Metabolomics in critical care medicine: A new approach to biomarker discovery

Clinical and Investigative Medicine

Volumn 37, Issue 6, 2014, Pages E363-E376

  Banoei, Mohammad M ^a   Donnelly, Sarah J ^a   Mickiewicz, Beata ^b   Weljie, Aalim ^b,c   Vogel, Hans J ^b   Winston, Brent W ^a,b  

^a UNIVERSITY OF CALGARY   (Canada)

^b UNIVERSITY OF CALGARY   (Canada)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER;

COMPARATIVE STUDY; DEVICES; HUMAN; INTENSIVE CARE; MEDLINE; METABOLISM; METABOLOMICS; PROCEDURES;

BIOLOGICAL MARKERS; CRITICAL CARE; HUMANS; METABOLOMICS; PUBMED;

EID: 84935459396     PISSN: 0147958X     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (76)

1. Collino, S., F.P. Martin, and S. Rezzi, Clinical metabolomics paves the way towards future healthcare strategies. Br J Clin Pharmacol, 2013. 75(3): p. 619-29.
2. Nicholson, J.K., J.C. Lindon, and E. Holmes, 'Metabonomics':understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica, 1999. 29(11):p. 1181-9.
3. Fiehn, O., Metabolomics--the link between genotypes and phenotypes. Plant Mol Biol, 2002. 48(1-2): p. 155-71.
4. Dunn, W.B., et al., Systems level studies of mammalian metabolomes:the roles of mass spectrometry and nuclear magnetic resonance spectroscopy. Chem Soc Rev, 2011. 40(1): pp. 387-426.
5. Nicholson, J.K. and J.C. Lindon, Systems biology: Metabonomics. Nature, 2008. 455(7216): p. 1054-6.
6. Leon, Z., et al., Mammalian cell metabolomics: experimental design and sample preparation. Electrophoresis, 2013. 34(19): pp. 2762-75.
7. Kaddurah-Daouk, R., B.S. Kristal, and R.M. Weinshilboum, Metabolomics: a global biochemical approach to drug response and disease. Annu Rev Pharmacol Toxicol, 2008. 48: p. 653-83.
8. Lacy, P., Metabolomics of sepsis-induced acute lung injury: a new approach for biomarkers. Am J Physiol Lung Cell Mol Physiol, 2011. 300(1): p. L1-3.
9. Nicholson, J.K., M.J. Buckingham, and P.J. Sadler, High resolution 1H n.m.r. studies of vertebrate blood and plasma. Biochem J, 1983. 211(3): p. 605-15.
10. Nicholson, J.K., et al., Quantitative high resolution 1H NMR urinalysis studies on the biochemical effects of cadmium in the rat. Mol Pharmacol, 1989. 36(3): pp. 398-404.
11. Moka, D., et al., Biochemical classification of kidney carcinoma biopsy samples using magic-angle-spinning 1H nuclear magnetic resonance spectroscopy. J Pharm Biomed Anal, 1998. 17(1): pp. 125-32.
12. Bharti, S.K. and R. Roy, Quantitative 1H NMR spectroscopy. Trends Analyt Chem, 2012. 35: p. 5-26.
13. Friebolin, H., Basic One- and Two-Dimensional NMR Spectroscopy. 5th ed. 2011, Weinheim, Germany: WILEY-VCH Verlag GmbH & Co. KGaA.
14. Villas-Bôas, S.G., et al., Metabolome Analysis: An Introduction. 2007: John Wiley & Sons, Inc.
15. Mickiewicz, B., et al., Metabolic Profiling of Serum Samples by 1H Nuclear Magnetic Resonance Spectroscopy as a Potential Diagnostic Approach for Septic Shock*. Crit Care Med, 2014. 42(5): pp. 1140-9.
16. Tiziani, S., et al., Optimized metabolite extraction from blood serum for 1H nuclear magnetic resonance spectroscopy. Anal Biochem, 2008. 377(1): pp. 16-23.
17. Lindon, J.C., et al., Metabonomics: metabolic processes studied by NMR spectroscopy of biofluids. Concepts Magn Reson, 2000. 12(5): pp. 289-320.
18. Beckonert, O., et al., Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc, 2007. 2(11): pp. 2692-703.
19. Dieterle, F., et al., NMR and MS methods for metabonomics. Methods Mol Biol, 2011. 691: p. 385-415.
20. Verwaest, K.A., et al., (1)H NMR based metabolomics of CSF and blood serum: a metabolic profile for a transgenic rat model of Huntington disease. Biochim Biophys Acta, 2011. 1812(11): pp. 1371-9.
21. Bouatra, S., et al., The human urine metabolome. Plos One, 2013. 8 (9): p. e73076.
22. Psychogios, N., et al., The human serum metabolome. PLoS ONE, 2011. 6(2): pp. e16957.
