Application of 1H NMR spectroscopy-based metabolomics to sera of tuberculosis patients

Journal of Proteome Research

Volumn 12, Issue 10, 2013, Pages 4642-4649

  Zhou, Aiping ^a   Ni, Jinjing ^a   Xu, Zhihong ^a   Wang, Ying ^b   Lu, Shuihua ^c   Sha, Wei ^d   Karakousis, Petros C ^e   Yao, Yu Feng ^a  

^a SHANGHAI JIAO TONG UNIVERSITY SCHOOL OF MEDICINE   (China)

^b Shanghai Institute of Immunology   (China)

^c SHANGHAI PUBLIC HEALTH CLINICAL CENTER   (China)

^d TONGJI UNIVERSITY SCHOOL OF MEDICINE   (China)

^e JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

metabolomics; NMR; serum; systems biology; tuberculosis

Indexed keywords

ACETOACETIC ACID; ACETONE; FORMIC ACID; GLUTAMIC ACID; GLUTAMINE; GLYCINE; ISOLEUCINE; LACTIC ACID; LOW DENSITY LIPOPROTEIN; LYSINE; NICOTINIC ACID; PHENYLALANINE; PYRUVIC ACID; TYROSINE;

ADOLESCENT; ADULT; ARTICLE; CHILD; CLINICAL ARTICLE; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DISCRIMINANT ANALYSIS; DOWN REGULATION; FEMALE; HUMAN; MALE; METABOLOMICS; PATTERN RECOGNITION; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN SYNTHESIS; PROTON NUCLEAR MAGNETIC RESONANCE; SCHOOL CHILD; TUBERCULOSIS; UPREGULATION;

ADOLESCENT; ADULT; AGED; BIOLOGICAL MARKERS; BLOOD CHEMICAL ANALYSIS; CASE-CONTROL STUDIES; CHILD; FEMALE; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MALE; METABOLOME; METABOLOMICS; MIDDLE AGED; MULTIVARIATE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; TUBERCULOSIS, PULMONARY; YOUNG ADULT;

EID: 84885206980     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr4007359     Document Type: Article

References (48)

