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MicroRNA (miRNA) Profiling

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Cancer Gene Profiling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1381))

Abstract

MicroRNAs (miRNAs) are small, highly conserved noncoding RNA molecules involved in the regulation of gene expression. Since each miRNA regulates the expression of hundreds of target mRNAs, miRNAs could function as master coordinators, efficiently regulating fundamental cellular processes, including proliferation, apoptosis, and development. Furthermore, miRNAs may provide useful diagnostic and therapeutic targets in a variety of diseases. However, miRNA expression profiling is essential for the investigation of the biological functions and clinical applications of miRNAs. Therefore, in this chapter, we review and discuss commonly used techniques for miRNAs profiling, as well as their advantages and restrictions.

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References

  1. Lee RC, Ambros V (2001) An extensive class of small RNAs in Caenorhabditis elegans. Science 294:862–864

    Article  CAS  PubMed  Google Scholar 

  2. Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T (2002) Identification of tissue-specific microRNAs from mouse. Curr Biol 12:735–739

    Article  CAS  PubMed  Google Scholar 

  3. Sunkar R, Girke T, Jain PK, Zhu JK (2005) Cloning and characterization of microRNAs from rice. Plant Cell 17:1397–1411

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  4. Lai EC, Tomancak P, Williams RW, Rubin GM (2003) Computational identification of Drosophila microRNA genes. Genome Biol 4:R42

    Article  PubMed Central  PubMed  Google Scholar 

  5. Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799

    Article  CAS  PubMed  Google Scholar 

  6. Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J (2003) Computational and experimental identification of C. elegans microRNAs. Mol Cell 11:1253–1263

    Article  CAS  PubMed  Google Scholar 

  7. Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP (2003) The microRNAs of Caenorhabditis elegans. Genes Dev 17:991–1008

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  8. Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP (2003) Vertebrate microRNA genes. Science 299:1540

    Article  CAS  PubMed  Google Scholar 

  9. Mendes ND, Freitas AT, Sagot MF (2009) Current tools for the identification of miRNA genes and their targets. Nucleic Acids Res 37:2419–2433

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33, e179

    Article  PubMed Central  PubMed  Google Scholar 

  11. Yu Z, Zhu Y, Zhang Y, Li J, Fang Q, Xi J, Yao B (2011) Nanoliter droplet array for microRNA detection based on enzymatic stem-loop probes ligation and SYBR Green real-time PCR. Talanta 85:1760–1765

    Article  CAS  PubMed  Google Scholar 

  12. Rajwanshi VK, Hakansson AE, Sorensen MD, Pitsch S, Singh SK, Kumar R, Nielsen P, Wengel J (2000) The eight stereoisomers of LNA (locked nucleic acid): A remarkable family of strong RNA binding molecules. We acknowledge the Danish Natural Science Research Council, the Danish Technical Research Council, and Exiqon A/S for financial support. Ms Britta M. Dahl is thanked for oligonucleotide synthesis, Dr. Carl E. Olsen for MALDI-MS analysis, and Ms. Karen Jorgensen for recording CD spectra. Angew Chem Int Ed Engl 39:1656–1659

    Article  CAS  PubMed  Google Scholar 

  13. Lin SL, Chang D, Ying SY (2005) Asymmetry of intronic pre-miRNA structures in functional RISC assembly. Gene 356:32–38

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  14. Zhou S, Liu M, An W, Liang X, Yu W, Piao F (2014) A new method for analyzing the Duffy blood group genotype by TaqMan minor groove binding probes. J Clin Lab Anal 29(3):203–207

    Article  PubMed  Google Scholar 

  15. 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  PubMed Central  CAS  PubMed  Google Scholar 

  16. Liu CG, Calin GA, Volinia S, Croce CM (2008) MicroRNA expression profiling using microarrays. Nat Protoc 3:563–578

    Article  CAS  PubMed  Google Scholar 

  17. Xu G, Chen J, Pan Q, Huang K, Pan J, Zhang W, Yu F, Zhou T, Wang Y (2014) Long noncoding RNA expression profiles of lung adenocarcinoma ascertained by microarray analysis. PLoS One 9, e104044

    Article  PubMed Central  PubMed  Google Scholar 

  18. Liu CG, Calin GA, Meloon B, Gamliel N, Sevignani C, Ferracin M, Dumitru CD, Shimizu M, Zupo S, Dono M, Alder H, Bullrich F, Negrini M, Croce CM (2004) An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci U S A 101:9740–9744

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Dee S, Getts RC (2012) MicroRNA expression analysis using the Affymetrix Platform. Methods Mol Biol 822:117–129

