Mina Jahandideh Ebrahim Barzegari https://orcid.org/0000-0002-4412-6129


     MicroRNAs are interesting as cancer diagnostic and prognostic biomarkers because of their unique tissue expression profiles, higher stability in the blood in comparison to mRNAs, and the possibility for reliable quantification. In the case of prostate cancer (PCa), it is currently emphasized to explore new biomarkers, particularly from microRNAs which are freely available in the bloodstream. In this study, the gene expression omnibus database (GEO), a repository of microarray data for PCa circulating extracellular vesicle-free microRNAs profiling, was analyzed for differentially expressed miRNAs (DE-miRs). Top 20 most differentially expressed miRs with significant (adjusted p-value < 0.01) high expression (fold change) levels were extracted by the simultaneous application of different filtering criteria. Then, microRNA-gene networks were constructed for the two sets of positively (n=20) or negatively (n=20) regulated miRNAs. Gene ontology annotations of the target gene sets were also extracted and analyzed. Results indicated that human miR-1587, miR-223-3p, miR-3125, and miR-642b-3p are highly significant DE-miRs in PCa. In addition, human miR-4459, miR-1273g, miR 642a-3p, and miR-642b-3p were identified as top-ranked hubs in the relevant miRNA-gene networks. FOXK1, PML, CD24, ATN1, BAZ2A, CDKN1A, NUFIP2, and HARNPU were identified as microRNA target genes with significant dysregulation. miR-4459, miR-1273g-3p, miR-3135b, miR-5001-5p, and miR-1587 were proposed as novel microRNAs with the potential to be utilized as diagnostic biomarkers of prostate cancer among circulating vesicle-free miRNAs.

Article Details


Prostate Cancer, Diagnosis, Biomarker, Vesicle-free microRNA, Gene ontology

Abramovic I., Ulamec M., Bojanac A. K., Bulic-Jakus F., Jezek D. and Sincic N. (2020) miRNA in prostate cancer: challenges toward translation. Epigenomics 12:543-558.
Aghaee-Bakhtiari S. H., Arefian E., Naderi M., Noorbakhsh F., Nodouzi V., Asgari M., Fard-Esfahani P., Mahdian R. and Soleimani M. (2015) MAPK and JAK/STAT pathways targeted by miR-23a and miR-23b in prostate cancer: computational and in vitro approaches. Tumour Biology 36:4203-4212.
Bahtiyar N., Onaran I., Aydemir B., Baykara O., Toplan S., Agaoglu F. Y. and Akyolcu M. C. (2018) Monitoring of platelet function parameters and microRNA expression levels in patients with prostate cancer treated with volumetric modulated arc radiotherapy. Oncology Letters 16:4745-4753.
Bendoraite A., Knouf E. C., Garg K. S., Parkin R. K., Kroh E. M., O'Briant K. C., Ventura A. P., Godwin A. K., Karlan B. Y., Drescher C. W., Urban N., Knudsen B. S. and Tewari M. (2010) Regulation of miR-200 family microRNAs and ZEB transcription factors in ovarian cancer: evidence supporting a mesothelial-to-epithelial transition. Gynecologic Oncology 116:117-125.
Boesen L., Norgaard N., Logager V., Balslev I., Bisbjerg R., Thestrup K. C., Winther M. D., Jakobsen H. and Thomsen H. S. (2018) Assessment of the diagnostic accuracy of biparametric magnetic resonance imaging for prostate cancer in biopsy-naive men: the biparametric MRI for detection of prostate cancer (BIDOC) study. JAMA Network Open 1: e180219.
Bolla M. and van Poppel H. (2012) Management of prostate cancer: a multidisciplinary approach. Springer-Verlag, Berlin Heidelberg. VIII, 334.
Bray F., Ferlay J., Soerjomataram I., Siegel R. L., Torre L. A. and Jemal A. (2018) Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185countries. CA: A Cancer Journal of Clinicians 68:394-424.
Burri R. J., Stock R. G., Cesaretti J. A., Atencio D. P., Peters S., Peters C. A., Fan G., Stone N. N., Ostrer H. and Rosenstein B. S. (2008) Association of single nucleotide polymorphisms in SOD2, XRCC1 and XRCC3 with susceptibility for the development of adverse effects resulting from radiotherapy for prostate cancer. Radiation Research 170:49-59.
