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Oncotarget. 2016 Apr 19;7(16):22566-78. doi: 10.18632/oncotarget.8124.

Non‑invasive prostate cancer detection by measuring miRNA variants (isomiRs) in urine extracellular vesicles.

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Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
Department of Neurosurgery, Neuro-Oncology Research Group, VU University Medical Center, Amsterdam, The Netherlands.
Exbiome B.V., 1016 PL Amsterdam, The Netherlands.
Department of Genetics, Computational Genomics and Bioinformatics Group, University of Granada, Granada Spain.
Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands.
Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
Department of Urology, VU University Medical Center, Amsterdam, The Netherlands.
CNR-National Research Council of Italy, IGM, Bologna, Italy.
SC Laboratory of Musculoskeletal Cell Biology, IOR-IRCCS, Bologna, Italy.
Department of Urology, Academic Medical Centre, Amsterdam, The Netherlands.
Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA.


In many cancer types, the expression and function of ~22 nucleotide-long microRNAs (miRNA) is deregulated. Mature miRNAs can be stably detected in extracellular vesicles (EVs) in biofluids, therefore they are considered to have great potential as biomarkers. In the present study, we investigated whether miRNAs have a distinct expression pattern in urine-EVs of prostate cancer (PCa) patients compared to control males. By next generation sequencing, we determined the miRNA expression in a discovery cohort of 4 control men and 9 PCa patients. miRNAs were validated by using a stemloop RT-PCR in an independent cohort of 74 patients (26 control and 48 PCa-patients). Whereas standard mapping protocols identified > 10 PCa associated miRNAs in urinary EVs, miR-21, miR-375 and miR-204 failed to robustly discriminate for disease in a validation study with RT-PCR-detection of mature miRNA sequences. In contrast, we observed that miRNA isoforms (isomiRs) with 3' end modifications were highly discriminatory between samples from control men and PCa patients. Highly differentially expressed isomiRs of miR-21, miR-204 and miR-375 were subsequently validated in an independent group of 74 patients. Receiver-operating characteristic analysis was performed to evaluate the diagnostic performance of three isomiRs, resulting in a 72.9% sensitivity with a high (88%) specificity and an area under the curve (AUC) of 0.866. In comparison, prostate specific antigen had an AUC of 0.707 and measuring the mature form of these miRNAs yielded a lower 70.8% sensitivity and 72% specificity (AUC 0.766). We propose that isomiRs may carry discriminatory information which is useful to generate stronger biomarkers.


RNA sequencing; extracellular vesicles; isomiRs; liquid biopsy; miRNA

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