Normalization of gene expression using SYBR green qPCR: A case for paraoxonase 1 and 2 in Alzheimer's disease brains

Journal of Neuroscience Methods

Volumn 200, Issue 1, 2011, Pages 14-19

  Leduc, Valérie ^a,b   Legault, Véronique ^a,b,d   Dea, Doris ^a   Poirier, Judes ^a,b,c  

^a DOUGLAS MENTAL HEALTH UNIVERSITY INSTITUTE   (Canada)

^b MCGILL UNIVERSITY   (Canada)

^c MCGILL UNIVERSITY   (Canada)

^d CENTRE HOSPITALIER DE L UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

Alzheimer's disease; Normalization; Paraoxonase 1; Paraoxonase 2; QPCR; Reference gene

Indexed keywords

ARYLDIALKYLPHOSPHATASE 1; ARYLDIALKYLPHOSPHATASE 2; BETA ACTIN; BETA GLUCURONIDASE; CYCLOPHILIN A; G PROTEIN PATHWAY SUPPRESSOR 1; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; GUANINE NUCLEOTIDE BINDING PROTEIN; MESSENGER RNA; MYOSIN PHOPHATASE RHO INTERACTING PROTEIN; NUCLEOTIDYLTRANSFERASE; PHOSPHOGLYCERATE KINASE; PHOSPHOGLYCERATE KINASE 1; POLYMERASE II POLYPEPTIDE F; PROTEIN KINASE YES; RHO KINASE; UBIQUITIN CONJUGATING ENZYME; UBIQUITIN CONJUGATING ENZYME E2D2; UNCLASSIFIED DRUG;

ADULT; AGED; ALZHEIMER DISEASE; ARTICLE; AUTOPSY; BRAIN TISSUE; CADAVER; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; FEMALE; FRONTAL CORTEX; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC ANALYSIS; GENETIC ASSOCIATION; HUMAN; HUMAN CELL; HUMAN TISSUE; MALE; PRIORITY JOURNAL; PROTEIN STABILITY; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; UPREGULATION;

ADULT; AGED; AGED, 80 AND OVER; ALZHEIMER DISEASE; ARYLDIALKYLPHOSPHATASE; BRAIN; COHORT STUDIES; FEMALE; FLUORESCENT DYES; GENE EXPRESSION REGULATION, ENZYMOLOGIC; HUMANS; MALE; MIDDLE AGED; ORGANIC CHEMICALS; RANDOM ALLOCATION; REAL-TIME POLYMERASE CHAIN REACTION; UP-REGULATION;

EID: 79960889419     PISSN: 01650270     EISSN: 1872678X     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2011.05.026     Document Type: Article

References (27)

