Inter- and intra-laboratory study to determine the reproducibility of toxicogenomics datasets

Toxicology

Volumn 290, Issue 1, 2011, Pages 50-58

  Scott, D J ^a   Devonshire, A S ^a   Adeleye, Y A ^b   Schutte, M E ^a   Rodrigues, M R ^c   Wilkes, T M ^a   Sacco, M G ^c   Gribaldo, L ^c   Fabbri, M ^c   Coecke, S ^c   Whelan, M ^c   Skinner, N ^d   Bennett, A ^e   White, A ^b   Foy, C A ^a  

^a LGC   (United Kingdom)

^b UNILEVER RESEARCH   (United Kingdom)

^c JOINT RESEARCH CENTRE   (Italy)

^d AGILENT TECHNOLOGIES   (United Kingdom)

^e UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

Benzo a pyrene; HepG2; In vitro; Inter laboratory; Reproducibility; Toxicogenomics

Indexed keywords

BENZO[A]PYRENE; TRANSCRIPTOME;

ARTICLE; CELL CULTURE; CELL STRAIN HEPG2; EXPOSURE; GENE EXPRESSION; GENOMICS; HUMAN; HUMAN CELL; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROSPECTIVE STUDY; REPRODUCIBILITY; RNA EXTRACTION; TOXICOGENOMICS; TOXICOLOGY;

DATABASES, GENETIC; HEP G2 CELLS; HUMANS; LABORATORIES; PRINCIPAL COMPONENT ANALYSIS; PROSPECTIVE STUDIES; PROTEIN ARRAY ANALYSIS; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; TOXICOGENETICS;

EID: 80053622829     PISSN: 0300483X     EISSN: 18793185     Source Type: Journal    
DOI: 10.1016/j.tox.2011.08.015     Document Type: Article

References (25)

