Isotope enhanced approaches in metabolomics

Advances in Experimental Medicine and Biology

Volumn 992, Issue , 2012, Pages 147-164

  Gowda, G A Nagana ^a   Shanaiah, Narasimhamurthy ^a   Raftery, Daniel ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON 13; DEUTERIUM; GLUCOSE; GLUTAMINE; MYC PROTEIN; NITROGEN 15; PHOSPHORUS 31; SERINE;

AMINO ACID METABOLISM; ANALYTIC METHOD; ARTICLE; BLOOD SAMPLING; CONCENTRATION (PARAMETERS); EX VIVO STUDY; HETERONUCLEAR SINGLE QUANTUM COHERENCE; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; IN VIVO STUDY; ISOTOPE LABELING; METABOLIC FLUX ANALYSIS; METABOLOMICS; MOLECULAR BIOLOGY; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; ONCOGENE MYC; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; SENSITIVITY ANALYSIS; TRANSCRIPTION REGULATION; TWO DIMENSIONAL NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

EID: 84870436793     PISSN: 00652598     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-94-007-4954-2_8     Document Type: Article

References (106)

1. Nicholson JK, Lindon JC, Holmes E (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. Fiehn O (2002) Metabolomics-the link between genotype and phenotype. Plant Mol Biol 48:155-171
3. Saghatelian A, Cravatt BF (2005) Global strategies to integrate the proteome and metabolome. Curr Opin Chem Biol 9:62-68
4. Assfalg M, Bertini I, Colangiuli D et al (2008) Evidence of different metabolic phenotypes in humans. Proc Natl Acad Sci USA 105:1420-1424
5. Nicholson JK, Lindon JC (2008) Systems biology: Metabonomics. Nature 455:1054-1056
6. van der Greef J, Smilde AK (2005) Symbiosis of chemometrics and metabolomics: Past, present, and future. J Chemom 19:376-386
7. Nagana Gowda GA, Zhang S, Gu H et al (2008) Metabolomics based methods for early disease diagnostics: A review. Exp Rev Mol Diagn 8:627-633
8. NaganaGowda GA, Ijare OB, Shanaiah N et al (2009) Combining NMR spectroscopy and mass spectrometry in biomarker discovery. Biomark Med 3:307-322
9. Holmes E, Wilson ID, Nicholson JK (2008) Metabolic phenotyping in health and disease. Cell 134:714-717
10. Weljie AM, Newton J, Mercier P et al (2006) Targeted pro fi ling: Quantitative analysis of 1 H NMR metabolomics data. Anal Chem 78:4430-4442
11. Lewis IA, Schommer SC, Hodis B et al (2007) Method for determining molar concentrations of metabolites in complex solutions from two-dimensional 1 H- 13 C NMR spectra. Anal Chem 79:9385-9390
12. Robinette SL, Zhang F, Brüschweiler-Li L et al (2008) Web server based complex mixture analysis by NMR. Anal Chem 80:3606-3611
13. Chikayama E, Sekiyama Y, Okamoto M et al (2010) Statistical indices for simultaneous large-scale metabolite detections for a single NMR spectrum. Anal Chem 82:1653-1658
14. Keun HC (2006) Metabonomic modeling of drug toxicity. Pharmacol Ther 109:92-106
15. Coen M, Holmes E, Lindon JC et al (2008) NMR-based metabolic pro fi ling and metabonomic approaches to problems in molecular toxicology. Chem Res Toxicol 2:9-27
16. Bollard ME, Stanley EG, Lindon JC et al (2005) NMR-based metabonomic approaches for evaluating physiological Influences on bio fl uid composition. NMR Biomed 18:143-162
17. Nagana Gowda GA, Ijare OB, Somashekar BS et al (2006) Single-step analysis of individual conjugated bile acids in human bile using 1 H NMR spectroscopy. Lipids 41:591-603
18. Nagana Gowda GA (2010) Human bile as a rich source of biomarkers for hepatopancreatobiliary cancers. Biomark Med 4:299-314
19. Nagana Gowda GA (2011) NMR spectroscopy for discovery and quantitation of biomarkers of disease in human bile. Bioanalysis 3:1877-1890
20. Bala L, Ghoshal UC, Ghoshal U et al (2006) Malabsorption syndrome with and without small intestinal bacterial overgrowth: A study on upper-gut aspirate using 1 H NMR spectroscopy. Magn Reson Med 56:738-744
