Selection of suitable housekeeping genes for expression analysis in glioblastoma using quantitative RT-PCR

Abstract

Background: Considering the broad variation in the expression of housekeeping genes among tissues and experimental situations, studies using quantitative RT-PCR require strict definition of adequate endogenous controls. for glioblastoma, the most common type of tumor in the central nervous system, there was no previous report regarding this issue.Results: Here we show that amongst seven frequently used housekeeping genes TBP and HPRT1 are adequate references for glioblastoma gene expression analysis. Evaluation of the expression levels of 12 target genes utilizing different endogenous controls revealed that the normalization method applied might introduce errors in the estimation of relative quantities. Genes presenting expression levels which do not significantly differ between tumor and normal tissues can be considered either increased or decreased if unsuitable reference genes are applied. Most importantly, genes showing significant differences in expression levels between tumor and normal tissues can be missed. We also demonstrated that the Holliday Junction Recognizing Protein, a novel DNA repair protein over expressed in lung cancer, is extremely over-expressed in glioblastoma, with a median change of about 134 fold.Conclusion: Altogether, our data show the relevance of previous validation of candidate control genes for each experimental model and indicate TBP plus HPRT1 as suitable references for studies on glioblastoma gene expression.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)FAEPA-FMRUniv São Paulo, Fac Med, Dept Surg & Anat, BR-14049090 Ribeirao Preto, SP, BrazilUniv São Paulo, Fac Med, Dept Cellular & Mol Biol, BR-14049090 Ribeirao Preto, SP, BrazilUniv São Paulo, Fac Med, Dept Pathol, BR-14049090 Ribeirao Preto, SP, BrazilUniversidade Federal de São Paulo, Dept Neurol & Neurosurg, BR-04023900 São Paulo, BrazilUniv São Paulo, Sch Med, Dept Neurol, BR-01246903 São Paulo, BrazilUniv São Paulo, Fac Med, Dept Pediat, BR-14049090 Ribeirao Preto, SP, BrazilUniversidade Federal de São Paulo, Dept Neurol & Neurosurg, BR-04023900 São Paulo, BrazilFAPESP: 04/12133-6FAPESP: 06/57602-9CNPq: 485342/2006Web of Scienc