Skip to main content
SpringerLink
Log in

MiRNA Expression Assays

  • Chapter
  • First Online:
Genomic Applications in Pathology

  • 2187 Accesses

Abstract

MicroRNAs (miRNAs) are small noncoding RNAs. Evaluation of miRNA expression profiles has come to play an important role in diverse physiological and pathological processes. In this chapter, we provide an overview of several of the most recently developed assays, methods, and technologies used to identify, characterize, and confirm miRNA expression in human pathologies. We also outline principal workflows for different preparations of biological samples, taking into account advantages and disadvantages of each approach. Furthermore, we discuss the diagnostic and therapeutic efficacy of miRNAs as well as their future roles in personalized medicine. This complete picture can help pathologists combine new methods and classical ones for diagnostic and therapeutic purposes.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 239.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Shah MY, Calin GA. The mix of two worlds: non-coding RNAs and hormones. Nucleic Acid Ther. 2012;23(1):2–8.

    PubMed  Google Scholar 

  2. Redis RS, Calin S, Yang Y, et al. Cell-to-cell miRNA transfer: from body homeostasis to therapy. Pharmacol Ther. 2012;136:169–74.

    PubMed  CAS  Google Scholar 

  3. Enfield KS, Pikor LA, Martinez VD, Lam WL. Mechanistic roles of noncoding RNAs in lung cancer biology and their clinical implications. Genet Res Int. 2012;2012:737416.

    PubMed  PubMed Central  Google Scholar 

  4. Fire A, Xu S, Montgomery MK, et al. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature. 1998;391:806–11.

    PubMed  CAS  Google Scholar 

  5. Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004;116:281–97.

    PubMed  CAS  Google Scholar 

  6. Negrini M, Nicoloso M, Calin G. MicroRNAs and cancer—new paradigms in molecular oncology. Curr Opin Cell Biol. 2009;21:470–9.

    PubMed  CAS  Google Scholar 

  7. Pritchard CC, Cheng HH, Tewari M. MicroRNA profiling: approaches and considerations. Nat Rev Genet. 2012;13(5):358–69.

    PubMed  CAS  Google Scholar 

  8. Yoshizawa JM, Wong DT. Salivary microRNAs and oral cancer detection. Methods Mol Biol. 2013;936:313–24.

    PubMed  CAS  PubMed Central  Google Scholar 

  9. Allegra A, Alonci A, Campo S, et al. Circulating microRNAs: new biomarkers in diagnosis, prognosis and treatment of cancer (review). Int J Oncol. 2012;41(6):1897–912. doi:10.3892/ijo.2012.1647.

    PubMed  CAS  Google Scholar 

  10. Li J, Smyth P, Flavin R, et al. Comparison of miRNA expression patterns using total RNA extracted from matched samples of formalin-fixed paraffin-embedded (FFPE) cells and snap frozen cells. BMC Biotechnol. 2007;29:36.

    Google Scholar 

  11. Calin GA, Croce CM. MicroRNA signatures in human cancers. Nat Rev Cancer. 2006;6(11):857–66.

    PubMed  CAS  Google Scholar 

  12. Etheridge A, Lee I, Hood L, et al. Extracellular microRNA: a new source of biomarkers. Mutat Res. 2011;717(1–2):85–90.

    PubMed  CAS  PubMed Central  Google Scholar 

  13. Krichevsky AM. MicroRNA profiling: from dark matter to white matter, or identifying new players in neurobiology. Scientific World Journal. 2007;7:155–66.

    PubMed  Google Scholar 

  14. Bommer GT, Gerin I, Feng Y, Kaczorowski AJ, Kuick R, Love RE, Zhai Y, Giordano TJ, Qin ZS, Moore BB, et al. p53-mediated activation of miRNA34 candidate tumor-suppressor genes. Curr Biol. 2007;17:1298–307.

    PubMed  CAS  Google Scholar 

  15. Mendell J, Olson E. MicroRNAs in stress signaling and human disease. Cell. 2012;148(6):1172–87.

    PubMed  CAS  PubMed Central  Google Scholar 

  16. Shi XB, Xue L, Yang J, et al. An androgen-regulated miRNA suppresses Bak1 expression and induces androgen-independent growth of prostate cancer cells. Proc Natl Acad Sci U S A. 2007;104:19983–8.

