Normalizing to GADPH jeopardises correct quantification of gene expression in ovarian tumours - IPO8 and RPL4 are reliable reference genes

Journal of Ovarian Research

Volumn 6, Issue 1, 2013, Pages

  Kolkova, Zuzana ^a   Arakelyan, Arsen ^b   Casslén, Bertil ^a   Hansson, Stefan ^a   Kriegova, Eva ^c  

^a LUND UNIVERSITY   (Sweden)

^b INSTITUTE OF MOLECULAR BIOLOGY   (Armenia)

^c PALACKÝ UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

ABL1 PROTEIN; BETA ACTIN; BETA GLUCURONIDASE; CYCLIN DEPENDENT KINASE INHIBITOR 1A; CYCLOPHILIN A; G PROTEIN COUPLED RECEPTOR 30; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; HEAT SHOCK PROTEIN; HEAT SHOCK PROTEIN 90AB; HYPOXANTHINE PHOSPHORIBOSYL TRANSFERASE 1; HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE; IMPORTIN 8; KARYOPHERIN; MESSENGER RNA; NUCLEAR PROTEIN; ONCOPROTEIN; RIBOSOMAL PROTEIN L30; RIBOSOMAL PROTEIN L4; RIBOSOMAL PROTEIN LARGE PO; RIBOSOME PROTEIN; TATA BINDING PROTEIN; TUMOR SUPPRESSOR PROTEIN; UNCLASSIFIED DRUG; UROKINASE RECEPTOR;

ADULT; AGED; ARTICLE; CANCER PATIENT; CANCER SURGERY; CANCER TISSUE; CLINICAL ARTICLE; CONTROLLED STUDY; DISEASE SEVERITY; FEMALE; GENE EXPRESSION; GENE TARGETING; GENETIC ANALYSIS; GENETIC VARIABILITY; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; NUCLEOTIDE SEQUENCE; OVARIECTOMY; OVARY TUMOR; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STABILITY; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

EID: 84883141057     PISSN: None     EISSN: 17572215     Source Type: Journal    
DOI: 10.1186/1757-2215-6-60     Document Type: Article

References (32)

1. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT, Clin Chem 2009 55 4 611 622 10.1373/clinchem.2008.112797 19246619
2. New insights into an old protein: the functional diversity of mammalian glyceraldehyde-3-phosphate dehydrogenase. Sirover MA, Biochimica et biophysica acta 1999 1432 2 159 184 10.1016/S0167-4838(99)00119-3 10407139 (Pubitemid 29304525)
3. Up-regulation of beta-actin, cyclophilin and GAPDH in N1S1 rat hepatoma. Chang TJ, Juan CC, Yin PH, Chi CW, Tsay HJ, Oncol Rep 1998 5 2 469 471 9468581
4. Identification of suitable reference genes for gene expression studies of human serous ovarian cancer by real-time polymerase chain reaction. Li YL, Ye F, Hu Y, Lu WG, Xie X, Anal Biochem 2009 394 1 110 116 10.1016/j.ab.2009.07.022 19622337
5. Pseudogenes as weaknesses of ACTB (Actb) and GAPDH (Gapdh) used as reference genes in reverse transcription and polymerase chain reactions. Sun Y, Li Y, Luo D, Liao DJ, PloS One 2012 7 8 41659 10.1371/journal.pone.0041659 22927912
6. Identification of genes for normalization of quantitative real-time PCR data in ovarian tissues. Fu J, Bian L, Zhao L, Dong Z, Gao X, Luan H, Sun Y, Song H, Acta biochimica et biophysica Sinica 2010 42 8 568 574 10.1093/abbs/gmq062 20705598
7. Stefan W, Testing Statistical Hypotheses of Equivalence and Noninferiority 2003
8. Equivalence test in quantitative reverse transcription polymerase chain reaction: confirmation of reference genes suitable for normalization. Haller F, Kulle B, Schwager S, Gunawan B, von Heydebreck A, Sultmann H, Fuzesi L, Anal Biochem 2004 335 1 1 9 10.1016/j.ab.2004.08.024 15519565 (Pubitemid 39446224)
9. PSMB2 and RPL32 are suitable denominators to normalize gene expression profiles in bronchoalveolar cells. Kriegova E, Arakelyan A, Fillerova R, Zatloukal J, Mrazek F, Navratilova Z, Kolek V, du Bois RM, Petrek M, BMC Mol Biol 2008 9 69 10.1186/1471-2199-9-69 18671841
10. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-excel-based tool using pair-wise correlations. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP, Biotechnol Lett 2004 26 6 509 515 15127793 (Pubitemid 38448421)
11. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F, Genome Biol 2002 3 7 RESEARCH0034
12. 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. Andersen CL, Jensen JL, Orntoft TF, Cancer Res 2004 64 15 5245 5250 10.1158/0008-5472.CAN-04- 0496 15289330 (Pubitemid 39006544)
13. The G protein-coupled estrogen receptor 1 (GPER/GPR30) does not predict survival in patients with ovarian cancer. Kolkova Z, Casslen V, Henic E, Ahmadi S, Ehinger A, Jirstrom K, Casslen B, J Ovarian Res 2012 5 9 10.1186/1757-2215-5- 9 22424333
14. Dedifferentiation of serous ovarian cancer from cystic to solid tumors is associated with increased expression of mRNA for urokinase plasminogen activator (uPA), its receptor (uPAR) and its inhibitor (PAI-1). Borgfeldt C, Hansson SR, Gustavsson B, Masback A, Casslen B, Int J Cancer 2001 92 4 497 502 10.1002/ijc.1215 11304683 (Pubitemid 32319422)
15. Signal recognition particle protein 19 is imported into the nucleus by importin 8 (RanBP8) and transportin. Dean KA, von Ahsen O, Gorlich D, Fried HM, J Cell Sci 2001 114 Pt 19 3479 3485 11682607 (Pubitemid 33019764)
16. Identification of importin 8 (IPO8) as the most accurate reference gene for the clinicopathological analysis of lung specimens. Nguewa PA, Agorreta J, Blanco D, Lozano MD, Gomez-Roman J, Sanchez BA, Valles I, Pajares MJ, Pio R, Rodriguez MJ, Montuenga LM, Calvo A, BMC Mol Biol 2008 9 103 10.1186/1471-2199-9-103 19014639
17. Identification of valid endogenous control genes for determining gene expression in human glioma. Kreth S, Heyn J, Grau S, Kretzschmar HA, Egensperger R, Kreth FW, Neuro Oncol 2010 12 6 570 579 10.1093/neuonc/nop072 20511187
18. Evaluation of suitable reference genes for normalization of real-time reverse transcription PCR analysis in colon cancer. Sorby LA, Andersen SN, Bukholm IR, Jacobsen MB, J Exp Clin Cancer Res 2010 29 144 10.1186/1756-9966-29- 144 21059236
19. Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6. Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N, Science 2011 334 6058 941 948 10.1126/science.1211204 22052974
20. DNA and RNA references for qRT-PCR assays in exfoliated cervical cells. Steinau M, Rajeevan MS, Unger ER, JMD 2006 8 1 113 118 16436642 (Pubitemid 43257442)
21. Validation of reference genes in cervical cell samples from human papillomavirus-infected and -uninfected women for quantitative reverse transcription-PCR assays. Daud II, Scott ME, CVI 2008 15 9 1369 1373 18632922
22. Estrogen, tamoxifen, and Akt modulate expression of putative housekeeping genes in breast cancer cells. Shah KN, Faridi JS, J Steroid Biochem Mol Biol 2011 125 3-5 219 225 21420492
23. Suitable reference genes for real-time PCR in human HBV-related hepatocellular carcinoma with different clinical prognoses. Fu LY, Jia HL, Dong QZ, Wu JC, Zhao Y, Zhou HJ, Ren N, Ye QH, Qin LX, BMC Cancer 2009 9 49 10.1186/1471-2407-9-49 19200351
24. In search of suitable reference genes for gene expression studies of human renal cell carcinoma by real-time PCR. Jung M, Ramankulov A, Roigas J, Johannsen M, Ringsdorf M, Kristiansen G, Jung K, BMC Mol Biol 2007 8 47 10.1186/1471-2199-8-47 17559644 (Pubitemid 47054425)
25. Identification of genes for normalization of real-time RT-PCR data in breast carcinomas. Lyng MB, Laenkholm AV, Pallisgaard N, Ditzel HJ, BMC Cancer 2008 8 20 10.1186/1471-2407-8-20 18211679 (Pubitemid 351689709)
26. ABL tyrosine kinases: evolution of function, regulation, and specificity. Colicelli J, Sci Signal 2010 3 139 e6 10.1126/scisignal.3139re6 20841568
27. Cell cycle genes and ovarian cancer susceptibility: a tagSNP analysis. Cunningham JM, Vierkant RA, Sellers TA, Phelan C, Rider DN, Liebow M, Schildkraut J, Berchuck A, Couch FJ, Wang X, Fridley BL, Gentry-Maharaj A, Menon U, Hogdall E, Kjaer S, Whittemore A, DiCioccio R, Song H, Gayther SA, Ramus SJ, Pharaoh PD, Goode EL, Br J Cancer 2009 101 8 1461 1468 10.1038/sj.bjc.6605284 19738611
28. The cyclin-dependent kinase inhibitor p21CDKN1A as a target of anti-cancer drugs. Stivala LA, Cazzalini O, Prosperi E, Curr Cancer Drug Targets 2012 12 2 85 96 10.2174/156800912799095126 22165965
29. Cytoplasmic p21 is a potential predictor for cisplatin sensitivity in ovarian cancer. Xia X, Ma Q, Li X, Ji T, Chen P, Xu H, Li K, Fang Y, Weng D, Weng Y, Liao S, Han Z, Liu R, Zhu T, Wang S, Xu G, Meng L, Zhou J, Ma D, BMC Cancer 2011 11 399 10.1186/1471-2407-11-399 21933447
30. The expression of glyceraldehyde-3-phosphate dehydrogenase associated cell cycle (GACC) genes correlates with cancer stage and poor survival in patients with solid tumors. Wang D, Moothart DR, Lowy DR, Qian X, PloS One 2013 8 4 61262 10.1371/journal.pone.0061262 23620736
31. Minireview: human ovarian cancer: biology, current management, and paths to personalizing therapy. Romero I, Bast RC Jr, Endocrinology 2012 153 4 1593 1602 10.1210/en.2011-2123 22416079
32. Molecular characterization of ovarian cancer by gene-expression profiling. Gomez-Raposo C, Mendiola M, Barriuso J, Hardisson D, Redondo A, Gynecol Oncol 2010 118 1 88 92 10.1016/j.ygyno.2010.03.012 20439111