Cai S., Chen R., Li X., Cai Y., Ye Z., Li S., Li J., Huang H., Peng S., Wang J., Tao Y., Wen X., Mo J., Deng Z., Zhang Y. and Gao X. (2015) Downregulation of microRNA-23a suppresses prostate cancer metastasis by targeting the PAK6-LIMK1 signaling pathway. Oncotarget 6:3904-3917.
Cao L., Zhang X., Cao F., Wang Y., Shen Y., Yang C., Uzan G., Peng B. and Zhang D. (2015) Inhibiting inducible miR-223 further reduces viable cells in human cancer cell lines MCF-7 and PC3 treated by celastrol. BMC Cancer 15:873.
Chang L., Zhou G., Soufan O. and Xia J. (2020) miRNet 2.0 - network-based visual analytics for miRNA functional analysis and systems biology. Nucleic Acids Research 48:W244-W251.
Chen D., Wang K., Li X., Jiang M., Ni L., Xu B., Chu Y., Wang W., Wang H., Kang H., Wu K., Liang J. and Ren G. (2017) FOXK1 plays an oncogenic role in the development of esophageal cancer. Biochemical and Biophysical Research Communications 494:88-94.
Chen Q. G., Zhou W., Han T., Du S. Q., Li Z. H., Zhang Z., Shan G. Y. and Kong C. Z. (2016) MiR-345 suppresses proliferation, migration and invasion by targeting Smad1 in human prostate cancer. Journal of Cancer Research and Clinical Oncology 142:213-224.
Chen R., Sheng L., Zhang H. J., Ji M. and Qian W. Q. (2018) miR-15b-5p facilitates the tumorigenicity by targeting RECK and predicts tumour recurrence in prostate cancer. Journal of Cellular and Molecular Medicine 22:1855-1863.
Elkjaer M. C., Andersen M. H., Hoyer S., Pedersen B. G. and Borre M. (2018) Multi-parametric magnetic resonance imaging monitoring patients in active surveillance for prostate cancer: a prospective cohort study. Scandinavian Journal of Urology 52:8-13.
Endzelins E., Berger A., Melne V., Bajo-Santos C., Sobolevska K., Abols A., Rodriguez M., Santare D., Rudnickiha A., Lietuvietis V., Llorente A. and LineA. (2017) Detection of circulating miRNAs: comparative analysis of extracellular vesicle-incorporated miRNAs and cell-free miRNAs in whole plasma of prostate cancer patients. BMC Cancer 17:730.
Fabris L., Ceder Y., Chinnaiyan A. M., Jenster G. W., Sorensen K. D., Tomlins S., Visakorpi T. and Calin G. A. (2016) The potential of microRNAs as prostate cancer biomarkers. European Urology 70:312-322.
Fendler A., Stephan C., Yousef G. M., Kristiansen G. and Jung K. (2016) The translational potential of microRNAs as biofluid markers of urological tumours. Nature Reviews in Urology 13:734-752.
Feng Q., He P. and Wang Y. (2018) MicroRNA-223-3p regulates cell chemo-sensitivity by targeting FOXO3 in prostatic cancer. Gene 658:152-158.
Ferracin M., Veronese A. and Negrini M. (2010) Micromarkers: miRNAs in cancer diagnosis and prognosis. Expert Reviews of Molecular Diagnostics 10:297-308.
Findlay V. J., Turner D. P., Moussa O. and Watson D. K. (2008) MicroRNA-mediated inhibition of prostate-derived Ets factor messenger RNA translation affects prostate-derived Ets factor regulatory networks in human breast cancer. Cancer Research 68:8499-8506.
Fredsoe J., Rasmussen A. K. I., Mouritzen P., Bjerre M. T., Ostergren P., Fode M., Borre M. and Sorensen K. D. (2020) Profiling of circulating microRNAs in prostate cancer reveals diagnostic biomarker potential. Diagnostics (Basel) 10:188.
Ge Y., Wang Q., Shao W., Zhao Y., Shi Q., Yuan Q. and Cui L. (2020) Circulating let-7f-5p improve risk prediction of prostate cancer in patients with benign prostatic hyperplasia. Journal of Cancer 11:4542-4549.
