Open Access Highly Accessed Research article

Microarray-based approach identifies microRNAs and their target functional patterns in polycystic kidney disease

Priyanka Pandey1, Benedikt Brors2, Prashant K Srivastava3, Andrea Bott1, Susanne NE Boehn1, Herrmann-Josef Groene3 and Norbert Gretz1*

Author Affiliations

1 Medical Research Center, University Hospital Mannheim, D-68167 Mannheim, Germany

2 Department of Theoretical Bioinformatics, German Cancer Research Center, D-69120 Heidelberg, Germany

3 Department of Cellular and Molecular Pathology, German Cancer Research Center, D-69120 Heidelberg, Germany

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BMC Genomics 2008, 9:624  doi:10.1186/1471-2164-9-624

Published: 23 December 2008



MicroRNAs (miRNAs) play key roles in mammalian gene expression and several cellular processes, including differentiation, development, apoptosis and cancer pathomechanisms. Recently the biological importance of primary cilia has been recognized in a number of human genetic diseases. Numerous disorders are related to cilia dysfunction, including polycystic kidney disease (PKD). Although involvement of certain genes and transcriptional networks in PKD development has been shown, not much is known how they are regulated molecularly.


Given the emerging role of miRNAs in gene expression, we explored the possibilities of miRNA-based regulations in PKD. Here, we analyzed the simultaneous expression changes of miRNAs and mRNAs by microarrays. 935 genes, classified into 24 functional categories, were differentially regulated between PKD and control animals. In parallel, 30 miRNAs were differentially regulated in PKD rats: our results suggest that several miRNAs might be involved in regulating genetic switches in PKD. Furthermore, we describe some newly detected miRNAs, miR-31 and miR-217, in the kidney which have not been reported previously. We determine functionally related gene sets, or pathways to reveal the functional correlation between differentially expressed mRNAs and miRNAs.


We find that the functional patterns of predicted miRNA targets and differentially expressed mRNAs are similar. Our results suggest an important role of miRNAs in specific pathways underlying PKD.