21. Griffin JL, Kauppinen RA (2007) Tumour metabolomics in animal models of human cancer. J Proteome Res 6:498-505
22. Villas-Boas SG, Hojer-Pedersen J, Akesson M et al (2005) Global metabolite analysis of yeast: Evaluation of sample preparation methods. Yeast 22:1155-1169
23. Bollard ME, Xu JS, Purcell W et al (2002) Metabolic pro fi ling of the effects of D-galactosamine in liver spheroids using 1 H NMR and MAS-NMR spectroscopy. Chem Res Toxicol 15:1351-1359
24. Boroujerdi AF, Vizcaino MI, Meyers A et al (2009) NMR-based microbial metabolomics and the temperaturedependent coral pathogen Vibrio coralliilyticus. Environ Sci Technol 43:7658-7664
25. Lyng H, Sitter B, Bathen TF et al (2007) Metabolic mapping by use of high-resolution magic angle spinning 1 H MR spectroscopy for assessment of apoptosis in cervical carcinomas. BMC Cancer 7:11
26. Sitter B, Bathen T, Hagen B et al (2004) Cervical cancer tissue characterized by high-resolution magic angle spinning MR spectroscopy. Magn Reson Mater Phys Biol Med 16:174-181
27. Schenetti L, Mucci A, Parenti F et al (2006) HR-MAS NMR spectroscopy in the characterization of human tissues: Application to healthy gastric mucosa. Concepts Magn Reson A 28A:430-443
28. Beckonert O, Keun HC, Ebbels TMD et al (2007) Metabolic pro fi ling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2:2692-2703
29. Beckonert O, Coen M, Keun HC et al (2010) High-resolution magic-angle-spinning NMR spectroscopy for metabolic pro fi ling of intact tissues. Nat Protoc 5:1019-1032
30. Nicholson JK, Foxall PJD, Spraul M et al (1995) 750 MHz 1 H and 1 H- 13 C NMR spectroscopy of human blood-plasma. Anal Chem 67:793-811
31. Balayssac S, DelsucM-A GV et al (2009) Two-dimensional DOSY experiment with Excitation Sculpting water suppression for the analysis of natural and biological media. J Magn Reson 196:78-83
32. Van Lokeren L, Kerssebaum R, Willem R et al (2008) ERETIC implemented in diffusion-ordered NMR as a diffusion reference. Magn Reson Chem 46:S63-S71
33. Smith LM, Maher AD, Cloarec O et al (2007) Statistical correlation and projection methods for improved information recovery from diffusion-edited NMR spectra of biological samples. Anal Chem 79:5682-5689
34. Simpson AJ, Brown SA (2005) Purge NMR: Effective and easy solvent suppression. J Magn Reson 175:340-346
35. Ogg RJ, Kingsley PB, Taylor JS (1994) Wet, a T-1-insensitive and B-1-insensitive water-suppression method for in-vivo localized 1 H NMR spectroscopy. J Magn Reson B 104:1-10
36. Mo H, Raftery D (2008) Improved residual water suppression: WET180. J Biomol NMR 41:105-111
37. Hoult DI (1976) Solvent peak saturation with single-phase and quadrature fourier transformation. J Magn Reson 21:337-347
38. Sandusky P, Raftery D (2005) Use of selective TOCSY NMR experiments for quantifying minor components in complex mixtures: Application to the metabonomics of amino acids in honey. Anal Chem 77:2455-2463
39. Sandusky P, Raftery D (2005) Use of semiselective TOCSY and the pearson correlation for the metabonomic analysis of bio fl uid mixtures: Application to urine. Anal Chem 77:7717-7723
40. Sandusky P, Appiah-Amponsah E, Raftery D (2011) Use of optimized 1D TOCSY NMR for improved quantitation and metabolomic analysis of bio fl uids. J Biomol NMR 49:281-290
41. Dumas ME, Canlet C, André F et al (2002) Metabonomic assessment of physiological disruptions using 1 H- 13 C HMBC-NMR spectroscopy combined with pattern recognition procedures performed on fi ltered variables. Anal Chem 74:2261-2273
