StoneMod: a database for kidney stone modulatory proteins with experimental evidence

Abstract

Better understanding of molecular mechanisms for kidney stone formation is required to improve management of kidney stone disease with better therapeutic outcome. Recent kidney stone research has indicated critical roles of a group of proteins, namely ‘stone modulators’, in promotion or inhibition of the stone formation. Nevertheless, such information is currently dispersed and difficult to obtain. Herein, we present the kidney stone modulator database (StoneMod), which is a curated resource by obtaining necessary information of such stone modulatory proteins, which can act as stone promoters or inhibitors, with experimental evidence from previously published studies. Currently, the StoneMod database contains 10, 16, 13, 8 modulatory proteins that affect calcium oxalate crystallization, crystal growth, crystal aggregation, and crystal adhesion on renal tubular cells, respectively. Informative details of each modulatory protein and PubMed links to the published articles are provided. Additionally, hyperlinks to other protein/gene databases (e.g., UniProtKB, Swiss-Prot, Human Protein Atlas, PeptideAtlas, and Ensembl) are made available for the users to obtain additional in-depth information of each protein. Moreover, this database provides a user-friendly web interface, in which the users can freely access to the information and/or submit their data to deposit or update. Database URL:https://www.stonemod.org.

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“…Протромбин, фактор свертывания крови, состоит из трёх фрагментов: тромбина, фрагмента 1 и фрагмента 2. Фрагмент 1 был назван фрагментом мочевого протромбина (UPTF1) из-за его высвобождения в моче [46]. Ранее обнаружено, что он избирательно связывается с кристаллами оксалатов кальция.…”

On the protein content of kidney stones: an explorative study

“…The formation of kidney stones is a complex phenomenon. Apart from the limited solubility of certain compounds, kidney stone formation is modulated by urinary proteins [2][3][4]. Modern attenuated total-reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy of kidney stones allows a detailed quantitative analysis of the organic and inorganic compounds.…”

“…Tamm-Horsfall protein (THP) or uromodulin, a 90-kDa protein, produced in the kidney by the epithelial cells lining the thick ascending limb of the loop of Henle and early distal tubules, is the most abundant protein in healthy urine [7][8][9][10]. Proteomics analyses have been carried out in previous published studies on calcium oxalate, calcium phosphate and uric acid kidney stones, with the characterization of hundreds of proteins [4,[11][12][13]. This for a better understanding of the kidney stone matrix protein composition and the molecular mechanisms for kidney stone formation to improve management of kidney stone disease [11][12][13].…”

“…Recent kidney stone research has indicated critical roles of a group of proteins, namely stone modulatory proteins, which can act as stone promotors or inhibitors [4]. Given the growing insight that urinary proteins play a major role in stone formation [14], there may be an increasing interest in detecting the relative expression of proteins in kidney stones by ATR-FTIR spectroscopy.…”

Editorial: Immunity and Inflammatory Response in Kidney Stone Disease

“…Some of the stones form as an overgrowth on crystalline deposits within the terminal collecting ducts of the kidney ( 13 ). Both pathogenic mechanisms require periodic urinary supersaturation with respect to CaOx (i.e., hypercalciuria and hyperoxaluria) in association with low levels of its inhibitors (e.g., citrate and other urinary macromolecular inhibitors) ( 13 , 14 ).…”