NPC transcriptome disection
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ABSTRACT:
PROVIDER: PRJNA751056 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of differential expression between NPC and non-NPC tissues at miRNA expression level. We used a miRNA microarray platform to investigate the profile between NPC tissues and normal nasopharyngeal tissues to evaluate the relationship between miRNA expression and NPC. Recognition of the aberrant miRNAs and enrichment pathway analysis of predicted target gene may provide some clues to estimate the mechanism of miRNA effects on NPC carcinogenesis mediated by miRNA-mRNA regulation.
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Project description:Analysis of differential expression between NPC and non-NPC tissues at miRNA expression level. We used a miRNA microarray platform to investigate the profile between NPC tissues and normal nasopharyngeal tissues to evaluate the relationship between miRNA expression and NPC. Recognition of the aberrant miRNAs and enrichment pathway analysis of predicted target gene may provide some clues to estimate the mechanism of miRNA effects on NPC carcinogenesis mediated by miRNA-mRNA regulation. Total RNA was extracted from 8 NPC tissues compared to 4 nasopharyngeal tissues. We peformed the Illumina miRNA microarray to identify the differentially expressed miRNA between NPC tissues and normal nasopharyngeal tissues.
2013-06-25 | E-GEOD-22587 | biostudies-arrayexpress
Project description:We report the application for high-throughput profiling of transcriptome, chromatin-associated proteins on a genome-wide level in NPC CNE2 cells.
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Project description:Epstein-Barr virus (EBV) is a ubiquitous human herpesvirus associated with nasopharyngeal carcinoma (NPC). EBV encodes two groups of microRNAs (miRNAs) which are divided into BamHI fragment H rightward open reading frame 1 (BHRF1) and BamHI-A rightward transcripts (BART) microRNAs. EBV miR-BARTs have been found to be involved in the development and progression of NPC. However, the role of EBV-miR-BARTs in NPC progression remains illusive. This study aimed to investigate the role of EBV-miR-BARTs in NPC and explore the underlying mechanisms.
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Project description:Analysis of differential expression genes in NESG1-overexpressed and negative nasopharyngeal carcinoma. NESG1 is a candidate tumor suppressor in NPC. Results provide insight into the molecular pathogenesis of NESG1 in NPC. NESG1 cDNA was transfected into NESG1-negative NPC 5-8F cells and affymetrix microarrays HG-U133_Plus_2 were used to analyze the differential genes in NESG1-overexpressed NPC cells and their control NESG1-negative NPC cells.
2011-02-15 | E-GEOD-27318 | biostudies-arrayexpress
Project description:Nasopharyngeal carcinoma (NPC) is a challenging cancer that is rare in the United States but shows exceptionally high incidence in Southern China, Indonesia, and Malaysia. While the hallmark of NPC is striking geographic variation, early detection and clinical management are also critical characteristics of this cancer. The etiology of NPC is complex, involving the interplay of multiple factors, including Epstein Barr Virus (EBV), which appears to play an oncogenic role. While multimodality therapy is the mainstay of treatment for NPC, the impact of this treatment is greatly influenced by the presenting tumor stage, tumor size, nodal involvement, and the histologic subtype classification. Up to 40% percent of NPC cases present at an advanced stage, likely due to its deep location in the lymphatic-rich nasopharynx and its propensity for early lymphatic spread. Recent modifications in the TNM staging schema have attempted to improve prognostic accuracy, but variations in clinical outcome are still reported in patients with the same stage and similar treatment regimens. The various molecular markers developed to monitor disease progression have also proven unreliable. Hence, there is a significant need for a new kind of prognostic biomarker for NPC. Herein different approaches were applied to a set of samples to detect NPC-related miRNAs, potential circulating biomarkers. We have optimized the extraction of total RNA from NPC Formalin-fixed, paraffin-embedded (FFPE) samples and sera from four patients and matched controls and analyzed the miRNA expression profile by microarray, qPCR and RNAseq. The microarray analysis showed that 46 miRNAs were found to be differentially and significantly expressed in carcinogenic tissue compared to healthy tissue. Twenty-three (23) microRNAs were significantly upregulated (21 human microRNAs and 2 EBV miRNAs), whereas 13 were down-regulated.
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Project description:To investigate the function of KRAS activation in the regulation of neoplastic features, we established NPC-KRASG13D cell lines in which KRAS has been overexpressed. We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells (NPC cells, NPC-KRASG13D, U251-GSC, and U118MG-GSC).
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Project description:We Report the genome-wide RNA expression levels in control and schizophrenia hiPSC dervied NPC treated with neuronal media for 2 days. In total, 440 microRNA expression were detected in all samples, of which 16 were dysregualted.
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Project description:Nasopharyngeal carcinoma (NPC) is a challenging cancer that is rare in the United States but shows exceptionally high incidence in Southern China, Indonesia, and Malaysia. While the hallmark of NPC is striking geographic variation, early detection and clinical management are also critical characteristics of this cancer. The etiology of NPC is complex, involving the interplay of multiple factors, including Epstein Barr Virus (EBV), which appears to play an oncogenic role. While multimodality therapy is the mainstay of treatment for NPC, the impact of this treatment is greatly influenced by the presenting tumor stage, tumor size, nodal involvement, and the histologic subtype classification. Up to 40% percent of NPC cases present at an advanced stage, likely due to its deep location in the lymphatic-rich nasopharynx and its propensity for early lymphatic spread. Recent modifications in the TNM staging schema have attempted to improve prognostic accuracy, but variations in clinical outcome are still reported in patients with the same stage and similar treatment regimens. The various molecular markers developed to monitor disease progression have also proven unreliable. Hence, there is a significant need for a new kind of prognostic biomarker for NPC. Herein different approaches were applied to a set of samples to detect NPC-related miRNAs, potential circulating biomarkers. We have optimized the extraction of total RNA from NPC Formalin-fixed, paraffin-embedded (FFPE) samples and sera from four patients and matched controls and analyzed the miRNA expression profile by microarray, qPCR and RNAseq. The microarray analysis showed that 46 miRNAs were found to be differentially and significantly expressed in carcinogenic tissue compared to healthy tissue. Twenty-three (23) microRNAs were significantly upregulated (21 human microRNAs and 2 EBV miRNAs), whereas 13 were down-regulated. A total of 8 unique samples were analyzed on Agilent human miRNA microarray (miRBase Release 16.0). Of the 8 samples, 4 are from Non-keratinizing NPC tissue. Non-NPC (normal) tissue were taken from 4 individuals that were diagnosed with NPC (2 of which were matched/paired from the NPC case).
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Project description:This submission contains a result of a study of transcriptiomic profiles of the IPSC and NPC, derived from PD discordant monozygous twins.
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