Abstract
The advent of omics technologies has enhanced significantly our capacity to interpret mechanistically the association between environmental exposure and disease. Although understanding these interactions requires capturing perturbations at different levels of biological organization, transcriptomics holds a key role. Modulation of gene expression represents the initial biological perturbations due to environmental exposure. This is of particular importance when assessing real-life exposure that involves multiple stressors in highly variable time regimes. This chapter aims at (a) demonstrating the place of transcriptomics in modern risk assessment and environmental health associations, highlighting the respective bioinformatics tools that are necessary for the interpretation and (b) demonstrating the feasibility of transcriptomics of understanding environmental risk associated to real-life ubiquitous mixtures. Although environmental exposures occur to mixtures of chemicals rather than to individual agents, most of the toxic effects of air pollutants are ascribed to single chemicals. There is a growing feeling in both the scientific and regulatory communities, however, that there is a need for more comprehensive approaches toward managing the potential impact of complex environmental chemical mixtures on human health. In this perspective, it is expected that toxicogenomics would be the appropriate screening method for assessing biological effects of complex chemical mixtures, allowing us to review the whole spectrum of potential biological response rather than focusing on a predefined number of endpoints as in classical toxicological analysis. In this chapter, beyond the overview of the analytical and computational aspects necessary for implementing toxicogenomics in the context of the exposome, a concrete example of such an application on a typical indoor air mixture as defined in the EU-wide review study INDEX and on a mixture of polyaromatic hydrocarbons (PAHs) isolated from urban air in the city of Milan is given with the aim to identify specific sets of biomarkers for each of the two types of exposure (indoor or outdoor). A human cell line derived from a bronco-pulmonary system (A549) was used as the appropriate in vitro model to support the investigation of the molecular basis for adverse outcomes that are attributed to indoor and/or outdoor air pollution based on epidemiological evidence. Applying a Total Gene Expression assay by Applied Biosystems Microarrays, large sets of genes modulated by single mixtures exposure were profiled. This process led us to identify common biochemical pathways and specific molecular responses. Indoor air mixtures induced a higher level of gene modulation than ambient air PAHs. A closer look at the differences in biological response confirmed major discrepancies in the mode of action of the two mixtures. Indoor air induced primarily modulation of genes associated to protein targeting and localization including in particular cytoskeletal organization; PAHs modulated mostly the expression of genes related to cell motility and gene networks regulating cell–cell signaling, as well as cell proliferation and differentiation. These results provide biological information useful for articulating mechanistic hypotheses linking exposure to xenobiotic mixtures and physiological responses. The evidence on the latter is supported by a large amount of epidemiological evidence, associating exposure to urban air pollution with respiratory allergies, chronic obstructive pulmonary disease, cardiovascular disease, and cancer. Lately, such evidence has been extended to include associations of exposure to polluted ambient and indoor air with kidney disease and even neurodegenerative disorders, and in particular dementia.
