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Title: Microarray analysis of microRNAs in NPC FFPE tissue samples      
dateReleased:
01-13-2014
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).
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-46172
refinement:
raw
alternateIdentifiers:
46172
keywords:
functional genomics
dateModified:
06-03-2014
availability:
available
types:
gene expression
name:
Homo sapiens
ID:
A-GEOD-16770
name:
Agilent-031181 Unrestricted_Human_miRNA_V16.0_Microarray (miRBase release 16.0 miRNA ID version)
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-46172/E-GEOD-46172.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-46172/E-GEOD-46172.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE46172
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress
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