1. Brindle, J. T.; Antti, H.; Holmes, E.; Tranter, G.; Nicholson, J. K.; Bethell, H. W.; Clarke, S.; Schofield, P. M.; McKilligin, E.; Mosedale, D. E.; Grainger, D. J. Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics Nat. Med. 2002, 8 (12) 1439-44
2. Maher, A. D.; Crockford, D.; Toft, H.; Malmodin, D.; Faber, J. H.; McCarthy, M. I.; Barrett, A.; Allen, M.; Walker, M.; Holmes, E.; Lindon, J. C.; Nicholson, J. K. Optimization of human plasma 1H NMR spectroscopic data processing for high-throughput metabolic phenotyping studies and detection of insulin resistance related to type 2 diabetes Anal. Chem. 2008, 80 (19) 7354-62
3. Ludwig, C.; Ward, D. G.; Martin, A.; Viant, M. R.; Ismail, T.; Johnson, P. J.; Wakelam, M. J.; Gunther, U. L. Fast targeted multidimensional NMR metabolomics of colorectal cancer Magn. Reson. Chem. 2009, 47 (Suppl 1) S68-73
4. Tiziani, S.; Lopes, V.; Gunther, U. L. Early stage diagnosis of oral cancer using 1H NMR-based metabolomics Neoplasia 2009, 11 (3) 269-76
5. Sinclair, A. J.; Viant, M. R.; Ball, A. K.; Burdon, M. A.; Walker, E. A.; Stewart, P. M.; Rauz, S.; Young, S. P. NMR-based metabolomic analysis of cerebrospinal fluid and serum in neurological diseases - a diagnostic tool? NMR Biomed. 2010, 23 (2) 123-32
6. The Sixteenth Global Report on Tuberculosis; World Health Organization: Geneva, Switzerland, 2011.
7. Multidrug and Extensively Drug-Resistant TB (M/XDR-TB): 2010 Global Report on Surveillance and Response; World Health Organization: Geneva, Switzerland, 2010.
8. Zumla, A.; Abubakar, I.; Raviglione, M.; Hoelscher, M.; Ditiu, L.; McHugh, T. D.; Squire, S. B.; Cox, H.; Ford, N.; McNerney, R.; Marais, B.; Grobusch, M.; Lawn, S. D.; Migliori, G. B.; Mwaba, P.; O'Grady, J.; Pletschette, M.; Ramsay, A.; Chakaya, J.; Schito, M.; Swaminathan, S.; Memish, Z.; Maeurer, M.; Atun, R. Drug-resistant tuberculosis - current dilemmas, unanswered questions, challenges, and priority needs J. Infect. Dis. 2012, 205 (Suppl 2) S228-40
9. Macallan, D. C.; McNurlan, M. A.; Kurpad, A. V.; de Souza, G.; Shetty, P. S.; Calder, A. G.; Griffin, G. E. Whole body protein metabolism in human pulmonary tuberculosis and undernutrition: evidence for anabolic block in tuberculosis Clin. Sci. 1998, 94 (3) 321-31
10. Pacchiarotta, T.; Deelder, A. M.; Mayboroda, O. A. Metabolomic investigations of human infections Bioanalysis 2012, 4 (8) 919-25
11. Somashekar, B. S.; Amin, A. G.; Rithner, C. D.; Troudt, J.; Basaraba, R.; Izzo, A.; Crick, D. C.; Chatterjee, D. Metabolic profiling of lung granuloma in Mycobacterium tuberculosis infected guinea pigs: ex vivo 1H magic angle spinning NMR studies J. Proteome Res. 2011, 10 (9) 4186-95
12. Shin, J. H.; Yang, J. Y.; Jeon, B. Y.; Yoon, Y. J.; Cho, S. N.; Kang, Y. H.; Ryu do, H.; Hwang, G. S. (1)H NMR-based metabolomic profiling in mice infected with Mycobacterium tuberculosis J. Proteome Res. 2011, 10 (5) 2238-47
13. Weiner, J., 3rd; Parida, S. K.; Maertzdorf, J.; Black, G. F.; Repsilber, D.; Telaar, A.; Mohney, R. P.; Arndt-Sullivan, C.; Ganoza, C. A.; Fae, K. C.; Walzl, G.; Kaufmann, S. H. Biomarkers of inflammation, immunosuppression and stress with active disease are revealed by metabolomic profiling of tuberculosis patients PLoS One 2012, 7 (7) e40221
14. Nicholson, J. K.; Foxall, P. J.; Spraul, M.; Farrant, R. D.; Lindon, J. C. 750 MHz 1H and 1H-13C NMR spectroscopy of human blood plasma Anal. Chem. 1995, 67 (5) 793-811
15. Trygg, J.; Holmes, E.; Lundstedt, T. Chemometrics in metabonomics J. Proteome Res. 2007, 6 (2) 469-79
16. Ni, Y.; Su, M.; Lin, J.; Wang, X.; Qiu, Y.; Zhao, A.; Chen, T.; Jia, W. Metabolic profiling reveals disorder of amino acid metabolism in four brain regions from a rat model of chronic unpredictable mild stress FEBS Lett. 2008, 582 (17) 2627-36