1. Andersen C.L., Jensen J.L., Orntoft T.F. 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.
2. Aviram M., Hussein O., Rosenblat M., Schlezinger S., Hayek T., Keidar S. Interactions of platelets, macrophages, and lipoproteins in hypercholesterolemia: antiatherogenic effects of HMG-CoA reductase inhibitor therapy. J Cardiovasc Pharmacol 1998, 31:39-45.
3. Barrachina M., Castano E., Ferrer I. TaqMan PCR assay in the control of RNA normalization in human post-mortem brain tissue. Neurochem Int 2006, 49:276-284.
4. Bustin S.A. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 2000, 25:169-193.
5. Ceelen L., De Spiegelaere W., David M., De Craene J., Vinken M., Vanhaecke T., et al. Critical selection of reliable reference genes for gene expression study in the HepaRG cell line. Biochem Pharmacol 2011.
6. Chang T.J., Juan C.C., Yin P.H., Chi C.W., Tsay H.J. Up-regulation of beta-actin, cyclophilin and GAPDH in N1S1 rat hepatoma. Oncol Rep 1998, 5:469-471.
7. Coulson D.T., Brockbank S., Quinn J.G., Murphy S., Ravid R., Irvine G.B., et al. Identification of valid reference genes for the normalization of RT qPCR gene expression data in human brain tissue. BMC Mol Biol 2008, 9:46.
8. Gibson G.E., Karuppagounder S.S., Shi Q. Oxidant-induced changes in mitochondria and calcium dynamics in the pathophysiology of Alzheimer's disease. Ann N Y Acad Sci 2008, 1147:221-232.
9. Gutala R.V., Reddy P.H. The use of real-time PCR analysis in a gene expression study of Alzheimer's disease post-mortem brains. J Neurosci Methods 2004, 132:101-107.
10. Hoerndli F.J., Toigo M., Schild A., Gotz J., Day P.J. Reference genes identified in SH-SY5Y cells using custom-made gene arrays with validation by quantitative polymerase chain reaction. Anal Biochem 2004, 335:30-41.
11. Hsiao L.L., Dangond F., Yoshida T., Hong R., Jensen R.V., Misra J., et al. A compendium of gene expression in normal human tissues. Physiol Genomics 2001, 7:97-104.
12. Kern A., Behl C. The unsolved relationship of brain aging and late-onset Alzheimer disease. Biochim Biophys Acta 2009, 1790:1124-1132.
13. Khachaturian Z.S. Diagnosis of Alzheimer's disease. Arch Neurol 1985, 42:1097-1105.
14. Leduc V., Jasmin-Belanger S., Poirier J. APOE and cholesterol homeostasis in Alzheimer's disease. Trends Mol Med 2010.
15. Leduc V., Theroux L., Dea D., Robitaille Y., Poirier J. Involvement of paraoxonase 1 genetic variants in Alzheimer's disease neuropathology. Eur J Neurosci 2009, 30:1823-1830.
16. Livak K.J., Schmittgen T.D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 2001, 25:402-408.
17. Logan J., Edwards K., Saunders N. Real-time PCR: current technology and applications 2009, Caister Academic Press, London, GB.
18. Lyahyai J., Serrano C., Ranera B., Badiola J.J., Zaragoza P., Martin-Burriel I. Effect of scrapie on the stability of housekeeping genes. Anim Biotechnol 2010, 21:1-13.
19. Mackness B., Beltran-Debon R., Aragones G., Joven J., Camps J., Mackness M. Human tissue distribution of paraoxonases 1 and 2 mRNA. IUBMB Life 2010, 62:480-482.
20. McKhann G., Drachman D., Folstein M., Katzman R., Price D., Stadlan E.M. Clinical diagnosis of Alzheimer's disease: report of the NINCDS-ADRDA Work Group under the auspices of Department of Health and Human Services Task Force on Alzheimer's Disease. Neurology 1984, 34:939-944.
21. Ng C.J., Wadleigh D.J., Gangopadhyay A., Hama S., Grijalva V.R., Navab M., et al. Paraoxonase-2 is a ubiquitously expressed protein with antioxidant properties and is capable of preventing cell-mediated oxidative modification of low density lipoprotein. J Biol Chem 2001, 276:44444-44449.
22. Nishimura M., Naito S. Tissue-specific mRNA expression profiles of human ATP-binding cassette and solute carrier transporter superfamilies. Drug Metab Pharmacokinet 2005, 20:452-477.
23. Pfaffl M.W., Horgan G.W., Dempfle L. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 2002, 30:e36.
24. Pfaffl M.W., Tichopad A., Prgomet C., Neuvians T.P. 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.
25. Schroder A.L., Pelch K.E., Nagel S.C. Estrogen modulates expression of putative housekeeping genes in the mouse uterus. Endocrine 2009, 35:211-219.
26. Vandesompele J., De Preter K., Pattyn F., Poppe B., Van Roy N., De Paepe A., et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002, 3. RESEARCH0034.
27. Warrington J.A., Nair A., Mahadevappa M., Tsyganskaya M. Comparison of human adult and fetal expression and identification of 535 housekeeping/maintenance genes. Physiol Genomics 2000, 2:143-147.