State-of-the-art non-targeted metabolomics in the study of chronic kidney disease

Metabolomics

Volumn 10, Issue 3, 2014, Pages 425-442

  Boelaert, J ^b   t'Kindt, R ^a   Schepers, E ^c   Jorge, L ^a   Glorieux, G ^c   Neirynck, N ^c   Lynen, F ^b   Sandra, P ^a   Vanholder, R ^c   Sandra, K ^a  

^a Metablys   (Belgium)

^b GHENT UNIVERSITY   (Belgium)

^c GHENT UNIVERSITY HOSPITAL   (Belgium)

Author keywords

Chronic kidney disease; GC MS; LC MS; Metabolomics; Q TOF; Serum

Indexed keywords

1 METHYLURIC ACID; 1, 3 DIMETHYLURIC ACID; 5 METHOXYSALICYLIC ACID; ALANINE; BIOLOGICAL MARKER; CREATININE; GLUCONIC ACID; INDICAN; KYNURENIC ACID; KYNURENINE; N ACETYLGLUCOSAMINE; N ACETYLNEURAMINIC ACID; OLEIC ACID; PANTOTHENIC ACID; PRASTERONE SULFATE; PROLINE; PSEUDOURIDINE; PYRIDINOL; PYRIDOXIC ACID; PYROGLUTAMIC ACID; QUINIC ACID; QUINOLINIC ACID; SALICYLURIC ACID; SIALIC ACID; SUCROSE; TRYPTOPHAN; UNCLASSIFIED DRUG; URIC ACID; XANTHOSINE;

ARTICLE; BLOOD CHEMISTRY; BLOOD SAMPLING; CHEMICAL ANALYSIS; CHRONIC KIDNEY DISEASE; CONTROLLED STUDY; ELECTROSPRAY; END STAGE RENAL DISEASE; FRAGMENTATION REACTION; GLOMERULUS FILTRATION RATE; HEMODIALYSIS; HUMAN; KIDNEY FUNCTION; MAJOR CLINICAL STUDY; MASS FRAGMENTOGRAPHY; METABOLIC ACTIVATION; METABOLOME; METABOLOMICS; MODERATE RENAL IMPAIRMENT; REVERSED PHASE LIQUID CHROMATOGRAPHY; TIME OF FLIGHT MASS SPECTROMETRY; UPREGULATION;

EID: 84898539018     PISSN: 15733882     EISSN: 15733890     Source Type: Journal    
DOI: 10.1007/s11306-013-0592-z     Document Type: Article

References (71)