    PubMed  CAS  PubMed Central  Google Scholar 

  17. Cao P, Deng Z, Wan M, et al. MicroRNA-101 negatively regulates Ezh2 and its expression is modulated by androgen receptor and HIF-1alpha/HIF-1beta. Mol Cancer. 2010;9:108.

    PubMed  PubMed Central  Google Scholar 

  18. Poliseno L, Salmena L, Riccardi A, et al. Identification of the miR-106b 25 microRNA cluster as a proto-oncogenic PTEN-targeting intron that cooperates with its host gene MCM7 in transformation. Sci Signal. 2010;3:ra29.

    PubMed  PubMed Central  Google Scholar 

  19. Zaman MS, Thamminana S, Shahryari V, et al. Inhibition of PTEN gene expression by oncogenic miR-23b-3p in renal cancer. PLoS One. 2012;7:e50203.

    PubMed  CAS  PubMed Central  Google Scholar 

  20. Mlcochova H, Hezova R, Stanik M, Slaby O. Urine microRNAs as potential noninvasive biomarkers in urologic cancers. Urol Oncol. 2014;32(1):41.e1–9. pii: S1078-1439(13)00197-X.

    CAS  Google Scholar 

  21. Calin GA, Sevignani C, Dumitru CD, Hyslop T, Noch E, Yendamuri S, Shimizu M, Rattan S, Bullrich F, Negrini M, et al. Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers. Proc Natl Acad Sci U S A. 2004;101:2999–3004.

    PubMed  CAS  PubMed Central  Google Scholar 

  22. Alvarez-Garcia I, Miska EA. MicroRNA functions in animal development and human disease. Development. 2005;132(21):4653–62.

    PubMed  CAS  Google Scholar 

  23. Lu M, Zhang Q, Deng M, Miao J, Guo Y, et al. An analysis of human MicroRNA and disease associations. PLoS One. 2008;3(10):e3420.

    PubMed  PubMed Central  Google Scholar 

  24. Calin GA, Dumitru CD, Shimizu M, et al. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A. 2002;99(24):15524–9.

    PubMed  CAS  PubMed Central  Google Scholar 

  25. Cimmino A, Calin GA, Fabbri M, et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci U S A. 2005;102(39):13944–9.

    PubMed  CAS  PubMed Central  Google Scholar 

  26. Calin GA, Ferracin M, Cimmino A, et al. A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med. 2005;353:1793–801.

    PubMed  CAS  Google Scholar 

  27. Pekarsky Y, Santanam U, Cimmino A, et al. Tcl1 expression in chronic lymphocytic leukemia is regulated by miR-29 and miR-181. Cancer Res. 2006;66(24):11590–3.

    PubMed  CAS  Google Scholar 

  28. Calin GA, Pekarsky Y, Croce CM. The role of microRNA and other non-coding RNA in the pathogenesis of chronic lymphocytic leukemia. Best Pract Res Clin Haematol. 2007;20(3):425–37.

    PubMed  CAS  Google Scholar 

  29. Rossi S, Shimizu M, Barbarotto E, et al. microRNA fingerprinting of CLL patients with chromosome 17p deletion identify a miR-21 score that stratifies early survival. Blood. 2010;116(6):945–52.

    PubMed  CAS  Google Scholar 

  30. Ferrajoli A, Shanafelt TD, Ivan C, et al. Prognostic value of miR-155 in individuals with monoclonal B-cell lymphocytosis and patients with B chronic lymphocytic leukemia. Blood. 2013;122(11):1891–9.

    PubMed  CAS  PubMed Central  Google Scholar 

  31. Wang JL, Hu Y, Kong X, et al. Candidate microRNA biomarkers in human gastric cancer: a systematic review and validation study. PLoS One. 2013;8(9):e73683.

    PubMed  CAS  PubMed Central  Google Scholar 

  32. Wang Y, Li J, Tong L, et al. The prognostic value of miR-21 and miR-155 in non-small-cell lung cancer: a meta-analysis. Jpn J Clin Oncol. 2013;43(8):813–20.

    PubMed  Google Scholar 

  33. Menéndez P, Padilla D, Villarejo P, et al. Prognostic implications of serum microRNA-21 in colorectal cancer. J Surg Oncol. 2013;108(6):369–73. doi:10.1002/jso.23415.

