Metabolomics, a novel tool for studies of nutrition, metabolism and lipid dysfunction

Nutrition, Metabolism and Cardiovascular Diseases

Volumn 19, Issue 11, 2009, Pages 816-824

  Oresic M ^a  

^a VTT TECHNICAL RESEARCH CENTRE OF FINLAND   (Finland)

Author keywords

Lipid metabolism; Lipidomics; Mass spectrometry; Metabolomics; Nutrition; Systems biology

Indexed keywords

BIOLOGY; DYSLIPIDEMIA; HISTORY; HUMAN; LIPID METABOLISM; METABOLIC DISORDER; METABOLISM; METABOLOMICS; METHODOLOGY; NUTRITION; PATHOPHYSIOLOGY; PHENOTYPE; REVIEW; SYSTEMS BIOLOGY;

COMPUTATIONAL BIOLOGY; DYSLIPIDEMIAS; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; HUMANS; LIPID METABOLISM; METABOLIC DISEASES; METABOLOMICS; NUTRITIONAL PHYSIOLOGICAL PHENOMENA; PHENOTYPE; SYSTEMS BIOLOGY;

EID: 70449726556     PISSN: 09394753     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.numecd.2009.04.018     Document Type: Review

References (80)

1. 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 3 (2009) e35
2. Bäckhed F., Ley R.E., Sonnenburg J.L., Peterson D.A., and Gordon J.I. Host-bacterial mutualism in the human intestine. Science 307 5717 (2005) 1915-1920
3. Cascante M., Boros L.G., Comin-Anduix B., de Atauri P., Centelles J.J., and Lee P.W.-N. Metabolic control analysis in drug discovery and disease. Nat Biotechnol 20 (2002) 243-249
4. Oresic M., Vidal-Puig A., and Hänninen V. Metabolomic approaches to phenotype characterization and applications to complex diseases. Expert Rev Mol Diagn 6 4 (2006) 575-585
5. van Ommen B. Nutrigenomics: exploiting systems biology in the nutrition and health arenas. Nutrition 20 1 (2004) 4-8
6. In: Vance D.E., and Vance J.E. (Eds). Biochemistry of lipids, lipoproteins and membranes. 5th ed (2008), Elsevier B.V, Amsterdam, The Netherlands
7. Oresic M., Hänninen V.A., and Vidal-Puig A. Lipidomics: a new window to biomedical frontiers. Trends Biotechnol 26 12 (2008) 647-652
8. Jänis M., Laaksonen R., and Oresic M. Metabolomic strategies to identify tissue specific effects of cardiovascular drugs. Exp Opin Drug Metab Toxicol 4 6 (2008) 665-680
9. Oresic M., Simell S., Sysi-Aho M., Näntö-Salonen K., Seppänen-Laakso T., Parikka V., et al. Dysregulation of lipid and amino acid metabolism precedes islet autoimmunity in children who later progress to type 1 diabetes. J Exp Med 205 13 (2008) 2975-2984
10. Unger R. Lipotoxic diseases. Annu Rev Med 53 (2002) 319-336
11. Medina-Gomez G., Gray S., Yetukuri L., Shimomura K., Campbell M., Curtis K., et al. PPAR gamma 2 prevents lipotoxicity by controlling adipose tissue expandability and peripheral lipid metabolism. PLoS Genet 3 4 (2007) e64
12. Hartmann T., Kuchenbecker J., and Grimm M.O.W. Alzheimer's disease: the lipid connection. J Neurochem 103 s1 (2007) 159-170
13. Han X., Holtzman D.M., and McKeel D.W. Plasmalogen deficiency in early Alzheimer's disease subjects and in animal models: molecular characterization using electrospray ionization mass spectrometry. J Neurochem 77 4 (2001) 1168-1180
14. Kaddurah-Daouk R., McEvoy J., Baillie R.A., Lee D., Yao J.K., Doraiswamy P.M., et al. Metabolomic mapping of atypical antipsychotic effects in schizophrenia. Mol Psychiatry 12 10 (2007) 934-945
