Identification of suitable endogenous control genes for microRNA gene expression analysis in human breast cancer

BMC Molecular Biology

Volumn 9, Issue , 2008, Pages

  Davoren, Pamela A ^a   McNeill, Roisin E ^a   Lowery, Aoife J ^a   Kerin, Michael J ^a   Miller, Nicola ^a  

^a NATIONAL UNIVERSITY OF IRELAND   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; SMALL NUCLEOLAR RNA; SMALL NUCLEAR RNA;

ADULT; AGED; ARTICLE; BONE METASTASIS; BREAST CANCER; BREAST CARCINOGENESIS; CLINICAL ARTICLE; CONTROLLED STUDY; FEMALE; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; HUMAN; HUMAN TISSUE; MASTECTOMY; NUCLEOTIDE SEQUENCE; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RELIABILITY; RNA ANALYSIS; VISCERAL METASTASIS; BREAST TUMOR; GENE EXPRESSION REGULATION; GENE SILENCING; GENETICS; POLYMERASE CHAIN REACTION; STANDARD; TUMOR GENE;

BREAST NEOPLASMS; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENE SILENCING; GENES, NEOPLASM; HUMANS; MICRORNAS; POLYMERASE CHAIN REACTION; REFERENCE STANDARDS; RNA, SMALL NUCLEAR;

EID: 51349111360     PISSN: None     EISSN: 14712199     Source Type: Journal    
DOI: 10.1186/1471-2199-9-76     Document Type: Article

References (63)

