Global gene expression changes in human embryonic lung fibroblasts induced by organic extracts from respirable air particles

Particle and Fibre Toxicology

Volumn 9, Issue , 2012, Pages

  Líbalová, Helena ^a,b   Uhlířová, Kateřina ^a   Kléma, Jiří ^c   Machala, Miroslav ^d   Šrám, Radim J ^a   Ciganek, Miroslav ^d   Topinka, Jan ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Czech Republic)

^b CHARLES UNIVERSITY   (Czech Republic)

^c CZECH TECHNICAL UNIVERSITY IN PRAGUE   (Czech Republic)

^d VETERINARY RESEARCH INSTITUTE   (Czech Republic)

Author keywords

Ahr; Air pollution; Complex mixtures; Cyp1b1; Gene expression profile; Hel cells

Indexed keywords

ABC TRANSPORTER; CYTOCHROME P450; DIMETHYL SULFOXIDE; GLYCEROLIPID; ORGANIC MATTER; STEROID HORMONE; TRANSFORMING GROWTH FACTOR BETA; WNT PROTEIN; XENOBIOTIC AGENT; ORGANIC COMPOUND;

AIR POLLUTANT; AIR POLLUTION; AMBIENT AIR; ARTICLE; CONCENTRATION RESPONSE; CONTROLLED STUDY; CYP1B1 GENE; DNA REPAIR; ENZYME ACTIVITY; ENZYME INDUCTION; GENE; GENE EXPRESSION; GENETIC SCREENING; HUMAN; HUMAN CELL; HUMAN GENOME; INCUBATION TIME; LIPID METABOLISM; LUNG FIBROBLAST; MEMBRANE TRANSPORT; MICROARRAY ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; STEROIDOGENESIS; TRANSCRIPTION REGULATION; TUMOR GROWTH; XENOBIOTIC METABOLISM; CHEMISTRY; CYTOLOGY; CZECH REPUBLIC; DOSE RESPONSE; DRUG EFFECT; FIBROBLAST; GENE EXPRESSION PROFILING; LUNG; METABOLISM; OXIDATION REDUCTION REACTION; PARTICULATE MATTER; PHYSIOLOGY;

AIR POLLUTANTS; CZECH REPUBLIC; DOSE-RESPONSE RELATIONSHIP, DRUG; FIBROBLASTS; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMANS; LUNG; MICROARRAY ANALYSIS; ORGANIC CHEMICALS; OXIDATION-REDUCTION; PARTICULATE MATTER;

EID: 84856745498     PISSN: None     EISSN: 17438977     Source Type: Journal    
DOI: 10.1186/1743-8977-9-1     Document Type: Article

References (64)