15. Schwarz E., Prabakaran S., Whitfield P., Major H., Leweke F.M., Koethe D., et al. High throughput lipidomic profiling of schizophrenia and bipolar disorder brain tissue reveals alterations of free fatty acids, phosphatidylcholines, and ceramides. J Proteome Res 7 10 (2008) 4266-4277
16. Menendez J.A., and Lupu R. Fatty acid synthase and the lipogenic phenotype in cancer pathogenesis. Nat Rev Cancer 7 10 (2007) 763-777
17. Kobayashi N., Barnard R.J., Henning S.M., Elashoff D., Reddy S.T., Cohen P., et al. Effect of altering dietary {omega}-6/{omega}-3 fatty acid ratios on prostate cancer membrane composition, cyclooxygenase-2, and prostaglandin E2. Clin Cancer Res 12 15 (2006) 4662-4670
18. Lusis A.J. Atherosclerosis. Nature 407 6801 (2000) 233-241
19. Haughey N.J., Steiner J., Nath A., McArthur J.C., Sacktor N., Pardo C., et al. Converging roles for sphingolipids and cell stress in the progression of neuro-AIDS. Front Biosci 13 (2008) 5120-5130
20. Wikoff W.R., Pendyala G., Siuzdak G., and Fox H.S. Metabolomic analysis of the cerebrospinal fluid reveals changes in phospholipase expression in the CNS of SIV-infected macaques. J Clin Invest 118 7 (2008) 2661-2669
21. Wenk M.R. The emerging field of lipidomics. Nat Rev Drug Discov 4 (2005) 594-610
22. Pauling L., Robinson A.B., Teranishi R., and Cary P. Quantitative analysis of urine vapor and breath by gas-liquid partition chromatography. Proc Nat Acad Sci U S A 68 (1971) 2374-2376
23. Venter J.C., Adams M.D., Myers E.W., Li P.W., Mural R.J., Sutton G.G., et al. The sequence of the human genome. Science 291 5507 (2001) 1304-1351
24. Collins F., Green E., Guttmacher A., and Guyer M. A vision for the future of genomics research. Nature 422 (2003) 835-847
25. Fenn J., Mann M., Meng C., Wong S., and Whitehouse C. Electrospray ionization for mass spectrometry of large biomolecules. Science 246 4926 (1989) 64-71
26. Goodacre R., Vaidyanathan S., Dunn W.B., Harrigan G.G., and Kell D.B. Metabolomics by numbers: acquiring and understanding global metabolite data. Trends Biotechnol 22 5 (2004) 245-252
27. van der Greef J., and Stroobant P. Heijden Rvd. The role of analytical sciences in medical systems biology. Curr Opin Chem Biol 8 5 (2004) 559-565
28. Lindon J.C., Holmes E., and Nicholson J.K. Metabonomics and its role in drug development and disease diagnosis. Expert Rev Mol Diag 4 2 (2004) 189-199
29. Ståhlman M, Ejsing CS, Tarasov K, Perman J, Borén J, Ekroos K. High-throughput shotgun lipidomics by quadrupole time-of-flight mass spectrometry. J Chromatogr B 2009:doi:10.1016/j.jchromb.2009.02.037.
30. Han X., and Gross R.W. Shotgun lipidomics: electrospray ionization mass spectrometric analysis and quantitation of cellular lipidomes directly from crude extracts of biological samples. Mass Spectrom Rev 24 (2005) 367-412
31. Schwudke D., Liebisch G., Herzog R., Schmitz G., and Shevchenko A. Shotgun lipidomics by tandem mass spectrometry under data-dependent acquisition control. Methods Enzymol 433 (2007) 175-191
32. Nordstrom A., O'Maille G., Qin C., and Siuzdak G. Nonlinear data alignment for UPLC-MS and HPLC-MS based metabolomics: quantitative analysis of endogenous and exogenous metabolites in human serum. Anal Chem 78 10 (2006) 3289-3295
33. Murphy R.C., Barkley R.M., Zemski Berry K., Hankin J., Harrison K., Johnson C., et al. Electrospray ionization and tandem mass spectrometry of eicosanoids. Anal Biochem 346 1 (2005) 1-42
