Modulatory effects of fibronectin on calcium oxalate crystallization, growth, aggregation, adhesion on renal tubular cells, and invasion through extracellular matrix

E53, E96, D162, E247 and D322 in Ca2+-binding domains of annexin A2 are essential for regulating intracellular [Ca2+] and crystal adhesion to renal cells via ERK1/2 and JNK signaling pathways

Annexin A2 (ANXA2) is expressed inside the cytoplasm and on the surface of renal tubular epithelial cells (RTECs) and is documented as a calcium oxalate monohydrate (COM) crystal-binding protein. Nevertheless, its molecular mechanism involved in kidney stone disease (KSD) remains underinvestigated. Herein, we performed various molecular assays to unravel the roles of ANXA2 and core residues (E53, E96, D162, E247 and D322) in its Ca2+-binding domains in the stone formation mechanism, particularly at crystal-cell adhesion step and downstream signaling cascade. ANXA2 was up-regulated in apical membranes, not cytosol, of RTECs after COM crystal exposure. Neutralizing the surface expression of ANXA2 by a specific monoclonal antibody and silencing its expression by small interfering RNA (siRNA) significantly decreased COM crystal-cell adhesion. siRNA also suppressed the COM-induced up-regulation of phospho-ERK1/2 and phospho-JNK, but not that of phospho-p38. Overexpression of ANXA2 wild-type (WT), but not that of E53A, E96A, D162A, E247A and D322A mutants of its Ca2+-binding domains, significantly increased intracellular [Ca2+], COM-cell adhesion, and phospho-ERK1/2 level. Therefore, E53, E96, D162, E247 and D322 in the Ca2+-binding domains of annexin A2 are essential for regulating intracellular [Ca2+] and COM crystal-cell adhesion via ERK1/2 and JNK signaling pathways.

The direct inhibitory effects of an antioxidant, N-acetylcysteine, against calcium oxalate crystal growth, aggregation and adhesion to MDCK renal cells

N-acetylcysteine (NAC), a potent antioxidant, can reduce nephrolithiatic pathogenesis by diminishing oxidative assault during crystalluria. However, its direct effects on calcium oxalate (CaOx) crystals that affect stone development were unknown. Herein, we examined the direct effects of NAC (at 1, 10 or 100 μM) on CaOx crystal formation, growth, aggregation, adhesion to MDCK renal cells, and internalization into the cells. The findings demonstrated that NAC at all these concentrations did not significantly affect size, number and mass of the newly generated CaOx crystals and their internalization into renal cells. However, NAC dose-dependently inhibited CaOx self-aggregation. Additionally, NAC at all concentrations significantly decreased the enlargement (growth) of the already-formed CaOx crystals and their adhesion to renal cells. Its dose-dependent inhibitory effects on crystal growth and adhesion were demonstrated at lower concentrations (0.01 and 0.1 μM). Measurement of adsorption energy (Eadsorption) between NAC molecule and Ca2+ ion revealed adsorption or affinity between NAC and Ca2+. Their affinity/binding was also confirmed by an ion-selective electrode (ISE)-based titration assay. These data have shown, for the first time, the direct inhibitory effects of NAC against CaOx crystal growth, aggregation and crystal adhesion to renal cells via Ca2+ binding that may impact the prevention of nephrolithiasis.

Urinary proteins from stone formers promote calcium oxalate crystallization, growth and aggregation via oxidative modifications

INTRODUCTION

Various urinary parameters are used for determining kidney stone risk. However, almost all of the widely used lithogenic indices rely on urinary concentrations of small molecules/ions and pH.

OBJECTIVE

To address whether urinary macromolecules (especially oxidatively modified proteins) also play a critical role in determining the stone risk.

METHODS

Complexed urinary proteins (proteome) were purified from healthy individuals and calcium oxalate (CaOx) stone formers and performed various crystal assays and quantitative proteomics to compare them. Bioinformatic analyses were performed to gain additional insights, and the obtained data were verified by ELISA.

RESULTS

While the normal urinary proteome inhibited CaOx stone-forming mechanisms (i.e., crystallization, growth and aggregation), the stone formers' urinary proteome promoted all these CaOx crystal parameters. Descriptive proteomics by nanoLC-ESI-LTQ-Orbitrap-MS/MS analysis identified 203 and 381 proteins in the urine of healthy individuals and stone formers, respectively. Analyses of physicochemical properties revealed only molecular mass and isoelectric point that slightly increased in the stone formers' urine, whereas instability index, grand average of hydrophathicity (GRAVY) and amino acid composition were comparable. Interestingly, proportion of oxidatively modified proteins (particularly those with methionine oxidation, methionine dioxidation and cysteine trioxidation) markedly increased (∼2.5-fold) in the stone formers' urine. Quantitative proteomics revealed 89 increased and 56 decreased proteins in the stone formers' urine. The oxidized proteins had a greater proportion (>3-fold) in the increased proteins (77 %) compared with the decreased ones (23 %), whereas the non-oxidized proteins showed comparable proportions (54 % and 46 %, respectively). Functional enrichment analyses revealed a correlation between the increased proteins and oxidative stress biological processes and molecular functions. Finally, ELISA confirmed the significantly increased levels of oxidized proteins in the stone formers' urine compared with that of healthy individuals.

CONCLUSION

These data implicate that oxidatively modified proteome serves as a key pathogenic factor or risk for CaOx kidney stone formation.