    PubMed  Google Scholar 

  34. Lee JA, Lee HY, Lee ES, Kim I, Bae JW. Prognostic implications of microRNA-21 overexpression in invasive ductal carcinomas of the breast. J Breast Cancer. 2011;14(4):269–75.

    PubMed  PubMed Central  Google Scholar 

  35. Ota A, Tagawa H, Karnan S, et al. Identification and characterization of a novel gene, C13orf25, as a target for 13q31-q32 amplification in malignant lymphoma. Cancer Res. 2004;64(9):3087–95.

    PubMed  CAS  Google Scholar 

  36. Chang CC, Yang YJ, Li YJ, et al. MicroRNA-17/20a functions to inhibit cell migration and can be used a prognostic marker in oral squamous cell carcinoma. Oral Oncol. 2013;49(9):923–31.

    PubMed  CAS  Google Scholar 

  37. Gao X, Zhang R, Qu X, et al. MiR-15a, miR-16-1 and miR-17-92 cluster expression are linked to poor prognosis in multiple myeloma. Leuk Res. 2012;36(12):1505–9.

    PubMed  CAS  Google Scholar 

  38. Yu G, Tang JQ, Tian ML, et al. Prognostic values of the miR-17-92 cluster and its paralogs in colon cancer. J Surg Oncol. 2012;106(3):232–7.

    PubMed  CAS  Google Scholar 

  39. Hanke M, Hoefig K, Merz H, et al. A robust methodology to study urine microRNA as tumor marker: microRNA-126 and microRNA-182 are related to urinary bladder cancer. Urol Oncol. 2010;28(6):655–61.

    PubMed  CAS  Google Scholar 

  40. Zhong S, Li W, Chen Z, Xu J, Zhao J. miR-222 and miR-29a contribute to the drug-resistance of breast cancer cells. Gene. 2013;531(1):8–14. pii: S0378-1119(13)01122-0.

    PubMed  CAS  Google Scholar 

  41. Yu PN, Yan MD, Lai HC, et al. Downregulation of miR-29 contributes to cisplatin resistance of ovarian cancer cells. Int J Cancer. 2013;134(3):542–51.

    PubMed  Google Scholar 

  42. Wong KY, Yim RL, Kwong YL, et al. Epigenetic inactivation of the MIR129-2 in hematological malignancies. J Hematol Oncol. 2013;6:16.

    PubMed  CAS  PubMed Central  Google Scholar 

  43. Lu CY, Lin KY, Tien MT, et al. Frequent DNA methylation of MiR-129-2 and its potential clinical implication in hepatocellular carcinoma. Genes Chromosomes Cancer. 2013;52:636–43.

    PubMed  CAS  Google Scholar 

  44. Fabbri M, Garzon R, Cimmino A, et al. MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proc Natl Acad Sci U S A. 2007;104:15805–10.

    PubMed  CAS  PubMed Central  Google Scholar 

  45. Sacco J, Adeli K. MicroRNAs: emerging roles in lipid and lipoprotein metabolism. Curr Opin Lipidol. 2012;23(3):220–5.

    PubMed  CAS  Google Scholar 

  46. Romao JM, Jin W, Dodson MV, Hausman GJ, Moore SS, Guan LL. MicroRNA regulation in mammalian adipogenesis. Exp Biol Med (Maywood). 2011;236(9):997–1004.

    CAS  Google Scholar 

  47. Ortega FJ, Mercader JM, Catalán V, Moreno-Navarrete JM, Pueyo N, Sabater M, Gómez-Ambrosi J, Anglada R, Fernández-Formoso JA, Ricart W, Frühbeck G, Fernández-Real JM. Targeting the circulating microRNA signature of obesity. Clin Chem. 2013;59(5):781–92.

    PubMed  CAS  Google Scholar 

  48. McGregor RA, Choi MS. microRNAs in the regulation of adipogenesis and obesity. Curr Mol Med. 2011;11(4):304–16.

    PubMed  CAS  PubMed Central  Google Scholar 

  49. Ono K, Kuwabara Y, Han J. MicroRNAs and cardiovascular diseases. FEBS J. 2011;278(10):1619–33. doi:10.1111/j.1742-4658.2011.08090.x. Epub 2011 Mar 30.

    PubMed  CAS  PubMed Central  Google Scholar 

  50. Thum T, Catalucci D, Bauersachs J. MicroRNAs: novel regulators in cardiac development and disease. Cardiovasc Res. 2008;79:562–70.