34. Hagio M., Matsumoto M., Fukushima M., Hara H., and Ishizuka S. Improved analysis of bile acids in tissues and intestinal contents of rats using LC/ESI-MS. J Lipid Res 50 1 (2009) 173-180
35. Pilvi TK, Seppänen-Laakso T, Simolin H, Finckenberg P, Huotari A, Herzig K-H, et al. Metabolomic changes in fatty liver can be modified by dietary protein and calcium during energy restriction. World J Gastroenterol 2008;14(28):4462-72.
36. Shaham O., Wei R., Wang T.J., Ricciardi C., Lewis G.D., Vasan R.S., et al. Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity. Mol Syst Biol 4 (2008) e214
37. Sabatine M.S., Liu E., Morrow D.A., Heller E., McCarroll R., Wiegand R., et al. Metabolomic identification of novel biomarkers of myocardial ischemia. Circulation 112 25 (2005) 3868-3875
38. Broadhurst D., and Kell D. Statistical strategies for avoiding false discoveries in metabolomics and related experiments. Metabolomics 2 4 (2006) 171-196
39. Thissen U., Wopereis S., van den Berg S., Bobeldijk I., Kleemann R., Kooistra T., et al. Improving the analysis of designed studies by combining statistical modelling with study design information. BMC Bioinformatics 10 1 (2009) e52
40. Niemelä PS, Castillo S, Sysi-Aho M, Oresic M. Bioinformatics and computational methods for lipidomics. J Chromatogr B: doi: 10.1016/j.jchromb.2009.01.025.
41. Katajamaa M., and Oresic M. Data processing for mass spectrometry-based metabolomics. J Chromatogr A 1158 1-2 (2007) 318-328
42. Katajamaa M., and Oresic M. Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics 6 (2005) 179
43. Katajamaa M., Miettinen J., and Oresic M. MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 22 5 (2006) 634-636
44. Kind T., Tolstikov V., Fiehn O., and Weiss R.H. A comprehensive urinary metabolomic approach for identifying kidney cancer. Anal Biochem 363 2 (2007) 185-195
45. Timischl B., Dettmer K., Kaspar H., Thieme M., and Oefner P.J. Development of a quantitative, validated capillary electrophoresis-time of flight - mass spectrometry method with integrated high-confidence analyte identification for metabolomics. Electrophoresis 29 10 (2008) 2203-2214
46. Rogers S., Scheltema R.A., Girolami M., and Breitling R. Probabilistic assignment of formulas to mass peaks in metabolomics experiments. Bioinformatics 25 4 (2009) 512-518
47. Welthagen W., Shellie R.A., Spranger J., Ristow M., Zimmermann R., and Fiehn O. Comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (GC-GC-TOF) for high resolution metabolomics: biomarker discovery on spleen tissue extracts of obese NZO compared to lean C57BL/6 mice. Metabolomics 1 1 (2005) 65-73
48. Koek M.M., Muilwijk B., van Stee L.L.P., and Hankemeier T. Higher mass loadability in comprehensive two-dimensional gas chromatography-mass spectrometry for improved analytical performance in metabolomics analysis. J Chromatogr A 1186 1-2 (2008) 420-429
49. Bobeldijk I., Hekman M., de Vries-van der Weij J., Coulier L., Ramaker R., Kleemann R., et al. Quantitative profiling of bile acids in biofluids and tissues based on accurate mass high resolution LC-FT-MS: compound class targeting in a metabolomics workflow. J Chromatogr B 871 2 (2008) 306-313
50. Sysi-Aho M., Katajamaa M., Yetukuri L., and Oresic M. Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformatics 8 (2007) e93