1. Ahmad, S., Dasgupta, A., & Kenny, M. A. (1989). Fatty acid abnormalities in haemodialysis patients: Effect of l-carnitine administration. Kidney International Supplement, 27, S243-S246.
2. Aronov, P. A., Luo, F. J., Plummer, N. S., et al. (2011). Colonic contribution to uremic solutes. Journal of the American Society of Nephrology, 22, 1769-1776.
3. Begley, P., Francis-McIntyre, S., Dunn, W. B., et al. (2009). Development and performance of a gas chromatography-time-of-flight mass spectrometry analysis for large-scale nontargeted metabolomic studies of human serum. Analytical Chemistry, 81, 7038-7046.
4. Bellinghieri, G., Santoro, D., Calvani, M., Mallamace, A., & Savica, V. (2003). Carnitine and haemodialysis. American Journal of Kidney Diseases, 41(3), S116-S122.
5. Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society: Series B, 57(1), 289-300.
6. Benton, H. P., Wong, D. M., Trauger, S. A., & Siuzdak, G. (2008). XCMS2: processing tandem mass spectrometry data for metabolite identification and structural characterization. Analytical Chemistry, 80(16), 6382-6389.
7. Bultitude, F. W., & Newham, S. J. (1975). Identification of some abnormal metabolites in plasma from uremic subjects. Clinical Chemistry, 21, 1329-1334.
8. Busch, M., Gobert, A., Franke, S., et al. (2010). Vitamin B-6 metabolism in chronic kidney disease-Relation to transsulfuration, advanced glycation and cardiovascular disease. Nephron Clinical Practice, 114, C38-C46.
9. Chen, J., Zhao, X., Fritsche, J., et al. (2008). Practical approach for the identification and isomer elucidation of biomarkers detected in a metabonomic study for the discovery of individuals at risk for diabetes by integrating the chromatographic and mass spectrometric information. Analytical Chemistry, 80(4), 1280-1289.
10. Cohen, G., Raupachova, J., Wimmer, T., Deicher, R., & Hörl, W. H. (2008). The uraemic retention solute para-hydroxy-hippuric acid attenuates apoptosis of polymorphonuclear leukocytes from healthy subjects but not from haemodialysis patients. Nephrol. Dialysis Transplantation, 23(8), 2512-2519.
11. Dasgupta, A., Kenny, M. A., & Ahmad, S. (1990). Abnormal fatty-acid profile in chronic-haemodialysis patients-Possible deficiency of essential fatty-acids. Clinical Physiology & Biochemistry, 8, 238-243.
12. Dudley, E., Lemière, F., van Dongen, W., et al. (2004). Analysis of urinary nucleosides. IV. Identification of urinary purine nucleosides by liquid chromatography/electrospray mass spectrometry. Rapid Communications in Mass Spectrometry, 18, 2730-2738.
13. Dudley, E., Tuytten, R., Bond, A., et al. (2005). Study of the mass spectrometric fragmentation of pseudouridine: comparison of fragmentation data obtained by matrix-assisted laser desorption/ionisation post-source decay, electrospray ion trap multistage mass spectrometry, and by a method utilising electrospray quadrupole time-of-flight tandem mass spectrometry and in-source fragmentation. Rapid Communications in Mass Spectrometry, 19, 3075-3085.
14. Duranton, F., Cohen, G., De Smet, R., et al. (2012). Normal and pathologic concentrations of uremic toxins. Journal of the American Society of Nephrology, 23, 1258-1270.
15. Fiehn, O., & Kind, T. (2007). Metabolite profiling in blood plasma. Methods in Molecular Biology, 358, 3-17.
16. Flugel-Link, R. M., Jones, M. R., & Kopple, J. D. (1983). Red cell and plasma amino acid concentrations in renal failure. Journal of Parenteral and Enteral Nutrition, 7, 450-456.
17. Hayashi, K., Sasamura, H., Hishiki, T., et al. (2011). Use of serum and urine metabolome analysis for the detection of metabolic changes in patients with stage 1-2 chronic kidney disease. Nephro-Urology Monthly, 3(3), 164-171.
18. Herget-Rosenthal, S., Glorieux, G., Jankowski, J., & Jankowski, V. (2009). Uremic toxins in acute kidney injury. Seminars in Dialysis, 22, 445-448.
19. Hill, A. W., & Mortishire-Smith, R. J. (2005). Automated assignment of high-resolution collisionally activated dissociation mass spectra using a systematic bond disconnection approach. Rapid Communications in Mass Spectrometry, 19, 3111-3118.
20. Jankowski, J., Tepel, M., Stephan, N., et al. (2001). Characterization of p-hydroxy-hippuric acid as an inhibitor of Ca2+ -ATPase in end-stage renal failure. Kidney International Supplement, 78, S84-S88.
21. Jia, L., Chen, J., Yin, P., Lu, X., & Xu, G. (2008a). Serum metabonomics study of chronic renal failure by ultra performance liquid chromatography coupled with Q-TOF mass spectrometry. Metabolomics, 4, 183-189.
22. Jia, L., Schweikart, K., Tomaszewski, J., et al. (2008b). Toxicology and pharmacokinetics of 1-methyl-d-tryptophan: absence of toxicity due to saturating absorption. Food and Chemical Toxicology, 46, 203-211.
