Gene and protein responses of human lung tissue explants exposed to ambient particulate matter of different sizes

Inhalation Toxicology

Volumn 24, Issue 14, 2012, Pages 966-975

  Hoogendoorn, Bastiaan ^a   Berube, Kelly ^b   Gregory, Clive ^a   Jones, Tim ^c   Sexton, Keith ^b   Brennan, Paul ^c   Brewis, Ian A ^c   Murison, Alexander ^b   Arthur, Robert ^a   Price, Heather ^c   Morgan, Huw ^d   Matthews, Ian P ^a  

^a Neuadd Meirionnydd   (United Kingdom)

^b CARDIFF UNIVERSITY   (United Kingdom)

^c CARDIFF UNIVERSITY   (United Kingdom)

^d City and County of Swansea   (United Kingdom)

Author keywords

Gene expression; Gene pathway; ITRAQ proteomics; Particulate matter; Ultrafine particles

Indexed keywords

PROTEOME;

AIR POLLUTION; ARTICLE; BRONCHUS MUCOSA; CONTROLLED STUDY; EXPLANT; GENE EXPRESSION; HUMAN; HUMAN CELL; HUMAN TISSUE; IN VITRO STUDY; LUNG PARENCHYMA; NUCLEOTIDE SEQUENCE; PARTICLE SIZE; PARTICULATE MATTER; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; REAL TIME POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; TISSUE CULTURE; UNINDEXED SEQUENCE;

ADENOSINE TRIPHOSPHATE; CELL LINE; ELECTRIC IMPEDANCE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENOMICS; HUMANS; LUNG; PARTICLE SIZE; PARTICULATE MATTER; POLYMERASE CHAIN REACTION; PROTEIN INTERACTION MAPPING; PROTEINS; PROTEOMICS; RESPIRATORY MUCOSA; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 84870826485     PISSN: 08958378     EISSN: 10917691     Source Type: Journal    
DOI: 10.3109/08958378.2012.742600     Document Type: Article

References (52)

