Identification of circulating miRNA biomarkers based on global quantitative real-time PCR profiling

Journal of Animal Science and Biotechnology

Volumn 3, Issue 1, 2012, Pages

  Kang, Kang ^a,b   Peng, Xiao ^a   Luo, Jun ^b   Gou, Deming ^a  

^a SHENZHEN UNIVERSITY   (China)

^b NORTHWEST A F UNIVERSITY   (China)

Author keywords

biomarker; circulating microRNAs; profiling; quantitative real time PCR

Indexed keywords

EID: 84885687775     PISSN: 16749782     EISSN: 20491891     Source Type: Journal    
DOI: 10.1186/2049-1891-3-4     Document Type: Review

References (58)

1. Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell 2009, 136:215-233. 10.1016/j.cell.2009.01.002, 19167326.
2. Zhang S, Chen L, Jung EJ, Calin GA. Targeting microRNAs with small molecules: from dream to reality. Clin Pharmacol Ther 2010, 87:754-758. 10.1038/clpt.2010.46, 20428111.
3. 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. Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 2008, 105:10513-10518. 10.1073/pnas.0804549105, 2492472, 18663219.
4. Brase JC, Wuttig D, Kuner R, Sultmann H. Serum microRNAs as non-invasive biomarkers for cancer. Mol Cancer 2010, 9:306-315. 10.1186/1476-4598-9-306, 3002336, 21110877.
5. Yu DC, Li QG, Ding XW, Ding YT. Circulating MicroRNAs: Potential Biomarkers for Cancer. Int J Mol Sci 2011, 12:2055-2063. 10.3390/ijms12032055, 3111650, 21673939.
6. D'Alessandra Y, Devanna P, Limana F, Straino S, Di Carlo A, Brambilla PG, Rubino M, Carena MC, Spazzafumo L, De Simone M, Micheli B, Biglioli P, Achilli F, Martelli F, Maggiolini S, Marenzi G, Pompilio G, Capogrossi MC. Circulating microRNAs are new and sensitive biomarkers of myocardial infarction. Eur Heart J 2010, 31:2765-2773. 10.1093/eurheartj/ehq167, 2980809, 20534597.
7. Dimmeler S, Zeiher AM. Circulating microRNAs: novel biomarkers for cardiovascular diseases?. Eur Heart J 2010, 31:2705-2707. 10.1093/eurheartj/ehq221, 20605798.
8. Valoczi A, Hornyik C, Varga N, Burgyan J, Kauppinen S, Havelda Z. Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res 2004, 32:175-183.
9. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR. MicroRNA expression profiles classify human cancers. Nature 2005, 435:834-838. 10.1038/nature03702, 15944708.
10. Fichtlscherer S, De Rosa S, Fox H, Schwietz T, Fischer A, Liebetrau C, Weber M, Hamm CW, Roxe T, Muller-Ardogan M, Bonauer A, Zeiher AM, Dimmeler S. Circulating microRNAs in patients with coronary artery disease. Circ Res 2010, 107:677-684. 10.1161/CIRCRESAHA.109.215566, 20595655.
11. Zhao H, Shen J, Medico L, Wang D, Ambrosone CB, Liu S. A pilot study of circulating miRNAs as potential biomarkers of early stage breast cancer. PLoS One 2010, 5:13735-13747.
12. 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. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005, 33:179-188.
13. Yang H, Schmuke JJ, Flagg LM, Roberts JK, Allen EM, Ivashuta S, Gilbertson LA, Armstrong TA, Christian AT. A novel real-time polymerase chain reaction method for high throughput quantification of small regulatory RNAs. Plant Biotechnol J 2009, 7:621-630. 10.1111/j.1467-7652.2009.00429.x, 19619184.
14. Benes V, Castoldi M. Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available. Methods 2010, 50:244-249. 10.1016/j.ymeth.2010.01.026, 20109550.
15. Hu Z, Chen X, Zhao Y, Tian T, Jin G, Shu Y, Chen Y, Xu L, Zen K, Zhang C, Shen H. Serum microRNA signatures identified in a genome-wide serum microRNA expression profiling predict survival of non-small-cell lung cancer. J Clin Oncol 2010, 28:1721-1726. 10.1200/JCO.2009.24.9342, 20194856.
