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Novel and Alternative Bioinformatics Approaches to Understand miRNA-mRNA Interactome in Cancer Research

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Systems Biology in Cancer Research and Drug Discovery

Abstract

MicroRNAs (miRNAs) are short, non-coding RNAs which play important regulatory roles on target messenger RNAs (mRNAs) that in turn, result into posttranslational repression. This intricate interplay between miRNAs and mRNA plays significant roles in complex diseases such as cancer. In this review we will introduce the role of several miRNAs known to be associated with different human cancers. More importantly, we will outline many existing computational algorithms that predict miRNA targets. These target prediction algorithms can potentially provide valuable data-based information for further experimental validation of meaningful miRNA-mRNA interactomes responsible for serious diseases including cancer.

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Abbreviations

miRNA:

MicroRNA

mRNA:

Messenger RNA

ncRNA:

Non coding RNA

tRNA:

Translational RNA

UTR:

Untranslated region

piRNA:

PIWI interacting RNA

siRNA:

Short interfering RNA

PicTar:

Probabilistic identification of combinations of target sites

IPA:

Ingenuity pathway analysis

RISC:

RNA-induced silencing complex

APC:

Adenomatous polyposis coli gene

SNP:

Single nucleotide polymorphism

DsRNA:

Double stranded RNA

DsRBD:

dsRNA binding domain protein

CBC:

Components of the cap binding complex

ORF:

Open reading frame

AGO:

Argonaut protein

References

  • Adams BD, Furneaux H, White BA (2007) The micro-ribonucleic acid (miRNA) miR-206 targets the human estrogen receptor-{alpha} (ER{alpha}) and represses ER{alpha} messenger RNA and protein expression in breast cancer cell lines. Mol Endocrinol 21:1132–1147

    Article  CAS  PubMed  Google Scholar 

  • Ahnen DJ (2011) The American College of Gastroenterology Emily Couric lecture[mdash]the adenoma-carcinoma sequence revisited: has the era of genetic tailoring finally arrived[quest]. Am J Gastroenterol 106:190–198

    Article  PubMed  Google Scholar 

  • Akao Y, Nakagawa Y, Naoe T (2006) MicroRNAs 143 and 145 are possible common onco-microRNAs in human cancers. Oncol Rep 16:845–850

    CAS  PubMed  Google Scholar 

  • Alexiou P, Maragkakis M, Papadopoulos GL, Reczko M, Hatzigeorgiou AG (2009) Lost in translation: an assessment and perspective for computational microRNA target identification. Bioinformatics 25:3049–3055

    Article  CAS  PubMed  Google Scholar 

  • Ameres SL, Martinez J, Schroeder R (2007) Molecular basis for target RNA recognition and cleavage by human RISC. Cell 130:101–112

    Article  CAS  PubMed  Google Scholar 

  • Aqeilan RI, Calin GA, Croce CM (2009) miR-15a and miR-16-1 in cancer: discovery, function and future perspectives. Cell Death Differ 17:215–220

    Article  PubMed  CAS  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  CAS  PubMed  Google Scholar 

  • Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bartels CL, Tsongalis GJ (2009) MicroRNAs: novel biomarkers for human cancer. Clin Chem 55:623–631

    Article  CAS  PubMed  Google Scholar 

  • Berkhout B, Jeang K-T (2007) RISCy business: microRNAs, pathogenesis, and viruses. J Biol Chem 282:26641–26645

    Article  CAS  PubMed  Google Scholar 

  • Betel D, Wilson M, Gabow A, Marks DS, Sander C (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res 36:D149–D153

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blaxter M (2010) Revealing the dark matter of the genome. Science 330:1758–1759

    Article  CAS  PubMed  Google Scholar 

  • Blenkiron C, Goldstein LD, Thorne NP et al (2007) MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biol 8:R214

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Brabletz S, Brabletz T (2010) The ZEB/miR-200 feedback loop–a motor of cellular plasticity in development and cancer? EMBO Rep 11:670–677

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bracken CP, Gregory PA, Kolesnikoff N et al (2008) A double-negative feedback loop between ZEB1-SIP1 and the microRNA-200 family regulates epithelial-mesenchymal transition. Cancer Res 68:7846–7854

    Article  CAS  PubMed  Google Scholar 

  • Brennecke J, Stark A, Russell RB, Cohen SM (2005) Principles of microRNA-target recognition. PLoS Biol 3:e85