The inhibitory effects of proteins secreted from trigonelline-treated renal cells on calcium oxalate crystals in vitro: Implications for kidney stone prevention

Trigonelline is a bioactive alkaloid with therapeutic effects on various kidney diseases. Although previous studies have implicated its potential to prevent kidney stone disease (KSD), its anti-lithiatic mechanisms were poorly understood and thus addressed herein. Secretome (a set of secreted proteins) was collected and purified from MDCK renal cells treated with 100 µM trigonelline (termed "trigonelline-treated secretome") to examine its effects on calcium oxalate (CaOx) crystals compared with that derived from untreated cells (termed "control secretome"). Trigonelline-treated secretome significantly reduced CaOx crystal size, number and abundance during initial crystallization, and also inhibited crystal growth, aggregation and adhesion to renal cells. Quantitative proteomics using nanoLC-ESI-Qq-TOF tandem mass spectrometry revealed 46 differentially secreted (11 decreased and 35 increased) proteins, mainly from extracellular compartments, in the trigonelline-treated secretome. While most of the identified proteins were acidic, significantly increased secreted proteins had an increased proportion of basic proteins, resulting in a slightly greater isoelectric point. In concordance, significantly increased secreted proteins had a greater proportion of positively charged amino acids as compared with significantly decreased secreted proteins. However, proportions of aromatic, polar, non-polar, and negatively charged amino acids were comparable. In summary, we report herein direct evidence of the inhibitory effects of trigonelline against CaOx crystallization, growth, aggregation and adhesion to renal cells via the altered secreted proteins that show some unique physicochemical properties when the increased secreted proteins were compared with the decreased compartments. These data may lead to a better understanding of mechanisms underlying the anti-lithiatic effects of trigonelline to prevent KSD.

The relevance of calcium-binding domains to promoting activities of annexin A2 in calcium oxalate stone formation

Annexin A2 (ANXA2) is a Ca2+-binding protein involved in kidney stone disease (KSD) but with unclear mechanism. Herein, five Ca2+-binding domains of ANXA2 were mutated by substituting glutamic acid (E) at positions 53rd (domain I), 96th (domain II) and 247th (domain IV), and aspartic acid (D) at positions 162nd (domain III) and 322nd (domain V) with alanine (A). Recombinant ANXA2 wide type (WT) and mutants (E53A, E96A, D162A, E247A and D322A) were constructed, produced, purified and subjected to multiple crystal and functional assays. Crystal assays revealed that ANXA2 WT increased calcium oxalate monohydrate (COM) crystal size during crystallization and enhanced growth and crystal-cell adhesion phases compared with blank and negative controls. However, crystals exposed to all ANXA2 mutants had comparable or slightly lower parameters compared with controls. Although ANXA2 WT did not affect crystal aggregation, its mutants still showed a lower degree of crystal aggregation. Immunofluorescence staining and Ca2+-binding assay demonstrated that ANXA2 WT had the greatest affinity to COM crystals and free Ca2+ ions, whereas all the mutants showed lower affinity. Taken together, all five Ca2+-binding domains are relevant to the promoting activities of ANXA2 in COM stone formation by interacting with COM crystal surfaces and free Ca2+ ions.

Promoting activities of human cyclophilin A on calcium oxalate stone formation at crystal growth, aggregation and crystal-cell adhesion phases

Kidney stone is a specialized form of biomineralization involving complex interactions between crystals and urinary macromolecules. Renal tubular cells secrete cyclophilin A (CyPA), a protein whose elevated level is associated with various kidney diseases. Nevertheless, its role in kidney stone formation has not previously been explored. This study thus aimed to investigate roles of CyPA in kidney stone formation through various calcium oxalate (CaOx) crystal assays. Recombinant human CyPA was generated to mimic its secretory form excreted into the urine. Crystal assays yielded the first evidence demonstrating that CyPA significantly promoted CaOx growth, aggregation and crystal-cell adhesion, all of which are the critical steps during initial CaOx stone formation. Despite the lack of specific Ca2+-binding and Ox2--binding domains and its inability to bind free Ca2+/Ox2- ions in solution, CyPA demonstrated a distinct ability to bind CaOx crystals. Upon binding, CyPA facilitated further CaOx growth, aggregation of adjacent crystals and crystal-cell adhesion. These findings unravel a novel mechanism of kidney stone pathogenesis, expanding the known functions of CyPA. This research also provides solid evidence of how CyPA became one of the compositions in the stone matrix and highlights its potential to be a therapeutic/preventive target for management/prevention of kidney stone disease.

Comprehensive identification of stone-promoting proteins in the urine of kidney stone formers

Urinary proteins have crucial roles in modulating kidney stone formation. While stone-inhibiting urinary proteins are well characterized, stone-promoting urinary proteins are insufficiently explored. This knowledge gap limits our ability to fully comprehend the pathogenic mechanisms underlying nephrolithiasis and hampers the development of targeted therapeutic/preventive interventions. Therefore, we systematically identified stone-promoting proteins from the urine of 30 calcium oxalate (CaOx) nephrolithiatic patients (stone formers). Urinary proteins were fractionated by anion exchange and size-exclusion chromatography. A total of 15 protein fractions (SF1-SF15) were tested for their modulating activities on CaOx crystals by various assays compared with the control. The fractions with net CaOx-promoting activities were then identified by nanoLC-ESI-Qq-TOF MS/MS. From 15 fractions, 9 had net CaOx-promoting activities in all crystal assays. Among 3-99 proteins identified from these fractions, alpha-1acid glycoprotein 2, alpha-1-antitrypsin, apolipoprotein D, CD44 antigen, endosialin, fibrinogen alpha chain, interleukin-18-binding protein, kallikrein-1, retinol-binding protein 4, and titin have been found to increase in the urine of stone formers compared with controls, reinforcing their potential roles as CaOx stone promoters. This study offers the largest collection of CaOx stone-promoting proteins that will shed light on pathogenic mechanisms of nephrolithiasis and may allow further development of new drug targets to treat/prevent nephrolithiasis.

Advances in the mechanism of urinary proteins in calcium oxalate kidney stone formation

Kidney stones are a common urological disease worldwide, imposing a significant burden on healthcare systems. Calcium oxalate stones are the predominant form of urinary calculi, with two main theoretical models explaining their pathogenesis: the fixed particle and free particle models. Regardless of the model, the formation of calcium oxalate kidney stones is inseparably linked to crystal nucleation, growth, aggregation, and adhesion in urine. Growing evidence highlights the significant role of urinary proteins, particularly matrix proteins, in the development of calcium oxalate stones. The review classifies urinary proteins impacting calcium oxalate stone formation into three groups: inhibitors, promoters, and dual-regulators, outlining their contributions to the formation process.