17. Xia, J.; Wishart, D. S. MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data Nucleic Acids Res. 2010, 38 (Web Server issue) W71-7
18. Pontoizeau, C.; Fearnside, J. F.; Navratil, V.; Domange, C.; Cazier, J. B.; Fernandez-Santamaria, C.; Kaisaki, P. J.; Emsley, L.; Toulhoat, P.; Bihoreau, M. T.; Nicholson, J. K.; Gauguier, D.; Dumas, M. E. Broad-ranging natural metabotype variation drives physiological plasticity in healthy control inbred rat strains J. Proteome. Res. 2011, 10 (4) 1675-89
19. Subramanian, A.; Tamayo, P.; Mootha, V. K.; Mukherjee, S.; Ebert, B. L.; Gillette, M. A.; Paulovich, A.; Pomeroy, S. L.; Golub, T. R.; Lander, E. S.; Mesirov, J. P. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles Proc. Natl. Acad. Sci. U. S. A. 2005, 102 (43) 15545-50
20. Tailleux, L.; Waddell, S. J.; Pelizzola, M.; Mortellaro, A.; Withers, M.; Tanne, A.; Castagnoli, P. R.; Gicquel, B.; Stoker, N. G.; Butcher, P. D.; Foti, M.; Neyrolles, O. Probing host pathogen cross-talk by transcriptional profiling of both Mycobacterium tuberculosis and infected human dendritic cells and macrophages PLoS One 2008, 3 (1) e1403
21. Blumenthal, A.; Isovski, F.; Rhee, K. Y. Tuberculosis and host metabolism: ancient associations, fresh insights Transl. Res. 2009, 154 (1) 7-14
22. Zhivotovsky, B.; Orrenius, S. The Warburg Effect returns to the cancer stage Semin. Cancer Biol. 2009, 19 (1) 1-3
23. Rohde, K. H.; Veiga, D. F.; Caldwell, S.; Balazsi, G.; Russell, D. G. Linking the transcriptional profiles and the physiological states of Mycobacterium tuberculosis during an extended intracellular infection PLoS Pathog. 2012, 8 (6) e1002769
24. McKinney, J. D.; Honer zu Bentrup, K.; Munoz-Elias, E. J.; Miczak, A.; Chen, B.; Chan, W. T.; Swenson, D.; Sacchettini, J. C.; Jacobs, W. R., Jr.; Russell, D. G. Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase Nature 2000, 406 (6797) 735-8
25. Munoz-Elias, E. J.; Upton, A. M.; Cherian, J.; McKinney, J. D. Role of the methylcitrate cycle in Mycobacterium tuberculosis metabolism, intracellular growth, and virulence Mol. Microbiol. 2006, 60 (5) 1109-22
26. De Backer, D. Lactic acidosis Intensive Care Med. 2003, 29 (5) 699-702
27. Via, L. E.; Lin, P. L.; Ray, S. M.; Carrillo, J.; Allen, S. S.; Eum, S. Y.; Taylor, K.; Klein, E.; Manjunatha, U.; Gonzales, J.; Lee, E. G.; Park, S. K.; Raleigh, J. A.; Cho, S. N.; McMurray, D. N.; Flynn, J. L.; Barry, C. E., 3rd Tuberculous granulomas are hypoxic in guinea pigs, rabbits, and nonhuman primates Infect. Immun. 2008, 76 (6) 2333-40
28. Cheng, L. L.; Chang, I. W.; Smith, B. L.; Gonzalez, R. G. Evaluating human breast ductal carcinomas with high-resolution magic-angle spinning proton magnetic resonance spectroscopy J. Magn. Reson. 1998, 135 (1) 194-202
29. Zhuang, H.; Alavi, A. 18-fluorodeoxyglucose positron emission tomographic imaging in the detection and monitoring of infection and inflammation Semin. Nucl. Med. 2002, 32 (1) 47-59
30. Macallan, D. C. Malnutrition in tuberculosis Diagn. Microbiol. Infect. Dis. 1999, 34 (2) 153-7
31. Paton, N. I.; Chua, Y. K.; Earnest, A.; Chee, C. B. Randomized controlled trial of nutritional supplementation in patients with newly diagnosed tuberculosis and wasting Am. J. Clin. Nutr. 2004, 80 (2) 460-5
32. Schwenk, A.; Macallan, D. C. Tuberculosis, malnutrition and wasting Curr. Opin. Clin. Nutr. Metab. Care 2000, 3 (4) 285-91
33. Kim, M. J.; Wainwright, H. C.; Locketz, M.; Bekker, L. G.; Walther, G. B.; Dittrich, C.; Visser, A.; Wang, W.; Hsu, F. F.; Wiehart, U.; Tsenova, L.; Kaplan, G.; Russell, D. G. Caseation of human tuberculosis granulomas correlates with elevated host lipid metabolism EMBO Mol. Med. 2010, 2 (7) 258-74
34. Wolfe, R. R.; Shaw, J. H.; Durkot, M. J. Energy metabolism in trauma and sepsis: the role of fat Prog. Clin. Biol. Res. 1983, 111, 89-109
