Method validation for preparing urine samples for downstream proteomic and metabolomic applications

Biopreservation and Biobanking

Volumn 12, Issue 5, 2014, Pages 351-357

  Ammerlaan, Wim ^a   Trezzi, Jean Pierre ^a,b   Mathay, Conny ^a   Hiller, Karsten ^b   Betsou, Fay ^a  

^a INTEGRATED BIOBANK OF LUXEMBOURG   (Luxembourg)

^b UNIVERSITY OF LUXEMBOURG   (Luxembourg)

Author keywords

[No Author keywords available]

Indexed keywords

CREATININE; CYSTATIN C; CYSTATIN; PROTEOME;

ARTICLE; CENTRIFUGATION; FITNESS; METABOLOMICS; PROTEOMICS; REPRODUCIBILITY; ROOM TEMPERATURE; TEMPERATURE; URINALYSIS; ADULT; CELL FREE SYSTEM; FEMALE; HUMAN; MALE; MEMBRANE MICROPARTICLE; METABOLISM; METABOLOME; MIDDLE AGED; PROCEDURES; URINE;

ADULT; CELL-DERIVED MICROPARTICLES; CELL-FREE SYSTEM; CREATININE; CYSTATINS; FEMALE; HUMANS; MALE; METABOLOME; MIDDLE AGED; PROTEOME; REPRODUCIBILITY OF RESULTS; TEMPERATURE; URINE SPECIMEN COLLECTION;

EID: 84912017031     PISSN: 19475535     EISSN: 19475543     Source Type: Journal    
DOI: 10.1089/bio.2014.0013     Document Type: Article

References (40)

