Kidney stone matrix proteins: Role in 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.

Post-ESWL urinary osteopontin level and ion-activity product of calcium oxalate are associated with stone recurrence after 5-year follow-up

BACKGROUND

Calcium oxalate (CaOx) is the predominant component in over 80% of kidney stones. The formation and retention of kidney stones involve multiple mechanisms, including overgrowth on Randall's plaques-subepithelial calcium phosphate deposits in the renal papillae-and interactions between urinary crystals and renal tubular epithelial cells. Previous studies have shown that specific urinary proteins can either promote or inhibit CaOx crystal nucleation, growth, and retention. This study investigates changes in the urinary excretion of CaOx-related proteins before and after extracorporeal shock wave lithotripsy (ESWL), aiming to identify protein markers associated with stone formation and recurrence over a 5-year follow-up.

METHODS

This study enrolled 54 patients with renal or ureteral stones treated with ESWL and 13 healthy controls. 24-hour urine samples were collected preoperatively and at 2 and 4 weeks post-ESWL for biochemical analysis. CaOx-related proteins were measured semi-quantitatively in urine samples before and after ESWL, including nucleolin-related protein (NRP), nuclear pore complex p62 (NPC), hyaluronic acid (HA), SLC26A6, CXCR4, osteopontin (OPN), Tamm-Horsfall protein (THP) and Matrix Metalloproteinase (MMPs). Statistical analyses, including Pearson correlation and logistic regression, were performed to identify factors related to 5-year stone recurrence. Statistical significance was set at p < 0.05.

RESULTS

Before ESWL, stone patients exhibited significantly higher levels of NPC, HA, and CXCR4. All examined markers, except for Tamm-Horsfall protein, increased significantly at two weeks after ESWL. At four weeks post-EWSL, OPN and SLC26A6 remained higher. Correlations were observed between CXCR4, MMPs, stone size and ion-activity product of calcium oxalate (APCaOX), a measure of urinary calcium oxalate supersaturation. Logistic regression identified urinary OPN and APCaOX at 4 weeks post-ESWL as significant factors influencing 5-year stone recurrence, with a recurrence rate of 48.4%.

CONCLUSIONS

The persistence of certain urinary proteins after ESWL implied the risk of stone recurrence despite stone removal. The stone recurrence at 5 years was significantly associated with higher urinary OPN and higher APCaOX levels at four weeks post-ESWL, suggesting the potential predictive value of these markers.

TRIAL REGISTRATION

Approval was obtained from the ethics committee of National Taiwan University Hospital (National Taiwan University Hospital Ethics Committee approval: 200706054M).

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.

Integrated proteomics reveals enrichment of oxidative stress and inflammatory proteins in the urine and stone matrix of calcium oxalate stone formers

Nephrolithiasis is a multifactorial disease associated with urinary and matrix proteins that become a focal point of research for diagnostic and preventative strategies. The functional relevance of these proteins in lithogenesis, along with their origins and impacts, remains a major subject of ongoing lithogenic research. Here, an integrated analysis was done on multiple proteome datasets compiled from various studies of normal urine (NU), urine from calcium oxalate stone formers (SFU), and calcium oxalate stone matrix (SM). Functional annotation and network analysis revealed the profound enrichment of proteins associated with oxidative stress and inflammation only in the stone-related samples (both "SFU but not NU" and "SM but not NU" cohorts). The oxidative stress and inflammation-related proteins were most abundant in the "SM but not NU" cohort and had higher proportions in the "SFU but not NU" cohort than the "NU only" cohort. KEGG pathway analysis corroborated such observation and highlighted the inclusion of proteins in the complement and coagulation pathways, particularly in SM. The findings of this study inform some mechanistic insights into the roles of calcium oxalate stone-related proteins and may help develop effective prevention and treatment strategies for nephrolithiasis.

Association between magnesium depletion score and the prevalence of kidney stones in the low primary income ratio: a cross-sectional study of NHANES 2007-2018

INTRODUCTION

To explore the association between magnesium depletion score (MgDS) and the prevalence of kidney stones in the low primary income ratio (PIR).

METHOD

A cross-sectional study was conducted using data from the National Health and Nutrition Examination Survey 2007-2018. Within the low PIR, people aged ≥20 years with complete information on MgDS and kidney stones questionnaires were enrolled. Multivariable logistic regression and stratified logistic regression analyses were performed to examine the association between MgDS and the prevalence of kidney stones and the recurrence of kidney stones by confounding factors adjusted. Stratified and interaction analysis was conducted to find whether some factors modified the association. In addition, sensitive analyses were also conducted to observe the stability. The work has been reported in line with the strengthening the reporting of cohort, cross-sectional, and case-control studies in surgery (STROCSS) criteria (Supplemental Digital Content 1, http://links.lww.com/JS9/C781 ).