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References
Aebersold R, Mann M (2003) Mass spectrometry-based proteomics. Nature 422(6928):198–207
Agrawal R, Srikant R (1994) Fast algorithms for mining association rules in large databases. In: VLDB conference, pp 487–499
Agyeman AS, Chaerkady R, Shaw PG, Davidson NE, Visvanathan K, Pandey A, Kensler TW (2012) Transcriptomic and proteomic profiling of KEAP1 disrupted and sulforaphane-treated human breast epithelial cells reveals common expression profiles. Breast Cancer Res Treat 132(1):175–187. https://doi.org/10.1007/s10549-011-1536-9
Allison DB, Cui X, Page GP, Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet 7(1):55–65. https://doi.org/10.1038/nrg1749
Altman RB, Raychaudhuri S (2001) Whole-genome expression analysis: challenges beyond clustering. Curr Opin Struct Biol 11(3):340–347. https://doi.org/10.1016/s0959-440x(00)00212-8
Ankley GT, Bennett RS, Erickson RJ, Hoff DJ, Hornung MW, Johnson RD, Mount DR, Nichols JW, Russom CL, Schmieder PK, Serrrano JA, Tietge JE, Villeneuve DL (2010) Adverse outcome pathways: a conceptual framework to support ecotoxicology research and risk assessment. Environ Toxicol Chem 29(3):730–741
Audouze K, Juncker AS, Roque FJ, Krysiak-Baltyn K, Weinhold N, Taboureau O, Jensen TS, Brunak S (2010) Deciphering diseases and biological targets for environmental chemicals using toxicogenomics networks. PLoS Comput Biol 6(5):e1000788. https://doi.org/10.1371/journal.pcbi.1000788
Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. J Comput Biol 63(3/4):281–297
Boezio B, Audouze K, Ducrot P, Taboureau O (2017) Network-based approaches in pharmacology. Molecular Inform 36(10), Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Borkowski K, Wrzesinski K, Rogowska-Wrzesinska A, Audouze K, Bakke J, Petersen RK, Haj FG, Madsen L, Kristiansen K (2014) Proteomic analysis of cAMP-mediated signaling during differentiation of 3 T3-L1 preadipocytes. Biochim Biophys Acta 1844(12):2096–2107. https://doi.org/10.1016/j.bbapap.2014.07.015
Breiman L (1996) Bagging predictors. Mach Learn 24(2):123–140
Breiman L (1998) Arcing classifiers (with discussion). Ann Stat 26(3):801–849
Breiman L (2001) Random forests. Mach Learn 45(1):5–32. https://doi.org/10.1023/a:1010933404324
Brunekreef B, Holgate ST (2002) Air pollution and health. Lancet 360(9341):1233–1242. https://doi.org/10.1016/s0140-6736(02)11274-8
Chang B, Halgamuge SK (2002) Protein motif extraction with neuro-fuzzy optimization. Bioinformatics 18(8):1084–1090
Ciriello G, Gatza ML, Beck AH, Wilkerson MD, Rhie SK, Pastore A, Zhang H, McLellan M, Yau C, Kandoth C, Bowlby R, Shen H, Hayat S, Fieldhouse R, Lester SC, Tse GM, Factor RE, Collins LC, Allison KH, Chen YY, Jensen K, Johnson NB, Oesterreich S, Mills GB, Cherniack AD, Robertson G, Benz C, Sander C, Laird PW, Hoadley KA, King TA, Perou CM (2015) Comprehensive molecular portraits of invasive lobular breast cancer. Cell 163(2):506–519. https://doi.org/10.1016/j.cell.2015.09.033
Dasgupta A, Raftery AE (1998) Detecting features in spatial point processes with clutter via model-based clustering. J Am Stat Assoc 93(441):294–302
Dong G, Zhang X, Wong L, Li J (1999) CAEP: classification by aggregating emerging patterns. In: Springer-Verlag (ed) Proceedings of the second international conference on discovery science, pp 30–42
Dubes R (1988) Algorithms for clustering data. Prentice Hall, Englewood Cliffs, NJ
Dumas ME, Domange C, Calderari S, Martinez AR, Ayala R, Wilder SP, Suarez-Zamorano N, Collins SC, Wallis RH, Gu Q, Wang Y, Hue C, Otto GW, Argoud K, Navratil V, Mitchell SC, Lindon JC, Holmes E, Cazier JB, Nicholson JK, Gauguier D (2016) Topological analysis of metabolic networks integrating co-segregating transcriptomes and metabolomes in type 2 diabetic rat congenic series. Genome Med 8(1):101. https://doi.org/10.1186/s13073-016-0352-6