1. Bowers J. CAP takes the reins on biorepository accreditation. CAP Today Coll Am Pathol. October 2012. http:// www.cap.org/apps/cap.portal. Reference resources and publications/CAP Today/2012 Articles.
2. Technical Standard NF S96-900. [Quality in the Biology Resource Centers (BRC) - Management system of a BRC and quality of the biological resources] in French. September 2011.
3. Ammerlaan W, Trezzi J, Lescuyer P, et al. Method validation for preparing serum and plasma samples from human blood for downstream proteomic, metabolomic and circulating nucleic acid-based applications. Biopreserv Biobank 2014;12:269-280.
4. Lafitte D, Dussol B, Andersen S, et al. Optimized preparation of urine samples for two-dimensional electrophoresis and initial application to patient samples. Clin Biochem 2002;35:581-589.
5. Latterich M, Abramovitz M, Leyland-Jones B. Proteomics: New technologies and clinical applications. Eur J Cancer 2008;44:2737-2741.
6. Sharma K, Karl B, Mathew AV, et al. Metabolomics reveals signature of mitochondrial dysfunction in diabetic kidney disease. J Am Soc Nephrol 2013;24:1901-1912.
7. Fanos V, Locci E, Noto A, et al. Urinary metabolomics in newborns infected by human cytomegalovirus: A preliminary investigation. Early Hum Dev 2013;89 Suppl 1:S58-61.
8. Nair H, Woo F, Hoofnagle AN, et al. Clinical validation of a highly sensitive GC-MS platform for routine urine drug screening and real-time Rreporting of up to 212 drugs. J Toxicol 2013;2013:329407.
9. Kim JW, Ryu SH, Kim S, et al. Pattern recognition analysis for hepatotoxicity induced by acetaminophen using plasma and urinary 1H NMR-based metabolomics in humans. Anal Chem 2013;85:11326-11334.
10. Favé G, Beckmann M, Lloyd AJ, et al. Development and validation of a standardized protocol to monitor human dietary exposure by metabolite fingerprinting of urine samples. Metabolomics 2011;7:469-484.
11. International Society for Biological and Environmental Repositories (ISBER). 2012 Best Practices for Repositories. Collection, storage, retrieval and distribution of biological materials for research. Third edition. Biopreserv Biobank 2012;10:79-161.
12. Canadian Tumor Repository Network. Standard Operating Procedures. https://www.ctrnet.ca/operating-procedures. Accessed February 2014.
13. Guerin J, Murray D, McGrath M, et al. Molecular Medicine Ireland Guidelines for Standardized Biobanking. Biopreserv Biobank 2010;8:3-63.
14. Lehmann S, Roche S, Allory Y, et al. [Preanalytical guidelines for clinical proteomics investigation of biological fluids] in French. Ann Biol Clin (Paris) 2009;67:629-639.
15. Thomas CE, Sexton W, Benson K, et al. Urine collection and processing for protein biomarker discovery and quantification. Cancer Epidemiol Biomarkers Prev 2010;19:953-959.
16. Human Kidney and Urine Proteome Project (HKUPP). Standard Protocol for Urine Collection and Storage (applicable for the analysis of soluble urine proteins; not for exosome analysis). Normal Urine (Adults). http://www.hkupp.org/Urine%20 collectiion%20Documents.html. Accessed February 2014.
17. Medeiros M, Sharma VK, Ding R, et al. Optimization of RNA yield, purity and mRNA copy number by treatment of urine cell pellets with RNAlater. J Immunol Methods 2003;279:135-142.
18. Gaydos CA, Quinn TC. Urine nucleic acid amplification tests for the diagnosis of sexually transmitted infections in clinical practice. Curr Opin Infect Dis 2005;18:55-66.
19. Pisitkun T, Shen R-F, Knepper MA. Identification and proteomic profiling of exosomes in human urine. PNAS 2004;101:13368-13373.
20. Hayward RM, Kirk MJ, Sproull M, et al. Post-collection, pre-measurement variables affecting VEGF levels in urine biospecimens. J Cell Mol Med 2008;12:343-350.
21. Zhou H, Yuen PST, Pisitkun T, et al. Collection, storage, preservation, and normalization of human urinary exosomes for biomarker discovery. Kidney Int 2006;69:1471-1476.
22. Uchida K, Gotoh A. Measurement of cystatin-C and creatinine in urine. Clin Chim Acta 2002;323:121-128.
23. Hiller K, Hangebrauk J, Jäger C, et al. MetaboliteDetector: Comprehensive analysis tool for targeted and nontargeted GC/ MS based metabolome analysis. Anal Chem 2009;81:3429-3439.
24. Yan L, Borregaard N, Kjeldsen L, et al. The high molecular weight urinary matrix metalloproteinase (MMP) activity is a complex of gelatinase B/MMP-9 and neutrophil gelatinaseassociated lipocalin (NGAL). Modulation of MMP-9 activity by NGAL. J Biol Chem 2001;276:37258-37265.
25. Quinto BM, Juliano MA, Hirata I, et al. Characterization of a prolyl endopeptidase (kininase) from human urine using fluorogenic quenched substrates. Int J Biochem Cell Biol 2000;32:1161-1172.
26. Schauer-Vukasinovic V, Langen H, Giller T. Detection of immunoreactive napsin A in human urine. Biochim Biophys Acta 2001;1524:51-56.
27. Saude EJ, Sykes BD. Urine stability for metabolomic studies: effects of preparation and storage. Metabolomics 2007;3:19-27.
28. Lewis DA, Brown R, Williams J, et al. The human urinary microbiome; bacterial DNA in voided urine of asymptomatic adults. Front Cell Infect Microbiol 2013;3:41.
29. Froom P, Bieganiec B, Ehrenrich Z, et al. Stability of common analytes in urine refrigerated for 24 h before automated analysis by test strips. Clin Chem 2000;46:1384-1386.
30. Kouri T, Malminiemi O, Penders J, et al. Limits of preservation of samples for urine strip tests and particle counting. Clin Chem Lab Med 2008;46:703-713.
31. Papale M, Pedicillo MC, Thatcher BJ, et al. Urine profiling by SELDI-TOF/MS: Monitoring of the critical steps in sample collection, handling and analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2007;856:205-213.
32. Spierto FW, Hannon WH, Gunter EW, et al. Stability of urine creatinine. Clin Chim Acta 1997;264:227-232.
33. Herget-Rosenthal S, Feldkamp T, Volbracht L, et al. Measurement of urinary cystatin C by particle-enhanced nephelometric immunoassay: Precision, interferences, stability and reference range. Ann Clin Biochem 2004;41:111-118.
34. Parikh CR, Butrymowicz I, Yu A, et al. Urine stability studies for novel biomarkers of acute kidney injury. Am J Kidney Dis 2014;63:567-572.
35. Vu NT, Chaturvedi AK, Canfield DV. Genotyping for DQA1 and PM loci in urine using PCR-based amplification: Effects of sample volume, storage temperature, preservatives, and aging on DNA extraction and typing. Forensic Sci Int 1999;102:23-34.
36. Gonzales PA, Zhou H, Pisitkun T, et al. Isolation and purification of exosomes in urine. MethodsMol Biol 2010;641:89-99.
37. Calvano CD, Aresta A, Iacovone M, et al. Optimization of analytical and pre-analytical conditions for MALDI-TOFMS human urine protein profiles. J Pharm Biomed Anal 2010;51:907-914.
38. Court M, Selevsek N, Matondo M, et al. Toward a standardized urine proteome analysis methodology. Proteomics 2011;11:1160-1171.
39. Betsou F, Lehmann S, Ashton G, et al. Standard preanalytical coding for biospecimens: Defining the sample PREanalytical code. Cancer Epidemiol Biomarkers Prev 2010;19:1004-1011.
40. Lehmann R, F. Guadagni, H. Moore, et al. Standard preanalytical coding for biospecimens: Review and implementation of the Sample PREanalytical Code (SPREC). Biopreserv Biobank 2012;10:366-374.