16. Wu Q, Lu Z, Li H, Lu J, Guo L, Ge Q. Next-generation sequencing of microRNAs for breast cancer detection. J Biomed Biotechnol 2011, 2011:597145-597152. 3118289, 21716661.
17. Kong W, Zhao JJ, He L, Cheng JQ. Strategies for profiling microRNA expression. J Cell Physiol 2009, 218:22-25. 10.1002/jcp.21577, 18767038.
18. Tang F, Hajkova P, Barton SC, Lao K, Surani MA. MicroRNA expression profiling of single whole embryonic stem cells. Nucleic Acids Res 2006, 34:9-16.
19. Mestdagh P, Feys T, Bernard N, Guenther S, Chen C, Speleman F, Vandesompele J. High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA. Nucleic Acids Res 2008, 36:143-151.
20. Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 2011, 39:152-157.
21. Ng EK, Chong WW, Jin H, Lam EK, Shin VY, Yu J, Poon TC, Ng SS, Sung JJ. Differential expression of microRNAs in plasma of patients with colorectal cancer: a potential marker for colorectal cancer screening. Gut 2009, 58:1375-1381. 10.1136/gut.2008.167817, 19201770.
22. McDonald JS, Milosevic D, Reddi HV, Grebe SK, Algeciras-Schimnich A. Analysis of circulating microRNA: preanalytical and analytical challenges. Clin Chem 2011, 57:833-840. 10.1373/clinchem.2010.157198, 21487102.
23. Kroh EM, Parkin RK, Mitchell PS, Tewari M. Analysis of circulating microRNA biomarkers in plasma and serum using quantitative reverse transcription-PCR (qRT-PCR). Methods 2010, 50:298-301. 10.1016/j.ymeth.2010.01.032, 20146939.
24. Gui J, Tian Y, Wen X, Zhang W, Zhang P, Gao J, Run W, Tian L, Jia X, Gao Y. Serum microRNA characterization identifies miR-885-5p as a potential marker for detecting liver pathologies. Clin Sci (Lond) 2011, 120:183-193.
25. Zhu HT, Dong QZ, Wang G, Zhou HJ, Ren N, Jia HL, Ye QH, Qin LX. Identification of Suitable Reference Genes for qRT-PCR Analysis of Circulating microRNAs in Hepatitis B Virus-Infected Patients. Mol Biotechnol 2012, 50:49-56. 10.1007/s12033-011-9414-6, 21567136.
26. Lao K, Xu NL, Sun YA, Livak KJ, Straus NA. Real time PCR profiling of 330 human micro-RNAs. Biotechnol J 2007, 2:33-35. 10.1002/biot.200600119, 17124719.
27. Resnick KE, Alder H, Hagan JP, Richardson DL, Croce CM, Cohn DE. The detection of differentially expressed microRNAs from the serum of ovarian cancer patients using a novel real-time PCR platform. Gynecol Oncol 2009, 112:55-59. 10.1016/j.ygyno.2008.08.036, 18954897.
28. Brase JC, Johannes M, Schlomm T, Falth M, Haese A, Steuber T, Beissbarth T, Kuner R, Sultmann H. Circulating miRNAs are correlated with tumor progression in prostate cancer. Int J Cancer 2011, 128:608-616. 10.1002/ijc.25376, 20473869.
29. Ji F, Yang B, Peng X, Ding H, You H, Tien P. Circulating microRNAs in hepatitis B virus-infected patients. J Viral Hepat 2011, 18:242-251.
30. Zahm AM, Thayu M, Hand NJ, Horner A, Leonard MB, Friedman JR. Circulating microRNA is a biomarker of pediatric Crohn disease. J Pediatr Gastroenterol Nutr 2011, 53:26-33. 10.1097/MPG.0b013e31822200cc, 21546856.
31. Varkonyi-Gasic E, Wu R, Wood M, Walton EF, Hellens RP. Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 2007, 3:12-24. 10.1186/1746-4811-3-12, 2225395, 17931426.
32. Reichenstein I, Aizenberg N, Goshen M, Bentwich Z, Avni YS. A novel qPCR assay for viral encoded microRNAs. J Virol Methods 2010, 163:323-328. 10.1016/j.jviromet.2009.10.018, 19879298.
33. Shi R, Chiang VL. Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 2005, 39:519-525. 10.2144/000112010, 16235564.
34. Zhang Y, Li M, Wang H, Fisher WE, Lin PH, Yao Q, Chen C. Profiling of 95 microRNAs in pancreatic cancer cell lines and surgical specimens by real-time PCR analysis. World J Surg 2009, 33:698-709. 10.1007/s00268-008-9833-0, 2933040, 19030927.
