The MicroRNA Expression Signature of Bladder Cancer by Deep Sequencing: The Functional Significance of the <i>miR-195/497</i> Cluster

<div><p>Current genome-wide microRNA (miRNA) expression signature analysis using deep sequencing technologies can drive the discovery of novel cancer pathways regulated by oncogenic and/or tumor suppressive miRNAs. We determined the genome-wide miRNA expression signature in bladder cancer (BC) by deep sequencing technology. A total of ten small RNA libraries were sequenced (five BCs and five samples of histologically normal bladder epithelia (NBE)), and 13,190,619 to 18,559,060 clean small RNA reads were obtained. A total of 933 known miRNAs and 17 new miRNA candidates were detected in this analysis. Among the known miRNAs, a total of 60 miRNAs were significantly downregulated in BC compared with NBE. We also found that several miRNAs, such as <i>miR-1/133a</i>, <i>miR-206/133b</i>, <i>let-7c/miR-99a</i>, <i>miR-143/145</i> and <i>miR-195/497</i>, were located close together at five distinct loci and constituted clustered miRNAs. Among these clustered miRNAs, we focused on the <i>miR-195/497</i> cluster because this clustered miRNA had not been analyzed in BC. Transfection of mature <i>miR-195</i> or <i>miR-497</i> in two BC cell lines (BOY and T24) significantly inhibited cancer cell proliferation, migration and invasion, suggesting that the <i>miR-195/497</i> cluster functioned as tumor suppressors in BC. Regarding the genes targeted by the <i>miR-195/497</i> cluster, the TargetScan algorithm showed that 6,730 genes were putative <i>miR-195/497</i> targets, and 113 significantly enriched signaling pathways were identified in this analysis. The “Pathways in cancer” category was the most enriched, involving 104 candidate target genes. Gene expression data revealed that 27 of 104 candidate target genes were actually upregulated in BC clinical specimens. Luciferase reporter assays and Western blotting demonstrated that <i>BIRC5</i> and <i>WNT7A</i> were directly targeted by <i>miR-195/497</i>. In conclusion, aberrant expression of clustered miRNAs was identified by deep sequencing, and downregulation of <i>miR-195/497</i> contributed to BC progression and metastasis. Tumor suppressive miRNA-mediated cancer pathways provide new insights into the potential mechanisms of BC oncogenesis.</p></div

Effect of mature <i>miR-195</i> and <i>miR-497</i> transfection of BC cell lines (BOY, T24).

<p>Gain-of-function studies were performed by using <i>miR-195</i> and <i>miR-497</i>-transfected BOY and T24 in comparison with the miR-control transfectants. A) Cell proliferation determined by the XTT assay. B) Cell invasion activity demonstrated by the Matrigel invasion assay. C) Cell migration activity determined by the wound healing assay. *, P<0.0001; **, P = 0.009.</p

<i>BIRC5</i> and <i>WNT7A</i> as target genes of the <i>miR-195/497</i> cluster in BC.

<p>Luminescence intensity was measured in <i>miR-195-</i> and <i>miR-497-</i>transfectants in comparison with the miR-control transfectant. A) <i>miR-195/497</i> cluster binding sites in the 3′-UTR of <i>BIRC5</i> mRNA. Luciferase reporter assay vector used the encoding 3′-UTR region of <i>BIRC5</i> including putative <i>miR-195/497</i> target sites. <i>Renilla</i> luciferase values were normalized to firefly luciferase values. *P<0.01. B) <i>miR-195/497</i> cluster binding sites in the 3′-UTR of <i>WNT7A</i> mRNA. Luciferase reporter assay vector is the encoding 3′-UTR region of <i>WNT7A</i> including putative <i>miR-195/497</i> target site. *P<0.01.</p

Patient characteristics for real-time RT-PCR.

<p>Patient characteristics for real-time RT-PCR.</p

Patient characteristics for deep sequencing.

<p>Patient characteristics for deep sequencing.</p

Differentially expressed clustered miRNAs, their target mRNAs, and associated pathways in BC.

<p>Differentially expressed clustered miRNAs, their target mRNAs, and associated pathways in BC.</p

<i>BIRC5</i> and <i>WNT7A</i> mRNA and protein expression levels were suppressed by <i>miR-195</i> and <i>miR-497</i> transfection in comparison with the miR-control transfection in BC cell lines (BOY and T24).

<p>A) <i>BIRC5</i> and <i>WNT7A</i> mRNA expression 72 h after transfection with <i>miR-195</i>, <i>miR-497</i>, and the miR-control. <i>GUSB</i> expression was used for normalization. B) <i>BIRC5</i> and <i>WNT7A</i> protein expression 72 h after transfection with <i>miR-195</i>, <i>miR-497</i>, and the miR-control. <i>GAPDH</i> was used as a loading control. The ratio of <i>BIRC5</i> or <i>WNT7A</i> to <i>GAPDH</i> expression was evaluated using ImageJ software (ver. 1.43; <a href="http://rsbweb.nih.gov/ij/index.htmL" target="_blank">http://rsbweb.nih.gov/ij/index.htmL</a>). *P<0.01.</p

Expression levels of <i>miR-195</i> and <i>miR-497</i> in BC clinical specimens, and noncancerous bladder tissues.

<p>A, B) The expression of <i>miR-195</i> and <i>miR-497</i> was significantly lower in 20 clinical BC specimens than in 29 adjacent noncancerous specimens. <i>RNU48</i> was used as the internal control. *, P<0.0001. C) Significant positive correlation between miRNA expression patterns of <i>miR-195</i> and <i>miR-497</i> (rank test Spearman's correlation coefficient r = 0.984, P<0.0001).</p

Details of sequence reads in BCs (#1 – #5) and NBEs (#6 – #10).

<p>Details of sequence reads in BCs (#1 – #5) and NBEs (#6 – #10).</p