23. Jia, L., Wang, C., Zhao, S., Lu, X., & Xu, G. (2007). Metabolomic identification of potential phospholipid biomarkers for chronic glomerulonephritis by using high performance liquid chromatography-mass spectrometry. Journal of Chromatography B, 860, 134-140.
24. Jiye, A., Trygg, J., Gullberg, J., et al. (2005). Extraction and GC/MS analysis of the human blood plasma metabolome. Analytical Chemistry, 77, 8086-8094.
25. Jourde-Chiche, N., Dou, L., Cerini, C., Dignat-George, F., Vanholder, R., & Brunet, P. (2009). Protein-bound toxins-update 2009. Seminars in Dialysis, 22, 334-339.
26. Ju, W., Smith, S., & Kretzler, M. (2012). Genomic biomarkers for chronic kidney disease. Translational Research, 159, 290-302.
27. Kikuchi, K., Itoh, Y., Tateoka, R., Ezawa, A., Murakami, K., & Niwa, T. (2010). Metabolomic analysis of uremic toxins by liquid chromatography/electrospray ionization-tandem mass spectrometry. Journal of Chromatography B, 878, 1662-1668.
28. Kind, T., Wohlgemuth, G., Lee, D. Y., et al. (2009). FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Analytical Chemistry, 81, 10038-10048.
29. Kumps, A., Duez, P., & Mardens, Y. (2002). Metabolic, nutritional, iatrogenic, and artifactual sources of urinary organic acids: a comprehensive table. Clinical Chemistry, 48, 708-717.
30. Kussmann, M., Raymond, F., & Affolter, M. (2006). OMICS-driven biomarker discovery in nutrition and health. Journal of Biotechnology, 124, 758-787.
31. Lawrence, J. R., Peter, R., Baxter, G. J., Robson, J., Graham, A. B., & Paterson, J. R. (2003). Urinary excretion of salicyluric and salicylic acids by non-vegetarians, vegetarians, and patients taking low dose aspirin. Journal of Clinical Pathology, 56(9), 651-653.
32. Lees, H., Swann, J. R., Wilson, I. D., Nicholson, J. K., & Holmes, E. (2013). Hippurate: the natural history of a mammalian-microbial co-metabolite. Journal of Proteome Research. doi: 10. 1021/pr300900b.
33. Levey, A. S., Coresh, J., Balk, E., et al. (2003). National kidney foundation practice guidelines for chronic kidney disease: evaluation, classification, and stratification. Annals of Internal Medicine, 139, 137-147.
34. Lipkin, G. W., Forbes, M. A., Cooper, E. H., & Turney, J. H. (1993). Hyaluronic acid metabolism and its clinical significance in patients treated by continuous ambulatory peritoneal dialysis. Nephrology Dialysis Transplantation, 8(4), 357-360.
35. Meert, N., Schepers, E., Glorieux, G., et al. (2012). Novel method for simultaneous determination of p-cresylsulphate and p-cresylglucuronide: Clinical data and pathophysiological implications. Nephrology Dialysis Transplantation, 27, 2388-2396.
36. Mischak, H., Allmaier, G., Apweiler, R., et al. (2010). Recommendations for biomarker identification and qualification in clinical proteomics. Science Translational Medicicne, 2(46), 46ps42.
37. Mischak, H., Massy, Z. A., & Jankowski, J. (2009). Proteomics in uremia and renal disease. Seminars in Dialysis, 22, 409-416.
38. Niwa, T., Takeda, N., & Yoshizumi, H. (1998). RNA metabolism in uremic patients: Accumulation of modified ribonucleosides in uremic serum-Technical note. Kidney International, 53, 1801-1806.
39. Palazoglu, M., & Fiehn, O. (2009). Metabolite identification in blood plasma using GC/MS and the Agilent Fiehn GC/MS metabolomics RTL library. Agilent Application Note 5990-3638EN. Palo Alto, CA: Agilent Technologies.
40. Perco, P., Pleban, C., Kainz, A., et al. (2006). Protein biomarkers associated with acute renal failure and chronic kidney disease. European Journal of Clinical Investigation, 36, 753-763.
41. Pero, R. W. (2010). Health consequences of catabolic synthesis of hippuric acid in humans. Current Clinical Pharmacology, 5(1), 67-73.
42. Pletinck, A., Vanholder, R., & Glorieux, G. (2012). p-Cresyl sulfate. In T. Niwa (Ed.), Uremic toxins. Hoboken: Wiley. doi: 10. 1002/9781118424032. ch5.
43. Qi, S., Ouyang, X., Wang, L., Peng, W., Wen, J., & Dai, Y. (2012). A pilot metabolic profiling study in serum of patients with chronic kidney disease based on (1) H-NMR-spectroscopy. Clinical and Translational Science, 5(5), 379-385.
44. Rechner, A. R., Spencer, J. P., Kuhnle, G., Hahn, U., & Rice-Evans, C. A. (2001). Novel biomarkers of the metabolism of caffeic acid derivatives in vivo. Free Radical Biology & Medicine, 30(11), 1213-1222.
45. Rhee, E. P., Souza, A., Farrell, L., et al. (2010). Metabolite profiling identifies markers of uremia. Journal of the American Society of Nephrology, 21, 1041-1051.
46. Salisbury, P. F., Dunn, M. S., & Murphy, E. A. (1957). Apparent free amino acids in deproteinized plasma of normal and uremic persons. Journal of clinical Investigation, 36, 1227-1232.
47. Sana, T. R., Roark, J. C., Li, X., Waddell, K., & Fischer, S. M. (2008). Molecular formula and METLIN personal metabolite database matching applied to the identification of compounds generated by LC/TOF-MS. Journal of Biomolecular Techniques, 19(4), 258-266.
