Download PDF
Thromb Haemost 2012; 108(04): 592-598
DOI: 10.1160/TH12-02-0097
Theme Issue Article
Schattauer GmbH

Analytical challenges and technical limitations in assessing circulating MiRNAs

Anna Zampetaki
1   King’s British Heart Foundation Centre, King’s College London, London, UK
,
Manuel Mayr
1   King’s British Heart Foundation Centre, King’s College London, London, UK
› Author Affiliations
Further Information

Publication History

Received: 17 February 2012

Accepted after minor revision: 17 April 2012

Publication Date:
29 November 2017 (online)

    Permissions and Reprints

Summary

MiRNAs are emerging as promising biomarkers in cardiovascular diseases and may constitute a novel mechanism of intercellular communication. Accurate quantification of circulating miRNAs is essential. A variety of technological approaches and platforms have been developed with increased sensitivity and specificity for the detection and quantification of circulating miRNAs. In this review, we focus on the technical aspects and discuss the analytical challenges in profiling circulating miRNAs.

Keywords

microRNA - biomarker - cardiovascular - diabetes
 

  • References

  • 1 Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116: 281-297.
    CrossrefPubMedGoogle Scholar
  • 2 Lee Y, Ahn C, Han J. et al. The nuclear RNase III Drosha initiates microRNA processing. Nature 2003; 425: 415-419.
    CrossrefPubMedGoogle Scholar
  • 3 Denli AM, Tops BB, Plasterk RH. et al. Processing of primary microRNAs by the Microprocessor complex. Nature 2004; 432: 231-235.
    CrossrefPubMedGoogle Scholar
  • 4 Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009; 136: 215-233.
    CrossrefPubMedGoogle Scholar
  • 5 Guo H, Ingolia NT, Weissman JS. et al. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010; 466: 835-840.
    CrossrefPubMedGoogle Scholar
  • 6 Zampetaki A, Mayr M. MicroRNAs in Vascular and Metabolic Disease. Circ Res 2012; 110: 508-522.
    CrossrefPubMedGoogle Scholar
  • 7 Zampetaki A, Willeit P, Drozdov I. et al. Profiling of circulating microRNAs: from single biomarkers to re-wired networks. Cardiovasc Res 2012; 93: 555-562.
    CrossrefPubMedGoogle Scholar
  • 8 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: 10513-10518.
    CrossrefPubMedGoogle Scholar
  • 9 Zernecke A, Bidzhekov K, Noels H. et al. Delivery of microRNA-126 by apoptotic bodies induces CXCL12-dependent vascular protection. Sci Signal 2009; 02: ra81.
    PubMedGoogle Scholar
  • 10 Skog J, Wurdinger T, van Rijn S. et al. Glioblastoma microvesicles transport RNA and proteins that promote tumour growth and provide diagnostic biomarkers. Nature Cell Biol 2008; 10: 1470-1476.
    CrossrefPubMedGoogle Scholar
  • 11 Pegtel DM, Cosmopoulos K, Thorley-Lawson DA. et al. Functional delivery of viral miRNAs via exosomes. Proc Natl Acad Sci USA 2010; 107: 6328-6333.
    CrossrefPubMedGoogle Scholar
  • 12 Arroyo JD, Chevillet JR, Kroh EM. et al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci USA 2011; 108: 5003-5008.
    CrossrefPubMedGoogle Scholar
  • 13 Wang K, Zhang S, Weber J. et al. Export of microRNAs and microRNA-protective protein by mammalian cells. Nucleic Acids Res 2010; 38: 7248-7259.
    CrossrefPubMedGoogle Scholar
  • 14 Vickers KC, Palmisano BT, Shoucri BM. et al. MicroRNAs are transported in plasma and delivered to recipient cells by highdensity lipoproteins. Nature Cell Biol 2011; 13: 423-433.
    CrossrefPubMedGoogle Scholar
  • 15 Kirschner MB, Kao SC, Edelman JJ. et al. Haemolysis during sample preparation alters microRNA content of plasma. PloS One 2011; 06: e24145.
    CrossrefPubMedGoogle Scholar
  • 16 Duttagupta R, Jiang R, Gollub J. et al. Impact of Cellular miRNAs on Circulating miRNA Biomarker Signatures. PloS One 2011; 06: e20769.
    CrossrefPubMedGoogle Scholar
  • 17 McDonald JS, Milosevic D, Reddi HV. et al. Analysis of Circulating MicroRNA: Preanalytical and Analytical Challenges. Clin Chem 2011; 57: 833-840.
    CrossrefPubMedGoogle Scholar