51. Bijlsma S., Bobeldijk I., Verheij E.R., Ramaker R., Kochhar S., Macdonald I.A., et al. Large-scale human metabolomics studies: a strategy for data (pre-) processing and validation. Anal Chem 78 2 (2006) 567-574
52. Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., et al. KEGG for linking genomes to life and the environment. Nucl Acids Res 36 (2008) D480-D484
53. Wishart D.S., Knox C., Guo A.C., Eisner R., Young N., Gautam B., et al. HMDB: a knowledgebase for the human metabolome. Nucl Acids Res 37 (2009) D603-D610
54. Aura A.M., Mattila I., Seppänen-Laakso T., Miettinen J., Oksman-Caldentey K.M., and Oresic M. Microbial metabolism of catechin stereoisomers by human faecal microbiota: comparison of targeted analysis and a non-targeted metabolomics method. Phytochem Lett 1 (2008) 18-22
55. Nikkilä J., Sysi-Aho M., Ermolov A., Seppänen-Laakso T., Simell O., Kaski S., et al. Gender dependent progression of systemic metabolic states in early childhood. Mol Syst Biol 4 (2008) e197
56. Lenz E.M., Bright J., Wilson I.D., Hughes A., Morrisson J., Lindberg H., et al. Metabonomics, dietary influences and cultural differences: a 1H NMR-based study of urine samples obtained from healthy British and Swedish subjects. J Pharm Biomed Anal 36 4 (2004) 841-849
57. Bäckhed F., Ding H., Wang T., Hooper L.V., Koh G.Y., Nagy A., et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 101 44 (2004) 15718-15723
58. Ley R.E., Bäckhed F., Turnbaugh P., Lozupone C.A., Knight R.D., and Gordon J.I. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 102 31 (2005) 11070-11075
59. Ley R.E., Turnbaugh P.J., Klein S., and Gordon J.I. Microbial ecology: human gut microbes associated with obesity. Nature 444 7122 (2006) 1022-1023
60. Wikoff W.R., Anfora A.T., Liu J., Schultz P.G., Lesley S.A., Peters E.C., et al. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci USA 106 10 (2009) 3698-3703
61. Pietiläinen K.H., Sysi-Aho M., Rissanen A., Seppänen-Laakso T., Yki-Järvinen H., Kaprio J., et al. Acquired obesity is associated with changes in the serum lipidomic profile independent of genetic effects - a monozygotic twin study. PLoS ONE 2 2 (2007) e218
62. Pietiläinen K.H., Naukkarinen J., Rissanen A., Saharinen J., Ellonen P., Keränen H., et al. Global transcript profiles of fat in monozygotic twins discordant for BMI: pathways behind acquired obesity. PLoS Med 5 3 (2008) e51
63. Kolak M., Westerbacka J., Velagapudi V.R., Wagsater D., Yetukuri L., Makkonen J., et al. Adipose tissue inflammation and increased ceramide content characterize subjects with high liver fat content independent of obesity. Diabetes 56 8 (2007) 1960-1968
64. Virtue S., and Vidal-Puig A. It's not how fat you are, it's what you do with it that counts. PLoS Biol 6 9 (2008) e237
65. Grundy S., and Denke M. Dietary influences on serum lipids and lipoproteins. J Lipid Res 31 7 (1990) 1149-1172
66. Kotronen A., Velagapudi V.R., Yetukuri L., Westerbacka J., Bergholm R., Ekroos K., et al. Saturated fatty acids containing triacylglycerols are better markers of insulin resistance than total serum triacylglycerol concentrations. Diabetologia 52 4 (2009) 684-690
67. Maeba R., Maeda T., Kinoshita M., Takao K., Takenaka H., Kusano J., et al. Plasmalogens in human serum positively correlate with high-density lipoprotein and decrease with aging. J Atheroscler Thromb 14 1 (2007) 12-18
