Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies
Stokman, Marijn F.; Bijnsdorp, Irene V.; Schelfhorst, Tim; Pham, Thang V.; Piersma, Sander R.; Knol, Jaco C.; Giles, Rachel H.; Bongers, Ernie M.H.F.; Knoers, Nine V.A.M.; Lilien, Marc R.; Jiménez, Connie R.; Renkema, Kirsten Y.
(2019) Journal of Proteomics, volume 192, pp. 27 - 36
(Article)
Abstract
Nephronophthisis is one of the leading genetic causes of end-stage renal disease in childhood. Early diagnostics and prognostics for nephronophthisis are currently limited. We aimed to identify non-invasive protein biomarkers for nephronophthisis in urinary extracellular vesicles. Extracellular vesicles were isolated from urine of 12 patients with a nephronophthisis-related ciliopathy and
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12 age- and gender-matched controls, followed by in-depth label-free LC-MS/MS proteomics analysis of gel fractionated extracellular vesicle proteins. Supervised cluster analysis of proteomic profiles separated patients from controls. We identified 156 differentially expressed proteins with fold change ≥4 in patients compared to controls (P <.05). Importantly, expression levels of discriminating proteins were correlated with chronic kidney disease stage, suggesting possible applications for urinary extracellular vesicle biomarkers in prognostics for nephronophthisis. Enrichment analysis of gene ontology terms revealed GO terms including signaling, actin cytoskeleton and endocytosis among the downregulated proteins in patients, whereas terms related to response to wounding and extracellular matrix organization were enriched among upregulated proteins. Our findings represent the first step towards a non-invasive diagnostic test for nephronophthisis. Further research is needed to determine specificity of the candidate biomarkers. In conclusion, proteomic profiles of urinary extracellular vesicles differentiate nephronophthisis-related ciliopathy patients from healthy controls. Significance: Nephronophthisis is an important cause of end-stage renal disease in children and is associated with an average diagnostic delay of 3.5 years. This is the first study investigating candidate biomarkers for nephronophthisis using global proteomics analysis of urinary extracellular vesicles in patients with nephronophthisis compared to control individuals. We show that measuring protein markers in urinary extracellular vesicles is a promising approach for non-invasive early diagnostics of nephronophthisis.
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Keywords: Biomarker, Extracellular vesicle, Nephronophthisis, Proteomics, Renal ciliopathy, Urine, Biophysics, Biochemistry
ISSN: 1874-3919
Publisher: Elsevier
Note: Funding Information: We thank the patients, healthy control individuals, and parents for participation in this study and donating urine samples. The authors thank Albertien M. van Eerde (Dept. of Genetics, UMC Utrecht), Marie-Jose H. van den Boogaard (Department of Genetics, UMC Utrecht), Hester Y. Kroes (Department of Genetics, UMC Utrecht), Mandy G. Keijzer-Veen (Department of Pediatric Nephrology, UMC Utrecht) and Mieke M. van Haelst (Department of Medical Genetics, VUMC) for their clinical contribution and Adele van Dijk (Department of Nephrology, UMC Utrecht) for measurement of protein and creatinine in urine samples. This study was financially supported by an Impulsion Grant of the ERA-EDTA Working Group on Inherited Kidney Disorders (WGIKD) to K.Y.R. The researchers received funding from the Dutch Kidney Foundation under grant agreement CP11.18; Kouncil to N.V.A.M.K. and the European Community's Seventh Framework Programme (FP7/2009) under grant agreement 305608; EURenOmics to N.V.A.M.K. Funding Information: We thank the patients, healthy control individuals, and parents for participation in this study and donating urine samples. The authors thank Albertien M. van Eerde (Dept. of Genetics, UMC Utrecht ), Marie-Jose H. van den Boogaard ( Department of Genetics , UMC Utrecht ), Hester Y. Kroes ( Department of Genetics , UMC Utrecht ), Mandy G. Keijzer-Veen (Department of Pediatric Nephrology, UMC Utrecht ) and Mieke M. van Haelst (Department of Medical Genetics, VUMC) for their clinical contribution and Adele van Dijk (Department of Nephrology, UMC Utrecht ) for measurement of protein and creatinine in urine samples. This study was financially supported by an Impulsion Grant of the ERA-EDTA Working Group on Inherited Kidney Disorders (WGIKD) to K.Y.R. The researchers received funding from the Dutch Kidney Foundation under grant agreement CP11.18; Kouncil to N.V.A.M.K. and the European Community's Seventh Framework Programme (FP7/2009) under grant agreement 305608; EURenOmics to N.V.A.M.K. Publisher Copyright: © 2018 The Authors
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