Assessment of RT-qPCR normalization strategies for accurate quantification of extracellular microRNAs in murine Serum

PLoS ONE

Volumn 9, Issue 2, 2014, Pages

  Roberts, Thomas C ^a,b   Coenen Stass, Anna M L ^a   Wood, Matthew J A ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; MICRORNA; MICRORNA 16; MICRORNA 223; MICRORNA 31;

ANIMAL EXPERIMENT; ARTICLE; DISEASE COURSE; DUCHENNE MUSCULAR DYSTROPHY; GENE EXPRESSION; INTERMETHOD COMPARISON; MALE; MOUSE; NONHUMAN; PROCESS OPTIMIZATION; QUANTITATIVE STUDY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SENSITIVITY ANALYSIS; VALIDATION PROCESS;

ANALYSIS OF VARIANCE; ANIMALS; BIOLOGICAL MARKERS; CAENORHABDITIS ELEGANS; CALIBRATION; MICE; MICRORNAS; RESEARCH DESIGN; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 84895875247     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0089237     Document Type: Article

References (38)

1. Ivey KN, Srivastava D (2010) MicroRNAs as regulators of differentiation and cell fate decisions. Cell Stem Cell 7: 36-41. doi:10.1016/j.stem.2010.06. 012.
2. Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, et al. (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 105: 10513-10518. doi:10.1073/pnas.0804549105.
3. Gilad S, Meiri E, Yogev Y, Benjamin S, Lebanony D, et al. (2008) Serum microRNAs are promising novel biomarkers. PLoS ONE 3: e3148. doi:10.1371/journal.pone.0003148.
4. Russo F, Di Bella S, Nigita G, Macca V, Laganà A, et al. (2012) miRandola: extracellular circulating microRNAs database. PLoS ONE 7: e47786. doi:10.1371/journal.pone.0047786.
5. Vickers KC, Palmisano BT, Shoucri BM, Shamburek RD, Remaley AT (2011) MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins. Nat Cell Biol 13: 423-433. doi:10.1038/ncb2210.
6. Turchinovich A, Weiz L, Langheinz A, Burwinkel B (2011) Characterization of extracellular circulating microRNA. Nucleic Acids Res 39: 7223-7233. doi:10.1093/nar/gkr254.
7. Turchinovich A, Burwinkel B (2012) Distinct AGO1 and AGO2 associated miRNA profiles in human cells and blood plasma. RNA Biol 9: 1066-1075.
8. Kosaka N, Iguchi H, Yoshioka Y, Takeshita F, Matsuki Y, et al. (2010) Secretory mechanisms and intercellular transfer of microRNAs in living cells. J Biol Chem 285: 17442-17452. doi:10.1074/jbc.M110.107821.
9. Valadi H, Ekström K, Bossios A, Sjöstrand M, Lee JJ, et al. (2007) Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells. Nat Cell Biol 9: 654-659. doi:10.1038/ncb1596. (Pubitemid 47214727)
10. Hoffman EP, Brown RH Jr, Kunkel LM (1987) Dystrophin: the protein product of the Duchenne muscular dystrophy locus. Cell 51: 919-928.
11. Kinali M, Arechavala-Gomeza V, Feng L, Cirak S, Hunt D, et al. (2009) Local restoration of dystrophin expression with the morpholino oligomer AVI-4658 in Duchenne muscular dystrophy: a single-blind, placebo-controlled, dose-escalation, proof-of-concept study. Lancet Neurol 8: 918-928. doi:10.1016/S1474-4422(09)70211-X.
12. Van Deutekom JC, Janson AA, Ginjaar IB, FrankhuizenWS, Aartsma-Rus A, et al. (2007) Local dystrophin restoration with antisense oligonucleotide PRO051. N Engl J Med 357: 2677-2686. doi:10.1056/NEJMoa073108.
13. Mizuno H, Nakamura A, Aoki Y, Ito N, Kishi S, et al. (2011) Identification of muscle-specific microRNAs in serum of muscular dystrophy animal models: promising novel blood-based markers for muscular dystrophy. PLoS ONE 6: e18388. doi:10.1371/journal.pone.0018388.
14. Cacchiarelli D, Legnini I, Martone J, Cazzella V, D'Amico A, et al. (2011) miRNAs as serum biomarkers for Duchenne muscular dystrophy. EMBO Mol Med 3: 258-265. doi:10.1002/emmm.201100133.
15. Roberts TC, Blomberg KEM, McClorey G, Andaloussi SE, Godfrey C, et al. (2012) Expression Analysis in Multiple Muscle Groups and Serum Reveals Complexity in the MicroRNA Transcriptome of the mdx Mouse with Implications for Therapy. Molecular Therapy - Nucleic Acids 1: e39. doi:10.1038/mtna.2012.26.
16. Hori SS, Gambhir SS (2011) Mathematical model identifies blood biomarker-based early cancer detection strategies and limitations. Sci Transl Med 3: 109ra116. doi:10.1126/scitranslmed.3003110.