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Brown JR, Sanseau P (2005) A computational view of microRNAs and their targets. Drug Discov Today 10:595–601

    Article  CAS  PubMed  Google Scholar 

  • Brueckner B, Stresemann C, Kuner R et al (2007) The human let-7a-3 locus contains an epigenetically regulated MicroRNA gene with oncogenic function. Cancer Res 67:1419–1423

    Article  CAS  PubMed  Google Scholar 

  • Cagle PT, Allen TC, Dacic S et al (2011) Revolution in lung cancer: new challenges for the surgical pathologist. Arch Pathol Lab Med 135:110–116

    Article  PubMed  Google Scholar 

  • Calin GA, Croce CM (2006) MicroRNA-cancer connection: the beginning of a new tale. Cancer Res 66:7390–7394

    Article  CAS  PubMed  Google Scholar 

  • Calin GA, Dumitru CD, Shimizu M et al (2002) Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci 99:15524–15529

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Catto JWF, Alcaraz A, Bjartell AS et al (2011) MicroRNA in prostate, bladder, and kidney cancer: a systematic review. Eur Urol 59:671–681

    Article  CAS  PubMed  Google Scholar 

  • Chan JA, Krichevsky AM, Kosik KS (2005) MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells. Cancer Res 65:6029–6033

    Article  CAS  PubMed  Google Scholar 

  • Chendrimada TP, Finn KJ, Ji X et al (2007) MicroRNA silencing through RISC recruitment of eIF6. Nature 447:823–828

    Article  CAS  PubMed  Google Scholar 

  • Chin LJ, Ratner E, Leng S et al (2008) A SNP in a let-7 microRNA complementary site in the KRAS 3′ untranslated region increases Non-small cell lung cancer risk. Cancer Res 68:8535–8540

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chou Y-T, Lin H-H, Lien Y-C et al (2010) EGFR promotes lung tumorigenesis by activating miR-7 through a Ras/ERK/Myc pathway that targets the Ets2 transcriptional repressor ERF. Cancer Res 70:8822–8831

    Article  CAS  PubMed  Google Scholar 

  • Cimmino A, Calin GA, Fabbri M et al (2005) miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci 102:13944–13949

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cuellar TL, McManus MT (2005) MicroRNAs and endocrine biology. J Endocrinol 187:327–332

    Article  CAS  PubMed  Google Scholar 

  • Cummins JM, Velculescu VE (2006) Implications of micro-RNA profiling for cancer diagnosis. Oncogene 25:6220–6227

    Article  CAS  PubMed  Google Scholar 

  • Dacic S (2011) Molecular diagnostics of lung carcinomas. Arch Pathol Lab Med 135:622–629

    Article  CAS  PubMed  Google Scholar 

  • Datta S (2001) Exploring relationships in gene expressions: a partial least squares approach. Gene Expr 9:249–255

    Article  CAS  PubMed  Google Scholar 

  • Datta S, Le-Rademacher J, Datta S (2007) Predicting patient survival from microarray data by accelerated failure time modeling using partial least squares and LASSO. Biometrics 63:259–271

    Article  CAS  PubMed  Google Scholar 

  • Davis-Dusenbery BN, Hata A (2010) Mechanisms of control of microRNA biogenesis. J Biochem 148:381–392

    CAS  PubMed  PubMed Central  Google Scholar 

  • Deng N, Puetter A, Zhang K et al (2011) Isoform-level microRNA-155 target prediction using RNA-seq. Nucleic Acids Res 39(9):e61

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Diederichs S, Haber DA (2006) Sequence variations of microRNAs in human cancer: alterations in predicted secondary structure do not affect processing. Cancer Res 66:6097–6104

    Article  CAS  PubMed  Google Scholar 

  • ENCODE (2007) ENCODE, project and consortium: Identification and analysis of functional elements in 1 % of the human genome by the ENCODE pilot project. Nature 447:799–816

    Article  CAS  Google Scholar 

  • Friedman RC, Farh KK-H, Burge CB, Bartel D (2008) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res: gr.082701.082108

    Google Scholar 

  • Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92–105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fukuda T, Yamagata K, Fujiyama S et al (2007) DEAD-box RNA helicase subunits of the Drosha complex are required for processing of rRNA and a subset of microRNAs. Nat Cell Biol 9:604–611