Glinge C., Clauss S., Boddum K., Jabbari R., Jabbari J., Risgaard B., Tomsits P., Hildebrand B., Kaab S., Wakili R., Jespersen T. and Tfelt-Hansen J. (2017) Stability of circulating blood-based microRNAs - pre-analytic methodological considerations. PLoS One 12: e0167969.
Gu L., Frommel S. C., Oakes C. C., Simon R., Grupp K., Gerig C. Y., Bar D., Robinson M. D., Baer C., Weiss M., Gu Z., Schapira M., Kuner R., Sultmann H., Provenzano M., Yaspo M. L., Brors B., Korbel J., Schlomm T., Sauter G., Eils R., Plass C. and Santoro R. (2015) BAZ2A (TIP5) is involved in epigenetic alterations in prostate cancer and its overexpression predicts disease recurrence. Nature Genetics 47:22-30.
Gurrieri C., Capodieci P., Bernardi R., Scaglioni P. P., Nafa K., Rush L. J., Verbel D. A., Cordon-Cardo C. and Pandolfi P. P. (2004) Loss of the tumor suppressor PML in human cancers of multiple histologic origins. Journal of the National Cancer Institute 96:269-279.
Hamdy F. C., Donovan J. L., Lane J. A., Mason M., Metcalfe C., Holding P., Davis M., Peters T. J., Turner E. L., Martin R. M., Oxley J., Robinson M., Staffurth J., Walsh E., Bollina P., Catto J., Doble A., Doherty A., Gillatt D., Kockelbergh R., Kynaston H., Paul A., Powell P., Prescott S., Rosario D. J., Rowe E. and Neal D. E. (2016) 10-Year outcomes after monitoring, surgery, or radiotherapy for localized prostate cancer. The New England Journal of Medicine 375:1415-1424.
Helgstrand J. T., Roder M. A., Klemann N., Toft B. G., Lichtensztajn D. Y., Brooks J. D., Brasso K., Vainer B. and Iversen P. (2018) Trends in incidence and 5-year mortality in men with newly diagnosed, metastatic prostate cancer-A population-based analysis of 2 national cohorts. Cancer 124:2931-2938.
Huang X., Yuan T., Tschannen M., Sun Z., Jacob H., Du M., Liang M., Dittmar R. L., Liu Y., Kohli M., Thibodeau S. N., Boardman L. and Wang L. (2013) Characterization of human plasma-derived exosomal RNAs by deep sequencing. BMC Genomics 14:319.
Huang Z., Shi J., Gao Y., Cui C., Zhang S., Li J., Zhou Y. and Cui Q. (2019) HMDD v3.0: a database for experimentally supported human microRNA-disease associations. Nucleic Acids Research 47: D1013-D1017.
Jiang J., Lee E. J., Gusev Y. and Schmittgen T. D. (2005) Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Research 33:5394-5403.
Kurozumi A., Goto Y., Matsushita R., Fukumoto I., Kato M., Nishikawa R., Sakamoto S., Enokida H., Nakagawa M., Ichikawa T. and Seki N. (2016) Tumor-suppressive microRNA-223 inhibits cancer cell migration and invasion by targeting ITGA3/ITGB1 signaling in prostate cancer. Cancer Science 107:84-94.
Laursen E. B., Fredsoe J., Schmidt L., Strand S. H., Kristensen H., Rasmussen A. K. I., Daugaard T. F., Mouritzen P., Hoyer S., Kristensen G., Stroomberg H. V., Brasso K., Roder M. A., Borre M. and Sorensen K. D. (2019) Elevated miR-615-3pexpression predicts adverse clinical outcome and promotes proliferation and migration of prostate cancer cells. The American Journal of Pathology 189:2377-2388.
Lim Y. B., Park T. J. and Lim I. K. (2008) B cell translocation gene 2 enhances susceptibility of HeLa cells to doxorubicin-induced oxidative damage. Journal of Biological Chemistry 283:33110-33118.
Lin S. and Gregory R. I. (2015) MicroRNA biogenesis pathways in cancer. Nature Reviews in Cancer 15:321-333.
Liu R. S. C., Olkhov-Mitsel E., Jeyapala R., Zhao F., Commisso K., Klotz L., Loblaw A., Liu S. K., Vesprini D., Fleshner N. E. and Bapat B. (2018) Assessment of serum microRNA biomarkers to predict reclassification of prostate cancer in patients on active surveillance. Journal of Urology 199:1475-1481.
