Metabonomic Applications in Toxicity Screening and Disease Diagnosis

Integrated Strategies for Drug Discovery Using Mass Spectrometry

Volumn , Issue , 2005, Pages 121-147

  Shockcor, John P ^a   Holmes, Elaine ^b  

^a WATERS CORPORATION   (United States)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

1H NMR; Biomarkers; Chemometrics; Functional Genomics; LC NMR; Metabonomics; Physiological variation; Toxicity

Indexed keywords

EID: 84888009630     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/0471721034.ch5     Document Type: Chapter

References (79)

1. Nicholson, J.K., Lindon, J.C., Holmes, E. " 'Metabonomics':Understanding the Metabolic Responses of Living Systems to Pathophysiological Stimuli via Multivariate Statistical Analysis of Biological NMR Spectroscopic Data," Xenobiotica 11, 1181-1189 (1999).
2. Sinclair, B. "Everything's Great When It Sits on a Chip: A bright future for DNA arrays," The Scientist 13, 11, 18-20 (1999).
3. Geisow, M.J. "Proteomics: One Small Step for a Digital Computer, One Giant Leap for Humankind," Nature Biotechnol. 16, 206 (1998).
4. Smith, L.L. "Key Challenges for Toxicologists in the 21st Century," Trends Pharm. Sci. 22(6), 281-285 (2001).
5. Beckwith-Hall, B.M., Nicholson, J.K., Nicholls, A., Foxall, P.J.D., Lindon, J.C., Connor, S.C., Abdi, M., Connelly, J., Holmes, E. "Nuclear Magnetic Resonance Spectroscopic and Principal Components Analysis Investigations into Biochemical Effects of Three Model Hepatotoxins," Chem. Res. Toxicol. 11, 260-272 (1998).
6. Anthony, M.L., Beddell, C.R., Lindon, J.C., Nicholson, J.K. "Studies on the Comparative Toxicity of S-(1,2-dichlorovinyl)-L-homocysteine (DCVHC), S-(1,2-dichlorovinyl)-L-cysteine (DCVC) and 1,1,2-trichloro-3,3,3-trifluoro-1-propene (TCTFP) in the Fischer 344 rat," Arch. Toxicol. 69(2), 99-110 (1994).
7. Holmes, E., Nicholls, A.W., Lindon, J.C., Ramos, S., Spraul, M., Neidig, P., Connor, S.C., Connelly, J., Damment, S.J.P., Haselden, J.N., Nicholson, J.K. "Development of a Model for Classification of Toxin-induced Lesions with 1H NMRSpectroscopy of Urine Combined with Pattern Recognition,"NMRBiomed. 11, 1-10 (1998).
8. Maxwell, R.J., Martinez-Perez, I., Cerdan, S., Cabanas, M.E., Arus, C., Moreno, A., Capdevila, A., Ferrer, E., Bartomeus, F., Aparicio, A., Conesa, G., Roda, J.M., Carcellar, F., Pascual, J.M., Howells, S.L., Mazucco, R., Griffiths, J.R. "Pattern Recognition Analysis of 1H NMR Spectra from Perchloric Acid Extracts of Human Brain Tumour Biopsies," Magn. Res. Med. 39, 869-877 (1998).
9. El-Deredy, W. "Pattern Recognition Approaches in Biomedical and Clinical Magnetic Resonance Spectroscopy: A Review," NMR Biomed. 10, 99-124 (1997).
10. Howells, S.L., Maxwell, R.J., Peet, A.C., Griffiths, J.R. "An Investigation of Tumour 1H Nuclear Magnetic Resonance Spectra by the Application of Chemometric Techniques," Mag. Res. Med. 28, 214-236 (1992).
11. Nicholson, J.K., Wilson, I.D. "High Resolution Proton NMR Spectroscopy of Biological Fluids," Prog. NMR Spectrosc. 21, 444-501 (1989).
12. Robertson, D.G., Reily, M.D., Sigler, R.E., Wells, D.F., Paterson, D.A., Braden, T.K. "Metabonomics: Evaluation of Nuclear Magnetic Resonance (NMR) and Pattern Recognition Technology for Rapid in vivo Screening of Liver and Kidney Toxicants," Toxicol. Sci. 57(2), 326-337 (2000).
