Next Generation Sequencing Analysis of USP2-AS1_KD A549 cell line
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE169138 | GEO | 2021/03/19
REPOSITORIES: GEO
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Project description:Next Generation Sequencing Analysis of USP2-AS1_KD A549 cell line
| PRJNA715397 | ENA
Project description:Purpose:The goals of this study to compare NGS-derived transcriptome profiling (RNA-seq) to examine differentially expressed genes berween A549 infected with Zika virus and A549 Control . Methods: A549 cells mRNA profiles of A549 cells-infected with Zika virus and aun-infected A549 cells were generated by deep sequencing, in triplicate, using Illumina Hiseq4000. The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Results: Using an optimized data analysis workflow, we mapped about identified 11124 transcripts in the A549 cells of control and Zika virus with Cuffcompare workflow. RNA-seq data confirmed stable expression of 20 known housekeeping genes, and 10 of these were validated with qRT–PCR. Approximately 10% of the transcripts showed differential expression between the control and DV, with a fold change >1 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of A549 cells transcriptomes, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2020-03-06 | GSE146423 | GEO
Project description:Ubiquitylation plays an important role in the control of Na+ homeostasis by the kidney. It is well established that the epithelial Na+ channel ENaC is regulated by the ubiquitin-protein ligase NEDD4-2, limiting ENaC cell surface expression and activity. Ubiquitylation can be reversed by the action of deubiquitylating enzymes (DUBs). One such DUB, USP2-45, was identified previously as an aldosterone-induced protein in the kidney, and is also a circadian output gene. In heterologous expression systems USP2-45 binds to ENaC, deubiquitylates it and enhances channel density and activity at the cell surface. Because the role of USP2-45 in renal Na+ transport had not been studied in vivo, we investigated here the effect of Usp2 gene inactivation in this process. We demonstrate first that the USP2-45 protein has a rhythmic expression with a peak at ZT12. Usp2-KO mice did not show any differences to wild-type littermates with respect to the diurnal control of Na+ or K+ urinary excretion and plasma levels neither on standard diet, nor after acute and chronic changes to low and high Na+ diets, respectively. Moreover, they had similar aldosterone levels either at low or high Na+ diet. Blood pressure measurements using telemetry did not reveal variations as compared to control mice. Usp2-KO did neither display alternations in ENaC or Na+,Cl--cotransporter (NCC) expression, nor were there any changes in regulatory protein levels, as evidenced by immunoblotting and transcriptome analysis. We conclude that USP2-45 is not crucial for the regulation of Na+ balance or maintenance of blood pressure in vivo.
2013-01-16 | GSE43517 | GEO
Project description:Ubiquitylation plays an important role in the control of Na+ homeostasis by the kidney. It is well established that the epithelial Na+ channel ENaC is regulated by the ubiquitin-protein ligase NEDD4-2, limiting ENaC cell surface expression and activity. Ubiquitylation can be reversed by the action of deubiquitylating enzymes (DUBs). One such DUB, USP2-45, was identified previously as an aldosterone-induced protein in the kidney, and is also a circadian output gene. In heterologous expression systems USP2-45 binds to ENaC, deubiquitylates it and enhances channel density and activity at the cell surface. Because the role of USP2-45 in renal Na+ transport had not been studied in vivo, we investigated here the effect of Usp2 gene inactivation in this process. We demonstrate first that the USP2-45 protein has a rhythmic expression with a peak at ZT12. Usp2-KO mice did not show any differences to wild-type littermates with respect to the diurnal control of Na+ or K+ urinary excretion and plasma levels neither on standard diet, nor after acute and chronic changes to low and high Na+ diets, respectively. Moreover, they had similar aldosterone levels either at low or high Na+ diet. Blood pressure measurements using telemetry did not reveal variations as compared to control mice. Usp2-KO did neither display alternations in ENaC or Na+,Cl--cotransporter (NCC) expression, nor were there any changes in regulatory protein levels, as evidenced by immunoblotting and transcriptome analysis. We conclude that USP2-45 is not crucial for the regulation of Na+ balance or maintenance of blood pressure in vivo. We compared gene expression in kidneys from Usp2 Knock-Out versus Wild-Type. Six pairs of male littermates Usp2-KO and WT were combined in two pools per condition (3 animals per pool) keeping the littermate pairing between pools.
