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Exosomes in Urine Biomarker Discovery

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Book cover Urine Proteomics in Kidney Disease Biomarker Discovery

Abstract

Nanovesicles present in urine the so-called urinary exosomes have been found to be secreted by every epithelial cell type lining the urinary tract system in human. Urinary exosomes are an appealing source for biomarker discovery as they contain molecular constituents of their cell of origin, including proteins and genetic materials, and they can be isolated in a non-invasive manner. Following the discovery of urinary exosomes in 2004, many studies have been performed using urinary exosomes as a starting material to identify biomarkers in various renal, urogenital, and systemic diseases. Here, we describe the discovery of urinary exosomes and address the issues on the collection, isolation, and normalization of urinary exosomes as well as delineate the systems biology approach to biomarker discovery using urinary exosomes.

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References

  1. Bobrie A, Colombo M, Raposo G, Thery C (2011) Exosome secretion: molecular mechanisms and roles in immune responses. Traffic 12(12):1659–1668. doi:10.1111/j.1600-0854.2011.01225.x

    Article  PubMed  CAS  Google Scholar 

  2. Pisitkun T, Shen RF, Knepper MA (2004) Identification and proteomic profiling of exosomes in human urine. Proc Natl Acad Sci USA 101(36):13368–13373. doi:10.1073/pnas.0403453101

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  3. Cheruvanky A, Zhou H, Pisitkun T, Kopp JB, Knepper MA, Yuen PS, Star RA (2007) Rapid isolation of urinary exosomal biomarkers using a nanomembrane ultrafiltration concentrator. Am J Physiol Ren Physiol 292(5):F1657–1661. doi:10.1152/ajprenal.00434.2006

    Article  CAS  Google Scholar 

  4. Hoorn EJ, Pisitkun T, Zietse R, Gross P, Frokiaer J, Wang NS, Gonzales PA, Star RA, Knepper MA (2005) Prospects for urinary proteomics: exosomes as a source of urinary biomarkers. Nephrology 10(3):283–290. doi:10.1111/j.1440-1797.2005.00387.x

    Article  PubMed  CAS  Google Scholar 

  5. Miranda KC, Bond DT, McKee M, Skog J, Paunescu TG, Da Silva N, Brown D, Russo LM (2010) Nucleic acids within urinary exosomes/microvesicles are potential biomarkers for renal disease. Kidney Int 78(2):191–199. doi:10.1038/ki.2010.106

    Article  PubMed  Google Scholar 

  6. Pisitkun T, Gandolfo MT, Das S, Knepper MA, Bagnasco SM (2012) Application of systems biology principles to protein biomarker discovery: urinary exosomal proteome in renal transplantation. Proteomics Clin Appl 6(5–6):268–278. doi:10.1002/prca.201100108

    Article  PubMed  CAS  Google Scholar 

  7. Pisitkun T, Johnstone R, Knepper MA (2006) Discovery of urinary biomarkers. Mol Cell Proteomics 5(10):1760–1771. doi:10.1074/mcp.R600004-MCP200

    Article  PubMed  CAS  Google Scholar 

  8. van Balkom BW, Pisitkun T, Verhaar MC, Knepper MA (2011) Exosomes and the kidney: prospects for diagnosis and therapy of renal diseases. Kidney Int 80(11):1138–1145. doi:10.1038/ki.2011.292

    Article  PubMed  PubMed Central  Google Scholar 

  9. van der Lubbe N, Jansen PM, Salih M, Fenton RA, van den Meiracker AH, Danser AH, Zietse R, Hoorn EJ (2012) The phosphorylated sodium chloride cotransporter in urinary exosomes is superior to prostasin as a marker for aldosteronism. Hypertension 60(3):741–748. doi:10.1161/HYPERTENSIONAHA.112.198135

    Article  PubMed  Google Scholar 

  10. Zhou H, Cheruvanky A, Hu X, Matsumoto T, Hiramatsu N, Cho ME, Berger A, Leelahavanichkul A, Doi K, Chawla K, Illei LS, Kopp GG, Balow JE, Austin HA 3rd, Yuen PS, Star RA (2008) Urinary exosomal transcription factors, a new class of biomarkers for renal disease. Kidney Int 74(5):613–621. doi:10.1038/ki.2008.206

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  11. Zhou H, Pisitkun T, Aponte A, Yuen PS, Hoffert JD, Yasuda H, Hu X, Chawla L, Shen RF, Knepper MA, Star RA (2006) Exosomal Fetuin-A identified by proteomics: a novel urinary biomarker for detecting acute kidney injury. Kidney Int 70(10):1847–1857. doi:10.1038/sj.ki.5001874