    PubMed  CAS  Google Scholar 

  51. Care A, Catalucci D, Felicetti F, Bonci D, Addario A, Gallo P, et al. MicroRNA-133 controls cardiac hypertrophy. Nat Med. 2007;13:613–8.

    PubMed  CAS  Google Scholar 

  52. Yang B, Lin H, Xiao J, Lu Y, Luo X, Li B, et al. The muscle-specific microRNA miR-1 regulates cardiac arrhythmogenic potential by targeting GJA1 and KCNJ2. Nat Med. 2007;13:486–91.

    PubMed  CAS  Google Scholar 

  53. Oliveira-Carvalho V, da Silva MM, Guimarães GV, Bacal F, Bocchi EA. MicroRNAs: new players in heart failure. Mol Biol Rep. 2013;40(3):2663–70.

    PubMed  CAS  Google Scholar 

  54. Fichtlscherer S, Zeiher AM, Dimmeler S. Circulating microRNAs: biomarkers or mediators of cardiovascular diseases? Arterioscler Thromb Vasc Biol. 2011;31(11):2383–90.

    PubMed  CAS  Google Scholar 

  55. Hu R, O’Connell M. MicroRNA control in the development of systemic autoimmunity. Arthritis Res Ther. 2013;15(1):202. doi:10.1186/ar413.

    PubMed  CAS  PubMed Central  Google Scholar 

  56. Meisgen F, Xu N, Wei T, Janson PC, Obad S, Broom O, Nagy N, Kauppinen S, Kemény L, Ståhle M, Pivarcsi A, Sonkoly E. MiR-21 is up-regulated in psoriasis and suppresses T cell apoptosis. Exp Dermatol. 2012;15:312–4.

    Google Scholar 

  57. Mi QS, He HZ, Dong Z, Isales C, Zhou L. microRNA deficiency in pancreatic islet cells exacerbates streptozotocin-induced murine autoimmune diabetes. Cell Cycle. 2010;15:3127–9.

    Google Scholar 

  58. Yanaihara N, Caplen N, Bowman E, et al. Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell. 2006;9(3):189–98.

    PubMed  CAS  Google Scholar 

  59. Liu A, Xu X. MicroRNA isolation from formalin-fixed, paraffin-embedded tissues. Methods Mol Biol. 2011;724:259–67.

    PubMed  CAS  Google Scholar 

  60. Nelson PT, Wang WX, Wilfred BR, Tang G. Technical variables in high-throughput miRNA expression profiling: much work remains to be done. Biochim Biophys Acta. 2008;1779(11):758–65.

    PubMed  CAS  PubMed Central  Google Scholar 

  61. Mraz M, Malinova K, Mayer J, Pospisilova S. MicroRNA isolation and stability in stored RNA samples. Biochem Biophys Res Commun. 2009;390(1):1–4.

    PubMed  CAS  Google Scholar 

  62. Wang K, Yuan Y, Cho J-H, McClarty S, Baxter D, et al. Comparing the MicroRNA spectrum between serum and plasma. PLoS One. 2012;7(7):e41561. doi:10.1371/journal.pone.0041561.

    PubMed  CAS  PubMed Central  Google Scholar 

  63. Becker C, Hammerle-Fickinger A, Riedmaier I, Pfaffl MW. mRNA and microRNA quality control for RT-qPCR analysis. Methods. 2010;50(4):237–43.

    PubMed  CAS  Google Scholar 

  64. Rio DC, Ares Jr M, Hannon GJ, Nilsen TW. Purification of RNA using TRIzol (TRI reagent). Cold Spring Harb Protoc. 2010;2010(6):pdb.prot5439.

    PubMed  Google Scholar 

  65. Ach RA, Wang H, Curry B. Measuring microRNAs: comparisons of microarray and quantitative PCR measurements, and of different total RNA prep methods. BMC Biotechnol. 2008;8:69.

    PubMed  PubMed Central  Google Scholar 

  66. Bustin SA, Benes V, Garson JA, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55(4):611–22.

    PubMed  CAS  Google Scholar 

  67. Kim YK, Yeo J, Kim B, Ha M, Kim VN. Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Mol Cell. 2012;46(6):893–5.

    PubMed  CAS  Google Scholar 

  68. Yoo CE, Kim G, Kim M, et al. A direct extraction method for microRNAs from exosomes captured by immunoaffinity beads. Anal Biochem. 2012;431(2):96–8.