13. Lindon, J.C., Holmes, E., Nicholson, J.K. "Pattern Recognition Methods and Applications in Biomedical Magnetic Resonance," Prog. NMR Spectros. 39(1), 1-40 (2001).
14. Lindon, J.C., Nicholson, J.K., Holmes, E., Everett, J.R. "Metabonomics: Metabolic Processes Studied byNMRSpectroscopy of Biofluids," ConceptsMag. Res. 12(5), 289-320 (2000).
15. Moreda-Pineiro, A., Marcos, A., Fisher, A., Hill, S.J. "Evaluation of the Effect of Data Pretreatment Procedures on Classical Pattern Recognition and Principal Components Analysis: A Case Study for the Geographical Classification of Tea," J. Environ. Monit. 3(4), 352-360 (2001).
16. Queralto, J.M., Torres, J., Guinot, M. "Neural Networks for the Biochemical Prediction of Bone Mass Loss." Clin. Chem. Lab. Med. 37(8), 831-838 (1999).
17. Halket, J.M., Przyborowska, A., Stein, S.E., Mallard,W.G., Down, S., Chalmers, R.A. "Deconvolution of Gas Chromatography/Mass Spectrometry of Urinary Organic Acids-Potential for Pattern Recognition and Automated Identification of Metabolic Disorders," Rapid Commun. Mass Spectrom. 13(4), 279-284 (1999).
18. Goodacre, R., Rooney, P.J., Kell, D.B. "Discrimination Between Methicillin-Resistant and Methicillin-Susceptible Staphylococcus Aureus Using Pyrolysis Mass Spectrometry and Artificial Neural Networks," J. Antimicrob. Chemother. 41(1), 27-34 (1998).
19. Kim, K.R., Kim, J.H., Cheong, E,; Jeong, C. "Gas Chromatographic Amino acid Profiling of Wine Samples for Pattern Recognition," J. Chromatogr. A 722(1-2), 303-309 (1996).
20. Freeman, R., Goodacre, R., Sisson, P.R., Magee, J.G., Ward, A.C., Lightfoot, N.F. "Rapid Identification of Species within the Mycobacterium Tuberculosis Complex by Artificial Neural Network Analysis of Pyrolysis Mass Spectra," J. Med. Microbiol. 40(3), 170-173 (1994).
21. Ramos L.S. "Characterisation of Mycobacteria species by HPLC and Pattern Recognition," J. Chromatogr. Sci. 32(6), 219-227 (1994).
22. Gartland, K.P.R., Bonner, F.W., Nicholson, J.K. "Investigations into the Biochemical Effects of Region-specific Nephrotoxins," Mol. Pharmacol. 35, 242-250 (1989).
23. Gavaghan, C.L., Holmes, E., Lenz, E., Wilson, I.D., Nicholson, J.K. "An NMRbased Metabonomic Approach to Investigate the Biochemical Consequences of Genetic Strain Differences: Application to the C57BL10J and Alpk:ApfCD Mouse," Febs. Lett. 484, 169-174 (2000).
24. Gavaghan, C.L., Nicholson, J.K., Connor, S.C., Wilson, I.D., Wright, B., Holmes, E. "HPLC-NMR Spectroscopic and Chemometric Studies on Metabolic Variation in Sprague Dawley Rats," Anal. Biochem. 291 (2), 245-252 (2001).
25. Phipps, A.N., Stewart, J., Wright, B., Wilson, I.D. "Effect of Diet on the Urinary Excretion of Hippuric Acid and Other Dietary-derived Aromatics in Rat," Xenobiotica, 28(5), 527-537 (1998).
26. Anthony, M.L., Sweatman, B.C., Beddell, C.R., Lindon, J.C., Nicholson, J.K. "Pattern Recognition Classification of the Site of Nephrotoxicity Based on Metabolic Data Derived from High Resolution Proton Nuclear Magnetic Resonance Spectra of Urine," Mol. Pharmacol. 46, 199-211 (1994).