1. Mattick JS Non-coding RNAs: The architects of eukaryotic complexity EMBO Rep 2001, 2(11):986-991 1084129 11713189 10.1093/embo-reports/kve230
2. Mattick JS Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms. Bioessays 2003:930-935 10.1002/bies.10332 14505360
3. 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):843-854 10.1016/0092-8674(93)90529-Y 8252621
4. Griffiths-Jones S Grocock RJ van Dongen S Bateman A Enright AJ miRBase: microRNA sequences, targets and gene nomenclature Nucleic Acids Res 2006, 34 Database issue D140-4 1347474 16381832 10.1093/nar/gkj112
5. Griffiths-Jones S The microRNA Registry Nucleic Acids Res 2004, 32 Database issue D109-11 308757 14681370 10.1093/nar/gkh023
6. O'Donnell KA Wentzel EA Zeller KI Dang CV Mendell JT c-Myc-regulated microRNAs modulate E2F1 expression Nature 2005, 435(7043):839-843 10.1038/nature03677 15944709
7. Cimmino A Calin GA Fabbri M Iorio MV Ferracin M Shimizu M Wojcik SE Aqeilan RI Zupo S Dono M Rassenti L Alder H Volinia S Liu CG Kipps TJ Negrini M Croce CM miR-15 and miR-16 induce apoptosis by targeting BCL2 Proc Natl Acad Sci U S A 2005, 102(39):13944-13949 1236577 16166262 10.1073/pnas.0506654102
8. Kent OA Mendell JT A small piece in the cancer puzzle: MicroRNAs as tumor suppressors and oncogenes Oncogene 2006, 25(46):6188-6196 10.1038/ sj.onc.1209913 17028598
9. Esquela-Kerscher A Slack FJ Oncomirs - microRNAs with a role in cancer Nat Rev Cancer 2006, 6(4):259-269 10.1038/nrc1840 16557279
10. Fidler IJ The pathogenesis of cancer metastasis: The 'seed and soil' hypothesis revisited Nat Rev Cancer 2003, 3(6):453-458 10.1038/nrc1098 12778135
11. Gupta GP Massague J Cancer metastasis: Building a framework Cell 2006, 127(4):679-695 10.1016/j.cell.2006.11.001 17110329
12. Tavazoie SF Alarcon C Oskarsson T Padua D Wang Q Bos PD Gerald WL Massague J Endogenous human microRNAs that suppress breast cancer metastasis Nature 2008, 451(7175);147-152 10.1038/nature06487 18185580
13. Ma L Teruya-Feldstein J Weinberg RA Tumour invasion and metastasis initiated by microRNA-10b in breast cancer Nature 2007, 449(7163):682-688 10.1038/nature06174 17898713
14. Budhu A Jia HL Forgues M Liu CG Goldstein D Lam A Zanetti KA Ye QH Qin LX Croce CM Tang ZY Wang XW Identification of metastasis-related microRNAs in hepatocellular carcinoma Hepatology 2008, 47(3):897-907 10.1002/hep.22160 18176954
15. Sempere LF Freemantle S Pitha-Rowe I Moss E Dmitrovsky E Ambros V 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(3):R13 395763 15003116 10.1186/gb-2004-5-3-r13
16. 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(7043):834-838 10.1038/nature03702 15944708
17. Miska EA Alvarez-Saavedra E Townsend M Yoshii A Sestan N Rakic P Constantine-Paton M Horvitz HR Microarray analysis of microRNA expression in the developing mammalian brain Genome Biol 2004, 5(9):R68 522875 15345052 10.1186/gb-2004-5-9-r68
18. 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(20):e179 1292995 16314309 10.1093/nar/gni178
19. Tang F Hajkova P Barton SC Lao K Surani MA MicroRNA expression profiling of single whole embryonic stem cells Nucleic Acids Res 2006, 34(2):e9 1351374 16434699 10.1093/nar/gnj009
20. Lao K Xu NL Yeung V Chen C Livak KJ Straus NA Multiplexing RT-PCR for the detection of multiple miRNA species in small samples Biochem Biophys Res Commun 2006, 343(1):85-89 10.1016/j.bbrc.2006.02.106 16529715
21. McNeill RE Miller N Kerin MJ Evaluation and validation of candidate endogenous control genes for real-time quantitative PCR studies of breast cancer BMC Mol Biol 2007, 8:107 2211316 18042273 10.1186/ 1471-2199-8-107
22. Wong ML Medrano JF Real-time PCR for mRNA quantitation Biotechniques 2005, 39(1):75-85 16060372
23. Schmittgen TD Zakrajsek BA Effect of experimental treatment on housekeeping gene expression: Validation by real-time, quantitative RT-PCR J Biochem Biophys Methods 2000, 46(1-2):69-81 10.1016/ S0165-022X(00)00129-9 11086195
24. 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 1563474 16784538 10.1186/ 1476-4598-5-24