  • 18 George JN, Thoi LL, McManus LM. et al. Isolation of human platelet membrane microparticles from plasma and serum. Blood 1982; 60: 834-840.
    PubMedGoogle Scholar
  • 19 Garcia ME, Blanco JL, Caballero J. et al. Anticoagulants interfere with PCR used to diagnose invasive aspergillosis. J Clin Microbiol 2002; 40: 1567-1568.
    CrossrefPubMedGoogle Scholar
  • 20 Willems M, Moshage H, Nevens F. et al. Plasma collected from heparinized blood is not suitable for HCV-RNA detection by conventional RT-PCR assay. J Virol Methods 1993; 42: 127-130.
    CrossrefPubMedGoogle Scholar
  • 21 Cui W, Ma J, Wang Y. et al. Plasma miRNA as biomarkers for assessment of totalbody radiation exposure dosimetry. PloS One 2011; 06: e22988.
    CrossrefPubMedGoogle Scholar
  • 22 Gilad S, Meiri E, Yogev Y. et al. Serum microRNAs are promising novel biomarkers. PloS One 2008; 03: e3148.
    CrossrefPubMedGoogle Scholar
  • 23 Rio DC, Ares Jr M, Hannon GJ. et al. Purification of RNA using TRIzol (TRI reagent). Cold Spring Harbor Prot 2010. 2010 pdb prot5439.
    PubMedGoogle Scholar
  • 24 Zampetaki A, Kiechl S, Drozdov I. et al. Plasma microRNA profiling reveals loss of endothelial miR-126 and other microRNAs in type 2 diabetes. Circ Res 2010; 107: 810-817.
    CrossrefPubMedGoogle Scholar
  • 25 Fichtlscherer S, De Rosa S, Fox H. et al. Circulating microRNAs in patients with coronary artery disease. Circ Res 2010; 107: 677-684.
    CrossrefPubMedGoogle Scholar
  • 26 Andreasen D, Fog JU, Biggs W. et al. Improved microRNA quantification in total RNA from clinical samples. Methods 2010; 50: S6-9.
    CrossrefPubMedGoogle Scholar
  • 27 Turchinovich A, Weiz L, Langheinz A. et al. Characterization of extracellular circulating microRNA. Nucleic Acids Res 2011; 39: 7223-7233.
    CrossrefPubMedGoogle Scholar
  • 28 Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nature Rev Genet 2011; 12: 87-98.
    CrossrefPubMedGoogle Scholar
  • 29 Chen X, Ba Y, Ma L. et al. Characterization of microRNAs in serum: a novel class of biomarkers for diagnosis of cancer and other diseases. Cell Res 2008; 18: 997-1006.
    CrossrefPubMedGoogle Scholar
  • 30 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; 08: 69.
    CrossrefPubMedGoogle Scholar
  • 31 Raymond CK, Roberts BS, Garrett-Engele P. et al. Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. RNA 2005; 11: 1737-1744.
    CrossrefPubMedGoogle Scholar
  • 32 Pradervand S, Weber J, Lemoine F. et al. Concordance among digital gene expression, microarrays, and qPCR when measuring differential expression of microRNAs. BioTechniques 2010; 48: 219-222.
    CrossrefPubMedGoogle Scholar
  • 33 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.
    CrossrefPubMedGoogle Scholar
  • 34 Ansorge WJ. Next-generation DNA sequencing techniques. New Biotechnol 2009; 25: 195-203.
    CrossrefPubMedGoogle Scholar
  • 35 Creighton CJ, Reid JG, Gunaratne PH. Expression profiling of microRNAs by deep sequencing. Briefings Bioinformatics 2009; 10: 490-497.
    CrossrefPubMedGoogle Scholar
  • 36 Yin JQ, Zhao RC, Morris KV. Profiling microRNA expression with microarrays. Trends Biotechnol 2008; 26: 70-76.
    CrossrefPubMedGoogle Scholar
  • 37 Bargaje R, Hariharan M, Scaria V. et al. Consensus miRNA expression profiles derived from interplatform normalization of microarray data. RNA 2010; 16: 16-25.
    CrossrefPubMedGoogle Scholar
  • 38 Shingara J, Keiger K, Shelton J. et al. An optimized isolation and labeling platform for accurate microRNA expression profiling. RNA 2005; 11: 1461-1470.
    CrossrefPubMedGoogle Scholar
  • 39 Wang H, Ach RA, Curry B. Direct and sensitive miRNA profiling from low-input total RNA. RNA 2007; 13: 151-159.
    PubMedGoogle Scholar
  • 40 Chen TS, Lai RC, Lee MM. et al. Mesenchymal stem cell secretes microparticles enriched in pre-microRNAs. Nucleic Acids Res 2010; 38: 215-224.
    CrossrefPubMedGoogle Scholar
  • 41 Sah S, McCall MN, Eveleigh D. et al. Performance evaluation of commercial miRNA expression array platforms. BMC Res Notes 2010; 03: 80.
