Large-Scale Proteomic Assessment of Urinary Extracellular Vesicles Highlights Their Reliability in Reflecting Protein Changes in the Kidney

Visual Abstract Significance Statement Measurement of urinary extracellular vesicle (uEV) protein abundances is frequently used to reflect ongoing (patho)physiologic processes in the kidney. However, whether protein abundances in uEVs and the kidney directly correlate, or whether (patho)physiologic alterations in protein levels in the kidney can be determined by assessing protein changes in uEVs, has never been comprehensively determined. Here, quantitative proteomic data indicate protein abundances in uEVs and kidney in rats are correlated, with a monotonic relationship between altered transporter protein abundance in uEVs and the kidney after a physiologic stimulation. Therefore, it is valid to draw conclusions from altered protein levels in uEVs for particular protein classes and relate them to changes in the kidney. Background Urinary extracellular vesicles (uEVs) are secreted into urine by cells from the kidneys and urinary tract. Although changes in uEV proteins are used for quantitative assessment of protein levels in the kidney or biomarker discovery, whether they faithfully reflect (patho)physiologic changes in the kidney is a matter of debate. Methods Mass spectrometry was used to compare in an unbiased manner the correlations between protein levels in uEVs and kidney tissue from the same animal. Studies were performed on rats fed a normal or high K+ diet. Results Absolute quantification determined a positive correlation (Pearson R=0.46 or 0.45, control or high K+ respectively, P<0.0001) between the approximately 1000 proteins identified in uEVs and corresponding kidney tissue. Transmembrane proteins had greater positive correlations relative to cytoplasmic proteins. Proteins with high correlations (R>0.9), included exosome markers Tsg101 and Alix. Relative quantification highlighted a monotonic relationship between altered transporter/channel abundances in uEVs and the kidney after dietary K+ manipulation. Analysis of genetic mouse models also revealed correlations between uEVs and kidney. Conclusion This large-scale unbiased analysis identifies uEV proteins that track the abundance of the parent proteins in the kidney. The data form a novel resource for the kidney community and support the reliability of using uEV protein changes to monitor specific physiologic responses and disease mechanisms.