Gene expression results in lipopolysaccharide-stimulated monocytes depend significantly on the choice of reference genes

BMC Immunology

Volumn 11, Issue , 2010, Pages

  Piehler, Armin P ^a   Grimholt, Runa M ^a   Øvstebø, Reidun ^a   Berg, Jens P ^a  

^a ULLEVÅL UNIVERSITY HOSPITAL   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM LIPOPOLYSACCHARIDE; BETA 2 MICROGLOBULIN; CYCLOPHILIN A; CYCLOPHILIN B; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; INTERLEUKIN 10; TATA BINDING PROTEIN; TUMOR NECROSIS FACTOR ALPHA; LIPOPOLYSACCHARIDE;

ARTICLE; DATA ANALYSIS SOFTWARE; EVALUATION; GENE EXPRESSION PROFILING; HUMAN; HUMAN CELL; MONOCYTE; NORMAL HUMAN; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STANDARD; COMPUTER PROGRAM; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; IMMUNOLOGY; METABOLISM; METHODOLOGY; REGRESSION ANALYSIS;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; HUMANS; INTERLEUKIN-10; LIPOPOLYSACCHARIDES; MONOCYTES; REFERENCE STANDARDS; REGRESSION ANALYSIS; SOFTWARE; TUMOR NECROSIS FACTOR-ALPHA;

EID: 77952856143     PISSN: None     EISSN: 14712172     Source Type: Journal    
DOI: 10.1186/1471-2172-11-21     Document Type: Article

References (36)