    Article  CAS  PubMed  Google Scholar 

  • Gao W, Shen H, Liu L, Xu J, Xu J, Shu Y (2011a) MiR-21 overexpression in human primary squamous cell lung carcinoma is associated with poor patient prognosis. J Cancer Res Clin Oncol 137:557–566

    Article  CAS  PubMed  Google Scholar 

  • Gao W, Liu L, Lu X, Shu Y (2011b) Circulating microRNAs: possible prediction biomarkers for personalized therapy of non-small-cell lung carcinoma. Clin Lung Cancer 12:14–17

    Article  CAS  PubMed  Google Scholar 

  • Gaur A, Jewell DA, Liang Y et al (2007) Characterization of microRNA expression levels and their biological correlates in human cancer cell lines. Cancer Res 67:2456–2468

    Article  CAS  PubMed  Google Scholar 

  • Giannakakis A, Coukos G, Hatzigeorgiou A, Sandaltzopoulos R, Zhang L (2007) miRNA genetic alterations in human cancers. Expert Opin Biol Ther 7:1375–1386

    Article  CAS  PubMed  Google Scholar 

  • Gong X, Wu R, Wang H et al (2011) Evaluating the consistency of differential expression of microRNA detected in human cancers. Mol Cancer Ther 10:752–760

    Article  CAS  PubMed  Google Scholar 

  • Gramantieri L, Ferracin M, Fornari F et al (2007) Cyclin G1 is a target of miR-122a, a microRNA frequently down-regulated in human hepatocellular carcinoma. Cancer Res 67:6092–6099

    Article  CAS  PubMed  Google Scholar 

  • Gregory RI, K-p Y, Amuthan G et al (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432:235–240

    Article  CAS  PubMed  Google Scholar 

  • Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36:D154–D158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gruber JJ, Zatechka DS, Sabin LR et al (2009) Ars2 links the nuclear cap-binding complex to RNA interference and cell proliferation. Cell 138:328–339

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gusev Y, Schmittgen TD, Lerner M, Postier R, Brackett D (2007) Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer. BMC Bioinform 8 Suppl 7: S16

    Google Scholar 

  • Hammell M, Long D, Zhang L et al (2008) mirWIP: microRNA target prediction based on microRNA-containing ribonucleoprotein-enriched transcripts. Nat Methods 5:813–819

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hammond SM (2005) MicroRNAs as oncogenes. Curr Opin Genet Dev 16:4–9

    Article  PubMed  CAS  Google Scholar 

  • Hayashita Y, Osada H, Tatematsu Y et al (2005) A polycistronic MicroRNA cluster, miR-17-92, is overexpressed in human lung cancers and enhances cell proliferation. Cancer Res 65:9628–9632

    Article  CAS  PubMed  Google Scholar 

  • Heegaard NH, Schetter AJ, Welsh JA, Yoneda M, Bowman ED, Harris CC (2011) Circulating microRNA expression profiles in early stage non-small cell lung cancer. Int J Cancer 130(6):1378–1386

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Heikkinen L, Kolehmainen M, Wong G (2011) Prediction of microRNA targets in Caenorhabditis elegans using a self-organizing map. Bioinformatics 27(9):1247–1254

    Article  CAS  PubMed  Google Scholar 

  • Hinske L, Galante P, Kuo W, Ohno-Machado L (2010) A potential role for intragenic miRNAs on their hosts’ interactome. BMC Genomics 11:533

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hock J, Meister G (2008) The Argonaute protein family. Genome Biol 9:210

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hossain A, Kuo MT, Saunders GF (2006) Mir-17-5p regulates breast cancer cell proliferation by inhibiting translation of AIB1 mRNA. Mol Cell Biol 26:8191–8201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang JC, Babak T, Corson TW et al (2007) Using expression profiling data to identify human microRNA targets. Nat Methods 4:1045–1049

    Article  CAS  PubMed  Google Scholar 

  • Hurteau GJ, Carlson JA, Spivack SD, Brock GJ (2007) Overexpression of the microRNA hsa-miR-200c leads to reduced expression of transcription factor 8 and increased expression of E-cadherin. Cancer Res 67:7972–7976

    Article  CAS  PubMed  Google Scholar 

  • Iorio MV, Ferracin M, Liu C-G et al (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65:7065–7070

