In silico Meta-Analysis of Circulatory microRNAs in Prostate Cancer


  • Anshika N. Singh Symbiosis School of Biomedical Sciences, Symbiosis International University, Gram- Lavale, Taluka- Mulshi, Pune, India
  • Neeti Sharma Symbiosis School of Biomedical Sciences, Symbiosis International University, Gram- Lavale, Taluka- Mulshi, Pune, India



Prostate Cancer, microRNA, Target prediction, Cancer hallmarks.


 Circulatory microRNAs (miRNAs) have emerged as a new class of non coding RNA molecules which regulate many crucial molecular and biological processes. We have aimed to shed light on the roles of circulatory miRNAs in Prostate Cancer (PCa) using an integrative in silico bioinformatics approach. We have described a new protocol for target prediction and functional analysis which was applied to 40 highly differentially dysregulatedcirculatory miRNAs in PCa. This framework comprises: (i) evidence of involvement of these circulatory miRNAs from previous literature and microarray analysis (ii) overlap of prediction results by target prediction tools, including miRTarBase, miRDB, DIANA- microT 4.0 and TargetScan (combining computational learning, alignment, interaction energy and statistical tests for minimization of false positives), (iii) gene ontology (GO) along with pathway enrichment analysis of the miRNA targets and their pathways and (iv) linking these pathways to oncogenesis and cancer hallmarks. More than 200 target genes and 40 regulatory pathways were retrieved and analysed which was followed by associating their roles with cancer hallmark processes. Wnt signalling, Cell cycle, MAPK signalling, Cadherin signalling, Integrin signalling and Ras pathways were some of the identified regulatory pathways during bioinformatics analysis. These signalling and developmental pathways crosstalk and regulate stem cell renewal thus indicating a definite role of circulatory miRNAs in PCa development. Our study identified miR-181, miR-9, Let-7 family, miR-26b circulatory miRNAs, to be contributing majorly in the oncogenic pathways, thus proposing their role as potential biomarkers in PCa initiation and progression.


Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116(2): 281-297.

Singh, AN, Khandwekar AP, & Sharma N. Cancer Stem-Cell Related miRNAs: Novel Potential Targets for Metastatic PCa. Journal of Analytical Oncology 2015; 4(4): 146-156.

Kosaka N, Iguchi H, & Ochiya T. Circulating microRNA in body fluid: a new potential biomarker for cancer diagnosis and prognosis. Cancer Science 2010; 101(10): 2087-2092.

Qiu C, Chen G, & Cui Q. Towards the understanding of microRNA and environmental factor interactions and their relationships to human diseases. Scientific Reports 2012; 2.

Wang WT, Chen YQ. Circulating miRNAs in cancer: from detection to therapy. Journal of hematology & oncology 2014; 7(1): 86.

Peng Y, Croce CM. The role of MicroRNAs in human cancer. Signal Transduction and Targeted Therapy 2016; 1: 15004.

Sita-Lumsden A, Dart DA, Waxman J, & Bevan CL. Circulating microRNAs as potential new biomarkers for PCa. British journal of cancer 2013; 108(10): 1925-1930.

Mendes ND, Freitas AT, & Sagot MF. Current tools for the identification of miRNA genes and their targets. Nucleic acids research 2009; 37(8): 2419-2433.

Watanabe Y, Tomita M, & Kanai A. Computational methods for microRNA target prediction. Methods in enzymology 2007; 427: 65-86.

Min H, & Yoon S. Got target?: computational methods for microRNA target prediction and their extension. Experimental & molecular medicine 2010; 42(4): 233-244.

Rahman ME, Islam R, Islam S, Mondal SI, Amin MR. MiRANN: a reliable approach for improved classification of precursor microRNA using Artificial Neural Network model. Genomics 2012; 99(4): 189-194.

Jiang Q, Wang G, Jin S, Li Y, Wang Y. Predicting human microRNA-disease associations based on support vector machine. International journal of data mining and bioinformatics 2013; 8(3): 282-293.

Paller CJ, & Antonarakis ES. Management of biochemically recurrent PCa after local therapy: evolving standards of care and new directions. Clinical advances in hematology & oncology: H&O 2013; 11(1): 14.

Loeb S, Bjurlin MA, Nicholson J, et al. Overdiagnosis and over-treatment of PCa. European urology 2014; 65(6): 1046-1055.

