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. SignificanceNephronophthisis 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.
Highlights
Nephronophthisis is an important genetic cause of end-stage renal disease (ESRD) in children and young adults, accounting for 2.4% to 15% of pediatric ESRD cases [1,2,3]
By using an in-depth proteomics analysis using 140 nanoLC-MS/MS runs on a high resolution fast scanning tandem mass spectrometer, combined with statistical and quantitative filtering, we identified 156 promising candidate protein biomarkers
neutrophil gelatinase-associated lipocalin (NGAL) is the only biomarker for kidney injury in general that was previously identified in nephronophthisis-related ciliopathies (NPH-RC) patients
Summary
Nephronophthisis is an important genetic cause of end-stage renal disease (ESRD) in children and young adults, accounting for 2.4% to 15% of pediatric ESRD cases [1,2,3]. Nephronophthisis is known to result from defective ciliary signaling and has been classified as a renal ciliopathy It is characterized by chronic tubulointerstitial nephritis leading to loss of renal function and a reduced concentrating ability of the kidney. As a result of the variable and non-specific presenting symptoms, nephronophthisis is diagnosed on average 3.5 years after symptom onset, often in advanced stages of CKD when kidney damage is irreversible [7]. This diagnostic delay occurs especially in Journal of Proteomics 192 (2019) 27–36 nephronophthisis patients without extra-renal manifestations (e.g. retinitis pigmentosa or neurological signs) that could be indicative of a ciliopathy and would usually prompt monitoring of renal function. Early detection of nephronophthisis may be indispensable for the success of future targeted therapies
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