Suitable reference genes for relative quantification of miRNA expression in prostate cancer

Experimental and Molecular Medicine

Volumn 42, Issue 11, 2010, Pages 749-758

  Schaefer, Annika ^a,b,c   Jung, Monika ^a   Miller, Kurt ^a   Lein, Michael ^a,b   Kristiansen, Glen ^d   Erbersdobler, Andreas ^e   Jung, Klaus ^a,b  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b Berlin Institute for Urologic Research   (Germany)

^c FREIE UNIVERSITÄT BERLIN   (Germany)

^d UNIVERSITY HOSPITAL ZURICH   (Switzerland)

^e ROSTOCK UNIVERSITY MEDICAL CENTER   (Germany)

Author keywords

Gene expression profiling; MicroRNA; Polymerase chain reaction; Prostate neoplasms

Indexed keywords

MICRORNA; MICRORNA 130B; MICRORNA 16; SMALL NUCLEOLAR RNA; SMALL NUCLEOLAR RNA CD BOX 7; U6 SMALL NUCLEOLAR RNA 2; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; GENE EXPRESSION PROFILING; GENETIC REGULATION; HUMAN; HUMAN CELL; HUMAN TISSUE; MAJOR CLINICAL STUDY; MALE; PREDICTION; PROSTATE CANCER; PROSTATECTOMY; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION;

EID: 78649785019     PISSN: 12263613     EISSN: 20926413     Source Type: Journal    
DOI: 10.3858/emm.2010.42.11.076     Document Type: Article

References (47)

