Metabonomics: NMR spectroscopy and pattern recognition analysis of body fluids and tissues for characterisation of xenobiotic toxicity and disease diagnosis

Current Opinion in Chemical Biology

Volumn 7, Issue 5, 2003, Pages 648-654

  Griffin, Julian L ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

XENOBIOTIC AGENT;

APOPTOSIS; BODY FLUID; BRAIN; CAENORHABDITIS ELEGANS; CARBON NUCLEAR MAGNETIC RESONANCE; COMET ASSAY; DISEASE SEVERITY; DNA MODIFICATION; GENE THERAPY; GENOMICS; GLIOMA; HUMAN; ISCHEMIC HEART DISEASE; LIVER TOXICITY; METABOLIC DISORDER; METABOLITE; MUSCULAR DYSTROPHY; NONHUMAN; PATHOLOGY; PATTERN RECOGNITION; PHENOTYPE; PRINCIPAL COMPONENT ANALYSIS; PROTON NUCLEAR MAGNETIC RESONANCE; REVIEW; STATISTICAL ANALYSIS; TOXICITY; TOXICOLOGY; YEAST;

CAENORHABDITIS; CAENORHABDITIS ELEGANS;

EID: 0142138236     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2003.08.008     Document Type: Review

References (33)

1. Raamsdonk L.M., Teusink B., Broadhurst D., Zhang N., Hayes A., Walsh M.C., Berden J.A., Brindle K.M., Kell D.B., Rowland J.J.et al. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat Biotechnol. 19:2001;45-50.
2. Fiehn O. Metabolomics - the link between genotypes and phenotypes. Plant Mol Biol. 48:2002;155-171 This review provides many of the details for the use of MS for metabonomics, especially in plants. Metabolic profiling in plants is a particular challenge given the huge number of potential metabolites.
3. Nicholson J.K., Connelly J., Lindon J.C., Holmes E. Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov. 1:2002;153-161 A review demonstrating the ability of NMR-based metabonomics as a tool in the drug discovery process.
4. Fiehn O. Combining genomics, metabolome analysis and biochemical modeling to understand metabolic networks. Comp Funct Genomics. 2:2001;155-168.
5. Stitt M., Fernie A.R. From measurements of metabolites to metabolomics: an 'on the fly' perspective illustrated by recent studies of carbon-nitrogen interactions. Curr Opin Biotechnol. 14:2003;136-144.
6. Plumb R.S., Stumpf C.L., Gorenstein M.V., Castro-Perez J.M., Dear G.J., Anthony M., Sweatman A., Connor S.C., Haselden J.C. Metabonomics: the use of electrospray mass spectrometry coupled to reversed-phase liquid chromatography shows potential for the screening of rat urine in drug development. Rapid Commun Mass Spectrum. 16:2002;1991-1996.
7. Allen J., Davey H.M., Broadhurst D., Heald J.K., Rowland J.J., Oliver S.G., Kell D.B. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol. 21:2003;692-696.
8. 13C NMR spectroscopy of urine for metabonomic studies. Anal Chem. 74:2002;4588-4593.
9. Griffin J.L., Nicholls A.W., Keun H.C., Mortishire-Smith R.J., Nicholson J.K., Kuehn T. Metabolic profiling of rodent biological fluids via 1H NMR spectroscopy using a 1mm Microlitre probe. Analyst. 127:2002;582-584.
10. Lindon J.C., Nicholson J.K., Holmes E., Antii H., Bollard M.E., Keun H., Beckonert O., Ebbels T.M., Reily M.D., Robertson D.et al. The role of metabonomics in toxicology and its evaluation by the COMET project. Toxicol Appl Pharmacol. 187:2003;137-146 This paper details how high-throughput NMR spectroscopy can be used in drug safety assessment.
11. Lindon J.C., Holmes E., Nicholson J.K. Pattern recognition methods and applications in biomedical magnetic resonance. Prog Nucl Magnetic Res. 39:2001;1-40.
12. Valafar F. Pattern recognition techniques in microarray data analysis. Ann N Y Acad Sci. 980:2002;41-64 Although concerning microarray data, this is an excellent review of pattern recognition techniques that are equally applicable to any large multivariate datasets. Perhaps what is most refreshing about this review is that the author provides unbiased criticism on each technique.
13. Eriksson L, Johansson E, Kettaneh-Wold N, Wold S: Introduction to Multi- and Megavariate Data Analysis Using Projection Methods (PCA & PLS). Umea, Sweden: Umetrics; 1999.