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  12. Zhou H, Yuen PS, Pisitkun T, Gonzales PA, Yasuda H, Dear JW, Gross P, Knepper MA, Star RA (2006) Collection, storage, preservation, and normalization of human urinary exosomes for biomarker discovery. Kidney Int 69(8):1471–1476. doi:10.1038/sj.ki.5000273

    PubMed  CAS  PubMed Central  Google Scholar 

  13. Kanno K, Sasaki S, Hirata Y, Ishikawa S, Fushimi K, Nakanishi S, Bichet DG, Marumo F (1995) Urinary excretion of aquaporin-2 in patients with diabetes insipidus. N Engl J Med 332(23):1540–1545. doi:10.1056/NEJM199506083322303

    Article  PubMed  CAS  Google Scholar 

  14. Wen H, Frokiaer J, Kwon TH, Nielsen S (1999) Urinary excretion of aquaporin-2 in rat is mediated by a vasopressin-dependent apical pathway. J Am Soc Nephrol 10(7):1416–1429

    PubMed  CAS  Google Scholar 

  15. Ishikawa SE, Schrier RW (2003) Pathophysiological roles of arginine vasopressin and aquaporin-2 in impaired water excretion. Clin Endocrinol 58(1):1–17

    Article  CAS  Google Scholar 

  16. McKee JA, Kumar S, Ecelbarger CA, Fernandez-Llama P, Terris J, Knepper MA (2000) Detection of Na(+) transporter proteins in urine. J Am Soc Nephrol 11(11):2128–2132

    PubMed  CAS  Google Scholar 

  17. Thery C, Zitvogel L, Amigorena S (2002) Exosomes: composition, biogenesis and function. Nat Rev Immunol 2(8):569–579. doi:10.1038/nri855

    PubMed  CAS  Google Scholar 

  18. Stoorvogel W, Kleijmeer MJ, Geuze HJ, Raposo G (2002) The biogenesis and functions of exosomes. Traffic 3(5):321–330

    Article  PubMed  CAS  Google Scholar 

  19. Gonzales PA, Pisitkun T, Hoffert JD, Tchapyjnikov D, Star RA, Kleta R, Wang NS, Knepper MA (2009) Large-scale proteomics and phosphoproteomics of urinary exosomes. J Am Soc Nephrol 20(2):363–379. doi:10.1681/ASN.2008040406

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  20. Wang Z, Hill S, Luther JM, Hachey DL, Schey KL (2012) Proteomic analysis of urine exosomes by multidimensional protein identification technology (MudPIT). Proteomics 12(2):329–338. doi:10.1002/pmic.201100477

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  21. Street JM, Birkhoff W, Menzies RI, Webb DJ, Bailey MA, Dear JW (2011) Exosomal transmission of functional aquaporin 2 in kidney cortical collecting duct cells. J Physiol 589(Pt 24):6119–6127. doi:10.1113/jphysiol.2011.220277

    PubMed  CAS  PubMed Central  Google Scholar 

  22. Oosthuyzen W, Sime NE, Ivy JR, Turtle EJ, Street JM, Pound J, Bath LE, Webb DJ, Gregory CD, Bailey MA, Dear JW (2013) Quantification of human urinary exosomes by nanoparticle tracking analysis. J Physiol. doi:10.1113/jphysiol.2013.264069

    PubMed  Google Scholar 

  23. Raj DA, Fiume I, Capasso G, Pocsfalvi G (2012) A multiplex quantitative proteomics strategy for protein biomarker studies in urinary exosomes. Kidney Int 81(12):1263–1272. doi:10.1038/ki.2012.25

    Article  PubMed  CAS  Google Scholar 

  24. Chen CY, Hogan MC, Ward CJ (2013) Purification of exosome-like vesicles from urine. Methods Enzymol 524:225–241. doi:10.1016/B978-0-12-397945-2.00013-5

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  25. Rood IM, Deegens JK, Merchant ML, Tamboer WP, Wilkey DW, Wetzels JF, Klein JB (2010) Comparison of three methods for isolation of urinary microvesicles to identify biomarkers of nephrotic syndrome. Kidney Int 78(8):810–816. doi:10.1038/ki.2010.262

    Article  PubMed  CAS  Google Scholar 

  26. Merchant ML, Powell DW, Wilkey DW, Cummins TD, Deegens JK, Rood IM, McAfee KJ, Fleischer C, Klein E, Klein JB (2010) Microfiltration isolation of human urinary exosomes for characterization by MS. Proteomics Clin Appl 4(1):84–96. doi:10.1002/prca.200800093

    Article  PubMed  CAS  Google Scholar 

  27. Alvarez ML, Khosroheidari M, Kanchi Ravi R, DiStefano JK (2012) Comparison of protein, microRNA, and mRNA yields using different methods of urinary exosome isolation for the discovery of kidney disease biomarkers. Kidney Int 82(9):1024–1032. doi:10.1038/ki.2012.256