Liu Y., Jovanovic B., Pins M., Lee C. and Bergan R. C. (2002) Over expression of endoglin in human prostate cancer suppresses cell detachment, migration and invasion. Oncogene 21:8272-8281.
Maugham M. L., Thomas P. B., Crisp G. J., Philp L. K., Shah E. T., Herington A. C., Chen C., Gregory L. S., Nelson C. C., Seim I., Jeffery P. L. and Chopin L. K. (2017) Insights from engraftable immunodeficient mouse models of hyperinsulinaemia. Scientific Reports 7:491.
McDonald A. C., Vira M., Shen J., Sanda M., Raman J. D., Liao J., Patil D. and Taioli E. (2018) Circulating microRNAs in plasma as potential biomarkers for the early detection of prostate cancer. Prostate 78:411-418.
Mello-Grand M., Gregnanin I., Sacchetto L., Ostano P., Zitella A., Bottoni G., Oderda M., Marra G., Munegato S., Pardini B., Naccarati A., Gasparini M., Gontero P. and Chiorino G. (2019) Circulating microRNAs combined with PSA for accurate and non-invasive prostate cancer detection. Carcinogenesis 40:246-253.
Mi S., Lu J., Sun M., Li Z., Zhang H., Neilly M. B., Wang Y., Qian Z., Jin J., Zhang Y., Bohlander S. K., Le Beau M. M., Larson R. A., Golub T. R., Rowley J. D. and Chen J. (2007) MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia. Proceedings of the National Academy of Sciences of the United States of America 104:19971-19976.
Mitchell K. O. and El-Deiry W. S. (1999) Overexpression of c-Myc inhibits p21WAF1/CIP1 expression and induces S-phase entry in 12-O-tetradecanoylphorbol-13-acetate (TPA)-sensitive human cancer cells. Cell Growth & Differentiation 10:223-230.
Movahedpour A., Ahmadi N., Ghasemi Y., Savardashtaki A. and Shabaninejad Z. (2019) Circulating microRNAs as potential diagnostic biomarkers and therapeutic targets in prostate cancer: current status and future perspectives. Journal of Cellular Biochemistry 120:16316-16329.
Musumeci M., Coppola V., Addario A., Patrizii M., Maugeri-Sacca M., Memeo L., Colarossi C., Francescangeli F., Biffoni M., Collura D., Giacobbe A., D'Urso L., Falchi M., Venneri M. A., Muto G., De Maria R. and Bonci D. (2011) Control of tumor and microenvironment cross-talk by miR-15a and miR-16 in prostate cancer. Oncogene 30:4231-4242.
Navon R., Wang H., Steinfeld I., Tsalenko A., Ben-Dor A. and Yakhini Z. (2009) Novel rank-based statistical methods reveal microRNAs with differential expression in multiple cancer types. PLoS One 4:e8003.
Pomaznoy M., Ha B. and Peters B. (2018) GOnet: a tool for interactive gene ontology analysis. BMC Bioinformatics 19:470.
Porkka K. P., Pfeiffer M. J., Waltering K. K., Vessella R. L., Tammela T. L. and Visakorpi T. (2007) MicroRNA expression profiling in prostate cancer. Cancer Research 67:6130-6135.
Rouhrazi H., Turgan N. and Oktem G. (2018) Zoledronic acid overcomes chemoresistance by sensitizing cancer stem cells to apoptosis. Biotechnic & Histochemistry 93:77-88.
Sayed D., Hong C., Chen I. Y., Lypowy J. and Abdellatif M. (2007) MicroRNAs play an essential role in the development of cardiac hypertrophy. Circulation Research 100:416-424.
Schmidt L., Fredsoe J., Kristensen H., Strand S. H., Rasmussen A., Hoyer S., Borre M., Mouritzen P., Orntoft T. and Sorensen K. D. (2018) Training and validation of a novel 4-miRNA ratio model (MiCaP) for prediction of postoperative outcome in prostate cancer patients. Annals of Oncology 29:2003-2009.
