J Cancer 2017; 8(14):2729-2739. doi:10.7150/jca.18396
Discovering the miR-26a-5p Targetome in Prostate Cancer Cells
1. Non-coding RNA Laboratory, Institute of Clinical Physiology (IFC), CNR, Pisa, Italy;
2. Tuscan Tumor Institute (ITT), Firenze, Italy;
3. Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics (IIT) and Institute of Clinical Physiology (IFC), CNR, Pisa, Italy;
4. Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
Rizzo M, Berti G, Russo F, Fazio S, Evangelista M, D'Aurizio R, Pellegrini M, Rainaldi G. Discovering the miR-26a-5p Targetome in Prostate Cancer Cells. J Cancer 2017; 8(14):2729-2739. doi:10.7150/jca.18396. Available from http://www.jcancer.org/v08p2729.htm
Purpose. miR-26a-5p is a tumor suppressor (TS) miRNA often downregulated in several tumor tissues and tumor cell lines. In this work, we performed the re-expression of the miR-26a-5p in DU-145 prostate cancer cells to collect genes interacting with miR-26a-5p and analyzed their integration in the tumorigenesis related pathways.
Methods. The transfection of DU-145 prostate cancer cells with miR-26a-5p was done using nucleofection. The biological effects induced by miR-26a-5p re-expression were detected with routine assays for cell proliferation, cell cycle, survival, apoptosis and cell migration. The miRNA pull out technique was used to collect and next generation sequencing to identify the complete repertoire of the miR-26a-5p targets (miR-26a-5p/targetome). TargetScan 7, PITA and RNA22 were used to find the predicted miR-26a-5p targets in the miR-26a-5p/targetome. Gene set enrichment analysis were used to integrate target genes in KEGG pathways and Protein-Protein Interaction networks (PPINs) and modules were built.
Results. miR-26a-5p exerted an anti-proliferative effect acting at several levels, by decreasing survival and migration and inducing both cell cycle block and apoptosis. The analysis of the miR-26a-5p/targetome showed that 1423 (1352 coding and 71 non-coding) transcripts interacted with miR-26a-5p. Filtering the miR-26a-5p/targetome with prediction algorithms, 628 out of 1353 transcripts were miR-26a-5p predicted targets and 73 of them were already validated miR-26a-5p targets. Finally, miR-26a-5p targets were involved in 22 KEGG pathways and 20 significant protein-protein interaction modules
Conclusion. The TS-miR-26a-5p/targetome is a platform that shows both unknown and known miRNA/target interactions thus offering the possibility to validate genes and discover pathways in which these genes could be involved.
Keywords: re-expression of miR-26a-5p, DU-145 prostate cancer cells, miRNA pull out assay, next generation sequencing, miR-26a-5p/targetome, pathway in cancer.