Existence of inverted profile in chemically responsive molecular pathways in the zebrafish liver

PLoS ONE

Volumn 6, Issue 11, 2011, Pages

  Ung, Choong Yong ^a   Lam, Siew Hong ^a   Zhang, Xun ^a   Li, Hu ^b   Ma, Jing ^a   Zhang, Louxin ^a   Li, Baowen ^a   Gong, Zhiyuan ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; ENVIRONMENTAL EXPOSURE; GENE EXPRESSION REGULATION; HOMEOSTASIS; LIVER METABOLISM; LIVER PARENCHYMA; MALE; MOLECULAR DYNAMICS; NONHUMAN; PHYSIOLOGICAL PROCESS; SIGNAL TRANSDUCTION; TRANSCRIPTOMICS; ZEBRA FISH; ANIMAL; BIOLOGICAL MODEL; FEMALE; HUMAN; LIVER; MAMMAL; METABOLISM; MOUSE; PATHOLOGY; RAT;

ANIMALS; FEMALE; HUMANS; LIVER; MALE; MAMMALS; MICE; MODELS, BIOLOGICAL; RATS; SIGNAL TRANSDUCTION; ZEBRAFISH;

EID: 82255195413     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0027819     Document Type: Article

References (56)

1. Hillenmeyer ME, Fung E, Wildenhain J, Pierce SE, Hoon S, et al. (2008) The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science 320: 362-365.
2. Yang L, Kemadjou JR, Zinsmeister C, Bauer M, Legradi J, et al. (2007) Transcriptional profiling reveals barcode-like toxicogenomic responses in the zebrafish embryo. Genome Biol 8: R227.
3. Lam SH, Winata CL, Tong Y, Korzh S, Lim WS, et al. (2006) Transcriptome kinetics of arsenic-induced adaptive response in zebrafish liver. Physiol Genomics 27: 351-361.
4. Lam SH, Mathavan S, Tong Y, Li H, Karuturi RK, et al. (2008) Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology. PLoS Genet 4: e1000121.
5. Ung CY, Lam SH, Hlaing MM, Winata CL, Korzh S, et al. (2010) Mercury-induced hepatotoxicity in zebrafish: in vivo mechanistic insights from transcriptome analysis, phenotype anchoring and targeted gene expression validation. BMC Genomics 11: 212.
6. Hamadeh HK, Bushel PR, Jayadev S, Martin K, DiSorbo O, et al. (2002) Gene expression analysis reveals chemical-specific profiles. Toxicol Sci 67: 219-231.
7. Yang M, Park MS, Lee HS, (2006) Endocrine disrupting chemicals: human exposure and health risks. J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 24: 183-224.
8. Kummer V, Masková J, Zralý Z, Neca J, Simecková P, et al. (2008) Estrogenic activity of environmental polycyclic aromatic hydrocarbons in uterus of immature Wistar rats. Toxicol Lett 180: 212-221.
9. Chowdhury TR, Basu GK, Mandel BK, Biswass BK, Samanta G, et al. (1999) Arsenic poisoning in the Ganges delta. Nature 401: 545-546.
10. Hylande LD, Goodsite ME, (2006) Environmental costs of mercury pollution. Sci Total Environ 368: 352-370.
11. Esteban E, Rubin C, Hill R, Olson D, Pearce K, (1996) Association between indoor residential contamination with methyl parathion and urinary para-nitrophenol. J Expo Anal Environ Epidemiol 6: 375-387.
12. Pizon AF, Schwartz AR, Shum LM, Rittenberger JC, Lower DR, et al. (2009) Toxicology laboratory analysis and human exposure to p-chloroaniline. Clin Toxicol 47: 132-136.
13. Smith LW, Hall GT, Kennedy GL, (1988) Acute and repeated dose inhalation toxicity of para-nitrophenol sodium salt in rats. Drug Chem Toxicol 11: 319-327.
14. Li C TS, Suzuki AK, Furuta C, Watanabe G, Taya K, (2006) Estrogenic and anti-androgenic activities of 4-nitrophenol in diesel exhaust particles. Toxicol Appl Pharmacol 217: 1-6.