23. Soininen, P. et al., High-throughput serum NMR metabonomics for cost-effective holistic studies on systemic metabolism. Analyst, 2009. 134(9): pp. 1781-1785.
24. Roberts, L.D., A. Koulman, and J.L. Griffin, Towards metabolic biomarkers of insulin resistance and type 2 diabetes: progress from the metabolome. Lancet Diabetes Endocrinol, 2014. 2(1):p. 65-75.
25. Bodi, V., et al., Metabolomics in the diagnosis of acute myocardial ischemia. J Cardiovasc Transl Res, 2013. 6(5): pp. 808-15.
26. Gupta, S. and K. Chawla, Oncometabolomics in cancer research. Expert Rev Proteomics, 2013. 10(4): p. 325-36.
27. Pacchiarotta, T., A.M. Deelder, and O.A. Mayboroda, Metabolomic investigations of human infections. Bioanalysis, 2012. 4(8): p. 919-25.
28. Trushina, E. and M.M. Mielke, Recent advances in the application of metabolomics to Alzheimer's Disease. Biochim Biophys Acta, 2013.
29. Diabetes: Fact sheet No312. 2013 April 23, 2014]; Available from: http://www.who.int/mediacentre/factsheets/fs312/en/.
30. Makinen, V.P., et al., Sphingomyelin is associated with kidney disease in type 1 diabetes (The FinnDiane Study). Metabolomics, 2012. 8(3): pp. 369-375.
31. Deja, S., et al., 1H NMR-based metabolomics studies of urine reveal differences between type 1 diabetic patients with high and low HbAc1 values. J Pharm Biomed Anal, 2013. 83: p. 43-8.
32. Mickiewicz, B., et al., Metabolomics as a novel approach for early diagnosis of pediatric septic shock and its mortality. Am J Respir Crit Care Med, 2013. 187(9): pp. 967-76.
33. Kumar, A., et al., Duration of hypotension before initiation of effective antimicrobial therapy is the critical determinant of survival in human septic shock*. Critical Care Medicine, 2006. 34(6): pp. 1589-1596.
34. Theodoridis, G.A., et al., Liquid chromatography-mass spectrometry based global metabolite profiling: a review. Anal Chim Acta, 2012. 711: p. 7-16.
35. Dunn, W.B., Current trends and future requirements for the mass spectrometric investigation of microbial, mammalian and plant metabolomes. Phys Biol, 2008. 5(1): p. 011001.
36. Lei, Z., D. Huhman, and L.W. Sumner, Mass Spectrometry Strategies in Metabolomics. Journal of Biological Chemistry, 2011.
37. Dunn, W.B., et al., A GC-TOF-MS study of the stability of serum and urine metabolomes during the UK Biobank sample collection and preparation protocols. Int J Epidemiol, 2008. 37 Suppl 1: p. i23-30.
38. Ma, B., et al., GC-TOF/MS-based metabolomic profiling of estrogen deficiency-induced obesity in ovariectomized rats. Acta Pharmacol Sin, 2011. 32(2): pp. 270-8.
39. Barding, G.A., Jr., R. Salditos, and C.K. Larive, Quantitative NMR for bioanalysis and metabolomics. Anal Bioanal Chem, 2012. 404(4): p. 1165-79.
40. Tolstikov, V.V., Metabolic analysis. Methods Mol Biol, 2009. 544: p. 343-53.
41. Mayr, M., Metabolomics: Ready for the Prime Time? Circulation:Cardiovascular Genetics, 2008. 1(1): p. 58-65.
42. Issaq, H.J., et al., Global proteomics and metabolomics in cancer biomarker discovery. J Sep Sci, 2011. 34(24): pp. 3484-92.
43. Guo, X., ed. Advances in Gas Chromatography. 2014, AvE4EvA.
44. Dunn, W.B., et al., Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc, 2011. 6(7): pp. 1060-83.
45. Rabinowitz, J.D., et al., Metabolomics in drug target discovery. Cold Spring Harb Symp Quant Biol, 2011. 76: p. 235-46.
46. Livengood, P., et al., OmicsVis: an interactive tool for visually analyzing metabolomics data. BMC Bioinformatics, 2012. 13 Suppl 8: p. S6.
47. Zhang, A., et al., Modern analytical techniques in metabolomics analysis. Analyst, 2012. 137(2): pp. 293-300.
48. Harkewicz, R. and E.A. Dennis, Applications of Mass Spectrometry to Lipids and Membranes. Annual Review of Biochemistry, 2010. 80(1): p. 110301095147058.
49. Blekherman, G., et al., Bioinformatics tools for cancer metabolomics. Metabolomics, 2011. 7(3): pp. 329-343.
50. Johnson, C.H. and F.J. Gonzalez, Challenges and opportunities of metabolomics. J Cell Physiol, 2012. 227(8): p. 2975-81.
