Quantitative assessment of biological impact using transcriptomic data and mechanistic network models

Toxicology and Applied Pharmacology

Volumn 272, Issue 3, 2013, Pages 863-878

  Thomson, Ty M ^a   Sewer, Alain ^b   Martin, Florian ^b   Belcastro, Vincenzo ^b   Frushour, Brian P ^a   Gebel, Stephan ^c   Park, Jennifer ^a   Schlage, Walter K ^c   Talikka, Marja ^b   Vasilyev, Dmitry M ^a   Westra, Jurjen W ^a   Hoeng, Julia ^b   Peitsch, Manuel C ^b  

^a Selventa   (United States)

^b PHILIP MORRIS PRODUCTS S A   (Switzerland)

^c Philip Morris Research Laboratories GmbH   (Germany)

Author keywords

Bioactive substance; Biological impact; Mechanisms; Network model; Quantification; Transcriptome

Indexed keywords

ARTICLE; ENVIRONMENTAL EXPOSURE; ENVIRONMENTAL IMPACT; HUMAN; HUMAN CELL; IN VITRO STUDY; MODEL; NETWORK MODEL; PHENOTYPE; QUANTITATIVE ANALYSIS; SYSTEMS BIOLOGY; TRANSCRIPTOMICS;

BIOACTIVE SUBSTANCE; BIOLOGICAL IMPACT; MECHANISMS; NETWORK MODEL; QUANTIFICATION; TRANSCRIPTOME;

ANIMALS; CELL CYCLE; COMPUTER SIMULATION; GENE REGULATORY NETWORKS; HUMANS; MICE; MICE, KNOCKOUT; RESPIRATORY MUCOSA; TOBACCO SMOKE POLLUTION; TRANSCRIPTOME;

EID: 84884695502     PISSN: 0041008X     EISSN: 10960333     Source Type: Journal    
DOI: 10.1016/j.taap.2013.07.007     Document Type: Article

References (52)

