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. 2016 Mar 31;25(Suppl 1):143–151. doi: 10.1007/s10068-016-0111-x

Data mining of micrornas in breast carcinogenesis which may be a potential target for cancer prevention

Jin-Wook Kang 1,2, Min-Ji Kim 1,2, Hyun-Ah Baek 3, Jeong-Sang Lee 1,2,3,✉
PMCID: PMC6049403  PMID: 30263499

Abstract

The microRNAs (miRNAs) negatively regulate the stability and translation of target messenger RNAs by selectively binding. It has been implicated in diverse processes such as cellular differentiation, cell-cycle control, apoptosis, and carcinogenesis. Examination of tumor-specific miRNA expression profiles has revealed wide spread dysregulation of these molecules in diverse cancers. The available genomic bulk evidences were extracted from The Cancer Genome Atlas by using IluminaGA_miRNASeq platform in human breast cancer samples. After mining collected data, group of each miRNA ID was analyzed through five D/Bs (mirWalk, miranda, mirDB, RNA22, and TargetScan) on predicted and validated miRNA targets. Oncogenes known to have a high correlation with breast cancer (C-myc, HER2, cyclin D-1, N-RAS, FGF-4, FGF-3, BRCA1, and BRCA2) are subject in this study to select their relevant miRNAs. Function of miRNA regulation will be essential to achieve a complete understanding of carcinogenesis and these miRNAs would be potential target for breast cancer prevention.

