Systems biology strategy to study lipotoxicity and the metabolic syndrome

Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids

Volumn 1801, Issue 3, 2010, Pages 235-239

  Orešič, Matej ^a  

^a VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

Author keywords

Allostasis; Gene network; Lipid metabolism; Lipidomics; Metabolomics; Systems biology

Indexed keywords

PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA 2;

ENERGY; GENE EXPRESSION; GENE INTERACTION; HEREDITY; HUMAN; INSULIN DEPENDENT DIABETES MELLITUS; INSULIN RESISTANCE; INTESTINE FLORA; LIPID METABOLISM; LIPIDOMICS; LIPOTOXICITY; METABOLIC SYNDROME X; NONHUMAN; OXIDATIVE STRESS; PRIORITY JOURNAL; REVIEW; SYSTEMS BIOLOGY; TOXICITY; TRANSCRIPTOMICS;

ANIMALS; ENVIRONMENT; GENETIC PREDISPOSITION TO DISEASE; HUMANS; LIPID METABOLISM; METABOLIC SYNDROME X; MODELS, BIOLOGICAL; SYSTEMS BIOLOGY;

EID: 76049112961     PISSN: 13881981     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbalip.2009.11.003     Document Type: Review

References (62)

1. Obesity: preventing and managing the global epidemic. Report of a WHO consultation. World Health Organ Tech Rep Ser. 894 I-xii (2000) 1-253
2. Kitano H., Oda K., Kimura T., Matsuoka Y., Csete M., Doyle J., and Muramatsu M. Metabolic syndrome and robustness tradeoffs. Diabetes 53 (2004) S6-S15
3. Breitling R. Robust signaling networks of the adipose secretome. Trends Endocrinol. Metab. 20 (2009) 1-7
4. Lusis A.J., Attie A.D., and Reue K. Metabolic syndrome: from epidemiology to systems biology. Nat. Genet. 9 (2008) 819-830
5. Ge H., Walhout A., and Vidal M. Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet 19 (2003) 551-560
6. Ideker T., Galitski T., and Hood L. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2 (2001) 343-372
7. van der Greef J., Stroobant P., and Heijden R.v.d. The role of analytical sciences in medical systems biology. Curr. Opin. Chem. Biol 8 (2004) 559-565
8. Oresic M. Metabolomics, a novel tool for studies of nutrition, metabolism and lipid dysfunction. Nutr. Metab. Cardiovasc. Dis. (2009) 10.1016/j.numecd.2009.04.018
9. Oresic M., Hänninen V.A., and Vidal-Puig A. Lipidomics: a new window to biomedical frontiers. Trends Biotechnol 26 (2008) 647-652
10. Duarte N.C., Becker S.A., Jamshidi N., Thiele I., Mo M.L., Vo T.D., Srivas R., and Palsson B.O. Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc. Natl. Acad. Sci. USA 104 (2007) 1777-1782
11. Oresic M., Vidal-Puig A., and Hänninen V. Metabolomic approaches to phenotype characterization and applications to complex diseases. Expert Rev. Mol. Diagn. 6 (2006) 575-585
12. Unger R.H., and Orci L. Diseases of liporegulation: new perspective on obesity and related disorders. FASEB J 15 (2001) 312-321
13. Unger R. How obesity causes diabetes in Zucker diabetic fatty rats. Trends Endocrinol. Metab. 7 (1997) 276-282
14. Lelliott C., and Vidal-Puig A.J. Lipotoxicity, an imbalance between lipogenesis de novo and fatty acid oxidation. Int. J. Obes. relat. Metab. Disord. 28 Suppl. 4 (2005) S22-S28
15. Vance D.E., and Vance J.E. In: Bernardi G. (Ed) (2008), Elsevier B. V., Amsterdam, The Netherlands
16. Fahy E., Subramaniam S., Brown H.A., Glass C.K., Merrill A.H., Murphy R.C., Raetz C.R.H., Russell D.W., Seyama Y., Shaw W., Shimizu T., Spener F., van Meer G., VanNieuwenhze M.S., White S.H., Witztum J.L., and Dennis E.A. A comprehensive classification system for lipids. J. Lipid Res. 46 (2005) 839-862