Yu DC, Li QG, Ding XW, & Ding YT. Circulating microRNAs: potential biomarkers for cancer. International journal of molecular sciences 2011; 12(3): 2055-2063.

Srivastava A, Suy S, Collins SP, & Kumar D. Circulating MicroRNA as biomarkers: An update in PCa. Molecular and cellular pharmacology 2011; 3(3): 115.

Russo F, Di Bella S, Nigita G, et al. miRandola: extracellular circulating microRNAs database. PloS one 2012; 7(10): e47786.

Xie B, Ding Q, Han H, et al. miRCancer: a microRNA-cancer association database constructed by text mining on literature. Bioinformatics. 2013; btt014.

Li Y, Qiu C, Tu J, et al. HMDD v2. 0: a database for experimentally supported human microRNA and disease associations. Nucleic acids research 2013; gkt1023.

Chou CH, Chang NW, Shrestha S, Hsu SD, Lin YL, Lee WH. miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. Nucleic acids research 2016; 44(D1): D239-D247.

Wong N, Wang X. miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic acids research 2014; gku1104.

Maragkakis M, Vergoulis T, Alexiou P, et al. DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. Nucleic acids research 2011; 39(suppl 2): W145-W148.

Agarwal V, Bell GW, Nam J, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. eLife 2015; 4:e05005.

Mi H, Poudel S, Muruganujan A, Casagrande JT, Thomas PD. PANTHER version 10: expanded protein families and functions, and analysis tools. Nucleic acids research 2016; 44(D1): D336-D342.

Tabas-Madrid D, Nogales-Cadenas R, Pascual-Montano A. GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. Nucleic acids research 2012; 40(W1): W478-W483.

Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic acids research 2010; 38(suppl 1): D355-D360.

Croft D, O’Kelly G, Wu G, et al. Reactome: a database of reactions, pathways and biological processes. Nucleic acids research 2010; gkq1018.

Chen ZH, Zhang GL, Li HR, et al. A panel of five circulating microRNAs as potential biomarkers for PCa. Prostate 2012; 72(13): 1443-1452.

Ryant RJ, Pawlowski T, Catto JW, et al. Changes in circulating microRNA levels associated with PCa. Br J Cancer 2012; 106(4): 768-774.

Agaoglu FY, Kovancilar M, Dizdar Y, et al. Investigation of miR-21, miR-141, and miR-221 in blood circulation of patients with PCa. Tumor Biology 2011; 32(3): 583-588.

Shen J, Hruby GW, McKiernan JM, et al. Dysregulation of circulating microRNAs and prediction of aggressive PCa. Prostate 2012; 72(13): 1469-1477.

Selth LA, Townley S, Gillis JL, et al. Discovery of circulating microRNAs associated with human PCa using a mouse model of disease. Int J Cancer 2012; 131(3): 652-661.

Moltzahn F, Olshen AB, Baehner L, et al. Microfluidic-based multiplex qRTPCR identifies diagnostic and prognostic microRNA signatures in the sera of PCa patients. Cancer Res 2011; 71(2): 550-560.

Mahn R, Heukamp LC, Rogenhofer S, von Ruecker A, Muller SC, Ellinger J. Circulating microRNAs (miRNA) in serum of patients with PCa. Urology 2011; 77(5): 1265, e9-e16.

Brase JC, Johannes M, Schlomm T, Falth M, et al. Circulating miRNAs are correlated with tumor progression in PCa. Int J Cancer 2011; 128(3): 608-616.

Mitchell PS, Parkin RK, Kroh EM, et al. Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 2008; 105(30): 10513-10518.

Lodes MJ, Caraballo M, Suciu D, Munro S, Kumar A, Anderson B. Detection of cancer with serum miRNAs on an oligonucleotide microarray. PLoS One 2009; 4(7): e6229.

Baruah MM, Khandwekar AP, & Sharma N. Quercetin modulates Wnt signalling components in PCa cell line by inhibiting cell viability, migration, and metastases. Tumor Biology 2016; 37(10): 14025-14034.

MacDonald BT, Tamai K, & He X. Wnt/β-catenin signaling: components, mechanisms, and diseases. Developmental cell 2009; 17(1): 9-26.

De Ferrari GV, Moon RT. The ups and downs of Wnt signaling in prevalent neurological disorders. Oncogene 2006; 25(57): 7545-7553.

