Systematic Identification of MicroRNAs That Impact on Proliferation of Prostate Cancer Cells and Display Changed Expression in Tumor Tissue.
Systematic approaches to functionally identify key players in microRNA (miRNA)-target networks regulating prostate cancer (PCa) proliferation are still missing.



To comprehensively map miRNA regulation of genes relevant for PCa proliferation through phenotypic screening and tumor expression data.



Gain-of-function screening with 1129 miRNA molecules was performed in five PCa cell lines, measuring proliferation, viability, and apoptosis. These results were integrated with changes in miRNA expression from two cohorts of human PCa (188 tumors in total). For resulting miRNAs, the predicted targets were collected and analyzed for patterns with gene set enrichment analysis, and for their association with biochemical recurrence free survival.



Rank product statistical analysis was used to evaluate miRNA effects in phenotypic screening and for expression differences in the prostate tumor cohorts. Expression data were analyzed using the significance analysis of microarrays (SAM) method and the patient material was subjected to Kaplan-Meier statistics.



Functional screening identified 25 miRNAs increasing and 48 miRNAs decreasing cell viability. Data integration resulted in 14 miRNAs, with aberrant expression and effect on proliferation. These miRNAs are predicted to regulate >3700 genes, of which 28 were found up-regulated and 127 down-regulated in PCa compared with benign tissue. Seven genes, FLNC, MSRB3, PARVA, PCDH7, PRNP, RAB34, and SORBS1, showed an inverse association to their predicted miRNA, and were identified to significantly correlate with biochemical recurrence free survival in PCa patients.



A systematic in vitro screening approach combined with in vivo expression and gene set enrichment analysis provide unbiased means for revealing novel miRNA-target links, possibly driving the oncogenic processes in PCa.



This study identified novel regulatory molecules, which impact on PCa proliferation and are aberrantly expressed in clinical tumors. Thus, our study reveals regulatory nodes with potential for therapy.
Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland; VTT Technical Research Centre of Finland, Medical Biotechnology, Turku, Finland(1); Turku Centre for Biotechnology, University of Turku, Turku, Finland(1). Electronic address: anna.aakula@fimm.fi.
Anna
A
Aakula
VTT Technical Research Centre of Finland, Medical Biotechnology, Turku, Finland(1); Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden.
Pekka
P
Kohonen
VTT Technical Research Centre of Finland, Medical Biotechnology, Turku, Finland(1); Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland.
Suvi-Katri
SK
Leivonen
VTT Technical Research Centre of Finland, Medical Biotechnology, Turku, Finland(1); Misvik Biology Corporation, Turku, Finland.
Rami
R
Mäkelä
Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
Petteri
P
Hintsanen
Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland; VTT Technical Research Centre of Finland, Medical Biotechnology, Turku, Finland(1).
John Patrick
JP
Mpindi
Department of Urology, Erasmus MC, Rotterdam, The Netherlands.
Elena
E
Martens-Uzunova
Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
Tero
T
Aittokallio
Department of Urology, Erasmus MC, Rotterdam, The Netherlands.
Guido
G
Jenster
VTT Technical Research Centre of Finland, Medical Biotechnology, Turku, Finland(1); Natural Resources Institute Finland (Luke), Helsinki, Finland.
Merja
M
Perälä
Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland; VTT Technical Research Centre of Finland, Medical Biotechnology, Turku, Finland(1).
Olli
O
Kallioniemi
Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland; VTT Technical Research Centre of Finland, Medical Biotechnology, Turku, Finland(1).
Päivi
P
Östling
D017209:Apoptosis / Q000235:genetics; D015820:Cadherins / Q000235:genetics; D045744:Cell Line, Tumor; D049109:Cell Proliferation / Q000235:genetics; D002470:Cell Survival / Q000235:genetics; D018572:Disease-Free Survival; D015536:Down-Regulation; D064448:Filamins / Q000235:genetics; D005786:Gene Expression Regulation; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D051150:Methionine Sulfoxide Reductases / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism*; D008840:Microfilament Proteins / Q000235:genetics; D009687:Nuclear Proteins; D000072002:Prion Proteins / Q000235:genetics; D017430:Prostate-Specific Antigen / Q000097:blood; D011471:Prostatic Neoplasms / Q000235:genetics*; D000091363:Protocadherins; D015854:Up-Regulation; D020691:rab GTP-Binding Proteins / Q000235:genetics; D000096985:Calponins
D015820:Cadherins; D064448:Filamins; D051150:Methionine Sulfoxide Reductases; D035683:MicroRNAs; D008840:Microfilament Proteins; D009687:Nuclear Proteins; D000072002:Prion Proteins; D017430:Prostate-Specific Antigen; D000091363:Protocadherins; D020691:rab GTP-Binding Proteins; C578661:FLNC protein, human; C486590:PARVA protein, human; D000096985:Calponins; C113391:PCDH7 protein, human; C512656:PRNP protein, human; C567953:RAB34 protein, human; C432967:SORBS1 protein, human; C524352:MSRB3 protein, human
Functional high-throughput screening; MicroRNA; Prostate cancer; Reverse-phase protein array