Determination of variability due to biological and technical variation in urinary extracellular vesicles as a crucial step in biomarker discovery studies

References

• Al-Nedawi K. The yin-yang of microvesicles (exosomes) in cancer biology. Front Oncol. 2014;4:172.
   Google Scholar
• Corrado C, Raimondo S, Saieva L, et al. Exosome-mediated crosstalk between chronic myelogenous leukemia cells and human bone marrow stromal cells triggers an interleukin 8-dependent survival of leukemia cells. Cancer Lett. 2014;348(1–2):71–10.
   Web of Science ®Google Scholar
• Spanu S, van Roeyen CRC, Denecke B, et al. Urinary exosomes: a novel means to non-invasively assess changes in renal gene and protein expression. PLoS One. 2014;9(10):e109631.
   Web of Science ®Google Scholar
• Barros ER, Carvajal CA. Urinary exosomes and their cargo: potential biomarkers for mineralocorticoid arterial hypertension? Front Endocrinol. 2017;8:230.
   Web of Science ®Google Scholar
• Nawaz M, Camussi G, Valadi H, et al. The emerging role of extracellular vesicles as biomarkers for urogenital cancers. Nat Rev Urol. 2014;11(12):688–701.
   PubMed Web of Science ®Google Scholar
• Zhou H, Yuen PST, Pisitkun T, et al. Collection, storage, preservation, and normalization of human urinary exosomes for biomarker discovery. Kidney Int. 2006;69(8):1471–1476.
   PubMed Web of Science ®Google Scholar
• Maes E, Valkenborg D, Baggerman G, et al. Determination of variation parameters as a crucial step in designing TMT-based clinical proteomics experiments. PLoS One. 2015;10(3):e0120115.
   Web of Science ®Google Scholar
• Cairns DA. Statistical issues in quality control of proteomic analyses: good experimental design and planning. Proteomics. 2011;11(6):1037–1048.
   Web of Science ®Google Scholar
• Batista-Miranda JE, Molinuevo B, Pardo Y. Impact of lower urinary tract symptoms on quality of life using functional assessment cancer therapy scale. Urology. 2007;69(2):285–288.
   PubMed Web of Science ®Google Scholar
• Lawhorne LW, Ouslander JG, Parmelee PA, et al. Urinary incontinence: a neglected geriatric syndrome in nursing facilities. J Am Med Dir Assoc. 2008;9(1):29–35.
   Web of Science ®Google Scholar
• Oeyen E, Van Mol K, Baggerman G, et al. Ultrafiltration and size exclusion chromatography combined with asymmetrical-flow field-flow fractionation for the isolation and characterisation of extracellular vesicles from urine. J Extracell Vesicles. 2018;7(1):1490143.
   PubMed Web of Science ®Google Scholar
• t’Kindt R, Telenga ED, Jorge L, et al. Profiling over 1500 lipids in induced lung sputum and the implications in studying lung diseases. Anal Chem. 2015;87(9):4957–4964.
   Web of Science ®Google Scholar
• Matyash V, Liebisch G, Kurzchalia TVet al. Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. J Lipid Res. 2008;49(5):1137–1146.
   PubMed Web of Science ®Google Scholar
• Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol. 2008;26(12):1367–1372.
   PubMed Web of Science ®Google Scholar
• Tyanova S, Temu T, Cox J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat Protoc. 2016;11(12):2301–2319.
   PubMed Web of Science ®Google Scholar
• MacLean B, Tomazela DM, Shulman N, et al. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics. 2010;26(7):966–968.
   PubMed Web of Science ®Google Scholar
• Megger DA, Bracht T, Meyer HE, et al. Label-free quantification in clinical proteomics. Biochim Biophys Acta. 2013;1834(8):1581–1590.
   PubMed Web of Science ®Google Scholar
• Thery C, Ostrowski M, Segura E. Membrane vesicles as conveyors of immune responses. Nat Rev Immunol. 2009;9(8):581–593.
   PubMed Web of Science ®Google Scholar
• Chawade A, Alexandersson E, Levander F. Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets. J Proteome Res. 2014;13(6):3114–3120.
   PubMed Web of Science ®Google Scholar
• Sun Y, Liu J. Potential of cancer cell-derived exosomes in clinical application: a review of recent research advances. Clin Ther. 2014;36(6):863–872.
   Web of Science ®Google Scholar
• Hoorn EJ, Pisitkun T, Zietse R, et al. Prospects for urinary proteomics: exosomes as a source of urinary biomarkers. Nephrology (Carlton). 2005;10(3):283–290.
   PubMed Web of Science ®Google Scholar
• Jia S, Zocco D, Samuels ML, et al. Emerging technologies in extracellular vesicle-based molecular diagnostics. Expert Rev Mol Diagn. 2014;14(3):307–321.
   PubMed Web of Science ®Google Scholar
• Trajkovic K, Hsu C, Chiantia S, et al. Ceramide triggers budding of exosome vesicles into multivesicular endosomes. Science. 2008;319(5867):1244–1247.