    Article  CAS  PubMed  Google Scholar 

  • Izumiya M, Okamoto K, Tsuchiya N, Nakagama H (2010) Functional screening using a microRNA virus library and microarrays: a new high-throughput assay to identify tumor-suppressive microRNAs. Carcinogenesis 31:1354–1359

    Article  CAS  PubMed  Google Scholar 

  • Jemal A, Siegel R, Xu J, Ward E (2010) Cancer statistics, 2010. CA Cancer J Clin: caac.20073

    Google Scholar 

  • Jiang J, Lee EJ, Gusev Y, Schmittgen TD (2005) Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res 33:5394–5403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • John B, Enright AJ, Aravin A, Tuschl T, Sander C, Marks DS (2004) Human microRNA targets. PLoS Biol 2:e363

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Johnson SM, Grosshans H, Shingara J et al (2005) RAS is regulated by the let-7 MicroRNA family. Cell 120:635–647

    Article  CAS  PubMed  Google Scholar 

  • Johnson CD, Esquela-Kerscher A, Stefani G et al (2007) The let-7 microRNA represses cell proliferation pathways in human cells. Cancer Res 67:7713–7722

    Article  CAS  PubMed  Google Scholar 

  • Kanemitsu K, Kawasaki K, Nakamura M et al (2007) MSI is frequently recognized among gastric cancer patients with a family history of cancer. Hepatogastroenterology 54:2410–2414

    PubMed  Google Scholar 

  • Kapranov P, Cheng J, Dike S et al (2007) RNA maps reveal New RNA classes and a possible function for pervasive transcription. Science 316:1484–1488

    Article  CAS  PubMed  Google Scholar 

  • Kapranov P, St Laurent G, Raz T et al (2010) The majority of total nuclear-encoded non-ribosomal RNA in a human cell is ‘dark matter’ un-annotated RNA. BMC Biol 8:149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Katahira J, Yoneda Y (2011) Nucleocytoplasmic transport of microRNAs and related small RNAs. Traffic 12(11):1468–1474

    Article  CAS  PubMed  Google Scholar 

  • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007) The role of site accessibility in microRNA target recognition. Nat Genet 39:1278–1284

    Article  CAS  PubMed  Google Scholar 

  • Kim SK, Nam JW, Rhee JK, Lee WJ, Zhang BT (2006) miTarget: microRNA target gene prediction using a support vector machine. BMC Bioinformatics 7:411

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kohonen T (1995/1997/2001) Self-organizing maps, 3rd edn, Springer series in information sciences, vol. 30. Springer, Berlin/Heidelberg/New York

    Book  Google Scholar 

  • Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39:D152–D157

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Krek A, Grun D, Poy MN et al (2005) Combinatorial microRNA target predictions. Nat Genet 37:495–500

    Article  CAS  PubMed  Google Scholar 

  • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854

    Article  CAS  PubMed  Google Scholar 

  • Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115:787–798

    Article  CAS  PubMed  Google Scholar 

  • Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20

    Article  CAS  PubMed  Google Scholar 

  • Li X, Gill R, Cooper NG, Yoo JK, Datta S (2011) Modeling microRNA-mRNA interactions using PLS regression in human colon cancer. BMC Med Genomics 4:44

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin PY, Yu SL, Yang PC (2010) MicroRNA in lung cancer. Br J Cancer 103:1144–1148

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu X, Sempere LF, Guo Y et al (2011) Involvement of microRNAs in lung cancer biology and therapy. Transl Res 157:200–208

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Long D, Lee R, Williams P, Chan CY, Ambros V, Ding Y (2007) Potent effect of target structure on microRNA function. Nat Struct Mol Biol 14:287–294

    Article  CAS  PubMed  Google Scholar 

  • Lowery AJ, Miller N, McNeill RE, Kerin MJ (2008) MicroRNAs as prognostic indicators and therapeutic targets: potential effect on breast cancer management. Clin Cancer Res 14:360–365

    Article  CAS  PubMed  Google Scholar 

  • Lu Z, Liu M, Stribinskis V et al (2008) MicroRNA-21 promotes cell transformation by targeting the programmed cell death 4 gene. Oncogene 27:4373–4379

