Stone former urine proteome demonstrates a cationic shift in protein distribution compared to normal

Bioinformatics and computational analyses of kidney stone modulatory proteins lead to solid experimental evidence and therapeutic potential

In recent biomedical research, bioinformatics and computational analyses have played essential roles for examining experimental findings and database information. Several bioinformatic tools have been developed and made publicly available for analyzing protein sequence, structure, functional motif/domain, and interactions network. Such properties are very helpful to define biochemical and functional roles of the protein(s) of interest. During the past few decades, bioinformatics and computational biotechnology have been widely applied to kidney stone research. This review summarizes commonly used tools and evidence of bioinformatics and computational biotechnology applied to kidney stone disease (KSD) with special emphasis on analyses of the stone modulatory proteins that play critical roles in kidney stone formation. Such analyses lead to solid experimental evidence to demonstrate mechanisms underlying their stone modulatory activities. The findings obtained from such analyses may also lead to better understanding of KSD pathogenesis and to further development of new therapeutic and preventive strategies.

Comparison of cat and human calcium oxalate monohydrate kidney stone matrix proteomes

Despite its critical nature, the role of matrix in calcium oxalate stone formation is poorly understood. The wide diversity of proteins comprising matrix has contributed to the ambiguity. This study compares the protein distributions measured by mass spectrometry in human calcium oxalate stone matrix to that observed in cat stone matrix, because cats share many clinical characteristics of their stone disease with humans. The observed protein distributions were analyzed in the context of a recent model based on the aggregation of strongly anionic and strongly cationic proteins which includes selective adsorption of other proteins based on total charge. Matrix protein distributions shared many common features between species, including enrichment of both strongly anionic and strongly cationic proteins, increased total charge in matrix proteins compared to urine proteins, and a high degree of similarity of prominent strongly anionic proteins in the matrix of both species. However, there was weaker overlap of the specific dominant proteins in other regions of the net charge distribution. Collectively, these observations support the conceptual model where the strongly anionic proteins associate most strongly with the calcium oxalate crystal surfaces, while the other proteins associate with the strongly anionic proteins through non-specific, charge interactions with each other to create stones. Also, cats appear to be the best animal model of human stone disease identified to date based on these similarities.

A urinary proteomic study in hypercalciuric dogs with and without calcium oxalate urolithiasis

Background and Aims

Hypercalciuria is an important predisposing factor commonly found in humans and dogs with calcium oxalate (CaOx) urolithiasis. Calcium oxalate crystals can induce an inflammatory reaction that subsequently produces several proteins that have an inhibitory or stimulatory effect on stone formation. This study aimed to evaluate the differences in urinary proteomic profiles between hypercalciuric CaOx stone dogs and hypercalciuric stone-free dogs (CaOx stone and control groups, respectively).

Materials and Methods

Seven dogs with hypercalciuric CaOx urolithiasis and breed-, sex-, and aged-matched controls with hypercalciuria were included in the study. Serum and urine samples were obtained from all dogs to analyze electrolytes. Urinary proteomic profiles were analyzed using liquid chromatography-mass spectrometry. Student's t-test was used to compare the differences between groups.

Results

Forty-nine urinary proteins were identified in the stone-free and CaOx stone groups, whereas 19 and 6 proteins were unique in the CaOx stone and stone-free groups, respectively. The urinary thrombomodulin level was significantly higher in the CaOx stone group (relative ratio = 1.8, p < 0.01) than in the stone-free group.

Conclusion

This study demonstrated that urinary proteomic profiles may be used as a candidate biomarker for urinary tract injury in CaOx urolithiasis in dogs.

Effect of urinary glucose concentration and pH on signal intensity in magnetic resonance images

Purpose

With advances in anti-diabetes drugs, increasing numbers of patients have high urinary glucose concentrations, which may alter magnetic resonance (MR) signal intensity. We sought to elucidate the effect of urinary glucose concentration and pH on transverse relaxation and MR signal intensity.

Materials and methods

The transverse relaxation rate (R₂) was measured in samples with different glucose concentrations (in vitro) and in the urinary bladder of seven patients with diabetes and nine healthy volunteers (in vivo). The glucose concentration and pH in the in vitro samples and urine were measured. The signal intensity ratio of the bladder to adjacent tissues was obtained on T2-weighted imaging (WI), T1WI, and MR urography (in vivo). To clarify the effect of pH further, the urine of two healthy subjects was adjusted with acid and/or base to obtain various pH values (ex vivo).

Results

R₂ increased significantly with high glucose concentrations in the in vitro study. In the in vivo study, high glucose concentration (p < 0.001) and low pH (p = 0.005) were significantly associated with high R₂. R₂ was higher (p = 0.002) and the signal in maximum-intensity projection images of MR urography was lower (p = 0.005) in patients with diabetes than in healthy subjects. Ex vivo study revealed that a decrease in pH in acid portion resulted in increased R₂.

