Identification of suitable reference genes for gene expression studies using quantitative polymerase chain reaction in lung cancer in vitro

Molecular Medicine Reports

Volumn 11, Issue 5, 2015, Pages 3767-3773

  Ali, Hassan ^a,b   Du, Zhenwu ^a   Li, Xiuying ^a   Yang, Qiwei ^a   Zhang, Yu Cheng ^a   Wu, Mei ^a   Li, Yi ^b   Zhang, Guizhen ^a  

^a JILIN UNIVERSITY   (China)

^b Basic Medical College   (China)

Author keywords

Housekeeping genes; Lung cancer; Normalization; Reverse transcription quantitative polymerase chain reaction

Indexed keywords

BETA 2 MICROGLOBULIN; BETA ACTIN; GLYCERALDEHYDE 3 PHOSPHATE DEHYDROGENASE; HYPOXANTHINE PHOSPHORIBOSYLTRANSFERASE; MESSENGER RNA; PEPTIDYLPROLYL ISOMERASE; PEPTIDYLPROLYL ISOMERASE A; PHOSPHOGLYCERATE KINASE; RIBOSOMAL PROTEIN LARGE P0; RIBOSOMAL PROTEIN LI3A; RIBOSOME PROTEIN; RNA 18S; TATA BINDING PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; GENE EXPRESSION; GENE IDENTIFICATION; GENETIC ANALYSIS; GENETIC PURITY; GENETIC STABILITY; HOUSEKEEPING GENE; HUMAN; HUMAN CELL; IN VITRO STUDY; LUNG CANCER; LUNG CANCER CELL LINE; PROTEIN EXPRESSION; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; STABLE EXPRESSION; ESSENTIAL GENE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION STUDY; GENETICS; LUNG TUMOR; REAL TIME POLYMERASE CHAIN REACTION; STATISTICAL MODEL;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, NEOPLASTIC; GENES, ESSENTIAL; GENETIC ASSOCIATION STUDIES; HUMANS; LUNG NEOPLASMS; MODELS, STATISTICAL; REAL-TIME POLYMERASE CHAIN REACTION;

EID: 84922271504     PISSN: 17912997     EISSN: 17913004     Source Type: Journal    
DOI: 10.3892/mmr.2015.3159     Document Type: Article

References (38)