Defining physicochemical properties of urinary proteins that determine their inhibitory activities against calcium oxalate kidney stone formation

We have recently reported a set of urinary proteins that inhibited calcium oxalate (CaOx) stone development. However, physicochemical properties that determine their inhibitory activities remained unknown. Herein, human urinary proteins were chromatographically fractionated into 15 fractions and subjected to various CaOx crystal assays and identification by nanoLC-ESI-Qq-TOF MS/MS. Their physicochemical properties and crystal inhibitory activities were subjected to Pearson correlation analysis. The data showed that almost all urinary protein fractions had crystal inhibitory activities. Up to 128 proteins were identified from each fraction. Crystallization inhibitory activity correlated with percentages of Ca2+-binding proteins, stable proteins, polar amino acids, alpha helix, beta turn, and random coil, but inversely correlated with number of Ox2--binding motifs/protein and percentage of unstable proteins. Crystal aggregation inhibitory activity correlated with percentage of stable proteins but inversely correlated with percentage of unstable proteins. Crystal adhesion inhibitory activity correlated with percentage of stable proteins and GRAVY, but inversely correlated with pI, instability index and percentages of unstable proteins and positively charged amino acids. However, there was no correlation between crystal growth inhibitory activity and any physicochemical properties. In summary, some physicochemical properties of urinary proteins can determine and may be able to predict their CaOx stone inhibitory activities.

The direct inhibitory effects of Lactobacillus acidophilus, a commensal urinary bacterium, on calcium oxalate stone development

BACKGROUND

Lactobacillus acidophilus is a commensal urinary bacterium found more abundantly in healthy individuals than in stone patients. Hence, it has been proposed to play an inhibitory role in kidney stone disease (KSD) but with unclear mechanisms. We therefore investigated the direct effects of L. acidophilus on calcium oxalate (CaOx) stone development compared with Escherichia coli, which is known to promote CaOx stone formation.

RESULTS

L. acidophilus at 1 × 103 CFU/ml  significantly reduced the abundance of newly formed crystals, enlargement and aggregation of seeded crystals, and crystal adhesion on renal cell membranes. By contrast, E. coli at 1 × 103 CFU/ml significantly enhanced crystal growth and aggregation but did not affect crystallization and crystal-cell adhesion. Oxalate consumption assay showed that neither L. acidophilus nor E. coli significantly reduced the remaining oxalate level after 1 - 3 h incubation. However, both of them adhered to CaOx crystals. Surface component detection revealed that only L. acidophilus expressed S-layer protein, whereas only E. coli exhibited flagella on their surfaces. Removal of L. acidophilus S-layer protein and E. coli flagella completely abolished the inhibitory and promoting effects of L. acidophilus and E. coli, respectively.

CONCLUSIONS

L. acidophilus inhibits CaOx stone development by hampering crystallization, growth, aggregation and cell-adhesive ability of CaOx. By contrast, E. coli enhances CaOx stone development by promoting CaOx growth and aggregation. Their contradictory effects are most likely from differential surface components (i.e., S-layer protein on L. acidophilus and flagella on E. coli) not from oxalate-degrading ability. Video Abstract.

Large-scale identification of calcium oxalate stone inhibitory proteins in normal human urine

Recent evidence has shown that proteins in normal human urine can inhibit calcium oxalate (CaOx) kidney stone formation. Herein, we performed fast protein liquid chromatography (FPLC) to fractionate normal human urinary proteins using anion-exchange (DEAE) and size-exclusion (Superdex 200) materials. FPLC fractions (F1-F15) were examined by CaOx crystallization, growth, aggregation and crystal-cell adhesion assays. The fractions with potent inhibitory activities against CaOx crystals were then subjected to mass spectrometric protein identification. The data revealed that 13 of 15 fractions showed inhibitory activities in at least one crystal assay. Integrating CaOx inhibitory scores demonstrated that F6, F7 and F8 had the most potent inhibitory activities. NanoLC-ESI-Qq-TOF MS/MS identified 105, 93 and 53 proteins in F6, F7 and F8, respectively. Among them, 60 were found in at least two fractions and/or listed among known inhibitors with solid experimental evidence in the StoneMod database (https://www.stonemod.org). Interestingly, 10 of these 60 potential inhibitors have been reported with lower urinary levels in CaOx stone formers compared with healthy (non-stone) individuals, strengthening their roles as potent CaOx stone inhibitors. Our study provides the largest dataset of potential CaOx stone inhibitory proteins that will be useful for further elucidations of stone-forming mechanisms and ultimately for therapeutic/preventive applications.

Machine learning and 4D-LFQ quantitative proteomic analysis explore the molecular mechanism of kidney stone formation

Background

Nephrolithiasis, a common and chronic urological condition, exerts significant pressure on both the general public and society as a whole. The precise mechanisms of nephrolith formation remain inadequately comprehended. Nevertheless, the utilization of proteomics methods has not been employed to examine the development of renal calculi in order to efficiently hinder and manage the creation and reappearance of nephrolith. Nowadays, with the rapid development of proteomics techniques, more efficient and more accurate proteomics technique is utilized to uncover the mechanisms underlying diseases. The objective of this study was to investigate the possible alterations of HK-2 cells when exposed to varying amounts of calcium oxalate (CaOx). The aim was to understand the precise development of stone formation and recurrence, in order to find effective preventive and treatment methods.

Methods

To provide a complete view of the proteins involved in the development of nephrolithiasis, we utilized an innovative proteomics method called 4D-LFQ proteomic quantitative techniques. HK-2 cells were selected as our experimental subjects. Three groups (n = 3) of HK-2 cells were treated with intervention solutions containing 0 (negative control, NC), 1 mM, and 2 mM CaOx, respectively. For the proteins that showed differential expression, various analyses were conducted including examination of Gene Ontology (GO), Clusters of Orthologous Groups of proteins (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, enrichment analysis of protein domains, and hierarchical clustering analysis. The STRING database was used to identify the interaction network of the chosen proteins. Candidate proteins were validated using parallel reaction monitoring (PRM) in the end.