    PubMed  CAS  Google Scholar 

  69. Bravo V, Rosero S, Ricordi C, Pastori RL. Instability of miRNA and cDNAs derivatives in RNA preparations. Biochem Biophys Res Commun. 2007;353(4):1052–5.

    PubMed  CAS  Google Scholar 

  70. Vaz C, Ahmad HM, Sharma P, et al. Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genomics. 2010;11:288.

    PubMed  PubMed Central  Google Scholar 

  71. Jensen SG, Lamy P, Rasmussen MH, et al. Evaluation of two commercial global miRNA expression profiling platforms for detection of less abundant miRNAs. BMC Genomics. 2011;12:435.

    PubMed  CAS  PubMed Central  Google Scholar 

  72. Sablok G, Milev I, Minkov G, et al. isomiRex: web-based identification of microRNAs, isomiR variations and differential expression using next-generation sequencing datasets. FEBS Lett. 2013;587(16):2629–34.

    PubMed  CAS  Google Scholar 

  73. Kim SW, Li Z, Moore PS, et al. A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Res. 2010;38(7):e98.

    PubMed  PubMed Central  Google Scholar 

  74. Wang B, Howel P, Bruheim S, et al. Systematic evaluation of three microRNA profiling platforms: microarray, beads array, and quantitative real-time PCR array. PLoS One. 2011;6(2):e17167.

    PubMed  CAS  PubMed Central  Google Scholar 

  75. Sempere LF, Freemantle S, Pitha-Rowe I, et al. Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation. Genome Biol. 2004;5:R13.

    PubMed  PubMed Central  Google Scholar 

  76. Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell. 1993;75(5):843–54.

    PubMed  CAS  Google Scholar 

  77. Setoyama T, Ling H, Natsugoe S, Calin GA. Non-coding RNAs for medical practice in oncology. Keio J Med. 2011;60(4):106–13.

    PubMed  CAS  Google Scholar 

  78. de Planell-Saguer M, Rodicio MC. Analytical aspects of microRNA in diagnostics: a review. Anal Chim Acta. 2011;699(2):134–52.

    PubMed  Google Scholar 

  79. Kumar P, Johnston BH, Kazakov SA. miR-ID: a novel, circularization-based platform for detection of microRNAs. RNA. 2011;17(2):365–80.

    PubMed  CAS  PubMed Central  Google Scholar 

  80. Schmittgen TD, Jiang J, Liu Q, Yang L. A high-throughput method to monitor the expression of microRNAs precursor. Nucleic Acids Res. 2004;32:43–53.

    Google Scholar 

  81. Reichenstein I, Aizenberg N, Goshen M, et al. A novel qPCR assay for viral encoded microRNAs. J Virol Methods. 2010;163:323–8.

    PubMed  CAS  Google Scholar 

  82. Ro S, Park C, Jin J, et al. A PCR-based method for detection and quantification of small RNAs. Biochem Biophys Res Commun. 2006;351:756–63.

    PubMed  CAS  PubMed Central  Google Scholar 

  83. Stratagene® qRT-PCR platforms. http://www.stratagene.com/products/displayProduct.aspx?pid=820. Accessed Dec 2012.

  84. Highly-specific miRNA QRT-PCR detection. http://www.genomics.agilent.com/CollectionSubpage.aspx?PageType=Product&SubPageType=ProductData&PageID=308. Accessed Feb 2013.

  85. NCode™ miRNA amplification system. http://tools.invitrogen.com/content/sfs/manuals/ncode_rna_amp_man.pdf. Accessed Feb 2013.

  86. Raymond CJ, Roberts BS, Garrett-Engele P. Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. RNA. 2005;11:1737–44.

    PubMed  CAS  PubMed Central  Google Scholar 

  87. Locked nucleic acids. http://www.eurogentec.com/EGT/files/GOL-LNALEAFLET-1107-V1.pdf. Accessed Feb 2013.

  88. Leung AK, Sharp PA. Function and localization of microRNAs in mammalian cells. Cold Spring Harb Symp Quant Biol. 2006;71:29–38.

    PubMed  CAS  Google Scholar 

  89. Nass D, Rosenwald S, Meiri E, et al. MiR-92b and miR-9/9* are specifically expressed in brain primary tumors and can be used to differentiate primary from metastatic brain tumors. Brain Pathol. 2009;19(3):375–83.

