Systematic Re-evaluation of the Long-used Standard Protocol of Urease-dependent Metabolome Sample Preparation

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2020 Mar 18

PMID 32182259

Citations 5

Authors

Jungyeon Kim

Joong Kyong Ahn

Yu Eun Cheong

Sung-Joon Lee

Hoon-Suk Cha

Kyoung Heon Kim

Affiliations

Soon will be listed here.

Abstract

In the urinary metabolomics for finding biomarkers in urine, owing to high concentrations of urea, for chromatography-based metabolomic analysis, urea needed to be degraded by urease. This urease pretreatment has been the key step of sample preparation for standard urinary metabolomics until today even for mass spectrometry-based analysis. The urease pretreatment involving incubation of urine with urease contradicts the concept of metabolome sampling, which should immediately arrest metabolic reactions to prevent alterations of a metabolite profile. Nonetheless, the impact of urease pretreatment has not been clearly elucidated yet. We found that activities of urease and endogenous urinary enzymes and metabolite contaminants from the urease preparations introduce artefacts into metabolite profiles, thus leading to misinterpretation.

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References

Kamijo A, Sugaya T, Hikawa A, Okada M, Okumura F, Yamanouchi M . Urinary excretion of fatty acid-binding protein reflects stress overload on the proximal tubules. Am J Pathol. 2004; 165(4):1243-55. PMC: 1618632. DOI: 10.1016/S0002-9440(10)63384-6. View

Hult K, Berglund P . Enzyme promiscuity: mechanism and applications. Trends Biotechnol. 2007; 25(5):231-8. DOI: 10.1016/j.tibtech.2007.03.002. View

Kind T, Wohlgemuth G, Lee D, Lu Y, Palazoglu M, Shahbaz S . FiehnLib: mass spectral and retention index libraries for metabolomics based on quadrupole and time-of-flight gas chromatography/mass spectrometry. Anal Chem. 2009; 81(24):10038-48. PMC: 2805091. DOI: 10.1021/ac9019522. View

Johnson C, Ivanisevic J, Siuzdak G . Metabolomics: beyond biomarkers and towards mechanisms. Nat Rev Mol Cell Biol. 2016; 17(7):451-9. PMC: 5729912. DOI: 10.1038/nrm.2016.25. View

Masson P, Alves A, Ebbels T, Nicholson J, Want E . Optimization and evaluation of metabolite extraction protocols for untargeted metabolic profiling of liver samples by UPLC-MS. Anal Chem. 2010; 82(18):7779-86. DOI: 10.1021/ac101722e. View

Dixon N, Riddles P, Gazzola C, Blakeley R, ZERNER B . Jack bean urease (EC 3.5.1.5). V. On the mechanism of action of urease on urea, formamide, acetamide, N-methylurea, and related compounds. Can J Biochem. 1980; 58(12):1335-44. DOI: 10.1139/o80-181. View

Tekiner P, Percin I, Ergun B, Yavuz H, Aksoz E . Purification of urease from jack bean (Canavalia ensiformis) with copper (II) chelated poly(hydroxyethyl methacrylate-N-methacryloyl-(L)-histidine methyl ester) cryogels. J Mol Recognit. 2012; 25(11):549-54. DOI: 10.1002/jmr.2204. View

Idborg H, Zamani L, Edlund P, Schuppe-Koistinen I, Jacobsson S . Metabolic fingerprinting of rat urine by LC/MS Part 1. Analysis by hydrophilic interaction liquid chromatography-electrospray ionization mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2005; 828(1-2):9-13. DOI: 10.1016/j.jchromb.2005.07.031. View

Shin M, Lee D, Liu K, Fiehn O, Kim K . Evaluation of sampling and extraction methodologies for the global metabolic profiling of Saccharophagus degradans. Anal Chem. 2010; 82(15):6660-6. DOI: 10.1021/ac1012656. View

10.

Menzies I . Quantitative estimation of sugars in blood and urine by paper chromatography using direct densitometry. J Chromatogr. 1973; 81(1):109-27. DOI: 10.1016/s0021-9673(01)82322-0. View

11.

Bornscheuer U, Kazlauskas R . Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways. Angew Chem Int Ed Engl. 2004; 43(45):6032-40. DOI: 10.1002/anie.200460416. View

12.

Ni Y, Xie G, Jia W . Metabonomics of human colorectal cancer: new approaches for early diagnosis and biomarker discovery. J Proteome Res. 2014; 13(9):3857-70. DOI: 10.1021/pr500443c. View

13.

Chu V, Gottardo R, Raftery A, Bumgarner R, Yeung K . MeV+R: using MeV as a graphical user interface for Bioconductor applications in microarray analysis. Genome Biol. 2008; 9(7):R118. PMC: 2530872. DOI: 10.1186/gb-2008-9-7-r118. View

14.

Kasai T, Ogo Y, Otobe Y, Kiriyama S . Accumulation of hypotaurine in tissues and urine of rats fed an excess methionine diet. J Nutr Sci Vitaminol (Tokyo). 1992; 38(1):93-101. DOI: 10.3177/jnsv.38.93. View

15.

Thevenot E, Roux A, Xu Y, Ezan E, Junot C . Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses. J Proteome Res. 2015; 14(8):3322-35. DOI: 10.1021/acs.jproteome.5b00354. View

16.

Ferrannini E, Muscelli E, Frascerra S, Baldi S, Mari A, Heise T . Metabolic response to sodium-glucose cotransporter 2 inhibition in type 2 diabetic patients. J Clin Invest. 2014; 124(2):499-508. PMC: 3904627. DOI: 10.1172/JCI72227. View

17.

So A, Thorens B . Uric acid transport and disease. J Clin Invest. 2010; 120(6):1791-9. PMC: 2877959. DOI: 10.1172/JCI42344. View

18.

Thompson J, Markey S . Quantitative metabolic profiling of urinary organic acids by gas chromatography-mass spectrometry: comparison of isolation methods. Anal Chem. 1975; 47(8):1313-21. DOI: 10.1021/ac60358a074. View

19.

Fiehn O . Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. Comp Funct Genomics. 2008; 2(3):155-68. PMC: 2447208. DOI: 10.1002/cfg.82. View

20.

Mashego M, Rumbold K, De Mey M, Vandamme E, Soetaert W, Heijnen J . Microbial metabolomics: past, present and future methodologies. Biotechnol Lett. 2006; 29(1):1-16. DOI: 10.1007/s10529-006-9218-0. View