Application of a fuzzy neural network model in predicting polycyclic aromatic hydrocarbon-mediated perturbations of the Cyp1b1 transcriptional regulatory network in mouse skin

Toxicology and Applied Pharmacology

Volumn 267, Issue 2, 2013, Pages 192-199

  Larkin, Andrew ^a   Siddens, Lisbeth K ^a   Krueger, Sharon K ^a,b   Tilton, Susan C ^a,c   Waters, Katrina M ^a,c   Williams, David E ^a,b   Baird, William M ^a  

^a OREGON STATE UNIVERSITY   (United States)

^b OREGON STATE UNIVERSITY   (United States)

^c PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Ahrr; Cyp1b1; Mixtures; Modeling; PAHs; Skin

Indexed keywords

ARYL HYDROCARBON RECEPTOR REPRESSOR; BENZO[A]PYRENE; CIGARETTE SMOKE CONDENSATE; COAL TAR; CYTOCHROME P450 1A1; CYTOCHROME P450 1B1; DIBENZO[DEF,P]CHRYSENE; HEAT SHOCK PROTEIN 90; HERPESVIRUS ENTRY MEDIATOR; MESSENGER RNA; POLYCYCLIC AROMATIC HYDROCARBON; PROTEIN; RETINOBLASTOMA BINDING PROTEIN 4; TOLUENE; TRANSCRIPTION FACTOR E2F6; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ARTICLE; ARTIFICIAL NEURAL NETWORK; DOWN REGULATION; FUZZY NEURAL NETWORK; GENE EXPRESSION; MICROARRAY ANALYSIS; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN EXPRESSION; RISK ASSESSMENT; SKIN;

ANIMALS; ARYL HYDROCARBON HYDROXYLASES; FEMALE; FUZZY LOGIC; GENE REGULATORY NETWORKS; MICE; NEURAL NETWORKS (COMPUTER); POLYCYCLIC HYDROCARBONS, AROMATIC; RISK ASSESSMENT; SKIN;

EID: 84873807426     PISSN: 0041008X     EISSN: 10960333     Source Type: Journal    
DOI: 10.1016/j.taap.2012.12.011     Document Type: Article

References (45)