1. Koutsokera A, Kiagia M, Saif MW, Souliotis K and Syrigos KN: Nutrition habits, physical activity and lung cancer: an authoritative review. Clin Lung Cancer 14: 342-350, 2013.
2. Perroud MW, Jr, Honma HN, Barbeiro AS, et al: Mature autologous dendritic cell vaccines in advanced non-small cell lung cancer: a phase I pilot study. J Exp Clin Cancer Res: 30: 65, 2011.
3. Travis WD: Pathology of lung cancer. Clin Chest Med 32: 669-692, 2011.
4. Watanabe T, Miura T, Degawa Y, et al: Comparison of lung cancer cell lines representing four histopathological subtypes with gene expression profiling using quantitative real-time PCR. Cancer Cell Int 10: 2, 2010.
5. Guenin S, Mauriat M, Pelloux J, Van Wuytswinkel O, Bellini C and Gutierrez L: Normalization of qRT-PCR data: the necessity of adopting a systematic, experimental conditions-specific, validation of references. J Exp Bot 60: 487-493, 2009.
6. Dheda K, Huggett JF, Bustin SA, Johnson MA, Rook G and Zumla A: Validation of housekeeping genes for normalizing RNA expression in real-time PCR. Biotechniques 37: 112-114, 2004.
7. Hendriks-Balk MC, Michel MC and Alewijnse AE: Pitfalls in the normalization of real-time polymerase chain reaction data. Basic Res Cardiol 102: 195-197, 2007.
8. Eisenberg E and Levanon EY: Human housekeeping genes, revisited. Trends Genet 29: 569-574, 2013.
9. Arenas-Hernandez M and Vega-Sanchez R: Housekeeping gene expression stability in reproductive tissues after mitogen stimulation. BMC Res Notes 6: 285, 2013.
10. Huggett J, Dheda K, Bustin S and Zumla A: Real-time RT-PCR normalisation; strategies and considerations. Genes Immun 6: 279-284, 2005.
11. Barber RD, Harmer DW, Coleman RA and Clark BJ: GAPDH as a housekeeping gene: analysis of GAPDH mRNA expression in a panel of 72 human tissues. Physiol Genomics 21: 389-395, 2005.
12. Bas A, Forsberg G, Hammarstrom S and Hammarstrom ML: Utility of the housekeeping genes 18S rRNA, beta-actin and glyceraldehyde-3-phosphate-dehydrogenase for normalization in real-time quantitative reverse transcriptase-polymerase chain reaction analysis of gene expression in human T lymphocytes. Scand J Immun 59: 566-573, 2004.
13. Selvey S, Thompson EW, Matthaei K, Lea RA, Irving MG and Griffiths LR: Beta-actin - an unsuitable internal control for RT-PCR. Mol Cell Probes 15: 307-311, 2001.
14. Andersen CL, Jensen JL and 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. Can Res 64: 5245-5250, 2004.
15. Rodriguez-Mulero S and Montanya E: Selection of a suitable internal control gene for expression studies in pancreatic islet grafts. Transplantation 80: 650-652, 2005.
16. Sorby LA, Andersen SN, Bukholm IR and Jacobsen MB: Evaluation of suitable reference genes for normalization of real-time reverse transcription PCR analysis in colon cancer. J Exp Clinical Cancer Res 29: 144, 2010.
17. Chua SL, See Too WC, Khoo BY and Few LL: UBC and YWHAZ as suitable reference genes for accurate normalisation of gene expression using MCF7, HCT116 and HepG2 cell lines. Cytotechnology 63: 645-654, 2011.
18. Kim B, Lee HJ, Choi HY, et al: Clinical validity of the lung cancer biomarkers identified by bioinformatics analysis of public expression data. Cancer Res 67: 7431-7438, 2007.
19. Schlotter YM, Veenhof EZ, Brinkhof B, et al: A GeNorm algorithm-based selection of reference genes for quantitative real-time PCR in skin biopsies of healthy dogs and dogs with atopic dermatitis. Vet Immunol Immunopathol 129: 115-118, 2009.
20. Wang Q, Ishikawa T, Michiue T, Zhu BL, Guan DW and Maeda H: Stability of endogenous reference genes in postmortem human brains for normalization of quantitative real-time PCR data: comprehensive evaluation using geNorm, NormFinder and BestKeeper. Int J Legal Med 126: 943-952, 2012.
21. Pfaffl MW, Tichopad A, Prgomet C and Neuvians TP: Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper - Excel-based tool using pair-wise correlations. Biotechno Lett 26: 509-515, 2004.
22. de Oliveira LA, Breton MC, Bastolla FM, et al: Reference genes for the normalization of gene expression in eucalyptus species. Plant Cell Physiol 53: 405-422, 2012.
23. Bunn PA, Jr: Worldwide overview of the current status of lung cancer diagnosis and treatment. Arch Pathology Lab Med 136: 1478-1481, 2012.
24. Tsuboi M, Ohira T, Saji H, et al: The present status of postoperative adjuvant chemotherapy for completely resected non-small cell lung cancer. Ann Thoracic Cardiovasc Surg 13: 73-77, 2007.
25. Liu J, Lee W, Jiang Z, et al: Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing events. Genome Res 22: 2315-2327, 2012.
26. Sokilde R, Kaczkowski B, Podolska A, et al: Global microRNA analysis of the NCI-60 cancer cell panel. Mol Cancer The 10: 375-384, 2011.
27. Che CL, Zhang YM, Zhang HH, et al: DNA microarray reveals different pathways responding to paclitaxel and docetaxel in non-small cell lung cancer cell line. Int J Clin Exp Path 6: 1538-1548, 2013.
28. Gazdar AF, Girard L, Lockwood WW, Lam WL and Minna JD: Lung cancer cell lines as tools for biomedical discovery and research. J Natl Cancer Inst 102: 1310-1321, 2010.
29. Gazdar AF, Gao B and Minna JD: Lung cancer cell lines: Useless artifacts or invaluable tools for medical science? Lung Cancer 68: 309-318, 2010.
30. van Eijk R, Licht J, Schrumpf M, et al: Rapid KRAS, EGFR, BRAF and PIK3CA mutation analysis of fine needle aspirates from non-small-cell lung cancer using allele-specific qPCR. PloS One 6: e17791, 2011.
31. Saviozzi S, Cordero F, Lo Iacono M, Novello S, Scagliotti GV and Calogero RA: Selection of suitable reference genes for accurate normalization of gene expression profile studies in non-small cell lung cancer. BMC Cancer 6: 200, 2006.
32. Ho-Pun-Cheung A, Bascoul-Mollevi C, Assenat E, et al: Validation of an appropriate reference gene for normalization of reverse transcription-quantitative polymerase chain reaction data from rectal cancer biopsies. Anal Biochem 388: 348-350, 2009.
33. Ohl F, Jung M, Xu C, et al: Gene expression studies in prostate cancer tissue: which reference gene should be selected for normalization? J Mol Medicine 83: 1014-1024, 2005.
34. Jacob F, Guertler R, Naim S, et al: Careful selection of reference genes is required for reliable performance of RT-qPCR in human normal and cancer cell lines. PloS One 8: e59180, 2013.
35. Mafra V, Kubo KS, Alves-Ferreira M, et al: Reference genes for accurate transcript normalization in citrus genotypes under different experimental conditions. PloS One 7: e31263, 2012.
36. Mallona I, Lischewski S, Weiss J, Hause B and Egea-Cortines M: Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida. BMC Plant Biol 10: 4, 2010.
37. Liu DW, Chen ST and Liu HP: Choice of endogenous control for gene expression in nonsmall cell lung cancer. Eur Respir J 26: 1002-1008, 2005.
38. Gresner P, Gromadzinska J and Wasowicz W: Reference genes for gene expression studies on non-small cell lung cancer. Acta Biochim Pol 56: 307-316, 2009.