27. Manley, B.F.J. Multivariate Statistical Methods: A Primer, Chapman & Hall, London (1986).
28. Beebe, K.R., Pell, R.J., Seahsholt, M.B. Chemometrics: A Practical Guide, Wiley, New York (1998).
29. Jurs, P.C. "Pattern Recognition Used to Investigate Multivariate Data in Analytical Chemistry," Science 232, 1219-1224 (1986).
30. Eriksson, L., Johansson, E., Kettanah-Wold, N., Wold, S. "Introduction to Multi and Megavariate Data Analysis Using Projection Methods (PCA and PLS) UMETRICS ACADEMY (1999).
31. Holmes, E., Nicholson, J.K., Tranter, G. "Metabonomic Characterization of Genetic Variations in Toxicological and Metabolic Responses Using Probabilistic Neural Networks," Chem. Res. Toxicol. 14(2), 182-191 (2001).
32. Gartland, K.P.R., Beddell, C.R., Lindon, J.C., Nicholson, J.K. "Application of Pattern-Recognition Methods to the Analysis and Classification of Toxicological Data Derived from Proton Nuclear-Magnetic-Resonance Spectroscopy of Urine." Mol. Pharmacol. 39(5), 629-642 (1991).
33. Kosir, I.J.,Kocjancic, M., Ogrinc, N., Kidric, J. "Use of SNIF-NMR and IRMS in Combination with Chemometric Methods for the Determination of Chaptalisation and Geographical Origin of Wines (the Example of Slovenian wines)," Anal. Chimica Acta 429(2), 195-206 (2001).
34. Zamora, R., Alba,V., Hidalgo, F.J. "Use of high-resolution C-13 nuclear magnetic resonance spectroscopy for the screening of virgin olive oils," J. Am. Oil Chem. Soc. 78(1), 89-94 (2001).
35. "Characterization of the Geographic Origin of Bordeaux Wines by a Combined Use of Isotopic and Trace Element Measurements," Am. J. Enology Viticulture 50(4), 409-417 (1999).
36. Belton, P.S., Colquhoun, I.J., Kemsley, E.K., Delgadillo, I., Roma, P., Dennis, M.J., Sharman, M., Holmes, E., Nicholson, J.K., Spraul, M. "Application of Chemometrics to the H-1 NMR Spectra of Apple Juices: Discrimination between Apple Varieties," Food Chem. 61(1-2), 207-213 (1998).
37. Vogels, J.T.W.E.,Terwel, L.,Tas, A.C., vandenBerg, F., Dukel, F.,VanderGreef, J. "Detection of Adulteration in Orange Juices by a New Screening Method Using Proton NMR Spectroscopy in Combination with Pattern Recognition Techniques," J. Agric. Food Chem. 44(1), 175-180 (1996).
38. Bundy, J.G., Osborn, D., Weeks, J.M., Lindon, J.C., Nicholson, J.K. "An NMRbased Metabonomic Approach to the Investigation of Coelomic Fluid Biochemistry in Earthworms under Toxic Stress," FEBS Letters 500(1-2), 31-35 (2001).
39. Warne, M.A., Lenz, E.M., Osborn, D., Weeks, J.M., Nicholson, J.K. "An NMRbased metabonomic investigation of the toxic effects of 3-trifluoromethyl-aniline on the earthworm Eisenia veneta," Biomarkers 5(1), 56-72 (2000).
40. Gibb, J.O.T., Holmes, E., Nicholson, J.K., Weeks, J.M. "Proton NMR Spectroscopic Studies on Tissue Extracts of Invertebrate Species with Pollution Indicator Potential," Comp. Biochem. Physiol. B-Biochem. Mol. Biol. 118(3), 587-598 (1997).
41. Griffin, J.L., Williams, H.J., Sang, E., Clarke, K., Rae, C., Nicholson, J.K. "Metabolic Profiling of Genetic Disorders: A Multitissue H-1 Nuclear Magnetic Resonance Spectroscopic and Pattern Recognition Study into Dystrophic Tissue," Anal. Biochem. 293(1), 16-21 (2001).