1. Ambs S, Prueitt RL, Yi M, Hudson RS, Howe TM, Petrocca F, Wallace TA, Liu CG, Volinia S, Calin GA, Yfantis HG, Stephens RM, Croce CM. Genomic profiling of microRNA and messenger RNA reveals deregulated microRNA expression in prostate cancer. Cancer Res 2008;68:6162-70
2. 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;64:5245-50
3. Bartels CL, Tsongalis GJ. MicroRNAs: novel biomarkers for human cancer. Clin Chem 2009;55:623-31
4. Berezikov E, Guryev V, van de BJ, Wienholds E, Plasterk RH, Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell 2005;120: 21-4
5. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93
6. Bonci D, Coppola V, Musumeci M, Addario A, Giuffrida R, Memeo L, D'Urso L, Pagliuca A, Biffoni M, Labbaye C, Bartucci M, Muto G, Peschle C, De MR. The miR-15amiR- 16-1 cluster controls prostate cancer by targeting multiple oncogenic activities. Nat Med 2008;14:1271-7
7. Bustin SA, Nolan T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J Biomol Tech 2004;15:155-66
8. 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;55:611-22
9. Chang KH, Mestdagh P, Vandesompele J, Kerin MJ, Miller N. MicroRNA expression profiling to identify and validate reference genes for relative quantification in colorectal cancer. BMC Cancer 2010;10:173
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. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005;33:e179
11. 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
12. Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, Johnson MA, Rook GA, Zumla A. The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Anal Biochem 2005;344: 141-3
13. Epstein JI, Allsbrook WC Jr, Amin MB, Egevad LL. The 2005 International Society of Urological Pathology (ISUP) Consensus Conference on Gleason Grading of Prostatic Carcinoma. Am J Surg Pathol 2005;29:1228-42
14. Filipowicz W, Jaskiewicz L, Kolb FA, Pillai RS. Posttranscriptional gene silencing by siRNAs and miRNAs. Curr Opin Struct Biol 2005;15:331-41
15. Gandellini P, Folini M, Longoni N, Pennati M, Binda M, Colecchia M, Salvioni R, Supino R, Moretti R, Limonta P, Valdagni R, Daidone MG, Zaffaroni N. miR-205 Exerts tumor-suppressive functions in human prostate through down-regulation of protein kinase Cepsilon. Cancer Res 2009;69:2287-95
16. Garzon R, Calin GA, Croce CM. MicroRNAs in Cancer. Annu Rev Med 2009;60:167-79
17. Haller F, Kulle B, Schwager S, Gunawan B, von HA, Sultmann H, Fuzesi L. Equivalence test in quantitative reverse transcription polymerase chain reaction: confirmation of reference genes suitable for normalization. Anal Biochem 2004;335:1-9
18. Huang Q, Gumireddy K, Schrier M, le Sage C, Nagel R, Nair S, Egan DA, Li A, Huang G, Klein-Szanto AJ, Gimotty PA, Katsaros D, Coukos G, Zhang L, Pure E, Agami R. The microRNAs miR-373 and miR-520c promote tumour invasion and metastasis. Nat Cell Biol 2008;10:202-10
19. Jiang J, Lee EJ, Gusev Y, Schmittgen TD. Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucleic Acids Res 2005;33:5394-403
20. Josson S, Sung SY, Lao K, Chung LW, Johnstone PA. Radiation modulation of microRNA in prostate cancer cell lines. Prostate 2008;68:1599-606
21. Jung M, Mollenkopf HJ, Grimm C, Wagner I, Albrecht M, Waller T, Pilarsky C, Johannsen M, Stephan C, Lehrach H, Nietfeld W, Rudel T, Jung K, Kristiansen G. MicroRNA profiling of clear cell renal cell cancer identifies a robust signature to define renal malignancy. J Cell Mol Med 2009;13:3918-28
22. Kubista M, Andrade JM, Bengtsson M, Forootan A, Jonak J, Lind K, Sindelka R, Sjoback R, Sjogreen B, Strombom L, Stahlberg A, Zoric N. The real-time polymerase chain reaction. Mol Aspects Med 2006;27:95-125
23. Lee YS, Dutta A. MicroRNAs in cancer. Annu Rev Pathol 2009;4:199-227
24. Leite KR, Sousa-Canavez JM, Reis ST, Tomiyama AH, Camara-Lopes LH, Sanudo A, Antunes AA, Srougi M. Change in expression of miR-let7c, miR-100, and miR-218 from high grade localized prostate cancer to metastasis. Urol Oncol 2009; in press: doi:10.1016/j.urolonc.2009.02.002
25. Mattie MD, Benz CC, Bowers J, Sensinger K, Wong L, Scott GK, Fedele V, Ginzinger D, Getts R, Haqq C. Optimized high-throughput microRNA expression profiling provides novel biomarker assessment of clinical prostate and breast cancer biopsies. Mol Cancer 2006;5:24
26. 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:R64
27. 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: 1777-88
28. Min H, Yoon S. Got target? Computational methods for microRNA target prediction and their extension. Exp Mol Med 2010;42:233-44
29. 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;105:10513-8
30. Nolan T, Hands RE, Bustin SA. Quantification of mRNA using real-time RT-PCR. Nat Protoc 2006;1:1559-82
31. Noonan EJ, Place RF, Pookot D, Basak S, Whitson JM, Hirata H, Giardina C, Dahiya R. miR-449a targets HDAC-1 and induces growth arrest in prostate cancer. Oncogene 2009;28:1714-24
32. Ohl F, Jung M, Xu C, Stephan C, Rabien A, Burkhardt M, Nitsche A, Kristiansen G, Loening SA, Radonic A, Jung K. Gene expression studies in prostate cancer tissue: which reference gene should be selected for normalization? J Mol Med 2005;83:1014-24
33. Ozen M, Creighton CJ, Ozdemir M, Ittmann M. Widespread deregulation of microRNA expression in human prostate cancer. Oncogene 2008;27:1788-93
34. 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;14:844-52
35. Place RF, Li LC, Pookot D, Noonan EJ, Dahiya R. MicroRNA- 373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci USA 2008;105: 1608-13
36. Porkka KP, Pfeiffer MJ, Waltering KK, Vessella RL, Tammela TL, Visakorpi T. MicroRNA expression profiling in prostate cancer. Cancer Res 2007;67:6130-5
37. Pradervand S, Weber J, Thomas J, Bueno M, Wirapati P, Lefort K, Dotto GP, Harshman K. Impact of normalization on miRNA microarray expression profiling. RNA 2009;15:493-501
38. Prueitt RL, Yi M, Hudson RS, Wallace TA, Howe TM, Yfantis HG, Lee DH, Stephens RM, Liu CG, Calin GA, Croce CM, Ambs S. Expression of microRNAs and protein-coding genes associated with perineural invasion in prostate cancer. Prostate 2008;68:1152-64
39. Rokhlin OW, Scheinker VS, Taghiyev AF, Bumcrot D, Glover RA, Cohen MB. MicroRNA-34 mediates AR-dependent p53-induced apoptosis in prostate cancer. Cancer Biol Ther 2008;7:1288-96
40. Rondinelli RH, Epner DE, Tricoli JV. Increased glyceraldehyde- 3-phosphate dehydrogenase gene expression in late pathological stage human prostate cancer. Prostate Cancer Prostatic Dis 1997;1:66-72
41. Schaefer A, Jung M, Mollenkopf H-J, Wagner I, Stephan C, Jentzmik F, Miller K, Lein M, Kristiansen G, Jung K. Diagnostic and prognostic implications of microRNA profiling in prostate carcinoma. Int J Cancer 2010a;126:1166-76
42. Schaefer A, Stephan C, Busch J, Yousef GM, Jung K. Diagnostic, prognostic, and therapeutic implications of miRNAs in urologic tumors. Nat Rev Urol 2010b;7:286-97
43. Siva AC, Nelson LJ, Fleischer CL, Majlessi M, Becker MM, Vessella RL, Reynolds MA. Molecular assays for the detection of microRNAs in prostate cancer. Mol Cancer 2009;8:17
44. Sobin LH, Wittekind C. TNM Classification of Malignant Tumours, 6th Ed, 2002, Wiley-Liss, New York, NY.
45. Spahn M, Kneitz S, Scholz CJ, Nico S, Rudiger T, Strobel P, Riedmiller H, Kneitz B. Expression of microRNA-221 is progressively reduced in aggressive prostate cancer and metastasis and predicts clinical recurrence. Int J Cancer 2010;127:394-403
46. Tong AW, Fulgham P, Jay C, Chen P, Khalil I, Liu S, Senzer N, Eklund AC, Han J, Nemunaitis J. MicroRNA profile analysis of human prostate cancers. Cancer Gene Ther 2009;16:206-16
47. 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: RESEARCH0034