in facilitating both short-term and long-term adaptation to hypoxia. Alignment of the sequences encompassing all well-characterized HIF-1 binding sites has revealed a consensus core HRE motif of 5'-RCGTG-3' (R = A or G). Since the consensus HIF-1 binding motif is too promiscuous to accurately predict binding a priori, we used ChIP-chip to define HIF-1 chromatin binding on a genome-wide level. We integrated these results with gene expression profiling to interrogate mechanisms regulating hypoxia-induced gene expression, and to more comprehensively identify direct targets of HIF-1 transactivation.
2009-06-02 | GSE16347 | GEO
Project description:To study the effects of miR--210 on 293T cells and hypoxia response, we used the CRISPR/Cas9 system to knockout (KO) the human miR-210 gene in 293T cells. We then added DMOG to mimic hypoxia condition and analyzed the RNA expression profile of wildtype (WT) and KO cells under normal and hypoxic conditions. DMOG treatment and RNA-seq were performed three times (experiment 1, 2, and 3).
2024-12-31 | GSE243063 | GEO
Project description:The faecal indicator bacterium Escherichia coli K12 was used to study the cellular events that take place at the transcription level using the microarray technology during short-term (physiological) and long-term (genetic) adaptation to slow growth under limited nutrient supply. Short-term and long-term adaptation were assessed by comparing the mRNA levels isolated after 40 or 500 hours of glucose-limited continuous culture at a dilution rate of 0.3 h-1 with those from batch culture with glucose excess. Keywords: glucose-limited continuous culture, adaptation, microarray, high affinity transport systems, transcriptome, Escherichia coli
2006-04-26 | GSE4706 | GEO
Project description:Background/Aims: Tibetan chickens, a unique plateau breed, have good performances to adapt to high-altitude hypoxic environments. A number of positively selected genes have been reported in Tibetan chickens; however, the mechanisms of gene expression for hypoxia adaptation are not fully understood. Methods: Eggs from Tibetan (TC) and Chahua (CH) chickens were incubated under hypoxic and normoxic conditions, and vessel density index (VDI) in the chorioallantoic membrane (CAM) of embryos was measured. Meanwhile, Transcriptomic and proteomic analyses of CAM tissues were performed in TC and CH embryos under hypoxic incubation using RNA-seq and iTRAQ. Results: We found that the vessel density index (VDI) in CAM of TCs was lower than in CHs under hypoxia incubation. In the transcriptomic and proteomic analyses, 160 differentially expressed genes (DEGs) and 387 differentially expressed proteins (DEPs) that were mainly enriched in angiogenesis, vasculature development, blood vessel morphogenesis, blood circulation, renin-angiotensin system, and HIF-1 and VEGF signaling pathways. Twenty-six genes involved in angiogenesis and blood circulation, two genes involved in ion transport, and six genes that regulated energy metabolism were identified as candidate functional genes in regulating hypoxic adaption of chicken embryos. Conclusion: Combination of transcriptomic and proteomic data revealed several key candidate regulators and pathways that might play high-priority roles in the hypoxic adaptation of Tibetan chickens by regulating angiogenesis and promoting blood circulation, thus explaining the blunt responses to hypoxic conditions on CAM angiogenesis in Tibetan chicken embryos. This research provided insights into the molecular mechanism of hypoxia adaptation in Tibetan chickens.
2020-07-13 | GSE126082 | GEO
Project description:To reveal the molecular basis of the long-term sperm storage mechanisms in ant queens, protein profiles enriched in the spermathecal fluid relative to the hemolymph were identified in Lasius japonicus using data-independent acquisition (DIA)-based quantitative proteomics technology.
2024-02-01 | PXD041534 | JPOST Repository