Technology Insight: Metabonomics in gastroenterology - Basic principles and potential clinical applications

Nature Clinical Practice Gastroenterology and Hepatology

Volumn 5, Issue 6, 2008, Pages 332-343

  Bjerrum, Jacob T ^a   Nielsen, Ole H ^a   Wang, Yulan L ^b   Olsen, Jørgen ^c  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b Wuhan National Laboratory for Optoelectronics   (China)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; HEPATOCYTE NUCLEAR FACTOR 4; HYPOXIA INDUCIBLE FACTOR 1BETA; MESALAZINE; PREDNISOLONE;

BIOTECHNOLOGY; CHEMOMETRIC ANALYSIS; CLINICAL RESEARCH; COLORECTAL CANCER; DIAGNOSTIC ACCURACY; ELECTROMAGNETIC FIELD; ENTERITIS; GASTROENTEROLOGY; GASTROINTESTINAL DISEASE; GENE EXPRESSION PROFILING; GENE OVEREXPRESSION; GENOMICS; HUMAN; LIVER TOXICITY; MALIGNANT NEOPLASTIC DISEASE; METABOLIC DISORDER; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MULTIVARIATE ANALYSIS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROGNOSIS; PROTEOMICS; PROTON NUCLEAR MAGNETIC RESONANCE; REVIEW; TRANSCRIPTOMICS;

GASTROENTEROLOGY; GASTROINTESTINAL DISEASES; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; METABOLISM;

EID: 44949190481     PISSN: 17434378     EISSN: 17434386     Source Type: Journal    
DOI: 10.1038/ncpgasthep1125     Document Type: Review

References (101)

