Comparative study of candidate housekeeping genes for quantification of target gene messenger RNA expression by real-time PCR in patients with inflammatory bowel disease

Inflammatory Bowel Diseases

Volumn 19, Issue 13, 2013, Pages 2840-2847

  Bamias, Giorgos ^a   Goukos, Dimitris ^a   Laoudi, Eyfrosyni ^a   Balla, Iliana G ^a   Siakavellas, Spyros I ^a   Daikos, George L ^a   Ladas, Spiros D ^a  

^a UNIVERSITY OF ATHENS   (Greece)

Author keywords

Housekeeping genes; Inflammatory bowel disease; Real time PCR; Target mRNA expression

Indexed keywords

ABL1 PROTEIN; BETA 2 MICROGLOBULIN; BETA ACTIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; GUSB PROTEIN; HPRT1 PROTEIN; MESSENGER RNA; POLR2A PROTEIN; PPIA PROTEIN; PROTEIN; RIBOSOME PROTEIN; RPLPO PROTEIN; RPS9 PROTEIN; TUMOR NECROSIS FACTOR ALPHA; UNCLASSIFIED DRUG;

ARTICLE; CLINICAL ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; ENDOSCOPY; GENE EXPRESSION; GENETIC STABILITY; HOUSEKEEPING GENE; HUMAN; HUMAN TISSUE; INFLAMMATORY BOWEL DISEASE; INTESTINE BIOPSY; INTESTINE MUCOSA; PRIORITY JOURNAL; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RNA EXTRACTION;

CASE-CONTROL STUDIES; GENES, ESSENTIAL; HUMANS; INFLAMMATORY BOWEL DISEASES; INTESTINAL MUCOSA; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, MESSENGER;

EID: 84893724270     PISSN: 10780998     EISSN: 15364844     Source Type: Journal    
DOI: 10.1097/01.MIB.0000435440.22484.e8     Document Type: Article

References (29)

1. Abraham C, Cho JH. Inflammatory bowel disease. N Engl J Med. 2009; 361:2066-2078.
2. Bamias G, Nyce MR, De La Rue SA, et al. New concepts in the pathophysiology of inflammatory bowel disease. Ann Intern Med. 2005;143:895-904.
3. Bamias G, Cominelli F. Novel strategies to attenuate immune activation in Crohn's disease. Curr Opin Pharmacol. 2006;6:401-407.
4. Huggett J, Dheda K, Bustin S, et al. Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005;6:279-284.
5. Suzuki T, Higgins PJ, Crawford DR. Control selection for RNA quantitation. Biotechniques. 2000;29:332-337.
6. Tricarico C, Pinzani P, Bianchi S, et al. 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.
7. Wu YY, Rees JL. Variation in epidermal housekeeping gene expression in different pathological states. Acta Derm Venereol. 2000;80:2-3.
8. Zhong H, Simons JW. Direct comparison of GAPDH, beta-actin, cyclophilin, and 28S rRNA as internal standards for quantifying RNA levels under hypoxia. Biochem Biophys Res Commun. 1999;259:523-526.
9. Marten NW, Burke EJ, Hayden JM, et al. Effect of amino acid limitation on the expression of 19 genes in rat hepatoma cells. FASEB J. 1994;8:538-544.
10. Blanquicett C, Johnson MR, Heslin M, et al. Housekeeping gene variability in normal and carcinomatous colorectal and liver tissues: applications in pharmacogenomic gene expression studies. Anal Biochem. 2002;303:209-214.
11. Thellin O, Zorzi W, Lakaye B, et al. Housekeeping genes as internal standards: use and limits. J Biotechnol. 1999;75:291-295.
12. Taylor S, Wakem M, Dijkman G, et al. A practical approach to RTqPCR -publishing data that conform to the MIQE guidelines. Methods. 2010;50:S1-S5.
13. Bustin SA, Benes V, Garson JA, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009;55:611-622.
14. Chechi K, Gelinas Y, Mathieu P, et al. Validation of reference genes for the relative quantification of gene expression in human epicardial adipose tissue. PLoS One. 2012;7:e32265.
15. Dydensborg AB, Herring E, Auclair J, et al. Normalizing genes for quantitative RT-PCR in differentiating human intestinal epithelial cells and adenocarcinomas of the colon. Am J Physiol Gastrointest Liver Physiol. 2006;290:G1067-G1074.
16. Stern-Straeter J, Bonaterra GA, Hormann K, et al. Identification of valid reference genes during the differentiation of human myoblasts. BMC Mol Biol. 2009;10:66.
17. Lindstrom MS, Zhang Y. Ribosomal protein S9 is a novel B23/NPMbinding protein required for normal cell proliferation. J Biol Chem. 2008; 283:15568-15576.
18. Pfaffl MW, Tichopad A, Prgomet C, et al. 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.
19. 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.
20. Vandesompele J, De Preter K, Pattyn F, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002;3:RESEARCH0034.
21. Silver N, Best S, Jiang J, et al. Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR. BMC Mol Biol. 2006;7:33.
22. Meyer FR, Grausgruber H, Binter C, et al. Cross-platform microarray meta-analysis for the mouse jejunum selects novel reference genes with highly uniform levels of expression. PLoS One. 2013;8:e63125.
23. Rubie C, Kempf K, Hans J, et al. Housekeeping gene variability in normal and cancerous colorectal, pancreatic, esophageal, gastric and hepatic tissues. Mol Cell Probes. 2005;19:101-109.
24. Yang X, Hatfield JT, Hinze SJ, et al. Bone to pick: the importance of evaluating reference genes for RT-qPCR quantification of gene expression in craniosynostosis and bone-related tissues and cells. BMC Res Notes. 2012;5:222.
25. Adamski MG, Li Y, Wagner E, et al. Next-generation qPCR for the highthroughput measurement of gene expression in multiple leukocyte subsets. J Biomol Screen. 2013;18:1008-1017.
26. Tchórzewski M, Krokowski D, Rzeski W, et al. The subcellular distribution of the human ribosomal "stalk" components: P1, P2 and P0 proteins. Int J Biochem Cell Biol. 2003;35:203-211.
27. Hashemi A, Roohvand F, Ghahremani MH. Selection of valid reference genes for expression studies of hepatic cell lines under IFN-alpha treatment. Biochem Biophys Res Commun. 2012;426:649-653.
28. Albershardt TC, Iritani BM, Ruddell A. Evaluation of reference genes for quantitative PCR analysis of mouse lymphocytes. J Immunol Methods. 2012;384:196-199.
29. Taylor CF, Field D, Sansone SA, et al. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol. 2008;26:889-896.