Conclusion

High concentrations of urinary glucose and low pH both enhance transverse relaxation, which, in turn, causes low signal intensity in urinary bladder on long echo time (TE) images, such as MR urography. Radiologists should be aware of this phenomenon when interpreting abnormally low-intensity bladders on long TE images.

Systematic analysis of modulating activities of native human urinary Tamm-Horsfall protein on calcium oxalate crystallization, growth, aggregation, crystal-cell adhesion and invasion through extracellular matrix

Functions of Tamm-Horsfall protein (THP), the most abundant human urinary protein, have been studied for decades. However, its precise roles in kidney stone formation remain controversial. In this study, we aimed to clarify the roles of native human urinary THP in calcium oxalate monohydrate (COM) kidney stone formation. THP was purified from the human urine by adsorption method using diatomaceous earth (DE). Its effects on stone formation processes, including COM crystallization, crystal growth, aggregation, crystal-cell adhesion and invasion through extracellular matrix (ECM), were examined. SDS-PAGE and Western blotting confirmed that DE adsorption yielded 84.9% purity of the native THP isolated from the human urine. Systematic analyses revealed that THP (at 0.4-40 μg/ml) concentration-dependently reduced COM crystal size but did not affect the crystal mass during initial crystallization. At later steps, THP concentration-dependently inhibited COM crystal growth and aggregation, and prevented crystal-cell adhesion only at 40 μg/ml. However, THP did not affect crystal invasion through the ECM. Sequence analysis revealed two large calcium-binding domains (residues 65-107 and 108-149) and three small oxalate-binding domains (residues 199-207, 361-368 and 601-609) in human THP. Immunofluorescence study confirmed the binding of THP to COM crystals. Analyses for calcium-affinity and/or oxalate-affinity demonstrated that THP exerted a high affinity with only calcium, not oxalate. Functional validation revealed that saturation of THP with calcium, not with oxalate, could abolish the inhibitory effects of THP on COM crystal growth, aggregation and crystal-cell adhesion. These data highlight the inhibitory roles of the native human urinary THP in COM crystal growth, aggregation and crystal-cell adhesion, which are the important processes for kidney stone formation. Such inhibitory effects of THP are most likely mediated via its high affinity with calcium ions.

Analysis of Threshold Effect of Urinary Heavy Metal Elements on the High Prevalence of Nephrolithiasis in Men

Exposure to heavy metals in the environment exerts serious effects on kidney health. However, the effects of joint exposure on the kidneys have been rarely studied, particularly in non-occupational exposure high-risk populations. This study provided a reference threshold range of heavy metals in urine and explored the effect of joint exposure on nephrolithiasis in men. The data were obtained from the China Multi-Ethnic Cohort database, and 1502 men were included in the study. A two-piece-wise regression model was used to assess the dose-response relationship between heavy metal exposure and nephrolithiasis. The least absolute shrinkage and selection operator regression model was used to calculate the score of joint exposure to heavy metals. The threshold effect analysis revealed a linear relationship between the concentration of arsenic (As) in the urine and the prevalence of nephrolithiasis, whereas a nonlinear relationship was observed with cadmium (Cd), chromium (Cr), mercury (Hg), and lead (Pb). In addition, As, Cd, Cr, Hg, and Pb may significantly affect the joint exposure effect. Moreover, the final risk of nephrolithiasis increased by 123% (P for trend < 0.001). This study found a threshold relationship between heavy metals (Cd, Cr, Hg, Pb) in male urine and the occurrence of nephrolithiasis. Joint exposure to heavy metals in urine caused a high-risk effect on nephrolithiasis. The study provided a reference threshold value of related studies and indicated that environmental pollution caused by heavy metals should be reduced.

Combined effect of polyacrylic acid and vitamin E in preventing calcium oxalate crystal deposition in the kidneys of experimental hyperoxaluric rats

Our study explores the combined effect of polyacrylic acid and vitamin E as prophylactic and curative agent against ethylene glycol (EG) induced calcium oxalate stone formation in Wistar rats. Male Wistar rats (54) were divided into nine groups, including control. The experimental groups were equally segregated into two for preventive study (4) and curative study (4). Urolithiasis was induced with 0.75% (v/v) EG in drinking water. Polyacrylic acid (10 mg/kg) and vitamin E (300 IU/day) were supplemented from day 1 for preventive and day 30 for curative studies. Restoration of urinary lithogenic factors (calcium, oxalate, phosphate, citrate and magnesium) and renal function (urea and creatinine in serum) by intervening agents were accomplished compared to urolithic rats (P < .001). Abnormal localization and increased expression of Tamm-Horsfall Protein, osteopontin and transferrin were observed in the kidneys of urolithic rats (P < .001) from immunohistochemistry and immunoblotting analysis. Polyacrylic acid and vitamin E supplementation have regulated the expression of the urinary macromolecules. Pro-inflammatory cytokines in kidney were significantly reduced (P < .001) by the intervening agents compared to urolithic rats. Therefore, polyacrylic acid and vitamin E in combination could be a potential formulation for better management of urolithiasis.