    Article  CAS  PubMed  Google Scholar 

  20. D’Andrade PN, Fulmer-Smentek S (2012) Agilent microRNA microarray profiling system. Methods Mol Biol 822:85–102

    Article  PubMed  Google Scholar 

  21. Tsao J, Yau P, Winegarden N (2010) Profiling microRNA expression with the Illumina BeadChip platform. Methods Mol Biol 632:73–86

    Article  CAS  PubMed  Google Scholar 

  22. Shen J, Jiang F (2012) Applications of MicroRNAs in the diagnosis and prognosis of lung cancer. Expert Opin Med Diagn 6:197–207

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Sanger F, Air GM, Barrell BG, Brown NL, Coulson AR, Fiddes CA, Hutchison CA, Slocombe PM, Smith M (1977) Nucleotide sequence of bacteriophage phi X174 DNA. Nature 265:687–695

    Article  CAS  PubMed  Google Scholar 

  24. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer ML, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    PubMed Central  CAS  PubMed  Google Scholar 

  25. Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C (2010) Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 16:991–1006

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Schee K, Lorenz S, Worren MM, Gunther CC, Holden M, Hovig E, Fodstad O, Meza-Zepeda LA, Flatmark K (2013) Deep sequencing the MicroRNA transcriptome in colorectal cancer. PLoS One 8, e66165

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Hu Z, Chen X, Zhao Y, Tian T, Jin G, Shu Y, Chen Y, Xu L, Zen K, Zhang C, Shen H (2010) Serum microRNA signatures identified in a genome-wide serum microRNA expression profiling predict survival of non-small-cell lung cancer. J Clin Oncol 28:1721–1726

    Article  PubMed  Google Scholar 

  28. Keller A, Backes C, Leidinger P, Kefer N, Boisguerin V, Barbacioru C, Vogel B, Matzas M, Huwer H, Katus HA, Stahler C, Meder B, Meese E (2011) Next-generation sequencing identifies novel microRNAs in peripheral blood of lung cancer patients. Mol Biosyst 7:3187–3199

    Article  CAS  PubMed  Google Scholar 

  29. Ma J, Mannoor K, Gao L, Tan A, Guarnera MA, Zhan M, Shetty A, Stass SA, Xing L, Jiang F (2014) Characterization of microRNA transcriptome in lung cancer by next-generation deep sequencing. Mol Oncol 8:1208–1219

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  30. Ekblom R, Slate J, Horsburgh GJ, Birkhead T, Burke T (2012) Comparison between normalised and unnormalised 454-sequencing libraries for small-scale RNA-Seq studies. Comp Funct Genomics 2012:281693

    Article  PubMed Central  PubMed  Google Scholar 

  31. Bentley DR (2006) Whole-genome re-sequencing. Curr Opin Genet Dev 16:545–552

    Article  CAS  PubMed  Google Scholar 

  32. Li S, Wang H, Qi Y, Tu J, Bai Y, Tian T, Huang N, Wang Y, Xiong F, Lu Z, Xiao Z (2011) Assessment of nanomaterial cytotoxicity with SOLiD sequencing-based microRNA expression profiling. Biomaterials 32:9021–9030

    Article  CAS  PubMed  Google Scholar 

  33. Shen J, Stass SA, Jiang F (2013) MicroRNAs as potential biomarkers in human solid tumors. Cancer Lett 329:125–136

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  34. Shen J, Liu Z, Todd NW, Zhang H, Liao J, Yu L, Guarnera MA, Li R, Cai L, Zhan M, Jiang F (2011) Diagnosis of lung cancer in individuals with solitary pulmonary nodules by plasma microRNA biomarkers. BMC Cancer 11:374

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  35. Shen J, Todd NW, Zhang H, Yu L, Lingxiao X, Mei Y, Guarnera M, Liao J, Chou A, Lu CL, Jiang Z, Fang H, Katz RL, Jiang F (2011) Plasma microRNAs as potential biomarkers for non-small-cell lung cancer. Lab Invest 91:579–587

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Dodd DW, Gagnon KT, Corey DR (2013) Digital quantitation of potential therapeutic target RNAs. Nucleic Acid Ther 23:188–194

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  37. Whale AS, Huggett JF, Cowen S, Speirs V, Shaw J, Ellison S, Foy CA, Scott DJ (2012) Comparison of microfluidic digital PCR and conventional quantitative PCR for measuring copy number variation. Nucleic Acids Res 40, e82

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  38. Warren L, Bryder D, Weissman IL, Quake SR (2006) Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR. Proc Natl Acad Sci U S A 103:17807–17812