    Article  PubMed  CAS  Google Scholar 

  28. Fernandez-Llama P, Khositseth S, Gonzales PA, Star RA, Pisitkun T, Knepper MA (2010) Tamm-Horsfall protein and urinary exosome isolation. Kidney Int 77(8):736–742. doi:10.1038/ki.2009.550

    Article  PubMed  PubMed Central  Google Scholar 

  29. Pisitkun T, Hoffert JD, Yu MJ, Knepper MA (2007) Tandem mass spectrometry in physiology. Physiology 22:390–400. doi:10.1152/physiol.00025.2007

    Article  PubMed  CAS  Google Scholar 

  30. Wang G, Wu WW, Zeng W, Chou CL, Shen RF (2006) Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes. J Proteome Res 5(5):1214–1223. doi:10.1021/pr050406g

    Article  PubMed  CAS  Google Scholar 

  31. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ (2004) Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 3(12):1154–1169. doi:10.1074/mcp.M400129-MCP200

    Article  PubMed  CAS  Google Scholar 

  32. Thompson A, Schafer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AK, Hamon C (2003) Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem 75(8):1895–1904

    Article  PubMed  CAS  Google Scholar 

  33. Yocum AK, Chinnaiyan AM (2009) Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry. Brief Funct Genomic Proteomic 8(2):145–157. doi:10.1093/bfgp/eln056

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  34. Lv LL, Cao YH, Ni HF, Xu M, Liu D, Liu H, Chen PS, Liu BC (2013) MicroRNA-29c in urinary exosome/microvesicle as a biomarker of renal fibrosis. Am J Physiol Ren Physiol 305(8):F1220–1227. doi:10.1152/ajprenal.00148.2013

    Article  CAS  Google Scholar 

  35. Lv LL, Cao YH, Pan MM, Liu H, Tang RN, Ma KL, Chen PS, Liu BC (2013) CD2AP mRNA in urinary exosome as biomarker of kidney disease. Clin Chim Acta. doi:10.1016/j.cca.2013.10.003

  36. Nilsson J, Skog J, Nordstrand A, Baranov V, Mincheva-Nilsson L, Breakefield XO, Widmark A (2009) Prostate cancer-derived urine exosomes: a novel approach to biomarkers for prostate cancer. Br J Cancer 100(10):1603–1607. doi:10.1038/sj.bjc.6605058

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  37. Sonoda H, Yokota-Ikeda N, Oshikawa S, Kanno Y, Yoshinaga K, Uchida K, Ueda Y, Kimiya K, Uezono S, Ueda A, Ito K, Ikeda M (2009) Decreased abundance of urinary exosomal aquaporin-1 in renal ischemia-reperfusion injury. Am J Physiol Ren Physiol 297(4):F1006–1016. doi:10.1152/ajprenal.00200.2009

    Article  CAS  Google Scholar 

  38. Isobe K, Mori T, Asano T, Kawaguchi H, Nonoyama S, Kumagai N, Kamada F, Morimoto T, Hayashi M, Sohara E, Rai T, Sasaki S, Uchida S (2013) Development of enzyme-linked immunosorbent assays for urinary thiazide-sensitive Na-Cl cotransporter (NCC) measurement. Am J Physiol Ren Physiol. doi:10.1152/ajprenal.00208.2013

    Google Scholar 

  39. Joo KW, Lee JW, Jang HR, Heo NJ, Jeon US, Oh YK, Lim CS, Na KY, Kim J, Cheong HI, Han JS (2007) Reduced urinary excretion of thiazide-sensitive Na-Cl cotransporter in Gitelman syndrome: preliminary data. Am J Kidney Dis 50(5):765–773. doi:10.1053/j.ajkd.2007.07.022

    Article  PubMed  CAS  Google Scholar 

  40. Welton JL, Khanna S, Giles PJ, Brennan P, Brewis IA, Staffurth J, Mason MD, Clayton A (2010) Proteomics analysis of bladder cancer exosomes. Mol Cell Proteomics 9(6):1324–1338. doi:10.1074/mcp.M000063-MCP201

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  41. Li Y, Zhang Y, Qiu F, Qiu Z (2011) Proteomic identification of exosomal LRG1: a potential urinary biomarker for detecting NSCLC. Electrophoresis 32(15):1976–1983. doi:10.1002/elps.201000598

    Article  PubMed  CAS  Google Scholar 

  42. Raimondo F, Morosi L, Corbetta S, Chinello C, Brambilla P, Della Mina P, Villa A, Albo G, Battaglia C, Bosari S, Magni F, Pitto M (2013) Differential protein profiling of renal cell carcinoma urinary exosomes. Mol BioSyst 9(6):1220–1233. doi:10.1039/c3mb25582d

