Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies

Marijn F. Stokman, Irene V. Bijnsdorp, Tim Schelfhorst, Thang V. Pham, Sander R. Piersma, Jaco C. Knol, Rachel H. Giles, Ernie M. H. F. Bongers, Nine V. A. M. Knoers, Marc R. Lilien, Connie R. Jiménez, Kirsten Y. Renkema

Research output: Contribution to journalArticleAcademicpeer-review

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 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.
Original languageEnglish
Pages (from-to)27-36
Number of pages10
JournalJournal of Proteomics
Volume192
Early online date2018
DOIs
Publication statusPublished - 10 Feb 2019

Cite this

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. / Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies. In: Journal of Proteomics. 2019 ; Vol. 192. pp. 27-36.
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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 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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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.

In: Journal of Proteomics, Vol. 192, 10.02.2019, p. 27-36.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies

AU - Stokman, Marijn F.

AU - Bijnsdorp, Irene V.

AU - Schelfhorst, Tim

AU - Pham, Thang V.

AU - Piersma, Sander R.

AU - Knol, Jaco C.

AU - Giles, Rachel H.

AU - Bongers, Ernie M. H. F.

AU - Knoers, Nine V. A. M.

AU - Lilien, Marc R.

AU - Jiménez, Connie R.

AU - Renkema, Kirsten Y.

PY - 2019/2/10

Y1 - 2019/2/10

N2 - 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 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.

AB - 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 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.

KW - Biomarker

KW - Extracellular vesicle

KW - Nephronophthisis

KW - Proteomics

KW - Renal ciliopathy

KW - Urine

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UR - https://www.ncbi.nlm.nih.gov/pubmed/30071318

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DO - 10.1016/j.jprot.2018.07.008

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JF - Journal of Proteomics

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