42. Holmes, E., Foxall, P.J.D., Spraul, M., Farrant, R.D., Nicholson, J.K., Lindon, J.C. "750 MHz H-1 NMR Spectroscopy Characterisation of the Complex Metabolic Pattern of Urine from Patients with Inborn Errors of Metabolism: 2-Hydroxyglutaric Aciduria and Maple Syrup Urine Disease," J. Pharm. Biomed. Anal. 15(11), 1647-1659 (1997).
43. Alanen, A., Komu, M., Penttinen, M., Leino, R. "Magnetic Resonance Imaging and ProtonMRSpectroscopy in Wilson's disease." Br. J. Radiol. 72(860), 749-56 (1999).
44. Burtscher, I.M., Holtas, S. "Proton Magnetic Resonance Spectroscopy in Brain Tumours: Clinical Applications," Neuroradiology 43(5), 345-352 (2001).
45. Roda, J.M., Pascual, J.M., Carceller, F., Gonzalez-Llanos, F., Perez-Higueras, A., Solivera, J., Barrios, L., Cerdan, S. "Nonhistological Diagnosis of Human Cerebral Tumors by H-1 Magnetic Resonance Spectroscopy and Amino Acid Analysis," Clin. Cancer Res. 6(10), 3983-3993 (2000).
46. Tate, A.R., Foxall, P.J.D., Holmes, E., Moka, D., Spraul, M., Nicholson, J.K., Lindon, J.C. "Distinction between Normal and Renal Cell Carcinoma Kidney Cortical Biopsy Samples Using Pattern Recognition of H-1 Magic Angle Spinning (MAS) NMR Spectra," Nmr Biomed. 13(2), 64-71 (2000).
47. Morales, F., Ballesteros, P., Cerdan, S. "Neural Networks in Automatic Diagnosis Malignant Brain Tumors," Eng. Appl. Bio-Inspired Artificial Neural Networks 607, 778-787 (1999).
48. Hagberg, G. "From Magnetic Resonance Spectroscopy to Classification of Tumors. A Review of Pattern Recognition Methods," NMR Biomed. 11(4-5), 148-156 (1998).
49. Connor, S.C., Hughes, M.G., Moore, G., Lister, C.A., Smith, S.A. Antidiabetic Efficacy of BRL49653 a Potent Orally Active Insulin Sensitising Agent, Assessed in the C57BL/KsJ db/db Diabetic Mouse by Non Invasive Proton NMR Studies in Urine," J. Pharm. Pharmacol. 49, 336-344 (1997).
50. Warne, M.A., Lenz, E.M., Osborn, D., Weeks, J.M., Nicholson, J.K. "Comparative Biochemistry and Short-term Starvation Effects on the Earthworms Eisenia veneta and Lumbricus terrestris Studied by H-1 NMR Spectroscopy and Pattern Recognition," Soil Biol. Biochem. 33(9), 1171-1180 (2001).
51. Holmes, E., Foxall, P.J.D., Nicholson, J.K., Neild, G.H., Brown, S.M., Beddell, C.R., Sweatman, B.C., Rahr, E., Lindon, J.C., Spraul, M., Neidig, P. "Automatic Data Reduction and Pattern-Recognition Methods for Analysis Of H-1 Nuclear-Magnetic-Resonance Spectra of Human Urine from Normal and Pathological States." Anal. Biochem. 220(2), 284-296 (1994).
52. Nicholson, J.K., Timbrell, J.A., Sadler, P.J. Proton NMR Spectra of Urine as Indicators of Renal Damage: Mercury Nephrotoxicity in Rats. Mol. Pharmacol. 27, 644-651 (1985).
53. Nicholson, J.K., O'Flynn, N., Sadler, P.J., Mcleod, P., Juul, S.M., Sonksen, P.H. "Proton-Nuclear-Magnetic-Resonance Studies of Serum, Plasma and Urine from Fasting Normal and Diabetic Subjects." Biochem. J. 217, 365-375 (1984).
54. Nicholson, J.K., Higham, D., Timbrell, J.A., Sadler, P.J. Quantitative 1H NMR Urinalysis Studies on the Biochemical Effects of Acute Cadmium Exposure in the Rat." Mol. Pharmacol. 36, 398-404 (1989).