1. Lewtas J. Air pollution combustion emissions: characterisation of causative agents and mechanisms associated with cancer, reproductive and cardiovascular effects. Mutat Res 2007, 636:95-133. 10.1016/j.mrrev.2007.08.003, 17951105.
2. Harrison RM, Smith DJT, Kibble AJ. What is responsible for the carcinogenicity of PM2.5?. Occup Environ Med 2004, 61:799-805. 10.1136/oem.2003.010504, 1740668, 15377764.
3. Claxton LD, Woodall GM. A review of the mutagenicity and rodent carcinogenicity of ambient air. Mutat Res 2007, 636:36-94. 10.1016/j.mrrev.2007.01.001, 17451995.
4. Topinka J, Hovorka J, Milcova A, Schmuczerova J, Krouzek J, Rossner P, Sram RJ. Acellular assay to assess genotoxicity of complex mixtures of organic pollutants bound on size segregated aerosol. Part I: DNA adducts. Toxocol Lett 2010, 198:304-311.
5. Marvin CH, Hewitt LM. Analytical methods in bioassay-directed investigations of mutagenicity of air particulate material. Mutat Res 2007, 636:4-35. 10.1016/j.mrrev.2006.05.001, 17468041.
6. Karlsson HL, Nygren J, Moller L. Genotoxicity of airborne particulate matter: the role of cell-particle interaction and of substances with adduct-forming and oxidizing capacity. Mutat Res 2004, 565:1-10.
7. Steenhof M, Gosens I, Strak M, Godri K, Hoek G, Cassee FR, Mudway IS, Kelly FJ, Harrison RM, Lebret E, Brunekreef B, Janssen NAH, Pieters HHP. In vitro toxicity of particulate matter (PM) collected at different sites in t5he Netherlands is associated with PM composition, size fraction and oxidative potential - the RAPTES project. Particle and Fibre Toxicology 2011, 8:26. 10.1186/1743-8977-8-26, 3180259, 21888644.
8. Topinka J, Schwarz LR, Wiebel FJ, Cerna M, Wolff T. Genotoxicity of urban air pollutants in the Czech Republic Part II. DNA adduct formation in mammalian cells by extractable organic matter. Mutat Res 2000, 469:83-93.
9. Binkova B, Sram RJ. The genotoxic effect of carcinogenic PAHs, their artificial and environmental mixtures (EOM) on human diploid lung fibroblasts. Mutat Res 2004, 547:109-121. 10.1016/j.mrfmmm.2003.12.006, 15013705.
10. Ghio AJ, Stonehuerner J, Dailey LA, Carter JD. Metals associated with both the water soluble and insoluble fractions of an ambient air pollution particles catalyze an oxidative stress. Inhal Toxicol 1999, 11:37-49. 10.1080/089583799197258, 10380158.
11. Prahalad AK, Inmon J, Dailey LA, Madden MC, Ghio AJ, Gallagher JE. Air pollution particles mediated oxidative DNA base damage in a cell free system and in human airway epithelial cells in relation to particulate metal content and bioreactivity. Chem Res Toxicol 2001, 14:879-887. 10.1021/tx010022e, 11453735.
12. Knaapen AM, Shi T, Borm PJ, Schins RP. Soluble metals as well as insoluble particle fraction are involved in cellular DNA damage induced by particulate matter. Mol Cell Biochem 2002, 234:317-326. 10.1023/A:1015970023889, 12162450.
13. Upham BL, Bláha L, Babica P, Park JS, Sovadinová I, Pudrith C, Rummel AM, Weis LM, Sai K, Tithof PK, Guzvić M, Vondráček J, Machala M, Trosko JE. Tumor promoting properties of a cigarette smoke prevalent polycyclic aromatic hydrocarbon as indicated by the inhibition of gap junctional intercellular communication via phosphatidylcholine-specific phospholipase C. Cancer Sci 2008, 99:696-705. 10.1111/j.1349-7006.2008.00752.x, 3023995, 18377422.