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  39. Chen X, Ba Y, Ma L, Cai X, Yin Y, Wang K, Guo J, Zhang Y, Chen J, Guo X, Li Q, Li X, Wang W, Wang J, Jiang X, Xiang Y, Xu C, Zheng P, Zhang J, Li R, Zhang H, Shang X, Gong T, Ning G, Zen K, Zhang CY (2008) Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 18:997–1006

    Article  CAS  PubMed  Google Scholar 

  40. Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O’Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 105:10513–10518

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  41. Pritchard CC, Kroh E, Wood B, Arroyo JD, Dougherty KJ, Miyaji MM, Tait JF, Tewari M (2012) Blood cell origin of circulating microRNAs: a cautionary note for cancer biomarker studies. Cancer Prev Res (Phila) 5:492–497

    Article  CAS  Google Scholar 

  42. Bhat S, Herrmann J, Armishaw P, Corbisier P, Emslie KR (2009) Single molecule detection in nanofluidic digital array enables accurate measurement of DNA copy number. Anal Bioanal Chem 394:457–467

    Article  CAS  PubMed  Google Scholar 

  43. Kiss MM, Ortoleva-Donnelly L, Beer NR, Warner J, Bailey CG, Colston BW, Rothberg JM, Link DR, Leamon JH (2008) High-throughput quantitative polymerase chain reaction in picoliter droplets. Anal Chem 80:8975–8981

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  44. Kreutz JE, Munson T, Huynh T, Shen F, Du W, Ismagilov RF (2011) Theoretical design and analysis of multivolume digital assays with wide dynamic range validated experimentally with microfluidic digital PCR. Anal Chem 83:8158–8168

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  45. Pinheiro LB, Coleman VA, Hindson CM, Herrmann J, Hindson BJ, Bhat S, Emslie KR (2012) Evaluation of a droplet digital polymerase chain reaction format for DNA copy number quantification. Anal Chem 84:1003–1011

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Pohl G, Shih Ie M (2004) Principle and applications of digital PCR. Expert Rev Mol Diagn 4:41–47

    Article  CAS  PubMed  Google Scholar 

  47. Vogelstein B, Kinzler KW (1999) Digital PCR. Proc Natl Acad Sci U S A 96:9236–9241

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  48. Hayden RT, Gu Z, Ingersoll J, Abdul-Ali D, Shi L, Pounds S, Caliendo AM (2013) Comparison of droplet digital PCR to real-time PCR for quantitative detection of cytomegalovirus. J Clin Microbiol 51:540–546

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  49. Day E, Dear PH, McCaughan F (2013) Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine. Methods 59:101–107

    Article  CAS  PubMed  Google Scholar 

  50. Diehl F, Diaz LA Jr (2007) Digital quantification of mutant DNA in cancer patients. Curr Opin Oncol 19:36–42

    Article  CAS  PubMed  Google Scholar 

  51. Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, Kitano TK, Hodel MR, Petersen JF, Wyatt PW, Steenblock ER, Shah PH, Bousse LJ, Troup CB, Mellen JC, Wittmann DK, Erndt NG, Cauley TH, Koehler RT, So AP, Dube S, Rose KA, Montesclaros L, Wang S, Stumbo DP, Hodges SP, Romine S, Milanovich FP, White HE, Regan JF, Karlin-Neumann GA, Hindson CM, Saxonov S, Colston BW (2011) High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem 83:8604–8610

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  52. Sanders R, Huggett JF, Bushell CA, Cowen S, Scott DJ, Foy CA (2011) Evaluation of digital PCR for absolute DNA quantification. Anal Chem 83:6474–6484

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This work was supported in part by NCI R01CA161837, VA merit Award I01 CX000512, LUNGevity/Upstage Foundation Early Detection Award, and Award from the Geaton and JoAnn DeCesaris Family Foundation (F. J.).

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Authors and Affiliations

  1. Department of Pathology, University of Maryland School of Medicine, 10 South Pine Street, MSTF 7th Floor, Baltimore, MD, 21201-1192, USA

    Lu Gao & Feng Jiang

Authors
  1. Lu Gao
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  2. Feng Jiang
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Corresponding author

Correspondence to Feng Jiang .

Editor information

Editors and Affiliations

  1. Department of Surgery, Universitätsklinikum Erlangen, Erlangen, Germany

    Robert Grützmann

  2. Department of Surgery, TU-Dresden, Dresden, Germany

    Christian Pilarsky

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Gao, L., Jiang, F. (2016). MicroRNA (miRNA) Profiling. In: Grützmann, R., Pilarsky, C. (eds) Cancer Gene Profiling. Methods in Molecular Biology, vol 1381. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3204-7_8

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  • DOI: https://doi.org/10.1007/978-1-4939-3204-7_8

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-3203-0

  • Online ISBN: 978-1-4939-3204-7

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