48. Sato, E., Kohno, M., Yamamoto, M., Fujisawa, T., Fujiwara, K., & Tanaka, N. (2011). Metabolomic analysis of human plasma from haemodialysis patients. European Journal of Clinical Investigation, 41, 241-255.
49. Seppala, R., Renlund, M., Bernardini, I., Tietze, F., & Gahl, W. A. (1990). Renal handling of free sialic acid in normal humans and patients with Salla disease or renal disease. Laboratory Investigation, 63(2), 197-203.
50. Shah, V. O., Townsend, R. R., Feldman, H. I., Pappan, K. L., Kensicki, E., & Vander Jagt, D. L. (2013). Plasma metabolomic profiles in different stages of CKD. Clinical Journal of the American Society of Nephrology. doi: 10. 2215/CJN. 05540512.
51. Smith, C. A., O'Maille, G., Want, E. J., et al. (2005). METLIN: A metabolite mass spectral database. Therapeutic Drug Monitoring, 27(6), 747-751.
52. Smith, C. A., Want, E. J., O'Maille, G., Abagyan, R., & Siuzdak, G. (2006). XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Analytical Chemistry, 78(3), 779-787.
53. Spagou, K., Wilson, I. D., Masson, P., et al. (2011). HILIC-UPLC-MS for exploratory urinary metabolic profiling in toxicological studies. Analytical Chemistry, 83, 382-390.
54. Spasovski, G., Ortiz, A., Vanholder, R., & El Nahas, M. (2011). Proteomics in chronic kidney disease: The issues clinical nephrologists need an answer for. Proteomics Clinical Applications, 5, 233-240.
55. Stanislaus, A., Guo, K., & Li, L. (2012). Development of an isotope labeling ultra-high performance liquid chromatography mass spectrometric method for quantification of acylglycines in human urine. Analytica Chimica Acta, 750, 161-172.
56. T'Kindt, R., Scheltema, R. A., Jankevics, A., et al. (2010). Metabolomics to unveil and understand phenotypic diversity between pathogen populations. PLoS Neglected Tropical Diseases, 4(11), e904.
57. Tao, X., Liu, Y., Wang, Y., et al. (2008). GC-MS with ethyl chloroformate derivatization for comprehensive analysis of metabolites in serum and its application to human uremia. Analytical and Bioanalytical Chemistry, 391, 2881-2889.
58. Tautenhahn, R., Cho, K., Uritboonthai, W., Zhu, Z., Patti, G. J., & Siuzdak, G. (2012). An accelerated workflow for untargeted metabolomics using the METLIN database. Nature Biotechnology, 30(9), 826-828.
59. Toyohara, T., Akiyama, Y., Suzuki, T., et al. (2010). Metabolomic profiling of uremic solutes in CKD patients. Hypertension Research, 33, 944-952.
60. Turney, J. H., Davison, A. M., Forbes, M. A., & Cooper, E. H. (1991). Hyaluronic acid in end-stage renal failure treated by haemodialysis: clinical correlates and implications. Nephrology Dialysis Transplantation, 6, 566-570.
61. Vanholder, R., Bammens, B., de Loor, H., et al. (2011). Warning: the unfortunate end of p-cresol as a uraemic toxin. Nephrology Dialysis Transplantation, 26, 1464-1467.
62. Vanholder, R., De Smet, R., Glorieux, G., et al. (2003a). Review on uremic toxins: Classification, concentration, and interindividual variability. Kidney International, 63, 1934-1943.
63. Vanholder, R., Glorieux, G., De Smet, R., & Lameire, N. (2003b). New insights in uremic toxins. Kidney International, 63, S6-S10.
64. Vaziri, N. D. (2012). CKD impairs barrier function and alters microbial flora of the intestine: a major link to inflammation and uremic toxicity. Current Opinion in Nephrology and Hypertension, 21(6), 587-592.
65. Vazquez, S., Truscott, R. J., O'Hair, R. A., Weimann, A., & Sheil, M. M. (2001). A study of kynurenine fragmentation using electrospray tandem mass spectrometry. Journal of the American Society for Mass Spectrometry, 12(7), 786-794.
66. Weimann, A., Sabroe, M., & Poulsen, H. E. (2005). Measurement of caffeine and five of the major metabolites in urine by high-performance liquid chromatography/tandem mass spectrometry. Journal of Mass Spectrometry, 40, 307-316.
67. Weiss, R. H., & Kim, K. (2012). Metabolomics in the study of kidney diseases. Nature Reviews Nephrology, 8, 22-33.
68. Wu, I., & Parikh, C. R. (2008). Screening for kidney diseases: Older measures versus novel biomarkers. Clinical Journal American Society of Nephrology, 3, 1895-1901.
69. Zhao, Y. Y., Cheng, X. L., Wei, F., et al. (2012a). Serum metabonomics study of adenine-induced chronic renal failure in rats by ultra performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Biomarkers, 17, 48-55.
70. Zhao, Y. Y., Liu, J., Cheng, X. L., Bai, X., & Lin, R. C. (2012b). Urinary metabonomics study on biochemical changes in an experimental model of chronic renal failure by adenine based on UPLC Q-TOF/MS. Clinica Chimica Acta, 413, 642-649.
71. Zhu, Z. J., Schultz, A. W., Wang, J., et al. (2013). Liquid chromatography quadrupole time-of-flight mass spectrometry characterization of metabolites guided by the METLIN database. Nature Protocols, 8(3), 451-460.