14. Andrysík Z, Vondráček J, Marvanová S, Cigánek M, Neča J, Pěnčíková K, Mahadevan B, Topinka J, Baird WM, Kozubík A, Machala M. Activation of the aryl hydrocarbon receptor is the major toxic mode of action of an organic extract of a reference urban dust particulate matter mixture: The role of polycyclic aromatic hydrocarbons. Mutation Res 2011, 714:53-62. 10.1016/j.mrfmmm.2011.06.011, 21762708.
15. IARC Monographs on the Evaluation of Carcinogenic Risks to Humans. 2009, , http://monographs.iarc.fr/ENG/Classification/index.php
16. Hemminki K, Dipple A, Shuker DEG, Kadlubar FF, Segerbäck D, Bartsch H. DNA Adducts: Identification and Biological Significance. IARC, Lyon 1994,
17. Dipple A. DNA adducts of chemical carcinogens. Carcinogenesis 1995, 16:437-441. 10.1093/carcin/16.3.437, 7697795.
18. Khalili H, Zhang FJ, Harvey RG, Dipple A. Mutagenicity of benzo[a]pyrene-deoxyadenosine adducts in a sequence context derived from the p53 gene. Mutat Res 2000, 465:39-44.
19. Puga A, Tomlinson CR, Xia Y. Ah receptor signals cross-talk with multiple developmental pathways. Biochem Pharmacol 2005, 69:199-207. 10.1016/j.bcp.2004.06.043, 15627472.
20. Chopra M, Schrenk D. Dioxin toxicity, aryl hydrocarbon receptor signaling, and apoptosis-persistent pollutants affect programmed cell death. Crit Rev Toxicol 2011, 41:292-320. 10.3109/10408444.2010.524635, 21323611.
21. Ferecatu I, Borot M-C, Bossard C, Leroux M, Boggetto N, Marano F, Baeza-Squiban A, Andreau K. Polycyclic aromatic hydrocarbon components contribute to the mitochondria-antiapoptotic effect of fine particulate matter on human bronchial epithelial cells via the aryl hydrocarbon receptor. Particle and Fibre Toxicology 2010, 7:8-18. 10.1186/1743-8977-7-8, 2861638, 20359338.
22. Bláha L, Kapplová P, Vondráček J, Upham B, Machala M. Inhibition of gap-junctional intercellular communication by environmentally occurring polycyclic aromatic hydrocarbons. Toxicol Sci 2002, 65:43-51. 10.1093/toxsci/65.1.43, 11752684.
23. Mahadevan B, Parsons H, Musafia T, Sharma AK, Amin S, et al. Effect of artificial mixtures of environmental polycyclic aromatic hydrocarbons present in coal tar, urban dust, and diesel exhaust particulates on MCF-7 cells in culture. Environ Mol Mutagen 2004, 44:99-107. 10.1002/em.20039, 15278913.
24. Sen B, Mahadevan B, DeMarini D. Transcriptional responses of the complex mixtures - A review. Mutat Res 2007, 636:144-177. 10.1016/j.mrrev.2007.08.002, 17888717.
25. Mahadevan B, Keshava C, Musafia-Jeknic T, Pecaj A, Weston A, Baird WM. Altered gene expression patterns in MCF-7 cells induced by the urban dust particulate complex mixture standard reference material 1649a. Cancer Res 2005, 65:1251-1258. 10.1158/0008-5472.CAN-04-2357, 15735009.
26. Aung HH, Lame MW, Gohil K, He G, Denison M, Rutledge JC, Wilson DW. Comparative gene responses to collected ambient particles in vitro: endothelial responses. Physiol Genomics 2011, 43:917-929. 10.1152/physiolgenomics.00051.2011, 21652769.
27. Binkova B, Giguere Y, Rossner P, Dostal M, Sram RJ. The effect of dibenzo[al]pyrene on human diploid fibroblasts; the induction of DNA adducts, expression of p53 and p21WAF1 proteins and cell cycle distribution. Mutat Res 2000, 471:57-70.
28. Ravindra K, Sokhi R, van Grieken R. Atmospheric polycyclic aromatic hydrocarbons: source attribution, emission factors and regulation. Atmosph Environ 2008, 42:2895-2921.
29. Yang Y, Guo P, Zhang Li D, Zhao L, Mu D. Seasonal variation, sources and gas/particle partitioning of polycyclic aromatic hydrocarbons in Guangzhou, China. Science Tot Environ 2010, 408:2492-2500.