    CrossrefPubMedGoogle Scholar
  • 42 Wang K, Zhang S, Marzolf B. et al. Circulating microRNAs, potential biomarkers for drug-induced liver injury. Proc Natl Acad Sci USA 2009; 106: 4402-4407.
    CrossrefPubMedGoogle Scholar
  • 43 Castoldi M, Schmidt S, Benes V. et al. A sensitive array for microRNA expression profiling (miChip) based on locked nucleic acids (LNA). RNA 2006; 12: 913-920.
    CrossrefPubMedGoogle Scholar
  • 44 Castoldi M, Schmidt S, Benes V. et al. miChip: an array-based method for microRNA expression profiling using locked nucleic acid capture probes. Nature Protocols 2008; 03: 321-329.
    CrossrefPubMedGoogle Scholar
  • 45 Li S, Zhu J, Zhang W. et al. Signature microRNA expression profile of essential hypertension and its novel link to human cytomegalovirus infection. Circulation 2011; 124: 175-184.
    CrossrefPubMedGoogle Scholar
  • 46 Chen J, Lozach J, Garcia EW. et al. Highly sensitive and specific microRNA expression profiling using BeadArray technology. Nucleic Acids Res 2008; 36: e87.
    CrossrefPubMedGoogle Scholar
  • 47 Lu J, Getz G, Miska EA. et al. MicroRNA expression profiles classify human cancers. Nature 2005; 435: 834-838.
    CrossrefPubMedGoogle Scholar
  • 48 Jay C, Nemunaitis J, Chen P. et al. miRNA profiling for diagnosis and prognosis of human cancer. DNA Cell Biol 2007; 26: 293-300.
    CrossrefPubMedGoogle Scholar
  • 49 Liu CG, Calin GA, Volinia S. et al. MicroRNA expression profiling using microarrays. Nature Protocols 2008; 03: 563-578.
    CrossrefPubMedGoogle Scholar
  • 50 Tijsen AJ, Creemers EE, Moerland PD. et al. MiR423-5p as a circulating biomarker for heart failure. Circ Res 2010; 106: 1035-1039.
    CrossrefPubMedGoogle Scholar
  • 51 Vorwerk S, Ganter K, Cheng Y. et al. Microfluidic-based enzymatic on-chip labeling of miRNAs. New Biotechnol 2008; 25: 142-149.
    CrossrefPubMedGoogle Scholar
  • 52 Chen Y, Gelfond JA, McManus LM. et al. Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis. BMC Genomics 2009; 10: 407.
    CrossrefPubMedGoogle Scholar
  • 53 Chen C, Ridzon DA, Broomer AJ. et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005; 33: e179.
    CrossrefPubMedGoogle Scholar
  • 54 Mestdagh P, Feys T, Bernard N. et al. High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA. Nucleic Acids Res 2008; 36: e143.
    CrossrefPubMedGoogle Scholar
  • 55 Linsen SE, de Wit E, Janssens G. et al. Limitations and possibilities of small RNA digital gene expression profiling. Nature Methods 2009; 06: 474-476.
    CrossrefPubMedGoogle Scholar
  • 56 Bryant RJ, Pawlowski T, Catto JW. et al. Changes in circulating microRNA levels associated with prostate cancer. Br J Cancer 2012; 106: 768-774.
    CrossrefPubMedGoogle Scholar
  • 57 Ballantyne KN, van Oorschot RA, Mitchell RJ. Locked nucleic acids in PCR primers increase sensitivity and performance. Genomics 2008; 91: 301-305.
    CrossrefPubMedGoogle Scholar
  • 58 Latorra D, Arar K, Hurley JM. Design considerations and effects of LNA in PCR primers. Mol Cell Probes 2003; 17: 253-259.
    CrossrefPubMedGoogle Scholar
  • 59 Levin JD, Fiala D, Samala MF. et al. Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers. Nucleic Acids Res 2006; 34: e142.
    CrossrefPubMedGoogle Scholar
  • 60 D'Alessandra Y, Devanna P, Limana F. et al. Circulating microRNAs are new and sensitive biomarkers of myocardial infarction. Eur Heart J 2010; 31: 2765-2773.
    CrossrefPubMedGoogle Scholar
  • 61 Ji X, Takahashi R, Hiura Y. et al. Plasma miR-208 as a biomarker of myocardial injury. Clin Chem 2009; 55: 1944-1949.
    CrossrefPubMedGoogle Scholar
  • 62 Zhang Y, Liu D, Chen X. et al. Secreted monocytic miR-150 enhances targeted endothelial cell migration. Mol Cell 2010; 39: 133-144.
    CrossrefPubMedGoogle Scholar
  • 63 Zampetaki A, Willeit P, Tilling L. et al. Prospective Study on Circulating MicroRNAs and Risk of Myocardial Infarction. JACC. 2012 in press.
    PubMedGoogle Scholar