1. Abdo K.M., Haseman J.K., Nyska A. Isobutyraldehyde administered by inhalation (whole body exposure) for up to thirteen weeks or two years was a respiratory tract toxicant but was not carcinogenic in F344/N rats and B6C3F1 mice. Toxicol. Sci. 1998, 42:136-151.
2. Andersen M.E., Clewell H.J., Bermudez E., Dodd D.E., Willson G.A., Campbell J.L., Thomas R.S. Formaldehyde: integrating dosimetry, cytotoxicity, and genomics to understand dose-dependent transitions for an endogenous compound. Toxicol. Sci. 2010, 118:716-731.
3. Barabasi A.L., Gulbahce N., Loscalzo J. Network medicine: a network-based approach to human disease. Nat. Rev. Genet. 2011, 12:56-68.
4. Barrett T., Wilhite S.E., Ledoux P., Evangelista C., Kim I.F., Tomashevsky M., Marshall K.A., Phillippy K.H., Sherman P.M., Holko M. NCBI GEO: archive for functional genomics data sets - update. Nucleic Acids Res. 2013, 41:D991-D995.
5. Belcastro V., Poussin C., Gebel S., Mathis C., Schlage W.K., Lichtner R.B., Quadt-Humme S., Wagner S., Hoeng J., Peitsch M.C. Systematic verification of upstream regulators of a computable cellular proliferation network model on non-diseased lung cells using a dedicated dataset. Bioinform. Biol. Insights 2013, 7:217-230.
6. Bhattacharya S., Zhang Q., Carmichael P.L., Boekelheide K., Andersen M.E. Toxicity testing in the 21st century: defining new risk assessment approaches based on perturbation of intracellular toxicity pathways. PLoS One 2011, 6:e20887.
7. Cao Z., Xiong J., Takeuchi M., Kurama T., Goeddel D.V. TRAF6 is a signal transducer for interleukin-1. Nature 1996, 383:443-446.
8. Caron de Fromentel C., Soussi T. TP53 tumor suppressor gene: a model for investigating human mutagenesis. Gene Chromosome Cancer 1992, 4:1-15.
9. Catlett N.L., Bargnesi A.J., Ungerer S., Seagaran T., Ladd W., Elliston K., Pratt D. Reverse causal reasoning: applying qualitative causal knowledge to the interpretation of high-throughput data. BMC Genomics 2013, (submitted for publication).
10. Committee on Toxicity Testing and Assessment of Environmental Agents, N.R.C. Toxicity testing in the 21st century: a vision and a strategy 2007, The National Academies Press.
11. Conolly R.B., Andersen M.E. An approach to mechanism-based cancer risk assessment for formaldehyde. Environ. Heal. Perspect. 1993, 101(Suppl. 6):169-176.
12. Cosma G.N., Wilhite A.S., Marchok A.C. The detection of DNA-protein cross-links in rat tracheal implants exposed in vivo to benzo[a]pyrene and formaldehyde. Cancer Lett. 1988, 42:13-21.
13. Enright P.L., Kaminsky D.A. Strategies for screening for chronic obstructive pulmonary disease. Respir. Care 2003, 48:1194-1201. (discussion 1201-1193).
14. Fry D.W., Harvey P.J., Keller P.R., Elliott W.L., Meade M., Trachet E., Albassam M., Zheng X., Leopold W.R., Pryer N.K., Toogood P.L. Specific inhibition of cyclin-dependent kinase 4/6 by PD 0332991 and associated antitumor activity in human tumor xenografts. Mol. Cancer Ther. 2004, 3:1427-1438.
15. Gebel S., Lichtner R.B., Frushour B.P., Schlage W.K., Hoang V., Talikka M., Hengstermann A., Mathis C., Veljkovic E., Peck M., Peitsch M.C., Deehan R., Hoeng J., Westra J.W. Construction of a computable network model for DNA damage, autophagy, cell death, and senescence. Bioinform. Biol. Insights 2013, 7:1-21.
16. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y., Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
17. Harman A.E., Voigt J.M., Frame S.R., Bogdanffy M.S. Mitogenic responses of rat nasal epithelium to hexamethylphosphoramide inhalation exposure. Mutat. Res. 1997, 380:155-165.
18. Hoeng J., Deehan R., Pratt D., Martin F., Sewer A., Thomson T.M., Drubin D.A., Waters C.A., de Graaf D., Peitsch M.C. A network-based approach to quantifying the impact of biologically active substances. Drug Discov. Today 2012, 17:413-418.
19. Irizarry R.A., Hobbs B., Collin F., Beazer-Barclay Y.D., Antonellis K.J., Scherf U., Speed T.P. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4:249-264.
20. Iskandar A.R., Martin F., Talikka M., Schlage W.K., Kostadinova R., Mathis C., Hoeng J. Systems approaches evaluating the perturbation of xenobiotic metabolism in response to cigarette smoke exposure in nasal and bronchial tissues 2013, BioMed Res. Int. (submitted for publication).
21. Kanehisa M., Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28:27-30.
22. Karlebach G., Shamir R. Modelling and analysis of gene regulatory networks. Nat. Rev. Mol. Cell Biol. 2008, 9:770-780.
23. Keller D.A., Juberg D.R., Catlin N., Farland W.H., Hess F.G., Wolf D.C., Doerrer N.G. Identification and characterization of adverse effects in 21st century toxicology. Toxicol. Sci. 2012, 126:291-297.
24. Kerns W.D., Pavkov K.L., Donofrio D.J., Gralla E.J., Swenberg J.A. Carcinogenicity of formaldehyde in rats and mice after long-term inhalation exposure. Cancer Res. 1983, 43:4382-4392.
25. Kiyosawa N., Manabe S., Yamoto T., Sanbuissho A. Practical application of toxicogenomics for profiling toxicant-induced biological perturbations. Int. J. Mol. Sci. 2010, 11:3397-3412.
26. Kleiman R., Westra W., Schlage W.K., Park J., Hayes W., Talikka M., Ansari S., Martin F., Veljkovic E., Kenney R., Peitsch M.C., Hoeng J. CausalBioNet: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems 2013, (in preparation).