    PubMed  CAS  PubMed Central  Google Scholar 

  90. Bustos-Sanmamed P, Laffont C, Frugier F, Lelandais-Brière C, Crespi M. Analyzing small and long RNAs in plant development using non-radioactive in situ hybridization. Methods Mol Biol. 2013;959:303–16.

    PubMed  Google Scholar 

  91. Obernosterer G, Leuschner PJ, Alenius M, Martinez J. Post-transcriptional regulation of microRNA expression. RNA. 2006;12(7):1161–7.

    PubMed  CAS  PubMed Central  Google Scholar 

  92. Shi Z, Johnson J, Sharon Stack M. Fluorescence in situ hybridization for microRNA detection in archived oral cancer tissues. J Oncol. 2012;2012:903581.

    PubMed  PubMed Central  Google Scholar 

  93. Yauk CL, Rowan-Carroll A, Stead JD, Williams A. Cross-platform analysis of global microRNA expression technologies. BMC Genomics. 2010;11:330.

    PubMed  PubMed Central  Google Scholar 

  94. Aldridge S, Hadfield J. Introduction to miRNA profiling technologies and cross-platform comparison. Methods Mol Biol. 2012;822:19–31.

    PubMed  CAS  Google Scholar 

  95. Duttagupta R, DiRienzo S, Jiang R, et al. Genome-wide maps of circulating miRNA biomarkers for ulcerative colitis. PLoS One. 2012;7(2):e31241.

    PubMed  CAS  PubMed Central  Google Scholar 

  96. Chen J, April CS, Fan JB. miRNA expression profiling using Illumina Universal BeadChips. Methods Mol Biol. 2012;822:103–16.

    PubMed  CAS  Google Scholar 

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

    PubMed  Google Scholar 

  98. Benes V, Castoldi M. Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available. Methods. 2010;50(4):244–9.

    PubMed  CAS  Google Scholar 

  99. Liu J, Jenning S, Tong W, Hong H. Next generation sequencing for profiling expression of miRNAs: technical progress and applications in drug development. J Biomed Sci Eng. 2011;4:666–76.

    PubMed  CAS  PubMed Central  Google Scholar 

  100. Yang Q, Lu J, Wang S, Li H, Ge Q, Lu Z, et al. Application of next-generation sequencing technology to profile the circulating microRNAs in the serum of preeclampsia versus normal pregnant women. Clin Chim Acta. 2011;412:2167–73.

    PubMed  CAS  Google Scholar 

  101. Schulte JH, Marschall T, Martin M, et al. Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma. Nucleic Acids Res. 2010;38:5919–28.

    PubMed  CAS  PubMed Central  Google Scholar 

  102. Wang H, Ach RA, Curry B. Direct and sensitive miRNA profiling from low-input total RNA. RNA. 2007;13:151–9.

    PubMed  CAS  PubMed Central  Google Scholar 

  103. Lu C, Meyers BC, Green PJ. Construction of small RNA cDNA libraries for deep sequencing. Methods. 2007;43:110–7.

    PubMed  Google Scholar 

  104. Buermans HP, Ariyurek Y, van Ommen G, et al. New methods for next generation sequencing based microRNA expression profiling. BMC Genomics. 2010;11:716.

    PubMed  CAS  PubMed Central  Google Scholar 

  105. Tian G, Yin X, Luo H, et al. Sequencing bias: comparison of different protocols of microRNA library construction. BMC Biotechnol. 2010;10:64.

    PubMed  PubMed Central  Google Scholar 

  106. Friedländer MR, Chen W, Adamidi C, et al. Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol. 2008;26:407–15.

    PubMed  Google Scholar 

  107. Wang WC, Lin FM, Chang WC. miRExpress: analyzing high-throughput sequencing data for profiling microRNA expression. BMC Bioinformatics. 2009;10:328.

    PubMed  PubMed Central  Google Scholar 

  108. Hackenberg M, Sturm M, Langenberger D. miRanalyzer: a microRNA detection and analysis tool for next-generation sequencing experiments. Nucleic Acids Res. 2009;37:W68–76.