Results

All three groups verified the repeatability of samples. According to the results of 4D-LFQ proteomic quantitative analysis, there were 120, 262, and 81 differentially expressed proteins (DEPs) in the 1 mM-VS-NC, 2 mM-VS-NC, and 2 mM-VS-1mM conditions, respectively. According to GO annotation, the functional enrichment analysis indicates that the differentially expressed proteins (DEPs) were notably enriched in promoting cell migration and the extracellular matrix, among other functions. Analysis of enrichment, based on the KEGG pathway, revealed significant enrichment of DEPs in complement and coagulation cascades, as well as in ECM-receptor (extracellular matrix-receptor) interaction and other related pathways. 14 DEPs of great interest were selected as candidate proteins, including FN1, TFRC, ITGA3, FBN1, HYOU1, SPP1, HSPA5, COL6A1, MANF, HIP1R, JUP, AXL, CTNNB1 and DSG2.The data from PRM demonstrated the variation trend of 14 DEPs was identical as 4D-LFQ proteomic quantitative analysis.

Conclusion

Proteomics studies of CaOx-induced HK-2 cells using 4D-LFQ proteomic quantitative analysis and PRM may help to provide crucial potential target proteins and signaling pathways for elucidating the mechanism of nephrolithiasis and better treating nephrolithiasis.

Resveratrol inhibits calcium oxalate crystal growth, reduces adhesion to renal cells and induces crystal internalization into the cells, but promotes crystal aggregation

Resveratrol is a natural phenolic compound that belongs to stilbenoid group found in diverse plants. Health benefits and therapeutic potentials of resveratrol have been widely recognized in various diseases. In kidney stone disease, it can alleviate oxalate-induced hyperproduction of free radicals in renal epithelial cells. Nevertheless, its direct effects on calcium oxalate (CaOx) crystal, which is the major stone component, remained unclear. This study therefore addressed the direct effects of resveratrol (at 1, 10 or 100 μM) on each step of CaOx kidney stone formation. The results revealed that resveratrol had no significant effects on CaOx crystallization. However, resveratrol significantly decreased CaOx crystal growth and adhesion to renal epithelial cells at all concentrations, and induced crystal internalization into the cells (a process related to crystal degradation by endolysosomes) in a concentration-dependent manner. On the other hand, resveratrol promoted crystal aggregation. These data indicate that resveratrol serves as a dual modulator on CaOx stone formation. While it inhibits CaOx stone development by reducing crystal growth and adhesion to renal cells and by inducing crystal internalization into the cells, resveratrol promotes crystal aggregation, which is one of the mechanisms leading to kidney stone formation.

Understanding formation processes of calcareous nephrolithiasis in renal interstitium and tubule lumen

Kidney stone, one of the oldest known diseases, has plagued humans for centuries, consistently imposing a heavy burden on patients and healthcare systems worldwide due to their high incidence and recurrence rates. Advancements in endoscopy, imaging, genetics, molecular biology and bioinformatics have led to a deeper and more comprehensive understanding of the mechanism behind nephrolithiasis. Kidney stone formation is a complex, multi-step and long-term process involving the transformation of stone-forming salts from free ions into asymptomatic or symptomatic stones influenced by physical, chemical and biological factors. Among the various types of kidney stones observed in clinical practice, calcareous nephrolithiasis is currently the most common and exhibits the most intricate formation mechanism. Extensive research suggests that calcareous nephrolithiasis primarily originates from interstitial subepithelial calcified plaques and/or calcified blockages in the openings of collecting ducts. These calcified plaques and blockages eventually come into contact with urine in the renal pelvis, serving as a nidus for crystal formation and subsequent stone growth. Both pathways of stone formation share similar mechanisms, such as the drive of abnormal urine composition, involvement of oxidative stress and inflammation, and an imbalance of stone inhibitors and promoters. However, they also possess unique characteristics. Hence, this review aims to provide detailed description and present recent discoveries regarding the formation processes of calcareous nephrolithiasis from two distinct birthplaces: renal interstitium and tubule lumen.

The modulatory effects of large and small extracellular vesicles from normal human urine on calcium oxalate crystallization, growth, aggregation, adhesion on renal cells, and invasion through extracellular matrix: An in vitro study

Urinary extracellular vesicles (uEVs) play important roles in physiologic condition and various renal/urological disorders. However, their roles in kidney stone disease remain unclear. This study aimed to examine modulatory effects of large and small uEVs derived from normal human urine on calcium oxalate (CaOx) crystals (the main component in kidney stones). After isolation, large uEVs, small uEVs and total urinary proteins (TUPs) with equal (protein equivalent) concentration were added into various crystal assays to compare with the control (without uEVs or TUPs). TUPs strongly inhibited CaOx crystallization, growth, aggregation and crystal-cell adhesion. Large uEVs had lesser degree of inhibition against crystallization, growth and crystal-cell adhesion, and comparable degree of aggregation inhibition compared with TUPs. Small uEVs had comparable inhibitory effects as of TUPs for all these crystal assays. However, TUPs and large uEVs slightly promoted CaOx invasion through extracellular matrix, whereas small uEVs did not affect this. Matching of the proteins reported in six uEVs datasets with those in the kidney stone modulator (StoneMod) database revealed that uEVs contained 18 known CaOx stone modulators (mainly inhibitors). These findings suggest that uEVs derived from normal human urine serve as CaOx stone inhibitors to prevent healthy individuals from kidney stone formation.