17. Williams Z, Ben-Dov IZ, Elias R, Mihailovic A, Brown M, et al. (2013) Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations. Proc Natl Acad Sci U S A 110: 4255-4260. doi:10.1073/pnas.1214046110.
18. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, et al. (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33: e179. doi:10.1093/nar/gni178.
19. Fu H-J, Zhu J, Yang M, Zhang Z-Y, Tie Y, et al. (2006) A novel method to monitor the expression of microRNAs. Mol Biotechnol 32: 197-204. doi:10.1385/MB:32:3:197. (Pubitemid 43787131)
20. Jones LJ, Yue ST, Cheung CY, Singer VL (1998) RNA quantitation by fluorescence-based solution assay: RiboGreen reagent characterization. Anal Biochem 265: 368-374. doi:10.1006/abio.1998.2914. (Pubitemid 29002085)
21. Blondal T, Jensby Nielsen S, Baker A, Andreasen D, Mouritzen P, et al. (2013) Assessing sample and miRNA profile quality in serum and plasma or other biofluids. Methods 59: S1-6. doi:10.1016/j.ymeth.2012.09.015.
22. Roberts TC, Godfrey C, McClorey G, Vader P, Briggs D, et al. (2013) Extracellular microRNAs are dynamic non-vesicular biomarkers of muscle turnover. Nucl Acids Res 41: 9500-9513. doi:10.1093/nar/gkt724.
23. Mestdagh P, Van Vlierberghe P, De Weer A, Muth D, Westermann F, et al. (2009) A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol 10: R64. doi:10.1186/gb-2009-10-6-r64.
24. Mattie MD, Benz CC, Bowers J, Sensinger K, Wong L, et al. (2006) Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 5: 24. doi:10.1186/1476-4598-5-24.
25. Goyenvalle A, Babbs A, Powell D, Kole R, Fletcher S, et al. (2010) Prevention of dystrophic pathology in severely affected dystrophin/utrophin- deficient mice by morpholino-oligomer-mediated exon-skipping. Mol Ther 18: 198-205. doi:10.1038/mt.2009.248.
26. Vignier N, Amor F, Fogel P, Duvallet A, Poupiot J, et al. (2013) Distinctive serum miRNA profile in mouse models of striated muscular pathologies. PLoS ONE 8: e55281. doi:10.1371/journal.pone.0055281.
27. Betts C, Saleh AF, Arzumanov AA, Hammond SM, Godfrey C, et al. (2012) Pip6-PMO, A New Generation of Peptide-oligonucleotide Conjugates With Improved Cardiac Exon Skipping Activity for DMD Treatment. Molecular Therapy - Nucleic Acids 1: e38. doi:10.1038/mtna.2012.30.
28. Fichtlscherer S, De Rosa S, Fox H, Schwietz T, Fischer A, et al. (2010) Circulating microRNAs in patients with coronary artery disease. Circ Res 107: 677-684. doi:10.1161/CIRCRESAHA.109.215566.
29. Kroh EM, Parkin RK, Mitchell PS, Tewari M (2010) Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR). Methods 50: 298-301. doi:10.1016/ j.ymeth.2010.01.032.
30. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 55: 611-622. doi:10.1373/clinchem.2008.112797.
31. Taylor S, Wakem M, Dijkman G, Alsarraj M, Nguyen M (2010) A practical approach to RT-qPCR-Publishing data that conform to the MIQE guidelines. Methods 50: S1-5. doi:10.1016/j.ymeth.2010.01.005.
32. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: e45.
33. Ramakers C, Ruijter JM, Deprez RHL, Moorman AFM (2003) Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci Lett 339: 62-66. (Pubitemid 36263221)
34. Andersen CL, Jensen JL, Ørntoft TF (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64: 5245-5250. doi:10.1158/0008-5472.CAN-04-0496. (Pubitemid 39006544)
35. Wang Y, Tang N, Hui T, Wang S, Zeng X, et al. (2013) Identification of endogenous reference genes for RT-qPCR analysis of plasma microRNAs levels in rats with acetaminophen-induced hepatotoxicity. J Appl Toxicol 33: 1330-1336. doi:10.1002/jat.2864.
36. Sanders I, Holdenrieder S, Walgenbach-Brünagel G, von Ruecker A, Kristiansen G, et al. (2012) Evaluation of reference genes for the analysis of serum miRNA in patients with prostate cancer, bladder cancer and renal cell carcinoma. Int J Urol 19: 1017-1025. doi:10.1111/j.1442-2042.2012.03082.x.
37. Mi Q-S, Weiland M, Qi R-Q, Gao X-H, Poisson LM, et al. (2012) Identification of mouse serum miRNA endogenous references by global gene expression profiles. PLoS ONE 7: e31278. doi:10.1371/journal.pone.0031278.
38. Song J, Bai Z, Han W, Zhang J, Meng H, et al. (2012) Identification of suitable reference genes for qPCR analysis of serum microRNA in gastric cancer patients. Dig Dis Sci 57: 897-904. doi:10.1007/s10620-011-1981-7.