25. Liu CG Calin GA Meloon B Gamliel N Sevignani C Ferracin M Dumitru CD Shimizu M Zupo S Dono M Alder H Bullrich F Negrini M Croce CM An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues Proc Natl Acad Sci U S A 2004, 101(26):9740-9744 470744 15210942 10.1073/pnas.0403293101
26. Kulshreshtha R Ferracin M Wojcik SE Garzon R Alder H Agosto-Perez FJ Davuluri R Liu CG Croce CM Negrini M Calin GA Ivan M A microRNA signature of hypoxia Mol Cell Biol 2007, 27(5):1859-1867 1820461 17194750 10.1128/MCB.01395-06
27. Chang XZ Li DQ Hou YF Wu J Lu JS Di GH Jin W Ou ZL Shen ZZ Shao ZM Identification of the functional role of peroxiredoxin 6 in the progression of breast cancer Breast Cancer Res 2007, 9(6):R76 2246172 17980029 10.1186/bcr1789
28. Liang Z Wu H Reddy S Zhu A Wang S Blevins D Yoon Y Zhang Y Shim H Blockade of invasion and metastasis of breast cancer cells via targeting CXCR4 with an artificial microRNA Biochem Biophys Res Commun 2007, 363(3):542-546 10.1016/j.bbrc.2007.09.007 17889832
29. Bustin SA Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays J Mol Endocrinol 2000, 25(2):169-193 10.1677/jme.0.0250169 11013345
30. 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(7):RESEARCH0034 126239 12184808 10.1186/gb-2002-3-7-research0034
31. Nadano D Sato TA Caspase-3-dependent and -independent degradation of 28 S ribosomal RNA may be involved in the inhibition of protein synthesis during apoptosis initiated by death receptor engagement J Biol Chem 2000, 275(18):13967-13973 10.1074/jbc.275.18.13967 10788523
32. 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(2):66-72 10.1038/ sj.pcan.4500208 12496918
33. Tokunaga K Nakamura Y Sakata K Fujimori K Ohkubo M Sawada K Sakiyama S Enhanced expression of a glyceraldehyde-3-phosphate dehydrogenase gene in human lung cancers Cancer Res 1987, 47(21):5616-5619 3664468
34. Weisman AS Tixier-Vidal A Gourdji D Thyrotropin-releasing hormone increases the levels of c-fos and beta-actin mRNA in GH3/B6 pituitary tumor cells In Vitro Cell Dev Biol 1987, 23(8):585-590 10.1007/ BF02620977 3114226
35. Cavaille J Bachellerie JP SnoRNA-guided ribose methylation of rRNA: structural features of the guide RNA duplex influencing the extent of the reaction Nucleic Acids Res 1998, 26(7):1576-1587 147472 9512526 10.1093/nar/26.7.1576
36. Ganot P Jady BE Bortolin ML Darzacq X Kiss T Nucleolar factors direct the 2′-O-ribose methylation and pseudouridylation of U6 spliceosomal RNA Mol Cell Biol 1999, 19(10):6906-6917 84686 10490628
37. Cavaille J Buiting K Kiefmann M Lalande M Brannan CI Horsthemke B Bachellerie JP Brosius J Huttenhofer A Identification of brain-specific and imprinted small nucleolar RNA genes exhibiting an unusual genomic organization Proc Natl Acad Sci U S A 2000, 97(26):14311-14316 18915 11106375 10.1073/pnas.250426397
38. Nakamoto M Jin P O'Donnell WT Warren ST Physiological identification of human transcripts translationally regulated by a specific microRNA Hum Mol Genet 2005, 14(24):3813-3821 10.1093/hmg/ddi397 16239240
39. Nolan T Hands RE Bustin SA Quantification of mRNA using real-time RT-PCR Nat Protoc 2006, 1(3):1559-1582 10.1038/nprot.2006.236 17406449
40. Ohl F Jung M Radonic A Sachs M Loening SA Jung K Identification and validation of suitable endogenous reference genes for gene expression studies of human bladder cancer J Urol 2006, 175(5):1915-1920 10.1016/ S0022-5347(05)00919-5 16600798
41. Haller F Kulle B Schwager S Gunawan B von Heydebreck A 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):1-9 10.1016/j.ab.2004.08.024 15519565
42. Chan JA Krichevsky AM Kosik KS MicroRNA-21 is an antiapoptotic factor in human glioblastoma cells Cancer Res 2005, 65(14):6029-6033 10.1158/ 0008-5472.CAN-05-0137 16024602
43. Calin GA Dumitru CD Shimizu M Bichi R Zupo S Noch E Aldler H Rattan S Keating M Rai K Rassenti L Kipps T Negrini M Bullrich F Croce CM 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):15524-15529 137750 12434020 10.1073/pnas.242606799