    Article  CAS  PubMed  Google Scholar 

  • Lujambio A, Ropero S, Ballestar E et al (2007) Genetic unmasking of an epigenetically silenced microRNA in human cancer cells. Cancer Res 67:1424–1429

    Article  CAS  PubMed  Google Scholar 

  • Mattie MD, Benz CC, Bowers J et al (2006) Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 5:24

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Maziere P, Enright AJ (2007) Prediction of microRNA targets. Drug Discov Today 12:452–458

    Article  CAS  PubMed  Google Scholar 

  • Megraw M, Sethupathy P, Corda B, Hatzigeorgiou AG (2007) miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res 35:D149–D155

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Melo SA, Moutinho C, Ropero S et al (2010) A genetic defect in exportin-5 traps precursor microRNAs in the nucleus of cancer cells. Cancer Cell 18:303–315

    Article  CAS  PubMed  Google Scholar 

  • Meng F, Henson R, Wehbe-Janek H, Ghoshal K, Jacob ST, Patel T (2007) MicroRNA-21 regulates expression of the PTEN tumor suppressor gene in human hepatocellular cancer. Gastroenterology 133:647–658

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miranda KC, Huynh T, Tay Y et al (2006) A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126:1203–1217

    Article  CAS  PubMed  Google Scholar 

  • Muckstein U, Tafer H, Hackermuller J, Bernhart SH, Stadler PF, Hofacker IL (2006) Thermodynamics of RNA-RNA binding. Bioinformatics 22:1177–1182

    Article  PubMed  CAS  Google Scholar 

  • Nagayama K, Kohno T, Sato M, Arai Y, Minna JD, Yokota J (2007) Homozygous deletion scanning of the lung cancer genome at a 100-kb resolution. Genes Chromosomes Cancer 46:1000–1010

    Article  CAS  PubMed  Google Scholar 

  • Nagel R, le Sage C, Diosdado B et al (2008) Regulation of the adenomatous polyposis coli gene by the miR-135 family in colorectal cancer. Cancer Res 68:5795–5802

    Article  CAS  PubMed  Google Scholar 

  • Nguyen DV, Rocke DM (2002) Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 18:39–50

    Article  CAS  PubMed  Google Scholar 

  • Nicoloso MS, Sun H, Spizzo R et al (2010) Single-nucleotide polymorphisms inside MicroRNA target sites influence tumor susceptibility. Cancer Res 70:2789–2798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • O’Day E, Lal A (2010) MicroRNAs and their target gene networks in breast cancer. Breast Cancer Res 12(2):201

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Osada H, Takahashi T (2007) MicroRNAs in biological processes and carcinogenesis. Carcinogenesis 28:2–12

    Article  CAS  PubMed  Google Scholar 

  • Pasquinelli AE, Hunter S, Bracht J (2005) MicroRNAs: a developing story. Curr Opin Genet Dev 15:200–205

    Article  CAS  PubMed  Google Scholar 

  • Peng X, Li Y, Walters KA et al (2009) Computational identification of hepatitis C virus associated microRNA-mRNA regulatory modules in human livers. BMC Genomics 10:373

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pickering BF, Yu D, Van Dyke MW (2011) Nucleolin interacts with the microprocessor complex to affect microRNAs 15a and 16 biogenesis. J Biol Chem 286(51):44095–44103

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pillai RS, Bhattacharyya SN, Filipowicz W (2007) Repression of protein synthesis by miRNAs: how many mechanisms? Trends Cell Biol 17:118–126

    Article  CAS  PubMed  Google Scholar 

  • Porkka KP, Pfeiffer MJ, Waltering KK, Vessella RL, Tammela TLJ, Visakorpi T (2007) MicroRNA expression profiling in prostate cancer. Cancer Res 67:6130–6135

    Article  CAS  PubMed  Google Scholar 

  • Purohit PV, Rocke DM (2003) Discriminant models for high-throughput proteomics mass spectrometer data. Proteomics 3:1699–1703

    Article  CAS  PubMed  Google Scholar 

  • Rabinowits G, Gercel-Taylor C, Day JM, Taylor DD, Kloecker GH (2009) Exosomal microRNA: a diagnostic marker for lung cancer. Clin Lung Cancer 10:42–46

    Article  CAS  PubMed  Google Scholar 

  • Ragan C, Zuker M, Ragan MA (2011) Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations. PLoS Comput Biol 7:e1001090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reinhart BJ, Slack FJ, Basson M et al (2000) The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature 403:901–906