55. Sanins, S.M., Timbrell, J.A., Elcombe, C.R., Nicholson, J.K. "Hepatotoxininduced Hypertaurinuria: A Proton NMR Study," Arch. Toxicol. 64, 407-411 (1990).
56. Holmes, E., Bonner, F.W., Sweatman, B.C., Lindon, J.C., Beddell, C.R., Rahr, E., Nicholson, J.K. "NMR Spectroscopy and Pattern Recognition Analysis of the Biochemical Processes Associated with the Progression and Recovery from Nephrotoxic Lesions in the Rat Induced by Mercury (II) Chloride and 2-Bromoethanamine," Mol. Pharmacol. 42, 922-930 (1992).
57. Tjiong, H.B., Debuch H. "Lysosomal bis (monoacylglycerol)phosphate of Rat Liver, Its Induction by Chloroquine and Its Structure. Hoppe-Seyler's Physil. Chem. 359, 71-79 (1978).
58. Espina, J.R., Herron,W.J., Shockcor, J.P., Car, B.D., Contel, N.R., Ciaccio, P.J., Lindon, J.C., Holmes. E., Nicholson, J.K. "Detection of in vivo Biomarkers of Phospholipidosis Using NMR-based Metabonomic Approaches," J. Mag. Res. Chem. 39, 559-565 (2001).
59. Wold, S., Antti, H., Lindgren, F., Öhman, J. "Orthogonal Signal Correction of Near-Infrared Spectra, "Chemomet. Intelligent Lab. Systems 44, 175-185 (1998).
60. Nicholls, A.W., Nicholson, J.K., Haselden, J.H.,Waterfield, C.J. "Metabonomic Investigations into HydrazineToxicity in the Rat." Biomarkers 5, 410-423 (2000).
61. Holmes, E., Foxall, P.J.D., Nicholson, J.K., Neild, G.H., Brown, S.M., Beddell, C., Sweatman, B.C., Rahr, E., Lindon, J.C,; Spraul, M., Neidig, P. "Automatic Data Reduction and Pattern Recognition Methods for Analysis of 1H Nuclear Magnetic Resonance Spectra of Human Urine form Normal and Pathological States," Anal. Biochem. 220, 284-296 (1994).
62. Bollard, M.E., Holmes, E., Lindon, J.C., Mitchell, S.C., Branstetter, D., Zhang, W., Nicholson, J.K. "Investigations into Biochemical Changes Due to Diurnal Variation and Estrus Cycle in Female Rats Using High Resolution 1H NMR Spectroscopy of Urine and Pattern Recognition," Anal. Biochem. 295, 194-202 (2001).
63. Nicholson, J.K., Wilson I.D. "High Resolution Proton NMR Spectroscopy of Biological Fluids," Prog. NMR Spectrosc. 21, 444-501 (1989).
64. Holmes, E., Bonner, F.W., Nicholson, J.K. 1H NMR Spectroscopic and Histopathological Studies on Propyleneimine-induced Renal Papillary Necrosis in the Fischer 344 rat and the Multimammate Desert Mouse (Mastomys natalensis). Compar. Biochem. Pharmacol. (C) 116(2), 125-134 (1997).
65. Holmes, E., Bonner, F.W., Nicholson, J.K. "Comparative Studies on the Nephrotoxicity of 2-bromoethanamine in the Fischer 344 and Multimammate Desert Rats (Mastomys natalensis)" Arch. Toxicol. 70, 89-95 (1995).
66. Nicholls,A.W., Holmes, E., Lindon, J.C., Shockcor, J.P., Farrant, R.D., Haselden, J.N., Damment, S.J.P.,Waterfield, C.J., Nicholson, J.K. "Metabonomic Investigations into Hydrazine Toxicity in the Rat," Chemical Research in Tox. 14, 975-987.
67. Andrew, E.R., Eades, R.G. "Removal of Dipolar Broadening of NMR Spectra of Solids by Specimen Rotation," Nature 183, 1802 (1959).