Keywords: microRNA, breast cancer, data mining, chemoprevention, target

References

  • 1.Graveel CR, Calderone HM, Westerhuis JJ, Winn ME, Sempere LF. Critical analysis of the potential for microRNA biomarkers in breast cancer management. Breast Cancer. 2015;7:59–79. doi: 10.2147/BCTT.S43799. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 2.André F, Cortés J. Rationale for targeting fibroblast growth factor receptor signaling in breast cancer. Breast Cancer Res. Tr. 2015;150:1–8. doi: 10.1007/s10549-015-3301-y. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 3.Rebecca S, Jiemin M, Zhaohui Z, Ahmedin Jemal. Cancer statistics, 2014. CA-Cancer J. Clin. 2014;64:9–29. doi: 10.3322/caac.21208. [DOI] [PubMed] [Google Scholar]
  • 4.Somnay Y, Schneider D, Mazeh H. Thyroid: Medullary carcinoma. Atlas Genet. Cytogenet. Oncol. Haematol. 2013;17:291–296. doi: 10.4267/2042/48876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 5.Zheng ZY, Tian L, Bu W, Fan C, Gao X, Wang H, Liao YH, Li Y, Lewis MT, Edwards D, Zwaka TP, Hilsenbeck SG, Medina D, Perou CM, Creighton CJ, Zhang XH, Chang EC. Wild-type N-Ras, overexpressed in basal-like breast cancer, promotes tumor formation by inducing IL-8 secretion via JAK2 activation. Cell Rep. 2015;12:511–524. doi: 10.1016/j.celrep.2015.06.044. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Chung IF, Chen CY, Su SC, Li CY, Wu KJ, Wang HW, Cheng WC. Nucleic Acids Res. 2015. DriverDBv2: A database for human cancer driver gene research. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Baldin V, Lukas J, Marcote MJ, Pagano M, Draetta G. Cyclin D1 is a nuclear protein required for cell cycle progression in G1. Gene. Dev. 1993;7:812–821. doi: 10.1101/gad.7.5.812. [DOI] [PubMed] [Google Scholar]
  • 8.He Y, Liu Z, Qiao C, Xu M, Yu J, Li G. Expression and significance of Wnt signaling components and their target genes in breast carcinoma. Mol. Med. Rep. 2014;9:137–143. doi: 10.3892/mmr.2013.1774. [DOI] [PubMed] [Google Scholar]
  • 9.Mitri Z, Constantine T, O’Regan R. Chemother. Res. Pract. 2012. The HER2 receptor in breast cancer: Pathophysiology, clinical use, and new advances in therapy; p. 743193. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Lee M, Beggs SM, Gildea D, Bupp S, Lichtenberg J, Trivedi NS, NISC Comperatibe Sequencing Program Necdin is a breast cancer metastasis suppressor that regulates the transcription of c-Myc. Oncotarget. 2015;6:31557–31568. doi: 10.18632/oncotarget.5230. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Welcsh PL, Owens KN, King MC. Insights into the functions of BRCA1 and BRCA2. Trends Genet. 2000;16:69–74. doi: 10.1016/S0168-9525(99)01930-7. [DOI] [PubMed] [Google Scholar]
  • 12.Kuhn DE, Martin MM, Feldman DS, Terry AV, Nuovo GJ, Elton TS. Experimental validation of miRNA targets. Methods. 2008;44:47–54. doi: 10.1016/j.ymeth.2007.09.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Mathe A, Scott RJ, Avery-Kiejda KA. MiRNAs and other epigenetic changes as biomarkers in triple negative breast cancer. Int. J. Mol. Sci. 2015;16:28347–28376. doi: 10.3390/ijms161226090. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Kloosterman WP, Plasterk RH. The diverse functions of microRNAs in animal development and disease. Dev. Cell. 2006;11:441–450. doi: 10.1016/j.devcel.2006.09.009. [DOI] [PubMed] [Google Scholar]
  • 15.Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR. MicroRNA expression profiles classify human cancers. Nature. 2005;435:834–838. doi: 10.1038/nature03702. [DOI] [PubMed] [Google Scholar]
  • 16.Sui X, Wang X, Han W, Li D, Xu Y, Lou F, Zhou J, Gu X, Zhu J, Zhang C, Pan H. MicroRNAs-mediated cell fate in triple negative breast cancers. Cancer Lett. 2015;361:8–12. doi: 10.1016/j.canlet.2015.02.048. [DOI] [PubMed] [Google Scholar]
  • 17.Garnier D, Magnus N, D’Asti E, Hashemi M, Meehan B, Milsom C, Rak J. Genetic pathways linking hemostasis and cancer. Thromb. Res. 2012;129:S22–S29. doi: 10.1016/S0049-3848(12)70012-9. [DOI] [PubMed] [Google Scholar]
  • 18.Motameny S, Wolters S, Nürnberg P, Schumacher B. Next generation sequencing of miRNAs-strategies, resources and methods. Genes. 2010;1:70–84. doi: 10.3390/genes1010070. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.Osanto S, Qin Y, Buermans HP, Berkers J, Lerut E, Goeman JJ, van Poppel H. Genome-wide microRNA expression analysis of clear cell renal cell carcinoma by next generation deep sequencing. PLoS ONE. 2012;7:e38298. doi: 10.1371/journal.pone.0038298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Heneghan HM, Miller N, Kerin MJ. MiRNAs as biomarkers and therapeutic targets in cancer. Curr. Opin. Pharmacol. 2010;10:543–550. doi: 10.1016/j.coph.2010.05.010. [DOI] [PubMed] [Google Scholar]
