Global gene expression analysis reveals reduced abundance of putative microRNA targets in human prostate tumours

Ruping Sun, Xuping Fu, Yao Li, Yi Xie, Yumin Mao

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38 Scopus citations


Background: Recently, microRNAs (miRNAs) have taken centre stage in the field of human molecular oncology. Several studies have shown that miRNA profiling analyses offer new possibilities in cancer classification, diagnosis and prognosis. However, the function of miRNAs that are dysregulated in tumours remains largely a mystery. Global analysis of miRNA-target gene expression has helped illuminate the role of miRNAs in developmental gene expression programs, but such an approach has not been reported in cancer transcriptomics. Results: In this study, we globally analysed the expression patterns of miRNA target genes in prostate cancer by using several public microarray datasets. Intriguingly, we found that, in contrast to global mRNA transcript levels, putative miRNA targets showed a reduced abundance in prostate tumours relative to benign prostate tissue. Additionally, the down-regulation of these miRNA targets positively correlated with the number of types of miRNA target-sites in the 3′ untranslated regions of these targets. Further investigation revealed that the globally low expression was mainly driven by the targets of 36 specific miRNAs that were reported to be up-regulated in prostate cancer by a miRNA expression profiling study. We also found that the transcript levels of miRNA targets were lower in androgen-independent prostate cancer than in androgen-dependent prostate cancer. Moreover, when the global analysis was extended to four other cancers, significant differences in transcript levels between miRNA targets and total mRNA backgrounds were found. Conclusion: Global gene expression analysis, along with further investigation, suggests that miRNA targets have a significantly reduced transcript abundance in prostate cancer, when compared with the combined pool of all mRNAs. The abnormal expression pattern of miRNA targets in human cancer could be a common feature of the human cancer transcriptome. Our study may help to shed new light on the functional roles of miRNAs in cancer transcriptomics.

Original languageEnglish (US)
Article number93
JournalBMC Genomics
StatePublished - Feb 26 2009
Externally publishedYes

Bibliographical note

Funding Information:
We are grateful to two anonymous reviewers for their thoughtful criticisms, comments and suggestions on early version of the manuscript. We also thank Ms. Zhaorong Ma for copyediting of the manuscript. This work is supported by a grant 2006AA02Z324 from the National High Technology Research and Development Program of China (863 Program). This work is also supported by Shanghai Leading Academic Discipline Project, Project Number: B111.


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