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Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GAN, Raftery D, Steinbeck C, Salek RM, Wishart DS. Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis. J Proteome Res 2016; 15:360-73. [PMID: 26745651 PMCID: PMC4865177 DOI: 10.1021/acs.jproteome.5b00885] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many "unwanted" or "undesirable" compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment.
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Affiliation(s)
- Abdul-Hamid Emwas
- Imaging and Characterization Core Lab, KAUST , Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Raja Roy
- Centre of Biomedical Research, formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus , Lucknow, Uttar Pradesh, India
| | - Ryan T McKay
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada
| | - Danielle Ryan
- School of Agricultural and Wine Sciences, Charles Sturt University , Bathurst, New South Wales, Australia
| | - Lorraine Brennan
- UCD Insitute of Food and Health, UCD , Belfield, Dublin, Ireland
| | - Leonardo Tenori
- FiorGen Foundation , 50019 Sesto Fiorentino, Florence, Italy
| | - Claudio Luchinat
- Centro Risonanze Magnetiche - CERM, University of Florence , Florence, Italy
| | - Xin Gao
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ana Carolina Zeri
- Brazilian Biosciences National Laboratory, LNBio , Campinas, São Paulo, Brazil
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States.,Fred Hutchinson Cancer Research Center , 1100 Fairview Avenue, Seattle, Washington 98109, United States
| | - Christoph Steinbeck
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David S Wishart
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta, Canada
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Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS. Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review. Metabolomics 2015; 11:872-894. [PMID: 26109927 PMCID: PMC4475544 DOI: 10.1007/s11306-014-0746-7] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 10/27/2014] [Indexed: 02/08/2023]
Abstract
The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.
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Affiliation(s)
- Abdul-Hamid Emwas
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology, KSA, Thuwal, Saudi Arabia
| | - Claudio Luchinat
- Centro Risonanze Magnetiche – CERM, University of Florence, Florence, Italy
| | - Paola Turano
- Centro Risonanze Magnetiche – CERM, University of Florence, Florence, Italy
| | | | - Raja Roy
- Centre of Biomedical Research, Formerly known as Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow, India
| | - Reza M. Salek
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD UK
| | - Danielle Ryan
- School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Jasmeen S. Merzaban
- Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, KSA, Thuwal, Saudi Arabia
| | - Rima Kaddurah-Daouk
- Pharmacometabolomics Center, School of Medicine, Duke University, Durham, USA
| | - Ana Carolina Zeri
- Brazilian Biosciences National Laboratory, LNBio, Campinas, SP Brazil
| | - G. A. Nagana Gowda
- Department of Anethesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, 850 Republican St., Seattle, WA 98109 USA
| | - Daniel Raftery
- Department of Anethesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, 850 Republican St., Seattle, WA 98109 USA
| | - Yulan Wang
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Beijing, China
| | - Lorraine Brennan
- Institute of Food and Health and Conway Institute, School of Agriculture & Food Science, Dublin 4, Ireland
| | - David S. Wishart
- Department of Computing Science, University of Alberta, Edmonton, Alberta Canada
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Duarte ML, Zeri AC, Krieger JE, Schechtman D. Identifying targets and characterizing the role of aPKCs in murine embryonic stem cells. FASEB J 2012. [DOI: 10.1096/fasebj.26.1_supplement.985.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mariana Lemos Duarte
- Departamento de Bioquímica do Instituto de QuímicaUniverisdade de São PauloSão PauloBrazil
| | | | | | - Deborah Schechtman
- Departamento de Bioquímica do Instituto de QuímicaUniverisdade de São PauloSão PauloBrazil
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de Oliveira JF, Castilho BA, Sforça ML, Krieger MA, Zeri AC, Guimarães BG, Zanchin NI. Characterization of the Trypanosoma cruzi ortholog of the SBDS protein reveals an intrinsically disordered extended C-terminal region showing RNA-interacting activity. Biochimie 2009; 91:475-83. [DOI: 10.1016/j.biochi.2008.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Accepted: 12/05/2008] [Indexed: 10/21/2022]
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Affiliation(s)
- Stanley J. Opella
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093;
| | - Ana Carolina Zeri
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093;
| | - Sang Ho Park
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093;
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Zeri AC, Mesleh MF, Nevzorov AA, Opella SJ. Structure of the coat protein in fd filamentous bacteriophage particles determined by solid-state NMR spectroscopy. Proc Natl Acad Sci U S A 2003; 100:6458-63. [PMID: 12750469 PMCID: PMC164468 DOI: 10.1073/pnas.1132059100] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The atomic resolution structure of fd coat protein determined by solid-state NMR spectroscopy of magnetically aligned filamentous bacteriophage particles differs from that previously determined by x-ray fiber diffraction. Most notably, the 50-residue protein is not a single curved helix, but rather is a nearly ideal straight helix between residues 7 and 38, where there is a distinct kink, and then a straight helix with a different orientation between residues 39 and 49. Residues 1-5 have been shown to be mobile and unstructured, and proline 6 terminates the helix. The structure of the coat protein in virus particles, in combination with the structure of the membrane-bound form of the same protein in bilayers, also recently determined by solid-state NMR spectroscopy, provides insight into the viral assembly process. In addition to their roles in molecular biology and biotechnology, the filamentous bacteriophages continue to serve as model systems for the development of experimental methods for determining the structures of proteins in biological supramolecular assemblies. New NMR results include the complete sequential assignment of the two-dimensional polarization inversion spin-exchange at the magic angle spectrum of a uniformly 15N-labeled 50-residue protein in a 1.6 x 107 Da particle in solution, and the calculation of the three-dimensional structure of the protein from orientational restraints with an accuracy equivalent to an rms deviation of approximately 1A.