Ebrahim A, Brunk E, Tan J, O’Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A, Feist AM, Palsson BO (2016) Multi-omic data integration enables discovery of hidden biological regularities. Nat Commun 7:13091. https://doi.org/10.1038/ncomms13091
Fayyad UM, Piatetsky-Shapiro G, Smyth P (1996) Knowledge discovery and data mining: towards a unifying framework. In: Proceedings of the second international conference on knowledge discovery and data mining, p 82
Fiedler N, Laumbach R, Kelly-McNeil K, Lioy P, Fan ZH, Zhang J, Ottenweller J, Ohman-Strickland P, Kipen H (2005) Health effects of a mixture of indoor air volatile organics, their ozone oxidation products, and stress. Environ Health Perspect 113(11):1542–1548
Fraley C, Raftery AE (1998) How many clusters? Which clustering method? Answers via model-based cluster analysis. Comput J 41(8):586–588
Freund Y, Schapire R (1996) Experiments with a new boosting algorithm. In: Proceedings of the thirteenth national conference on machine learning, pp 148–156
Garcia-Reyero N (2015) Are adverse outcome pathways here to stay? Environ Sci Technol 49(1):3–9. https://doi.org/10.1021/es504976d
Gasch A, Eisen M (2002) Exploring the conditional corregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol 3:1–22
Gevaert O, De Smet F, Timmerman D, Moreau Y, De Moor B (2006) Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks. Bioinformatics 22(14):e184–e190. https://doi.org/10.1093/bioinformatics/btl230
Hackett JL, Lesko LJ (2003) Microarray data--the US FDA, industry and academia. Nat Biotechnol 21(7):742–743. https://doi.org/10.1038/nbt0703-742
Han J, Pei H, Yin Y (2000) Mining frequent patterns without candidate generation. In: Conference on the management of data, ACM Press, Dalas
Han J, Pei J, Yin Y, Mao R (2003) Mining frequent patterns without candidate generation: a frequent-pattern tree approach. Data Min Knowl Discov 8:53–87
Hao Q, Yadav R, Basse AL, Petersen S, Sonne SB, Rasmussen S, Zhu Q, Lu Z, Wang J, Audouze K, Gupta R, Madsen L, Kristiansen K, Hansen JB (2015) Transcriptome profiling of brown adipose tissue during cold exposure reveals extensive regulation of glucose metabolism. Am J Phys Endocrinol Metab 308(5):E380–E392. https://doi.org/10.1152/ajpendo.00277.2014
Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and complex traits. Nat Rev Genet 6(2):95–108. https://doi.org/10.1038/nrg1521
Jiang D, Pei J, Zhang A (2003a) Interactive exploration of coherent patterns in time-series gene expression data. In: Proceedings of the ACM SIGKDD international conference on knowledge discovery and data mining, pp 565–570. https://doi.org/10.1145/956750.956820
Jiang D, Pei J, Zhang A (2003b) DHC: a density-based hierarchical clustering method for timeseries gene expression data. In: BIBE2003 (ed) 3rd IEEE international symposium on bioinformatics and bioengineering, Bethesda, Maryland, 10–12 Mar 2003
Jones DT (2001) Protein structure prediction in genomics. Brief Bioinform 2(2):111–125
Kaufman L, Rousseeuw PJ (2008) Finding groups in data: an introduction to cluster analysis. Wiley, New York
Kohonen T (1984) Self-organization and associative memory. Spring, Berlin
Kongsbak K, Vinggaard AM, Hadrup N, Audouze K (2014) A computational approach to mechanistic and predictive toxicology of pesticides. ALTEX 31(1):11–22. https://doi.org/10.14573/altex.1304241
Kotzias P, Koistinen K, Kephalopoulos S, Schlitt C, Carrer P, Maroni VI, Jantunen MJ, Cochet C, Kirchner S, Lindvall T, McLaughlin J, Molhave L, Fernandes E, Seifert B (2005) The INDEX project: critical appraisal of the setting and implementation of indoor exposure limits in the EU. EUR 21590 EN. doi:Cited By (since 1996) 1 Export Date 17 April 2012