Comprehensive proteomic quantification of bladder stone progression in a cystinuric mouse model using data-independent acquisitions

Cystinuria is one of various disorders that cause biomineralization in the urinary system, including bladder stone formation in humans. It is most prevalent in children and adolescents and more aggressive in males. There is no cure, and only limited disease management techniques help to solubilize the stones. Recurrence, even after treatment, occurs frequently. Other than a buildup of cystine, little is known about factors involved in the formation, expansion, and recurrence of these stones. This study sought to define the growth of bladder stones, guided by micro-computed tomography imaging, and to profile dynamic stone proteome changes in a cystinuria mouse model. After bladder stones developed in vivo, they were harvested and separated into four developmental stages (sand, small, medium and large stone), based on their size. Data-dependent and data-independent acquisitions allowed deep profiling of stone proteomics. The proteomic signatures and pathways illustrated major changes as the stones grew. Stones initiate from a small nidus, grow outward, and show major enrichment in ribosomal proteins and factors related to coagulation and platelet degranulation, suggesting a major dysregulation in specific pathways that can be targeted for new therapeutic options.

Differential biomolecular recognition by synthetic vs. biologically-derived components in the stone-forming process using 3D microfluidics

Calcium phosphate (CaP) biomineralization is the hallmark of extra-skeletal tissue calcification and renal calcium stones. Although such a multistep process starts with CaP crystal formation, the mechanism is still poorly understood due to the complexity of the in vivo system and the lack of a suitable approach to simulate a truly in vivo-like environment. Although endogenous proteins and lipids are engaged with CaP crystals in such a biological process of stone formation, most in vitro studies use synthetic materials that can display differential bioreactivity and molecular recognition by the cellular component. Here, we used our in vitro microfluidic (MF) tubular structure, which is the first completely cylindrical platform, with renal tubular cellular microenvironments closest to the functional human kidney tubule, to understand the precise role of biological components in this process. We systematically evaluated the contribution of synthetic and biological components in the stone-forming process in the presence of dynamic microenvironmental cues that originated due to cellular pathophysiology, which are critical for the nucleation, aggregation, and growth of CaP crystals. Our results show that crystal aggregation and growth were enhanced by immunoglobulin G (IgG), which was further inhibited by etidronic acid due to the chelation of extracellular Ca²⁺. Interestingly, biogenic CaP crystals from mice urine, when applied with cell debris and non-specific protein (bovine serum albumin), exhibited a more discrete crystal growth pattern, compared to exposure to synthetic CaP crystals under similar conditions. Furthermore, proteins found on those calcium crystals from mice urine produced discriminatory effects on crystal-protein attachment. Specifically, such biogenic crystals exhibited enhanced affinity to the proteins inherent to those crystals. More importantly, a physiological comparison of crystal induction in renal tubular cells revealed that biogenic crystals are less effective at producing a sustained rise in cytosolic Ca²⁺ compared to synthetic crystals, suggesting a milder detrimental effect to downstream signaling. Finally, synthetic crystal-internalized cells induced more oxidative stress, inflammation, and cellular damage compared to the biogenic crystal-internalized cells. Together, these results suggest that the intrinsic nature of biogenically derived components are appropriate to generate the molecular recognition needed for spatiotemporal effects and are critical towards understanding the process of kidney stone formation.

Protein primary structure correlates with calcium oxalate stone matrix preference

Despite the apparent importance of matrix proteins in calcium oxalate kidney stone formation, the complexity of the protein mixture continues to elude explanation. Based on a series of experiments, we have proposed a model where protein aggregates formed from a mixture containing both strongly charged polyanions and strongly charged polycations could initiate calcium oxalate crystal formation and crystal aggregation to create a stone. These protein aggregates also preferentially adsorb many weakly charged proteins from the urine to create a complex protein mixture that mimics the protein distributions observed in patient samples. To verify essential details of this model and identify an explanation for phase selectivity observed in weakly charged proteins, we have examined primary structures of major proteins preferring either the matrix phase or the urine phase for their contents of aspartate, glutamate, lysine and arginine; amino acids that would represent fixed charges at normal urine pH of 6–7. We verified enrichment in stone matrix of proteins with a large number of charged residues exhibiting extreme isoelectric points, both low (pI<5) and high (pI>9). We found that the many proteins with intermediate isoelectric points exhibiting preference for stone matrix contained a smaller number of charge residues, though still more total charges than the intermediate isoelectric point proteins preferring the urine phase. While other sources of charge have yet to be considered, protein preference for stone matrix appears to correlate with high total charge content.