35. Jensen SG, Lamy P, Rasmussen MH, Ostenfeld MS, Dyrskjot L, Orntoft TF, Andersen CL. Evaluation of two commercial global miRNA expression profiling platforms for detection of less abundant miRNAs. BMC Genomics 2011, 12:435-461. 10.1186/1471-2164-12-435, 3184117, 21867561.
36. Balcells I, Cirera S, Busk PK. Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol 2011, 11:70-81. 10.1186/1472-6750-11-70, 3135530, 21702990.
37. Wei J, Gao W, Zhu CJ, Liu YQ, Mei Z, Cheng T, Shu YQ. Identification of plasma microRNA-21 as a biomarker for early detection and chemosensitivity of non-small cell lung cancer. Chin J Cancer 2011, 30:407-414. 10.5732/cjc.010.10522, 21627863.
38. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3:34-46.
39. Wu F, Zhang S, Dassopoulos T, Harris ML, Bayless TM, Meltzer SJ, Brant SR, Kwon JH. Identification of microRNAs associated with ileal and colonic Crohn's disease. Inflamm Bowel Dis 2010, 16:1729-1738. 10.1002/ibd.21267, 2946509, 20848482.
40. Davoren PA, McNeill RE, Lowery AJ, Kerin MJ, Miller N. Identification of suitable endogenous control genes for microRNA gene expression analysis in human breast cancer. BMC Mol Biol 2008, 9:76-87. 10.1186/1471-2199-9-76, 2533012, 18718003.
41. Peltier HJ, Latham GJ. Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues. RNA 2008, 14:844-852. 10.1261/rna.939908, 2327352, 18375788.
42. Andersen CL, Jensen JL, Orntoft TF. 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 2004, 64:5245-5250. 10.1158/0008-5472.CAN-04-0496, 15289330.
43. Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol 2007, 8:19-33.
44. The qRT-PCR data analysis software qBaseplus. , http://www.biogazelle.com/products
45. The qRT-PCR data analysis software GenEx. , http://www.multid.se/
46. Mestdagh P, Van Vlierberghe P, De Weer A, Muth D, Westermann F, Speleman F, Vandesompele J. A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol 2009, 10:64-74.
47. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009, 55:611-622. 10.1373/clinchem.2008.112797, 19246619.
48. Bustin SA. Why the need for qPCR publication guidelines?--The case for MIQE. Methods 2010, 50:217-226. 10.1016/j.ymeth.2009.12.006, 20025972.
49. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 2008, 3:1101-1108. 10.1038/nprot.2008.73, 18546601.
50. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25:402-408. 10.1006/meth.2001.1262, 11846609.
51. Hunter MP, Ismail N, Zhang X, Aguda BD, Lee EJ, Yu L, Xiao T, Schafer J, Lee ML, Schmittgen TD, Nana-Sinkam SP, Jarjoura D, Marsh CB. Detection of microRNA expression in human peripheral blood microvesicles. PLoS One 2008, 3:3694-3705.
52. Arroyo JD, Chevillet JR, Kroh EM, Ruf IK, Pritchard CC, Gibson DF, Mitchell PS, Bennett CF, Pogosova-Agadjanyan EL, Stirewalt DL, Tait JF, Tewari M. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc Natl Acad Sci USA 2011, 108:5003-5008. 10.1073/pnas.1019055108, 3064324, 21383194.
53. Chen X, Gao C, Li H, Huang L, Sun Q, Dong Y, Tian C, Gao S, Dong H, Guan D, Hu X, Zhao S, Li L, Zhu L, Yan Q, Zhang J, Zen K, Zhang CY. Identification and characterization of microRNAs in raw milk during different periods of lactation, commercial fluid, and powdered milk products. Cell Res 2010, 20:1128-1137. 10.1038/cr.2010.80, 20548333.
54. Applied Biosystems Megaplex™ Pools. , http://www.appliedbiosystems.com/absite/us/en/home.html
55. System Biosciences QuantiMir™. , http://www.systembio.com/
56. SABiosciences RT2 miRNA PCR Array. , http://www.sabiosciences.com/
57. Invitrogen NCode EXPRESS SYBR GreenER miRNA qRT-PCR Kit. , http://www.invitrogen.com/site/us/en/home.html
58. Exiqon miRCURY LNA™ Universal RT microRNA PCR. , http://www.exiqon.com/