Metabolic changes in flatfish hepatic tumours revealed by NMR-based metabolomics and metabolic correlation networks

Journal of Proteome Research

Volumn 7, Issue 12, 2008, Pages 5277-5285

  Southam, Andrew D ^a   Easton, John M ^a   Stentiford, Grant D ^b   Ludwig, Christian ^a   Arvanitis, Theodoras N ^a   Viant, Mark R ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^b CENTRE FOR ENVIRONMENT   (United Kingdom)

Author keywords

Cancer; Dab flatfish; Environment; False discovery rate; FDR; Fingerprinting; Hepatocellular adenoma; Metabolic networks; Profiling; Succinate

Indexed keywords

ACETIC ACID; ALANINE; CHOLINE; PROLINE;

ANAEROBIC METABOLISM; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CORRELATIONAL STUDY; DATA ANALYSIS; FEMALE; FLATFISH; LIVER TUMOR; MALE; METABOLIC PARAMETERS; METABOLOMICS; MULTIVARIATE ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN METABOLISM; PROTON NUCLEAR MAGNETIC RESONANCE;

ADENOMA; ANIMALS; CHOLINE; COMPUTATIONAL BIOLOGY; ENVIRONMENT; FALSE POSITIVE REACTIONS; FLATFISHES; GENE EXPRESSION REGULATION, NEOPLASTIC; LIVER; LIVER NEOPLASMS; MAGNETIC RESONANCE SPECTROSCOPY; METABOLOMICS; PROTEOME; PROTEOMICS;

PLEURONECTIFORMES;

EID: 61349135679     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800353t     Document Type: Article

References (41)