    PubMed  CAS  PubMed Central  Google Scholar 

  109. Moxon S, Schwach F, Dalmay T. A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics. 2008;24:2252–3.

    PubMed  CAS  Google Scholar 

  110. Bargaje R, Hariharan M, Scaria V, Pillai B, et al. Consensus miRNA expression profiles derived from interplatform normalization of microarray data. RNA. 2010;16(1):16–25.

    PubMed  CAS  PubMed Central  Google Scholar 

  111. Meyer SU, Pfaffl MW, Ulbrich SE. Normalization strategies for microRNA profiling experiments: a ‘normal’ way to a hidden layer of complexity? Biotechnol Lett. 2010;32(12):1777–88.

    PubMed  CAS  Google Scholar 

  112. Deo A, Carlsson J, Lindldof A. How to choose a normalization strategy for miRNA quantitative real-time (qPCR) arrays. J Bioinform Comput Biol. 2011;9:795–812.

    PubMed  Google Scholar 

  113. Volinia S, Calin GA, Liu CG, et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci U S A. 2006;103:2257–61.

    PubMed  CAS  PubMed Central  Google Scholar 

  114. SAM: significance analysis of microarrays. http://www-stat.stanford.edu/~tibs/SAM/index.html. Accessed Feb 2013.

  115. PAM: prediction analysis for microarrays. http://www-stat.stanford.edu/~tibs/PAM/index.html. Accessed Feb 2013.

  116. Liu CG, Calin GA, Meloon B, et al. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proc Natl Acad Sci U S A. 2004;101(26):9740–4.

    PubMed  CAS  PubMed Central  Google Scholar 

  117. Iorio MV, Ferracin M, Liu CG, et al. MicroRNA gene expression deregulation in human breast cancer. Cancer Res. 2005;65(16):7065–70.

    PubMed  CAS  Google Scholar 

  118. Williams MD, Mitchell GM. MicroRNA in insulin resistance and obesity. Exp Diabetes Res. 2012;2012:484696.

    PubMed  PubMed Central  Google Scholar 

  119. Mo YY. MicroRNA regulatory networks and human disease. Cell Mol Life Sci. 2012;69:3529–31.

    PubMed  CAS  PubMed Central  Google Scholar 

  120. Salmena L, Poliseno LB, Tay Y, Kats L, Pandolfi PP, et al. A ceRNA hypothesis: the Rosetta Stone of a hidden RAN language? Cell. 2011;146:353–8.

    PubMed  CAS  PubMed Central  Google Scholar 

  121. Dillman W. Cardiac hypertrophy and thyroid hormone signaling. Heart Fail Rev. 2010;15:125–32.

    Google Scholar 

  122. Callis TE, Pandya K, Seok HY, et al. MicroRNA-208a is a regulator of cardiac hypertrophy and conduction in mice. J Clin Invest. 2009;119:2772–27786.

    PubMed  CAS  PubMed Central  Google Scholar 

  123. Jopling CL, Yi M, Lancaster AM, Lemon SM, Sarnow P. Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science. 2005;309:1577–81.

    PubMed  CAS  Google Scholar 

  124. Yue J. miRNA and vascular cell movement. Adv Drug Deliv Rev. 2011;63(8):616–22.

    PubMed  CAS  PubMed Central  Google Scholar 

  125. Li W, Szoka Jr FC. Lipid-based nanoparticles for nucleic acid delivery. Pharm Res. 2007;24:438–49.

    PubMed  Google Scholar 

  126. Walther W, Stain U. Viral vectors for gene transfer: a review of their use in the treatment of human diseases. Drugs. 2000;60:249–71.

    PubMed  CAS  Google Scholar 

  127. Al-Dosari MS, Gao X. Nonviral gene delivery: principle, limitations and recent progress. AAPS J. 2009;11(4):671–81.

    PubMed  CAS  PubMed Central  Google Scholar 

  128. Couto LB, High KA. Viral vector-mediated RNA interference. Curr Opin Pharmacol. 2010;10(5):534–42.

    PubMed  CAS  Google Scholar 

  129. Rai K, Takigawa N, Ito S, et al. Liposomal delivery of microRNA-7-expression plasmid epidermal growth factor receptor tyrosine kinase inhibitor-resistance in lung cancer cells. Mol Cancer Ther. 2011;10(9):1720–7.