1. (EPAQS) EPoAQS. 1998. Final report of the Expert Panel on Air Quality Standards on Particles. In: Department for Environment FaRA (ed.). Te stationery ofce. National Publishing: London, UK.
2. Ammirante M, Rosati A, Gentilella A, Festa M, Petrella A, Marzullo L, Pascale M, Belisario MA, Leone A, Turco MC. 2008. Te activity of hsp90 alpha promoter is regulated by NF-kappa B transcription factors. Oncogene 27:1175-1178.
3. Araujo JA, Nel AE. 2009. Particulate matter and atherosclerosis: role of particle size, composition and oxidative stress. Part Fibre Toxicol 6:24.
4. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. 2000. Gene ontology: tool for the unifcation of biology. Te Gene Ontology Consortium. Nat Genet 25:25-29.
5. Ayres JG, Borm P, Cassee FR, Castranova V, Donaldson K, Ghio A, Harrison RM, Hider R, Kelly F, Kooter IM, Marano F, Maynard RL, Mudway I, Nel A, Sioutas C, Smith S, Baeza-Squiban A, Cho A, Duggan S, Froines J. 2008. Evaluating the toxicity of airborne particulate matter and nanoparticles by measuring oxidative stress potential-a workshop report and consensus statement. Inhal Toxicol 20:75-99.
6. Balharry D, Sexton K, BéruBé KA. 2008. An in vitro approach to assess the toxicity of inhaled tobacco smoke components: nicotine, cadmium, formaldehyde and urethane. Toxicology 244:66-76.
7. Beelen R, Hoek G, van den Brandt PA, Goldbohm RA, Fischer P, Schouten LJ, Jerrett M, Hughes E, Armstrong B, Brunekreef B. 2008. Long-term efects of trafc-related air pollution on mortality in a Dutch cohort (NLCS-AIR study). Environ Health Perspect 116:196-202.
8. Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Royal Statistical Society Series B (Methodological) 57:289-300.
9. Blachly-Dyson E, Zambronicz EB, Yu WH, Adams V, McCabe ER, Adelman J, Colombini M, Forte M. 1993. Cloning and functional expression in yeast of two human isoforms of the outer mitochondrial membrane channel, the voltage-dependent anion channel. J Biol Chem 268:1835-1841.
10. Borm PJ, Kelly F, Künzli N, Schins RP, Donaldson K. 2007. Oxidant generation by particulate matter: from biologically efective dose to a promising, novel metric. Occup Environ Med 64:73-74.
11. Brennan P, Shore AM, Clement M, Hewamana S, Jones CM, Giles P, Fegan C, Pepper C, Brewis IA. 2009. Quantitative nuclear proteomics reveals new phenotypes altered in lymphoblastoid cells. PROTEOMICS-Clinical Applications 3:359-369.
12. Brook RD. 2008. Cardiovascular efects of air pollution. Clin Sci 115:175-187.
13. Cederholm A, Frostegård J. 2007. Annexin A5 as a novel player in prevention of atherothrombosis in SLE and in the general population. Ann N Y Acad Sci 1108:96-103.
14. Cui Y, Wang J, Zhang X, Lang R, Bi M, Guo L, Lu SH. 2003. ECRG2, a novel candidate of tumor suppressor gene in the esophageal carcinoma, interacts directly with metallothionein 2A and links to apoptosis. Biochem Biophys Res Commun 302:904-915.
15. Donaldson K, Tran L, Jimenez LA, Dufn R, Newby DE, Mills N, MacNee W, Stone V. 2005. Combustion-derived nanoparticles: a review of their toxicology following inhalation exposure. Part Fibre Toxicol 2:10.
16. Gauderman WJ, Avol E, Gilliland F, Vora H, Tomas D, Berhane K, McConnell R, Kuenzli N, Lurmann F, Rappaport E, Margolis H, Bates D, Peters J. 2004. Te efect of air pollution on lung development from 10 to 18 years of age. N Engl J Med 351:1057-1067.
17. Harrison RM, Giorio C, Beddows DC, Dall'Osto M. 2010. Size distribution of airborne particles controls outcome of epidemiological studies. Sci Total Environ 409:289-293.
18. HEI. 2010. HEI Panel on the Health Efects of Trafc-Related Air Pollution. Trafc-related air pollution: a critical review of the literature on emissions, exposure and health efects. HEI Special Report 17. Health Efects Institute: Boston, MA.
19. Hintze A, Adami C. 2008. Evolution of complex modular biological networks. PLoS Comput Biol 4:e23.
20. Hofmann B, Moebus S, Stang A, Beck EM, Dragano N, Möhlenkamp S, Schmermund A, Memmesheimer M, Mann K, Erbel R, Jöckel KH; Heinz Nixdorf RECALL Study Investigative Group. 2006. Residence close to high trafc and prevalence of coronary heart disease. Eur Heart J 27:2696-2702.
21. Huang da W, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4:44-57.
22. Jones T, Moreno T, BéruBé K, Richards R. 2006. Te physicochemical characterisation of microscopic airborne particles in south Wales: a review of the locations and methodologies. Sci Total Environ 360:43-59.
23. Jung EJ, Avliyakulov NK, Boontheung P, Loo JA, Nel AE. 2007. Pro-oxidative DEP chemicals induce heat shock proteins and an unfolding protein response in a bronchial epithelial cell line as determined by DIGE analysis. Proteomics 7:3906-3918.
24. Keskinen J, Pietarinen K, Lehtimäki M. 1992. Electrical low pressure impactor. J Aerosol Sci 23:353-360.
25. Khatri P, Draghici S. 2005. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics 21:3587-3595.
26. Knol AB, de Hartog JJ, Boogaard H, Slottje P, van der Sluijs JP, Lebret E, Cassee FR, Wardekker JA, Ayres JG, Borm PJ, Brunekreef B, Donaldson K, Forastiere F, Holgate ST, Kreyling WG, Nemery B, Pekkanen J, Stone V, Wichmann HE, Hoek G. 2009. Expert elicitation on ultrafne particles: likelihood of health efects and causal pathways. Part Fibre Toxicol 6:19.