2013-01-16 | E-GEOD-43517 | biostudies-arrayexpress
Project description:In prostate cancer, the development of resistance to androgen receptor (AR)-targeted therapies (ATTs) and chemotherapies is associated with the emergence of new phenotypic states with altered molecular features. Here, we identify ubiquitin-specific peptidase 2 (USP2) as a mediator of this phenomenon. USP2 is induced in response to ATTs and more highly expressed in aggressive, castration-resistant prostate tumours that have lost dependence on AR as an oncogenic driver. Over-expression of USP2 in prostate cancer cells elicited elevated rates of glycolysis, neuroendocrine features and resistance to docetaxel, a taxane chemotherapeutic that is a mainstay treatment for advanced prostate cancer. USP2 stabilises key oncoproteins including Aurora kinase A, cyclin D1 and fatty acid synthase. An unbiased proteomic approach identified potential new USP2 substrates and a USP2-regulated proteome that is associated with metastatic disease. Genetic or pharmacological targeting of USP2 caused cell death in human and mouse models of aggressive prostate cancer, and the USP2 inhibitor ML364 exhibited potent anti-tumour effects against an orthotopic xenograft model of AR-null disease. Collectively, this study identifies USP2 as a key regulator of proteins involved in prostate cancer progression and therapy resistance, positioning it as a viable therapeutic target.
2025-10-08 | GSE297844 | GEO
Project description:Renal transcriptome analysis of Usp2 knockout mice. Please note 'Zeitgeber time 12' means 12 hours after light onset in 12h: light 12h dark housing conditions. It is of importance in the present design because of the strong circadian oscillation of the interest gene. In the Characteristics[genetic modification] column Usp2-Lac0-SA-IRES-lacZ-WT Neo/Kan is the name of the targeting cassette which was inserted in the gene, in opposition to non for the WT who carry no mutation.
2013-03-20 | E-MTAB-1442 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) of human transcriptome of over 20,000 genes to compare gene expression of wild-type versus designed IFNG partial agonsits Methods: A549 cells were treated with either wild-type IFNG or partial agonists for 48 hours. RNA was extracted and prepared for NGS on using Thermo Ampliseq human transriptome kit on an Ion S5 XL system (Thermo). Relative expression was determined from the data. Results: Over 20,000 transcripts were matched to the human transcriptome to compare expression between protein treatments. We find genes that are stably expressed regardless of protein agonist treatment and other genes that have altered expression levels compared to wild-type. Conclusions: Our study represents a comprehensive list of genes along with their sensitivity to IFNG induced signaling.
2019-03-07 | GSE122672 | GEO
Project description:So far, we have found PMA induced USP2b isoform in myeloid leukemia cell lines such as HL60, THP-1, and U937. To explore molecular function of USP2 in the cells, we assess expression profiles of HL60-derivatives continuously expressing shRNA for USP2 and control shRNA.
2013-08-27 | GSE20476 | GEO
Project description:So far, we have found PMA induced USP2b isoform in myeloid leukemia cell lines such as HL60, THP-1, and U937. To explore molecular function of USP2 in the cells, we assess expression profiles of HL60-derivatives continuously expressing shRNA for USP2 and control shRNA. HL60 derivatives continuously expressing shRNA for USP2 and control shRNA were treated with PMA (30nM) for 0, 1, 2, and 3 days. Total RNA was extracted from the cells and subjected to microarray experiments using Human Genome U133 GeneChips.
2013-08-27 | E-GEOD-20476 | biostudies-arrayexpress
Project description:Ubiquitin specifc protease (USP) 2 modulates various cellular responces including carcinogenesis, spermatogenesis, and glucose metabolism. So far, we established USP2 knockdown HL-60 cells to explore roles of USP2 in macrophages. In this experiment, we investigated whether USP2 knockdown HL-60 cells more prominently modulate function of adipocytes compared with control cells.
2013-08-27 | GSE43313 | GEO