42. Tang HR, Wang Y, Nicholson JK et al (2004) Use of relaxation-edited one-dimensional and two dimensional nuclear magnetic resonance spectroscopy to improve detection of small metabolites in blood plasma. Anal Biochem 325:260-272
43. Xi Y, de Ropp JS, Viant MR et al (2006) Automated screening for metabolites in complex mixtures using 2D COSY NMR spectroscopy. Metabolomics 2:221-233
44. Chikayama E, Suto M, Nishihara T et al (2008) Systematic NMR analysis of stable isotope labeled metabolite mixtures in plant and animal systems: Coarse grained views of metabolic pathways. PLoS One 3:e3805
45. Fan TWM, Bandura LL, Higashi RM et al (2005) Metabolomics-edited transcriptomics analysis of Se anticancer action in human lung cancer cells. Metabolomics 1:325-339
46. Ludwig C, Viant MR (2010) Two-dimensional J-resolved NMR spectroscopy: Review of a key methodology in the metabolomics toolbox. Phytochem Anal 21:22-32
47. Parsons HM, Ludwig C, Gunther UL et al (2007) Improved classi fi cation accuracy in 1-and 2-dimensional NMR metabolomics data using the variance stabilising generalised logarithm transformation. BMC Bioinform 8:234
48. Hyberts SG, Heffron GJ, Tarragona NG et al (2007) Ultrahigh-resolution 1 H- 13 C HSQC spectra of metabolite mixtures using nonlinear sampling and forward maximum entropy reconstruction. J Am Chem Soc 129:5108-5116
49. Viant MR (2003) Improved methods for the acquisition and interpretation of NMR metabolomic data. Biochem Biophys Res Commun 310:943-948
50. Lindon JC, Holmes E, Nicholson JK (2006) Metabonomics techniques and applications to pharmaceutical research & development. Pharm Res 23:1075-1088
51. Kind T, Tolstikov V, Fiehn O et al (2007) A comprehensive urinary metabolomic approach for identifying kidney cancer. Anal Biochem 363:185-195
52. Wilson ID, Nicholson JK, Castro-Perez J et al (2005) High resolution "ultra performance" liquid chromatography coupled to a-TOF mass spectrometry as a tool for differential metabolic pathway pro fi ling in functional genomic studies. J Proteome Res 4:591-598
53. Spraul M, Freund AS, Nast RE et al (2003) Advancing NMR sensitivity for LC-NMR-MS using a cryo- fl ow probe: Application to the analysis of acetaminophen metabolites in urine. Anal Chem 75:1536-1541
54. Lacey ME, Subramanian R, Olson DL et al (1999) High-resolution NMR spectroscopy of sample volumes from 1 nL to 10 m L. Chem Rev 99:3133-3152
55. Olson DL, Peck TL, Webb AG et al (1995) High-resolution microcoil 1 H-NMR for mass-limited, nanoliter-volume samples. Science 270:1967-1970
56. Webb AG (2005) Microcoil nuclear magnetic resonance spectroscopy. J Pharm Biomed Anal 38:892-903
57. Kc R, Henry ID, Park GHJ et al (2009) Design and construction of a versatile dual volume heteronuclear double resonance microcoil NMR probe. J Magn Reson 197:186-192
58. Henry D, Park GHJ, Kc R et al (2008) Design and construction of a microcoil NMR probe for the routine analysis of 20-mu L samples. Concepts Magn Reson B Magn Reson Eng 33B:1-8
59. Bergeron SJ, Henry ID, Santini RE et al (2008) Saturation transfer double-difference NMR spectroscopy using a dual solenoid microcoil difference probe. Magn Reson Chem 46:925-929
60. Kc R, Gowda YN, Djukovic D et al (2010) Susceptibility-matched plugs for microcoil NMR probes. J Magn Reson 205:63-68
61. Guo K, Bamforth F, Li L (2011) Qualitative metabolome analysis of human cerebrospinal fl uid by 13C-/12Cisotope dansylation labeling combined with liquid chromatography fourier transform ion cyclotron resonance mass spectrometry. J Am Soc Mass Spectrom 22:339-347
62. Huang X, Regnier FE (2008) Differential metabolomics using stable isotope labeling and two-dimensional gas chromatography with time-of- fl ight mass spectrometry. Anal Chem 80:107-114
