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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 26, 2011 |
| Title |
The mRNA and microRNA expression profile of the RNA-induced silencing complex in human U-87 astrocytoma cells and primary human astrocytes |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Non-coding RNA profiling by array
Other
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| Summary |
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.
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| Overall design |
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.
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| Contributor(s) |
Moser JJ, Fritzler MJ |
| Citation(s) |
20976148 |
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| Submission date |
Apr 26, 2010 |
| Last update date |
Mar 25, 2019 |
| Contact name |
Joanna Moser |
| Organization name |
University of Calgary
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| Department |
Biochemistry and Molecular Biology
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| Lab |
Dr. Marvin Fritzler
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| Street address |
3330 Hospital Drive N.W.
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| City |
Calgary |
| State/province |
AB |
| ZIP/Postal code |
T2N 4N1 |
| Country |
Canada |
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| Platforms (2) |
| GPL570 |
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array |
| GPL10358 |
LC_MRA-1001_miRHuman_11.0_080411 (miRNA ID version) |
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| Samples (8)
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| GSM537469 |
astrocytoma_global mRNA (S803681.H42.1) |
| GSM537470 |
astrocyte_global mRNA (S803681.H52) |
| GSM537471 |
astrocyte_RISC-IP mRNA (S905515.K438) |
| GSM537472 |
astrocytoma_RISC-IP mRNA (S905515.K439) |
| GSM537491 |
astrocytoma_global microRNA (01_H11.0_081771) |
| GSM537492 |
astrocyte_global microRNA (02_H11.0_081772) |
| GSM537493 |
astrocyte_RISC-IP microRNA (01_H11.0_092342) |
| GSM537494 |
astrocytoma_RISC-IP microRNA (02_H11.0_092343) |
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| Relations |
| BioProject |
PRJNA125971 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE21514_RAW.tar |
20.3 Mb |
(http)(custom) |
TAR (of CEL, TXT) |
| Processed data included within Sample table |
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