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

Valéria Valente1, Silvia A. Teixeira1, Luciano Neder2, Oswaldo Keith Okamoto3, Sueli Mieko Oba‐Shinjo4, Suely Kazue Nagahashi Marie4, Carlos Alberto Scrideli5, Maria Luisa Paçó‐Larson6, Carlos Gilberto Carlotti1
1Department of Surgery and Anatomy, Faculty of Medicine, University of São Paulo, Ribeirão Preto, Brazil
2Department of Pathology, Faculty of Medicine, University of São Paulo, Ribeirão Preto, Brazil
3Department of Neurology and Neurosurgery, Federal University of Sao Paulo, Sao Paulo, Brazil
4Department of Neurology, School of Medicine, University of São Paulo, São Paulo, Brazil
5Department of Pediatrics, Faculty of Medicine, University of São Paulo, Ribeirão Preto, Brazil
6Department of Cellular and Molecular Biology, Faculty of Medicine, University of São Paulo, Ribeirão Preto, Brazil

Tóm tắt

Từ khóa


Tài liệu tham khảo

Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A: Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun. 2004, 313 (4): 856-862. 10.1016/j.bbrc.2003.11.177

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 (1): 112-114.

de Kok JB, Roelofs RW, Giesendorf BA, Pennings JL, Waas ET, Feuth T, Swinkels DW, Span PN: Normalization of gene expression measurements in tumor tissues: comparison of 13 endogenous control genes. Lab Invest. 2005, 85 (1): 154-159.

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 (5): 307-311. 10.1006/mcpr.2001.0376

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 (9): 765-770. 10.1136/thorax.57.9.765

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 (2): 293-300. 10.1016/S0003-2697(02)00311-1

Ohl F, Jung M, Xu C, Stephan C, Rabien A, Burkhardt M, Nitsche A, Kristiansen G, Loening SA, Radonic A, et al: Gene expression studies in prostate cancer tissue: which reference gene should be selected for normalization?. J Mol Med. 2005, 83 (12): 1014-1024. 10.1007/s00109-005-0703-z

Toegel S, Huang W, Piana C, Unger FM, Wirth M, Goldring MB, Gabor F, Viernstein H: Selection of reliable reference genes for qPCR studies on chondroprotective action. BMC Mol Biol. 2007, 8: 13- 10.1186/1471-2199-8-13

Silver N, Cotroneo E, Proctor G, Osailan S, Paterson KL, Carpenter GH: Selection of housekeeping genes for gene expression studies in the adult rat submandibular gland under normal, inflamed, atrophic and regenerative states. BMC Mol Biol. 2008, 9: 64-

Calcagno AM, Chewning KJ, Wu CP, Ambudkar SV: Plasma membrane calcium ATPase (PMCA4): a housekeeper for RT-PCR relative quantification of polytopic membrane proteins. BMC Mol Biol. 2006, 7: 29- 10.1186/1471-2199-7-29

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 (3): 523-526. 10.1006/bbrc.1999.0815

Hamalainen HK, Tubman JC, Vikman S, Kyrola T, Ylikoski E, Warrington JA, Lahesmaa R: Identification and validation of endogenous reference genes for expression profiling of T helper cell differentiation by quantitative real-time RT-PCR. Anal Biochem. 2001, 299 (1): 63-70. 10.1006/abio.2001.5369

Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 2002, 3 (7): RESEARCH0034- 10.1186/gb-2002-3-7-research0034

Louis DN, Ohgaki H, Wiestler OD, Cavenee WK, Burger PC, Jouvet A, Scheithauer BW, Kleihues P: The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol. 2007, 114 (2): 97-109. 10.1007/s00401-007-0243-4

Behin A, Hoang-Xuan K, Carpentier AF, Delattre JY: Primary brain tumours in adults. Lancet. 2003, 361 (9354): 323-331. 10.1016/S0140-6736(03)12328-8

Louis DN: Molecular pathology of malignant gliomas. Annu Rev Pathol. 2006, 1: 97-117. 10.1146/annurev.pathol.1.110304.100043

Omuro AM, Delattre JY: Editorial: what is new in the treatment of gliomas?. Curr Opin Neurol. 2007, 20 (6): 704-707. 10.1097/WCO.0b013e3282f1beef

Omuro AM, Faivre S, Raymond E: Lessons learned in the development of targeted therapy for malignant gliomas. Mol Cancer Ther. 2007, 6 (7): 1909-1919. 10.1158/1535-7163.MCT-07-0047

Dent P, Yacoub A, Park M, Sarkar D, Shah K, Curiel DT, Grant S: Searching for a cure: Gene therapy for glioblastoma. Cancer Biol Ther. 2008, 7 (9): 1335-1340.

Idbaih A, Omuro A, Ducray F, Hoang-Xuan K: Molecular genetic markers as predictors of response to chemotherapy in gliomas. Curr Opin Oncol. 2007, 19 (6): 606-611. 10.1097/CCO.0b013e3282f075f3

Colman H, Aldape K: Molecular predictors in glioblastoma: toward personalized therapy. Arch Neurol. 2008, 65 (7): 877-883. 10.1001/archneur.65.7.877

Maier MS, Legare ME, Hanneman WH: The aryl hydrocarbon receptor agonist 3, 3', 4, 4', 5-pentachlorobiphenyl induces distinct patterns of gene expression between hepatoma and glioma cells: chromatin remodeling as a mechanism for selective effects. Neurotoxicology. 2007, 28 (3): 594-612. 10.1016/j.neuro.2007.01.002

Schmitz M, Temme A, Senner V, Ebner R, Schwind S, Stevanovic S, Wehner R, Schackert G, Schackert HK, Fussel M, et al: Identification of SOX2 as a novel glioma-associated antigen and potential target for T cell-based immunotherapy. Br J Cancer. 2007, 96 (8): 1293-1301. 10.1038/sj.bjc.6603696