    Article  PubMed  CAS  Google Scholar 

  43. Chen CL, Lai YF, Tang P, Chien KY, Yu JS, Tsai CH, Chen HW, Wu CC, Chung T, Hsu CW, Chen CD, Chang YS, Chang PL, Chen YT (2012) Comparative and targeted proteomic analyses of urinary microparticles from bladder cancer and hernia patients. J Proteome Res 11(12):5611–5629. doi:10.1021/pr3008732

    PubMed  CAS  Google Scholar 

  44. Benito-Martin A, Ucero AC, Zubiri I, Posada-Ayala M, Fernandez-Fernandez B, Cannata-Ortiz P, Sanchez-Nino MD, Ruiz-Ortega M, Egido J, Alvarez-Llamas G, Ortiz A (2013) Osteoprotegerin in exosome-like vesicles from human cultured tubular cells and urine. PLoS ONE 8(8):e72387. doi:10.1371/journal.pone.0072387

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  45. Moon PG, Lee JE, You S, Kim TK, Cho JH, Kim IS, Kwon TH, Kim CD, Park SH, Hwang D, Kim YL, Baek MC (2011) Proteomic analysis of urinary exosomes from patients of early IgA nephropathy and thin basement membrane nephropathy. Proteomics 11(12):2459–2475. doi:10.1002/pmic.201000443

    Article  PubMed  CAS  Google Scholar 

  46. Raimondo F, Corbetta S, Morosi L, Chinello C, Gianazza E, Castoldi G, Di Gioia C, Bombardi C, Stella A, Battaglia C, Bianchi C, Magni F, Pitto M (2013) Urinary exosomes and diabetic nephropathy: a proteomic approach. Mol BioSyst 9(6):1139–1146. doi:10.1039/c2mb25396h

    Article  PubMed  CAS  Google Scholar 

  47. Kalani A, Mohan A, Godbole MM, Bhatia E, Gupta A, Sharma RK, Tiwari S (2013) Wilm’s tumor-1 protein levels in urinary exosomes from diabetic patients with or without proteinuria. PLoS ONE 8(3):e60177. doi:10.1371/journal.pone.0060177

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  48. Zhou H, Kajiyama H, Tsuji T, Hu X, Leelahavanichkul A, Vento S, Frank R, Kopp JB, Trachtman H, Star RA, Yuen PS (2013) Urinary exosomal Wilms’ tumor-1 as a potential biomarker for podocyte injury. Am J Physiol Ren Physiol 305(4):F553–559. doi:10.1152/ajprenal.00056.2013

    Article  CAS  Google Scholar 

  49. Conde-Vancells J, Rodriguez-Suarez E, Gonzalez E, Berisa A, Gil D, Embade N, Valle M, Luka Z, Elortza F, Wagner C, Lu SC, Mato JM, Falcon-Perez M (2010) Candidate biomarkers in exosome-like vesicles purified from rat and mouse urine samples. Proteomics Clin Appl 4(4):416–425. doi:10.1002/prca.200900103

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  50. Ramirez-Alvarado M, Ward CJ, Huang BQ, Gong X, Hogan MC, Madden BJ, Charlesworth MC, Leung N (2012) Differences in immunoglobulin light chain species found in urinary exosomes in light chain amyloidosis (Al). PLoS ONE 7(6):e38061. doi:10.1371/journal.pone.0038061

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  51. Li ZZ, Zhao ZZ, Wen JG, Xing L, Zhang H, Zhang Y (2012) Early alteration of urinary exosomal aquaporin 1 and transforming growth factor beta1 after release of unilateral pelviureteral junction obstruction. J Pediatr Surg 47(8):1581–1586. doi:10.1016/j.jpedsurg.2011.12.024

    Article  PubMed  Google Scholar 

  52. Gildea JJ, Carlson JM, Schoeffel CD, Carey RM, Felder RA (2013) Urinary exosome miRNome analysis and its applications to salt sensitivity of blood pressure. Clin Biochem 46(12):1131–1134. doi:10.1016/j.clinbiochem.2013.05.052

    Article  PubMed  CAS  PubMed Central  Google Scholar 

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Acknowledgments

This work was supported by the Lundbeck Foundation, Danish Medical Research Foundation, Novo Nordisk Foundation, Carlsberg Foundation, Aarhus University Research Foundation, and the Ratchadapiseksomphot Endowment Fund of Chulalongkorn University (RES560530124-HR).

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Correspondence to Trairak Pisitkun .

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Huebner, A.R. et al. (2015). Exosomes in Urine Biomarker Discovery. In: Gao, Y. (eds) Urine Proteomics in Kidney Disease Biomarker Discovery. Advances in Experimental Medicine and Biology, vol 845. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9523-4_5

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