Kidney stone proteomics: an update and perspectives

INTRODUCTION

Main problems of kidney stone disease are its increasing prevalence and high recurrence rate after calculi removal in almost all areas around the globe. Despite enormous efforts in the past, its pathogenic mechanisms remain unclear and need further elucidations. Proteomics has thus become an essential tool to unravel such sophisticated disease mechanisms at cellular, subcellular, molecular, tissue, and whole organism levels.

AREAS COVERED

This review provides abrief overview of kidney stone disease followed by updates on proteomics for investigating urinary stone modulators, matrix proteins, cellular responses to different types/doses of calcium oxalate (CaOx) crystals, sex hormones and other stimuli, crystal-cell interactions, crystal receptors, secretome, and extracellular vesicles (EVs), all of which lead to better understanding of the disease mechanisms. Finally, the future challenges and translation of these obtained data to the clinic are discussed.

EXPERT OPINION

Knowledge from urinary proteomics for exploring the important stone modulators (either inhibitors or promoters) will be helpful for early detection of asymptomatic cases for prompt prevention of symptoms, complications, and new stone formation. Moreover, these modulators may serve as the new therapeutic targets in the future for successful treatment and prevention of kidney stone disease by medications or other means of intervention.

Exploring mechanisms of protein influence on calcium oxalate kidney stone formation

Calcium oxalate monohydrate (COM) crystals are the primary constituent of most kidney stones, but urine proteins in stone matrix are believed to be critical elements for stone formation from these crystals. Recent data have shown that hundreds of proteins appear in the stone matrix with no explanation for inclusion of so many proteins. We have proposed a stone formation model with protein stimulated COM aggregation based on polyanion-polycation aggregation, which is supported by finding that matrix is highly enriched in strongly anionic and strongly cationic proteins. Many other proteins may be drawn to such aggregates due to their limited solubility in water or charge effects. Finding similar protein enrichment in both polyarginine (pR) induced aggregates of urine proteins and COM stone matrix would support this hypothesis. Purified proteins (PP) were obtained from random urine samples of six healthy adults by ultradiafiltration. Protein aggregation was induced by adding pR to PP solutions at two concentrations; 0.25 and 0.5 µg pR/µg of PP. Samples of each fraction and the original PP mixture were lyophilized and analyzed by tandem mass spectrometry. Aggregates induced by pR addition to PP samples collected a protein mixture that mimicked the protein distribution observed in COM matrix, supporting our hypothesis. The apparently discordant behavior of certain abundant anionic proteins preferentially joining the pR aggregate, when they had demonstrated reduced abundance in COM stone matrix, suggests that this model was overdriven to aggregate. The reversal of aggregate preference of albumin at low pR addition supports this interpretation.

Selective protein enrichment in calcium oxalate stone matrix: a window to pathogenesis?

Urine proteins are thought to control calcium oxalate stone formation, but over 1000 proteins have been reported in stone matrix obscuring their relative importance. Proteins critical to stone formation should be present at increased relative abundance in stone matrix compared to urine, so quantitative protein distribution data were obtained for stone matrix compared to prior urine proteome data. Matrix proteins were isolated from eight stones (> 90% calcium oxalate content) by crystal dissolution and further purified by ultradiafiltration (> 10 kDa membrane). Proteomic analyses were performed using label-free spectral counting tandem mass spectrometry, followed by stringent filtering. The average matrix proteome was compared to the average urine proteome observed in random urine samples from 25 calcium oxalate stone formers reported previously. Five proteins were prominently enriched in matrix, accounting for a mass fraction of > 30% of matrix protein, but only 3% of urine protein. Many highly abundant urinary proteins, like albumin and uromodulin, were present in matrix at reduced relative abundance compared to urine, likely indicating non-selective inclusion in matrix. Furthermore, grouping proteins by isoelectric point demonstrated that the stone matrix proteome was highly enriched in both strongly anionic (i.e., osteopontin) and strongly cationic (i.e., histone) proteins, most of which are normally found in intracellular or nuclear compartments. The fact that highly anionic and highly cationic proteins aggregate at low concentrations and these aggregates can induce crystal aggregation suggests that protein aggregation may facilitate calcium oxalate stone formation, while cell injury processes are implicated by the presence of many intracellular proteins.