StoneMod 2.0: Database and prediction of kidney stone modulatory proteins

Stone modulators are various kinds of molecules that play crucial roles in promoting/inhibiting kidney stone formation. Several recent studies have extensively characterized the stone modulatory proteins with the ultimate goal of preventing kidney stone formation. Herein, we introduce the StoneMod 2.0 database (https://www.stonemod.org), which has been dramatically improved from the previous version by expanding the number of the modulatory proteins in the list (from 32 in the initial version to 17,130 in this updated version). The stone modulatory proteins were recruited from solid experimental evidence (via PubMed) and/or predicted evidence (via UniProtKB, QuickGO, ProRule, STITCH and OxaBIND to retrieve calcium-binding and oxalate-binding proteins). Additionally, StoneMod 2.0 has implemented a scoring system that can be used to determine the likelihood and to classify the potential stone modulatory proteins as either "solid" (modulator score ≥ 50) or "weak" (modulator score < 50) modulators. Furthermore, the updated version has been designed with more user-friendly interfaces and advanced visualization tools. In addition to the monthly scheduled update, the users can directly submit their experimental evidence online anytime. Therefore, StoneMod 2.0 is a powerful database with prediction scores that will be very useful for many future studies on the stone modulatory proteins.

The inhibitory effects of epigallocatechin-3-gallate on calcium oxalate monohydrate crystal growth, aggregation and crystal-cell adhesion

Epigallocatechin-3-gallate (EGCG), a predominant phytochemical in tea plant, has been reported to prevent kidney stone formation but with vague mechanism. We investigated modulatory effects of EGCG (at 0.1-100 µM) on calcium oxalate monohydrate (COM) crystals at various stages of kidney stone development. EGCG significantly increased crystal size (at 1-100 µM), but decreased crystal number (at 10-100 µM), resulting in unchanged crystal mass and volume. Interestingly, EGCG at 10-100 µM caused morphological change of the crystals from typical monoclinic prismatic to coffee-bean-like shape, which represented atypical/aberrant form of COM as confirmed by attenuated total reflection - Fourier transform infrared (ATR-FTIR) spectroscopy. EGCG at all concentrations significantly inhibited crystal growth in a concentration-dependent manner. However, only 100 µM and 10-100 µM of EGCG significantly inhibited crystal aggregation and crystal-cell adhesion, respectively. Immunofluorescence staining (without permeabilization) revealed that surface expression of heat shock protein 90 (HSP90) (a COM crystal receptor) on MDCK renal cells was significantly decreased by 10 µM EGCG, whereas other surface COM receptors (annexin A1, annexin A2, enolase 1 and ezrin) remained unchanged. Immunoblotting showed that 10 µM EGCG did not alter total level of HSP90 in MDCK cells, implicating that its decreased surface expression was due to translocation. Our data provide a piece of evidence explaining mechanism underlying the anti-lithiatic property of EGCG by inhibition of COM crystal growth, aggregation and crystal-cell adhesion via reduced surface expression of HSP90, which is an important COM crystal receptor.

Quercetin inhibits calcium oxalate crystallization and growth but promotes crystal aggregation and invasion

Recent evidence has shown an association between kidney stone pathogenesis and oxidative stress. Many anti-oxidants have been studied with an aim for stone prevention. Quercetin, a natural flavonol, is one among those eminent anti-oxidants with satisfactory anti-inflammatory property to cope with renal tissue injury in kidney stone disease. Nevertheless, its direct effect (if any) on calcium oxalate (CaOx) crystals and the stone formation mechanism had not been previously explored. This study has addressed the ability of quercetin at various concentrations (2.5, 5, 10, 20, 40, 80 and 160 μM) to directly modulate CaOx crystallization, growth, aggregation, adhesion on kidney cells, and invasion through the matrix. The data have shown that quercetin significantly inhibits CaOx crystallization and crystal growth but promotes crystal aggregation in concentration-dependent manner. However, quercetin at all these concentrations do not affect CaOx adhesion on kidney cells. For the invasion, quercetin at all concentrations constantly promotes CaOx invasion through the matrix without concentration-dependent pattern. These discoveries have demonstrated for the first time that quercetin has direct but dual modulatory effects on CaOx crystals. While quercetin inhibits CaOx crystallization and growth, on the other hand, it promotes CaOx crystal aggregation and invasion through the matrix. These data highlight the role for quercetin in direct modulation of the CaOx crystals that may intervene the stone pathogenesis.

Calcineurin B inhibits calcium oxalate crystallization, growth and aggregation via its high calcium-affinity property

Calcineurin inhibitors (CNIs) are widely used in organ transplantation to suppress immunity and prevent allograft rejection. However, some transplant patients receiving CNIs have hypocitraturia, hyperoxaluria and kidney stone with unclear mechanism. We hypothesized that CNIs suppress activities of urinary calcineurin, which may serve as the stone inhibitor. This study aimed to investigate effects of calcineurin B (CNB) on calcium oxalate monohydrate (COM) stone formation. Sequence and structural analyses revealed that CNB contained four EF-hand (Ca2+-binding) domains, which are known to regulate Ca2+ homeostasis and likely to affect COM crystals. Various crystal assays revealed that CNB dramatically inhibited COM crystallization, crystal growth and crystal aggregation. At an equal amount, degrees of its inhibition against crystallization and crystal growth were slightly inferior to total urinary proteins (TUPs) from healthy subjects that are known to strongly inhibit COM stone formation. Surprisingly, its inhibitory effect against crystal aggregation was slightly superior to TUPs. While TUPs dramatically inhibited crystal-cell adhesion, CNB had no effect on this process. Ca2+-affinity assay revealed that CNB strongly bound Ca2+ at a comparable degree as of TUPs. These findings indicate that CNB serves as a novel inhibitor of COM crystallization, growth and aggregation via its high Ca2+-affinity property.