Kuncheva L (2004) Combining pattern classifiers: methods and algorithms. Wiley, New York
Larranaga P, Calvo B, Santana R, Bielza C, Galdiano J (2003) Machine learning in bioinformatics. Brief Bioinform 7(1):86–112
Lesko LJ, Woodcock J (2004) Translation of pharmacogenomics and pharmacogenetics: a regulatory perspective. Nat Rev Drug Discov 3(9):763–769. https://doi.org/10.1038/nrd1499
Li T, Wernersson R, Hansen RB (2017) A scored human protein-protein interaction network to catalyze genomic interpretation. Nat Methods 14(1):61–64. https://doi.org/10.1038/nmeth.4083
Linkov I, Massey O, Keisler J, Rusyn I, Hartung T (2015) From “weight of evidence” to quantitative data integration using multicriteria decision analysis and Bayesian methods. ALTEX 32(1):3–8. https://doi.org/10.14573/altex.1412231
Manrai AK, Cui Y, Bushel PR, Hall M, Karakitsios S, Mattingly C, Ritchie M, Schmitt C, Sarigiannis DA, Thomas DC, Wishart D, Balshaw DM, Patel CJ (2016) Informatics and data analytics to support exposome-based discovery for public health. Annu Rev Public Health 38:279–294. https://doi.org/10.1146/annurev-publhealth-082516-012737
Martinez R, Collard M (2007) Extracted knowledge: interpretation in mining biological data, a survey. Int J Comput Sci Appl 1:1–21
McQueen JB (1967) Some methods for classification and analysis of multivariate observations. In: Press UoC (ed) Fifth Berkeley symposium on mathematical statistics and probability, University of California Press, Berkeley, pp 281–297
Perkins EJ, Antczak P, Burgoon L, Falciani F, Garcia-Reyero N, Gutsell S, Hodges G, Kienzler A, Knapen D, McBride M, Willett C (2015) Adverse outcome pathways for regulatory applications: examination of four case studies with different degrees of completeness and scientific confidence. Toxicol Sci 148(1):14–25. https://doi.org/10.1093/toxsci/kfv181
Pleil JD (2012) Categorizing biomarkers of the human exposome and developing metrics for assessing environmental sustainability. J Toxicol Environ Health B Crit Rev 15(4):264–280. https://doi.org/10.1080/10937404.2012.672148
Sarigiannis D, Gotti A, Cimino Reale G, Marafante E (2009) Reflections on new directions for risk assessment of environmental chemical mixtures. Int J Risk Assess Manag 13(3-4):216–241
Sarigiannis DA, Kermenidou M, Nikolaki S, Zikopoulos D, Karakitsios SP (2015) Mortality and morbidity attributed to aerosol and gaseous emissions from biomass use for space heating. Aerosol Air Qual Res 15(7):2496–2507
Saykin AJ, Shen L, Yao X, Kim S, Nho K, Risacher SL, Ramanan VK, Foroud TM, Faber KM, Sarwar N, Munsie LM, Hu X, Soares HD, Potkin SG, Thompson PM, Kauwe JS, Kaddurah-Daouk R, Green RC, Toga AW, Weiner MW (2015) Genetic studies of quantitative MCI and AD phenotypes in ADNI: progress, opportunities, and plans. Alzheimers Dement 11(7):792–814. https://doi.org/10.1016/j.jalz.2015.05.009
Schapire R, Freund Y, Bartlett P, Lee WS (1998) Boosting the margin: a new explanation for the effectiveness of voting methods. Ann Stat 26(5):1651–1686
Seno M, Karypis G (2001) LPMiner: an algorithm for finding frequent itemsets using length-decreasing support constraint. In: 1st IEEE conference on data mining
Shamir R, Sharan R (2000) Click: a clustering algorithm for gene expression analysis. In: AAAI Press (ed) 8th international conference on intelligent systems for molecular biology (ISMB ‘00)
Shatkay H, Edwards S, Wilbur WJ, Boguski M (2000) Genes, themes, microarrays: using information retrieval for large-scale gene analysis. Proc Int Conf Intell Syst Mol Biol 8:340–347