63. Yang WC, Adamec J, Regnier FE (2007) Enhancement of the LC/MS analysis of fatty acids through derivatization and stable isotope coding. Anal Chem 79:5150-5157
64. Yang WC, Regnier FE, Sliva D et al (2008) Stable isotope-coded quaternization for comparative quanti fi cation of estrogen metabolites by high-performance liquid chromatography-electrospray ionization mass spectrometry. J Chromatogr B Anal Technol Biomed Life Sci 870:233-240
65. Lane AN, Fan TWM, Bousamra M II et al (2011) Stable isotope-resolved metabolomics (SIRM) in cancer research with clinical application to nonsmall cell lung cancer. OMICS A J Integr Biol 15:173-182
66. Fan TW, Lane AN, Higashi RM et al (2011) Stable isotope resolved metabolomics of lung cancer in a SCID mouse model. Metabolomics 7:257-269
67. Fan TW, Lane AN, Higashi RM et al (2009) Altered regulation of metabolic pathways in human lung cancer discerned by (13)C stable isotope-resolved metabolomics (SIRM). Mol Cancer 8:41
68. Locasale JW, Grassian AR, Melman T et al (2011) Phosphoglycerate dehydrogenase diverts glycolytic fl ux and contributes to oncogenesis. Nat Genet 43:869-874
69. Fan TW, Lane AN (2011) NMR-based stable isotope resolved metabolomics in systems biochemistry. J Biomol NMR 49:267-280
70. Petch D, Butler M (1994) Pro fi le of energy metabolism in a murine hybridoma: Glucose and glutamine utilization. J Cell Physiol 161:71-76
71. Portais JC, Voisin P, Merle M et al (1996) Glucose and glutamine metabolism in C6 glioma cells studied by carbon-13 NMR. Biochimie 78:155-164
72. Mazurek S, Grimm H, Oehmke M et al (2000) Tumor M2-PK and glutaminolytic enzymes in the metabolic shift of tumor cells. Anticancer Res 20(6D):5151-5154
73. DeBerardinis RJ, Mancuso A, Daikhin E et al (2007) Beyond aerobic glycolysis: Transformed cells can engage in glutamine metabolism that exceeds the requirement for protein and nucleotide synthesis. Proc Natl Acad Sci USA 104:19345-19350
74. Lane AN, Fan TW, Higashi RM et al (2009) Prospects for clinical cancer metabolomics using stable isotope tracers. Exp Mol Pathol 86:165-173
75. Lloyd SG, Zeng H, Wang P et al (2004) Lactate isotopomer analysis by 1 H NMR spectroscopy: Consideration of long-range nuclear spin-spin interactions. Magn Reson Med 51:1279-1282
76. Lane AN, Fan TW (2007) Quanti fi cation and identi fi cation of isotopomer distributions of metabolites in crude cell extracts using 1 H TOCSY. Metabolomics 3:79-86
77. Burgess SC, Babcock EE, Jeffrey FM et al (2001) NMR indirect detection of glutamate to measure citric acid cycle fl ux in the isolated perfused mouse heart. FEBS Lett 505:163-167
78. Perdigoto R, Furtado AL, Porto A et al (2003) Sources of glucose production in cirrhosis by 2 H 2 O ingestion and 2 H NMR analysis of plasma glucose. Biochim Biophys Acta 1637:156-163
79. Kikuchi J, Shinozaki K, Hirayama T (2004) Stable isotope labeling of Arabidopsis thaliana for an NMR-based metabolomics approach. Plant Cell Physiol 45:1099-1104
80. Lane AN, Fan TW, Higashi RM (2008) Isotopomer based metabolic analysis by NMR and mass spectrometry. Biophys Tools Biol 84:541-588
81. Lane AN, Fan TW, Xie Z et al (2009) Isotopomer analysis of lipid biosynthesis by high resolution mass spectrometry and NMR. Anal Chim Acta 651:201-208
82. Coles NW, Johnstone RM (1962) Glutamine metabolism in Ehrlich ascites-carcinoma cells. Biochem J J83:284-291
83. Eagle H (1955) Nutrition needs of mammalian cells in tissue culture. Science 122:501-514
84. Wise DR, DeBerardinis RJ, Mancuso A et al (2008) Myc regulates a transcriptional program that stimulates mitochondrial glutaminolysis and leads to glutamine addiction. Proc Natl Acad Sci USA 105:18782-18787
85. Weis BC, Margolis D, Burgess SC et al (2004) Glucose production pathways by 2 H and 13 C NMR in patients with HIV-associated lipoatrophy. Magn Reson Med 51:649-654