OxaBIND: A tool for identifying oxalate-binding domain(s)/motif(s) in protein(s)

High oxalate level in blood and urine may cause oxalate-related disorders, particularly kidney stone disease. To unravel disease mechanisms, investigations of oxalate level and its binding proteins are required. However, the information on oxalate-binding proteins is limited due to a lack of appropriate tool for their investigations. Therefore, we have developed a freely accessible web-based tool, namely OxaBIND (https://www.stonemod.org/oxabind.php), to identify oxalate-binding site(s) in any proteins of interest. The prediction model was generated by recruiting all of the known oxalate-binding proteins with solid experimental evidence (from PubMed and RCSB Protein Data Bank). The potential oxalate-binding domains/motifs were predicted from these oxalate-binding proteins using PRATT tool and used to discriminate these known oxalate-binding proteins from the known non-oxalate-binding proteins. The best one, which provided highest fitness score, sensitivity and specificity, was then implemented to create the OxaBIND tool. After inputting protein identifier or sequence (which can be single or multiple), details of all the identified oxalate-binding site(s), if any, are presented in both textual and graphical formats. OxaBIND also provides theoretical three-dimensional (3D) structure of the protein with oxalate-binding site(s) being highlighted. This tool will be beneficial for future research on the oxalate-binding proteins, which play important roles in the oxalate-related disorders.

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.

Evolution of nacre- and prisms-related shell matrix proteins in the pen shell, Atrina pectinata

The molluscan shell is a good model for understanding the mechanisms underlying biomineralization. It is composed of calcium carbonate crystals and many types of organic molecules, such as the matrix proteins, polysaccharides, and lipids. The pen shell Atrina pectinata (Pterioida, Pinnidae) has two shell microstructures: an outer prismatic layer and an inner nacreous layer. Similar microstructures are well known in pearl oysters (Pteriidae), such as Pinctada fucata, and many kinds of shell matrix proteins (SMPs) have been identified from their shells. However, the members of SMPs that consist of the nacreous and prismatic layers of Pinnidae bivalves remain unclear. In this study, we identified 114 SMPs in the nacreous and prismatic layers of A. pectinata, of which only seven were found in both microstructures. 54 of them were found to bind calcium carbonate. Comparative analysis of nine molluscan shell proteomes showed that 69 of 114 SMPs of A. pectinata were found to have sequential similarity with at least one or more SMPs of other molluscan species. For instance, nacrein, tyrosinase, Pif/BMSP-like, chitinase (CN), chitin-binding proteins, CD109, and Kunitz-type serine proteinase inhibitors are widely shared among bivalves and gastropods. Our results provide new insights for understanding the complex evolution of SMPs related to nacreous and prismatic layer formation in the pteriomorph bivalves.

Roles of heat-shock protein 90 and its four domains (N, LR, M and C) in calcium oxalate stone-forming processes

Human heat-shock protein 90 (HSP90) has four functional domains, including NH₂-terminal (N), charged linker region (LR), middle (M) and COOH-terminal (C) domains. In kidney stone disease (or nephrolithiasis/urolithiasis), HSP90 serves as a receptor for calcium oxalate monohydrate (COM), which is the most common crystal to form kidney stones. Nevertheless, roles of HSP90 and its four domains in kidney stone formation remained unclear and under-investigated. We thus examined and compared their effects on COM crystals during physical (crystallization, growth and aggregation) and biological (crystal–cell adhesion and crystal invasion through extracellular matrix (ECM)) pathogenic processes of kidney stone formation. The analyses revealed that full-length (FL) HSP90 obviously increased COM crystal size and abundance during crystallization and markedly promoted crystal growth, aggregation, adhesion onto renal cells and ECM invasion. Comparing among four individual domains, N and C domains exhibited the strongest promoting effects, whereas LR domain had the weakest promoting effects on COM crystals. In summary, our findings indicate that FL-HSP90 and its four domains (N, LR, M and C) promote COM crystallization, crystal growth, aggregation, adhesion onto renal cells and invasion through the ECM, all of which are the important physical and biological pathogenic processes of kidney stone formation.

Trigonelline prevents kidney stone formation processes by inhibiting calcium oxalate crystallization, growth and crystal-cell adhesion, and downregulating crystal receptors

Trigonelline is the second most abundant bioactive alkaloid found in coffee. It is classified as a phytoestrogen with similar structure as of estradiol and exhibits an estrogenic effect. A previous study has reported that fenugreek seed extract rich with trigonelline can reduce renal crystal deposition in ethylene glycol-induced nephrolithiatic rats. However, direct evidence of such anti-lithogenic effects of trigonelline and underlying mechanisms have not previously been reported. Our study therefore addressed the protective effects and mechanisms of trigonelline against kidney stone-forming processes using crystallization, crystal growth, aggregation and crystal-cell adhesion assays. Also, proteomics was applied to identify changes in receptors for calcium oxalate monohydrate (COM), the most common stone-forming crystal, on apical membranes of trigonelline-treated renal tubular cells. The analyses revealed that trigonelline significantly reduced COM crystal size, number and mass during crystallization. Additionally, trigonelline dose-dependently inhibited crystal growth and crystal-cell adhesion, but did not affect crystal aggregation. Mass spectrometric protein identification showed the smaller number of COM crystal receptors on apical membranes of the trigonelline-treated cells. Western blotting confirmed the decreased levels of some of these crystal receptors by trigonelline. These data highlight the protective mechanisms of trigonelline against kidney stone development by inhibiting COM crystallization, crystal growth and crystal-cell adhesion via downregulation of the crystal receptors on apical membranes of renal tubular cells.

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.

Oxidative Modifications Switch Modulatory Activities of Urinary Proteins From Inhibiting to Promoting Calcium Oxalate Crystallization, Growth, and Aggregation

The incidence/prevalence of kidney stone disease has been increasing around the globe, but its pathogenic mechanisms remained unclear. We evaluated effects of oxidative modifications of urinary proteins on calcium oxalate (CaOx) stone formation processes. Urinary proteins derived from 20 healthy individuals were modified by performic oxidation, and the presence of oxidatively modified urinary proteins was verified, quantified, and characterized by Oxyblot assay and tandem MS (nanoLC-electrospray ionization-linear trap quadrupole-Orbitrap-MS/MS). Subsequently, activities of oxidatively modified urinary proteins on CaOx stone formation processes were examined. Oxyblot assay confirmed the marked increase in protein oxidation level in the modified urine. NanoLC-electrospray ionization-linear trap quadrupole-Orbitrap-MS/MS identified a total of 193 and 220 urinary proteins in nonmodified and modified urine samples, respectively. Among these, there were 1121 and 5297 unambiguous oxidatively modified peptides representing 42 and 136 oxidatively modified proteins in the nonmodified and modified urine samples, respectively. Crystal assays revealed that oxidatively modified urinary proteins significantly promoted CaOx crystallization, crystal growth, and aggregation. By contrast, the nonmodified urinary proteins had inhibitory activities. This is the first direct evidence demonstrating that oxidative modifications of urinary proteins increase the risk of kidney stone disease by switching their modulatory activities from inhibiting to promoting CaOx crystallization, crystal growth, and aggregation.