    Article  CAS  PubMed  Google Scholar 

  • Robins H, Li Y, Padgett RW (2005) Incorporating structure to predict microRNA targets. Proc Natl Acad Sci USA 102:4006–4009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ruby JG, Jan C, Player C et al (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193–1207

    Article  CAS  PubMed  Google Scholar 

  • Sachdeva M, Zhu S, Wu F et al (2009) p53 represses c-Myc through induction of the tumor suppressor miR-145. Proc Natl Acad Sci 106:3207–3212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saini HK, Griffiths-Jones S, Enright AJ (2007) Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci 104:17719–17724

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saito M, Schetter AJ, Mollerup S et al (2011) The association of microRNA expression with prognosis and progression in early-stage, non–small cell lung adenocarcinoma: a retrospective analysis of three cohorts. Clin Cancer Res 17:1875–1882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sarver AL, Li L, Subramanian S (2010) MicroRNA miR-183 functions as an oncogene by targeting the transcription factor EGR1 and promoting tumor cell migration. Cancer Res 70:9570–9580

    Article  CAS  PubMed  Google Scholar 

  • Sayed D, Abdellatif M (2011) MicroRNAs in development and disease. Physiol Rev 91:827–887

    Article  CAS  PubMed  Google Scholar 

  • Schepeler T, Reinert JT, Ostenfeld MS et al (2008) Diagnostic and prognostic microRNAs in stage II colon cancer. Cancer Res 68:6416–6424

    Article  CAS  PubMed  Google Scholar 

  • Scott GK, Mattie MD, Berger CE, Benz SC, Benz CC (2006) Rapid alteration of microRNA levels by histone deacetylase inhibition. Cancer Res 66:1277–1281

    Article  CAS  PubMed  Google Scholar 

  • Scott GK, Goga A, Bhaumik D, Berger CE, Sullivan CS, Benz CC (2007) Coordinate suppression of ERBB2 and ERBB3 by enforced expression of micro-RNA miR-125a or miR-125b. J Biol Chem 282:1479–1486

    Article  CAS  PubMed  Google Scholar 

  • Seike M, Goto A, Okano T et al (2009) MiR-21 is an EGFR-regulated anti-apoptotic factor in lung cancer in never-smokers. Proc Natl Acad Sci 106:12085–12090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Selbach M, Schwanhausser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N (2008) Widespread changes in protein synthesis induced by microRNAs. Nature 455:58–63

    Article  CAS  PubMed  Google Scholar 

  • Sempere LF, Christensen M, Silahtaroglu A et al (2007) Altered MicroRNA expression confined to specific epithelial cell subpopulations in breast cancer. Cancer Res 67:11612–11620

    Article  CAS  PubMed  Google Scholar 

  • Sen GL, Blau HM (2006) A brief history of RNAi: the silence of the genes. FASEB J 20:1293–1299

    Article  CAS  PubMed  Google Scholar 

  • Si ML, Zhu S, Wu H, Lu Z, Wu F, Mo YY (2007) miR-21-mediated tumor growth. Oncogene 26:2799–2803

    Article  CAS  PubMed  Google Scholar 

  • Siegel R, Ward E, Brawley O, Jemal A (2011) Cancer statistics, 2011. CA Cancer J Clin 61:212–236

    Article  PubMed  Google Scholar 

  • Suzuki HI, Miyazono K (2011) Emerging complexity of microRNA generation cascades. J Biochem 149:15–25

    Article  CAS  PubMed  Google Scholar 

  • Suzuki HI, Yamagata K, Sugimoto K, Iwamoto T, Kato S, Miyazono K (2009) Modulation of microRNA processing by p53. Nature 460:529–533

    Article  CAS  PubMed  Google Scholar 

  • Taft RJ, Pang KC, Mercer TR, Dinger M, Mattick JS (2010) Non-coding RNAs: regulators of disease. J Pathol 220:126–139

    Article  CAS  PubMed  Google Scholar 

  • Takamizawa J, Konishi H, Yanagisawa K et al (2004) Reduced expression of the let-7 MicroRNAs in human lung cancers in association with shortened postoperative survival. Cancer Res 64:3753–3756