   PubMed Web of Science ®Google Scholar
• Marimpietri D, Petretto A, Raffaghello L, et al. Proteome profiling of neuroblastoma-derived exosomes reveal the expression of proteins potentially involved in tumor progression. PLoS One. 2013;8(9):e75054.
   PubMed Web of Science ®Google Scholar
• Hosseini-Beheshti E, Pham S, Adomat H, et al. Exosomes as biomarker enriched microvesicles: characterization of exosomal proteins derived from a panel of prostate cell lines with distinct AR phenotypes. Mol Cell Proteomics. 2012;11(10):863–885.
   PubMed Web of Science ®Google Scholar
• Kim CW, Lee HM, Lee TH, et al. Extracellular membrane vesicles from tumor cells promote angiogenesis via sphingomyelin. Cancer Res. 2002;62(21):6312–6317.
   PubMed Web of Science ®Google Scholar
• Del Boccio P, Raimondo F, Pieragostino D, et al. A hyphenated microLC-Q-TOF-MS platform for exosomal lipidomics investigations: application to RCC urinary exosomes. Electrophoresis. 2012;33(4):689–696.
   PubMed Web of Science ®Google Scholar
• Choi DS, Lee J, Go G, et al. Circulating extracellular vesicles in cancer diagnosis and monitoring: an appraisal of clinical potential. Mol Diagn Ther. 2013;17(5):265–271.
   Web of Science ®Google Scholar
• Taylor DD, Gercel-Taylor C. MicroRNA signatures of tumor-derived exosomes as diagnostic biomarkers of ovarian cancer. Gynecol Oncol. 2008;110(1):13–21.
   PubMed Web of Science ®Google Scholar
• Liang LG, Kong M-Q, Zhou S, et al. An integrated double-filtration microfluidic device for isolation, enrichment and quantification of urinary extracellular vesicles for detection of bladder cancer. Sci Rep. 2017;7:46224.
   PubMed Web of Science ®Google Scholar
• Oeyen E, Hoekx L, De Wachter S, et al. Bladder cancer diagnosis and follow-up: the current status and possible role of extracellular vesicles. Int J Mol Sci. 2019;20(4).
   Web of Science ®Google Scholar
• Lin SY, Lin Z, Buawangpong N, et al. Proteome profiling of urinary exosomes identifies alpha 1-antitrypsin and H2B1K as diagnostic and prognostic biomarkers for urothelial carcinoma. Sci Rep. 2016;6:34446.
   PubMed Web of Science ®Google Scholar
• Long JD, Sullivan TB, Humphrey J, et al. A non-invasive miRNA based assay to detect bladder cancer in cell-free urine. Am J Transl Res. 2015;7(11):2500–2509.
   PubMed Web of Science ®Google Scholar
• Nagaraj N, Mann M. Quantitative analysis of the intra- and inter-individual variability of the normal urinary proteome. J Proteome Res. 2011;10(2):637–645.
   PubMed Web of Science ®Google Scholar
• Yanez-Mo M, Siljander PR, Andreu Z, et al. Biological properties of extracellular vesicles and their physiological functions. J Extracell Vesicles. 2015;4:27066.
   PubMed Web of Science ®Google Scholar
• Filipazzi P, Bürdek M, Villa A, et al. Recent advances on the role of tumor exosomes in immunosuppression and disease progression. Semin Cancer Biol. 2012;22(4):342–349.
   PubMed Web of Science ®Google Scholar
• Franzen CA, Blackwell RH, Todorovic V, et al. Urothelial cells undergo epithelial-to-mesenchymal transition after exposure to muscle invasive bladder cancer exosomes. Oncogenesis. 2015;4:e163.
   PubMed Web of Science ®Google Scholar
• Yuana Y, Böing AN, Grootemaat AE, et al. Handling and storage of human body fluids for analysis of extracellular vesicles. J Extracell Vesicles. 2015;4:29260.
   PubMed Web of Science ®Google Scholar
• Abramowicz A, Widlak P, Pietrowska M. Proteomic analysis of exosomal cargo: the challenge of high purity vesicle isolation. Mol Biosyst. 2016;12(5):1407–1419.
   PubMedGoogle Scholar
• Webber J, Clayton A. How pure are your vesicles? J Extracell Vesicles. 2013;2:19861.
   PubMedGoogle Scholar
• Sandra K, Pereira ADS, Vanhoenacker G, et al. Comprehensive blood plasma lipidomics by liquid chromatography/quadrupole time-of-flight mass spectrometry. J Chromatogr A. 2010;1217(25):4087–4099.
   PubMed Web of Science ®Google Scholar
• Team, R.C. R: a language and environment for statistical computing. R foundation for statistical computing. 2018. Available from: https://www.R-project.org/
   Google Scholar
• Gentleman RC, Carey VJ, Bates DM, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5(10):R80.
   PubMed Web of Science ®Google Scholar
• Consortium E-T, Van Deun J, Mestdagh P, et al. EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research. Nat Methods. 2017;14(3):228–232.
   PubMed Web of Science ®Google Scholar