1. Abraham V.C., Towne D.L., Waring J.F., Warrior U., Burns D.J. Application of a high-content multiparameter cytotoxicity assay to prioritize compounds based on toxicity potential in humans. J. Biomol. Screen. 2008, 13:527-537.
2. Barnes M., Freudenberg J., Thompson S., Aronow B., Pavlidis P. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res. 2005, 33:5914-5923.
3. Beekman J.M., Boess F., Hildebrand H., Kalkuhl A., Suter L. Gene expression analysis of the hepatotoxicant methapyrilene in primary rat hepatocytes: an interlaboratory study. Environ. Health Perspect. 2006, 114:92-99.
4. Burczynski M.E., McMillian M., Ciervo J., Li L., Parker J.B., Dunn R.T., Hicken S., Farr S., Johnson M.D. Toxicogenomics-based discrimination of toxic mechanism in HepG2 human hepatoma cells. Toxicol. Sci. 2000, 58:399-415.
5. Castorena-Torres F., Bermudez de Leon M., Cisneros B., Zapata-Perez O., Salinas J.E., Albores A. Changes in gene expression induced by polycyclic aromatic hydrocarbons in the human cell lines HepG2 and A549. Toxicol. In Vitro 2008, 22:411-421.
6. Dennis G., Sherman B.T., Hosack D.A., Yang J., Gao W., Lane H.C., Lempicki R.A. DAVID: Database for Annotation. Visualization, and Integrated Discovery. Genome Biology 2003, 4:3.
7. Ellinger-Ziegelbauer H., Stuart B., Wahle B., Bomann W., Ahr H.J. Comparison of the expression profiles induced by genotoxic and nongenotoxic carcinogens in rat liver. Mutat. Res. 2005, 575:61-84.
8. Guler G., Himmetoglu C., Jimenez R.E., Geyer S.M., Wang W.P., Costinean S., Pilarski R.T., Morrison C., Suren D., Liu J., Chen J., Kamal J., Shapiro C.L., Huebner K. Aberrant expression of DNA damage response proteins is associated with breast cancer subtype and clinical features. Breast Cancer Res. Treat. 2010.
9. Guler G., Huebner K., Himmetoglu C., Jimenez R.E., Costinean S., Volinia S., Pilarski R.T., Hayran M., Shapiro C.L. Fragile histidine triad protein, WW domain-containing oxidoreductase protein Wwox, and activator protein 2gamma expression levels correlate with basal phenotype in breast cancer. Cancer 2009, 115:899-908.
10. Hockley S.L., Arlt V.M., Brewer D., Giddings I., Phillips D.H. Time- and concentration-dependent changes in gene expression induced by benzo(a)pyrene in two human cell lines. MCF-7 and HepG2. BMC Genomics 2006, 7:260.
11. Hockley S.L., Mathijs K., Staal Y.C., Brewer D., Giddings I., van Delft J.H., Phillips D.H. Interlaboratory and interplatform comparison of microarray gene expression analysis of HepG2 cells exposed to benzo(a)pyrene. Omics 2009, 13:115-125.
12. Jarvinen A.K., Hautaniemi S., Edgren H., Auvinen P., Saarela J., Kallioniemi O.P., Monni O. Are data from different gene expression microarray platforms comparable?. Genomics 2004, 83:1164-1168.
13. Kuo W.P., Jenssen T.K., Butte A.J., Ohno-Machado L., Kohane I.S. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 2002, 18:405-412.
14. Lee C.M., Chen S.Y., Lee Y.C., Huang C.Y., Chen Y.M. Benzo[a]pyrene and glycine N-methyltransferse interactions: gene expression profiles of the liver detoxification pathway. Toxicol. Appl. Pharmacol. 2006, 214:126-135.
15. 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.
16. O'Brien P.J., Irwin W., Diaz D., Howard-Cofield H., Krejsa C.M., Slaughter M.R., Gao B., Kaludercic N., Angeline N., Bernardi P., Brain P., Hougham C. High concordance of drug-induced human hepatotoxicity with in vitro cytotoxicity measured in a novel cell-based model using high content screening. Arch. Toxicol. 2006, 80:580-604.
17. O'Keefe L.V., Colella A., Dayan S., Chen Q., Choo A., Jacob R., Price G., Venter D., Richards R.I. Drosophila orthologue of WWOX, the chromosomal fragile site FRA16D tumour suppressor gene, functions in aerobic metabolism and regulates reactive oxygen species. Hum. Mol. Genet. 2010.
18. Shi L., Reid L.H., Jones W.D., Shippy R., Warrington J.A., Baker S.C., Collins P.J., de Longueville F., Kawasaki E.S., Lee K.Y., et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat. Biotechnol. 2006, 24:1151-1161.
19. Staal Y.C., van Herwijnen M.H., van Schooten F.J., van Delft J.H. Modulation of gene expression and DNA adduct formation in HepG2 cells by polycyclic aromatic hydrocarbons with different carcinogenic potencies. Carcinogenesis 2006, 27:646-655.
20. Tan P.K., Downey T.J., Spitznagel E.L., Xu P., Fu D., Dimitrov D.S., Lempicki R.A., Raaka B.M., Cam M.C. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 2003, 31:5676-5684.
21. Thavathiru E., Ludes-Meyers J.H., MacLeod M.C., Aldaz C.M. Expression of common chromosomal fragile site genes, WWOX/FRA16D and FHIT/FRA3B is downregulated by exposure to environmental carcinogens, UV, and BPDE but not by IR. Mol. Carcinog. 2005, 44:174-182.
22. Ulrich R.G., Rockett J.C., Gibson G.G., Pettit S.D. Overview of an interlaboratory collaboration on evaluating the effects of model hepatotoxicants on hepatic gene expression. Environ. Health Perspect. 2004, 112:423-427.
23. van Delft J.H., van Agen E., van Breda S.G., Herwijnen M.H., Staal Y.C., Kleinjans J.C. Discrimination of genotoxic from non-genotoxic carcinogens by gene expression profiling. Carcinogenesis 2004, 25:1265-1276.
24. 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. RESEARCH0034.
25. Wilkening S., Stahl F., Bader A. Comparison of primary human hepatocytes and hepatoma cell line Hepg2 with regard to their biotransformation properties. Drug Metab. Dispos. 2003, 31:1035-1042.