15. Luch A, (2005) Nature and nurture- lessons from chemical carcinogenesis. Nat Rev Cancer 5: 113-125.
16. Clarkson TW, (2002) The Three Modern Faces of Mercury. Environ Health Perspect 110 (suppl 1): 11-23.
17. Spicker JS, Brunak S, Frederiksen KS, Toft H, (2008) Integration of clinical chemistry, expression, and metabolite data leads to better toxicological class separation. Toxicol Sci 102: 444-454.
18. Chen F, Zhu HH, Zhou LF, Li J, Zhao LY, et al. (2010) Genes related to the very early stage of ConA-induced fulminant hepatitis: a gene-chip-based study in a mouse model. BMC Genomics 11: 240.
19. Tugues S, Morales-Ruiz M, Fernandez-Varo G, Ros J, Arteta D, et al. (2005) Microarray analysis of endothelial differentially expressed genes in liver of cirrhotic rats. Gastroenterology 129: 1686-1695.
20. Drew RE, Rodnick KJ, Settles M, Wacyk J, Churchill E, et al. (2008) Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio). Physiol Genomics 35: 283-295.
21. Robison BD, Drew RE, Murdoch GK, Powell M, Rodnick KJ, et al. (2008) Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio), Comparative Biochemistry and Physiology Part D. Genomics and Proteomics 3: 141-154.
22. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, et al. (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 15545-15550.
23. Hoffmann JL, Torontali SP, Thomason RG, Lee DM, Brill JL, et al. (2006) Hepatic gene expression profiling using Genechips in zebrafish exposed to 17alpha-ethynylestradiol. Aquat Toxicol 79: 233-246.
24. De Wit M, Keil D, van der Ven K, Vandamme S, Witters E, et al. (2010) An integrated transcriptomic and proteomic approach characterizing estrogenic and metabolic effects of 17 alpha-ethinylestradiol in zebrafish (Danio rerio). Gen Comp Endocrinol 167: 190-201.
25. Ortiz PA, Bruno ME, Moore T, Nesnow S, Winnik W, et al. (2010) Proteomic analysis of propiconazole responses in mouse liver: comparison of genomic and proteomic profiles. J Proteome Res 9: 1268-1278.
26. Ruepp SU, Tonge RP, Shaw J, Wallis N, Pognan F, (2002) Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Toxicol Sci 65: 135-150.
27. Heinloth AN, Irwin RD, Boorman GA, Nettesheim P, Fannin RD, et al. (2004) Gene expression profiling of rat livers reveals indicators of potential adverse effects. Toxicol Sci 80: 193-202.
28. Huang Q, Jin X, Gaillard ET, Knight BL, Pack FD, et al. (2004) Gene expression profiling reveals multiple toxicity endpoints induced by hepatotoxicants. Mutat Res 549: 147-167.
29. Vanhooren V, Liu XE, Franceschi C, Gao CF, Libert C, et al. (2009) N-glycan profiles as tools in diagnosis of hepatocellular carcinoma and prediction of healthy human ageing. Mech Ageing Dev 130: 92-97.
30. Liu XE, Dewaele S, Vanhooren V, Fan YD, Wang L, et al. (2010) Alteration of N-glycome in diethylnitrosamine-induced hepatocellular carcinoma mice: a non-invasive monitoring tool for liver cancer. Liver Int 30: 1221-1228.
31. Reddy AB, Karp NA, Maywood ES, Sage EA, Deery M, et al. (2006) Circadian orchestration of the hepatic proteome. Curr Biol 16: 1107-1115.
32. Michalak A, Rose C, Butterworth J, Butterworth RF, (1996) Neuroactive amino acids and glutamate (NMDA) receptors in frontal cortex of rats with experimental acute liver failure. Hepatology 24: 908-913.