27. Kreyling WG, Semmler-Behnke M, Möller W. 2006. Ultrafne particle-lung interactions: does size matter? J Aerosol Med 19:74-83.
28. Laden F, Schwartz J, Speizer FE, Dockery DW. 2006. Reduction in fne particulate air pollution and mortality: Extended follow-up of the Harvard Six Cities study. Am J Respir Crit Care Med 173:667-672.
29. Lamarche BJ, Orazio NI, Weitzman MD. 2010. Te MRN complex in double-strand break repair and telomere maintenance. FEBS Lett 584:3682-3695.
30. Lau AT, Chiu JF. 2009. Biomarkers of lung-related diseases: current knowledge by proteomic approaches. J Cell Physiol 221:535-543.
31. Li N, Sioutas C, Cho A, Schmitz D, Misra C, Sempf J, Wang M, Oberley T, Froines J, Nel A. 2003. Ultrafne particulate pollutants induce oxidative stress and mitochondrial damage. Environ Health Perspect 111:455-460.
32. Li N, Xia T, Nel AE. 2008. Te role of oxidative stress in ambient particulate matter-induced lung diseases and its implications in the toxicity of engineered nanoparticles. Free Radic Biol Med 44:1689-1699.
33. Magrane M, Consortium U. 2011. UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford) 2011:bar009.
34. Miller KA, Siscovick DS, Sheppard L, Shepherd K, Sullivan JH, Anderson GL, Kaufman JD. 2007. Long-term exposure to air pollution and incidence of cardiovascular events in women. N Engl J Med 356:447-458.
35. Parker D, Prince A. 2011. Innate immunity in the respiratory epithelium. Am J Respir Cell Mol Biol 45:189-201.
36. Prahalad AK, Soukup JM, Inmon J, Willis R, Ghio AJ, Becker S, Gallagher JE. 1999. Ambient air particles: efects on cellular oxidant radical generation in relation to particulate elemental chemistry. Toxicol Appl Pharmacol 158:81-91.
37. Price H, Arthur R, Sexton K, Gregory C, Hoogendoorn B, Matthews I, Jones T, BéruBé K. 2010. Airborne particles in Swansea, UK: their collection and characterization. J Toxicol Environ Health Part A 73:355-367.
38. Putaud JP, Van Dingenen R, Alastuey A, Bauer H, Birmili W, Cyrys J, Flentje H, Fuzzi S, Gehrig R, Hansson HC, Harrison RM, Herrmann H, Hitzenberger R, Hüglin C, Jones AM, Kasper-Giebl A, Kiss G, Kousa A, Kuhlbusch TAJ, Löschau G, Maenhaut W, Molnar A, Moreno T, Pekkanen J, Perrino C, Pitz M, Puxbaum H, Querol X, Rodriguez S, Salma I, Schwarz J, Smolik J, Schneider J, Spindler G, ten Brink H, Tursic J, Viana M, Wiedensohler A, Raes F. 2010. A European aerosol phenomenology-3: Physical and chemical characteristics of particulate matter from 60 rural, urban, and kerbside sites across Europe. Atmospheric Environ 44:1308-1320.
39. Ren D, Kim H, Tu HC, Westergard TD, Fisher JK, Rubens JA, Korsmeyer SJ, Hsieh JJ, Cheng EH. 2009. Te VDAC2-BAK rheostat controls thymocyte survival. Sci Signal 2:ra48.
40. Richards AL, Holmans P, O'Donovan MC, Owen MJ, Jones L. 2008. A comparison of four clustering methods for brain expression microarray data. BMC Bioinformatics 9:490.
41. Sexton K, Balharry D, BéruBé KA. 2008. Genomic biomarkers of pulmonary exposure to tobacco smoke components. Pharmacogenet Genomics 18:853-860.
42. Shilov I V, Seymour SL, Patel AA, Loboda A, Tang WH, Keating SP, Hunter CL, Nuwaysir LM, Schaefer DA. 2007. Te Paragon Algorithm, a next generation search engine that uses sequence temperature values and feature probabilities to identify peptides from tandem mass spectra. Mol Cell Proteomics 6:1638-1655.
43. Simkhovich BZ, Kleinman MT, Kloner RA. 2008. Air pollution and cardiovascular injury epidemiology, toxicology, and mechanisms. J Am Coll Cardiol 52:719-726.
44. Staversky RJ, Vitiello PF, Yee M, Callahan LM, Dean DA, O'Reilly MA. 2010. Epithelial ablation of Bcl-XL increases sensitivity to oxygen without disrupting lung development. Am J Respir Cell Mol Biol 43:376-385.
45. Tonne C, Melly S, Mittleman M, Coull B, Goldberg R, Schwartz J. 2007. A case-control analysis of exposure to trafc and acute myocardial infarction. Environ Health Perspect 115:53-57.
46. Ueno K, Koga T, Kato K, Golenbock DT, Gendler SJ, Kai H, Kim KC. 2008. MUC1 mucin is a negative regulator of toll-like receptor signaling. Am J Respir Cell Mol Biol 38:263-268.
47. Voynow JA, Rubin BK. 2009. Mucins, mucus, and sputum. Chest 135:505-512.
48. Xia T, Korge P, Weiss JN, Li N, Venkatesen MI, Sioutas C, Nel A. 2004. Quinones and aromatic chemical compounds in particulate matter induce mitochondrial dysfunction: implications for ultrafne particle toxicity. Environ Health Perspect 112:1347-1358.
49. Xiao GG, Wang M, Li N, Loo JA, Nel AE. 2003. Use of proteomics to demonstrate a hierarchical oxidative stress response to diesel exhaust particle chemicals in a macrophage cell line. J Biol Chem 278:50781-50790.
50. Yip AM, Horvath S. 2007. Gene network interconnectedness and the generalized topological overlap measure. BMC Bioinformatics 8:22.
51. Zervas E, Dorlhène P. 2006. Comparison of exhaust particle number measured by EEPS, CPC, and ELPI. Aerosol Science and Technology 40:977-984.
52. Zhang L, Wang M, Kang X, Boontheung P, Li N, Nel AE, Loo JA. 2009. Oxidative stress and asthma: proteome analysis of chitinase-like proteins and FIZZ1 in lung tissue and bronchoalveolar lavage fuid. J Proteome Res 8:1631-1638.