Ling XH, Chen ZY, Luo HW, et al. BCL9, a coactivator for Wnt/β-catenin transcription, is targeted by miR 30c and is associated with PCa progression. Oncology letters 2016; 11(3): 2001-2008.

Verras M, Sun, Z. Roles and regulation of Wnt signaling and β-catenin in PCa. Cancer letters 2006; 237(1): 22-32.

Lu W, Tinsley HN, Keeton A, Qu Z, Piazza GA, Li Y. Suppression of Wnt/β-catenin signaling inhibits PCa cell proliferation. European journal of pharmacology 2009; 602(1): 8-14.

Bisson I, Prowse DM. WNT signaling regulates self-renewal and differentiation of PCa cells with stem cell characteristics. Cell research 2009; 19(6): 683-697.

Sun J, Yan P, Chen Y, et al. MicroRNA-26b inhibits cell proliferation and cytokine secretion in human RASF cells via the Wnt/GSK-3β/β-catenin pathway.Diagnostic pathology 2015; 10(1): 1.

Saydam O, Shen Y, Würdinger T. et al. Downregulated microRNA-200a in meningiomas promotes tumor growth by reducing E-cadherin and activating the Wnt/β-catenin signaling pathway. Molecular and cellular biology 2009; 29(21): 5923-5940.

Lindsey S & Langhans SA. Crosstalk of oncogenic signaling pathways during epithelial-mesenchymal transition. Cellular and Phenotypic Plasticity in Cancer 2015; 8.

Wang X, Wang K, Han L, et al. PRDM1 is directly targeted by miR-30a-5p and modulates the Wnt/β-catenin pathway in a Dkk1-dependent manner during glioma growth. Cancer letters 2013; 331(2): 211-219.

Maeda M, Johnson KR, Wheelock MJ. Cadherin switching: essential for behavioral but not morphological changes during an epithelium-to-mesenchyme transition. J Cell Sci 2005; 118(5): 873-887.

Heuberger J, Birchmeier W. Interplay of cadherin-mediated cell adhesion and canonical Wnt signaling. Cold Spring Harbor perspectives in biology 2010; 2(2): a002915.

Wong TS, Gao W, Chan JYW. Interactions between E-Cadherin and MicroRNA Deregulation in Head and Neck Cancers: The Potential Interplay. BioMed research international 2014; 126038.

Romero-Pérez L, López-García MÁ, Díaz-Martín J, et al. ZEB1 overexpression associated with E-cadherin and microRNA-200 downregulation is characteristic of undifferentiated endometrial carcinoma. Modern Pathology 2013; 26(11): 1514-1524.

Ma L, Young J, Prabhala H, et al. miR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis. Nature cell biology 2010; 12(3): 247-256.

Nishida N, Yano H, Nishida T, Kamura T, Kojiro M. Angiogenesis in cancer. Vascular health and risk management 2006; 2(3): 213.

Carmeliet P, & Jain RK. Angiogenesis in cancer and other diseases. Nature 2000; 407(6801): 249-257.

Folkman J. Angiogenesis in cancer, vascular, rheumatoid and other disease. Nature medicine 1995; 1(1): 27-30.

Wang S, & Olson EN. AngiomiRs—key regulators of angiogenesis. Current opinion in genetics & development 2009; 19(3): 205-211.

Kuehbacher A, Urbich C, & Dimmeler S. Targeting microRNA expression to regulate angiogenesis. Trends in pharmacological sciences 2008; 29(1): 12-15.

Derynck R, Akhurst RJ, & Balmain A. TGF-β signaling in tumor suppression and cancer progression. Nature genetics 2001; 29(2): 117-129.

Wakefield LM, & Roberts AB. TGF-β signaling: positive and negative effects on tumorigenesis. Current opinion in genetics & development 2002; 12(1): 22-29.

Buck MB, & Knabbe C. TGF‐Beta Signaling in Breast Cancer. Annals of the New York Academy of Sciences 2006; 1089(1): 119-126.

Cao Z, & Kyprianou N. Mechanisms navigating the TGF-β pathway in PCa. Asian Journal of Urology 2015; 2(1): 11-18.

Katz LH, Li Y, Chen JS, et al. Targeting TGF-β signaling in cancer. Expert opinion on therapeutic targets 2013; 17(7): 743-760.