1. Nicholson JK et al. (1999) 'Metabonomics': Understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29: 1181-1189
2. Mitchell S and Carmichael PL (2005) Metabonomics and the endocrine system. Mol Cell Endocrinol 244: 10-14
3. Raamsdonk LM et al. (2001) A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol 19: 45-50
4. Schmidt C (2004) Metabolomics takes its place as latest up-and-coming "omic" science. J Natl Cancer Inst 96: 732-734
5. 1H magnetic resonance spectroscopy in inflammatory bowel diseases: Distinguishing ulcerative colitis from Crohn's disease. Am J Gastroenterol 96: 442-448
6. Marchesi JR et al. (2007) Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 6: 546-551
7. 1H-NMR-based metabonomics. Nat Med 8: 1439-1444
8. Kirschenlohr HL et al. (2006) Proton NMR analysis of plasma is a weak predictor of coronary artery disease. Nat Med 12: 705-710
9. Griffin JL et al. (2002) Metabolic profiles of dystrophin and utrophin expression in mouse models of Duchenne muscular dystrophy. FEBS Lett 530: 109-116
10. Prabakaran S et al. (2004) Mitochondrial dysfunction in schizophrenia: Evidence for compromised brain metabolism and oxidative stress. Mol Psychiatry 9: 684-697
11. Griffin JL and Bollard ME (2004) Metabonomics: Its potential as a tool in toxicology for safety assessment and data integration. Curr Drug Metab 5: 389-398
12. Nicholson JK et al. (2002) Metabonomics: A platform for studying drug toxicity and gone function. Nat Rev Drug Discov 1: 153-161
13. Coen M et al. (2004) Integrated application of transcriptomics and metabonomics yields new insight into the toxicity due to paracetamol in the mouse. J Pharm Biomed Anal 35: 93-105
14. Craig A et al. (2006) Systems toxicology: Integrated genomic, proteomic and metabonomic analysis of methapyrilene induced hepatotoxicity in the rat. J Proteome Res 5: 1586-1601
15. Griffin JL et al. (2004) An integrated reverse functional genomic and metabolic approach to understanding orotic acid-induced fatty liver. Physiol Genomics 17: 140-149
16. Schnackenberg LK et al. (2006) An integrated study of acute effects of valproic acid in the liver using metabonomics, proteomics, and transcriptomics platforms. OMICS 10: 1-14
17. Tang W (2007) Drug metabolite profiling and elucidation of drug-induced hepatotoxicity. Expert Opin Drug Metab Toxicol 3: 407-420
18. Rezzi S et al. (2007) Nutritional metabonomics: Applications and perspectives. J Proteome Res 6: 513-525
19. Kemsley EK et al. (2007) Multivariate techniques and their application in nutrition: A metabolomics case study. Br J Nutr 98: 1-14
20. Fiehn O et al. (2000) Metabolite profiling for plant functional genomics. Nat Biotechnol 18: 1157-1161
21. Allen J et al. (2003) High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 21: 692-696
22. Macomber RS (1998) A Complete Introduction to Modern NMR Spectroscopy New York: John Wiley & Sons Inc.
23. Lindon JC et al. (2003) So what's the deal with metabonomics? Anal Chem 75: 384A-391A
24. Nicholson JK and Wilson ID (2003) Opinion: Understanding 'global' systems biology: Metabonomics and the continuum of metabolism. Nat Rev Drug Discov 2: 668-676
25. Reo NV (2002) NMR-based metabolomics. Drug Chem Toxicol 25: 375-382
26. 1H NMR spectroscopic studies on intact rat renal cortex and medulla. Magn Reson Med 41: 1108-1118
27. 1H nuclear magnetic resonance spectroscopy. J Pharm Biomed Anal 17: 125-132
28. Cheng LL et al. (1997) Quantitative neuropathology by high resolution magic angle spinning proton magnetic resonance spectroscopy. Proc Natl Acad Sci USA 94: 6408-6413
29. Millis KK et al. (1997) Gradient, high-resolution, magic-angle spinning nuclear magnetic resonance spectroscopy of human adipocyte tissue. Magn Reson Med 38: 399-403
30. 1H NMR spectroscopic studies on dynamic biochemical processes in incubated human seminal fluid samples. Biochim Biophys Acta 1379: 367-380
31. Lenz EM and Wilson ID (2007) Analytical strategies in metabonomics. J Proteome Res 6: 443-458
32. 1H NMR-based metabonomic urinalysis. Chem Res Toxicol 15: 1380-1386
33. Chen JH et al. (2001) Biochemical analysis using high-resolution magic angle spinning NMR spectroscopy distinguishes lipoma-like well-differentiated liposarcoma from normal fat. J Am Chem Soc 123: 9200-9201
34. 1H NMR spectroscopy. Biochim Biophys Acta 1619: 151-158
35. 1H nuclear magnetic resonance spectroscopy of liver tissues. Anal Biochem 323: 26-32
36. 1H diffusion-edited total-correlation NMR spectroscopy. Anal Chem 69: 1504-1509
37. Cheng LL et al. (1998) Evaluating human breast ductal carcinomas with high-resolution magic-angle spinning proton magnetic resonance spectroscopy. J Magn Reson 135: 194-202