86. Jones JG, Solomon MA, Cole SM et al (2001) An integrated (2)H and (13)C NMR study of gluconeogenesis and TCA cycle fl ux in humans. Am J Physiol Endocrinol Metab 281:E848-E856
87. Hausler N, Browning J, Merritt M et al (2006) Effects of insulin and cytosolic redox state on glucose production pathways in the isolated perfused mouse liver measured by integrated 2 H and 13 C NMR. Biochem J 394(Pt 2): 465-473, Erratum in: Biochem J 2006; 395:663
88. Perdigoto R, Rodrigues TB, Furtado AL et al (2003) Integration of [U-13C]glucose and 2 H 2 O for quanti fi cation of hepatic glucose production and gluconeogenesis. NMR Biomed 16:189-198
89. Jin ES, Jones JG, Merritt M et al (2004) Glucose production, gluconeogenesis, and hepatic tricarboxylic acid cycle fl uxes measured by nuclear magnetic resonance analysis of a single glucose derivative. Anal Biochem 327:149-155
90. Burgess SC, Weis B, Jones JG et al (2003) Noninvasive evaluation of liver metabolism by 2 H and 13 C NMR isotopomer analysis of human urine. Anal Biochem 312:228-234
91. Merritt ME, Harrison C, Sherry AD et al (2011) Flux through hepatic pyruvate carboxylase and phosphoenolpyruvatecarboxykinase detected by hyperpolarized 13 C magnetic resonance. Proc Natl Acad Sci USA 108:19084-19089
92. Schroeder MA, Atherton HJ, Ball DR et al (2009) Real-time assessment of Krebs cycle metabolism using hyperpolarized 13 C magnetic resonance spectroscopy. FASEB J 23:2529-2538
93. Lewis IA, Karsten RH, Norton ME et al (2010) NMR method for measuring carbon-13 isotopic enrichment of metabolites in complex solutions. Anal Chem 82:4558-4563
94. Fernie AR, Trethewey RN, Krotzky AJ et al (2004) Metabolite pro fi ling: From diagnostics to systems biology. Nat Rev Mol Cell Biol 5:763-769
95. Shanaiah N, Desilva A, Nagana Gowda GA et al (2007) Metabolite class selection of amino acids in bio fl uids using chemical derivatization and their enhanced 13 C NMR. Proc Natl Acad Sci USA 104:11540-11544
96. Ye T, Mo H, Shanaiah N et al (2009) Chemoselective 15 N tag for sensitive and high-resolution nuclear magnetic resonance pro fi ling of the carboxyl-containing metabolome. Anal Chem 81:4882-4888
97. Ye T, Zhang S, Mo H et al (2010) 13 C-formylation for improved NMR pro fi ling of amino metabolites in bio fl uids. Anal Chem 82:2303-2309
98. DeSilva MA, Shanaiah N, Nagana Gowda GA et al (2009) Application of 31 P NMR spectroscopy and chemical derivatization for metabolite pro fi ling of lipophilic compounds in human serum. Magn Reson Chem 47:S74-S80
99. NaganaGowda GA, Tayyari F, Ye T et al (2010) Quantitative analysis of blood plasma metabolites using isotope enhanced NMR methods. Anal Chem 82:8983-8990
100. Fan TW (1996) Metabolite pro fi ling by one- and two-dimensional NMR analysis of complex mixtures. Prog NMR Spectrosc 28:161-219
101. Hu K, Ellinger JJ, Chylla RA et al (2011) Measurement of absolute concentrations of individual compounds in metabolite mixtures by gradient-selective time-zero (1)H-(13)C HSQC with two concentration references and fast maximum likelihood reconstruction analysis. Anal Chem 83:9352-9360
102. Hu K, Wyche TP, Bugni TS et al (2011) Selective quanti fi cation by 2D HSQC(0) spectroscopy of thiocoraline in an extract from a sponge-derived Verrucosispora sp. J Nat Prod 74:2295-2298
103. Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry. W. H. Freeman & Co, New York
104. Sakami W, Harrington H (1963) Amino acid metabolism. Annu Rev Biochem 32:355-398
105. Brosnan JT (2000) Glutamate, at the interface between amino acid and carbohydrate metabolism. J Nutr 130: 988S-990S
106. Young VR, Ajami AM (2001) Glutamine: The emperor or his clothes? J Nutr 131:2449S-2459S