RESULT

A total of 7600 adults were involved in the study, and the individuals were classified into four groups: 0 points for MgDS ( n =3814), 1 point for MgDS ( n =2229), 2 points for MgDS ( n =1020), and ≥3 points for MgDS ( n =537). The multivariable logistic regression suggested that a positive association between MgDS and the prevalence of kidney stones (OR=1.123, 95% CI: 1.019-1.238) in the fully adjusted model. Compared with the lowest group, people with ≥3 points of MgDS had a significant relationship with kidney stones (OR=1.417, 95% CI: 1.013-1.983). No significant association was observed between the recurrence of kidney stones and MgDS. The result of the sensitive analysis showed the robustness of the main analysis.

CONCLUSION

The prevalence of kidney stones is positively correlated with MgDS, which suggests that maintaining a higher MgDS is accompanied by higher prevalence rates of kidney stones in the low PIR.

Aortic Calcification in Patients with Nephrolithiasis: A Cross-Sectional Case-Control Study

Background

Nephrolithiasis is a common condition that has been linked to various systemic diseases. Recent studies have suggested that young patients with nephrolithiasis are at increased risk of developing premature atherosclerosis. This study aims to investigate the relationship between nephrolithiasis and systemic disease by examining the association between aortic calcification and the severity of kidney stone disease.

Methods

This study employed a matched case-control design involving 144 patients with kidney stones and 144 non-stone formers. All participants underwent non-contrast abdominal and pelvic CT scans. The Agatston score was used to quantify the severity of aortic calcification. The data were analyzed and compared between the two groups. Quantitative data were analyzed using Pearson's chi-square test. Non-parametric data were analyzed using the Mann-Whitney test.

Results

The Agatston score was measured in both case and control groups, with mean values of 316±734 and 231±706, respectively. However, the difference between the two groups was not statistically significant (P = 0.122). Notably, a significant correlation was observed between Agatston score and stone size (P = 0.014). The value of the correlation coefficient is 0.23, which shows the increase in severity of aortic calcification with increasing stone size. A comparison of the Agatston score between male kidney stone formers patients aged 45 years or younger and controls revealed a statistically significant difference, with a p-value of 0.049, indicating more pronounced aortic calcification in the patient group.

Conclusion

These results suggest that there may be a shared pathophysiological mechanism underlying both nephrolithiasis and atherosclerosis.

The Caenorhabditis elegans cuticle and precuticle: a model for studying dynamic apical extracellular matrices in vivo

Apical extracellular matrices (aECMs) coat the exposed surfaces of animal bodies to shape tissues, influence social interactions, and protect against pathogens and other environmental challenges. In the nematode Caenorhabditis elegans, collagenous cuticle and zona pellucida protein-rich precuticle aECMs alternately coat external epithelia across the molt cycle and play many important roles in the worm's development, behavior, and physiology. Both these types of aECMs contain many matrix proteins related to those in vertebrates, as well as some that are nematode-specific. Extensive differences observed among tissues and life stages demonstrate that aECMs are a major feature of epithelial cell identity. In addition to forming discrete layers, some cuticle components assemble into complex substructures such as ridges, furrows, and nanoscale pillars. The epidermis and cuticle are mechanically linked, allowing the epidermis to sense cuticle damage and induce protective innate immune and stress responses. The C. elegans model, with its optical transparency, facilitates the study of aECM cell biology and structure/function relationships and all the myriad ways by which aECM can influence an organism.

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.

Management of urinary stones: state of the art and future perspectives by experts in stone disease