Regulation of Laminaria Polysaccharides with Different Degrees of Sulfation during the Growth of Calcium Oxalate Crystals and their Protective Effects on Renal Epithelial Cells

The original Laminaria polysaccharide (LP0) was sulfated using the sulfur trioxide-pyridine method, and four sulfated Laminaria polysaccharides (SLPs) were obtained, namely, SLP1, SLP2, SLP3, and SLP4. The sulfated (-OSO3 -) contents were 8.58%, 15.1%, 22.8%, and 31.3%, respectively. The structures of the polysaccharides were characterized using a Fourier transform infrared (FT-IR) spectrometer and nuclear magnetic resonance (NMR) techniques. SLPs showed better antioxidant activity than LP0, increased the concentration of soluble Ca2+ in the solution, reduced the amount of CaOx precipitation and degree of CaOx crystal aggregation, induced COD crystal formation, and protected HK-2 cells from damage caused by nanometer calcium oxalate crystals. These effects can inhibit the formation of CaOx kidney stones. The biological activity of the polysaccharides increased with the content of -OSO3 -, that is, the biological activities of the polysaccharides had the following order: LP0 < SLP1 < SLP2 < SLP3 < SLP4. These results reveal that SLPs with high -OSO3 - contents are potential drugs for effectively inhibiting the formation of CaOx stones.

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.

Optimizing Decellularization Strategies for the Efficient Production of Whole Rat Kidney Scaffolds

BACKGROUND

Renal dysfunction remains a global issue, with chronic kidney disease being the 18th most leading cause of death, worldwide. The increased demands in kidney transplants, led the scientific society to seek alternative strategies, utilizing mostly the tissue engineering approaches. Unlike to perfusion decellularization of kidneys, we proposed alternative decellularization strategies to obtain acellular kidney scaffolds. The aim of this study was the evaluation of two different decellularization approaches for producing kidney bioscaffolds.

METHODS

Rat kidneys from Wistar rats, were submitted to decellularization, followed two different strategies. The decellularization solutions used in both approaches were the same and involved the use of 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate and sodium dodecyl sulfate buffers for 12 h each, followed by incubation in a serum medium. Both approaches involved 3 decellularization cycles. Histological analysis, biochemical and DNA quantification were performed. Cytotoxicity assay and repopulation of acellular kidneys were also applied.

RESULTS

Histological, biochemical and DNA quantification confirmed that the 2nd approach had the best outcome regarding the kidney composition and cell elimination. Acellular kidneys from both approaches were successfully recellularized.

CONCLUSION

Based on the above data, the production of kidney scaffolds with the proposed cost- effective decellularization approaches, was efficient.

Dual modulatory effects of diosmin on calcium oxalate kidney stone formation processes: Crystallization, growth, aggregation, crystal-cell adhesion, internalization into renal tubular cells, and invasion through extracellular matrix

Diosmin is a natural flavone glycoside (bioflavonoid) found in fruits and plants with several pharmacological activities. It has been widely used as a dietary supplement or therapeutic agent in various diseases/disorders. Although recommended, evidence of its protective mechanisms against kidney stone disease (nephrolithiasis/urolithiasis), especially calcium oxalate (CaOx) monohydrate (COM) that is the most common type, remained unclear. In this study, we thus systematically evaluated the effects of diosmin (at 2.5-160 nM) on various stages of kidney stone formation processes, including COM crystallization, crystal growth, aggregation, crystal-cell adhesion, internalization into renal tubular cells and invasion through extracellular matrix (ECM). The results showed that diosmin had dose-dependent modulatory effects on all the mentioned COM kidney stone processes. Diosmin significantly increased COM crystal number and mass during crystallization, but reduced crystal size and growth. While diosmin promoted crystal aggregation, it inhibited crystal-cell adhesion and internalization into renal tubular cells. Finally, diosmin promoted crystal invasion through the ECM. Our data provide evidence demonstrating both inhibiting and promoting effects of diosmin on COM kidney stone formation processes. Based on these dual modulatory activities of diosmin, its anti-urolithiasis role is doubtful and cautions should be made for its use in kidney stone disease.

In Vitro Cell Culture Models of Hyperoxaluric States: Calcium Oxalate and Renal Epithelial Cell Interactions

Urolithiasis is a multifactorial disease with a high incidence and high recurrence rate, characterized by formation of solid deposits in the urinary tract. The most common type of these stones are calcium oxalate stones. Calcium oxalate crystals can, in hyperoxaluric states, interact with renal epithelial cells, causing injury to the renal epithelia. Pathogenesis of urolithiasis is widely investigated, but underlying mechanisms are still not completely clarified. In vitro models offer insight into molecular processes which lead to renal stone formation and are significant for evaluation of prophylactic and therapeutic management of patients with urolithiasis. In this review, we summarize recently published data from in vitro studies investigating interactions of calcium oxalate crystals with renal epithelial cell lines, anti-urolithiatic mechanisms, and the results from studies exploring possible therapeutic and prophylactic options for calcium oxalate urolithiasis in cell cultures.

