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Title: The mRNA and microRNA expression profile of the RNA-induced silencing complex in human U-87 astrocytoma cells and primary human astrocytes      
availability:
available
aggregation:
instance of dataset
privacy:
not applicable
refinement:
curated
dateReleased:
06-02-2014
ID:
E-GEOD-21514
description:
mRNA and microRNA expression was examined in global cellular fractions and in RNA-induced silencing complex (RISC)-immunoprecipitated cell fractions in cultured primary human astrocytes (ScienCell) and in cultured human U-87 MG astrocytoma cells (ATCC). ABSTRACT: Background: GW/P bodies are cytoplasmic ribonucleoprotein-rich foci that are involved in microRNA (miRNA)-mediated messenger RNA (mRNA) silencing and degradation. These mRNA regulatory functions within GW/P bodies are mediated by GW182 and its binding partner hAgo2 when bound to miRNA within the RNA-induced silencing complex (RISC). Although miRNAs and mRNAs are known to be localized to RISC in a variety of cells, to date no published study has examined the profile of specific miRNA and mRNA targeted to the RISC. Methodology/Principle Findings: In this study, RISC mRNA and miRNA components were profiled by microarray analysis of human U-87 astrocytoma cells and primary human astrocytes with total RNA extracted from the RISC as well as the global cellular fractions. The novel findings of this study were fourfold: (1) miRNAs are highly enriched in primary astrocyte RISC compared to U-87 astrocytoma RISC, (2) astrocytoma cells and primary astrocytes each contain unique RISC miRNA profiles as compared to their respective cellular miRNA profiles, (3) miR-195, 10b, 29b, 19b, 34a and 455-3p were upregulated and miR-181b was downregulated in U-87 astrocytoma RISC as compared to primary astrocyte RISC, and (4) RISC contain mostly downregulated mRNAs in primary astrocytes and U-87 astrocytoma cells. Conclusions/Significance: We show that in U-87 astrocytoma cells, miR-34a and miR-195 were upregulated in RISC suggesting an oncogenic role for these miRNAs. Three miR34a-targeted mRNAs and two miR-195-targeted mRNAs were downregulated. One miR-195-targeted mRNA was upregulated. Biological pathway analysis of RISC mRNA components suggests that the RISC plays a pivotal role in cancer, inflammatory disease, immunological disease, the cell cycle, cellular movement and numerous cell signaling pathways. This study points to the importance of the RISC and ultimately GW/P body composition and function and in miRNA and mRNA deregulation in astrocytoma cells and possibly for other brain tumors. Experiments outsourced to LC Sciences who are partnered with an Affymetrix® Authorized Service Provider, SeqWright DNA Technology Services (Houston, TX). Using Affymetrix Human Genome U133A 2.0 Array, they analyzed 14,500 well-characterized human genes across 4 replicates in each of the 4 sample groups: (1) global cellular U-87 astrocytoma, (2) global cellular primary astrocyte, (3) RISC-IP U-87 astrocytoma, and (4) RISC-IP primary astrocyte. Experiments outsourced to LC Sciences (Houston, TX). Using µParaflo microfluidic chips, they analyzed 6211 target human miRNAs (Sanger miRBase version 11, http://microrna.sanger.ac.uk/sequences/) or control RNAs (array hybridization controls and single-base mismatch targets) and a polyethylene glycol spacer segment to extend the coding segment away from the substrate across 4 replicates in each of the 4 sample groups: (1) global cellular U-87 astrocytoma, (2) global cellular primary astrocyte, (3) RISC-IP U-87 astrocytoma, and (4) RISC-IP primary astrocyte.
keywords:
other
transcription profiling by array
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HTML
storedIn:
Array Express
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not compressed
accessType:
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primary:
true
accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21514
format:
JSON
storedIn:
OmicsDI
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accessType:
download
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none
authentication:
none
primary:
false
accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-21514.json
format:
XML
storedIn:
OmicsDI
qualifier:
not compressed
accessType:
download
authorization:
none
authentication:
none
primary:
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accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-GEOD-21514.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/