27. Kode A., Yang S.R., Rahman I. Differential effects of cigarette smoke on oxidative stress and proinflammatory cytokine release in primary human airway epithelial cells and in a variety of transformed alveolar epithelial cells. Respir. Res. 2006, 7:132.
28. Kosmider B., Messier E.M., Chu H.W., Mason R.J. Human alveolar epithelial cell injury induced by cigarette smoke. PLoS One 2011, 6:e26059.
29. Krewski D., Westphal M., Al-Zoughool M., Croteau M.C., Andersen M.E. New directions in toxicity testing. Annu. Rev. Public Health 2011, 32:161-178.
30. Kuykendall J.R., Trela B.A., Bogdanffy M.S. DNA-protein crosslink formation in rat nasal epithelial cells by hexamethylphosphoramide and its correlation with formaldehyde production. Mutat. Res. Genet. Toxicol. 1995, 343:209-218.
31. Loboda A., Nebozhyn M., Klinghoffer R., Frazier J., Chastain M., Arthur W., Roberts B., Zhang T., Chenard M., Haines B. A gene expression signature of RAS pathway dependence predicts response to PI3K and RAS pathway inhibitors and expands the population of RAS pathway activated tumors. BMC Med. Genet. 2010, 3:26.
32. Martin F., Thomson T.M., Sewer A., Drubin D.A., Mathis C., Weisensee D., Pratt D., Hoeng J., Peitsch M.C. Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks. BMC Syst. Biol. 2012, 6:54.
33. Ohtsuka R., Shuto Y., Fujie H., Takeda M., Harada T., Itagaki S. Response of respiratory epithelium of BN and F344 rats to formaldehyde inhalation. Exp. Anim. 1997, 46:279-286.
34. Parkinson H., Sarkans U., Kolesnikov N., Abeygunawardena N., Burdett T., Dylag M., Emam I., Farne A., Hastings E., Holloway E., Kurbatova N., Lukk M., Malone J., Mani R., Pilicheva E., Rustici G., Sharma A., Williams E., Adamusiak T., Brandizi M., Sklyar N., Brazma A. ArrayExpress update - an archive of microarray and high-throughput sequencing-based functional genomics experiments. Nucleic Acids Res. 2011, 39:D1002-D1004.
35. R Core Team R: A Language and Environment for Statistical Computing 2013, R Foundation for Statistical Computing, Vienna.
36. Recio L., Sisk S., Pluta L., Bermudez E., Gross E.A., Chen Z., Morgan K., Walker C. p53 mutations in formaldehyde-induced nasal squamous cell carcinomas in rats. Cancer Res. 1992, 52:6113-6116.
37. Rodgman A., Perfetti T.A. The chemical components of tobacco and tobacco smoke 2013, CRC press.
38. Schadt E.E. Molecular networks as sensors and drivers of common human diseases. Nature 2009, 461:218-223.
39. Schlage W., Westra J., Gebel S., Catlett N., Mathis C., Frushour B., Hengstermann A., Van Hooser A., Poussin C., Wong B., Lietz M., Park J., Drubin D., Veljkovic E., Peitsch M., Hoeng J., Deehan R. A computable cellular stress network model for non-diseased pulmonary and cardiovascular tissue. BMC Syst. Biol. 2011, 5:168.
40. Selventa The openBEL Portal http://www.openbel.org/.
41. Selventa The BEL Large Corpus, Version 1.4 http://resource.belframework.org/belframework/1.0/knowledge/large_corpus.bel.
42. Selventa Reverse Causal Reasoning Methods Whitepaper http://www.selventa.com/technology/white-papers.
43. Sha Y., Markovic-Plese S. A role of IL-1R1 signaling in the differentiation of Th17 cells and the development of autoimmune diseases. Self/Nonself 2011, 2:35-42.
44. Sridhar S., Schembri F., Zeskind J., Shah V., Gustafson A.M., Steiling K., Liu G., Dumas Y.M., Zhang X., Brody J.S., Lenburg M.E., Spira A. Smoking-induced gene expression changes in the bronchial airway are reflected in nasal and buccal epithelium. BMC Genomics 2008, 9:259.
45. Subramanian A., Tamayo P., Mootha V.K., Mukherjee S., Ebert B.L., Gillette M.A., Paulovich A., Pomeroy S.L., Golub T.R., Lander E.S., Mesirov J.P. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:15545-15550.
46. Tominaga K., Yoshimoto T., Torigoe K., Kurimoto M., Matsui K., Hada T., Okamura H., Nakanishi K. IL-12 synergizes with IL-18 or IL-1β for IFN-γ production from human T cells. Int. Immunol. 2000, 12:151-160.
47. Vandenabeele P., Galluzzi L., Berghe T.V., Kroemer G. Molecular mechanisms of necroptosis: an ordered cellular explosion. Nat. Rev. Mol. Cell Biol. 2010, 11:700-714.
48. Vasilyev D.M., Thomson T.M., Frushour B.P., Martin F., Sewer A. A method of score aggregation over biological networks based on random walk. BMC Res. Notes 2013, (submitted for publication).
49. Washko G.R. Diagnostic imaging in COPD. Semin. Respir. Crit. Care Med. 2010, 31:276-285.
50. Westra J.W., Schlage W.K., Frushour B.P., Gebel S., Catlett N.L., Han W., Eddy S.F., Hengstermann A., Matthews A.L., Mathis C., Lichtner R.B., Poussin C., Talikka M., Veljkovic E., Van Hooser A.A., Wong B., Maria M.J., Peitsch M.C., Deehan R., Hoeng J. Construction of a computable cell proliferation network focused on non-diseased lung cells. BMC Syst. Biol. 2011, 5:105.
51. Westra J.W., Schlage W.K., Hengstermann A., Gebel S., Mathis C., Thomson T., Wong B., Hoang V., Veljkovic E., Peck M., Lichtner R.B., Weisensee D., Talikka M., Deehan R., Hoeng J., Peitsch M.C. A modular cell-type focused inflammatory process network model for non-diseased pulmonary tissue. Bioinform. Biol. Insights 2013, 7:167-192.
52. Zhang X., Sebastiani P., Liu G., Schembri F., Zhang X., Dumas Y.M., Langer E.M., Alekseyev Y., O'Connor G.T., Brooks D.R., Lenburg M.E., Spira A. Similarities and differences between smoking-related gene expression in nasal and bronchial epithelium. Physiol. Genomics 2010, 41:1-8.