Cerebrospinal Fluid of Preeclamptic and Normotensive Pregnant Women Compared to Nonpregnant Women Analyzed with Mass Spectrometry

Preeclampsia is a pregnancy-specific multiorgan disorder in which impaired placental functioning and excessive oxidative stress play an important role. We previously showed distinct differences between cerebrospinal fluid proteins in patients with preeclampsia and normotensive pregnant women. An additional group of nonpregnant women was included to study the presence of pregnancy-related proteins in normotensive and preeclamptic pregnancies and whether pregnancy-related proteins were associated with preeclampsia. Cerebrospinal fluid samples were tryptically digested and subsequently measured with a nano-LC-tribrid Orbitrap mass spectrometry system. Proteins were identified by shotgun proteomic analysis based on a data-dependent acquisition method. Proteins identified in preeclampsia, normotensive pregnant controls, and nonpregnant groups were compared to the Progenesis method according to the criteria as previously described and with a secondary analysis using a Scaffold method including Benjamini-Hochberg correction for multiple testing. For preeclampsia, the Progenesis and the Scaffold method together identified 15 (eight proteins for both analyses with one overlap) proteins that were significantly different compared to normotensive control pregnancies. Three of these 15 proteins, which were elevated in cerebrospinal fluid of preeclamptic women, were described to be pregnancy proteins with a calcium-binding function. Using two analysis methods (Progenesis and Scaffold), four out of 15 differential proteins were associated with pregnancy, as described in the literature. Three out of the four pregnancy-related proteins were elevated in preeclampsia. Furthermore, the contribution of elevated (n = 4/15) and downregulated (n = 2/15) calcium-binding proteins in preeclampsia is remarkably high (40%) and needs to be elucidated further.

Evolution of Biomineralization Genes in the Prismatic Layer of the Pen Shell Atrina pectinata

Molluscan shells are composed of calcium carbonates, with small amounts of extracellular matrices secreted from mantle epithelial cells. Many types of shell matrix proteins (SMPs) have been identified from molluscan shells or mantle cells. The pen shell Atrina pectinata (Pinnidae) has two different shell microstructures, the nacreous and prismatic layers. Nacreous and prismatic layer-specific matrix proteins have been reported in Pteriidae bivalves, but remain unclear in Pinnidae. We performed transcriptome analysis using the mantle cells of A. pectinata to screen the candidate transcripts involved in its prismatic layer formation. We found Asprich and nine highly conserved prismatic layer-specific SMPs encoding transcript in P. fucata, P. margaritifera, and P. maxima (Tyrosinase, Chitinase, EGF-like proteins, Fibronectin, valine-rich proteins, and prismatic uncharacterized shell protein 2 [PUSP2]) using molecular phylogenetic analysis or multiple alignment. We confirmed these genes were expressed in the epithelial cells of the mantle edge (outer surface of the outer fold) and the mantle pallium. Phylogenetic character mapping of these SMPs was used to infer a possible evolutionary scenario of them in Pteriomorphia. EGF-like proteins, Fibronectin, and valine-rich proteins encoding genes each evolved in the linage leading to four Pteriomorphia (Mytilidae, Pinnidae, Ostreidae, and Pteriidae), PUSP2 evolved in the linage leading to three Pteriomorphia families (Pinnidae, Ostreidae, and Pteriidae), and chitinase was independently evolved as SMPs in Mytilidae and in other Pteriomorphia (Pinnidae, Ostreidae, and Pteriidae). Our results provide a new dataset for A. pectinata SMP annotation, and a basis for understanding the evolution of prismatic layer formation in bivalves.

Differential bound proteins and adhesive capabilities of calcium oxalate monohydrate crystals with various sizes

Adhesion of calcium oxalate (CaOx) crystals onto renal tubular epithelial cells is one of the critical steps in kidney stone formation. However, effects of crystal size on the crystal adhesive capability remained unclear. This study compared the adhesive capabilities of CaOx monohydrate (COM) crystals with various sizes (<10 μm, 20-30 μm, 50-60 μm, and > 80 μm). Crystal-cell adhesion assay showed size-dependent increase of COM crystal adhesion onto epithelial cell surface using the larger crystals. Identification of apical membrane proteins that could bind to COM crystals by tandem mass spectrometry (nanoLC-ESI-ETD MS/MS) demonstrated size-specific sets of the COM crystal-binding proteins. Among these, numbers of known oxalate-binding proteins and COM crystal receptors were greatest in the set of the largest size (>80 μm). Atomic force microscopy (AFM) revealed that adhesive forces between carboxylic-immobilized AFM tip and COM crystal surface and between COM-mounted AFM tip and renal epithelial cell surface were size-dependent (greater for the larger crystals). In summary, the adhesive capability of COM crystals is size-dependent - the larger the greater adhesive capability. These data may help better understanding of the pathogenic mechanisms of kidney stone formation at an initial stage when renal tubular cells are exposed to various sizes of COM crystals.

Flagellum Is Responsible for Promoting Effects of Viable Escherichia coli on Calcium Oxalate Crystallization, Crystal Growth, and Crystal Aggregation

Urease-producing bacteria (especially Proteus mirabilis) can cause infection kidney stone. However, recent studies have shown that intact viable non-urease-producing bacteria such as Escherichia coli might also promote calcium oxalate (CaOx) kidney stone formation but with unclear mechanism. We thus hypothesized that some relevant bacterial components might be responsible for such promoting effects of the intact viable E. coli. Flagella, capsule, lipopolysaccharide (LPS), and outer membrane vesicles (OMVs) were isolated/purified and their stone modulatory activities were evaluated using CaOx crystallization, crystal growth, and crystal aggregation assays. Among these, flagella had the most potent promoting effects on CaOx crystallization, crystal growth, and crystal aggregation. Validation was performed by deflagellation demonstrating that the deflagellated intact viable E. coli had markedly reduced CaOx crystal modulatory activities in all aspects (comparable to those of the negative controls). Similarly, neutralization of the isolated/purified flagella using a specific anti-flagellin antibody, not an isotype control, could abolish the promoting effects of flagella. These findings provide direct evidence indicating that flagellum is responsible for the promoting effects of the viable E. coli on CaOx crystallization, crystal growth and aggregation.