35. Lin, Z. Y.; Xu, P. B.; Yan, S. K.; Meng, H. B.; Yang, G. J.; Dai, W. X.; Liu, X. R.; Li, J. B.; Deng, X. M.; Zhang, W. D. A metabonomic approach to early prognostic evaluation of experimental sepsis by (1)H NMR and pattern recognition NMR Biomed. 2009, 22 (6) 601-8
36. Gao, H.; Lu, Q.; Liu, X.; Cong, H.; Zhao, L.; Wang, H.; Lin, D. Application of 1H NMR-based metabonomics in the study of metabolic profiling of human hepatocellular carcinoma and liver cirrhosis Cancer Sci. 2009, 100 (4) 782-785
37. Lanza, I. R.; Zhang, S.; Ward, L. E.; Karakelides, H.; Raftery, D.; Nair, K. S. Quantitative metabolomics by 1H-NMR and LC-MS/MS confirms altered metabolic pathways in diabetes PloS One 2010, 5 (5) e10538
38. Zhao, L.; Liu, X.; Xie, L.; Gao, H.; Lin, D. 1 H NMR-based Metabonomic Analysis of Metabolic Changes in Streptozotocin-induced Diabetic Rats Anal. Sci. 2010, 26 (12) 1277-1282
39. Blasco, H.; Corcia, P.; Moreau, C.; Veau, S.; Fournier, C.; Vourc'h, P.; Emond, P.; Gordon, P.; Pradat, P.-F.; Praline, J. 1H-NMR-based metabolomic profiling of CSF in early amyotrophic lateral sclerosis PloS One 2010, 5 (10) e13223
40. Rao, J. U.; Engelke, U.; Rodenburg, R.; Wevers, R.; Pacak, K.; Eisenhofer, G.; Qin, N.; Kusters, B.; Goudswaard, A.; Lenders, J. W. Genotype-specific abnormalities in mitochondrial function associate with distinct profiles of energy metabolism and catecholamine content in pheochromocytoma and paraganglioma Clin. Cancer Res. 2013, 19, 3787-3795
41. Bylesjö, M.; Rantalainen, M.; Cloarec, O.; Nicholson, J. K.; Holmes, E.; Trygg, J. OPLS discriminant analysis: combining the strengths of PLS-DA and SIMCA classification J. Chemom. 2006, 20 (8-10) 341-351
42. Winnike, J. H.; Li, Z.; Wright, F. A.; Macdonald, J. M.; O'Connell, T. M.; Watkins, P. B. Use of pharmaco-metabonomics for early prediction of acetaminophen-induced hepatotoxicity in humans Clin. Pharmacol. Ther. Ser. 2010, 88 (1) 45-51
43. Jung, J. Y.; Lee, H. S.; Kang, D. G.; Kim, N. S.; Cha, M. H.; Bang, O. S.; Ryu do, H.; Hwang, G. S. 1H-NMR-based metabolomics study of cerebral infarction Stroke 2011, 42 (5) 1282-8
44. Holmes, E.; Loo, R. L.; Cloarec, O.; Coen, M.; Tang, H.; Maibaum, E.; Bruce, S.; Chan, Q.; Elliott, P.; Stamler, J.; Wilson, I. D.; Lindon, J. C.; Nicholson, J. K. Detection of urinary drug metabolite (xenometabolome) signatures in molecular epidemiology studies via statistical total correlation (NMR) spectroscopy Anal. Chem. 2007, 79 (7) 2629-40
45. Chan, E. C.; Koh, P. K.; Mal, M.; Cheah, P. Y.; Eu, K. W.; Backshall, A.; Cavill, R.; Nicholson, J. K.; Keun, H. C. Metabolic profiling of human colorectal cancer using high-resolution magic angle spinning nuclear magnetic resonance (HR-MAS NMR) spectroscopy and gas chromatography mass spectrometry (GC/MS) J. Proteome Res. 2009, 8 (1) 352-61
46. Li, M.; Wang, B.; Zhang, M.; Rantalainen, M.; Wang, S.; Zhou, H.; Zhang, Y.; Shen, J.; Pang, X.; Zhang, M.; Wei, H.; Chen, Y.; Lu, H.; Zuo, J.; Su, M.; Qiu, Y.; Jia, W.; Xiao, C.; Smith, L. M.; Yang, S.; Holmes, E.; Tang, H.; Zhao, G.; Nicholson, J. K.; Li, L.; Zhao, L. Symbiotic gut microbes modulate human metabolic phenotypes Proc. Natl. Acad. Sci. U. S. A. 2008, 105 (6) 2117-22
47. Wiklund, S.; Johansson, E.; Sjostrom, L.; Mellerowicz, E. J.; Edlund, U.; Shockcor, J. P.; Gottfries, J.; Moritz, T.; Trygg, J. Visualization of GC/TOF-MS-based metabolomics data for identification of biochemically interesting compounds using OPLS class models Anal. Chem. 2008, 80 (1) 115-22
48. Wang, X.; Zhang, A.; Han, Y.; Wang, P.; Sun, H.; Song, G.; Dong, T.; Yuan, Y.; Yuan, X.; Zhang, M.; Xie, N.; Zhang, H.; Dong, H.; Dong, W. Urine metabolomics analysis for biomarker discovery and detection of jaundice syndrome in patients with liver disease Mol. Cell. Proteomics 2012, 11 (8) 370-80