17. Yetukuri L., Ekroos K., Vidal-Puig A., and Oresic M. Informatics and computational strategies for the study of lipids. Mol. BioSyst. 4 (2008) 121-127
18. Alberts B., Johnson A., Lewis J., Raff M., Roberts K., and Walter P. Molecular Biology of the Cell. 5th ed. (2007), Garland Science, New York
19. Han X., and Gross R.W. Global analyses of cellular lipidomes directly from crude extracts of biological samples by ESI mass spectrometry: a bridge to lipidomics. J. Lipid Res. 44 (2003) 1071-1079
20. Lagarde M., Geloen A., Record M., Vance D., and Spener F. Lipidomics is emerging. Biochim. Biophys. Acta 1634 (2003) 61
21. Wenk M.R. The emerging field of lipidomics. Nat. Rev. Drug Discov. 4 (2005) 594-610
22. Han X. Lipidomics: developments and applications. J. Chromatogr. B 877 (2009) 2663
23. Ståhlman M., Ejsing C.S., Tarasov K., Perman J., Borén J., and Ekroos K. High-throughput shotgun lipidomics by quadrupole time-of-flight mass spectrometry. J. Chromatogr. B 877 (2009) 2664-2672
24. Cui Z., and Thomas M.J. Phospholipid profiling by tandem mass spectrometry. J. Chromatogr. B 877 (2009) 2709-2715
25. Haynes C.A., Allegood J.C., Park H., and Sullards M.C. Sphingolipidomics: methods for the comprehensive analysis of sphingolipids. J. Chromatogr. B 877 (2009) 2696-2708
26. Mesaros C., Lee S.H., and Blair I.A. Targeted quantitative analysis of eicosanoid lipids in biological samples using liquid chromatography-tandem mass spectrometry. J. Chromatogr. B 877 (2009) 2736-2745
27. Song H., Ladenson J., and Turk J. Algorithms for automatic processing of data from mass spectrometric analyses of lipids. J. Chromatogr. B 877 (2009) 2847-2854
28. Niemelä P.S., Castillo S., Sysi-Aho M., and Oresic M. Bioinformatics and computational methods for lipidomics. J. Chromatogr. B 877 (2009) 2855-2862
29. King R.A., Rotter J.I., and Motulsky A.G. The Genetic Basis of Common Diseases (2002), Oxford University Press, New York
30. Walley A.J., Asher J.E., and Froguel P. The genetic contribution to non-syndromic human obesity. Nat. Rev. Genet. 10 (2009) 431-442
31. Maher B. Personal genomes: the case of the missing heritability. Nature 456 (2008) 18-21
32. Schadt E.E., Lamb J., Yang X., Zhu J., Edwards S., GuhaThakurta D., Sieberts S.K., Monks S., Reitman M., Zhang C., Lum P.Y., Leonardson A., Thieringer R., Metzger J.M., Yang L., Castle J., Zhu H., Kash S.F., Drake T.A., Sachs A., and Lusis A.J. An integrative genomics approach to infer causal associations between gene expression and disease. Nat. Genet. 37 (2005) 710-717
33. Schadt E.E. Molecular networks as sensors and drivers of common human diseases. Nature 461 (2009) 218-223
34. Chen Y., Zhu J., Lum P.Y., Yang X., Pinto S., MacNeil D.J., Zhang C., Lamb J., Edwards S., Sieberts S.K., Leonardson A., Castellini L.W., Wang S., Champy M.-F., Zhang B., Emilsson V., Doss S., Ghazalpour A., Horvath S., Drake T.A., Lusis A.J., and Schadt E.E. Variations in DNA elucidate molecular networks that cause disease. Nature 452 (2008) 429-435