1. Abdelaziz A., Shushko I., Wolfram T., Körner R., Novotarskyi S., Tetko I.V. QSAR modeling for in vitro assays: linking ToxCast™ database to the integrated modeling framework "OCHEM". J. Chem. Inf. 2012, 4:62.
2. Agrafiotis D.K., Cedeno W., Lobanov V.S. On the use of neural network ensembles in QSAR and QSPR. J. Chem. Inf. Comput. Sci. 2002, 42:903-911.
3. Altenburger R., Scholz S., Mechthild S., Busch W., Escher B.I. Mixture toxicity revisited from a toxicogenomic perspective. Environ. Sci. Technol. 2012, 46:2508-2522.
4. Baird W.M., Hooven L.A., Mahadevan B. Carcinogenic aromatic hydrocarbon-DNA adducts and mechanism of action. Environ. Mol. Mutagen. 2005, 45:106-114.
5. Benjamini Y., Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B 1995, 57:289-300.
6. Billiard S.M., Timme-Laragy A.R., Wassenberg D.M., Cockman C., Di Giulio R.T. The role of the aryl hydrocarbon receptor pathway in mediating synergistic developmental toxicity of polycyclic aromatic hydrocarbons to zebrafish. Toxicol. Sci. 2006, 92:526-536.
7. Bolstad B.M., Irizarry R.A., Åstrand M., Speed T.P. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19:185-193.
8. Burke K.E., Wei H. Synergistic damage by UVA radiation and pollutants. Toxicol. Ind. Health 2009, 25(4-5):219-224.
9. Buters J.T., Sakai S., Richter T., Pineau T., Alexander D.L., Savas U., Doehmer J., Ward J.M., Jefcoate C.R., Gonzalez F.J. Cytochrome P450 CYP1B1 determines susceptibility to 7,12-dimethylbenz[a]thracene-induced lymphomas. Proc. Natl. Acad. Sci. U. S. A. 1999, 96:1977-1982.
10. Buters J.T., Mahadevan B., Quintanilla-Martinez L., Gonzalez F.J., Greim H., Baird W.M., Luch A. Cytochrome P450 1B1 determines susceptibility to dibenzo[a, l]pyrene-induced tumor formation. Chem. Res. Toxicol. 2002, 15:1127-1135.
11. Castro D.J., Baird W.M., Pereira C.B., Giovanini J., Löhr C.V., Fischer K.A., Yu Z., Gonzalez F.J., Krueger S.K., Williams D.E. Fetal mouse Cyp1b1 and transplacental carcinogenesis from maternal exposure to dibenzo(a, l)pyrene. Cancer Prev. Res. 2008, 1:128-134.
12. Cavalieri E.L., Rogan E.G. Central role of radical cations in metabolic activation of polycyclic aromatic hydrocarbons. Xenobiotica 1995, 25:677-688.
13. Courter L.A., Musafia-Jeknic T., Fischer K., Bildfell R., Giovanini J., Pereira C., Baird W.M. Urban dust particulate matter alters PAH-induced carcinogenesis by inhibition of CYP1A1 and CYP1B1. Toxicol. Sci. 2007, 95:63-73.
14. Courter L.A., Pereira C., Baird W.M. Diesel exhaust influences carcinogenic PAH-induced genotoxicity and gene expression in human breast epithelial cells in culture. Mutat. Res. 2007, 625:72-82.
15. Damon D.A. Toxic equivalency factor approach for assessment of polycyclic aromatic hydrocarbons. Toxicol. Environ. Chem. 1997, 64:81-108.
16. DiGiovanni J. Multistage carcinogenesis in mouse skin. Pharmacol. Ther. 1992, 54:63-128.
17. Fujii-Kuriyama Y., Mimura J. Molecular mechanisms of AhR functions in the regulation of cytochrome P450 genes. Biochem. Biophys. Res. Commun. 2005, 338:311-317.
18. Garson G.D. Interpreting neural-network connection weights. AI Expert 1991, 6:46-51.
19. Hahn M.E., Allan L.L., Sherr D.H. Regulation of constitutive and inducible AHR signaling: complex interactions involving the AHR repressor. Biochem. Pharmacol. 2009, 77:485-497.
20. Halgamuge S.K., Glesner M. Neural networks in designing fuzzy systems for real world applications. Fuzzy Set Syst. 1994, 65:1-12.
21. Hosoya T., Harada N., Mimura J., Motohashi H., Takahashi S., Nakajima O., Morita M., Kawauchi S., Yamamoto M., Fujii-Kuriyama Y. Inducibility of cytochrome P450 1A1 and chemical carcinogenesis by benzo[a]pyrene in AhR repressor-deficient mice. Biochem. Biophys. Res. Commun. 2008, 365:562-567.
22. IARC Some non-heterocyclic polycyclicaromatic hydrocarbons and some related exposures. Monographs on the Evaluation of Carcinogenic Risks to Humans. Lyon, France 2010, (http://monographs.iarc.fr/ENG/Monographs/vol92/mono92.pdf).
23. Kawajiri K., Fujii-Kuriyama Y. Cytochrome P450 gene regulation and physiological functions mediated by the aryl hydrocarbon receptor. Arch. Biochem. Biophys. 2007, 2:207-212.
24. Kerr M.K., Martin M., Churchill G.A. Analysis of variance for gene expression microarray data. J. Comput. Biol. 2000, 7:819-837.