14. Kell D.B. Metabolomics and machine learning: explanatory analysis of complex metabolome data using genetic programming to produce simple, robust rules. Mol Biol Rep. 29:2002;237-241.
15. Wold S., Antti H., Lingren F., Ohman J. Orthogonal signal correction of near-infrared spectra. Chemometrics and Intelligent Lab Systems. 44:1998;175-185.
16. Brindle JT, Antii H, Holmes E, Tranter G, Nicholson JK, Bethell HWL, Clarke S, Schofield PM, McKilligin E, Mosedale DE, Grainger DJ: Rapid and non-invasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics. 2002, 8:1439-44.
17. Griffin J.L., Williams H.J., Sang E., Nicholson J.K. Abnormal lipid profile of dystrophic cardiac tissue as demonstrated by one- and two-dimensional magic-angle spinning (1)H NMR spectroscopy. Magn Reson Med. 46:2001;249-255.
18. Styles P., Soffe N.F., Scott C.A., Cragg D.A., Row F., White D.J., White P.C.J. A High resolution NMR probe in which the coil and preamplifier are cooled with liquid helium. J Magn Reson. 60:1984;397-404.
19. Andrew E.R., Bradbury A., Eades R.G. Removal of dipolar broadening of NMR spectra of solids by specimen rotation. Nature. 183:1959;1802.
20. Cheng L.L., Lean C.L., Bogdanova A., Wright S.C., Ackerman J.L., Brady T.J., Garrido L. Enhanced resolution of proton NMR spectra of malignant lymph nodes using magic angle spinning. Magn Reson Med. 36:1996;653-658.
21. Wind R.A., Zhi Hu J., Rommereim D.N. High-resolution (1)H NMR spectroscopy in organs and tissues using slow magic angle spinning. Magn Reson Med. 46:2001;213-218.
22. 1H nuclear magnetic resonance spectroscopy of intact cells. Magn Reson Med. 39:1998;337-344.
23. Chen J.-H., Enloe B.M., Fletcher C.D., Cory D.G., Singer S. Biochemical analysis using high-resolution magic angle spinning NMR spectroscopy distinguishes lipoma-like well-differentiated liposarcoma from normal fat. J Am Chem Soc. 123:2001;9200-9201.
24. 1H NMR spectroscopy. BBA General Subjects. 1619:2003;151-158.
25. Griffin J.L., Sang E., Evens T., Davies K., Clarke K. Metabolic profiles of dystrophin and utrophin expression in mouse models of Duchenne muscular dystrophy. FEBS Lett. 530:2002;109-116.
26. Rabenstein D.L., Millis K.K., Straus E.J. Proton NMR spectroscopy of human blood plasma and red blood cells. Anal Chem. 1560:1988;1380A-1391A.
27. Wu D., Chen A., Johnson C.S. An improved diffusion-ordered spectroscopy experiment incorporating bipolar-gradient pulses. J Magn Reson. 115:1995;260-264.
28. Thrippleton M.J., Loening N.M., Keeler J. A fast method for the measurement of diffusion coefficients: one-dimensional DOSY. Mag Res Chem. 41:2003;441-447.
29. Brindle K.M. Metabolomics: Pandora's Box or Aladdin's Cave? The Biochemist. 25:2003;15-17 A simple and brief introduction to metabonomics, aimed at the non-expert. This commentary has a nice discussion of why metabonomics might work.
30. Ravasz E., Somera A.L., Mongru D.A., Oltvai Z.N., Barabasi A.-L. Hierarchial organization of modularity in metabolic networks. Science. 297:2002;1551-1555 This manuscript may represent the cornerstone as to why metabonomics/metabolomics is potentially such a ubiquitous functional genomic tool. It represents a detailed examination of metabolic networks and how they interact.
31. Fraser A.G., Kamath R.S., Zipperlen P., Martinez-Campos M., Sohrmann M., Ahringer J. Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature. 408:2000;325-330.
32. Pfeuffer J., Tkac I., Provencher S.W., Gruetter R. Towards an in vivo neurochemical profile: quantification of 18 metabolites in short-echo-time 1H NMR spectra of the rat brain. J Mag Reson. 141:1999;104-120.
33. Griffin JL, Valonen PK, Grohn OHJ, Kettunen MI, Yla-Herttuala S, Pitkanen A, Nicholson JK, Kauppinen RA: Assignment Of 1H NMR visible polyunsaturated fatty acids in BT4C gliomas undergoing ganciclovir-thymidine kinase gene-therapy induced programmed cell death. Cancer Res 2003, in press.