38. 13C NMR spectroscopy of urine for metabonomic studies. Anal Chem 74: 4588-4593
39. Deming SN (1986) Chemometrics: An overview. Clin Chem 32: 1702-1706
40. Eriksson L et al. (2004) Using chemometrics for navigating in the large data sets of genomics proteomics, and metabonomics (gpm). Anal Bioanal Chem 380: 419-429
41. Eriksson L et al. (2006) Megavariate analysis of environmental QSAR data. Part I-a basic framework founded on principal component analysis (PCA), partial least squares (PLS), and statistical molecular design (SMD). Mol Divers 110: 169-186
42. Eriksson L et al. (2006) Megavariate analysis of environmental QSAR data. Part II - investigating very complex problem formulations using hierarchical, non-linear and batch-wise extensions of PCA and PLS. Mol Divers 10: 187-205
43. Lindon JC et al. (2001) Pattern recognition methods and applications in biomedical magnetic resonance. Prog NMR Spect 39: 1-40
44. Trygg J et al. (2007) Chemometrics in metabonomics. J Proteome Res 6: 469-479
45. Lavine B and Workman JJ Jr (2004) Chemometrics. Anal Chem 76 3365-3371
46. 31P heteronuclear statistical total correlation spectroscopy of intact human gut biopsies. Anal Chem 80: 1058-1066
47. Schlens J (online 10 December 2005) A tutorial on principal component analysis. [http://www.snl.salk.edu/~shlens/pub/notes/pca.pdf] (accessed 4 March 2008)
48. 1H NMR data sets. Anal Chem 77 1282-1289
49. Trygg J and Wold S (2003) O2-PLS, a two-block (X-Y) latent variable regression (LVR) method with an integral OSC filter. J Chemomet 17: 53-64
50. Trygg J (2002) O2-PLS for qualitative and quantitative analysis in multivadate calibration. J Chemomet 16: 283-293
51. Holmes E et al. (2007) Detection of urinary drug metabolite (xenometabolome) signatures in molecular epidemiology studies via statistical total correlation (NMR) spectroscopy. Anal Chem 79 2629-2640
52. 31P statistical total correlation NMR spectroscopy of intact liver for metabolic biomarker assignment: Application to galactosamine-induced hepatotoxicity. Anal Chem 79: 8956-8966
53. Geboes K and De HG (2003) Indeterminate colitis. Inflamm Bowel Dis 9: 324-331
54. Hildebrand H et al. (1991) Chronic inflammatory bowel disease in children and adolescents in Sweden. J Pediatir Gastroenterol Nutr 13: 293-297
55. Lennard-Jones JE and Shivananda S (1997) Clinical uniformity of inflammatory bowel disease at presentation and during the first year of disease in the north and south of Europe. Eur J Gastroenterol Hepatol 9: 353-359
56. Meucci G et al. (1999) Frequency and clinical evolution of indeterminate colitis: A retrospective multi-centre study in northern Italy. Eur J Gastroenterol Hepatol 11: 909-913
57. Nicholls RJ and Wells AD (1992) Indeterminate colitis. Baillieres Clin Gastroenterol 6: 105-112
58. Riegler G et al. (1997) Clinical evolution in an outpatient series with indeterminate colitis. Dis Colon Rectum 40: 437-439
59. Csillag C et al. (2007) Clinical phenotype and gene expression profile in Crohn's disease. Am J Physiol Gastrointest Liver Physiol 292: G298-G304
60. Distler P and Holt PR (1997) Are right- and left-sided colon neoplasms distinct tumors? Dig Dis 15: 302-311
61. Glebov OK et al. (2003) Distinguishing right from left colon by the pattern of gene expression. Cancer Epidemiol Biomarkers Prev 12: 755-762
62. 1H NMR spectroscopy and multivariate data analysis. J Proteome Res 4 1324-1329
63. Bates MD et al. (2002) Novel genes and functional relationships in the adult mouse gastrointestinal tract identified by microarray analysis. Gastroenterology 122: 1467-1482
64. 1H NMR spectroscopy. J Proteome Res 6: 3944-3951
65. Saric J et al. (2008) Species variation in the fecal metabolome gives insight into differential gastrointestinal function. J Proteome Res 7: 352-360
66. Nielbn OH et al. (2000) Clinical reviews: Established and emerging biological activity markers of inflammatory bowel disease. Am J Gastroenterol 95: 359-367
67. Wang Y et al. (2004) Metabonomic investigations in mice infected with Schistosoma mansoni: An approach for biomarker identification. Proc Natl Acad Sci USA 101: 12676-12681
68. Gerstle RJ et al. (2000) The role of neural networks in improving the accuracy of MR spectroscopy for the diagnosis of head and neck squamous cell carcinoma. AJNR Am J Neuroradiol 21: 1133-1138
69. Griffin JL and Shockcor JP (2004) Metabolic profiles of cancer cells. Nat Rev Cancer 4: 551-561
70. Hagberg G (1998) From magnetic resonance spectroscopy to classification of tumors: A review of pattern recognition methods. NMR Biomed 11: 148-156
