Comparative proteomic profiling of uric acid, ammonium acid urate, and calcium-based kidney stones

Introduction: Kidney stone matrix proteins may help explain cellular mechanisms of stone genesis. However, most existing proteomic studies have focused on calcium oxalate stones. Here, we present a comparative proteomic analysis of different kidney stone types. Methods: Proteins were extracted from the stones of patients undergoing percutaneous nephrolithotomy (PCNL). Approximately 20 mu g of protein was digested into tryptic peptides using filter aided sample preparation, followed by liquid chromatography tandem-mass-spectrometry using an EASY-nLC 1200 and Orbitrap Fusion Lumos mass spectrometer. A standard false discovery rate cutoff of 1% was used for protein identification. Stone analysis was used to organize stone samples into similar groups. We selected the top 5% of proteins based on total ion intensities and used DAVID and Ingenuity Pathway Analysis to identify and compare significantly enriched gene ontologies and pathways between groups. Results: Six specimens were included and organized into the following four groups: 1) mixed uric acid (UA) and calcium-based, 2) pure UA, 3) pure ammonium acid urate (AAU), and 4) pure calcium-based. We identified 2,426 unique proteins (1,310-1,699 per sample), with 11-16 significantly enriched KEGG pathways identified per group and compared via heatmap. Based on number of unique proteins identified, this is the deepest proteomic study of kidney stones to date and the first such study of an AAU stone. Conclusions: The results indicate that mixed UA and calcium-based kidney stones are more similar to pure UA stones than pure calcium-based stones. AAU stones appear more similar to pure calcium-based stones than UA containing stones and may be related to parasitic infections. Further research with larger cohorts and histopathologic correlation is warranted.