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Affiliation(s)
- Ana Carolina Zeri
- Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla 92093, USA
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Veglia G, Zeri AC, Ma C, Opella SJ. Deuterium/hydrogen exchange factors measured by solution nuclear magnetic resonance spectroscopy as indicators of the structure and topology of membrane proteins. Biophys J 2002; 82:2176-83. [PMID: 11916873 PMCID: PMC1302011 DOI: 10.1016/s0006-3495(02)75564-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Deuterium/hydrogen exchange factors (chi) were measured for the backbone amide sites of the membrane-bound forms of the 50-residue fd coat protein and the 23-residue magainin2 peptide in lipid micelles by solution nuclear magnetic resonance spectroscopy. By combining kinetic and thermodynamic effects, deuterium/hydrogen exchange factors overcome the principal limitations encountered in the measurements of kinetic protection factors and thermodynamic fractionation factors for membrane proteins. The magnitudes of the exchange factors can be correlated with the structure and topology of membrane-associated polypeptides. In fd coat protein, residues in the transmembrane helix have exchange factors that are substantially smaller than those in the amphipathic surface helix or the loop connecting the two helices. For the amphipathic helical peptide, magainin2, the exchange factors of residues exposed to the solvent are appreciably larger than those that face the hydrocarbon portion of membrane bilayers. These examples demonstrate that deuterium/hydrogen exchange factors can be measured by solution NMR spectroscopy and used to identify residues in transmembrane helices as well as to determine the polarity of amphipathic helices in membrane proteins.
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Affiliation(s)
- Gianluigi Veglia
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Abstract
We report direct measurements of entropic interactions of colloidal spheres in suspensions of rodlike fd bacteriophage. We investigate the influence of sphere size, rod concentration, and ionic strength on these interactions. Although the results compare favorably with a recent calculation, small discrepancies reveal entropic effects due to rod flexibility. At high salt concentrations, the potential turns repulsive as a result of viral adsorption on the spheres and viral bridging between the spheres.
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Affiliation(s)
- K Lin
- Department of Physics and Astronomy, University of Pennsylvania, 209 S. 33rd Street, Philadelphia, Pennsylvania 19104-6396, USA
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Rosay M, Zeri AC, Astrof NS, Opella SJ, Herzfeld J, Griffin RG. Sensitivity-enhanced NMR of biological solids: dynamic nuclear polarization of Y21M fd bacteriophage and purple membrane. J Am Chem Soc 2001; 123:1010-1. [PMID: 11456650 DOI: 10.1021/ja005659j] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M Rosay
- Department of Chemistry and Francis Bitter Magnet Laboratory Massachusetts Institute of Technology Cambridge, Massachusetts 02139, USA
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Abstract
Triple-resonance solid-state NMR spectroscopy is demonstrated to sequentially assign the 13C' and 15N amide backbone resonances of adjacent residues in an oriented protein sample. The observed 13C' chemical shift frequency provides an orientational constraint complementary to those measured from the 1H and 15N amide resonances in double-resonance experiments.
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Affiliation(s)
- W M Tan
- Department of Chemistry, University of Pennsylvania, Philadelphia 19104, USA
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