35. Emilsson V., Thorleifsson G., Zhang B., Leonardson A.S., Zink F., Zhu J., Carlson S., Helgason A., Walters G.B., Gunnarsdottir S., Mouy M., Steinthorsdottir V., Eiriksdottir G.H., Bjornsdottir G., Reynisdottir I., Gudbjartsson D., Helgadottir A., Jonasdottir A., Jonasdottir A., Styrkarsdottir U., Gretarsdottir S., Magnusson K.P., Stefansson H., Fossdal R., Kristjansson K., Gislason H.G., Stefansson T., Leifsson B.G., Thorsteinsdottir U., Lamb J.R., Gulcher J.R., Reitman M.L., Kong A., Schadt E.E., and Stefansson K. Genetics of gene expression and its effect on disease. Nature 452 (2008) 423-428
36. Tang J., Tan C.Y., Oresic M., and Vidal-Puig A. Integrating post-genomic approaches as a strategy to advance our understanding of health and disease. Genome Med 1 (2009) e35
37. Bäckhed F., and Crawford P.A. Coordinated regulation of the metabolome and lipidome at the host-microbial interface. Biochim. Biophys. Acta (2009) 10.1016/j.bbalip.2009.09.009
38. Claus S.P., Tsang T.M., Wang Y., Cloarec O., Skordi E., Martin F.-P., Rezzi S., Ross A., Kochhar S., Holmes E., and Nicholson J.K. Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes. Mol. Syst. Biol. 4 (2008) 219
39. Gopalacharyulu P.V., Velagapudi V., Lindfors E., Halperin E., and Oresic M. Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast. Mol. BioSyst. 5 (2009) 276-287
40. Jamieson D.J. Oxidative stress responses of the yeast Saccharomyces cerevisiae. Yeast 14 (1998) 1511-1527
41. Gasch A.P., Spellman P.T., Kao C.M., Carmel-Harel O., Eisen M.B., Storz G., Botstein D., and Brown P.O. Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell 11 (2000) 4241-4257
42. Bougneres P., and Valleron A.-J. Causes of early-onset type 1 diabetes: toward data-driven environmental approaches. J. Exp. Med. 205 (2008) 2953-2957
43. Oresic M., Simell S., Sysi-Aho M., Näntö-Salonen K., Seppänen-Laakso T., Parikka V., Katajamaa M., Hekkala A., Mattila I., Keskinen P., Yetukuri L., Reinikainen A., Lähde J., Suortti T., Hakalax J., Simell T., Hyöty H., Veijola R., Ilonen J., Lahesmaa R., Knip M., and Simell O. Dysregulation of lipid and amino acid metabolism precedes islet autoimmunity in children who later progress to type 1 diabetes. J. Exp. Med. 205 (2008) 2975-2984
44. Nikkilä J., Sysi-Aho M., Ermolov A., Seppänen-Laakso T., Simell O., Kaski S., and Oresic M. Gender dependent progression of systemic metabolic states in early childhood. Mol. Syst. Biol. 4 (2008) e197
45. Rabiner L. A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77 (1989) 257-286
46. Atherton H.J., Gulston M.K., Bailey N.J., Cheng K.-K., Zhang W., Clarke K., and Griffin J.L. Metabolomics of the interaction between PPAR-[alpha] and age in the PPAR-[alpha]-null mouse. Mol. Syst. Biol. 5 (2009) e259
47. Reddy J.K., and Hashimoto T. Peroxisomal beta-oxidation and peroxisome proliferator-activated receptor alpha: an adaptive metabolic system. Annu. Rev. Nutr. 21 (2003) 193-230
48. Noble D. The Music of Life: Biology Beyond the Genome (2006), Oxford University Press, Oxford
49. Pietiläinen K.H., Rissanen A., Laamanen M., Lindholm A.K., Markkula H., Yki-Järvinen H., and Kaprio J. Growth patterns in young adult monozygotic twin pairs discordant and concordant for obesity. Twin Res 7 (2004) 421-429
50. Pietiläinen K.H., Naukkarinen J., Rissanen A., Saharinen J., Ellonen P., Keränen H., Suomalainen A., Götz A., Suortti T., Yki-Järvinen H., Oresic M., Kaprio J., and Peltonen L. Global transcript profiles of fat in monozygotic twins discordant for BMI: pathways behind acquired obesity. PLoS Med 5 (2008) e51