AIM

To present state of the art on the management of urinary stones from a panel of globally recognized urolithiasis experts who met during the Experts in Stone Disease Congress in Valencia in January 2024. Options of treatment: The surgical treatment modalities of renal and ureteral stones are well defined by the guidelines of international societies, although for some index cases more alternative options are possible. For 1.5 cm renal stones, both m-PCNL and RIRS have proven to be valid treatment alternatives with comparable stone-free rates. The m-PCNL has proven to be more cost effective and requires a shorter operative time, while the RIRS has demonstrated lower morbidity in terms of blood loss and shorter recovery times. SWL has proven to be less effective at least for lower calyceal stones but has the highest safety profile. For a 6mm obstructing stone of the pelviureteric junction (PUJ) stone, SWL should be the first choice for a stone less than 1 cm, due to less invasiveness and lower risk of complications although it has a lower stone free-rate. RIRS has advantages in certain conditions such as anticoagulant treatment, obesity, or body deformity. Technical issues of the surgical procedures for stone removal: In patients receiving antithrombotic therapy, SWL, PCN and open surgery are at elevated risk of hemorrhage or perinephric hematoma. URS, is associated with less morbidity in these cases. An individualized combined evaluation of risks of bleeding and thromboembolism should determine the perioperative thromboprophylactic strategy. Pre-interventional urine culture and antibiotic therapy are mandatory although UTI treatment is becoming more challenging due to increasing resistance to routinely applied antibiotics. The use of an intrarenal urine culture and stone culture is recommended to adapt antibiotic therapy in case of postoperative infectious complications. Measurements of temperature and pressure during RIRS are vital for ensuring patient safety and optimizing surgical outcomes although techniques of measurements and methods for data analysis are still to be refined. Ureteral stents were improved by the development of new biomaterials, new coatings, and new stent designs. Topics of current research are the development of drug eluting and bioresorbable stents. Complications of endoscopic treatment: PCNL is considered the most invasive surgical option. Fever and sepsis were observed in 11 and 0.5% and need for transfusion and embolization for bleeding in 7 and 0.4%. Major complications, as colonic, splenic, liver, gall bladder and bowel injuries are quite rare but are associated with significant morbidity. Ureteroscopy causes less complications, although some of them can be severe. They depend on high pressure in the urinary tract (sepsis or renal bleeding) or application of excessive force to the urinary tract (ureteral avulsion or stricture). Diagnostic work up:  Genetic testing consents the diagnosis of monogenetic conditions causing stones. It should be carried out in children and in selected adults. In adults, monogenetic diseases can be diagnosed by systematic genetic testing in no more than 4%, when cystinuria, APRT deficiency, and xanthinuria are excluded. A reliable stone analysis by infrared spectroscopy or X-ray diffraction is mandatory and should be associated to examination of the stone under a stereomicroscope. The analysis of digital images of stones by deep convolutional neural networks in dry laboratory or during endoscopic examination could allow the classification of stones based on their color and texture. Scanning electron microscopy (SEM) in association with energy dispersive spectrometry (EDS) is another fundamental research tool for the study of kidney stones. The combination of metagenomic analysis using Next Generation Sequencing (NGS) techniques and the enhanced quantitative urine culture (EQUC) protocol can be used to evaluate the urobiome of renal stone formers. Twenty-four hour urine analysis has a place during patient evaluation together with repeated measurements of urinary pH with a digital pH meter. Urinary supersaturation is the most comprehensive physicochemical risk factor employed in urolithiasis research. Urinary macromolecules can act as both promoters or inhibitors of stone formation depending on the chemical composition of urine in which they are operating. At the moment, there are no clinical applications of macromolecules in stone management or prophylaxis. Patients should be evaluated for the association with systemic pathologies.

PROPHYLAXIS

Personalized medicine and public health interventions are complementary to prevent stone recurrence. Personalized medicine addresses a small part of stone patients with a high risk of recurrence and systemic complications requiring specific dietary and pharmacological treatment to prevent stone recurrence and complications of associated systemic diseases. The more numerous subjects who form one or a few stones during their entire lifespan should be treated by modifications of diet and lifestyle. Primary prevention by public health interventions is advisable to reduce prevalence of stones in the general population. Renal stone formers at "high-risk" for recurrence need early diagnosis to start specific treatment. Stone analysis allows the identification of most "high-risk" patients forming non-calcium stones: infection stones (struvite), uric acid and urates, cystine and other rare stones (dihydroxyadenine, xanthine). Patients at "high-risk" forming calcium stones require a more difficult diagnosis by clinical and laboratory evaluation. Particularly, patients with cystinuria and primary hyperoxaluria should be actively searched.

FUTURE RESEARCH

Application of Artificial Intelligence are promising for automated identification of ureteral stones on CT imaging, prediction of stone composition and 24-hour urinary risk factors by demographics and clinical parameters, assessment of stone composition by evaluation of endoscopic images and prediction of outcomes of stone treatments. The synergy between urologists, nephrologists, and scientists in basic kidney stone research will enhance the depth and breadth of investigations, leading to a more comprehensive understanding of kidney stone formation.

Carboxymethylated Desmodium styracifolium polysaccharide reduces the risk of calcium oxalate kidney stone formation by inhibiting crystal adhesion and promoting crystal endocytosis

The inhibition of cell surface crystal adhesion and an appropriate increase in crystal endocytosis contribute to the inhibition of kidney stone formation. In this study, we investigated the effects of different degrees of carboxymethylation on these processes. An injury model was established by treating human renal proximal tubular epithelial (HK-2) cells with 98.3 ± 8.1 nm calcium oxalate dihydrate (nanoCOD) crystals. The HK-2 cells were protected with carboxy (-COOH) Desmodium styracifolium polysaccharides at 1.17% (DSP0), 7.45% (CDSP1), 12.2% (CDSP2), and 17.7% (CDSP3). Changes in biochemical indexes and effects on nanoCOD adhesion and endocytosis were detected. The protection of HK-2 cells from nanoCOD-induced oxidative damage by carboxymethylated Desmodium styracifolium polysaccharides (CDSPs) is closely related to the protection of subcellular organelles, such as mitochondria. CDSPs can reduce crystal adhesion on the cell surface and maintain appropriate crystal endocytosis, thereby reducing the risk of kidney stone formation. CDSP2 with moderate -COOH content showed the strongest protective activity among the CDSPs.