    Article  CAS  PubMed  Google Scholar 

  • Tavazoie SF, Alarcon C, Oskarsson T et al (2008) Endogenous human microRNAs that suppress breast cancer metastasis. Nature 451:147–152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomson JM, Newman M, Parker JS, Morin-Kensicki EM, Wright T, Hammond SM (2006) Extensive post-transcriptional regulation of microRNAs and its implications for cancer. Genes Dev 20:2202–2207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsang WP, Ng EKO, Ng SSM et al (2010) Oncofetal H19-derived miR-675 regulates tumor suppressor RB in human colorectal cancer. Carcinogenesis 31:350–358

    Article  CAS  PubMed  Google Scholar 

  • Tsuchiya N, Izumiya M, Ogata-Kawata H et al (2011) Tumor suppressor miR-22 determines p53-dependent cellular fate through post-transcriptional regulation of p21. Cancer Res 71:4628–4639

    Article  CAS  PubMed  Google Scholar 

  • Tuteja R, Tuteja N (1998) Nucleolin: a multifunctional major nucleolar phosphoprotein. Crit Rev Biochem Mol Biol 33:407–436

    Article  CAS  PubMed  Google Scholar 

  • Vasudevan S, Tong Y, Steitz J (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science 318:1931–1934

    Article  CAS  PubMed  Google Scholar 

  • Verghese ET, Hanby AM, Speirs V, Hughes TA (2008) Small is beautiful: microRNAs and breast cancer-where are we now? J Pathol 215:214–221

    Article  CAS  PubMed  Google Scholar 

  • Volinia S, Calin GA, Liu C-G et al (2006) A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci 103:2257–2261

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang X, El Naqa IM (2008) Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics 24:325–332

    Article  PubMed  CAS  Google Scholar 

  • Wang Y, Juranek S, Li H, Sheng G, Tuschl T, Patel DJ (2008) Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex. Nature 456:921–926

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang R, Wang ZX, Yang JS, Pan X, De W, Chen LB (2011) MicroRNA-451 functions as a tumor suppressor in human non-small cell lung cancer by targeting ras-related protein 14 (RAB14). Oncogene 30:2644–2658

    Article  CAS  PubMed  Google Scholar 

  • Wery M, Kwapisz M, Morillon A (2011) Noncoding RNAs in gene regulation. Wiley Interdiscip Rev Syst Biol Med 3(6):728–738

    Article  CAS  PubMed  Google Scholar 

  • Wickramasinghe N, Manavalan T, Dougherty S, Riggs K, Li Y, Klinge C (2009) Estradiol downregulates miR-21 expression and increases miR-21 target gene expression in MCF-7 breast cancer cells. Nucleic Acids Res 37:2584–2595

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu M, Jolicoeur N, Li Z et al (2008) Genetic variations of microRNAs in human cancer and their effects on the expression of miRNAs. Carcinogenesis 29:1710–1716

    Article  CAS  PubMed  Google Scholar 

  • Wuchty S, Fontana W, Hofacker IL, Schuster P (1999) Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49:145–165

    Article  CAS  PubMed  Google Scholar 

  • Yanaihara N, Caplen N, Bowman E et al (2006) Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9:189–198

    Article  CAS  PubMed  Google Scholar 

  • Yousef M, Jung S, Kossenkov AV, Showe LC, Showe MK (2007) Naive Bayes for microRNA target predictions–machine learning for microRNA targets. Bioinformatics 23:2987–2992

    Article  CAS  PubMed  Google Scholar 

  • Zhang L, Huang J, Yang N et al (2006) microRNAs exhibit high frequency genomic alterations in human cancer. PNAS 103:9136–9141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou Y, Yau C, Gray JW et al (2007) Enhanced NF kappa B and AP-1 transcriptional activity associated with antiestrogen resistant breast cancer. BMC Cancer 7:59

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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Acknowledgements

We would like to thank Dr. Timothy O’Toole for assistance with manuscript preparation. This work was supported by NIH-CA133844 (S. Datta), NIH-R01 CA138410 (C. M. Klinge) and the center grant NIH-P20RR16481.

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Correspondence to Susmita Datta .

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Li, X., Klinge, C.M., Datta, S. (2012). Novel and Alternative Bioinformatics Approaches to Understand miRNA-mRNA Interactome in Cancer Research. In: Azmi, A.S. (eds) Systems Biology in Cancer Research and Drug Discovery. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4819-4_11

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