MicroRNA expression and identification of putative miRNA targets in ovarian cancer - PubMed (original) (raw)

MicroRNA expression and identification of putative miRNA targets in ovarian cancer

Neetu Dahiya et al. PLoS One. 2008.

Abstract

Background: MicroRNAs (miRNAs) represent a class of small non-coding RNAs that control gene expression by targeting mRNAs and triggering either translation repression or RNA degradation. Emerging evidence suggests the potential involvement of altered regulation of miRNA in the pathogenesis of cancers, and these genes are thought to function as both tumor suppressors and oncogenes.

Methodology/principal findings: Using microRNA microarrays, we identify several miRNAs aberrantly expressed in human ovarian cancer tissues and cell lines. miR-221 stands out as a highly elevated miRNA in ovarian cancer, while miR-21 and several members of the let-7 family are found downregulated. Public databases were used to reveal potential targets for the highly differentially expressed miRNAs. In order to experimentally identify transcripts whose stability may be affected by the differentially expressed miRNAs, we transfected precursor miRNAs into human cancer cell lines and used oligonucleotide microarrays to examine changes in the mRNA levels. Interestingly, there was little overlap between the predicted and the experimental targets or pathways, or between experimental targets/pathways obtained using different cell lines, highlighting the complexity of miRNA target selection.

Conclusion/significance: Our results identify several differentially expressed miRNAs in ovarian cancer and identify potential target transcripts that may be regulated by these miRNAs. These miRNAs and their targets may have important roles in the initiation and development of ovarian cancer.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Cluster analysis of miRNA expression.

Tree generated by cluster analysis of ovarian cancer tissues and cell lines based on (A) all tested miRNAs in tissues and cell lines, and (B) differentially regulated miRNAs (Fold change >2.0 or <0.5 in greater than 60% of the samples) in tissues and cell lines compared to the normal control HOSE-B cells.

Figure 2

Figure 2. Principal component analysis of ovarian cancer samples (PCA) based on global miRNA expression.

Two-dimensional PCA shows that global miRNA expression patterns are different in ovarian cancer cell lines (indicated in blue), ovarian cancer tissues (indicated in green), and the non-tumorigenic HOSE-B cells (in red).

Figure 3

Figure 3. Comparisons of miRNA expression in ovarian tissues.

(A) The Venn diagram shows the number miRNAs differentially expressed in ovarian cell lines, in ovarian cancer tissues and in both. For each category, the miRNAs elevated (indicated in red) and downregulated (indicated in green) are indicated below the diagram. (B) The Venn diagram shows the number of differentially expressed miRNAs identified in the current study and the number of miRNAs indentified in 3 previous ovarian cancer studies. The miRNAs in common are indicated below the diagram and color-coded (red: elevated; green: decreased).

Figure 4

Figure 4. Forced overexpression of selected miRNAs in ovarian cancer cell lines.

Pre-miR-34c, Pre-miR-98, Pre-miR-424, Pre-let-7f were overexpressed in BG-1 and UCI-101. The products for each of the miRNAs is shown in duplicate for the two cell lines used. Significant overexpression of the miRNAs is confirmed. RT-PCR of 18S RNA is shown for each condition to demonstrate equal loading.

Figure 5

Figure 5. Validation of illumina arrays data for let-7f.

Transcripts identified by illumina arrays to be altered following let-7f overexpression are validated by RT-PCR. Fold changes for genes KIF1A, ASS, FDPS, NTS (in UCI-101 cells), and TFF1, EEF1A2, ESM1, VIM (in BG-1 cells) are shown and confirm the changes identified by illumina arrays.

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