44. 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(2):202-210 10.1038/ncb1681 18193036
45. Raymond CK Roberts BS Garrett-Engele P Lim LP Johnson JM Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs Rna 2005, 11(11):1737-1744 1370860 16244135 10.1261/rna.2148705
46. Tricarico C Pinzani P Bianchi S Paglierani M Distante V Pazzagli M Bustin SA Orlando C Quantitative real-time reverse transcription polymerase chain reaction: Normalization to rRNA or single housekeeping genes is inappropriate for human tissue biopsies Anal Biochem 2002, 309(2):293-300 10.1016/S0003-2697(02)00311-1 12413463
47. Chan MW Wei SH Wen P Wang Z Matei DE Liu JC Liyanarachchi S Brown R Nephew KP Yan PS Huang TH Hypermethylation of 18S and 28S ribosomal DNAs predicts progression-free survival in patients with ovarian cancer Clin Cancer Res 2005, 11(20):7376-7383 10.1158/1078-0432.CCR-05-1100 16243810
48. Runte M Huttenhofer A Gross S Kiefmann M Horsthemke B Buiting K The IC-SNURF-SNRPN transcript serves as a host for multiple small nucleolar RNA species and as an antisense RNA for UBE3A Hum Mol Genet 2001, 10(23):2687-2700 10.1093/hmg/10.23.2687 11726556
49. Takamizawa J Konishi H Yanagisawa K Tomida S Osada H Endoh H Harano T Yatabe Y Nagino M Nimura Y Mitsudomi T Takahashi T Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival Cancer Res 2004, 64(11):3753-3756 10.1158/ 0008-5472.CAN-04-0637 15172979
50. Pineles BL Romero R Montenegro D Tarca AL Han YM Kim YM Draghici S Espinoza J Kusanovic JP Mittal P Hassan SS Kim CJ Distinct subsets of microRNAs are expressed differentially in the human placentas of patients with preeclampsia Am J Obstet Gynecol 2007, 196(3):261 e1-6 10.1016/j.ajog.2007.01.008
51. 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 18375788
52. Popescu NC Genetic alterations in cancer as a result of breakage at fragile sites Cancer Lett 2003, 192(1):1-17 10.1016/ S0304-3835(02)00596-7 12637148
53. Calin GA Sevignani C Dumitru CD Hyslop T Noch E Yendamuri S Shimizu M Rattan S Bullrich F Negrini M Croce CM Human microRNA genes are frequently located at fragile sites and genomic regions involved in cancers Proc Natl Acad Sci U S A 2004, 101(9):2999-3004 365734 14973191 10.1073/pnas.0307323101
54. 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(15):5245-5250 10.1158/ 0008-5472.CAN-04-0496 15289330
55. Bustin SA Nolan T Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction J Biomol Tech 2004, 15(3):155-166 2291693 15331581
56. Goossens K Van Poucke M Van Soom A Vandesompele J Van Zeveren A Peelman LJ Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos BMC Dev Biol 2005, 5:27 1315359 16324220 10.1186/ 1471-213X-5-27
57. Johnson SM Grosshans H Shingara J Byrom M Jarvis R Cheng A Labourier E Reinert KL Brown D Slack FJ RAS is regulated by the let-7 microRNA family Cell 2005, 120(5):635-647 10.1016/j.cell.2005.01.014 15766527
58. Liang Y Ridzon D Wong L Chen C Characterization of microRNA expression profiles in normal human tissues BMC Genomics 2007, 8:166 1904203 17565689 10.1186/1471-2164-8-166
59. Bortolin ML Kiss T Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding Rna 1998, 4(4):445-454 1369630 9630250
60. Ganot P Bortolin ML Kiss T Site-specific pseudouridine formation in preribosomal RNA is guided by small nucleolar RNAs Cell 1997, 89(5):799-809 10.1016/S0092-8674(00)80263-9 9182768
61. Kiss T Bortolin ML Filipowicz W Characterization of the intron-encoded U19 RNA, a new mammalian small nucleolar RNA that is not associated with fibrillarin Mol Cell Biol 1996, 16(4):1391-1400 231123 8657112
62. Galardi S Fatica A Bachi A Scaloni A Presutti C Bozzoni I Purified box C/ D snoRNPs are able to reproduce site-specific 2′-O-methylation of target RNA in vitro Mol Cell Biol 2002, 22(19):6663-6668 134041 12215523 10.1128/MCB.22.19.6663-6668.2002
63. Zhou H Chen YQ Du YP Qu LH The Schizosaccharomyces pombe mgU6-47 gene is required for 2′-O-methylation of U6 snRNA at A41 Nucleic Acids Res 2002, 30(4):894-902 100344 11842100 10.1093/nar/30.4.894