68. Moka, D., Vorreuther, R., Schicha, H., Spraul, M., Humpfer, E., Lipinski, M., Foxall, P.J.D., Nicholson, J.K., Lindon, J.C. "Magic Angle Spinning Proton Nuclear Magnetic Resonance Spectroscopic Analysis of Intact Kidney Tissue Samples." Anal. Comm. 34, 107-109 (1997).
69. Moka, D., Vorreuther, R., Schicha, H., Spraul, M., Humpfer, E., Lipinski, M., Foxall, P.J.D., Nicholson, J.K., Lindon, J.C. "Biochemical Classification of Kidney Carcinoma Biopsy Samples Using Magic-Angle-Spinning 1H Nuclear Magnetic Resonance Spectroscopy," J. Pharm. Biomed. Anal. May; 17(1), 125-32 (1998).
70. Millis, K., Maas, E., Cory, D.G., Singer, S. "Gradient High Resolution Magic Angle Spinning Nuclear Magnetic Resonance Spectroscopy of Human Adipocyte Tissue," Mag. Res. Med. 38, 399-403 (1997).
71. Humpfer, E., Spraul, M., Nicholls, A.W., Nicholson, J.K., Lindon, J.C. "Direct Observation of Resolved Intracellular and Extracellular Water Signals in Intact Human Red Blood Cells Using 1H MAS NMR Spectroscopy," Mag. Res. Med. 38, 334-336 (1997).
72. Tomlins, A., Foxall, P.J.D., Lindon, J.C., Lynch, M.J., Spraul, M., Everett, J., Nicholson, J.K. "High Resolution Magic Angle Spinning 1H Nuclear Magnetic Resonance Analysis of Intact Prostatic Hyperplastic and Tumour Tissues. Anal. Comm. 35, 113-115 (1998).
73. Cheng, L.L., Ma, M.J., Becerra, L., Hale, T., Tracey, I., Lackner, A., Gonzalez, R.G. "Quantitative Neuropathology by High Resolution Magic Angle Spinning Proton Magnetic Resonance Spectroscopy," Proc. Natl. Acad. Sci. USA 94, 6408-6413 (1997).
74. Cheng, L.L., Lean, C.L., Bogdanova, A., Wright, Jr., S.C., Ackerman, J.L., Brady, T.J., Garrido, L. "Enhanced Resolution of Proton NMR Spectra of Malignant Lymph Nodes Using Magic Angle Spinning." Mag. Res. Med. 36, 653-658 (1996).
75. Garrod, S., Humpher, E., Connor, S.C., Connelly, J.C., Spraul, M., Nicholson, J.K., Holmes, E. "High Resolution 1H NMR and Magic Angle Spinning NMR Spectroscopic Investigation of the Biochemical Effects of 2-Bromoethanamine in Intact Renal and Hepatic Tissue," Mag. Res. Med. 45(5), 781-790 (2001).
76. Foxall, P.J., Singer, J.M., Hartley, J.M., Neild, G.H., Lapsley, M., Nicholson, J.K. "Urinary Proton Magnetic Resonance Studies of Early Ifosfamide-induced Nephrotoxicity and Encephalopathy," Clin. Cancer Res. 3(9), 1507-1518 (1997).
77. Halligan, S., Byard, S.J., Spencer, A.J., Gray, T.J., Harpur, E.S., Bonner, F.W. "A study of the Nephrotoxicity of Three Cephalosporins in Rabbits Using 1H NMR Spectroscopy," Toxicol. Lett. 81(1), 15-21 (1995).
78. Harrison, M.P., Jones, D.V., Pickford, R.J.,Wilson, I.D. "Beta-Hydroxybutyrate: AUrinary Marker of Imipenem Induced Nephrotoxicity in the Cynomolgus Monkey Detected by High Field NMR Spectroscopy," Biochem. Pharmacol. 41(12), 2045-2049 (1991).
79. Bairaktari, E., Katopodis, K., Siamopoulos, K.C., Tsolas, O. "Paraquat-Induced Renal Injury Studied by 1H NMR Spectroscopy of Urine," Clin. Chem. 44(6), 1256-1261 (1998).