  • 21.Dweep H, Sticht C, Pandey P, Gretz N. miRWalk-database: P rediction of possible miRNA binding sites by "walking" the genes of three genomes. J. Biomed. Inform. 2011;44:839–847. doi: 10.1016/j.jbi.2011.05.002. [DOI] [PubMed] [Google Scholar]
  • 22.Betel D, Wilson M, Gabow A, Marks DS, Sander C. The microRNA.org resource: Targets and expression. Nucleic Acids Res. 2008;36:D149–D153. doi: 10.1093/nar/gkm995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Wang X. miRDB: A microRNA target prediction and functional annotation database with a wiki interface. RNA. 2008;14:1012–1017. doi: 10.1261/rna.965408. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 24.Loher P, Rigoutsos I. Interactive exploration of RNA22 microRNA target predictions. Bioinformatics. 2012;28:3322–3323. doi: 10.1093/bioinformatics/bts615. [DOI] [PubMed] [Google Scholar]
  • 25.Agarwal V, Bell GW, Nam JW, Bartel DP. Predicting effective microRNA target sites in mammalian mRNAs. Elife. 2015;4:e05005. doi: 10.7554/eLife.05005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Witkos TM, Koscianska E, Krzyzosiak WJ. Practical aspects of microRNA target prediction. Curr. Mol. Med. 2011;11:93–109. doi: 10.2174/156652411794859250. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Alvarez-Garcia I, Eric EA. MicroRNA functions in animal development and human disease. Development. 2005;132:4653–4662. doi: 10.1242/dev.02073. [DOI] [PubMed] [Google Scholar]
  • 28.Kuhn DE, Martin MM, Feldman DS, Terry Jr A, Nuovo GJ, Elton TS. Experimental validation of miRNA targets. Methods. 2008;44:47–54. doi: 10.1016/j.ymeth.2007.09.005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 29.Soifer HS, Rossi JJ, Sætrom P. MicroRNAs in disease and potential therapeutic applications. Mol. Thet. 2007;15:2070–2079. doi: 10.1038/sj.mt.6300311. [DOI] [PubMed] [Google Scholar]
  • 30.Choi SW, Friso S. Epigenetics: A new bridge between nutrition and health. Adv. Nutr. 2010;1:8–16. doi: 10.3945/an.110.1004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Landecker H. Food as exposure: Nutritional epigenetics and the new metabolism. Biosocieties. 2011;6:167–194. doi: 10.1057/biosoc.2011.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Paul B, Barnes S, Demark-Wahnefried W, Morrow C, Salvador C, Skibola C, Tollefsbol TO. Influences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases. Clin. Epigenetics. 2015;7:112. doi: 10.1186/s13148-015-0144-7. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Mishra PJ. MicroRNAs as promising biomarkers in cancer diagnostics. Biomark. Res. 2014;2:19. doi: 10.1186/2050-7771-2-19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Ali MA, Mozhgan MN. The role of microRNAs in human diseases. Avicenna J. Med. Biotechnol. 2010;2:161–180. [PMC free article] [PubMed] [Google Scholar]
  • 35.Garzon R, Pichiorri F, Palumbo T, Visentini M, Aqeilan R, Cimmino A, Wang H, Sun H, Volinia S, Alder H, Calin GA, Liu CG, Andreeff M, Croce CM. MicroRNA gene expression during retinoic acid-induced differentiation of human acute promyelocytic leukemia. Oncogene. 2007;26:4148–4157. doi: 10.1038/sj.onc.1210186. [DOI] [PubMed] [Google Scholar]
  • 36.Marsit CJ, Eddy K, Kelsey KT. MicroRNA responses to cellular stress. Cancer Res. 2006;66:10843–10848. doi: 10.1158/0008-5472.CAN-06-1894. [DOI] [PubMed] [Google Scholar]
  • 37.Mudduluru G, George-William JN, Muppala S, Asangani IA, Kumarswamy R, Nelson LD, Allgayer H. Curcumin regulates miR-21 expression and inhibits invasion and metastasis in colorectal cancer. Biosci. Rep. 2011;3:185–197. doi: 10.1042/BSR20100065. [DOI] [PubMed] [Google Scholar]
  • 38.Dhar S, Hicks C, Levenson AS. Resveratrol and prostate cancer: Promising role for microRNAs. Mol. Nutr. Food Res. 2011;55:1219–1229. doi: 10.1002/mnfr.201100141. [DOI] [PubMed] [Google Scholar]
  • 39.Li Y, Vandenboom T 2, Wang Z, Kong D, Ali S, Philip PA, Sarkar FH. miR-146a suppresses invasion of pancreatic cancer cells. Cancer Res. 2010;70:1486–1495. doi: 10.1158/0008-5472.CAN-09-2792. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 40.Zhang L, Hou D, Chen X, Li D, Zhu L, Zhang Y, Li J, Bian Z, Liang X, Cai X, Yin Y, Wang C, Zhang T, Zhu D, Zhang D, Xu J, Chen Q, Ba Y, Liu J, Wang Q, Chen J, Wang J, Wang M, Zhang Q, Zhang J, Zen K, Zhang CY. Exogenous plant MIR168a specifically targets mammalian LDLRAP1: Evidence of cross-kingdom regulation by microRNA. Cell Res. 2012;22:107–126. doi: 10.1038/cr.2011.158. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 41.Philip A, Ferro VA, Tate RJ. Determination of the potential bioavailability of plant microRNAs using a simulated human digestion process. Mol. Nutr. Food Res. 2015;59:1962–1972. doi: 10.1002/mnfr.201500137. [DOI] [PubMed] [Google Scholar]

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