    PubMed  CAS  Google Scholar 

  130. Gondi CS, Rao JS. Concepts in in vivo siRNA delivery for cancer therapy. J Cell Physiol. 2009;220(2):285–91.

    PubMed  CAS  PubMed Central  Google Scholar 

  131. Lujambio A, Lowe SW. The microcosmos of cancer. Nature. 2012;482:347–55.

    PubMed  CAS  PubMed Central  Google Scholar 

  132. Ferracin M, Zagatti B, Rizzotto L, et al. MicroRNAs involvement in fludarabine refractory chronic lymphocytic leukemia. Mol Cancer. 2010;9:123.

    PubMed  PubMed Central  Google Scholar 

  133. Ru P, Steele R, Newhall P, et al. MicroRNA-29b suppresses prostate cancer metastasis by regulating epithelial-mesenchymal transition signaling. Mol Cancer Ther. 2012;11:1166–73.

    PubMed  CAS  Google Scholar 

  134. Kandalam MM, Beta M, Maheswari UK, et al. Oncogenic microRNA 17-92 cluster is regulated by epithelial cell adhesion molecule and could be a potential therapeutic target in retinoblastoma. Mol Vis. 2012;18:2279–87.

    PubMed  CAS  PubMed Central  Google Scholar 

  135. Fassina A, Marino F, Siri M, et al. The miR-17-92 microRNA cluster: a novel diagnostic tool in large B-cell malignancies. Lab Invest. 2012;92(11):1574–82.

    PubMed  CAS  Google Scholar 

  136. Lu J, Getz G, Miska EA, et al. MicroRNA expression profiles classify human cancers. Nature. 2005;435(7043):834–8.

    PubMed  CAS  Google Scholar 

Download references

Acknowledgements

Dr. Calin is the Alan M. Gewirtz Leukemia & Lymphoma Society Scholar. He is supported as a fellow of the University of Texas MD Anderson Cancer Center Research Trust, as the University of Texas System Regents Research Scholar, and by the CLL Global Research Foundation. Work in Dr. Calin’s laboratory is supported in part by the National Institutes of Health/National Cancer Institute (CA135444); a Department of Defense Breast Cancer Idea Award; Developmental Research Awards in Breast Cancer, Ovarian Cancer, Brain Cancer, Prostate Cancer, Multiple Myeloma, Leukemia (P50 CA100632), and Head and Neck (P50 CA097007) Specialized Program of Research Excellence grants; Sister Institution Network Fund grants in CLL and colon cancer; the Laura and John Arnold Foundation; the RGK Foundation; and the Estate of C. G. Johnson, Jr. Drs. Berindan-Neagoe and Braicu were financed by a POSCCE grant (709/2010) entitled Clinical and Economical Impact of Proteome and Transcriptome Molecular Profiling in Neoadjuvant Therapy of Triple Negative Breast Cancer (BREASTIMPACT). This research is supported in part by the MD Anderson Cancer Center Support Grant CA016672. We thank Don Norwood in the Department of Scientific Publications at MD Anderson for expert editorial assistance.

Author information

Authors and Affiliations

  1. Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania

    Cornelia Braicu

  2. Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    Beatriz M. Maia

  3. Research Center for Functional Genomics, Biomedicine and Translational Medicine and The Department of Immunology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania

    Ioana Berindan-Neagoe

  4. Department of Functional Genomics and Experimental Pathology, The Oncological Institute “Prof. Dr. Ion Chiricuta”, Cluj-Napoca, Romania

    Ioana Berindan-Neagoe

  5. Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    George A. Calin

  6. Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA

    George A. Calin

Authors
  1. Cornelia Braicu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Beatriz M. Maia
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ioana Berindan-Neagoe
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. George A. Calin
    View author publications

    You can also search for this author in PubMed Google Scholar

Editor information

Editors and Affiliations

  1. Departments of Pathology, Oncology and Urology, Johns Hopkins University, Baltimore, Maryland, USA

    George Jabboure Netto

  2. Department of Pathology, Stanford University School of Medicine, Stanford, California, USA

    Iris Schrijver

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this chapter

Cite this chapter

Braicu, C., Maia, B.M., Berindan-Neagoe, I., Calin, G.A. (2015). MiRNA Expression Assays. In: Netto, G., Schrijver, I. (eds) Genomic Applications in Pathology. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-0727-4_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-0727-4_4

  • Published:

  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-4939-0726-7

  • Online ISBN: 978-1-4939-0727-4

  • eBook Packages: MedicineMedicine (R0)

Publish with us

Policies and ethics

Search

Navigation