Svihalkova-Sindlerova L, Machala M, Pencikova K, Marvanova S, Neca J, Topinka J, Sevastyanova O, Kozubik A, Vondracek J (2007) Dibenzanthracenes and benzochrysenes elicit both genotoxic and nongenotoxic events in rat liver ‘stem-like’ cells. Toxicology 232(1–2):147–159. https://doi.org/10.1016/j.tox.2006.12.024
Szklarczyk D, Morris JH, Cook H, Kuhn M, Wyder S, Simonovic M, Santos A, Doncheva NT, Roth A, Bork P, Jensen LJ, von Mering C (2017) The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res 45(D1):D362–d368. https://doi.org/10.1093/nar/gkw937
Taboureau O, Audouze K (2017) Human Environmental Disease Network: a computational model to assess toxicology of contaminants. ALTEX 34(2):289–300. https://doi.org/10.14573/altex.1607201
Taboureau O, Jacobsen UP, Kalhauge C, Edsgard D, Rigina O, Gupta R, Audouze K (2013) HExpoChem: a systems biology resource to explore human exposure to chemicals. Bioinformatics 29(9):1231–1232. https://doi.org/10.1093/bioinformatics/btt112
TCGA (2011) Integrated genomic analyses of ovarian carcinoma. Nature 474(7353):609–615. https://doi.org/10.1038/nature10166
TCGA (2014) Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507(7492):315–322. https://doi.org/10.1038/nature12965
Valencia A, Pazos F (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 12(3):368–373. https://doi.org/10.1016/s0959-440x(02)00333-0
Villeneuve DL, Crump D, Garcia-Reyero N, Hecker M, Hutchinson TH, LaLone CA, Landesmann B, Lettieri T, Munn S, Nepelska M, Ottinger MA, Vergauwen L, Whelan M (2014) Adverse outcome pathway development II: best practices. Toxicol Sci 142(2):321–330. https://doi.org/10.1093/toxsci/kfu200
Vitkina TI, Yankova VI, Gvozdenko TA, Kuznetsov VL, Krasnikov DV, Nazarenko AV, Chaika VV, Smagin SV, Tsatsakis AΜ, Engin AB, Karakitsios SP, Sarigiannis DA, Golokhvast KS (2016) The impact of multi-walled carbon nanotubes with different amount of metallic impurities on immunometabolic parameters in healthy volunteers. Food Chem Toxicol 87:138–147. https://doi.org/10.1016/j.fct.2015.11.023
Webb G, Zheng Z (2004) Multistrategy ensemble learning: reducing error by combining ensemble learning techniques. IEEE Trans Knowl Data Eng 16(8):980–991
Weiner MW, Aisen PS, Jack CR Jr, Jagust WJ, Trojanowski JQ, Shaw L, Saykin AJ, Morris JC, Cairns N, Beckett LA, Toga A, Green R, Walter S, Soares H, Snyder P, Siemers E, Potter W, Cole PE, Schmidt M (2010) The Alzheimer’s disease neuroimaging initiative: progress report and future plans. Alzheimers Dement 6(3):202–211.e207. https://doi.org/10.1016/j.jalz.2010.03.007
Yan J, Risacher SL, Shen L, Saykin AJ (2017) Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data. Brief Bioinform. https://doi.org/10.1093/bib/bbx066
Yang Y, Blomme EA, Waring JF (2004) Toxicogenomics in drug discovery: from preclinical studies to clinical trials. Chem Biol Interact 150(1):71–85. https://doi.org/10.1016/j.cbi.2004.09.013
Zeng J, Zhu S, Yan H (2009) Towards accurate human promoter recognition: a review of currently used sequence features and classification methods. Brief Bioinform 10(5):498–508. https://doi.org/10.1093/bib/bbp027
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The author gratefully acknowledges the support of the European Commission through the grant No. 603946 (HEALS—Health and Environment-wide Associations via Large Population Studies) funded through the 7th Framework Program for Research and Technological Development of the EU.
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Sarigiannis, D.A. (2019). Transcriptomics within the Exposome Paradigm. In: Dagnino, S., Macherone, A. (eds) Unraveling the Exposome. Springer, Cham. https://doi.org/10.1007/978-3-319-89321-1_7
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