Song C., Chen H., Wang T., Zhang W., Ru G. and Lang J. (2015) Expression profile analysis of microRNAs in prostate cancer by next-generation sequencing. Prostate 75:500-516.
Tinay I., Tan M., Gui B., Werner L., Kibel A. S. and Jia L. (2018) Functional roles and potential clinical application of miRNA-345-5p in prostate cancer.Prostate 78:927-937.
Triozzi P. L., Achberger S., Aldrich W., Elson P., Garcia J. and Dreicer R. (2012) Differential immunologic and microRNA effects of 2 dosing regimens of recombinant human granulocyte/macrophage colony stimulating factor. Journal of Immunotherapy 35:587-594.
Urabe F., Matsuzaki J., Yamamoto Y., Kimura T., Hara T., Ichikawa M., Takizawa S., Aoki Y., Niida S., Sakamoto H., Kato K., Egawa S., Fujimoto H. and Ochiya T. (2019) Large-scale circulating microRNA profiling for the liquid biopsy of prostate cancer. Clinical Cancer Research 25:3016-3025.
Valadi H., Ekstrom K., Bossios A., Sjostrand M., Lee J. J. and Lotvall J. O. (2007) Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nature Cell Biology 9:654-659.
Volinia S., Calin G. A., Liu C. G., Ambs S., Cimmino A., Petrocca F., Visone R., Iorio M., Roldo C., Ferracin M., Prueitt R. L., Yanaihara N., Lanza G., Scarpa A., Vecchione A., Negrini M., Harris C. C. and Croce C. M. (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proceedings of the National Academy of Sciences of the United States of America 103:2257-2261.
Wang C., Peng G., Huang H., Liu F., Kong D. P., Dong K. Q., Dai L. H., Zhou Z., Wang K. J., Yang J., Cheng Y. Q., Gao X., Qu M., Wang H. R., Zhu F., Tian Q. Q., Liu D., Cao L., Cui X. G., Xu C. L., Xu D. F. and Sun Y. H. (2018) Blocking the feedback loop between neuroendocrine differentiation and macrophages improves the therapeutic effects of enzalutamide (MDV3100) on prostate cancer. Clinical Cancer Research 24:708-723.
Wang K., Zhang S., Weber J., Baxter D. and Galas D. J. (2010) Export of microRNAs and microRNA-protective protein by mammalian cells. Nucleic Acids Research 38:7248-7259.
Wang S. Y., Shiboski S., Belair C. D., Cooperberg M. R., Simko J. P., Stoppler H., Cowan J., Carroll P. R. and Blelloch R. (2014) miR-19, miR-345, miR-519c-5p serum levels predict adverse pathology in prostate cancer patients eligible for active surveillance. PLoS One 9: e98597.
Wei Y., Yang J., Yi L., Wang Y., Dong Z., Liu Z., Ou-yang S., Wu H., Zhong Z., Yin Z., Zhou K., Gao Y., Yan B. and Wang Z. (2014) MiR-223-3p targeting SEPT6 promotes the biological behavior of prostate cancer. Scientific Reports 4:7546.
Wen Y. C., Lee W. J., Tan P., Yang S. F., Hsiao M., Lee L. M. and Chien M. H. (2015) By inhibiting snail signaling and miR-23a-3p, osthole suppresses the EMT-mediated metastatic ability in prostate cancer. Oncotarget 6:21120-21136.
Yao L., Li Y., Du F., Han X., Li X., Niu Y., Ren S. and Sun Y. (2014) Histone H4 Lys 20 methyltransferase SET8 promotes androgen receptor-mediated transcription activation in prostate cancer. Biochemical and Biophysical Research Communications 450:692-696.
Zhang W., Zang J., Jing X., Sun Z., Yan W., Yang D., Shen B. and Guo F. (2014) Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer. Journal of Translational Medicine 12:66.
Zhou G., Soufan O., Ewald J., Hancock R. E. W., Basu N. and Xia J. (2019) NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis. Nucleic Acids Research 47: W234-W241.
How to Cite
JahandidehM., & BarzegariE. (2020). Identification and Functional Profiling of Differentially Expressed Extracellular Vesicle-free MicroRNAs for Efficient Prostate Cancer Diagnosis. Journal of Cell and Molecular Research, 12(1), 10-21. https://doi.org/10.22067/jcmr.v12i1.87155
Research Articles