30. Gupta S, Kumar K, Srivastava A, Srivastava VK. Size distribution and source apportionment of polycyclic aromatic hydrocarbons (PAHs) in aerosol particle samples from the atmospheric environment of Delhi, India. Science of the Total Environment 2011, 409:4674-4680. 10.1016/j.scitotenv.2011.08.008, 21889785.
31. Topinka J, Rossner P, Milcova A, Schmuczerova J, Svecova V, Sram RJ. DNA adducts and oxidative DNA damage induced by organic extracts from PM2.5 in an acellular assay. Toxicol Lett 2011, 202:186-192. 10.1016/j.toxlet.2011.02.005, 21329747.
32. Guengerich FP, Parikh A, Yun CH, Kim D, Nakamura K, Notley LM, Gillam EM. What makes P450s work? Searches for answers with known and new P450s. Drug Metab Rev 2000, 32:267-281. 10.1081/DMR-100102334, 11139129.
33. Nebert DW, Russell DW. Clinical importance of the cytochromes P450. Lancet 2002, 360:1155-62. 10.1016/S0140-6736(02)11203-7, 12387968.
34. Port JL, Yamaguchi K, Du B, De Lorenzo M, Chang M, Heerdt PM, Kopelovich R, Marcus CB, Altorki NK, Subbaramaiah K, Dannenberg A. Tobacco smoke induces CYP1B1 in the aerodigestive tract. Carcinogenesis 2004, 25:2275-2281. 10.1093/carcin/bgh243, 15297370.
35. Tsuchiya Y, Nakajima M, Kyo S, Kanaya T, Inoue M, Yokoi T. Human CYP1B1 is regulated by estradiol via estrogen receptor. Cancer Res 2004, 64:3119-3125. 10.1158/0008-5472.CAN-04-0166, 15126349.
36. Nebert DW, Roe AL, Dieter MZ, Solis WA, Yang Y, Dalton TP. Role of the aromatic hydrocarbon receptor and [Ah] gene battery in the oxidative stress response, cell cycle control, and apoptosis. Biochem Pharmacol 2000, 59:65-85. 10.1016/S0006-2952(99)00310-X, 10605936.
37. Kung T, Murphy KA, White LA. The aryl hydrocarbon receptor (AhR) pathway as a regulatory pathway for cell adhesion and matrix metabolism. Biochem Pharmacol 2009, 77:536-546. 10.1016/j.bcp.2008.09.031, 2699768, 18940186.
38. Kelner MJ, Stokely MN, Stoval NE, Montoya MA. Structural organization of the human microsomal glutathione S-transferase gene (GST12). Genomics 1996, 36:100-103. 10.1006/geno.1996.0429, 8812420.
39. Xu S, Wang Y, Roe B, Pearson WR. Characterization of the human class Mu glutathione S-transferase gene cluster and the GSTM1 deletion. J Biol Chem 1998, 6:3517-3527.
40. Whitbread AK, Masoumi A, Tetlow N, Schmuck E, Coggan M, Board PG. Characterization of the omega class of glutathione transferases. Methods Enzymol 2005, 401:78-99.
41. Sanderson JT. The steroid hormone biosynthesis pathway as a target for endocrine-disrupting chemicals. Toxicol Sci 2006, 94:3-21. 10.1093/toxsci/kfl051, 16807284.
42. Tsuchiya Y, Nakajima M, Yokoi T. Cytochrome P450-mediated metabolism of estrogens and its regulation in human. Cancer Lett 2005, 227:115-124. 10.1016/j.canlet.2004.10.007, 16112414.
43. Ohtake F, Baba A, Fujii-Kuriyama Y, Kato S. Intrinsic AhR function underlies cross-talk of dioxins with sex hormone signalings. Biochem Biophysis Res Commun 2008, 370:541-546.
44. Shanle EK, Xu W. Endocrine disrupting chemicals targeting estrogen receptor signaling: identification and mechanisms of action. Chem Res Toxicol 2011, 24:6-19. 10.1021/tx100231n, 3119362, 21053929.
45. Mathew LR, Simonich MT, Tanguay RL. AhR-dependent misregulation of Wnt signalling disrupts tissue regeneration. Biochem Pharmacol 2009, 77:498-507. 10.1016/j.bcp.2008.09.025, 2658594, 18938144.