33. Anderson SP, Yoon L, Richard EB, Dunn CS, Cattley RC, et al. (2002) Delayed liver regeneration in peroxisome proliferator-activated receptor-alpha-null mice. Hepatology 36: 544-554.
34. Lam SH, Wu YL, Vega VB, Miller LD, Spitsbergen J, et al. (2006) Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression. Nat Biotechnol 24: 73-75.
35. Shapiro B, (1967) Lipid metabolism. Annu Rev Biochem 36: 247-270.
36. Yi CX, la Fleur SE, Fliers E, Kalsbeek A, (2010) The role of the autonomic nervous liver innervation in the control of energy metabolism. Biochim Biophys Acta 1802: 416-431.
37. Symonds ME, Sebert SP, Hyatt MA, Budge H, (2009) Nutritional programming of the metabolic syndrome. Nat Rev Endocrinol 5: 604-610.
38. Alkhouri N, Dixon LJ, Feldstein AE, (2009) Lipotoxicity in nonalcoholic fatty liver disease: not all lipids are created equal. Expert Rev Gastroenterol Hepatol 3: 445-451.
39. Gatfield D, Schibler U, (2007) Proteasomes keep the circadian clock ticking. Science 316: 1135-1136.
40. Bass J, Takahashi JS, (2010) Circadian integration of metabolism and energetics. Science 330: 1349-1354.
41. Dennis JW, Nabi IR, Demetriou M, (2009) Metabolism, cell surface organization, and disease. Cell 139: 1229-1241.
42. Hamel FG, Upward JL, Siford GL, Duckworth WC, (2003) Inhibition of proteasome activity by selected amino acids. Metabolism 52: 810-814.
43. Dueber JE, Yeh BJ, Bhattacharyya RP, Lim WA, (2004) Rewiring cell signaling: the logic and plasticity of eukaryotic protein circuitry. Curr Opin Struct Biol 14: 690-699.
44. Lehár J, Zimmermann GR, Krueger AS, Molnar RA, Ledell JT, et al. (2007) Chemical combination effects predict connectivity in biological systems. Mol Syst Biol 3: 80.
45. Strogatz SH, (2001) Nonlinear dynamics and chaos: with applications to physics, biology, chemistry, and engineering Westview Press.
46. Macarthur BD, Ma'ayan A, Lemischka IR, (2009) Systems biology of stem cell fate and cellular reprogramming. Nat Rev Mol Cell Biol 10: 672-681.
47. Ou B, Huang D, Hampsch-Woodill M, Flanagan JA, (2003) When east meets west: the relationship between yin-yang and antioxidation-oxidation. FASEB J 17: 127-129.
48. La Thangue NB, (2003) The yin and yang of E2F-1: balancing life and death. Nat Cell Biol 5: 587-589.
49. Sachdeva M, Mo YY, (2009) p53 and c-myc: how does the cell balance "yin" and "yang"? Cell Cycle 8: 1303.
50. Ji J, Wang XW, (2010) A Yin-Yang balancing act of the lin28/let-7 link in tumorigenesis. J Hepatol 53: 974-975.
51. Barabási AL, Gulbahce N, Loscalzo J, (2011) Network medicine: a network-based approach to human disease. Nat Rev Genet 12: 56-68.
52. Zimmermann GR, Lehár J, Keith CT, (2007) Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discov Today 12: 34-42.
53. Hopkins AL, (2008) Network pharmacology: the next paradigm in drug discovery. Nat Chem Biol 4: 682-690.
54. Kitano H, (2007) A robustness-based approach to systems-oriented drug design. Nat Rev Drug Discov 6: 202-210.
55. Lam SH, Mathavan S, Gong Z, (2009) Zebrafish spotted-microarray for genome-wide expression profiling experiments. Part I: array printing and hybridization. Methods Mol Biol 546: 175-195.
56. Lam SH, Krishna MKR, Gong Z, (2009) Zebrafish spotted-microarray for genome-wide expression profiling experiments: data acquisition and analysis. Methods Mol Biol 546: 197-226.