68. Wopereis S., Rubingh C.M., van Erk M.J., Verheij E.R., van Vliet T., Cnubben N.H.P., et al. Metabolic profiling of the response to an oral glucose tolerance test detects subtle metabolic changes. PLoS ONE 4 2 (2009) e4525
69. Zhao X., Peter A., Fritsche J., Elcnerova M., Fritsche A., Haring H.-U., et al. Changes of the plasma metabolome during an oral glucose tolerance test: is there more than glucose to look at?. Am J Physiol Endocrinol Metab 296 2 (2009) E384-E393
70. Walsh M.C., Brennan L., Malthouse J.P.G., Roche H.M., and Gibney M.J. Effect of acute dietary standardization on the urinary, plasma, and salivary metabolomic profiles of healthy humans. Am J Clin Nutr 84 3 (2006) 531-539
71. Fardet A., Llorach R., Orsoni A., Martin J.-F., Pujos-Guillot E., Lapierre C., et al. Metabolomics provide new insight on the metabolism of dietary phytochemicals in rats. J Nutr 138 7 (2008) 1282-1287
72. Aura A.-M., Oikarinen S., Mutanen M., Heinonen S.-M., Adlercreutz H., Virtanen H., et al. Suitability of a batch in vitro fermentation model using human faecal microbiota for prediction of conversion of flaxseed lignans to enterolactone with reference to an in vivo rat model. Eur J Nutr 45 1 (2006) 45-51
73. Aura A.-M., Martin-Lopez P., O'Leary K.A., Williamson G., Oksman-Caldentey K.-M., Poutanen K., et al. In vitro metabolism of anthocyanins by human gut microflora. Eur J Nutr 44 3 (2005) 133-142
74. Heinonen S.-M., Wahala K., Liukkonen K.-H., Aura A.-M., Poutanen K., and Adlercreutz H. Studies of the in vitro intestinal metabolism of isoflavones aid in the identification of their urinary metabolites. J Agric Food Chem 52 9 (2004) 2640-2646
75. Kong H., Wang M., Venema K., Maathuis A., van der Heijden R., van der Greef J., et al. Bioconversion of red ginseng saponins in the gastro-intestinal tract in vitro model studied by high-performance liquid chromatography-high resolution Fourier transform ion cyclotron resonance mass spectrometry. J Chromatogr A 1216 11 (2009) 2195-2203
76. Lankinen M, Schwab U, Gopalacharyulu PV, Seppänen-Laakso T, Yetukuri L, Sysi-Aho M, et al. Dietary carbohydrate modification alters serum metabolic profiles in individuals with the metabolic syndrome. Nutr Metab Cardiovasc Dis 2009:In press, doi:10.1016/j.numecd.2009.04.009.
77. Lankinen M., Schwab U., Erkkilä A., Seppänen-Laakso T., Hannila M.-L., Mussalo H., et al. Fatty fish intake decreases lipids related to inflammation and insulin signaling - a lipidomics approach. PLoS ONE 4 4 (2009) e5258
78. Schwab U., Seppänen-Laakso T., Yetukuri L., Ågren J., Kolehmainen M., Laaksonen D.E., et al. Triacylglycerol fatty acid composition in diet-induced weight loss in subjects with abnormal glucose metabolism - the GENOBIN Study. PLoS ONE 3 7 (2008) e2630
79. Smilowitz J.T., Wiest M.M., Watkins S.M., Teegarden D., Zemel M.B., German J.B., et al. Lipid metabolism predicts changes in body composition during energy restriction in overweight humans. J Nutr 139 2 (2009) 222-229
80. Chorell E, Moritz T, Branth S, Antti H, Svensson M. A predictive metabolomics evaluation of nutrition-modulated metabolic stress responses in human blood serum during the early recovery phase of strenuous physical exercise. J Proteome Res 2009:doi:10.1021/pr900081q.