46. Procházková J, Kabátková M, Bryja V, Umannová L, Bernatík O, Kozubík A, Machala M, Vondráček J. The Interplay of the Aryl Hydrocarbon Receptor and β-Catenin Alters Both AhR-Dependent Transcription and Wnt/β-Catenin Signaling in Liver Progenitors. Toxicol Sci 2011, 122:349-360. 10.1093/toxsci/kfr129, 21602191.
47. Katoh M. Molecular cloning, gene structure, and expression analyses of NKD1 and NKD2. Int J Oncol 2001, 19:963-969.
48. Shi Y, Massague J. Mechanisms of TGF-beta signaling from cell membrane to the nucleus. Cell 113:685-700.
49. McLean K, Gong Y, Choi Y, Deng N, Yang K, Bai S, Cabrera L, Keller E, McCauley L, Cho KR, Buckanovich RJ. Human ovarian carcinoma-associated mesenchymal stem cells regulate cancer stem cells and tumorigenesis via altered BMP production. J Clin Invest 2011, 121:3206-3219. 10.1172/JCI45273, 3148732, 21737876.
50. Langlands K, Yin X, Anand G, Prochownik EV. Differential interactions of Id proteins with basic-helix-loop-helix transcription factors. J Biol Chem 1997, 272:19785-19793. 10.1074/jbc.272.32.19785, 9242638.
51. Gomez-Duran A, Carvajal-Gonzalez JM, Mulero-Navarro S, Santiago-Josefat B, Puga A, Fernandez-Salguero PM. Fitting a xenobiotic receptor into cell homeostasis: how the dioxin receptor interacts with TGFbeta signaling. Biochem Pharmacol 2009, 15:700-712.
52. Vasiliou V, Vasiliou K, Nebert DW. Human ATP-binding cassette (ABC) transporter family. Hum Genomics 2009, 3:281-290. 2752038, 19403462.
53. Davidson AL, Dassa E, Orelle C, Chen J. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol Mol Biol Rev 2008, 72:317-364. 10.1128/MMBR.00031-07, 2415747, 18535149.
54. Xu S, Weerachayaphorn J, Cai SY, Soroka CJ, Boyer JL. Aryl hydrocarbon receptor and NF-E2-related factor 2 are key regulators of human MRP4 expression. Am J Physiol Gastrointest Liver Physiol 2010, 99:G126-G135.
55. Henry EC, Welle SL, Gasiewicz TA. TCDD and a Putative Endogenous AhR Ligand, ITE, Elicit the Same Immediate Changes in Gene Expression in Mouse Lung Fibroblasts. Toxicol Sci 2010, 114:90-100. 10.1093/toxsci/kfp285, 2819971, 19933214.
56. Nishimura C, Matsuura Y, Kohai Y, Ahera T, Carper D, Morjana N, Lyons C, Flynn TG. Cloning and expression of human aldose-reductase. J Biol Chem 1990, 265:9788-9792.
57. Sevastyanova O, Novakova Z, Hanzalova K, Binkova B, Sram RJ, Topinka J. Temporal variation in the genotoxic potential of urban air particulate matter. Mutat Res 2008, 649:179-186.
58. Du P, Kibbe W, Lin SM. Lumi: a pipeline for processing Illumina microarray. Bioinformatics 2008, 24:1547-1548. 10.1093/bioinformatics/btn224, 18467348.
59. Smyth GK. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 2004, 3. Article 3.
60. Oliveros JC. VENNY. An interactive tool for comparing lists with Venn Diagrams. , http://bioinfogp.cnb.csic.es/tools/venny/index.html
61. Goeman JJ, van de Geer SA, de Kort F, van Houwelingen JC. A global test for groups of genes: testing association with a clinical outcome. Bioinformatics 2004, 20:93-99. 10.1093/bioinformatics/btg382, 14693814.
62. Holm S. A simple sequentially rejective multiple test procedure. Scand J Stat 1979, 6:65-70.
63. Jonckheere AR. A test of significance for the relation between m rankings and k ranked categories. Brit J Stat Psychol 1954, 7:93-100.
64. Bewick V, Cheek L, Ball J. Statistics review 10: Further nonparametric methods. Crit Care 2004, 8:196-199. 10.1186/cc2857, 468904, 15153238.