51. Langley, R.J., et al., An integrated clinico-metabolomic model improves prediction of death in sepsis. Sci Transl Med, 2013. 5(195): pp. 195ra95.
52. Rogers, A.J., et al., Metabolomic derangements are associated with mortality in critically ill adult patients. PLoS ONE, 2014. 9(1): pp. e87538.
53. Fanos, V., et al., Urinary (1)H-NMR and GC-MS metabolomics predicts early and late onset neonatal sepsis. Early Hum Dev, 2014. 90 Suppl 1: p. S78-83.
54. Schubert, J.K., et al., Application of a new method for analysis of exhaled gas in critically ill patients. Intensive Care Med, 1998. 24(5): pp. 415-21.
55. Zhou, B., et al., LC-MS-based metabolomics. Mol Biosyst, 2012. 8(2): pp. 470-81.
56. Dunn, W.B. and D.I. Ellis, Metabolomics: Current analytical platforms and methodologies. Trac-Trends in Analytical Chemistry, 2005. 24(4): p. 285-294.
57. Bedair, M. and L.W. Smner, Current and emerging massspectrometry technologies for metabolomics. TrAC Trends in Analytical Chemistry, 2008. 27 (3): p. 238- 250.
58. Plumb, R., et al., Ultra-performance liquid chromatography coupled to quadrupole-orthogonal time-of-flight mass spectrometry. Rapid Commun Mass Spectrom, 2004. 18(19): pp. 2331-7.
59. Dunn, W.B., N.J. Bailey, and H.E. Johnson, Measuring the metabolome:current analytical technologies. Analyst, 2005. 130(5): p. 606-25.
60. De Vos, R.C., et al., Untargeted large-scale plant metabolomics using liquid chromatography coupled to mass spectrometry. Nat Protoc, 2007. 2(4): pp. 778-91.
61. Stoyanov, A.V., et al., Isotope dilution assay in peptide quantification:the challenge of microheterogeneity of internal standard. Proteomics Clin Appl, 2013. 7(11-12): p. 825-8.
62. Zhu, Z.J., et al., Liquid chromatography quadrupole time-offlight mass spectrometry characterization of metabolites guided by the METLIN database. Nat Protoc, 2013. 8(3): pp. 451-60.
63. Zhang, G.F., et al., Metabolomics, pathway regulation, and pathway discovery. J Biol Chem, 2011. 286(27): pp. 23631-5.
64. Issaq, H.J., T.D. Abbott E Fau - Veenstra, and T.D. Veenstra, Utility of separation science in metabolomic studies. 2008(1615-9314 (Electronic)).
65. Verpoorte, R., et al., Metabolomics: Back to basics. Phytochemistry Reviews, 2008. 7(3): pp. 525-537.
66. Bundy, J.G., M.P. Davey, and M.R. Viant, Environmental metabolomics:A critical review and future perspectives. Metabolomics, 2009. 5(1): p. 3-21.
67. Becker, S., et al., LC-MS-based metabolomics in the clinical laboratory. J Chromatogr B Analyt Technol Biomed Life Sci, 2012. 883-884: p. 68-75.
68. Cui, L., et al., Serum metabolome and lipidome changes in adult patients with primary dengue infection. PLoS Negl Trop Dis, 2013. 7(8): pp. e2373.
69. Seymour, C.W., et al., Metabolomics in pneumonia and sepsis:an analysis of the GenIMS cohort study. Intensive Care Med, 2013. 39(8): pp. 1423-34.
70. Bartel, J., J. Krumsiek, and F.J. Theis, Statistical methods for the analysis of high-throughput metabolomics data. Computational and Structural Biotechnology Journal, 2013. 4(5).
71. Eriksson, L., et al., Multi- and Megavariate Data Analysis Part I:Basic Principles and Applications. 2006, Umeå, Sweden: Umetrics AB. 425.
72. Zweig, M.H. and G. Campbell, Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clin Chem, 1993. 39(4): p. 561-77.
73. Xia, J., et al., MetaboAnalyst 2.0--a comprehensive server for metabolomic data analysis. Nucleic Acids Res, 2012. 40(Web Server issue): p. W127-33.
74. Viswanathan, G.A., et al., Getting started in biological pathway construction and analysis. PLoS Comput Biol, 2008. 4(2): pp. e16.
75. Booth, S.C., A.M. Weljie, and R.J. Turner, Computational tools for the secondary analysis of metabolomics experiments. Computational and Structural Biotechnology Journal, 2013. 4(5).
76. Evans, C.R., et al., Untargeted LC-MS metabolomics of bronchoalveolar lavage fluid differentiates acute respiratory distress syndrome from health. J Proteome Res, 2014. 13(2): pp. 640-9.