25. Lee C.C. Fuzzy logic in control systems: fuzzy logic controller. IEEE Trans. Syst. Man Cybern. 1990, 20:404-418.
26. Lek S., Guégan J.F. Artificial neural networks as a tool in ecological modelling, an introduction. Ecol. Model. 1999, 120:65-73.
27. Leondes C.T. Fuzzy Logic and Expert Systems Applications 1998, Academic Press, San Diego.
28. Lin P., Hu S.W., Chang T.H. Correlation between gene expression of aryl hydrocarbon receptor (AhR), hydrocarbon receptor nuclear translocator (Arnt), cytochromes P4501A1 (CYP1A1) and 1B1 (CYP1B1), and inducibility of CYP1A1 and CYP1B1 in human lymphocytes. Toxicol. Sci. 2003, 71:20-26.
29. Lomas A., Leonardi-Bee J., Bath-Hextall F. A systematic review of worldwide incidence of non-melanoma skin cancer. Br. J. Dermatol. 2012, 166:1069-1080.
30. Mamdani E.H. Application of fuzzy logic to approximate reasoning using linguistic synthesis. IEEE Trans. Comput. 1977, 100:1182-1191.
31. Marston C.P., Pereira C., Ferguson J., Fischer K., Hedstrom O., Dashwood W.M., Baird W.M. Effect of a complex environmental mixture from coal tar containing polycyclic aromatic hydrocarbons (PAH) on the tumor initiation, PAH-DNA binding and metabolic activation of carcinogenic PAH in mouse epidermis. Carcinogenesis 2001, 22:1077-1086.
32. Moldoveanu S. Toxicological and environmental aspects of polycyclic aromatic hydrocarbons (PAHs) and related compounds. Tech. Instrum. Anal. Chem. 2010, 28:693-699.
33. Penning T.M., Burczynski M.E., Hung C.-F., McCoull K.D., Palackal N.T., Tsuruda L.S. Dihydrodiol dehydrogenases and polycyclic aromatic hydrocarbon activation: generation of reactive and redox-active o-quinones. Chem. Res. Toxicol. 1999, 12:1-18.
34. Pham D., Liu X. Neural Networks for Identification, Prediction, and Control 1995, Springer-Verlag, London.
35. Pollenz R.S. The mechanism of AH receptor protein down-regulation (degradation) and its impact on AH receptor-mediated gene regulation. Chem. Biol. Interact. 2002, 141:41-61.
36. Schauer C., Niessner R., Pöschl U. Polycyclic aromatic hydrocarbons in urban air particulate matter: decadal and seasonal trends, chemical degradation, and sampling artifacts. Environ. Sci. Technol. 2003, 37:2861-2868.
37. Siddens L.K., Larkin A., Krueger S.K., Bradfield C.A., Waters K.M., Tilton S.C., Pereira C.B., Löjr C.V., Arlt V.M., Phillips D.H., Williams D.E., Baird W.M. Polycyclic aromatic hydrocarbons as skin carcinogens: comparison of benzo[a]pyrene, dibenzo[def, p]chrysene and three environmental mixtures in the FVB/N mouse. Toxicol. Appl. Pharmacol. 2012, 264:377-386.
38. Siegel R., Ward E., Brawley O., Jeimal A. Cancer statistics, 2011. The impact of eliminating socieoeconomic and racial disparities on premature cancer deaths. CA Cancer J. Clin. 2011, 61:212-236.
39. Sipes N.S., Martin M.T., Reif D.M., Kleinstreuer N.C., Judson R.S., Singh A.V., Chandler K.J., Dix D.J., Kavlock R.J., Knudsen T.B. Predictive models of prenatal developmental toxicity from ToxCast high-throughput screening data. Toxicol. Sci. 2011, 124:109-127.
40. Timme-Laragy A.R., Cockman C.J., Matson C.W., Di Giulio R.T. Synergistic induction of AHR regulated genes in developmental toxicity from co-exposure to two model PAHs in zebrafish. Aquat. Toxicol. 2007, 85:241-250.
41. Toyooka T., Ibuki Y., Takabayashi F., Goto R. Coexposure to benzo[a]pyrene and UVA induces DNA damage: first proof of double-strand breaks in a cell-free system. Environ. Mol. Mutagen. 2006, 47:38-47.
42. Uno S., Dalton T.P., Dragin N., Curran C.P., Derkenne S., Miller M.L., Shertzer H.G., Gonzalez F.J., Nebert D.W. Oral benzo[a]pyrene in Cyp1 knockout mouse lines: CYP1A1 important in detoxication, CYP1B1 metabolism required for immune damage independent of total-body burden and clearance rate. Mol. Pharmacol. 2006, 69:1103-1114.
43. Vasilakos C., Kalabokidis K., Hatzopoulos J., Matsinos I. Identifying wildland fire ignition factors through sensitivity analysis of a neural network. Nat. Hazards 2009, 50:125-143.
44. Yuspa S.H., Poirier M.C. Chemical carcinogenesis: from animal models to molecular models in one decade. Adv. Cancer Res. 1988, 50:25-70.
45. Zhang Y., Tao S. Global atmospheric emission inventory of polycyclic aromatic hydrocarbons (PAHs) for 2004. Atmos. Environ. 2009, 43:812-819.