1. Auffray C, Sieweke MH, Geissmann F. Blood monocytes: development, heterogeneity, and relationship with dendritic cells. Annu Rev Immunol 2009, 27:669-692. 10.1146/annurev.immunol.021908.132557, 19132917.
2. Serbina NV, Jia T, Hohl TM, Pamer EG. Monocyte-mediated defense against microbial pathogens. Annu Rev Immunol 2008, 26:421-452. 10.1146/annurev.immunol.26.021607.090326, 18303997.
3. Brandtzaeg P, Bjerre A, Ovstebo R, Brusletto B, Joo GB, Kierulf P. Neisseria meningitidis lipopolysaccharides in human pathology. J Endotoxin Res 2001, 7:401-420.
4. Toltl LJ, Beaudin S, Liaw PC. Activated protein C up-regulates IL-10 and inhibits tissue factor in blood monocytes. J Immunol 2008, 181:2165-2173.
5. Ovstebo R, Olstad OK, Brusletto B, Moller AS, Aase A, Haug KB, Brandtzaeg P, Kierulf P. Identification of genes particularly sensitive to lipopolysaccharide (LPS) in human monocytes induced by wild-type versus LPS-deficient Neisseria meningitidis strains. Infect Immun 2008, 76:2685-2695. 10.1128/IAI.01625-07, 2423066, 18362127.
6. Martin M, Rehani K, Jope RS, Michalek SM. Toll-like receptor-mediated cytokine production is differentially regulated by glycogen synthase kinase 3. Nat Immunol 2005, 6:777-784. 10.1038/ni1221, 1933525, 16007092.
7. Hashimoto S, Morohoshi K, Suzuki T, Matsushima K. Lipopolysaccharide-inducible gene expression profile in human monocytes. Scand J Infect Dis 2003, 35:619-627. 10.1080/00365540310015926, 14620145.
8. Moller AS, Ovstebo R, Westvik AB, Joo GB, Haug KB, Kierulf P. Effects of bacterial cell wall components (PAMPs) on the expression of monocyte chemoattractant protein-1 (MCP-1), macrophage inflammatory protein-1alpha (MIP-1alpha) and the chemokine receptor CCR2 by purified human blood monocytes. J Endotoxin Res 2003, 9:349-360.
9. Ahamed J, Niessen F, Kurokawa T, Lee YK, Bhattacharjee G, Morrissey JH, Ruf W. Regulation of macrophage procoagulant responses by the tissue factor cytoplasmic domain in endotoxemia. Blood 2007, 109:5251-5259. 10.1182/blood-2006-10-051334, 1890821, 17332247.
10. Luyendyk JP, Schabbauer GA, Tencati M, Holscher T, Pawlinski R, Mackman N. Genetic analysis of the role of the PI3K-Akt pathway in lipopolysaccharide-induced cytokine and tissue factor gene expression in monocytes/macrophages. J Immunol 2008, 180:4218-4226. 2834303, 18322234.
11. Huggett J, Dheda K, Bustin S, Zumla A. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 2005, 6:279-284. 10.1038/sj.gene.6364190, 15815687.
12. 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.
13. 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, 344:141-143. 10.1016/j.ab.2005.05.022, 16054107.
14. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper--Excel-based tool using pair-wise correlations. Biotechnol Lett 2004, 26:509-515. 10.1023/B:BILE.0000019559.84305.47, 15127793.
15. Vandesompele J, De PK, Pattyn F, Poppe B, Van RN, De PA, Speleman F. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3:RESEARCH0034. 10.1186/gb-2002-3-7-research0034, 126239, 12184808.
16. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, et al. 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.
17. geNorm. , http://medgen.ugent.be/~jvdesomp/genorm/
18. Normfinder. , http://www.mdl.dk/publicationsnormfinder.htm
19. BestKeeper. , http://gene-quantification.com/bestkeeper.html
20. Hellemans J, Mortier G, De PA, 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:R19. 10.1186/gb-2007-8-2-r19, 1852402, 17291332.
21. Suzuki T, Higgins PJ, Crawford DR. Control selection for RNA quantitation. Biotechniques 2000, 29:332-337.
22. Lee S, Jo M, Lee J, Koh SS, Kim S. Identification of novel universal housekeeping genes by statistical analysis of microarray data. J Biochem Mol Biol 2007, 40:226-231.
23. Dheda K, Huggett JF, Bustin SA, Johnson MA, Rook G, Zumla A. Validation of housekeeping genes for normalizing RNA expression in real-time PCR. Biotechniques 2004, 37:112-119.
24. Schmittgen TD, Zakrajsek BA. Effect of experimental treatment on housekeeping gene expression: validation by real-time, quantitative RT-PCR. J Biochem Biophys Methods 2000, 46:69-81. 10.1016/S0165-022X(00)00129-9, 11086195.
25. Arukwe A. Toxicological housekeeping genes: do they really keep the house?. Environ Sci Technol 2006, 40:7944-7949. 10.1021/es0615223, 17256553.
26. Bustin SA, Nolan T. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J Biomol Tech 2004, 15:155-166. 2291693, 15331581.
27. Selvey S, Thompson EW, Matthaei K, Lea RA, Irving MG, Griffiths LR. Beta-actin--an unsuitable internal control for RT-PCR. Mol Cell Probes 2001, 15:307-311. 10.1006/mcpr.2001.0376, 11735303.
28. 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, 309:293-300. 10.1016/S0003-2697(02)00311-1, 12413463.
29. Glare EM, Divjak M, Bailey MJ, Walters EH. beta-Actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalising mRNA levels. Thorax 2002, 57:765-770. 10.1136/thorax.57.9.765, 1746418, 12200519.
30. Hibbeler S, Scharsack JP, Becker S. Housekeeping genes for quantitative expression studies in the three-spined stickleback Gasterosteus aculeatus. BMC Mol Biol 2008, 9:18. 10.1186/1471-2199-9-18, 2254436, 18230138.
31. Guenin S, Mauriat M, Pelloux J, Van WO, Bellini C, Gutierrez L. Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references. J Exp Bot 2009, 60:487-493. 10.1093/jxb/ern305, 19264760.
32. Lund PK, Joo GB, Westvik AB, Ovstebo R, Kierulf P. Isolation of monocytes from whole blood by density gradient centrifugation and counter-current elutriation followed by cryopreservation: six years' experience. Scand J Clin Lab Invest 2000, 60:357-365. 10.1080/003655100750019260, 11003255.
33. Brandtzaeg P, Bryn K, Kierulf P, Ovstebo R, Namork E, Aase B, Jantzen E. Meningococcal endotoxin in lethal septic shock plasma studied by gas chromatography, mass-spectrometry, ultracentrifugation, and electron microscopy. J Clin Invest 1992, 89:816-823. 10.1172/JCI115660, 442926, 1541674.
34. Fleige S, Pfaffl MW. RNA integrity and the effect on the real-time qRT-PCR performance. Mol Aspects Med 2006, 27:126-139. 10.1016/j.mam.2005.12.003, 16469371.
35. Coulson DT, Brockbank S, Quinn JG, Murphy S, Ravid R, Irvine GB, Johnston JA. Identification of valid reference genes for the normalization of RT qPCR gene expression data in human brain tissue. BMC Mol Biol 2008, 9:46. 10.1186/1471-2199-9-46, 2396658, 18460208.
36. Pfaffl MW. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 2001, 29:e45. 10.1093/nar/29.9.e45, 55695, 11328886.