51. Pietiläinen K.H., Sysi-Aho M., Rissanen A., Seppänen-Laakso T., Yki-Järvinen H., Kaprio J., and Oresic M. Acquired obesity is associated with changes in the serum lipidomic profile independent of genetic effects-a monozygotic twin study. PLoS ONE 2 (2007) e218
52. Hicks A.A., Pramstaller P.P., Johansson Å., Vitart V., Rudan I., Ugocsai P., Aulchenko Y., Franklin C.S., Liebisch G., Erdmann J., Jonasson I., Zorkoltseva I.V., Pattaro C., Hayward C., Isaacs A., Hengstenberg C., Campbell S., Gnewuch C., Janssens A.C.W., Kirichenko A.V., König I.R., Marroni F., Polasek O., Demirkan A., Kolcic I., Schwienbacher C., Igl W., Biloglav Z., Witteman J.C.M., Pichler I., Zaboli G., Axenovich T.I., Peters A., Schreiber S., Wichmann H.-E., Schunkert H., Hastie N., Oostra B.A., Wild S.H., Meitinger T., Gyllensten U., van Duijn C.M., Wilson J.F., Wright A., Schmitz G., and Campbell H. Genetic determinants of circulating sphingolipid concentrations in European populations. PLoS Genet. 5 (2009) e1000672
53. Kotronen A., Seppänen-Laakso T., Westerbacka J., Kiviluoto T., Arola J.T., Ruskeepää A.-L., Yki-Järvinen H., and Oresic M. Comparison of lipid and fatty acid composition of the liver, subcutaneous and intra-abdominal adipose tissue, and serum in humans. Obesity (2009) 10.1038/oby.2009.326
54. Puri P., Baillie R.A., Wiest M.M., Mirshahi F., Choudhury J., Cheung O., Sargeant C., Contos M.J., and Sanyal A.J. A lipidomic analysis of nonalcoholic fatty liver disease. Hepatology 46 (2007) 1081-1090
55. Damian D., Oresic M., Verheij E., Meulman J.J., Friedman J., Adouran A., Morel N., Smilde A.K., and van der Greef J. Applications of a new subspace clustering algorithm (COSA) in medical systems biology. Metabolomics 3 (2007) 69-77
56. Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., Katayama T., Kawashima S., Okuda S., Tokimatsu T., and Yamanishi Y. KEGG for linking genomes to life and the environment. Nucl. Acids Res. 36 (2008) D480-D484
57. Yetukuri L., Katajamaa M., Medina-Gomez G., Seppanen-Laakso T., Vidal-Puig A., and Oresic M. Bioinformatics strategies for lipidomics analysis: characterization of obesity related hepatic steatosis. BMC Syst. Biol. 1 (2007) e12
58. Serhan C.N., Lu Y., Hong S., and Yang R. Mediator lipidomics: search algorithms for eicosanoids, resolvins, and protectins. Methods Enzymol 432 (2007) 275-317
59. Medina-Gomez G., Gray S., Yetukuri L., Shimomura K., Campbell M., Curtis K., Virtue S., Jimenez-Linan M., Blount M., Yeo G., Lopez M., Seppänen-Laakso T., Ashcroft F.M., Oresic M., and Vidal-Puig A. PPAR gamma 2 prevents lipotoxicity by controlling adipose tissue expandability and peripheral lipid metabolism. PLoS Genet. 3 (2007) e64
60. Niemelä P.S., Ollila S., Hyvönen M.T., Karttunen M., and Vattulainen I. Assessing the nature of lipid raft membranes. PLoS Comp. Biol. 3 (2007) e34
61. Wheeler D., Bandaru V.V.R., Calabresi P.A., Nath A., and Haughey N.J. A defect of sphingolipid metabolism modifies the properties of normal appearing white matter in multiple sclerosis. Brain 131 (2008) 3092-3102
62. Virtue S., and Vidal-Puig A. IIt's not how fat you are, it's what you do with it that counts. PLoS Biol 6 (2008) e237