Haque T, Faury D, Albrecht S, Lopez-Aguilar E, Hauser P, Garami M, Hanzely Z, Bognar L, Del Maestro RF, Atkinson J, et al: Gene expression profiling from formalin-fixed paraffin-embedded tumors of pediatric glioblastoma. Clin Cancer Res. 2007, 13 (21): 6284-6292. 10.1158/1078-0432.CCR-07-0525

Bozinov O, Kohler S, Samans B, Benes L, Miller D, Ritter M, Sure U, Bertalanffy H: Candidate genes for the progression of malignant gliomas identified by microarray analysis. Neurosurg Rev. 2008, 31 (1): 83-89. discussion 89–90 10.1007/s10143-007-0107-3

Scrideli CA, Carlotti CG, Okamoto OK, Andrade VS, Cortez MA, Motta FJ, Lucio-Eterovic AK, Neder L, Rosemberg S, Oba-Shinjo SM, et al: Gene expression profile analysis of primary glioblastomas and non-neoplastic brain tissue: identification of potential target genes by oligonucleotide microarray and real-time quantitative PCR. J Neurooncol. 2008, 88 (3): 281-291. 10.1007/s11060-008-9579-4

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 (15): 5245-5250. 10.1158/0008-5472.CAN-04-0496

Haller F, Kulle B, Schwager S, Gunawan B, von Heydebreck A, Sultmann H, Fuzesi L: Equivalence test in quantitative reverse transcription polymerase chain reaction: confirmation of reference genes suitable for normalization. Anal Biochem. 2004, 335 (1): 1-9. 10.1016/j.ab.2004.08.024

Noor A, Windpassinger C, Patel M, Stachowiak B, Mikhailov A, Azam M, Irfan M, Siddiqui ZK, Naeem F, Paterson AD, et al: CC2D2A, encoding a coiled-coil and C2 domain protein, causes autosomal-recessive mental retardation with retinitis pigmentosa. Am J Hum Genet. 2008, 82 (4): 1011-1018. 10.1016/j.ajhg.2008.01.021

Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M: Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell. 2006, 127 (3): 635-648. 10.1016/j.cell.2006.09.026

Lefevre C, Bouadjar B, Karaduman A, Jobard F, Saker S, Ozguc M, Lathrop M, Prud'homme JF, Fischer J: Mutations in ichthyin a new gene on chromosome 5q33 in a new form of autosomal recessive congenital ichthyosis. Hum Mol Genet. 2004, 13 (20): 2473-2482. 10.1093/hmg/ddh263

Rui Y, Xu Z, Xiong B, Cao Y, Lin S, Zhang M, Chan SC, Luo W, Han Y, Lu Z, et al: A beta-catenin-independent dorsalization pathway activated by Axin/JNK signaling and antagonized by aida. Dev Cell. 2007, 13 (2): 268-282. 10.1016/j.devcel.2007.07.006

Douglas J, Cilliers D, Coleman K, Tatton-Brown K, Barker K, Bernhard B, Burn J, Huson S, Josifova D, Lacombe D, et al: Mutations in RNF135, a gene within the NF1 microdeletion region, cause phenotypic abnormalities including overgrowth. Nat Genet. 2007, 39 (8): 963-965. 10.1038/ng2083

Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, et al: Complete sequencing and characterization of 21, 243 full-length human cDNAs. Nat Genet. 2004, 36 (1): 40-45. 10.1038/ng1285

Eilbracht J, Reichenzeller M, Hergt M, Schnolzer M, Heid H, Stohr M, Franke WW, Schmidt-Zachmann MS: NO66, a highly conserved dual location protein in the nucleolus and in a special type of synchronously replicating chromatin. Mol Biol Cell. 2004, 15 (4): 1816-1832. 10.1091/mbc.E03-08-0623

Kato T, Sato N, Hayama S, Yamabuki T, Ito T, Miyamoto M, Kondo S, Nakamura Y, Daigo Y: Activation of Holliday junction recognizing protein involved in the chromosomal stability and immortality of cancer cells. Cancer Res. 2007, 67 (18): 8544-8553. 10.1158/0008-5472.CAN-07-1307

Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W: The LIFEdb database in 2006. Nucleic Acids Res. 2006, D415-418. 34 Database

Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, et al: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004, 14 (10B): 2121-2127. 10.1101/gr.2596504

Ohl F, Jung M, Radonic A, Sachs M, Loening SA, Jung K: Identification and validation of suitable endogenous reference genes for gene expression studies of human bladder cancer. J Urol. 2006, 175 (5): 1915-1920. 10.1016/S0022-5347(05)00919-5

Schmid H, Cohen CD, Henger A, Irrgang S, Schlondorff D, Kretzler M: Validation of endogenous controls for gene expression analysis in microdissected human renal biopsies. Kidney Int. 2003, 64 (1): 356-360. 10.1046/j.1523-1755.2003.00074.x

Solanas M, Moral R, Escrich E: Unsuitability of using ribosomal RNA as loading control for Northern blot analyses related to the imbalance between messenger and ribosomal RNA content in rat mammary tumors. Anal Biochem. 2001, 288 (1): 99-102. 10.1006/abio.2000.4889

Marie SK, Okamoto OK, Uno M, Hasegawa AP, Oba-Shinjo SM, Cohen T, Camargo AA, Kosoy A, Carlotti CG, Toledo S, et al: Maternal embryonic leucine zipper kinase transcript abundance correlates with malignancy grade in human astrocytomas. Int J Cancer. 2008, 122 (4): 807-815. 10.1002/ijc.23189

Livak KJ, Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001, 25 (4): 402-408. 10.1006/meth.2001.1262