1. Anon UK national marine monitoring programme; Second report (1999-2001). Marine environment monitoring group, CEFAS, U.K. 2004.
2. Feist, S. W.; Lang, T.; Stentiford, G. D.; Köhler, A. Biological effects of contaminants: Use of liver pathology of the European flatfish dab (Limanda limanda L.) and flounder (Platichthys flesus L.) for monitoring. ICES Tech. Mar. Environ. Sci. 2004, 38, 1-42.
3. Koehler, A. The gender-specific risk to liver toxicity and cancer of flounder (Platichthys flesus (L.)) at the German Wadden Sea coast. Aquat. Toxicol. 2004, 70, 257-276.
4. Stentiford, G. D.; Longshaw, M.; Lyons, B. P.; Jones, G.; Green, M.; Feist, S. W. Histopathological biomarkers in estuarine fish species for the assessment of biological effects of contaminants. Mar. Environ. Res. 2003, 55, 137-159.
5. Viant, M. R. Metabolomics of aquatic organisms: the new 'omics' on the block. Mar. Ecol: Prog. Ser. 2007, 332, 301-306.
6. Griffin, J. L.; Kauppinen, R. A. Tumour metabolomics in animal models of human cancer. J. Proteome Res. 2007, 6, 498-505.
7. Mazurek, S.; Eigenbrodt, E. The tumor metabolome. Anticancer Res. 2003, 23, 1149-1154.
8. Griffiths, J. R.; Stubbs, M. Opportunities for studying cancer by metabolomics: preliminary observations on tumors deficient in hypoxia-inducible factor 1. Adv. Enzyme Regul. 2003, 43, 67-76.
9. Warburg, O. Origin of cancer cells. Science 1956, 123, 309-314.
10. Vaupel, P. The role of hypoxia-induced factors in tumor progression. Oncologist 2004, 9, 10-17.
11. Semenza, G. L. Hypoxia, clonal selection, and the role of HIF-1 in tumor progression. Crit. Rev. Biochem. Mol. Biol. 2000, 35, 71-103.
12. Ackerstaff, E.; Glunde, K.; Bhujwalla, Z. M. Choline phospholipid metabolism: A target in cancer cells? J. Cell. Biochem. 2003, 90, 525-533.
13. Podo, F. Tumour phospholipid metabolism. NMR Biomed. 1999, 12, 413-439.
14. Lindon, J. C.; Holmes, E.; Nicholson, J. K. So whats the deal with metabonomics? Metabonomics measures the fingerprint of biochemical perturbations caused by disease, drugs, and toxins. Anal. Chem. 2003, 75, 384A-391A.
15. Stella, C.; Beckwith-Hall, B.; Cloarec, O.; Holmes, E.; Lindon, J. C.; Powell, J.; van der Ouderaa, F.; Bingham, S.; Cross, A. J.; Nicholson, J. K. Susceptibility of human metabolic phenotypes to dietary modulation. J. Proteome Res. 2006, 5, 2780-2788.
16. Viant, M. R.; Rosenblum, E. S.; Tjeerdema, R. S. NMR-based metabolomics: A powerful approach for characterizing the effects of environmental stressors on organism health. Environ. Sci. Technol. 2003, 37, 4982-4989.
17. Denken, C.; Budczies, J.; Kind, T.; Weichen, W.; Tablack, P.; Sehouli, J.; Niesporek, S.; Konsgen, D.; Dietel, M.; Fiehn, O. Mass spectrometry-based metabolic profiling reveals different metabolite patterns in invasive ovarian carcinomas and ovarian borderline tumors. Cancer Res. 2006, 66, 10795-10804.
18. Schauer, N.; Semel, Y.; Roessner, U.; Gur, A.; Balbo, I.; Carrari, F.; Pleban, T.; Perez-Melis, A.; Bruedigam, C.; Kopka, J.; Willmitzer, L.; Zamir, D.; Fernie, A. R. Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat. Biotechnol. 2006, 24, 447-454.
19. Weljie, A. M.; Newton, J.; Mercier, P.; Carlson, E.; Slupsky, C. M. Targeted profiling: Quantitative analysis of H-1 NMR metabolomics data. Anal. Chem. 2006, 78, 4430-4442.
20. Camacho, D.; de la Fuente, A.; Mendes, P. The origin of correlations in metabolomics data. Metabolomics 2005, 1, 53-63.
21. Weckwerth, W.; Loureiro, M. E.; Wenzel, K.; Fiehn, O. Differential metabolic networks unravel the effects of silent plant phenotypes. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7809-7814.
22. Viant, M. R. Improved methods for the acquisition and interpretation of NMR metabolomic data. Biochem. Biophys. Res. Commun. 2003, 310 (3), 943-948.
23. Parsons, H. M.; Ludwig, C.; Gunther, U. L.; Viant, M. R. Improved classification accuracy in 1-and 2-dimensional NMR metabolomics data using the variance stabilising generalised logarithm transformation. BMC Bioinf. 2007, 8.
24. Purohit, P. V.; Rocke, D. M.; Viant, M. R.; Woodruff, D. L. Discrimination models using variance stabilizing transformation of metabolomic NMR data. OMICS 2004, 8, 118-130.
25. Benjamini, Y.; Hochberg, Y. Controlling the false discovery rate - a practical and powerful approach to multiple testing. J. R. Stat. Soc., Ser. B 1995, 57, 289-300.
26. Dang, C. V.; Semenza, G. L. Oncogenic alterations of metabolism. Trends Biochem. Sci. 1999, 24, 68-72.
27. Gatenby, R. A.; Gillies, R. J. Why do cancers have high aerobic glycolysis? Nat. Rev. Cancer 2004, 4, 891-899.
28. Pugh, C. W.; Ratcliffe, P. J. The von Hippel-Lindau tumor suppressor, hypoxia-inducible factor-1 (HIF-1) degradation, and cancer pathogenesis. Sem. Cancer Biol. 2003, 13, 83-89.
29. Wang, G. L.; Jiang, B. H.; Rue, E. A.; Semenza, G. L. Hypoxia-inducible factor-1 is a basic-helix-loop-helix-Pas heterodimer regulated by cellular O-2 tension. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 5510-5514.
30. Selak, M. A.; Armour, S. M.; MacKenzie, E. D.; Boulahbel, H.; Watson, D. G.; Mansfield, K. D.; Pan, Y.; Simon, M. C.; Thompson, C. B.; Gottlieb, E. Succinate links TCA cycle dysfunction to oncogenesis by inhibiting HIF-alpha prolyl hydroxylase. Cancer Cell 2005, 7, 77-85.
31. King, A.; Selak, M. A.; Gottlieb, E. Succinate dehydrogenase and fumarate hydratase: linking mitochondrial dysfunction and cancer. Oncogene 2006, 25, 4675-4682.
32. Soitamo, A. J.; Rabergh, C. M. I.; Gassmann, M.; Sistonen, L.; Nikinmaa, M. Characterization of a hypoxia-inducible factor (HIF-1 alpha) from rainbow trout - Accumulation of protein occurs at normal venous oxygen tension. J. Biol. Chem. 2001, 276, 19699-19705.
33. Rytkonen, K. T.; Vuori, K. A. M.; Primmer, C. R.; Nikinmaa, M. Comparison of hypoxia-inducible factor-1 alpha in hypoxia-sensitive and hypoxia-tolerant fish species. Comp. Biochem. Physiol., Part D:Genomics Proteomics 2007, 2, 177-186.
34. Mazurek, S.; Boschek, C. B.; Hugo, F.; Eigenbrodt, E. Pyruvate kinase type M2 and its role in tumor growth and spreading. Sem. Cancer Biol. 2005, 15, 300-308.
35. Hensgens, H.; Meijer, A. J.; Williamson, J. R.; Gimpel, J. A.; Tager, J. M. Proline metabolism in isolated rat-liver cells. Biochem. J. 1978, 170, 699-707.
36. Michel, V.; Yuan, Z. F.; Ramsubir, S.; Bakovic, M. Choline transport for phospholipid synthesis. Exp. Biol. Med. 2006, 231, 490-504.
37. DeLong, C. J.; Hicks, A. M.; Cui, Z. Disruption of choline methyl group donation for phosphatidylethanolamine methylation in hepatocarcinoma cells. J. Biol. Chem. 2002, 277, 17217-17225.
38. Ishidate, K. In Phosphatidylcholine Metabolism, Vance, D. E., Ed.; CRC Press: Boca Raton, FL, 1989; pp 9-32.
39. Davis, C. D.; Uthus, E. O. DNA methylation, cancer susceptibility, and nutrient interactions. Exp. Biol. Med. 2004, 229, 988-995.
40. Nakae, D.; Yoshiji, H.; Mizumoto, Y.; Horiguchi, K.; Shiraiwa, K.; Tamura, K.; Denda, A.; Konishi, Y. High-incidence of hepatocellular carcinomas induced by a choline-deficient L-amino-acid defined diet in rats. Cancer Res. 1992, 52, 5042-5045.
41. Avila, M. A.; Berasain, C.; Tones, L.; Martin-Duce, A.; Conales, F. J.; Yang, H. P.; Prieto, J.; Lu, S. C.; Caballeria, J.; Rodes, J.; Mato, J. M. Reduced mRNA abundance of the main enzymes involved in methionine metabolism in human liver cirrhosis and hepatocellular carcinoma. J. Hepatol. 2000, 33, 907-914.