Taylor MA, Sossey-Alaoui K, Thompson CL, Danielpour D, & Schiemann WP. TGF-β upregulates miR-181a expression to promote breast cancer metastasis. The Journal of clinical investigation 2013; 123(1): 150-163.

Kim YJ, Hwang SJ, Bae YC, & Jung JS. MiR‐21 Regulates Adipogenic Differentiation through the Modulation of TGF‐β Signaling in Mesenchymal Stem Cells Derived from Human Adipose Tissue. Stem cells 2009; 27(12): 3093-3102.

Gregory PA, Bracken CP, Smith E, et al. An autocrine TGF-β/ZEB/miR-200 signaling network regulates establishment and maintenance of epithelial-mesenchymal transition. Molecular biology of the cell 2011; 22(10): 1686-1698.

Varner JA, & Cheresh DA. Integrins and cancer. Current opinion in cell biology 1996; 8(5): 724-730.

Desgrosellier JS, & Cheresh DA. Integrins in cancer: biological implications and therapeutic opportunities. Nature Reviews Cancer 2010; 10(1): 9-22.

Chen W, Harbeck MC, Zhang W, & Jacobson JR. MicroRNA regulation of integrins. Translational Research 2013; 162(3): 133-143.

Bertoli G, Cava C, & Castiglioni I. MicroRNAs as Biomarkers for Diagnosis, Prognosis and Theranostics in PCa. International journal of molecular sciences 2016; 17(3): 421.

Di Lorenzo G, Tortora G, D’Armiento FP, et al. Expression of epidermal growth factor receptor correlates with disease relapse and progression to androgen-independence in human PCa. Clinical Cancer Research 2002; 8(11): 3438-3444.

Marks RA, Zhang S, Montironi R, et al. Epidermal growth factor receptor (EGFR) expression in prostatic adenocarcinoma after hormonal therapy: a fluorescence in situ hybridization and immunohistochemical analysis. The Prostate 2008; 68(9): 919-923.

Seshacharyulu P, Ponnusamy MP, Haridas D, Jain M, Ganti AK., Batra SK. Targeting the EGFR signaling pathway in cancer therapy. Expert opinion on therapeutic targets 2012; 16(1): 15-31.

Huang Y, & Chang Y. Epidermal growth factor receptor (EGFR) phosphorylation, signaling and trafficking in PCa. INTECH Open Access Publisher; 2011.

Wang F, Chan LW, Law HK, et al. Exploring microRNA-mediated alteration of EGFR signaling pathway in non-small cell lung cancer using an mRNA: miRNA regression model supported by target prediction databases. Genomics 2014; 104(6): 504-511.

Han F, He J, Li F, et al. Emerging roles of microRNAs in EGFR-targeted therapies for lung cancer. BioMed research international 2015; 672759.

Uhlmann S, Mannsperger H, Zhang JD, et al. Global microRNA level regulation of EGFR‐driven cell‐cycle protein network in breast cancer.Molecular systems biology 2012; 8(1): 570.

Gomez GG, Wykosky J, Zanca C, Furnari FB, & Cavenee WK. Therapeutic resistance in cancer: microRNA regulation of EGFR signaling networks. Cancer biology & medicine 2013; 10(4): 192-205.

Jechlinger M, Sommer A, Moriggl R, et al. Autocrine PDGFR signaling promotes mammary cancer metastasis. The Journal of clinical investigation 2006; 116(6): 1561-1570.

Raica M, Cimpean AM. Platelet-derived growth factor (PDGF)/PDGF receptors (PDGFR) axis as target for antitumor and antiangiogenic therapy.Pharmaceuticals 2010; 3(3): 572-599.

Heldin CH. Targeting the PDGF signaling pathway in tumor treatment. Cell Communication and Signalling 2013; 11(1): 1.

Peng Y, Guo JJ, Liu YM, Wu XL. MicroRNA-34A inhibits the growth, invasion and metastasis of gastric cancer by targeting PDGFR and MET expression. Bioscience reports 2014; 34(3): e00112.

Kong D, Li Y, Wang Z, et al. miR‐200 Regulates PDGF‐D‐Mediated Epithelial-Mesenchymal Transition, Adhesion, and Invasion of PCa Cells. Stem cells 2009; 27(8): 1712-1721.




How to Cite

Anshika N. Singh, & Neeti Sharma. (2017). In silico Meta-Analysis of Circulatory microRNAs in Prostate Cancer. Journal of Analytical Oncology, 6(2), 107–116.