71. 1H nuclear magnetic resonance spectra by the application of chemometric techniques. Magn Reson Med 28: 214-236
72. Preul MC et al. (1998) Using pattern analysis of in vivo proton MRSI data to improve the diagnosis and surgical management of patients with brain tumors. NMR Biomed 11: 192-200
73. 1H magnetic resonance spectroscopic metabolite phenotypes. Neuroreport 7 1597-1600
74. Nelson SJ and Cha S (2003) Imaging glioblastoma multiforme. Cancer J 9: 134-145
75. Preul MC et al. (1996) Accurate, noninvasive diagnosis of human brain tumors by using proton magnetic resonance spectroscopy. Nat Med 2: 323-325
76. Guillevin R et al. (2007) Proton magnetic resonance spectroscopy predicts proliferative activity in diffuse low-grade gliomas. J Neurooncol [doi:10.1007/s11060-007-9508-y]
77. 31P MR spectroscopy from pretreatment relative phosphomonoester levels. Acad Radiol 9: 688-694
78. 1H MR spectroscopy. Magn Reson Med 50: 1134-1143
79. 1H MR spectroscopy - a pilot study at 4 T. Radiology 233: 424-431
80. Claudino WM et al. (2007) Metabolomics: Available results, current research projects in breast cancer, and future applications. J Clin Oncol 25: 2840-2846
81. 31P MR spectral alterations in human hepatic tumours. NMR Biomed 11 354-359
82. Li CW et al. (2005) Quantification of choline compounds in human hepatic tumors by proton MR spectroscopy at 3 T. Magn Reson Med 53: 770-776
83. 1H MR spectroscopy and MR imaging: Clinicopathologic case-controlled study. Radiology 221: 380-390
84. 1H MR spectroscopic imaging of human prostate cancer. J Magn Reson Imaging 20: 279-287
85. Arias-Mendoza F et al. (2004) Predicting treatment response in non-Hodgkin's lymphoma from the pretreatment tumor content of phosphoethanolamine plus phosphocholine. Acad Radiol 11: 368-376
86. Griffiths JR et al. (2002) Metabolic changes detected by in vivo magnetic resonance studies of HEPA-1 wild-type tumors and tumors deficient in hypoxia-inducible factor-1 β (HIF-1β): Evidence of an anabolic role for the HIF-1 pathway. Cancer Res 62: 688-695
87. Griffiths JR and Stubbs M (2003) Opportunities for studying cancer by metabolomics: Preliminary observations on tumors deficient in hypoxia-inducible factor 1. Adv Enzyme Regul 43: 67-76
88. Zhong H et al. (1999) Overexpression of hypoxia-inducible factor 1α in common human cancers and their metastases. Cancer Res 59 5830-5835
89. Clish CB et al. (2004) Integrative biological analysis of the APOE*3-leiden transgenic mouse. OMICS 8: 3-13
90. Mayr M et al. (2004) Proteomic and metabolomic analysis of vascular smooth muscle cells: Role of PKCδ. Circ Res 94: e87-e96
91. Verhoeckx KC et al. (2004) Characterization of anti-inflammatory compounds using transcriptomics, proteomics, and metabolomics in combination with multivariate data analysis. Int Immunopharmacol 4: 1499-1514
92. Wong MS et al. (2004) Metabolic and transcriptional patterns accompanying glutamine depletion and repletion in mouse hepatoma cells: a model for physiological regulatory networks. Physiol Genomics 16: 247-255
93. Griffin JL et al. (2007) The influence of pharmacogenetics on fatty liver disease in the Wistar and Kyoto rats: A combined transcriptomic and metabonomic study. J Proteome Res 6: 54-61
94. Heijne WH et al. (2003) Toxicogenomics of bromobenzene hepatotoxicity: A combined transcriptomics and proteomics approach. Biochem Pharmacol 65: 857-875
95. Heijne WH et al. (2005) Systems toxicology: Applications of toxicogenomics, transcriptomics, proteomics and metabolomics in toxicology. Expert Rev Proteomics 2: 767-780
96. Heijne WH et al. (2005) Profiles of metabolites and gene expression in rats with chemically induced hepatic necrosis. Toxicol Pathol 33: 425-433
97. Kleno TG et al. (2004) Combination of 'omics' data to investigate the mechanism(s) of hydrazine-induced hepatotoxicity in rats and to identify potential biomarkers. Biomarkers 9: 116-138
98. Ruepp SU et al. (2002) Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Toxicol Sci 65: 135-150
99. Stegmann A et al. (2006) Metabolome, transcriptome, and bioinformatic cis-element analyses point to HNF-4 as a central regulator of gene expression during enterocyte differentiation. Physiol Genomics 27:141-155
100. Dumas ME et al. (2007) Direct quantitative trait locus mapping of mammalian metabolic phenotypes in diabetic and normoglycemic rat models. Nat Genet 39: 666-672
101. Gupta RB et al. (2007) Histologic inflammation is a risk factor for progression to colorectal neoplasia in ulcerative colitis: A cohort study. Gastroenterology 133: 1099-1105